From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun Dec 5 17:24:07 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2C2015065@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory pub.open-bio.org:/tmp/cvs-serv14933/src/Clients/help Modified Files: MobyCmdLineClient_usage.txt Log Message: a lot of changes in docs; but also in code moby-live/Java/src/Clients/help MobyCmdLineClient_usage.txt,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2004/11/12 23:02:31 1.6 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2004/12/05 22:28:02 1.7 @@ -131,7 +131,7 @@ points to your HTTP space to a place where an RDF describing this service will be -rs-rdfpath - if the service registration is succesful, the returned + if the service registration is successful, the returned RDF is copied to a file given by (which completes the registration process); use it, however, with caution because this client From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun Dec 5 17:24:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2cf014998@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/docs/dist In directory pub.open-bio.org:/tmp/cvs-serv14933/docs/dist Modified Files: _README_ Log Message: a lot of changes in docs; but also in code moby-live/Java/docs/dist _README_,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/dist/_README_,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/docs/dist/_README_ 2004/05/18 10:13:16 1.2 +++ /home/repository/moby/moby-live/Java/docs/dist/_README_ 2004/12/05 22:28:02 1.3 @@ -18,6 +18,10 @@ You should consider to change some parameters in provided web.xml (it appears in 'jmoby/WEB-INF' after unpacking). +Binary distribution with RDF agent: + rdfagent-.tar.gz + rdfagent-.zip + -------------------------------------------------------------------- File: README Comments to the biomoby mailing lists, or directly to Martin Senger (senger@ebi.ac.uk). From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun Dec 5 17:24:11 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2oZ014956@pub.open-bio.org> senger Sun Dec 5 17:28:01 EST 2004 Update of /home/repository/moby/moby-live/Java In directory pub.open-bio.org:/tmp/cvs-serv14933 Modified Files: README build.xml Log Message: a lot of changes in docs; but also in code moby-live/Java README,1.7,1.8 build.xml,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Java/README,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/README 2003/11/08 00:27:23 1.7 +++ /home/repository/moby/moby-live/Java/README 2004/12/05 22:28:01 1.8 @@ -73,13 +73,15 @@ After building it all, invoke available clients using provided (and very simple) scripts: - ./run-cmdline-client -help - ./run-testing-central + ./build/run/run-cmdline-client -help + ./build/run/run-testing-central or, on Windows platforms: - run-cmdline-client.bat -help - run-testing-central.bat + build/run/run-cmdline-client.bat -help + build/run/run-testing-central.bat + +There are more scripts available - check the 'build/run' directory. Enjoy it! =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/build.xml 2004/11/01 19:21:42 1.9 +++ /home/repository/moby/moby-live/Java/build.xml 2004/12/05 22:28:01 1.10 @@ -421,26 +421,30 @@ + description="Create binary distribution with basic jMoby clients."> + + + + - - + + - + - - + + - + - + + + + - + - - + + @@ -489,18 +496,18 @@ - + - + - + - + - - + + @@ -608,7 +615,7 @@ - From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun Dec 5 17:24:11 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2je015039@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/src/Clients In directory pub.open-bio.org:/tmp/cvs-serv14933/src/Clients Modified Files: MobyCmdLineClient.java Log Message: a lot of changes in docs; but also in code moby-live/Java/src/Clients MobyCmdLineClient.java,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/11/12 23:02:30 1.7 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/12/05 22:28:02 1.8 @@ -367,9 +367,17 @@ if ((param = cmd.getParam ("-rs-out")) != null ) { String[] outs = StringUtils.split (param, ","); for (int i = 0; i < outs.length; i++) { - MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy"); - data.setDataType (new MobyDataType (outs[i])); - service.addOutput (data); + String[] parts = StringUtils.split (outs[i], "="); + if (parts.length >= 2) { + MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy"); + data.setDataType (new MobyDataType (parts[0])); + data.addNamespace (new MobyNamespace (parts[1])); + service.addOutput (data); + } else { + MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy"); + data.setDataType (new MobyDataType (parts[0])); + service.addOutput (data); + } } } if ((param = cmd.getParam ("-rs-ofile")) != null ) { From senger at pub.open-bio.org Sun Dec 5 17:28:03 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun Dec 5 17:24:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2kR015109@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv14933/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: a lot of changes in docs; but also in code moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.18,1.19 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/11/22 17:22:22 1.18 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/12/05 22:28:02 1.19 @@ -138,6 +138,7 @@ Service service = new Service(); call = (Call) service.createCall(); call.setTargetEndpointAddress (endpoint); + call.setTimeout (new Integer (0)); call.setSOAPActionURI (uri + "#" + method); @@ -1291,7 +1292,7 @@ pattern = new MobyService ("dummy"); String result = - getServicesAsXML (pattern, keywords, includeParentDataTypes, includeChildrenServiceTypes); + getServicesAsXML (pattern, keywords, includeChildrenServiceTypes, includeParentDataTypes); MobyService[] services = extractServices (result); return services; } From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun Dec 5 17:24:13 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2Rx015086@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/src/config In directory pub.open-bio.org:/tmp/cvs-serv14933/src/config Modified Files: run-digest-client Log Message: a lot of changes in docs; but also in code moby-live/Java/src/config run-digest-client,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-digest-client,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/config/run-digest-client 2004/11/14 16:43:49 1.1 +++ /home/repository/moby/moby-live/Java/src/config/run-digest-client 2004/12/05 22:28:02 1.2 @@ -1,8 +1,8 @@ #!/bin/sh # -# Run MobyDigest client. +# Run MobyDigestClient. # -# Use ./build/run/run-digets-client -help for list of +# Use ./build/run/run-digest-client -help for list of # all available arguments. # # $Id$ From senger at pub.open-bio.org Sun Dec 5 17:28:03 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun Dec 5 17:24:13 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS3HO015127@pub.open-bio.org> senger Sun Dec 5 17:28:03 EST 2004 Update of /home/repository/moby/moby-live/Java/src/support In directory pub.open-bio.org:/tmp/cvs-serv14933/src/support Added Files: run-cache-client run-cache-client.bat run-digest-client run-digest-client.bat Log Message: a lot of changes in docs; but also in code moby-live/Java/src/support run-cache-client,NONE,1.1 run-cache-client.bat,NONE,1.1 run-digest-client,NONE,1.1 run-digest-client.bat,NONE,1.1 From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun Dec 5 17:24:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2B0015020@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/docs/images In directory pub.open-bio.org:/tmp/cvs-serv14933/docs/images Modified Files: whale.gif Added Files: blue.gif orange.gif red.gif Log Message: a lot of changes in docs; but also in code moby-live/Java/docs/images blue.gif,NONE,1.1 orange.gif,NONE,1.1 red.gif,NONE,1.1 whale.gif,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/images/whale.gif,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 Binary files /home/repository/moby/moby-live/Java/docs/images/whale.gif 2004/11/14 17:33:57 1.1 and /home/repository/moby/moby-live/Java/docs/images/whale.gif 2004/12/05 22:28:02 1.2 differ rcsdiff: /home/repository/moby/moby-live/Java/docs/images/whale.gif: diff failed From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun Dec 5 17:24:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS29D014979@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv14933/docs Modified Files: ChangeLog index.html Added Files: CmdLineClients.html Download.html MOBYSHoundGetGenBankff-result.xml.txt RDFAgent.html SimpleClient.html TavernaGuide.html Testing_service.rdf ToDo.html Log Message: a lot of changes in docs; but also in code moby-live/Java/docs CmdLineClients.html,NONE,1.1 Download.html,NONE,1.1 MOBYSHoundGetGenBankff-result.xml.txt,NONE,1.1 RDFAgent.html,NONE,1.1 SimpleClient.html,NONE,1.1 TavernaGuide.html,NONE,1.1 Testing_service.rdf,NONE,1.1 ToDo.html,NONE,1.1 ChangeLog,1.26,1.27 index.html,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.26 retrieving revision 1.27 diff -u -r1.26 -r1.27 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/11/14 16:43:49 1.26 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/12/05 22:28:02 1.27 @@ -1,3 +1,13 @@ +2004-12-05 Martin Senger + + * Updated documentation (significantly, but not yet finished). + +2004-11-30 Martin Senger + + * Fixed CentralImpl dealing now better with + 1 and + 1. + 2004-11-14 Martin Senger * Added MobyDigestClient for retrieving cummulative (digested) =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/index.html,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/docs/index.html 2004/11/14 17:33:57 1.5 +++ /home/repository/moby/moby-live/Java/docs/index.html 2004/12/05 22:28:02 1.6 @@ -3,83 +3,72 @@ - +
-

BioMoby in Java

+

jMoby - BioMoby in Java

-This is a sub-project of the BioMoby project. -It aims to develop an access to the Moby registry using pure Java, and later perhaps to -develop a stand-alone Java Moby server. It will also provide Java support for providers -of the Moby-compliant services. -

- -This is the overview of the current Moby java clients, and their -relationship to the whole BioMoby project. -

- - -

- - -

Java API

-The detailed documentation of the involved classes and interfaces -is available +This is a sub-project of the BioMoby project. It aims to develop tools in Java +in order: +
    +
  • to access BioMoby registries, allowing all features provided by +such registries, including but not limited to registering and +deregistering of the BioMoby services and their parts, discovering +them, and understanding their data in various formats (such as RDF),

    - -

    Moby Java Clients - download and use

    +
  • to create Java implementations of BioMoby services, especially +to help service providers with creating BioMoby data containers (input +and output data) without exposing providers to the complexity of the +XML required and produced by BioMoby services, and finally

    -The Moby Java clients are part of the -Moby CVS repository -but for convenience they can be downloaded also separately from -http://industry.ebi.ac.uk/~senger/jMoby/dist/ -(take the latest version, pick up either .tar.gz or .zip - both are equivalent). -

    +

  • to provide support for those writing Java clients accessing +both BioMoby registries and BioMoby services.

    -After downloading, unpack it, check the README file and start using it: -

      -
    • sh run-testing-central -
    • sh run-cmdline-client -help -
    -

    -or on the Windows platform: -

      -
    • run-testing-central.bat -
    • run-cmdline-client.bat -help

    -Latest changes are available either as a -summary or in details from the -CVS repository. -

    +

    Where to go now

    -Please report all problems, or submit features and wishes to -Martin Senger. +
    +
    +
    How to get jMoby +

    + +

    How to use jMoby +
    +
    Command-line clients +
    Integration with Taverna +
    RDF Agent +
    +

    + +

    How to develop with jMoby +
    +
    Available APIs (more explanation coming...) +
    How to develop a client talking to a BioMoby service +
    How to develop a BioMoby service (coming...) +
    +

    + +

    Next plans +
    +
    - -

    Next steps

    - -The future plans and steps in this sub-project may or should include -
      -
    • Design and implement Java interfaces that can be used for the providers - of the Moby-compliant services -
    • Start to work on a pure Java Moby server (talk to Brian Gilman who had already started to work on it) -
    - -

    Acknowledgements

    -The work on BioMoby Java sub-project is supported by +The work on BioMoby Java sub-project is partly supported by
    myGrid, a multi-organisational project developing the infrastructural middleware for an e-Biologist's workbench, funded by EPSRC. +

    - +Other parts of jMoby are funded from the same sources as the BioMoby +itself.

    @@ -87,7 +76,7 @@

    Martin Senger
    -Last modified: Sun Nov 14 17:29:05 2004 +Last modified: Sun Dec 5 21:32:23 2004
    From nopushneva at pub.open-bio.org Tue Dec 7 22:29:06 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue Dec 7 22:24:26 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412080329.iB83T65F024862@pub.open-bio.org> nopushneva Tue Dec 7 22:29:05 EST 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib In directory pub.open-bio.org:/tmp/cvs-serv24837 Removed Files: activation.jar concurrent.jar icu4j.jar Log Message: remove libs from RDFAgent directory moby-live/Agents/MOBY-S/RDFAgent/lib activation.jar,1.3,NONE concurrent.jar,1.1,NONE icu4j.jar,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/activation.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/concurrent.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/icu4j.jar,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:20 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:39:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFK2W026995@pub.open-bio.org> yanwong Wed Dec 8 06:15:20 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched Removed Files: CHANGES MANIFEST PKG-INFO README setup.cfg setup.py Log Message: moby-live/Python/ZSI-1.5.0-patched CHANGES,1.1.1.1,NONE MANIFEST,1.1.1.1,NONE PKG-INFO,1.1.1.1,NONE README,1.1.1.1,NONE setup.cfg,1.1.1.1,NONE setup.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/CHANGES,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/MANIFEST,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/PKG-INFO,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/setup.cfg,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/setup.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:39:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFLc0027079@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/ZSI/wstools/test Removed Files: __init__.py test_t1.py test_wsdl.py test_wstools.py test_wstools_net.py Log Message: moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test __init__.py,1.1.1.1,NONE test_t1.py,1.1.1.1,NONE test_wsdl.py,1.1.1.1,NONE test_wstools.py,1.1.1.1,NONE test_wstools_net.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/__init__.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/test_t1.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/test_wsdl.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/test_wstools.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/test_wstools_net.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:20 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:39:59 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFKo8026975@pub.open-bio.org> yanwong Wed Dec 8 06:15:20 EST 2004 Update of /home/repository/moby/moby-live/Python In directory pub.open-bio.org:/tmp/cvs-serv26947/Python Removed Files: PKG-INFO README TODO changelog setup.py Log Message: moby-live/Python PKG-INFO,1.1.1.1,NONE README,1.1.1.1,NONE TODO,1.1.1.1,NONE changelog,1.1.1.1,NONE setup.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/RCS/PKG-INFO,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/RCS/TODO,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/RCS/changelog,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/RCS/setup.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:00 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFLB3027059@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/ZSI/wstools Removed Files: TimeoutSocket.py UserTuple.py Utility.py WSDLTools.py XMLSchema.py XMLname.py __init__.py Log Message: moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools TimeoutSocket.py,1.1.1.1,NONE UserTuple.py,1.1.1.1,NONE Utility.py,1.1.1.1,NONE WSDLTools.py,1.1.1.1,NONE XMLSchema.py,1.1.1.1,NONE XMLname.py,1.1.1.1,NONE __init__.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/TimeoutSocket.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/UserTuple.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/Utility.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/WSDLTools.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/XMLSchema.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/XMLname.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/__init__.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFKbl027032@pub.open-bio.org> yanwong Wed Dec 8 06:15:20 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/ZSI Removed Files: ServiceProxy.py TC.py TCapache.py TCcompound.py TCnumbers.py TCtimes.py __init__.py auth.py client.py compat.py dispatch.py fault.py parse.py resolvers.py typeinterpreter.py version.py writer.py wsdl2python.py wsdlInterface.py Log Message: moby-live/Python/ZSI-1.5.0-patched/ZSI ServiceProxy.py,1.1.1.1,NONE TC.py,1.1.1.1,NONE TCapache.py,1.1.1.1,NONE TCcompound.py,1.1.1.1,NONE TCnumbers.py,1.1.1.1,NONE TCtimes.py,1.1.1.1,NONE __init__.py,1.1.1.1,NONE auth.py,1.1.1.1,NONE client.py,1.1.1.1,NONE compat.py,1.1.1.1,NONE dispatch.py,1.1.1.1,NONE fault.py,1.1.1.1,NONE parse.py,1.1.1.1,NONE resolvers.py,1.1.1.1,NONE typeinterpreter.py,1.1.1.1,NONE version.py,1.1.1.1,NONE writer.py,1.1.1.1,NONE wsdl2python.py,1.1.1.1,NONE wsdlInterface.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/ServiceProxy.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/TC.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/TCapache.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/TCcompound.py,v: No such 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/home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/parse.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/resolvers.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/typeinterpreter.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/version.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/writer.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/wsdl2python.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/wsdlInterface.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:02 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFLVu027159@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/samples In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/samples Removed Files: README poly.py Log Message: moby-live/Python/ZSI-1.5.0-patched/samples README,1.1.1.1,NONE poly.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/samples/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/samples/RCS/poly.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:22 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:02 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFM1A027210@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/test Removed Files: README cgicli.py test_t1.py test_t2.py test_t3.py test_t4.py test_t5.py test_t6.py test_t7.py test_zsi.py test_zsi_net.py tests_bad.py tests_good.py Log Message: moby-live/Python/ZSI-1.5.0-patched/test README,1.1.1.1,NONE cgicli.py,1.1.1.1,NONE test_t1.py,1.1.1.1,NONE test_t2.py,1.1.1.1,NONE test_t3.py,1.1.1.1,NONE test_t4.py,1.1.1.1,NONE test_t5.py,1.1.1.1,NONE test_t6.py,1.1.1.1,NONE test_t7.py,1.1.1.1,NONE test_zsi.py,1.1.1.1,NONE test_zsi_net.py,1.1.1.1,NONE tests_bad.py,1.1.1.1,NONE tests_good.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/cgicli.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/test_t1.py,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/tests_bad.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/tests_good.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:03 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFLq3027176@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/scripts In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/scripts Removed Files: wsdl2py Log Message: moby-live/Python/ZSI-1.5.0-patched/scripts wsdl2py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/scripts/RCS/wsdl2py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:04 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFL70027139@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/interop Removed Files: InteropTest.wsdl InteropTestB.wsdl README client.py cpackets.py echoHeaderBindings.wsdl sclasses.py server.py Log Message: moby-live/Python/ZSI-1.5.0-patched/interop InteropTest.wsdl,1.1.1.1,NONE InteropTestB.wsdl,1.1.1.1,NONE README,1.1.1.1,NONE client.py,1.1.1.1,NONE cpackets.py,1.1.1.1,NONE echoHeaderBindings.wsdl,1.1.1.1,NONE sclasses.py,1.1.1.1,NONE server.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/InteropTest.wsdl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/InteropTestB.wsdl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/client.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/cpackets.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/echoHeaderBindings.wsdl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/sclasses.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/server.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:05 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFL1V027116@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/doc Removed Files: .cvsignore Makefile c01-intro.tex c02-samples.tex c02a-coverage.tex c03-except.tex c04-utils.tex c05-parse.tex c06-tc.tex c07-writer.tex c08-fault.tex c09-resolve.tex c10-dispatch.tex c11-wsdl.tex zsi.tex zsi.xsd Log Message: moby-live/Python/ZSI-1.5.0-patched/doc .cvsignore,1.1.1.1,NONE Makefile,1.1.1.1,NONE c01-intro.tex,1.1.1.1,NONE c02-samples.tex,1.1.1.1,NONE c02a-coverage.tex,1.1.1.1,NONE c03-except.tex,1.1.1.1,NONE c04-utils.tex,1.1.1.1,NONE c05-parse.tex,1.1.1.1,NONE c06-tc.tex,1.1.1.1,NONE c07-writer.tex,1.1.1.1,NONE c08-fault.tex,1.1.1.1,NONE c09-resolve.tex,1.1.1.1,NONE c10-dispatch.tex,1.1.1.1,NONE c11-wsdl.tex,1.1.1.1,NONE zsi.tex,1.1.1.1,NONE zsi.xsd,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/.cvsignore,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c07-writer.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c08-fault.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c09-resolve.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c10-dispatch.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c11-wsdl.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/zsi.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/zsi.xsd,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:22 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFMuO027232@pub.open-bio.org> yanwong Wed Dec 8 06:15:22 EST 2004 Update of /home/repository/moby/moby-live/Python/doc In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/doc Removed Files: epydoc.css howto.pdf index.html Log Message: moby-live/Python/doc epydoc.css,1.1.1.1,NONE howto.pdf,1.1.1.1,NONE index.html,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/doc/RCS/epydoc.css,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/RCS/howto.pdf,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/RCS/index.html,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:07 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFV9F028121@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/utils/wx In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/utils/wx Removed Files: README objectBrowser.py Log Message: moby-live/Python/utils/wx README,1.1.1.1,NONE objectBrowser.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/utils/wx/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/utils/wx/RCS/objectBrowser.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:08 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFVEv028079@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/webservices In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/tutorials/webservices Removed Files: Clustalw-mod_python.py Clustalw.py Stride.py dispatcher1.py dispatcherCMD.py Log Message: moby-live/Python/tutorials/webservices Clustalw-mod_python.py,1.1.1.1,NONE Clustalw.py,1.1.1.1,NONE Stride.py,1.1.1.1,NONE dispatcher1.py,1.1.1.1,NONE dispatcherCMD.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/Clustalw-mod_python.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/Clustalw.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/Stride.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/dispatcher1.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/dispatcherCMD.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:26 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:09 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFQb8027557@pub.open-bio.org> yanwong Wed Dec 8 06:15:25 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/private In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/doc/private Removed Files: __builtin__.object-class.html __builtin__.type-class.html bioMoby-module.html bioMoby.mobyClient-module.html bioMoby.mobyClient.Central-class.html bioMoby.mobyClient.Client-class.html bioMoby.mobyDataTypes-module.html bioMoby.mobyDataTypes.MobyContent-class.html bioMoby.mobyDataTypes.MobyFloat-class.html bioMoby.mobyDataTypes.MobyInteger-class.html bioMoby.mobyDataTypes.MobyObject-class.html bioMoby.mobyDataTypes.MobySequence-class.html bioMoby.mobyDataTypes.MobyString-class.html bioMoby.mobyDataTypes.MobyXref-class.html bioMoby.mobyDataTypes.MobyZmPDB-class.html bioMoby.mobyDataTypes.Parameter-class.html bioMoby.mobyExceptions-module.html bioMoby.mobyExceptions.EInvalidArgument-class.html bioMoby.mobyExceptions.EInvalidType-class.html bioMoby.mobyExceptions.EMethodRetrieveError-class.html bioMoby.mobyExceptions.ENotAWSMethod-class.html bioMoby.mobyExceptions.ETypeMismatch-class.html 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/home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.ontology.Wildcard_Query-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.webservice-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.webservice.Dispatcher-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.webservice.Invocators-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-everything.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/trees.html,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:30 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:22 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFUNc027999@pub.open-bio.org> yanwong Wed Dec 8 06:15:30 EST 2004 Update of /home/repository/moby/moby-live/Python/src/ontology In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/src/ontology Removed Files: AGI_LocusCode.py Allele_freq.py AminoAcidSequence.py B64_Encoded_PNG.py B64_Encoded_Postscript.py B64_encoded_PDB.py B64_encoded_gif.py B64_encoded_jpeg.py BasicGFFSequenceFeature.py DNASequence.py DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py Edge.py EmblFlatfile.py FASTA.py GFF.py GFF1.py GFF2.py GFF2_5.py GFF3.py GO_Term.py GenbankFlatfile.py GenericSequence.py GeneticElement.py Germplasm_Details.py Germplasm_List.py Global_Keyword.py HCA_picture.py Haplotyping_Study_obj.py ICIS_Query.py ICIS_Query2.py ICIS_Query3.py IntAct_XML.py Interaction.py InteractionMethod.py Interaction_partner.py Interactor.py MMP_Locus.py MO_Term_Test.py Multi_key_value_pair.py MyTree.py NCBI_BLAST_Text.py NCBI_Blast_XML.py NucleotideSequence.py PDBFormattedText.py PDGJOB.py PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py SchematikonMotifID.py SchematikonMotifSupport.py SchematikonSegmentAttributes.py SchematikonSegmentID.py SchematikonStructureAnnotation.py SchematikonVorocodeName.py Scored_acronym_string.py SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py Simple_key_value_pair.py Snp_allele.py Snp_genotype.py Study.py TargetP_result.py Testout.py TextBase64.py TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py TextXml.py Text_plain.py Trait_Details.py Tree.py VirtualSequence.py WU_BLAST_Text.py Wildcard_Query.py __init__.py Log Message: moby-live/Python/src/ontology AGI_LocusCode.py,1.1.1.1,NONE Allele_freq.py,1.1.1.1,NONE AminoAcidSequence.py,1.1.1.1,NONE B64_Encoded_PNG.py,1.1.1.1,NONE B64_Encoded_Postscript.py,1.1.1.1,NONE B64_encoded_PDB.py,1.1.1.1,NONE B64_encoded_gif.py,1.1.1.1,NONE B64_encoded_jpeg.py,1.1.1.1,NONE BasicGFFSequenceFeature.py,1.1.1.1,NONE 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/home/repository/moby/moby-live/Python/src/ontology/RCS/TextUuencoded.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/TextXml.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Text_plain.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Trait_Details.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Tree.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/VirtualSequence.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/WU_BLAST_Text.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Wildcard_Query.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/__init__.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFV5j028099@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/utils In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/utils Removed Files: moby2python.py Log Message: moby-live/Python/utils moby2python.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/utils/RCS/moby2python.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:50 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFVRn028039@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/Mobycentral In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/tutorials/Mobycentral Removed Files: deregisterService.py registerService.py retrieveServices.py servicesDump.py Log Message: moby-live/Python/tutorials/Mobycentral deregisterService.py,1.1.1.1,NONE registerService.py,1.1.1.1,NONE retrieveServices.py,1.1.1.1,NONE servicesDump.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/RCS/deregisterService.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/RCS/registerService.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/RCS/retrieveServices.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/RCS/servicesDump.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:29 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:51 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFT1L027878@pub.open-bio.org> yanwong Wed Dec 8 06:15:27 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/public In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/doc/public Removed Files: __builtin__.object-class.html __builtin__.type-class.html bioMoby-module.html bioMoby.mobyClient-module.html bioMoby.mobyClient.Central-class.html bioMoby.mobyClient.Client-class.html bioMoby.mobyDataTypes-module.html bioMoby.mobyDataTypes.MobyContent-class.html bioMoby.mobyDataTypes.MobyFloat-class.html bioMoby.mobyDataTypes.MobyInteger-class.html bioMoby.mobyDataTypes.MobyObject-class.html bioMoby.mobyDataTypes.MobySequence-class.html bioMoby.mobyDataTypes.MobyString-class.html bioMoby.mobyDataTypes.MobyXref-class.html bioMoby.mobyDataTypes.MobyZmPDB-class.html bioMoby.mobyDataTypes.Parameter-class.html bioMoby.mobyExceptions-module.html bioMoby.mobyExceptions.EInvalidArgument-class.html bioMoby.mobyExceptions.EInvalidType-class.html bioMoby.mobyExceptions.EMethodRetrieveError-class.html bioMoby.mobyExceptions.ENotAWSMethod-class.html 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bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html bioMoby.ontology.B64_Encoded_PNG-module.html bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html bioMoby.ontology.B64_Encoded_Postscript-module.html bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html bioMoby.ontology.B64_encoded_PDB-module.html bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html bioMoby.ontology.B64_encoded_gif-module.html bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html bioMoby.ontology.B64_encoded_jpeg-module.html bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg-class.html bioMoby.ontology.BasicGFFSequenceFeature-module.html bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature-class.html bioMoby.ontology.DNASequence-module.html bioMoby.ontology.DNASequence.MobyDNASequence-class.html bioMoby.ontology.DNASequenceWithGFFFeatures-module.html bioMoby.ontology.DNASequenceWithGFFFeatures.MobyDNASequenceWithGFFFeatures-class.html bioMoby.ontology.DateTime-module.html bioMoby.ontology.DateTime.MobyDateTime-class.html bioMoby.ontology.Decypher_Text-module.html bioMoby.ontology.Decypher_Text.MobyDecypher_Text-class.html bioMoby.ontology.Edge-module.html bioMoby.ontology.Edge.MobyEdge-class.html bioMoby.ontology.EmblFlatfile-module.html bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile-class.html bioMoby.ontology.FASTA-module.html bioMoby.ontology.FASTA.MobyFASTA-class.html bioMoby.ontology.GFF-module.html bioMoby.ontology.GFF.MobyGFF-class.html bioMoby.ontology.GFF1-module.html bioMoby.ontology.GFF1.MobyGFF1-class.html bioMoby.ontology.GFF2-module.html bioMoby.ontology.GFF2.MobyGFF2-class.html bioMoby.ontology.GFF2_5-module.html bioMoby.ontology.GFF2_5.MobyGFF2_5-class.html bioMoby.ontology.GFF3-module.html bioMoby.ontology.GFF3.MobyGFF3-class.html bioMoby.ontology.GO_Term-module.html bioMoby.ontology.GO_Term.MobyGO_Term-class.html bioMoby.ontology.GenbankFlatfile-module.html bioMoby.ontology.GenbankFlatfile.MobyGenbankFlatfile-class.html bioMoby.ontology.GenericSequence-module.html bioMoby.ontology.GenericSequence.MobyGenericSequence-class.html bioMoby.ontology.GeneticElement-module.html bioMoby.ontology.GeneticElement.MobyGeneticElement-class.html bioMoby.ontology.Germplasm_Details-module.html bioMoby.ontology.Germplasm_Details.MobyGermplasm_Details-class.html bioMoby.ontology.Germplasm_List-module.html bioMoby.ontology.Germplasm_List.MobyGermplasm_List-class.html bioMoby.ontology.Global_Keyword-module.html bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword-class.html bioMoby.ontology.HCA_picture-module.html bioMoby.ontology.HCA_picture.MobyHCA_picture-class.html bioMoby.ontology.Haplotyping_Study_obj-module.html bioMoby.ontology.Haplotyping_Study_obj.MobyHaplotyping_Study_obj-class.html bioMoby.ontology.ICIS_Query-module.html bioMoby.ontology.ICIS_Query.MobyICIS_Query-class.html bioMoby.ontology.ICIS_Query2-module.html bioMoby.ontology.ICIS_Query2.MobyICIS_Query2-class.html bioMoby.ontology.ICIS_Query3-module.html bioMoby.ontology.ICIS_Query3.MobyICIS_Query3-class.html bioMoby.ontology.IntAct_XML-module.html bioMoby.ontology.IntAct_XML.MobyIntAct_XML-class.html bioMoby.ontology.Interaction-module.html bioMoby.ontology.Interaction.MobyInteraction-class.html bioMoby.ontology.InteractionMethod-module.html bioMoby.ontology.InteractionMethod.MobyInteractionMethod-class.html bioMoby.ontology.Interaction_partner-module.html bioMoby.ontology.Interaction_partner.MobyInteraction_partner-class.html bioMoby.ontology.Interactor-module.html bioMoby.ontology.Interactor.MobyInteractor-class.html bioMoby.ontology.MMP_Locus-module.html bioMoby.ontology.MMP_Locus.MobyMMP_Locus-class.html bioMoby.ontology.MO_Term_Test-module.html bioMoby.ontology.MO_Term_Test.MobyMO_Term_Test-class.html bioMoby.ontology.Multi_key_value_pair-module.html bioMoby.ontology.Multi_key_value_pair.MobyMulti_key_value_pair-class.html bioMoby.ontology.MyTree-module.html bioMoby.ontology.MyTree.MobyMyTree-class.html bioMoby.ontology.NCBI_BLAST_Text-module.html bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text-class.html bioMoby.ontology.NCBI_Blast_XML-module.html bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML-class.html bioMoby.ontology.NucleotideSequence-module.html bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence-class.html bioMoby.ontology.PDBFormattedText-module.html bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText-class.html bioMoby.ontology.PDGJOB-module.html bioMoby.ontology.PDGJOB.MobyPDGJOB-class.html bioMoby.ontology.PhenotypeDescription-module.html bioMoby.ontology.PhenotypeDescription.MobyPhenotypeDescription-class.html bioMoby.ontology.PubMedMEDLINE-module.html bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE-class.html bioMoby.ontology.RNASequence-module.html bioMoby.ontology.RNASequence.MobyRNASequence-class.html bioMoby.ontology.SchematikonMotifID-module.html bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID-class.html bioMoby.ontology.SchematikonMotifSupport-module.html bioMoby.ontology.SchematikonMotifSupport.MobySchematikonMotifSupport-class.html bioMoby.ontology.SchematikonSegmentAttributes-module.html bioMoby.ontology.SchematikonSegmentAttributes.MobySchematikonSegmentAttributes-class.html bioMoby.ontology.SchematikonSegmentID-module.html bioMoby.ontology.SchematikonSegmentID.MobySchematikonSegmentID-class.html bioMoby.ontology.SchematikonStructureAnnotation-module.html bioMoby.ontology.SchematikonStructureAnnotation.MobySchematikonStructureAnnotation-class.html bioMoby.ontology.SchematikonVorocodeName-module.html bioMoby.ontology.SchematikonVorocodeName.MobySchematikonVorocodeName-class.html bioMoby.ontology.Scored_acronym_string-module.html bioMoby.ontology.Scored_acronym_string.MobyScored_acronym_string-class.html bioMoby.ontology.SimpleAnnotatedGIFImage-module.html bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage-class.html bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage-class.html bioMoby.ontology.Simple_key_value_pair-module.html bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair-class.html bioMoby.ontology.Snp_allele-module.html bioMoby.ontology.Snp_allele.MobySnp_allele-class.html bioMoby.ontology.Snp_genotype-module.html bioMoby.ontology.Snp_genotype.MobySnp_genotype-class.html bioMoby.ontology.Study-module.html bioMoby.ontology.Study.MobyStudy-class.html bioMoby.ontology.TargetP_result-module.html bioMoby.ontology.TargetP_result.MobyTargetP_result-class.html bioMoby.ontology.Testout-module.html bioMoby.ontology.Testout.MobyTestout-class.html bioMoby.ontology.TextBase64-module.html bioMoby.ontology.TextBase64.MobyTextBase64-class.html bioMoby.ontology.TextFormatted-module.html bioMoby.ontology.TextFormatted.MobyTextFormatted-class.html bioMoby.ontology.TextHtml-module.html bioMoby.ontology.TextHtml.MobyTextHtml-class.html bioMoby.ontology.TextPlain-module.html bioMoby.ontology.TextPlain.MobyTextPlain-class.html bioMoby.ontology.TextUuencoded-module.html bioMoby.ontology.TextUuencoded.MobyTextUuencoded-class.html bioMoby.ontology.TextXml-module.html bioMoby.ontology.TextXml.MobyTextXml-class.html bioMoby.ontology.Text_plain-module.html bioMoby.ontology.Text_plain.MobyText_plain-class.html bioMoby.ontology.Trait_Details-module.html bioMoby.ontology.Trait_Details.MobyTrait_Details-class.html bioMoby.ontology.Tree-module.html bioMoby.ontology.Tree.MobyTree-class.html bioMoby.ontology.VirtualSequence-module.html bioMoby.ontology.VirtualSequence.MobyVirtualSequence-class.html bioMoby.ontology.WU_BLAST_Text-module.html bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text-class.html bioMoby.ontology.Wildcard_Query-module.html bioMoby.ontology.Wildcard_Query.MobyWildcard_Query-class.html bioMoby.webservice-module.html bioMoby.webservice.Dispatcher-module.html bioMoby.webservice.Dispatcher.Dispatcher-class.html bioMoby.webservice.Dispatcher.EDispatchError-class.html bioMoby.webservice.Dispatcher.LockedIterator-class.html bioMoby.webservice.Dispatcher.MultiThread-class.html bioMoby.webservice.Dispatcher.SingleThread-class.html bioMoby.webservice.Invocators-module.html bioMoby.webservice.Invocators.CGIPostInvocator-class.html bioMoby.webservice.Invocators.CGIPostMInvocator-class.html bioMoby.webservice.Invocators.GeneralInvocator-class.html bioMoby.webservice.Invocators.InvocatorError-class.html bioMoby.webservice.Invocators.LocalInvocator-class.html epydoc.css exceptions.Exception-class.html frames.html help.html index.html indices.html threading.Thread-class.html toc-bioMoby-module.html toc-bioMoby.mobyClient-module.html toc-bioMoby.mobyDataTypes-module.html toc-bioMoby.mobyExceptions-module.html toc-bioMoby.mobyMarshal-module.html toc-bioMoby.mobyRegister-module.html toc-bioMoby.mobyService-module.html toc-bioMoby.ontology-module.html toc-bioMoby.ontology.AGI_LocusCode-module.html toc-bioMoby.ontology.Allele_freq-module.html toc-bioMoby.ontology.AminoAcidSequence-module.html toc-bioMoby.ontology.B64_Encoded_PNG-module.html toc-bioMoby.ontology.B64_Encoded_Postscript-module.html toc-bioMoby.ontology.B64_encoded_PDB-module.html toc-bioMoby.ontology.B64_encoded_gif-module.html toc-bioMoby.ontology.B64_encoded_jpeg-module.html toc-bioMoby.ontology.BasicGFFSequenceFeature-module.html toc-bioMoby.ontology.DNASequence-module.html toc-bioMoby.ontology.DNASequenceWithGFFFeatures-module.html toc-bioMoby.ontology.DateTime-module.html toc-bioMoby.ontology.Decypher_Text-module.html toc-bioMoby.ontology.Edge-module.html toc-bioMoby.ontology.EmblFlatfile-module.html toc-bioMoby.ontology.FASTA-module.html toc-bioMoby.ontology.GFF-module.html toc-bioMoby.ontology.GFF1-module.html toc-bioMoby.ontology.GFF2-module.html toc-bioMoby.ontology.GFF2_5-module.html toc-bioMoby.ontology.GFF3-module.html toc-bioMoby.ontology.GO_Term-module.html toc-bioMoby.ontology.GenbankFlatfile-module.html toc-bioMoby.ontology.GenericSequence-module.html toc-bioMoby.ontology.GeneticElement-module.html toc-bioMoby.ontology.Germplasm_Details-module.html toc-bioMoby.ontology.Germplasm_List-module.html toc-bioMoby.ontology.Global_Keyword-module.html toc-bioMoby.ontology.HCA_picture-module.html toc-bioMoby.ontology.Haplotyping_Study_obj-module.html toc-bioMoby.ontology.ICIS_Query-module.html toc-bioMoby.ontology.ICIS_Query2-module.html toc-bioMoby.ontology.ICIS_Query3-module.html toc-bioMoby.ontology.IntAct_XML-module.html toc-bioMoby.ontology.Interaction-module.html toc-bioMoby.ontology.InteractionMethod-module.html toc-bioMoby.ontology.Interaction_partner-module.html toc-bioMoby.ontology.Interactor-module.html toc-bioMoby.ontology.MMP_Locus-module.html toc-bioMoby.ontology.MO_Term_Test-module.html toc-bioMoby.ontology.Multi_key_value_pair-module.html toc-bioMoby.ontology.MyTree-module.html toc-bioMoby.ontology.NCBI_BLAST_Text-module.html toc-bioMoby.ontology.NCBI_Blast_XML-module.html toc-bioMoby.ontology.NucleotideSequence-module.html toc-bioMoby.ontology.PDBFormattedText-module.html toc-bioMoby.ontology.PDGJOB-module.html toc-bioMoby.ontology.PhenotypeDescription-module.html toc-bioMoby.ontology.PubMedMEDLINE-module.html toc-bioMoby.ontology.RNASequence-module.html toc-bioMoby.ontology.SchematikonMotifID-module.html toc-bioMoby.ontology.SchematikonMotifSupport-module.html toc-bioMoby.ontology.SchematikonSegmentAttributes-module.html toc-bioMoby.ontology.SchematikonSegmentID-module.html toc-bioMoby.ontology.SchematikonStructureAnnotation-module.html toc-bioMoby.ontology.SchematikonVorocodeName-module.html toc-bioMoby.ontology.Scored_acronym_string-module.html toc-bioMoby.ontology.SimpleAnnotatedGIFImage-module.html toc-bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html toc-bioMoby.ontology.Simple_key_value_pair-module.html toc-bioMoby.ontology.Snp_allele-module.html toc-bioMoby.ontology.Snp_genotype-module.html toc-bioMoby.ontology.Study-module.html toc-bioMoby.ontology.TargetP_result-module.html toc-bioMoby.ontology.Testout-module.html toc-bioMoby.ontology.TextBase64-module.html toc-bioMoby.ontology.TextFormatted-module.html toc-bioMoby.ontology.TextHtml-module.html toc-bioMoby.ontology.TextPlain-module.html toc-bioMoby.ontology.TextUuencoded-module.html toc-bioMoby.ontology.TextXml-module.html toc-bioMoby.ontology.Text_plain-module.html toc-bioMoby.ontology.Trait_Details-module.html toc-bioMoby.ontology.Tree-module.html toc-bioMoby.ontology.VirtualSequence-module.html toc-bioMoby.ontology.WU_BLAST_Text-module.html toc-bioMoby.ontology.Wildcard_Query-module.html toc-bioMoby.webservice-module.html toc-bioMoby.webservice.Dispatcher-module.html toc-bioMoby.webservice.Invocators-module.html toc-everything.html toc.html trees.html Log Message: moby-live/Python/doc/public __builtin__.object-class.html,1.1.1.1,NONE __builtin__.type-class.html,1.1.1.1,NONE bioMoby-module.html,1.1.1.1,NONE bioMoby.mobyClient-module.html,1.1.1.1,NONE bioMoby.mobyClient.Central-class.html,1.1.1.1,NONE bioMoby.mobyClient.Client-class.html,1.1.1.1,NONE bioMoby.mobyDataTypes-module.html,1.1.1.1,NONE bioMoby.mobyDataTypes.MobyContent-class.html,1.1.1.1,NONE bioMoby.mobyDataTypes.MobyFloat-class.html,1.1.1.1,NONE bioMoby.mobyDataTypes.MobyInteger-class.html,1.1.1.1,NONE bioMoby.mobyDataTypes.MobyObject-class.html,1.1.1.1,NONE bioMoby.mobyDataTypes.MobySequence-class.html,1.1.1.1,NONE bioMoby.mobyDataTypes.MobyString-class.html,1.1.1.1,NONE bioMoby.mobyDataTypes.MobyXref-class.html,1.1.1.1,NONE bioMoby.mobyDataTypes.MobyZmPDB-class.html,1.1.1.1,NONE bioMoby.mobyDataTypes.Parameter-class.html,1.1.1.1,NONE bioMoby.mobyExceptions-module.html,1.1.1.1,NONE bioMoby.mobyExceptions.EInvalidArgument-class.html,1.1.1.1,NONE bioMoby.mobyExceptions.EInva! lidType-class.html,1.1.1.1,NONE bioMoby.mobyExceptions.EMethodRetrieveError-class.html,1.1.1.1,NONE bioMoby.mobyExceptions.ENotAWSMethod-class.html,1.1.1.1,NONE bioMoby.mobyExceptions.ETypeMismatch-class.html,1.1.1.1,NONE bioMoby.mobyMarshal-module.html,1.1.1.1,NONE bioMoby.mobyMarshal.MobyMarshaller-class.html,1.1.1.1,NONE bioMoby.mobyMarshal.MobyUnmarshaller-class.html,1.1.1.1,NONE bioMoby.mobyRegister-module.html,1.1.1.1,NONE bioMoby.mobyRegister.GeneralInformations-class.html,1.1.1.1,NONE bioMoby.mobyRegister.Namespace-class.html,1.1.1.1,NONE bioMoby.mobyRegister.ObjectClass-class.html,1.1.1.1,NONE bioMoby.mobyRegister.RegistrationObject-class.html,1.1.1.1,NONE bioMoby.mobyRegister.ServiceType-class.html,1.1.1.1,NONE bioMoby.mobyService-module.html,1.1.1.1,NONE bioMoby.mobyService.Service-class.html,1.1.1.1,NONE bioMoby.mobyService.ServiceArticle-class.html,1.1.1.1,NONE 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bioMoby.ontology.Decypher_Text.MobyDecypher_Text-class.html,1.1.1.1,NONE bioMoby.ontology.Edge-module.html,1.1.1.1,NONE bioMoby.ontology.Edge.MobyEdge-class.html,1.1.1.1,NONE bioMoby.ontology.EmblFlatfile-module.h! tml,1.1.1.1,NONE bioMoby.ontology.EmblFlatfile.MobyEmblFlatfi! le-class.html,1.1.1.1,NONE bioMoby.ontology.FASTA-module.html,1.1.1.1,NONE bioMoby.ontology.FASTA.MobyFASTA-class.html,1.1.1.1,NONE bioMoby.ontology.GFF-module.html,1.1.1.1,NONE bioMoby.ontology.GFF.MobyGFF-class.html,1.1.1.1,NONE bioMoby.ontology.GFF1-module.html,1.1.1.1,NONE bioMoby.ontology.GFF1.MobyGFF1-class.html,1.1.1.1,NONE bioMoby.ontology.GFF2-module.html,1.1.1.1,NONE bioMoby.ontology.GFF2.MobyGFF2-class.html,1.1.1.1,NONE bioMoby.ontology.GFF2_5-module.html,1.1.1.1,NONE bioMoby.ontology.GFF2_5.MobyGFF2_5-class.html,1.1.1.1,NONE bioMoby.ontology.GFF3-module.html,1.1.1.1,NONE bioMoby.ontology.GFF3.MobyGFF3-class.html,1.1.1.1,NONE bioMoby.ontology.GO_Term-module.html,1.1.1.1,NONE 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/home/repository/moby/moby-live/Python/doc/public/RCS/toc-bioMoby.webservice.Invocators-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/toc-everything.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/toc.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/trees.html,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:52 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFVTo028018@pub.open-bio.org> yanwong Wed Dec 8 06:15:30 EST 2004 Update of /home/repository/moby/moby-live/Python/src/webservice In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/src/webservice Removed Files: Dispatcher.py Invocators.py __init__.py Log Message: moby-live/Python/src/webservice Dispatcher.py,1.1.1.1,NONE Invocators.py,1.1.1.1,NONE __init__.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/src/webservice/RCS/Dispatcher.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/webservice/RCS/Invocators.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/webservice/RCS/__init__.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:30 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:54 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFUEx027900@pub.open-bio.org> yanwong Wed Dec 8 06:15:30 EST 2004 Update of /home/repository/moby/moby-live/Python/src In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/src Removed Files: __init__.py mobyClient.py mobyDataTypes.py mobyExceptions.py mobyMarshal.py mobyRegister.py mobyService.py Log Message: moby-live/Python/src __init__.py,1.1.1.1,NONE mobyClient.py,1.1.1.1,NONE mobyDataTypes.py,1.1.1.1,NONE mobyExceptions.py,1.1.1.1,NONE mobyMarshal.py,1.1.1.1,NONE mobyRegister.py,1.1.1.1,NONE mobyService.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/__init__.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyClient.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyDataTypes.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyExceptions.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyMarshal.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyRegister.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyService.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:55 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFVfY028059@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/Service In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/tutorials/Service Removed Files: testMarshaller.py testMobyService.py testMobyService2.py Log Message: moby-live/Python/tutorials/Service testMarshaller.py,1.1.1.1,NONE testMobyService.py,1.1.1.1,NONE testMobyService2.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Service/RCS/testMarshaller.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Service/RCS/testMobyService.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Service/RCS/testMobyService2.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:21:20 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:56 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081121.iB8BLKrP028288@pub.open-bio.org> yanwong Wed Dec 8 06:21:20 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby In directory pub.open-bio.org:/tmp/cvs-serv28264/bioMoby Log Message: Directory /home/repository/moby/moby-live/Python/bioMoby added to the repository moby-live/Python/bioMoby - New directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:21:44 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:57 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081121.iB8BLi3H028331@pub.open-bio.org> yanwong Wed Dec 8 06:21:44 EST 2004 Update of /home/repository/moby/moby-live/Python/packages In directory pub.open-bio.org:/tmp/cvs-serv28307/packages Log Message: Directory /home/repository/moby/moby-live/Python/packages added to the repository moby-live/Python/packages - New directory rcsdiff: /home/repository/moby/moby-live/Python/packages/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/packages/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/packages/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:24:34 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081124.iB8BOYLA028461@pub.open-bio.org> yanwong Wed Dec 8 06:24:34 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby/webservice In directory pub.open-bio.org:/tmp/cvs-serv28419/webservice Log Message: Directory /home/repository/moby/moby-live/Python/bioMoby/webservice added to the repository moby-live/Python/bioMoby/webservice - New directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/webservice/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/webservice/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/webservice/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:24:34 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:40:59 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081124.iB8BOY8f028443@pub.open-bio.org> yanwong Wed Dec 8 06:24:34 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby/ontology In directory pub.open-bio.org:/tmp/cvs-serv28419/ontology Log Message: Directory /home/repository/moby/moby-live/Python/bioMoby/ontology added to the repository moby-live/Python/bioMoby/ontology - New directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/ontology/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/ontology/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/ontology/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:25:23 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081125.iB8BPNdV028520@pub.open-bio.org> yanwong Wed Dec 8 06:25:23 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/src In directory pub.open-bio.org:/tmp/cvs-serv28496/src Log Message: Directory /home/repository/moby/moby-live/Python/doc/src added to the repository moby-live/Python/doc/src - New directory rcsdiff: /home/repository/moby/moby-live/Python/doc/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/src/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:26:02 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:02 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081126.iB8BQ2tq028580@pub.open-bio.org> yanwong Wed Dec 8 06:26:02 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby In directory pub.open-bio.org:/tmp/cvs-serv28528/Python/bioMoby Added Files: __init__.py mobyClient.py mobyDataTypes.py mobyExceptions.py mobyMarshal.py mobyRegister.py mobyService.py Log Message: moby-live/Python/bioMoby __init__.py,NONE,1.1 mobyClient.py,NONE,1.1 mobyDataTypes.py,NONE,1.1 mobyExceptions.py,NONE,1.1 mobyMarshal.py,NONE,1.1 mobyRegister.py,NONE,1.1 mobyService.py,NONE,1.1 From yanwong at pub.open-bio.org Wed Dec 8 06:26:02 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:03 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081126.iB8BQ2Ja028565@pub.open-bio.org> yanwong Wed Dec 8 06:26:01 EST 2004 Update of /home/repository/moby/moby-live/Python In directory pub.open-bio.org:/tmp/cvs-serv28528/Python Added Files: PKG-INFO README changelog setup.py Log Message: moby-live/Python PKG-INFO,1.2,1.3 README,1.2,1.3 changelog,1.2,1.3 setup.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/PKG-INFO,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/PKG-INFO 2004/12/08 11:15:20 1.2 +++ /home/repository/moby/moby-live/Python/PKG-INFO 2004/12/08 11:26:01 1.3 @@ -1,10 +1,10 @@ Metadata-Version: 1.0 Name: bioMoby -Version: 0.5 +Version: 0.7p1 Summary: Python interface for bioMoby Home-page: http://bioserv.rpbs.jussieu.fr Author: Yan Wong Author-email: yanwong@ebgm.jussieu.fr License: -Description: Python's version of Moby's API 0.7 +Description: Python's version of Moby's API 0.8 Platform: UNKNOWN =================================================================== RCS file: /home/repository/moby/moby-live/Python/README,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/README 2004/12/08 11:15:20 1.2 +++ /home/repository/moby/moby-live/Python/README 2004/12/08 11:26:01 1.3 @@ -6,11 +6,13 @@ -Python 2.3 -SOAPpy : http://pywebsvcs.sourceforge.net/ -xml libraries for python: http://pyxml.sourceforge.net (generally already included in python 2.2+) + however if you have some troubles you may need to install PyXML 0.8.3 -if you plan to build webservices with Python, have a look on ZSI gived in this distribution (ZSI-1.5.0-patched) the ZSI here has been patched due to some trouble with CDATA section node __init__.py has been modified in order to solve this problem -pyipc: http://www.theory.org/~mac4/software/ for ipc management with Python (the Dispatcher class needs it) +All these libraries has been added in the packages directory. How to setup bioMoby-python? =================================================================== RCS file: /home/repository/moby/moby-live/Python/changelog,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/changelog 2004/12/08 11:15:20 1.2 +++ /home/repository/moby/moby-live/Python/changelog 2004/12/08 11:26:01 1.3 @@ -31,4 +31,28 @@ add a __setitem__ method to the MobyContent class queries are now accessible via the key directly, use mobycontent['querykey'] to access the data and parameters inside a tool in the utils/wx, objectBrowser is a GUI program to browse the bioMoby Ontology - + +0.6: Bug in the MobyObject corrected + Bug in the Dispatcher corrected (troubles with handling multiple queries) + added signatureURL and RDF for Registration process (in Service, ServiceList) + debug option when executing a service (trace of HTTP calls) in Central and Service Class + (allows you to have the dump of all your SOAP transaction with the webservice) + if you want to trace a SOAP call while executing a service just put: + service.execute(mobyqueries, debug=True) and you'll have the complete trace of the execution + when you deal with the Moby Central Server, just add client.server.config.debug=1 in order to trace execution of your queries + +0.7: Create a class AbstractDispatcher, SimpleDispatcher in order to create other types of dispatchers + On PBSDispatcher, a class qsubParameters designed to store parameters for the qsub command + Class Parameter deserialisation (fromMoby) + Some cleaning on the code, and even more debugging;) + Documentation has been updated + Libraries that were used to build this packages has been added into the packages directory + +0.7p1: Dispatchers can deserialize MobyContent that were in Body tag people using mod_python will have + to patch their ZSI package again. + just do a: + cd packages/ZSI-1.5.0-patched + python setup.py install + (normally just the dispatch.py was modified) + + tutorials/webservice and documentations have been updated. =================================================================== RCS file: /home/repository/moby/moby-live/Python/setup.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/setup.py 2004/12/08 11:15:20 1.2 +++ /home/repository/moby/moby-live/Python/setup.py 2004/12/08 11:26:01 1.3 @@ -9,4 +9,4 @@ author_email="yanwong@ebgm.jussieu.fr", url="http://bioserv.rpbs.jussieu.fr", packages=['bioMoby', 'bioMoby.ontology', 'bioMoby.webservice'], - package_dir={'bioMoby':'src', 'bioMoby.ontology':'src/ontology', 'bioMoby.webservice':'src/webservice'}) + package_dir={'bioMoby':'bioMoby', 'bioMoby.ontology':'bioMoby/ontology', 'bioMoby.webservice':'bioMoby/webservice'}) From yanwong at pub.open-bio.org Wed Dec 8 09:46:40 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:04 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081446.iB8EkeMG029581@pub.open-bio.org> yanwong Wed Dec 8 09:46:40 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby/webservice In directory pub.open-bio.org:/tmp/cvs-serv29560 Added Files: Dispatcher.py Invocators.py TCBioMoby.py __init__.py Log Message: moby-live/Python/bioMoby/webservice Dispatcher.py,NONE,1.1 Invocators.py,NONE,1.1 TCBioMoby.py,NONE,1.1 __init__.py,NONE,1.1 From yanwong at pub.open-bio.org Wed Dec 8 09:47:49 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081447.iB8ElnHb029634@pub.open-bio.org> yanwong Wed Dec 8 09:47:49 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby/ontology In directory pub.open-bio.org:/tmp/cvs-serv29613 Added Files: AlleleAssociation.py Allele_freq.py AminoAcidSequence.py B64_Encoded_PNG.py B64_Encoded_Postscript.py B64_encoded_PDB.py B64_encoded_gif.py B64_encoded_jpeg.py BLASTText.py BasicGFFSequenceFeature.py ClustalAlnFormattedText.py ClustalMsfFormattedText.py CommentedAASequence.py CommentedDNASequence.py CommentedRNASequence.py DNASequence.py DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py Edge.py EmblFlatfile.py FASTA.py FASTA_AA.py FASTA_NA.py FASTA_Text.py GFF.py GFF1.py GFF2.py GFF2_5.py GFF3.py GO_Term.py GenbankFlatfile.py GenericSequence.py GeneticElement.py Genotype.py Germplasm_Details.py Germplasm_List.py Global_Keyword.py HBond_Pair.py HFormatText.py Haplotyping_Study_obj.py ICIS_Query.py ICIS_Query2.py ICIS_Query3.py IntAct_XML.py Interaction.py InteractionMethod.py Interaction_partner.py Interactor.py MEME_Text.py MGIS_ACCESSION.py MMP_Locus.py MO_Term_Test.py MmCIFText.py Multi_key_value_pair.py MyTestingDataType_11024145298313.py MyTree.py NCBI_BLAST_Text.py NCBI_Blast_XML.py NCBI_Blast_XML_Gif.py NCBI_Blast_XML_Gif_Map.py NCBI_MEME_Text.py NucleotideSequence.py PDBFormattedText.py PDBText.py PDGJOB.py PHDText.py PMUTText.py PSeaTextFormatted.py PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py SINGER_ACCESSION.py Sample.py SchematikonMotifID.py SchematikonMotifSupport.py SchematikonSegmentAttributes.py SchematikonSegmentID.py SchematikonStructureAnnotation.py SchematikonVorocodeName.py Scored_acronym_string.py SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py Simple_key_value_pair.py Snp_allele.py Snp_genotype.py Study.py TEST.py TargetP_result.py Testout.py TextBase64.py TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py TextXml.py Text_plain.py Trait_Details.py Tree.py TropGENE_ACCESSION.py TropGENE_Diversity_Matrix.py TropGENE_LOCUS.py VirtualSequence.py WU_BLAST_Text.py Wildcard_Query.py __init__.py Log Message: moby-live/Python/bioMoby/ontology AlleleAssociation.py,NONE,1.1 Allele_freq.py,NONE,1.1 AminoAcidSequence.py,NONE,1.1 B64_Encoded_PNG.py,NONE,1.1 B64_Encoded_Postscript.py,NONE,1.1 B64_encoded_PDB.py,NONE,1.1 B64_encoded_gif.py,NONE,1.1 B64_encoded_jpeg.py,NONE,1.1 BLASTText.py,NONE,1.1 BasicGFFSequenceFeature.py,NONE,1.1 ClustalAlnFormattedText.py,NONE,1.1 ClustalMsfFormattedText.py,NONE,1.1 CommentedAASequence.py,NONE,1.1 CommentedDNASequence.py,NONE,1.1 CommentedRNASequence.py,NONE,1.1 DNASequence.py,NONE,1.1 DNASequenceWithGFFFeatures.py,NONE,1.1 DateTime.py,NONE,1.1 Decypher_Text.py,NONE,1.1 Edge.py,NONE,1.1 EmblFlatfile.py,NONE,1.1 FASTA.py,NONE,1.1 FASTA_AA.py,NONE,1.1 FASTA_NA.py,NONE,1.1 FASTA_Text.py,NONE,1.1 GFF.py,NONE,1.1 GFF1.py,NONE,1.1 GFF2.py,NONE,1.1 GFF2_5.py,NONE,1.1 GFF3.py,NONE,1.1 GO_Term.py,NONE,1.1 GenbankFlatfile.py,NONE,1.1 GenericSequence.py,NONE,1.1 GeneticElement.py,NONE,1.1 Genotype.py,NONE,1.1 Germplasm_Details.py,NONE,1.1 Germplasm_List.py,NO! NE,1.1 Global_Keyword.py,NONE,1.1 HBond_Pair.py,NONE,1.1 HFormatText.py,NONE,1.1 Haplotyping_Study_obj.py,NONE,1.1 ICIS_Query.py,NONE,1.1 ICIS_Query2.py,NONE,1.1 ICIS_Query3.py,NONE,1.1 IntAct_XML.py,NONE,1.1 Interaction.py,NONE,1.1 InteractionMethod.py,NONE,1.1 Interaction_partner.py,NONE,1.1 Interactor.py,NONE,1.1 MEME_Text.py,NONE,1.1 MGIS_ACCESSION.py,NONE,1.1 MMP_Locus.py,NONE,1.1 MO_Term_Test.py,NONE,1.1 MmCIFText.py,NONE,1.1 Multi_key_value_pair.py,NONE,1.1 MyTestingDataType_11024145298313.py,NONE,1.1 MyTree.py,NONE,1.1 NCBI_BLAST_Text.py,NONE,1.1 NCBI_Blast_XML.py,NONE,1.1 NCBI_Blast_XML_Gif.py,NONE,1.1 NCBI_Blast_XML_Gif_Map.py,NONE,1.1 NCBI_MEME_Text.py,NONE,1.1 NucleotideSequence.py,NONE,1.1 PDBFormattedText.py,NONE,1.1 PDBText.py,NONE,1.1 PDGJOB.py,NONE,1.1 PHDText.py,NONE,1.1 PMUTText.py,NONE,1.1 PSeaTextFormatted.py,NONE,1.1 PhenotypeDescription.py,NONE,1.1 PubMedMEDLINE.py,NONE,1.1 RNASequence.py,NONE,1.1 SINGER_ACCESSION.py,NONE,1.1 Sample.py,NONE,1.1 Schemat! ikonMotifID.py,NONE,1.1 SchematikonMotifSupport.py,NONE,1.1 S! chematikonSegmentAttributes.py,NONE,1.1 SchematikonSegmentID.py,NONE,1.1 SchematikonStructureAnnotation.py,NONE,1.1 SchematikonVorocodeName.py,NONE,1.1 Scored_acronym_string.py,NONE,1.1 SimpleAnnotatedGIFImage.py,NONE,1.1 SimpleAnnotatedJPEGImage.py,NONE,1.1 Simple_key_value_pair.py,NONE,1.1 Snp_allele.py,NONE,1.1 Snp_genotype.py,NONE,1.1 Study.py,NONE,1.1 TEST.py,NONE,1.1 TargetP_result.py,NONE,1.1 Testout.py,NONE,1.1 TextBase64.py,NONE,1.1 TextFormatted.py,NONE,1.1 TextHtml.py,NONE,1.1 TextPlain.py,NONE,1.1 TextUuencoded.py,NONE,1.1 TextXml.py,NONE,1.1 Text_plain.py,NONE,1.1 Trait_Details.py,NONE,1.1 Tree.py,NONE,1.1 TropGENE_ACCESSION.py,NONE,1.1 TropGENE_Diversity_Matrix.py,NONE,1.1 TropGENE_LOCUS.py,NONE,1.1 VirtualSequence.py,NONE,1.1 WU_BLAST_Text.py,NONE,1.1 Wildcard_Query.py,NONE,1.1 __init__.py,NONE,1.1 From yanwong at pub.open-bio.org Wed Dec 8 09:48:40 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:07 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081448.iB8EmeLf029679@pub.open-bio.org> yanwong Wed Dec 8 09:48:40 EST 2004 Update of /home/repository/moby/moby-live/Python/packages In directory pub.open-bio.org:/tmp/cvs-serv29658 Added Files: PyIPC.tar.bz2 PyXML-0.8.3.tar.bz2 SOAPpy-0.11.4.tar.bz2 ZSI-1.5.0-patched-2.tar.bz2 fpconst-0.6.0.tar.bz2 Log Message: moby-live/Python/packages PyIPC.tar.bz2,NONE,1.1 PyXML-0.8.3.tar.bz2,NONE,1.1 SOAPpy-0.11.4.tar.bz2,NONE,1.1 ZSI-1.5.0-patched-2.tar.bz2,NONE,1.1 fpconst-0.6.0.tar.bz2,NONE,1.1 From yanwong at pub.open-bio.org Wed Dec 8 09:53:40 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:09 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081453.iB8ErePs029779@pub.open-bio.org> yanwong Wed Dec 8 09:53:40 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/webservices In directory pub.open-bio.org:/tmp/cvs-serv29748 Added Files: Clustalw-mod_python.py Clustalw.py blastpgp.py wsStride.py Log Message: wsStride is an example of wrapping Stride as a webservice: to query it, just give a PDB id like namespace="PDB" id="1AKQ" the service queries the PDB and calculate stride with it moby-live/Python/tutorials/webservices Clustalw-mod_python.py,1.2,1.3 Clustalw.py,1.2,1.3 blastpgp.py,NONE,1.1 wsStride.py,NONE,1.1 =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw-mod_python.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw-mod_python.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw-mod_python.py 2004/12/08 14:53:40 1.3 @@ -36,7 +36,11 @@ d=Dispatcher(mobyContent, LocalInvocator, _toParameters) return d.execute() - + +from ZSI import dispatch +from mod_python import apache +from bioMoby.webservice import TCBioMoby + def handler(req): if req.method=='GET': if req.args=='wsdl': @@ -50,6 +54,6 @@ req.write("ClustalwClustalw") else: - dispatch.AsHandler(modules=(Clustalw,),request=req) + dispatch.AsHandler(modules=(Clustalw,),request=req, typesmodule=TCBioMoby) return apache.OK =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw.py 2004/12/08 14:53:40 1.3 @@ -31,12 +31,21 @@ return (commandName, " type=p -align "+" ".join(parameters), tempfiles, outputfiles) +def ClustalFormatter(results): + def ClustalFormatter(results): + """Return the results in a MobyClustalAlnFormattedText object + """ + from bioMoby import MobyClustalAlnFormattedText + + return [MobyClustalAlnFormattedText(content=results)] + def clustalw(mobyContent): from bioMoby import Dispatcher, LocalInvocator - d=Dispatcher(mobyContent, LocalInvocator, commandBuilder) + d=Dispatcher(mobyContent, LocalInvocator, commandBuilder, formatter=ClustalFormatter) return d.execute() from ZSI import dispatch -dispatch.asCGI() \ No newline at end of file +from bioMoby.webservice import TCBioMoby +dispatch.asCGI(typesmodule=TCBioMoby) From yanwong at pub.open-bio.org Wed Dec 8 09:54:50 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081454.iB8EsoS9029833@pub.open-bio.org> yanwong Wed Dec 8 09:54:50 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/Service In directory pub.open-bio.org:/tmp/cvs-serv29800 Added Files: async.py blastpgp.py testMarshaller.py testMobyService.py testMobyService2.py Log Message: moby-live/Python/tutorials/Service async.py,NONE,1.1 blastpgp.py,NONE,1.1 testMarshaller.py,1.2,1.3 testMobyService.py,1.2,1.3 testMobyService2.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Service/testMarshaller.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Service/testMarshaller.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Service/testMarshaller.py 2004/12/08 14:54:50 1.3 @@ -29,7 +29,7 @@ o=um.loads(s) -print "content of the object" -for object in o.queryData: - print str(object) +print "contents:" +for query in o.keys(): + print o[query][0].content =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService.py 2004/12/08 14:54:50 1.3 @@ -30,7 +30,7 @@ print "Service getNASC_codebyAGI_locus executed with query1 namespace=AGI_LocusCode and id=At3g19100...\n" - resultat=myService.execute(query) + resultat=myService.execute(query, debug=True) print "the xml form\n" =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService2.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService2.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService2.py 2004/12/08 14:54:50 1.3 @@ -16,7 +16,7 @@ object=MobyObject(namespace='DragonDB_Allele',id='cho') print "Service executed with query namespace=DragonDB_Allele and id=cho" -resultat=service.execute(MobyContent({'query1':[object]})) +resultat=service.execute(MobyContent({'query1':[object]}), debug=True) print resultat From yanwong at pub.open-bio.org Wed Dec 8 09:55:22 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:11 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081455.iB8EtMBX029887@pub.open-bio.org> yanwong Wed Dec 8 09:55:22 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/Mobycentral In directory pub.open-bio.org:/tmp/cvs-serv29854 Added Files: registerService.py retrieveServices.py servicesDump.py Log Message: moby-live/Python/tutorials/Mobycentral registerService.py,1.2,1.3 retrieveServices.py,1.2,1.3 servicesDump.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/registerService.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Mobycentral/registerService.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Mobycentral/registerService.py 2004/12/08 14:55:22 1.3 @@ -43,6 +43,7 @@ 'name':'getStrideFromPDB', 'type':'Analysis', 'url':'http://prot3.rpbs.jussieu.fr:8080/ZStrideService/ZStrideService.py', + 'signatureURL':'http://prot3.rpbs.jussieu.fr:8080/RDF', 'authoritative':0, 'contactEmail':'yanwong@ebgm.jussieu.fr', 'authURI':'prot3.rpbs.jussieu.fr', @@ -56,6 +57,7 @@ if resultat.isSuccess(): print "Service registration successful" + print resultat.RDF else: print resultat.message raise Exception =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/retrieveServices.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/servicesDump.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Mobycentral/servicesDump.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Mobycentral/servicesDump.py 2004/12/08 14:55:22 1.3 @@ -2,7 +2,7 @@ from bioMoby import Client, ServiceQuery, ServiceArticle, ServiceSecondary -client=Client() +client=Client(url="http://mips.gsf.de/cgi-bin/proj/planet/moby/MOBY-Central.pl", ns="http://mips.gsf.de/MOBY/Central") dsn=client.retrieveServiceNames() From yanwong at pub.open-bio.org Wed Dec 8 09:57:28 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081457.iB8EvS4x029956@pub.open-bio.org> yanwong Wed Dec 8 09:57:28 EST 2004 Update of /home/repository/moby/moby-live/Python In directory pub.open-bio.org:/tmp/cvs-serv29919 Modified Files: PKG-INFO README changelog setup.py Log Message: moby-live/Python PKG-INFO,1.3,1.4 README,1.3,1.4 changelog,1.3,1.4 setup.py,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Python/PKG-INFO,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Python/README,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Python/changelog,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Python/setup.py,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 From yanwong at pub.open-bio.org Thu Dec 9 09:07:37 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091407.iB9E7bpV003498@pub.open-bio.org> yanwong Thu Dec 9 09:07:32 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/private In directory pub.open-bio.org:/tmp/cvs-serv2265 Added Files: ZSI.TC.TypeCode-class.html __builtin__.object-class.html __builtin__.type-class.html bioMoby-module.html bioMoby.mobyClient-module.html bioMoby.mobyClient.Central-class.html bioMoby.mobyClient.Client-class.html bioMoby.mobyDataTypes-module.html bioMoby.mobyDataTypes.MobyContent-class.html bioMoby.mobyDataTypes.MobyFloat-class.html bioMoby.mobyDataTypes.MobyInteger-class.html bioMoby.mobyDataTypes.MobyObject-class.html bioMoby.mobyDataTypes.MobySequence-class.html bioMoby.mobyDataTypes.MobyString-class.html bioMoby.mobyDataTypes.MobyXref-class.html bioMoby.mobyDataTypes.MobyZmPDB-class.html bioMoby.mobyDataTypes.Parameter-class.html bioMoby.mobyExceptions-module.html 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bioMoby.webservice.Dispatcher.Dispatcher-class.html bioMoby.webservice.Dispatcher.EDispatchError-class.html bioMoby.webservice.Dispatcher.LockedIterator-class.html bioMoby.webservice.Dispatcher.MultiThread-class.html bioMoby.webservice.Dispatcher.PBSDispatcher-class.html bioMoby.webservice.Dispatcher.SimpleDispatcher-class.html bioMoby.webservice.Dispatcher.SingleThread-class.html bioMoby.webservice.Invocators-module.html bioMoby.webservice.Invocators.CGIPostInvocator-class.html bioMoby.webservice.Invocators.CGIPostMInvocator-class.html bioMoby.webservice.Invocators.GeneralInvocator-class.html bioMoby.webservice.Invocators.InvocatorError-class.html bioMoby.webservice.Invocators.LocalInvocator-class.html bioMoby.webservice.Invocators.PBSInvocator-class.html bioMoby.webservice.Invocators.QsubParameters-class.html bioMoby.webservice.TCBioMoby-module.html bioMoby.webservice.TCBioMoby.Body-class.html bioMoby.webservice.TCBioMoby._TCBody-class.html exceptions.Exception-class.html frames.html help.html index.html indices.html threading.Thread-class.html threading._Verbose-class.html toc-bioMoby-module.html toc-bioMoby.mobyClient-module.html toc-bioMoby.mobyDataTypes-module.html toc-bioMoby.mobyExceptions-module.html toc-bioMoby.mobyMarshal-module.html toc-bioMoby.mobyRegister-module.html toc-bioMoby.mobyService-module.html toc-bioMoby.ontology-module.html toc-bioMoby.ontology.AGI_LocusCode-module.html toc-bioMoby.ontology.Allele_freq-module.html toc-bioMoby.ontology.AminoAcidSequence-module.html toc-bioMoby.ontology.B64_Encoded_PNG-module.html toc-bioMoby.ontology.B64_Encoded_Postscript-module.html toc-bioMoby.ontology.B64_encoded_PDB-module.html toc-bioMoby.ontology.B64_encoded_gif-module.html toc-bioMoby.ontology.B64_encoded_jpeg-module.html toc-bioMoby.ontology.BasicGFFSequenceFeature-module.html toc-bioMoby.ontology.ClustalAlnFormattedText-module.html toc-bioMoby.ontology.CommentedAASequence-module.html toc-bioMoby.ontology.CommentedDNASequence-module.html toc-bioMoby.ontology.CommentedRNASequence-module.html toc-bioMoby.ontology.DNASequence-module.html toc-bioMoby.ontology.DNASequenceWithGFFFeatures-module.html toc-bioMoby.ontology.DateTime-module.html toc-bioMoby.ontology.Decypher_Text-module.html toc-bioMoby.ontology.Edge-module.html toc-bioMoby.ontology.EmblFlatfile-module.html toc-bioMoby.ontology.FASTA-module.html toc-bioMoby.ontology.FASTA_AA-module.html toc-bioMoby.ontology.FASTA_NA-module.html toc-bioMoby.ontology.GFF-module.html toc-bioMoby.ontology.GFF1-module.html toc-bioMoby.ontology.GFF2-module.html toc-bioMoby.ontology.GFF2_5-module.html toc-bioMoby.ontology.GFF3-module.html toc-bioMoby.ontology.GO_Term-module.html toc-bioMoby.ontology.GenbankFlatfile-module.html toc-bioMoby.ontology.GenericSequence-module.html toc-bioMoby.ontology.GeneticElement-module.html toc-bioMoby.ontology.Germplasm_Details-module.html toc-bioMoby.ontology.Germplasm_List-module.html toc-bioMoby.ontology.Global_Keyword-module.html toc-bioMoby.ontology.HBond_Pair-module.html toc-bioMoby.ontology.HCA_picture-module.html toc-bioMoby.ontology.Haplotyping_Study_obj-module.html toc-bioMoby.ontology.ICIS_Query-module.html toc-bioMoby.ontology.ICIS_Query2-module.html toc-bioMoby.ontology.ICIS_Query3-module.html toc-bioMoby.ontology.IntAct_XML-module.html toc-bioMoby.ontology.Interaction-module.html toc-bioMoby.ontology.InteractionMethod-module.html toc-bioMoby.ontology.Interaction_partner-module.html toc-bioMoby.ontology.Interactor-module.html toc-bioMoby.ontology.MEME_Text-module.html toc-bioMoby.ontology.MGIS_ACCESSION-module.html toc-bioMoby.ontology.MMP_Locus-module.html toc-bioMoby.ontology.MO_Term_Test-module.html toc-bioMoby.ontology.Multi_key_value_pair-module.html toc-bioMoby.ontology.MyTree-module.html toc-bioMoby.ontology.NCBI_BLAST_Text-module.html toc-bioMoby.ontology.NCBI_Blast_XML-module.html toc-bioMoby.ontology.NCBI_MEME_Text-module.html toc-bioMoby.ontology.NucleotideSequence-module.html toc-bioMoby.ontology.PDBFormattedText-module.html toc-bioMoby.ontology.PDGJOB-module.html toc-bioMoby.ontology.PhenotypeDescription-module.html toc-bioMoby.ontology.PubMedMEDLINE-module.html toc-bioMoby.ontology.RNASequence-module.html toc-bioMoby.ontology.SINGER_ACCESSION-module.html toc-bioMoby.ontology.SchematikonMotifID-module.html toc-bioMoby.ontology.SchematikonMotifSupport-module.html toc-bioMoby.ontology.SchematikonSegmentAttributes-module.html toc-bioMoby.ontology.SchematikonSegmentID-module.html toc-bioMoby.ontology.SchematikonStructureAnnotation-module.html toc-bioMoby.ontology.SchematikonVorocodeName-module.html toc-bioMoby.ontology.Scored_acronym_string-module.html toc-bioMoby.ontology.SimpleAnnotatedGIFImage-module.html toc-bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html toc-bioMoby.ontology.Simple_key_value_pair-module.html toc-bioMoby.ontology.Snp_allele-module.html toc-bioMoby.ontology.Snp_genotype-module.html toc-bioMoby.ontology.Study-module.html toc-bioMoby.ontology.TEST-module.html toc-bioMoby.ontology.TargetP_result-module.html toc-bioMoby.ontology.Testout-module.html toc-bioMoby.ontology.TextBase64-module.html toc-bioMoby.ontology.TextFormatted-module.html toc-bioMoby.ontology.TextHtml-module.html toc-bioMoby.ontology.TextPlain-module.html toc-bioMoby.ontology.TextUuencoded-module.html toc-bioMoby.ontology.TextXml-module.html toc-bioMoby.ontology.Text_plain-module.html toc-bioMoby.ontology.Trait_Details-module.html toc-bioMoby.ontology.Tree-module.html toc-bioMoby.ontology.TropGENE_ACCESSION-module.html toc-bioMoby.ontology.TropGENE_Diversity_Matrix-module.html toc-bioMoby.ontology.TropGENE_LOCUS-module.html toc-bioMoby.ontology.VirtualSequence-module.html toc-bioMoby.ontology.WU_BLAST_Text-module.html toc-bioMoby.ontology.Wildcard_Query-module.html toc-bioMoby.webservice-module.html toc-bioMoby.webservice.Dispatcher-module.html toc-bioMoby.webservice.Invocators-module.html toc-bioMoby.webservice.TCBioMoby-module.html toc-everything.html toc.html trees.html Log Message: moby-live/Python/doc/private ZSI.TC.TypeCode-class.html,NONE,1.1 __builtin__.object-class.html,1.2,1.3 __builtin__.type-class.html,1.2,1.3 bioMoby-module.html,1.2,1.3 bioMoby.mobyClient-module.html,1.2,1.3 bioMoby.mobyClient.Central-class.html,1.2,1.3 bioMoby.mobyClient.Client-class.html,1.2,1.3 bioMoby.mobyDataTypes-module.html,1.2,1.3 bioMoby.mobyDataTypes.MobyContent-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyFloat-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyInteger-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyObject-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobySequence-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyString-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyXref-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyZmPDB-class.html,1.2,1.3 bioMoby.mobyDataTypes.Parameter-class.html,1.2,1.3 bioMoby.mobyExceptions-module.html,1.2,1.3 bioMoby.mobyExceptions.EInvalidArgument-class.html,1.2,1.3 bioMoby.mobyExceptions.EInvalidType-class.html,1.2,1.3 bioMoby.mobyExceptions.EMe! thodRetrieveError-class.html,1.2,1.3 bioMoby.mobyExceptions.ENotAWSMethod-class.html,1.2,1.3 bioMoby.mobyExceptions.ETypeMismatch-class.html,1.2,1.3 bioMoby.mobyMarshal-module.html,1.2,1.3 bioMoby.mobyMarshal.MobyMarshaller-class.html,1.2,1.3 bioMoby.mobyMarshal.MobyUnmarshaller-class.html,1.2,1.3 bioMoby.mobyRegister-module.html,1.2,1.3 bioMoby.mobyRegister.GeneralInformations-class.html,1.2,1.3 bioMoby.mobyRegister.Namespace-class.html,1.2,1.3 bioMoby.mobyRegister.ObjectClass-class.html,1.2,1.3 bioMoby.mobyRegister.RegistrationObject-class.html,1.2,1.3 bioMoby.mobyRegister.ServiceType-class.html,1.2,1.3 bioMoby.mobyService-module.html,1.2,1.3 bioMoby.mobyService.Service-class.html,1.2,1.3 bioMoby.mobyService.ServiceArticle-class.html,1.2,1.3 bioMoby.mobyService.ServiceList-class.html,1.2,1.3 bioMoby.mobyService.ServiceQuery-class.html,1.2,1.3 bioMoby.mobyService.ServiceSecondary-class.html,1.2,1.3 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bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg-class.html,1.2,1.3 bioMoby.ontology.BasicGFFSequenceFeature-module.html,1.2,1.3 bioMoby.ontology! .BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature-class.html,1.2,1.3 bioMoby.ontology.ClustalAlnFormattedText-module.html,NONE,1.1 bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText-class.html,NONE,1.1 bioMoby.ontology.CommentedAASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence-class.html,NONE,1.1 bioMoby.ontology.CommentedDNASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence-class.html,NONE,1.1 bioMoby.ontology.CommentedRNASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence-class.html,NONE,1.1 bioMoby.ontology.DNASequence-module.html,1.2,1.3 bioMoby.ontology.DNASequence.MobyDNASequence-class.html,1.2,1.3 bioMoby.ontology.DNASequenceWithGFFFeatures-module.html,1.2,1.3 bioMoby.ontology.DNASequenceWithGFFFeatures.MobyDNASequenceWithGFFFeatures-class.html,1.2,1.3 bioMoby.ontology.DateTime-module.html,1.2,1.3 bioMoby.ontology.DateTime.! 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ext-class.html,1.2,1.3 bioMoby.ontology.NCBI_Blast_XML-module! .html,1.2,1.3 bioMoby.ontology.NCBI _Blast_XML.MobyNCBI_Blast_XML-class.html,1.2,1.3 bioMoby.ontology.NCBI_MEME_Text-module.html,NONE,1.1 bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text-class.html,NONE,1.1 bioMoby.ontology.NucleotideSequence-module.html,1.2,1.3 bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence-class.html,1.2,1.3 bioMoby.ontology.PDBFormattedText-module.html,1.2,1.3 bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText-class.html,1.2,1.3 bioMoby.ontology.PDGJOB-module.html,1.2,1.3 bioMoby.ontology.PDGJOB.MobyPDGJOB-class.html,1.2,1.3 bioMoby.ontology.PhenotypeDescription-module.html,1.2,1.3 bioMoby.ontology.PhenotypeDescription.MobyPhenotypeDescription-class.html,1.2,1.3 bioMoby.ontology.PubMedMEDLINE-module.html,1.2,1.3 bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE-class.html,1.2,1.3 bioMoby.ontology.RNASequence-module.html,1.2,1.3 bioMoby.ontology.RNASequence.MobyRNASequence-class.html,1.2,1.3 bioMoby.ontology.SINGER_ACCESSION-module.html,NONE,1.1 bioMoby.ontology.SINGER_ACCES! 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MobyScored_acronym_string-class.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedGIFImage-module.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage-class.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage-class.html,1.2,1.3 bioMoby.ontology.Simple_key_value_pair-module.html,1.2,1.3 bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair-class.html,1.2,1.3 bioMoby.ontology.Snp_allele-module.html,1.2,1.3 bioMoby.ontology.Snp_allele.MobySnp_allele-class.html,1.2,1.3 bioMoby.ontology.Snp_genotype-module.html,1.2,1.3 bioMoby.ontology.Snp_genotype.MobySnp_genotype-class.html,1.2,1.3 bioMoby.ontology.Study-module.html,1.2,1.3 bioMoby.ontology.Study.MobyStudy-class.html,1.2,1.3 bioMoby.ontology.TEST-module.html,NONE,1.1 bioMoby.ontology.TEST.MobyTEST-class.html,NONE,1.1 bioMoby.ontology.TargetP_result-module.html,1.2,1.3 bioMoby.ontology.TargetP_result.M! obyTargetP_result-class.html,1.2,1.3 bioMoby.ontology.Testout-module.html,1.2,1.3 bioMoby.ontology.Testout.MobyTestout-class.html,1.2,1.3 bioMoby.ontology.TextBase64-module.html,1.2,1.3 bioMoby.ontology.TextBase64.MobyTextBase64-class.html,1.2,1.3 bioMoby.ontology.TextFormatted-module.html,1.2,1.3 bioMoby.ontology.TextFormatted.MobyTextFormatted-class.html,1.2,1.3 bioMoby.ontology.TextHtml-module.html,1.2,1.3 bioMoby.ontology.TextHtml.MobyTextHtml-class.html,1.2,1.3 bioMoby.ontology.TextPlain-module.html,1.2,1.3 bioMoby.ontology.TextPlain.MobyTextPlain-class.html,1.2,1.3 bioMoby.ontology.TextUuencoded-module.html,1.2,1.3 bioMoby.ontology.TextUuencoded.MobyTextUuencoded-class.html,1.2,1.3 bioMoby.ontology.TextXml-module.html,1.2,1.3 bioMoby.ontology.TextXml.MobyTextXml-class.html,1.2,1.3 bioMoby.ontology.Text_plain-module.html,1.2,1.3 bioMoby.ontology.Text_plain.MobyText_plain-class.html,1.2,1.3 bioMoby.ontology.Trait_Details-module.html,1.2,1.3 bioMoby.ontology.Trait_Details! .MobyTrait_Details-class.html,1.2,1.3 bioMoby.ontology.Tree-m! odule.html,1.2,1.3 bioMoby.ontology.Tree.MobyTree-class.html,1.2,1.3 bioMoby.ontology.TropGENE_ACCESSION-module.html,NONE,1.1 bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION-class.html,NONE,1.1 bioMoby.ontology.TropGENE_Diversity_Matrix-module.html,NONE,1.1 bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix-class.html,NONE,1.1 bioMoby.ontology.TropGENE_LOCUS-module.html,NONE,1.1 bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS-class.html,NONE,1.1 bioMoby.ontology.VirtualSequence-module.html,1.2,1.3 bioMoby.ontology.VirtualSequence.MobyVirtualSequence-class.html,1.2,1.3 bioMoby.ontology.WU_BLAST_Text-module.html,1.2,1.3 bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text-class.html,1.2,1.3 bioMoby.ontology.Wildcard_Query-module.html,1.2,1.3 bioMoby.ontology.Wildcard_Query.MobyWildcard_Query-class.html,1.2,1.3 bioMoby.webservice-module.html,1.2,1.3 bioMoby.webservice.Dispatcher-module.html,1.2,1.3 bioMoby.webservice.Dispatcher.AbstractDispatcher! -class.html,NONE,1.1 bioMoby.webservice.Dispatcher.Dispatcher-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.EDispatchError-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.LockedIterator-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.MultiThread-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.PBSDispatcher-class.html,NONE,1.1 bioMoby.webservice.Dispatcher.SimpleDispatcher-class.html,NONE,1.1 bioMoby.webservice.Dispatcher.SingleThread-class.html,1.2,1.3 bioMoby.webservice.Invocators-module.html,1.2,1.3 bioMoby.webservice.Invocators.CGIPostInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.CGIPostMInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.GeneralInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.InvocatorError-class.html,1.2,1.3 bioMoby.webservice.Invocators.LocalInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.PBSInvocator-class.html,NONE,1.1 bioMoby.webservice.Invocators.QsubParameters-class.html,NONE,1.1 bioMoby.webservice.TC! BioMoby-module.html,NONE,1.1 bioMoby.webservice.TCBioMoby.Bod! y-class.html,NONE,1.1 bioMoby.webservice.TCBioMoby._TCBody-class.html,NONE,1.1 exceptions.Exception-class.html,1.2,1.3 frames.html,1.2,1.3 help.html,1.2,1.3 index.html,1.2,1.3 indices.html,1.2,1.3 threading.Thread-class.html,1.2,1.3 threading._Verbose-class.html,1.2,1.3 toc-bioMoby-module.html,1.2,1.3 toc-bioMoby.mobyClient-module.html,1.2,1.3 toc-bioMoby.mobyDataTypes-module.html,1.2,1.3 toc-bioMoby.mobyExceptions-module.html,1.2,1.3 toc-bioMoby.mobyMarshal-module.html,1.2,1.3 toc-bioMoby.mobyRegister-module.html,1.2,1.3 toc-bioMoby.mobyService-module.html,1.2,1.3 toc-bioMoby.ontology-module.html,1.2,1.3 toc-bioMoby.ontology.AGI_LocusCode-module.html,1.2,1.3 toc-bioMoby.ontology.Allele_freq-module.html,1.2,1.3 toc-bioMoby.ontology.AminoAcidSequence-module.html,1.2,1.3 toc-bioMoby.ontology.B64_Encoded_PNG-module.html,1.2,1.3 toc-bioMoby.ontology.B64_Encoded_Postscript-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encoded_PDB-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encode! d_gif-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encoded_jpeg-module.html,1.2,1.3 toc-bioMoby.ontology.BasicGFFSequenceFeature-module.html,1.2,1.3 toc-bioMoby.ontology.ClustalAlnFormattedText-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedAASequence-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedDNASequence-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedRNASequence-module.html,NONE,1.1 toc-bioMoby.ontology.DNASequence-module.html,1.2,1.3 toc-bioMoby.ontology.DNASequenceWithGFFFeatures-module.html,1.2,1.3 toc-bioMoby.ontology.DateTime-module.html,1.2,1.3 toc-bioMoby.ontology.Decypher_Text-module.html,1.2,1.3 toc-bioMoby.ontology.Edge-module.html,1.2,1.3 toc-bioMoby.ontology.EmblFlatfile-module.html,1.2,1.3 toc-bioMoby.ontology.FASTA-module.html,1.2,1.3 toc-bioMoby.ontology.FASTA_AA-module.html,NONE,1.1 toc-bioMoby.ontology.FASTA_NA-module.html,NONE,1.1 toc-bioMoby.ontology.GFF-module.html,1.2,1.3 toc-bioMoby.ontology.GFF1-module.html,1.2,1.3 toc-bioMoby.ontology! .GFF2-module.html,1.2,1.3 toc-bioMoby.ontology.GFF2_5-module.! html,1.2,1.3 toc-bioMoby.ontology.G FF3-module.html,1.2,1.3 toc-bioMoby.ontology.GO_Term-module.html,1.2,1.3 toc-bioMoby.ontology.GenbankFlatfile-module.html,1.2,1.3 toc-bioMoby.ontology.GenericSequence-module.html,1.2,1.3 toc-bioMoby.ontology.GeneticElement-module.html,1.2,1.3 toc-bioMoby.ontology.Germplasm_Details-module.html,1.2,1.3 toc-bioMoby.ontology.Germplasm_List-module.html,1.2,1.3 toc-bioMoby.ontology.Global_Keyword-module.html,1.2,1.3 toc-bioMoby.ontology.HBond_Pair-module.html,NONE,1.1 toc-bioMoby.ontology.HCA_picture-module.html,1.2,1.3 toc-bioMoby.ontology.Haplotyping_Study_obj-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query2-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query3-module.html,1.2,1.3 toc-bioMoby.ontology.IntAct_XML-module.html,1.2,1.3 toc-bioMoby.ontology.Interaction-module.html,1.2,1.3 toc-bioMoby.ontology.InteractionMethod-module.html,1.2,1.3 toc-bioMoby.ontology.Interaction_partner-module.html,1.2,1.3 toc-bioMoby.ontology.In! teractor-module.html,1.2,1.3 toc-bioMoby.ontology.MEME_Text-module.html,NONE,1.1 toc-bioMoby.ontology.MGIS_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.MMP_Locus-module.html,1.2,1.3 toc-bioMoby.ontology.MO_Term_Test-module.html,1.2,1.3 toc-bioMoby.ontology.Multi_key_value_pair-module.html,1.2,1.3 toc-bioMoby.ontology.MyTree-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_BLAST_Text-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_Blast_XML-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_MEME_Text-module.html,NONE,1.1 toc-bioMoby.ontology.NucleotideSequence-module.html,1.2,1.3 toc-bioMoby.ontology.PDBFormattedText-module.html,1.2,1.3 toc-bioMoby.ontology.PDGJOB-module.html,1.2,1.3 toc-bioMoby.ontology.PhenotypeDescription-module.html,1.2,1.3 toc-bioMoby.ontology.PubMedMEDLINE-module.html,1.2,1.3 toc-bioMoby.ontology.RNASequence-module.html,1.2,1.3 toc-bioMoby.ontology.SINGER_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.SchematikonMotifID-module.html,1.2,1.3 toc-bioMoby! .ontology.SchematikonMotifSupport-module.html,1.2,1.3 toc-bio! Moby.ontology.SchematikonSegmentAttributes-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonSegmentID-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonStructureAnnotation-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonVorocodeName-module.html,1.2,1.3 toc-bioMoby.ontology.Scored_acronym_string-module.html,1.2,1.3 toc-bioMoby.ontology.SimpleAnnotatedGIFImage-module.html,1.2,1.3 toc-bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html,1.2,1.3 toc-bioMoby.ontology.Simple_key_value_pair-module.html,1.2,1.3 toc-bioMoby.ontology.Snp_allele-module.html,1.2,1.3 toc-bioMoby.ontology.Snp_genotype-module.html,1.2,1.3 toc-bioMoby.ontology.Study-module.html,1.2,1.3 toc-bioMoby.ontology.TEST-module.html,NONE,1.1 toc-bioMoby.ontology.TargetP_result-module.html,1.2,1.3 toc-bioMoby.ontology.Testout-module.html,1.2,1.3 toc-bioMoby.ontology.TextBase64-module.html,1.2,1.3 toc-bioMoby.ontology.TextFormatted-module.html,1.2,1.3 toc-bioMoby.ontology.TextHtml-module.html,1.2,1.3 toc-bioM! oby.ontology.TextPlain-module.html,1.2,1.3 toc-bioMoby.ontology.TextUuencoded-module.html,1.2,1.3 toc-bioMoby.ontology.TextXml-module.html,1.2,1.3 toc-bioMoby.ontology.Text_plain-module.html,1.2,1.3 toc-bioMoby.ontology.Trait_Details-module.html,1.2,1.3 toc-bioMoby.ontology.Tree-module.html,1.2,1.3 toc-bioMoby.ontology.TropGENE_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.TropGENE_Diversity_Matrix-module.html,NONE,1.1 toc-bioMoby.ontology.TropGENE_LOCUS-module.html,NONE,1.1 toc-bioMoby.ontology.VirtualSequence-module.html,1.2,1.3 toc-bioMoby.ontology.WU_BLAST_Text-module.html,1.2,1.3 toc-bioMoby.ontology.Wildcard_Query-module.html,1.2,1.3 toc-bioMoby.webservice-module.html,1.2,1.3 toc-bioMoby.webservice.Dispatcher-module.html,1.2,1.3 toc-bioMoby.webservice.Invocators-module.html,1.2,1.3 toc-bioMoby.webservice.TCBioMoby-module.html,NONE,1.1 toc-everything.html,1.2,1.3 toc.html,1.2,1.3 trees.html,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/__builtin__.object-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/__builtin__.object-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/__builtin__.object-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + @@ -246,13 +252,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/__builtin__.type-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/__builtin__.type-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/__builtin__.type-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -489,13 +495,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -58,6 +64,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -65,6 +75,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -78,6 +90,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -87,12 +100,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -109,10 +125,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -123,6 +141,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -131,6 +152,7 @@

  • @@ -143,13 +165,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -57,13 +63,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Central-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Central-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Central-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,7 +60,8 @@ @@ -77,7 +84,8 @@
      __init__(self, url, - ns) + ns, + debug)
    Changes url and ns parameters if you want to use another moby server
    - +

    __init__(self, url='http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral..., - ns='http://mobycentral.cbr.nrc.ca/MOBY/Central') + ns='http://mobycentral.cbr.nrc.ca/MOBY/Central', + debug=False)
    (Constructor)

    Changes url and ns parameters if you want to use another moby @@ -106,13 +114,19 @@
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Client-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Client-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Client-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,12 +60,10 @@ - +
    Method Summary
     __init__(self, + __init__(self, url, ns) -
    -Changes url and ns parameters if you want to use another moby -server
      findService(self, mobyQuery) @@ -141,23 +145,6 @@ Method Details
    - -
    -

    __init__(self, - url='http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral..., - ns='http://mobycentral.cbr.nrc.ca/MOBY/Central') -
    (Constructor) -

    - Changes url and ns parameters if you want to use another moby - server -
    -
    Overrides:
    -
    bioMoby.mobyClient.Central.__init__ (inherited documentation) -
    -
    -
    -
    - - +

    findService(self, @@ -298,13 +285,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -80,13 +86,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyContent-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyContent-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyContent-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -116,13 +122,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyFloat-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyFloat-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyFloat-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -110,13 +116,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyInteger-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyInteger-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyInteger-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -110,13 +116,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyObject-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyObject-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyObject-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -49,6 +55,7 @@ MobyGlobal_Keyword, MobyGO_Term, MobyHaplotyping_Study_obj, + MobyHBond_Pair, MobyICIS_Query, MobyICIS_Query2, MobyICIS_Query3, @@ -57,6 +64,7 @@ MobyInteraction_partner, MobyInteractionMethod, MobyInteractor, + MobyMGIS_ACCESSION, MobyMMP_Locus, MobyMO_Term_Test, MobyMulti_key_value_pair, @@ -70,11 +78,14 @@ MobyScored_acronym_string, MobySequence, MobySimple_key_value_pair, + MobySINGER_ACCESSION, MobyString, MobyStudy, MobyTargetP_result, MobyTestout, MobyTrait_Details, + MobyTropGENE_ACCESSION, + MobyTropGENE_LOCUS, MobyVirtualSequence, MobyWildcard_Query, MobyXref, @@ -162,13 +173,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobySequence-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobySequence-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobySequence-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -57,7 +63,8 @@ - +
    __init__(self, sequence, namespace, - id) + id, + articleName)
      fromMoby(self, @@ -110,13 +117,19 @@    Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyString-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyString-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyString-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -99,13 +105,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyXref-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyXref-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyXref-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -124,13 +130,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyZmPDB-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyZmPDB-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyZmPDB-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -183,13 +189,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.Parameter-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.Parameter-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.Parameter-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -104,13 +110,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -66,13 +72,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidArgument-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidArgument-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidArgument-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidType-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidType-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidType-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EMethodRetrieveError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EMethodRetrieveError-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EMethodRetrieveError-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ENotAWSMethod-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ENotAWSMethod-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ENotAWSMethod-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ETypeMismatch-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ETypeMismatch-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ETypeMismatch-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -57,13 +63,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyMarshaller-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyMarshaller-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyMarshaller-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,10 +54,11 @@ - +
    +Serialize the object into a Moby XML object - +
    +this method do the serialization of the object
    Method Summary
     dumps(self, + dumps(self, value, articleName) -
      m_dict(self, value, @@ -114,10 +121,11 @@
    transforms an object and all properties into a XML
     _marshal(self, + _marshal(self, value, articleName) -

    @@ -127,6 +135,17 @@ Method Details + +
    +

    dumps(self, + value, + articleName='') +

    + Serialize the object into a Moby XML object +
    +
    +
    +

    m_dict(self, @@ -222,6 +241,17 @@

    + + +
    +

    _marshal(self, + value, + articleName='') +

    + this method do the serialization of the object +
    +
    +

    @@ -232,13 +262,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyUnmarshaller-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyUnmarshaller-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyUnmarshaller-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,9 +54,10 @@ - +
    +Deserializes an xml string and return a bioMoby-Python object
    Method Summary
     loads(self, + loads(self, xml) -
      m_Collection(self, value) @@ -98,6 +105,16 @@ Method Details
    + +
    +

    loads(self, + xml) +

    + Deserializes an xml string and return a bioMoby-Python object +
    +
    +
    + - +

    m_Collection(self, @@ -180,13 +197,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -67,13 +73,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.GeneralInformations-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.GeneralInformations-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.GeneralInformations-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -154,13 +160,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.Namespace-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.Namespace-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.Namespace-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -136,13 +142,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ObjectClass-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ObjectClass-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ObjectClass-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -138,13 +144,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.RegistrationObject-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.RegistrationObject-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.RegistrationObject-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -121,13 +127,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ServiceType-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ServiceType-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ServiceType-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -158,13 +164,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -67,13 +73,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.Service-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.Service-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.Service-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -70,7 +76,8 @@ @@ -82,7 +89,8 @@ +Register the service on the Moby server has been added here a code to +verify that signatureURL is not empty :)
    execute(self, query, method, - returnXml) + returnXml, + debug)
    Executes the web service v0.5: return either the XML form or try to unmarshall the result and return a MobyContent Object
      register(self)
    -Register the service on the Moby server

    @@ -151,7 +159,8 @@

    execute(self, query, method='', - returnXml=True) + returnXml=True, + debug=False)

    Executes the web service v0.5: return either the XML form or try to unmarshall the result and return a MobyContent Object @@ -173,7 +182,8 @@

    register(self)

    - Register the service on the Moby server + Register the service on the Moby server has been added here a code + to verify that signatureURL is not empty :)
    @@ -187,13 +197,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceArticle-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceArticle-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceArticle-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -113,13 +119,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceList-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceList-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceList-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -204,13 +210,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceQuery-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceQuery-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceQuery-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -128,13 +134,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceSecondary-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceSecondary-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceSecondary-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -116,13 +122,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -51,6 +57,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -58,6 +68,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -71,6 +83,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -80,12 +93,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -102,10 +118,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -116,6 +134,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -130,13 +151,19 @@
  • - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -58,13 +64,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -113,13 +119,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -90,13 +96,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,6 +54,10 @@ MobyAminoAcidSequence
    +
    Known Subclasses:
    +
    + MobyCommentedAASequence
    +
    Description: Lightweight representation an amino acid sequence Author: @@ -117,13 +127,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_Postscript-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_Postscript-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_Postscript-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
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    +

    + bioMoby-python +

    +
    @@ -120,13 +126,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_PDB-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_PDB-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_PDB-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
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    +

    + bioMoby-python +

    +
    @@ -116,13 +122,19 @@ - +
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    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_gif-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_gif-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_gif-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
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    + bioMoby-python +

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    @@ -52,6 +58,7 @@
    Known Subclasses:
    + MobyCommentedDNASequence, MobyDNASequenceWithGFFFeatures

    @@ -123,13 +130,19 @@ - +
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    +
    @@ -50,6 +56,11 @@ MobyFASTA
    +
    Known Subclasses:
    +
    + MobyFASTA_AA, + MobyFASTA_NA
    +
    Description: FASTA formatted sequence Author: www.sdsc.edu Contact: @@ -118,13 +129,19 @@ - +
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    Known Subclasses:
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    Description: Lightweight representation an RNA sequence Author: @@ -119,13 +129,19 @@ - +
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    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Snp_allele-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Snp_allele-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Snp_allele-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -50,16 +56,21 @@
    Known Subclasses:
    + MobyClustalAlnFormattedText, MobyDecypher_Text, MobyEmblFlatfile, MobyFASTA, MobyGenbankFlatfile, MobyGFF, + MobyMEME_Text, MobyMyTree, MobyNCBI_BLAST_Text, + MobyNCBI_MEME_Text, MobyPDBFormattedText, MobyPubMedMEDLINE, + MobyTEST, MobyTree, + MobyTropGENE_Diversity_Matrix, MobyWU_BLAST_Text

    @@ -130,13 +141,19 @@ - +
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    +
    @@ -44,6 +50,7 @@

    @@ -55,13 +62,19 @@    Trees       Index       Help    - + + +
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    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -43,6 +49,10 @@ + + + + + +
    Classes
    + AbstractDispatcherSubclass this one to create your own dispatcher class a Dispatcher +class must have a execute method
    Dispatcher All Queries in the MobyContent Object are splitted and executed
    @@ -52,6 +62,12 @@ MultiThread Several threads
    + PBSDispatcherDispatcher for PBS jobs
    + SimpleDispatcherA simple dispatcher, without execute method
    SingleThread Definition of a single Thread

    @@ -74,13 +90,19 @@    Trees       Index       Help    - + + +
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    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.Dispatcher-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.Dispatcher-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.Dispatcher-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -38,6 +44,12 @@

    Class Dispatcher

    +
    +AbstractDispatcher --+
    +                     |
    +                    Dispatcher
    +

    +
    All Queries in the MobyContent Object are splitted and executed @@ -104,6 +116,9 @@ [queryData]-->("commandName","commandArgs", ["tempfiles"])
    +
    Overrides:
    +
    bioMoby.webservice.Dispatcher.AbstractDispatcher.__init__
    +
    @@ -115,6 +130,9 @@ Execute the queries with a pool of threads, store the results in a mobyContent Object
    +
    Overrides:
    +
    bioMoby.webservice.Dispatcher.AbstractDispatcher.execute
    +
    @@ -147,13 +165,19 @@    Trees       Index       Help    - + + +
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    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.EDispatchError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.EDispatchError-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.EDispatchError-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.SingleThread-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.SingleThread-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.SingleThread-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -163,13 +169,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,11 +60,24 @@ GeneralInvocator - - + + + + +
    General class for other invocators
    - InvocatorErrorError during an invocation of method
    LocalInvocator Invokes local command
    + PBSInvocatorInvokes a command in a qsub
    + QsubParametersParameters for the qsub command

    + + + + + + + +
    Exceptions
    + InvocatorErrorError during an invocation of method

    @@ -69,13 +88,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostInvocator-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostInvocator-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -68,7 +74,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -111,13 +118,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -89,7 +95,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -151,13 +158,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.GeneralInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.GeneralInvocator-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.GeneralInvocator-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -55,17 +61,51 @@ - +
    +queryid is the identifier of a query, userdir is the session +directory, timeout the limit time of execution of the query - +
    Method Summary
     __init__(self, + __init__(self, queryid, userdir, timeout) -
     getResults(self) -
    getResults(self) +
    +retrieve the results if available

    + + + + +
    Method Details
    + + +
    +

    __init__(self, + queryid, + userdir='/tmp', + timeout=None) +
    (Constructor) +

    + queryid is the identifier of a query, userdir is the session + directory, timeout the limit time of execution of the query +
    +
    +
    + + +
    +

    getResults(self) +

    + retrieve the results if available +
    +
    +
    +
    + + @@ -73,13 +113,19 @@ - + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.InvocatorError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.InvocatorError-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.InvocatorError-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -38,6 +44,12 @@

    Class InvocatorError

    +
    +Exception --+
    +            |
    +           InvocatorError
    +

    +
    Error during an invocation of method @@ -51,6 +63,14 @@ + + + + + +
      __str__(self)
        Inherited from Exception
     __init__(...) +
     __getitem__(...) +

    @@ -61,13 +81,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.LocalInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.LocalInvocator-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.LocalInvocator-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -44,6 +50,10 @@ LocalInvocator
    +
    Known Subclasses:
    +
    + PBSInvocator
    +
    Invokes local command @@ -69,7 +79,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -105,13 +116,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/exceptions.Exception-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/exceptions.Exception-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/exceptions.Exception-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -43,7 +49,8 @@ EInvalidType, EMethodRetrieveError, ENotAWSMethod, - ETypeMismatch + ETypeMismatch, + InvocatorError
    @@ -74,13 +81,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/frames.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/frames.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/frames.html 2004/12/09 14:07:31 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/help.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/help.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/help.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -32,7 +38,7 @@

    API Documentation

    This document contains the API (Application Programming Interface) -documentation for this project. Documentation for the Python +documentation for bioMoby-python. Documentation for the Python objects defined by the project is divided into separate pages for each package, module, and class. The API documentation also includes two pages containing information about the project as a whole: a trees @@ -209,13 +215,19 @@

    - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/index.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/index.html 2004/12/09 14:07:31 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/indices.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/indices.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/indices.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:10 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -74,6 +80,8 @@ + + @@ -136,6 +144,14 @@ + + + + + + + + @@ -150,6 +166,10 @@ + + + + @@ -174,6 +194,8 @@ + + @@ -194,6 +216,10 @@ + + + + @@ -206,6 +232,8 @@ + + @@ -218,6 +246,8 @@ + + @@ -244,6 +274,8 @@ + + @@ -266,18 +298,30 @@ + + + + + + + + + + + + @@ -288,6 +332,10 @@ + + + + @@ -384,6 +432,8 @@ + + @@ -394,12 +444,16 @@ + + + + @@ -430,6 +484,8 @@ + + @@ -438,8 +494,20 @@ + + + + + + + + + + + + @@ -506,16 +574,26 @@ + + + + + + + + + + @@ -550,6 +628,14 @@ + + + + + + + + @@ -564,6 +650,10 @@ + + + + @@ -588,6 +678,8 @@ + + @@ -608,6 +700,10 @@ + + + + @@ -620,6 +716,8 @@ + + @@ -632,6 +730,8 @@ + + @@ -658,6 +758,8 @@ + + @@ -680,6 +782,12 @@ + + + + + + @@ -706,6 +814,8 @@ + + @@ -734,6 +844,8 @@ + + @@ -806,6 +918,10 @@ + + + + @@ -830,6 +946,14 @@ + + + + + + + + @@ -850,6 +974,10 @@ + + + + @@ -878,6 +1006,8 @@ + + @@ -902,6 +1032,10 @@ + + + + @@ -914,6 +1048,8 @@ + + @@ -954,6 +1090,8 @@ + + @@ -964,6 +1102,8 @@ + + @@ -984,6 +1124,12 @@ + + + + + + @@ -1004,14 +1150,20 @@ + + + + + + @@ -1022,6 +1174,16 @@ + + + + + + + + + + @@ -1034,6 +1196,8 @@ + + @@ -1088,6 +1252,10 @@ + + + + @@ -1104,12 +1272,22 @@ + + + + + + + + + + @@ -1124,8 +1302,14 @@ + + + + + + @@ -1168,8 +1352,22 @@ + + + + + + + + + + + + + + @@ -1188,13 +1386,19 @@ - +
    Method in class __builtin__.object
    __hash__ Method in class __builtin__.type
    __init__Method in class ZSI.TC.TypeCode
    __init__ Method in class __builtin__.object
    __init__Method in class bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg
    __init__ Method in class bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    __init__Method in class bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    __init__Method in class bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    __init__Method in class bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    __init__Method in class bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    __init__ Method in class bioMoby.ontology.DNASequence.MobyDNASequence
    __init__Method in class bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    __init__ Method in class bioMoby.ontology.FASTA.MobyFASTA
    __init__Method in class bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    __init__Method in class bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    __init__ Method in class bioMoby.ontology.GFF.MobyGFF
    __init__Method in class bioMoby.ontology.Germplasm_List.MobyGermplasm_List
    __init__ Method in class bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    __init__Method in class bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    __init__ Method in class bioMoby.ontology.HCA_picture.MobyHCA_picture
    __init__Method in class bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    __init__ Method in class bioMoby.ontology.Interactor.MobyInteractor
    __init__Method in class bioMoby.ontology.MEME_Text.MobyMEME_Text
    __init__Method in class bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    __init__ Method in class bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    __init__Method in class bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    __init__ Method in class bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    __init__Method in class bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    __init__ Method in class bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    __init__Method in class bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE
    __init__ Method in class bioMoby.ontology.RNASequence.MobyRNASequence
    __init__Method in class bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    __init__ Method in class bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID
    __init__Method in class bioMoby.ontology.Snp_genotype.MobySnp_genotype
    __init__ Method in class bioMoby.ontology.Study.MobyStudy
    __init__Method in class bioMoby.ontology.TEST.MobyTEST
    __init__ Method in class bioMoby.ontology.TargetP_result.MobyTargetP_result
    __init__Method in class bioMoby.ontology.Trait_Details.MobyTrait_Details
    __init__ Method in class bioMoby.ontology.Tree.MobyTree
    __init__Method in class bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    __init__Method in class bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    __init__Method in class bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    __init__ Method in class bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    __init__ Method in class bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text
    __init__ Method in class bioMoby.ontology.Wildcard_Query.MobyWildcard_Query
    __init__Method in class bioMoby.webservice.Dispatcher.AbstractDispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.Dispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.LockedIterator
    __init__ Method in class bioMoby.webservice.Dispatcher.MultiThread
    __init__Method in class bioMoby.webservice.Dispatcher.PBSDispatcher
    __init__Method in class bioMoby.webservice.Dispatcher.SimpleDispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.SingleThread
    __init__Method in class bioMoby.webservice.Invocators.GeneralInvocator
    __init__ Method in class bioMoby.webservice.Invocators.LocalInvocator
    __init__Method in class bioMoby.webservice.Invocators.PBSInvocator
    __init__Method in class bioMoby.webservice.Invocators.QsubParameters
    __init__ Method in class exceptions.Exception
    __init__Method in class bioMoby.webservice.Dispatcher.Dispatcher
    _fetchAnswers Method in class bioMoby.webservice.Dispatcher.Dispatcher
    _getResultsMethod in class bioMoby.webservice.Dispatcher.PBSDispatcher
    _getSem Method in class bioMoby.webservice.Dispatcher.Dispatcher
    _marshalMethod in class threading.Thread
    _tailRecurse Method in class bioMoby.webservice.Dispatcher.MultiThread
    _TCBodyClass in module bioMoby.webservice.TCBioMoby
    __initialized Variable in class threading.Thread
    __initialized Variable in class threading.Thread
    _Verbose Class in module threading
    AbstractDispatcherClass in module bioMoby.webservice.Dispatcher
    AGI_LocusCode Module in package bioMoby.ontology
    Allele_freqModule in package bioMoby.ontology
    bioMoby Package
    BodyClass in module bioMoby.webservice.TCBioMoby
    call_method Method in class bioMoby.mobyClient.Central
    CentralClass in module bioMoby.webservice.Invocators
    CGIPostMInvocator Class in module bioMoby.webservice.Invocators
    checknameMethod in class ZSI.TC.TypeCode
    checktypeMethod in class ZSI.TC.TypeCode
    Client Class in module bioMoby.mobyClient
    ClustalAlnFormattedTextModule in package bioMoby.ontology
    CommentedAASequenceModule in package bioMoby.ontology
    CommentedDNASequenceModule in package bioMoby.ontology
    CommentedRNASequenceModule in package bioMoby.ontology
    compress Method in class bioMoby.mobyDataTypes.MobyZmPDB
    contactClass in module exceptions
    execute Method in class bioMoby.mobyService.Service
    executeMethod in class bioMoby.webservice.Dispatcher.AbstractDispatcher
    execute Method in class bioMoby.webservice.Dispatcher.Dispatcher
    executeMethod in class bioMoby.webservice.Dispatcher.PBSDispatcher
    execute Method in class bioMoby.webservice.Invocators.CGIPostInvocator
    execute Method in class bioMoby.webservice.Invocators.CGIPostMInvocator
    execute Method in class bioMoby.webservice.Invocators.LocalInvocator
    executeMethod in class bioMoby.webservice.Invocators.PBSInvocator
    FASTA Module in package bioMoby.ontology
    FASTA_AAModule in package bioMoby.ontology
    FASTA_NAModule in package bioMoby.ontology
    findService Method in class bioMoby.mobyClient.Client
    fromMobyMethod in class bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg
    fromMoby Method in class bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    fromMobyMethod in class bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    fromMobyMethod in class bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    fromMobyMethod in class bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    fromMobyMethod in class bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    fromMoby Method in class bioMoby.ontology.DNASequence.MobyDNASequence
    fromMobyMethod in class bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    fromMoby Method in class bioMoby.ontology.FASTA.MobyFASTA
    fromMobyMethod in class bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    fromMobyMethod in class bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    fromMoby Method in class bioMoby.ontology.GFF.MobyGFF
    fromMobyMethod in class bioMoby.ontology.Germplasm_List.MobyGermplasm_List
    fromMoby Method in class bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    fromMobyMethod in class bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    fromMoby Method in class bioMoby.ontology.HCA_picture.MobyHCA_picture
    fromMobyMethod in class bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    fromMoby Method in class bioMoby.ontology.Interactor.MobyInteractor
    fromMobyMethod in class bioMoby.ontology.MEME_Text.MobyMEME_Text
    fromMobyMethod in class bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    fromMoby Method in class bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    fromMobyMethod in class bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    fromMoby Method in class bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    fromMobyMethod in class bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    fromMoby Method in class bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    fromMobyMethod in class bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE
    fromMoby Method in class bioMoby.ontology.RNASequence.MobyRNASequence
    fromMobyMethod in class bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    fromMoby Method in class bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID
    fromMobyMethod in class bioMoby.ontology.Snp_genotype.MobySnp_genotype
    fromMoby Method in class bioMoby.ontology.Study.MobyStudy
    fromMobyMethod in class bioMoby.ontology.TEST.MobyTEST
    fromMoby Method in class bioMoby.ontology.TargetP_result.MobyTargetP_result
    fromMobyMethod in class bioMoby.ontology.Trait_Details.MobyTrait_Details
    fromMoby Method in class bioMoby.ontology.Tree.MobyTree
    fromMobyMethod in class bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    fromMobyMethod in class bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    fromMobyMethod in class bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    fromMoby Method in class bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    fromMobyModule in package bioMoby.ontology
    get_content_type Method in class bioMoby.webservice.Invocators.CGIPostMInvocator
    get_parse_and_errorlistMethod in class ZSI.TC.TypeCode
    getInfo Method in class bioMoby.mobyDataTypes.MobyObject
    getMethodsModule in package bioMoby.ontology
    Haplotyping_Study_obj Module in package bioMoby.ontology
    HBond_PairModule in package bioMoby.ontology
    HCA_picture Module in package bioMoby.ontology
    ICIS_QueryMethod in class bioMoby.mobyMarshal.MobyMarshaller
    m_unicode Method in class bioMoby.mobyMarshal.MobyMarshaller
    MEME_TextModule in package bioMoby.ontology
    MGIS_ACCESSIONModule in package bioMoby.ontology
    MMP_Locus Module in package bioMoby.ontology
    MO_Term_TestClass in module bioMoby.ontology.BasicGFFSequenceFeature
    mobyClient Module in package bioMoby
    MobyClustalAlnFormattedTextClass in module bioMoby.ontology.ClustalAlnFormattedText
    MobyCommentedAASequenceClass in module bioMoby.ontology.CommentedAASequence
    MobyCommentedDNASequenceClass in module bioMoby.ontology.CommentedDNASequence
    MobyCommentedRNASequenceClass in module bioMoby.ontology.CommentedRNASequence
    MobyContent Class in module bioMoby.mobyDataTypes
    mobyDataTypesModule in package bioMoby
    MobyFASTA Class in module bioMoby.ontology.FASTA
    MobyFASTA_AAClass in module bioMoby.ontology.FASTA_AA
    MobyFASTA_NAClass in module bioMoby.ontology.FASTA_NA
    MobyFloat Class in module bioMoby.mobyDataTypes
    MobyGenbankFlatfileClass in module bioMoby.ontology.GO_Term
    MobyHaplotyping_Study_obj Class in module bioMoby.ontology.Haplotyping_Study_obj
    MobyHBond_PairClass in module bioMoby.ontology.HBond_Pair
    MobyHCA_picture Class in module bioMoby.ontology.HCA_picture
    MobyICIS_QueryModule in package bioMoby
    MobyMarshaller Class in module bioMoby.mobyMarshal
    MobyMEME_TextClass in module bioMoby.ontology.MEME_Text
    MobyMGIS_ACCESSIONClass in module bioMoby.ontology.MGIS_ACCESSION
    MobyMMP_Locus Class in module bioMoby.ontology.MMP_Locus
    MobyMO_Term_TestClass in module bioMoby.ontology.NCBI_BLAST_Text
    MobyNCBI_Blast_XML Class in module bioMoby.ontology.NCBI_Blast_XML
    MobyNCBI_MEME_TextClass in module bioMoby.ontology.NCBI_MEME_Text
    MobyNucleotideSequence Class in module bioMoby.ontology.NucleotideSequence
    MobyObjectClass in module bioMoby.ontology.SimpleAnnotatedGIFImage
    MobySimpleAnnotatedJPEGImage Class in module bioMoby.ontology.SimpleAnnotatedJPEGImage
    MobySINGER_ACCESSIONClass in module bioMoby.ontology.SINGER_ACCESSION
    MobySnp_allele Class in module bioMoby.ontology.Snp_allele
    MobySnp_genotypeClass in module bioMoby.ontology.Study
    MobyTargetP_result Class in module bioMoby.ontology.TargetP_result
    MobyTESTClass in module bioMoby.ontology.TEST
    MobyTestout Class in module bioMoby.ontology.Testout
    MobyText_plainClass in module bioMoby.ontology.Trait_Details
    MobyTree Class in module bioMoby.ontology.Tree
    MobyTropGENE_ACCESSIONClass in module bioMoby.ontology.TropGENE_ACCESSION
    MobyTropGENE_Diversity_MatrixClass in module bioMoby.ontology.TropGENE_Diversity_Matrix
    MobyTropGENE_LOCUSClass in module bioMoby.ontology.TropGENE_LOCUS
    MobyUnmarshaller Class in module bioMoby.mobyMarshal
    MobyVirtualSequenceClass in module bioMoby.webservice.Dispatcher
    MyTree Module in package bioMoby.ontology
    name_matchMethod in class ZSI.TC.TypeCode
    Namespace Class in module bioMoby.mobyRegister
    NCBI_BLAST_Text Module in package bioMoby.ontology
    NCBI_Blast_XML Module in package bioMoby.ontology
    NCBI_MEME_TextModule in package bioMoby.ontology
    next Method in class bioMoby.webservice.Dispatcher.LockedIterator
    nilledMethod in class ZSI.TC.TypeCode
    NucleotideSequence Module in package bioMoby.ontology
    objectPackage in package bioMoby
    Parameter Class in module bioMoby.mobyDataTypes
    parseMethod in class ZSI.TC.TypeCode
    parseMethod in class bioMoby.webservice.TCBioMoby._TCBody
    parselistVariable in class bioMoby.webservice.TCBioMoby.Body
    PBSDispatcherClass in module bioMoby.webservice.Dispatcher
    PBSInvocatorClass in module bioMoby.webservice.Invocators
    PDBFormattedText Module in package bioMoby.ontology
    PDGJOBMethod in class bioMoby.webservice.Invocators.CGIPostMInvocator
    PubMedMEDLINE Module in package bioMoby.ontology
    QsubParametersClass in module bioMoby.webservice.Invocators
    register Method in class bioMoby.mobyRegister.Namespace
    registerModule in package bioMoby.ontology
    Scored_acronym_string Module in package bioMoby.ontology
    serializeMethod in class bioMoby.webservice.TCBioMoby.Body
    seriallistVariable in class bioMoby.webservice.TCBioMoby.Body
    Service Class in module bioMoby.mobyService
    ServiceArticleMethod in class threading.Thread
    setName Method in class threading.Thread
    setParametersMethod in class bioMoby.webservice.Invocators.PBSInvocator
    Simple_key_value_pair Module in package bioMoby.ontology
    simple_valueMethod in class ZSI.TC.TypeCode
    SimpleAnnotatedGIFImage Module in package bioMoby.ontology
    SimpleAnnotatedJPEGImage Module in package bioMoby.ontology
    SimpleDispatcherClass in module bioMoby.webservice.Dispatcher
    SimpleHREFMethod in class ZSI.TC.TypeCode
    SINGER_ACCESSIONModule in package bioMoby.ontology
    SingleThread Class in module bioMoby.webservice.Dispatcher
    Snp_alleleModule in package bioMoby.ontology
    submits2XML Method in class bioMoby.mobyService.ServiceQuery
    tagVariable in class bioMoby.webservice.TCBioMoby.Body
    TargetP_result Module in package bioMoby.ontology
    TCBioMobyModule in package bioMoby.webservice
    TESTModule in package bioMoby.ontology
    Testout Module in package bioMoby.ontology
    Text_plainModule in package bioMoby.ontology
    Tree Module in package bioMoby.ontology
    TropGENE_ACCESSIONModule in package bioMoby.ontology
    TropGENE_Diversity_MatrixModule in package bioMoby.ontology
    TropGENE_LOCUSModule in package bioMoby.ontology
    type Class in module __builtin__
    typechecksVariable in class ZSI.TC.TypeCode
    typechecksVariable in class ZSI.TC.TypeCode
    TypeCodeClass in module ZSI.TC
    typecodeVariable in class bioMoby.webservice.TCBioMoby.Body
    VirtualSequence Module in package bioMoby.ontology
    webservice   Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/threading.Thread-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/threading.Thread-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/threading.Thread-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -197,13 +203,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/threading._Verbose-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/threading._Verbose-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/threading._Verbose-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -112,13 +118,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyClient-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyDataTypes-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyExceptions-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyMarshal-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyRegister-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyService-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology-module.html 2004/12/09 14:07:31 1.3 @@ -22,6 +22,10 @@ B64_Encoded_PNG
    B64_Encoded_Postscript
    BasicGFFSequenceFeature
    +ClustalAlnFormattedText
    +CommentedAASequence
    +CommentedDNASequence
    +CommentedRNASequence
    DateTime
    Decypher_Text
    DNASequence
    @@ -29,6 +33,8 @@ Edge
    EmblFlatfile
    FASTA
    +FASTA_AA
    +FASTA_NA
    GenbankFlatfile
    GenericSequence
    GeneticElement
    @@ -42,6 +48,7 @@ Global_Keyword
    GO_Term
    Haplotyping_Study_obj
    +HBond_Pair
    HCA_picture
    ICIS_Query
    ICIS_Query2
    @@ -51,12 +58,15 @@ Interaction_partner
    InteractionMethod
    Interactor
    +MEME_Text
    +MGIS_ACCESSION
    MMP_Locus
    MO_Term_Test
    Multi_key_value_pair
    MyTree
    NCBI_BLAST_Text
    NCBI_Blast_XML
    +NCBI_MEME_Text
    NucleotideSequence
    PDBFormattedText
    PDGJOB
    @@ -73,10 +83,12 @@ Simple_key_value_pair
    SimpleAnnotatedGIFImage
    SimpleAnnotatedJPEGImage
    +SINGER_ACCESSION
    Snp_allele
    Snp_genotype
    Study
    TargetP_result
    +TEST
    Testout
    Text_plain
    TextBase64
    @@ -87,6 +99,9 @@ TextXml
    Trait_Details
    Tree
    +TropGENE_ACCESSION
    +TropGENE_Diversity_Matrix
    +TropGENE_LOCUS
    VirtualSequence
    Wildcard_Query
    WU_BLAST_Text
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revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Testout-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextBase64-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextFormatted-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextHtml-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextPlain-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextUuencoded-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextXml-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Text_plain-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Trait_Details-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Tree-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.VirtualSequence-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.WU_BLAST_Text-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Wildcard_Query-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice-module.html 2004/12/09 14:07:31 1.3 @@ -15,6 +15,7 @@ Modules
    Dispatcher
    Invocators
    +TCBioMoby


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Dispatcher-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Dispatcher-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Dispatcher-module.html 2004/12/09 14:07:31 1.3 @@ -13,9 +13,12 @@ Classes
    +AbstractDispatcher
    Dispatcher
    LockedIterator
    MultiThread
    +PBSDispatcher
    +SimpleDispatcher
    SingleThread

    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Invocators-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Invocators-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Invocators-module.html 2004/12/09 14:07:31 1.3 @@ -16,8 +16,14 @@ CGIPostInvocator
    CGIPostMInvocator
    GeneralInvocator
    -InvocatorError
    LocalInvocator
    +PBSInvocator
    +QsubParameters
    +
    + + +Exceptions
    +InvocatorError


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-everything.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-everything.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-everything.html 2004/12/09 14:07:31 1.3 @@ -45,6 +45,10 @@ bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG
    bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript
    bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    +bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    +bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    +bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    +bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    bioMoby.ontology.DateTime.MobyDateTime
    bioMoby.ontology.Decypher_Text.MobyDecypher_Text
    bioMoby.ontology.DNASequence.MobyDNASequence
    @@ -52,6 +56,8 @@ bioMoby.ontology.Edge.MobyEdge
    bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    bioMoby.ontology.FASTA.MobyFASTA
    +bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    +bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    bioMoby.ontology.GenbankFlatfile.MobyGenbankFlatfile
    bioMoby.ontology.GenericSequence.MobyGenericSequence
    bioMoby.ontology.GeneticElement.MobyGeneticElement
    @@ -65,6 +71,7 @@ bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    bioMoby.ontology.GO_Term.MobyGO_Term
    bioMoby.ontology.Haplotyping_Study_obj.MobyHaplotyping_Study_obj
    +bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    bioMoby.ontology.HCA_picture.MobyHCA_picture
    bioMoby.ontology.ICIS_Query.MobyICIS_Query
    bioMoby.ontology.ICIS_Query2.MobyICIS_Query2
    @@ -74,12 +81,15 @@ bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    bioMoby.ontology.InteractionMethod.MobyInteractionMethod
    bioMoby.ontology.Interactor.MobyInteractor
    +bioMoby.ontology.MEME_Text.MobyMEME_Text
    +bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    bioMoby.ontology.MO_Term_Test.MobyMO_Term_Test
    bioMoby.ontology.Multi_key_value_pair.MobyMulti_key_value_pair
    bioMoby.ontology.MyTree.MobyMyTree
    bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    +bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText
    bioMoby.ontology.PDGJOB.MobyPDGJOB
    @@ -96,10 +106,12 @@ bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair
    bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage
    bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage
    +bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    bioMoby.ontology.Snp_allele.MobySnp_allele
    bioMoby.ontology.Snp_genotype.MobySnp_genotype
    bioMoby.ontology.Study.MobyStudy
    bioMoby.ontology.TargetP_result.MobyTargetP_result
    +bioMoby.ontology.TEST.MobyTEST
    bioMoby.ontology.Testout.MobyTestout
    bioMoby.ontology.Text_plain.MobyText_plain
    bioMoby.ontology.TextBase64.MobyTextBase64
    @@ -110,18 +122,27 @@ bioMoby.ontology.TextXml.MobyTextXml
    bioMoby.ontology.Trait_Details.MobyTrait_Details
    bioMoby.ontology.Tree.MobyTree
    +bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    +bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    +bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    bioMoby.ontology.Wildcard_Query.MobyWildcard_Query
    bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text
    +bioMoby.webservice.Dispatcher.AbstractDispatcher
    bioMoby.webservice.Dispatcher.Dispatcher
    bioMoby.webservice.Dispatcher.LockedIterator
    bioMoby.webservice.Dispatcher.MultiThread
    +bioMoby.webservice.Dispatcher.PBSDispatcher
    +bioMoby.webservice.Dispatcher.SimpleDispatcher
    bioMoby.webservice.Dispatcher.SingleThread
    bioMoby.webservice.Invocators.CGIPostInvocator
    bioMoby.webservice.Invocators.CGIPostMInvocator
    bioMoby.webservice.Invocators.GeneralInvocator
    -bioMoby.webservice.Invocators.InvocatorError
    bioMoby.webservice.Invocators.LocalInvocator
    +bioMoby.webservice.Invocators.PBSInvocator
    +bioMoby.webservice.Invocators.QsubParameters
    +bioMoby.webservice.TCBioMoby._TCBody
    +bioMoby.webservice.TCBioMoby.Body

    @@ -132,6 +153,7 @@ bioMoby.mobyExceptions.ENotAWSMethod
    bioMoby.mobyExceptions.ETypeMismatch
    bioMoby.webservice.Dispatcher.EDispatchError
    +bioMoby.webservice.Invocators.InvocatorError


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc.html 2004/12/09 14:07:31 1.3 @@ -35,6 +35,10 @@ bioMoby.ontology.B64_Encoded_PNG
    bioMoby.ontology.B64_Encoded_Postscript
    bioMoby.ontology.BasicGFFSequenceFeature
    +bioMoby.ontology.ClustalAlnFormattedText
    +bioMoby.ontology.CommentedAASequence
    +bioMoby.ontology.CommentedDNASequence
    +bioMoby.ontology.CommentedRNASequence
    bioMoby.ontology.DateTime
    bioMoby.ontology.Decypher_Text
    bioMoby.ontology.DNASequence
    @@ -42,6 +46,8 @@ bioMoby.ontology.Edge
    bioMoby.ontology.EmblFlatfile
    bioMoby.ontology.FASTA
    +bioMoby.ontology.FASTA_AA
    +bioMoby.ontology.FASTA_NA
    bioMoby.ontology.GenbankFlatfile
    bioMoby.ontology.GenericSequence
    bioMoby.ontology.GeneticElement
    @@ -55,6 +61,7 @@ bioMoby.ontology.Global_Keyword
    bioMoby.ontology.GO_Term
    bioMoby.ontology.Haplotyping_Study_obj
    +bioMoby.ontology.HBond_Pair
    bioMoby.ontology.HCA_picture
    bioMoby.ontology.ICIS_Query
    bioMoby.ontology.ICIS_Query2
    @@ -64,12 +71,15 @@ bioMoby.ontology.Interaction_partner
    bioMoby.ontology.InteractionMethod
    bioMoby.ontology.Interactor
    +bioMoby.ontology.MEME_Text
    +bioMoby.ontology.MGIS_ACCESSION
    bioMoby.ontology.MMP_Locus
    bioMoby.ontology.MO_Term_Test
    bioMoby.ontology.Multi_key_value_pair
    bioMoby.ontology.MyTree
    bioMoby.ontology.NCBI_BLAST_Text
    bioMoby.ontology.NCBI_Blast_XML
    +bioMoby.ontology.NCBI_MEME_Text
    bioMoby.ontology.NucleotideSequence
    bioMoby.ontology.PDBFormattedText
    bioMoby.ontology.PDGJOB
    @@ -86,10 +96,12 @@ bioMoby.ontology.Simple_key_value_pair
    bioMoby.ontology.SimpleAnnotatedGIFImage
    bioMoby.ontology.SimpleAnnotatedJPEGImage
    +bioMoby.ontology.SINGER_ACCESSION
    bioMoby.ontology.Snp_allele
    bioMoby.ontology.Snp_genotype
    bioMoby.ontology.Study
    bioMoby.ontology.TargetP_result
    +bioMoby.ontology.TEST
    bioMoby.ontology.Testout
    bioMoby.ontology.Text_plain
    bioMoby.ontology.TextBase64
    @@ -100,11 +112,15 @@ bioMoby.ontology.TextXml
    bioMoby.ontology.Trait_Details
    bioMoby.ontology.Tree
    +bioMoby.ontology.TropGENE_ACCESSION
    +bioMoby.ontology.TropGENE_Diversity_Matrix
    +bioMoby.ontology.TropGENE_LOCUS
    bioMoby.ontology.VirtualSequence
    bioMoby.ontology.Wildcard_Query
    bioMoby.ontology.WU_BLAST_Text
    bioMoby.webservice.Dispatcher
    bioMoby.webservice.Invocators
    +bioMoby.webservice.TCBioMoby


    [show private | hide private] =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/trees.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/trees.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/trees.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -51,6 +57,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -58,6 +68,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -71,6 +83,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -80,12 +93,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -102,10 +118,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -116,6 +134,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -124,6 +145,7 @@ @@ -131,6 +153,12 @@

    Class Hierarchy

    @@ -483,8 +564,19 @@
  • bioMoby.ontology.Snp_genotype.MobySnp_genotype: Description: Snp Genotypes Author: www.hapmap.org Contact: hapmap@hapmap.edu +
  • bioMoby.webservice.Dispatcher.AbstractDispatcher: +Subclass this one to create your own dispatcher class a Dispatcher +class must have a execute method +
  • bioMoby.webservice.Dispatcher.LockedIterator: Avoid concurrency on the iterator
  • bioMoby.webservice.Dispatcher.MultiThread: @@ -500,9 +592,14 @@ CGI script in Post multipart
  • bioMoby.webservice.Invocators.LocalInvocator: Invokes local command + -
  • bioMoby.webservice.Invocators.InvocatorError: -Error during an invocation of method + +
  • bioMoby.webservice.Invocators.QsubParameters: +Parameters for the qsub command +
  • bioMoby.webservice.TCBioMoby._TCBody
  • exceptions.Exception: Common base class for all exceptions. @@ -523,13 +622,19 @@
  • - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + From yanwong at pub.open-bio.org Thu Dec 9 09:38:10 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091438.iB9EcAo2003626@pub.open-bio.org> yanwong Thu Dec 9 09:38:10 EST 2004 Update of /home/repository/moby/moby-live/Python/utils In directory pub.open-bio.org:/tmp/cvs-serv3601 Added Files: moby2python.py Log Message: moby-live/Python/utils moby2python.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/utils/moby2python.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/utils/moby2python.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/utils/moby2python.py 2004/12/09 14:38:10 1.3 @@ -1,4 +1,4 @@ -#!/bin/env python +#!/usr/bin/env python #This program will retrieve all objects definitions stored on a bioMoby Server #and generate the corresponding Python Object From yanwong at pub.open-bio.org Thu Dec 9 09:39:05 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:29 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091439.iB9Ed5el003686@pub.open-bio.org> yanwong Thu Dec 9 09:39:05 EST 2004 Update of /home/repository/moby/moby-live/Python/utils/wx In directory pub.open-bio.org:/tmp/cvs-serv3657 Added Files: README objectBrowser.py Log Message: moby-live/Python/utils/wx README,1.2,1.3 objectBrowser.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/utils/wx/README,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/utils/wx/objectBrowser.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From yanwong at pub.open-bio.org Thu Dec 9 09:41:33 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:30 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091441.iB9EfX1b003758@pub.open-bio.org> yanwong Thu Dec 9 09:41:33 EST 2004 Update of /home/repository/moby/moby-live/Python/doc In directory pub.open-bio.org:/tmp/cvs-serv3725 Added Files: api.pdf api.ps epydoc.css howto.pdf index.html Log Message: moby-live/Python/doc api.pdf,NONE,1.1 api.ps,NONE,1.1 epydoc.css,1.2,1.3 howto.pdf,1.2,1.3 index.html,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/epydoc.css,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/howto.pdf,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 Binary files /home/repository/moby/moby-live/Python/doc/howto.pdf 2004/12/08 11:15:22 1.2 and /home/repository/moby/moby-live/Python/doc/howto.pdf 2004/12/09 14:41:33 1.3 differ rcsdiff: /home/repository/moby/moby-live/Python/doc/howto.pdf: diff failed =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/index.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/index.html 2004/12/09 14:41:33 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python From yanwong at pub.open-bio.org Thu Dec 9 09:41:39 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:32 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091441.iB9EfdKr005007@pub.open-bio.org> yanwong Thu Dec 9 09:41:39 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/src In directory pub.open-bio.org:/tmp/cvs-serv3725/src Added Files: howto.sxw Log Message: moby-live/Python/doc/src howto.sxw,NONE,1.1 From yanwong at pub.open-bio.org Thu Dec 9 09:41:39 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu Dec 9 09:41:40 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091441.iB9Efdre004992@pub.open-bio.org> yanwong Thu Dec 9 09:41:35 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/public In directory pub.open-bio.org:/tmp/cvs-serv3725/public Added Files: ZSI.TC.TypeCode-class.html __builtin__.object-class.html __builtin__.type-class.html bioMoby-module.html bioMoby.mobyClient-module.html bioMoby.mobyClient.Central-class.html bioMoby.mobyClient.Client-class.html bioMoby.mobyDataTypes-module.html bioMoby.mobyDataTypes.MobyContent-class.html bioMoby.mobyDataTypes.MobyFloat-class.html bioMoby.mobyDataTypes.MobyInteger-class.html bioMoby.mobyDataTypes.MobyObject-class.html bioMoby.mobyDataTypes.MobySequence-class.html bioMoby.mobyDataTypes.MobyString-class.html bioMoby.mobyDataTypes.MobyXref-class.html 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bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html,1.2,1.3 bioMoby.ontology.B64_encoded_gif-module.html,1.2,1.3 bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html,1.2,1.3 bioMoby.ontology.B64_encoded_jpeg-module.html,1.2,1.3 bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg-class.html,1.2,1.3 bioMoby.ontology.BasicGFFSequenceFeature-module.html,1.2,1.3 bioMoby.ontology.! BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature-class.html,1.2,1.3 bioMoby.ontology.ClustalAlnFormattedText-module.html,NONE,1.1 bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText-class.html,NONE,1.1 bioMoby.ontology.CommentedAASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence-class.html,NONE,1.1 bioMoby.ontology.CommentedDNASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence-class.html,NONE,1.1 bioMoby.ontology.CommentedRNASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence-class.html,NONE,1.1 bioMoby.ontology.DNASequence-module.html,1.2,1.3 bioMoby.ontology.DNASequence.MobyDNASequence-class.html,1.2,1.3 bioMoby.ontology.DNASequenceWithGFFFeatures-module.html,1.2,1.3 bioMoby.ontology.DNASequenceWithGFFFeatures.MobyDNASequenceWithGFFFeatures-class.html,1.2,1.3 bioMoby.ontology.DateTime-module.html,1.2,1.3 bioMoby.ontology.DateTime.M! obyDateTime-class.html,1.2,1.3 bioMoby.ontology.Decypher_Text! 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3 bioMoby.ontology.Interaction_partner.MobyInteraction_partner-class.html,1.2,1.3 bioMoby.ontology.Interactor-module.html,1.2,1.3 bioMoby.ontology.Interactor.MobyInteractor-class.html,1.2,1.3 bioMoby.ontology.MEME_Text-module.html,NONE,1.1 bioMoby.ontology.MEME_Text.MobyMEME_Text-class.html,NONE,1.1 bioMoby.ontology.MGIS_ACCESSION-module.html,NONE,1.1 bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION-class.html,NONE,1.1 bioMoby.ontology.MMP_Locus-module.html,1.2,1.3 bioMoby.ontology.MMP_Locus.MobyMMP_Locus-class.html,1.2,1.3 bioMoby.ontology.MO_Term_Test-module.html,1.2,1.3 bioMoby.ontology.MO_Term_Test.MobyMO_Term_Test-class.html,1.2,1.3 bioMoby.ontology.Multi_key_value_pair-module.html,1.2,1.3 bioMoby.ontology.Multi_key_value_pair.MobyMulti_key_value_pair-class.html,1.2,1.3 bioMoby.ontology.MyTree-module.html,1.2,1.3 bioMoby.ontology.MyTree.MobyMyTree-class.html,1.2,1.3 bioMoby.ontology.NCBI_BLAST_Text-module.html,1.2,1.3 bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Te! xt-class.html,1.2,1.3 bioMoby.ontology.NCBI_Blast_XML-module.! html,1.2,1.3 bioMoby.ontology.NCBI_ Blast_XML.MobyNCBI_Blast_XML-class.html,1.2,1.3 bioMoby.ontology.NCBI_MEME_Text-module.html,NONE,1.1 bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text-class.html,NONE,1.1 bioMoby.ontology.NucleotideSequence-module.html,1.2,1.3 bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence-class.html,1.2,1.3 bioMoby.ontology.PDBFormattedText-module.html,1.2,1.3 bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText-class.html,1.2,1.3 bioMoby.ontology.PDGJOB-module.html,1.2,1.3 bioMoby.ontology.PDGJOB.MobyPDGJOB-class.html,1.2,1.3 bioMoby.ontology.PhenotypeDescription-module.html,1.2,1.3 bioMoby.ontology.PhenotypeDescription.MobyPhenotypeDescription-class.html,1.2,1.3 bioMoby.ontology.PubMedMEDLINE-module.html,1.2,1.3 bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE-class.html,1.2,1.3 bioMoby.ontology.RNASequence-module.html,1.2,1.3 bioMoby.ontology.RNASequence.MobyRNASequence-class.html,1.2,1.3 bioMoby.ontology.SINGER_ACCESSION-module.html,NONE,1.1 bioMoby.ontology.SINGER_ACCESS! ION.MobySINGER_ACCESSION-class.html,NONE,1.1 bioMoby.ontology.SchematikonMotifID-module.html,1.2,1.3 bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID-class.html,1.2,1.3 bioMoby.ontology.SchematikonMotifSupport-module.html,1.2,1.3 bioMoby.ontology.SchematikonMotifSupport.MobySchematikonMotifSupport-class.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentAttributes-module.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentAttributes.MobySchematikonSegmentAttributes-class.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentID-module.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentID.MobySchematikonSegmentID-class.html,1.2,1.3 bioMoby.ontology.SchematikonStructureAnnotation-module.html,1.2,1.3 bioMoby.ontology.SchematikonStructureAnnotation.MobySchematikonStructureAnnotation-class.html,1.2,1.3 bioMoby.ontology.SchematikonVorocodeName-module.html,1.2,1.3 bioMoby.ontology.SchematikonVorocodeName.MobySchematikonVorocodeName-class.html,1.2,1.3 bioMoby.ontology.Scored_acronym_string! -module.html,1.2,1.3 bioMoby.ontology.Scored_acronym_string.M! obyScored_acronym_string-class.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedGIFImage-module.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage-class.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage-class.html,1.2,1.3 bioMoby.ontology.Simple_key_value_pair-module.html,1.2,1.3 bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair-class.html,1.2,1.3 bioMoby.ontology.Snp_allele-module.html,1.2,1.3 bioMoby.ontology.Snp_allele.MobySnp_allele-class.html,1.2,1.3 bioMoby.ontology.Snp_genotype-module.html,1.2,1.3 bioMoby.ontology.Snp_genotype.MobySnp_genotype-class.html,1.2,1.3 bioMoby.ontology.Study-module.html,1.2,1.3 bioMoby.ontology.Study.MobyStudy-class.html,1.2,1.3 bioMoby.ontology.TEST-module.html,NONE,1.1 bioMoby.ontology.TEST.MobyTEST-class.html,NONE,1.1 bioMoby.ontology.TargetP_result-module.html,1.2,1.3 bioMoby.ontology.TargetP_result.Mo! byTargetP_result-class.html,1.2,1.3 bioMoby.ontology.Testout-module.html,1.2,1.3 bioMoby.ontology.Testout.MobyTestout-class.html,1.2,1.3 bioMoby.ontology.TextBase64-module.html,1.2,1.3 bioMoby.ontology.TextBase64.MobyTextBase64-class.html,1.2,1.3 bioMoby.ontology.TextFormatted-module.html,1.2,1.3 bioMoby.ontology.TextFormatted.MobyTextFormatted-class.html,1.2,1.3 bioMoby.ontology.TextHtml-module.html,1.2,1.3 bioMoby.ontology.TextHtml.MobyTextHtml-class.html,1.2,1.3 bioMoby.ontology.TextPlain-module.html,1.2,1.3 bioMoby.ontology.TextPlain.MobyTextPlain-class.html,1.2,1.3 bioMoby.ontology.TextUuencoded-module.html,1.2,1.3 bioMoby.ontology.TextUuencoded.MobyTextUuencoded-class.html,1.2,1.3 bioMoby.ontology.TextXml-module.html,1.2,1.3 bioMoby.ontology.TextXml.MobyTextXml-class.html,1.2,1.3 bioMoby.ontology.Text_plain-module.html,1.2,1.3 bioMoby.ontology.Text_plain.MobyText_plain-class.html,1.2,1.3 bioMoby.ontology.Trait_Details-module.html,1.2,1.3 bioMoby.ontology.Trait_Details.! MobyTrait_Details-class.html,1.2,1.3 bioMoby.ontology.Tree-mo! dule.html,1.2,1.3 bioMoby.ontology.Tree.MobyTree-class.html,1.2,1.3 bioMoby.ontology.TropGENE_ACCESSION-module.html,NONE,1.1 bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION-class.html,NONE,1.1 bioMoby.ontology.TropGENE_Diversity_Matrix-module.html,NONE,1.1 bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix-class.html,NONE,1.1 bioMoby.ontology.TropGENE_LOCUS-module.html,NONE,1.1 bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS-class.html,NONE,1.1 bioMoby.ontology.VirtualSequence-module.html,1.2,1.3 bioMoby.ontology.VirtualSequence.MobyVirtualSequence-class.html,1.2,1.3 bioMoby.ontology.WU_BLAST_Text-module.html,1.2,1.3 bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text-class.html,1.2,1.3 bioMoby.ontology.Wildcard_Query-module.html,1.2,1.3 bioMoby.ontology.Wildcard_Query.MobyWildcard_Query-class.html,1.2,1.3 bioMoby.webservice-module.html,1.2,1.3 bioMoby.webservice.Dispatcher-module.html,1.2,1.3 bioMoby.webservice.Dispatcher.AbstractDispatcher-! class.html,NONE,1.1 bioMoby.webservice.Dispatcher.Dispatcher-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.EDispatchError-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.LockedIterator-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.MultiThread-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.PBSDispatcher-class.html,NONE,1.1 bioMoby.webservice.Dispatcher.SimpleDispatcher-class.html,NONE,1.1 bioMoby.webservice.Dispatcher.SingleThread-class.html,1.2,1.3 bioMoby.webservice.Invocators-module.html,1.2,1.3 bioMoby.webservice.Invocators.CGIPostInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.CGIPostMInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.GeneralInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.InvocatorError-class.html,1.2,1.3 bioMoby.webservice.Invocators.LocalInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.PBSInvocator-class.html,NONE,1.1 bioMoby.webservice.Invocators.QsubParameters-class.html,NONE,1.1 bioMoby.webservice.TCB! ioMoby-module.html,NONE,1.1 bioMoby.webservice.TCBioMoby.Body! -class.html,NONE,1.1 exceptions.Exception-class.html,1.2,1.3 frames.html,1.2,1.3 help.html,1.2,1.3 index.html,1.2,1.3 indices.html,1.2,1.3 threading.Thread-class.html,1.2,1.3 toc-bioMoby-module.html,1.2,1.3 toc-bioMoby.mobyClient-module.html,1.2,1.3 toc-bioMoby.mobyDataTypes-module.html,1.2,1.3 toc-bioMoby.mobyExceptions-module.html,1.2,1.3 toc-bioMoby.mobyMarshal-module.html,1.2,1.3 toc-bioMoby.mobyRegister-module.html,1.2,1.3 toc-bioMoby.mobyService-module.html,1.2,1.3 toc-bioMoby.ontology-module.html,1.2,1.3 toc-bioMoby.ontology.AGI_LocusCode-module.html,1.2,1.3 toc-bioMoby.ontology.Allele_freq-module.html,1.2,1.3 toc-bioMoby.ontology.AminoAcidSequence-module.html,1.2,1.3 toc-bioMoby.ontology.B64_Encoded_PNG-module.html,1.2,1.3 toc-bioMoby.ontology.B64_Encoded_Postscript-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encoded_PDB-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encoded_gif-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encoded_jpeg-module.html,1.2,1.3 toc-bioMoby.! ontology.BasicGFFSequenceFeature-module.html,1.2,1.3 toc-bioMoby.ontology.ClustalAlnFormattedText-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedAASequence-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedDNASequence-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedRNASequence-module.html,NONE,1.1 toc-bioMoby.ontology.DNASequence-module.html,1.2,1.3 toc-bioMoby.ontology.DNASequenceWithGFFFeatures-module.html,1.2,1.3 toc-bioMoby.ontology.DateTime-module.html,1.2,1.3 toc-bioMoby.ontology.Decypher_Text-module.html,1.2,1.3 toc-bioMoby.ontology.Edge-module.html,1.2,1.3 toc-bioMoby.ontology.EmblFlatfile-module.html,1.2,1.3 toc-bioMoby.ontology.FASTA-module.html,1.2,1.3 toc-bioMoby.ontology.FASTA_AA-module.html,NONE,1.1 toc-bioMoby.ontology.FASTA_NA-module.html,NONE,1.1 toc-bioMoby.ontology.GFF-module.html,1.2,1.3 toc-bioMoby.ontology.GFF1-module.html,1.2,1.3 toc-bioMoby.ontology.GFF2-module.html,1.2,1.3 toc-bioMoby.ontology.GFF2_5-module.html,1.2,1.3 toc-bioMoby.ontology.G! FF3-module.html,1.2,1.3 toc-bioMoby.ontology.GO_Term-module.h! tml,1.2,1.3 toc-bioMoby.ontology.Ge nbankFlatfile-module.html,1.2,1.3 toc-bioMoby.ontology.GenericSequence-module.html,1.2,1.3 toc-bioMoby.ontology.GeneticElement-module.html,1.2,1.3 toc-bioMoby.ontology.Germplasm_Details-module.html,1.2,1.3 toc-bioMoby.ontology.Germplasm_List-module.html,1.2,1.3 toc-bioMoby.ontology.Global_Keyword-module.html,1.2,1.3 toc-bioMoby.ontology.HBond_Pair-module.html,NONE,1.1 toc-bioMoby.ontology.HCA_picture-module.html,1.2,1.3 toc-bioMoby.ontology.Haplotyping_Study_obj-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query2-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query3-module.html,1.2,1.3 toc-bioMoby.ontology.IntAct_XML-module.html,1.2,1.3 toc-bioMoby.ontology.Interaction-module.html,1.2,1.3 toc-bioMoby.ontology.InteractionMethod-module.html,1.2,1.3 toc-bioMoby.ontology.Interaction_partner-module.html,1.2,1.3 toc-bioMoby.ontology.Interactor-module.html,1.2,1.3 toc-bioMoby.ontology.MEME_Text-module.html,NONE,1.1 toc-bioMoby.ont! ology.MGIS_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.MMP_Locus-module.html,1.2,1.3 toc-bioMoby.ontology.MO_Term_Test-module.html,1.2,1.3 toc-bioMoby.ontology.Multi_key_value_pair-module.html,1.2,1.3 toc-bioMoby.ontology.MyTree-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_BLAST_Text-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_Blast_XML-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_MEME_Text-module.html,NONE,1.1 toc-bioMoby.ontology.NucleotideSequence-module.html,1.2,1.3 toc-bioMoby.ontology.PDBFormattedText-module.html,1.2,1.3 toc-bioMoby.ontology.PDGJOB-module.html,1.2,1.3 toc-bioMoby.ontology.PhenotypeDescription-module.html,1.2,1.3 toc-bioMoby.ontology.PubMedMEDLINE-module.html,1.2,1.3 toc-bioMoby.ontology.RNASequence-module.html,1.2,1.3 toc-bioMoby.ontology.SINGER_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.SchematikonMotifID-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonMotifSupport-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonSegmentAtt! ributes-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonS! egmentID-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonStructureAnnotation-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonVorocodeName-module.html,1.2,1.3 toc-bioMoby.ontology.Scored_acronym_string-module.html,1.2,1.3 toc-bioMoby.ontology.SimpleAnnotatedGIFImage-module.html,1.2,1.3 toc-bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html,1.2,1.3 toc-bioMoby.ontology.Simple_key_value_pair-module.html,1.2,1.3 toc-bioMoby.ontology.Snp_allele-module.html,1.2,1.3 toc-bioMoby.ontology.Snp_genotype-module.html,1.2,1.3 toc-bioMoby.ontology.Study-module.html,1.2,1.3 toc-bioMoby.ontology.TEST-module.html,NONE,1.1 toc-bioMoby.ontology.TargetP_result-module.html,1.2,1.3 toc-bioMoby.ontology.Testout-module.html,1.2,1.3 toc-bioMoby.ontology.TextBase64-module.html,1.2,1.3 toc-bioMoby.ontology.TextFormatted-module.html,1.2,1.3 toc-bioMoby.ontology.TextHtml-module.html,1.2,1.3 toc-bioMoby.ontology.TextPlain-module.html,1.2,1.3 toc-bioMoby.ontology.TextUuencoded-module.html,1.2,1.! 3 toc-bioMoby.ontology.TextXml-module.html,1.2,1.3 toc-bioMoby.ontology.Text_plain-module.html,1.2,1.3 toc-bioMoby.ontology.Trait_Details-module.html,1.2,1.3 toc-bioMoby.ontology.Tree-module.html,1.2,1.3 toc-bioMoby.ontology.TropGENE_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.TropGENE_Diversity_Matrix-module.html,NONE,1.1 toc-bioMoby.ontology.TropGENE_LOCUS-module.html,NONE,1.1 toc-bioMoby.ontology.VirtualSequence-module.html,1.2,1.3 toc-bioMoby.ontology.WU_BLAST_Text-module.html,1.2,1.3 toc-bioMoby.ontology.Wildcard_Query-module.html,1.2,1.3 toc-bioMoby.webservice-module.html,1.2,1.3 toc-bioMoby.webservice.Dispatcher-module.html,1.2,1.3 toc-bioMoby.webservice.Invocators-module.html,1.2,1.3 toc-bioMoby.webservice.TCBioMoby-module.html,NONE,1.1 toc-everything.html,1.2,1.3 toc.html,1.2,1.3 trees.html,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/__builtin__.object-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/__builtin__.object-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/__builtin__.object-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -245,13 +251,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/__builtin__.type-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/__builtin__.type-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/__builtin__.type-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -489,13 +495,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -58,6 +64,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -65,6 +75,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -78,6 +90,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -87,12 +100,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -109,10 +125,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -123,6 +141,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -131,6 +152,7 @@

  • @@ -143,13 +165,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -57,13 +63,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Central-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Central-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Central-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,7 +60,8 @@ @@ -77,7 +84,8 @@
      __init__(self, url, - ns) + ns, + debug)
    Changes url and ns parameters if you want to use another moby server
    - +

    __init__(self, url='http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral..., - ns='http://mobycentral.cbr.nrc.ca/MOBY/Central') + ns='http://mobycentral.cbr.nrc.ca/MOBY/Central', + debug=False)
    (Constructor)

    Changes url and ns parameters if you want to use another moby @@ -106,13 +114,19 @@
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Client-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Client-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Client-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,12 +60,10 @@ - +
    Method Summary
     __init__(self, + __init__(self, url, ns) -
    -Changes url and ns parameters if you want to use another moby -server
      findService(self, mobyQuery) @@ -141,23 +145,6 @@ Method Details
    - -
    -

    __init__(self, - url='http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral..., - ns='http://mobycentral.cbr.nrc.ca/MOBY/Central') -
    (Constructor) -

    - Changes url and ns parameters if you want to use another moby - server -
    -
    Overrides:
    -
    bioMoby.mobyClient.Central.__init__ (inherited documentation) -
    -
    -
    -
    - - +

    findService(self, @@ -298,13 +285,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -80,13 +86,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyContent-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyContent-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyContent-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +
    @@ -116,13 +122,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyFloat-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyFloat-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyFloat-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
    @@ -110,13 +116,19 @@ - +
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    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyInteger-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyInteger-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyInteger-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -110,13 +116,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyObject-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyObject-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyObject-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -49,6 +55,7 @@ MobyGlobal_Keyword, MobyGO_Term, MobyHaplotyping_Study_obj, + MobyHBond_Pair, MobyICIS_Query, MobyICIS_Query2, MobyICIS_Query3, @@ -57,6 +64,7 @@ MobyInteraction_partner, MobyInteractionMethod, MobyInteractor, + MobyMGIS_ACCESSION, MobyMMP_Locus, MobyMO_Term_Test, MobyMulti_key_value_pair, @@ -70,11 +78,14 @@ MobyScored_acronym_string, MobySequence, MobySimple_key_value_pair, + MobySINGER_ACCESSION, MobyString, MobyStudy, MobyTargetP_result, MobyTestout, MobyTrait_Details, + MobyTropGENE_ACCESSION, + MobyTropGENE_LOCUS, MobyVirtualSequence, MobyWildcard_Query, MobyXref, @@ -162,13 +173,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobySequence-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobySequence-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobySequence-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -57,7 +63,8 @@ - +
    __init__(self, sequence, namespace, - id) + id, + articleName)
      fromMoby(self, @@ -110,13 +117,19 @@    Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyString-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyString-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyString-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
    @@ -99,13 +105,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyXref-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyXref-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyXref-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyZmPDB-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyZmPDB-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyZmPDB-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EInvalidType-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EInvalidType-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EInvalidType-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EMethodRetrieveError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EMethodRetrieveError-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EMethodRetrieveError-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ENotAWSMethod-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ENotAWSMethod-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ENotAWSMethod-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ETypeMismatch-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ETypeMismatch-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ETypeMismatch-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -57,13 +63,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyMarshaller-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyMarshaller-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyMarshaller-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,10 +54,11 @@ - +
    +Serialize the object into a Moby XML object
    Method Summary
     dumps(self, + dumps(self, value, articleName) -
      m_dict(self, value, @@ -115,6 +122,17 @@ Method Details
    + +
    +

    dumps(self, + value, + articleName='') +

    + Serialize the object into a Moby XML object +
    +
    +
    + - +

    m_dict(self, @@ -208,13 +226,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyUnmarshaller-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyUnmarshaller-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyUnmarshaller-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +

    + bioMoby-python +

    +
    @@ -48,9 +54,10 @@ - +
    +Deserializes an xml string and return a bioMoby-Python object
    Method Summary
     loads(self, + loads(self, xml) -
      m_Collection(self, value) @@ -93,6 +100,16 @@ Method Details
    + +
    +

    loads(self, + xml) +

    + Deserializes an xml string and return a bioMoby-Python object +
    +
    +
    + - +

    m_Collection(self, @@ -165,13 +182,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyRegister-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyRegister-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyRegister-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    +
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    +
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    +
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    +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -67,13 +73,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.Service-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.Service-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.Service-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -70,7 +76,8 @@ @@ -82,7 +89,8 @@ +Register the service on the Moby server has been added here a code to +verify that signatureURL is not empty :)
    execute(self, query, method, - returnXml) + returnXml, + debug)
    Executes the web service v0.5: return either the XML form or try to unmarshall the result and return a MobyContent Object
      register(self)
    -Register the service on the Moby server

    @@ -151,7 +159,8 @@

    execute(self, query, method='', - returnXml=True) + returnXml=True, + debug=False)

    Executes the web service v0.5: return either the XML form or try to unmarshall the result and return a MobyContent Object @@ -173,7 +182,8 @@

    register(self)

    - Register the service on the Moby server + Register the service on the Moby server has been added here a code + to verify that signatureURL is not empty :)
    @@ -187,13 +197,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceArticle-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceArticle-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceArticle-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -113,13 +119,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceList-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceList-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceList-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -204,13 +210,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceQuery-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceQuery-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceQuery-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -128,13 +134,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceSecondary-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceSecondary-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceSecondary-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -116,13 +122,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -51,6 +57,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -58,6 +68,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -71,6 +83,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -80,12 +93,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -102,10 +118,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -116,6 +134,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -130,13 +151,19 @@
  • - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -58,13 +64,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -113,13 +119,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -90,13 +96,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,6 +54,10 @@ MobyAminoAcidSequence
    +
    Known Subclasses:
    +
    + MobyCommentedAASequence
    +
    Description: Lightweight representation an amino acid sequence Author: @@ -117,13 +127,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
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    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
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    + bioMoby-python +

    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -116,13 +122,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif-module.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

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    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    @@ -52,6 +58,7 @@
    Known Subclasses:
    + MobyCommentedDNASequence, MobyDNASequenceWithGFFFeatures

    @@ -123,13 +130,19 @@ - +
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    @@ -50,6 +56,11 @@ MobyFASTA
    +
    Known Subclasses:
    +
    + MobyFASTA_AA, + MobyFASTA_NA
    +
    Description: FASTA formatted sequence Author: www.sdsc.edu Contact: @@ -118,13 +129,19 @@ - +
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    Known Subclasses:
    + MobyClustalAlnFormattedText, MobyDecypher_Text, MobyEmblFlatfile, MobyFASTA, MobyGenbankFlatfile, MobyGFF, + MobyMEME_Text, MobyMyTree, MobyNCBI_BLAST_Text, + MobyNCBI_MEME_Text, MobyPDBFormattedText, MobyPubMedMEDLINE, + MobyTEST, MobyTree, + MobyTropGENE_Diversity_Matrix, MobyWU_BLAST_Text

    @@ -130,13 +141,19 @@ - +
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    +
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    @@ -55,13 +62,19 @@    Trees       Index       Help    - + + +
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    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher-module.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher-module.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -43,6 +49,10 @@ + + + + + +
    Classes
    + AbstractDispatcherSubclass this one to create your own dispatcher class a Dispatcher +class must have a execute method
    Dispatcher All Queries in the MobyContent Object are splitted and executed
    @@ -52,6 +62,12 @@ MultiThread Several threads
    + PBSDispatcherDispatcher for PBS jobs
    + SimpleDispatcherA simple dispatcher, without execute method
    SingleThread Definition of a single Thread

    @@ -74,13 +90,19 @@    Trees       Index       Help    - + + +
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    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.Dispatcher-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.Dispatcher-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.Dispatcher-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -38,6 +44,12 @@

    Class Dispatcher

    +
    +AbstractDispatcher --+
    +                     |
    +                    Dispatcher
    +

    +
    All Queries in the MobyContent Object are splitted and executed @@ -92,6 +104,9 @@ [queryData]-->("commandName","commandArgs", ["tempfiles"])
    +
    Overrides:
    +
    bioMoby.webservice.Dispatcher.AbstractDispatcher.__init__
    +
    @@ -103,6 +118,9 @@ Execute the queries with a pool of threads, store the results in a mobyContent Object
    +
    Overrides:
    +
    bioMoby.webservice.Dispatcher.AbstractDispatcher.execute
    +

    @@ -115,13 +133,19 @@    Trees       Index       Help    - + + +
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    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.EDispatchError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.EDispatchError-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.EDispatchError-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -54,11 +60,24 @@ GeneralInvocator - - + + + + +
    General class for other invocators
    - InvocatorErrorError during an invocation of method
    LocalInvocator Invokes local command
    + PBSInvocatorInvokes a command in a qsub
    + QsubParametersParameters for the qsub command

    + + + + + + + +
    Exceptions
    + InvocatorErrorError during an invocation of method

    @@ -69,13 +88,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostInvocator-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostInvocator-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -68,7 +74,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -111,13 +118,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -89,7 +95,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -151,13 +158,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.GeneralInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.GeneralInvocator-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.GeneralInvocator-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -55,17 +61,51 @@ - +
    +queryid is the identifier of a query, userdir is the session +directory, timeout the limit time of execution of the query - +
    Method Summary
     __init__(self, + __init__(self, queryid, userdir, timeout) -
     getResults(self) -
    getResults(self) +
    +retrieve the results if available

    + + + + +
    Method Details
    + + +
    +

    __init__(self, + queryid, + userdir='/tmp', + timeout=None) +
    (Constructor) +

    + queryid is the identifier of a query, userdir is the session + directory, timeout the limit time of execution of the query +
    +
    +
    + + +
    +

    getResults(self) +

    + retrieve the results if available +
    +
    +
    +
    + + @@ -73,13 +113,19 @@ - + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.InvocatorError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.InvocatorError-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.InvocatorError-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -38,6 +44,12 @@

    Class InvocatorError

    +
    +Exception --+
    +            |
    +           InvocatorError
    +

    +
    Error during an invocation of method @@ -51,6 +63,14 @@ + + + + + +
      __str__(self)
        Inherited from Exception
     __init__(...) +
     __getitem__(...) +

    @@ -61,13 +81,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.LocalInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.LocalInvocator-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.LocalInvocator-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -44,6 +50,10 @@ LocalInvocator
    +
    Known Subclasses:
    +
    + PBSInvocator
    +
    Invokes local command @@ -69,7 +79,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -105,13 +116,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/exceptions.Exception-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/exceptions.Exception-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/exceptions.Exception-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -43,7 +49,8 @@ EInvalidType, EMethodRetrieveError, ENotAWSMethod, - ETypeMismatch + ETypeMismatch, + InvocatorError
    @@ -74,13 +81,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/frames.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/frames.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/frames.html 2004/12/09 14:41:34 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/help.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/help.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/help.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -32,7 +38,7 @@

    API Documentation

    This document contains the API (Application Programming Interface) -documentation for this project. Documentation for the Python +documentation for bioMoby-python. Documentation for the Python objects defined by the project is divided into separate pages for each package, module, and class. The API documentation also includes two pages containing information about the project as a whole: a trees @@ -209,13 +215,19 @@

    - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/index.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/index.html 2004/12/09 14:41:34 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/indices.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/indices.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/indices.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:10 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -70,6 +76,8 @@ + + @@ -132,6 +140,14 @@ + + + + + + + + @@ -146,6 +162,10 @@ + + + + @@ -170,6 +190,8 @@ + + @@ -190,6 +212,10 @@ + + + + @@ -202,6 +228,8 @@ + + @@ -214,6 +242,8 @@ + + @@ -240,6 +270,8 @@ + + @@ -262,18 +294,30 @@ + + + + + + + + + + + + @@ -284,6 +328,10 @@ + + + + @@ -368,6 +416,8 @@ + + @@ -398,6 +448,8 @@ + + @@ -406,8 +458,20 @@ + + + + + + + + + + + + @@ -474,16 +538,26 @@ + + + + + + + + + + @@ -518,6 +592,14 @@ + + + + + + + + @@ -532,6 +614,10 @@ + + + + @@ -556,6 +642,8 @@ + + @@ -576,6 +664,10 @@ + + + + @@ -588,6 +680,8 @@ + + @@ -600,6 +694,8 @@ + + @@ -626,6 +722,8 @@ + + @@ -648,6 +746,12 @@ + + + + + + @@ -674,6 +778,8 @@ + + @@ -702,6 +808,8 @@ + + @@ -774,6 +882,10 @@ + + + + @@ -798,6 +910,14 @@ + + + + + + + + @@ -818,6 +938,10 @@ + + + + @@ -846,6 +970,8 @@ + + @@ -870,6 +996,10 @@ + + + + @@ -882,6 +1012,8 @@ + + @@ -922,6 +1054,8 @@ + + @@ -932,6 +1066,8 @@ + + @@ -952,6 +1088,12 @@ + + + + + + @@ -972,14 +1114,20 @@ + + + + + + @@ -990,6 +1138,14 @@ + + + + + + + + @@ -1002,6 +1158,8 @@ + + @@ -1056,6 +1214,10 @@ + + + + @@ -1072,12 +1234,22 @@ + + + + + + + + + + @@ -1092,8 +1264,14 @@ + + + + + + @@ -1136,8 +1314,22 @@ + + + + + + + + + + + + + + @@ -1156,13 +1348,19 @@ - +
    Method in class __builtin__.object
    __hash__ Method in class __builtin__.type
    __init__Method in class ZSI.TC.TypeCode
    __init__ Method in class __builtin__.object
    __init__Method in class bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg
    __init__ Method in class bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    __init__Method in class bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    __init__Method in class bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    __init__Method in class bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    __init__Method in class bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    __init__ Method in class bioMoby.ontology.DNASequence.MobyDNASequence
    __init__Method in class bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    __init__ Method in class bioMoby.ontology.FASTA.MobyFASTA
    __init__Method in class bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    __init__Method in class bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    __init__ Method in class bioMoby.ontology.GFF.MobyGFF
    __init__Method in class bioMoby.ontology.Germplasm_List.MobyGermplasm_List
    __init__ Method in class bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    __init__Method in class bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    __init__ Method in class bioMoby.ontology.HCA_picture.MobyHCA_picture
    __init__Method in class bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    __init__ Method in class bioMoby.ontology.Interactor.MobyInteractor
    __init__Method in class bioMoby.ontology.MEME_Text.MobyMEME_Text
    __init__Method in class bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    __init__ Method in class bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    __init__Method in class bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    __init__ Method in class bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    __init__Method in class bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    __init__ Method in class bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    __init__Method in class bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE
    __init__ Method in class bioMoby.ontology.RNASequence.MobyRNASequence
    __init__Method in class bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    __init__ Method in class bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID
    __init__Method in class bioMoby.ontology.Snp_genotype.MobySnp_genotype
    __init__ Method in class bioMoby.ontology.Study.MobyStudy
    __init__Method in class bioMoby.ontology.TEST.MobyTEST
    __init__ Method in class bioMoby.ontology.TargetP_result.MobyTargetP_result
    __init__Method in class bioMoby.ontology.Trait_Details.MobyTrait_Details
    __init__ Method in class bioMoby.ontology.Tree.MobyTree
    __init__Method in class bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    __init__Method in class bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    __init__Method in class bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    __init__ Method in class bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    __init__ Method in class bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text
    __init__ Method in class bioMoby.ontology.Wildcard_Query.MobyWildcard_Query
    __init__Method in class bioMoby.webservice.Dispatcher.AbstractDispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.Dispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.LockedIterator
    __init__ Method in class bioMoby.webservice.Dispatcher.MultiThread
    __init__Method in class bioMoby.webservice.Dispatcher.PBSDispatcher
    __init__Method in class bioMoby.webservice.Dispatcher.SimpleDispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.SingleThread
    __init__Method in class bioMoby.webservice.Invocators.GeneralInvocator
    __init__ Method in class bioMoby.webservice.Invocators.LocalInvocator
    __init__Method in class bioMoby.webservice.Invocators.PBSInvocator
    __init__Method in class bioMoby.webservice.Invocators.QsubParameters
    __init__ Method in class exceptions.Exception
    __init__Method in class __builtin__.type
    __weakrefoffset__ Variable in class __builtin__.type
    AbstractDispatcherClass in module bioMoby.webservice.Dispatcher
    AGI_LocusCode Module in package bioMoby.ontology
    Allele_freqModule in package bioMoby.ontology
    bioMoby Package
    BodyClass in module bioMoby.webservice.TCBioMoby
    call_method Method in class bioMoby.mobyClient.Central
    CentralClass in module bioMoby.webservice.Invocators
    CGIPostMInvocator Class in module bioMoby.webservice.Invocators
    checknameMethod in class ZSI.TC.TypeCode
    checktypeMethod in class ZSI.TC.TypeCode
    Client Class in module bioMoby.mobyClient
    ClustalAlnFormattedTextModule in package bioMoby.ontology
    CommentedAASequenceModule in package bioMoby.ontology
    CommentedDNASequenceModule in package bioMoby.ontology
    CommentedRNASequenceModule in package bioMoby.ontology
    compress Method in class bioMoby.mobyDataTypes.MobyZmPDB
    contactClass in module exceptions
    execute Method in class bioMoby.mobyService.Service
    executeMethod in class bioMoby.webservice.Dispatcher.AbstractDispatcher
    execute Method in class bioMoby.webservice.Dispatcher.Dispatcher
    executeMethod in class bioMoby.webservice.Dispatcher.PBSDispatcher
    execute Method in class bioMoby.webservice.Invocators.CGIPostInvocator
    execute Method in class bioMoby.webservice.Invocators.CGIPostMInvocator
    execute Method in class bioMoby.webservice.Invocators.LocalInvocator
    executeMethod in class bioMoby.webservice.Invocators.PBSInvocator
    FASTA Module in package bioMoby.ontology
    FASTA_AAModule in package bioMoby.ontology
    FASTA_NAModule in package bioMoby.ontology
    findService Method in class bioMoby.mobyClient.Client
    fromMobyMethod in class bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg
    fromMoby Method in class bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    fromMobyMethod in class bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    fromMobyMethod in class bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    fromMobyMethod in class bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    fromMobyMethod in class bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    fromMoby Method in class bioMoby.ontology.DNASequence.MobyDNASequence
    fromMobyMethod in class bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    fromMoby Method in class bioMoby.ontology.FASTA.MobyFASTA
    fromMobyMethod in class bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    fromMobyMethod in class bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    fromMoby Method in class bioMoby.ontology.GFF.MobyGFF
    fromMobyMethod in class bioMoby.ontology.Germplasm_List.MobyGermplasm_List
    fromMoby Method in class bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    fromMobyMethod in class bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    fromMoby Method in class bioMoby.ontology.HCA_picture.MobyHCA_picture
    fromMobyMethod in class bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    fromMoby Method in class bioMoby.ontology.Interactor.MobyInteractor
    fromMobyMethod in class bioMoby.ontology.MEME_Text.MobyMEME_Text
    fromMobyMethod in class bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    fromMoby Method in class bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    fromMobyMethod in class bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    fromMoby Method in class bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    fromMobyMethod in class bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    fromMoby Method in class bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    fromMobyMethod in class bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE
    fromMoby Method in class bioMoby.ontology.RNASequence.MobyRNASequence
    fromMobyMethod in class bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    fromMoby Method in class bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID
    fromMobyMethod in class bioMoby.ontology.Snp_genotype.MobySnp_genotype
    fromMoby Method in class bioMoby.ontology.Study.MobyStudy
    fromMobyMethod in class bioMoby.ontology.TEST.MobyTEST
    fromMoby Method in class bioMoby.ontology.TargetP_result.MobyTargetP_result
    fromMobyMethod in class bioMoby.ontology.Trait_Details.MobyTrait_Details
    fromMoby Method in class bioMoby.ontology.Tree.MobyTree
    fromMobyMethod in class bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    fromMobyMethod in class bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    fromMobyMethod in class bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    fromMoby Method in class bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    fromMobyModule in package bioMoby.ontology
    get_content_type Method in class bioMoby.webservice.Invocators.CGIPostMInvocator
    get_parse_and_errorlistMethod in class ZSI.TC.TypeCode
    getInfo Method in class bioMoby.mobyDataTypes.MobyObject
    getMethodsModule in package bioMoby.ontology
    Haplotyping_Study_obj Module in package bioMoby.ontology
    HBond_PairModule in package bioMoby.ontology
    HCA_picture Module in package bioMoby.ontology
    ICIS_QueryMethod in class bioMoby.mobyMarshal.MobyMarshaller
    m_unicode Method in class bioMoby.mobyMarshal.MobyMarshaller
    MEME_TextModule in package bioMoby.ontology
    MGIS_ACCESSIONModule in package bioMoby.ontology
    MMP_Locus Module in package bioMoby.ontology
    MO_Term_TestClass in module bioMoby.ontology.BasicGFFSequenceFeature
    mobyClient Module in package bioMoby
    MobyClustalAlnFormattedTextClass in module bioMoby.ontology.ClustalAlnFormattedText
    MobyCommentedAASequenceClass in module bioMoby.ontology.CommentedAASequence
    MobyCommentedDNASequenceClass in module bioMoby.ontology.CommentedDNASequence
    MobyCommentedRNASequenceClass in module bioMoby.ontology.CommentedRNASequence
    MobyContent Class in module bioMoby.mobyDataTypes
    mobyDataTypesModule in package bioMoby
    MobyFASTA Class in module bioMoby.ontology.FASTA
    MobyFASTA_AAClass in module bioMoby.ontology.FASTA_AA
    MobyFASTA_NAClass in module bioMoby.ontology.FASTA_NA
    MobyFloat Class in module bioMoby.mobyDataTypes
    MobyGenbankFlatfileClass in module bioMoby.ontology.GO_Term
    MobyHaplotyping_Study_obj Class in module bioMoby.ontology.Haplotyping_Study_obj
    MobyHBond_PairClass in module bioMoby.ontology.HBond_Pair
    MobyHCA_picture Class in module bioMoby.ontology.HCA_picture
    MobyICIS_QueryModule in package bioMoby
    MobyMarshaller Class in module bioMoby.mobyMarshal
    MobyMEME_TextClass in module bioMoby.ontology.MEME_Text
    MobyMGIS_ACCESSIONClass in module bioMoby.ontology.MGIS_ACCESSION
    MobyMMP_Locus Class in module bioMoby.ontology.MMP_Locus
    MobyMO_Term_TestClass in module bioMoby.ontology.NCBI_BLAST_Text
    MobyNCBI_Blast_XML Class in module bioMoby.ontology.NCBI_Blast_XML
    MobyNCBI_MEME_TextClass in module bioMoby.ontology.NCBI_MEME_Text
    MobyNucleotideSequence Class in module bioMoby.ontology.NucleotideSequence
    MobyObjectClass in module bioMoby.ontology.SimpleAnnotatedGIFImage
    MobySimpleAnnotatedJPEGImage Class in module bioMoby.ontology.SimpleAnnotatedJPEGImage
    MobySINGER_ACCESSIONClass in module bioMoby.ontology.SINGER_ACCESSION
    MobySnp_allele Class in module bioMoby.ontology.Snp_allele
    MobySnp_genotypeClass in module bioMoby.ontology.Study
    MobyTargetP_result Class in module bioMoby.ontology.TargetP_result
    MobyTESTClass in module bioMoby.ontology.TEST
    MobyTestout Class in module bioMoby.ontology.Testout
    MobyText_plainClass in module bioMoby.ontology.Trait_Details
    MobyTree Class in module bioMoby.ontology.Tree
    MobyTropGENE_ACCESSIONClass in module bioMoby.ontology.TropGENE_ACCESSION
    MobyTropGENE_Diversity_MatrixClass in module bioMoby.ontology.TropGENE_Diversity_Matrix
    MobyTropGENE_LOCUSClass in module bioMoby.ontology.TropGENE_LOCUS
    MobyUnmarshaller Class in module bioMoby.mobyMarshal
    MobyVirtualSequenceClass in module bioMoby.webservice.Dispatcher
    MyTree Module in package bioMoby.ontology
    name_matchMethod in class ZSI.TC.TypeCode
    Namespace Class in module bioMoby.mobyRegister
    NCBI_BLAST_Text Module in package bioMoby.ontology
    NCBI_Blast_XML Module in package bioMoby.ontology
    NCBI_MEME_TextModule in package bioMoby.ontology
    next Method in class bioMoby.webservice.Dispatcher.LockedIterator
    nilledMethod in class ZSI.TC.TypeCode
    NucleotideSequence Module in package bioMoby.ontology
    objectPackage in package bioMoby
    Parameter Class in module bioMoby.mobyDataTypes
    parseMethod in class ZSI.TC.TypeCode
    parselistVariable in class bioMoby.webservice.TCBioMoby.Body
    PBSDispatcherClass in module bioMoby.webservice.Dispatcher
    PBSInvocatorClass in module bioMoby.webservice.Invocators
    PDBFormattedText Module in package bioMoby.ontology
    PDGJOBMethod in class bioMoby.webservice.Invocators.CGIPostMInvocator
    PubMedMEDLINE Module in package bioMoby.ontology
    QsubParametersClass in module bioMoby.webservice.Invocators
    register Method in class bioMoby.mobyRegister.Namespace
    registerModule in package bioMoby.ontology
    Scored_acronym_string Module in package bioMoby.ontology
    serializeMethod in class bioMoby.webservice.TCBioMoby.Body
    seriallistVariable in class bioMoby.webservice.TCBioMoby.Body
    Service Class in module bioMoby.mobyService
    ServiceArticleMethod in class threading.Thread
    setName Method in class threading.Thread
    setParametersMethod in class bioMoby.webservice.Invocators.PBSInvocator
    Simple_key_value_pair Module in package bioMoby.ontology
    simple_valueMethod in class ZSI.TC.TypeCode
    SimpleAnnotatedGIFImage Module in package bioMoby.ontology
    SimpleAnnotatedJPEGImage Module in package bioMoby.ontology
    SimpleDispatcherClass in module bioMoby.webservice.Dispatcher
    SimpleHREFMethod in class ZSI.TC.TypeCode
    SINGER_ACCESSIONModule in package bioMoby.ontology
    SingleThread Class in module bioMoby.webservice.Dispatcher
    Snp_alleleModule in package bioMoby.ontology
    submits2XML Method in class bioMoby.mobyService.ServiceQuery
    tagVariable in class bioMoby.webservice.TCBioMoby.Body
    TargetP_result Module in package bioMoby.ontology
    TCBioMobyModule in package bioMoby.webservice
    TESTModule in package bioMoby.ontology
    Testout Module in package bioMoby.ontology
    Text_plainModule in package bioMoby.ontology
    Tree Module in package bioMoby.ontology
    TropGENE_ACCESSIONModule in package bioMoby.ontology
    TropGENE_Diversity_MatrixModule in package bioMoby.ontology
    TropGENE_LOCUSModule in package bioMoby.ontology
    type Class in module __builtin__
    typechecksVariable in class ZSI.TC.TypeCode
    typechecksVariable in class ZSI.TC.TypeCode
    TypeCodeClass in module ZSI.TC
    typecodeVariable in class bioMoby.webservice.TCBioMoby.Body
    VirtualSequence Module in package bioMoby.ontology
    webservice   Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/threading.Thread-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/threading.Thread-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/threading.Thread-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -140,13 +146,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyClient-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyDataTypes-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyExceptions-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyMarshal-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyRegister-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyService-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology-module.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology-module.html 2004/12/09 14:41:35 1.3 @@ -22,6 +22,10 @@ B64_Encoded_PNG
    B64_Encoded_Postscript
    BasicGFFSequenceFeature
    +ClustalAlnFormattedText
    +CommentedAASequence
    +CommentedDNASequence
    +CommentedRNASequence
    DateTime
    Decypher_Text
    DNASequence
    @@ -29,6 +33,8 @@ Edge
    EmblFlatfile
    FASTA
    +FASTA_AA
    +FASTA_NA
    GenbankFlatfile
    GenericSequence
    GeneticElement
    @@ -42,6 +48,7 @@ Global_Keyword
    GO_Term
    Haplotyping_Study_obj
    +HBond_Pair
    HCA_picture
    ICIS_Query
    ICIS_Query2
    @@ -51,12 +58,15 @@ Interaction_partner
    InteractionMethod
    Interactor
    +MEME_Text
    +MGIS_ACCESSION
    MMP_Locus
    MO_Term_Test
    Multi_key_value_pair
    MyTree
    NCBI_BLAST_Text
    NCBI_Blast_XML
    +NCBI_MEME_Text
    NucleotideSequence
    PDBFormattedText
    PDGJOB
    @@ -73,10 +83,12 @@ Simple_key_value_pair
    SimpleAnnotatedGIFImage
    SimpleAnnotatedJPEGImage
    +SINGER_ACCESSION
    Snp_allele
    Snp_genotype
    Study
    TargetP_result
    +TEST
    Testout
    Text_plain
    TextBase64
    @@ -87,6 +99,9 @@ TextXml
    Trait_Details
    Tree
    +TropGENE_ACCESSION
    +TropGENE_Diversity_Matrix
    +TropGENE_LOCUS
    VirtualSequence
    Wildcard_Query
    WU_BLAST_Text
    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology.AGI_LocusCode-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology.Allele_freq-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology.AminoAcidSequence-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology.B64_Encoded_PNG-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 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    Dispatcher
    Invocators
    +TCBioMoby


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Dispatcher-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Dispatcher-module.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Dispatcher-module.html 2004/12/09 14:41:35 1.3 @@ -13,9 +13,12 @@ Classes
    +AbstractDispatcher
    Dispatcher
    LockedIterator
    MultiThread
    +PBSDispatcher
    +SimpleDispatcher
    SingleThread

    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Invocators-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Invocators-module.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Invocators-module.html 2004/12/09 14:41:35 1.3 @@ -16,8 +16,14 @@ CGIPostInvocator
    CGIPostMInvocator
    GeneralInvocator
    -InvocatorError
    LocalInvocator
    +PBSInvocator
    +QsubParameters
    +
    + + +Exceptions
    +InvocatorError


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-everything.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc-everything.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc-everything.html 2004/12/09 14:41:35 1.3 @@ -45,6 +45,10 @@ bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG
    bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript
    bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    +bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    +bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    +bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    +bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    bioMoby.ontology.DateTime.MobyDateTime
    bioMoby.ontology.Decypher_Text.MobyDecypher_Text
    bioMoby.ontology.DNASequence.MobyDNASequence
    @@ -52,6 +56,8 @@ bioMoby.ontology.Edge.MobyEdge
    bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    bioMoby.ontology.FASTA.MobyFASTA
    +bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    +bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    bioMoby.ontology.GenbankFlatfile.MobyGenbankFlatfile
    bioMoby.ontology.GenericSequence.MobyGenericSequence
    bioMoby.ontology.GeneticElement.MobyGeneticElement
    @@ -65,6 +71,7 @@ bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    bioMoby.ontology.GO_Term.MobyGO_Term
    bioMoby.ontology.Haplotyping_Study_obj.MobyHaplotyping_Study_obj
    +bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    bioMoby.ontology.HCA_picture.MobyHCA_picture
    bioMoby.ontology.ICIS_Query.MobyICIS_Query
    bioMoby.ontology.ICIS_Query2.MobyICIS_Query2
    @@ -74,12 +81,15 @@ bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    bioMoby.ontology.InteractionMethod.MobyInteractionMethod
    bioMoby.ontology.Interactor.MobyInteractor
    +bioMoby.ontology.MEME_Text.MobyMEME_Text
    +bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    bioMoby.ontology.MO_Term_Test.MobyMO_Term_Test
    bioMoby.ontology.Multi_key_value_pair.MobyMulti_key_value_pair
    bioMoby.ontology.MyTree.MobyMyTree
    bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    +bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText
    bioMoby.ontology.PDGJOB.MobyPDGJOB
    @@ -96,10 +106,12 @@ bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair
    bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage
    bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage
    +bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    bioMoby.ontology.Snp_allele.MobySnp_allele
    bioMoby.ontology.Snp_genotype.MobySnp_genotype
    bioMoby.ontology.Study.MobyStudy
    bioMoby.ontology.TargetP_result.MobyTargetP_result
    +bioMoby.ontology.TEST.MobyTEST
    bioMoby.ontology.Testout.MobyTestout
    bioMoby.ontology.Text_plain.MobyText_plain
    bioMoby.ontology.TextBase64.MobyTextBase64
    @@ -110,18 +122,26 @@ bioMoby.ontology.TextXml.MobyTextXml
    bioMoby.ontology.Trait_Details.MobyTrait_Details
    bioMoby.ontology.Tree.MobyTree
    +bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    +bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    +bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    bioMoby.ontology.Wildcard_Query.MobyWildcard_Query
    bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text
    +bioMoby.webservice.Dispatcher.AbstractDispatcher
    bioMoby.webservice.Dispatcher.Dispatcher
    bioMoby.webservice.Dispatcher.LockedIterator
    bioMoby.webservice.Dispatcher.MultiThread
    +bioMoby.webservice.Dispatcher.PBSDispatcher
    +bioMoby.webservice.Dispatcher.SimpleDispatcher
    bioMoby.webservice.Dispatcher.SingleThread
    bioMoby.webservice.Invocators.CGIPostInvocator
    bioMoby.webservice.Invocators.CGIPostMInvocator
    bioMoby.webservice.Invocators.GeneralInvocator
    -bioMoby.webservice.Invocators.InvocatorError
    bioMoby.webservice.Invocators.LocalInvocator
    +bioMoby.webservice.Invocators.PBSInvocator
    +bioMoby.webservice.Invocators.QsubParameters
    +bioMoby.webservice.TCBioMoby.Body

    @@ -132,6 +152,7 @@ bioMoby.mobyExceptions.ENotAWSMethod
    bioMoby.mobyExceptions.ETypeMismatch
    bioMoby.webservice.Dispatcher.EDispatchError
    +bioMoby.webservice.Invocators.InvocatorError


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc.html 2004/12/09 14:41:35 1.3 @@ -35,6 +35,10 @@ bioMoby.ontology.B64_Encoded_PNG
    bioMoby.ontology.B64_Encoded_Postscript
    bioMoby.ontology.BasicGFFSequenceFeature
    +bioMoby.ontology.ClustalAlnFormattedText
    +bioMoby.ontology.CommentedAASequence
    +bioMoby.ontology.CommentedDNASequence
    +bioMoby.ontology.CommentedRNASequence
    bioMoby.ontology.DateTime
    bioMoby.ontology.Decypher_Text
    bioMoby.ontology.DNASequence
    @@ -42,6 +46,8 @@ bioMoby.ontology.Edge
    bioMoby.ontology.EmblFlatfile
    bioMoby.ontology.FASTA
    +bioMoby.ontology.FASTA_AA
    +bioMoby.ontology.FASTA_NA
    bioMoby.ontology.GenbankFlatfile
    bioMoby.ontology.GenericSequence
    bioMoby.ontology.GeneticElement
    @@ -55,6 +61,7 @@ bioMoby.ontology.Global_Keyword
    bioMoby.ontology.GO_Term
    bioMoby.ontology.Haplotyping_Study_obj
    +bioMoby.ontology.HBond_Pair
    bioMoby.ontology.HCA_picture
    bioMoby.ontology.ICIS_Query
    bioMoby.ontology.ICIS_Query2
    @@ -64,12 +71,15 @@ bioMoby.ontology.Interaction_partner
    bioMoby.ontology.InteractionMethod
    bioMoby.ontology.Interactor
    +bioMoby.ontology.MEME_Text
    +bioMoby.ontology.MGIS_ACCESSION
    bioMoby.ontology.MMP_Locus
    bioMoby.ontology.MO_Term_Test
    bioMoby.ontology.Multi_key_value_pair
    bioMoby.ontology.MyTree
    bioMoby.ontology.NCBI_BLAST_Text
    bioMoby.ontology.NCBI_Blast_XML
    +bioMoby.ontology.NCBI_MEME_Text
    bioMoby.ontology.NucleotideSequence
    bioMoby.ontology.PDBFormattedText
    bioMoby.ontology.PDGJOB
    @@ -86,10 +96,12 @@ bioMoby.ontology.Simple_key_value_pair
    bioMoby.ontology.SimpleAnnotatedGIFImage
    bioMoby.ontology.SimpleAnnotatedJPEGImage
    +bioMoby.ontology.SINGER_ACCESSION
    bioMoby.ontology.Snp_allele
    bioMoby.ontology.Snp_genotype
    bioMoby.ontology.Study
    bioMoby.ontology.TargetP_result
    +bioMoby.ontology.TEST
    bioMoby.ontology.Testout
    bioMoby.ontology.Text_plain
    bioMoby.ontology.TextBase64
    @@ -100,11 +112,15 @@ bioMoby.ontology.TextXml
    bioMoby.ontology.Trait_Details
    bioMoby.ontology.Tree
    +bioMoby.ontology.TropGENE_ACCESSION
    +bioMoby.ontology.TropGENE_Diversity_Matrix
    +bioMoby.ontology.TropGENE_LOCUS
    bioMoby.ontology.VirtualSequence
    bioMoby.ontology.Wildcard_Query
    bioMoby.ontology.WU_BLAST_Text
    bioMoby.webservice.Dispatcher
    bioMoby.webservice.Invocators
    +bioMoby.webservice.TCBioMoby


    [show private | hide private] =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/trees.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/trees.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/trees.html 2004/12/09 14:41:35 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -51,6 +57,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -58,6 +68,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -71,6 +83,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -80,12 +93,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -102,10 +118,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -116,6 +134,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -124,6 +145,7 @@ @@ -131,6 +153,12 @@

    Class Hierarchy

    @@ -477,8 +558,19 @@
  • bioMoby.ontology.Snp_genotype.MobySnp_genotype: Description: Snp Genotypes Author: www.hapmap.org Contact: hapmap@hapmap.edu +
  • bioMoby.webservice.Dispatcher.AbstractDispatcher: +Subclass this one to create your own dispatcher class a Dispatcher +class must have a execute method +
  • bioMoby.webservice.Dispatcher.LockedIterator: Avoid concurrency on the iterator
  • bioMoby.webservice.Dispatcher.MultiThread: @@ -494,9 +586,13 @@ CGI script in Post multipart
  • bioMoby.webservice.Invocators.LocalInvocator: Invokes local command + -
  • bioMoby.webservice.Invocators.InvocatorError: -Error during an invocation of method + +
  • bioMoby.webservice.Invocators.QsubParameters: +Parameters for the qsub command
  • exceptions.Exception: Common base class for all exceptions. @@ -517,13 +615,19 @@
  • - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + From kawas at pub.open-bio.org Tue Dec 14 13:58:20 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 13:53:07 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141858.iBEIwKdZ009890@pub.open-bio.org> kawas Tue Dec 14 13:58:19 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv9852 Modified Files: Central.pm CommonSubs.pm CrossReference.pm OntologyServer.pm Log Message: hopefully fixed the cdata bug - eddie moby-live/Perl/MOBY Central.pm,1.142,1.143 CommonSubs.pm,1.54,1.55 CrossReference.pm,1.3,1.4 OntologyServer.pm,1.46,1.47 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.142 retrieving revision 1.143 diff -u -r1.142 -r1.143 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/11/18 17:41:14 1.142 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/12/14 18:58:19 1.143 @@ -392,7 +392,7 @@ my $obj = $Object->nodeName; return undef unless ( $obj eq 'registerObjectClass' ); my $term = &_nodeTextContent( $Object, "objectType" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my $authURI = &_nodeTextContent( $Object, "authURI" ); my $email = &_nodeTextContent( $Object, "contactEmail" ); my $clobber = &_nodeTextContent( $Object, "Clobber" ); @@ -696,7 +696,7 @@ my $type = &_nodeTextContent( $Object, "serviceType" ); my $email = &_nodeTextContent( $Object, "contactEmail" ); my $auth = &_nodeTextContent( $Object, "authURI" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my %relationships; my $x = $doc->getElementsByTagName( "Relationship" ); my $no_relationships = $x->size(); @@ -881,7 +881,7 @@ return undef unless ( $obj eq 'registerNamespace' ); my $type = &_nodeTextContent( $Object, "namespaceType" ); my $authURI = &_nodeTextContent( $Object, "authURI" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my $contact = &_nodeTextContent( $Object, "contactEmail" ); return ( $type, $authURI, $desc, $contact ); } @@ -1593,7 +1593,7 @@ &_nodeTextContent( $Object, "authoritativeService" ); my $URL = &_nodeTextContent( $Object, "URL" ); my $signatureURL = &_nodeTextContent( $Object, "signatureURL" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my $INPUTS = &_nodeRawContent( $Object, "Input" ); # returns array ref my $OUTPUTS = &_nodeRawContent( $Object, "Output" ); # returns array ref my $SECONDARIES = @@ -2388,6 +2388,9 @@ my $wsdl = &_getServiceWSDL( $SI, $InputXML, $OutputXML, $SecondaryXML ); if ( $wsdl ) { + if ($wsdl =~ /[^\]]+))\]\]>/) { + $wsdl = $1; + } $wsdls .= "\n"; } @@ -2519,6 +2522,9 @@ my %types = %{ $OS->retrieveAllServiceTypes() }; my $types = "\n"; while ( my ( $serv, $desc ) = each %types ) { + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $types .= "\n\n\n"; } @@ -2558,6 +2564,9 @@ while ( my ( $name, $authdesc ) = each %types ) { my $auth = $authdesc->[0]; my $desc = $authdesc->[1]; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $types .= "\n\n\n"; } @@ -2589,6 +2598,9 @@ my %types = %{ $OS->retrieveAllObjectTypes() }; my $obj = "\n"; while ( my ( $name, $desc ) = each %types ) { + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $obj .= "\n\n\n"; } @@ -2639,6 +2651,9 @@ ; # will return undef if this term does not exist, and does not look like an LSID return "" unless $def; my %def = %{ $OS->retrieveObject( node => $term ) }; + if ($def{description} =~ /[^\]]+))\]\]>/) { + $def{description}= $1; + } my $response; $response = " $def{objectType} @@ -2685,6 +2700,9 @@ my %types = %{ $OS->retrieveAllNamespaceTypes() }; my $ns = "\n"; while ( my ( $namespace, $desc ) = each %types ) { + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $ns .= "\n\n\n"; } @@ -3002,6 +3020,9 @@ $response .= "$cat\n"; $response .= "$type\n"; $response .= "$objectOUT\n"; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $response .= "\n"; $response .= "\n"; if ( $max_return ) { --$max_return; last unless $max_return } @@ -3035,6 +3056,9 @@ my $serviceName = $SI->servicename; my $AuthURI = $SI->authority_uri; my $desc = $SI->description; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } my $URL = $SI->url; my $IN = "NOT_YET_DEFINED_INPUTS"; my $OUT = "NOT_YET_DEFINED_OUTPUTS"; @@ -3075,6 +3099,9 @@ my $sth = $dbh->prepare( $sth{get_server_parameters} ); $sth->execute( $id ); my ( $Object, $sprintf, $in ) = $sth->fetchrow_array(); + if ($sprintf=~ /[^\]]+))\]\]>/) { + $sprintf = $1; + } return ""; } @@ -3197,7 +3224,30 @@ } return $content; } +sub _nodeCDATAContent{ + # will get text of **all** child $node from the given $DOM + # regardless of their depth!! + my ( $DOM, $node ) = @_; + $debug && &_LOG( "_nodeTextContent received DOM: ", + $DOM->toString, "\nsearching for node $node\n" ); + my $x = $DOM->getElementsByTagName( $node ); + return undef unless $x->get_node( 1 ); + my @child = $x->get_node( 1 )->childNodes; + my $content; + foreach ( @child ) { + $debug + && &_LOG( $_->nodeType, "\t", $_->toString, "\n" ); + + #next unless $_->nodeType == TEXT_NODE; + if ($_->toString =~ /[^\]]+))\]\]>/) { + $content .= $1; + } else { + $content .= $_->toString; + } + } + return $content; +} #Eddie - converted sub _nodeRawContent { @@ -3341,6 +3391,9 @@ $authoritative, $email, $signatureURL ) = $sth->fetchrow_array; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } #print "\n\nAFTER EXECUTE $category, $servicename, $service_type_uri, $authority_id, $desc, $authoritative\n\n"; $signatureURL ||= ""; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.54 retrieving revision 1.55 diff -u -r1.54 -r1.55 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/11/18 17:41:14 1.54 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/12/14 18:58:19 1.55 @@ -31,7 +31,7 @@ # [SIMPLE, $queryID, $simple] # the first element is an exported constant SIMPLE, COLLECTION, SECONDARY # the second element is the queryID (required for enumerating the responses) - # the third element is the XML::DOM for the Simple, Collection, or Parameter block + # the third element is the XML::LibXML for the Simple, Collection, or Parameter block my (@inputs)= genericServiceInputParser($data); # or fail properly with an empty response return SOAP::Data->type('base64' => responseHeader("my.authURI.com") . responseFooter()) unless (scalar(@inputs)); @@ -258,9 +258,9 @@ 1. COLLECTION|SIMPLE (i.e. constants 1, 2) 2. queryID 3. $data - the data takes several forms - a. $article XML::DOM node for Simples + a. $article XML::LibXML node for Simples ... - b. \@article XML:DOM nodes for Collections + b. \@article XML:LibXML nodes for Collections for example, the input message: @@ -303,7 +303,7 @@ my ( $message ) = @_; # get the incoming MOBY query XML my @inputs; # set empty response my @queries = - getInputs( $message ); # returns XML::DOM nodes ... + getInputs( $message ); # returns XML::LibXML nodes ... foreach my $query ( @queries ) { my $queryID = getInputID( $query ); # get the queryID attribute of the mobyData @@ -331,7 +331,7 @@ name : DO NOT USE!! function : to take a MOBY message and break the objects out of it. This is identical to the genericServiceInputParser method above, except that it returns the data as - Objects rather than XML::DOM nodes. This is an improvement! + Objects rather than XML::LibXML nodes. This is an improvement! usage : my @inputs = serviceInputParser($MOBY_mssage)); args : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message returns : @inputs - the structure of @inputs is a list of listrefs. @@ -346,7 +346,7 @@ my ( $message ) = @_; # get the incoming MOBY query XML my @inputs; # set empty response my @queries = - getInputs( $message ); # returns XML::DOM nodes ... + getInputs( $message ); # returns XML::LibXML nodes ... # mark, this doesn't work for complex services. We need to allow more than one input per invocation foreach my $query ( @queries ) { @@ -402,7 +402,7 @@ [SECONDARY, $DOM_cutoff] # $DOM_cutoff= block ] - Please see the XML::DOM pod documentation for information about how + Please see the XML::LibXML pod documentation for information about how to parse XML DOM objects. @@ -431,7 +431,7 @@ [SECONDARY, $DOM_cutoff] # $DOM_cutoff = Block ] - Please see the XML::DOM pod documentation for information about how + Please see the XML::LibXML pod documentation for information about how to parse XML DOM objects. @@ -441,7 +441,7 @@ my ( $message ) = @_; # get the incoming MOBY query XML my @inputs; # set empty response my @queries = - getInputs( $message ); # returns XML::DOM nodes ... + getInputs( $message ); # returns XML::LibXML nodes ... my %input_parameters; # $input_parameters{$queryID} = [ foreach my $query ( @queries ) { my $queryID = @@ -470,7 +470,7 @@ name : getArticles function : get the Simple/Collection/Parameter articles for a single mobyData usage : @articles = getArticles($XML) - args : raw XML or XML::DOM of a queryInput, mobyData, or queryResponse block (e.g. from getInputs) + args : raw XML or XML::LibXML of a queryInput, mobyData, or queryResponse block (e.g. from getInputs) returns : a list of listrefs; each listref is one component of the queryInput or mobyData block a single block may consist of one or more named or unnamed simple, collection, or parameter articles. @@ -508,7 +508,7 @@ sub getArticles { my ( $moby ) = @_; - unless ( ref( $moby ) =~ /XML\:\:DOM/ ) { + unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $moby ); $moby = $doc->getDocumentElement(); @@ -548,8 +548,8 @@ usage : my @ids = getSimpleArticleIDs("NCBI_gi", \@SimpleArticles); my @ids = getSimpleArticleIDs(\@SimpleArticles); args : $Namespace - (optional) a namespace stringfrom the MOBY namespace ontology, or undef if you don't care - \@Simples - (required) a listref of Simple XML::DOM nodes - i.e. the XML::DOM representing an XML structure like this: + \@Simples - (required) a listref of Simple XML::LibXML nodes + i.e. the XML::LibXML representing an XML structure like this: @@ -643,8 +643,8 @@ name : getSimpleArticleNamespaceURI function : to get the namespace of a simple article usage : my $ns = getSimpleArticleNamespaceURI($SimpleArticle); - args : $Simple - (required) a single XML::DOM node representing a Simple Article - i.e. the XML::DOM representing an XML structure like this: + args : $Simple - (required) a single XML::LibXML node representing a Simple Article + i.e. the XML::LibXML representing an XML structure like this: @@ -700,7 +700,7 @@ my ( $data, $articleName, $qID ) = @_; # articleName optional $qID = &_getQueryID( $qID ) if ref( $qID ) =~ - /XML::DOM/; # in case they send the DOM instead of the ID + /XML::LibXML/; # in case they send the DOM instead of the ID $data ||= ''; # initialize to avoid uninit value errors $qID ||= ""; $articleName ||= ""; @@ -726,7 +726,7 @@ #Eddie - converted sub _getQueryID { my ( $query ) = @_; - unless ( ref( $query ) =~ /XML\:\:DOM/ ) { + unless ( ref( $query ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $query ); $query = $doc->getDocumentElement(); @@ -849,10 +849,10 @@ =head2 getInputs name : getInputs - function : get the mobyData block(s) as XML::DOM nodes + function : get the mobyData block(s) as XML::LibXML nodes usage : @queryInputs = getInputArticles($XML) - args : the raw XML of a query, or an XML::DOM document - returns : a list of XML::DOM::Node's, each is a queryInput or mobyData block. + args : the raw XML of a query, or an XML::LibXML document + returns : a list of XML::LibXML::Node's, each is a queryInput or mobyData block. Note : Remember that these blocks are enumerated! This is what you pass as the third argument to the simpleResponse or collectionResponse subroutine to associate the numbered input to the numbered response @@ -863,7 +863,7 @@ sub getInputs { my ( $XML ) = @_; my $moby; - unless ( ref( $XML ) =~ /XML\:\:DOM/ ) { + unless ( ref( $XML ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $XML ); $moby = $doc->getDocumentElement(); @@ -887,7 +887,7 @@ name : getInputID function : get the value of the queryID element usage : @queryInputs = getInputID($XML) - args : the raw XML or XML::DOM of a queryInput or mobyData block (e.g. from getInputs) + args : the raw XML or XML::LibXML of a queryInput or mobyData block (e.g. from getInputs) returns : integer, or '' Note : Inputs and Responses are coordinately enumerated! The integer you get here is what you @@ -898,7 +898,7 @@ sub getInputID { my ( $XML ) = @_; - unless ( ref( $XML ) =~ /XML\:\:DOM/ ) { + unless ( ref( $XML ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $XML ); $XML = $doc->getDocumentElement(); @@ -918,7 +918,7 @@ or queryResponse node, rethrning them as SimpleArticle, SecondaryArticle, or ServiceInstance objects usage : @articles = getArticles($XML) - args : raw XML or XML::DOM of a moby:mobyData block + args : raw XML or XML::LibXML of a moby:mobyData block returns : =cut @@ -926,7 +926,7 @@ #Eddie - converted sub getArticlesAsObjects { my ( $moby ) = @_; - unless ( ref( $moby ) =~ /XML\:\:DOM/ ) { + unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $moby ); $moby = $doc->getDocumentElement(); @@ -964,14 +964,14 @@ name : getCollectedSimples function : get the Simple articles collected in a moby:Collection block usage : @Simples = getCollectedSimples($XML) - args : raw XML or XML::DOM of a moby:Collection block - returns : a list of XML::DOM nodes, each of which is a moby:Simple block + args : raw XML or XML::LibXML of a moby:Collection block + returns : a list of XML::LibXML nodes, each of which is a moby:Simple block =cut sub getCollectedSimples { my ( $moby ) = @_; - unless ( ref( $moby ) =~ /XML\:\:DOM/ ) { + unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $moby ); $moby = $doc->getDocumentElement(); @@ -997,7 +997,7 @@ args : the raw XML of a moby:MOBY query returns : a list of listrefs, each listref is the input to a single query. Remember that the input to a single query may be one or more Simple - and/or Collection articles. These are provided as XML::DOM nodes. + and/or Collection articles. These are provided as XML::LibXML nodes. i.e.: @queries = ([$SIMPLE_DOM_NODE], [$SIMPLE_DOM_NODE2]) or : @queries = ([$COLLECTION_DOM_NODE], [$COLLECTION_DOM_NODE2]) @@ -1024,7 +1024,7 @@ #Eddie - converted sub getInputArticles { my ( $moby ) = @_; - unless ( ref( $moby ) =~ /XML\:\:DOM/ ) { + unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $moby ); $moby = $doc->getDocumentElement(); @@ -1054,7 +1054,7 @@ name : isSimpleArticle function : tests XML (text) or an XML DOM node to see if it represents a Simple article usage : if (isSimpleArticle($node)){do something to it} - input : an XML::DOM node, an XML::DOM::Document or straight XML + input : an XML::LibXML node, an XML::LibXML::Document or straight XML returns : boolean =cut @@ -1062,7 +1062,7 @@ #Eddie - converted sub isSimpleArticle { my ( $DOM ) = @_; - unless ( ref( $DOM ) =~ /XML\:\:DOM/ ) { + unless ( ref( $DOM ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc; eval { $doc = $parser->parse_string( $DOM ); }; @@ -1079,7 +1079,7 @@ name : isCollectionArticle function : tests XML (text) or an XML DOM node to see if it represents a Collection article usage : if (isCollectionArticle($node)){do something to it} - input : an XML::DOM node, an XML::DOM::Document or straight XML + input : an XML::LibXML node, an XML::LibXML::Document or straight XML returns : boolean =cut @@ -1087,7 +1087,7 @@ #Eddie - converted sub isCollectionArticle { my ( $DOM ) = @_; - unless ( ref( $DOM ) =~ /XML\:\:DOM/ ) { + unless ( ref( $DOM ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc; eval { $doc = $parser->parse_string( $DOM ); }; @@ -1104,7 +1104,7 @@ name : isSecondaryArticle function : tests XML (text) or an XML DOM node to see if it represents a Secondary article usage : if (isSecondaryArticle($node)){do something to it} - input : an XML::DOM node, an XML::DOM::Document or straight XML + input : an XML::LibXML node, an XML::LibXML::Document or straight XML returns : boolean =cut @@ -1112,7 +1112,7 @@ #Eddie - converted sub isSecondaryArticle { my ( $DOM ) = @_; - unless ( ref( $DOM ) =~ /XML\:\:DOM/ ) { + unless ( ref( $DOM ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc; eval { $doc = $parser->parse( _string $DOM); }; @@ -1138,7 +1138,7 @@ sub extractRawContent { my ( $article ) = @_; return "" unless $article; - return "" unless ref( $article ) =~ /XML::DOM/; + return "" unless ref( $article ) =~ /XML::LibXML/; my $response; foreach ( $article->childNodes ) { $response .= $_->toString; @@ -1154,7 +1154,7 @@ or get the value of a Parameter element. usage : @strings = getNodeContentWithArticle($node, $tagname, $articleName) args : (in order) - $node - an XML::DOM node, or straight XML. It may even + $node - an XML::LibXML node, or straight XML. It may even be the entire mobyData block. $tagname - the tagname (effectively from the Object type ontology), or "Parameter" if you are trying to get secondaries @@ -1243,7 +1243,7 @@ # carriage returns, as these might be meaningful! my ( $node, $element, $articleName ) = @_; my @contents; - return () unless ref( $node ) =~ /XML::DOM/; + return () unless ref( $node ) =~ /XML::LibXML/; return () unless $element; return () unless $articleName; my $nodes = $node->getElementsByTagName( $element ); @@ -1355,9 +1355,9 @@ function : get the DOM nodes corresponding to individual Simple or Collection outputs from a MOBY Response usage : ($collections, $simples) = getResponseArticles($node) - args : $node - either raw XML or an XML::DOM::Document to be searched - returns : an array-ref of Collection article XML::DOM::Node's - an array-ref of Simple article XML::DOM::Node's + args : $node - either raw XML or an XML::LibXML::Document to be searched + returns : an array-ref of Collection article XML::LibXML::Node's + an array-ref of Simple article XML::LibXML::Node's =cut @@ -1369,7 +1369,7 @@ my ( $result ) = @_; return ( [], [] ) unless $result; my $moby; - unless ( ref( $result ) =~ /XML\:\:DOM/ ) { + unless ( ref( $result ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $result ); $moby = $doc->getDocumentElement(); @@ -1426,7 +1426,7 @@ name : getServiceNotes function : to get the content of the Service Notes block of the MOBY message usage : getServiceNotes($message) - args : $message is either the XML::DOM of the MOBY message, or plain XML + args : $message is either the XML::LibXML of the MOBY message, or plain XML returns : String content of the ServiceNotes block of the MOBY Message =cut @@ -1436,7 +1436,7 @@ my ( $result ) = @_; return ( "" ) unless $result; my $moby; - unless ( ref( $result ) =~ /XML\:\:DOM/ ) { + unless ( ref( $result ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $result ); $moby = $doc->getDocumentElement(); @@ -1470,7 +1470,7 @@ usage : @xrefs = getCrossReferences($XML) args : $XML is either a SIMPLE article (...) or an object (the payload of a Simple article), and - may be either raw XML or an XML::DOM node. + may be either raw XML or an XML::LibXML node. returns : an array of MOBY::CrossReference objects example : @@ -1492,7 +1492,7 @@ #Eddie - converted sub getCrossReferences { my ( $XML ) = @_; - unless ( ref( $XML ) =~ /XML::DOM/ ) { + unless ( ref( $XML ) =~ /XML::LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $XML ); $XML = $doc->getDocumentElement(); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CrossReference.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.46 retrieving revision 1.47 diff -u -r1.46 -r1.47 From kawas at pub.open-bio.org Tue Dec 14 13:58:20 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 13:53:29 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141858.iBEIwK9J009921@pub.open-bio.org> kawas Tue Dec 14 13:58:20 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv9852/Client Modified Files: Central.pm OntologyServer.pm Registration.pm Service.pm Log Message: hopefully fixed the cdata bug - eddie moby-live/Perl/MOBY/Client Central.pm,1.81,1.82 OntologyServer.pm,1.7,1.8 Registration.pm,1.7,1.8 Service.pm,1.13,1.14 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.81 retrieving revision 1.82 diff -u -r1.81 -r1.82 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/11/18 17:41:15 1.81 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/14 18:58:20 1.82 @@ -3,6 +3,7 @@ use SOAP::Lite; #use SOAP::Lite + trace; # for debugging + use strict; use Carp; use XML::LibXML; @@ -376,6 +377,9 @@ $term ||= ""; my $desc = $a{'description'}; $desc ||= ""; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } my $contactEmail = $a{'contactEmail'}; $contactEmail ||= ""; my $authURI = $a{'authURI'}; @@ -504,7 +508,7 @@ my $obj = $Object->nodeName; return undef unless ( $obj eq 'retrieveObjectDefinition' ); my $term = &_nodeTextContent( $Object, "objectType" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my $authURI = &_nodeTextContent( $Object, "authURI" ); my $email = &_nodeTextContent( $Object, "contactEmail" ); my %att_value; @@ -565,6 +569,9 @@ my $type = $a{'serviceType'}; $type ||= ""; my $desc = $a{'description'}; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $desc ||= ""; my $email = $a{'contactEmail'}; $email ||= ""; @@ -645,6 +652,9 @@ my $authURI = $a{'authURI'}; $authURI ||= ""; my $desc = $a{'description'}; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $desc ||= ""; my $contact = $a{'contactEmail'}; $contact ||= ""; @@ -758,6 +768,9 @@ $URL ||= ""; my $desc = $a{description}; $desc ||= ""; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } my $signatureURL = $a{signatureURL}; $signatureURL ||= ""; my $Category = lc( $a{category} ); @@ -1197,7 +1210,11 @@ foreach ( @child ) { $debug && &_LOG( getNodeTypeName($_), "\t", $_->toString, "\n" ); if ( $_->nodeType == TEXT_NODE ) { - $content .= $_->nodeValue; #else try $_->textContent + if ($_->nodeValue=~ /[^\]]+))\]\]>/) { + $content .= $1; + } else { + $content .= $_->nodeValue; #else try $_->textContent + } } else { $content .= $_->toString; } @@ -1305,6 +1322,9 @@ $types->get_node( $x )->getElementsByTagName( 'Description' ) ) { $desc = $elem->firstChild->toString; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } } $servicetypes{$type} = $desc; } @@ -1344,6 +1364,9 @@ $obnames->get_node( $x )->getElementsByTagName( 'Description' ) ) { $desc = $elem->firstChild->toString; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } } $objectnames{$name} = $desc; } @@ -1383,6 +1406,9 @@ { $desc = $elem->firstChild; $desc = $desc ? $desc->toString : ""; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } } $namespaces{$ns} = $desc; } @@ -1429,6 +1455,9 @@ $objects->get_node( $x )->getElementsByTagName( 'Schema' ) ) { $desc = $elem->firstChild->nodeValue; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } } $objects{$name} = $desc; } @@ -1628,7 +1657,7 @@ my $URL = &_nodeTextContent( $Service, 'URL' ); #my $Output = &_nodeTextContent($Service, 'outputObject'); - my $Description = &_nodeTextContent( $Service, 'Description' ); + my $Description = &_nodeCDATAContent( $Service, 'Description' ); my $cat = &_nodeTextContent( $Service, 'Category' ); my @INPUTS; my @OUTPUTS; @@ -1793,7 +1822,7 @@ return undef unless ( $obj eq 'MOBYRegistration' ); my $id = &_nodeTextContent( $Object, 'id' ); my $success = &_nodeTextContent( $Object, 'success' ); - my $message = &_nodeTextContent( $Object, 'message' ); + my $message = &_nodeCDATAContent( $Object, 'message' ); my $RDF = &_nodeRawContent( $Object, 'RDF' ); my $reg = MOBY::Client::Registration->new( success => $success, @@ -1814,7 +1843,25 @@ ); return $reg; } - +sub _nodeCDATAContent { + # will get text of **all** child $node from the given $DOM + # regardless of their depth!! + my ( $DOM, $node ) = @_; + my $x = $DOM->getElementsByTagName( $node ); + unless ( $x->get_node( 1 ) ) { return } + my @child = $x->get_node( 1 )->childNodes; + my $content; + foreach ( @child ) { + #print getNodeTypeName($_), "\t", $_->toString,"\n"; + next unless $_->nodeType == TEXT_NODE; + $content = $_->toString; + if ($content =~ /[^\]]+))\]\]>/) { + $content = $1; + return $content; + } + } + return $content; +} sub _nodeTextContent { # will get text of **all** child $node from the given $DOM @@ -1825,7 +1872,6 @@ my @child = $x->get_node( 1 )->childNodes; my $content; foreach ( @child ) { - #print getNodeTypeName($_), "\t", $_->toString,"\n"; next unless $_->nodeType == TEXT_NODE; $content = $_->toString; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 From kawas at pub.open-bio.org Tue Dec 14 14:10:19 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:05:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141910.iBEJAJcD010047@pub.open-bio.org> kawas Tue Dec 14 14:10:18 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv10008 Modified Files: Central.pm CommonSubs.pm CrossReference.pm OntologyServer.pm Log Message: hopefully fixed the cdata bug - eddie (part 2 - i hate cvs) moby-live/Perl/MOBY Central.pm,1.143,1.144 CommonSubs.pm,1.55,1.56 CrossReference.pm,1.4,1.5 OntologyServer.pm,1.47,1.48 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.143 retrieving revision 1.144 diff -u -r1.143 -r1.144 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.55 retrieving revision 1.56 diff -u -r1.55 -r1.56 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CrossReference.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.47 retrieving revision 1.48 diff -u -r1.47 -r1.48 From kawas at pub.open-bio.org Tue Dec 14 14:10:19 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:05:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141910.iBEJAJdX010079@pub.open-bio.org> kawas Tue Dec 14 14:10:19 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv10008/Client Modified Files: Central.pm OntologyServer.pm Registration.pm Service.pm Log Message: hopefully fixed the cdata bug - eddie (part 2 - i hate cvs) moby-live/Perl/MOBY/Client Central.pm,1.82,1.83 OntologyServer.pm,1.8,1.9 Registration.pm,1.8,1.9 Service.pm,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.82 retrieving revision 1.83 diff -u -r1.82 -r1.83 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:13 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXJw010917@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY added to the repository moby-live/Perl/MOBY/MOBY - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:14 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXdk010935@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/Adaptor Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor added to the repository moby-live/Perl/MOBY/MOBY/Adaptor - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXSU010953@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/Adaptor/moby Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby added to the repository moby-live/Perl/MOBY/MOBY/Adaptor/moby - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXol011011@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/RDF Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF added to the repository moby-live/Perl/MOBY/MOBY/RDF - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXjn010972@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/Adaptor/moby/queryapi Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi added to the repository moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:17 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiX7a010993@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/Client Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client added to the repository moby-live/Perl/MOBY/MOBY/Client - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiX1t011034@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/lsid Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid added to the repository moby-live/Perl/MOBY/MOBY/lsid - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:34 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:20 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiYiN011055@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/lsid/authority Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority added to the repository moby-live/Perl/MOBY/MOBY/lsid/authority - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:26 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJikC3011162@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11077 Added Files: MobyXMLRetriever.pl myScript.pl Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY MobyXMLRetriever.pl,NONE,1.1 myScript.pl,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 14:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiklW011100@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/Client Added Files: Central.pm CollectionArticle.pm Registration.pm SecondaryArticle.pm OntologyServer.pm ServiceInstance.pm SimpleArticle.pm SimpleInput.pm Service.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/Client Central.pm,NONE,1.1 CollectionArticle.pm,NONE,1.1 Registration.pm,NONE,1.1 SecondaryArticle.pm,NONE,1.1 OntologyServer.pm,NONE,1.1 ServiceInstance.pm,NONE,1.1 SimpleArticle.pm,NONE,1.1 SimpleInput.pm,NONE,1.1 Service.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 14:44:47 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiljX011182@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/Adaptor/moby Added Files: queryapi.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/Adaptor/moby queryapi.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 14:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:28 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJikZH011132@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY Added Files: service_type.pm collection_input.pm CommonSubs.pm Central.pm MobyXMLConstants.pm OntologyServer.pm secondary_input.pm simple_output.pm service_instance.pm CrossReference.pm collection_output.pm mysql.pm dbConfig.pm central_db_connection.pm Config.pm authority.pm simple_input.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY service_type.pm,NONE,1.1 collection_input.pm,NONE,1.1 CommonSubs.pm,NONE,1.1 Central.pm,NONE,1.1 MobyXMLConstants.pm,NONE,1.1 OntologyServer.pm,NONE,1.1 secondary_input.pm,NONE,1.1 simple_output.pm,NONE,1.1 service_instance.pm,NONE,1.1 CrossReference.pm,NONE,1.1 collection_output.pm,NONE,1.1 mysql.pm,NONE,1.1 dbConfig.pm,NONE,1.1 central_db_connection.pm,NONE,1.1 Config.pm,NONE,1.1 authority.pm,NONE,1.1 simple_input.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 14:44:47 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:29 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJilk8011199@pub.open-bio.org> kawas Tue Dec 14 14:44:47 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/Adaptor/moby/queryapi Added Files: mysql.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi mysql.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 14:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:30 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJikmA011115@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/lsid/authority Added Files: ClassResolver.pm authority.pl NamespaceResolver.pm RDFConfigure.pm dbConfigure.pm.template dbConnect.pm ServiceInstanceResolver.pm Error.pm ServiceResolver.pm PredicateResolver.pm lsid_resolver.kpf metadata.pl RelationshipResolver.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/lsid/authority ClassResolver.pm,NONE,1.1 authority.pl,NONE,1.1 NamespaceResolver.pm,NONE,1.1 RDFConfigure.pm,NONE,1.1 dbConfigure.pm.template,NONE,1.1 dbConnect.pm,NONE,1.1 ServiceInstanceResolver.pm,NONE,1.1 Error.pm,NONE,1.1 ServiceResolver.pm,NONE,1.1 PredicateResolver.pm,NONE,1.1 lsid_resolver.kpf,NONE,1.1 metadata.pl,NONE,1.1 RelationshipResolver.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 14:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 14:39:31 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJikRH011147@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/RDF Added Files: ServiceInstanceRDF.pm InOutArticlesRDF.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/RDF ServiceInstanceRDF.pm,NONE,1.1 InOutArticlesRDF.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 15:36:49 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 15:31:25 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142036.iBEKanI8011390@pub.open-bio.org> kawas Tue Dec 14 15:36:49 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11354/MOBY Modified Files: Central.pm Log Message: fixed typo - get_Node -> get_node moby-live/Perl/MOBY/MOBY Central.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Central.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/MOBY/Central.pm 2004/12/14 19:44:46 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/MOBY/Central.pm 2004/12/14 20:36:48 1.2 @@ -2431,7 +2431,7 @@ my $SECONDARY = $doc->getElementsByTagName( "Output" ); my $SecondaryXML = ""; if ( $SECONDARY->get_node( 1 ) ) { - $SecondaryXML = $SECONDARY->get_Node( 1 )->toString; + $SecondaryXML = $SECONDARY->get_node( 1 )->toString; } return ( $authURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML ); } From kawas at pub.open-bio.org Tue Dec 14 15:47:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 15:41:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl4Hs011664@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv11595/Client Modified Files: Central.pm OntologyServer.pm Registration.pm Service.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/Client Central.pm,1.83,1.84 OntologyServer.pm,1.9,1.10 Registration.pm,1.9,1.10 Service.pm,1.15,1.16 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.83 retrieving revision 1.84 diff -u -r1.83 -r1.84 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 From kawas at pub.open-bio.org Tue Dec 14 15:47:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 15:41:40 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl477011632@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11595 Modified Files: Central.pm CommonSubs.pm CrossReference.pm OntologyServer.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY Central.pm,1.144,1.145 CommonSubs.pm,1.56,1.57 CrossReference.pm,1.5,1.6 OntologyServer.pm,1.48,1.49 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.144 retrieving revision 1.145 diff -u -r1.144 -r1.145 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.56 retrieving revision 1.57 diff -u -r1.56 -r1.57 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CrossReference.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.48 retrieving revision 1.49 diff -u -r1.48 -r1.49 From kawas at pub.open-bio.org Tue Dec 14 15:47:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 15:41:41 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl43b011717@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/Adaptor/moby Removed Files: queryapi.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/Adaptor/moby queryapi.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/RCS/queryapi.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 15:47:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 15:41:44 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl4L9011701@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY Removed Files: Central.pm CommonSubs.pm Config.pm CrossReference.pm MobyXMLConstants.pm OntologyServer.pm authority.pm central_db_connection.pm collection_input.pm collection_output.pm dbConfig.pm mysql.pm secondary_input.pm service_instance.pm service_type.pm simple_input.pm simple_output.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY Central.pm,1.2,NONE CommonSubs.pm,1.1,NONE Config.pm,1.1,NONE CrossReference.pm,1.1,NONE MobyXMLConstants.pm,1.1,NONE OntologyServer.pm,1.1,NONE authority.pm,1.1,NONE central_db_connection.pm,1.1,NONE collection_input.pm,1.1,NONE collection_output.pm,1.1,NONE dbConfig.pm,1.1,NONE mysql.pm,1.1,NONE secondary_input.pm,1.1,NONE service_instance.pm,1.1,NONE service_type.pm,1.1,NONE simple_input.pm,1.1,NONE simple_output.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/Central.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/CommonSubs.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/Config.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/CrossReference.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/MobyXMLConstants.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/OntologyServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/authority.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/central_db_connection.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/collection_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/collection_output.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/dbConfig.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/mysql.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/secondary_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/service_instance.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/service_type.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/simple_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/simple_output.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 15:47:05 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 15:41:45 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl5i8011815@pub.open-bio.org> kawas Tue Dec 14 15:47:05 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/lsid/authority Removed Files: ClassResolver.pm Error.pm NamespaceResolver.pm PredicateResolver.pm RDFConfigure.pm RelationshipResolver.pm ServiceInstanceResolver.pm ServiceResolver.pm authority.pl dbConfigure.pm.template dbConnect.pm lsid_resolver.kpf metadata.pl Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/lsid/authority ClassResolver.pm,1.1,NONE Error.pm,1.1,NONE NamespaceResolver.pm,1.1,NONE PredicateResolver.pm,1.1,NONE RDFConfigure.pm,1.1,NONE RelationshipResolver.pm,1.1,NONE ServiceInstanceResolver.pm,1.1,NONE ServiceResolver.pm,1.1,NONE authority.pl,1.1,NONE dbConfigure.pm.template,1.1,NONE dbConnect.pm,1.1,NONE lsid_resolver.kpf,1.1,NONE metadata.pl,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/ClassResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/Error.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/NamespaceResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/PredicateResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/RDFConfigure.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/RelationshipResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/ServiceInstanceResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/ServiceResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/authority.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/dbConfigure.pm.template,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/dbConnect.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/lsid_resolver.kpf,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/metadata.pl,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 15:47:05 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 15:41:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl54D011734@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/Adaptor/moby/queryapi Removed Files: mysql.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi mysql.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi/RCS/mysql.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 15:47:05 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 15:43:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl5HZ011764@pub.open-bio.org> kawas Tue Dec 14 15:47:05 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/Client Removed Files: Central.pm CollectionArticle.pm OntologyServer.pm Registration.pm SecondaryArticle.pm Service.pm ServiceInstance.pm SimpleArticle.pm SimpleInput.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/Client Central.pm,1.1,NONE CollectionArticle.pm,1.1,NONE OntologyServer.pm,1.1,NONE Registration.pm,1.1,NONE SecondaryArticle.pm,1.1,NONE Service.pm,1.1,NONE ServiceInstance.pm,1.1,NONE SimpleArticle.pm,1.1,NONE SimpleInput.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/Central.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/CollectionArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/OntologyServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/Registration.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/SecondaryArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/Service.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/ServiceInstance.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/SimpleArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/SimpleInput.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 15:47:05 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 15:43:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl5td011783@pub.open-bio.org> kawas Tue Dec 14 15:47:05 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/RDF Removed Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/RDF InOutArticlesRDF.pm,1.1,NONE ServiceInstanceRDF.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/InOutArticlesRDF.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/ServiceInstanceRDF.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 15:55:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 15:49:43 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142055.iBEKtBYf011949@pub.open-bio.org> kawas Tue Dec 14 15:55:11 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11923 Modified Files: Central.pm Log Message: fix type in get_node moby-live/Perl/MOBY Central.pm,1.145,1.146 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.145 retrieving revision 1.146 diff -u -r1.145 -r1.146 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/12/14 20:47:04 1.145 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/12/14 20:55:11 1.146 @@ -2431,7 +2431,7 @@ my $SECONDARY = $doc->getElementsByTagName( "Output" ); my $SecondaryXML = ""; if ( $SECONDARY->get_node( 1 ) ) { - $SecondaryXML = $SECONDARY->get_Node( 1 )->toString; + $SecondaryXML = $SECONDARY->get_node( 1 )->toString; } return ( $authURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML ); } From kawas at pub.open-bio.org Tue Dec 14 17:31:30 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 17:26:08 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142231.iBEMVUnp012494@pub.open-bio.org> kawas Tue Dec 14 17:31:30 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv12457/MOBY/Client Modified Files: Central.pm CollectionArticle.pm SimpleArticle.pm SecondaryArticle.pm Log Message: updated the check for dom to check for libxml moby-live/Perl/MOBY/Client Central.pm,1.84,1.85 CollectionArticle.pm,1.10,1.11 SimpleArticle.pm,1.6,1.7 SecondaryArticle.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.84 retrieving revision 1.85 diff -u -r1.84 -r1.85 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/14 20:47:04 1.84 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/14 22:31:30 1.85 @@ -847,6 +847,7 @@ $message .= "\n"; } my ( $type, $Namespaces ) = @{$objectdef}; + $type ||=""; $message .= "$type\n"; unless ( ref( $Namespaces ) =~ /array/i ) { return $self->errorRegXML( =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2004/11/18 17:41:16 1.10 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2004/12/14 22:31:30 1.11 @@ -255,7 +255,7 @@ } if ( $self->XML && ref( $self->XML ) ) { return 0; - } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /dom/i ) ) { + } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /libxml/i ) ) { return 0; } $self->createFromXML if ( $self->XML ); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm 2004/11/18 17:41:16 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm 2004/12/14 22:31:30 1.7 @@ -225,7 +225,7 @@ } if ( $self->XML && ref( $self->XML ) ) { return 0; - } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /dom/i ) ) { + } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /libxml/i ) ) { return 0; } $self->createFromXML if ( $self->XML ); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/11/18 17:41:16 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/12/14 22:31:30 1.6 @@ -201,7 +201,7 @@ $self->{enum} = [] unless $self->enum; if ( $self->XML && ref( $self->XML ) ) { return 0; - } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /dom/i ) ) { + } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /libxml/i ) ) { return 0; } $self->createFromXML if ( $self->XML ); From kawas at pub.open-bio.org Tue Dec 14 23:13:47 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Dec 14 23:08:22 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412150413.iBF4DlbY013910@pub.open-bio.org> kawas Tue Dec 14 23:13:47 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv13883/MOBY/Client Modified Files: Central.pm Log Message: checked for CDATA and tried to excise it - eddie moby-live/Perl/MOBY/Client Central.pm,1.85,1.86 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.85 retrieving revision 1.86 diff -u -r1.85 -r1.86 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/14 22:31:30 1.85 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/15 04:13:47 1.86 @@ -3,7 +3,6 @@ use SOAP::Lite; #use SOAP::Lite + trace; # for debugging - use strict; use Carp; use XML::LibXML; @@ -377,7 +376,7 @@ $term ||= ""; my $desc = $a{'description'}; $desc ||= ""; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } my $contactEmail = $a{'contactEmail'}; @@ -507,15 +506,17 @@ my $Object = $doc->getDocumentElement(); my $obj = $Object->nodeName; return undef unless ( $obj eq 'retrieveObjectDefinition' ); - my $term = &_nodeTextContent( $Object, "objectType" ); - my $desc = &_nodeCDATAContent( $Object, "Description" ); + my $term = &_nodeTextContent( $Object, "objectType" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); + if ( $desc =~ /[^\]]+))\]\]>/ ) { + $desc = $1; + } my $authURI = &_nodeTextContent( $Object, "authURI" ); my $email = &_nodeTextContent( $Object, "contactEmail" ); my %att_value; my %relationships; my $x = $doc->getElementsByTagName( "Relationship" ); my $no_relationships = $x->size(); - for ( my $n = 1 ; $n <= $no_relationships ; ++$n ) { #get_node starts at one my $relationshipType = $x->get_node( $n )->getAttributeNode( 'relationshipType' ) @@ -569,7 +570,7 @@ my $type = $a{'serviceType'}; $type ||= ""; my $desc = $a{'description'}; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } $desc ||= ""; @@ -652,7 +653,7 @@ my $authURI = $a{'authURI'}; $authURI ||= ""; my $desc = $a{'description'}; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } $desc ||= ""; @@ -768,7 +769,8 @@ $URL ||= ""; my $desc = $a{description}; $desc ||= ""; - if ($desc =~ /[^\]]+))\]\]>/) { + + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } my $signatureURL = $a{signatureURL}; @@ -847,7 +849,7 @@ $message .= "\n"; } my ( $type, $Namespaces ) = @{$objectdef}; - $type ||=""; + $type ||= ""; $message .= "$type\n"; unless ( ref( $Namespaces ) =~ /array/i ) { return $self->errorRegXML( @@ -1209,18 +1211,16 @@ my @child = $de->childNodes; my $content; foreach ( @child ) { - $debug && &_LOG( getNodeTypeName($_), "\t", $_->toString, "\n" ); + $debug && &_LOG( getNodeTypeName( $_ ), "\t", $_->toString, "\n" ); if ( $_->nodeType == TEXT_NODE ) { - if ($_->nodeValue=~ /[^\]]+))\]\]>/) { - $content .= $1; - } else { - $content .= $_->nodeValue; #else try $_->textContent - } + $content .= $_->nodeValue; #else try $_->textContent } else { $content .= $_->toString; } } $content =~ s/^\n//gs; + $content =~ s/[^\]]+))\]\]>/$1/gs; + return $content; } @@ -1323,10 +1323,11 @@ $types->get_node( $x )->getElementsByTagName( 'Description' ) ) { $desc = $elem->firstChild->toString; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } } + $desc =~ s/[^\]]+))\]\]>/$1/gs; $servicetypes{$type} = $desc; } return \%servicetypes; @@ -1365,10 +1366,11 @@ $obnames->get_node( $x )->getElementsByTagName( 'Description' ) ) { $desc = $elem->firstChild->toString; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } } + $desc =~ s/[^\]]+))\]\]>/$1/gs; $objectnames{$name} = $desc; } return \%objectnames; @@ -1407,10 +1409,11 @@ { $desc = $elem->firstChild; $desc = $desc ? $desc->toString : ""; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } } + $desc =~ s/[^\]]+))\]\]>/$1/gs; $namespaces{$ns} = $desc; } return \%namespaces; @@ -1456,10 +1459,11 @@ $objects->get_node( $x )->getElementsByTagName( 'Schema' ) ) { $desc = $elem->firstChild->nodeValue; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } } + $desc =~ s/[^\]]+))\]\]>/$1/gs; $objects{$name} = $desc; } return \%objects; @@ -1659,7 +1663,8 @@ #my $Output = &_nodeTextContent($Service, 'outputObject'); my $Description = &_nodeCDATAContent( $Service, 'Description' ); - my $cat = &_nodeTextContent( $Service, 'Category' ); + $Description =~ s/[^\]]+))\]\]>/$1/gs; + my $cat = &_nodeTextContent( $Service, 'Category' ); my @INPUTS; my @OUTPUTS; foreach my $inout ( "Input", "Output" ) { @@ -1821,10 +1826,10 @@ my $Object = $doc->getDocumentElement(); my $obj = $Object->nodeName; return undef unless ( $obj eq 'MOBYRegistration' ); - my $id = &_nodeTextContent( $Object, 'id' ); - my $success = &_nodeTextContent( $Object, 'success' ); + my $id = &_nodeTextContent( $Object, 'id' ); + my $success = &_nodeTextContent( $Object, 'success' ); my $message = &_nodeCDATAContent( $Object, 'message' ); - my $RDF = &_nodeRawContent( $Object, 'RDF' ); + my $RDF = &_nodeRawContent( $Object, 'RDF' ); my $reg = MOBY::Client::Registration->new( success => $success, message => $message, @@ -1844,7 +1849,9 @@ ); return $reg; } + sub _nodeCDATAContent { + # will get text of **all** child $node from the given $DOM # regardless of their depth!! my ( $DOM, $node ) = @_; @@ -1853,16 +1860,15 @@ my @child = $x->get_node( 1 )->childNodes; my $content; foreach ( @child ) { + #print getNodeTypeName($_), "\t", $_->toString,"\n"; next unless $_->nodeType == TEXT_NODE; $content = $_->toString; - if ($content =~ /[^\]]+))\]\]>/) { - $content = $1; - return $content; - } } + $content =~ s/[^\]]+))\]\]>/$1/gs; return $content; } + sub _nodeTextContent { # will get text of **all** child $node from the given $DOM @@ -1873,6 +1879,7 @@ my @child = $x->get_node( 1 )->childNodes; my $content; foreach ( @child ) { + #print getNodeTypeName($_), "\t", $_->toString,"\n"; next unless $_->nodeType == TEXT_NODE; $content = $_->toString; From kawas at pub.open-bio.org Wed Dec 15 12:49:44 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed Dec 15 12:44:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412151749.iBFHniXc016480@pub.open-bio.org> kawas Wed Dec 15 12:49:44 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv16454/MOBY Modified Files: CommonSubs.pm Log Message: fixed typo -> getNodeValue :-> nodeValue - eddie moby-live/Perl/MOBY CommonSubs.pm,1.57,1.58 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.57 retrieving revision 1.58 diff -u -r1.57 -r1.58 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/12/14 20:47:04 1.57 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/12/15 17:49:44 1.58 @@ -1456,7 +1456,7 @@ foreach my $response_component ( $resp->childNodes ) { # $content .= $response_component->toString; - $content .= $response_component->getNodeValue + $content .= $response_component->nodeValue if ( $response_component->nodeType == TEXT_NODE ); } } From mwilkinson at pub.open-bio.org Wed Dec 15 14:37:12 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Dec 15 14:31:41 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412151937.iBFJbCc5016846@pub.open-bio.org> mwilkinson Wed Dec 15 14:37:12 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv16827 Modified Files: Central.pm Log Message: one more uninitialized value moby-live/Perl/MOBY/Client Central.pm,1.86,1.87 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.86 retrieving revision 1.87 diff -u -r1.86 -r1.87 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/15 04:13:47 1.86 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/15 19:37:12 1.87 @@ -1865,6 +1865,7 @@ next unless $_->nodeType == TEXT_NODE; $content = $_->toString; } + $content ||=""; $content =~ s/[^\]]+))\]\]>/$1/gs; return $content; } From kawas at pub.open-bio.org Sat Dec 18 13:33:44 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat Dec 18 13:27:55 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181833.iBIIXiGm030170@pub.open-bio.org> kawas Sat Dec 18 13:33:43 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv30145/org/biomoby/client/gui/util Modified Files: REGEXP.java Log Message: fixed the uri regular expression so that it handles uris like: illuminae.com, and not just www.illuminae.com moby-live/Java/src/main/org/biomoby/client/gui/util REGEXP.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/11/22 17:48:45 1.4 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/12/18 18:33:43 1.5 @@ -21,7 +21,7 @@ private final static String URI = //"(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|www\\.|http:\\/\\/|HTTP:\\/\\/)?[\\w]+\\.[\\w].*\\w$)"; //"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\\?([^#]*))?(#(.*))?"; // as per rfc 2396 appendix a. - "^([\\w]+\\.[\\w]+(\\.[\\w]+)+)$"; + "^([\\w]+\\.[\\w]+(\\.[\\w]+)*)$"; private final static String URL = "(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|http:\\/\\/|HTTP:\\/\\/)[\\w]+\\.[\\w].*(\\/\\w+(\\.{1}\\w+)*)$)"; From kawas at pub.open-bio.org Sat Dec 18 13:48:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat Dec 18 13:42:34 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181848.iBIImQxQ030233@pub.open-bio.org> kawas Sat Dec 18 13:48:26 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv30212/org/biomoby/client/gui/util Added Files: ObjectXMLWriter.java Log Message: a class that helps retrieve xml information on moby datatypes. used when we want to display the xml format of an object. requires the file /usr/local/apache2/cgi-bin/applets/retrieveObjectXML.cgi moby-live/Java/src/main/org/biomoby/client/gui/util ObjectXMLWriter.java,NONE,1.1 From kawas at pub.open-bio.org Sat Dec 18 13:51:27 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat Dec 18 13:45:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181851.iBIIpRcD030279@pub.open-bio.org> kawas Sat Dec 18 13:51:27 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv30254/org/biomoby/client/gui/serviceInstanceCreationTool Modified Files: ServiceInstancePanelFactory.java Log Message: fixed the edit details page so that it is more consistent with the applet. Other small revisions made. moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool ServiceInstancePanelFactory.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/11/17 17:15:26 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/18 18:51:27 1.3 @@ -629,7 +629,6 @@ // ButtonBeautifier.enhanceButton(done, 11, tool.getClass()); JButton add = new JButton(" Add Data Type To The Collection "); - //TODO press this and ask to choose another object or to add the // collection to the service add.setActionCommand("addDataType"); add.setName("addDataType"); // adds the data type @@ -1059,7 +1058,6 @@ + "of allowable values." + "Once you have inputted all of the appropriate details, click on the button

    " + "labelled 'Add to Service' to add the secondary input to your service."); - //TODO String[] theLabels = { "Secondary Input Name REQUIRED :", // required @@ -1101,7 +1099,7 @@ // goes back to the input/output radio panel done.addActionListener(ioal); - JButton cancel = new JButton(" Cancel "); //TODO + JButton cancel = new JButton(" Cancel "); ButtonBeautifier.enhanceButton(cancel, 6, tool.getClass()); cancel.setActionCommand("back"); cancel.setName("back"); // goes back to the input/output radio panel @@ -1244,22 +1242,63 @@ JLabel signatureUrlLabel = new JLabel( "Signature URL (Optional)"); - JLabel serviceNameLabel2 = new JLabel( - " Must be in valid XML format"); - JLabel authorityLabel2 = new JLabel( - " Must be a valid URI - e.g. www.biomoby.org"); - JLabel emailLabel2 = new JLabel( - " Must be a valid email address"); - JLabel descriptionLabel2 = new JLabel( - ""); - JLabel authoritativeLabel2 = new JLabel( - ""); - JLabel typeLabel2 = new JLabel( - ""); - JLabel urlLabel2 = new JLabel( - " Must be a valid URL - e.g. http://some.domain/something"); - JLabel signatureUrlLabel2 = new JLabel( - " Must be a valid URL - e.g. http://some.domain/something"); + JButton serviceNameLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(serviceNameLabel2, 14, tool.getClass()); + serviceNameLabel2 + .setToolTipText(" Name cannot contain spaces nor start with special characters "); + serviceNameLabel2.setActionCommand("1"); + serviceNameLabel2.addActionListener(hal); + + JButton authorityLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(authorityLabel2, 14, tool.getClass()); + authorityLabel2 + .setToolTipText(" Must be a valid URI "); + authorityLabel2.setActionCommand("2"); + authorityLabel2.addActionListener(hal); + + JButton emailLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(emailLabel2, 14, tool.getClass()); + emailLabel2 + .setToolTipText(" Must be a valid email address "); + emailLabel2.setActionCommand("3"); + emailLabel2.addActionListener(hal); + + JButton descriptionLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(descriptionLabel2, 14, tool.getClass()); + descriptionLabel2 + .setToolTipText("Please provide a comprehensive description "); + descriptionLabel2.setActionCommand("4"); + descriptionLabel2.addActionListener(hal); + + JButton authoritativeLabel2 = new JButton(""); + ButtonBeautifier + .enhanceButton(authoritativeLabel2, 14, tool.getClass()); + authoritativeLabel2 + .setToolTipText("Is your service authoritative?"); + authoritativeLabel2.setActionCommand("5"); + authoritativeLabel2.addActionListener(hal); + + JButton typeLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(typeLabel2, 14, tool.getClass()); + typeLabel2 + .setToolTipText("What type of service instance are you creating?"); + typeLabel2.setActionCommand("6"); + typeLabel2.addActionListener(hal); + + JButton urlLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(urlLabel2, 14, tool.getClass()); + urlLabel2 + .setToolTipText(" Must be a valid URL "); + urlLabel2.setActionCommand("7"); + urlLabel2.addActionListener(hal); + + JButton signatureUrlLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(signatureUrlLabel2, 14, tool.getClass()); + signatureUrlLabel2 + .setToolTipText(" Must be a valid URL "); + signatureUrlLabel2.setActionCommand("8"); + signatureUrlLabel2.addActionListener(hal); + // check if we need to fill in the service fields Service s = tool.getService(); @@ -1316,33 +1355,67 @@ else authoritativeComboBox.setSelectedIndex(1); - // add the items to a panel with 2 columns +// add the items to a panel with 2 columns JPanel itemPanel = null; itemPanel = initPanel(itemPanel, "itemPanel", 3); itemPanel.add(serviceNameLabel); itemPanel.add(serviceNameField); - itemPanel.add(serviceNameLabel2); + // the help1 panels ensure that the button is fitted + JPanel help1 = null; + help1 = initPanel(help1, "", -1); + help1.add(serviceNameLabel2,BorderLayout.LINE_START); + itemPanel.add(help1); + + itemPanel.add(descriptionLabel); itemPanel.add(descriptionField); - itemPanel.add(descriptionLabel2); + JPanel help2 = null; + help2 = initPanel(help1, "", -1); + help2.add(descriptionLabel2,BorderLayout.LINE_START); + itemPanel.add(help2); + itemPanel.add(emailLabel); itemPanel.add(emailField); - itemPanel.add(emailLabel2); + JPanel help3 = null; + help3 = initPanel(help3, "", -1); + help3.add(emailLabel2,BorderLayout.LINE_START); + itemPanel.add(help3); + itemPanel.add(urlLabel); itemPanel.add(urlField); - itemPanel.add(urlLabel2); + JPanel help4 = null; + help4 = initPanel(help1, "", -1); + help4.add(urlLabel2,BorderLayout.LINE_START); + itemPanel.add(help4); + + itemPanel.add(authoritativeLabel); itemPanel.add(authoritativeComboBox); - itemPanel.add(authoritativeLabel2); + JPanel help5 = null; + help5 = initPanel(help1, "", -1); + help5.add(authoritativeLabel2,BorderLayout.LINE_START); + itemPanel.add(help5); + itemPanel.add(typeLabel); itemPanel.add(categoryComboBox); - itemPanel.add(typeLabel2); + JPanel help6 = null; + help6 = initPanel(help1, "", -1); + help6.add(typeLabel2,BorderLayout.LINE_START); + itemPanel.add(help6); + itemPanel.add(authorityLabel); itemPanel.add(authorityField); - itemPanel.add(authorityLabel2); + JPanel help7 = null; + help7 = initPanel(help1, "", -1); + help7.add(authorityLabel2,BorderLayout.LINE_START); + itemPanel.add(help7); + itemPanel.add(signatureUrlLabel); itemPanel.add(sigUrlField); - itemPanel.add(signatureUrlLabel2); + JPanel help8 = null; + help8 = initPanel(help1, "", -1); + help8.add(signatureUrlLabel2,BorderLayout.LINE_START); + itemPanel.add(help8); JButton next = new JButton(" Go Back To (In/Out)put Selection "); next.setActionCommand("backFromEdit"); From kawas at pub.open-bio.org Sat Dec 18 13:52:31 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat Dec 18 13:46:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181852.iBIIqVYQ030327@pub.open-bio.org> kawas Sat Dec 18 13:52:30 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv30302/org/biomoby/client/gui/serviceInstanceCreationTool Modified Files: MobyInputOutputData.java Log Message: added the code to display an objects details when requested. moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyInputOutputData.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyInputOutputData.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyInputOutputData.java 2004/09/27 21:29:15 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyInputOutputData.java 2004/12/18 18:52:30 1.2 @@ -7,6 +7,7 @@ import java.util.Enumeration; import org.biomoby.client.CentralImpl; +import org.biomoby.client.gui.util.ObjectXMLWriter; import org.biomoby.shared.Central; import org.biomoby.shared.MobyDataType; import org.biomoby.shared.MobyException; @@ -36,6 +37,7 @@ "http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl"; static final String NAMESPACE = "http://mobycentral.cbr.nrc.ca:8080/MOBY/Central"; + private static String _URL = "http://mobycentral.cbr.nrc.ca/cgi-bin/applets/retrieveObjectXML.cgi?name="; /** * @@ -187,14 +189,15 @@ } /** - * NOT YET IMPLEMENTED

    - * @param datatype - * @return should return the MobyData type in xml format. - *

    TODO implement this! - */ - public static String ObjectInXML(String datatype) { // TODO - create an xml view of the data type - String str = - "looking for a way to get the xml from a cgi script?\n is there one already?"; - return str; + * @param datatype - the name of the datatype to retrieve informationon. + * @return if we are able to retrieve information on the datatype, then we return the MobyData type in xml format. + */ + public static String ObjectInXML(String datatype) { + String content = null; + content = ObjectXMLWriter.generatePrettyXML(_URL+datatype); + if (content.equals("")) { + content = "Couldn't retrieve object details in xml format."; + } + return content; } } From kawas at pub.open-bio.org Sat Dec 18 14:00:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat Dec 18 13:55:02 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181900.iBIJ0t3l030373@pub.open-bio.org> kawas Sat Dec 18 14:00:55 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv30348/org/biomoby/client/gui/serviceInstanceCreationTool Modified Files: ServiceInstancePanelFactory.java Log Message: fixed bug where MOBY, CGI, WSDL appearred when in 'edit service details' view. moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool ServiceInstancePanelFactory.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/18 18:51:27 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/18 19:00:55 1.4 @@ -892,10 +892,9 @@ // create the text area to display the service info JTextArea area = new JTextArea(); - area.setText(/* tool.getService().getObjectString(name) */ - MobyInputOutputData.ObjectInXML(name)); + area.setText(MobyInputOutputData.ObjectInXML(name)); area.setCaretPosition(0); - + JScrollPane scrollableTextArea = new JScrollPane(area); // create a back button JButton back = new JButton(" Go Back "); back.setActionCommand("back2Object"); @@ -909,7 +908,7 @@ button.add(back); // add everything to the panel - panel.add(area, BorderLayout.CENTER); + panel.add(scrollableTextArea, BorderLayout.CENTER); panel.add(button, BorderLayout.PAGE_END); return panel; } @@ -1337,7 +1336,7 @@ if (SET) sigUrlField.setText(s.getSignatureURL()); // Create comboboxes - String[] typeItems = { "Moby", "CGI", "WSDL" }; + String[] typeItems = { "Moby"/*, "CGI", "WSDL" */}; JComboBox categoryComboBox = new JComboBox(typeItems); categoryComboBox.setName("category"); categoryComboBox.setActionCommand("category"); From kawas at pub.open-bio.org Mon Dec 20 12:13:06 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Dec 20 12:07:13 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412201713.iBKHD6ul013123@pub.open-bio.org> kawas Mon Dec 20 12:13:06 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv13098/org/biomoby/client/gui/util Modified Files: ObjectXMLWriter.java Log Message: Added/Modified documentation moby-live/Java/src/main/org/biomoby/client/gui/util ObjectXMLWriter.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/ObjectXMLWriter.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/ObjectXMLWriter.java 2004/12/18 18:48:26 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/ObjectXMLWriter.java 2004/12/20 17:13:06 1.2 @@ -6,8 +6,7 @@ /** * @author Eddie Kawas - *

    Created for - *

    This class was created to ... + *

    This class was created to query mobycentral in order to return the xml representation of a moby object. *

    For questions, comments, or bugs *

    email me at edward.kawas@gmail.com */ @@ -19,6 +18,13 @@ import org.jdom.output.XMLOutputter; public class ObjectXMLWriter { + /** + * + * PRE:unformattedXML is valid XML.

    + * POST:Pretty, i.e. tabbed, spaced, etc, XML is returned.

    + * @param unformattedXML - a string of xml that will be to look orderly. + * @return an XML string outputted neatly. + */ public static String generatePrettyXML(String unformattedXML) { try { ByteArrayOutputStream buf = new ByteArrayOutputStream(); From kawas at pub.open-bio.org Mon Dec 20 12:13:34 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Dec 20 12:07:33 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412201713.iBKHDYes013173@pub.open-bio.org> kawas Mon Dec 20 12:13:34 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv13136/org/biomoby/client/gui/serviceInstanceCreationTool Modified Files: TreeListener.java ServiceInstancePanelFactory.java NamespaceTree.java ServiceTypeTree.java Log Message: Added/Modified documentation moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool TreeListener.java,1.1,1.2 ServiceInstancePanelFactory.java,1.4,1.5 NamespaceTree.java,1.1,1.2 ServiceTypeTree.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/TreeListener.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/TreeListener.java 2004/09/27 21:29:15 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/TreeListener.java 2004/12/20 17:13:34 1.2 @@ -36,7 +36,7 @@ * POST: the tree listener is initialized. *

    * - * @param tool + * @param tool - the ServiceCreationTool that registered this listener. */ public TreeListener(ServiceCreationTool tool) { this.tool = tool; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/18 19:00:55 1.4 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/20 17:13:34 1.5 @@ -92,9 +92,6 @@ } }; worker.start(); - // before doing anything, load the service tree in a - // separate thread to increase performance - // also download the object tree for use final TreeLoaderThread workerTree = new TreeLoaderThread() { public Object construct() { mobyTree = new MobyTree(false, @@ -106,10 +103,6 @@ } }; workerTree.start(); - - // before doing anything, load the service tree in a - // separate thread to increase performance - // also download the object tree for use final TreeLoaderThread workerNamespace = new TreeLoaderThread() { public Object construct() { namespaceTree = new NamespaceTree(false, @@ -123,6 +116,12 @@ workerNamespace.start(); } + /** + * + * PRE:None.

    + * POST:The starting panel for the applet is returned.

    + * @return - the starting panel for the applet is returned. + */ public JPanel createStartingPanel() { /* all tabs go to the center of this panel */ @@ -372,6 +371,12 @@ return pan; } + /** + * + * PRE:None.

    + * POST:The add inputs/outputs panel is created for the applet.

    + * @return - a JPanel representing the input/output chooser for the applet. + */ public JPanel createChoosingPanel() { /* all tabs go to the center of this panel */ JPanel pan = null; @@ -447,6 +452,14 @@ return pan; } + /** + * + * PRE:Top and bottom are valid JPanels.

    + * POST:a JSplitPane is created with top placed at the top of the panel and bottom placed at the bottom

    + * @param top - a JPanel that will be the top component of the split pane. + * @param bottom - a JPanel that will be the bottom component of the split pane. + * @return - a JSplitPane with the top and bottom components initialized to top and bottom. + */ public JSplitPane createSplitePane(JPanel top, JPanel bottom) { JSplitPane vpane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, top, bottom); @@ -455,6 +468,11 @@ return vpane; } + /** + * PRE:None.

    + * POST:A JPanel containing the service type tree is returned.

    + * @return - a JPanel containing the service type tree. + */ public JPanel createServiceTypeChooserPanel() { JPanel panel = null; panel = initPanel(panel, "Choose the Service Type", @@ -489,6 +507,14 @@ return panel; } + /** + * + * PRE:dataTypeName is found in the mobycentral object ontology.

    + * POST:A JPanel containing the information of the recently chosen datatype, along with a namespace tree so that user can choose appropriate namespaces for their input/output.

    + * @param dataTypeName - a string name of a valid object in the moby object ontology. + * @param isInput - if isInput is true, then datatype is a primary input. Otherwise the datatype is an output. + * @return - a JPanel containing information on the datatype, as well as other widgets that aid in the supplementing of the input/output object. + */ public JPanel createSimplePrimaryPanel(String dataTypeName, boolean isInput) { JPanel panel = null; panel = initPanel(panel, "" @@ -609,6 +635,15 @@ return panel; } + /** + * + * PRE:datatype name is found in the moby object ontology.

    + * POST:a JPanel is returned that allows the user to add more information on the object contained in their collection

    + * @param dataTypeName - a valid object name found in the moby object ontology. + * @param isInput - if true, then collection (and object contained in collection) is an input, otherwise the collection is an output. + * @param collectionName - the name of the collection. + * @return - a JPanel with widgets that allow for the user to supplement the information on the collection. + */ public JPanel createCollectionPrimaryPanel(String dataTypeName, boolean isInput, String collectionName) { JPanel panel = null; @@ -764,6 +799,12 @@ return panel; } + /** + * + * PRE:None.

    + * POST:a JPanel containing an object tree that allows for object additions to the users current collection is returned

    + * @return - JPanel with an object tree allowing for the addition of the selected object to the users collection. + */ public JPanel createObjectTreePanelForAddingToCollections() { JPanel panel = null; panel = initPanel( @@ -850,6 +891,12 @@ return p; } + /** + * + * PRE:None.

    + * POST:An empty JPanel is returned.

    + * @return - a JPanel with nothing contained within. + */ public JPanel createEmptyPanel() { JPanel p = null; p = initPanel(p, "empty", -1); @@ -857,6 +904,12 @@ return p; } + /** + * + * PRE:None

    + * POST:A JPanel containing information about the users service is shown.

    + * @return - JPanel with information on the users service. + */ public JPanel createServiceViewPanel() { JPanel panel = null; panel = initPanel(panel, "Service View", -1); @@ -884,6 +937,12 @@ return panel; } + /** + * + * PRE:An object is selected in the object tree.

    + * POST:Information about the selected object is returned.

    + * @return - JPanel with information on the selected moby object. + */ public JPanel createObjectViewPanel() { String name = objectTreeListener.getSelectedNode(); JPanel panel = null; @@ -913,6 +972,12 @@ return panel; } + /** + * + * PRE:None.

    + * POST:JPanel with information and widgets that allow the user to supplement their collection is returned.

    + * @return - JPanel with information fields and widgets that allow the user to supplement their collection. + */ public JPanel createObjectViewPanelForCollection() { String name = objectTreeListener.getSelectedNode(); JPanel panel = null; @@ -942,6 +1007,12 @@ return panel; } + /** + * + * PRE:None.

    + * POST:JPanel displaying a tree of the moby object ontology is returned that aids in the addition of objects to the service.

    + * @return JPanel containing a tree representation of the moby object ontology. + */ public JPanel createObjectTreePanel() { JPanel panel = null; panel = initPanel(panel, "Choose an Object", -1); @@ -980,72 +1051,81 @@ } /** - * @return + * @return true if a radio button is selected, false otherwise. */ public boolean isRADIO_SELECTED() { return RADIO_SELECTED; } /** - * @param b + * @param b - set whether or not the radio button is selected. */ public void setRADIO_SELECTED(boolean b) { RADIO_SELECTED = b; } /** - * @return + * @return - return the service type tree. */ public ServiceTypeTree getTree() { return tree; } /** - * @param tree + * @param tree - the tree to set the service type tree to. */ public void setTree(ServiceTypeTree tree) { this.tree = tree; } /** - * @return + * @return - the TreeListener registered to this tool */ public TreeListener getMouseTreeListener() { return mtl; } /** - * @return + * @return - the moby tree registered to this tool. */ public MobyTree getMobyTree() { return mobyTree; } /** - * @return + * @return - the namespace tree. */ public NamespaceTree getNamespaceTree() { return namespaceTree; } /** - * @return + * @return - the listener associated with the namespace tree registered with this tool. */ public NamespaceListener getNamespaceListener() { return ntl; } /** - * @return + * @return - DefaultListModel for the namespace dropdown list. */ public DefaultListModel getNamespaceDropdownListModel() { return model; } + /** + * @return - the size of the namespace dropdown list. + */ public int getNamespaceDropdownListSize() { return namespaceDropdownList.getModel().getSize(); } + /** + * + * PRE:None.

    + * POST:JPanel with widgets required to add secondary input to the service instance is returned.

    + * @return - JPanel with various widgets that allow for the addition of secondary inputs to the service instance. + */ public JPanel createSecondaryPanel() { JPanel panel = null; panel = initPanel(panel, "Secondary Input Entry", -1); @@ -1138,6 +1218,9 @@ return panel; } + /** + * @return - an Enumeration of secondary data valid inputs + */ public Enumeration getSecondaryInputEnumeration() { Vector vec = new Vector(); StringTokenizer st = new StringTokenizer(InputOutputFocusListener @@ -1153,14 +1236,26 @@ return vec.elements(); } + /** + * @return - the secondary input datatype - Can be INTEGER, STRING, DATETIME or FLOAT + */ public static String getSecondaryDataType() { return ServiceInstancePanelFactory.datatype; } + /** + * @param datatype - the secondary input datatype - INTEGER, STRING, DATETIME, or FLOAT + */ public static void setSecondaryDataType(String datatype) { ServiceInstancePanelFactory.datatype = datatype; } + /** + * + * PRE:None.

    + * POST:JPanel that displays the service instance is returned.

    + * @return - JPanel that initiates submission of the service instance. + */ public JPanel createSubmissionPanel() { JPanel panel = null; panel = initPanel( @@ -1200,12 +1295,18 @@ } /** - * @return + * @return - the submit JButton. */ public JButton getSubmit() { return submit; } + /** + * + * PRE:None.

    + * POST:JPanel with various widgets for editing the details of the service instance is returned.

    + * @return - JPanel is returned that aids in the editing of the service instance details. + */ public JPanel createDetailEditingPanel() { /* all tabs go to the center of this panel */ @@ -1438,7 +1539,7 @@ } /** - * @return + * @return - the edit JButton */ public JButton getEdit() { return edit; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/NamespaceTree.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/NamespaceTree.java 2004/09/27 21:29:15 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/NamespaceTree.java 2004/12/20 17:13:34 1.2 @@ -40,9 +40,9 @@ private String rdf = ""; /** * PRE: None

    - * POST: A moby tree is constructed with the root node labeled as 'Service'

    + * POST: A moby tree is constructed with the root node labeled as 'Namespace'

    * and the material for the tree taken from the RDF located at - * @link http://biomoby.org/RESOURCES/MOBY-S/Service + * @link http://biomoby.org/RESOURCES/MOBY-S/Namespace * @param canEdit, if true, then the nodes are editable, else they are not. */ public NamespaceTree(boolean canEdit, String rdf) { @@ -84,7 +84,7 @@ /** * PRE: None.

    - * POST: The MobyTree object contains an empty tree with a single node labeled 'Object' + * POST: The MobyTree Namespace contains an empty tree with a single node labeled 'Namespace' * @return - none. * */ @@ -294,6 +294,12 @@ return tree; } + /** + * + * PRE:None.

    + * POST:THe Namespace tree is refreshed.

    + * + */ public void reload() { hashmap = new Construct(rdf).createHomes(); makeObjectTree(); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceTypeTree.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceTypeTree.java 2004/09/27 21:29:15 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceTypeTree.java 2004/12/20 17:13:34 1.2 @@ -298,6 +298,12 @@ return tree; } + /** + * + * PRE:None.

    + * POST:The Service Type tree for this tool is refreshed.

    + * + */ public void reload() { hashmap = new Construct(rdf).createHomes(); makeObjectTree(); From kawas at pub.open-bio.org Wed Dec 22 09:33:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed Dec 22 09:27:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221433.iBMEXatx001964@pub.open-bio.org> kawas Wed Dec 22 09:33:36 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv1939/org/biomoby/client/gui/objectCreationTool Modified Files: MobyTree.java Log Message: Revised MobyTree.java moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool MobyTree.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/MobyTree.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/MobyTree.java 2004/09/27 22:15:13 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/MobyTree.java 2004/12/22 14:33:36 1.2 @@ -66,7 +66,17 @@ tree.setEditable(canEdit); tree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION); tree.setShowsRootHandles(true); - + } + + /** + * + * PRE:tree is a valid JTree.

    + * POST:JTree is collapsed at root node.

    + * + */ + public void collapseMobyTree() { + tree.clearSelection(); + tree.collapseRow(0); } /** From kawas at pub.open-bio.org Wed Dec 22 09:34:58 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed Dec 22 09:28:44 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221434.iBMEYwdL002035@pub.open-bio.org> kawas Wed Dec 22 09:34:58 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2014/org/biomoby/client/gui/objectCreationTool Added Files: TreeWindow.java PopUpWindow.java TreeMouseListener.java SubmissionWindow.java Log Message: Revised Object Creation Tool - newly updated moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool TreeWindow.java,NONE,1.1 PopUpWindow.java,NONE,1.1 TreeMouseListener.java,NONE,1.1 SubmissionWindow.java,NONE,1.1 From kawas at pub.open-bio.org Wed Dec 22 09:40:50 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed Dec 22 09:34:30 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221440.iBMEeoVd002108@pub.open-bio.org> kawas Wed Dec 22 09:40:50 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main In directory pub.open-bio.org:/tmp/cvs-serv2087 Added Files: retrieveObjectXML.cgi Log Message: File needed for retrieving xml representations for moby objects. referenced in org\biomoby\client\gui\objectCreationTool\TreeWindow.java moby-live/Java/src/main retrieveObjectXML.cgi,NONE,1.1 From kawas at pub.open-bio.org Wed Dec 22 09:42:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed Dec 22 09:36:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221442.iBMEgaQG002142@pub.open-bio.org> kawas Wed Dec 22 09:42:36 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main In directory pub.open-bio.org:/tmp/cvs-serv2117 Modified Files: retrieveObjectXML.cgi Log Message: added the code to strip CDATA from returned xml moby-live/Java/src/main retrieveObjectXML.cgi,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/retrieveObjectXML.cgi,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/retrieveObjectXML.cgi 2004/12/22 14:40:50 1.1 +++ /home/repository/moby/moby-live/Java/src/main/retrieveObjectXML.cgi 2004/12/22 14:42:36 1.2 @@ -15,4 +15,5 @@ print "Content-type: text/plain\n\n"; my $output = $DEFS->{'XML'}; $output =~ s/retrieveObjectDefinition/objectDetails/g; + $output =~ s/[^\]]+))\]\]>/$1/gs; print $output; From kawas at pub.open-bio.org Wed Dec 22 09:48:43 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed Dec 22 09:42:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221448.iBMEmhs2002207@pub.open-bio.org> kawas Wed Dec 22 09:48:43 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2180 Removed Files: ButtonActions.java ButtonBeautifier.java FieldFocusListeners.java FieldKeyListener.java MobyUserPanel.java PanelFactory.java Log Message: removed - no longer necessary moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool ButtonActions.java,1.2,NONE ButtonBeautifier.java,1.1,NONE FieldFocusListeners.java,1.2,NONE FieldKeyListener.java,1.1,NONE MobyUserPanel.java,1.1,NONE PanelFactory.java,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/ButtonActions.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/ButtonBeautifier.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/FieldFocusListeners.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/FieldKeyListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/MobyUserPanel.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/PanelFactory.java,v: No such file or directory From kawas at pub.open-bio.org Wed Dec 22 09:49:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed Dec 22 09:43:17 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221449.iBMEnaa3002248@pub.open-bio.org> kawas Wed Dec 22 09:49:36 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2226 Removed Files: TreeListener.java Log Message: removed - no longer necessary moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool TreeListener.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/TreeListener.java,v: No such file or directory From kawas at pub.open-bio.org Wed Dec 22 11:01:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed Dec 22 10:55:23 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221601.iBMG1cvQ002501@pub.open-bio.org> kawas Wed Dec 22 11:01:38 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2460/org/biomoby/client/gui/objectCreationTool Modified Files: TreeWindow.java PopUpWindow.java Registration.java TreeMouseListener.java SubmissionWindow.java Log Message: Added documentation moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool TreeWindow.java,1.1,1.2 PopUpWindow.java,1.1,1.2 Registration.java,1.1,1.2 TreeMouseListener.java,1.1,1.2 SubmissionWindow.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeWindow.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeWindow.java 2004/12/22 14:34:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeWindow.java 2004/12/22 16:01:38 1.2 @@ -16,8 +16,11 @@ import org.biomoby.client.gui.util.ObjectXMLWriter; /** * @author Eddie Kawas - *

    Created for - *

    This class was created to ... + *

    This class was created with the purpose of + * displaying the mobycentral object ontology in + * tree format, as well as providing a way to + * retrieve information about objects from the + * mobycentral object ontology. *

    For questions, comments, or bugs *

    email me at edward.kawas@gmail.com */ =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/PopUpWindow.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/PopUpWindow.java 2004/12/22 14:34:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/PopUpWindow.java 2004/12/22 16:01:38 1.2 @@ -13,8 +13,8 @@ import javax.swing.ImageIcon; /** * @author Eddie Kawas - *

    Created for - *

    This class was created to ... + *

    This class was created to present a convenience class + * that presents modal pop up windows to the user. *

    For questions, comments, or bugs *

    email me at edward.kawas@gmail.com */ =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Registration.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Registration.java 2004/09/27 22:15:13 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Registration.java 2004/12/22 16:01:38 1.2 @@ -20,24 +20,47 @@ static final String ENDPOINT = "http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl"; static final String NAMESPACE = "http://mobycentral.cbr.nrc.ca:8080/MOBY/Central"; - - private static boolean PROTO = false; + /** + * + * Constructor + * @param name - the name of the moby data type + * @param proto - is this object a prototype? + */ public Registration(String name, boolean proto) { super(name); PROTO = proto; } + /** + * + * PRE:None.

    + * POST:The name of the data type is renamed to str.

    + * @param str - the new name of the data type. + */ public void setName(String str) { this.name = str; } - + /** + * + * PRE:Pair p is a well constructed Pair object.

    + * POST:Data from Pair p is added to the data type + * in the form of HASA relationship

    + * @param p - the pair to add to the HASA containment relationship for the data type + */ public void addHASAChildren(Pair p) { //System.out.println("ArticleName: " + p.getArticlename() + " DataType: " + p.getAttribute()); this.addChild(p.getArticlename(), p.getAttribute(), Central.iHASA); } + /** + * + * PRE:Pair p is a well constructed Pair object.

    + * POST:Data from Pair p is added to the data type + * in the form of HAS relationship

    + * @param p - the pair to add to the HAS containment relationship for the data type + */ public void addHASChildren(Pair p) { //System.out.println("ArticleName: " + p.getArticlename() + " DataType: " + p.getAttribute()); this.addChild(p.getArticlename(), p.getAttribute(), Central.iHAS); @@ -45,9 +68,11 @@ } /** - * - * PRE: - *

    POST:

    + * + * PRE:MobyDataType has been properly initialized.

    + * POST:MobyDataType is registered in the mobycentral object + * ontology and a string representing its LSID is returned.

    + * @param tool - the ObjectCreationTool that is registering this new data type. * @return 1 for success, 0 for failure and -1 for 'pending curation' */ public String performRegistration(ObjectCreationTool tool) { @@ -83,12 +108,10 @@ return reg; } + /** - * - * PRE: - *

    POST:

    - * @param name - * @return + * @deprecated - no longer used. + * TODO - remove method from class. */ public String getDataTypeInfo(String name) { String ret = ""; @@ -108,10 +131,19 @@ } + /** + * + * PRE:MobyDataType has been registered.

    + * POST:LSID is returned

    + * @return - the LSID of the moby data type. + */ public String getMobyID() { return this.getId(); } + /** + * TODO - remove from class. Shouldn't have this method. + */ public void setMobyID(String s) { this.setId(s); } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeMouseListener.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeMouseListener.java 2004/12/22 14:34:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeMouseListener.java 2004/12/22 16:01:38 1.2 @@ -10,8 +10,11 @@ import javax.swing.tree.TreePath; /** - * @author Eddie Kawas

    Created for

    This class was created to ...

    For - * questions, comments, or bugs

    email me at edward.kawas@gmail.com + * @author Eddie Kawas + *

    This class was created to implement the Mouselistener interface + * for use with a tree that displays the mobycentral object ontology. + *

    For questions, comments, or bugs + *

    email me at edward.kawas@gmail.com */ public class TreeMouseListener implements MouseListener { @@ -65,10 +68,11 @@ } /** - * PRE:

    POST:

    - * - * @param selected - * @return + * PRE: None.

    + * POST: THe name of the event originator is returned: ISA, HAS, HASA.

    + * @param selected - the integer value representing the event originator + * @see org.biomoby.client.gui.objectCreationTool + * @return String representing the event originator. */ private String getEventOriginatorName(int selected) { String str = null; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/SubmissionWindow.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/SubmissionWindow.java 2004/12/22 14:34:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/SubmissionWindow.java 2004/12/22 16:01:38 1.2 @@ -13,8 +13,9 @@ import javax.swing.ImageIcon; /** * @author Eddie Kawas - *

    Created for - *

    This class was created to ... + *

    This class was created to present a view to the user + * of the tool that displays their newly created object prior + * to registration. *

    For questions, comments, or bugs *

    email me at edward.kawas@gmail.com */ From kawas at pub.open-bio.org Wed Dec 22 11:07:03 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed Dec 22 11:00:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221607.iBMG73tG002580@pub.open-bio.org> kawas Wed Dec 22 11:07:03 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2555/org/biomoby/client/gui/serviceTypeCreationTool Modified Files: ServiceTypeApplet.java Log Message: Added documentation moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool ServiceTypeApplet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java 2004/09/27 21:06:17 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java 2004/12/22 16:07:03 1.3 @@ -35,14 +35,13 @@ import org.biomoby.shared.PendingCurationException; /** - * @author Eddie Created for - *

    - * This class was created to ... - *

    - * For questions, comments, or bugs - *

    - * email me at edward.kawas@gmail.com - *

    + * + * @author Eddie Kawas + *

    This class was created to present + * users of moby the chance to create + * new service types quickly and easily. + *

    For questions, comments, or bugs + *

    email me at edward.kawas@gmail.com */ public class ServiceTypeApplet extends JApplet { @@ -125,17 +124,20 @@ return super.getAppletContext(); } - /* - * (non-Javadoc) - *@see java.applet.Applet#getAppletInfo() - */ + /* + * (non-Javadoc) + *@see java.applet.Applet#getAppletInfo() + */ public String getAppletInfo() { - return "Title: Moby Service Type Construction Tool v1.00, 24 September 2004\n" - + "Author: Edward Kawas\n" - + "An interactive way to create Service Types for the MobyCentral Ontology." + - newline + "This is" + ((PROTOTYPE) ? "" : " not " ) + "a prototype!"; - } - + return "Title: Moby Service Type Construction Tool v1.00, 24 September 2004\n" + + "Author: Edward Kawas\n" + + "An interactive way to create Service Types for the MobyCentral Ontology." + + newline + + "This is" + + ((PROTOTYPE) ? "" : " not ") + + "a prototype!"; + } + /* * (non-Javadoc) * @@ -159,17 +161,17 @@ .getLastSelectedPathComponent().toString(); switch (arg0.getClickCount()) { - case 1: - break; - case 2: - //set text box to be this node, and close frame - parentTextField.setText(selected); - frame.dispose(); - frame = null; - break; - default: - // do nothing - break; + case 1: + break; + case 2: + //set text box to be this node, and close frame + parentTextField.setText(selected); + frame.dispose(); + frame = null; + break; + default: + // do nothing + break; } } @@ -229,9 +231,8 @@ title.setFont(new java.awt.Font("Dialog", java.awt.Font.BOLD, 24)); title.setHorizontalAlignment(javax.swing.SwingConstants.CENTER); title.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER); - title - .setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/moby.gif"))); + title.setIcon(new ImageIcon(getClass().getResource( + "/org/biomoby/client/gui/img/moby.gif"))); title.setOpaque(true); backgroundPane.add(title, java.awt.BorderLayout.NORTH); backgroundPane.add(getCenterPane(), java.awt.BorderLayout.CENTER); @@ -313,20 +314,24 @@ registerServiceType.setText("Create New Service Type"); registerServiceType.setCursor(new java.awt.Cursor( java.awt.Cursor.DEFAULT_CURSOR)); - registerServiceType.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/ComposeMail24.gif"))); + registerServiceType + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/ComposeMail24.gif"))); registerServiceType.setActionCommand("register"); registerServiceType .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { - + // check whether inputs is valid /* * data is an array of values: 0.service type name * 1.service type description 2.service type uri * 3.service type parent 4. valid email address */ - String[] data = { getNameTxtField().getText(), + String[] data = { + getNameTxtField().getText(), getDescTxtArea().getText(), getUriTxtField().getText(), getParentTextField().getText(), @@ -351,7 +356,7 @@ createPopUpMsg("Please enter a valid email address."); return; } - + Central worker = null; boolean success = false; String errorMsg = ""; @@ -560,8 +565,11 @@ private JButton getNamehelpBtn() { if (namehelpBtn == null) { namehelpBtn = new JButton(); - namehelpBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); + namehelpBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); namehelpBtn.setOpaque(false); namehelpBtn.setActionCommand("nameHelp"); namehelpBtn.setMaximumSize(new java.awt.Dimension(34, 26)); @@ -592,8 +600,11 @@ descHelpBtn.setMaximumSize(new java.awt.Dimension(34, 26)); descHelpBtn.setMinimumSize(new java.awt.Dimension(34, 26)); descHelpBtn.setOpaque(false); - descHelpBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); + descHelpBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); descHelpBtn.setActionCommand("descHelp"); descHelpBtn.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { @@ -619,8 +630,11 @@ emailHelpBtn.setMaximumSize(new java.awt.Dimension(34, 26)); emailHelpBtn.setMinimumSize(new java.awt.Dimension(34, 26)); emailHelpBtn.setOpaque(false); - emailHelpBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); + emailHelpBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); emailHelpBtn.setActionCommand("emailHelp"); emailHelpBtn.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { @@ -645,8 +659,11 @@ uriHelpBtn.setMaximumSize(new java.awt.Dimension(34, 26)); uriHelpBtn.setMinimumSize(new java.awt.Dimension(34, 26)); uriHelpBtn.setOpaque(false); - uriHelpBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); + uriHelpBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); uriHelpBtn.setActionCommand("uriHelp"); uriHelpBtn.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { @@ -686,8 +703,11 @@ chooseParentBtn = new JButton(); chooseParentBtn.setText("Choose Service Type Parent"); chooseParentBtn.setActionCommand("chooseParent"); - chooseParentBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Preferences24.gif"))); + chooseParentBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Preferences24.gif"))); chooseParentBtn.setOpaque(true); chooseParentBtn.setPreferredSize(new java.awt.Dimension(274, 27)); chooseParentBtn.setMinimumSize(new java.awt.Dimension(274, 27)); @@ -708,7 +728,8 @@ return; } frame = new JFrame("Service Type Chooser"); - JScrollPane scrollable = new JScrollPane(tree.getTree()); + JScrollPane scrollable = new JScrollPane(tree + .getTree()); frame.getContentPane().add(scrollable); frame .setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2C2015065@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory pub.open-bio.org:/tmp/cvs-serv14933/src/Clients/help Modified Files: MobyCmdLineClient_usage.txt Log Message: a lot of changes in docs; but also in code moby-live/Java/src/Clients/help MobyCmdLineClient_usage.txt,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2004/11/12 23:02:31 1.6 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2004/12/05 22:28:02 1.7 @@ -131,7 +131,7 @@ points to your HTTP space to a place where an RDF describing this service will be -rs-rdfpath - if the service registration is succesful, the returned + if the service registration is successful, the returned RDF is copied to a file given by (which completes the registration process); use it, however, with caution because this client From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2cf014998@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/docs/dist In directory pub.open-bio.org:/tmp/cvs-serv14933/docs/dist Modified Files: _README_ Log Message: a lot of changes in docs; but also in code moby-live/Java/docs/dist _README_,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/dist/_README_,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/docs/dist/_README_ 2004/05/18 10:13:16 1.2 +++ /home/repository/moby/moby-live/Java/docs/dist/_README_ 2004/12/05 22:28:02 1.3 @@ -18,6 +18,10 @@ You should consider to change some parameters in provided web.xml (it appears in 'jmoby/WEB-INF' after unpacking). +Binary distribution with RDF agent: + rdfagent-.tar.gz + rdfagent-.zip + -------------------------------------------------------------------- File: README Comments to the biomoby mailing lists, or directly to Martin Senger (senger at ebi.ac.uk). From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2oZ014956@pub.open-bio.org> senger Sun Dec 5 17:28:01 EST 2004 Update of /home/repository/moby/moby-live/Java In directory pub.open-bio.org:/tmp/cvs-serv14933 Modified Files: README build.xml Log Message: a lot of changes in docs; but also in code moby-live/Java README,1.7,1.8 build.xml,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Java/README,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/README 2003/11/08 00:27:23 1.7 +++ /home/repository/moby/moby-live/Java/README 2004/12/05 22:28:01 1.8 @@ -73,13 +73,15 @@ After building it all, invoke available clients using provided (and very simple) scripts: - ./run-cmdline-client -help - ./run-testing-central + ./build/run/run-cmdline-client -help + ./build/run/run-testing-central or, on Windows platforms: - run-cmdline-client.bat -help - run-testing-central.bat + build/run/run-cmdline-client.bat -help + build/run/run-testing-central.bat + +There are more scripts available - check the 'build/run' directory. Enjoy it! =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/build.xml 2004/11/01 19:21:42 1.9 +++ /home/repository/moby/moby-live/Java/build.xml 2004/12/05 22:28:01 1.10 @@ -421,26 +421,30 @@ + description="Create binary distribution with basic jMoby clients."> + + + + - - + + - + - - + + - + - + + + + - + - - + + @@ -489,18 +496,18 @@ - + - + - + - + - - + + @@ -608,7 +615,7 @@ - From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2je015039@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/src/Clients In directory pub.open-bio.org:/tmp/cvs-serv14933/src/Clients Modified Files: MobyCmdLineClient.java Log Message: a lot of changes in docs; but also in code moby-live/Java/src/Clients MobyCmdLineClient.java,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/11/12 23:02:30 1.7 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/12/05 22:28:02 1.8 @@ -367,9 +367,17 @@ if ((param = cmd.getParam ("-rs-out")) != null ) { String[] outs = StringUtils.split (param, ","); for (int i = 0; i < outs.length; i++) { - MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy"); - data.setDataType (new MobyDataType (outs[i])); - service.addOutput (data); + String[] parts = StringUtils.split (outs[i], "="); + if (parts.length >= 2) { + MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy"); + data.setDataType (new MobyDataType (parts[0])); + data.addNamespace (new MobyNamespace (parts[1])); + service.addOutput (data); + } else { + MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy"); + data.setDataType (new MobyDataType (parts[0])); + service.addOutput (data); + } } } if ((param = cmd.getParam ("-rs-ofile")) != null ) { From senger at pub.open-bio.org Sun Dec 5 17:28:03 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2kR015109@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv14933/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: a lot of changes in docs; but also in code moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.18,1.19 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/11/22 17:22:22 1.18 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/12/05 22:28:02 1.19 @@ -138,6 +138,7 @@ Service service = new Service(); call = (Call) service.createCall(); call.setTargetEndpointAddress (endpoint); + call.setTimeout (new Integer (0)); call.setSOAPActionURI (uri + "#" + method); @@ -1291,7 +1292,7 @@ pattern = new MobyService ("dummy"); String result = - getServicesAsXML (pattern, keywords, includeParentDataTypes, includeChildrenServiceTypes); + getServicesAsXML (pattern, keywords, includeChildrenServiceTypes, includeParentDataTypes); MobyService[] services = extractServices (result); return services; } From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2Rx015086@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/src/config In directory pub.open-bio.org:/tmp/cvs-serv14933/src/config Modified Files: run-digest-client Log Message: a lot of changes in docs; but also in code moby-live/Java/src/config run-digest-client,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-digest-client,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/config/run-digest-client 2004/11/14 16:43:49 1.1 +++ /home/repository/moby/moby-live/Java/src/config/run-digest-client 2004/12/05 22:28:02 1.2 @@ -1,8 +1,8 @@ #!/bin/sh # -# Run MobyDigest client. +# Run MobyDigestClient. # -# Use ./build/run/run-digets-client -help for list of +# Use ./build/run/run-digest-client -help for list of # all available arguments. # # $Id$ From senger at pub.open-bio.org Sun Dec 5 17:28:03 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS3HO015127@pub.open-bio.org> senger Sun Dec 5 17:28:03 EST 2004 Update of /home/repository/moby/moby-live/Java/src/support In directory pub.open-bio.org:/tmp/cvs-serv14933/src/support Added Files: run-cache-client run-cache-client.bat run-digest-client run-digest-client.bat Log Message: a lot of changes in docs; but also in code moby-live/Java/src/support run-cache-client,NONE,1.1 run-cache-client.bat,NONE,1.1 run-digest-client,NONE,1.1 run-digest-client.bat,NONE,1.1 From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2B0015020@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/docs/images In directory pub.open-bio.org:/tmp/cvs-serv14933/docs/images Modified Files: whale.gif Added Files: blue.gif orange.gif red.gif Log Message: a lot of changes in docs; but also in code moby-live/Java/docs/images blue.gif,NONE,1.1 orange.gif,NONE,1.1 red.gif,NONE,1.1 whale.gif,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/images/whale.gif,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 Binary files /home/repository/moby/moby-live/Java/docs/images/whale.gif 2004/11/14 17:33:57 1.1 and /home/repository/moby/moby-live/Java/docs/images/whale.gif 2004/12/05 22:28:02 1.2 differ rcsdiff: /home/repository/moby/moby-live/Java/docs/images/whale.gif: diff failed From senger at pub.open-bio.org Sun Dec 5 17:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS29D014979@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv14933/docs Modified Files: ChangeLog index.html Added Files: CmdLineClients.html Download.html MOBYSHoundGetGenBankff-result.xml.txt RDFAgent.html SimpleClient.html TavernaGuide.html Testing_service.rdf ToDo.html Log Message: a lot of changes in docs; but also in code moby-live/Java/docs CmdLineClients.html,NONE,1.1 Download.html,NONE,1.1 MOBYSHoundGetGenBankff-result.xml.txt,NONE,1.1 RDFAgent.html,NONE,1.1 SimpleClient.html,NONE,1.1 TavernaGuide.html,NONE,1.1 Testing_service.rdf,NONE,1.1 ToDo.html,NONE,1.1 ChangeLog,1.26,1.27 index.html,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.26 retrieving revision 1.27 diff -u -r1.26 -r1.27 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/11/14 16:43:49 1.26 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/12/05 22:28:02 1.27 @@ -1,3 +1,13 @@ +2004-12-05 Martin Senger + + * Updated documentation (significantly, but not yet finished). + +2004-11-30 Martin Senger + + * Fixed CentralImpl dealing now better with + 1 and + 1. + 2004-11-14 Martin Senger * Added MobyDigestClient for retrieving cummulative (digested) =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/index.html,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/docs/index.html 2004/11/14 17:33:57 1.5 +++ /home/repository/moby/moby-live/Java/docs/index.html 2004/12/05 22:28:02 1.6 @@ -3,83 +3,72 @@ - +

    -

    BioMoby in Java

    +

    jMoby - BioMoby in Java

    -This is a sub-project of the BioMoby project. -It aims to develop an access to the Moby registry using pure Java, and later perhaps to -develop a stand-alone Java Moby server. It will also provide Java support for providers -of the Moby-compliant services. -

    - -This is the overview of the current Moby java clients, and their -relationship to the whole BioMoby project. -

    - - -

    - - -

    Java API

    -The detailed documentation of the involved classes and interfaces -is available +This is a sub-project of the BioMoby project. It aims to develop tools in Java +in order: +
      +
    • to access BioMoby registries, allowing all features provided by +such registries, including but not limited to registering and +deregistering of the BioMoby services and their parts, discovering +them, and understanding their data in various formats (such as RDF),

      - -

      Moby Java Clients - download and use

      +
    • to create Java implementations of BioMoby services, especially +to help service providers with creating BioMoby data containers (input +and output data) without exposing providers to the complexity of the +XML required and produced by BioMoby services, and finally

      -The Moby Java clients are part of the -Moby CVS repository -but for convenience they can be downloaded also separately from -http://industry.ebi.ac.uk/~senger/jMoby/dist/ -(take the latest version, pick up either .tar.gz or .zip - both are equivalent). -

      +

    • to provide support for those writing Java clients accessing +both BioMoby registries and BioMoby services.

      -After downloading, unpack it, check the README file and start using it: -

        -
      • sh run-testing-central -
      • sh run-cmdline-client -help -
      -

      -or on the Windows platform: -

        -
      • run-testing-central.bat -
      • run-cmdline-client.bat -help

      -Latest changes are available either as a -summary or in details from the -CVS repository. -

      +

      Where to go now

      -Please report all problems, or submit features and wishes to -Martin Senger. +
      +
      +
      How to get jMoby +

      + +

      How to use jMoby +
      +
      Command-line clients +
      Integration with Taverna +
      RDF Agent +
      +

      + +

      How to develop with jMoby +
      +
      Available APIs (more explanation coming...) +
      How to develop a client talking to a BioMoby service +
      How to develop a BioMoby service (coming...) +
      +

      + +

      Next plans +
      +
      - -

      Next steps

      - -The future plans and steps in this sub-project may or should include -
        -
      • Design and implement Java interfaces that can be used for the providers - of the Moby-compliant services -
      • Start to work on a pure Java Moby server (talk to Brian Gilman who had already started to work on it) -
      - -

      Acknowledgements

      -The work on BioMoby Java sub-project is supported by +The work on BioMoby Java sub-project is partly supported by
      myGrid, a multi-organisational project developing the infrastructural middleware for an e-Biologist's workbench, funded by EPSRC. +

      - +Other parts of jMoby are funded from the same sources as the BioMoby +itself.

      @@ -87,7 +76,7 @@

      Martin Senger
      -Last modified: Sun Nov 14 17:29:05 2004 +Last modified: Sun Dec 5 21:32:23 2004
      From nopushneva at pub.open-bio.org Tue Dec 7 22:29:06 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue, 7 Dec 2004 22:29:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412080329.iB83T65F024862@pub.open-bio.org> nopushneva Tue Dec 7 22:29:05 EST 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib In directory pub.open-bio.org:/tmp/cvs-serv24837 Removed Files: activation.jar concurrent.jar icu4j.jar Log Message: remove libs from RDFAgent directory moby-live/Agents/MOBY-S/RDFAgent/lib activation.jar,1.3,NONE concurrent.jar,1.1,NONE icu4j.jar,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/activation.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/concurrent.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/icu4j.jar,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:20 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFK2W026995@pub.open-bio.org> yanwong Wed Dec 8 06:15:20 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched Removed Files: CHANGES MANIFEST PKG-INFO README setup.cfg setup.py Log Message: moby-live/Python/ZSI-1.5.0-patched CHANGES,1.1.1.1,NONE MANIFEST,1.1.1.1,NONE PKG-INFO,1.1.1.1,NONE README,1.1.1.1,NONE setup.cfg,1.1.1.1,NONE setup.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/CHANGES,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/MANIFEST,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/PKG-INFO,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/setup.cfg,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/setup.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFLc0027079@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/ZSI/wstools/test Removed Files: __init__.py test_t1.py test_wsdl.py test_wstools.py test_wstools_net.py Log Message: moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test __init__.py,1.1.1.1,NONE test_t1.py,1.1.1.1,NONE test_wsdl.py,1.1.1.1,NONE test_wstools.py,1.1.1.1,NONE test_wstools_net.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/__init__.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/test_t1.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/test_wsdl.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/test_wstools.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/test_wstools_net.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:20 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFKo8026975@pub.open-bio.org> yanwong Wed Dec 8 06:15:20 EST 2004 Update of /home/repository/moby/moby-live/Python In directory pub.open-bio.org:/tmp/cvs-serv26947/Python Removed Files: PKG-INFO README TODO changelog setup.py Log Message: moby-live/Python PKG-INFO,1.1.1.1,NONE README,1.1.1.1,NONE TODO,1.1.1.1,NONE changelog,1.1.1.1,NONE setup.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/RCS/PKG-INFO,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/RCS/TODO,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/RCS/changelog,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/RCS/setup.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFLB3027059@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/ZSI/wstools Removed Files: TimeoutSocket.py UserTuple.py Utility.py WSDLTools.py XMLSchema.py XMLname.py __init__.py Log Message: moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools TimeoutSocket.py,1.1.1.1,NONE UserTuple.py,1.1.1.1,NONE Utility.py,1.1.1.1,NONE WSDLTools.py,1.1.1.1,NONE XMLSchema.py,1.1.1.1,NONE XMLname.py,1.1.1.1,NONE __init__.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/TimeoutSocket.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/UserTuple.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/Utility.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/WSDLTools.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/XMLSchema.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/XMLname.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/__init__.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFKbl027032@pub.open-bio.org> yanwong Wed Dec 8 06:15:20 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/ZSI Removed Files: ServiceProxy.py TC.py TCapache.py TCcompound.py TCnumbers.py TCtimes.py __init__.py auth.py client.py compat.py dispatch.py fault.py parse.py resolvers.py typeinterpreter.py version.py writer.py wsdl2python.py wsdlInterface.py Log Message: moby-live/Python/ZSI-1.5.0-patched/ZSI ServiceProxy.py,1.1.1.1,NONE TC.py,1.1.1.1,NONE TCapache.py,1.1.1.1,NONE TCcompound.py,1.1.1.1,NONE TCnumbers.py,1.1.1.1,NONE TCtimes.py,1.1.1.1,NONE __init__.py,1.1.1.1,NONE auth.py,1.1.1.1,NONE client.py,1.1.1.1,NONE compat.py,1.1.1.1,NONE dispatch.py,1.1.1.1,NONE fault.py,1.1.1.1,NONE parse.py,1.1.1.1,NONE resolvers.py,1.1.1.1,NONE typeinterpreter.py,1.1.1.1,NONE version.py,1.1.1.1,NONE writer.py,1.1.1.1,NONE wsdl2python.py,1.1.1.1,NONE wsdlInterface.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/ServiceProxy.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/TC.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/TCapache.py,v: No such file or directory rcsdiff: 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file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/parse.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/resolvers.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/typeinterpreter.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/version.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/writer.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/wsdl2python.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/wsdlInterface.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFLVu027159@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/samples In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/samples Removed Files: README poly.py Log Message: moby-live/Python/ZSI-1.5.0-patched/samples README,1.1.1.1,NONE poly.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/samples/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/samples/RCS/poly.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:22 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFM1A027210@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/test Removed Files: README cgicli.py test_t1.py test_t2.py test_t3.py test_t4.py test_t5.py test_t6.py test_t7.py test_zsi.py test_zsi_net.py tests_bad.py tests_good.py Log Message: moby-live/Python/ZSI-1.5.0-patched/test README,1.1.1.1,NONE cgicli.py,1.1.1.1,NONE test_t1.py,1.1.1.1,NONE test_t2.py,1.1.1.1,NONE test_t3.py,1.1.1.1,NONE test_t4.py,1.1.1.1,NONE test_t5.py,1.1.1.1,NONE test_t6.py,1.1.1.1,NONE test_t7.py,1.1.1.1,NONE test_zsi.py,1.1.1.1,NONE test_zsi_net.py,1.1.1.1,NONE tests_bad.py,1.1.1.1,NONE tests_good.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/cgicli.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/test_t1.py,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/tests_bad.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/tests_good.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFLq3027176@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/scripts In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/scripts Removed Files: wsdl2py Log Message: moby-live/Python/ZSI-1.5.0-patched/scripts wsdl2py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/scripts/RCS/wsdl2py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFL70027139@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/interop Removed Files: InteropTest.wsdl InteropTestB.wsdl README client.py cpackets.py echoHeaderBindings.wsdl sclasses.py server.py Log Message: moby-live/Python/ZSI-1.5.0-patched/interop InteropTest.wsdl,1.1.1.1,NONE InteropTestB.wsdl,1.1.1.1,NONE README,1.1.1.1,NONE client.py,1.1.1.1,NONE cpackets.py,1.1.1.1,NONE echoHeaderBindings.wsdl,1.1.1.1,NONE sclasses.py,1.1.1.1,NONE server.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/InteropTest.wsdl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/InteropTestB.wsdl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/client.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/cpackets.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/echoHeaderBindings.wsdl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/sclasses.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/server.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFL1V027116@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/doc Removed Files: .cvsignore Makefile c01-intro.tex c02-samples.tex c02a-coverage.tex c03-except.tex c04-utils.tex c05-parse.tex c06-tc.tex c07-writer.tex c08-fault.tex c09-resolve.tex c10-dispatch.tex c11-wsdl.tex zsi.tex zsi.xsd Log Message: moby-live/Python/ZSI-1.5.0-patched/doc .cvsignore,1.1.1.1,NONE Makefile,1.1.1.1,NONE c01-intro.tex,1.1.1.1,NONE c02-samples.tex,1.1.1.1,NONE c02a-coverage.tex,1.1.1.1,NONE c03-except.tex,1.1.1.1,NONE c04-utils.tex,1.1.1.1,NONE c05-parse.tex,1.1.1.1,NONE c06-tc.tex,1.1.1.1,NONE c07-writer.tex,1.1.1.1,NONE c08-fault.tex,1.1.1.1,NONE c09-resolve.tex,1.1.1.1,NONE c10-dispatch.tex,1.1.1.1,NONE c11-wsdl.tex,1.1.1.1,NONE zsi.tex,1.1.1.1,NONE zsi.xsd,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/.cvsignore,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/Makefile,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c01-intro.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c02-samples.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c02a-coverage.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c03-except.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c04-utils.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c05-parse.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c06-tc.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c07-writer.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c08-fault.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c09-resolve.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c10-dispatch.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c11-wsdl.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/zsi.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/zsi.xsd,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:22 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFMuO027232@pub.open-bio.org> yanwong Wed Dec 8 06:15:22 EST 2004 Update of /home/repository/moby/moby-live/Python/doc In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/doc Removed Files: epydoc.css howto.pdf index.html Log Message: moby-live/Python/doc epydoc.css,1.1.1.1,NONE howto.pdf,1.1.1.1,NONE index.html,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/doc/RCS/epydoc.css,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/RCS/howto.pdf,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/RCS/index.html,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFV9F028121@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/utils/wx In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/utils/wx Removed Files: README objectBrowser.py Log Message: moby-live/Python/utils/wx README,1.1.1.1,NONE objectBrowser.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/utils/wx/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/utils/wx/RCS/objectBrowser.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFVEv028079@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/webservices In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/tutorials/webservices Removed Files: Clustalw-mod_python.py Clustalw.py Stride.py dispatcher1.py dispatcherCMD.py Log Message: moby-live/Python/tutorials/webservices Clustalw-mod_python.py,1.1.1.1,NONE Clustalw.py,1.1.1.1,NONE Stride.py,1.1.1.1,NONE dispatcher1.py,1.1.1.1,NONE dispatcherCMD.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/Clustalw-mod_python.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/Clustalw.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/Stride.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/dispatcher1.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/dispatcherCMD.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:26 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:26 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFQb8027557@pub.open-bio.org> yanwong Wed Dec 8 06:15:25 EST 2004 Update of 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or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.ontology.Study-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.ontology.TargetP_result-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.ontology.Testout-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.ontology.TextBase64-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.ontology.TextFormatted-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.ontology.TextHtml-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.ontology.TextPlain-module.html,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.ontology.Wildcard_Query-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.webservice-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.webservice.Dispatcher-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.webservice.Invocators-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-everything.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/trees.html,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:30 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFUNc027999@pub.open-bio.org> yanwong Wed Dec 8 06:15:30 EST 2004 Update of /home/repository/moby/moby-live/Python/src/ontology In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/src/ontology Removed Files: AGI_LocusCode.py Allele_freq.py AminoAcidSequence.py B64_Encoded_PNG.py B64_Encoded_Postscript.py B64_encoded_PDB.py B64_encoded_gif.py B64_encoded_jpeg.py BasicGFFSequenceFeature.py DNASequence.py DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py Edge.py EmblFlatfile.py FASTA.py GFF.py GFF1.py GFF2.py GFF2_5.py GFF3.py GO_Term.py GenbankFlatfile.py GenericSequence.py GeneticElement.py Germplasm_Details.py Germplasm_List.py Global_Keyword.py HCA_picture.py Haplotyping_Study_obj.py ICIS_Query.py ICIS_Query2.py ICIS_Query3.py IntAct_XML.py Interaction.py InteractionMethod.py Interaction_partner.py Interactor.py MMP_Locus.py MO_Term_Test.py Multi_key_value_pair.py MyTree.py NCBI_BLAST_Text.py NCBI_Blast_XML.py NucleotideSequence.py PDBFormattedText.py PDGJOB.py PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py SchematikonMotifID.py SchematikonMotifSupport.py SchematikonSegmentAttributes.py SchematikonSegmentID.py SchematikonStructureAnnotation.py SchematikonVorocodeName.py Scored_acronym_string.py SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py Simple_key_value_pair.py Snp_allele.py Snp_genotype.py Study.py TargetP_result.py Testout.py TextBase64.py TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py TextXml.py Text_plain.py Trait_Details.py Tree.py VirtualSequence.py WU_BLAST_Text.py Wildcard_Query.py __init__.py Log Message: moby-live/Python/src/ontology AGI_LocusCode.py,1.1.1.1,NONE Allele_freq.py,1.1.1.1,NONE AminoAcidSequence.py,1.1.1.1,NONE B64_Encoded_PNG.py,1.1.1.1,NONE B64_Encoded_Postscript.py,1.1.1.1,NONE B64_encoded_PDB.py,1.1.1.1,NONE B64_encoded_gif.py,1.1.1.1,NONE B64_encoded_jpeg.py,1.1.1.1,NONE BasicGFFSequenceFeature.py,1.1.1.1,NONE DNASequence.py,1.1.1.1,NONE DNASequenceWithGFFFeatures.py,1.1.1.1,NONE DateTime.py,1.1.1.1,NONE Decypher_Text.py,1.1.1.1,NONE Edge.py,1.1.1.1,NONE EmblFlatfile.py,1.1.1.1,NONE FASTA.py,1.1.1.1,NONE GFF.py,1.1.1.1,NONE GFF1.py,1.1.1.1,NONE GFF2.py,1.1.1.1,NONE GFF2_5.py,1.1.1.1,NONE GFF3.py,1.1.1.1,NONE GO_Term.py,1.1.1.1,NONE GenbankFlatfile.py,1.1.1.1,NONE GenericSequence.py,1.1.1.1,NONE GeneticElement.py,1.1.1.1,NONE Germplasm_Details.py,1.1.1.1,NONE Germplasm_List.py,1.1.1.1,NONE Global_Keyword.py,1.1.1.1,NONE HCA_picture.py,1.1.1.1,NONE Haplotyping_Study_obj.py,1.1.1.1,NONE ICIS_Query.py,1.1.1.1,NONE ICIS_Query2.py,1.1.1.1,NONE ICIS_Query3.py,1.1.! 1.1,NONE IntAct_XML.py,1.1.1.1,NONE Interaction.py,1.1.1.1,NONE InteractionMethod.py,1.1.1.1,NONE Interaction_partner.py,1.1.1.1,NONE Interactor.py,1.1.1.1,NONE MMP_Locus.py,1.1.1.1,NONE MO_Term_Test.py,1.1.1.1,NONE Multi_key_value_pair.py,1.1.1.1,NONE MyTree.py,1.1.1.1,NONE NCBI_BLAST_Text.py,1.1.1.1,NONE NCBI_Blast_XML.py,1.1.1.1,NONE NucleotideSequence.py,1.1.1.1,NONE PDBFormattedText.py,1.1.1.1,NONE PDGJOB.py,1.1.1.1,NONE PhenotypeDescription.py,1.1.1.1,NONE PubMedMEDLINE.py,1.1.1.1,NONE RNASequence.py,1.1.1.1,NONE SchematikonMotifID.py,1.1.1.1,NONE SchematikonMotifSupport.py,1.1.1.1,NONE SchematikonSegmentAttributes.py,1.1.1.1,NONE SchematikonSegmentID.py,1.1.1.1,NONE SchematikonStructureAnnotation.py,1.1.1.1,NONE SchematikonVorocodeName.py,1.1.1.1,NONE Scored_acronym_string.py,1.1.1.1,NONE SimpleAnnotatedGIFImage.py,1.1.1.1,NONE SimpleAnnotatedJPEGImage.py,1.1.1.1,NONE Simple_key_value_pair.py,1.1.1.1,NONE Snp_allele.py,1.1.1.1,NONE Snp_genotype.py,1.1.1.1,NONE Study.p! y,1.1.1.1,NONE TargetP_result.py,1.1.1.1,NONE Testout.py,1.1.! 1.1,NONE TextBase64.py,1.1.1.1,NONE TextFormatted.py,1.1.1.1,NONE TextHtml.py,1.1.1.1,NONE TextPlain.py,1.1.1.1,NONE TextUuencoded.py,1.1.1.1,NONE TextXml.py,1.1.1.1,NONE Text_plain.py,1.1.1.1,NONE Trait_Details.py,1.1.1.1,NONE Tree.py,1.1.1.1,NONE VirtualSequence.py,1.1.1.1,NONE WU_BLAST_Text.py,1.1.1.1,NONE Wildcard_Query.py,1.1.1.1,NONE __init__.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/AGI_LocusCode.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Allele_freq.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/AminoAcidSequence.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/B64_Encoded_PNG.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/B64_Encoded_Postscript.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/B64_encoded_PDB.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/B64_encoded_gif.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/B64_encoded_jpeg.py,v: No such file or directory 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/home/repository/moby/moby-live/Python/src/ontology/RCS/Snp_allele.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Snp_genotype.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Study.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/TargetP_result.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Testout.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/TextBase64.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/TextFormatted.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/TextHtml.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/TextPlain.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/TextUuencoded.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/TextXml.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Text_plain.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Trait_Details.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Tree.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/VirtualSequence.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/WU_BLAST_Text.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Wildcard_Query.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/__init__.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFV5j028099@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/utils In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/utils Removed Files: moby2python.py Log Message: moby-live/Python/utils moby2python.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/utils/RCS/moby2python.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFVRn028039@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/Mobycentral In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/tutorials/Mobycentral Removed Files: deregisterService.py registerService.py retrieveServices.py servicesDump.py Log Message: moby-live/Python/tutorials/Mobycentral deregisterService.py,1.1.1.1,NONE registerService.py,1.1.1.1,NONE retrieveServices.py,1.1.1.1,NONE servicesDump.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/RCS/deregisterService.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/RCS/registerService.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/RCS/retrieveServices.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/RCS/servicesDump.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:29 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFT1L027878@pub.open-bio.org> yanwong Wed Dec 8 06:15:27 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/public In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/doc/public Removed Files: __builtin__.object-class.html __builtin__.type-class.html bioMoby-module.html bioMoby.mobyClient-module.html bioMoby.mobyClient.Central-class.html bioMoby.mobyClient.Client-class.html bioMoby.mobyDataTypes-module.html bioMoby.mobyDataTypes.MobyContent-class.html bioMoby.mobyDataTypes.MobyFloat-class.html bioMoby.mobyDataTypes.MobyInteger-class.html bioMoby.mobyDataTypes.MobyObject-class.html bioMoby.mobyDataTypes.MobySequence-class.html bioMoby.mobyDataTypes.MobyString-class.html bioMoby.mobyDataTypes.MobyXref-class.html bioMoby.mobyDataTypes.MobyZmPDB-class.html bioMoby.mobyDataTypes.Parameter-class.html bioMoby.mobyExceptions-module.html bioMoby.mobyExceptions.EInvalidArgument-class.html bioMoby.mobyExceptions.EInvalidType-class.html bioMoby.mobyExceptions.EMethodRetrieveError-class.html 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/home/repository/moby/moby-live/Python/doc/public/RCS/toc-bioMoby.webservice.Invocators-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/toc-everything.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/toc.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/trees.html,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFVTo028018@pub.open-bio.org> yanwong Wed Dec 8 06:15:30 EST 2004 Update of /home/repository/moby/moby-live/Python/src/webservice In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/src/webservice Removed Files: Dispatcher.py Invocators.py __init__.py Log Message: moby-live/Python/src/webservice Dispatcher.py,1.1.1.1,NONE Invocators.py,1.1.1.1,NONE __init__.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/src/webservice/RCS/Dispatcher.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/webservice/RCS/Invocators.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/webservice/RCS/__init__.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:30 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFUEx027900@pub.open-bio.org> yanwong Wed Dec 8 06:15:30 EST 2004 Update of /home/repository/moby/moby-live/Python/src In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/src Removed Files: __init__.py mobyClient.py mobyDataTypes.py mobyExceptions.py mobyMarshal.py mobyRegister.py mobyService.py Log Message: moby-live/Python/src __init__.py,1.1.1.1,NONE mobyClient.py,1.1.1.1,NONE mobyDataTypes.py,1.1.1.1,NONE mobyExceptions.py,1.1.1.1,NONE mobyMarshal.py,1.1.1.1,NONE mobyRegister.py,1.1.1.1,NONE mobyService.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/__init__.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyClient.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyDataTypes.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyExceptions.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyMarshal.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyRegister.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyService.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFVfY028059@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/Service In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/tutorials/Service Removed Files: testMarshaller.py testMobyService.py testMobyService2.py Log Message: moby-live/Python/tutorials/Service testMarshaller.py,1.1.1.1,NONE testMobyService.py,1.1.1.1,NONE testMobyService2.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Service/RCS/testMarshaller.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Service/RCS/testMobyService.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Service/RCS/testMobyService2.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:21:20 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:21:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081121.iB8BLKrP028288@pub.open-bio.org> yanwong Wed Dec 8 06:21:20 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby In directory pub.open-bio.org:/tmp/cvs-serv28264/bioMoby Log Message: Directory /home/repository/moby/moby-live/Python/bioMoby added to the repository moby-live/Python/bioMoby - New directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:21:44 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:21:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081121.iB8BLi3H028331@pub.open-bio.org> yanwong Wed Dec 8 06:21:44 EST 2004 Update of /home/repository/moby/moby-live/Python/packages In directory pub.open-bio.org:/tmp/cvs-serv28307/packages Log Message: Directory /home/repository/moby/moby-live/Python/packages added to the repository moby-live/Python/packages - New directory rcsdiff: /home/repository/moby/moby-live/Python/packages/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/packages/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/packages/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:24:34 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:24:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081124.iB8BOYLA028461@pub.open-bio.org> yanwong Wed Dec 8 06:24:34 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby/webservice In directory pub.open-bio.org:/tmp/cvs-serv28419/webservice Log Message: Directory /home/repository/moby/moby-live/Python/bioMoby/webservice added to the repository moby-live/Python/bioMoby/webservice - New directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/webservice/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/webservice/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/webservice/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:24:34 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:24:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081124.iB8BOY8f028443@pub.open-bio.org> yanwong Wed Dec 8 06:24:34 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby/ontology In directory pub.open-bio.org:/tmp/cvs-serv28419/ontology Log Message: Directory /home/repository/moby/moby-live/Python/bioMoby/ontology added to the repository moby-live/Python/bioMoby/ontology - New directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/ontology/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/ontology/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/ontology/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:25:23 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:25:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081125.iB8BPNdV028520@pub.open-bio.org> yanwong Wed Dec 8 06:25:23 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/src In directory pub.open-bio.org:/tmp/cvs-serv28496/src Log Message: Directory /home/repository/moby/moby-live/Python/doc/src added to the repository moby-live/Python/doc/src - New directory rcsdiff: /home/repository/moby/moby-live/Python/doc/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/src/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 06:26:02 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:26:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081126.iB8BQ2tq028580@pub.open-bio.org> yanwong Wed Dec 8 06:26:02 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby In directory pub.open-bio.org:/tmp/cvs-serv28528/Python/bioMoby Added Files: __init__.py mobyClient.py mobyDataTypes.py mobyExceptions.py mobyMarshal.py mobyRegister.py mobyService.py Log Message: moby-live/Python/bioMoby __init__.py,NONE,1.1 mobyClient.py,NONE,1.1 mobyDataTypes.py,NONE,1.1 mobyExceptions.py,NONE,1.1 mobyMarshal.py,NONE,1.1 mobyRegister.py,NONE,1.1 mobyService.py,NONE,1.1 From yanwong at pub.open-bio.org Wed Dec 8 06:26:02 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:26:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081126.iB8BQ2Ja028565@pub.open-bio.org> yanwong Wed Dec 8 06:26:01 EST 2004 Update of /home/repository/moby/moby-live/Python In directory pub.open-bio.org:/tmp/cvs-serv28528/Python Added Files: PKG-INFO README changelog setup.py Log Message: moby-live/Python PKG-INFO,1.2,1.3 README,1.2,1.3 changelog,1.2,1.3 setup.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/PKG-INFO,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/PKG-INFO 2004/12/08 11:15:20 1.2 +++ /home/repository/moby/moby-live/Python/PKG-INFO 2004/12/08 11:26:01 1.3 @@ -1,10 +1,10 @@ Metadata-Version: 1.0 Name: bioMoby -Version: 0.5 +Version: 0.7p1 Summary: Python interface for bioMoby Home-page: http://bioserv.rpbs.jussieu.fr Author: Yan Wong Author-email: yanwong at ebgm.jussieu.fr License: -Description: Python's version of Moby's API 0.7 +Description: Python's version of Moby's API 0.8 Platform: UNKNOWN =================================================================== RCS file: /home/repository/moby/moby-live/Python/README,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/README 2004/12/08 11:15:20 1.2 +++ /home/repository/moby/moby-live/Python/README 2004/12/08 11:26:01 1.3 @@ -6,11 +6,13 @@ -Python 2.3 -SOAPpy : http://pywebsvcs.sourceforge.net/ -xml libraries for python: http://pyxml.sourceforge.net (generally already included in python 2.2+) + however if you have some troubles you may need to install PyXML 0.8.3 -if you plan to build webservices with Python, have a look on ZSI gived in this distribution (ZSI-1.5.0-patched) the ZSI here has been patched due to some trouble with CDATA section node __init__.py has been modified in order to solve this problem -pyipc: http://www.theory.org/~mac4/software/ for ipc management with Python (the Dispatcher class needs it) +All these libraries has been added in the packages directory. How to setup bioMoby-python? =================================================================== RCS file: /home/repository/moby/moby-live/Python/changelog,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/changelog 2004/12/08 11:15:20 1.2 +++ /home/repository/moby/moby-live/Python/changelog 2004/12/08 11:26:01 1.3 @@ -31,4 +31,28 @@ add a __setitem__ method to the MobyContent class queries are now accessible via the key directly, use mobycontent['querykey'] to access the data and parameters inside a tool in the utils/wx, objectBrowser is a GUI program to browse the bioMoby Ontology - + +0.6: Bug in the MobyObject corrected + Bug in the Dispatcher corrected (troubles with handling multiple queries) + added signatureURL and RDF for Registration process (in Service, ServiceList) + debug option when executing a service (trace of HTTP calls) in Central and Service Class + (allows you to have the dump of all your SOAP transaction with the webservice) + if you want to trace a SOAP call while executing a service just put: + service.execute(mobyqueries, debug=True) and you'll have the complete trace of the execution + when you deal with the Moby Central Server, just add client.server.config.debug=1 in order to trace execution of your queries + +0.7: Create a class AbstractDispatcher, SimpleDispatcher in order to create other types of dispatchers + On PBSDispatcher, a class qsubParameters designed to store parameters for the qsub command + Class Parameter deserialisation (fromMoby) + Some cleaning on the code, and even more debugging;) + Documentation has been updated + Libraries that were used to build this packages has been added into the packages directory + +0.7p1: Dispatchers can deserialize MobyContent that were in Body tag people using mod_python will have + to patch their ZSI package again. + just do a: + cd packages/ZSI-1.5.0-patched + python setup.py install + (normally just the dispatch.py was modified) + + tutorials/webservice and documentations have been updated. =================================================================== RCS file: /home/repository/moby/moby-live/Python/setup.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/setup.py 2004/12/08 11:15:20 1.2 +++ /home/repository/moby/moby-live/Python/setup.py 2004/12/08 11:26:01 1.3 @@ -9,4 +9,4 @@ author_email="yanwong at ebgm.jussieu.fr", url="http://bioserv.rpbs.jussieu.fr", packages=['bioMoby', 'bioMoby.ontology', 'bioMoby.webservice'], - package_dir={'bioMoby':'src', 'bioMoby.ontology':'src/ontology', 'bioMoby.webservice':'src/webservice'}) + package_dir={'bioMoby':'bioMoby', 'bioMoby.ontology':'bioMoby/ontology', 'bioMoby.webservice':'bioMoby/webservice'}) From yanwong at pub.open-bio.org Wed Dec 8 09:46:40 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:46:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081446.iB8EkeMG029581@pub.open-bio.org> yanwong Wed Dec 8 09:46:40 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby/webservice In directory pub.open-bio.org:/tmp/cvs-serv29560 Added Files: Dispatcher.py Invocators.py TCBioMoby.py __init__.py Log Message: moby-live/Python/bioMoby/webservice Dispatcher.py,NONE,1.1 Invocators.py,NONE,1.1 TCBioMoby.py,NONE,1.1 __init__.py,NONE,1.1 From yanwong at pub.open-bio.org Wed Dec 8 09:47:49 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:47:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081447.iB8ElnHb029634@pub.open-bio.org> yanwong Wed Dec 8 09:47:49 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby/ontology In directory pub.open-bio.org:/tmp/cvs-serv29613 Added Files: AlleleAssociation.py Allele_freq.py AminoAcidSequence.py B64_Encoded_PNG.py B64_Encoded_Postscript.py B64_encoded_PDB.py B64_encoded_gif.py B64_encoded_jpeg.py BLASTText.py BasicGFFSequenceFeature.py ClustalAlnFormattedText.py ClustalMsfFormattedText.py CommentedAASequence.py CommentedDNASequence.py CommentedRNASequence.py DNASequence.py DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py Edge.py EmblFlatfile.py FASTA.py FASTA_AA.py FASTA_NA.py FASTA_Text.py GFF.py GFF1.py GFF2.py GFF2_5.py GFF3.py GO_Term.py GenbankFlatfile.py GenericSequence.py GeneticElement.py Genotype.py Germplasm_Details.py Germplasm_List.py Global_Keyword.py HBond_Pair.py HFormatText.py Haplotyping_Study_obj.py ICIS_Query.py ICIS_Query2.py ICIS_Query3.py IntAct_XML.py Interaction.py InteractionMethod.py Interaction_partner.py Interactor.py MEME_Text.py MGIS_ACCESSION.py MMP_Locus.py MO_Term_Test.py MmCIFText.py Multi_key_value_pair.py MyTestingDataType_11024145298313.py MyTree.py NCBI_BLAST_Text.py NCBI_Blast_XML.py NCBI_Blast_XML_Gif.py NCBI_Blast_XML_Gif_Map.py NCBI_MEME_Text.py NucleotideSequence.py PDBFormattedText.py PDBText.py PDGJOB.py PHDText.py PMUTText.py PSeaTextFormatted.py PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py SINGER_ACCESSION.py Sample.py SchematikonMotifID.py SchematikonMotifSupport.py SchematikonSegmentAttributes.py SchematikonSegmentID.py SchematikonStructureAnnotation.py SchematikonVorocodeName.py Scored_acronym_string.py SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py Simple_key_value_pair.py Snp_allele.py Snp_genotype.py Study.py TEST.py TargetP_result.py Testout.py TextBase64.py TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py TextXml.py Text_plain.py Trait_Details.py Tree.py TropGENE_ACCESSION.py TropGENE_Diversity_Matrix.py TropGENE_LOCUS.py VirtualSequence.py WU_BLAST_Text.py Wildcard_Query.py __init__.py Log Message: moby-live/Python/bioMoby/ontology AlleleAssociation.py,NONE,1.1 Allele_freq.py,NONE,1.1 AminoAcidSequence.py,NONE,1.1 B64_Encoded_PNG.py,NONE,1.1 B64_Encoded_Postscript.py,NONE,1.1 B64_encoded_PDB.py,NONE,1.1 B64_encoded_gif.py,NONE,1.1 B64_encoded_jpeg.py,NONE,1.1 BLASTText.py,NONE,1.1 BasicGFFSequenceFeature.py,NONE,1.1 ClustalAlnFormattedText.py,NONE,1.1 ClustalMsfFormattedText.py,NONE,1.1 CommentedAASequence.py,NONE,1.1 CommentedDNASequence.py,NONE,1.1 CommentedRNASequence.py,NONE,1.1 DNASequence.py,NONE,1.1 DNASequenceWithGFFFeatures.py,NONE,1.1 DateTime.py,NONE,1.1 Decypher_Text.py,NONE,1.1 Edge.py,NONE,1.1 EmblFlatfile.py,NONE,1.1 FASTA.py,NONE,1.1 FASTA_AA.py,NONE,1.1 FASTA_NA.py,NONE,1.1 FASTA_Text.py,NONE,1.1 GFF.py,NONE,1.1 GFF1.py,NONE,1.1 GFF2.py,NONE,1.1 GFF2_5.py,NONE,1.1 GFF3.py,NONE,1.1 GO_Term.py,NONE,1.1 GenbankFlatfile.py,NONE,1.1 GenericSequence.py,NONE,1.1 GeneticElement.py,NONE,1.1 Genotype.py,NONE,1.1 Germplasm_Details.py,NONE,1.1 Germplasm_List.py,NO! NE,1.1 Global_Keyword.py,NONE,1.1 HBond_Pair.py,NONE,1.1 HFormatText.py,NONE,1.1 Haplotyping_Study_obj.py,NONE,1.1 ICIS_Query.py,NONE,1.1 ICIS_Query2.py,NONE,1.1 ICIS_Query3.py,NONE,1.1 IntAct_XML.py,NONE,1.1 Interaction.py,NONE,1.1 InteractionMethod.py,NONE,1.1 Interaction_partner.py,NONE,1.1 Interactor.py,NONE,1.1 MEME_Text.py,NONE,1.1 MGIS_ACCESSION.py,NONE,1.1 MMP_Locus.py,NONE,1.1 MO_Term_Test.py,NONE,1.1 MmCIFText.py,NONE,1.1 Multi_key_value_pair.py,NONE,1.1 MyTestingDataType_11024145298313.py,NONE,1.1 MyTree.py,NONE,1.1 NCBI_BLAST_Text.py,NONE,1.1 NCBI_Blast_XML.py,NONE,1.1 NCBI_Blast_XML_Gif.py,NONE,1.1 NCBI_Blast_XML_Gif_Map.py,NONE,1.1 NCBI_MEME_Text.py,NONE,1.1 NucleotideSequence.py,NONE,1.1 PDBFormattedText.py,NONE,1.1 PDBText.py,NONE,1.1 PDGJOB.py,NONE,1.1 PHDText.py,NONE,1.1 PMUTText.py,NONE,1.1 PSeaTextFormatted.py,NONE,1.1 PhenotypeDescription.py,NONE,1.1 PubMedMEDLINE.py,NONE,1.1 RNASequence.py,NONE,1.1 SINGER_ACCESSION.py,NONE,1.1 Sample.py,NONE,1.1 Schemat! ikonMotifID.py,NONE,1.1 SchematikonMotifSupport.py,NONE,1.1 S! chematikonSegmentAttributes.py,NONE,1.1 SchematikonSegmentID.py,NONE,1.1 SchematikonStructureAnnotation.py,NONE,1.1 SchematikonVorocodeName.py,NONE,1.1 Scored_acronym_string.py,NONE,1.1 SimpleAnnotatedGIFImage.py,NONE,1.1 SimpleAnnotatedJPEGImage.py,NONE,1.1 Simple_key_value_pair.py,NONE,1.1 Snp_allele.py,NONE,1.1 Snp_genotype.py,NONE,1.1 Study.py,NONE,1.1 TEST.py,NONE,1.1 TargetP_result.py,NONE,1.1 Testout.py,NONE,1.1 TextBase64.py,NONE,1.1 TextFormatted.py,NONE,1.1 TextHtml.py,NONE,1.1 TextPlain.py,NONE,1.1 TextUuencoded.py,NONE,1.1 TextXml.py,NONE,1.1 Text_plain.py,NONE,1.1 Trait_Details.py,NONE,1.1 Tree.py,NONE,1.1 TropGENE_ACCESSION.py,NONE,1.1 TropGENE_Diversity_Matrix.py,NONE,1.1 TropGENE_LOCUS.py,NONE,1.1 VirtualSequence.py,NONE,1.1 WU_BLAST_Text.py,NONE,1.1 Wildcard_Query.py,NONE,1.1 __init__.py,NONE,1.1 From yanwong at pub.open-bio.org Wed Dec 8 09:48:40 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:48:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081448.iB8EmeLf029679@pub.open-bio.org> yanwong Wed Dec 8 09:48:40 EST 2004 Update of /home/repository/moby/moby-live/Python/packages In directory pub.open-bio.org:/tmp/cvs-serv29658 Added Files: PyIPC.tar.bz2 PyXML-0.8.3.tar.bz2 SOAPpy-0.11.4.tar.bz2 ZSI-1.5.0-patched-2.tar.bz2 fpconst-0.6.0.tar.bz2 Log Message: moby-live/Python/packages PyIPC.tar.bz2,NONE,1.1 PyXML-0.8.3.tar.bz2,NONE,1.1 SOAPpy-0.11.4.tar.bz2,NONE,1.1 ZSI-1.5.0-patched-2.tar.bz2,NONE,1.1 fpconst-0.6.0.tar.bz2,NONE,1.1 From yanwong at pub.open-bio.org Wed Dec 8 09:53:40 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:53:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081453.iB8ErePs029779@pub.open-bio.org> yanwong Wed Dec 8 09:53:40 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/webservices In directory pub.open-bio.org:/tmp/cvs-serv29748 Added Files: Clustalw-mod_python.py Clustalw.py blastpgp.py wsStride.py Log Message: wsStride is an example of wrapping Stride as a webservice: to query it, just give a PDB id like namespace="PDB" id="1AKQ" the service queries the PDB and calculate stride with it moby-live/Python/tutorials/webservices Clustalw-mod_python.py,1.2,1.3 Clustalw.py,1.2,1.3 blastpgp.py,NONE,1.1 wsStride.py,NONE,1.1 =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw-mod_python.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw-mod_python.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw-mod_python.py 2004/12/08 14:53:40 1.3 @@ -36,7 +36,11 @@ d=Dispatcher(mobyContent, LocalInvocator, _toParameters) return d.execute() - + +from ZSI import dispatch +from mod_python import apache +from bioMoby.webservice import TCBioMoby + def handler(req): if req.method=='GET': if req.args=='wsdl': @@ -50,6 +54,6 @@ req.write("ClustalwClustalw") else: - dispatch.AsHandler(modules=(Clustalw,),request=req) + dispatch.AsHandler(modules=(Clustalw,),request=req, typesmodule=TCBioMoby) return apache.OK =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw.py 2004/12/08 14:53:40 1.3 @@ -31,12 +31,21 @@ return (commandName, " type=p -align "+" ".join(parameters), tempfiles, outputfiles) +def ClustalFormatter(results): + def ClustalFormatter(results): + """Return the results in a MobyClustalAlnFormattedText object + """ + from bioMoby import MobyClustalAlnFormattedText + + return [MobyClustalAlnFormattedText(content=results)] + def clustalw(mobyContent): from bioMoby import Dispatcher, LocalInvocator - d=Dispatcher(mobyContent, LocalInvocator, commandBuilder) + d=Dispatcher(mobyContent, LocalInvocator, commandBuilder, formatter=ClustalFormatter) return d.execute() from ZSI import dispatch -dispatch.asCGI() \ No newline at end of file +from bioMoby.webservice import TCBioMoby +dispatch.asCGI(typesmodule=TCBioMoby) From yanwong at pub.open-bio.org Wed Dec 8 09:54:50 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:54:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081454.iB8EsoS9029833@pub.open-bio.org> yanwong Wed Dec 8 09:54:50 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/Service In directory pub.open-bio.org:/tmp/cvs-serv29800 Added Files: async.py blastpgp.py testMarshaller.py testMobyService.py testMobyService2.py Log Message: moby-live/Python/tutorials/Service async.py,NONE,1.1 blastpgp.py,NONE,1.1 testMarshaller.py,1.2,1.3 testMobyService.py,1.2,1.3 testMobyService2.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Service/testMarshaller.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Service/testMarshaller.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Service/testMarshaller.py 2004/12/08 14:54:50 1.3 @@ -29,7 +29,7 @@ o=um.loads(s) -print "content of the object" -for object in o.queryData: - print str(object) +print "contents:" +for query in o.keys(): + print o[query][0].content =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService.py 2004/12/08 14:54:50 1.3 @@ -30,7 +30,7 @@ print "Service getNASC_codebyAGI_locus executed with query1 namespace=AGI_LocusCode and id=At3g19100...\n" - resultat=myService.execute(query) + resultat=myService.execute(query, debug=True) print "the xml form\n" =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService2.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService2.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService2.py 2004/12/08 14:54:50 1.3 @@ -16,7 +16,7 @@ object=MobyObject(namespace='DragonDB_Allele',id='cho') print "Service executed with query namespace=DragonDB_Allele and id=cho" -resultat=service.execute(MobyContent({'query1':[object]})) +resultat=service.execute(MobyContent({'query1':[object]}), debug=True) print resultat From yanwong at pub.open-bio.org Wed Dec 8 09:55:22 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:55:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081455.iB8EtMBX029887@pub.open-bio.org> yanwong Wed Dec 8 09:55:22 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/Mobycentral In directory pub.open-bio.org:/tmp/cvs-serv29854 Added Files: registerService.py retrieveServices.py servicesDump.py Log Message: moby-live/Python/tutorials/Mobycentral registerService.py,1.2,1.3 retrieveServices.py,1.2,1.3 servicesDump.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/registerService.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Mobycentral/registerService.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Mobycentral/registerService.py 2004/12/08 14:55:22 1.3 @@ -43,6 +43,7 @@ 'name':'getStrideFromPDB', 'type':'Analysis', 'url':'http://prot3.rpbs.jussieu.fr:8080/ZStrideService/ZStrideService.py', + 'signatureURL':'http://prot3.rpbs.jussieu.fr:8080/RDF', 'authoritative':0, 'contactEmail':'yanwong at ebgm.jussieu.fr', 'authURI':'prot3.rpbs.jussieu.fr', @@ -56,6 +57,7 @@ if resultat.isSuccess(): print "Service registration successful" + print resultat.RDF else: print resultat.message raise Exception =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/retrieveServices.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/servicesDump.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Mobycentral/servicesDump.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Mobycentral/servicesDump.py 2004/12/08 14:55:22 1.3 @@ -2,7 +2,7 @@ from bioMoby import Client, ServiceQuery, ServiceArticle, ServiceSecondary -client=Client() +client=Client(url="http://mips.gsf.de/cgi-bin/proj/planet/moby/MOBY-Central.pl", ns="http://mips.gsf.de/MOBY/Central") dsn=client.retrieveServiceNames() From yanwong at pub.open-bio.org Wed Dec 8 09:57:28 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:57:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081457.iB8EvS4x029956@pub.open-bio.org> yanwong Wed Dec 8 09:57:28 EST 2004 Update of /home/repository/moby/moby-live/Python In directory pub.open-bio.org:/tmp/cvs-serv29919 Modified Files: PKG-INFO README changelog setup.py Log Message: moby-live/Python PKG-INFO,1.3,1.4 README,1.3,1.4 changelog,1.3,1.4 setup.py,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Python/PKG-INFO,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Python/README,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Python/changelog,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Python/setup.py,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 From yanwong at pub.open-bio.org Thu Dec 9 09:07:37 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu, 9 Dec 2004 09:07:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091407.iB9E7bpV003498@pub.open-bio.org> yanwong Thu Dec 9 09:07:32 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/private In directory pub.open-bio.org:/tmp/cvs-serv2265 Added Files: ZSI.TC.TypeCode-class.html __builtin__.object-class.html __builtin__.type-class.html bioMoby-module.html bioMoby.mobyClient-module.html bioMoby.mobyClient.Central-class.html bioMoby.mobyClient.Client-class.html bioMoby.mobyDataTypes-module.html bioMoby.mobyDataTypes.MobyContent-class.html bioMoby.mobyDataTypes.MobyFloat-class.html bioMoby.mobyDataTypes.MobyInteger-class.html bioMoby.mobyDataTypes.MobyObject-class.html bioMoby.mobyDataTypes.MobySequence-class.html bioMoby.mobyDataTypes.MobyString-class.html bioMoby.mobyDataTypes.MobyXref-class.html bioMoby.mobyDataTypes.MobyZmPDB-class.html bioMoby.mobyDataTypes.Parameter-class.html bioMoby.mobyExceptions-module.html bioMoby.mobyExceptions.EInvalidArgument-class.html bioMoby.mobyExceptions.EInvalidType-class.html bioMoby.mobyExceptions.EMethodRetrieveError-class.html bioMoby.mobyExceptions.ENotAWSMethod-class.html bioMoby.mobyExceptions.ETypeMismatch-class.html bioMoby.mobyMarshal-module.html bioMoby.mobyMarshal.MobyMarshaller-class.html bioMoby.mobyMarshal.MobyUnmarshaller-class.html bioMoby.mobyRegister-module.html bioMoby.mobyRegister.GeneralInformations-class.html bioMoby.mobyRegister.Namespace-class.html bioMoby.mobyRegister.ObjectClass-class.html bioMoby.mobyRegister.RegistrationObject-class.html bioMoby.mobyRegister.ServiceType-class.html bioMoby.mobyService-module.html bioMoby.mobyService.Service-class.html bioMoby.mobyService.ServiceArticle-class.html bioMoby.mobyService.ServiceList-class.html bioMoby.mobyService.ServiceQuery-class.html bioMoby.mobyService.ServiceSecondary-class.html bioMoby.ontology-module.html bioMoby.ontology.AGI_LocusCode-module.html bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html bioMoby.ontology.Allele_freq-module.html bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html bioMoby.ontology.AminoAcidSequence-module.html bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html bioMoby.ontology.B64_Encoded_PNG-module.html bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html bioMoby.ontology.B64_Encoded_Postscript-module.html bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html bioMoby.ontology.B64_encoded_PDB-module.html bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html bioMoby.ontology.B64_encoded_gif-module.html bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html bioMoby.ontology.B64_encoded_jpeg-module.html bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg-class.html bioMoby.ontology.BasicGFFSequenceFeature-module.html bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature-class.html bioMoby.ontology.ClustalAlnFormattedText-module.html bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText-class.html bioMoby.ontology.CommentedAASequence-module.html bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence-class.html bioMoby.ontology.CommentedDNASequence-module.html bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence-class.html bioMoby.ontology.CommentedRNASequence-module.html bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence-class.html bioMoby.ontology.DNASequence-module.html bioMoby.ontology.DNASequence.MobyDNASequence-class.html bioMoby.ontology.DNASequenceWithGFFFeatures-module.html bioMoby.ontology.DNASequenceWithGFFFeatures.MobyDNASequenceWithGFFFeatures-class.html bioMoby.ontology.DateTime-module.html bioMoby.ontology.DateTime.MobyDateTime-class.html bioMoby.ontology.Decypher_Text-module.html bioMoby.ontology.Decypher_Text.MobyDecypher_Text-class.html bioMoby.ontology.Edge-module.html 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bioMoby.ontology.GenericSequence-module.html bioMoby.ontology.GenericSequence.MobyGenericSequence-class.html bioMoby.ontology.GeneticElement-module.html bioMoby.ontology.GeneticElement.MobyGeneticElement-class.html bioMoby.ontology.Germplasm_Details-module.html bioMoby.ontology.Germplasm_Details.MobyGermplasm_Details-class.html bioMoby.ontology.Germplasm_List-module.html bioMoby.ontology.Germplasm_List.MobyGermplasm_List-class.html bioMoby.ontology.Global_Keyword-module.html bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword-class.html bioMoby.ontology.HBond_Pair-module.html bioMoby.ontology.HBond_Pair.MobyHBond_Pair-class.html bioMoby.ontology.HCA_picture-module.html bioMoby.ontology.HCA_picture.MobyHCA_picture-class.html bioMoby.ontology.Haplotyping_Study_obj-module.html bioMoby.ontology.Haplotyping_Study_obj.MobyHaplotyping_Study_obj-class.html bioMoby.ontology.ICIS_Query-module.html bioMoby.ontology.ICIS_Query.MobyICIS_Query-class.html bioMoby.ontology.ICIS_Query2-module.html 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bioMoby.ontology.Study.MobyStudy-class.html bioMoby.ontology.TEST-module.html bioMoby.ontology.TEST.MobyTEST-class.html bioMoby.ontology.TargetP_result-module.html bioMoby.ontology.TargetP_result.MobyTargetP_result-class.html bioMoby.ontology.Testout-module.html bioMoby.ontology.Testout.MobyTestout-class.html bioMoby.ontology.TextBase64-module.html bioMoby.ontology.TextBase64.MobyTextBase64-class.html bioMoby.ontology.TextFormatted-module.html bioMoby.ontology.TextFormatted.MobyTextFormatted-class.html bioMoby.ontology.TextHtml-module.html bioMoby.ontology.TextHtml.MobyTextHtml-class.html bioMoby.ontology.TextPlain-module.html bioMoby.ontology.TextPlain.MobyTextPlain-class.html bioMoby.ontology.TextUuencoded-module.html bioMoby.ontology.TextUuencoded.MobyTextUuencoded-class.html bioMoby.ontology.TextXml-module.html bioMoby.ontology.TextXml.MobyTextXml-class.html bioMoby.ontology.Text_plain-module.html bioMoby.ontology.Text_plain.MobyText_plain-class.html bioMoby.ontology.Trait_Details-module.html bioMoby.ontology.Trait_Details.MobyTrait_Details-class.html bioMoby.ontology.Tree-module.html bioMoby.ontology.Tree.MobyTree-class.html bioMoby.ontology.TropGENE_ACCESSION-module.html bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION-class.html bioMoby.ontology.TropGENE_Diversity_Matrix-module.html bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix-class.html bioMoby.ontology.TropGENE_LOCUS-module.html bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS-class.html bioMoby.ontology.VirtualSequence-module.html bioMoby.ontology.VirtualSequence.MobyVirtualSequence-class.html bioMoby.ontology.WU_BLAST_Text-module.html bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text-class.html bioMoby.ontology.Wildcard_Query-module.html bioMoby.ontology.Wildcard_Query.MobyWildcard_Query-class.html bioMoby.webservice-module.html bioMoby.webservice.Dispatcher-module.html bioMoby.webservice.Dispatcher.AbstractDispatcher-class.html bioMoby.webservice.Dispatcher.Dispatcher-class.html bioMoby.webservice.Dispatcher.EDispatchError-class.html bioMoby.webservice.Dispatcher.LockedIterator-class.html bioMoby.webservice.Dispatcher.MultiThread-class.html bioMoby.webservice.Dispatcher.PBSDispatcher-class.html bioMoby.webservice.Dispatcher.SimpleDispatcher-class.html bioMoby.webservice.Dispatcher.SingleThread-class.html bioMoby.webservice.Invocators-module.html bioMoby.webservice.Invocators.CGIPostInvocator-class.html bioMoby.webservice.Invocators.CGIPostMInvocator-class.html bioMoby.webservice.Invocators.GeneralInvocator-class.html bioMoby.webservice.Invocators.InvocatorError-class.html bioMoby.webservice.Invocators.LocalInvocator-class.html bioMoby.webservice.Invocators.PBSInvocator-class.html bioMoby.webservice.Invocators.QsubParameters-class.html bioMoby.webservice.TCBioMoby-module.html bioMoby.webservice.TCBioMoby.Body-class.html bioMoby.webservice.TCBioMoby._TCBody-class.html exceptions.Exception-class.html frames.html help.html index.html indices.html threading.Thread-class.html threading._Verbose-class.html toc-bioMoby-module.html toc-bioMoby.mobyClient-module.html toc-bioMoby.mobyDataTypes-module.html toc-bioMoby.mobyExceptions-module.html toc-bioMoby.mobyMarshal-module.html toc-bioMoby.mobyRegister-module.html toc-bioMoby.mobyService-module.html toc-bioMoby.ontology-module.html toc-bioMoby.ontology.AGI_LocusCode-module.html toc-bioMoby.ontology.Allele_freq-module.html toc-bioMoby.ontology.AminoAcidSequence-module.html toc-bioMoby.ontology.B64_Encoded_PNG-module.html toc-bioMoby.ontology.B64_Encoded_Postscript-module.html toc-bioMoby.ontology.B64_encoded_PDB-module.html toc-bioMoby.ontology.B64_encoded_gif-module.html toc-bioMoby.ontology.B64_encoded_jpeg-module.html toc-bioMoby.ontology.BasicGFFSequenceFeature-module.html toc-bioMoby.ontology.ClustalAlnFormattedText-module.html toc-bioMoby.ontology.CommentedAASequence-module.html toc-bioMoby.ontology.CommentedDNASequence-module.html 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toc-bioMoby.ontology.HBond_Pair-module.html toc-bioMoby.ontology.HCA_picture-module.html toc-bioMoby.ontology.Haplotyping_Study_obj-module.html toc-bioMoby.ontology.ICIS_Query-module.html toc-bioMoby.ontology.ICIS_Query2-module.html toc-bioMoby.ontology.ICIS_Query3-module.html toc-bioMoby.ontology.IntAct_XML-module.html toc-bioMoby.ontology.Interaction-module.html toc-bioMoby.ontology.InteractionMethod-module.html toc-bioMoby.ontology.Interaction_partner-module.html toc-bioMoby.ontology.Interactor-module.html toc-bioMoby.ontology.MEME_Text-module.html toc-bioMoby.ontology.MGIS_ACCESSION-module.html toc-bioMoby.ontology.MMP_Locus-module.html toc-bioMoby.ontology.MO_Term_Test-module.html toc-bioMoby.ontology.Multi_key_value_pair-module.html toc-bioMoby.ontology.MyTree-module.html toc-bioMoby.ontology.NCBI_BLAST_Text-module.html toc-bioMoby.ontology.NCBI_Blast_XML-module.html toc-bioMoby.ontology.NCBI_MEME_Text-module.html toc-bioMoby.ontology.NucleotideSequence-module.html toc-bioMoby.ontology.PDBFormattedText-module.html toc-bioMoby.ontology.PDGJOB-module.html toc-bioMoby.ontology.PhenotypeDescription-module.html toc-bioMoby.ontology.PubMedMEDLINE-module.html toc-bioMoby.ontology.RNASequence-module.html toc-bioMoby.ontology.SINGER_ACCESSION-module.html toc-bioMoby.ontology.SchematikonMotifID-module.html toc-bioMoby.ontology.SchematikonMotifSupport-module.html toc-bioMoby.ontology.SchematikonSegmentAttributes-module.html toc-bioMoby.ontology.SchematikonSegmentID-module.html toc-bioMoby.ontology.SchematikonStructureAnnotation-module.html toc-bioMoby.ontology.SchematikonVorocodeName-module.html toc-bioMoby.ontology.Scored_acronym_string-module.html toc-bioMoby.ontology.SimpleAnnotatedGIFImage-module.html toc-bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html toc-bioMoby.ontology.Simple_key_value_pair-module.html toc-bioMoby.ontology.Snp_allele-module.html toc-bioMoby.ontology.Snp_genotype-module.html toc-bioMoby.ontology.Study-module.html toc-bioMoby.ontology.TEST-module.html toc-bioMoby.ontology.TargetP_result-module.html toc-bioMoby.ontology.Testout-module.html toc-bioMoby.ontology.TextBase64-module.html toc-bioMoby.ontology.TextFormatted-module.html toc-bioMoby.ontology.TextHtml-module.html toc-bioMoby.ontology.TextPlain-module.html toc-bioMoby.ontology.TextUuencoded-module.html toc-bioMoby.ontology.TextXml-module.html toc-bioMoby.ontology.Text_plain-module.html toc-bioMoby.ontology.Trait_Details-module.html toc-bioMoby.ontology.Tree-module.html toc-bioMoby.ontology.TropGENE_ACCESSION-module.html toc-bioMoby.ontology.TropGENE_Diversity_Matrix-module.html toc-bioMoby.ontology.TropGENE_LOCUS-module.html toc-bioMoby.ontology.VirtualSequence-module.html toc-bioMoby.ontology.WU_BLAST_Text-module.html toc-bioMoby.ontology.Wildcard_Query-module.html toc-bioMoby.webservice-module.html toc-bioMoby.webservice.Dispatcher-module.html toc-bioMoby.webservice.Invocators-module.html toc-bioMoby.webservice.TCBioMoby-module.html toc-everything.html toc.html trees.html Log Message: moby-live/Python/doc/private ZSI.TC.TypeCode-class.html,NONE,1.1 __builtin__.object-class.html,1.2,1.3 __builtin__.type-class.html,1.2,1.3 bioMoby-module.html,1.2,1.3 bioMoby.mobyClient-module.html,1.2,1.3 bioMoby.mobyClient.Central-class.html,1.2,1.3 bioMoby.mobyClient.Client-class.html,1.2,1.3 bioMoby.mobyDataTypes-module.html,1.2,1.3 bioMoby.mobyDataTypes.MobyContent-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyFloat-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyInteger-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyObject-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobySequence-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyString-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyXref-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyZmPDB-class.html,1.2,1.3 bioMoby.mobyDataTypes.Parameter-class.html,1.2,1.3 bioMoby.mobyExceptions-module.html,1.2,1.3 bioMoby.mobyExceptions.EInvalidArgument-class.html,1.2,1.3 bioMoby.mobyExceptions.EInvalidType-class.html,1.2,1.3 bioMoby.mobyExceptions.EMe! thodRetrieveError-class.html,1.2,1.3 bioMoby.mobyExceptions.ENotAWSMethod-class.html,1.2,1.3 bioMoby.mobyExceptions.ETypeMismatch-class.html,1.2,1.3 bioMoby.mobyMarshal-module.html,1.2,1.3 bioMoby.mobyMarshal.MobyMarshaller-class.html,1.2,1.3 bioMoby.mobyMarshal.MobyUnmarshaller-class.html,1.2,1.3 bioMoby.mobyRegister-module.html,1.2,1.3 bioMoby.mobyRegister.GeneralInformations-class.html,1.2,1.3 bioMoby.mobyRegister.Namespace-class.html,1.2,1.3 bioMoby.mobyRegister.ObjectClass-class.html,1.2,1.3 bioMoby.mobyRegister.RegistrationObject-class.html,1.2,1.3 bioMoby.mobyRegister.ServiceType-class.html,1.2,1.3 bioMoby.mobyService-module.html,1.2,1.3 bioMoby.mobyService.Service-class.html,1.2,1.3 bioMoby.mobyService.ServiceArticle-class.html,1.2,1.3 bioMoby.mobyService.ServiceList-class.html,1.2,1.3 bioMoby.mobyService.ServiceQuery-class.html,1.2,1.3 bioMoby.mobyService.ServiceSecondary-class.html,1.2,1.3 bioMoby.ontology-module.html,1.2,1.3 bioMoby.ontology.AGI_LocusCode-module.h! tml,1.2,1.3 bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-! class.html,1.2,1.3 bioMoby.ontology.Allele_freq-module.html,1.2,1.3 bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html,1.2,1.3 bioMoby.ontology.AminoAcidSequence-module.html,1.2,1.3 bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html,1.2,1.3 bioMoby.ontology.B64_Encoded_PNG-module.html,1.2,1.3 bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html,1.2,1.3 bioMoby.ontology.B64_Encoded_Postscript-module.html,1.2,1.3 bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html,1.2,1.3 bioMoby.ontology.B64_encoded_PDB-module.html,1.2,1.3 bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html,1.2,1.3 bioMoby.ontology.B64_encoded_gif-module.html,1.2,1.3 bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html,1.2,1.3 bioMoby.ontology.B64_encoded_jpeg-module.html,1.2,1.3 bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg-class.html,1.2,1.3 bioMoby.ontology.BasicGFFSequenceFeature-module.html,1.2,1.3 bioMoby.ontology! .BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature-class.html,1.2,1.3 bioMoby.ontology.ClustalAlnFormattedText-module.html,NONE,1.1 bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText-class.html,NONE,1.1 bioMoby.ontology.CommentedAASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence-class.html,NONE,1.1 bioMoby.ontology.CommentedDNASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence-class.html,NONE,1.1 bioMoby.ontology.CommentedRNASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence-class.html,NONE,1.1 bioMoby.ontology.DNASequence-module.html,1.2,1.3 bioMoby.ontology.DNASequence.MobyDNASequence-class.html,1.2,1.3 bioMoby.ontology.DNASequenceWithGFFFeatures-module.html,1.2,1.3 bioMoby.ontology.DNASequenceWithGFFFeatures.MobyDNASequenceWithGFFFeatures-class.html,1.2,1.3 bioMoby.ontology.DateTime-module.html,1.2,1.3 bioMoby.ontology.DateTime.! 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ext-class.html,1.2,1.3 bioMoby.ontology.NCBI_Blast_XML-module! .html,1.2,1.3 bioMoby.ontology.NCBI _Blast_XML.MobyNCBI_Blast_XML-class.html,1.2,1.3 bioMoby.ontology.NCBI_MEME_Text-module.html,NONE,1.1 bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text-class.html,NONE,1.1 bioMoby.ontology.NucleotideSequence-module.html,1.2,1.3 bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence-class.html,1.2,1.3 bioMoby.ontology.PDBFormattedText-module.html,1.2,1.3 bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText-class.html,1.2,1.3 bioMoby.ontology.PDGJOB-module.html,1.2,1.3 bioMoby.ontology.PDGJOB.MobyPDGJOB-class.html,1.2,1.3 bioMoby.ontology.PhenotypeDescription-module.html,1.2,1.3 bioMoby.ontology.PhenotypeDescription.MobyPhenotypeDescription-class.html,1.2,1.3 bioMoby.ontology.PubMedMEDLINE-module.html,1.2,1.3 bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE-class.html,1.2,1.3 bioMoby.ontology.RNASequence-module.html,1.2,1.3 bioMoby.ontology.RNASequence.MobyRNASequence-class.html,1.2,1.3 bioMoby.ontology.SINGER_ACCESSION-module.html,NONE,1.1 bioMoby.ontology.SINGER_ACCES! SION.MobySINGER_ACCESSION-class.html,NONE,1.1 bioMoby.ontology.SchematikonMotifID-module.html,1.2,1.3 bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID-class.html,1.2,1.3 bioMoby.ontology.SchematikonMotifSupport-module.html,1.2,1.3 bioMoby.ontology.SchematikonMotifSupport.MobySchematikonMotifSupport-class.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentAttributes-module.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentAttributes.MobySchematikonSegmentAttributes-class.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentID-module.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentID.MobySchematikonSegmentID-class.html,1.2,1.3 bioMoby.ontology.SchematikonStructureAnnotation-module.html,1.2,1.3 bioMoby.ontology.SchematikonStructureAnnotation.MobySchematikonStructureAnnotation-class.html,1.2,1.3 bioMoby.ontology.SchematikonVorocodeName-module.html,1.2,1.3 bioMoby.ontology.SchematikonVorocodeName.MobySchematikonVorocodeName-class.html,1.2,1.3 bioMoby.ontology.Scored_acronym_strin! g-module.html,1.2,1.3 bioMoby.ontology.Scored_acronym_string.! MobyScored_acronym_string-class.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedGIFImage-module.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage-class.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage-class.html,1.2,1.3 bioMoby.ontology.Simple_key_value_pair-module.html,1.2,1.3 bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair-class.html,1.2,1.3 bioMoby.ontology.Snp_allele-module.html,1.2,1.3 bioMoby.ontology.Snp_allele.MobySnp_allele-class.html,1.2,1.3 bioMoby.ontology.Snp_genotype-module.html,1.2,1.3 bioMoby.ontology.Snp_genotype.MobySnp_genotype-class.html,1.2,1.3 bioMoby.ontology.Study-module.html,1.2,1.3 bioMoby.ontology.Study.MobyStudy-class.html,1.2,1.3 bioMoby.ontology.TEST-module.html,NONE,1.1 bioMoby.ontology.TEST.MobyTEST-class.html,NONE,1.1 bioMoby.ontology.TargetP_result-module.html,1.2,1.3 bioMoby.ontology.TargetP_result.M! obyTargetP_result-class.html,1.2,1.3 bioMoby.ontology.Testout-module.html,1.2,1.3 bioMoby.ontology.Testout.MobyTestout-class.html,1.2,1.3 bioMoby.ontology.TextBase64-module.html,1.2,1.3 bioMoby.ontology.TextBase64.MobyTextBase64-class.html,1.2,1.3 bioMoby.ontology.TextFormatted-module.html,1.2,1.3 bioMoby.ontology.TextFormatted.MobyTextFormatted-class.html,1.2,1.3 bioMoby.ontology.TextHtml-module.html,1.2,1.3 bioMoby.ontology.TextHtml.MobyTextHtml-class.html,1.2,1.3 bioMoby.ontology.TextPlain-module.html,1.2,1.3 bioMoby.ontology.TextPlain.MobyTextPlain-class.html,1.2,1.3 bioMoby.ontology.TextUuencoded-module.html,1.2,1.3 bioMoby.ontology.TextUuencoded.MobyTextUuencoded-class.html,1.2,1.3 bioMoby.ontology.TextXml-module.html,1.2,1.3 bioMoby.ontology.TextXml.MobyTextXml-class.html,1.2,1.3 bioMoby.ontology.Text_plain-module.html,1.2,1.3 bioMoby.ontology.Text_plain.MobyText_plain-class.html,1.2,1.3 bioMoby.ontology.Trait_Details-module.html,1.2,1.3 bioMoby.ontology.Trait_Details! .MobyTrait_Details-class.html,1.2,1.3 bioMoby.ontology.Tree-m! odule.html,1.2,1.3 bioMoby.ontology.Tree.MobyTree-class.html,1.2,1.3 bioMoby.ontology.TropGENE_ACCESSION-module.html,NONE,1.1 bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION-class.html,NONE,1.1 bioMoby.ontology.TropGENE_Diversity_Matrix-module.html,NONE,1.1 bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix-class.html,NONE,1.1 bioMoby.ontology.TropGENE_LOCUS-module.html,NONE,1.1 bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS-class.html,NONE,1.1 bioMoby.ontology.VirtualSequence-module.html,1.2,1.3 bioMoby.ontology.VirtualSequence.MobyVirtualSequence-class.html,1.2,1.3 bioMoby.ontology.WU_BLAST_Text-module.html,1.2,1.3 bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text-class.html,1.2,1.3 bioMoby.ontology.Wildcard_Query-module.html,1.2,1.3 bioMoby.ontology.Wildcard_Query.MobyWildcard_Query-class.html,1.2,1.3 bioMoby.webservice-module.html,1.2,1.3 bioMoby.webservice.Dispatcher-module.html,1.2,1.3 bioMoby.webservice.Dispatcher.AbstractDispatcher! -class.html,NONE,1.1 bioMoby.webservice.Dispatcher.Dispatcher-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.EDispatchError-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.LockedIterator-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.MultiThread-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.PBSDispatcher-class.html,NONE,1.1 bioMoby.webservice.Dispatcher.SimpleDispatcher-class.html,NONE,1.1 bioMoby.webservice.Dispatcher.SingleThread-class.html,1.2,1.3 bioMoby.webservice.Invocators-module.html,1.2,1.3 bioMoby.webservice.Invocators.CGIPostInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.CGIPostMInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.GeneralInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.InvocatorError-class.html,1.2,1.3 bioMoby.webservice.Invocators.LocalInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.PBSInvocator-class.html,NONE,1.1 bioMoby.webservice.Invocators.QsubParameters-class.html,NONE,1.1 bioMoby.webservice.TC! BioMoby-module.html,NONE,1.1 bioMoby.webservice.TCBioMoby.Bod! y-class.html,NONE,1.1 bioMoby.webservice.TCBioMoby._TCBody-class.html,NONE,1.1 exceptions.Exception-class.html,1.2,1.3 frames.html,1.2,1.3 help.html,1.2,1.3 index.html,1.2,1.3 indices.html,1.2,1.3 threading.Thread-class.html,1.2,1.3 threading._Verbose-class.html,1.2,1.3 toc-bioMoby-module.html,1.2,1.3 toc-bioMoby.mobyClient-module.html,1.2,1.3 toc-bioMoby.mobyDataTypes-module.html,1.2,1.3 toc-bioMoby.mobyExceptions-module.html,1.2,1.3 toc-bioMoby.mobyMarshal-module.html,1.2,1.3 toc-bioMoby.mobyRegister-module.html,1.2,1.3 toc-bioMoby.mobyService-module.html,1.2,1.3 toc-bioMoby.ontology-module.html,1.2,1.3 toc-bioMoby.ontology.AGI_LocusCode-module.html,1.2,1.3 toc-bioMoby.ontology.Allele_freq-module.html,1.2,1.3 toc-bioMoby.ontology.AminoAcidSequence-module.html,1.2,1.3 toc-bioMoby.ontology.B64_Encoded_PNG-module.html,1.2,1.3 toc-bioMoby.ontology.B64_Encoded_Postscript-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encoded_PDB-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encode! d_gif-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encoded_jpeg-module.html,1.2,1.3 toc-bioMoby.ontology.BasicGFFSequenceFeature-module.html,1.2,1.3 toc-bioMoby.ontology.ClustalAlnFormattedText-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedAASequence-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedDNASequence-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedRNASequence-module.html,NONE,1.1 toc-bioMoby.ontology.DNASequence-module.html,1.2,1.3 toc-bioMoby.ontology.DNASequenceWithGFFFeatures-module.html,1.2,1.3 toc-bioMoby.ontology.DateTime-module.html,1.2,1.3 toc-bioMoby.ontology.Decypher_Text-module.html,1.2,1.3 toc-bioMoby.ontology.Edge-module.html,1.2,1.3 toc-bioMoby.ontology.EmblFlatfile-module.html,1.2,1.3 toc-bioMoby.ontology.FASTA-module.html,1.2,1.3 toc-bioMoby.ontology.FASTA_AA-module.html,NONE,1.1 toc-bioMoby.ontology.FASTA_NA-module.html,NONE,1.1 toc-bioMoby.ontology.GFF-module.html,1.2,1.3 toc-bioMoby.ontology.GFF1-module.html,1.2,1.3 toc-bioMoby.ontology! .GFF2-module.html,1.2,1.3 toc-bioMoby.ontology.GFF2_5-module.! html,1.2,1.3 toc-bioMoby.ontology.G FF3-module.html,1.2,1.3 toc-bioMoby.ontology.GO_Term-module.html,1.2,1.3 toc-bioMoby.ontology.GenbankFlatfile-module.html,1.2,1.3 toc-bioMoby.ontology.GenericSequence-module.html,1.2,1.3 toc-bioMoby.ontology.GeneticElement-module.html,1.2,1.3 toc-bioMoby.ontology.Germplasm_Details-module.html,1.2,1.3 toc-bioMoby.ontology.Germplasm_List-module.html,1.2,1.3 toc-bioMoby.ontology.Global_Keyword-module.html,1.2,1.3 toc-bioMoby.ontology.HBond_Pair-module.html,NONE,1.1 toc-bioMoby.ontology.HCA_picture-module.html,1.2,1.3 toc-bioMoby.ontology.Haplotyping_Study_obj-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query2-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query3-module.html,1.2,1.3 toc-bioMoby.ontology.IntAct_XML-module.html,1.2,1.3 toc-bioMoby.ontology.Interaction-module.html,1.2,1.3 toc-bioMoby.ontology.InteractionMethod-module.html,1.2,1.3 toc-bioMoby.ontology.Interaction_partner-module.html,1.2,1.3 toc-bioMoby.ontology.In! teractor-module.html,1.2,1.3 toc-bioMoby.ontology.MEME_Text-module.html,NONE,1.1 toc-bioMoby.ontology.MGIS_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.MMP_Locus-module.html,1.2,1.3 toc-bioMoby.ontology.MO_Term_Test-module.html,1.2,1.3 toc-bioMoby.ontology.Multi_key_value_pair-module.html,1.2,1.3 toc-bioMoby.ontology.MyTree-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_BLAST_Text-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_Blast_XML-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_MEME_Text-module.html,NONE,1.1 toc-bioMoby.ontology.NucleotideSequence-module.html,1.2,1.3 toc-bioMoby.ontology.PDBFormattedText-module.html,1.2,1.3 toc-bioMoby.ontology.PDGJOB-module.html,1.2,1.3 toc-bioMoby.ontology.PhenotypeDescription-module.html,1.2,1.3 toc-bioMoby.ontology.PubMedMEDLINE-module.html,1.2,1.3 toc-bioMoby.ontology.RNASequence-module.html,1.2,1.3 toc-bioMoby.ontology.SINGER_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.SchematikonMotifID-module.html,1.2,1.3 toc-bioMoby! .ontology.SchematikonMotifSupport-module.html,1.2,1.3 toc-bio! Moby.ontology.SchematikonSegmentAttributes-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonSegmentID-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonStructureAnnotation-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonVorocodeName-module.html,1.2,1.3 toc-bioMoby.ontology.Scored_acronym_string-module.html,1.2,1.3 toc-bioMoby.ontology.SimpleAnnotatedGIFImage-module.html,1.2,1.3 toc-bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html,1.2,1.3 toc-bioMoby.ontology.Simple_key_value_pair-module.html,1.2,1.3 toc-bioMoby.ontology.Snp_allele-module.html,1.2,1.3 toc-bioMoby.ontology.Snp_genotype-module.html,1.2,1.3 toc-bioMoby.ontology.Study-module.html,1.2,1.3 toc-bioMoby.ontology.TEST-module.html,NONE,1.1 toc-bioMoby.ontology.TargetP_result-module.html,1.2,1.3 toc-bioMoby.ontology.Testout-module.html,1.2,1.3 toc-bioMoby.ontology.TextBase64-module.html,1.2,1.3 toc-bioMoby.ontology.TextFormatted-module.html,1.2,1.3 toc-bioMoby.ontology.TextHtml-module.html,1.2,1.3 toc-bioM! oby.ontology.TextPlain-module.html,1.2,1.3 toc-bioMoby.ontology.TextUuencoded-module.html,1.2,1.3 toc-bioMoby.ontology.TextXml-module.html,1.2,1.3 toc-bioMoby.ontology.Text_plain-module.html,1.2,1.3 toc-bioMoby.ontology.Trait_Details-module.html,1.2,1.3 toc-bioMoby.ontology.Tree-module.html,1.2,1.3 toc-bioMoby.ontology.TropGENE_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.TropGENE_Diversity_Matrix-module.html,NONE,1.1 toc-bioMoby.ontology.TropGENE_LOCUS-module.html,NONE,1.1 toc-bioMoby.ontology.VirtualSequence-module.html,1.2,1.3 toc-bioMoby.ontology.WU_BLAST_Text-module.html,1.2,1.3 toc-bioMoby.ontology.Wildcard_Query-module.html,1.2,1.3 toc-bioMoby.webservice-module.html,1.2,1.3 toc-bioMoby.webservice.Dispatcher-module.html,1.2,1.3 toc-bioMoby.webservice.Invocators-module.html,1.2,1.3 toc-bioMoby.webservice.TCBioMoby-module.html,NONE,1.1 toc-everything.html,1.2,1.3 toc.html,1.2,1.3 trees.html,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/__builtin__.object-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/__builtin__.object-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/__builtin__.object-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@
    - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -246,13 +252,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/__builtin__.type-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/__builtin__.type-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/__builtin__.type-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -489,13 +495,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -58,6 +64,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -65,6 +75,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -78,6 +90,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -87,12 +100,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -109,10 +125,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -123,6 +141,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -131,6 +152,7 @@

  • @@ -143,13 +165,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -57,13 +63,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Central-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Central-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Central-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,7 +60,8 @@ @@ -77,7 +84,8 @@
      __init__(self, url, - ns) + ns, + debug)
    Changes url and ns parameters if you want to use another moby server
    - +

    __init__(self, url='http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral..., - ns='http://mobycentral.cbr.nrc.ca/MOBY/Central') + ns='http://mobycentral.cbr.nrc.ca/MOBY/Central', + debug=False)
    (Constructor)

    Changes url and ns parameters if you want to use another moby @@ -106,13 +114,19 @@
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Client-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Client-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Client-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,12 +60,10 @@ - +
    Method Summary
     __init__(self, + __init__(self, url, ns) -
    -Changes url and ns parameters if you want to use another moby -server
      findService(self, mobyQuery) @@ -141,23 +145,6 @@ Method Details
    - -
    -

    __init__(self, - url='http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral..., - ns='http://mobycentral.cbr.nrc.ca/MOBY/Central') -
    (Constructor) -

    - Changes url and ns parameters if you want to use another moby - server -
    -
    Overrides:
    -
    bioMoby.mobyClient.Central.__init__ (inherited documentation) -
    -
    -
    -
    - - +

    findService(self, @@ -298,13 +285,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -80,13 +86,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyContent-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyContent-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyContent-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -116,13 +122,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyFloat-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyFloat-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyFloat-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -110,13 +116,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyInteger-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyInteger-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyInteger-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -110,13 +116,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyObject-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyObject-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyObject-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -49,6 +55,7 @@ MobyGlobal_Keyword, MobyGO_Term, MobyHaplotyping_Study_obj, + MobyHBond_Pair, MobyICIS_Query, MobyICIS_Query2, MobyICIS_Query3, @@ -57,6 +64,7 @@ MobyInteraction_partner, MobyInteractionMethod, MobyInteractor, + MobyMGIS_ACCESSION, MobyMMP_Locus, MobyMO_Term_Test, MobyMulti_key_value_pair, @@ -70,11 +78,14 @@ MobyScored_acronym_string, MobySequence, MobySimple_key_value_pair, + MobySINGER_ACCESSION, MobyString, MobyStudy, MobyTargetP_result, MobyTestout, MobyTrait_Details, + MobyTropGENE_ACCESSION, + MobyTropGENE_LOCUS, MobyVirtualSequence, MobyWildcard_Query, MobyXref, @@ -162,13 +173,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobySequence-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobySequence-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobySequence-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -57,7 +63,8 @@ - +
    __init__(self, sequence, namespace, - id) + id, + articleName)
      fromMoby(self, @@ -110,13 +117,19 @@    Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyString-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyString-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyString-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -99,13 +105,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyXref-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyXref-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyXref-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -124,13 +130,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyZmPDB-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyZmPDB-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyZmPDB-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -183,13 +189,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.Parameter-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.Parameter-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.Parameter-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -104,13 +110,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -66,13 +72,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidArgument-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidArgument-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidArgument-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidType-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidType-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidType-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EMethodRetrieveError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EMethodRetrieveError-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EMethodRetrieveError-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ENotAWSMethod-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ENotAWSMethod-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ENotAWSMethod-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ETypeMismatch-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ETypeMismatch-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ETypeMismatch-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -57,13 +63,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyMarshaller-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyMarshaller-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyMarshaller-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,10 +54,11 @@ - +
    +Serialize the object into a Moby XML object - +
    +this method do the serialization of the object
    Method Summary
     dumps(self, + dumps(self, value, articleName) -
      m_dict(self, value, @@ -114,10 +121,11 @@
    transforms an object and all properties into a XML
     _marshal(self, + _marshal(self, value, articleName) -

    @@ -127,6 +135,17 @@ Method Details + +
    +

    dumps(self, + value, + articleName='') +

    + Serialize the object into a Moby XML object +
    +
    +
    +

    m_dict(self, @@ -222,6 +241,17 @@

    + + +
    +

    _marshal(self, + value, + articleName='') +

    + this method do the serialization of the object +
    +
    +

    @@ -232,13 +262,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyUnmarshaller-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyUnmarshaller-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyUnmarshaller-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,9 +54,10 @@ - +
    +Deserializes an xml string and return a bioMoby-Python object
    Method Summary
     loads(self, + loads(self, xml) -
      m_Collection(self, value) @@ -98,6 +105,16 @@ Method Details
    + +
    +

    loads(self, + xml) +

    + Deserializes an xml string and return a bioMoby-Python object +
    +
    +
    + - +

    m_Collection(self, @@ -180,13 +197,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -67,13 +73,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.GeneralInformations-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.GeneralInformations-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.GeneralInformations-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -154,13 +160,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.Namespace-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.Namespace-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.Namespace-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -136,13 +142,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ObjectClass-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ObjectClass-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ObjectClass-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -138,13 +144,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.RegistrationObject-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.RegistrationObject-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.RegistrationObject-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -121,13 +127,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ServiceType-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ServiceType-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ServiceType-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -158,13 +164,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -67,13 +73,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.Service-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.Service-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.Service-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -70,7 +76,8 @@ @@ -82,7 +89,8 @@ +Register the service on the Moby server has been added here a code to +verify that signatureURL is not empty :)
    execute(self, query, method, - returnXml) + returnXml, + debug)
    Executes the web service v0.5: return either the XML form or try to unmarshall the result and return a MobyContent Object
      register(self)
    -Register the service on the Moby server

    @@ -151,7 +159,8 @@

    execute(self, query, method='', - returnXml=True) + returnXml=True, + debug=False)

    Executes the web service v0.5: return either the XML form or try to unmarshall the result and return a MobyContent Object @@ -173,7 +182,8 @@

    register(self)

    - Register the service on the Moby server + Register the service on the Moby server has been added here a code + to verify that signatureURL is not empty :)
    @@ -187,13 +197,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceArticle-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceArticle-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceArticle-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -113,13 +119,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceList-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceList-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceList-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -204,13 +210,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceQuery-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceQuery-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceQuery-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -128,13 +134,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceSecondary-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceSecondary-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceSecondary-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -116,13 +122,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -51,6 +57,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -58,6 +68,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -71,6 +83,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -80,12 +93,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -102,10 +118,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -116,6 +134,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -130,13 +151,19 @@
  • - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -58,13 +64,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -113,13 +119,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -90,13 +96,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,6 +54,10 @@ MobyAminoAcidSequence
    +
    Known Subclasses:
    +
    + MobyCommentedAASequence
    +
    Description: Lightweight representation an amino acid sequence Author: @@ -117,13 +127,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_Postscript-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_Postscript-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_Postscript-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
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    +

    + bioMoby-python +

    +
    @@ -120,13 +126,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_PDB-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_PDB-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_PDB-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
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    +

    + bioMoby-python +

    +
    @@ -116,13 +122,19 @@ - +
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    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_gif-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_gif-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_encoded_gif-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
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    + bioMoby-python +

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    @@ -52,6 +58,7 @@
    Known Subclasses:
    + MobyCommentedDNASequence, MobyDNASequenceWithGFFFeatures

    @@ -123,13 +130,19 @@ - +
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    +
    @@ -50,6 +56,11 @@ MobyFASTA
    +
    Known Subclasses:
    +
    + MobyFASTA_AA, + MobyFASTA_NA
    +
    Description: FASTA formatted sequence Author: www.sdsc.edu Contact: @@ -118,13 +129,19 @@ - +
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    Known Subclasses:
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    Description: Lightweight representation an RNA sequence Author: @@ -119,13 +129,19 @@ - +
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    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Snp_allele-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Snp_allele-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Snp_allele-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -50,16 +56,21 @@
    Known Subclasses:
    + MobyClustalAlnFormattedText, MobyDecypher_Text, MobyEmblFlatfile, MobyFASTA, MobyGenbankFlatfile, MobyGFF, + MobyMEME_Text, MobyMyTree, MobyNCBI_BLAST_Text, + MobyNCBI_MEME_Text, MobyPDBFormattedText, MobyPubMedMEDLINE, + MobyTEST, MobyTree, + MobyTropGENE_Diversity_Matrix, MobyWU_BLAST_Text

    @@ -130,13 +141,19 @@ - +
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    +
    @@ -44,6 +50,7 @@

    @@ -55,13 +62,19 @@    Trees       Index       Help    - + + +
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    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -43,6 +49,10 @@ + + + + + +
    Classes
    + AbstractDispatcherSubclass this one to create your own dispatcher class a Dispatcher +class must have a execute method
    Dispatcher All Queries in the MobyContent Object are splitted and executed
    @@ -52,6 +62,12 @@ MultiThread Several threads
    + PBSDispatcherDispatcher for PBS jobs
    + SimpleDispatcherA simple dispatcher, without execute method
    SingleThread Definition of a single Thread

    @@ -74,13 +90,19 @@    Trees       Index       Help    - + + +
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    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.Dispatcher-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.Dispatcher-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.Dispatcher-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -38,6 +44,12 @@

    Class Dispatcher

    +
    +AbstractDispatcher --+
    +                     |
    +                    Dispatcher
    +

    +
    All Queries in the MobyContent Object are splitted and executed @@ -104,6 +116,9 @@ [queryData]-->("commandName","commandArgs", ["tempfiles"])
    +
    Overrides:
    +
    bioMoby.webservice.Dispatcher.AbstractDispatcher.__init__
    +
    @@ -115,6 +130,9 @@ Execute the queries with a pool of threads, store the results in a mobyContent Object
    +
    Overrides:
    +
    bioMoby.webservice.Dispatcher.AbstractDispatcher.execute
    +
    @@ -147,13 +165,19 @@    Trees       Index       Help    - + + +
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    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.EDispatchError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.EDispatchError-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.EDispatchError-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.SingleThread-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.SingleThread-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.SingleThread-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -163,13 +169,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,11 +60,24 @@ GeneralInvocator - - + + + + +
    General class for other invocators
    - InvocatorErrorError during an invocation of method
    LocalInvocator Invokes local command
    + PBSInvocatorInvokes a command in a qsub
    + QsubParametersParameters for the qsub command

    + + + + + + + +
    Exceptions
    + InvocatorErrorError during an invocation of method

    @@ -69,13 +88,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostInvocator-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostInvocator-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -68,7 +74,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -111,13 +118,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -89,7 +95,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -151,13 +158,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.GeneralInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.GeneralInvocator-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.GeneralInvocator-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -55,17 +61,51 @@ - +
    +queryid is the identifier of a query, userdir is the session +directory, timeout the limit time of execution of the query - +
    Method Summary
     __init__(self, + __init__(self, queryid, userdir, timeout) -
     getResults(self) -
    getResults(self) +
    +retrieve the results if available

    + + + + +
    Method Details
    + + +
    +

    __init__(self, + queryid, + userdir='/tmp', + timeout=None) +
    (Constructor) +

    + queryid is the identifier of a query, userdir is the session + directory, timeout the limit time of execution of the query +
    +
    +
    + + +
    +

    getResults(self) +

    + retrieve the results if available +
    +
    +
    +
    + + @@ -73,13 +113,19 @@ - + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.InvocatorError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.InvocatorError-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.InvocatorError-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -38,6 +44,12 @@

    Class InvocatorError

    +
    +Exception --+
    +            |
    +           InvocatorError
    +

    +
    Error during an invocation of method @@ -51,6 +63,14 @@ + + + + + +
      __str__(self)
        Inherited from Exception
     __init__(...) +
     __getitem__(...) +

    @@ -61,13 +81,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.LocalInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.LocalInvocator-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.LocalInvocator-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -44,6 +50,10 @@ LocalInvocator
    +
    Known Subclasses:
    +
    + PBSInvocator
    +
    Invokes local command @@ -69,7 +79,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -105,13 +116,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/exceptions.Exception-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/exceptions.Exception-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/exceptions.Exception-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -43,7 +49,8 @@ EInvalidType, EMethodRetrieveError, ENotAWSMethod, - ETypeMismatch + ETypeMismatch, + InvocatorError
    @@ -74,13 +81,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/frames.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/frames.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/frames.html 2004/12/09 14:07:31 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/help.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/help.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/help.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -32,7 +38,7 @@

    API Documentation

    This document contains the API (Application Programming Interface) -documentation for this project. Documentation for the Python +documentation for bioMoby-python. Documentation for the Python objects defined by the project is divided into separate pages for each package, module, and class. The API documentation also includes two pages containing information about the project as a whole: a trees @@ -209,13 +215,19 @@

    - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/index.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/index.html 2004/12/09 14:07:31 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/indices.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/indices.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/indices.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:10 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -74,6 +80,8 @@ + + @@ -136,6 +144,14 @@ + + + + + + + + @@ -150,6 +166,10 @@ + + + + @@ -174,6 +194,8 @@ + + @@ -194,6 +216,10 @@ + + + + @@ -206,6 +232,8 @@ + + @@ -218,6 +246,8 @@ + + @@ -244,6 +274,8 @@ + + @@ -266,18 +298,30 @@ + + + + + + + + + + + + @@ -288,6 +332,10 @@ + + + + @@ -384,6 +432,8 @@ + + @@ -394,12 +444,16 @@ + + + + @@ -430,6 +484,8 @@ + + @@ -438,8 +494,20 @@ + + + + + + + + + + + + @@ -506,16 +574,26 @@ + + + + + + + + + + @@ -550,6 +628,14 @@ + + + + + + + + @@ -564,6 +650,10 @@ + + + + @@ -588,6 +678,8 @@ + + @@ -608,6 +700,10 @@ + + + + @@ -620,6 +716,8 @@ + + @@ -632,6 +730,8 @@ + + @@ -658,6 +758,8 @@ + + @@ -680,6 +782,12 @@ + + + + + + @@ -706,6 +814,8 @@ + + @@ -734,6 +844,8 @@ + + @@ -806,6 +918,10 @@ + + + + @@ -830,6 +946,14 @@ + + + + + + + + @@ -850,6 +974,10 @@ + + + + @@ -878,6 +1006,8 @@ + + @@ -902,6 +1032,10 @@ + + + + @@ -914,6 +1048,8 @@ + + @@ -954,6 +1090,8 @@ + + @@ -964,6 +1102,8 @@ + + @@ -984,6 +1124,12 @@ + + + + + + @@ -1004,14 +1150,20 @@ + + + + + + @@ -1022,6 +1174,16 @@ + + + + + + + + + + @@ -1034,6 +1196,8 @@ + + @@ -1088,6 +1252,10 @@ + + + + @@ -1104,12 +1272,22 @@ + + + + + + + + + + @@ -1124,8 +1302,14 @@ + + + + + + @@ -1168,8 +1352,22 @@ + + + + + + + + + + + + + + @@ -1188,13 +1386,19 @@ - +
    Method in class __builtin__.object
    __hash__ Method in class __builtin__.type
    __init__Method in class ZSI.TC.TypeCode
    __init__ Method in class __builtin__.object
    __init__Method in class bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg
    __init__ Method in class bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    __init__Method in class bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    __init__Method in class bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    __init__Method in class bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    __init__Method in class bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    __init__ Method in class bioMoby.ontology.DNASequence.MobyDNASequence
    __init__Method in class bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    __init__ Method in class bioMoby.ontology.FASTA.MobyFASTA
    __init__Method in class bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    __init__Method in class bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    __init__ Method in class bioMoby.ontology.GFF.MobyGFF
    __init__Method in class bioMoby.ontology.Germplasm_List.MobyGermplasm_List
    __init__ Method in class bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    __init__Method in class bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    __init__ Method in class bioMoby.ontology.HCA_picture.MobyHCA_picture
    __init__Method in class bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    __init__ Method in class bioMoby.ontology.Interactor.MobyInteractor
    __init__Method in class bioMoby.ontology.MEME_Text.MobyMEME_Text
    __init__Method in class bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    __init__ Method in class bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    __init__Method in class bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    __init__ Method in class bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    __init__Method in class bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    __init__ Method in class bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    __init__Method in class bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE
    __init__ Method in class bioMoby.ontology.RNASequence.MobyRNASequence
    __init__Method in class bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    __init__ Method in class bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID
    __init__Method in class bioMoby.ontology.Snp_genotype.MobySnp_genotype
    __init__ Method in class bioMoby.ontology.Study.MobyStudy
    __init__Method in class bioMoby.ontology.TEST.MobyTEST
    __init__ Method in class bioMoby.ontology.TargetP_result.MobyTargetP_result
    __init__Method in class bioMoby.ontology.Trait_Details.MobyTrait_Details
    __init__ Method in class bioMoby.ontology.Tree.MobyTree
    __init__Method in class bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    __init__Method in class bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    __init__Method in class bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    __init__ Method in class bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    __init__ Method in class bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text
    __init__ Method in class bioMoby.ontology.Wildcard_Query.MobyWildcard_Query
    __init__Method in class bioMoby.webservice.Dispatcher.AbstractDispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.Dispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.LockedIterator
    __init__ Method in class bioMoby.webservice.Dispatcher.MultiThread
    __init__Method in class bioMoby.webservice.Dispatcher.PBSDispatcher
    __init__Method in class bioMoby.webservice.Dispatcher.SimpleDispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.SingleThread
    __init__Method in class bioMoby.webservice.Invocators.GeneralInvocator
    __init__ Method in class bioMoby.webservice.Invocators.LocalInvocator
    __init__Method in class bioMoby.webservice.Invocators.PBSInvocator
    __init__Method in class bioMoby.webservice.Invocators.QsubParameters
    __init__ Method in class exceptions.Exception
    __init__Method in class bioMoby.webservice.Dispatcher.Dispatcher
    _fetchAnswers Method in class bioMoby.webservice.Dispatcher.Dispatcher
    _getResultsMethod in class bioMoby.webservice.Dispatcher.PBSDispatcher
    _getSem Method in class bioMoby.webservice.Dispatcher.Dispatcher
    _marshalMethod in class threading.Thread
    _tailRecurse Method in class bioMoby.webservice.Dispatcher.MultiThread
    _TCBodyClass in module bioMoby.webservice.TCBioMoby
    __initialized Variable in class threading.Thread
    __initialized Variable in class threading.Thread
    _Verbose Class in module threading
    AbstractDispatcherClass in module bioMoby.webservice.Dispatcher
    AGI_LocusCode Module in package bioMoby.ontology
    Allele_freqModule in package bioMoby.ontology
    bioMoby Package
    BodyClass in module bioMoby.webservice.TCBioMoby
    call_method Method in class bioMoby.mobyClient.Central
    CentralClass in module bioMoby.webservice.Invocators
    CGIPostMInvocator Class in module bioMoby.webservice.Invocators
    checknameMethod in class ZSI.TC.TypeCode
    checktypeMethod in class ZSI.TC.TypeCode
    Client Class in module bioMoby.mobyClient
    ClustalAlnFormattedTextModule in package bioMoby.ontology
    CommentedAASequenceModule in package bioMoby.ontology
    CommentedDNASequenceModule in package bioMoby.ontology
    CommentedRNASequenceModule in package bioMoby.ontology
    compress Method in class bioMoby.mobyDataTypes.MobyZmPDB
    contactClass in module exceptions
    execute Method in class bioMoby.mobyService.Service
    executeMethod in class bioMoby.webservice.Dispatcher.AbstractDispatcher
    execute Method in class bioMoby.webservice.Dispatcher.Dispatcher
    executeMethod in class bioMoby.webservice.Dispatcher.PBSDispatcher
    execute Method in class bioMoby.webservice.Invocators.CGIPostInvocator
    execute Method in class bioMoby.webservice.Invocators.CGIPostMInvocator
    execute Method in class bioMoby.webservice.Invocators.LocalInvocator
    executeMethod in class bioMoby.webservice.Invocators.PBSInvocator
    FASTA Module in package bioMoby.ontology
    FASTA_AAModule in package bioMoby.ontology
    FASTA_NAModule in package bioMoby.ontology
    findService Method in class bioMoby.mobyClient.Client
    fromMobyMethod in class bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg
    fromMoby Method in class bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    fromMobyMethod in class bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    fromMobyMethod in class bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    fromMobyMethod in class bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    fromMobyMethod in class bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    fromMoby Method in class bioMoby.ontology.DNASequence.MobyDNASequence
    fromMobyMethod in class bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    fromMoby Method in class bioMoby.ontology.FASTA.MobyFASTA
    fromMobyMethod in class bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    fromMobyMethod in class bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    fromMoby Method in class bioMoby.ontology.GFF.MobyGFF
    fromMobyMethod in class bioMoby.ontology.Germplasm_List.MobyGermplasm_List
    fromMoby Method in class bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    fromMobyMethod in class bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    fromMoby Method in class bioMoby.ontology.HCA_picture.MobyHCA_picture
    fromMobyMethod in class bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    fromMoby Method in class bioMoby.ontology.Interactor.MobyInteractor
    fromMobyMethod in class bioMoby.ontology.MEME_Text.MobyMEME_Text
    fromMobyMethod in class bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    fromMoby Method in class bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    fromMobyMethod in class bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    fromMoby Method in class bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    fromMobyMethod in class bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    fromMoby Method in class bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    fromMobyMethod in class bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE
    fromMoby Method in class bioMoby.ontology.RNASequence.MobyRNASequence
    fromMobyMethod in class bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    fromMoby Method in class bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID
    fromMobyMethod in class bioMoby.ontology.Snp_genotype.MobySnp_genotype
    fromMoby Method in class bioMoby.ontology.Study.MobyStudy
    fromMobyMethod in class bioMoby.ontology.TEST.MobyTEST
    fromMoby Method in class bioMoby.ontology.TargetP_result.MobyTargetP_result
    fromMobyMethod in class bioMoby.ontology.Trait_Details.MobyTrait_Details
    fromMoby Method in class bioMoby.ontology.Tree.MobyTree
    fromMobyMethod in class bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    fromMobyMethod in class bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    fromMobyMethod in class bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    fromMoby Method in class bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    fromMobyModule in package bioMoby.ontology
    get_content_type Method in class bioMoby.webservice.Invocators.CGIPostMInvocator
    get_parse_and_errorlistMethod in class ZSI.TC.TypeCode
    getInfo Method in class bioMoby.mobyDataTypes.MobyObject
    getMethodsModule in package bioMoby.ontology
    Haplotyping_Study_obj Module in package bioMoby.ontology
    HBond_PairModule in package bioMoby.ontology
    HCA_picture Module in package bioMoby.ontology
    ICIS_QueryMethod in class bioMoby.mobyMarshal.MobyMarshaller
    m_unicode Method in class bioMoby.mobyMarshal.MobyMarshaller
    MEME_TextModule in package bioMoby.ontology
    MGIS_ACCESSIONModule in package bioMoby.ontology
    MMP_Locus Module in package bioMoby.ontology
    MO_Term_TestClass in module bioMoby.ontology.BasicGFFSequenceFeature
    mobyClient Module in package bioMoby
    MobyClustalAlnFormattedTextClass in module bioMoby.ontology.ClustalAlnFormattedText
    MobyCommentedAASequenceClass in module bioMoby.ontology.CommentedAASequence
    MobyCommentedDNASequenceClass in module bioMoby.ontology.CommentedDNASequence
    MobyCommentedRNASequenceClass in module bioMoby.ontology.CommentedRNASequence
    MobyContent Class in module bioMoby.mobyDataTypes
    mobyDataTypesModule in package bioMoby
    MobyFASTA Class in module bioMoby.ontology.FASTA
    MobyFASTA_AAClass in module bioMoby.ontology.FASTA_AA
    MobyFASTA_NAClass in module bioMoby.ontology.FASTA_NA
    MobyFloat Class in module bioMoby.mobyDataTypes
    MobyGenbankFlatfileClass in module bioMoby.ontology.GO_Term
    MobyHaplotyping_Study_obj Class in module bioMoby.ontology.Haplotyping_Study_obj
    MobyHBond_PairClass in module bioMoby.ontology.HBond_Pair
    MobyHCA_picture Class in module bioMoby.ontology.HCA_picture
    MobyICIS_QueryModule in package bioMoby
    MobyMarshaller Class in module bioMoby.mobyMarshal
    MobyMEME_TextClass in module bioMoby.ontology.MEME_Text
    MobyMGIS_ACCESSIONClass in module bioMoby.ontology.MGIS_ACCESSION
    MobyMMP_Locus Class in module bioMoby.ontology.MMP_Locus
    MobyMO_Term_TestClass in module bioMoby.ontology.NCBI_BLAST_Text
    MobyNCBI_Blast_XML Class in module bioMoby.ontology.NCBI_Blast_XML
    MobyNCBI_MEME_TextClass in module bioMoby.ontology.NCBI_MEME_Text
    MobyNucleotideSequence Class in module bioMoby.ontology.NucleotideSequence
    MobyObjectClass in module bioMoby.ontology.SimpleAnnotatedGIFImage
    MobySimpleAnnotatedJPEGImage Class in module bioMoby.ontology.SimpleAnnotatedJPEGImage
    MobySINGER_ACCESSIONClass in module bioMoby.ontology.SINGER_ACCESSION
    MobySnp_allele Class in module bioMoby.ontology.Snp_allele
    MobySnp_genotypeClass in module bioMoby.ontology.Study
    MobyTargetP_result Class in module bioMoby.ontology.TargetP_result
    MobyTESTClass in module bioMoby.ontology.TEST
    MobyTestout Class in module bioMoby.ontology.Testout
    MobyText_plainClass in module bioMoby.ontology.Trait_Details
    MobyTree Class in module bioMoby.ontology.Tree
    MobyTropGENE_ACCESSIONClass in module bioMoby.ontology.TropGENE_ACCESSION
    MobyTropGENE_Diversity_MatrixClass in module bioMoby.ontology.TropGENE_Diversity_Matrix
    MobyTropGENE_LOCUSClass in module bioMoby.ontology.TropGENE_LOCUS
    MobyUnmarshaller Class in module bioMoby.mobyMarshal
    MobyVirtualSequenceClass in module bioMoby.webservice.Dispatcher
    MyTree Module in package bioMoby.ontology
    name_matchMethod in class ZSI.TC.TypeCode
    Namespace Class in module bioMoby.mobyRegister
    NCBI_BLAST_Text Module in package bioMoby.ontology
    NCBI_Blast_XML Module in package bioMoby.ontology
    NCBI_MEME_TextModule in package bioMoby.ontology
    next Method in class bioMoby.webservice.Dispatcher.LockedIterator
    nilledMethod in class ZSI.TC.TypeCode
    NucleotideSequence Module in package bioMoby.ontology
    objectPackage in package bioMoby
    Parameter Class in module bioMoby.mobyDataTypes
    parseMethod in class ZSI.TC.TypeCode
    parseMethod in class bioMoby.webservice.TCBioMoby._TCBody
    parselistVariable in class bioMoby.webservice.TCBioMoby.Body
    PBSDispatcherClass in module bioMoby.webservice.Dispatcher
    PBSInvocatorClass in module bioMoby.webservice.Invocators
    PDBFormattedText Module in package bioMoby.ontology
    PDGJOBMethod in class bioMoby.webservice.Invocators.CGIPostMInvocator
    PubMedMEDLINE Module in package bioMoby.ontology
    QsubParametersClass in module bioMoby.webservice.Invocators
    register Method in class bioMoby.mobyRegister.Namespace
    registerModule in package bioMoby.ontology
    Scored_acronym_string Module in package bioMoby.ontology
    serializeMethod in class bioMoby.webservice.TCBioMoby.Body
    seriallistVariable in class bioMoby.webservice.TCBioMoby.Body
    Service Class in module bioMoby.mobyService
    ServiceArticleMethod in class threading.Thread
    setName Method in class threading.Thread
    setParametersMethod in class bioMoby.webservice.Invocators.PBSInvocator
    Simple_key_value_pair Module in package bioMoby.ontology
    simple_valueMethod in class ZSI.TC.TypeCode
    SimpleAnnotatedGIFImage Module in package bioMoby.ontology
    SimpleAnnotatedJPEGImage Module in package bioMoby.ontology
    SimpleDispatcherClass in module bioMoby.webservice.Dispatcher
    SimpleHREFMethod in class ZSI.TC.TypeCode
    SINGER_ACCESSIONModule in package bioMoby.ontology
    SingleThread Class in module bioMoby.webservice.Dispatcher
    Snp_alleleModule in package bioMoby.ontology
    submits2XML Method in class bioMoby.mobyService.ServiceQuery
    tagVariable in class bioMoby.webservice.TCBioMoby.Body
    TargetP_result Module in package bioMoby.ontology
    TCBioMobyModule in package bioMoby.webservice
    TESTModule in package bioMoby.ontology
    Testout Module in package bioMoby.ontology
    Text_plainModule in package bioMoby.ontology
    Tree Module in package bioMoby.ontology
    TropGENE_ACCESSIONModule in package bioMoby.ontology
    TropGENE_Diversity_MatrixModule in package bioMoby.ontology
    TropGENE_LOCUSModule in package bioMoby.ontology
    type Class in module __builtin__
    typechecksVariable in class ZSI.TC.TypeCode
    typechecksVariable in class ZSI.TC.TypeCode
    TypeCodeClass in module ZSI.TC
    typecodeVariable in class bioMoby.webservice.TCBioMoby.Body
    VirtualSequence Module in package bioMoby.ontology
    webservice   Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/threading.Thread-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/threading.Thread-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/threading.Thread-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -197,13 +203,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/threading._Verbose-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/threading._Verbose-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/threading._Verbose-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -112,13 +118,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyClient-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyDataTypes-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyExceptions-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyMarshal-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyRegister-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyService-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology-module.html 2004/12/09 14:07:31 1.3 @@ -22,6 +22,10 @@ B64_Encoded_PNG
    B64_Encoded_Postscript
    BasicGFFSequenceFeature
    +ClustalAlnFormattedText
    +CommentedAASequence
    +CommentedDNASequence
    +CommentedRNASequence
    DateTime
    Decypher_Text
    DNASequence
    @@ -29,6 +33,8 @@ Edge
    EmblFlatfile
    FASTA
    +FASTA_AA
    +FASTA_NA
    GenbankFlatfile
    GenericSequence
    GeneticElement
    @@ -42,6 +48,7 @@ Global_Keyword
    GO_Term
    Haplotyping_Study_obj
    +HBond_Pair
    HCA_picture
    ICIS_Query
    ICIS_Query2
    @@ -51,12 +58,15 @@ Interaction_partner
    InteractionMethod
    Interactor
    +MEME_Text
    +MGIS_ACCESSION
    MMP_Locus
    MO_Term_Test
    Multi_key_value_pair
    MyTree
    NCBI_BLAST_Text
    NCBI_Blast_XML
    +NCBI_MEME_Text
    NucleotideSequence
    PDBFormattedText
    PDGJOB
    @@ -73,10 +83,12 @@ Simple_key_value_pair
    SimpleAnnotatedGIFImage
    SimpleAnnotatedJPEGImage
    +SINGER_ACCESSION
    Snp_allele
    Snp_genotype
    Study
    TargetP_result
    +TEST
    Testout
    Text_plain
    TextBase64
    @@ -87,6 +99,9 @@ TextXml
    Trait_Details
    Tree
    +TropGENE_ACCESSION
    +TropGENE_Diversity_Matrix
    +TropGENE_LOCUS
    VirtualSequence
    Wildcard_Query
    WU_BLAST_Text
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revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Testout-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextBase64-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextFormatted-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextHtml-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextPlain-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextUuencoded-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextXml-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Text_plain-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Trait_Details-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Tree-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.VirtualSequence-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.WU_BLAST_Text-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Wildcard_Query-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice-module.html 2004/12/09 14:07:31 1.3 @@ -15,6 +15,7 @@ Modules
    Dispatcher
    Invocators
    +TCBioMoby


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Dispatcher-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Dispatcher-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Dispatcher-module.html 2004/12/09 14:07:31 1.3 @@ -13,9 +13,12 @@ Classes
    +AbstractDispatcher
    Dispatcher
    LockedIterator
    MultiThread
    +PBSDispatcher
    +SimpleDispatcher
    SingleThread

    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Invocators-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Invocators-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Invocators-module.html 2004/12/09 14:07:31 1.3 @@ -16,8 +16,14 @@ CGIPostInvocator
    CGIPostMInvocator
    GeneralInvocator
    -InvocatorError
    LocalInvocator
    +PBSInvocator
    +QsubParameters
    +
    + + +Exceptions
    +InvocatorError


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-everything.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-everything.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-everything.html 2004/12/09 14:07:31 1.3 @@ -45,6 +45,10 @@ bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG
    bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript
    bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    +bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    +bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    +bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    +bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    bioMoby.ontology.DateTime.MobyDateTime
    bioMoby.ontology.Decypher_Text.MobyDecypher_Text
    bioMoby.ontology.DNASequence.MobyDNASequence
    @@ -52,6 +56,8 @@ bioMoby.ontology.Edge.MobyEdge
    bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    bioMoby.ontology.FASTA.MobyFASTA
    +bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    +bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    bioMoby.ontology.GenbankFlatfile.MobyGenbankFlatfile
    bioMoby.ontology.GenericSequence.MobyGenericSequence
    bioMoby.ontology.GeneticElement.MobyGeneticElement
    @@ -65,6 +71,7 @@ bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    bioMoby.ontology.GO_Term.MobyGO_Term
    bioMoby.ontology.Haplotyping_Study_obj.MobyHaplotyping_Study_obj
    +bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    bioMoby.ontology.HCA_picture.MobyHCA_picture
    bioMoby.ontology.ICIS_Query.MobyICIS_Query
    bioMoby.ontology.ICIS_Query2.MobyICIS_Query2
    @@ -74,12 +81,15 @@ bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    bioMoby.ontology.InteractionMethod.MobyInteractionMethod
    bioMoby.ontology.Interactor.MobyInteractor
    +bioMoby.ontology.MEME_Text.MobyMEME_Text
    +bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    bioMoby.ontology.MO_Term_Test.MobyMO_Term_Test
    bioMoby.ontology.Multi_key_value_pair.MobyMulti_key_value_pair
    bioMoby.ontology.MyTree.MobyMyTree
    bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    +bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText
    bioMoby.ontology.PDGJOB.MobyPDGJOB
    @@ -96,10 +106,12 @@ bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair
    bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage
    bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage
    +bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    bioMoby.ontology.Snp_allele.MobySnp_allele
    bioMoby.ontology.Snp_genotype.MobySnp_genotype
    bioMoby.ontology.Study.MobyStudy
    bioMoby.ontology.TargetP_result.MobyTargetP_result
    +bioMoby.ontology.TEST.MobyTEST
    bioMoby.ontology.Testout.MobyTestout
    bioMoby.ontology.Text_plain.MobyText_plain
    bioMoby.ontology.TextBase64.MobyTextBase64
    @@ -110,18 +122,27 @@ bioMoby.ontology.TextXml.MobyTextXml
    bioMoby.ontology.Trait_Details.MobyTrait_Details
    bioMoby.ontology.Tree.MobyTree
    +bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    +bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    +bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    bioMoby.ontology.Wildcard_Query.MobyWildcard_Query
    bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text
    +bioMoby.webservice.Dispatcher.AbstractDispatcher
    bioMoby.webservice.Dispatcher.Dispatcher
    bioMoby.webservice.Dispatcher.LockedIterator
    bioMoby.webservice.Dispatcher.MultiThread
    +bioMoby.webservice.Dispatcher.PBSDispatcher
    +bioMoby.webservice.Dispatcher.SimpleDispatcher
    bioMoby.webservice.Dispatcher.SingleThread
    bioMoby.webservice.Invocators.CGIPostInvocator
    bioMoby.webservice.Invocators.CGIPostMInvocator
    bioMoby.webservice.Invocators.GeneralInvocator
    -bioMoby.webservice.Invocators.InvocatorError
    bioMoby.webservice.Invocators.LocalInvocator
    +bioMoby.webservice.Invocators.PBSInvocator
    +bioMoby.webservice.Invocators.QsubParameters
    +bioMoby.webservice.TCBioMoby._TCBody
    +bioMoby.webservice.TCBioMoby.Body

    @@ -132,6 +153,7 @@ bioMoby.mobyExceptions.ENotAWSMethod
    bioMoby.mobyExceptions.ETypeMismatch
    bioMoby.webservice.Dispatcher.EDispatchError
    +bioMoby.webservice.Invocators.InvocatorError


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc.html 2004/12/09 14:07:31 1.3 @@ -35,6 +35,10 @@ bioMoby.ontology.B64_Encoded_PNG
    bioMoby.ontology.B64_Encoded_Postscript
    bioMoby.ontology.BasicGFFSequenceFeature
    +bioMoby.ontology.ClustalAlnFormattedText
    +bioMoby.ontology.CommentedAASequence
    +bioMoby.ontology.CommentedDNASequence
    +bioMoby.ontology.CommentedRNASequence
    bioMoby.ontology.DateTime
    bioMoby.ontology.Decypher_Text
    bioMoby.ontology.DNASequence
    @@ -42,6 +46,8 @@ bioMoby.ontology.Edge
    bioMoby.ontology.EmblFlatfile
    bioMoby.ontology.FASTA
    +bioMoby.ontology.FASTA_AA
    +bioMoby.ontology.FASTA_NA
    bioMoby.ontology.GenbankFlatfile
    bioMoby.ontology.GenericSequence
    bioMoby.ontology.GeneticElement
    @@ -55,6 +61,7 @@ bioMoby.ontology.Global_Keyword
    bioMoby.ontology.GO_Term
    bioMoby.ontology.Haplotyping_Study_obj
    +bioMoby.ontology.HBond_Pair
    bioMoby.ontology.HCA_picture
    bioMoby.ontology.ICIS_Query
    bioMoby.ontology.ICIS_Query2
    @@ -64,12 +71,15 @@ bioMoby.ontology.Interaction_partner
    bioMoby.ontology.InteractionMethod
    bioMoby.ontology.Interactor
    +bioMoby.ontology.MEME_Text
    +bioMoby.ontology.MGIS_ACCESSION
    bioMoby.ontology.MMP_Locus
    bioMoby.ontology.MO_Term_Test
    bioMoby.ontology.Multi_key_value_pair
    bioMoby.ontology.MyTree
    bioMoby.ontology.NCBI_BLAST_Text
    bioMoby.ontology.NCBI_Blast_XML
    +bioMoby.ontology.NCBI_MEME_Text
    bioMoby.ontology.NucleotideSequence
    bioMoby.ontology.PDBFormattedText
    bioMoby.ontology.PDGJOB
    @@ -86,10 +96,12 @@ bioMoby.ontology.Simple_key_value_pair
    bioMoby.ontology.SimpleAnnotatedGIFImage
    bioMoby.ontology.SimpleAnnotatedJPEGImage
    +bioMoby.ontology.SINGER_ACCESSION
    bioMoby.ontology.Snp_allele
    bioMoby.ontology.Snp_genotype
    bioMoby.ontology.Study
    bioMoby.ontology.TargetP_result
    +bioMoby.ontology.TEST
    bioMoby.ontology.Testout
    bioMoby.ontology.Text_plain
    bioMoby.ontology.TextBase64
    @@ -100,11 +112,15 @@ bioMoby.ontology.TextXml
    bioMoby.ontology.Trait_Details
    bioMoby.ontology.Tree
    +bioMoby.ontology.TropGENE_ACCESSION
    +bioMoby.ontology.TropGENE_Diversity_Matrix
    +bioMoby.ontology.TropGENE_LOCUS
    bioMoby.ontology.VirtualSequence
    bioMoby.ontology.Wildcard_Query
    bioMoby.ontology.WU_BLAST_Text
    bioMoby.webservice.Dispatcher
    bioMoby.webservice.Invocators
    +bioMoby.webservice.TCBioMoby


    [show private | hide private] =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/trees.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/trees.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/trees.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -51,6 +57,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -58,6 +68,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -71,6 +83,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -80,12 +93,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -102,10 +118,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -116,6 +134,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -124,6 +145,7 @@ @@ -131,6 +153,12 @@

    Class Hierarchy

    @@ -483,8 +564,19 @@
  • bioMoby.ontology.Snp_genotype.MobySnp_genotype: Description: Snp Genotypes Author: www.hapmap.org Contact: hapmap@hapmap.edu +
  • bioMoby.webservice.Dispatcher.AbstractDispatcher: +Subclass this one to create your own dispatcher class a Dispatcher +class must have a execute method +
  • bioMoby.webservice.Dispatcher.LockedIterator: Avoid concurrency on the iterator
  • bioMoby.webservice.Dispatcher.MultiThread: @@ -500,9 +592,14 @@ CGI script in Post multipart
  • bioMoby.webservice.Invocators.LocalInvocator: Invokes local command + -
  • bioMoby.webservice.Invocators.InvocatorError: -Error during an invocation of method + +
  • bioMoby.webservice.Invocators.QsubParameters: +Parameters for the qsub command +
  • bioMoby.webservice.TCBioMoby._TCBody
  • exceptions.Exception: Common base class for all exceptions. @@ -523,13 +622,19 @@
  • - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + From yanwong at pub.open-bio.org Thu Dec 9 09:38:10 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu, 9 Dec 2004 09:38:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091438.iB9EcAo2003626@pub.open-bio.org> yanwong Thu Dec 9 09:38:10 EST 2004 Update of /home/repository/moby/moby-live/Python/utils In directory pub.open-bio.org:/tmp/cvs-serv3601 Added Files: moby2python.py Log Message: moby-live/Python/utils moby2python.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/utils/moby2python.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/utils/moby2python.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/utils/moby2python.py 2004/12/09 14:38:10 1.3 @@ -1,4 +1,4 @@ -#!/bin/env python +#!/usr/bin/env python #This program will retrieve all objects definitions stored on a bioMoby Server #and generate the corresponding Python Object From yanwong at pub.open-bio.org Thu Dec 9 09:39:05 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu, 9 Dec 2004 09:39:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091439.iB9Ed5el003686@pub.open-bio.org> yanwong Thu Dec 9 09:39:05 EST 2004 Update of /home/repository/moby/moby-live/Python/utils/wx In directory pub.open-bio.org:/tmp/cvs-serv3657 Added Files: README objectBrowser.py Log Message: moby-live/Python/utils/wx README,1.2,1.3 objectBrowser.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/utils/wx/README,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/utils/wx/objectBrowser.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From yanwong at pub.open-bio.org Thu Dec 9 09:41:33 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu, 9 Dec 2004 09:41:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091441.iB9EfX1b003758@pub.open-bio.org> yanwong Thu Dec 9 09:41:33 EST 2004 Update of /home/repository/moby/moby-live/Python/doc In directory pub.open-bio.org:/tmp/cvs-serv3725 Added Files: api.pdf api.ps epydoc.css howto.pdf index.html Log Message: moby-live/Python/doc api.pdf,NONE,1.1 api.ps,NONE,1.1 epydoc.css,1.2,1.3 howto.pdf,1.2,1.3 index.html,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/epydoc.css,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/howto.pdf,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 Binary files /home/repository/moby/moby-live/Python/doc/howto.pdf 2004/12/08 11:15:22 1.2 and /home/repository/moby/moby-live/Python/doc/howto.pdf 2004/12/09 14:41:33 1.3 differ rcsdiff: /home/repository/moby/moby-live/Python/doc/howto.pdf: diff failed =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/index.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/index.html 2004/12/09 14:41:33 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python From yanwong at pub.open-bio.org Thu Dec 9 09:41:39 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu, 9 Dec 2004 09:41:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091441.iB9EfdKr005007@pub.open-bio.org> yanwong Thu Dec 9 09:41:39 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/src In directory pub.open-bio.org:/tmp/cvs-serv3725/src Added Files: howto.sxw Log Message: moby-live/Python/doc/src howto.sxw,NONE,1.1 From yanwong at pub.open-bio.org Thu Dec 9 09:41:39 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu, 9 Dec 2004 09:41:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091441.iB9Efdre004992@pub.open-bio.org> yanwong Thu Dec 9 09:41:35 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/public In directory pub.open-bio.org:/tmp/cvs-serv3725/public Added Files: ZSI.TC.TypeCode-class.html __builtin__.object-class.html __builtin__.type-class.html bioMoby-module.html bioMoby.mobyClient-module.html bioMoby.mobyClient.Central-class.html bioMoby.mobyClient.Client-class.html bioMoby.mobyDataTypes-module.html bioMoby.mobyDataTypes.MobyContent-class.html bioMoby.mobyDataTypes.MobyFloat-class.html bioMoby.mobyDataTypes.MobyInteger-class.html bioMoby.mobyDataTypes.MobyObject-class.html bioMoby.mobyDataTypes.MobySequence-class.html bioMoby.mobyDataTypes.MobyString-class.html bioMoby.mobyDataTypes.MobyXref-class.html 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bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html,1.2,1.3 bioMoby.ontology.B64_encoded_gif-module.html,1.2,1.3 bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html,1.2,1.3 bioMoby.ontology.B64_encoded_jpeg-module.html,1.2,1.3 bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg-class.html,1.2,1.3 bioMoby.ontology.BasicGFFSequenceFeature-module.html,1.2,1.3 bioMoby.ontology.! BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature-class.html,1.2,1.3 bioMoby.ontology.ClustalAlnFormattedText-module.html,NONE,1.1 bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText-class.html,NONE,1.1 bioMoby.ontology.CommentedAASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence-class.html,NONE,1.1 bioMoby.ontology.CommentedDNASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence-class.html,NONE,1.1 bioMoby.ontology.CommentedRNASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence-class.html,NONE,1.1 bioMoby.ontology.DNASequence-module.html,1.2,1.3 bioMoby.ontology.DNASequence.MobyDNASequence-class.html,1.2,1.3 bioMoby.ontology.DNASequenceWithGFFFeatures-module.html,1.2,1.3 bioMoby.ontology.DNASequenceWithGFFFeatures.MobyDNASequenceWithGFFFeatures-class.html,1.2,1.3 bioMoby.ontology.DateTime-module.html,1.2,1.3 bioMoby.ontology.DateTime.M! obyDateTime-class.html,1.2,1.3 bioMoby.ontology.Decypher_Text! 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3 bioMoby.ontology.Interaction_partner.MobyInteraction_partner-class.html,1.2,1.3 bioMoby.ontology.Interactor-module.html,1.2,1.3 bioMoby.ontology.Interactor.MobyInteractor-class.html,1.2,1.3 bioMoby.ontology.MEME_Text-module.html,NONE,1.1 bioMoby.ontology.MEME_Text.MobyMEME_Text-class.html,NONE,1.1 bioMoby.ontology.MGIS_ACCESSION-module.html,NONE,1.1 bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION-class.html,NONE,1.1 bioMoby.ontology.MMP_Locus-module.html,1.2,1.3 bioMoby.ontology.MMP_Locus.MobyMMP_Locus-class.html,1.2,1.3 bioMoby.ontology.MO_Term_Test-module.html,1.2,1.3 bioMoby.ontology.MO_Term_Test.MobyMO_Term_Test-class.html,1.2,1.3 bioMoby.ontology.Multi_key_value_pair-module.html,1.2,1.3 bioMoby.ontology.Multi_key_value_pair.MobyMulti_key_value_pair-class.html,1.2,1.3 bioMoby.ontology.MyTree-module.html,1.2,1.3 bioMoby.ontology.MyTree.MobyMyTree-class.html,1.2,1.3 bioMoby.ontology.NCBI_BLAST_Text-module.html,1.2,1.3 bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Te! xt-class.html,1.2,1.3 bioMoby.ontology.NCBI_Blast_XML-module.! html,1.2,1.3 bioMoby.ontology.NCBI_ Blast_XML.MobyNCBI_Blast_XML-class.html,1.2,1.3 bioMoby.ontology.NCBI_MEME_Text-module.html,NONE,1.1 bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text-class.html,NONE,1.1 bioMoby.ontology.NucleotideSequence-module.html,1.2,1.3 bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence-class.html,1.2,1.3 bioMoby.ontology.PDBFormattedText-module.html,1.2,1.3 bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText-class.html,1.2,1.3 bioMoby.ontology.PDGJOB-module.html,1.2,1.3 bioMoby.ontology.PDGJOB.MobyPDGJOB-class.html,1.2,1.3 bioMoby.ontology.PhenotypeDescription-module.html,1.2,1.3 bioMoby.ontology.PhenotypeDescription.MobyPhenotypeDescription-class.html,1.2,1.3 bioMoby.ontology.PubMedMEDLINE-module.html,1.2,1.3 bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE-class.html,1.2,1.3 bioMoby.ontology.RNASequence-module.html,1.2,1.3 bioMoby.ontology.RNASequence.MobyRNASequence-class.html,1.2,1.3 bioMoby.ontology.SINGER_ACCESSION-module.html,NONE,1.1 bioMoby.ontology.SINGER_ACCESS! ION.MobySINGER_ACCESSION-class.html,NONE,1.1 bioMoby.ontology.SchematikonMotifID-module.html,1.2,1.3 bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID-class.html,1.2,1.3 bioMoby.ontology.SchematikonMotifSupport-module.html,1.2,1.3 bioMoby.ontology.SchematikonMotifSupport.MobySchematikonMotifSupport-class.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentAttributes-module.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentAttributes.MobySchematikonSegmentAttributes-class.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentID-module.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentID.MobySchematikonSegmentID-class.html,1.2,1.3 bioMoby.ontology.SchematikonStructureAnnotation-module.html,1.2,1.3 bioMoby.ontology.SchematikonStructureAnnotation.MobySchematikonStructureAnnotation-class.html,1.2,1.3 bioMoby.ontology.SchematikonVorocodeName-module.html,1.2,1.3 bioMoby.ontology.SchematikonVorocodeName.MobySchematikonVorocodeName-class.html,1.2,1.3 bioMoby.ontology.Scored_acronym_string! -module.html,1.2,1.3 bioMoby.ontology.Scored_acronym_string.M! obyScored_acronym_string-class.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedGIFImage-module.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage-class.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage-class.html,1.2,1.3 bioMoby.ontology.Simple_key_value_pair-module.html,1.2,1.3 bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair-class.html,1.2,1.3 bioMoby.ontology.Snp_allele-module.html,1.2,1.3 bioMoby.ontology.Snp_allele.MobySnp_allele-class.html,1.2,1.3 bioMoby.ontology.Snp_genotype-module.html,1.2,1.3 bioMoby.ontology.Snp_genotype.MobySnp_genotype-class.html,1.2,1.3 bioMoby.ontology.Study-module.html,1.2,1.3 bioMoby.ontology.Study.MobyStudy-class.html,1.2,1.3 bioMoby.ontology.TEST-module.html,NONE,1.1 bioMoby.ontology.TEST.MobyTEST-class.html,NONE,1.1 bioMoby.ontology.TargetP_result-module.html,1.2,1.3 bioMoby.ontology.TargetP_result.Mo! byTargetP_result-class.html,1.2,1.3 bioMoby.ontology.Testout-module.html,1.2,1.3 bioMoby.ontology.Testout.MobyTestout-class.html,1.2,1.3 bioMoby.ontology.TextBase64-module.html,1.2,1.3 bioMoby.ontology.TextBase64.MobyTextBase64-class.html,1.2,1.3 bioMoby.ontology.TextFormatted-module.html,1.2,1.3 bioMoby.ontology.TextFormatted.MobyTextFormatted-class.html,1.2,1.3 bioMoby.ontology.TextHtml-module.html,1.2,1.3 bioMoby.ontology.TextHtml.MobyTextHtml-class.html,1.2,1.3 bioMoby.ontology.TextPlain-module.html,1.2,1.3 bioMoby.ontology.TextPlain.MobyTextPlain-class.html,1.2,1.3 bioMoby.ontology.TextUuencoded-module.html,1.2,1.3 bioMoby.ontology.TextUuencoded.MobyTextUuencoded-class.html,1.2,1.3 bioMoby.ontology.TextXml-module.html,1.2,1.3 bioMoby.ontology.TextXml.MobyTextXml-class.html,1.2,1.3 bioMoby.ontology.Text_plain-module.html,1.2,1.3 bioMoby.ontology.Text_plain.MobyText_plain-class.html,1.2,1.3 bioMoby.ontology.Trait_Details-module.html,1.2,1.3 bioMoby.ontology.Trait_Details.! MobyTrait_Details-class.html,1.2,1.3 bioMoby.ontology.Tree-mo! dule.html,1.2,1.3 bioMoby.ontology.Tree.MobyTree-class.html,1.2,1.3 bioMoby.ontology.TropGENE_ACCESSION-module.html,NONE,1.1 bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION-class.html,NONE,1.1 bioMoby.ontology.TropGENE_Diversity_Matrix-module.html,NONE,1.1 bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix-class.html,NONE,1.1 bioMoby.ontology.TropGENE_LOCUS-module.html,NONE,1.1 bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS-class.html,NONE,1.1 bioMoby.ontology.VirtualSequence-module.html,1.2,1.3 bioMoby.ontology.VirtualSequence.MobyVirtualSequence-class.html,1.2,1.3 bioMoby.ontology.WU_BLAST_Text-module.html,1.2,1.3 bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text-class.html,1.2,1.3 bioMoby.ontology.Wildcard_Query-module.html,1.2,1.3 bioMoby.ontology.Wildcard_Query.MobyWildcard_Query-class.html,1.2,1.3 bioMoby.webservice-module.html,1.2,1.3 bioMoby.webservice.Dispatcher-module.html,1.2,1.3 bioMoby.webservice.Dispatcher.AbstractDispatcher-! class.html,NONE,1.1 bioMoby.webservice.Dispatcher.Dispatcher-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.EDispatchError-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.LockedIterator-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.MultiThread-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.PBSDispatcher-class.html,NONE,1.1 bioMoby.webservice.Dispatcher.SimpleDispatcher-class.html,NONE,1.1 bioMoby.webservice.Dispatcher.SingleThread-class.html,1.2,1.3 bioMoby.webservice.Invocators-module.html,1.2,1.3 bioMoby.webservice.Invocators.CGIPostInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.CGIPostMInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.GeneralInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.InvocatorError-class.html,1.2,1.3 bioMoby.webservice.Invocators.LocalInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.PBSInvocator-class.html,NONE,1.1 bioMoby.webservice.Invocators.QsubParameters-class.html,NONE,1.1 bioMoby.webservice.TCB! ioMoby-module.html,NONE,1.1 bioMoby.webservice.TCBioMoby.Body! -class.html,NONE,1.1 exceptions.Exception-class.html,1.2,1.3 frames.html,1.2,1.3 help.html,1.2,1.3 index.html,1.2,1.3 indices.html,1.2,1.3 threading.Thread-class.html,1.2,1.3 toc-bioMoby-module.html,1.2,1.3 toc-bioMoby.mobyClient-module.html,1.2,1.3 toc-bioMoby.mobyDataTypes-module.html,1.2,1.3 toc-bioMoby.mobyExceptions-module.html,1.2,1.3 toc-bioMoby.mobyMarshal-module.html,1.2,1.3 toc-bioMoby.mobyRegister-module.html,1.2,1.3 toc-bioMoby.mobyService-module.html,1.2,1.3 toc-bioMoby.ontology-module.html,1.2,1.3 toc-bioMoby.ontology.AGI_LocusCode-module.html,1.2,1.3 toc-bioMoby.ontology.Allele_freq-module.html,1.2,1.3 toc-bioMoby.ontology.AminoAcidSequence-module.html,1.2,1.3 toc-bioMoby.ontology.B64_Encoded_PNG-module.html,1.2,1.3 toc-bioMoby.ontology.B64_Encoded_Postscript-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encoded_PDB-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encoded_gif-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encoded_jpeg-module.html,1.2,1.3 toc-bioMoby.! ontology.BasicGFFSequenceFeature-module.html,1.2,1.3 toc-bioMoby.ontology.ClustalAlnFormattedText-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedAASequence-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedDNASequence-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedRNASequence-module.html,NONE,1.1 toc-bioMoby.ontology.DNASequence-module.html,1.2,1.3 toc-bioMoby.ontology.DNASequenceWithGFFFeatures-module.html,1.2,1.3 toc-bioMoby.ontology.DateTime-module.html,1.2,1.3 toc-bioMoby.ontology.Decypher_Text-module.html,1.2,1.3 toc-bioMoby.ontology.Edge-module.html,1.2,1.3 toc-bioMoby.ontology.EmblFlatfile-module.html,1.2,1.3 toc-bioMoby.ontology.FASTA-module.html,1.2,1.3 toc-bioMoby.ontology.FASTA_AA-module.html,NONE,1.1 toc-bioMoby.ontology.FASTA_NA-module.html,NONE,1.1 toc-bioMoby.ontology.GFF-module.html,1.2,1.3 toc-bioMoby.ontology.GFF1-module.html,1.2,1.3 toc-bioMoby.ontology.GFF2-module.html,1.2,1.3 toc-bioMoby.ontology.GFF2_5-module.html,1.2,1.3 toc-bioMoby.ontology.G! FF3-module.html,1.2,1.3 toc-bioMoby.ontology.GO_Term-module.h! tml,1.2,1.3 toc-bioMoby.ontology.Ge nbankFlatfile-module.html,1.2,1.3 toc-bioMoby.ontology.GenericSequence-module.html,1.2,1.3 toc-bioMoby.ontology.GeneticElement-module.html,1.2,1.3 toc-bioMoby.ontology.Germplasm_Details-module.html,1.2,1.3 toc-bioMoby.ontology.Germplasm_List-module.html,1.2,1.3 toc-bioMoby.ontology.Global_Keyword-module.html,1.2,1.3 toc-bioMoby.ontology.HBond_Pair-module.html,NONE,1.1 toc-bioMoby.ontology.HCA_picture-module.html,1.2,1.3 toc-bioMoby.ontology.Haplotyping_Study_obj-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query2-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query3-module.html,1.2,1.3 toc-bioMoby.ontology.IntAct_XML-module.html,1.2,1.3 toc-bioMoby.ontology.Interaction-module.html,1.2,1.3 toc-bioMoby.ontology.InteractionMethod-module.html,1.2,1.3 toc-bioMoby.ontology.Interaction_partner-module.html,1.2,1.3 toc-bioMoby.ontology.Interactor-module.html,1.2,1.3 toc-bioMoby.ontology.MEME_Text-module.html,NONE,1.1 toc-bioMoby.ont! ology.MGIS_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.MMP_Locus-module.html,1.2,1.3 toc-bioMoby.ontology.MO_Term_Test-module.html,1.2,1.3 toc-bioMoby.ontology.Multi_key_value_pair-module.html,1.2,1.3 toc-bioMoby.ontology.MyTree-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_BLAST_Text-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_Blast_XML-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_MEME_Text-module.html,NONE,1.1 toc-bioMoby.ontology.NucleotideSequence-module.html,1.2,1.3 toc-bioMoby.ontology.PDBFormattedText-module.html,1.2,1.3 toc-bioMoby.ontology.PDGJOB-module.html,1.2,1.3 toc-bioMoby.ontology.PhenotypeDescription-module.html,1.2,1.3 toc-bioMoby.ontology.PubMedMEDLINE-module.html,1.2,1.3 toc-bioMoby.ontology.RNASequence-module.html,1.2,1.3 toc-bioMoby.ontology.SINGER_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.SchematikonMotifID-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonMotifSupport-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonSegmentAtt! ributes-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonS! egmentID-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonStructureAnnotation-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonVorocodeName-module.html,1.2,1.3 toc-bioMoby.ontology.Scored_acronym_string-module.html,1.2,1.3 toc-bioMoby.ontology.SimpleAnnotatedGIFImage-module.html,1.2,1.3 toc-bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html,1.2,1.3 toc-bioMoby.ontology.Simple_key_value_pair-module.html,1.2,1.3 toc-bioMoby.ontology.Snp_allele-module.html,1.2,1.3 toc-bioMoby.ontology.Snp_genotype-module.html,1.2,1.3 toc-bioMoby.ontology.Study-module.html,1.2,1.3 toc-bioMoby.ontology.TEST-module.html,NONE,1.1 toc-bioMoby.ontology.TargetP_result-module.html,1.2,1.3 toc-bioMoby.ontology.Testout-module.html,1.2,1.3 toc-bioMoby.ontology.TextBase64-module.html,1.2,1.3 toc-bioMoby.ontology.TextFormatted-module.html,1.2,1.3 toc-bioMoby.ontology.TextHtml-module.html,1.2,1.3 toc-bioMoby.ontology.TextPlain-module.html,1.2,1.3 toc-bioMoby.ontology.TextUuencoded-module.html,1.2,1.! 3 toc-bioMoby.ontology.TextXml-module.html,1.2,1.3 toc-bioMoby.ontology.Text_plain-module.html,1.2,1.3 toc-bioMoby.ontology.Trait_Details-module.html,1.2,1.3 toc-bioMoby.ontology.Tree-module.html,1.2,1.3 toc-bioMoby.ontology.TropGENE_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.TropGENE_Diversity_Matrix-module.html,NONE,1.1 toc-bioMoby.ontology.TropGENE_LOCUS-module.html,NONE,1.1 toc-bioMoby.ontology.VirtualSequence-module.html,1.2,1.3 toc-bioMoby.ontology.WU_BLAST_Text-module.html,1.2,1.3 toc-bioMoby.ontology.Wildcard_Query-module.html,1.2,1.3 toc-bioMoby.webservice-module.html,1.2,1.3 toc-bioMoby.webservice.Dispatcher-module.html,1.2,1.3 toc-bioMoby.webservice.Invocators-module.html,1.2,1.3 toc-bioMoby.webservice.TCBioMoby-module.html,NONE,1.1 toc-everything.html,1.2,1.3 toc.html,1.2,1.3 trees.html,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/__builtin__.object-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/__builtin__.object-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/__builtin__.object-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -245,13 +251,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/__builtin__.type-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/__builtin__.type-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/__builtin__.type-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -489,13 +495,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -58,6 +64,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -65,6 +75,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -78,6 +90,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -87,12 +100,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -109,10 +125,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -123,6 +141,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -131,6 +152,7 @@

  • @@ -143,13 +165,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -57,13 +63,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Central-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Central-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Central-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,7 +60,8 @@ @@ -77,7 +84,8 @@
      __init__(self, url, - ns) + ns, + debug)
    Changes url and ns parameters if you want to use another moby server
    - +

    __init__(self, url='http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral..., - ns='http://mobycentral.cbr.nrc.ca/MOBY/Central') + ns='http://mobycentral.cbr.nrc.ca/MOBY/Central', + debug=False)
    (Constructor)

    Changes url and ns parameters if you want to use another moby @@ -106,13 +114,19 @@
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Client-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Client-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Client-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,12 +60,10 @@ - +
    Method Summary
     __init__(self, + __init__(self, url, ns) -
    -Changes url and ns parameters if you want to use another moby -server
      findService(self, mobyQuery) @@ -141,23 +145,6 @@ Method Details
    - -
    -

    __init__(self, - url='http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral..., - ns='http://mobycentral.cbr.nrc.ca/MOBY/Central') -
    (Constructor) -

    - Changes url and ns parameters if you want to use another moby - server -
    -
    Overrides:
    -
    bioMoby.mobyClient.Central.__init__ (inherited documentation) -
    -
    -
    -
    - - +

    findService(self, @@ -298,13 +285,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -80,13 +86,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyContent-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyContent-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyContent-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +
    @@ -116,13 +122,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyFloat-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyFloat-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyFloat-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
    @@ -110,13 +116,19 @@ - +
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    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyInteger-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyInteger-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyInteger-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -110,13 +116,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyObject-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyObject-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyObject-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -49,6 +55,7 @@ MobyGlobal_Keyword, MobyGO_Term, MobyHaplotyping_Study_obj, + MobyHBond_Pair, MobyICIS_Query, MobyICIS_Query2, MobyICIS_Query3, @@ -57,6 +64,7 @@ MobyInteraction_partner, MobyInteractionMethod, MobyInteractor, + MobyMGIS_ACCESSION, MobyMMP_Locus, MobyMO_Term_Test, MobyMulti_key_value_pair, @@ -70,11 +78,14 @@ MobyScored_acronym_string, MobySequence, MobySimple_key_value_pair, + MobySINGER_ACCESSION, MobyString, MobyStudy, MobyTargetP_result, MobyTestout, MobyTrait_Details, + MobyTropGENE_ACCESSION, + MobyTropGENE_LOCUS, MobyVirtualSequence, MobyWildcard_Query, MobyXref, @@ -162,13 +173,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobySequence-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobySequence-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobySequence-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -57,7 +63,8 @@ - +
    __init__(self, sequence, namespace, - id) + id, + articleName)
      fromMoby(self, @@ -110,13 +117,19 @@    Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyString-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyString-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyString-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
    @@ -99,13 +105,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyXref-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyXref-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyXref-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyZmPDB-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyZmPDB-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyZmPDB-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EInvalidType-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EInvalidType-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EInvalidType-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EMethodRetrieveError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EMethodRetrieveError-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EMethodRetrieveError-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ENotAWSMethod-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ENotAWSMethod-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ENotAWSMethod-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ETypeMismatch-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ETypeMismatch-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ETypeMismatch-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -57,13 +63,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyMarshaller-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyMarshaller-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyMarshaller-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,10 +54,11 @@ - +
    +Serialize the object into a Moby XML object
    Method Summary
     dumps(self, + dumps(self, value, articleName) -
      m_dict(self, value, @@ -115,6 +122,17 @@ Method Details
    + +
    +

    dumps(self, + value, + articleName='') +

    + Serialize the object into a Moby XML object +
    +
    +
    + - +

    m_dict(self, @@ -208,13 +226,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyUnmarshaller-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyUnmarshaller-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyUnmarshaller-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +

    + bioMoby-python +

    +
    @@ -48,9 +54,10 @@ - +
    +Deserializes an xml string and return a bioMoby-Python object
    Method Summary
     loads(self, + loads(self, xml) -
      m_Collection(self, value) @@ -93,6 +100,16 @@ Method Details
    + +
    +

    loads(self, + xml) +

    + Deserializes an xml string and return a bioMoby-Python object +
    +
    +
    + - +

    m_Collection(self, @@ -165,13 +182,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyRegister-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyRegister-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyRegister-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    +
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    +
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    +
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    +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -67,13 +73,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.Service-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.Service-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.Service-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -70,7 +76,8 @@ @@ -82,7 +89,8 @@ +Register the service on the Moby server has been added here a code to +verify that signatureURL is not empty :)
    execute(self, query, method, - returnXml) + returnXml, + debug)
    Executes the web service v0.5: return either the XML form or try to unmarshall the result and return a MobyContent Object
      register(self)
    -Register the service on the Moby server

    @@ -151,7 +159,8 @@

    execute(self, query, method='', - returnXml=True) + returnXml=True, + debug=False)

    Executes the web service v0.5: return either the XML form or try to unmarshall the result and return a MobyContent Object @@ -173,7 +182,8 @@

    register(self)

    - Register the service on the Moby server + Register the service on the Moby server has been added here a code + to verify that signatureURL is not empty :)
    @@ -187,13 +197,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceArticle-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceArticle-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceArticle-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -113,13 +119,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceList-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceList-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceList-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -204,13 +210,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceQuery-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceQuery-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceQuery-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -128,13 +134,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceSecondary-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceSecondary-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceSecondary-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -116,13 +122,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -51,6 +57,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -58,6 +68,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -71,6 +83,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -80,12 +93,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -102,10 +118,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -116,6 +134,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -130,13 +151,19 @@
  • - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -58,13 +64,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -113,13 +119,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -90,13 +96,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,6 +54,10 @@ MobyAminoAcidSequence
    +
    Known Subclasses:
    +
    + MobyCommentedAASequence
    +
    Description: Lightweight representation an amino acid sequence Author: @@ -117,13 +127,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
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    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
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    + bioMoby-python +

    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -116,13 +122,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif-module.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

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    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    @@ -52,6 +58,7 @@
    Known Subclasses:
    + MobyCommentedDNASequence, MobyDNASequenceWithGFFFeatures

    @@ -123,13 +130,19 @@ - +
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    @@ -50,6 +56,11 @@ MobyFASTA
    +
    Known Subclasses:
    +
    + MobyFASTA_AA, + MobyFASTA_NA
    +
    Description: FASTA formatted sequence Author: www.sdsc.edu Contact: @@ -118,13 +129,19 @@ - +
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    Known Subclasses:
    + MobyClustalAlnFormattedText, MobyDecypher_Text, MobyEmblFlatfile, MobyFASTA, MobyGenbankFlatfile, MobyGFF, + MobyMEME_Text, MobyMyTree, MobyNCBI_BLAST_Text, + MobyNCBI_MEME_Text, MobyPDBFormattedText, MobyPubMedMEDLINE, + MobyTEST, MobyTree, + MobyTropGENE_Diversity_Matrix, MobyWU_BLAST_Text

    @@ -130,13 +141,19 @@ - +
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    +
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    @@ -55,13 +62,19 @@    Trees       Index       Help    - + + +
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    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher-module.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher-module.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -43,6 +49,10 @@ + + + + + +
    Classes
    + AbstractDispatcherSubclass this one to create your own dispatcher class a Dispatcher +class must have a execute method
    Dispatcher All Queries in the MobyContent Object are splitted and executed
    @@ -52,6 +62,12 @@ MultiThread Several threads
    + PBSDispatcherDispatcher for PBS jobs
    + SimpleDispatcherA simple dispatcher, without execute method
    SingleThread Definition of a single Thread

    @@ -74,13 +90,19 @@    Trees       Index       Help    - + + +
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    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.Dispatcher-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.Dispatcher-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.Dispatcher-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -38,6 +44,12 @@

    Class Dispatcher

    +
    +AbstractDispatcher --+
    +                     |
    +                    Dispatcher
    +

    +
    All Queries in the MobyContent Object are splitted and executed @@ -92,6 +104,9 @@ [queryData]-->("commandName","commandArgs", ["tempfiles"])
    +
    Overrides:
    +
    bioMoby.webservice.Dispatcher.AbstractDispatcher.__init__
    +
    @@ -103,6 +118,9 @@ Execute the queries with a pool of threads, store the results in a mobyContent Object
    +
    Overrides:
    +
    bioMoby.webservice.Dispatcher.AbstractDispatcher.execute
    +

    @@ -115,13 +133,19 @@    Trees       Index       Help    - + + +
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    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.EDispatchError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.EDispatchError-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.EDispatchError-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -54,11 +60,24 @@ GeneralInvocator - - + + + + +
    General class for other invocators
    - InvocatorErrorError during an invocation of method
    LocalInvocator Invokes local command
    + PBSInvocatorInvokes a command in a qsub
    + QsubParametersParameters for the qsub command

    + + + + + + + +
    Exceptions
    + InvocatorErrorError during an invocation of method

    @@ -69,13 +88,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostInvocator-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostInvocator-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -68,7 +74,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -111,13 +118,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -89,7 +95,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -151,13 +158,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.GeneralInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.GeneralInvocator-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.GeneralInvocator-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -55,17 +61,51 @@ - +
    +queryid is the identifier of a query, userdir is the session +directory, timeout the limit time of execution of the query - +
    Method Summary
     __init__(self, + __init__(self, queryid, userdir, timeout) -
     getResults(self) -
    getResults(self) +
    +retrieve the results if available

    + + + + +
    Method Details
    + + +
    +

    __init__(self, + queryid, + userdir='/tmp', + timeout=None) +
    (Constructor) +

    + queryid is the identifier of a query, userdir is the session + directory, timeout the limit time of execution of the query +
    +
    +
    + + +
    +

    getResults(self) +

    + retrieve the results if available +
    +
    +
    +
    + + @@ -73,13 +113,19 @@ - + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.InvocatorError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.InvocatorError-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.InvocatorError-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -38,6 +44,12 @@

    Class InvocatorError

    +
    +Exception --+
    +            |
    +           InvocatorError
    +

    +
    Error during an invocation of method @@ -51,6 +63,14 @@ + + + + + +
      __str__(self)
        Inherited from Exception
     __init__(...) +
     __getitem__(...) +

    @@ -61,13 +81,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.LocalInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.LocalInvocator-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.LocalInvocator-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -44,6 +50,10 @@ LocalInvocator
    +
    Known Subclasses:
    +
    + PBSInvocator
    +
    Invokes local command @@ -69,7 +79,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -105,13 +116,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/exceptions.Exception-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/exceptions.Exception-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/exceptions.Exception-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -43,7 +49,8 @@ EInvalidType, EMethodRetrieveError, ENotAWSMethod, - ETypeMismatch + ETypeMismatch, + InvocatorError
    @@ -74,13 +81,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/frames.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/frames.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/frames.html 2004/12/09 14:41:34 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/help.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/help.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/help.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -32,7 +38,7 @@

    API Documentation

    This document contains the API (Application Programming Interface) -documentation for this project. Documentation for the Python +documentation for bioMoby-python. Documentation for the Python objects defined by the project is divided into separate pages for each package, module, and class. The API documentation also includes two pages containing information about the project as a whole: a trees @@ -209,13 +215,19 @@

    - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/index.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/index.html 2004/12/09 14:41:34 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/indices.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/indices.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/indices.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:10 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -70,6 +76,8 @@ + + @@ -132,6 +140,14 @@ + + + + + + + + @@ -146,6 +162,10 @@ + + + + @@ -170,6 +190,8 @@ + + @@ -190,6 +212,10 @@ + + + + @@ -202,6 +228,8 @@ + + @@ -214,6 +242,8 @@ + + @@ -240,6 +270,8 @@ + + @@ -262,18 +294,30 @@ + + + + + + + + + + + + @@ -284,6 +328,10 @@ + + + + @@ -368,6 +416,8 @@ + + @@ -398,6 +448,8 @@ + + @@ -406,8 +458,20 @@ + + + + + + + + + + + + @@ -474,16 +538,26 @@ + + + + + + + + + + @@ -518,6 +592,14 @@ + + + + + + + + @@ -532,6 +614,10 @@ + + + + @@ -556,6 +642,8 @@ + + @@ -576,6 +664,10 @@ + + + + @@ -588,6 +680,8 @@ + + @@ -600,6 +694,8 @@ + + @@ -626,6 +722,8 @@ + + @@ -648,6 +746,12 @@ + + + + + + @@ -674,6 +778,8 @@ + + @@ -702,6 +808,8 @@ + + @@ -774,6 +882,10 @@ + + + + @@ -798,6 +910,14 @@ + + + + + + + + @@ -818,6 +938,10 @@ + + + + @@ -846,6 +970,8 @@ + + @@ -870,6 +996,10 @@ + + + + @@ -882,6 +1012,8 @@ + + @@ -922,6 +1054,8 @@ + + @@ -932,6 +1066,8 @@ + + @@ -952,6 +1088,12 @@ + + + + + + @@ -972,14 +1114,20 @@ + + + + + + @@ -990,6 +1138,14 @@ + + + + + + + + @@ -1002,6 +1158,8 @@ + + @@ -1056,6 +1214,10 @@ + + + + @@ -1072,12 +1234,22 @@ + + + + + + + + + + @@ -1092,8 +1264,14 @@ + + + + + + @@ -1136,8 +1314,22 @@ + + + + + + + + + + + + + + @@ -1156,13 +1348,19 @@ - +
    Method in class __builtin__.object
    __hash__ Method in class __builtin__.type
    __init__Method in class ZSI.TC.TypeCode
    __init__ Method in class __builtin__.object
    __init__Method in class bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg
    __init__ Method in class bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    __init__Method in class bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    __init__Method in class bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    __init__Method in class bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    __init__Method in class bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    __init__ Method in class bioMoby.ontology.DNASequence.MobyDNASequence
    __init__Method in class bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    __init__ Method in class bioMoby.ontology.FASTA.MobyFASTA
    __init__Method in class bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    __init__Method in class bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    __init__ Method in class bioMoby.ontology.GFF.MobyGFF
    __init__Method in class bioMoby.ontology.Germplasm_List.MobyGermplasm_List
    __init__ Method in class bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    __init__Method in class bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    __init__ Method in class bioMoby.ontology.HCA_picture.MobyHCA_picture
    __init__Method in class bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    __init__ Method in class bioMoby.ontology.Interactor.MobyInteractor
    __init__Method in class bioMoby.ontology.MEME_Text.MobyMEME_Text
    __init__Method in class bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    __init__ Method in class bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    __init__Method in class bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    __init__ Method in class bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    __init__Method in class bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    __init__ Method in class bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    __init__Method in class bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE
    __init__ Method in class bioMoby.ontology.RNASequence.MobyRNASequence
    __init__Method in class bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    __init__ Method in class bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID
    __init__Method in class bioMoby.ontology.Snp_genotype.MobySnp_genotype
    __init__ Method in class bioMoby.ontology.Study.MobyStudy
    __init__Method in class bioMoby.ontology.TEST.MobyTEST
    __init__ Method in class bioMoby.ontology.TargetP_result.MobyTargetP_result
    __init__Method in class bioMoby.ontology.Trait_Details.MobyTrait_Details
    __init__ Method in class bioMoby.ontology.Tree.MobyTree
    __init__Method in class bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    __init__Method in class bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    __init__Method in class bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    __init__ Method in class bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    __init__ Method in class bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text
    __init__ Method in class bioMoby.ontology.Wildcard_Query.MobyWildcard_Query
    __init__Method in class bioMoby.webservice.Dispatcher.AbstractDispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.Dispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.LockedIterator
    __init__ Method in class bioMoby.webservice.Dispatcher.MultiThread
    __init__Method in class bioMoby.webservice.Dispatcher.PBSDispatcher
    __init__Method in class bioMoby.webservice.Dispatcher.SimpleDispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.SingleThread
    __init__Method in class bioMoby.webservice.Invocators.GeneralInvocator
    __init__ Method in class bioMoby.webservice.Invocators.LocalInvocator
    __init__Method in class bioMoby.webservice.Invocators.PBSInvocator
    __init__Method in class bioMoby.webservice.Invocators.QsubParameters
    __init__ Method in class exceptions.Exception
    __init__Method in class __builtin__.type
    __weakrefoffset__ Variable in class __builtin__.type
    AbstractDispatcherClass in module bioMoby.webservice.Dispatcher
    AGI_LocusCode Module in package bioMoby.ontology
    Allele_freqModule in package bioMoby.ontology
    bioMoby Package
    BodyClass in module bioMoby.webservice.TCBioMoby
    call_method Method in class bioMoby.mobyClient.Central
    CentralClass in module bioMoby.webservice.Invocators
    CGIPostMInvocator Class in module bioMoby.webservice.Invocators
    checknameMethod in class ZSI.TC.TypeCode
    checktypeMethod in class ZSI.TC.TypeCode
    Client Class in module bioMoby.mobyClient
    ClustalAlnFormattedTextModule in package bioMoby.ontology
    CommentedAASequenceModule in package bioMoby.ontology
    CommentedDNASequenceModule in package bioMoby.ontology
    CommentedRNASequenceModule in package bioMoby.ontology
    compress Method in class bioMoby.mobyDataTypes.MobyZmPDB
    contactClass in module exceptions
    execute Method in class bioMoby.mobyService.Service
    executeMethod in class bioMoby.webservice.Dispatcher.AbstractDispatcher
    execute Method in class bioMoby.webservice.Dispatcher.Dispatcher
    executeMethod in class bioMoby.webservice.Dispatcher.PBSDispatcher
    execute Method in class bioMoby.webservice.Invocators.CGIPostInvocator
    execute Method in class bioMoby.webservice.Invocators.CGIPostMInvocator
    execute Method in class bioMoby.webservice.Invocators.LocalInvocator
    executeMethod in class bioMoby.webservice.Invocators.PBSInvocator
    FASTA Module in package bioMoby.ontology
    FASTA_AAModule in package bioMoby.ontology
    FASTA_NAModule in package bioMoby.ontology
    findService Method in class bioMoby.mobyClient.Client
    fromMobyMethod in class bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg
    fromMoby Method in class bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    fromMobyMethod in class bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    fromMobyMethod in class bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    fromMobyMethod in class bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    fromMobyMethod in class bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    fromMoby Method in class bioMoby.ontology.DNASequence.MobyDNASequence
    fromMobyMethod in class bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    fromMoby Method in class bioMoby.ontology.FASTA.MobyFASTA
    fromMobyMethod in class bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    fromMobyMethod in class bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    fromMoby Method in class bioMoby.ontology.GFF.MobyGFF
    fromMobyMethod in class bioMoby.ontology.Germplasm_List.MobyGermplasm_List
    fromMoby Method in class bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    fromMobyMethod in class bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    fromMoby Method in class bioMoby.ontology.HCA_picture.MobyHCA_picture
    fromMobyMethod in class bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    fromMoby Method in class bioMoby.ontology.Interactor.MobyInteractor
    fromMobyMethod in class bioMoby.ontology.MEME_Text.MobyMEME_Text
    fromMobyMethod in class bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    fromMoby Method in class bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    fromMobyMethod in class bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    fromMoby Method in class bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    fromMobyMethod in class bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    fromMoby Method in class bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    fromMobyMethod in class bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE
    fromMoby Method in class bioMoby.ontology.RNASequence.MobyRNASequence
    fromMobyMethod in class bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    fromMoby Method in class bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID
    fromMobyMethod in class bioMoby.ontology.Snp_genotype.MobySnp_genotype
    fromMoby Method in class bioMoby.ontology.Study.MobyStudy
    fromMobyMethod in class bioMoby.ontology.TEST.MobyTEST
    fromMoby Method in class bioMoby.ontology.TargetP_result.MobyTargetP_result
    fromMobyMethod in class bioMoby.ontology.Trait_Details.MobyTrait_Details
    fromMoby Method in class bioMoby.ontology.Tree.MobyTree
    fromMobyMethod in class bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    fromMobyMethod in class bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    fromMobyMethod in class bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    fromMoby Method in class bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    fromMobyModule in package bioMoby.ontology
    get_content_type Method in class bioMoby.webservice.Invocators.CGIPostMInvocator
    get_parse_and_errorlistMethod in class ZSI.TC.TypeCode
    getInfo Method in class bioMoby.mobyDataTypes.MobyObject
    getMethodsModule in package bioMoby.ontology
    Haplotyping_Study_obj Module in package bioMoby.ontology
    HBond_PairModule in package bioMoby.ontology
    HCA_picture Module in package bioMoby.ontology
    ICIS_QueryMethod in class bioMoby.mobyMarshal.MobyMarshaller
    m_unicode Method in class bioMoby.mobyMarshal.MobyMarshaller
    MEME_TextModule in package bioMoby.ontology
    MGIS_ACCESSIONModule in package bioMoby.ontology
    MMP_Locus Module in package bioMoby.ontology
    MO_Term_TestClass in module bioMoby.ontology.BasicGFFSequenceFeature
    mobyClient Module in package bioMoby
    MobyClustalAlnFormattedTextClass in module bioMoby.ontology.ClustalAlnFormattedText
    MobyCommentedAASequenceClass in module bioMoby.ontology.CommentedAASequence
    MobyCommentedDNASequenceClass in module bioMoby.ontology.CommentedDNASequence
    MobyCommentedRNASequenceClass in module bioMoby.ontology.CommentedRNASequence
    MobyContent Class in module bioMoby.mobyDataTypes
    mobyDataTypesModule in package bioMoby
    MobyFASTA Class in module bioMoby.ontology.FASTA
    MobyFASTA_AAClass in module bioMoby.ontology.FASTA_AA
    MobyFASTA_NAClass in module bioMoby.ontology.FASTA_NA
    MobyFloat Class in module bioMoby.mobyDataTypes
    MobyGenbankFlatfileClass in module bioMoby.ontology.GO_Term
    MobyHaplotyping_Study_obj Class in module bioMoby.ontology.Haplotyping_Study_obj
    MobyHBond_PairClass in module bioMoby.ontology.HBond_Pair
    MobyHCA_picture Class in module bioMoby.ontology.HCA_picture
    MobyICIS_QueryModule in package bioMoby
    MobyMarshaller Class in module bioMoby.mobyMarshal
    MobyMEME_TextClass in module bioMoby.ontology.MEME_Text
    MobyMGIS_ACCESSIONClass in module bioMoby.ontology.MGIS_ACCESSION
    MobyMMP_Locus Class in module bioMoby.ontology.MMP_Locus
    MobyMO_Term_TestClass in module bioMoby.ontology.NCBI_BLAST_Text
    MobyNCBI_Blast_XML Class in module bioMoby.ontology.NCBI_Blast_XML
    MobyNCBI_MEME_TextClass in module bioMoby.ontology.NCBI_MEME_Text
    MobyNucleotideSequence Class in module bioMoby.ontology.NucleotideSequence
    MobyObjectClass in module bioMoby.ontology.SimpleAnnotatedGIFImage
    MobySimpleAnnotatedJPEGImage Class in module bioMoby.ontology.SimpleAnnotatedJPEGImage
    MobySINGER_ACCESSIONClass in module bioMoby.ontology.SINGER_ACCESSION
    MobySnp_allele Class in module bioMoby.ontology.Snp_allele
    MobySnp_genotypeClass in module bioMoby.ontology.Study
    MobyTargetP_result Class in module bioMoby.ontology.TargetP_result
    MobyTESTClass in module bioMoby.ontology.TEST
    MobyTestout Class in module bioMoby.ontology.Testout
    MobyText_plainClass in module bioMoby.ontology.Trait_Details
    MobyTree Class in module bioMoby.ontology.Tree
    MobyTropGENE_ACCESSIONClass in module bioMoby.ontology.TropGENE_ACCESSION
    MobyTropGENE_Diversity_MatrixClass in module bioMoby.ontology.TropGENE_Diversity_Matrix
    MobyTropGENE_LOCUSClass in module bioMoby.ontology.TropGENE_LOCUS
    MobyUnmarshaller Class in module bioMoby.mobyMarshal
    MobyVirtualSequenceClass in module bioMoby.webservice.Dispatcher
    MyTree Module in package bioMoby.ontology
    name_matchMethod in class ZSI.TC.TypeCode
    Namespace Class in module bioMoby.mobyRegister
    NCBI_BLAST_Text Module in package bioMoby.ontology
    NCBI_Blast_XML Module in package bioMoby.ontology
    NCBI_MEME_TextModule in package bioMoby.ontology
    next Method in class bioMoby.webservice.Dispatcher.LockedIterator
    nilledMethod in class ZSI.TC.TypeCode
    NucleotideSequence Module in package bioMoby.ontology
    objectPackage in package bioMoby
    Parameter Class in module bioMoby.mobyDataTypes
    parseMethod in class ZSI.TC.TypeCode
    parselistVariable in class bioMoby.webservice.TCBioMoby.Body
    PBSDispatcherClass in module bioMoby.webservice.Dispatcher
    PBSInvocatorClass in module bioMoby.webservice.Invocators
    PDBFormattedText Module in package bioMoby.ontology
    PDGJOBMethod in class bioMoby.webservice.Invocators.CGIPostMInvocator
    PubMedMEDLINE Module in package bioMoby.ontology
    QsubParametersClass in module bioMoby.webservice.Invocators
    register Method in class bioMoby.mobyRegister.Namespace
    registerModule in package bioMoby.ontology
    Scored_acronym_string Module in package bioMoby.ontology
    serializeMethod in class bioMoby.webservice.TCBioMoby.Body
    seriallistVariable in class bioMoby.webservice.TCBioMoby.Body
    Service Class in module bioMoby.mobyService
    ServiceArticleMethod in class threading.Thread
    setName Method in class threading.Thread
    setParametersMethod in class bioMoby.webservice.Invocators.PBSInvocator
    Simple_key_value_pair Module in package bioMoby.ontology
    simple_valueMethod in class ZSI.TC.TypeCode
    SimpleAnnotatedGIFImage Module in package bioMoby.ontology
    SimpleAnnotatedJPEGImage Module in package bioMoby.ontology
    SimpleDispatcherClass in module bioMoby.webservice.Dispatcher
    SimpleHREFMethod in class ZSI.TC.TypeCode
    SINGER_ACCESSIONModule in package bioMoby.ontology
    SingleThread Class in module bioMoby.webservice.Dispatcher
    Snp_alleleModule in package bioMoby.ontology
    submits2XML Method in class bioMoby.mobyService.ServiceQuery
    tagVariable in class bioMoby.webservice.TCBioMoby.Body
    TargetP_result Module in package bioMoby.ontology
    TCBioMobyModule in package bioMoby.webservice
    TESTModule in package bioMoby.ontology
    Testout Module in package bioMoby.ontology
    Text_plainModule in package bioMoby.ontology
    Tree Module in package bioMoby.ontology
    TropGENE_ACCESSIONModule in package bioMoby.ontology
    TropGENE_Diversity_MatrixModule in package bioMoby.ontology
    TropGENE_LOCUSModule in package bioMoby.ontology
    type Class in module __builtin__
    typechecksVariable in class ZSI.TC.TypeCode
    typechecksVariable in class ZSI.TC.TypeCode
    TypeCodeClass in module ZSI.TC
    typecodeVariable in class bioMoby.webservice.TCBioMoby.Body
    VirtualSequence Module in package bioMoby.ontology
    webservice   Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/threading.Thread-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/threading.Thread-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/threading.Thread-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -140,13 +146,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyClient-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyDataTypes-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyExceptions-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyMarshal-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyRegister-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyService-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology-module.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology-module.html 2004/12/09 14:41:35 1.3 @@ -22,6 +22,10 @@ B64_Encoded_PNG
    B64_Encoded_Postscript
    BasicGFFSequenceFeature
    +ClustalAlnFormattedText
    +CommentedAASequence
    +CommentedDNASequence
    +CommentedRNASequence
    DateTime
    Decypher_Text
    DNASequence
    @@ -29,6 +33,8 @@ Edge
    EmblFlatfile
    FASTA
    +FASTA_AA
    +FASTA_NA
    GenbankFlatfile
    GenericSequence
    GeneticElement
    @@ -42,6 +48,7 @@ Global_Keyword
    GO_Term
    Haplotyping_Study_obj
    +HBond_Pair
    HCA_picture
    ICIS_Query
    ICIS_Query2
    @@ -51,12 +58,15 @@ Interaction_partner
    InteractionMethod
    Interactor
    +MEME_Text
    +MGIS_ACCESSION
    MMP_Locus
    MO_Term_Test
    Multi_key_value_pair
    MyTree
    NCBI_BLAST_Text
    NCBI_Blast_XML
    +NCBI_MEME_Text
    NucleotideSequence
    PDBFormattedText
    PDGJOB
    @@ -73,10 +83,12 @@ Simple_key_value_pair
    SimpleAnnotatedGIFImage
    SimpleAnnotatedJPEGImage
    +SINGER_ACCESSION
    Snp_allele
    Snp_genotype
    Study
    TargetP_result
    +TEST
    Testout
    Text_plain
    TextBase64
    @@ -87,6 +99,9 @@ TextXml
    Trait_Details
    Tree
    +TropGENE_ACCESSION
    +TropGENE_Diversity_Matrix
    +TropGENE_LOCUS
    VirtualSequence
    Wildcard_Query
    WU_BLAST_Text
    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology.AGI_LocusCode-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology.Allele_freq-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology.AminoAcidSequence-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology.B64_Encoded_PNG-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 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    Dispatcher
    Invocators
    +TCBioMoby


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Dispatcher-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Dispatcher-module.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Dispatcher-module.html 2004/12/09 14:41:35 1.3 @@ -13,9 +13,12 @@ Classes
    +AbstractDispatcher
    Dispatcher
    LockedIterator
    MultiThread
    +PBSDispatcher
    +SimpleDispatcher
    SingleThread

    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Invocators-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Invocators-module.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Invocators-module.html 2004/12/09 14:41:35 1.3 @@ -16,8 +16,14 @@ CGIPostInvocator
    CGIPostMInvocator
    GeneralInvocator
    -InvocatorError
    LocalInvocator
    +PBSInvocator
    +QsubParameters
    +
    + + +Exceptions
    +InvocatorError


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-everything.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc-everything.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc-everything.html 2004/12/09 14:41:35 1.3 @@ -45,6 +45,10 @@ bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG
    bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript
    bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    +bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    +bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    +bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    +bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    bioMoby.ontology.DateTime.MobyDateTime
    bioMoby.ontology.Decypher_Text.MobyDecypher_Text
    bioMoby.ontology.DNASequence.MobyDNASequence
    @@ -52,6 +56,8 @@ bioMoby.ontology.Edge.MobyEdge
    bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    bioMoby.ontology.FASTA.MobyFASTA
    +bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    +bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    bioMoby.ontology.GenbankFlatfile.MobyGenbankFlatfile
    bioMoby.ontology.GenericSequence.MobyGenericSequence
    bioMoby.ontology.GeneticElement.MobyGeneticElement
    @@ -65,6 +71,7 @@ bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    bioMoby.ontology.GO_Term.MobyGO_Term
    bioMoby.ontology.Haplotyping_Study_obj.MobyHaplotyping_Study_obj
    +bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    bioMoby.ontology.HCA_picture.MobyHCA_picture
    bioMoby.ontology.ICIS_Query.MobyICIS_Query
    bioMoby.ontology.ICIS_Query2.MobyICIS_Query2
    @@ -74,12 +81,15 @@ bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    bioMoby.ontology.InteractionMethod.MobyInteractionMethod
    bioMoby.ontology.Interactor.MobyInteractor
    +bioMoby.ontology.MEME_Text.MobyMEME_Text
    +bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    bioMoby.ontology.MO_Term_Test.MobyMO_Term_Test
    bioMoby.ontology.Multi_key_value_pair.MobyMulti_key_value_pair
    bioMoby.ontology.MyTree.MobyMyTree
    bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    +bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText
    bioMoby.ontology.PDGJOB.MobyPDGJOB
    @@ -96,10 +106,12 @@ bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair
    bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage
    bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage
    +bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    bioMoby.ontology.Snp_allele.MobySnp_allele
    bioMoby.ontology.Snp_genotype.MobySnp_genotype
    bioMoby.ontology.Study.MobyStudy
    bioMoby.ontology.TargetP_result.MobyTargetP_result
    +bioMoby.ontology.TEST.MobyTEST
    bioMoby.ontology.Testout.MobyTestout
    bioMoby.ontology.Text_plain.MobyText_plain
    bioMoby.ontology.TextBase64.MobyTextBase64
    @@ -110,18 +122,26 @@ bioMoby.ontology.TextXml.MobyTextXml
    bioMoby.ontology.Trait_Details.MobyTrait_Details
    bioMoby.ontology.Tree.MobyTree
    +bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    +bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    +bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    bioMoby.ontology.Wildcard_Query.MobyWildcard_Query
    bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text
    +bioMoby.webservice.Dispatcher.AbstractDispatcher
    bioMoby.webservice.Dispatcher.Dispatcher
    bioMoby.webservice.Dispatcher.LockedIterator
    bioMoby.webservice.Dispatcher.MultiThread
    +bioMoby.webservice.Dispatcher.PBSDispatcher
    +bioMoby.webservice.Dispatcher.SimpleDispatcher
    bioMoby.webservice.Dispatcher.SingleThread
    bioMoby.webservice.Invocators.CGIPostInvocator
    bioMoby.webservice.Invocators.CGIPostMInvocator
    bioMoby.webservice.Invocators.GeneralInvocator
    -bioMoby.webservice.Invocators.InvocatorError
    bioMoby.webservice.Invocators.LocalInvocator
    +bioMoby.webservice.Invocators.PBSInvocator
    +bioMoby.webservice.Invocators.QsubParameters
    +bioMoby.webservice.TCBioMoby.Body

    @@ -132,6 +152,7 @@ bioMoby.mobyExceptions.ENotAWSMethod
    bioMoby.mobyExceptions.ETypeMismatch
    bioMoby.webservice.Dispatcher.EDispatchError
    +bioMoby.webservice.Invocators.InvocatorError


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc.html 2004/12/09 14:41:35 1.3 @@ -35,6 +35,10 @@ bioMoby.ontology.B64_Encoded_PNG
    bioMoby.ontology.B64_Encoded_Postscript
    bioMoby.ontology.BasicGFFSequenceFeature
    +bioMoby.ontology.ClustalAlnFormattedText
    +bioMoby.ontology.CommentedAASequence
    +bioMoby.ontology.CommentedDNASequence
    +bioMoby.ontology.CommentedRNASequence
    bioMoby.ontology.DateTime
    bioMoby.ontology.Decypher_Text
    bioMoby.ontology.DNASequence
    @@ -42,6 +46,8 @@ bioMoby.ontology.Edge
    bioMoby.ontology.EmblFlatfile
    bioMoby.ontology.FASTA
    +bioMoby.ontology.FASTA_AA
    +bioMoby.ontology.FASTA_NA
    bioMoby.ontology.GenbankFlatfile
    bioMoby.ontology.GenericSequence
    bioMoby.ontology.GeneticElement
    @@ -55,6 +61,7 @@ bioMoby.ontology.Global_Keyword
    bioMoby.ontology.GO_Term
    bioMoby.ontology.Haplotyping_Study_obj
    +bioMoby.ontology.HBond_Pair
    bioMoby.ontology.HCA_picture
    bioMoby.ontology.ICIS_Query
    bioMoby.ontology.ICIS_Query2
    @@ -64,12 +71,15 @@ bioMoby.ontology.Interaction_partner
    bioMoby.ontology.InteractionMethod
    bioMoby.ontology.Interactor
    +bioMoby.ontology.MEME_Text
    +bioMoby.ontology.MGIS_ACCESSION
    bioMoby.ontology.MMP_Locus
    bioMoby.ontology.MO_Term_Test
    bioMoby.ontology.Multi_key_value_pair
    bioMoby.ontology.MyTree
    bioMoby.ontology.NCBI_BLAST_Text
    bioMoby.ontology.NCBI_Blast_XML
    +bioMoby.ontology.NCBI_MEME_Text
    bioMoby.ontology.NucleotideSequence
    bioMoby.ontology.PDBFormattedText
    bioMoby.ontology.PDGJOB
    @@ -86,10 +96,12 @@ bioMoby.ontology.Simple_key_value_pair
    bioMoby.ontology.SimpleAnnotatedGIFImage
    bioMoby.ontology.SimpleAnnotatedJPEGImage
    +bioMoby.ontology.SINGER_ACCESSION
    bioMoby.ontology.Snp_allele
    bioMoby.ontology.Snp_genotype
    bioMoby.ontology.Study
    bioMoby.ontology.TargetP_result
    +bioMoby.ontology.TEST
    bioMoby.ontology.Testout
    bioMoby.ontology.Text_plain
    bioMoby.ontology.TextBase64
    @@ -100,11 +112,15 @@ bioMoby.ontology.TextXml
    bioMoby.ontology.Trait_Details
    bioMoby.ontology.Tree
    +bioMoby.ontology.TropGENE_ACCESSION
    +bioMoby.ontology.TropGENE_Diversity_Matrix
    +bioMoby.ontology.TropGENE_LOCUS
    bioMoby.ontology.VirtualSequence
    bioMoby.ontology.Wildcard_Query
    bioMoby.ontology.WU_BLAST_Text
    bioMoby.webservice.Dispatcher
    bioMoby.webservice.Invocators
    +bioMoby.webservice.TCBioMoby


    [show private | hide private] =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/trees.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/trees.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/trees.html 2004/12/09 14:41:35 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -51,6 +57,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -58,6 +68,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -71,6 +83,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -80,12 +93,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -102,10 +118,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -116,6 +134,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -124,6 +145,7 @@ @@ -131,6 +153,12 @@

    Class Hierarchy

    @@ -477,8 +558,19 @@
  • bioMoby.ontology.Snp_genotype.MobySnp_genotype: Description: Snp Genotypes Author: www.hapmap.org Contact: hapmap@hapmap.edu +
  • bioMoby.webservice.Dispatcher.AbstractDispatcher: +Subclass this one to create your own dispatcher class a Dispatcher +class must have a execute method +
  • bioMoby.webservice.Dispatcher.LockedIterator: Avoid concurrency on the iterator
  • bioMoby.webservice.Dispatcher.MultiThread: @@ -494,9 +586,13 @@ CGI script in Post multipart
  • bioMoby.webservice.Invocators.LocalInvocator: Invokes local command + -
  • bioMoby.webservice.Invocators.InvocatorError: -Error during an invocation of method + +
  • bioMoby.webservice.Invocators.QsubParameters: +Parameters for the qsub command
  • exceptions.Exception: Common base class for all exceptions. @@ -517,13 +615,19 @@
  • - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + From kawas at pub.open-bio.org Tue Dec 14 13:58:20 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 13:58:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141858.iBEIwKdZ009890@pub.open-bio.org> kawas Tue Dec 14 13:58:19 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv9852 Modified Files: Central.pm CommonSubs.pm CrossReference.pm OntologyServer.pm Log Message: hopefully fixed the cdata bug - eddie moby-live/Perl/MOBY Central.pm,1.142,1.143 CommonSubs.pm,1.54,1.55 CrossReference.pm,1.3,1.4 OntologyServer.pm,1.46,1.47 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.142 retrieving revision 1.143 diff -u -r1.142 -r1.143 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/11/18 17:41:14 1.142 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/12/14 18:58:19 1.143 @@ -392,7 +392,7 @@ my $obj = $Object->nodeName; return undef unless ( $obj eq 'registerObjectClass' ); my $term = &_nodeTextContent( $Object, "objectType" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my $authURI = &_nodeTextContent( $Object, "authURI" ); my $email = &_nodeTextContent( $Object, "contactEmail" ); my $clobber = &_nodeTextContent( $Object, "Clobber" ); @@ -696,7 +696,7 @@ my $type = &_nodeTextContent( $Object, "serviceType" ); my $email = &_nodeTextContent( $Object, "contactEmail" ); my $auth = &_nodeTextContent( $Object, "authURI" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my %relationships; my $x = $doc->getElementsByTagName( "Relationship" ); my $no_relationships = $x->size(); @@ -881,7 +881,7 @@ return undef unless ( $obj eq 'registerNamespace' ); my $type = &_nodeTextContent( $Object, "namespaceType" ); my $authURI = &_nodeTextContent( $Object, "authURI" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my $contact = &_nodeTextContent( $Object, "contactEmail" ); return ( $type, $authURI, $desc, $contact ); } @@ -1593,7 +1593,7 @@ &_nodeTextContent( $Object, "authoritativeService" ); my $URL = &_nodeTextContent( $Object, "URL" ); my $signatureURL = &_nodeTextContent( $Object, "signatureURL" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my $INPUTS = &_nodeRawContent( $Object, "Input" ); # returns array ref my $OUTPUTS = &_nodeRawContent( $Object, "Output" ); # returns array ref my $SECONDARIES = @@ -2388,6 +2388,9 @@ my $wsdl = &_getServiceWSDL( $SI, $InputXML, $OutputXML, $SecondaryXML ); if ( $wsdl ) { + if ($wsdl =~ /[^\]]+))\]\]>/) { + $wsdl = $1; + } $wsdls .= "\n"; } @@ -2519,6 +2522,9 @@ my %types = %{ $OS->retrieveAllServiceTypes() }; my $types = "\n"; while ( my ( $serv, $desc ) = each %types ) { + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $types .= "\n\n\n"; } @@ -2558,6 +2564,9 @@ while ( my ( $name, $authdesc ) = each %types ) { my $auth = $authdesc->[0]; my $desc = $authdesc->[1]; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $types .= "\n\n\n"; } @@ -2589,6 +2598,9 @@ my %types = %{ $OS->retrieveAllObjectTypes() }; my $obj = "\n"; while ( my ( $name, $desc ) = each %types ) { + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $obj .= "\n\n\n"; } @@ -2639,6 +2651,9 @@ ; # will return undef if this term does not exist, and does not look like an LSID return "" unless $def; my %def = %{ $OS->retrieveObject( node => $term ) }; + if ($def{description} =~ /[^\]]+))\]\]>/) { + $def{description}= $1; + } my $response; $response = " $def{objectType} @@ -2685,6 +2700,9 @@ my %types = %{ $OS->retrieveAllNamespaceTypes() }; my $ns = "\n"; while ( my ( $namespace, $desc ) = each %types ) { + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $ns .= "\n\n\n"; } @@ -3002,6 +3020,9 @@ $response .= "$cat\n"; $response .= "$type\n"; $response .= "$objectOUT\n"; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $response .= "\n"; $response .= "\n"; if ( $max_return ) { --$max_return; last unless $max_return } @@ -3035,6 +3056,9 @@ my $serviceName = $SI->servicename; my $AuthURI = $SI->authority_uri; my $desc = $SI->description; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } my $URL = $SI->url; my $IN = "NOT_YET_DEFINED_INPUTS"; my $OUT = "NOT_YET_DEFINED_OUTPUTS"; @@ -3075,6 +3099,9 @@ my $sth = $dbh->prepare( $sth{get_server_parameters} ); $sth->execute( $id ); my ( $Object, $sprintf, $in ) = $sth->fetchrow_array(); + if ($sprintf=~ /[^\]]+))\]\]>/) { + $sprintf = $1; + } return ""; } @@ -3197,7 +3224,30 @@ } return $content; } +sub _nodeCDATAContent{ + # will get text of **all** child $node from the given $DOM + # regardless of their depth!! + my ( $DOM, $node ) = @_; + $debug && &_LOG( "_nodeTextContent received DOM: ", + $DOM->toString, "\nsearching for node $node\n" ); + my $x = $DOM->getElementsByTagName( $node ); + return undef unless $x->get_node( 1 ); + my @child = $x->get_node( 1 )->childNodes; + my $content; + foreach ( @child ) { + $debug + && &_LOG( $_->nodeType, "\t", $_->toString, "\n" ); + + #next unless $_->nodeType == TEXT_NODE; + if ($_->toString =~ /[^\]]+))\]\]>/) { + $content .= $1; + } else { + $content .= $_->toString; + } + } + return $content; +} #Eddie - converted sub _nodeRawContent { @@ -3341,6 +3391,9 @@ $authoritative, $email, $signatureURL ) = $sth->fetchrow_array; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } #print "\n\nAFTER EXECUTE $category, $servicename, $service_type_uri, $authority_id, $desc, $authoritative\n\n"; $signatureURL ||= ""; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.54 retrieving revision 1.55 diff -u -r1.54 -r1.55 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/11/18 17:41:14 1.54 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/12/14 18:58:19 1.55 @@ -31,7 +31,7 @@ # [SIMPLE, $queryID, $simple] # the first element is an exported constant SIMPLE, COLLECTION, SECONDARY # the second element is the queryID (required for enumerating the responses) - # the third element is the XML::DOM for the Simple, Collection, or Parameter block + # the third element is the XML::LibXML for the Simple, Collection, or Parameter block my (@inputs)= genericServiceInputParser($data); # or fail properly with an empty response return SOAP::Data->type('base64' => responseHeader("my.authURI.com") . responseFooter()) unless (scalar(@inputs)); @@ -258,9 +258,9 @@ 1. COLLECTION|SIMPLE (i.e. constants 1, 2) 2. queryID 3. $data - the data takes several forms - a. $article XML::DOM node for Simples + a. $article XML::LibXML node for Simples ... - b. \@article XML:DOM nodes for Collections + b. \@article XML:LibXML nodes for Collections for example, the input message: @@ -303,7 +303,7 @@ my ( $message ) = @_; # get the incoming MOBY query XML my @inputs; # set empty response my @queries = - getInputs( $message ); # returns XML::DOM nodes ... + getInputs( $message ); # returns XML::LibXML nodes ... foreach my $query ( @queries ) { my $queryID = getInputID( $query ); # get the queryID attribute of the mobyData @@ -331,7 +331,7 @@ name : DO NOT USE!! function : to take a MOBY message and break the objects out of it. This is identical to the genericServiceInputParser method above, except that it returns the data as - Objects rather than XML::DOM nodes. This is an improvement! + Objects rather than XML::LibXML nodes. This is an improvement! usage : my @inputs = serviceInputParser($MOBY_mssage)); args : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message returns : @inputs - the structure of @inputs is a list of listrefs. @@ -346,7 +346,7 @@ my ( $message ) = @_; # get the incoming MOBY query XML my @inputs; # set empty response my @queries = - getInputs( $message ); # returns XML::DOM nodes ... + getInputs( $message ); # returns XML::LibXML nodes ... # mark, this doesn't work for complex services. We need to allow more than one input per invocation foreach my $query ( @queries ) { @@ -402,7 +402,7 @@ [SECONDARY, $DOM_cutoff] # $DOM_cutoff= block ] - Please see the XML::DOM pod documentation for information about how + Please see the XML::LibXML pod documentation for information about how to parse XML DOM objects. @@ -431,7 +431,7 @@ [SECONDARY, $DOM_cutoff] # $DOM_cutoff = Block ] - Please see the XML::DOM pod documentation for information about how + Please see the XML::LibXML pod documentation for information about how to parse XML DOM objects. @@ -441,7 +441,7 @@ my ( $message ) = @_; # get the incoming MOBY query XML my @inputs; # set empty response my @queries = - getInputs( $message ); # returns XML::DOM nodes ... + getInputs( $message ); # returns XML::LibXML nodes ... my %input_parameters; # $input_parameters{$queryID} = [ foreach my $query ( @queries ) { my $queryID = @@ -470,7 +470,7 @@ name : getArticles function : get the Simple/Collection/Parameter articles for a single mobyData usage : @articles = getArticles($XML) - args : raw XML or XML::DOM of a queryInput, mobyData, or queryResponse block (e.g. from getInputs) + args : raw XML or XML::LibXML of a queryInput, mobyData, or queryResponse block (e.g. from getInputs) returns : a list of listrefs; each listref is one component of the queryInput or mobyData block a single block may consist of one or more named or unnamed simple, collection, or parameter articles. @@ -508,7 +508,7 @@ sub getArticles { my ( $moby ) = @_; - unless ( ref( $moby ) =~ /XML\:\:DOM/ ) { + unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $moby ); $moby = $doc->getDocumentElement(); @@ -548,8 +548,8 @@ usage : my @ids = getSimpleArticleIDs("NCBI_gi", \@SimpleArticles); my @ids = getSimpleArticleIDs(\@SimpleArticles); args : $Namespace - (optional) a namespace stringfrom the MOBY namespace ontology, or undef if you don't care - \@Simples - (required) a listref of Simple XML::DOM nodes - i.e. the XML::DOM representing an XML structure like this: + \@Simples - (required) a listref of Simple XML::LibXML nodes + i.e. the XML::LibXML representing an XML structure like this: @@ -643,8 +643,8 @@ name : getSimpleArticleNamespaceURI function : to get the namespace of a simple article usage : my $ns = getSimpleArticleNamespaceURI($SimpleArticle); - args : $Simple - (required) a single XML::DOM node representing a Simple Article - i.e. the XML::DOM representing an XML structure like this: + args : $Simple - (required) a single XML::LibXML node representing a Simple Article + i.e. the XML::LibXML representing an XML structure like this: @@ -700,7 +700,7 @@ my ( $data, $articleName, $qID ) = @_; # articleName optional $qID = &_getQueryID( $qID ) if ref( $qID ) =~ - /XML::DOM/; # in case they send the DOM instead of the ID + /XML::LibXML/; # in case they send the DOM instead of the ID $data ||= ''; # initialize to avoid uninit value errors $qID ||= ""; $articleName ||= ""; @@ -726,7 +726,7 @@ #Eddie - converted sub _getQueryID { my ( $query ) = @_; - unless ( ref( $query ) =~ /XML\:\:DOM/ ) { + unless ( ref( $query ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $query ); $query = $doc->getDocumentElement(); @@ -849,10 +849,10 @@ =head2 getInputs name : getInputs - function : get the mobyData block(s) as XML::DOM nodes + function : get the mobyData block(s) as XML::LibXML nodes usage : @queryInputs = getInputArticles($XML) - args : the raw XML of a query, or an XML::DOM document - returns : a list of XML::DOM::Node's, each is a queryInput or mobyData block. + args : the raw XML of a query, or an XML::LibXML document + returns : a list of XML::LibXML::Node's, each is a queryInput or mobyData block. Note : Remember that these blocks are enumerated! This is what you pass as the third argument to the simpleResponse or collectionResponse subroutine to associate the numbered input to the numbered response @@ -863,7 +863,7 @@ sub getInputs { my ( $XML ) = @_; my $moby; - unless ( ref( $XML ) =~ /XML\:\:DOM/ ) { + unless ( ref( $XML ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $XML ); $moby = $doc->getDocumentElement(); @@ -887,7 +887,7 @@ name : getInputID function : get the value of the queryID element usage : @queryInputs = getInputID($XML) - args : the raw XML or XML::DOM of a queryInput or mobyData block (e.g. from getInputs) + args : the raw XML or XML::LibXML of a queryInput or mobyData block (e.g. from getInputs) returns : integer, or '' Note : Inputs and Responses are coordinately enumerated! The integer you get here is what you @@ -898,7 +898,7 @@ sub getInputID { my ( $XML ) = @_; - unless ( ref( $XML ) =~ /XML\:\:DOM/ ) { + unless ( ref( $XML ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $XML ); $XML = $doc->getDocumentElement(); @@ -918,7 +918,7 @@ or queryResponse node, rethrning them as SimpleArticle, SecondaryArticle, or ServiceInstance objects usage : @articles = getArticles($XML) - args : raw XML or XML::DOM of a moby:mobyData block + args : raw XML or XML::LibXML of a moby:mobyData block returns : =cut @@ -926,7 +926,7 @@ #Eddie - converted sub getArticlesAsObjects { my ( $moby ) = @_; - unless ( ref( $moby ) =~ /XML\:\:DOM/ ) { + unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $moby ); $moby = $doc->getDocumentElement(); @@ -964,14 +964,14 @@ name : getCollectedSimples function : get the Simple articles collected in a moby:Collection block usage : @Simples = getCollectedSimples($XML) - args : raw XML or XML::DOM of a moby:Collection block - returns : a list of XML::DOM nodes, each of which is a moby:Simple block + args : raw XML or XML::LibXML of a moby:Collection block + returns : a list of XML::LibXML nodes, each of which is a moby:Simple block =cut sub getCollectedSimples { my ( $moby ) = @_; - unless ( ref( $moby ) =~ /XML\:\:DOM/ ) { + unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $moby ); $moby = $doc->getDocumentElement(); @@ -997,7 +997,7 @@ args : the raw XML of a moby:MOBY query returns : a list of listrefs, each listref is the input to a single query. Remember that the input to a single query may be one or more Simple - and/or Collection articles. These are provided as XML::DOM nodes. + and/or Collection articles. These are provided as XML::LibXML nodes. i.e.: @queries = ([$SIMPLE_DOM_NODE], [$SIMPLE_DOM_NODE2]) or : @queries = ([$COLLECTION_DOM_NODE], [$COLLECTION_DOM_NODE2]) @@ -1024,7 +1024,7 @@ #Eddie - converted sub getInputArticles { my ( $moby ) = @_; - unless ( ref( $moby ) =~ /XML\:\:DOM/ ) { + unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $moby ); $moby = $doc->getDocumentElement(); @@ -1054,7 +1054,7 @@ name : isSimpleArticle function : tests XML (text) or an XML DOM node to see if it represents a Simple article usage : if (isSimpleArticle($node)){do something to it} - input : an XML::DOM node, an XML::DOM::Document or straight XML + input : an XML::LibXML node, an XML::LibXML::Document or straight XML returns : boolean =cut @@ -1062,7 +1062,7 @@ #Eddie - converted sub isSimpleArticle { my ( $DOM ) = @_; - unless ( ref( $DOM ) =~ /XML\:\:DOM/ ) { + unless ( ref( $DOM ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc; eval { $doc = $parser->parse_string( $DOM ); }; @@ -1079,7 +1079,7 @@ name : isCollectionArticle function : tests XML (text) or an XML DOM node to see if it represents a Collection article usage : if (isCollectionArticle($node)){do something to it} - input : an XML::DOM node, an XML::DOM::Document or straight XML + input : an XML::LibXML node, an XML::LibXML::Document or straight XML returns : boolean =cut @@ -1087,7 +1087,7 @@ #Eddie - converted sub isCollectionArticle { my ( $DOM ) = @_; - unless ( ref( $DOM ) =~ /XML\:\:DOM/ ) { + unless ( ref( $DOM ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc; eval { $doc = $parser->parse_string( $DOM ); }; @@ -1104,7 +1104,7 @@ name : isSecondaryArticle function : tests XML (text) or an XML DOM node to see if it represents a Secondary article usage : if (isSecondaryArticle($node)){do something to it} - input : an XML::DOM node, an XML::DOM::Document or straight XML + input : an XML::LibXML node, an XML::LibXML::Document or straight XML returns : boolean =cut @@ -1112,7 +1112,7 @@ #Eddie - converted sub isSecondaryArticle { my ( $DOM ) = @_; - unless ( ref( $DOM ) =~ /XML\:\:DOM/ ) { + unless ( ref( $DOM ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc; eval { $doc = $parser->parse( _string $DOM); }; @@ -1138,7 +1138,7 @@ sub extractRawContent { my ( $article ) = @_; return "" unless $article; - return "" unless ref( $article ) =~ /XML::DOM/; + return "" unless ref( $article ) =~ /XML::LibXML/; my $response; foreach ( $article->childNodes ) { $response .= $_->toString; @@ -1154,7 +1154,7 @@ or get the value of a Parameter element. usage : @strings = getNodeContentWithArticle($node, $tagname, $articleName) args : (in order) - $node - an XML::DOM node, or straight XML. It may even + $node - an XML::LibXML node, or straight XML. It may even be the entire mobyData block. $tagname - the tagname (effectively from the Object type ontology), or "Parameter" if you are trying to get secondaries @@ -1243,7 +1243,7 @@ # carriage returns, as these might be meaningful! my ( $node, $element, $articleName ) = @_; my @contents; - return () unless ref( $node ) =~ /XML::DOM/; + return () unless ref( $node ) =~ /XML::LibXML/; return () unless $element; return () unless $articleName; my $nodes = $node->getElementsByTagName( $element ); @@ -1355,9 +1355,9 @@ function : get the DOM nodes corresponding to individual Simple or Collection outputs from a MOBY Response usage : ($collections, $simples) = getResponseArticles($node) - args : $node - either raw XML or an XML::DOM::Document to be searched - returns : an array-ref of Collection article XML::DOM::Node's - an array-ref of Simple article XML::DOM::Node's + args : $node - either raw XML or an XML::LibXML::Document to be searched + returns : an array-ref of Collection article XML::LibXML::Node's + an array-ref of Simple article XML::LibXML::Node's =cut @@ -1369,7 +1369,7 @@ my ( $result ) = @_; return ( [], [] ) unless $result; my $moby; - unless ( ref( $result ) =~ /XML\:\:DOM/ ) { + unless ( ref( $result ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $result ); $moby = $doc->getDocumentElement(); @@ -1426,7 +1426,7 @@ name : getServiceNotes function : to get the content of the Service Notes block of the MOBY message usage : getServiceNotes($message) - args : $message is either the XML::DOM of the MOBY message, or plain XML + args : $message is either the XML::LibXML of the MOBY message, or plain XML returns : String content of the ServiceNotes block of the MOBY Message =cut @@ -1436,7 +1436,7 @@ my ( $result ) = @_; return ( "" ) unless $result; my $moby; - unless ( ref( $result ) =~ /XML\:\:DOM/ ) { + unless ( ref( $result ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $result ); $moby = $doc->getDocumentElement(); @@ -1470,7 +1470,7 @@ usage : @xrefs = getCrossReferences($XML) args : $XML is either a SIMPLE article (...) or an object (the payload of a Simple article), and - may be either raw XML or an XML::DOM node. + may be either raw XML or an XML::LibXML node. returns : an array of MOBY::CrossReference objects example : @@ -1492,7 +1492,7 @@ #Eddie - converted sub getCrossReferences { my ( $XML ) = @_; - unless ( ref( $XML ) =~ /XML::DOM/ ) { + unless ( ref( $XML ) =~ /XML::LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $XML ); $XML = $doc->getDocumentElement(); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CrossReference.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.46 retrieving revision 1.47 diff -u -r1.46 -r1.47 From kawas at pub.open-bio.org Tue Dec 14 13:58:20 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 13:58:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141858.iBEIwK9J009921@pub.open-bio.org> kawas Tue Dec 14 13:58:20 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv9852/Client Modified Files: Central.pm OntologyServer.pm Registration.pm Service.pm Log Message: hopefully fixed the cdata bug - eddie moby-live/Perl/MOBY/Client Central.pm,1.81,1.82 OntologyServer.pm,1.7,1.8 Registration.pm,1.7,1.8 Service.pm,1.13,1.14 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.81 retrieving revision 1.82 diff -u -r1.81 -r1.82 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/11/18 17:41:15 1.81 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/14 18:58:20 1.82 @@ -3,6 +3,7 @@ use SOAP::Lite; #use SOAP::Lite + trace; # for debugging + use strict; use Carp; use XML::LibXML; @@ -376,6 +377,9 @@ $term ||= ""; my $desc = $a{'description'}; $desc ||= ""; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } my $contactEmail = $a{'contactEmail'}; $contactEmail ||= ""; my $authURI = $a{'authURI'}; @@ -504,7 +508,7 @@ my $obj = $Object->nodeName; return undef unless ( $obj eq 'retrieveObjectDefinition' ); my $term = &_nodeTextContent( $Object, "objectType" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my $authURI = &_nodeTextContent( $Object, "authURI" ); my $email = &_nodeTextContent( $Object, "contactEmail" ); my %att_value; @@ -565,6 +569,9 @@ my $type = $a{'serviceType'}; $type ||= ""; my $desc = $a{'description'}; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $desc ||= ""; my $email = $a{'contactEmail'}; $email ||= ""; @@ -645,6 +652,9 @@ my $authURI = $a{'authURI'}; $authURI ||= ""; my $desc = $a{'description'}; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $desc ||= ""; my $contact = $a{'contactEmail'}; $contact ||= ""; @@ -758,6 +768,9 @@ $URL ||= ""; my $desc = $a{description}; $desc ||= ""; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } my $signatureURL = $a{signatureURL}; $signatureURL ||= ""; my $Category = lc( $a{category} ); @@ -1197,7 +1210,11 @@ foreach ( @child ) { $debug && &_LOG( getNodeTypeName($_), "\t", $_->toString, "\n" ); if ( $_->nodeType == TEXT_NODE ) { - $content .= $_->nodeValue; #else try $_->textContent + if ($_->nodeValue=~ /[^\]]+))\]\]>/) { + $content .= $1; + } else { + $content .= $_->nodeValue; #else try $_->textContent + } } else { $content .= $_->toString; } @@ -1305,6 +1322,9 @@ $types->get_node( $x )->getElementsByTagName( 'Description' ) ) { $desc = $elem->firstChild->toString; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } } $servicetypes{$type} = $desc; } @@ -1344,6 +1364,9 @@ $obnames->get_node( $x )->getElementsByTagName( 'Description' ) ) { $desc = $elem->firstChild->toString; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } } $objectnames{$name} = $desc; } @@ -1383,6 +1406,9 @@ { $desc = $elem->firstChild; $desc = $desc ? $desc->toString : ""; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } } $namespaces{$ns} = $desc; } @@ -1429,6 +1455,9 @@ $objects->get_node( $x )->getElementsByTagName( 'Schema' ) ) { $desc = $elem->firstChild->nodeValue; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } } $objects{$name} = $desc; } @@ -1628,7 +1657,7 @@ my $URL = &_nodeTextContent( $Service, 'URL' ); #my $Output = &_nodeTextContent($Service, 'outputObject'); - my $Description = &_nodeTextContent( $Service, 'Description' ); + my $Description = &_nodeCDATAContent( $Service, 'Description' ); my $cat = &_nodeTextContent( $Service, 'Category' ); my @INPUTS; my @OUTPUTS; @@ -1793,7 +1822,7 @@ return undef unless ( $obj eq 'MOBYRegistration' ); my $id = &_nodeTextContent( $Object, 'id' ); my $success = &_nodeTextContent( $Object, 'success' ); - my $message = &_nodeTextContent( $Object, 'message' ); + my $message = &_nodeCDATAContent( $Object, 'message' ); my $RDF = &_nodeRawContent( $Object, 'RDF' ); my $reg = MOBY::Client::Registration->new( success => $success, @@ -1814,7 +1843,25 @@ ); return $reg; } - +sub _nodeCDATAContent { + # will get text of **all** child $node from the given $DOM + # regardless of their depth!! + my ( $DOM, $node ) = @_; + my $x = $DOM->getElementsByTagName( $node ); + unless ( $x->get_node( 1 ) ) { return } + my @child = $x->get_node( 1 )->childNodes; + my $content; + foreach ( @child ) { + #print getNodeTypeName($_), "\t", $_->toString,"\n"; + next unless $_->nodeType == TEXT_NODE; + $content = $_->toString; + if ($content =~ /[^\]]+))\]\]>/) { + $content = $1; + return $content; + } + } + return $content; +} sub _nodeTextContent { # will get text of **all** child $node from the given $DOM @@ -1825,7 +1872,6 @@ my @child = $x->get_node( 1 )->childNodes; my $content; foreach ( @child ) { - #print getNodeTypeName($_), "\t", $_->toString,"\n"; next unless $_->nodeType == TEXT_NODE; $content = $_->toString; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 From kawas at pub.open-bio.org Tue Dec 14 14:10:19 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:10:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141910.iBEJAJcD010047@pub.open-bio.org> kawas Tue Dec 14 14:10:18 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv10008 Modified Files: Central.pm CommonSubs.pm CrossReference.pm OntologyServer.pm Log Message: hopefully fixed the cdata bug - eddie (part 2 - i hate cvs) moby-live/Perl/MOBY Central.pm,1.143,1.144 CommonSubs.pm,1.55,1.56 CrossReference.pm,1.4,1.5 OntologyServer.pm,1.47,1.48 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.143 retrieving revision 1.144 diff -u -r1.143 -r1.144 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.55 retrieving revision 1.56 diff -u -r1.55 -r1.56 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CrossReference.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.47 retrieving revision 1.48 diff -u -r1.47 -r1.48 From kawas at pub.open-bio.org Tue Dec 14 14:10:19 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:10:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141910.iBEJAJdX010079@pub.open-bio.org> kawas Tue Dec 14 14:10:19 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv10008/Client Modified Files: Central.pm OntologyServer.pm Registration.pm Service.pm Log Message: hopefully fixed the cdata bug - eddie (part 2 - i hate cvs) moby-live/Perl/MOBY/Client Central.pm,1.82,1.83 OntologyServer.pm,1.8,1.9 Registration.pm,1.8,1.9 Service.pm,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.82 retrieving revision 1.83 diff -u -r1.82 -r1.83 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXJw010917@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY added to the repository moby-live/Perl/MOBY/MOBY - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXdk010935@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/Adaptor Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor added to the repository moby-live/Perl/MOBY/MOBY/Adaptor - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXSU010953@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/Adaptor/moby Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby added to the repository moby-live/Perl/MOBY/MOBY/Adaptor/moby - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXol011011@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/RDF Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF added to the repository moby-live/Perl/MOBY/MOBY/RDF - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXjn010972@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/Adaptor/moby/queryapi Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi added to the repository moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiX7a010993@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/Client Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client added to the repository moby-live/Perl/MOBY/MOBY/Client - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiX1t011034@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/lsid Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid added to the repository moby-live/Perl/MOBY/MOBY/lsid - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:34 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiYiN011055@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/lsid/authority Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority added to the repository moby-live/Perl/MOBY/MOBY/lsid/authority - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 14:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJikC3011162@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11077 Added Files: MobyXMLRetriever.pl myScript.pl Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY MobyXMLRetriever.pl,NONE,1.1 myScript.pl,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 14:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiklW011100@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/Client Added Files: Central.pm CollectionArticle.pm Registration.pm SecondaryArticle.pm OntologyServer.pm ServiceInstance.pm SimpleArticle.pm SimpleInput.pm Service.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/Client Central.pm,NONE,1.1 CollectionArticle.pm,NONE,1.1 Registration.pm,NONE,1.1 SecondaryArticle.pm,NONE,1.1 OntologyServer.pm,NONE,1.1 ServiceInstance.pm,NONE,1.1 SimpleArticle.pm,NONE,1.1 SimpleInput.pm,NONE,1.1 Service.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 14:44:47 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiljX011182@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/Adaptor/moby Added Files: queryapi.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/Adaptor/moby queryapi.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 14:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJikZH011132@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY Added Files: service_type.pm collection_input.pm CommonSubs.pm Central.pm MobyXMLConstants.pm OntologyServer.pm secondary_input.pm simple_output.pm service_instance.pm CrossReference.pm collection_output.pm mysql.pm dbConfig.pm central_db_connection.pm Config.pm authority.pm simple_input.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY service_type.pm,NONE,1.1 collection_input.pm,NONE,1.1 CommonSubs.pm,NONE,1.1 Central.pm,NONE,1.1 MobyXMLConstants.pm,NONE,1.1 OntologyServer.pm,NONE,1.1 secondary_input.pm,NONE,1.1 simple_output.pm,NONE,1.1 service_instance.pm,NONE,1.1 CrossReference.pm,NONE,1.1 collection_output.pm,NONE,1.1 mysql.pm,NONE,1.1 dbConfig.pm,NONE,1.1 central_db_connection.pm,NONE,1.1 Config.pm,NONE,1.1 authority.pm,NONE,1.1 simple_input.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 14:44:47 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJilk8011199@pub.open-bio.org> kawas Tue Dec 14 14:44:47 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/Adaptor/moby/queryapi Added Files: mysql.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi mysql.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 14:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJikmA011115@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/lsid/authority Added Files: ClassResolver.pm authority.pl NamespaceResolver.pm RDFConfigure.pm dbConfigure.pm.template dbConnect.pm ServiceInstanceResolver.pm Error.pm ServiceResolver.pm PredicateResolver.pm lsid_resolver.kpf metadata.pl RelationshipResolver.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/lsid/authority ClassResolver.pm,NONE,1.1 authority.pl,NONE,1.1 NamespaceResolver.pm,NONE,1.1 RDFConfigure.pm,NONE,1.1 dbConfigure.pm.template,NONE,1.1 dbConnect.pm,NONE,1.1 ServiceInstanceResolver.pm,NONE,1.1 Error.pm,NONE,1.1 ServiceResolver.pm,NONE,1.1 PredicateResolver.pm,NONE,1.1 lsid_resolver.kpf,NONE,1.1 metadata.pl,NONE,1.1 RelationshipResolver.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 14:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJikRH011147@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/RDF Added Files: ServiceInstanceRDF.pm InOutArticlesRDF.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/RDF ServiceInstanceRDF.pm,NONE,1.1 InOutArticlesRDF.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 15:36:49 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:36:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142036.iBEKanI8011390@pub.open-bio.org> kawas Tue Dec 14 15:36:49 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11354/MOBY Modified Files: Central.pm Log Message: fixed typo - get_Node -> get_node moby-live/Perl/MOBY/MOBY Central.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Central.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/MOBY/Central.pm 2004/12/14 19:44:46 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/MOBY/Central.pm 2004/12/14 20:36:48 1.2 @@ -2431,7 +2431,7 @@ my $SECONDARY = $doc->getElementsByTagName( "Output" ); my $SecondaryXML = ""; if ( $SECONDARY->get_node( 1 ) ) { - $SecondaryXML = $SECONDARY->get_Node( 1 )->toString; + $SecondaryXML = $SECONDARY->get_node( 1 )->toString; } return ( $authURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML ); } From kawas at pub.open-bio.org Tue Dec 14 15:47:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl4Hs011664@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv11595/Client Modified Files: Central.pm OntologyServer.pm Registration.pm Service.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/Client Central.pm,1.83,1.84 OntologyServer.pm,1.9,1.10 Registration.pm,1.9,1.10 Service.pm,1.15,1.16 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.83 retrieving revision 1.84 diff -u -r1.83 -r1.84 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 From kawas at pub.open-bio.org Tue Dec 14 15:47:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl477011632@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11595 Modified Files: Central.pm CommonSubs.pm CrossReference.pm OntologyServer.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY Central.pm,1.144,1.145 CommonSubs.pm,1.56,1.57 CrossReference.pm,1.5,1.6 OntologyServer.pm,1.48,1.49 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.144 retrieving revision 1.145 diff -u -r1.144 -r1.145 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.56 retrieving revision 1.57 diff -u -r1.56 -r1.57 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CrossReference.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.48 retrieving revision 1.49 diff -u -r1.48 -r1.49 From kawas at pub.open-bio.org Tue Dec 14 15:47:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl43b011717@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/Adaptor/moby Removed Files: queryapi.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/Adaptor/moby queryapi.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/RCS/queryapi.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 15:47:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl4L9011701@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY Removed Files: Central.pm CommonSubs.pm Config.pm CrossReference.pm MobyXMLConstants.pm OntologyServer.pm authority.pm central_db_connection.pm collection_input.pm collection_output.pm dbConfig.pm mysql.pm secondary_input.pm service_instance.pm service_type.pm simple_input.pm simple_output.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY Central.pm,1.2,NONE CommonSubs.pm,1.1,NONE Config.pm,1.1,NONE CrossReference.pm,1.1,NONE MobyXMLConstants.pm,1.1,NONE OntologyServer.pm,1.1,NONE authority.pm,1.1,NONE central_db_connection.pm,1.1,NONE collection_input.pm,1.1,NONE collection_output.pm,1.1,NONE dbConfig.pm,1.1,NONE mysql.pm,1.1,NONE secondary_input.pm,1.1,NONE service_instance.pm,1.1,NONE service_type.pm,1.1,NONE simple_input.pm,1.1,NONE simple_output.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/Central.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/CommonSubs.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/Config.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/CrossReference.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/MobyXMLConstants.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/OntologyServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/authority.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/central_db_connection.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/collection_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/collection_output.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/dbConfig.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/mysql.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/secondary_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/service_instance.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/service_type.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/simple_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/simple_output.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 15:47:05 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl5i8011815@pub.open-bio.org> kawas Tue Dec 14 15:47:05 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/lsid/authority Removed Files: ClassResolver.pm Error.pm NamespaceResolver.pm PredicateResolver.pm RDFConfigure.pm RelationshipResolver.pm ServiceInstanceResolver.pm ServiceResolver.pm authority.pl dbConfigure.pm.template dbConnect.pm lsid_resolver.kpf metadata.pl Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/lsid/authority ClassResolver.pm,1.1,NONE Error.pm,1.1,NONE NamespaceResolver.pm,1.1,NONE PredicateResolver.pm,1.1,NONE RDFConfigure.pm,1.1,NONE RelationshipResolver.pm,1.1,NONE ServiceInstanceResolver.pm,1.1,NONE ServiceResolver.pm,1.1,NONE authority.pl,1.1,NONE dbConfigure.pm.template,1.1,NONE dbConnect.pm,1.1,NONE lsid_resolver.kpf,1.1,NONE metadata.pl,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/ClassResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/Error.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/NamespaceResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/PredicateResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/RDFConfigure.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/RelationshipResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/ServiceInstanceResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/ServiceResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/authority.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/dbConfigure.pm.template,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/dbConnect.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/lsid_resolver.kpf,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/metadata.pl,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 15:47:05 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl54D011734@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/Adaptor/moby/queryapi Removed Files: mysql.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi mysql.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi/RCS/mysql.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 15:47:05 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl5HZ011764@pub.open-bio.org> kawas Tue Dec 14 15:47:05 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/Client Removed Files: Central.pm CollectionArticle.pm OntologyServer.pm Registration.pm SecondaryArticle.pm Service.pm ServiceInstance.pm SimpleArticle.pm SimpleInput.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/Client Central.pm,1.1,NONE CollectionArticle.pm,1.1,NONE OntologyServer.pm,1.1,NONE Registration.pm,1.1,NONE SecondaryArticle.pm,1.1,NONE Service.pm,1.1,NONE ServiceInstance.pm,1.1,NONE SimpleArticle.pm,1.1,NONE SimpleInput.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/Central.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/CollectionArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/OntologyServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/Registration.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/SecondaryArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/Service.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/ServiceInstance.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/SimpleArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/SimpleInput.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 15:47:05 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl5td011783@pub.open-bio.org> kawas Tue Dec 14 15:47:05 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/RDF Removed Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/RDF InOutArticlesRDF.pm,1.1,NONE ServiceInstanceRDF.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/InOutArticlesRDF.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/ServiceInstanceRDF.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 15:55:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:55:11 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142055.iBEKtBYf011949@pub.open-bio.org> kawas Tue Dec 14 15:55:11 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11923 Modified Files: Central.pm Log Message: fix type in get_node moby-live/Perl/MOBY Central.pm,1.145,1.146 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.145 retrieving revision 1.146 diff -u -r1.145 -r1.146 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/12/14 20:47:04 1.145 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/12/14 20:55:11 1.146 @@ -2431,7 +2431,7 @@ my $SECONDARY = $doc->getElementsByTagName( "Output" ); my $SecondaryXML = ""; if ( $SECONDARY->get_node( 1 ) ) { - $SecondaryXML = $SECONDARY->get_Node( 1 )->toString; + $SecondaryXML = $SECONDARY->get_node( 1 )->toString; } return ( $authURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML ); } From kawas at pub.open-bio.org Tue Dec 14 17:31:30 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 17:31:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142231.iBEMVUnp012494@pub.open-bio.org> kawas Tue Dec 14 17:31:30 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv12457/MOBY/Client Modified Files: Central.pm CollectionArticle.pm SimpleArticle.pm SecondaryArticle.pm Log Message: updated the check for dom to check for libxml moby-live/Perl/MOBY/Client Central.pm,1.84,1.85 CollectionArticle.pm,1.10,1.11 SimpleArticle.pm,1.6,1.7 SecondaryArticle.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.84 retrieving revision 1.85 diff -u -r1.84 -r1.85 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/14 20:47:04 1.84 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/14 22:31:30 1.85 @@ -847,6 +847,7 @@ $message .= "\n"; } my ( $type, $Namespaces ) = @{$objectdef}; + $type ||=""; $message .= "$type\n"; unless ( ref( $Namespaces ) =~ /array/i ) { return $self->errorRegXML( =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2004/11/18 17:41:16 1.10 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2004/12/14 22:31:30 1.11 @@ -255,7 +255,7 @@ } if ( $self->XML && ref( $self->XML ) ) { return 0; - } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /dom/i ) ) { + } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /libxml/i ) ) { return 0; } $self->createFromXML if ( $self->XML ); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm 2004/11/18 17:41:16 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm 2004/12/14 22:31:30 1.7 @@ -225,7 +225,7 @@ } if ( $self->XML && ref( $self->XML ) ) { return 0; - } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /dom/i ) ) { + } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /libxml/i ) ) { return 0; } $self->createFromXML if ( $self->XML ); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/11/18 17:41:16 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/12/14 22:31:30 1.6 @@ -201,7 +201,7 @@ $self->{enum} = [] unless $self->enum; if ( $self->XML && ref( $self->XML ) ) { return 0; - } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /dom/i ) ) { + } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /libxml/i ) ) { return 0; } $self->createFromXML if ( $self->XML ); From kawas at pub.open-bio.org Tue Dec 14 23:13:47 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 23:13:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412150413.iBF4DlbY013910@pub.open-bio.org> kawas Tue Dec 14 23:13:47 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv13883/MOBY/Client Modified Files: Central.pm Log Message: checked for CDATA and tried to excise it - eddie moby-live/Perl/MOBY/Client Central.pm,1.85,1.86 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.85 retrieving revision 1.86 diff -u -r1.85 -r1.86 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/14 22:31:30 1.85 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/15 04:13:47 1.86 @@ -3,7 +3,6 @@ use SOAP::Lite; #use SOAP::Lite + trace; # for debugging - use strict; use Carp; use XML::LibXML; @@ -377,7 +376,7 @@ $term ||= ""; my $desc = $a{'description'}; $desc ||= ""; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } my $contactEmail = $a{'contactEmail'}; @@ -507,15 +506,17 @@ my $Object = $doc->getDocumentElement(); my $obj = $Object->nodeName; return undef unless ( $obj eq 'retrieveObjectDefinition' ); - my $term = &_nodeTextContent( $Object, "objectType" ); - my $desc = &_nodeCDATAContent( $Object, "Description" ); + my $term = &_nodeTextContent( $Object, "objectType" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); + if ( $desc =~ /[^\]]+))\]\]>/ ) { + $desc = $1; + } my $authURI = &_nodeTextContent( $Object, "authURI" ); my $email = &_nodeTextContent( $Object, "contactEmail" ); my %att_value; my %relationships; my $x = $doc->getElementsByTagName( "Relationship" ); my $no_relationships = $x->size(); - for ( my $n = 1 ; $n <= $no_relationships ; ++$n ) { #get_node starts at one my $relationshipType = $x->get_node( $n )->getAttributeNode( 'relationshipType' ) @@ -569,7 +570,7 @@ my $type = $a{'serviceType'}; $type ||= ""; my $desc = $a{'description'}; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } $desc ||= ""; @@ -652,7 +653,7 @@ my $authURI = $a{'authURI'}; $authURI ||= ""; my $desc = $a{'description'}; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } $desc ||= ""; @@ -768,7 +769,8 @@ $URL ||= ""; my $desc = $a{description}; $desc ||= ""; - if ($desc =~ /[^\]]+))\]\]>/) { + + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } my $signatureURL = $a{signatureURL}; @@ -847,7 +849,7 @@ $message .= "\n"; } my ( $type, $Namespaces ) = @{$objectdef}; - $type ||=""; + $type ||= ""; $message .= "$type\n"; unless ( ref( $Namespaces ) =~ /array/i ) { return $self->errorRegXML( @@ -1209,18 +1211,16 @@ my @child = $de->childNodes; my $content; foreach ( @child ) { - $debug && &_LOG( getNodeTypeName($_), "\t", $_->toString, "\n" ); + $debug && &_LOG( getNodeTypeName( $_ ), "\t", $_->toString, "\n" ); if ( $_->nodeType == TEXT_NODE ) { - if ($_->nodeValue=~ /[^\]]+))\]\]>/) { - $content .= $1; - } else { - $content .= $_->nodeValue; #else try $_->textContent - } + $content .= $_->nodeValue; #else try $_->textContent } else { $content .= $_->toString; } } $content =~ s/^\n//gs; + $content =~ s/[^\]]+))\]\]>/$1/gs; + return $content; } @@ -1323,10 +1323,11 @@ $types->get_node( $x )->getElementsByTagName( 'Description' ) ) { $desc = $elem->firstChild->toString; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } } + $desc =~ s/[^\]]+))\]\]>/$1/gs; $servicetypes{$type} = $desc; } return \%servicetypes; @@ -1365,10 +1366,11 @@ $obnames->get_node( $x )->getElementsByTagName( 'Description' ) ) { $desc = $elem->firstChild->toString; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } } + $desc =~ s/[^\]]+))\]\]>/$1/gs; $objectnames{$name} = $desc; } return \%objectnames; @@ -1407,10 +1409,11 @@ { $desc = $elem->firstChild; $desc = $desc ? $desc->toString : ""; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } } + $desc =~ s/[^\]]+))\]\]>/$1/gs; $namespaces{$ns} = $desc; } return \%namespaces; @@ -1456,10 +1459,11 @@ $objects->get_node( $x )->getElementsByTagName( 'Schema' ) ) { $desc = $elem->firstChild->nodeValue; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } } + $desc =~ s/[^\]]+))\]\]>/$1/gs; $objects{$name} = $desc; } return \%objects; @@ -1659,7 +1663,8 @@ #my $Output = &_nodeTextContent($Service, 'outputObject'); my $Description = &_nodeCDATAContent( $Service, 'Description' ); - my $cat = &_nodeTextContent( $Service, 'Category' ); + $Description =~ s/[^\]]+))\]\]>/$1/gs; + my $cat = &_nodeTextContent( $Service, 'Category' ); my @INPUTS; my @OUTPUTS; foreach my $inout ( "Input", "Output" ) { @@ -1821,10 +1826,10 @@ my $Object = $doc->getDocumentElement(); my $obj = $Object->nodeName; return undef unless ( $obj eq 'MOBYRegistration' ); - my $id = &_nodeTextContent( $Object, 'id' ); - my $success = &_nodeTextContent( $Object, 'success' ); + my $id = &_nodeTextContent( $Object, 'id' ); + my $success = &_nodeTextContent( $Object, 'success' ); my $message = &_nodeCDATAContent( $Object, 'message' ); - my $RDF = &_nodeRawContent( $Object, 'RDF' ); + my $RDF = &_nodeRawContent( $Object, 'RDF' ); my $reg = MOBY::Client::Registration->new( success => $success, message => $message, @@ -1844,7 +1849,9 @@ ); return $reg; } + sub _nodeCDATAContent { + # will get text of **all** child $node from the given $DOM # regardless of their depth!! my ( $DOM, $node ) = @_; @@ -1853,16 +1860,15 @@ my @child = $x->get_node( 1 )->childNodes; my $content; foreach ( @child ) { + #print getNodeTypeName($_), "\t", $_->toString,"\n"; next unless $_->nodeType == TEXT_NODE; $content = $_->toString; - if ($content =~ /[^\]]+))\]\]>/) { - $content = $1; - return $content; - } } + $content =~ s/[^\]]+))\]\]>/$1/gs; return $content; } + sub _nodeTextContent { # will get text of **all** child $node from the given $DOM @@ -1873,6 +1879,7 @@ my @child = $x->get_node( 1 )->childNodes; my $content; foreach ( @child ) { + #print getNodeTypeName($_), "\t", $_->toString,"\n"; next unless $_->nodeType == TEXT_NODE; $content = $_->toString; From kawas at pub.open-bio.org Wed Dec 15 12:49:44 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 15 Dec 2004 12:49:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412151749.iBFHniXc016480@pub.open-bio.org> kawas Wed Dec 15 12:49:44 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv16454/MOBY Modified Files: CommonSubs.pm Log Message: fixed typo -> getNodeValue :-> nodeValue - eddie moby-live/Perl/MOBY CommonSubs.pm,1.57,1.58 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.57 retrieving revision 1.58 diff -u -r1.57 -r1.58 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/12/14 20:47:04 1.57 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/12/15 17:49:44 1.58 @@ -1456,7 +1456,7 @@ foreach my $response_component ( $resp->childNodes ) { # $content .= $response_component->toString; - $content .= $response_component->getNodeValue + $content .= $response_component->nodeValue if ( $response_component->nodeType == TEXT_NODE ); } } From mwilkinson at pub.open-bio.org Wed Dec 15 14:37:12 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 15 Dec 2004 14:37:12 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412151937.iBFJbCc5016846@pub.open-bio.org> mwilkinson Wed Dec 15 14:37:12 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv16827 Modified Files: Central.pm Log Message: one more uninitialized value moby-live/Perl/MOBY/Client Central.pm,1.86,1.87 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.86 retrieving revision 1.87 diff -u -r1.86 -r1.87 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/15 04:13:47 1.86 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/15 19:37:12 1.87 @@ -1865,6 +1865,7 @@ next unless $_->nodeType == TEXT_NODE; $content = $_->toString; } + $content ||=""; $content =~ s/[^\]]+))\]\]>/$1/gs; return $content; } From kawas at pub.open-bio.org Sat Dec 18 13:33:44 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat, 18 Dec 2004 13:33:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181833.iBIIXiGm030170@pub.open-bio.org> kawas Sat Dec 18 13:33:43 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv30145/org/biomoby/client/gui/util Modified Files: REGEXP.java Log Message: fixed the uri regular expression so that it handles uris like: illuminae.com, and not just www.illuminae.com moby-live/Java/src/main/org/biomoby/client/gui/util REGEXP.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/11/22 17:48:45 1.4 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/12/18 18:33:43 1.5 @@ -21,7 +21,7 @@ private final static String URI = //"(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|www\\.|http:\\/\\/|HTTP:\\/\\/)?[\\w]+\\.[\\w].*\\w$)"; //"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\\?([^#]*))?(#(.*))?"; // as per rfc 2396 appendix a. - "^([\\w]+\\.[\\w]+(\\.[\\w]+)+)$"; + "^([\\w]+\\.[\\w]+(\\.[\\w]+)*)$"; private final static String URL = "(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|http:\\/\\/|HTTP:\\/\\/)[\\w]+\\.[\\w].*(\\/\\w+(\\.{1}\\w+)*)$)"; From kawas at pub.open-bio.org Sat Dec 18 13:48:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat, 18 Dec 2004 13:48:26 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181848.iBIImQxQ030233@pub.open-bio.org> kawas Sat Dec 18 13:48:26 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv30212/org/biomoby/client/gui/util Added Files: ObjectXMLWriter.java Log Message: a class that helps retrieve xml information on moby datatypes. used when we want to display the xml format of an object. requires the file /usr/local/apache2/cgi-bin/applets/retrieveObjectXML.cgi moby-live/Java/src/main/org/biomoby/client/gui/util ObjectXMLWriter.java,NONE,1.1 From kawas at pub.open-bio.org Sat Dec 18 13:51:27 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat, 18 Dec 2004 13:51:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181851.iBIIpRcD030279@pub.open-bio.org> kawas Sat Dec 18 13:51:27 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv30254/org/biomoby/client/gui/serviceInstanceCreationTool Modified Files: ServiceInstancePanelFactory.java Log Message: fixed the edit details page so that it is more consistent with the applet. Other small revisions made. moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool ServiceInstancePanelFactory.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/11/17 17:15:26 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/18 18:51:27 1.3 @@ -629,7 +629,6 @@ // ButtonBeautifier.enhanceButton(done, 11, tool.getClass()); JButton add = new JButton(" Add Data Type To The Collection "); - //TODO press this and ask to choose another object or to add the // collection to the service add.setActionCommand("addDataType"); add.setName("addDataType"); // adds the data type @@ -1059,7 +1058,6 @@ + "of allowable values." + "Once you have inputted all of the appropriate details, click on the button

    " + "labelled 'Add to Service' to add the secondary input to your service."); - //TODO String[] theLabels = { "Secondary Input Name REQUIRED :", // required @@ -1101,7 +1099,7 @@ // goes back to the input/output radio panel done.addActionListener(ioal); - JButton cancel = new JButton(" Cancel "); //TODO + JButton cancel = new JButton(" Cancel "); ButtonBeautifier.enhanceButton(cancel, 6, tool.getClass()); cancel.setActionCommand("back"); cancel.setName("back"); // goes back to the input/output radio panel @@ -1244,22 +1242,63 @@ JLabel signatureUrlLabel = new JLabel( "Signature URL (Optional)"); - JLabel serviceNameLabel2 = new JLabel( - " Must be in valid XML format"); - JLabel authorityLabel2 = new JLabel( - " Must be a valid URI - e.g. www.biomoby.org"); - JLabel emailLabel2 = new JLabel( - " Must be a valid email address"); - JLabel descriptionLabel2 = new JLabel( - ""); - JLabel authoritativeLabel2 = new JLabel( - ""); - JLabel typeLabel2 = new JLabel( - ""); - JLabel urlLabel2 = new JLabel( - " Must be a valid URL - e.g. http://some.domain/something"); - JLabel signatureUrlLabel2 = new JLabel( - " Must be a valid URL - e.g. http://some.domain/something"); + JButton serviceNameLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(serviceNameLabel2, 14, tool.getClass()); + serviceNameLabel2 + .setToolTipText(" Name cannot contain spaces nor start with special characters "); + serviceNameLabel2.setActionCommand("1"); + serviceNameLabel2.addActionListener(hal); + + JButton authorityLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(authorityLabel2, 14, tool.getClass()); + authorityLabel2 + .setToolTipText(" Must be a valid URI "); + authorityLabel2.setActionCommand("2"); + authorityLabel2.addActionListener(hal); + + JButton emailLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(emailLabel2, 14, tool.getClass()); + emailLabel2 + .setToolTipText(" Must be a valid email address "); + emailLabel2.setActionCommand("3"); + emailLabel2.addActionListener(hal); + + JButton descriptionLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(descriptionLabel2, 14, tool.getClass()); + descriptionLabel2 + .setToolTipText("Please provide a comprehensive description "); + descriptionLabel2.setActionCommand("4"); + descriptionLabel2.addActionListener(hal); + + JButton authoritativeLabel2 = new JButton(""); + ButtonBeautifier + .enhanceButton(authoritativeLabel2, 14, tool.getClass()); + authoritativeLabel2 + .setToolTipText("Is your service authoritative?"); + authoritativeLabel2.setActionCommand("5"); + authoritativeLabel2.addActionListener(hal); + + JButton typeLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(typeLabel2, 14, tool.getClass()); + typeLabel2 + .setToolTipText("What type of service instance are you creating?"); + typeLabel2.setActionCommand("6"); + typeLabel2.addActionListener(hal); + + JButton urlLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(urlLabel2, 14, tool.getClass()); + urlLabel2 + .setToolTipText(" Must be a valid URL "); + urlLabel2.setActionCommand("7"); + urlLabel2.addActionListener(hal); + + JButton signatureUrlLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(signatureUrlLabel2, 14, tool.getClass()); + signatureUrlLabel2 + .setToolTipText(" Must be a valid URL "); + signatureUrlLabel2.setActionCommand("8"); + signatureUrlLabel2.addActionListener(hal); + // check if we need to fill in the service fields Service s = tool.getService(); @@ -1316,33 +1355,67 @@ else authoritativeComboBox.setSelectedIndex(1); - // add the items to a panel with 2 columns +// add the items to a panel with 2 columns JPanel itemPanel = null; itemPanel = initPanel(itemPanel, "itemPanel", 3); itemPanel.add(serviceNameLabel); itemPanel.add(serviceNameField); - itemPanel.add(serviceNameLabel2); + // the help1 panels ensure that the button is fitted + JPanel help1 = null; + help1 = initPanel(help1, "", -1); + help1.add(serviceNameLabel2,BorderLayout.LINE_START); + itemPanel.add(help1); + + itemPanel.add(descriptionLabel); itemPanel.add(descriptionField); - itemPanel.add(descriptionLabel2); + JPanel help2 = null; + help2 = initPanel(help1, "", -1); + help2.add(descriptionLabel2,BorderLayout.LINE_START); + itemPanel.add(help2); + itemPanel.add(emailLabel); itemPanel.add(emailField); - itemPanel.add(emailLabel2); + JPanel help3 = null; + help3 = initPanel(help3, "", -1); + help3.add(emailLabel2,BorderLayout.LINE_START); + itemPanel.add(help3); + itemPanel.add(urlLabel); itemPanel.add(urlField); - itemPanel.add(urlLabel2); + JPanel help4 = null; + help4 = initPanel(help1, "", -1); + help4.add(urlLabel2,BorderLayout.LINE_START); + itemPanel.add(help4); + + itemPanel.add(authoritativeLabel); itemPanel.add(authoritativeComboBox); - itemPanel.add(authoritativeLabel2); + JPanel help5 = null; + help5 = initPanel(help1, "", -1); + help5.add(authoritativeLabel2,BorderLayout.LINE_START); + itemPanel.add(help5); + itemPanel.add(typeLabel); itemPanel.add(categoryComboBox); - itemPanel.add(typeLabel2); + JPanel help6 = null; + help6 = initPanel(help1, "", -1); + help6.add(typeLabel2,BorderLayout.LINE_START); + itemPanel.add(help6); + itemPanel.add(authorityLabel); itemPanel.add(authorityField); - itemPanel.add(authorityLabel2); + JPanel help7 = null; + help7 = initPanel(help1, "", -1); + help7.add(authorityLabel2,BorderLayout.LINE_START); + itemPanel.add(help7); + itemPanel.add(signatureUrlLabel); itemPanel.add(sigUrlField); - itemPanel.add(signatureUrlLabel2); + JPanel help8 = null; + help8 = initPanel(help1, "", -1); + help8.add(signatureUrlLabel2,BorderLayout.LINE_START); + itemPanel.add(help8); JButton next = new JButton(" Go Back To (In/Out)put Selection "); next.setActionCommand("backFromEdit"); From kawas at pub.open-bio.org Sat Dec 18 13:52:31 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat, 18 Dec 2004 13:52:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181852.iBIIqVYQ030327@pub.open-bio.org> kawas Sat Dec 18 13:52:30 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv30302/org/biomoby/client/gui/serviceInstanceCreationTool Modified Files: MobyInputOutputData.java Log Message: added the code to display an objects details when requested. moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyInputOutputData.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyInputOutputData.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyInputOutputData.java 2004/09/27 21:29:15 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyInputOutputData.java 2004/12/18 18:52:30 1.2 @@ -7,6 +7,7 @@ import java.util.Enumeration; import org.biomoby.client.CentralImpl; +import org.biomoby.client.gui.util.ObjectXMLWriter; import org.biomoby.shared.Central; import org.biomoby.shared.MobyDataType; import org.biomoby.shared.MobyException; @@ -36,6 +37,7 @@ "http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl"; static final String NAMESPACE = "http://mobycentral.cbr.nrc.ca:8080/MOBY/Central"; + private static String _URL = "http://mobycentral.cbr.nrc.ca/cgi-bin/applets/retrieveObjectXML.cgi?name="; /** * @@ -187,14 +189,15 @@ } /** - * NOT YET IMPLEMENTED

    - * @param datatype - * @return should return the MobyData type in xml format. - *

    TODO implement this! - */ - public static String ObjectInXML(String datatype) { // TODO - create an xml view of the data type - String str = - "looking for a way to get the xml from a cgi script?\n is there one already?"; - return str; + * @param datatype - the name of the datatype to retrieve informationon. + * @return if we are able to retrieve information on the datatype, then we return the MobyData type in xml format. + */ + public static String ObjectInXML(String datatype) { + String content = null; + content = ObjectXMLWriter.generatePrettyXML(_URL+datatype); + if (content.equals("")) { + content = "Couldn't retrieve object details in xml format."; + } + return content; } } From kawas at pub.open-bio.org Sat Dec 18 14:00:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat, 18 Dec 2004 14:00:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181900.iBIJ0t3l030373@pub.open-bio.org> kawas Sat Dec 18 14:00:55 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv30348/org/biomoby/client/gui/serviceInstanceCreationTool Modified Files: ServiceInstancePanelFactory.java Log Message: fixed bug where MOBY, CGI, WSDL appearred when in 'edit service details' view. moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool ServiceInstancePanelFactory.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/18 18:51:27 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/18 19:00:55 1.4 @@ -892,10 +892,9 @@ // create the text area to display the service info JTextArea area = new JTextArea(); - area.setText(/* tool.getService().getObjectString(name) */ - MobyInputOutputData.ObjectInXML(name)); + area.setText(MobyInputOutputData.ObjectInXML(name)); area.setCaretPosition(0); - + JScrollPane scrollableTextArea = new JScrollPane(area); // create a back button JButton back = new JButton(" Go Back "); back.setActionCommand("back2Object"); @@ -909,7 +908,7 @@ button.add(back); // add everything to the panel - panel.add(area, BorderLayout.CENTER); + panel.add(scrollableTextArea, BorderLayout.CENTER); panel.add(button, BorderLayout.PAGE_END); return panel; } @@ -1337,7 +1336,7 @@ if (SET) sigUrlField.setText(s.getSignatureURL()); // Create comboboxes - String[] typeItems = { "Moby", "CGI", "WSDL" }; + String[] typeItems = { "Moby"/*, "CGI", "WSDL" */}; JComboBox categoryComboBox = new JComboBox(typeItems); categoryComboBox.setName("category"); categoryComboBox.setActionCommand("category"); From kawas at pub.open-bio.org Mon Dec 20 12:13:06 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 20 Dec 2004 12:13:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412201713.iBKHD6ul013123@pub.open-bio.org> kawas Mon Dec 20 12:13:06 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv13098/org/biomoby/client/gui/util Modified Files: ObjectXMLWriter.java Log Message: Added/Modified documentation moby-live/Java/src/main/org/biomoby/client/gui/util ObjectXMLWriter.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/ObjectXMLWriter.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/ObjectXMLWriter.java 2004/12/18 18:48:26 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/ObjectXMLWriter.java 2004/12/20 17:13:06 1.2 @@ -6,8 +6,7 @@ /** * @author Eddie Kawas - *

    Created for - *

    This class was created to ... + *

    This class was created to query mobycentral in order to return the xml representation of a moby object. *

    For questions, comments, or bugs *

    email me at edward.kawas at gmail.com */ @@ -19,6 +18,13 @@ import org.jdom.output.XMLOutputter; public class ObjectXMLWriter { + /** + * + * PRE:unformattedXML is valid XML.

    + * POST:Pretty, i.e. tabbed, spaced, etc, XML is returned.

    + * @param unformattedXML - a string of xml that will be to look orderly. + * @return an XML string outputted neatly. + */ public static String generatePrettyXML(String unformattedXML) { try { ByteArrayOutputStream buf = new ByteArrayOutputStream(); From kawas at pub.open-bio.org Mon Dec 20 12:13:34 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 20 Dec 2004 12:13:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412201713.iBKHDYes013173@pub.open-bio.org> kawas Mon Dec 20 12:13:34 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv13136/org/biomoby/client/gui/serviceInstanceCreationTool Modified Files: TreeListener.java ServiceInstancePanelFactory.java NamespaceTree.java ServiceTypeTree.java Log Message: Added/Modified documentation moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool TreeListener.java,1.1,1.2 ServiceInstancePanelFactory.java,1.4,1.5 NamespaceTree.java,1.1,1.2 ServiceTypeTree.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/TreeListener.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/TreeListener.java 2004/09/27 21:29:15 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/TreeListener.java 2004/12/20 17:13:34 1.2 @@ -36,7 +36,7 @@ * POST: the tree listener is initialized. *

    * - * @param tool + * @param tool - the ServiceCreationTool that registered this listener. */ public TreeListener(ServiceCreationTool tool) { this.tool = tool; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/18 19:00:55 1.4 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/20 17:13:34 1.5 @@ -92,9 +92,6 @@ } }; worker.start(); - // before doing anything, load the service tree in a - // separate thread to increase performance - // also download the object tree for use final TreeLoaderThread workerTree = new TreeLoaderThread() { public Object construct() { mobyTree = new MobyTree(false, @@ -106,10 +103,6 @@ } }; workerTree.start(); - - // before doing anything, load the service tree in a - // separate thread to increase performance - // also download the object tree for use final TreeLoaderThread workerNamespace = new TreeLoaderThread() { public Object construct() { namespaceTree = new NamespaceTree(false, @@ -123,6 +116,12 @@ workerNamespace.start(); } + /** + * + * PRE:None.

    + * POST:The starting panel for the applet is returned.

    + * @return - the starting panel for the applet is returned. + */ public JPanel createStartingPanel() { /* all tabs go to the center of this panel */ @@ -372,6 +371,12 @@ return pan; } + /** + * + * PRE:None.

    + * POST:The add inputs/outputs panel is created for the applet.

    + * @return - a JPanel representing the input/output chooser for the applet. + */ public JPanel createChoosingPanel() { /* all tabs go to the center of this panel */ JPanel pan = null; @@ -447,6 +452,14 @@ return pan; } + /** + * + * PRE:Top and bottom are valid JPanels.

    + * POST:a JSplitPane is created with top placed at the top of the panel and bottom placed at the bottom

    + * @param top - a JPanel that will be the top component of the split pane. + * @param bottom - a JPanel that will be the bottom component of the split pane. + * @return - a JSplitPane with the top and bottom components initialized to top and bottom. + */ public JSplitPane createSplitePane(JPanel top, JPanel bottom) { JSplitPane vpane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, top, bottom); @@ -455,6 +468,11 @@ return vpane; } + /** + * PRE:None.

    + * POST:A JPanel containing the service type tree is returned.

    + * @return - a JPanel containing the service type tree. + */ public JPanel createServiceTypeChooserPanel() { JPanel panel = null; panel = initPanel(panel, "Choose the Service Type", @@ -489,6 +507,14 @@ return panel; } + /** + * + * PRE:dataTypeName is found in the mobycentral object ontology.

    + * POST:A JPanel containing the information of the recently chosen datatype, along with a namespace tree so that user can choose appropriate namespaces for their input/output.

    + * @param dataTypeName - a string name of a valid object in the moby object ontology. + * @param isInput - if isInput is true, then datatype is a primary input. Otherwise the datatype is an output. + * @return - a JPanel containing information on the datatype, as well as other widgets that aid in the supplementing of the input/output object. + */ public JPanel createSimplePrimaryPanel(String dataTypeName, boolean isInput) { JPanel panel = null; panel = initPanel(panel, "" @@ -609,6 +635,15 @@ return panel; } + /** + * + * PRE:datatype name is found in the moby object ontology.

    + * POST:a JPanel is returned that allows the user to add more information on the object contained in their collection

    + * @param dataTypeName - a valid object name found in the moby object ontology. + * @param isInput - if true, then collection (and object contained in collection) is an input, otherwise the collection is an output. + * @param collectionName - the name of the collection. + * @return - a JPanel with widgets that allow for the user to supplement the information on the collection. + */ public JPanel createCollectionPrimaryPanel(String dataTypeName, boolean isInput, String collectionName) { JPanel panel = null; @@ -764,6 +799,12 @@ return panel; } + /** + * + * PRE:None.

    + * POST:a JPanel containing an object tree that allows for object additions to the users current collection is returned

    + * @return - JPanel with an object tree allowing for the addition of the selected object to the users collection. + */ public JPanel createObjectTreePanelForAddingToCollections() { JPanel panel = null; panel = initPanel( @@ -850,6 +891,12 @@ return p; } + /** + * + * PRE:None.

    + * POST:An empty JPanel is returned.

    + * @return - a JPanel with nothing contained within. + */ public JPanel createEmptyPanel() { JPanel p = null; p = initPanel(p, "empty", -1); @@ -857,6 +904,12 @@ return p; } + /** + * + * PRE:None

    + * POST:A JPanel containing information about the users service is shown.

    + * @return - JPanel with information on the users service. + */ public JPanel createServiceViewPanel() { JPanel panel = null; panel = initPanel(panel, "Service View", -1); @@ -884,6 +937,12 @@ return panel; } + /** + * + * PRE:An object is selected in the object tree.

    + * POST:Information about the selected object is returned.

    + * @return - JPanel with information on the selected moby object. + */ public JPanel createObjectViewPanel() { String name = objectTreeListener.getSelectedNode(); JPanel panel = null; @@ -913,6 +972,12 @@ return panel; } + /** + * + * PRE:None.

    + * POST:JPanel with information and widgets that allow the user to supplement their collection is returned.

    + * @return - JPanel with information fields and widgets that allow the user to supplement their collection. + */ public JPanel createObjectViewPanelForCollection() { String name = objectTreeListener.getSelectedNode(); JPanel panel = null; @@ -942,6 +1007,12 @@ return panel; } + /** + * + * PRE:None.

    + * POST:JPanel displaying a tree of the moby object ontology is returned that aids in the addition of objects to the service.

    + * @return JPanel containing a tree representation of the moby object ontology. + */ public JPanel createObjectTreePanel() { JPanel panel = null; panel = initPanel(panel, "Choose an Object", -1); @@ -980,72 +1051,81 @@ } /** - * @return + * @return true if a radio button is selected, false otherwise. */ public boolean isRADIO_SELECTED() { return RADIO_SELECTED; } /** - * @param b + * @param b - set whether or not the radio button is selected. */ public void setRADIO_SELECTED(boolean b) { RADIO_SELECTED = b; } /** - * @return + * @return - return the service type tree. */ public ServiceTypeTree getTree() { return tree; } /** - * @param tree + * @param tree - the tree to set the service type tree to. */ public void setTree(ServiceTypeTree tree) { this.tree = tree; } /** - * @return + * @return - the TreeListener registered to this tool */ public TreeListener getMouseTreeListener() { return mtl; } /** - * @return + * @return - the moby tree registered to this tool. */ public MobyTree getMobyTree() { return mobyTree; } /** - * @return + * @return - the namespace tree. */ public NamespaceTree getNamespaceTree() { return namespaceTree; } /** - * @return + * @return - the listener associated with the namespace tree registered with this tool. */ public NamespaceListener getNamespaceListener() { return ntl; } /** - * @return + * @return - DefaultListModel for the namespace dropdown list. */ public DefaultListModel getNamespaceDropdownListModel() { return model; } + /** + * @return - the size of the namespace dropdown list. + */ public int getNamespaceDropdownListSize() { return namespaceDropdownList.getModel().getSize(); } + /** + * + * PRE:None.

    + * POST:JPanel with widgets required to add secondary input to the service instance is returned.

    + * @return - JPanel with various widgets that allow for the addition of secondary inputs to the service instance. + */ public JPanel createSecondaryPanel() { JPanel panel = null; panel = initPanel(panel, "Secondary Input Entry", -1); @@ -1138,6 +1218,9 @@ return panel; } + /** + * @return - an Enumeration of secondary data valid inputs + */ public Enumeration getSecondaryInputEnumeration() { Vector vec = new Vector(); StringTokenizer st = new StringTokenizer(InputOutputFocusListener @@ -1153,14 +1236,26 @@ return vec.elements(); } + /** + * @return - the secondary input datatype - Can be INTEGER, STRING, DATETIME or FLOAT + */ public static String getSecondaryDataType() { return ServiceInstancePanelFactory.datatype; } + /** + * @param datatype - the secondary input datatype - INTEGER, STRING, DATETIME, or FLOAT + */ public static void setSecondaryDataType(String datatype) { ServiceInstancePanelFactory.datatype = datatype; } + /** + * + * PRE:None.

    + * POST:JPanel that displays the service instance is returned.

    + * @return - JPanel that initiates submission of the service instance. + */ public JPanel createSubmissionPanel() { JPanel panel = null; panel = initPanel( @@ -1200,12 +1295,18 @@ } /** - * @return + * @return - the submit JButton. */ public JButton getSubmit() { return submit; } + /** + * + * PRE:None.

    + * POST:JPanel with various widgets for editing the details of the service instance is returned.

    + * @return - JPanel is returned that aids in the editing of the service instance details. + */ public JPanel createDetailEditingPanel() { /* all tabs go to the center of this panel */ @@ -1438,7 +1539,7 @@ } /** - * @return + * @return - the edit JButton */ public JButton getEdit() { return edit; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/NamespaceTree.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/NamespaceTree.java 2004/09/27 21:29:15 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/NamespaceTree.java 2004/12/20 17:13:34 1.2 @@ -40,9 +40,9 @@ private String rdf = ""; /** * PRE: None

    - * POST: A moby tree is constructed with the root node labeled as 'Service'

    + * POST: A moby tree is constructed with the root node labeled as 'Namespace'

    * and the material for the tree taken from the RDF located at - * @link http://biomoby.org/RESOURCES/MOBY-S/Service + * @link http://biomoby.org/RESOURCES/MOBY-S/Namespace * @param canEdit, if true, then the nodes are editable, else they are not. */ public NamespaceTree(boolean canEdit, String rdf) { @@ -84,7 +84,7 @@ /** * PRE: None.

    - * POST: The MobyTree object contains an empty tree with a single node labeled 'Object' + * POST: The MobyTree Namespace contains an empty tree with a single node labeled 'Namespace' * @return - none. * */ @@ -294,6 +294,12 @@ return tree; } + /** + * + * PRE:None.

    + * POST:THe Namespace tree is refreshed.

    + * + */ public void reload() { hashmap = new Construct(rdf).createHomes(); makeObjectTree(); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceTypeTree.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceTypeTree.java 2004/09/27 21:29:15 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceTypeTree.java 2004/12/20 17:13:34 1.2 @@ -298,6 +298,12 @@ return tree; } + /** + * + * PRE:None.

    + * POST:The Service Type tree for this tool is refreshed.

    + * + */ public void reload() { hashmap = new Construct(rdf).createHomes(); makeObjectTree(); From kawas at pub.open-bio.org Wed Dec 22 09:33:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 09:33:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221433.iBMEXatx001964@pub.open-bio.org> kawas Wed Dec 22 09:33:36 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv1939/org/biomoby/client/gui/objectCreationTool Modified Files: MobyTree.java Log Message: Revised MobyTree.java moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool MobyTree.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/MobyTree.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/MobyTree.java 2004/09/27 22:15:13 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/MobyTree.java 2004/12/22 14:33:36 1.2 @@ -66,7 +66,17 @@ tree.setEditable(canEdit); tree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION); tree.setShowsRootHandles(true); - + } + + /** + * + * PRE:tree is a valid JTree.

    + * POST:JTree is collapsed at root node.

    + * + */ + public void collapseMobyTree() { + tree.clearSelection(); + tree.collapseRow(0); } /** From kawas at pub.open-bio.org Wed Dec 22 09:34:58 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 09:34:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221434.iBMEYwdL002035@pub.open-bio.org> kawas Wed Dec 22 09:34:58 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2014/org/biomoby/client/gui/objectCreationTool Added Files: TreeWindow.java PopUpWindow.java TreeMouseListener.java SubmissionWindow.java Log Message: Revised Object Creation Tool - newly updated moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool TreeWindow.java,NONE,1.1 PopUpWindow.java,NONE,1.1 TreeMouseListener.java,NONE,1.1 SubmissionWindow.java,NONE,1.1 From kawas at pub.open-bio.org Wed Dec 22 09:40:50 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 09:40:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221440.iBMEeoVd002108@pub.open-bio.org> kawas Wed Dec 22 09:40:50 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main In directory pub.open-bio.org:/tmp/cvs-serv2087 Added Files: retrieveObjectXML.cgi Log Message: File needed for retrieving xml representations for moby objects. referenced in org\biomoby\client\gui\objectCreationTool\TreeWindow.java moby-live/Java/src/main retrieveObjectXML.cgi,NONE,1.1 From kawas at pub.open-bio.org Wed Dec 22 09:42:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 09:42:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221442.iBMEgaQG002142@pub.open-bio.org> kawas Wed Dec 22 09:42:36 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main In directory pub.open-bio.org:/tmp/cvs-serv2117 Modified Files: retrieveObjectXML.cgi Log Message: added the code to strip CDATA from returned xml moby-live/Java/src/main retrieveObjectXML.cgi,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/retrieveObjectXML.cgi,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/retrieveObjectXML.cgi 2004/12/22 14:40:50 1.1 +++ /home/repository/moby/moby-live/Java/src/main/retrieveObjectXML.cgi 2004/12/22 14:42:36 1.2 @@ -15,4 +15,5 @@ print "Content-type: text/plain\n\n"; my $output = $DEFS->{'XML'}; $output =~ s/retrieveObjectDefinition/objectDetails/g; + $output =~ s/[^\]]+))\]\]>/$1/gs; print $output; From kawas at pub.open-bio.org Wed Dec 22 09:48:43 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 09:48:43 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221448.iBMEmhs2002207@pub.open-bio.org> kawas Wed Dec 22 09:48:43 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2180 Removed Files: ButtonActions.java ButtonBeautifier.java FieldFocusListeners.java FieldKeyListener.java MobyUserPanel.java PanelFactory.java Log Message: removed - no longer necessary moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool ButtonActions.java,1.2,NONE ButtonBeautifier.java,1.1,NONE FieldFocusListeners.java,1.2,NONE FieldKeyListener.java,1.1,NONE MobyUserPanel.java,1.1,NONE PanelFactory.java,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/ButtonActions.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/ButtonBeautifier.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/FieldFocusListeners.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/FieldKeyListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/MobyUserPanel.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/PanelFactory.java,v: No such file or directory From kawas at pub.open-bio.org Wed Dec 22 09:49:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 09:49:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221449.iBMEnaa3002248@pub.open-bio.org> kawas Wed Dec 22 09:49:36 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2226 Removed Files: TreeListener.java Log Message: removed - no longer necessary moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool TreeListener.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/TreeListener.java,v: No such file or directory From kawas at pub.open-bio.org Wed Dec 22 11:01:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 11:01:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221601.iBMG1cvQ002501@pub.open-bio.org> kawas Wed Dec 22 11:01:38 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2460/org/biomoby/client/gui/objectCreationTool Modified Files: TreeWindow.java PopUpWindow.java Registration.java TreeMouseListener.java SubmissionWindow.java Log Message: Added documentation moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool TreeWindow.java,1.1,1.2 PopUpWindow.java,1.1,1.2 Registration.java,1.1,1.2 TreeMouseListener.java,1.1,1.2 SubmissionWindow.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeWindow.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeWindow.java 2004/12/22 14:34:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeWindow.java 2004/12/22 16:01:38 1.2 @@ -16,8 +16,11 @@ import org.biomoby.client.gui.util.ObjectXMLWriter; /** * @author Eddie Kawas - *

    Created for - *

    This class was created to ... + *

    This class was created with the purpose of + * displaying the mobycentral object ontology in + * tree format, as well as providing a way to + * retrieve information about objects from the + * mobycentral object ontology. *

    For questions, comments, or bugs *

    email me at edward.kawas at gmail.com */ =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/PopUpWindow.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/PopUpWindow.java 2004/12/22 14:34:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/PopUpWindow.java 2004/12/22 16:01:38 1.2 @@ -13,8 +13,8 @@ import javax.swing.ImageIcon; /** * @author Eddie Kawas - *

    Created for - *

    This class was created to ... + *

    This class was created to present a convenience class + * that presents modal pop up windows to the user. *

    For questions, comments, or bugs *

    email me at edward.kawas at gmail.com */ =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Registration.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Registration.java 2004/09/27 22:15:13 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Registration.java 2004/12/22 16:01:38 1.2 @@ -20,24 +20,47 @@ static final String ENDPOINT = "http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl"; static final String NAMESPACE = "http://mobycentral.cbr.nrc.ca:8080/MOBY/Central"; - - private static boolean PROTO = false; + /** + * + * Constructor + * @param name - the name of the moby data type + * @param proto - is this object a prototype? + */ public Registration(String name, boolean proto) { super(name); PROTO = proto; } + /** + * + * PRE:None.

    + * POST:The name of the data type is renamed to str.

    + * @param str - the new name of the data type. + */ public void setName(String str) { this.name = str; } - + /** + * + * PRE:Pair p is a well constructed Pair object.

    + * POST:Data from Pair p is added to the data type + * in the form of HASA relationship

    + * @param p - the pair to add to the HASA containment relationship for the data type + */ public void addHASAChildren(Pair p) { //System.out.println("ArticleName: " + p.getArticlename() + " DataType: " + p.getAttribute()); this.addChild(p.getArticlename(), p.getAttribute(), Central.iHASA); } + /** + * + * PRE:Pair p is a well constructed Pair object.

    + * POST:Data from Pair p is added to the data type + * in the form of HAS relationship

    + * @param p - the pair to add to the HAS containment relationship for the data type + */ public void addHASChildren(Pair p) { //System.out.println("ArticleName: " + p.getArticlename() + " DataType: " + p.getAttribute()); this.addChild(p.getArticlename(), p.getAttribute(), Central.iHAS); @@ -45,9 +68,11 @@ } /** - * - * PRE: - *

    POST:

    + * + * PRE:MobyDataType has been properly initialized.

    + * POST:MobyDataType is registered in the mobycentral object + * ontology and a string representing its LSID is returned.

    + * @param tool - the ObjectCreationTool that is registering this new data type. * @return 1 for success, 0 for failure and -1 for 'pending curation' */ public String performRegistration(ObjectCreationTool tool) { @@ -83,12 +108,10 @@ return reg; } + /** - * - * PRE: - *

    POST:

    - * @param name - * @return + * @deprecated - no longer used. + * TODO - remove method from class. */ public String getDataTypeInfo(String name) { String ret = ""; @@ -108,10 +131,19 @@ } + /** + * + * PRE:MobyDataType has been registered.

    + * POST:LSID is returned

    + * @return - the LSID of the moby data type. + */ public String getMobyID() { return this.getId(); } + /** + * TODO - remove from class. Shouldn't have this method. + */ public void setMobyID(String s) { this.setId(s); } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeMouseListener.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeMouseListener.java 2004/12/22 14:34:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeMouseListener.java 2004/12/22 16:01:38 1.2 @@ -10,8 +10,11 @@ import javax.swing.tree.TreePath; /** - * @author Eddie Kawas

    Created for

    This class was created to ...

    For - * questions, comments, or bugs

    email me at edward.kawas at gmail.com + * @author Eddie Kawas + *

    This class was created to implement the Mouselistener interface + * for use with a tree that displays the mobycentral object ontology. + *

    For questions, comments, or bugs + *

    email me at edward.kawas at gmail.com */ public class TreeMouseListener implements MouseListener { @@ -65,10 +68,11 @@ } /** - * PRE:

    POST:

    - * - * @param selected - * @return + * PRE: None.

    + * POST: THe name of the event originator is returned: ISA, HAS, HASA.

    + * @param selected - the integer value representing the event originator + * @see org.biomoby.client.gui.objectCreationTool + * @return String representing the event originator. */ private String getEventOriginatorName(int selected) { String str = null; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/SubmissionWindow.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/SubmissionWindow.java 2004/12/22 14:34:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/SubmissionWindow.java 2004/12/22 16:01:38 1.2 @@ -13,8 +13,9 @@ import javax.swing.ImageIcon; /** * @author Eddie Kawas - *

    Created for - *

    This class was created to ... + *

    This class was created to present a view to the user + * of the tool that displays their newly created object prior + * to registration. *

    For questions, comments, or bugs *

    email me at edward.kawas at gmail.com */ From kawas at pub.open-bio.org Wed Dec 22 11:07:03 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 11:07:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221607.iBMG73tG002580@pub.open-bio.org> kawas Wed Dec 22 11:07:03 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2555/org/biomoby/client/gui/serviceTypeCreationTool Modified Files: ServiceTypeApplet.java Log Message: Added documentation moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool ServiceTypeApplet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java 2004/09/27 21:06:17 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java 2004/12/22 16:07:03 1.3 @@ -35,14 +35,13 @@ import org.biomoby.shared.PendingCurationException; /** - * @author Eddie Created for - *

    - * This class was created to ... - *

    - * For questions, comments, or bugs - *

    - * email me at edward.kawas at gmail.com - *

    + * + * @author Eddie Kawas + *

    This class was created to present + * users of moby the chance to create + * new service types quickly and easily. + *

    For questions, comments, or bugs + *

    email me at edward.kawas at gmail.com */ public class ServiceTypeApplet extends JApplet { @@ -125,17 +124,20 @@ return super.getAppletContext(); } - /* - * (non-Javadoc) - *@see java.applet.Applet#getAppletInfo() - */ + /* + * (non-Javadoc) + *@see java.applet.Applet#getAppletInfo() + */ public String getAppletInfo() { - return "Title: Moby Service Type Construction Tool v1.00, 24 September 2004\n" - + "Author: Edward Kawas\n" - + "An interactive way to create Service Types for the MobyCentral Ontology." + - newline + "This is" + ((PROTOTYPE) ? "" : " not " ) + "a prototype!"; - } - + return "Title: Moby Service Type Construction Tool v1.00, 24 September 2004\n" + + "Author: Edward Kawas\n" + + "An interactive way to create Service Types for the MobyCentral Ontology." + + newline + + "This is" + + ((PROTOTYPE) ? "" : " not ") + + "a prototype!"; + } + /* * (non-Javadoc) * @@ -159,17 +161,17 @@ .getLastSelectedPathComponent().toString(); switch (arg0.getClickCount()) { - case 1: - break; - case 2: - //set text box to be this node, and close frame - parentTextField.setText(selected); - frame.dispose(); - frame = null; - break; - default: - // do nothing - break; + case 1: + break; + case 2: + //set text box to be this node, and close frame + parentTextField.setText(selected); + frame.dispose(); + frame = null; + break; + default: + // do nothing + break; } } @@ -229,9 +231,8 @@ title.setFont(new java.awt.Font("Dialog", java.awt.Font.BOLD, 24)); title.setHorizontalAlignment(javax.swing.SwingConstants.CENTER); title.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER); - title - .setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/moby.gif"))); + title.setIcon(new ImageIcon(getClass().getResource( + "/org/biomoby/client/gui/img/moby.gif"))); title.setOpaque(true); backgroundPane.add(title, java.awt.BorderLayout.NORTH); backgroundPane.add(getCenterPane(), java.awt.BorderLayout.CENTER); @@ -313,20 +314,24 @@ registerServiceType.setText("Create New Service Type"); registerServiceType.setCursor(new java.awt.Cursor( java.awt.Cursor.DEFAULT_CURSOR)); - registerServiceType.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/ComposeMail24.gif"))); + registerServiceType + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/ComposeMail24.gif"))); registerServiceType.setActionCommand("register"); registerServiceType .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { - + // check whether inputs is valid /* * data is an array of values: 0.service type name * 1.service type description 2.service type uri * 3.service type parent 4. valid email address */ - String[] data = { getNameTxtField().getText(), + String[] data = { + getNameTxtField().getText(), getDescTxtArea().getText(), getUriTxtField().getText(), getParentTextField().getText(), @@ -351,7 +356,7 @@ createPopUpMsg("Please enter a valid email address."); return; } - + Central worker = null; boolean success = false; String errorMsg = ""; @@ -560,8 +565,11 @@ private JButton getNamehelpBtn() { if (namehelpBtn == null) { namehelpBtn = new JButton(); - namehelpBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); + namehelpBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); namehelpBtn.setOpaque(false); namehelpBtn.setActionCommand("nameHelp"); namehelpBtn.setMaximumSize(new java.awt.Dimension(34, 26)); @@ -592,8 +600,11 @@ descHelpBtn.setMaximumSize(new java.awt.Dimension(34, 26)); descHelpBtn.setMinimumSize(new java.awt.Dimension(34, 26)); descHelpBtn.setOpaque(false); - descHelpBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); + descHelpBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); descHelpBtn.setActionCommand("descHelp"); descHelpBtn.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { @@ -619,8 +630,11 @@ emailHelpBtn.setMaximumSize(new java.awt.Dimension(34, 26)); emailHelpBtn.setMinimumSize(new java.awt.Dimension(34, 26)); emailHelpBtn.setOpaque(false); - emailHelpBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); + emailHelpBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); emailHelpBtn.setActionCommand("emailHelp"); emailHelpBtn.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { @@ -645,8 +659,11 @@ uriHelpBtn.setMaximumSize(new java.awt.Dimension(34, 26)); uriHelpBtn.setMinimumSize(new java.awt.Dimension(34, 26)); uriHelpBtn.setOpaque(false); - uriHelpBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); + uriHelpBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); uriHelpBtn.setActionCommand("uriHelp"); uriHelpBtn.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { @@ -686,8 +703,11 @@ chooseParentBtn = new JButton(); chooseParentBtn.setText("Choose Service Type Parent"); chooseParentBtn.setActionCommand("chooseParent"); - chooseParentBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Preferences24.gif"))); + chooseParentBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Preferences24.gif"))); chooseParentBtn.setOpaque(true); chooseParentBtn.setPreferredSize(new java.awt.Dimension(274, 27)); chooseParentBtn.setMinimumSize(new java.awt.Dimension(274, 27)); @@ -708,7 +728,8 @@ return; } frame = new JFrame("Service Type Chooser"); - JScrollPane scrollable = new JScrollPane(tree.getTree()); + JScrollPane scrollable = new JScrollPane(tree + .getTree()); frame.getContentPane().add(scrollable); frame .setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); From senger at pub.open-bio.org Sun Dec 5 22:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2C2015065@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory pub.open-bio.org:/tmp/cvs-serv14933/src/Clients/help Modified Files: MobyCmdLineClient_usage.txt Log Message: a lot of changes in docs; but also in code moby-live/Java/src/Clients/help MobyCmdLineClient_usage.txt,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2004/11/12 23:02:31 1.6 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2004/12/05 22:28:02 1.7 @@ -131,7 +131,7 @@ points to your HTTP space to a place where an RDF describing this service will be -rs-rdfpath - if the service registration is succesful, the returned + if the service registration is successful, the returned RDF is copied to a file given by (which completes the registration process); use it, however, with caution because this client From senger at pub.open-bio.org Sun Dec 5 22:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2cf014998@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/docs/dist In directory pub.open-bio.org:/tmp/cvs-serv14933/docs/dist Modified Files: _README_ Log Message: a lot of changes in docs; but also in code moby-live/Java/docs/dist _README_,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/dist/_README_,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/docs/dist/_README_ 2004/05/18 10:13:16 1.2 +++ /home/repository/moby/moby-live/Java/docs/dist/_README_ 2004/12/05 22:28:02 1.3 @@ -18,6 +18,10 @@ You should consider to change some parameters in provided web.xml (it appears in 'jmoby/WEB-INF' after unpacking). +Binary distribution with RDF agent: + rdfagent-.tar.gz + rdfagent-.zip + -------------------------------------------------------------------- File: README Comments to the biomoby mailing lists, or directly to Martin Senger (senger at ebi.ac.uk). From senger at pub.open-bio.org Sun Dec 5 22:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2oZ014956@pub.open-bio.org> senger Sun Dec 5 17:28:01 EST 2004 Update of /home/repository/moby/moby-live/Java In directory pub.open-bio.org:/tmp/cvs-serv14933 Modified Files: README build.xml Log Message: a lot of changes in docs; but also in code moby-live/Java README,1.7,1.8 build.xml,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Java/README,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/README 2003/11/08 00:27:23 1.7 +++ /home/repository/moby/moby-live/Java/README 2004/12/05 22:28:01 1.8 @@ -73,13 +73,15 @@ After building it all, invoke available clients using provided (and very simple) scripts: - ./run-cmdline-client -help - ./run-testing-central + ./build/run/run-cmdline-client -help + ./build/run/run-testing-central or, on Windows platforms: - run-cmdline-client.bat -help - run-testing-central.bat + build/run/run-cmdline-client.bat -help + build/run/run-testing-central.bat + +There are more scripts available - check the 'build/run' directory. Enjoy it! =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/build.xml 2004/11/01 19:21:42 1.9 +++ /home/repository/moby/moby-live/Java/build.xml 2004/12/05 22:28:01 1.10 @@ -421,26 +421,30 @@ + description="Create binary distribution with basic jMoby clients."> + + + + - - + + - + - - + + - + - + + + + - + - - + + @@ -489,18 +496,18 @@ - + - + - + - + - - + + @@ -608,7 +615,7 @@ - From senger at pub.open-bio.org Sun Dec 5 22:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2je015039@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/src/Clients In directory pub.open-bio.org:/tmp/cvs-serv14933/src/Clients Modified Files: MobyCmdLineClient.java Log Message: a lot of changes in docs; but also in code moby-live/Java/src/Clients MobyCmdLineClient.java,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/11/12 23:02:30 1.7 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/12/05 22:28:02 1.8 @@ -367,9 +367,17 @@ if ((param = cmd.getParam ("-rs-out")) != null ) { String[] outs = StringUtils.split (param, ","); for (int i = 0; i < outs.length; i++) { - MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy"); - data.setDataType (new MobyDataType (outs[i])); - service.addOutput (data); + String[] parts = StringUtils.split (outs[i], "="); + if (parts.length >= 2) { + MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy"); + data.setDataType (new MobyDataType (parts[0])); + data.addNamespace (new MobyNamespace (parts[1])); + service.addOutput (data); + } else { + MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy"); + data.setDataType (new MobyDataType (parts[0])); + service.addOutput (data); + } } } if ((param = cmd.getParam ("-rs-ofile")) != null ) { From senger at pub.open-bio.org Sun Dec 5 22:28:03 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2kR015109@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv14933/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: a lot of changes in docs; but also in code moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.18,1.19 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/11/22 17:22:22 1.18 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/12/05 22:28:02 1.19 @@ -138,6 +138,7 @@ Service service = new Service(); call = (Call) service.createCall(); call.setTargetEndpointAddress (endpoint); + call.setTimeout (new Integer (0)); call.setSOAPActionURI (uri + "#" + method); @@ -1291,7 +1292,7 @@ pattern = new MobyService ("dummy"); String result = - getServicesAsXML (pattern, keywords, includeParentDataTypes, includeChildrenServiceTypes); + getServicesAsXML (pattern, keywords, includeChildrenServiceTypes, includeParentDataTypes); MobyService[] services = extractServices (result); return services; } From senger at pub.open-bio.org Sun Dec 5 22:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2Rx015086@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/src/config In directory pub.open-bio.org:/tmp/cvs-serv14933/src/config Modified Files: run-digest-client Log Message: a lot of changes in docs; but also in code moby-live/Java/src/config run-digest-client,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-digest-client,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/config/run-digest-client 2004/11/14 16:43:49 1.1 +++ /home/repository/moby/moby-live/Java/src/config/run-digest-client 2004/12/05 22:28:02 1.2 @@ -1,8 +1,8 @@ #!/bin/sh # -# Run MobyDigest client. +# Run MobyDigestClient. # -# Use ./build/run/run-digets-client -help for list of +# Use ./build/run/run-digest-client -help for list of # all available arguments. # # $Id$ From senger at pub.open-bio.org Sun Dec 5 22:28:03 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS3HO015127@pub.open-bio.org> senger Sun Dec 5 17:28:03 EST 2004 Update of /home/repository/moby/moby-live/Java/src/support In directory pub.open-bio.org:/tmp/cvs-serv14933/src/support Added Files: run-cache-client run-cache-client.bat run-digest-client run-digest-client.bat Log Message: a lot of changes in docs; but also in code moby-live/Java/src/support run-cache-client,NONE,1.1 run-cache-client.bat,NONE,1.1 run-digest-client,NONE,1.1 run-digest-client.bat,NONE,1.1 From senger at pub.open-bio.org Sun Dec 5 22:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS2B0015020@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/docs/images In directory pub.open-bio.org:/tmp/cvs-serv14933/docs/images Modified Files: whale.gif Added Files: blue.gif orange.gif red.gif Log Message: a lot of changes in docs; but also in code moby-live/Java/docs/images blue.gif,NONE,1.1 orange.gif,NONE,1.1 red.gif,NONE,1.1 whale.gif,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/images/whale.gif,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 Binary files /home/repository/moby/moby-live/Java/docs/images/whale.gif 2004/11/14 17:33:57 1.1 and /home/repository/moby/moby-live/Java/docs/images/whale.gif 2004/12/05 22:28:02 1.2 differ rcsdiff: /home/repository/moby/moby-live/Java/docs/images/whale.gif: diff failed From senger at pub.open-bio.org Sun Dec 5 22:28:02 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Sun, 5 Dec 2004 17:28:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412052228.iB5MS29D014979@pub.open-bio.org> senger Sun Dec 5 17:28:02 EST 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv14933/docs Modified Files: ChangeLog index.html Added Files: CmdLineClients.html Download.html MOBYSHoundGetGenBankff-result.xml.txt RDFAgent.html SimpleClient.html TavernaGuide.html Testing_service.rdf ToDo.html Log Message: a lot of changes in docs; but also in code moby-live/Java/docs CmdLineClients.html,NONE,1.1 Download.html,NONE,1.1 MOBYSHoundGetGenBankff-result.xml.txt,NONE,1.1 RDFAgent.html,NONE,1.1 SimpleClient.html,NONE,1.1 TavernaGuide.html,NONE,1.1 Testing_service.rdf,NONE,1.1 ToDo.html,NONE,1.1 ChangeLog,1.26,1.27 index.html,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.26 retrieving revision 1.27 diff -u -r1.26 -r1.27 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/11/14 16:43:49 1.26 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/12/05 22:28:02 1.27 @@ -1,3 +1,13 @@ +2004-12-05 Martin Senger + + * Updated documentation (significantly, but not yet finished). + +2004-11-30 Martin Senger + + * Fixed CentralImpl dealing now better with + 1 and + 1. + 2004-11-14 Martin Senger * Added MobyDigestClient for retrieving cummulative (digested) =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/index.html,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/docs/index.html 2004/11/14 17:33:57 1.5 +++ /home/repository/moby/moby-live/Java/docs/index.html 2004/12/05 22:28:02 1.6 @@ -3,83 +3,72 @@ - +

    -

    BioMoby in Java

    +

    jMoby - BioMoby in Java

    -This is a sub-project of the BioMoby project. -It aims to develop an access to the Moby registry using pure Java, and later perhaps to -develop a stand-alone Java Moby server. It will also provide Java support for providers -of the Moby-compliant services. -

    - -This is the overview of the current Moby java clients, and their -relationship to the whole BioMoby project. -

    - - -

    - - -

    Java API

    -The detailed documentation of the involved classes and interfaces -is available +This is a sub-project of the BioMoby project. It aims to develop tools in Java +in order: +
      +
    • to access BioMoby registries, allowing all features provided by +such registries, including but not limited to registering and +deregistering of the BioMoby services and their parts, discovering +them, and understanding their data in various formats (such as RDF),

      - -

      Moby Java Clients - download and use

      +
    • to create Java implementations of BioMoby services, especially +to help service providers with creating BioMoby data containers (input +and output data) without exposing providers to the complexity of the +XML required and produced by BioMoby services, and finally

      -The Moby Java clients are part of the -Moby CVS repository -but for convenience they can be downloaded also separately from -http://industry.ebi.ac.uk/~senger/jMoby/dist/ -(take the latest version, pick up either .tar.gz or .zip - both are equivalent). -

      +

    • to provide support for those writing Java clients accessing +both BioMoby registries and BioMoby services.

      -After downloading, unpack it, check the README file and start using it: -

        -
      • sh run-testing-central -
      • sh run-cmdline-client -help -
      -

      -or on the Windows platform: -

        -
      • run-testing-central.bat -
      • run-cmdline-client.bat -help

      -Latest changes are available either as a -summary or in details from the -CVS repository. -

      +

      Where to go now

      -Please report all problems, or submit features and wishes to -Martin Senger. +
      +
      +
      How to get jMoby +

      + +

      How to use jMoby +
      +
      Command-line clients +
      Integration with Taverna +
      RDF Agent +
      +

      + +

      How to develop with jMoby +
      +
      Available APIs (more explanation coming...) +
      How to develop a client talking to a BioMoby service +
      How to develop a BioMoby service (coming...) +
      +

      + +

      Next plans +
      +
      - -

      Next steps

      - -The future plans and steps in this sub-project may or should include -
        -
      • Design and implement Java interfaces that can be used for the providers - of the Moby-compliant services -
      • Start to work on a pure Java Moby server (talk to Brian Gilman who had already started to work on it) -
      - -

      Acknowledgements

      -The work on BioMoby Java sub-project is supported by +The work on BioMoby Java sub-project is partly supported by
      myGrid, a multi-organisational project developing the infrastructural middleware for an e-Biologist's workbench, funded by EPSRC. +

      - +Other parts of jMoby are funded from the same sources as the BioMoby +itself.

      @@ -87,7 +76,7 @@

      Martin Senger
      -Last modified: Sun Nov 14 17:29:05 2004 +Last modified: Sun Dec 5 21:32:23 2004
      From nopushneva at pub.open-bio.org Wed Dec 8 03:29:06 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue, 7 Dec 2004 22:29:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412080329.iB83T65F024862@pub.open-bio.org> nopushneva Tue Dec 7 22:29:05 EST 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib In directory pub.open-bio.org:/tmp/cvs-serv24837 Removed Files: activation.jar concurrent.jar icu4j.jar Log Message: remove libs from RDFAgent directory moby-live/Agents/MOBY-S/RDFAgent/lib activation.jar,1.3,NONE concurrent.jar,1.1,NONE icu4j.jar,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/activation.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/concurrent.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/icu4j.jar,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:20 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFK2W026995@pub.open-bio.org> yanwong Wed Dec 8 06:15:20 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched Removed Files: CHANGES MANIFEST PKG-INFO README setup.cfg setup.py Log Message: moby-live/Python/ZSI-1.5.0-patched CHANGES,1.1.1.1,NONE MANIFEST,1.1.1.1,NONE PKG-INFO,1.1.1.1,NONE README,1.1.1.1,NONE setup.cfg,1.1.1.1,NONE setup.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/CHANGES,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/MANIFEST,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/PKG-INFO,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/setup.cfg,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/RCS/setup.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFLc0027079@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/ZSI/wstools/test Removed Files: __init__.py test_t1.py test_wsdl.py test_wstools.py test_wstools_net.py Log Message: moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test __init__.py,1.1.1.1,NONE test_t1.py,1.1.1.1,NONE test_wsdl.py,1.1.1.1,NONE test_wstools.py,1.1.1.1,NONE test_wstools_net.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/__init__.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/test_t1.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/test_wsdl.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/test_wstools.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/test/RCS/test_wstools_net.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:20 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFKo8026975@pub.open-bio.org> yanwong Wed Dec 8 06:15:20 EST 2004 Update of /home/repository/moby/moby-live/Python In directory pub.open-bio.org:/tmp/cvs-serv26947/Python Removed Files: PKG-INFO README TODO changelog setup.py Log Message: moby-live/Python PKG-INFO,1.1.1.1,NONE README,1.1.1.1,NONE TODO,1.1.1.1,NONE changelog,1.1.1.1,NONE setup.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/RCS/PKG-INFO,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/RCS/TODO,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/RCS/changelog,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/RCS/setup.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFLB3027059@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/ZSI/wstools Removed Files: TimeoutSocket.py UserTuple.py Utility.py WSDLTools.py XMLSchema.py XMLname.py __init__.py Log Message: moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools TimeoutSocket.py,1.1.1.1,NONE UserTuple.py,1.1.1.1,NONE Utility.py,1.1.1.1,NONE WSDLTools.py,1.1.1.1,NONE XMLSchema.py,1.1.1.1,NONE XMLname.py,1.1.1.1,NONE __init__.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/TimeoutSocket.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/UserTuple.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/Utility.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/WSDLTools.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/XMLSchema.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/XMLname.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/wstools/RCS/__init__.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFKbl027032@pub.open-bio.org> yanwong Wed Dec 8 06:15:20 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/ZSI Removed Files: ServiceProxy.py TC.py TCapache.py TCcompound.py TCnumbers.py TCtimes.py __init__.py auth.py client.py compat.py dispatch.py fault.py parse.py resolvers.py typeinterpreter.py version.py writer.py wsdl2python.py wsdlInterface.py Log Message: moby-live/Python/ZSI-1.5.0-patched/ZSI ServiceProxy.py,1.1.1.1,NONE TC.py,1.1.1.1,NONE TCapache.py,1.1.1.1,NONE TCcompound.py,1.1.1.1,NONE TCnumbers.py,1.1.1.1,NONE TCtimes.py,1.1.1.1,NONE __init__.py,1.1.1.1,NONE auth.py,1.1.1.1,NONE client.py,1.1.1.1,NONE compat.py,1.1.1.1,NONE dispatch.py,1.1.1.1,NONE fault.py,1.1.1.1,NONE parse.py,1.1.1.1,NONE resolvers.py,1.1.1.1,NONE typeinterpreter.py,1.1.1.1,NONE version.py,1.1.1.1,NONE writer.py,1.1.1.1,NONE wsdl2python.py,1.1.1.1,NONE wsdlInterface.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/ServiceProxy.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/TC.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/TCapache.py,v: No such file or directory rcsdiff: 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file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/parse.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/resolvers.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/typeinterpreter.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/version.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/writer.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/wsdl2python.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/ZSI/RCS/wsdlInterface.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFLVu027159@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/samples In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/samples Removed Files: README poly.py Log Message: moby-live/Python/ZSI-1.5.0-patched/samples README,1.1.1.1,NONE poly.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/samples/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/samples/RCS/poly.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:22 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFM1A027210@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/test Removed Files: README cgicli.py test_t1.py test_t2.py test_t3.py test_t4.py test_t5.py test_t6.py test_t7.py test_zsi.py test_zsi_net.py tests_bad.py tests_good.py Log Message: moby-live/Python/ZSI-1.5.0-patched/test README,1.1.1.1,NONE cgicli.py,1.1.1.1,NONE test_t1.py,1.1.1.1,NONE test_t2.py,1.1.1.1,NONE test_t3.py,1.1.1.1,NONE test_t4.py,1.1.1.1,NONE test_t5.py,1.1.1.1,NONE test_t6.py,1.1.1.1,NONE test_t7.py,1.1.1.1,NONE test_zsi.py,1.1.1.1,NONE test_zsi_net.py,1.1.1.1,NONE tests_bad.py,1.1.1.1,NONE tests_good.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/cgicli.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/test_t1.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/test_t2.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/test_t3.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/test_t4.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/test_t5.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/test_t6.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/test_t7.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/test_zsi.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/test_zsi_net.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/tests_bad.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/test/RCS/tests_good.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFLq3027176@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/scripts In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/scripts Removed Files: wsdl2py Log Message: moby-live/Python/ZSI-1.5.0-patched/scripts wsdl2py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/scripts/RCS/wsdl2py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFL70027139@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/interop Removed Files: InteropTest.wsdl InteropTestB.wsdl README client.py cpackets.py echoHeaderBindings.wsdl sclasses.py server.py Log Message: moby-live/Python/ZSI-1.5.0-patched/interop InteropTest.wsdl,1.1.1.1,NONE InteropTestB.wsdl,1.1.1.1,NONE README,1.1.1.1,NONE client.py,1.1.1.1,NONE cpackets.py,1.1.1.1,NONE echoHeaderBindings.wsdl,1.1.1.1,NONE sclasses.py,1.1.1.1,NONE server.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/InteropTest.wsdl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/InteropTestB.wsdl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/client.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/cpackets.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/echoHeaderBindings.wsdl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/sclasses.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/interop/RCS/server.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:21 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFL1V027116@pub.open-bio.org> yanwong Wed Dec 8 06:15:21 EST 2004 Update of /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/ZSI-1.5.0-patched/doc Removed Files: .cvsignore Makefile c01-intro.tex c02-samples.tex c02a-coverage.tex c03-except.tex c04-utils.tex c05-parse.tex c06-tc.tex c07-writer.tex c08-fault.tex c09-resolve.tex c10-dispatch.tex c11-wsdl.tex zsi.tex zsi.xsd Log Message: moby-live/Python/ZSI-1.5.0-patched/doc .cvsignore,1.1.1.1,NONE Makefile,1.1.1.1,NONE c01-intro.tex,1.1.1.1,NONE c02-samples.tex,1.1.1.1,NONE c02a-coverage.tex,1.1.1.1,NONE c03-except.tex,1.1.1.1,NONE c04-utils.tex,1.1.1.1,NONE c05-parse.tex,1.1.1.1,NONE c06-tc.tex,1.1.1.1,NONE c07-writer.tex,1.1.1.1,NONE c08-fault.tex,1.1.1.1,NONE c09-resolve.tex,1.1.1.1,NONE c10-dispatch.tex,1.1.1.1,NONE c11-wsdl.tex,1.1.1.1,NONE zsi.tex,1.1.1.1,NONE zsi.xsd,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/.cvsignore,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c07-writer.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c08-fault.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c09-resolve.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c10-dispatch.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/c11-wsdl.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/zsi.tex,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/ZSI-1.5.0-patched/doc/RCS/zsi.xsd,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:22 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFMuO027232@pub.open-bio.org> yanwong Wed Dec 8 06:15:22 EST 2004 Update of /home/repository/moby/moby-live/Python/doc In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/doc Removed Files: epydoc.css howto.pdf index.html Log Message: moby-live/Python/doc epydoc.css,1.1.1.1,NONE howto.pdf,1.1.1.1,NONE index.html,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/doc/RCS/epydoc.css,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/RCS/howto.pdf,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/RCS/index.html,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFV9F028121@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/utils/wx In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/utils/wx Removed Files: README objectBrowser.py Log Message: moby-live/Python/utils/wx README,1.1.1.1,NONE objectBrowser.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/utils/wx/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/utils/wx/RCS/objectBrowser.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFVEv028079@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/webservices In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/tutorials/webservices Removed Files: Clustalw-mod_python.py Clustalw.py Stride.py dispatcher1.py dispatcherCMD.py Log Message: moby-live/Python/tutorials/webservices Clustalw-mod_python.py,1.1.1.1,NONE Clustalw.py,1.1.1.1,NONE Stride.py,1.1.1.1,NONE dispatcher1.py,1.1.1.1,NONE dispatcherCMD.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/Clustalw-mod_python.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/Clustalw.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/Stride.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/dispatcher1.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/webservices/RCS/dispatcherCMD.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:26 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:26 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFQb8027557@pub.open-bio.org> yanwong Wed Dec 8 06:15:25 EST 2004 Update of 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bioMoby.mobyService.ServiceArticle-class.html,1.1.1.1,NONE bioMoby.mobyService.ServiceList-class.html,1.1.1.1,NONE bioMoby.mobyService.ServiceQuery-class.html,1! .1.1.1,NONE bioMoby.mobyService.ServiceSecondary-class.html,1! .1.1.1,NONE bioMoby.ontology-module.html,1.1.1.1,NONE bioMoby.ontology.AGI_LocusCode-module.html,1.1.1.1,NONE bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html,1.1.1.1,NONE bioMoby.ontology.Allele_freq-module.html,1.1.1.1,NONE bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html,1.1.1.1,NONE bioMoby.ontology.AminoAcidSequence-module.html,1.1.1.1,NONE bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html,1.1.1.1,NONE bioMoby.ontology.B64_Encoded_PNG-module.html,1.1.1.1,NONE bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html,1.1.1.1,NONE bioMoby.ontology.B64_Encoded_Postscript-module.html,1.1.1.1,NONE bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html,1.1.1.1,NONE 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bioMoby.ontology.Decypher_Text-module.html,1.1.1.1,NONE bioMoby.ontology.Decypher_Text.MobyDecypher_Text-class.html,1.1.1.1,NONE bioMoby.ontology.Edge-module.html,1.1.1.1,NONE bioMoby.ontology.Edge.MobyEdge-class.html,1.1.1.1,NONE bioMoby.ontology.EmblFlatfile-module.! html,1.1.1.1,NONE bioMoby.ontology.EmblFlatfile.MobyEmblFlatf! ile-class.html,1.1.1.1,NONE bioMoby.ontology.FASTA-module.html,1.1.1.1,NONE bioMoby.ontology.FASTA.MobyFASTA-class.html,1.1.1.1,NONE bioMoby.ontology.GFF-module.html,1.1.1.1,NONE bioMoby.ontology.GFF.MobyGFF-class.html,1.1.1.1,NONE bioMoby.ontology.GFF1-module.html,1.1.1.1,NONE bioMoby.ontology.GFF1.MobyGFF1-class.html,1.1.1.1,NONE bioMoby.ontology.GFF2-module.html,1.1.1.1,NONE bioMoby.ontology.GFF2.MobyGFF2-class.html,1.1.1.1,NONE bioMoby.ontology.GFF2_5-module.html,1.1.1.1,NONE bioMoby.ontology.GFF2_5.MobyGFF2_5-class.html,1.1.1.1,NONE bioMoby.ontology.GFF3-module.html,1.1.1.1,NONE bioMoby.ontology.GFF3.MobyGFF3-class.html,1.1.1.1,NONE bioMoby.ontology.GO_Term-module.html,1.1.1.1,NONE bioMoby.ontology.GO_Term.MobyGO_Term-class.html,1.1.1.1,NONE bioMoby.ontology.GenbankFlatfile-module.html,1.1.1.1,NONE bioMoby.ontology.GenbankFlatfile.MobyGenbankFlatfile-class.html,1.1.1.1,NONE bioMoby.ontology.GenericSequence-module.html,1.1.1.1,NONE bioMoby.ontology.GenericSequence.MobyGe! nericSequence-class.html,1.1.1.1,NONE bioMoby.ontology.GeneticElement-module.html,1.1.1.1,NONE bioMoby.ontology.GeneticElement.MobyGeneticElement-class.html,1.1.1.1,NONE bioMoby.ontology.Germplasm_Details-module.html,1.1.1.1,NONE bioMoby.ontology.Germplasm_Details.MobyGermplasm_Details-class.html,1.1.1.1,NONE bioMoby.ontology.Germplasm_List-module.html,1.1.1.1,NONE bioMoby.ontology.Germplasm_List.MobyGermplasm_List-class.html,1.1.1.1,NONE bioMoby.ontology.Global_Keyword-module.html,1.1.1.1,NONE bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword-class.html,1.1.1.1,NONE bioMoby.ontology.HCA_picture-module.html,1.1.1.1,NONE 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/home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.ontology.Wildcard_Query-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.webservice-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.webservice.Dispatcher-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-bioMoby.webservice.Invocators-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc-everything.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/toc.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/private/RCS/trees.html,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:30 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFUNc027999@pub.open-bio.org> yanwong Wed Dec 8 06:15:30 EST 2004 Update of /home/repository/moby/moby-live/Python/src/ontology In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/src/ontology Removed Files: AGI_LocusCode.py Allele_freq.py AminoAcidSequence.py B64_Encoded_PNG.py B64_Encoded_Postscript.py B64_encoded_PDB.py B64_encoded_gif.py B64_encoded_jpeg.py BasicGFFSequenceFeature.py DNASequence.py DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py Edge.py EmblFlatfile.py FASTA.py GFF.py GFF1.py GFF2.py GFF2_5.py GFF3.py GO_Term.py GenbankFlatfile.py GenericSequence.py GeneticElement.py Germplasm_Details.py Germplasm_List.py Global_Keyword.py HCA_picture.py Haplotyping_Study_obj.py ICIS_Query.py ICIS_Query2.py ICIS_Query3.py IntAct_XML.py Interaction.py InteractionMethod.py Interaction_partner.py Interactor.py MMP_Locus.py MO_Term_Test.py Multi_key_value_pair.py MyTree.py NCBI_BLAST_Text.py NCBI_Blast_XML.py NucleotideSequence.py PDBFormattedText.py PDGJOB.py PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py SchematikonMotifID.py SchematikonMotifSupport.py SchematikonSegmentAttributes.py SchematikonSegmentID.py SchematikonStructureAnnotation.py SchematikonVorocodeName.py Scored_acronym_string.py SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py Simple_key_value_pair.py Snp_allele.py Snp_genotype.py Study.py TargetP_result.py Testout.py TextBase64.py TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py TextXml.py Text_plain.py Trait_Details.py Tree.py VirtualSequence.py WU_BLAST_Text.py Wildcard_Query.py __init__.py Log Message: moby-live/Python/src/ontology AGI_LocusCode.py,1.1.1.1,NONE Allele_freq.py,1.1.1.1,NONE AminoAcidSequence.py,1.1.1.1,NONE B64_Encoded_PNG.py,1.1.1.1,NONE B64_Encoded_Postscript.py,1.1.1.1,NONE B64_encoded_PDB.py,1.1.1.1,NONE B64_encoded_gif.py,1.1.1.1,NONE B64_encoded_jpeg.py,1.1.1.1,NONE BasicGFFSequenceFeature.py,1.1.1.1,NONE 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NucleotideSequence.py,1.1.1.1,NONE PDBFormattedText.py,1.1.1.1,NONE PDGJOB.py,1.1.1.1,NONE PhenotypeDescription.py,1.1.1.1,NONE PubMedMEDLINE.py,1.1.1.1,NONE RNASequence.py,1.1.1.1,NONE SchematikonMotifID.py,1.1.1.1,NONE SchematikonMotifSupport.py,1.1.1.1,NONE SchematikonSegmentAttributes.py,1.1.1.1,NONE SchematikonSegmentID.py,1.1.1.1,NONE SchematikonStructureAnnotation.py,1.1.1.1,NONE SchematikonVorocodeName.py,1.1.1.1,NONE Scored_acronym_string.py,1.1.1.1,NONE SimpleAnnotatedGIFImage.py,1.1.1.1,NONE SimpleAnnotatedJPEGImage.py,1.1.1.1,NONE Simple_key_value_pair.py,1.1.1.1,NONE Snp_allele.py,1.1.1.1,NONE Snp_genotype.py,1.1.1.1,NONE Study.p! y,1.1.1.1,NONE TargetP_result.py,1.1.1.1,NONE Testout.py,1.1.! 1.1,NONE TextBase64.py,1.1.1.1,NONE TextFormatted.py,1.1.1.1,NONE TextHtml.py,1.1.1.1,NONE TextPlain.py,1.1.1.1,NONE TextUuencoded.py,1.1.1.1,NONE TextXml.py,1.1.1.1,NONE Text_plain.py,1.1.1.1,NONE Trait_Details.py,1.1.1.1,NONE Tree.py,1.1.1.1,NONE VirtualSequence.py,1.1.1.1,NONE 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/home/repository/moby/moby-live/Python/src/ontology/RCS/TextUuencoded.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/TextXml.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Text_plain.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Trait_Details.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Tree.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/VirtualSequence.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/WU_BLAST_Text.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/Wildcard_Query.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/ontology/RCS/__init__.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFV5j028099@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/utils In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/utils Removed Files: moby2python.py Log Message: moby-live/Python/utils moby2python.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/utils/RCS/moby2python.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFVRn028039@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/Mobycentral In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/tutorials/Mobycentral Removed Files: deregisterService.py registerService.py retrieveServices.py servicesDump.py Log Message: moby-live/Python/tutorials/Mobycentral deregisterService.py,1.1.1.1,NONE registerService.py,1.1.1.1,NONE retrieveServices.py,1.1.1.1,NONE servicesDump.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/RCS/deregisterService.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/RCS/registerService.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/RCS/retrieveServices.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/RCS/servicesDump.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:29 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFT1L027878@pub.open-bio.org> yanwong Wed Dec 8 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/home/repository/moby/moby-live/Python/doc/public/RCS/toc-bioMoby.ontology.Trait_Details-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/toc-bioMoby.ontology.Tree-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/toc-bioMoby.ontology.VirtualSequence-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/toc-bioMoby.ontology.WU_BLAST_Text-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/toc-bioMoby.ontology.Wildcard_Query-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/toc-bioMoby.webservice-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/toc-bioMoby.webservice.Dispatcher-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/toc-bioMoby.webservice.Invocators-module.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/toc-everything.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/toc.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/public/RCS/trees.html,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFVTo028018@pub.open-bio.org> yanwong Wed Dec 8 06:15:30 EST 2004 Update of /home/repository/moby/moby-live/Python/src/webservice In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/src/webservice Removed Files: Dispatcher.py Invocators.py __init__.py Log Message: moby-live/Python/src/webservice Dispatcher.py,1.1.1.1,NONE Invocators.py,1.1.1.1,NONE __init__.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/src/webservice/RCS/Dispatcher.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/webservice/RCS/Invocators.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/webservice/RCS/__init__.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:30 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFUEx027900@pub.open-bio.org> yanwong Wed Dec 8 06:15:30 EST 2004 Update of /home/repository/moby/moby-live/Python/src In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/src Removed Files: __init__.py mobyClient.py mobyDataTypes.py mobyExceptions.py mobyMarshal.py mobyRegister.py mobyService.py Log Message: moby-live/Python/src __init__.py,1.1.1.1,NONE mobyClient.py,1.1.1.1,NONE mobyDataTypes.py,1.1.1.1,NONE mobyExceptions.py,1.1.1.1,NONE mobyMarshal.py,1.1.1.1,NONE mobyRegister.py,1.1.1.1,NONE mobyService.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/__init__.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyClient.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyDataTypes.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyExceptions.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyMarshal.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyRegister.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/src/RCS/mobyService.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:15:31 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:15:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081115.iB8BFVfY028059@pub.open-bio.org> yanwong Wed Dec 8 06:15:31 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/Service In directory pub.open-bio.org:/tmp/cvs-serv26947/Python/tutorials/Service Removed Files: testMarshaller.py testMobyService.py testMobyService2.py Log Message: moby-live/Python/tutorials/Service testMarshaller.py,1.1.1.1,NONE testMobyService.py,1.1.1.1,NONE testMobyService2.py,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Service/RCS/testMarshaller.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Service/RCS/testMobyService.py,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/tutorials/Service/RCS/testMobyService2.py,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:21:20 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:21:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081121.iB8BLKrP028288@pub.open-bio.org> yanwong Wed Dec 8 06:21:20 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby In directory pub.open-bio.org:/tmp/cvs-serv28264/bioMoby Log Message: Directory /home/repository/moby/moby-live/Python/bioMoby added to the repository moby-live/Python/bioMoby - New directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:21:44 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:21:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081121.iB8BLi3H028331@pub.open-bio.org> yanwong Wed Dec 8 06:21:44 EST 2004 Update of /home/repository/moby/moby-live/Python/packages In directory pub.open-bio.org:/tmp/cvs-serv28307/packages Log Message: Directory /home/repository/moby/moby-live/Python/packages added to the repository moby-live/Python/packages - New directory rcsdiff: /home/repository/moby/moby-live/Python/packages/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/packages/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/packages/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:24:34 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:24:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081124.iB8BOYLA028461@pub.open-bio.org> yanwong Wed Dec 8 06:24:34 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby/webservice In directory pub.open-bio.org:/tmp/cvs-serv28419/webservice Log Message: Directory /home/repository/moby/moby-live/Python/bioMoby/webservice added to the repository moby-live/Python/bioMoby/webservice - New directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/webservice/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/webservice/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/webservice/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:24:34 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:24:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081124.iB8BOY8f028443@pub.open-bio.org> yanwong Wed Dec 8 06:24:34 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby/ontology In directory pub.open-bio.org:/tmp/cvs-serv28419/ontology Log Message: Directory /home/repository/moby/moby-live/Python/bioMoby/ontology added to the repository moby-live/Python/bioMoby/ontology - New directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/ontology/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/ontology/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/ontology/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:25:23 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:25:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081125.iB8BPNdV028520@pub.open-bio.org> yanwong Wed Dec 8 06:25:23 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/src In directory pub.open-bio.org:/tmp/cvs-serv28496/src Log Message: Directory /home/repository/moby/moby-live/Python/doc/src added to the repository moby-live/Python/doc/src - New directory rcsdiff: /home/repository/moby/moby-live/Python/doc/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Python/doc/src/RCS/directory,v: No such file or directory From yanwong at pub.open-bio.org Wed Dec 8 11:26:02 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:26:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081126.iB8BQ2tq028580@pub.open-bio.org> yanwong Wed Dec 8 06:26:02 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby In directory pub.open-bio.org:/tmp/cvs-serv28528/Python/bioMoby Added Files: __init__.py mobyClient.py mobyDataTypes.py mobyExceptions.py mobyMarshal.py mobyRegister.py mobyService.py Log Message: moby-live/Python/bioMoby __init__.py,NONE,1.1 mobyClient.py,NONE,1.1 mobyDataTypes.py,NONE,1.1 mobyExceptions.py,NONE,1.1 mobyMarshal.py,NONE,1.1 mobyRegister.py,NONE,1.1 mobyService.py,NONE,1.1 From yanwong at pub.open-bio.org Wed Dec 8 11:26:02 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 06:26:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081126.iB8BQ2Ja028565@pub.open-bio.org> yanwong Wed Dec 8 06:26:01 EST 2004 Update of /home/repository/moby/moby-live/Python In directory pub.open-bio.org:/tmp/cvs-serv28528/Python Added Files: PKG-INFO README changelog setup.py Log Message: moby-live/Python PKG-INFO,1.2,1.3 README,1.2,1.3 changelog,1.2,1.3 setup.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/PKG-INFO,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/PKG-INFO 2004/12/08 11:15:20 1.2 +++ /home/repository/moby/moby-live/Python/PKG-INFO 2004/12/08 11:26:01 1.3 @@ -1,10 +1,10 @@ Metadata-Version: 1.0 Name: bioMoby -Version: 0.5 +Version: 0.7p1 Summary: Python interface for bioMoby Home-page: http://bioserv.rpbs.jussieu.fr Author: Yan Wong Author-email: yanwong at ebgm.jussieu.fr License: -Description: Python's version of Moby's API 0.7 +Description: Python's version of Moby's API 0.8 Platform: UNKNOWN =================================================================== RCS file: /home/repository/moby/moby-live/Python/README,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/README 2004/12/08 11:15:20 1.2 +++ /home/repository/moby/moby-live/Python/README 2004/12/08 11:26:01 1.3 @@ -6,11 +6,13 @@ -Python 2.3 -SOAPpy : http://pywebsvcs.sourceforge.net/ -xml libraries for python: http://pyxml.sourceforge.net (generally already included in python 2.2+) + however if you have some troubles you may need to install PyXML 0.8.3 -if you plan to build webservices with Python, have a look on ZSI gived in this distribution (ZSI-1.5.0-patched) the ZSI here has been patched due to some trouble with CDATA section node __init__.py has been modified in order to solve this problem -pyipc: http://www.theory.org/~mac4/software/ for ipc management with Python (the Dispatcher class needs it) +All these libraries has been added in the packages directory. How to setup bioMoby-python? =================================================================== RCS file: /home/repository/moby/moby-live/Python/changelog,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/changelog 2004/12/08 11:15:20 1.2 +++ /home/repository/moby/moby-live/Python/changelog 2004/12/08 11:26:01 1.3 @@ -31,4 +31,28 @@ add a __setitem__ method to the MobyContent class queries are now accessible via the key directly, use mobycontent['querykey'] to access the data and parameters inside a tool in the utils/wx, objectBrowser is a GUI program to browse the bioMoby Ontology - + +0.6: Bug in the MobyObject corrected + Bug in the Dispatcher corrected (troubles with handling multiple queries) + added signatureURL and RDF for Registration process (in Service, ServiceList) + debug option when executing a service (trace of HTTP calls) in Central and Service Class + (allows you to have the dump of all your SOAP transaction with the webservice) + if you want to trace a SOAP call while executing a service just put: + service.execute(mobyqueries, debug=True) and you'll have the complete trace of the execution + when you deal with the Moby Central Server, just add client.server.config.debug=1 in order to trace execution of your queries + +0.7: Create a class AbstractDispatcher, SimpleDispatcher in order to create other types of dispatchers + On PBSDispatcher, a class qsubParameters designed to store parameters for the qsub command + Class Parameter deserialisation (fromMoby) + Some cleaning on the code, and even more debugging;) + Documentation has been updated + Libraries that were used to build this packages has been added into the packages directory + +0.7p1: Dispatchers can deserialize MobyContent that were in Body tag people using mod_python will have + to patch their ZSI package again. + just do a: + cd packages/ZSI-1.5.0-patched + python setup.py install + (normally just the dispatch.py was modified) + + tutorials/webservice and documentations have been updated. =================================================================== RCS file: /home/repository/moby/moby-live/Python/setup.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/setup.py 2004/12/08 11:15:20 1.2 +++ /home/repository/moby/moby-live/Python/setup.py 2004/12/08 11:26:01 1.3 @@ -9,4 +9,4 @@ author_email="yanwong at ebgm.jussieu.fr", url="http://bioserv.rpbs.jussieu.fr", packages=['bioMoby', 'bioMoby.ontology', 'bioMoby.webservice'], - package_dir={'bioMoby':'src', 'bioMoby.ontology':'src/ontology', 'bioMoby.webservice':'src/webservice'}) + package_dir={'bioMoby':'bioMoby', 'bioMoby.ontology':'bioMoby/ontology', 'bioMoby.webservice':'bioMoby/webservice'}) From yanwong at pub.open-bio.org Wed Dec 8 14:46:40 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:46:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081446.iB8EkeMG029581@pub.open-bio.org> yanwong Wed Dec 8 09:46:40 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby/webservice In directory pub.open-bio.org:/tmp/cvs-serv29560 Added Files: Dispatcher.py Invocators.py TCBioMoby.py __init__.py Log Message: moby-live/Python/bioMoby/webservice Dispatcher.py,NONE,1.1 Invocators.py,NONE,1.1 TCBioMoby.py,NONE,1.1 __init__.py,NONE,1.1 From yanwong at pub.open-bio.org Wed Dec 8 14:47:49 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:47:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081447.iB8ElnHb029634@pub.open-bio.org> yanwong Wed Dec 8 09:47:49 EST 2004 Update of /home/repository/moby/moby-live/Python/bioMoby/ontology In directory pub.open-bio.org:/tmp/cvs-serv29613 Added Files: AlleleAssociation.py Allele_freq.py AminoAcidSequence.py B64_Encoded_PNG.py B64_Encoded_Postscript.py B64_encoded_PDB.py B64_encoded_gif.py B64_encoded_jpeg.py BLASTText.py BasicGFFSequenceFeature.py ClustalAlnFormattedText.py ClustalMsfFormattedText.py CommentedAASequence.py CommentedDNASequence.py CommentedRNASequence.py DNASequence.py DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py Edge.py EmblFlatfile.py FASTA.py FASTA_AA.py FASTA_NA.py FASTA_Text.py GFF.py GFF1.py GFF2.py GFF2_5.py GFF3.py GO_Term.py GenbankFlatfile.py GenericSequence.py GeneticElement.py Genotype.py Germplasm_Details.py Germplasm_List.py Global_Keyword.py HBond_Pair.py HFormatText.py Haplotyping_Study_obj.py ICIS_Query.py ICIS_Query2.py ICIS_Query3.py IntAct_XML.py Interaction.py InteractionMethod.py Interaction_partner.py Interactor.py MEME_Text.py MGIS_ACCESSION.py MMP_Locus.py MO_Term_Test.py MmCIFText.py Multi_key_value_pair.py MyTestingDataType_11024145298313.py MyTree.py NCBI_BLAST_Text.py NCBI_Blast_XML.py NCBI_Blast_XML_Gif.py NCBI_Blast_XML_Gif_Map.py NCBI_MEME_Text.py NucleotideSequence.py PDBFormattedText.py PDBText.py PDGJOB.py PHDText.py PMUTText.py PSeaTextFormatted.py PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py SINGER_ACCESSION.py Sample.py SchematikonMotifID.py SchematikonMotifSupport.py SchematikonSegmentAttributes.py SchematikonSegmentID.py SchematikonStructureAnnotation.py SchematikonVorocodeName.py Scored_acronym_string.py SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py Simple_key_value_pair.py Snp_allele.py Snp_genotype.py Study.py TEST.py TargetP_result.py Testout.py TextBase64.py TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py TextXml.py Text_plain.py Trait_Details.py Tree.py TropGENE_ACCESSION.py TropGENE_Diversity_Matrix.py TropGENE_LOCUS.py VirtualSequence.py WU_BLAST_Text.py Wildcard_Query.py __init__.py Log Message: moby-live/Python/bioMoby/ontology AlleleAssociation.py,NONE,1.1 Allele_freq.py,NONE,1.1 AminoAcidSequence.py,NONE,1.1 B64_Encoded_PNG.py,NONE,1.1 B64_Encoded_Postscript.py,NONE,1.1 B64_encoded_PDB.py,NONE,1.1 B64_encoded_gif.py,NONE,1.1 B64_encoded_jpeg.py,NONE,1.1 BLASTText.py,NONE,1.1 BasicGFFSequenceFeature.py,NONE,1.1 ClustalAlnFormattedText.py,NONE,1.1 ClustalMsfFormattedText.py,NONE,1.1 CommentedAASequence.py,NONE,1.1 CommentedDNASequence.py,NONE,1.1 CommentedRNASequence.py,NONE,1.1 DNASequence.py,NONE,1.1 DNASequenceWithGFFFeatures.py,NONE,1.1 DateTime.py,NONE,1.1 Decypher_Text.py,NONE,1.1 Edge.py,NONE,1.1 EmblFlatfile.py,NONE,1.1 FASTA.py,NONE,1.1 FASTA_AA.py,NONE,1.1 FASTA_NA.py,NONE,1.1 FASTA_Text.py,NONE,1.1 GFF.py,NONE,1.1 GFF1.py,NONE,1.1 GFF2.py,NONE,1.1 GFF2_5.py,NONE,1.1 GFF3.py,NONE,1.1 GO_Term.py,NONE,1.1 GenbankFlatfile.py,NONE,1.1 GenericSequence.py,NONE,1.1 GeneticElement.py,NONE,1.1 Genotype.py,NONE,1.1 Germplasm_Details.py,NONE,1.1 Germplasm_List.py,NO! NE,1.1 Global_Keyword.py,NONE,1.1 HBond_Pair.py,NONE,1.1 HFormatText.py,NONE,1.1 Haplotyping_Study_obj.py,NONE,1.1 ICIS_Query.py,NONE,1.1 ICIS_Query2.py,NONE,1.1 ICIS_Query3.py,NONE,1.1 IntAct_XML.py,NONE,1.1 Interaction.py,NONE,1.1 InteractionMethod.py,NONE,1.1 Interaction_partner.py,NONE,1.1 Interactor.py,NONE,1.1 MEME_Text.py,NONE,1.1 MGIS_ACCESSION.py,NONE,1.1 MMP_Locus.py,NONE,1.1 MO_Term_Test.py,NONE,1.1 MmCIFText.py,NONE,1.1 Multi_key_value_pair.py,NONE,1.1 MyTestingDataType_11024145298313.py,NONE,1.1 MyTree.py,NONE,1.1 NCBI_BLAST_Text.py,NONE,1.1 NCBI_Blast_XML.py,NONE,1.1 NCBI_Blast_XML_Gif.py,NONE,1.1 NCBI_Blast_XML_Gif_Map.py,NONE,1.1 NCBI_MEME_Text.py,NONE,1.1 NucleotideSequence.py,NONE,1.1 PDBFormattedText.py,NONE,1.1 PDBText.py,NONE,1.1 PDGJOB.py,NONE,1.1 PHDText.py,NONE,1.1 PMUTText.py,NONE,1.1 PSeaTextFormatted.py,NONE,1.1 PhenotypeDescription.py,NONE,1.1 PubMedMEDLINE.py,NONE,1.1 RNASequence.py,NONE,1.1 SINGER_ACCESSION.py,NONE,1.1 Sample.py,NONE,1.1 Schemat! ikonMotifID.py,NONE,1.1 SchematikonMotifSupport.py,NONE,1.1 S! chematikonSegmentAttributes.py,NONE,1.1 SchematikonSegmentID.py,NONE,1.1 SchematikonStructureAnnotation.py,NONE,1.1 SchematikonVorocodeName.py,NONE,1.1 Scored_acronym_string.py,NONE,1.1 SimpleAnnotatedGIFImage.py,NONE,1.1 SimpleAnnotatedJPEGImage.py,NONE,1.1 Simple_key_value_pair.py,NONE,1.1 Snp_allele.py,NONE,1.1 Snp_genotype.py,NONE,1.1 Study.py,NONE,1.1 TEST.py,NONE,1.1 TargetP_result.py,NONE,1.1 Testout.py,NONE,1.1 TextBase64.py,NONE,1.1 TextFormatted.py,NONE,1.1 TextHtml.py,NONE,1.1 TextPlain.py,NONE,1.1 TextUuencoded.py,NONE,1.1 TextXml.py,NONE,1.1 Text_plain.py,NONE,1.1 Trait_Details.py,NONE,1.1 Tree.py,NONE,1.1 TropGENE_ACCESSION.py,NONE,1.1 TropGENE_Diversity_Matrix.py,NONE,1.1 TropGENE_LOCUS.py,NONE,1.1 VirtualSequence.py,NONE,1.1 WU_BLAST_Text.py,NONE,1.1 Wildcard_Query.py,NONE,1.1 __init__.py,NONE,1.1 From yanwong at pub.open-bio.org Wed Dec 8 14:48:40 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:48:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081448.iB8EmeLf029679@pub.open-bio.org> yanwong Wed Dec 8 09:48:40 EST 2004 Update of /home/repository/moby/moby-live/Python/packages In directory pub.open-bio.org:/tmp/cvs-serv29658 Added Files: PyIPC.tar.bz2 PyXML-0.8.3.tar.bz2 SOAPpy-0.11.4.tar.bz2 ZSI-1.5.0-patched-2.tar.bz2 fpconst-0.6.0.tar.bz2 Log Message: moby-live/Python/packages PyIPC.tar.bz2,NONE,1.1 PyXML-0.8.3.tar.bz2,NONE,1.1 SOAPpy-0.11.4.tar.bz2,NONE,1.1 ZSI-1.5.0-patched-2.tar.bz2,NONE,1.1 fpconst-0.6.0.tar.bz2,NONE,1.1 From yanwong at pub.open-bio.org Wed Dec 8 14:53:40 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:53:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081453.iB8ErePs029779@pub.open-bio.org> yanwong Wed Dec 8 09:53:40 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/webservices In directory pub.open-bio.org:/tmp/cvs-serv29748 Added Files: Clustalw-mod_python.py Clustalw.py blastpgp.py wsStride.py Log Message: wsStride is an example of wrapping Stride as a webservice: to query it, just give a PDB id like namespace="PDB" id="1AKQ" the service queries the PDB and calculate stride with it moby-live/Python/tutorials/webservices Clustalw-mod_python.py,1.2,1.3 Clustalw.py,1.2,1.3 blastpgp.py,NONE,1.1 wsStride.py,NONE,1.1 =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw-mod_python.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw-mod_python.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw-mod_python.py 2004/12/08 14:53:40 1.3 @@ -36,7 +36,11 @@ d=Dispatcher(mobyContent, LocalInvocator, _toParameters) return d.execute() - + +from ZSI import dispatch +from mod_python import apache +from bioMoby.webservice import TCBioMoby + def handler(req): if req.method=='GET': if req.args=='wsdl': @@ -50,6 +54,6 @@ req.write("ClustalwClustalw") else: - dispatch.AsHandler(modules=(Clustalw,),request=req) + dispatch.AsHandler(modules=(Clustalw,),request=req, typesmodule=TCBioMoby) return apache.OK =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/webservices/Clustalw.py 2004/12/08 14:53:40 1.3 @@ -31,12 +31,21 @@ return (commandName, " type=p -align "+" ".join(parameters), tempfiles, outputfiles) +def ClustalFormatter(results): + def ClustalFormatter(results): + """Return the results in a MobyClustalAlnFormattedText object + """ + from bioMoby import MobyClustalAlnFormattedText + + return [MobyClustalAlnFormattedText(content=results)] + def clustalw(mobyContent): from bioMoby import Dispatcher, LocalInvocator - d=Dispatcher(mobyContent, LocalInvocator, commandBuilder) + d=Dispatcher(mobyContent, LocalInvocator, commandBuilder, formatter=ClustalFormatter) return d.execute() from ZSI import dispatch -dispatch.asCGI() \ No newline at end of file +from bioMoby.webservice import TCBioMoby +dispatch.asCGI(typesmodule=TCBioMoby) From yanwong at pub.open-bio.org Wed Dec 8 14:54:50 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:54:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081454.iB8EsoS9029833@pub.open-bio.org> yanwong Wed Dec 8 09:54:50 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/Service In directory pub.open-bio.org:/tmp/cvs-serv29800 Added Files: async.py blastpgp.py testMarshaller.py testMobyService.py testMobyService2.py Log Message: moby-live/Python/tutorials/Service async.py,NONE,1.1 blastpgp.py,NONE,1.1 testMarshaller.py,1.2,1.3 testMobyService.py,1.2,1.3 testMobyService2.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Service/testMarshaller.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Service/testMarshaller.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Service/testMarshaller.py 2004/12/08 14:54:50 1.3 @@ -29,7 +29,7 @@ o=um.loads(s) -print "content of the object" -for object in o.queryData: - print str(object) +print "contents:" +for query in o.keys(): + print o[query][0].content =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService.py 2004/12/08 14:54:50 1.3 @@ -30,7 +30,7 @@ print "Service getNASC_codebyAGI_locus executed with query1 namespace=AGI_LocusCode and id=At3g19100...\n" - resultat=myService.execute(query) + resultat=myService.execute(query, debug=True) print "the xml form\n" =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService2.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService2.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Service/testMobyService2.py 2004/12/08 14:54:50 1.3 @@ -16,7 +16,7 @@ object=MobyObject(namespace='DragonDB_Allele',id='cho') print "Service executed with query namespace=DragonDB_Allele and id=cho" -resultat=service.execute(MobyContent({'query1':[object]})) +resultat=service.execute(MobyContent({'query1':[object]}), debug=True) print resultat From yanwong at pub.open-bio.org Wed Dec 8 14:55:22 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:55:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081455.iB8EtMBX029887@pub.open-bio.org> yanwong Wed Dec 8 09:55:22 EST 2004 Update of /home/repository/moby/moby-live/Python/tutorials/Mobycentral In directory pub.open-bio.org:/tmp/cvs-serv29854 Added Files: registerService.py retrieveServices.py servicesDump.py Log Message: moby-live/Python/tutorials/Mobycentral registerService.py,1.2,1.3 retrieveServices.py,1.2,1.3 servicesDump.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/registerService.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Mobycentral/registerService.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Mobycentral/registerService.py 2004/12/08 14:55:22 1.3 @@ -43,6 +43,7 @@ 'name':'getStrideFromPDB', 'type':'Analysis', 'url':'http://prot3.rpbs.jussieu.fr:8080/ZStrideService/ZStrideService.py', + 'signatureURL':'http://prot3.rpbs.jussieu.fr:8080/RDF', 'authoritative':0, 'contactEmail':'yanwong at ebgm.jussieu.fr', 'authURI':'prot3.rpbs.jussieu.fr', @@ -56,6 +57,7 @@ if resultat.isSuccess(): print "Service registration successful" + print resultat.RDF else: print resultat.message raise Exception =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/retrieveServices.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/tutorials/Mobycentral/servicesDump.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/tutorials/Mobycentral/servicesDump.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/tutorials/Mobycentral/servicesDump.py 2004/12/08 14:55:22 1.3 @@ -2,7 +2,7 @@ from bioMoby import Client, ServiceQuery, ServiceArticle, ServiceSecondary -client=Client() +client=Client(url="http://mips.gsf.de/cgi-bin/proj/planet/moby/MOBY-Central.pl", ns="http://mips.gsf.de/MOBY/Central") dsn=client.retrieveServiceNames() From yanwong at pub.open-bio.org Wed Dec 8 14:57:28 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Wed, 8 Dec 2004 09:57:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412081457.iB8EvS4x029956@pub.open-bio.org> yanwong Wed Dec 8 09:57:28 EST 2004 Update of /home/repository/moby/moby-live/Python In directory pub.open-bio.org:/tmp/cvs-serv29919 Modified Files: PKG-INFO README changelog setup.py Log Message: moby-live/Python PKG-INFO,1.3,1.4 README,1.3,1.4 changelog,1.3,1.4 setup.py,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Python/PKG-INFO,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Python/README,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Python/changelog,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Python/setup.py,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 From yanwong at pub.open-bio.org Thu Dec 9 14:07:37 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu, 9 Dec 2004 09:07:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091407.iB9E7bpV003498@pub.open-bio.org> yanwong Thu Dec 9 09:07:32 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/private In directory pub.open-bio.org:/tmp/cvs-serv2265 Added Files: ZSI.TC.TypeCode-class.html __builtin__.object-class.html __builtin__.type-class.html bioMoby-module.html bioMoby.mobyClient-module.html bioMoby.mobyClient.Central-class.html bioMoby.mobyClient.Client-class.html bioMoby.mobyDataTypes-module.html bioMoby.mobyDataTypes.MobyContent-class.html bioMoby.mobyDataTypes.MobyFloat-class.html bioMoby.mobyDataTypes.MobyInteger-class.html bioMoby.mobyDataTypes.MobyObject-class.html bioMoby.mobyDataTypes.MobySequence-class.html bioMoby.mobyDataTypes.MobyString-class.html bioMoby.mobyDataTypes.MobyXref-class.html bioMoby.mobyDataTypes.MobyZmPDB-class.html bioMoby.mobyDataTypes.Parameter-class.html bioMoby.mobyExceptions-module.html bioMoby.mobyExceptions.EInvalidArgument-class.html bioMoby.mobyExceptions.EInvalidType-class.html bioMoby.mobyExceptions.EMethodRetrieveError-class.html bioMoby.mobyExceptions.ENotAWSMethod-class.html bioMoby.mobyExceptions.ETypeMismatch-class.html bioMoby.mobyMarshal-module.html bioMoby.mobyMarshal.MobyMarshaller-class.html bioMoby.mobyMarshal.MobyUnmarshaller-class.html bioMoby.mobyRegister-module.html bioMoby.mobyRegister.GeneralInformations-class.html bioMoby.mobyRegister.Namespace-class.html bioMoby.mobyRegister.ObjectClass-class.html bioMoby.mobyRegister.RegistrationObject-class.html bioMoby.mobyRegister.ServiceType-class.html bioMoby.mobyService-module.html bioMoby.mobyService.Service-class.html bioMoby.mobyService.ServiceArticle-class.html bioMoby.mobyService.ServiceList-class.html bioMoby.mobyService.ServiceQuery-class.html bioMoby.mobyService.ServiceSecondary-class.html bioMoby.ontology-module.html bioMoby.ontology.AGI_LocusCode-module.html bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html bioMoby.ontology.Allele_freq-module.html bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html bioMoby.ontology.AminoAcidSequence-module.html bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html bioMoby.ontology.B64_Encoded_PNG-module.html bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html bioMoby.ontology.B64_Encoded_Postscript-module.html bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html bioMoby.ontology.B64_encoded_PDB-module.html bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html bioMoby.ontology.B64_encoded_gif-module.html bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html bioMoby.ontology.B64_encoded_jpeg-module.html bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg-class.html bioMoby.ontology.BasicGFFSequenceFeature-module.html bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature-class.html bioMoby.ontology.ClustalAlnFormattedText-module.html bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText-class.html bioMoby.ontology.CommentedAASequence-module.html bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence-class.html bioMoby.ontology.CommentedDNASequence-module.html bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence-class.html bioMoby.ontology.CommentedRNASequence-module.html bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence-class.html bioMoby.ontology.DNASequence-module.html bioMoby.ontology.DNASequence.MobyDNASequence-class.html bioMoby.ontology.DNASequenceWithGFFFeatures-module.html bioMoby.ontology.DNASequenceWithGFFFeatures.MobyDNASequenceWithGFFFeatures-class.html bioMoby.ontology.DateTime-module.html bioMoby.ontology.DateTime.MobyDateTime-class.html bioMoby.ontology.Decypher_Text-module.html bioMoby.ontology.Decypher_Text.MobyDecypher_Text-class.html bioMoby.ontology.Edge-module.html bioMoby.ontology.Edge.MobyEdge-class.html bioMoby.ontology.EmblFlatfile-module.html bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile-class.html bioMoby.ontology.FASTA-module.html bioMoby.ontology.FASTA.MobyFASTA-class.html bioMoby.ontology.FASTA_AA-module.html bioMoby.ontology.FASTA_AA.MobyFASTA_AA-class.html bioMoby.ontology.FASTA_NA-module.html bioMoby.ontology.FASTA_NA.MobyFASTA_NA-class.html bioMoby.ontology.GFF-module.html bioMoby.ontology.GFF.MobyGFF-class.html bioMoby.ontology.GFF1-module.html bioMoby.ontology.GFF1.MobyGFF1-class.html bioMoby.ontology.GFF2-module.html bioMoby.ontology.GFF2.MobyGFF2-class.html bioMoby.ontology.GFF2_5-module.html bioMoby.ontology.GFF2_5.MobyGFF2_5-class.html bioMoby.ontology.GFF3-module.html bioMoby.ontology.GFF3.MobyGFF3-class.html bioMoby.ontology.GO_Term-module.html bioMoby.ontology.GO_Term.MobyGO_Term-class.html bioMoby.ontology.GenbankFlatfile-module.html bioMoby.ontology.GenbankFlatfile.MobyGenbankFlatfile-class.html bioMoby.ontology.GenericSequence-module.html bioMoby.ontology.GenericSequence.MobyGenericSequence-class.html bioMoby.ontology.GeneticElement-module.html bioMoby.ontology.GeneticElement.MobyGeneticElement-class.html bioMoby.ontology.Germplasm_Details-module.html bioMoby.ontology.Germplasm_Details.MobyGermplasm_Details-class.html bioMoby.ontology.Germplasm_List-module.html bioMoby.ontology.Germplasm_List.MobyGermplasm_List-class.html bioMoby.ontology.Global_Keyword-module.html bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword-class.html bioMoby.ontology.HBond_Pair-module.html bioMoby.ontology.HBond_Pair.MobyHBond_Pair-class.html bioMoby.ontology.HCA_picture-module.html bioMoby.ontology.HCA_picture.MobyHCA_picture-class.html bioMoby.ontology.Haplotyping_Study_obj-module.html bioMoby.ontology.Haplotyping_Study_obj.MobyHaplotyping_Study_obj-class.html bioMoby.ontology.ICIS_Query-module.html bioMoby.ontology.ICIS_Query.MobyICIS_Query-class.html bioMoby.ontology.ICIS_Query2-module.html bioMoby.ontology.ICIS_Query2.MobyICIS_Query2-class.html bioMoby.ontology.ICIS_Query3-module.html bioMoby.ontology.ICIS_Query3.MobyICIS_Query3-class.html bioMoby.ontology.IntAct_XML-module.html bioMoby.ontology.IntAct_XML.MobyIntAct_XML-class.html bioMoby.ontology.Interaction-module.html bioMoby.ontology.Interaction.MobyInteraction-class.html bioMoby.ontology.InteractionMethod-module.html bioMoby.ontology.InteractionMethod.MobyInteractionMethod-class.html bioMoby.ontology.Interaction_partner-module.html bioMoby.ontology.Interaction_partner.MobyInteraction_partner-class.html bioMoby.ontology.Interactor-module.html bioMoby.ontology.Interactor.MobyInteractor-class.html bioMoby.ontology.MEME_Text-module.html bioMoby.ontology.MEME_Text.MobyMEME_Text-class.html bioMoby.ontology.MGIS_ACCESSION-module.html bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION-class.html bioMoby.ontology.MMP_Locus-module.html bioMoby.ontology.MMP_Locus.MobyMMP_Locus-class.html bioMoby.ontology.MO_Term_Test-module.html bioMoby.ontology.MO_Term_Test.MobyMO_Term_Test-class.html bioMoby.ontology.Multi_key_value_pair-module.html bioMoby.ontology.Multi_key_value_pair.MobyMulti_key_value_pair-class.html bioMoby.ontology.MyTree-module.html bioMoby.ontology.MyTree.MobyMyTree-class.html bioMoby.ontology.NCBI_BLAST_Text-module.html bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text-class.html bioMoby.ontology.NCBI_Blast_XML-module.html bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML-class.html bioMoby.ontology.NCBI_MEME_Text-module.html bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text-class.html bioMoby.ontology.NucleotideSequence-module.html bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence-class.html bioMoby.ontology.PDBFormattedText-module.html bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText-class.html bioMoby.ontology.PDGJOB-module.html bioMoby.ontology.PDGJOB.MobyPDGJOB-class.html bioMoby.ontology.PhenotypeDescription-module.html bioMoby.ontology.PhenotypeDescription.MobyPhenotypeDescription-class.html bioMoby.ontology.PubMedMEDLINE-module.html bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE-class.html bioMoby.ontology.RNASequence-module.html bioMoby.ontology.RNASequence.MobyRNASequence-class.html bioMoby.ontology.SINGER_ACCESSION-module.html bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION-class.html bioMoby.ontology.SchematikonMotifID-module.html bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID-class.html bioMoby.ontology.SchematikonMotifSupport-module.html bioMoby.ontology.SchematikonMotifSupport.MobySchematikonMotifSupport-class.html bioMoby.ontology.SchematikonSegmentAttributes-module.html bioMoby.ontology.SchematikonSegmentAttributes.MobySchematikonSegmentAttributes-class.html bioMoby.ontology.SchematikonSegmentID-module.html bioMoby.ontology.SchematikonSegmentID.MobySchematikonSegmentID-class.html bioMoby.ontology.SchematikonStructureAnnotation-module.html bioMoby.ontology.SchematikonStructureAnnotation.MobySchematikonStructureAnnotation-class.html bioMoby.ontology.SchematikonVorocodeName-module.html bioMoby.ontology.SchematikonVorocodeName.MobySchematikonVorocodeName-class.html bioMoby.ontology.Scored_acronym_string-module.html bioMoby.ontology.Scored_acronym_string.MobyScored_acronym_string-class.html bioMoby.ontology.SimpleAnnotatedGIFImage-module.html bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage-class.html bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage-class.html bioMoby.ontology.Simple_key_value_pair-module.html bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair-class.html bioMoby.ontology.Snp_allele-module.html bioMoby.ontology.Snp_allele.MobySnp_allele-class.html bioMoby.ontology.Snp_genotype-module.html bioMoby.ontology.Snp_genotype.MobySnp_genotype-class.html bioMoby.ontology.Study-module.html bioMoby.ontology.Study.MobyStudy-class.html bioMoby.ontology.TEST-module.html bioMoby.ontology.TEST.MobyTEST-class.html bioMoby.ontology.TargetP_result-module.html bioMoby.ontology.TargetP_result.MobyTargetP_result-class.html bioMoby.ontology.Testout-module.html bioMoby.ontology.Testout.MobyTestout-class.html bioMoby.ontology.TextBase64-module.html bioMoby.ontology.TextBase64.MobyTextBase64-class.html bioMoby.ontology.TextFormatted-module.html bioMoby.ontology.TextFormatted.MobyTextFormatted-class.html bioMoby.ontology.TextHtml-module.html bioMoby.ontology.TextHtml.MobyTextHtml-class.html bioMoby.ontology.TextPlain-module.html bioMoby.ontology.TextPlain.MobyTextPlain-class.html bioMoby.ontology.TextUuencoded-module.html bioMoby.ontology.TextUuencoded.MobyTextUuencoded-class.html bioMoby.ontology.TextXml-module.html bioMoby.ontology.TextXml.MobyTextXml-class.html bioMoby.ontology.Text_plain-module.html bioMoby.ontology.Text_plain.MobyText_plain-class.html bioMoby.ontology.Trait_Details-module.html bioMoby.ontology.Trait_Details.MobyTrait_Details-class.html bioMoby.ontology.Tree-module.html bioMoby.ontology.Tree.MobyTree-class.html bioMoby.ontology.TropGENE_ACCESSION-module.html bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION-class.html bioMoby.ontology.TropGENE_Diversity_Matrix-module.html bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix-class.html bioMoby.ontology.TropGENE_LOCUS-module.html bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS-class.html bioMoby.ontology.VirtualSequence-module.html bioMoby.ontology.VirtualSequence.MobyVirtualSequence-class.html bioMoby.ontology.WU_BLAST_Text-module.html bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text-class.html bioMoby.ontology.Wildcard_Query-module.html bioMoby.ontology.Wildcard_Query.MobyWildcard_Query-class.html bioMoby.webservice-module.html bioMoby.webservice.Dispatcher-module.html bioMoby.webservice.Dispatcher.AbstractDispatcher-class.html bioMoby.webservice.Dispatcher.Dispatcher-class.html bioMoby.webservice.Dispatcher.EDispatchError-class.html bioMoby.webservice.Dispatcher.LockedIterator-class.html bioMoby.webservice.Dispatcher.MultiThread-class.html bioMoby.webservice.Dispatcher.PBSDispatcher-class.html bioMoby.webservice.Dispatcher.SimpleDispatcher-class.html bioMoby.webservice.Dispatcher.SingleThread-class.html bioMoby.webservice.Invocators-module.html bioMoby.webservice.Invocators.CGIPostInvocator-class.html bioMoby.webservice.Invocators.CGIPostMInvocator-class.html bioMoby.webservice.Invocators.GeneralInvocator-class.html bioMoby.webservice.Invocators.InvocatorError-class.html bioMoby.webservice.Invocators.LocalInvocator-class.html bioMoby.webservice.Invocators.PBSInvocator-class.html bioMoby.webservice.Invocators.QsubParameters-class.html bioMoby.webservice.TCBioMoby-module.html bioMoby.webservice.TCBioMoby.Body-class.html bioMoby.webservice.TCBioMoby._TCBody-class.html exceptions.Exception-class.html frames.html help.html index.html indices.html threading.Thread-class.html threading._Verbose-class.html toc-bioMoby-module.html toc-bioMoby.mobyClient-module.html toc-bioMoby.mobyDataTypes-module.html toc-bioMoby.mobyExceptions-module.html toc-bioMoby.mobyMarshal-module.html toc-bioMoby.mobyRegister-module.html toc-bioMoby.mobyService-module.html toc-bioMoby.ontology-module.html toc-bioMoby.ontology.AGI_LocusCode-module.html toc-bioMoby.ontology.Allele_freq-module.html toc-bioMoby.ontology.AminoAcidSequence-module.html toc-bioMoby.ontology.B64_Encoded_PNG-module.html toc-bioMoby.ontology.B64_Encoded_Postscript-module.html toc-bioMoby.ontology.B64_encoded_PDB-module.html toc-bioMoby.ontology.B64_encoded_gif-module.html toc-bioMoby.ontology.B64_encoded_jpeg-module.html toc-bioMoby.ontology.BasicGFFSequenceFeature-module.html toc-bioMoby.ontology.ClustalAlnFormattedText-module.html toc-bioMoby.ontology.CommentedAASequence-module.html toc-bioMoby.ontology.CommentedDNASequence-module.html 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toc-bioMoby.ontology.HBond_Pair-module.html toc-bioMoby.ontology.HCA_picture-module.html toc-bioMoby.ontology.Haplotyping_Study_obj-module.html toc-bioMoby.ontology.ICIS_Query-module.html toc-bioMoby.ontology.ICIS_Query2-module.html toc-bioMoby.ontology.ICIS_Query3-module.html toc-bioMoby.ontology.IntAct_XML-module.html toc-bioMoby.ontology.Interaction-module.html toc-bioMoby.ontology.InteractionMethod-module.html toc-bioMoby.ontology.Interaction_partner-module.html toc-bioMoby.ontology.Interactor-module.html toc-bioMoby.ontology.MEME_Text-module.html toc-bioMoby.ontology.MGIS_ACCESSION-module.html toc-bioMoby.ontology.MMP_Locus-module.html toc-bioMoby.ontology.MO_Term_Test-module.html toc-bioMoby.ontology.Multi_key_value_pair-module.html toc-bioMoby.ontology.MyTree-module.html toc-bioMoby.ontology.NCBI_BLAST_Text-module.html toc-bioMoby.ontology.NCBI_Blast_XML-module.html toc-bioMoby.ontology.NCBI_MEME_Text-module.html toc-bioMoby.ontology.NucleotideSequence-module.html toc-bioMoby.ontology.PDBFormattedText-module.html toc-bioMoby.ontology.PDGJOB-module.html toc-bioMoby.ontology.PhenotypeDescription-module.html toc-bioMoby.ontology.PubMedMEDLINE-module.html toc-bioMoby.ontology.RNASequence-module.html toc-bioMoby.ontology.SINGER_ACCESSION-module.html toc-bioMoby.ontology.SchematikonMotifID-module.html toc-bioMoby.ontology.SchematikonMotifSupport-module.html toc-bioMoby.ontology.SchematikonSegmentAttributes-module.html toc-bioMoby.ontology.SchematikonSegmentID-module.html toc-bioMoby.ontology.SchematikonStructureAnnotation-module.html toc-bioMoby.ontology.SchematikonVorocodeName-module.html toc-bioMoby.ontology.Scored_acronym_string-module.html toc-bioMoby.ontology.SimpleAnnotatedGIFImage-module.html toc-bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html toc-bioMoby.ontology.Simple_key_value_pair-module.html toc-bioMoby.ontology.Snp_allele-module.html toc-bioMoby.ontology.Snp_genotype-module.html toc-bioMoby.ontology.Study-module.html toc-bioMoby.ontology.TEST-module.html toc-bioMoby.ontology.TargetP_result-module.html toc-bioMoby.ontology.Testout-module.html toc-bioMoby.ontology.TextBase64-module.html toc-bioMoby.ontology.TextFormatted-module.html toc-bioMoby.ontology.TextHtml-module.html toc-bioMoby.ontology.TextPlain-module.html toc-bioMoby.ontology.TextUuencoded-module.html toc-bioMoby.ontology.TextXml-module.html toc-bioMoby.ontology.Text_plain-module.html toc-bioMoby.ontology.Trait_Details-module.html toc-bioMoby.ontology.Tree-module.html toc-bioMoby.ontology.TropGENE_ACCESSION-module.html toc-bioMoby.ontology.TropGENE_Diversity_Matrix-module.html toc-bioMoby.ontology.TropGENE_LOCUS-module.html toc-bioMoby.ontology.VirtualSequence-module.html toc-bioMoby.ontology.WU_BLAST_Text-module.html toc-bioMoby.ontology.Wildcard_Query-module.html toc-bioMoby.webservice-module.html toc-bioMoby.webservice.Dispatcher-module.html toc-bioMoby.webservice.Invocators-module.html toc-bioMoby.webservice.TCBioMoby-module.html toc-everything.html toc.html trees.html Log Message: moby-live/Python/doc/private ZSI.TC.TypeCode-class.html,NONE,1.1 __builtin__.object-class.html,1.2,1.3 __builtin__.type-class.html,1.2,1.3 bioMoby-module.html,1.2,1.3 bioMoby.mobyClient-module.html,1.2,1.3 bioMoby.mobyClient.Central-class.html,1.2,1.3 bioMoby.mobyClient.Client-class.html,1.2,1.3 bioMoby.mobyDataTypes-module.html,1.2,1.3 bioMoby.mobyDataTypes.MobyContent-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyFloat-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyInteger-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyObject-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobySequence-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyString-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyXref-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyZmPDB-class.html,1.2,1.3 bioMoby.mobyDataTypes.Parameter-class.html,1.2,1.3 bioMoby.mobyExceptions-module.html,1.2,1.3 bioMoby.mobyExceptions.EInvalidArgument-class.html,1.2,1.3 bioMoby.mobyExceptions.EInvalidType-class.html,1.2,1.3 bioMoby.mobyExceptions.EMe! thodRetrieveError-class.html,1.2,1.3 bioMoby.mobyExceptions.ENotAWSMethod-class.html,1.2,1.3 bioMoby.mobyExceptions.ETypeMismatch-class.html,1.2,1.3 bioMoby.mobyMarshal-module.html,1.2,1.3 bioMoby.mobyMarshal.MobyMarshaller-class.html,1.2,1.3 bioMoby.mobyMarshal.MobyUnmarshaller-class.html,1.2,1.3 bioMoby.mobyRegister-module.html,1.2,1.3 bioMoby.mobyRegister.GeneralInformations-class.html,1.2,1.3 bioMoby.mobyRegister.Namespace-class.html,1.2,1.3 bioMoby.mobyRegister.ObjectClass-class.html,1.2,1.3 bioMoby.mobyRegister.RegistrationObject-class.html,1.2,1.3 bioMoby.mobyRegister.ServiceType-class.html,1.2,1.3 bioMoby.mobyService-module.html,1.2,1.3 bioMoby.mobyService.Service-class.html,1.2,1.3 bioMoby.mobyService.ServiceArticle-class.html,1.2,1.3 bioMoby.mobyService.ServiceList-class.html,1.2,1.3 bioMoby.mobyService.ServiceQuery-class.html,1.2,1.3 bioMoby.mobyService.ServiceSecondary-class.html,1.2,1.3 bioMoby.ontology-module.html,1.2,1.3 bioMoby.ontology.AGI_LocusCode-module.h! tml,1.2,1.3 bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-! class.html,1.2,1.3 bioMoby.ontology.Allele_freq-module.html,1.2,1.3 bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html,1.2,1.3 bioMoby.ontology.AminoAcidSequence-module.html,1.2,1.3 bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html,1.2,1.3 bioMoby.ontology.B64_Encoded_PNG-module.html,1.2,1.3 bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html,1.2,1.3 bioMoby.ontology.B64_Encoded_Postscript-module.html,1.2,1.3 bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html,1.2,1.3 bioMoby.ontology.B64_encoded_PDB-module.html,1.2,1.3 bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html,1.2,1.3 bioMoby.ontology.B64_encoded_gif-module.html,1.2,1.3 bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html,1.2,1.3 bioMoby.ontology.B64_encoded_jpeg-module.html,1.2,1.3 bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg-class.html,1.2,1.3 bioMoby.ontology.BasicGFFSequenceFeature-module.html,1.2,1.3 bioMoby.ontology! .BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature-class.html,1.2,1.3 bioMoby.ontology.ClustalAlnFormattedText-module.html,NONE,1.1 bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText-class.html,NONE,1.1 bioMoby.ontology.CommentedAASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence-class.html,NONE,1.1 bioMoby.ontology.CommentedDNASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence-class.html,NONE,1.1 bioMoby.ontology.CommentedRNASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence-class.html,NONE,1.1 bioMoby.ontology.DNASequence-module.html,1.2,1.3 bioMoby.ontology.DNASequence.MobyDNASequence-class.html,1.2,1.3 bioMoby.ontology.DNASequenceWithGFFFeatures-module.html,1.2,1.3 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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -58,6 +64,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -65,6 +75,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -78,6 +90,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -87,12 +100,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -109,10 +125,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -123,6 +141,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -131,6 +152,7 @@

  • @@ -143,13 +165,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -57,13 +63,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Central-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Central-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Central-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,7 +60,8 @@ @@ -77,7 +84,8 @@
      __init__(self, url, - ns) + ns, + debug)
    Changes url and ns parameters if you want to use another moby server
    - +

    __init__(self, url='http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral..., - ns='http://mobycentral.cbr.nrc.ca/MOBY/Central') + ns='http://mobycentral.cbr.nrc.ca/MOBY/Central', + debug=False)
    (Constructor)

    Changes url and ns parameters if you want to use another moby @@ -106,13 +114,19 @@
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Client-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Client-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyClient.Client-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,12 +60,10 @@ - +
    Method Summary
     __init__(self, + __init__(self, url, ns) -
    -Changes url and ns parameters if you want to use another moby -server
      findService(self, mobyQuery) @@ -141,23 +145,6 @@ Method Details
    - -
    -

    __init__(self, - url='http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral..., - ns='http://mobycentral.cbr.nrc.ca/MOBY/Central') -
    (Constructor) -

    - Changes url and ns parameters if you want to use another moby - server -
    -
    Overrides:
    -
    bioMoby.mobyClient.Central.__init__ (inherited documentation) -
    -
    -
    -
    - - +

    findService(self, @@ -298,13 +285,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -80,13 +86,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyContent-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyContent-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyContent-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -116,13 +122,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyFloat-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyFloat-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyFloat-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -110,13 +116,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyInteger-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyInteger-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyInteger-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -110,13 +116,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyObject-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyObject-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyObject-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -49,6 +55,7 @@ MobyGlobal_Keyword, MobyGO_Term, MobyHaplotyping_Study_obj, + MobyHBond_Pair, MobyICIS_Query, MobyICIS_Query2, MobyICIS_Query3, @@ -57,6 +64,7 @@ MobyInteraction_partner, MobyInteractionMethod, MobyInteractor, + MobyMGIS_ACCESSION, MobyMMP_Locus, MobyMO_Term_Test, MobyMulti_key_value_pair, @@ -70,11 +78,14 @@ MobyScored_acronym_string, MobySequence, MobySimple_key_value_pair, + MobySINGER_ACCESSION, MobyString, MobyStudy, MobyTargetP_result, MobyTestout, MobyTrait_Details, + MobyTropGENE_ACCESSION, + MobyTropGENE_LOCUS, MobyVirtualSequence, MobyWildcard_Query, MobyXref, @@ -162,13 +173,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobySequence-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobySequence-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobySequence-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -57,7 +63,8 @@ - +
    __init__(self, sequence, namespace, - id) + id, + articleName)
      fromMoby(self, @@ -110,13 +117,19 @@    Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyString-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyString-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyString-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -99,13 +105,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyXref-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyXref-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyXref-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -124,13 +130,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyZmPDB-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyZmPDB-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.MobyZmPDB-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -183,13 +189,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.Parameter-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.Parameter-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyDataTypes.Parameter-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -104,13 +110,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -66,13 +72,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidArgument-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidArgument-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidArgument-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidType-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidType-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EInvalidType-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EMethodRetrieveError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EMethodRetrieveError-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.EMethodRetrieveError-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ENotAWSMethod-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ENotAWSMethod-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ENotAWSMethod-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ETypeMismatch-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ETypeMismatch-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyExceptions.ETypeMismatch-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -71,13 +77,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -57,13 +63,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyMarshaller-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyMarshaller-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyMarshaller-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,10 +54,11 @@ - +
    +Serialize the object into a Moby XML object - +
    +this method do the serialization of the object
    Method Summary
     dumps(self, + dumps(self, value, articleName) -
      m_dict(self, value, @@ -114,10 +121,11 @@
    transforms an object and all properties into a XML
     _marshal(self, + _marshal(self, value, articleName) -

    @@ -127,6 +135,17 @@ Method Details + +
    +

    dumps(self, + value, + articleName='') +

    + Serialize the object into a Moby XML object +
    +
    +
    +

    m_dict(self, @@ -222,6 +241,17 @@

    + + +
    +

    _marshal(self, + value, + articleName='') +

    + this method do the serialization of the object +
    +
    +

    @@ -232,13 +262,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyUnmarshaller-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyUnmarshaller-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyMarshal.MobyUnmarshaller-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,9 +54,10 @@ - +
    +Deserializes an xml string and return a bioMoby-Python object
    Method Summary
     loads(self, + loads(self, xml) -
      m_Collection(self, value) @@ -98,6 +105,16 @@ Method Details
    + +
    +

    loads(self, + xml) +

    + Deserializes an xml string and return a bioMoby-Python object +
    +
    +
    + - +

    m_Collection(self, @@ -180,13 +197,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister-module.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -67,13 +73,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.GeneralInformations-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.GeneralInformations-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.GeneralInformations-class.html 2004/12/09 14:07:29 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -154,13 +160,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.Namespace-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.Namespace-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.Namespace-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -136,13 +142,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ObjectClass-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ObjectClass-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ObjectClass-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -138,13 +144,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.RegistrationObject-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.RegistrationObject-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.RegistrationObject-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -121,13 +127,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ServiceType-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ServiceType-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyRegister.ServiceType-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -158,13 +164,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -67,13 +73,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.Service-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.Service-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.Service-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -70,7 +76,8 @@ @@ -82,7 +89,8 @@ +Register the service on the Moby server has been added here a code to +verify that signatureURL is not empty :)
    execute(self, query, method, - returnXml) + returnXml, + debug)
    Executes the web service v0.5: return either the XML form or try to unmarshall the result and return a MobyContent Object
      register(self)
    -Register the service on the Moby server

    @@ -151,7 +159,8 @@

    execute(self, query, method='', - returnXml=True) + returnXml=True, + debug=False)

    Executes the web service v0.5: return either the XML form or try to unmarshall the result and return a MobyContent Object @@ -173,7 +182,8 @@

    register(self)

    - Register the service on the Moby server + Register the service on the Moby server has been added here a code + to verify that signatureURL is not empty :)
    @@ -187,13 +197,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceArticle-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceArticle-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceArticle-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -113,13 +119,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceList-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceList-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceList-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -204,13 +210,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceQuery-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceQuery-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceQuery-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -128,13 +134,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceSecondary-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceSecondary-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.mobyService.ServiceSecondary-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -116,13 +122,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -51,6 +57,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -58,6 +68,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -71,6 +83,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -80,12 +93,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -102,10 +118,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -116,6 +134,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -130,13 +151,19 @@
  • - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -58,13 +64,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -113,13 +119,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -90,13 +96,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,6 +54,10 @@ MobyAminoAcidSequence
    +
    Known Subclasses:
    +
    + MobyCommentedAASequence
    +
    Description: Lightweight representation an amino acid sequence Author: @@ -117,13 +127,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG-module.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG-module.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html 2004/12/09 14:07:30 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -52,6 +58,7 @@
    Known Subclasses:
    + MobyCommentedDNASequence, MobyDNASequenceWithGFFFeatures

    @@ -123,13 +130,19 @@ - +
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    @@ -50,6 +56,11 @@ MobyFASTA
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    Known Subclasses:
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    + MobyFASTA_AA, + MobyFASTA_NA
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    Description: FASTA formatted sequence Author: www.sdsc.edu Contact: @@ -118,13 +129,19 @@ - +
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    Description: Lightweight representation an RNA sequence Author: @@ -119,13 +129,19 @@ - +
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextBase64.MobyTextBase64-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextBase64.MobyTextBase64-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextBase64.MobyTextBase64-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
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    +
    @@ -122,13 +128,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextFormatted-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextFormatted-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextFormatted-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextFormatted.MobyTextFormatted-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextFormatted.MobyTextFormatted-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextFormatted.MobyTextFormatted-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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    +

    + bioMoby-python +

    +
    @@ -50,16 +56,21 @@
    Known Subclasses:
    + MobyClustalAlnFormattedText, MobyDecypher_Text, MobyEmblFlatfile, MobyFASTA, MobyGenbankFlatfile, MobyGFF, + MobyMEME_Text, MobyMyTree, MobyNCBI_BLAST_Text, + MobyNCBI_MEME_Text, MobyPDBFormattedText, MobyPubMedMEDLINE, + MobyTEST, MobyTree, + MobyTropGENE_Diversity_Matrix, MobyWU_BLAST_Text

    @@ -130,13 +141,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextHtml-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextHtml-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextHtml-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextHtml.MobyTextHtml-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextHtml.MobyTextHtml-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextHtml.MobyTextHtml-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
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    +
    @@ -114,13 +120,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextPlain-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextPlain-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextPlain-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextPlain.MobyTextPlain-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextPlain.MobyTextPlain-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextPlain.MobyTextPlain-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -118,13 +124,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextUuencoded-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextUuencoded-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextUuencoded-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextUuencoded.MobyTextUuencoded-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextUuencoded.MobyTextUuencoded-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextUuencoded.MobyTextUuencoded-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -114,13 +120,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextXml-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextXml-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextXml-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextXml.MobyTextXml-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextXml.MobyTextXml-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.TextXml.MobyTextXml-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
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    +

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    +
    @@ -119,13 +125,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Text_plain-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Text_plain-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Text_plain-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Text_plain.MobyText_plain-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Text_plain.MobyText_plain-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Text_plain.MobyText_plain-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
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    +

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    +
    @@ -114,13 +120,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Trait_Details-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Trait_Details-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Trait_Details-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Trait_Details.MobyTrait_Details-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Trait_Details.MobyTrait_Details-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Trait_Details.MobyTrait_Details-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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    +

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    +
    @@ -116,13 +122,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Tree-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Tree-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Tree-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Tree.MobyTree-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Tree.MobyTree-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Tree.MobyTree-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -118,13 +124,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.VirtualSequence-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.VirtualSequence-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.VirtualSequence-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.VirtualSequence.MobyVirtualSequence-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.VirtualSequence.MobyVirtualSequence-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.VirtualSequence.MobyVirtualSequence-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -119,13 +125,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.WU_BLAST_Text-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.WU_BLAST_Text-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.WU_BLAST_Text-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -118,13 +124,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Wildcard_Query-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Wildcard_Query-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Wildcard_Query-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Wildcard_Query.MobyWildcard_Query-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Wildcard_Query.MobyWildcard_Query-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.ontology.Wildcard_Query.MobyWildcard_Query-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

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    @@ -114,13 +120,19 @@ - +
       Trees       Index       Help    + +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
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    @@ -44,6 +50,7 @@

    @@ -55,13 +62,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -43,6 +49,10 @@ + + + + + +
    Classes
    + AbstractDispatcherSubclass this one to create your own dispatcher class a Dispatcher +class must have a execute method
    Dispatcher All Queries in the MobyContent Object are splitted and executed
    @@ -52,6 +62,12 @@ MultiThread Several threads
    + PBSDispatcherDispatcher for PBS jobs
    + SimpleDispatcherA simple dispatcher, without execute method
    SingleThread Definition of a single Thread

    @@ -74,13 +90,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.Dispatcher-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.Dispatcher-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.Dispatcher-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -38,6 +44,12 @@

    Class Dispatcher

    +
    +AbstractDispatcher --+
    +                     |
    +                    Dispatcher
    +

    +
    All Queries in the MobyContent Object are splitted and executed @@ -104,6 +116,9 @@ [queryData]-->("commandName","commandArgs", ["tempfiles"])
    +
    Overrides:
    +
    bioMoby.webservice.Dispatcher.AbstractDispatcher.__init__
    +
    @@ -115,6 +130,9 @@ Execute the queries with a pool of threads, store the results in a mobyContent Object
    +
    Overrides:
    +
    bioMoby.webservice.Dispatcher.AbstractDispatcher.execute
    +
    @@ -147,13 +165,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.EDispatchError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.EDispatchError-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.EDispatchError-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -75,13 +81,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.LockedIterator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.LockedIterator-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.LockedIterator-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -68,13 +74,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.MultiThread-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.MultiThread-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.MultiThread-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -74,13 +80,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.SingleThread-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.SingleThread-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Dispatcher.SingleThread-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -163,13 +169,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators-module.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,11 +60,24 @@ GeneralInvocator - - + + + + +
    General class for other invocators
    - InvocatorErrorError during an invocation of method
    LocalInvocator Invokes local command
    + PBSInvocatorInvokes a command in a qsub
    + QsubParametersParameters for the qsub command

    + + + + + + + +
    Exceptions
    + InvocatorErrorError during an invocation of method

    @@ -69,13 +88,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostInvocator-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostInvocator-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -68,7 +74,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -111,13 +118,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -89,7 +95,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -151,13 +158,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.GeneralInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.GeneralInvocator-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.GeneralInvocator-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -55,17 +61,51 @@ - +
    +queryid is the identifier of a query, userdir is the session +directory, timeout the limit time of execution of the query - +
    Method Summary
     __init__(self, + __init__(self, queryid, userdir, timeout) -
     getResults(self) -
    getResults(self) +
    +retrieve the results if available

    + + + + +
    Method Details
    + + +
    +

    __init__(self, + queryid, + userdir='/tmp', + timeout=None) +
    (Constructor) +

    + queryid is the identifier of a query, userdir is the session + directory, timeout the limit time of execution of the query +
    +
    +
    + + +
    +

    getResults(self) +

    + retrieve the results if available +
    +
    +
    +
    + + @@ -73,13 +113,19 @@ - + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.InvocatorError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.InvocatorError-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.InvocatorError-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -38,6 +44,12 @@

    Class InvocatorError

    +
    +Exception --+
    +            |
    +           InvocatorError
    +

    +
    Error during an invocation of method @@ -51,6 +63,14 @@ + + + + + +
      __str__(self)
        Inherited from Exception
     __init__(...) +
     __getitem__(...) +

    @@ -61,13 +81,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.LocalInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.LocalInvocator-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/bioMoby.webservice.Invocators.LocalInvocator-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -44,6 +50,10 @@ LocalInvocator
    +
    Known Subclasses:
    +
    + PBSInvocator
    +
    Invokes local command @@ -69,7 +79,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -105,13 +116,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/exceptions.Exception-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/exceptions.Exception-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/exceptions.Exception-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -43,7 +49,8 @@ EInvalidType, EMethodRetrieveError, ENotAWSMethod, - ETypeMismatch + ETypeMismatch, + InvocatorError
    @@ -74,13 +81,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/frames.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/frames.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/frames.html 2004/12/09 14:07:31 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/help.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/help.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/help.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -32,7 +38,7 @@

    API Documentation

    This document contains the API (Application Programming Interface) -documentation for this project. Documentation for the Python +documentation for bioMoby-python. Documentation for the Python objects defined by the project is divided into separate pages for each package, module, and class. The API documentation also includes two pages containing information about the project as a whole: a trees @@ -209,13 +215,19 @@

    - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/index.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/index.html 2004/12/09 14:07:31 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/indices.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/indices.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/indices.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:10 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -74,6 +80,8 @@ + + @@ -136,6 +144,14 @@ + + + + + + + + @@ -150,6 +166,10 @@ + + + + @@ -174,6 +194,8 @@ + + @@ -194,6 +216,10 @@ + + + + @@ -206,6 +232,8 @@ + + @@ -218,6 +246,8 @@ + + @@ -244,6 +274,8 @@ + + @@ -266,18 +298,30 @@ + + + + + + + + + + + + @@ -288,6 +332,10 @@ + + + + @@ -384,6 +432,8 @@ + + @@ -394,12 +444,16 @@ + + + + @@ -430,6 +484,8 @@ + + @@ -438,8 +494,20 @@ + + + + + + + + + + + + @@ -506,16 +574,26 @@ + + + + + + + + + + @@ -550,6 +628,14 @@ + + + + + + + + @@ -564,6 +650,10 @@ + + + + @@ -588,6 +678,8 @@ + + @@ -608,6 +700,10 @@ + + + + @@ -620,6 +716,8 @@ + + @@ -632,6 +730,8 @@ + + @@ -658,6 +758,8 @@ + + @@ -680,6 +782,12 @@ + + + + + + @@ -706,6 +814,8 @@ + + @@ -734,6 +844,8 @@ + + @@ -806,6 +918,10 @@ + + + + @@ -830,6 +946,14 @@ + + + + + + + + @@ -850,6 +974,10 @@ + + + + @@ -878,6 +1006,8 @@ + + @@ -902,6 +1032,10 @@ + + + + @@ -914,6 +1048,8 @@ + + @@ -954,6 +1090,8 @@ + + @@ -964,6 +1102,8 @@ + + @@ -984,6 +1124,12 @@ + + + + + + @@ -1004,14 +1150,20 @@ + + + + + + @@ -1022,6 +1174,16 @@ + + + + + + + + + + @@ -1034,6 +1196,8 @@ + + @@ -1088,6 +1252,10 @@ + + + + @@ -1104,12 +1272,22 @@ + + + + + + + + + + @@ -1124,8 +1302,14 @@ + + + + + + @@ -1168,8 +1352,22 @@ + + + + + + + + + + + + + + @@ -1188,13 +1386,19 @@ - +
    Method in class __builtin__.object
    __hash__ Method in class __builtin__.type
    __init__Method in class ZSI.TC.TypeCode
    __init__ Method in class __builtin__.object
    __init__Method in class bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg
    __init__ Method in class bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    __init__Method in class bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    __init__Method in class bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    __init__Method in class bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    __init__Method in class bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    __init__ Method in class bioMoby.ontology.DNASequence.MobyDNASequence
    __init__Method in class bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    __init__ Method in class bioMoby.ontology.FASTA.MobyFASTA
    __init__Method in class bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    __init__Method in class bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    __init__ Method in class bioMoby.ontology.GFF.MobyGFF
    __init__Method in class bioMoby.ontology.Germplasm_List.MobyGermplasm_List
    __init__ Method in class bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    __init__Method in class bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    __init__ Method in class bioMoby.ontology.HCA_picture.MobyHCA_picture
    __init__Method in class bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    __init__ Method in class bioMoby.ontology.Interactor.MobyInteractor
    __init__Method in class bioMoby.ontology.MEME_Text.MobyMEME_Text
    __init__Method in class bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    __init__ Method in class bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    __init__Method in class bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    __init__ Method in class bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    __init__Method in class bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    __init__ Method in class bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    __init__Method in class bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE
    __init__ Method in class bioMoby.ontology.RNASequence.MobyRNASequence
    __init__Method in class bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    __init__ Method in class bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID
    __init__Method in class bioMoby.ontology.Snp_genotype.MobySnp_genotype
    __init__ Method in class bioMoby.ontology.Study.MobyStudy
    __init__Method in class bioMoby.ontology.TEST.MobyTEST
    __init__ Method in class bioMoby.ontology.TargetP_result.MobyTargetP_result
    __init__Method in class bioMoby.ontology.Trait_Details.MobyTrait_Details
    __init__ Method in class bioMoby.ontology.Tree.MobyTree
    __init__Method in class bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    __init__Method in class bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    __init__Method in class bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    __init__ Method in class bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    __init__ Method in class bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text
    __init__ Method in class bioMoby.ontology.Wildcard_Query.MobyWildcard_Query
    __init__Method in class bioMoby.webservice.Dispatcher.AbstractDispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.Dispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.LockedIterator
    __init__ Method in class bioMoby.webservice.Dispatcher.MultiThread
    __init__Method in class bioMoby.webservice.Dispatcher.PBSDispatcher
    __init__Method in class bioMoby.webservice.Dispatcher.SimpleDispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.SingleThread
    __init__Method in class bioMoby.webservice.Invocators.GeneralInvocator
    __init__ Method in class bioMoby.webservice.Invocators.LocalInvocator
    __init__Method in class bioMoby.webservice.Invocators.PBSInvocator
    __init__Method in class bioMoby.webservice.Invocators.QsubParameters
    __init__ Method in class exceptions.Exception
    __init__Method in class bioMoby.webservice.Dispatcher.Dispatcher
    _fetchAnswers Method in class bioMoby.webservice.Dispatcher.Dispatcher
    _getResultsMethod in class bioMoby.webservice.Dispatcher.PBSDispatcher
    _getSem Method in class bioMoby.webservice.Dispatcher.Dispatcher
    _marshalMethod in class threading.Thread
    _tailRecurse Method in class bioMoby.webservice.Dispatcher.MultiThread
    _TCBodyClass in module bioMoby.webservice.TCBioMoby
    __initialized Variable in class threading.Thread
    __initialized Variable in class threading.Thread
    _Verbose Class in module threading
    AbstractDispatcherClass in module bioMoby.webservice.Dispatcher
    AGI_LocusCode Module in package bioMoby.ontology
    Allele_freqModule in package bioMoby.ontology
    bioMoby Package
    BodyClass in module bioMoby.webservice.TCBioMoby
    call_method Method in class bioMoby.mobyClient.Central
    CentralClass in module bioMoby.webservice.Invocators
    CGIPostMInvocator Class in module bioMoby.webservice.Invocators
    checknameMethod in class ZSI.TC.TypeCode
    checktypeMethod in class ZSI.TC.TypeCode
    Client Class in module bioMoby.mobyClient
    ClustalAlnFormattedTextModule in package bioMoby.ontology
    CommentedAASequenceModule in package bioMoby.ontology
    CommentedDNASequenceModule in package bioMoby.ontology
    CommentedRNASequenceModule in package bioMoby.ontology
    compress Method in class bioMoby.mobyDataTypes.MobyZmPDB
    contactClass in module exceptions
    execute Method in class bioMoby.mobyService.Service
    executeMethod in class bioMoby.webservice.Dispatcher.AbstractDispatcher
    execute Method in class bioMoby.webservice.Dispatcher.Dispatcher
    executeMethod in class bioMoby.webservice.Dispatcher.PBSDispatcher
    execute Method in class bioMoby.webservice.Invocators.CGIPostInvocator
    execute Method in class bioMoby.webservice.Invocators.CGIPostMInvocator
    execute Method in class bioMoby.webservice.Invocators.LocalInvocator
    executeMethod in class bioMoby.webservice.Invocators.PBSInvocator
    FASTA Module in package bioMoby.ontology
    FASTA_AAModule in package bioMoby.ontology
    FASTA_NAModule in package bioMoby.ontology
    findService Method in class bioMoby.mobyClient.Client
    fromMobyMethod in class bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg
    fromMoby Method in class bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    fromMobyMethod in class bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    fromMobyMethod in class bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    fromMobyMethod in class bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    fromMobyMethod in class bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    fromMoby Method in class bioMoby.ontology.DNASequence.MobyDNASequence
    fromMobyMethod in class bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    fromMoby Method in class bioMoby.ontology.FASTA.MobyFASTA
    fromMobyMethod in class bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    fromMobyMethod in class bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    fromMoby Method in class bioMoby.ontology.GFF.MobyGFF
    fromMobyMethod in class bioMoby.ontology.Germplasm_List.MobyGermplasm_List
    fromMoby Method in class bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    fromMobyMethod in class bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    fromMoby Method in class bioMoby.ontology.HCA_picture.MobyHCA_picture
    fromMobyMethod in class bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    fromMoby Method in class bioMoby.ontology.Interactor.MobyInteractor
    fromMobyMethod in class bioMoby.ontology.MEME_Text.MobyMEME_Text
    fromMobyMethod in class bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    fromMoby Method in class bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    fromMobyMethod in class bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    fromMoby Method in class bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    fromMobyMethod in class bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    fromMoby Method in class bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    fromMobyMethod in class bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE
    fromMoby Method in class bioMoby.ontology.RNASequence.MobyRNASequence
    fromMobyMethod in class bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    fromMoby Method in class bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID
    fromMobyMethod in class bioMoby.ontology.Snp_genotype.MobySnp_genotype
    fromMoby Method in class bioMoby.ontology.Study.MobyStudy
    fromMobyMethod in class bioMoby.ontology.TEST.MobyTEST
    fromMoby Method in class bioMoby.ontology.TargetP_result.MobyTargetP_result
    fromMobyMethod in class bioMoby.ontology.Trait_Details.MobyTrait_Details
    fromMoby Method in class bioMoby.ontology.Tree.MobyTree
    fromMobyMethod in class bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    fromMobyMethod in class bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    fromMobyMethod in class bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    fromMoby Method in class bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    fromMobyModule in package bioMoby.ontology
    get_content_type Method in class bioMoby.webservice.Invocators.CGIPostMInvocator
    get_parse_and_errorlistMethod in class ZSI.TC.TypeCode
    getInfo Method in class bioMoby.mobyDataTypes.MobyObject
    getMethodsModule in package bioMoby.ontology
    Haplotyping_Study_obj Module in package bioMoby.ontology
    HBond_PairModule in package bioMoby.ontology
    HCA_picture Module in package bioMoby.ontology
    ICIS_QueryMethod in class bioMoby.mobyMarshal.MobyMarshaller
    m_unicode Method in class bioMoby.mobyMarshal.MobyMarshaller
    MEME_TextModule in package bioMoby.ontology
    MGIS_ACCESSIONModule in package bioMoby.ontology
    MMP_Locus Module in package bioMoby.ontology
    MO_Term_TestClass in module bioMoby.ontology.BasicGFFSequenceFeature
    mobyClient Module in package bioMoby
    MobyClustalAlnFormattedTextClass in module bioMoby.ontology.ClustalAlnFormattedText
    MobyCommentedAASequenceClass in module bioMoby.ontology.CommentedAASequence
    MobyCommentedDNASequenceClass in module bioMoby.ontology.CommentedDNASequence
    MobyCommentedRNASequenceClass in module bioMoby.ontology.CommentedRNASequence
    MobyContent Class in module bioMoby.mobyDataTypes
    mobyDataTypesModule in package bioMoby
    MobyFASTA Class in module bioMoby.ontology.FASTA
    MobyFASTA_AAClass in module bioMoby.ontology.FASTA_AA
    MobyFASTA_NAClass in module bioMoby.ontology.FASTA_NA
    MobyFloat Class in module bioMoby.mobyDataTypes
    MobyGenbankFlatfileClass in module bioMoby.ontology.GO_Term
    MobyHaplotyping_Study_obj Class in module bioMoby.ontology.Haplotyping_Study_obj
    MobyHBond_PairClass in module bioMoby.ontology.HBond_Pair
    MobyHCA_picture Class in module bioMoby.ontology.HCA_picture
    MobyICIS_QueryModule in package bioMoby
    MobyMarshaller Class in module bioMoby.mobyMarshal
    MobyMEME_TextClass in module bioMoby.ontology.MEME_Text
    MobyMGIS_ACCESSIONClass in module bioMoby.ontology.MGIS_ACCESSION
    MobyMMP_Locus Class in module bioMoby.ontology.MMP_Locus
    MobyMO_Term_TestClass in module bioMoby.ontology.NCBI_BLAST_Text
    MobyNCBI_Blast_XML Class in module bioMoby.ontology.NCBI_Blast_XML
    MobyNCBI_MEME_TextClass in module bioMoby.ontology.NCBI_MEME_Text
    MobyNucleotideSequence Class in module bioMoby.ontology.NucleotideSequence
    MobyObjectClass in module bioMoby.ontology.SimpleAnnotatedGIFImage
    MobySimpleAnnotatedJPEGImage Class in module bioMoby.ontology.SimpleAnnotatedJPEGImage
    MobySINGER_ACCESSIONClass in module bioMoby.ontology.SINGER_ACCESSION
    MobySnp_allele Class in module bioMoby.ontology.Snp_allele
    MobySnp_genotypeClass in module bioMoby.ontology.Study
    MobyTargetP_result Class in module bioMoby.ontology.TargetP_result
    MobyTESTClass in module bioMoby.ontology.TEST
    MobyTestout Class in module bioMoby.ontology.Testout
    MobyText_plainClass in module bioMoby.ontology.Trait_Details
    MobyTree Class in module bioMoby.ontology.Tree
    MobyTropGENE_ACCESSIONClass in module bioMoby.ontology.TropGENE_ACCESSION
    MobyTropGENE_Diversity_MatrixClass in module bioMoby.ontology.TropGENE_Diversity_Matrix
    MobyTropGENE_LOCUSClass in module bioMoby.ontology.TropGENE_LOCUS
    MobyUnmarshaller Class in module bioMoby.mobyMarshal
    MobyVirtualSequenceClass in module bioMoby.webservice.Dispatcher
    MyTree Module in package bioMoby.ontology
    name_matchMethod in class ZSI.TC.TypeCode
    Namespace Class in module bioMoby.mobyRegister
    NCBI_BLAST_Text Module in package bioMoby.ontology
    NCBI_Blast_XML Module in package bioMoby.ontology
    NCBI_MEME_TextModule in package bioMoby.ontology
    next Method in class bioMoby.webservice.Dispatcher.LockedIterator
    nilledMethod in class ZSI.TC.TypeCode
    NucleotideSequence Module in package bioMoby.ontology
    objectPackage in package bioMoby
    Parameter Class in module bioMoby.mobyDataTypes
    parseMethod in class ZSI.TC.TypeCode
    parseMethod in class bioMoby.webservice.TCBioMoby._TCBody
    parselistVariable in class bioMoby.webservice.TCBioMoby.Body
    PBSDispatcherClass in module bioMoby.webservice.Dispatcher
    PBSInvocatorClass in module bioMoby.webservice.Invocators
    PDBFormattedText Module in package bioMoby.ontology
    PDGJOBMethod in class bioMoby.webservice.Invocators.CGIPostMInvocator
    PubMedMEDLINE Module in package bioMoby.ontology
    QsubParametersClass in module bioMoby.webservice.Invocators
    register Method in class bioMoby.mobyRegister.Namespace
    registerModule in package bioMoby.ontology
    Scored_acronym_string Module in package bioMoby.ontology
    serializeMethod in class bioMoby.webservice.TCBioMoby.Body
    seriallistVariable in class bioMoby.webservice.TCBioMoby.Body
    Service Class in module bioMoby.mobyService
    ServiceArticleMethod in class threading.Thread
    setName Method in class threading.Thread
    setParametersMethod in class bioMoby.webservice.Invocators.PBSInvocator
    Simple_key_value_pair Module in package bioMoby.ontology
    simple_valueMethod in class ZSI.TC.TypeCode
    SimpleAnnotatedGIFImage Module in package bioMoby.ontology
    SimpleAnnotatedJPEGImage Module in package bioMoby.ontology
    SimpleDispatcherClass in module bioMoby.webservice.Dispatcher
    SimpleHREFMethod in class ZSI.TC.TypeCode
    SINGER_ACCESSIONModule in package bioMoby.ontology
    SingleThread Class in module bioMoby.webservice.Dispatcher
    Snp_alleleModule in package bioMoby.ontology
    submits2XML Method in class bioMoby.mobyService.ServiceQuery
    tagVariable in class bioMoby.webservice.TCBioMoby.Body
    TargetP_result Module in package bioMoby.ontology
    TCBioMobyModule in package bioMoby.webservice
    TESTModule in package bioMoby.ontology
    Testout Module in package bioMoby.ontology
    Text_plainModule in package bioMoby.ontology
    Tree Module in package bioMoby.ontology
    TropGENE_ACCESSIONModule in package bioMoby.ontology
    TropGENE_Diversity_MatrixModule in package bioMoby.ontology
    TropGENE_LOCUSModule in package bioMoby.ontology
    type Class in module __builtin__
    typechecksVariable in class ZSI.TC.TypeCode
    typechecksVariable in class ZSI.TC.TypeCode
    TypeCodeClass in module ZSI.TC
    typecodeVariable in class bioMoby.webservice.TCBioMoby.Body
    VirtualSequence Module in package bioMoby.ontology
    webservice   Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/threading.Thread-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/threading.Thread-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/threading.Thread-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -197,13 +203,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/threading._Verbose-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/threading._Verbose-class.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/threading._Verbose-class.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -112,13 +118,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyClient-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyDataTypes-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyExceptions-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyMarshal-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyRegister-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.mobyService-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology-module.html 2004/12/09 14:07:31 1.3 @@ -22,6 +22,10 @@ B64_Encoded_PNG
    B64_Encoded_Postscript
    BasicGFFSequenceFeature
    +ClustalAlnFormattedText
    +CommentedAASequence
    +CommentedDNASequence
    +CommentedRNASequence
    DateTime
    Decypher_Text
    DNASequence
    @@ -29,6 +33,8 @@ Edge
    EmblFlatfile
    FASTA
    +FASTA_AA
    +FASTA_NA
    GenbankFlatfile
    GenericSequence
    GeneticElement
    @@ -42,6 +48,7 @@ Global_Keyword
    GO_Term
    Haplotyping_Study_obj
    +HBond_Pair
    HCA_picture
    ICIS_Query
    ICIS_Query2
    @@ -51,12 +58,15 @@ Interaction_partner
    InteractionMethod
    Interactor
    +MEME_Text
    +MGIS_ACCESSION
    MMP_Locus
    MO_Term_Test
    Multi_key_value_pair
    MyTree
    NCBI_BLAST_Text
    NCBI_Blast_XML
    +NCBI_MEME_Text
    NucleotideSequence
    PDBFormattedText
    PDGJOB
    @@ -73,10 +83,12 @@ Simple_key_value_pair
    SimpleAnnotatedGIFImage
    SimpleAnnotatedJPEGImage
    +SINGER_ACCESSION
    Snp_allele
    Snp_genotype
    Study
    TargetP_result
    +TEST
    Testout
    Text_plain
    TextBase64
    @@ -87,6 +99,9 @@ TextXml
    Trait_Details
    Tree
    +TropGENE_ACCESSION
    +TropGENE_Diversity_Matrix
    +TropGENE_LOCUS
    VirtualSequence
    Wildcard_Query
    WU_BLAST_Text
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-r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextPlain-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextUuencoded-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.TextXml-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Text_plain-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Trait_Details-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Tree-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.VirtualSequence-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.WU_BLAST_Text-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.ontology.Wildcard_Query-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice-module.html 2004/12/09 14:07:31 1.3 @@ -15,6 +15,7 @@ Modules
    Dispatcher
    Invocators
    +TCBioMoby


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Dispatcher-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Dispatcher-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Dispatcher-module.html 2004/12/09 14:07:31 1.3 @@ -13,9 +13,12 @@ Classes
    +AbstractDispatcher
    Dispatcher
    LockedIterator
    MultiThread
    +PBSDispatcher
    +SimpleDispatcher
    SingleThread

    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Invocators-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Invocators-module.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-bioMoby.webservice.Invocators-module.html 2004/12/09 14:07:31 1.3 @@ -16,8 +16,14 @@ CGIPostInvocator
    CGIPostMInvocator
    GeneralInvocator
    -InvocatorError
    LocalInvocator
    +PBSInvocator
    +QsubParameters
    +
    + + +Exceptions
    +InvocatorError


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc-everything.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc-everything.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc-everything.html 2004/12/09 14:07:31 1.3 @@ -45,6 +45,10 @@ bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG
    bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript
    bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    +bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    +bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    +bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    +bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    bioMoby.ontology.DateTime.MobyDateTime
    bioMoby.ontology.Decypher_Text.MobyDecypher_Text
    bioMoby.ontology.DNASequence.MobyDNASequence
    @@ -52,6 +56,8 @@ bioMoby.ontology.Edge.MobyEdge
    bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    bioMoby.ontology.FASTA.MobyFASTA
    +bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    +bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    bioMoby.ontology.GenbankFlatfile.MobyGenbankFlatfile
    bioMoby.ontology.GenericSequence.MobyGenericSequence
    bioMoby.ontology.GeneticElement.MobyGeneticElement
    @@ -65,6 +71,7 @@ bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    bioMoby.ontology.GO_Term.MobyGO_Term
    bioMoby.ontology.Haplotyping_Study_obj.MobyHaplotyping_Study_obj
    +bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    bioMoby.ontology.HCA_picture.MobyHCA_picture
    bioMoby.ontology.ICIS_Query.MobyICIS_Query
    bioMoby.ontology.ICIS_Query2.MobyICIS_Query2
    @@ -74,12 +81,15 @@ bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    bioMoby.ontology.InteractionMethod.MobyInteractionMethod
    bioMoby.ontology.Interactor.MobyInteractor
    +bioMoby.ontology.MEME_Text.MobyMEME_Text
    +bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    bioMoby.ontology.MO_Term_Test.MobyMO_Term_Test
    bioMoby.ontology.Multi_key_value_pair.MobyMulti_key_value_pair
    bioMoby.ontology.MyTree.MobyMyTree
    bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    +bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText
    bioMoby.ontology.PDGJOB.MobyPDGJOB
    @@ -96,10 +106,12 @@ bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair
    bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage
    bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage
    +bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    bioMoby.ontology.Snp_allele.MobySnp_allele
    bioMoby.ontology.Snp_genotype.MobySnp_genotype
    bioMoby.ontology.Study.MobyStudy
    bioMoby.ontology.TargetP_result.MobyTargetP_result
    +bioMoby.ontology.TEST.MobyTEST
    bioMoby.ontology.Testout.MobyTestout
    bioMoby.ontology.Text_plain.MobyText_plain
    bioMoby.ontology.TextBase64.MobyTextBase64
    @@ -110,18 +122,27 @@ bioMoby.ontology.TextXml.MobyTextXml
    bioMoby.ontology.Trait_Details.MobyTrait_Details
    bioMoby.ontology.Tree.MobyTree
    +bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    +bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    +bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    bioMoby.ontology.Wildcard_Query.MobyWildcard_Query
    bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text
    +bioMoby.webservice.Dispatcher.AbstractDispatcher
    bioMoby.webservice.Dispatcher.Dispatcher
    bioMoby.webservice.Dispatcher.LockedIterator
    bioMoby.webservice.Dispatcher.MultiThread
    +bioMoby.webservice.Dispatcher.PBSDispatcher
    +bioMoby.webservice.Dispatcher.SimpleDispatcher
    bioMoby.webservice.Dispatcher.SingleThread
    bioMoby.webservice.Invocators.CGIPostInvocator
    bioMoby.webservice.Invocators.CGIPostMInvocator
    bioMoby.webservice.Invocators.GeneralInvocator
    -bioMoby.webservice.Invocators.InvocatorError
    bioMoby.webservice.Invocators.LocalInvocator
    +bioMoby.webservice.Invocators.PBSInvocator
    +bioMoby.webservice.Invocators.QsubParameters
    +bioMoby.webservice.TCBioMoby._TCBody
    +bioMoby.webservice.TCBioMoby.Body

    @@ -132,6 +153,7 @@ bioMoby.mobyExceptions.ENotAWSMethod
    bioMoby.mobyExceptions.ETypeMismatch
    bioMoby.webservice.Dispatcher.EDispatchError
    +bioMoby.webservice.Invocators.InvocatorError


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/toc.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/toc.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/toc.html 2004/12/09 14:07:31 1.3 @@ -35,6 +35,10 @@ bioMoby.ontology.B64_Encoded_PNG
    bioMoby.ontology.B64_Encoded_Postscript
    bioMoby.ontology.BasicGFFSequenceFeature
    +bioMoby.ontology.ClustalAlnFormattedText
    +bioMoby.ontology.CommentedAASequence
    +bioMoby.ontology.CommentedDNASequence
    +bioMoby.ontology.CommentedRNASequence
    bioMoby.ontology.DateTime
    bioMoby.ontology.Decypher_Text
    bioMoby.ontology.DNASequence
    @@ -42,6 +46,8 @@ bioMoby.ontology.Edge
    bioMoby.ontology.EmblFlatfile
    bioMoby.ontology.FASTA
    +bioMoby.ontology.FASTA_AA
    +bioMoby.ontology.FASTA_NA
    bioMoby.ontology.GenbankFlatfile
    bioMoby.ontology.GenericSequence
    bioMoby.ontology.GeneticElement
    @@ -55,6 +61,7 @@ bioMoby.ontology.Global_Keyword
    bioMoby.ontology.GO_Term
    bioMoby.ontology.Haplotyping_Study_obj
    +bioMoby.ontology.HBond_Pair
    bioMoby.ontology.HCA_picture
    bioMoby.ontology.ICIS_Query
    bioMoby.ontology.ICIS_Query2
    @@ -64,12 +71,15 @@ bioMoby.ontology.Interaction_partner
    bioMoby.ontology.InteractionMethod
    bioMoby.ontology.Interactor
    +bioMoby.ontology.MEME_Text
    +bioMoby.ontology.MGIS_ACCESSION
    bioMoby.ontology.MMP_Locus
    bioMoby.ontology.MO_Term_Test
    bioMoby.ontology.Multi_key_value_pair
    bioMoby.ontology.MyTree
    bioMoby.ontology.NCBI_BLAST_Text
    bioMoby.ontology.NCBI_Blast_XML
    +bioMoby.ontology.NCBI_MEME_Text
    bioMoby.ontology.NucleotideSequence
    bioMoby.ontology.PDBFormattedText
    bioMoby.ontology.PDGJOB
    @@ -86,10 +96,12 @@ bioMoby.ontology.Simple_key_value_pair
    bioMoby.ontology.SimpleAnnotatedGIFImage
    bioMoby.ontology.SimpleAnnotatedJPEGImage
    +bioMoby.ontology.SINGER_ACCESSION
    bioMoby.ontology.Snp_allele
    bioMoby.ontology.Snp_genotype
    bioMoby.ontology.Study
    bioMoby.ontology.TargetP_result
    +bioMoby.ontology.TEST
    bioMoby.ontology.Testout
    bioMoby.ontology.Text_plain
    bioMoby.ontology.TextBase64
    @@ -100,11 +112,15 @@ bioMoby.ontology.TextXml
    bioMoby.ontology.Trait_Details
    bioMoby.ontology.Tree
    +bioMoby.ontology.TropGENE_ACCESSION
    +bioMoby.ontology.TropGENE_Diversity_Matrix
    +bioMoby.ontology.TropGENE_LOCUS
    bioMoby.ontology.VirtualSequence
    bioMoby.ontology.Wildcard_Query
    bioMoby.ontology.WU_BLAST_Text
    bioMoby.webservice.Dispatcher
    bioMoby.webservice.Invocators
    +bioMoby.webservice.TCBioMoby


    [show private | hide private] =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/private/trees.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/private/trees.html 2004/12/08 11:15:24 1.2 +++ /home/repository/moby/moby-live/Python/doc/private/trees.html 2004/12/09 14:07:31 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -51,6 +57,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -58,6 +68,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -71,6 +83,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -80,12 +93,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -102,10 +118,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -116,6 +134,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -124,6 +145,7 @@ @@ -131,6 +153,12 @@

    Class Hierarchy

    @@ -483,8 +564,19 @@
  • bioMoby.ontology.Snp_genotype.MobySnp_genotype: Description: Snp Genotypes Author: www.hapmap.org Contact: hapmap@hapmap.edu +
  • bioMoby.webservice.Dispatcher.AbstractDispatcher: +Subclass this one to create your own dispatcher class a Dispatcher +class must have a execute method +
  • bioMoby.webservice.Dispatcher.LockedIterator: Avoid concurrency on the iterator
  • bioMoby.webservice.Dispatcher.MultiThread: @@ -500,9 +592,14 @@ CGI script in Post multipart
  • bioMoby.webservice.Invocators.LocalInvocator: Invokes local command + -
  • bioMoby.webservice.Invocators.InvocatorError: -Error during an invocation of method + +
  • bioMoby.webservice.Invocators.QsubParameters: +Parameters for the qsub command +
  • bioMoby.webservice.TCBioMoby._TCBody
  • exceptions.Exception: Common base class for all exceptions. @@ -523,13 +622,19 @@
  • - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + From yanwong at pub.open-bio.org Thu Dec 9 14:38:10 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu, 9 Dec 2004 09:38:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091438.iB9EcAo2003626@pub.open-bio.org> yanwong Thu Dec 9 09:38:10 EST 2004 Update of /home/repository/moby/moby-live/Python/utils In directory pub.open-bio.org:/tmp/cvs-serv3601 Added Files: moby2python.py Log Message: moby-live/Python/utils moby2python.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/utils/moby2python.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/utils/moby2python.py 2004/12/08 11:15:31 1.2 +++ /home/repository/moby/moby-live/Python/utils/moby2python.py 2004/12/09 14:38:10 1.3 @@ -1,4 +1,4 @@ -#!/bin/env python +#!/usr/bin/env python #This program will retrieve all objects definitions stored on a bioMoby Server #and generate the corresponding Python Object From yanwong at pub.open-bio.org Thu Dec 9 14:39:05 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu, 9 Dec 2004 09:39:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091439.iB9Ed5el003686@pub.open-bio.org> yanwong Thu Dec 9 09:39:05 EST 2004 Update of /home/repository/moby/moby-live/Python/utils/wx In directory pub.open-bio.org:/tmp/cvs-serv3657 Added Files: README objectBrowser.py Log Message: moby-live/Python/utils/wx README,1.2,1.3 objectBrowser.py,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/utils/wx/README,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/utils/wx/objectBrowser.py,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From yanwong at pub.open-bio.org Thu Dec 9 14:41:33 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu, 9 Dec 2004 09:41:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091441.iB9EfX1b003758@pub.open-bio.org> yanwong Thu Dec 9 09:41:33 EST 2004 Update of /home/repository/moby/moby-live/Python/doc In directory pub.open-bio.org:/tmp/cvs-serv3725 Added Files: api.pdf api.ps epydoc.css howto.pdf index.html Log Message: moby-live/Python/doc api.pdf,NONE,1.1 api.ps,NONE,1.1 epydoc.css,1.2,1.3 howto.pdf,1.2,1.3 index.html,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/epydoc.css,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/howto.pdf,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 Binary files /home/repository/moby/moby-live/Python/doc/howto.pdf 2004/12/08 11:15:22 1.2 and /home/repository/moby/moby-live/Python/doc/howto.pdf 2004/12/09 14:41:33 1.3 differ rcsdiff: /home/repository/moby/moby-live/Python/doc/howto.pdf: diff failed =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/index.html 2004/12/08 11:15:22 1.2 +++ /home/repository/moby/moby-live/Python/doc/index.html 2004/12/09 14:41:33 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python From yanwong at pub.open-bio.org Thu Dec 9 14:41:39 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu, 9 Dec 2004 09:41:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091441.iB9EfdKr005007@pub.open-bio.org> yanwong Thu Dec 9 09:41:39 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/src In directory pub.open-bio.org:/tmp/cvs-serv3725/src Added Files: howto.sxw Log Message: moby-live/Python/doc/src howto.sxw,NONE,1.1 From yanwong at pub.open-bio.org Thu Dec 9 14:41:39 2004 From: yanwong at pub.open-bio.org (Yan Wong) Date: Thu, 9 Dec 2004 09:41:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412091441.iB9Efdre004992@pub.open-bio.org> yanwong Thu Dec 9 09:41:35 EST 2004 Update of /home/repository/moby/moby-live/Python/doc/public In directory pub.open-bio.org:/tmp/cvs-serv3725/public Added Files: ZSI.TC.TypeCode-class.html __builtin__.object-class.html __builtin__.type-class.html bioMoby-module.html bioMoby.mobyClient-module.html bioMoby.mobyClient.Central-class.html bioMoby.mobyClient.Client-class.html bioMoby.mobyDataTypes-module.html bioMoby.mobyDataTypes.MobyContent-class.html bioMoby.mobyDataTypes.MobyFloat-class.html bioMoby.mobyDataTypes.MobyInteger-class.html bioMoby.mobyDataTypes.MobyObject-class.html bioMoby.mobyDataTypes.MobySequence-class.html bioMoby.mobyDataTypes.MobyString-class.html bioMoby.mobyDataTypes.MobyXref-class.html bioMoby.mobyDataTypes.MobyZmPDB-class.html bioMoby.mobyDataTypes.Parameter-class.html bioMoby.mobyExceptions-module.html bioMoby.mobyExceptions.EInvalidArgument-class.html bioMoby.mobyExceptions.EInvalidType-class.html bioMoby.mobyExceptions.EMethodRetrieveError-class.html bioMoby.mobyExceptions.ENotAWSMethod-class.html bioMoby.mobyExceptions.ETypeMismatch-class.html bioMoby.mobyMarshal-module.html bioMoby.mobyMarshal.MobyMarshaller-class.html bioMoby.mobyMarshal.MobyUnmarshaller-class.html bioMoby.mobyRegister-module.html bioMoby.mobyRegister.GeneralInformations-class.html bioMoby.mobyRegister.Namespace-class.html bioMoby.mobyRegister.ObjectClass-class.html bioMoby.mobyRegister.RegistrationObject-class.html bioMoby.mobyRegister.ServiceType-class.html bioMoby.mobyService-module.html bioMoby.mobyService.Service-class.html bioMoby.mobyService.ServiceArticle-class.html bioMoby.mobyService.ServiceList-class.html bioMoby.mobyService.ServiceQuery-class.html bioMoby.mobyService.ServiceSecondary-class.html bioMoby.ontology-module.html bioMoby.ontology.AGI_LocusCode-module.html bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html bioMoby.ontology.Allele_freq-module.html bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html bioMoby.ontology.AminoAcidSequence-module.html bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html bioMoby.ontology.B64_Encoded_PNG-module.html bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html bioMoby.ontology.B64_Encoded_Postscript-module.html bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html bioMoby.ontology.B64_encoded_PDB-module.html bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html bioMoby.ontology.B64_encoded_gif-module.html bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html bioMoby.ontology.B64_encoded_jpeg-module.html bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg-class.html bioMoby.ontology.BasicGFFSequenceFeature-module.html bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature-class.html bioMoby.ontology.ClustalAlnFormattedText-module.html bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText-class.html bioMoby.ontology.CommentedAASequence-module.html bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence-class.html bioMoby.ontology.CommentedDNASequence-module.html bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence-class.html bioMoby.ontology.CommentedRNASequence-module.html bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence-class.html bioMoby.ontology.DNASequence-module.html bioMoby.ontology.DNASequence.MobyDNASequence-class.html bioMoby.ontology.DNASequenceWithGFFFeatures-module.html bioMoby.ontology.DNASequenceWithGFFFeatures.MobyDNASequenceWithGFFFeatures-class.html bioMoby.ontology.DateTime-module.html bioMoby.ontology.DateTime.MobyDateTime-class.html bioMoby.ontology.Decypher_Text-module.html bioMoby.ontology.Decypher_Text.MobyDecypher_Text-class.html bioMoby.ontology.Edge-module.html bioMoby.ontology.Edge.MobyEdge-class.html bioMoby.ontology.EmblFlatfile-module.html bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile-class.html bioMoby.ontology.FASTA-module.html bioMoby.ontology.FASTA.MobyFASTA-class.html bioMoby.ontology.FASTA_AA-module.html bioMoby.ontology.FASTA_AA.MobyFASTA_AA-class.html bioMoby.ontology.FASTA_NA-module.html bioMoby.ontology.FASTA_NA.MobyFASTA_NA-class.html bioMoby.ontology.GFF-module.html bioMoby.ontology.GFF.MobyGFF-class.html bioMoby.ontology.GFF1-module.html bioMoby.ontology.GFF1.MobyGFF1-class.html bioMoby.ontology.GFF2-module.html bioMoby.ontology.GFF2.MobyGFF2-class.html bioMoby.ontology.GFF2_5-module.html bioMoby.ontology.GFF2_5.MobyGFF2_5-class.html bioMoby.ontology.GFF3-module.html bioMoby.ontology.GFF3.MobyGFF3-class.html bioMoby.ontology.GO_Term-module.html 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toc-bioMoby.ontology.NCBI_Blast_XML-module.html toc-bioMoby.ontology.NCBI_MEME_Text-module.html toc-bioMoby.ontology.NucleotideSequence-module.html toc-bioMoby.ontology.PDBFormattedText-module.html toc-bioMoby.ontology.PDGJOB-module.html toc-bioMoby.ontology.PhenotypeDescription-module.html toc-bioMoby.ontology.PubMedMEDLINE-module.html toc-bioMoby.ontology.RNASequence-module.html toc-bioMoby.ontology.SINGER_ACCESSION-module.html toc-bioMoby.ontology.SchematikonMotifID-module.html toc-bioMoby.ontology.SchematikonMotifSupport-module.html toc-bioMoby.ontology.SchematikonSegmentAttributes-module.html toc-bioMoby.ontology.SchematikonSegmentID-module.html toc-bioMoby.ontology.SchematikonStructureAnnotation-module.html toc-bioMoby.ontology.SchematikonVorocodeName-module.html toc-bioMoby.ontology.Scored_acronym_string-module.html toc-bioMoby.ontology.SimpleAnnotatedGIFImage-module.html toc-bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html toc-bioMoby.ontology.Simple_key_value_pair-module.html toc-bioMoby.ontology.Snp_allele-module.html toc-bioMoby.ontology.Snp_genotype-module.html toc-bioMoby.ontology.Study-module.html toc-bioMoby.ontology.TEST-module.html toc-bioMoby.ontology.TargetP_result-module.html toc-bioMoby.ontology.Testout-module.html toc-bioMoby.ontology.TextBase64-module.html toc-bioMoby.ontology.TextFormatted-module.html toc-bioMoby.ontology.TextHtml-module.html toc-bioMoby.ontology.TextPlain-module.html toc-bioMoby.ontology.TextUuencoded-module.html toc-bioMoby.ontology.TextXml-module.html toc-bioMoby.ontology.Text_plain-module.html toc-bioMoby.ontology.Trait_Details-module.html toc-bioMoby.ontology.Tree-module.html toc-bioMoby.ontology.TropGENE_ACCESSION-module.html toc-bioMoby.ontology.TropGENE_Diversity_Matrix-module.html toc-bioMoby.ontology.TropGENE_LOCUS-module.html toc-bioMoby.ontology.VirtualSequence-module.html toc-bioMoby.ontology.WU_BLAST_Text-module.html toc-bioMoby.ontology.Wildcard_Query-module.html toc-bioMoby.webservice-module.html toc-bioMoby.webservice.Dispatcher-module.html toc-bioMoby.webservice.Invocators-module.html toc-bioMoby.webservice.TCBioMoby-module.html toc-everything.html toc.html trees.html Log Message: moby-live/Python/doc/public ZSI.TC.TypeCode-class.html,NONE,1.1 __builtin__.object-class.html,1.2,1.3 __builtin__.type-class.html,1.2,1.3 bioMoby-module.html,1.2,1.3 bioMoby.mobyClient-module.html,1.2,1.3 bioMoby.mobyClient.Central-class.html,1.2,1.3 bioMoby.mobyClient.Client-class.html,1.2,1.3 bioMoby.mobyDataTypes-module.html,1.2,1.3 bioMoby.mobyDataTypes.MobyContent-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyFloat-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyInteger-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyObject-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobySequence-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyString-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyXref-class.html,1.2,1.3 bioMoby.mobyDataTypes.MobyZmPDB-class.html,1.2,1.3 bioMoby.mobyDataTypes.Parameter-class.html,1.2,1.3 bioMoby.mobyExceptions-module.html,1.2,1.3 bioMoby.mobyExceptions.EInvalidArgument-class.html,1.2,1.3 bioMoby.mobyExceptions.EInvalidType-class.html,1.2,1.3 bioMoby.mobyExceptions.EMet! hodRetrieveError-class.html,1.2,1.3 bioMoby.mobyExceptions.ENotAWSMethod-class.html,1.2,1.3 bioMoby.mobyExceptions.ETypeMismatch-class.html,1.2,1.3 bioMoby.mobyMarshal-module.html,1.2,1.3 bioMoby.mobyMarshal.MobyMarshaller-class.html,1.2,1.3 bioMoby.mobyMarshal.MobyUnmarshaller-class.html,1.2,1.3 bioMoby.mobyRegister-module.html,1.2,1.3 bioMoby.mobyRegister.GeneralInformations-class.html,1.2,1.3 bioMoby.mobyRegister.Namespace-class.html,1.2,1.3 bioMoby.mobyRegister.ObjectClass-class.html,1.2,1.3 bioMoby.mobyRegister.RegistrationObject-class.html,1.2,1.3 bioMoby.mobyRegister.ServiceType-class.html,1.2,1.3 bioMoby.mobyService-module.html,1.2,1.3 bioMoby.mobyService.Service-class.html,1.2,1.3 bioMoby.mobyService.ServiceArticle-class.html,1.2,1.3 bioMoby.mobyService.ServiceList-class.html,1.2,1.3 bioMoby.mobyService.ServiceQuery-class.html,1.2,1.3 bioMoby.mobyService.ServiceSecondary-class.html,1.2,1.3 bioMoby.ontology-module.html,1.2,1.3 bioMoby.ontology.AGI_LocusCode-module.ht! ml,1.2,1.3 bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-c! lass.html,1.2,1.3 bioMoby.ontology.Allele_freq-module.html,1.2,1.3 bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html,1.2,1.3 bioMoby.ontology.AminoAcidSequence-module.html,1.2,1.3 bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html,1.2,1.3 bioMoby.ontology.B64_Encoded_PNG-module.html,1.2,1.3 bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html,1.2,1.3 bioMoby.ontology.B64_Encoded_Postscript-module.html,1.2,1.3 bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html,1.2,1.3 bioMoby.ontology.B64_encoded_PDB-module.html,1.2,1.3 bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html,1.2,1.3 bioMoby.ontology.B64_encoded_gif-module.html,1.2,1.3 bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html,1.2,1.3 bioMoby.ontology.B64_encoded_jpeg-module.html,1.2,1.3 bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg-class.html,1.2,1.3 bioMoby.ontology.BasicGFFSequenceFeature-module.html,1.2,1.3 bioMoby.ontology.! BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature-class.html,1.2,1.3 bioMoby.ontology.ClustalAlnFormattedText-module.html,NONE,1.1 bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText-class.html,NONE,1.1 bioMoby.ontology.CommentedAASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence-class.html,NONE,1.1 bioMoby.ontology.CommentedDNASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence-class.html,NONE,1.1 bioMoby.ontology.CommentedRNASequence-module.html,NONE,1.1 bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence-class.html,NONE,1.1 bioMoby.ontology.DNASequence-module.html,1.2,1.3 bioMoby.ontology.DNASequence.MobyDNASequence-class.html,1.2,1.3 bioMoby.ontology.DNASequenceWithGFFFeatures-module.html,1.2,1.3 bioMoby.ontology.DNASequenceWithGFFFeatures.MobyDNASequenceWithGFFFeatures-class.html,1.2,1.3 bioMoby.ontology.DateTime-module.html,1.2,1.3 bioMoby.ontology.DateTime.M! obyDateTime-class.html,1.2,1.3 bioMoby.ontology.Decypher_Text! -module.html,1.2,1.3 bioMoby.ontology.Decypher_Text.MobyDecypher_Text-class.html,1.2,1.3 bioMoby.ontology.Edge-module.html,1.2,1.3 bioMoby.ontology.Edge.MobyEdge-class.html,1.2,1.3 bioMoby.ontology.EmblFlatfile-module.html,1.2,1.3 bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile-class.html,1.2,1.3 bioMoby.ontology.FASTA-module.html,1.2,1.3 bioMoby.ontology.FASTA.MobyFASTA-class.html,1.2,1.3 bioMoby.ontology.FASTA_AA-module.html,NONE,1.1 bioMoby.ontology.FASTA_AA.MobyFASTA_AA-class.html,NONE,1.1 bioMoby.ontology.FASTA_NA-module.html,NONE,1.1 bioMoby.ontology.FASTA_NA.MobyFASTA_NA-class.html,NONE,1.1 bioMoby.ontology.GFF-module.html,1.2,1.3 bioMoby.ontology.GFF.MobyGFF-class.html,1.2,1.3 bioMoby.ontology.GFF1-module.html,1.2,1.3 bioMoby.ontology.GFF1.MobyGFF1-class.html,1.2,1.3 bioMoby.ontology.GFF2-module.html,1.2,1.3 bioMoby.ontology.GFF2.MobyGFF2-class.html,1.2,1.3 bioMoby.ontology.GFF2_5-module.html,1.2,1.3 bioMoby.ontology.GFF2_5.MobyGFF2_5-class.html,1.2,1.3 bioMoby.ontolo! gy.GFF3-module.html,1.2,1.3 bioMoby.ontology.GFF3.MobyGFF3-class.html,1.2,1.3 bioMoby.ontology.GO_Term-module.html,1.2,1.3 bioMoby.ontology.GO_Term.MobyGO_Term-class.html,1.2,1.3 bioMoby.ontology.GenbankFlatfile-module.html,1.2,1.3 bioMoby.ontology.GenbankFlatfile.MobyGenbankFlatfile-class.html,1.2,1.3 bioMoby.ontology.GenericSequence-module.html,1.2,1.3 bioMoby.ontology.GenericSequence.MobyGenericSequence-class.html,1.2,1.3 bioMoby.ontology.GeneticElement-module.html,1.2,1.3 bioMoby.ontology.GeneticElement.MobyGeneticElement-class.html,1.2,1.3 bioMoby.ontology.Germplasm_Details-module.html,1.2,1.3 bioMoby.ontology.Germplasm_Details.MobyGermplasm_Details-class.html,1.2,1.3 bioMoby.ontology.Germplasm_List-module.html,1.2,1.3 bioMoby.ontology.Germplasm_List.MobyGermplasm_List-class.html,1.2,1.3 bioMoby.ontology.Global_Keyword-module.html,1.2,1.3 bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword-class.html,1.2,1.3 bioMoby.ontology.HBond_Pair-module.html,NONE,1.1 bioMoby.ontolo! gy.HBond_Pair.MobyHBond_Pair-class.html,NONE,1.1 bioMoby.onto! logy.HCA_picture-module.html,1.2,1.3 bioMoby.ontology.HCA_picture.MobyHCA_picture-class.html,1.2,1.3 bioMoby.ontology.Haplotyping_Study_obj-module.html,1.2,1.3 bioMoby.ontology.Haplotyping_Study_obj.MobyHaplotyping_Study_obj-class.html,1.2,1.3 bioMoby.ontology.ICIS_Query-module.html,1.2,1.3 bioMoby.ontology.ICIS_Query.MobyICIS_Query-class.html,1.2,1.3 bioMoby.ontology.ICIS_Query2-module.html,1.2,1.3 bioMoby.ontology.ICIS_Query2.MobyICIS_Query2-class.html,1.2,1.3 bioMoby.ontology.ICIS_Query3-module.html,1.2,1.3 bioMoby.ontology.ICIS_Query3.MobyICIS_Query3-class.html,1.2,1.3 bioMoby.ontology.IntAct_XML-module.html,1.2,1.3 bioMoby.ontology.IntAct_XML.MobyIntAct_XML-class.html,1.2,1.3 bioMoby.ontology.Interaction-module.html,1.2,1.3 bioMoby.ontology.Interaction.MobyInteraction-class.html,1.2,1.3 bioMoby.ontology.InteractionMethod-module.html,1.2,1.3 bioMoby.ontology.InteractionMethod.MobyInteractionMethod-class.html,1.2,1.3 bioMoby.ontology.Interaction_partner-module.html,1.2,1.! 3 bioMoby.ontology.Interaction_partner.MobyInteraction_partner-class.html,1.2,1.3 bioMoby.ontology.Interactor-module.html,1.2,1.3 bioMoby.ontology.Interactor.MobyInteractor-class.html,1.2,1.3 bioMoby.ontology.MEME_Text-module.html,NONE,1.1 bioMoby.ontology.MEME_Text.MobyMEME_Text-class.html,NONE,1.1 bioMoby.ontology.MGIS_ACCESSION-module.html,NONE,1.1 bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION-class.html,NONE,1.1 bioMoby.ontology.MMP_Locus-module.html,1.2,1.3 bioMoby.ontology.MMP_Locus.MobyMMP_Locus-class.html,1.2,1.3 bioMoby.ontology.MO_Term_Test-module.html,1.2,1.3 bioMoby.ontology.MO_Term_Test.MobyMO_Term_Test-class.html,1.2,1.3 bioMoby.ontology.Multi_key_value_pair-module.html,1.2,1.3 bioMoby.ontology.Multi_key_value_pair.MobyMulti_key_value_pair-class.html,1.2,1.3 bioMoby.ontology.MyTree-module.html,1.2,1.3 bioMoby.ontology.MyTree.MobyMyTree-class.html,1.2,1.3 bioMoby.ontology.NCBI_BLAST_Text-module.html,1.2,1.3 bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Te! xt-class.html,1.2,1.3 bioMoby.ontology.NCBI_Blast_XML-module.! html,1.2,1.3 bioMoby.ontology.NCBI_ Blast_XML.MobyNCBI_Blast_XML-class.html,1.2,1.3 bioMoby.ontology.NCBI_MEME_Text-module.html,NONE,1.1 bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text-class.html,NONE,1.1 bioMoby.ontology.NucleotideSequence-module.html,1.2,1.3 bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence-class.html,1.2,1.3 bioMoby.ontology.PDBFormattedText-module.html,1.2,1.3 bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText-class.html,1.2,1.3 bioMoby.ontology.PDGJOB-module.html,1.2,1.3 bioMoby.ontology.PDGJOB.MobyPDGJOB-class.html,1.2,1.3 bioMoby.ontology.PhenotypeDescription-module.html,1.2,1.3 bioMoby.ontology.PhenotypeDescription.MobyPhenotypeDescription-class.html,1.2,1.3 bioMoby.ontology.PubMedMEDLINE-module.html,1.2,1.3 bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE-class.html,1.2,1.3 bioMoby.ontology.RNASequence-module.html,1.2,1.3 bioMoby.ontology.RNASequence.MobyRNASequence-class.html,1.2,1.3 bioMoby.ontology.SINGER_ACCESSION-module.html,NONE,1.1 bioMoby.ontology.SINGER_ACCESS! ION.MobySINGER_ACCESSION-class.html,NONE,1.1 bioMoby.ontology.SchematikonMotifID-module.html,1.2,1.3 bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID-class.html,1.2,1.3 bioMoby.ontology.SchematikonMotifSupport-module.html,1.2,1.3 bioMoby.ontology.SchematikonMotifSupport.MobySchematikonMotifSupport-class.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentAttributes-module.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentAttributes.MobySchematikonSegmentAttributes-class.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentID-module.html,1.2,1.3 bioMoby.ontology.SchematikonSegmentID.MobySchematikonSegmentID-class.html,1.2,1.3 bioMoby.ontology.SchematikonStructureAnnotation-module.html,1.2,1.3 bioMoby.ontology.SchematikonStructureAnnotation.MobySchematikonStructureAnnotation-class.html,1.2,1.3 bioMoby.ontology.SchematikonVorocodeName-module.html,1.2,1.3 bioMoby.ontology.SchematikonVorocodeName.MobySchematikonVorocodeName-class.html,1.2,1.3 bioMoby.ontology.Scored_acronym_string! -module.html,1.2,1.3 bioMoby.ontology.Scored_acronym_string.M! obyScored_acronym_string-class.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedGIFImage-module.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage-class.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html,1.2,1.3 bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage-class.html,1.2,1.3 bioMoby.ontology.Simple_key_value_pair-module.html,1.2,1.3 bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair-class.html,1.2,1.3 bioMoby.ontology.Snp_allele-module.html,1.2,1.3 bioMoby.ontology.Snp_allele.MobySnp_allele-class.html,1.2,1.3 bioMoby.ontology.Snp_genotype-module.html,1.2,1.3 bioMoby.ontology.Snp_genotype.MobySnp_genotype-class.html,1.2,1.3 bioMoby.ontology.Study-module.html,1.2,1.3 bioMoby.ontology.Study.MobyStudy-class.html,1.2,1.3 bioMoby.ontology.TEST-module.html,NONE,1.1 bioMoby.ontology.TEST.MobyTEST-class.html,NONE,1.1 bioMoby.ontology.TargetP_result-module.html,1.2,1.3 bioMoby.ontology.TargetP_result.Mo! byTargetP_result-class.html,1.2,1.3 bioMoby.ontology.Testout-module.html,1.2,1.3 bioMoby.ontology.Testout.MobyTestout-class.html,1.2,1.3 bioMoby.ontology.TextBase64-module.html,1.2,1.3 bioMoby.ontology.TextBase64.MobyTextBase64-class.html,1.2,1.3 bioMoby.ontology.TextFormatted-module.html,1.2,1.3 bioMoby.ontology.TextFormatted.MobyTextFormatted-class.html,1.2,1.3 bioMoby.ontology.TextHtml-module.html,1.2,1.3 bioMoby.ontology.TextHtml.MobyTextHtml-class.html,1.2,1.3 bioMoby.ontology.TextPlain-module.html,1.2,1.3 bioMoby.ontology.TextPlain.MobyTextPlain-class.html,1.2,1.3 bioMoby.ontology.TextUuencoded-module.html,1.2,1.3 bioMoby.ontology.TextUuencoded.MobyTextUuencoded-class.html,1.2,1.3 bioMoby.ontology.TextXml-module.html,1.2,1.3 bioMoby.ontology.TextXml.MobyTextXml-class.html,1.2,1.3 bioMoby.ontology.Text_plain-module.html,1.2,1.3 bioMoby.ontology.Text_plain.MobyText_plain-class.html,1.2,1.3 bioMoby.ontology.Trait_Details-module.html,1.2,1.3 bioMoby.ontology.Trait_Details.! MobyTrait_Details-class.html,1.2,1.3 bioMoby.ontology.Tree-mo! dule.html,1.2,1.3 bioMoby.ontology.Tree.MobyTree-class.html,1.2,1.3 bioMoby.ontology.TropGENE_ACCESSION-module.html,NONE,1.1 bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION-class.html,NONE,1.1 bioMoby.ontology.TropGENE_Diversity_Matrix-module.html,NONE,1.1 bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix-class.html,NONE,1.1 bioMoby.ontology.TropGENE_LOCUS-module.html,NONE,1.1 bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS-class.html,NONE,1.1 bioMoby.ontology.VirtualSequence-module.html,1.2,1.3 bioMoby.ontology.VirtualSequence.MobyVirtualSequence-class.html,1.2,1.3 bioMoby.ontology.WU_BLAST_Text-module.html,1.2,1.3 bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text-class.html,1.2,1.3 bioMoby.ontology.Wildcard_Query-module.html,1.2,1.3 bioMoby.ontology.Wildcard_Query.MobyWildcard_Query-class.html,1.2,1.3 bioMoby.webservice-module.html,1.2,1.3 bioMoby.webservice.Dispatcher-module.html,1.2,1.3 bioMoby.webservice.Dispatcher.AbstractDispatcher-! class.html,NONE,1.1 bioMoby.webservice.Dispatcher.Dispatcher-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.EDispatchError-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.LockedIterator-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.MultiThread-class.html,1.2,1.3 bioMoby.webservice.Dispatcher.PBSDispatcher-class.html,NONE,1.1 bioMoby.webservice.Dispatcher.SimpleDispatcher-class.html,NONE,1.1 bioMoby.webservice.Dispatcher.SingleThread-class.html,1.2,1.3 bioMoby.webservice.Invocators-module.html,1.2,1.3 bioMoby.webservice.Invocators.CGIPostInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.CGIPostMInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.GeneralInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.InvocatorError-class.html,1.2,1.3 bioMoby.webservice.Invocators.LocalInvocator-class.html,1.2,1.3 bioMoby.webservice.Invocators.PBSInvocator-class.html,NONE,1.1 bioMoby.webservice.Invocators.QsubParameters-class.html,NONE,1.1 bioMoby.webservice.TCB! ioMoby-module.html,NONE,1.1 bioMoby.webservice.TCBioMoby.Body! -class.html,NONE,1.1 exceptions.Exception-class.html,1.2,1.3 frames.html,1.2,1.3 help.html,1.2,1.3 index.html,1.2,1.3 indices.html,1.2,1.3 threading.Thread-class.html,1.2,1.3 toc-bioMoby-module.html,1.2,1.3 toc-bioMoby.mobyClient-module.html,1.2,1.3 toc-bioMoby.mobyDataTypes-module.html,1.2,1.3 toc-bioMoby.mobyExceptions-module.html,1.2,1.3 toc-bioMoby.mobyMarshal-module.html,1.2,1.3 toc-bioMoby.mobyRegister-module.html,1.2,1.3 toc-bioMoby.mobyService-module.html,1.2,1.3 toc-bioMoby.ontology-module.html,1.2,1.3 toc-bioMoby.ontology.AGI_LocusCode-module.html,1.2,1.3 toc-bioMoby.ontology.Allele_freq-module.html,1.2,1.3 toc-bioMoby.ontology.AminoAcidSequence-module.html,1.2,1.3 toc-bioMoby.ontology.B64_Encoded_PNG-module.html,1.2,1.3 toc-bioMoby.ontology.B64_Encoded_Postscript-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encoded_PDB-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encoded_gif-module.html,1.2,1.3 toc-bioMoby.ontology.B64_encoded_jpeg-module.html,1.2,1.3 toc-bioMoby.! ontology.BasicGFFSequenceFeature-module.html,1.2,1.3 toc-bioMoby.ontology.ClustalAlnFormattedText-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedAASequence-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedDNASequence-module.html,NONE,1.1 toc-bioMoby.ontology.CommentedRNASequence-module.html,NONE,1.1 toc-bioMoby.ontology.DNASequence-module.html,1.2,1.3 toc-bioMoby.ontology.DNASequenceWithGFFFeatures-module.html,1.2,1.3 toc-bioMoby.ontology.DateTime-module.html,1.2,1.3 toc-bioMoby.ontology.Decypher_Text-module.html,1.2,1.3 toc-bioMoby.ontology.Edge-module.html,1.2,1.3 toc-bioMoby.ontology.EmblFlatfile-module.html,1.2,1.3 toc-bioMoby.ontology.FASTA-module.html,1.2,1.3 toc-bioMoby.ontology.FASTA_AA-module.html,NONE,1.1 toc-bioMoby.ontology.FASTA_NA-module.html,NONE,1.1 toc-bioMoby.ontology.GFF-module.html,1.2,1.3 toc-bioMoby.ontology.GFF1-module.html,1.2,1.3 toc-bioMoby.ontology.GFF2-module.html,1.2,1.3 toc-bioMoby.ontology.GFF2_5-module.html,1.2,1.3 toc-bioMoby.ontology.G! FF3-module.html,1.2,1.3 toc-bioMoby.ontology.GO_Term-module.h! tml,1.2,1.3 toc-bioMoby.ontology.Ge nbankFlatfile-module.html,1.2,1.3 toc-bioMoby.ontology.GenericSequence-module.html,1.2,1.3 toc-bioMoby.ontology.GeneticElement-module.html,1.2,1.3 toc-bioMoby.ontology.Germplasm_Details-module.html,1.2,1.3 toc-bioMoby.ontology.Germplasm_List-module.html,1.2,1.3 toc-bioMoby.ontology.Global_Keyword-module.html,1.2,1.3 toc-bioMoby.ontology.HBond_Pair-module.html,NONE,1.1 toc-bioMoby.ontology.HCA_picture-module.html,1.2,1.3 toc-bioMoby.ontology.Haplotyping_Study_obj-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query2-module.html,1.2,1.3 toc-bioMoby.ontology.ICIS_Query3-module.html,1.2,1.3 toc-bioMoby.ontology.IntAct_XML-module.html,1.2,1.3 toc-bioMoby.ontology.Interaction-module.html,1.2,1.3 toc-bioMoby.ontology.InteractionMethod-module.html,1.2,1.3 toc-bioMoby.ontology.Interaction_partner-module.html,1.2,1.3 toc-bioMoby.ontology.Interactor-module.html,1.2,1.3 toc-bioMoby.ontology.MEME_Text-module.html,NONE,1.1 toc-bioMoby.ont! ology.MGIS_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.MMP_Locus-module.html,1.2,1.3 toc-bioMoby.ontology.MO_Term_Test-module.html,1.2,1.3 toc-bioMoby.ontology.Multi_key_value_pair-module.html,1.2,1.3 toc-bioMoby.ontology.MyTree-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_BLAST_Text-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_Blast_XML-module.html,1.2,1.3 toc-bioMoby.ontology.NCBI_MEME_Text-module.html,NONE,1.1 toc-bioMoby.ontology.NucleotideSequence-module.html,1.2,1.3 toc-bioMoby.ontology.PDBFormattedText-module.html,1.2,1.3 toc-bioMoby.ontology.PDGJOB-module.html,1.2,1.3 toc-bioMoby.ontology.PhenotypeDescription-module.html,1.2,1.3 toc-bioMoby.ontology.PubMedMEDLINE-module.html,1.2,1.3 toc-bioMoby.ontology.RNASequence-module.html,1.2,1.3 toc-bioMoby.ontology.SINGER_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.SchematikonMotifID-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonMotifSupport-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonSegmentAtt! ributes-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonS! egmentID-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonStructureAnnotation-module.html,1.2,1.3 toc-bioMoby.ontology.SchematikonVorocodeName-module.html,1.2,1.3 toc-bioMoby.ontology.Scored_acronym_string-module.html,1.2,1.3 toc-bioMoby.ontology.SimpleAnnotatedGIFImage-module.html,1.2,1.3 toc-bioMoby.ontology.SimpleAnnotatedJPEGImage-module.html,1.2,1.3 toc-bioMoby.ontology.Simple_key_value_pair-module.html,1.2,1.3 toc-bioMoby.ontology.Snp_allele-module.html,1.2,1.3 toc-bioMoby.ontology.Snp_genotype-module.html,1.2,1.3 toc-bioMoby.ontology.Study-module.html,1.2,1.3 toc-bioMoby.ontology.TEST-module.html,NONE,1.1 toc-bioMoby.ontology.TargetP_result-module.html,1.2,1.3 toc-bioMoby.ontology.Testout-module.html,1.2,1.3 toc-bioMoby.ontology.TextBase64-module.html,1.2,1.3 toc-bioMoby.ontology.TextFormatted-module.html,1.2,1.3 toc-bioMoby.ontology.TextHtml-module.html,1.2,1.3 toc-bioMoby.ontology.TextPlain-module.html,1.2,1.3 toc-bioMoby.ontology.TextUuencoded-module.html,1.2,1.! 3 toc-bioMoby.ontology.TextXml-module.html,1.2,1.3 toc-bioMoby.ontology.Text_plain-module.html,1.2,1.3 toc-bioMoby.ontology.Trait_Details-module.html,1.2,1.3 toc-bioMoby.ontology.Tree-module.html,1.2,1.3 toc-bioMoby.ontology.TropGENE_ACCESSION-module.html,NONE,1.1 toc-bioMoby.ontology.TropGENE_Diversity_Matrix-module.html,NONE,1.1 toc-bioMoby.ontology.TropGENE_LOCUS-module.html,NONE,1.1 toc-bioMoby.ontology.VirtualSequence-module.html,1.2,1.3 toc-bioMoby.ontology.WU_BLAST_Text-module.html,1.2,1.3 toc-bioMoby.ontology.Wildcard_Query-module.html,1.2,1.3 toc-bioMoby.webservice-module.html,1.2,1.3 toc-bioMoby.webservice.Dispatcher-module.html,1.2,1.3 toc-bioMoby.webservice.Invocators-module.html,1.2,1.3 toc-bioMoby.webservice.TCBioMoby-module.html,NONE,1.1 toc-everything.html,1.2,1.3 toc.html,1.2,1.3 trees.html,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/__builtin__.object-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/__builtin__.object-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/__builtin__.object-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -245,13 +251,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/__builtin__.type-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/__builtin__.type-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/__builtin__.type-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -489,13 +495,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -58,6 +64,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -65,6 +75,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -78,6 +90,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -87,12 +100,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -109,10 +125,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -123,6 +141,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -131,6 +152,7 @@

  • @@ -143,13 +165,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -57,13 +63,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Central-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Central-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Central-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,7 +60,8 @@ @@ -77,7 +84,8 @@
      __init__(self, url, - ns) + ns, + debug)
    Changes url and ns parameters if you want to use another moby server
    - +

    __init__(self, url='http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral..., - ns='http://mobycentral.cbr.nrc.ca/MOBY/Central') + ns='http://mobycentral.cbr.nrc.ca/MOBY/Central', + debug=False)
    (Constructor)

    Changes url and ns parameters if you want to use another moby @@ -106,13 +114,19 @@
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Client-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Client-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyClient.Client-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -54,12 +60,10 @@ - +
    Method Summary
     __init__(self, + __init__(self, url, ns) -
    -Changes url and ns parameters if you want to use another moby -server
      findService(self, mobyQuery) @@ -141,23 +145,6 @@ Method Details
    - -
    -

    __init__(self, - url='http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral..., - ns='http://mobycentral.cbr.nrc.ca/MOBY/Central') -
    (Constructor) -

    - Changes url and ns parameters if you want to use another moby - server -
    -
    Overrides:
    -
    bioMoby.mobyClient.Central.__init__ (inherited documentation) -
    -
    -
    -
    - - +

    findService(self, @@ -298,13 +285,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -80,13 +86,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyContent-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyContent-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyContent-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +
    @@ -116,13 +122,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyFloat-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyFloat-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyFloat-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
    @@ -110,13 +116,19 @@ - +
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    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyInteger-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyInteger-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyInteger-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -110,13 +116,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyObject-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyObject-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyObject-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -49,6 +55,7 @@ MobyGlobal_Keyword, MobyGO_Term, MobyHaplotyping_Study_obj, + MobyHBond_Pair, MobyICIS_Query, MobyICIS_Query2, MobyICIS_Query3, @@ -57,6 +64,7 @@ MobyInteraction_partner, MobyInteractionMethod, MobyInteractor, + MobyMGIS_ACCESSION, MobyMMP_Locus, MobyMO_Term_Test, MobyMulti_key_value_pair, @@ -70,11 +78,14 @@ MobyScored_acronym_string, MobySequence, MobySimple_key_value_pair, + MobySINGER_ACCESSION, MobyString, MobyStudy, MobyTargetP_result, MobyTestout, MobyTrait_Details, + MobyTropGENE_ACCESSION, + MobyTropGENE_LOCUS, MobyVirtualSequence, MobyWildcard_Query, MobyXref, @@ -162,13 +173,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobySequence-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobySequence-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobySequence-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -57,7 +63,8 @@ - +
    __init__(self, sequence, namespace, - id) + id, + articleName)
      fromMoby(self, @@ -110,13 +117,19 @@    Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyString-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyString-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyString-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
    @@ -99,13 +105,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyXref-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyXref-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyXref-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyZmPDB-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyZmPDB-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyDataTypes.MobyZmPDB-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EInvalidType-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EInvalidType-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EInvalidType-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EMethodRetrieveError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EMethodRetrieveError-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.EMethodRetrieveError-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ENotAWSMethod-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ENotAWSMethod-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ENotAWSMethod-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ETypeMismatch-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ETypeMismatch-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyExceptions.ETypeMismatch-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -57,13 +63,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyMarshaller-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyMarshaller-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyMarshaller-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,10 +54,11 @@ - +
    +Serialize the object into a Moby XML object
    Method Summary
     dumps(self, + dumps(self, value, articleName) -
      m_dict(self, value, @@ -115,6 +122,17 @@ Method Details
    + +
    +

    dumps(self, + value, + articleName='') +

    + Serialize the object into a Moby XML object +
    +
    +
    + - +

    m_dict(self, @@ -208,13 +226,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyUnmarshaller-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyUnmarshaller-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyMarshal.MobyUnmarshaller-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +

    + bioMoby-python +

    +
    @@ -48,9 +54,10 @@ - +
    +Deserializes an xml string and return a bioMoby-Python object
    Method Summary
     loads(self, + loads(self, xml) -
      m_Collection(self, value) @@ -93,6 +100,16 @@ Method Details
    + +
    +

    loads(self, + xml) +

    + Deserializes an xml string and return a bioMoby-Python object +
    +
    +
    + - +

    m_Collection(self, @@ -165,13 +182,19 @@

       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyRegister-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyRegister-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyRegister-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    +
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    +
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    +
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    +
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    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -67,13 +73,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.Service-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.Service-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.Service-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -70,7 +76,8 @@ @@ -82,7 +89,8 @@ +Register the service on the Moby server has been added here a code to +verify that signatureURL is not empty :)
    execute(self, query, method, - returnXml) + returnXml, + debug)
    Executes the web service v0.5: return either the XML form or try to unmarshall the result and return a MobyContent Object
      register(self)
    -Register the service on the Moby server

    @@ -151,7 +159,8 @@

    execute(self, query, method='', - returnXml=True) + returnXml=True, + debug=False)

    Executes the web service v0.5: return either the XML form or try to unmarshall the result and return a MobyContent Object @@ -173,7 +182,8 @@

    register(self)

    - Register the service on the Moby server + Register the service on the Moby server has been added here a code + to verify that signatureURL is not empty :)
    @@ -187,13 +197,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceArticle-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceArticle-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceArticle-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -113,13 +119,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceList-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceList-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceList-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -204,13 +210,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceQuery-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceQuery-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceQuery-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -128,13 +134,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceSecondary-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceSecondary-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.mobyService.ServiceSecondary-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -116,13 +122,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -51,6 +57,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -58,6 +68,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -71,6 +83,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -80,12 +93,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -102,10 +118,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -116,6 +134,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -130,13 +151,19 @@
  • - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -58,13 +64,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -113,13 +119,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.Allele_freq.MobyAllele_freq-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -90,13 +96,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -48,6 +54,10 @@ MobyAminoAcidSequence
    +
    Known Subclasses:
    +
    + MobyCommentedAASequence
    +
    Description: Lightweight representation an amino acid sequence Author: @@ -117,13 +127,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG-module.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
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    +

    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG-class.html 2004/12/09 14:41:33 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

    +
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    + bioMoby-python +

    +
    @@ -56,13 +62,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
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    + bioMoby-python +

    +
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    + bioMoby-python +

    +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -116,13 +122,19 @@ - +
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    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif-module.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif-module.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    + bioMoby-python +

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    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html 2004/12/08 11:15:26 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    @@ -52,6 +58,7 @@
    Known Subclasses:
    + MobyCommentedDNASequence, MobyDNASequenceWithGFFFeatures

    @@ -123,13 +130,19 @@ - +
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    @@ -50,6 +56,11 @@ MobyFASTA
    +
    Known Subclasses:
    +
    + MobyFASTA_AA, + MobyFASTA_NA
    +
    Description: FASTA formatted sequence Author: www.sdsc.edu Contact: @@ -118,13 +129,19 @@ - +
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    Known Subclasses:
    + MobyClustalAlnFormattedText, MobyDecypher_Text, MobyEmblFlatfile, MobyFASTA, MobyGenbankFlatfile, MobyGFF, + MobyMEME_Text, MobyMyTree, MobyNCBI_BLAST_Text, + MobyNCBI_MEME_Text, MobyPDBFormattedText, MobyPubMedMEDLINE, + MobyTEST, MobyTree, + MobyTropGENE_Diversity_Matrix, MobyWU_BLAST_Text

    @@ -130,13 +141,19 @@ - +
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    +
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    @@ -55,13 +62,19 @@    Trees       Index       Help    - + + +
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    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher-module.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher-module.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -43,6 +49,10 @@ + + + + + +
    Classes
    + AbstractDispatcherSubclass this one to create your own dispatcher class a Dispatcher +class must have a execute method
    Dispatcher All Queries in the MobyContent Object are splitted and executed
    @@ -52,6 +62,12 @@ MultiThread Several threads
    + PBSDispatcherDispatcher for PBS jobs
    + SimpleDispatcherA simple dispatcher, without execute method
    SingleThread Definition of a single Thread

    @@ -74,13 +90,19 @@    Trees       Index       Help    - + + +
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    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.Dispatcher-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.Dispatcher-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.Dispatcher-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -38,6 +44,12 @@

    Class Dispatcher

    +
    +AbstractDispatcher --+
    +                     |
    +                    Dispatcher
    +

    +
    All Queries in the MobyContent Object are splitted and executed @@ -92,6 +104,9 @@ [queryData]-->("commandName","commandArgs", ["tempfiles"])
    +
    Overrides:
    +
    bioMoby.webservice.Dispatcher.AbstractDispatcher.__init__
    +
    @@ -103,6 +118,9 @@ Execute the queries with a pool of threads, store the results in a mobyContent Object
    +
    Overrides:
    +
    bioMoby.webservice.Dispatcher.AbstractDispatcher.execute
    +

    @@ -115,13 +133,19 @@    Trees       Index       Help    - + + +
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    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.EDispatchError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.EDispatchError-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Dispatcher.EDispatchError-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
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    +
    @@ -54,11 +60,24 @@ GeneralInvocator - - + + + + +
    General class for other invocators
    - InvocatorErrorError during an invocation of method
    LocalInvocator Invokes local command
    + PBSInvocatorInvokes a command in a qsub
    + QsubParametersParameters for the qsub command

    + + + + + + + +
    Exceptions
    + InvocatorErrorError during an invocation of method

    @@ -69,13 +88,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostInvocator-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostInvocator-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -68,7 +74,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -111,13 +118,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.CGIPostMInvocator-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -89,7 +95,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -151,13 +158,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.GeneralInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.GeneralInvocator-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.GeneralInvocator-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:08 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -55,17 +61,51 @@ - +
    +queryid is the identifier of a query, userdir is the session +directory, timeout the limit time of execution of the query - +
    Method Summary
     __init__(self, + __init__(self, queryid, userdir, timeout) -
     getResults(self) -
    getResults(self) +
    +retrieve the results if available

    + + + + +
    Method Details
    + + +
    +

    __init__(self, + queryid, + userdir='/tmp', + timeout=None) +
    (Constructor) +

    + queryid is the identifier of a query, userdir is the session + directory, timeout the limit time of execution of the query +
    +
    +
    + + +
    +

    getResults(self) +

    + retrieve the results if available +
    +
    +
    +
    + + @@ -73,13 +113,19 @@ - + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.InvocatorError-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.InvocatorError-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.InvocatorError-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:05 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -38,6 +44,12 @@

    Class InvocatorError

    +
    +Exception --+
    +            |
    +           InvocatorError
    +

    +
    Error during an invocation of method @@ -51,6 +63,14 @@ + + + + + +
      __str__(self)
        Inherited from Exception
     __init__(...) +
     __getitem__(...) +

    @@ -61,13 +81,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.LocalInvocator-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.LocalInvocator-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/bioMoby.webservice.Invocators.LocalInvocator-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -44,6 +50,10 @@ LocalInvocator
    +
    Known Subclasses:
    +
    + PBSInvocator
    +
    Invokes local command @@ -69,7 +79,8 @@ +
    +retrieve the results if available
        Inherited from GeneralInvocator
      getResults(self) -

    @@ -105,13 +116,19 @@    Trees       Index       Help    - + + +
    +

    + bioMoby-python +

    + - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/exceptions.Exception-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/exceptions.Exception-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/exceptions.Exception-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:27 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:07 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -43,7 +49,8 @@ EInvalidType, EMethodRetrieveError, ENotAWSMethod, - ETypeMismatch + ETypeMismatch, + InvocatorError
    @@ -74,13 +81,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/frames.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/frames.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/frames.html 2004/12/09 14:41:34 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/help.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/help.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/help.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:28 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -32,7 +38,7 @@

    API Documentation

    This document contains the API (Application Programming Interface) -documentation for this project. Documentation for the Python +documentation for bioMoby-python. Documentation for the Python objects defined by the project is divided into separate pages for each package, module, and class. The API documentation also includes two pages containing information about the project as a whole: a trees @@ -209,13 +215,19 @@

    - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/index.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/index.html 2004/12/09 14:41:34 1.3 @@ -1,7 +1,7 @@ - API Documentation + bioMoby-python =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/indices.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/indices.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/indices.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:10 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -70,6 +76,8 @@ + + @@ -132,6 +140,14 @@ + + + + + + + + @@ -146,6 +162,10 @@ + + + + @@ -170,6 +190,8 @@ + + @@ -190,6 +212,10 @@ + + + + @@ -202,6 +228,8 @@ + + @@ -214,6 +242,8 @@ + + @@ -240,6 +270,8 @@ + + @@ -262,18 +294,30 @@ + + + + + + + + + + + + @@ -284,6 +328,10 @@ + + + + @@ -368,6 +416,8 @@ + + @@ -398,6 +448,8 @@ + + @@ -406,8 +458,20 @@ + + + + + + + + + + + + @@ -474,16 +538,26 @@ + + + + + + + + + + @@ -518,6 +592,14 @@ + + + + + + + + @@ -532,6 +614,10 @@ + + + + @@ -556,6 +642,8 @@ + + @@ -576,6 +664,10 @@ + + + + @@ -588,6 +680,8 @@ + + @@ -600,6 +694,8 @@ + + @@ -626,6 +722,8 @@ + + @@ -648,6 +746,12 @@ + + + + + + @@ -674,6 +778,8 @@ + + @@ -702,6 +808,8 @@ + + @@ -774,6 +882,10 @@ + + + + @@ -798,6 +910,14 @@ + + + + + + + + @@ -818,6 +938,10 @@ + + + + @@ -846,6 +970,8 @@ + + @@ -870,6 +996,10 @@ + + + + @@ -882,6 +1012,8 @@ + + @@ -922,6 +1054,8 @@ + + @@ -932,6 +1066,8 @@ + + @@ -952,6 +1088,12 @@ + + + + + + @@ -972,14 +1114,20 @@ + + + + + + @@ -990,6 +1138,14 @@ + + + + + + + + @@ -1002,6 +1158,8 @@ + + @@ -1056,6 +1214,10 @@ + + + + @@ -1072,12 +1234,22 @@ + + + + + + + + + + @@ -1092,8 +1264,14 @@ + + + + + + @@ -1136,8 +1314,22 @@ + + + + + + + + + + + + + + @@ -1156,13 +1348,19 @@ - +
    Method in class __builtin__.object
    __hash__ Method in class __builtin__.type
    __init__Method in class ZSI.TC.TypeCode
    __init__ Method in class __builtin__.object
    __init__Method in class bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg
    __init__ Method in class bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    __init__Method in class bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    __init__Method in class bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    __init__Method in class bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    __init__Method in class bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    __init__ Method in class bioMoby.ontology.DNASequence.MobyDNASequence
    __init__Method in class bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    __init__ Method in class bioMoby.ontology.FASTA.MobyFASTA
    __init__Method in class bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    __init__Method in class bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    __init__ Method in class bioMoby.ontology.GFF.MobyGFF
    __init__Method in class bioMoby.ontology.Germplasm_List.MobyGermplasm_List
    __init__ Method in class bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    __init__Method in class bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    __init__ Method in class bioMoby.ontology.HCA_picture.MobyHCA_picture
    __init__Method in class bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    __init__ Method in class bioMoby.ontology.Interactor.MobyInteractor
    __init__Method in class bioMoby.ontology.MEME_Text.MobyMEME_Text
    __init__Method in class bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    __init__ Method in class bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    __init__Method in class bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    __init__ Method in class bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    __init__Method in class bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    __init__ Method in class bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    __init__Method in class bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE
    __init__ Method in class bioMoby.ontology.RNASequence.MobyRNASequence
    __init__Method in class bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    __init__ Method in class bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID
    __init__Method in class bioMoby.ontology.Snp_genotype.MobySnp_genotype
    __init__ Method in class bioMoby.ontology.Study.MobyStudy
    __init__Method in class bioMoby.ontology.TEST.MobyTEST
    __init__ Method in class bioMoby.ontology.TargetP_result.MobyTargetP_result
    __init__Method in class bioMoby.ontology.Trait_Details.MobyTrait_Details
    __init__ Method in class bioMoby.ontology.Tree.MobyTree
    __init__Method in class bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    __init__Method in class bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    __init__Method in class bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    __init__ Method in class bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    __init__ Method in class bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text
    __init__ Method in class bioMoby.ontology.Wildcard_Query.MobyWildcard_Query
    __init__Method in class bioMoby.webservice.Dispatcher.AbstractDispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.Dispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.LockedIterator
    __init__ Method in class bioMoby.webservice.Dispatcher.MultiThread
    __init__Method in class bioMoby.webservice.Dispatcher.PBSDispatcher
    __init__Method in class bioMoby.webservice.Dispatcher.SimpleDispatcher
    __init__ Method in class bioMoby.webservice.Dispatcher.SingleThread
    __init__Method in class bioMoby.webservice.Invocators.GeneralInvocator
    __init__ Method in class bioMoby.webservice.Invocators.LocalInvocator
    __init__Method in class bioMoby.webservice.Invocators.PBSInvocator
    __init__Method in class bioMoby.webservice.Invocators.QsubParameters
    __init__ Method in class exceptions.Exception
    __init__Method in class __builtin__.type
    __weakrefoffset__ Variable in class __builtin__.type
    AbstractDispatcherClass in module bioMoby.webservice.Dispatcher
    AGI_LocusCode Module in package bioMoby.ontology
    Allele_freqModule in package bioMoby.ontology
    bioMoby Package
    BodyClass in module bioMoby.webservice.TCBioMoby
    call_method Method in class bioMoby.mobyClient.Central
    CentralClass in module bioMoby.webservice.Invocators
    CGIPostMInvocator Class in module bioMoby.webservice.Invocators
    checknameMethod in class ZSI.TC.TypeCode
    checktypeMethod in class ZSI.TC.TypeCode
    Client Class in module bioMoby.mobyClient
    ClustalAlnFormattedTextModule in package bioMoby.ontology
    CommentedAASequenceModule in package bioMoby.ontology
    CommentedDNASequenceModule in package bioMoby.ontology
    CommentedRNASequenceModule in package bioMoby.ontology
    compress Method in class bioMoby.mobyDataTypes.MobyZmPDB
    contactClass in module exceptions
    execute Method in class bioMoby.mobyService.Service
    executeMethod in class bioMoby.webservice.Dispatcher.AbstractDispatcher
    execute Method in class bioMoby.webservice.Dispatcher.Dispatcher
    executeMethod in class bioMoby.webservice.Dispatcher.PBSDispatcher
    execute Method in class bioMoby.webservice.Invocators.CGIPostInvocator
    execute Method in class bioMoby.webservice.Invocators.CGIPostMInvocator
    execute Method in class bioMoby.webservice.Invocators.LocalInvocator
    executeMethod in class bioMoby.webservice.Invocators.PBSInvocator
    FASTA Module in package bioMoby.ontology
    FASTA_AAModule in package bioMoby.ontology
    FASTA_NAModule in package bioMoby.ontology
    findService Method in class bioMoby.mobyClient.Client
    fromMobyMethod in class bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg
    fromMoby Method in class bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    fromMobyMethod in class bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    fromMobyMethod in class bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    fromMobyMethod in class bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    fromMobyMethod in class bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    fromMoby Method in class bioMoby.ontology.DNASequence.MobyDNASequence
    fromMobyMethod in class bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    fromMoby Method in class bioMoby.ontology.FASTA.MobyFASTA
    fromMobyMethod in class bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    fromMobyMethod in class bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    fromMoby Method in class bioMoby.ontology.GFF.MobyGFF
    fromMobyMethod in class bioMoby.ontology.Germplasm_List.MobyGermplasm_List
    fromMoby Method in class bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    fromMobyMethod in class bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    fromMoby Method in class bioMoby.ontology.HCA_picture.MobyHCA_picture
    fromMobyMethod in class bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    fromMoby Method in class bioMoby.ontology.Interactor.MobyInteractor
    fromMobyMethod in class bioMoby.ontology.MEME_Text.MobyMEME_Text
    fromMobyMethod in class bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    fromMoby Method in class bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    fromMobyMethod in class bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    fromMoby Method in class bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    fromMobyMethod in class bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    fromMoby Method in class bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    fromMobyMethod in class bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE
    fromMoby Method in class bioMoby.ontology.RNASequence.MobyRNASequence
    fromMobyMethod in class bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    fromMoby Method in class bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID
    fromMobyMethod in class bioMoby.ontology.Snp_genotype.MobySnp_genotype
    fromMoby Method in class bioMoby.ontology.Study.MobyStudy
    fromMobyMethod in class bioMoby.ontology.TEST.MobyTEST
    fromMoby Method in class bioMoby.ontology.TargetP_result.MobyTargetP_result
    fromMobyMethod in class bioMoby.ontology.Trait_Details.MobyTrait_Details
    fromMoby Method in class bioMoby.ontology.Tree.MobyTree
    fromMobyMethod in class bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    fromMobyMethod in class bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    fromMobyMethod in class bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    fromMoby Method in class bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    fromMobyModule in package bioMoby.ontology
    get_content_type Method in class bioMoby.webservice.Invocators.CGIPostMInvocator
    get_parse_and_errorlistMethod in class ZSI.TC.TypeCode
    getInfo Method in class bioMoby.mobyDataTypes.MobyObject
    getMethodsModule in package bioMoby.ontology
    Haplotyping_Study_obj Module in package bioMoby.ontology
    HBond_PairModule in package bioMoby.ontology
    HCA_picture Module in package bioMoby.ontology
    ICIS_QueryMethod in class bioMoby.mobyMarshal.MobyMarshaller
    m_unicode Method in class bioMoby.mobyMarshal.MobyMarshaller
    MEME_TextModule in package bioMoby.ontology
    MGIS_ACCESSIONModule in package bioMoby.ontology
    MMP_Locus Module in package bioMoby.ontology
    MO_Term_TestClass in module bioMoby.ontology.BasicGFFSequenceFeature
    mobyClient Module in package bioMoby
    MobyClustalAlnFormattedTextClass in module bioMoby.ontology.ClustalAlnFormattedText
    MobyCommentedAASequenceClass in module bioMoby.ontology.CommentedAASequence
    MobyCommentedDNASequenceClass in module bioMoby.ontology.CommentedDNASequence
    MobyCommentedRNASequenceClass in module bioMoby.ontology.CommentedRNASequence
    MobyContent Class in module bioMoby.mobyDataTypes
    mobyDataTypesModule in package bioMoby
    MobyFASTA Class in module bioMoby.ontology.FASTA
    MobyFASTA_AAClass in module bioMoby.ontology.FASTA_AA
    MobyFASTA_NAClass in module bioMoby.ontology.FASTA_NA
    MobyFloat Class in module bioMoby.mobyDataTypes
    MobyGenbankFlatfileClass in module bioMoby.ontology.GO_Term
    MobyHaplotyping_Study_obj Class in module bioMoby.ontology.Haplotyping_Study_obj
    MobyHBond_PairClass in module bioMoby.ontology.HBond_Pair
    MobyHCA_picture Class in module bioMoby.ontology.HCA_picture
    MobyICIS_QueryModule in package bioMoby
    MobyMarshaller Class in module bioMoby.mobyMarshal
    MobyMEME_TextClass in module bioMoby.ontology.MEME_Text
    MobyMGIS_ACCESSIONClass in module bioMoby.ontology.MGIS_ACCESSION
    MobyMMP_Locus Class in module bioMoby.ontology.MMP_Locus
    MobyMO_Term_TestClass in module bioMoby.ontology.NCBI_BLAST_Text
    MobyNCBI_Blast_XML Class in module bioMoby.ontology.NCBI_Blast_XML
    MobyNCBI_MEME_TextClass in module bioMoby.ontology.NCBI_MEME_Text
    MobyNucleotideSequence Class in module bioMoby.ontology.NucleotideSequence
    MobyObjectClass in module bioMoby.ontology.SimpleAnnotatedGIFImage
    MobySimpleAnnotatedJPEGImage Class in module bioMoby.ontology.SimpleAnnotatedJPEGImage
    MobySINGER_ACCESSIONClass in module bioMoby.ontology.SINGER_ACCESSION
    MobySnp_allele Class in module bioMoby.ontology.Snp_allele
    MobySnp_genotypeClass in module bioMoby.ontology.Study
    MobyTargetP_result Class in module bioMoby.ontology.TargetP_result
    MobyTESTClass in module bioMoby.ontology.TEST
    MobyTestout Class in module bioMoby.ontology.Testout
    MobyText_plainClass in module bioMoby.ontology.Trait_Details
    MobyTree Class in module bioMoby.ontology.Tree
    MobyTropGENE_ACCESSIONClass in module bioMoby.ontology.TropGENE_ACCESSION
    MobyTropGENE_Diversity_MatrixClass in module bioMoby.ontology.TropGENE_Diversity_Matrix
    MobyTropGENE_LOCUSClass in module bioMoby.ontology.TropGENE_LOCUS
    MobyUnmarshaller Class in module bioMoby.mobyMarshal
    MobyVirtualSequenceClass in module bioMoby.webservice.Dispatcher
    MyTree Module in package bioMoby.ontology
    name_matchMethod in class ZSI.TC.TypeCode
    Namespace Class in module bioMoby.mobyRegister
    NCBI_BLAST_Text Module in package bioMoby.ontology
    NCBI_Blast_XML Module in package bioMoby.ontology
    NCBI_MEME_TextModule in package bioMoby.ontology
    next Method in class bioMoby.webservice.Dispatcher.LockedIterator
    nilledMethod in class ZSI.TC.TypeCode
    NucleotideSequence Module in package bioMoby.ontology
    objectPackage in package bioMoby
    Parameter Class in module bioMoby.mobyDataTypes
    parseMethod in class ZSI.TC.TypeCode
    parselistVariable in class bioMoby.webservice.TCBioMoby.Body
    PBSDispatcherClass in module bioMoby.webservice.Dispatcher
    PBSInvocatorClass in module bioMoby.webservice.Invocators
    PDBFormattedText Module in package bioMoby.ontology
    PDGJOBMethod in class bioMoby.webservice.Invocators.CGIPostMInvocator
    PubMedMEDLINE Module in package bioMoby.ontology
    QsubParametersClass in module bioMoby.webservice.Invocators
    register Method in class bioMoby.mobyRegister.Namespace
    registerModule in package bioMoby.ontology
    Scored_acronym_string Module in package bioMoby.ontology
    serializeMethod in class bioMoby.webservice.TCBioMoby.Body
    seriallistVariable in class bioMoby.webservice.TCBioMoby.Body
    Service Class in module bioMoby.mobyService
    ServiceArticleMethod in class threading.Thread
    setName Method in class threading.Thread
    setParametersMethod in class bioMoby.webservice.Invocators.PBSInvocator
    Simple_key_value_pair Module in package bioMoby.ontology
    simple_valueMethod in class ZSI.TC.TypeCode
    SimpleAnnotatedGIFImage Module in package bioMoby.ontology
    SimpleAnnotatedJPEGImage Module in package bioMoby.ontology
    SimpleDispatcherClass in module bioMoby.webservice.Dispatcher
    SimpleHREFMethod in class ZSI.TC.TypeCode
    SINGER_ACCESSIONModule in package bioMoby.ontology
    SingleThread Class in module bioMoby.webservice.Dispatcher
    Snp_alleleModule in package bioMoby.ontology
    submits2XML Method in class bioMoby.mobyService.ServiceQuery
    tagVariable in class bioMoby.webservice.TCBioMoby.Body
    TargetP_result Module in package bioMoby.ontology
    TCBioMobyModule in package bioMoby.webservice
    TESTModule in package bioMoby.ontology
    Testout Module in package bioMoby.ontology
    Text_plainModule in package bioMoby.ontology
    Tree Module in package bioMoby.ontology
    TropGENE_ACCESSIONModule in package bioMoby.ontology
    TropGENE_Diversity_MatrixModule in package bioMoby.ontology
    TropGENE_LOCUSModule in package bioMoby.ontology
    type Class in module __builtin__
    typechecksVariable in class ZSI.TC.TypeCode
    typechecksVariable in class ZSI.TC.TypeCode
    TypeCodeClass in module ZSI.TC
    typecodeVariable in class bioMoby.webservice.TCBioMoby.Body
    VirtualSequence Module in package bioMoby.ontology
    webservice   Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/threading.Thread-class.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/threading.Thread-class.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/threading.Thread-class.html 2004/12/09 14:41:34 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:30 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:09 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -140,13 +146,19 @@ - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyClient-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyDataTypes-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyExceptions-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyMarshal-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyRegister-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.mobyService-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology-module.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology-module.html 2004/12/09 14:41:35 1.3 @@ -22,6 +22,10 @@ B64_Encoded_PNG
    B64_Encoded_Postscript
    BasicGFFSequenceFeature
    +ClustalAlnFormattedText
    +CommentedAASequence
    +CommentedDNASequence
    +CommentedRNASequence
    DateTime
    Decypher_Text
    DNASequence
    @@ -29,6 +33,8 @@ Edge
    EmblFlatfile
    FASTA
    +FASTA_AA
    +FASTA_NA
    GenbankFlatfile
    GenericSequence
    GeneticElement
    @@ -42,6 +48,7 @@ Global_Keyword
    GO_Term
    Haplotyping_Study_obj
    +HBond_Pair
    HCA_picture
    ICIS_Query
    ICIS_Query2
    @@ -51,12 +58,15 @@ Interaction_partner
    InteractionMethod
    Interactor
    +MEME_Text
    +MGIS_ACCESSION
    MMP_Locus
    MO_Term_Test
    Multi_key_value_pair
    MyTree
    NCBI_BLAST_Text
    NCBI_Blast_XML
    +NCBI_MEME_Text
    NucleotideSequence
    PDBFormattedText
    PDGJOB
    @@ -73,10 +83,12 @@ Simple_key_value_pair
    SimpleAnnotatedGIFImage
    SimpleAnnotatedJPEGImage
    +SINGER_ACCESSION
    Snp_allele
    Snp_genotype
    Study
    TargetP_result
    +TEST
    Testout
    Text_plain
    TextBase64
    @@ -87,6 +99,9 @@ TextXml
    Trait_Details
    Tree
    +TropGENE_ACCESSION
    +TropGENE_Diversity_Matrix
    +TropGENE_LOCUS
    VirtualSequence
    Wildcard_Query
    WU_BLAST_Text
    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology.AGI_LocusCode-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology.Allele_freq-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology.AminoAcidSequence-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.ontology.B64_Encoded_PNG-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 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    Dispatcher
    Invocators
    +TCBioMoby


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Dispatcher-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Dispatcher-module.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Dispatcher-module.html 2004/12/09 14:41:35 1.3 @@ -13,9 +13,12 @@ Classes
    +AbstractDispatcher
    Dispatcher
    LockedIterator
    MultiThread
    +PBSDispatcher
    +SimpleDispatcher
    SingleThread

    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Invocators-module.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Invocators-module.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc-bioMoby.webservice.Invocators-module.html 2004/12/09 14:41:35 1.3 @@ -16,8 +16,14 @@ CGIPostInvocator
    CGIPostMInvocator
    GeneralInvocator
    -InvocatorError
    LocalInvocator
    +PBSInvocator
    +QsubParameters
    +
    + + +Exceptions
    +InvocatorError


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc-everything.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc-everything.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc-everything.html 2004/12/09 14:41:35 1.3 @@ -45,6 +45,10 @@ bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG
    bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript
    bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
    +bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
    +bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
    +bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
    +bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
    bioMoby.ontology.DateTime.MobyDateTime
    bioMoby.ontology.Decypher_Text.MobyDecypher_Text
    bioMoby.ontology.DNASequence.MobyDNASequence
    @@ -52,6 +56,8 @@ bioMoby.ontology.Edge.MobyEdge
    bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
    bioMoby.ontology.FASTA.MobyFASTA
    +bioMoby.ontology.FASTA_AA.MobyFASTA_AA
    +bioMoby.ontology.FASTA_NA.MobyFASTA_NA
    bioMoby.ontology.GenbankFlatfile.MobyGenbankFlatfile
    bioMoby.ontology.GenericSequence.MobyGenericSequence
    bioMoby.ontology.GeneticElement.MobyGeneticElement
    @@ -65,6 +71,7 @@ bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
    bioMoby.ontology.GO_Term.MobyGO_Term
    bioMoby.ontology.Haplotyping_Study_obj.MobyHaplotyping_Study_obj
    +bioMoby.ontology.HBond_Pair.MobyHBond_Pair
    bioMoby.ontology.HCA_picture.MobyHCA_picture
    bioMoby.ontology.ICIS_Query.MobyICIS_Query
    bioMoby.ontology.ICIS_Query2.MobyICIS_Query2
    @@ -74,12 +81,15 @@ bioMoby.ontology.Interaction_partner.MobyInteraction_partner
    bioMoby.ontology.InteractionMethod.MobyInteractionMethod
    bioMoby.ontology.Interactor.MobyInteractor
    +bioMoby.ontology.MEME_Text.MobyMEME_Text
    +bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
    bioMoby.ontology.MMP_Locus.MobyMMP_Locus
    bioMoby.ontology.MO_Term_Test.MobyMO_Term_Test
    bioMoby.ontology.Multi_key_value_pair.MobyMulti_key_value_pair
    bioMoby.ontology.MyTree.MobyMyTree
    bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
    bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
    +bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
    bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
    bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText
    bioMoby.ontology.PDGJOB.MobyPDGJOB
    @@ -96,10 +106,12 @@ bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair
    bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage
    bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage
    +bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
    bioMoby.ontology.Snp_allele.MobySnp_allele
    bioMoby.ontology.Snp_genotype.MobySnp_genotype
    bioMoby.ontology.Study.MobyStudy
    bioMoby.ontology.TargetP_result.MobyTargetP_result
    +bioMoby.ontology.TEST.MobyTEST
    bioMoby.ontology.Testout.MobyTestout
    bioMoby.ontology.Text_plain.MobyText_plain
    bioMoby.ontology.TextBase64.MobyTextBase64
    @@ -110,18 +122,26 @@ bioMoby.ontology.TextXml.MobyTextXml
    bioMoby.ontology.Trait_Details.MobyTrait_Details
    bioMoby.ontology.Tree.MobyTree
    +bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
    +bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
    +bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
    bioMoby.ontology.VirtualSequence.MobyVirtualSequence
    bioMoby.ontology.Wildcard_Query.MobyWildcard_Query
    bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text
    +bioMoby.webservice.Dispatcher.AbstractDispatcher
    bioMoby.webservice.Dispatcher.Dispatcher
    bioMoby.webservice.Dispatcher.LockedIterator
    bioMoby.webservice.Dispatcher.MultiThread
    +bioMoby.webservice.Dispatcher.PBSDispatcher
    +bioMoby.webservice.Dispatcher.SimpleDispatcher
    bioMoby.webservice.Dispatcher.SingleThread
    bioMoby.webservice.Invocators.CGIPostInvocator
    bioMoby.webservice.Invocators.CGIPostMInvocator
    bioMoby.webservice.Invocators.GeneralInvocator
    -bioMoby.webservice.Invocators.InvocatorError
    bioMoby.webservice.Invocators.LocalInvocator
    +bioMoby.webservice.Invocators.PBSInvocator
    +bioMoby.webservice.Invocators.QsubParameters
    +bioMoby.webservice.TCBioMoby.Body

    @@ -132,6 +152,7 @@ bioMoby.mobyExceptions.ENotAWSMethod
    bioMoby.mobyExceptions.ETypeMismatch
    bioMoby.webservice.Dispatcher.EDispatchError
    +bioMoby.webservice.Invocators.InvocatorError


    =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/toc.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/toc.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/toc.html 2004/12/09 14:41:35 1.3 @@ -35,6 +35,10 @@ bioMoby.ontology.B64_Encoded_PNG
    bioMoby.ontology.B64_Encoded_Postscript
    bioMoby.ontology.BasicGFFSequenceFeature
    +bioMoby.ontology.ClustalAlnFormattedText
    +bioMoby.ontology.CommentedAASequence
    +bioMoby.ontology.CommentedDNASequence
    +bioMoby.ontology.CommentedRNASequence
    bioMoby.ontology.DateTime
    bioMoby.ontology.Decypher_Text
    bioMoby.ontology.DNASequence
    @@ -42,6 +46,8 @@ bioMoby.ontology.Edge
    bioMoby.ontology.EmblFlatfile
    bioMoby.ontology.FASTA
    +bioMoby.ontology.FASTA_AA
    +bioMoby.ontology.FASTA_NA
    bioMoby.ontology.GenbankFlatfile
    bioMoby.ontology.GenericSequence
    bioMoby.ontology.GeneticElement
    @@ -55,6 +61,7 @@ bioMoby.ontology.Global_Keyword
    bioMoby.ontology.GO_Term
    bioMoby.ontology.Haplotyping_Study_obj
    +bioMoby.ontology.HBond_Pair
    bioMoby.ontology.HCA_picture
    bioMoby.ontology.ICIS_Query
    bioMoby.ontology.ICIS_Query2
    @@ -64,12 +71,15 @@ bioMoby.ontology.Interaction_partner
    bioMoby.ontology.InteractionMethod
    bioMoby.ontology.Interactor
    +bioMoby.ontology.MEME_Text
    +bioMoby.ontology.MGIS_ACCESSION
    bioMoby.ontology.MMP_Locus
    bioMoby.ontology.MO_Term_Test
    bioMoby.ontology.Multi_key_value_pair
    bioMoby.ontology.MyTree
    bioMoby.ontology.NCBI_BLAST_Text
    bioMoby.ontology.NCBI_Blast_XML
    +bioMoby.ontology.NCBI_MEME_Text
    bioMoby.ontology.NucleotideSequence
    bioMoby.ontology.PDBFormattedText
    bioMoby.ontology.PDGJOB
    @@ -86,10 +96,12 @@ bioMoby.ontology.Simple_key_value_pair
    bioMoby.ontology.SimpleAnnotatedGIFImage
    bioMoby.ontology.SimpleAnnotatedJPEGImage
    +bioMoby.ontology.SINGER_ACCESSION
    bioMoby.ontology.Snp_allele
    bioMoby.ontology.Snp_genotype
    bioMoby.ontology.Study
    bioMoby.ontology.TargetP_result
    +bioMoby.ontology.TEST
    bioMoby.ontology.Testout
    bioMoby.ontology.Text_plain
    bioMoby.ontology.TextBase64
    @@ -100,11 +112,15 @@ bioMoby.ontology.TextXml
    bioMoby.ontology.Trait_Details
    bioMoby.ontology.Tree
    +bioMoby.ontology.TropGENE_ACCESSION
    +bioMoby.ontology.TropGENE_Diversity_Matrix
    +bioMoby.ontology.TropGENE_LOCUS
    bioMoby.ontology.VirtualSequence
    bioMoby.ontology.Wildcard_Query
    bioMoby.ontology.WU_BLAST_Text
    bioMoby.webservice.Dispatcher
    bioMoby.webservice.Invocators
    +bioMoby.webservice.TCBioMoby


    [show private | hide private] =================================================================== RCS file: /home/repository/moby/moby-live/Python/doc/public/trees.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Python/doc/public/trees.html 2004/12/08 11:15:27 1.2 +++ /home/repository/moby/moby-live/Python/doc/public/trees.html 2004/12/09 14:41:35 1.3 @@ -16,7 +16,13 @@ - +
    Generated by Epydoc 2.1 on Tue Aug 10 13:53:29 2004Generated by Epydoc 2.1 on Tue Dec 7 11:28:06 2004 http://epydoc.sf.net
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    @@ -51,6 +57,10 @@
  • B64_Encoded_PNG
  • B64_Encoded_Postscript
  • BasicGFFSequenceFeature +
  • ClustalAlnFormattedText +
  • CommentedAASequence +
  • CommentedDNASequence +
  • CommentedRNASequence
  • DateTime
  • Decypher_Text
  • DNASequence @@ -58,6 +68,8 @@
  • Edge
  • EmblFlatfile
  • FASTA +
  • FASTA_AA +
  • FASTA_NA
  • GenbankFlatfile
  • GenericSequence
  • GeneticElement @@ -71,6 +83,7 @@
  • Global_Keyword
  • GO_Term
  • Haplotyping_Study_obj +
  • HBond_Pair
  • HCA_picture
  • ICIS_Query
  • ICIS_Query2 @@ -80,12 +93,15 @@
  • Interaction_partner
  • InteractionMethod
  • Interactor +
  • MEME_Text +
  • MGIS_ACCESSION
  • MMP_Locus
  • MO_Term_Test
  • Multi_key_value_pair
  • MyTree
  • NCBI_BLAST_Text
  • NCBI_Blast_XML +
  • NCBI_MEME_Text
  • NucleotideSequence
  • PDBFormattedText
  • PDGJOB @@ -102,10 +118,12 @@
  • Simple_key_value_pair
  • SimpleAnnotatedGIFImage
  • SimpleAnnotatedJPEGImage +
  • SINGER_ACCESSION
  • Snp_allele
  • Snp_genotype
  • Study
  • TargetP_result +
  • TEST
  • Testout
  • Text_plain
  • TextBase64 @@ -116,6 +134,9 @@
  • TextXml
  • Trait_Details
  • Tree +
  • TropGENE_ACCESSION +
  • TropGENE_Diversity_Matrix +
  • TropGENE_LOCUS
  • VirtualSequence
  • Wildcard_Query
  • WU_BLAST_Text @@ -124,6 +145,7 @@ @@ -131,6 +153,12 @@

    Class Hierarchy

    @@ -477,8 +558,19 @@
  • bioMoby.ontology.Snp_genotype.MobySnp_genotype: Description: Snp Genotypes Author: www.hapmap.org Contact: hapmap@hapmap.edu +
  • bioMoby.webservice.Dispatcher.AbstractDispatcher: +Subclass this one to create your own dispatcher class a Dispatcher +class must have a execute method +
  • bioMoby.webservice.Dispatcher.LockedIterator: Avoid concurrency on the iterator
  • bioMoby.webservice.Dispatcher.MultiThread: @@ -494,9 +586,13 @@ CGI script in Post multipart
  • bioMoby.webservice.Invocators.LocalInvocator: Invokes local command + -
  • bioMoby.webservice.Invocators.InvocatorError: -Error during an invocation of method + +
  • bioMoby.webservice.Invocators.QsubParameters: +Parameters for the qsub command
  • exceptions.Exception: Common base class for all exceptions. @@ -517,13 +615,19 @@
  • - +
       Trees       Index       Help    + +
    +

    + bioMoby-python +

    +
    - + From kawas at pub.open-bio.org Tue Dec 14 18:58:20 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 13:58:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141858.iBEIwKdZ009890@pub.open-bio.org> kawas Tue Dec 14 13:58:19 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv9852 Modified Files: Central.pm CommonSubs.pm CrossReference.pm OntologyServer.pm Log Message: hopefully fixed the cdata bug - eddie moby-live/Perl/MOBY Central.pm,1.142,1.143 CommonSubs.pm,1.54,1.55 CrossReference.pm,1.3,1.4 OntologyServer.pm,1.46,1.47 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.142 retrieving revision 1.143 diff -u -r1.142 -r1.143 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/11/18 17:41:14 1.142 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/12/14 18:58:19 1.143 @@ -392,7 +392,7 @@ my $obj = $Object->nodeName; return undef unless ( $obj eq 'registerObjectClass' ); my $term = &_nodeTextContent( $Object, "objectType" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my $authURI = &_nodeTextContent( $Object, "authURI" ); my $email = &_nodeTextContent( $Object, "contactEmail" ); my $clobber = &_nodeTextContent( $Object, "Clobber" ); @@ -696,7 +696,7 @@ my $type = &_nodeTextContent( $Object, "serviceType" ); my $email = &_nodeTextContent( $Object, "contactEmail" ); my $auth = &_nodeTextContent( $Object, "authURI" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my %relationships; my $x = $doc->getElementsByTagName( "Relationship" ); my $no_relationships = $x->size(); @@ -881,7 +881,7 @@ return undef unless ( $obj eq 'registerNamespace' ); my $type = &_nodeTextContent( $Object, "namespaceType" ); my $authURI = &_nodeTextContent( $Object, "authURI" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my $contact = &_nodeTextContent( $Object, "contactEmail" ); return ( $type, $authURI, $desc, $contact ); } @@ -1593,7 +1593,7 @@ &_nodeTextContent( $Object, "authoritativeService" ); my $URL = &_nodeTextContent( $Object, "URL" ); my $signatureURL = &_nodeTextContent( $Object, "signatureURL" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my $INPUTS = &_nodeRawContent( $Object, "Input" ); # returns array ref my $OUTPUTS = &_nodeRawContent( $Object, "Output" ); # returns array ref my $SECONDARIES = @@ -2388,6 +2388,9 @@ my $wsdl = &_getServiceWSDL( $SI, $InputXML, $OutputXML, $SecondaryXML ); if ( $wsdl ) { + if ($wsdl =~ /[^\]]+))\]\]>/) { + $wsdl = $1; + } $wsdls .= "\n"; } @@ -2519,6 +2522,9 @@ my %types = %{ $OS->retrieveAllServiceTypes() }; my $types = "\n"; while ( my ( $serv, $desc ) = each %types ) { + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $types .= "\n\n\n"; } @@ -2558,6 +2564,9 @@ while ( my ( $name, $authdesc ) = each %types ) { my $auth = $authdesc->[0]; my $desc = $authdesc->[1]; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $types .= "\n\n\n"; } @@ -2589,6 +2598,9 @@ my %types = %{ $OS->retrieveAllObjectTypes() }; my $obj = "\n"; while ( my ( $name, $desc ) = each %types ) { + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $obj .= "\n\n\n"; } @@ -2639,6 +2651,9 @@ ; # will return undef if this term does not exist, and does not look like an LSID return "" unless $def; my %def = %{ $OS->retrieveObject( node => $term ) }; + if ($def{description} =~ /[^\]]+))\]\]>/) { + $def{description}= $1; + } my $response; $response = " $def{objectType} @@ -2685,6 +2700,9 @@ my %types = %{ $OS->retrieveAllNamespaceTypes() }; my $ns = "\n"; while ( my ( $namespace, $desc ) = each %types ) { + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $ns .= "\n\n\n"; } @@ -3002,6 +3020,9 @@ $response .= "$cat\n"; $response .= "$type\n"; $response .= "$objectOUT\n"; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $response .= "\n"; $response .= "\n"; if ( $max_return ) { --$max_return; last unless $max_return } @@ -3035,6 +3056,9 @@ my $serviceName = $SI->servicename; my $AuthURI = $SI->authority_uri; my $desc = $SI->description; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } my $URL = $SI->url; my $IN = "NOT_YET_DEFINED_INPUTS"; my $OUT = "NOT_YET_DEFINED_OUTPUTS"; @@ -3075,6 +3099,9 @@ my $sth = $dbh->prepare( $sth{get_server_parameters} ); $sth->execute( $id ); my ( $Object, $sprintf, $in ) = $sth->fetchrow_array(); + if ($sprintf=~ /[^\]]+))\]\]>/) { + $sprintf = $1; + } return ""; } @@ -3197,7 +3224,30 @@ } return $content; } +sub _nodeCDATAContent{ + # will get text of **all** child $node from the given $DOM + # regardless of their depth!! + my ( $DOM, $node ) = @_; + $debug && &_LOG( "_nodeTextContent received DOM: ", + $DOM->toString, "\nsearching for node $node\n" ); + my $x = $DOM->getElementsByTagName( $node ); + return undef unless $x->get_node( 1 ); + my @child = $x->get_node( 1 )->childNodes; + my $content; + foreach ( @child ) { + $debug + && &_LOG( $_->nodeType, "\t", $_->toString, "\n" ); + + #next unless $_->nodeType == TEXT_NODE; + if ($_->toString =~ /[^\]]+))\]\]>/) { + $content .= $1; + } else { + $content .= $_->toString; + } + } + return $content; +} #Eddie - converted sub _nodeRawContent { @@ -3341,6 +3391,9 @@ $authoritative, $email, $signatureURL ) = $sth->fetchrow_array; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } #print "\n\nAFTER EXECUTE $category, $servicename, $service_type_uri, $authority_id, $desc, $authoritative\n\n"; $signatureURL ||= ""; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.54 retrieving revision 1.55 diff -u -r1.54 -r1.55 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/11/18 17:41:14 1.54 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/12/14 18:58:19 1.55 @@ -31,7 +31,7 @@ # [SIMPLE, $queryID, $simple] # the first element is an exported constant SIMPLE, COLLECTION, SECONDARY # the second element is the queryID (required for enumerating the responses) - # the third element is the XML::DOM for the Simple, Collection, or Parameter block + # the third element is the XML::LibXML for the Simple, Collection, or Parameter block my (@inputs)= genericServiceInputParser($data); # or fail properly with an empty response return SOAP::Data->type('base64' => responseHeader("my.authURI.com") . responseFooter()) unless (scalar(@inputs)); @@ -258,9 +258,9 @@ 1. COLLECTION|SIMPLE (i.e. constants 1, 2) 2. queryID 3. $data - the data takes several forms - a. $article XML::DOM node for Simples + a. $article XML::LibXML node for Simples ... - b. \@article XML:DOM nodes for Collections + b. \@article XML:LibXML nodes for Collections for example, the input message: @@ -303,7 +303,7 @@ my ( $message ) = @_; # get the incoming MOBY query XML my @inputs; # set empty response my @queries = - getInputs( $message ); # returns XML::DOM nodes ... + getInputs( $message ); # returns XML::LibXML nodes ... foreach my $query ( @queries ) { my $queryID = getInputID( $query ); # get the queryID attribute of the mobyData @@ -331,7 +331,7 @@ name : DO NOT USE!! function : to take a MOBY message and break the objects out of it. This is identical to the genericServiceInputParser method above, except that it returns the data as - Objects rather than XML::DOM nodes. This is an improvement! + Objects rather than XML::LibXML nodes. This is an improvement! usage : my @inputs = serviceInputParser($MOBY_mssage)); args : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message returns : @inputs - the structure of @inputs is a list of listrefs. @@ -346,7 +346,7 @@ my ( $message ) = @_; # get the incoming MOBY query XML my @inputs; # set empty response my @queries = - getInputs( $message ); # returns XML::DOM nodes ... + getInputs( $message ); # returns XML::LibXML nodes ... # mark, this doesn't work for complex services. We need to allow more than one input per invocation foreach my $query ( @queries ) { @@ -402,7 +402,7 @@ [SECONDARY, $DOM_cutoff] # $DOM_cutoff= block ] - Please see the XML::DOM pod documentation for information about how + Please see the XML::LibXML pod documentation for information about how to parse XML DOM objects. @@ -431,7 +431,7 @@ [SECONDARY, $DOM_cutoff] # $DOM_cutoff = Block ] - Please see the XML::DOM pod documentation for information about how + Please see the XML::LibXML pod documentation for information about how to parse XML DOM objects. @@ -441,7 +441,7 @@ my ( $message ) = @_; # get the incoming MOBY query XML my @inputs; # set empty response my @queries = - getInputs( $message ); # returns XML::DOM nodes ... + getInputs( $message ); # returns XML::LibXML nodes ... my %input_parameters; # $input_parameters{$queryID} = [ foreach my $query ( @queries ) { my $queryID = @@ -470,7 +470,7 @@ name : getArticles function : get the Simple/Collection/Parameter articles for a single mobyData usage : @articles = getArticles($XML) - args : raw XML or XML::DOM of a queryInput, mobyData, or queryResponse block (e.g. from getInputs) + args : raw XML or XML::LibXML of a queryInput, mobyData, or queryResponse block (e.g. from getInputs) returns : a list of listrefs; each listref is one component of the queryInput or mobyData block a single block may consist of one or more named or unnamed simple, collection, or parameter articles. @@ -508,7 +508,7 @@ sub getArticles { my ( $moby ) = @_; - unless ( ref( $moby ) =~ /XML\:\:DOM/ ) { + unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $moby ); $moby = $doc->getDocumentElement(); @@ -548,8 +548,8 @@ usage : my @ids = getSimpleArticleIDs("NCBI_gi", \@SimpleArticles); my @ids = getSimpleArticleIDs(\@SimpleArticles); args : $Namespace - (optional) a namespace stringfrom the MOBY namespace ontology, or undef if you don't care - \@Simples - (required) a listref of Simple XML::DOM nodes - i.e. the XML::DOM representing an XML structure like this: + \@Simples - (required) a listref of Simple XML::LibXML nodes + i.e. the XML::LibXML representing an XML structure like this: @@ -643,8 +643,8 @@ name : getSimpleArticleNamespaceURI function : to get the namespace of a simple article usage : my $ns = getSimpleArticleNamespaceURI($SimpleArticle); - args : $Simple - (required) a single XML::DOM node representing a Simple Article - i.e. the XML::DOM representing an XML structure like this: + args : $Simple - (required) a single XML::LibXML node representing a Simple Article + i.e. the XML::LibXML representing an XML structure like this: @@ -700,7 +700,7 @@ my ( $data, $articleName, $qID ) = @_; # articleName optional $qID = &_getQueryID( $qID ) if ref( $qID ) =~ - /XML::DOM/; # in case they send the DOM instead of the ID + /XML::LibXML/; # in case they send the DOM instead of the ID $data ||= ''; # initialize to avoid uninit value errors $qID ||= ""; $articleName ||= ""; @@ -726,7 +726,7 @@ #Eddie - converted sub _getQueryID { my ( $query ) = @_; - unless ( ref( $query ) =~ /XML\:\:DOM/ ) { + unless ( ref( $query ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $query ); $query = $doc->getDocumentElement(); @@ -849,10 +849,10 @@ =head2 getInputs name : getInputs - function : get the mobyData block(s) as XML::DOM nodes + function : get the mobyData block(s) as XML::LibXML nodes usage : @queryInputs = getInputArticles($XML) - args : the raw XML of a query, or an XML::DOM document - returns : a list of XML::DOM::Node's, each is a queryInput or mobyData block. + args : the raw XML of a query, or an XML::LibXML document + returns : a list of XML::LibXML::Node's, each is a queryInput or mobyData block. Note : Remember that these blocks are enumerated! This is what you pass as the third argument to the simpleResponse or collectionResponse subroutine to associate the numbered input to the numbered response @@ -863,7 +863,7 @@ sub getInputs { my ( $XML ) = @_; my $moby; - unless ( ref( $XML ) =~ /XML\:\:DOM/ ) { + unless ( ref( $XML ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $XML ); $moby = $doc->getDocumentElement(); @@ -887,7 +887,7 @@ name : getInputID function : get the value of the queryID element usage : @queryInputs = getInputID($XML) - args : the raw XML or XML::DOM of a queryInput or mobyData block (e.g. from getInputs) + args : the raw XML or XML::LibXML of a queryInput or mobyData block (e.g. from getInputs) returns : integer, or '' Note : Inputs and Responses are coordinately enumerated! The integer you get here is what you @@ -898,7 +898,7 @@ sub getInputID { my ( $XML ) = @_; - unless ( ref( $XML ) =~ /XML\:\:DOM/ ) { + unless ( ref( $XML ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $XML ); $XML = $doc->getDocumentElement(); @@ -918,7 +918,7 @@ or queryResponse node, rethrning them as SimpleArticle, SecondaryArticle, or ServiceInstance objects usage : @articles = getArticles($XML) - args : raw XML or XML::DOM of a moby:mobyData block + args : raw XML or XML::LibXML of a moby:mobyData block returns : =cut @@ -926,7 +926,7 @@ #Eddie - converted sub getArticlesAsObjects { my ( $moby ) = @_; - unless ( ref( $moby ) =~ /XML\:\:DOM/ ) { + unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $moby ); $moby = $doc->getDocumentElement(); @@ -964,14 +964,14 @@ name : getCollectedSimples function : get the Simple articles collected in a moby:Collection block usage : @Simples = getCollectedSimples($XML) - args : raw XML or XML::DOM of a moby:Collection block - returns : a list of XML::DOM nodes, each of which is a moby:Simple block + args : raw XML or XML::LibXML of a moby:Collection block + returns : a list of XML::LibXML nodes, each of which is a moby:Simple block =cut sub getCollectedSimples { my ( $moby ) = @_; - unless ( ref( $moby ) =~ /XML\:\:DOM/ ) { + unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $moby ); $moby = $doc->getDocumentElement(); @@ -997,7 +997,7 @@ args : the raw XML of a moby:MOBY query returns : a list of listrefs, each listref is the input to a single query. Remember that the input to a single query may be one or more Simple - and/or Collection articles. These are provided as XML::DOM nodes. + and/or Collection articles. These are provided as XML::LibXML nodes. i.e.: @queries = ([$SIMPLE_DOM_NODE], [$SIMPLE_DOM_NODE2]) or : @queries = ([$COLLECTION_DOM_NODE], [$COLLECTION_DOM_NODE2]) @@ -1024,7 +1024,7 @@ #Eddie - converted sub getInputArticles { my ( $moby ) = @_; - unless ( ref( $moby ) =~ /XML\:\:DOM/ ) { + unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $moby ); $moby = $doc->getDocumentElement(); @@ -1054,7 +1054,7 @@ name : isSimpleArticle function : tests XML (text) or an XML DOM node to see if it represents a Simple article usage : if (isSimpleArticle($node)){do something to it} - input : an XML::DOM node, an XML::DOM::Document or straight XML + input : an XML::LibXML node, an XML::LibXML::Document or straight XML returns : boolean =cut @@ -1062,7 +1062,7 @@ #Eddie - converted sub isSimpleArticle { my ( $DOM ) = @_; - unless ( ref( $DOM ) =~ /XML\:\:DOM/ ) { + unless ( ref( $DOM ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc; eval { $doc = $parser->parse_string( $DOM ); }; @@ -1079,7 +1079,7 @@ name : isCollectionArticle function : tests XML (text) or an XML DOM node to see if it represents a Collection article usage : if (isCollectionArticle($node)){do something to it} - input : an XML::DOM node, an XML::DOM::Document or straight XML + input : an XML::LibXML node, an XML::LibXML::Document or straight XML returns : boolean =cut @@ -1087,7 +1087,7 @@ #Eddie - converted sub isCollectionArticle { my ( $DOM ) = @_; - unless ( ref( $DOM ) =~ /XML\:\:DOM/ ) { + unless ( ref( $DOM ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc; eval { $doc = $parser->parse_string( $DOM ); }; @@ -1104,7 +1104,7 @@ name : isSecondaryArticle function : tests XML (text) or an XML DOM node to see if it represents a Secondary article usage : if (isSecondaryArticle($node)){do something to it} - input : an XML::DOM node, an XML::DOM::Document or straight XML + input : an XML::LibXML node, an XML::LibXML::Document or straight XML returns : boolean =cut @@ -1112,7 +1112,7 @@ #Eddie - converted sub isSecondaryArticle { my ( $DOM ) = @_; - unless ( ref( $DOM ) =~ /XML\:\:DOM/ ) { + unless ( ref( $DOM ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc; eval { $doc = $parser->parse( _string $DOM); }; @@ -1138,7 +1138,7 @@ sub extractRawContent { my ( $article ) = @_; return "" unless $article; - return "" unless ref( $article ) =~ /XML::DOM/; + return "" unless ref( $article ) =~ /XML::LibXML/; my $response; foreach ( $article->childNodes ) { $response .= $_->toString; @@ -1154,7 +1154,7 @@ or get the value of a Parameter element. usage : @strings = getNodeContentWithArticle($node, $tagname, $articleName) args : (in order) - $node - an XML::DOM node, or straight XML. It may even + $node - an XML::LibXML node, or straight XML. It may even be the entire mobyData block. $tagname - the tagname (effectively from the Object type ontology), or "Parameter" if you are trying to get secondaries @@ -1243,7 +1243,7 @@ # carriage returns, as these might be meaningful! my ( $node, $element, $articleName ) = @_; my @contents; - return () unless ref( $node ) =~ /XML::DOM/; + return () unless ref( $node ) =~ /XML::LibXML/; return () unless $element; return () unless $articleName; my $nodes = $node->getElementsByTagName( $element ); @@ -1355,9 +1355,9 @@ function : get the DOM nodes corresponding to individual Simple or Collection outputs from a MOBY Response usage : ($collections, $simples) = getResponseArticles($node) - args : $node - either raw XML or an XML::DOM::Document to be searched - returns : an array-ref of Collection article XML::DOM::Node's - an array-ref of Simple article XML::DOM::Node's + args : $node - either raw XML or an XML::LibXML::Document to be searched + returns : an array-ref of Collection article XML::LibXML::Node's + an array-ref of Simple article XML::LibXML::Node's =cut @@ -1369,7 +1369,7 @@ my ( $result ) = @_; return ( [], [] ) unless $result; my $moby; - unless ( ref( $result ) =~ /XML\:\:DOM/ ) { + unless ( ref( $result ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $result ); $moby = $doc->getDocumentElement(); @@ -1426,7 +1426,7 @@ name : getServiceNotes function : to get the content of the Service Notes block of the MOBY message usage : getServiceNotes($message) - args : $message is either the XML::DOM of the MOBY message, or plain XML + args : $message is either the XML::LibXML of the MOBY message, or plain XML returns : String content of the ServiceNotes block of the MOBY Message =cut @@ -1436,7 +1436,7 @@ my ( $result ) = @_; return ( "" ) unless $result; my $moby; - unless ( ref( $result ) =~ /XML\:\:DOM/ ) { + unless ( ref( $result ) =~ /XML\:\:LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $result ); $moby = $doc->getDocumentElement(); @@ -1470,7 +1470,7 @@ usage : @xrefs = getCrossReferences($XML) args : $XML is either a SIMPLE article (...) or an object (the payload of a Simple article), and - may be either raw XML or an XML::DOM node. + may be either raw XML or an XML::LibXML node. returns : an array of MOBY::CrossReference objects example : @@ -1492,7 +1492,7 @@ #Eddie - converted sub getCrossReferences { my ( $XML ) = @_; - unless ( ref( $XML ) =~ /XML::DOM/ ) { + unless ( ref( $XML ) =~ /XML::LibXML/ ) { my $parser = XML::LibXML->new(); my $doc = $parser->parse_string( $XML ); $XML = $doc->getDocumentElement(); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CrossReference.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.46 retrieving revision 1.47 diff -u -r1.46 -r1.47 From kawas at pub.open-bio.org Tue Dec 14 18:58:20 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 13:58:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141858.iBEIwK9J009921@pub.open-bio.org> kawas Tue Dec 14 13:58:20 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv9852/Client Modified Files: Central.pm OntologyServer.pm Registration.pm Service.pm Log Message: hopefully fixed the cdata bug - eddie moby-live/Perl/MOBY/Client Central.pm,1.81,1.82 OntologyServer.pm,1.7,1.8 Registration.pm,1.7,1.8 Service.pm,1.13,1.14 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.81 retrieving revision 1.82 diff -u -r1.81 -r1.82 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/11/18 17:41:15 1.81 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/14 18:58:20 1.82 @@ -3,6 +3,7 @@ use SOAP::Lite; #use SOAP::Lite + trace; # for debugging + use strict; use Carp; use XML::LibXML; @@ -376,6 +377,9 @@ $term ||= ""; my $desc = $a{'description'}; $desc ||= ""; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } my $contactEmail = $a{'contactEmail'}; $contactEmail ||= ""; my $authURI = $a{'authURI'}; @@ -504,7 +508,7 @@ my $obj = $Object->nodeName; return undef unless ( $obj eq 'retrieveObjectDefinition' ); my $term = &_nodeTextContent( $Object, "objectType" ); - my $desc = &_nodeTextContent( $Object, "Description" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); my $authURI = &_nodeTextContent( $Object, "authURI" ); my $email = &_nodeTextContent( $Object, "contactEmail" ); my %att_value; @@ -565,6 +569,9 @@ my $type = $a{'serviceType'}; $type ||= ""; my $desc = $a{'description'}; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $desc ||= ""; my $email = $a{'contactEmail'}; $email ||= ""; @@ -645,6 +652,9 @@ my $authURI = $a{'authURI'}; $authURI ||= ""; my $desc = $a{'description'}; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } $desc ||= ""; my $contact = $a{'contactEmail'}; $contact ||= ""; @@ -758,6 +768,9 @@ $URL ||= ""; my $desc = $a{description}; $desc ||= ""; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } my $signatureURL = $a{signatureURL}; $signatureURL ||= ""; my $Category = lc( $a{category} ); @@ -1197,7 +1210,11 @@ foreach ( @child ) { $debug && &_LOG( getNodeTypeName($_), "\t", $_->toString, "\n" ); if ( $_->nodeType == TEXT_NODE ) { - $content .= $_->nodeValue; #else try $_->textContent + if ($_->nodeValue=~ /[^\]]+))\]\]>/) { + $content .= $1; + } else { + $content .= $_->nodeValue; #else try $_->textContent + } } else { $content .= $_->toString; } @@ -1305,6 +1322,9 @@ $types->get_node( $x )->getElementsByTagName( 'Description' ) ) { $desc = $elem->firstChild->toString; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } } $servicetypes{$type} = $desc; } @@ -1344,6 +1364,9 @@ $obnames->get_node( $x )->getElementsByTagName( 'Description' ) ) { $desc = $elem->firstChild->toString; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } } $objectnames{$name} = $desc; } @@ -1383,6 +1406,9 @@ { $desc = $elem->firstChild; $desc = $desc ? $desc->toString : ""; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } } $namespaces{$ns} = $desc; } @@ -1429,6 +1455,9 @@ $objects->get_node( $x )->getElementsByTagName( 'Schema' ) ) { $desc = $elem->firstChild->nodeValue; + if ($desc =~ /[^\]]+))\]\]>/) { + $desc = $1; + } } $objects{$name} = $desc; } @@ -1628,7 +1657,7 @@ my $URL = &_nodeTextContent( $Service, 'URL' ); #my $Output = &_nodeTextContent($Service, 'outputObject'); - my $Description = &_nodeTextContent( $Service, 'Description' ); + my $Description = &_nodeCDATAContent( $Service, 'Description' ); my $cat = &_nodeTextContent( $Service, 'Category' ); my @INPUTS; my @OUTPUTS; @@ -1793,7 +1822,7 @@ return undef unless ( $obj eq 'MOBYRegistration' ); my $id = &_nodeTextContent( $Object, 'id' ); my $success = &_nodeTextContent( $Object, 'success' ); - my $message = &_nodeTextContent( $Object, 'message' ); + my $message = &_nodeCDATAContent( $Object, 'message' ); my $RDF = &_nodeRawContent( $Object, 'RDF' ); my $reg = MOBY::Client::Registration->new( success => $success, @@ -1814,7 +1843,25 @@ ); return $reg; } - +sub _nodeCDATAContent { + # will get text of **all** child $node from the given $DOM + # regardless of their depth!! + my ( $DOM, $node ) = @_; + my $x = $DOM->getElementsByTagName( $node ); + unless ( $x->get_node( 1 ) ) { return } + my @child = $x->get_node( 1 )->childNodes; + my $content; + foreach ( @child ) { + #print getNodeTypeName($_), "\t", $_->toString,"\n"; + next unless $_->nodeType == TEXT_NODE; + $content = $_->toString; + if ($content =~ /[^\]]+))\]\]>/) { + $content = $1; + return $content; + } + } + return $content; +} sub _nodeTextContent { # will get text of **all** child $node from the given $DOM @@ -1825,7 +1872,6 @@ my @child = $x->get_node( 1 )->childNodes; my $content; foreach ( @child ) { - #print getNodeTypeName($_), "\t", $_->toString,"\n"; next unless $_->nodeType == TEXT_NODE; $content = $_->toString; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 From kawas at pub.open-bio.org Tue Dec 14 19:10:19 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:10:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141910.iBEJAJcD010047@pub.open-bio.org> kawas Tue Dec 14 14:10:18 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv10008 Modified Files: Central.pm CommonSubs.pm CrossReference.pm OntologyServer.pm Log Message: hopefully fixed the cdata bug - eddie (part 2 - i hate cvs) moby-live/Perl/MOBY Central.pm,1.143,1.144 CommonSubs.pm,1.55,1.56 CrossReference.pm,1.4,1.5 OntologyServer.pm,1.47,1.48 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.143 retrieving revision 1.144 diff -u -r1.143 -r1.144 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.55 retrieving revision 1.56 diff -u -r1.55 -r1.56 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CrossReference.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.47 retrieving revision 1.48 diff -u -r1.47 -r1.48 From kawas at pub.open-bio.org Tue Dec 14 19:10:19 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:10:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141910.iBEJAJdX010079@pub.open-bio.org> kawas Tue Dec 14 14:10:19 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv10008/Client Modified Files: Central.pm OntologyServer.pm Registration.pm Service.pm Log Message: hopefully fixed the cdata bug - eddie (part 2 - i hate cvs) moby-live/Perl/MOBY/Client Central.pm,1.82,1.83 OntologyServer.pm,1.8,1.9 Registration.pm,1.8,1.9 Service.pm,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.82 retrieving revision 1.83 diff -u -r1.82 -r1.83 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 From kawas at pub.open-bio.org Tue Dec 14 19:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXJw010917@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY added to the repository moby-live/Perl/MOBY/MOBY - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 19:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXdk010935@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/Adaptor Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor added to the repository moby-live/Perl/MOBY/MOBY/Adaptor - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 19:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXSU010953@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/Adaptor/moby Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby added to the repository moby-live/Perl/MOBY/MOBY/Adaptor/moby - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 19:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXol011011@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/RDF Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF added to the repository moby-live/Perl/MOBY/MOBY/RDF - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 19:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiXjn010972@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/Adaptor/moby/queryapi Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi added to the repository moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 19:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiX7a010993@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/Client Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client added to the repository moby-live/Perl/MOBY/MOBY/Client - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 19:44:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiX1t011034@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/lsid Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid added to the repository moby-live/Perl/MOBY/MOBY/lsid - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 19:44:34 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiYiN011055@pub.open-bio.org> kawas Tue Dec 14 14:44:33 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY/lsid/authority Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority added to the repository moby-live/Perl/MOBY/MOBY/lsid/authority - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 19:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJikC3011162@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11077 Added Files: MobyXMLRetriever.pl myScript.pl Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY MobyXMLRetriever.pl,NONE,1.1 myScript.pl,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 19:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiklW011100@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/Client Added Files: Central.pm CollectionArticle.pm Registration.pm SecondaryArticle.pm OntologyServer.pm ServiceInstance.pm SimpleArticle.pm SimpleInput.pm Service.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/Client Central.pm,NONE,1.1 CollectionArticle.pm,NONE,1.1 Registration.pm,NONE,1.1 SecondaryArticle.pm,NONE,1.1 OntologyServer.pm,NONE,1.1 ServiceInstance.pm,NONE,1.1 SimpleArticle.pm,NONE,1.1 SimpleInput.pm,NONE,1.1 Service.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 19:44:47 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJiljX011182@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/Adaptor/moby Added Files: queryapi.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/Adaptor/moby queryapi.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 19:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJikZH011132@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY Added Files: service_type.pm collection_input.pm CommonSubs.pm Central.pm MobyXMLConstants.pm OntologyServer.pm secondary_input.pm simple_output.pm service_instance.pm CrossReference.pm collection_output.pm mysql.pm dbConfig.pm central_db_connection.pm Config.pm authority.pm simple_input.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY service_type.pm,NONE,1.1 collection_input.pm,NONE,1.1 CommonSubs.pm,NONE,1.1 Central.pm,NONE,1.1 MobyXMLConstants.pm,NONE,1.1 OntologyServer.pm,NONE,1.1 secondary_input.pm,NONE,1.1 simple_output.pm,NONE,1.1 service_instance.pm,NONE,1.1 CrossReference.pm,NONE,1.1 collection_output.pm,NONE,1.1 mysql.pm,NONE,1.1 dbConfig.pm,NONE,1.1 central_db_connection.pm,NONE,1.1 Config.pm,NONE,1.1 authority.pm,NONE,1.1 simple_input.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 19:44:47 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJilk8011199@pub.open-bio.org> kawas Tue Dec 14 14:44:47 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/Adaptor/moby/queryapi Added Files: mysql.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi mysql.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 19:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJikmA011115@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/lsid/authority Added Files: ClassResolver.pm authority.pl NamespaceResolver.pm RDFConfigure.pm dbConfigure.pm.template dbConnect.pm ServiceInstanceResolver.pm Error.pm ServiceResolver.pm PredicateResolver.pm lsid_resolver.kpf metadata.pl RelationshipResolver.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/lsid/authority ClassResolver.pm,NONE,1.1 authority.pl,NONE,1.1 NamespaceResolver.pm,NONE,1.1 RDFConfigure.pm,NONE,1.1 dbConfigure.pm.template,NONE,1.1 dbConnect.pm,NONE,1.1 ServiceInstanceResolver.pm,NONE,1.1 Error.pm,NONE,1.1 ServiceResolver.pm,NONE,1.1 PredicateResolver.pm,NONE,1.1 lsid_resolver.kpf,NONE,1.1 metadata.pl,NONE,1.1 RelationshipResolver.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 19:44:46 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 14:44:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412141944.iBEJikRH011147@pub.open-bio.org> kawas Tue Dec 14 14:44:46 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv11077/MOBY/RDF Added Files: ServiceInstanceRDF.pm InOutArticlesRDF.pm Log Message: CDATA bug - Take 3 - Eddie moby-live/Perl/MOBY/MOBY/RDF ServiceInstanceRDF.pm,NONE,1.1 InOutArticlesRDF.pm,NONE,1.1 From kawas at pub.open-bio.org Tue Dec 14 20:36:49 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:36:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142036.iBEKanI8011390@pub.open-bio.org> kawas Tue Dec 14 15:36:49 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11354/MOBY Modified Files: Central.pm Log Message: fixed typo - get_Node -> get_node moby-live/Perl/MOBY/MOBY Central.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Central.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/MOBY/Central.pm 2004/12/14 19:44:46 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/MOBY/Central.pm 2004/12/14 20:36:48 1.2 @@ -2431,7 +2431,7 @@ my $SECONDARY = $doc->getElementsByTagName( "Output" ); my $SecondaryXML = ""; if ( $SECONDARY->get_node( 1 ) ) { - $SecondaryXML = $SECONDARY->get_Node( 1 )->toString; + $SecondaryXML = $SECONDARY->get_node( 1 )->toString; } return ( $authURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML ); } From kawas at pub.open-bio.org Tue Dec 14 20:47:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl4Hs011664@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv11595/Client Modified Files: Central.pm OntologyServer.pm Registration.pm Service.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/Client Central.pm,1.83,1.84 OntologyServer.pm,1.9,1.10 Registration.pm,1.9,1.10 Service.pm,1.15,1.16 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.83 retrieving revision 1.84 diff -u -r1.83 -r1.84 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 From kawas at pub.open-bio.org Tue Dec 14 20:47:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl477011632@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11595 Modified Files: Central.pm CommonSubs.pm CrossReference.pm OntologyServer.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY Central.pm,1.144,1.145 CommonSubs.pm,1.56,1.57 CrossReference.pm,1.5,1.6 OntologyServer.pm,1.48,1.49 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.144 retrieving revision 1.145 diff -u -r1.144 -r1.145 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.56 retrieving revision 1.57 diff -u -r1.56 -r1.57 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CrossReference.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.48 retrieving revision 1.49 diff -u -r1.48 -r1.49 From kawas at pub.open-bio.org Tue Dec 14 20:47:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl43b011717@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/Adaptor/moby Removed Files: queryapi.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/Adaptor/moby queryapi.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/RCS/queryapi.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 20:47:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl4L9011701@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY Removed Files: Central.pm CommonSubs.pm Config.pm CrossReference.pm MobyXMLConstants.pm OntologyServer.pm authority.pm central_db_connection.pm collection_input.pm collection_output.pm dbConfig.pm mysql.pm secondary_input.pm service_instance.pm service_type.pm simple_input.pm simple_output.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY Central.pm,1.2,NONE CommonSubs.pm,1.1,NONE Config.pm,1.1,NONE CrossReference.pm,1.1,NONE MobyXMLConstants.pm,1.1,NONE OntologyServer.pm,1.1,NONE authority.pm,1.1,NONE central_db_connection.pm,1.1,NONE collection_input.pm,1.1,NONE collection_output.pm,1.1,NONE dbConfig.pm,1.1,NONE mysql.pm,1.1,NONE secondary_input.pm,1.1,NONE service_instance.pm,1.1,NONE service_type.pm,1.1,NONE simple_input.pm,1.1,NONE simple_output.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/Central.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/CommonSubs.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/Config.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/CrossReference.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/MobyXMLConstants.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/OntologyServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/authority.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/central_db_connection.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/collection_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/collection_output.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/dbConfig.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/mysql.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/secondary_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/service_instance.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/service_type.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/simple_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RCS/simple_output.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 20:47:05 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl5i8011815@pub.open-bio.org> kawas Tue Dec 14 15:47:05 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/lsid/authority Removed Files: ClassResolver.pm Error.pm NamespaceResolver.pm PredicateResolver.pm RDFConfigure.pm RelationshipResolver.pm ServiceInstanceResolver.pm ServiceResolver.pm authority.pl dbConfigure.pm.template dbConnect.pm lsid_resolver.kpf metadata.pl Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/lsid/authority ClassResolver.pm,1.1,NONE Error.pm,1.1,NONE NamespaceResolver.pm,1.1,NONE PredicateResolver.pm,1.1,NONE RDFConfigure.pm,1.1,NONE RelationshipResolver.pm,1.1,NONE ServiceInstanceResolver.pm,1.1,NONE ServiceResolver.pm,1.1,NONE authority.pl,1.1,NONE dbConfigure.pm.template,1.1,NONE dbConnect.pm,1.1,NONE lsid_resolver.kpf,1.1,NONE metadata.pl,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/ClassResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/Error.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/NamespaceResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/PredicateResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/RDFConfigure.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/RelationshipResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/ServiceInstanceResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/ServiceResolver.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/authority.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/dbConfigure.pm.template,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/dbConnect.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/lsid_resolver.kpf,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/lsid/authority/RCS/metadata.pl,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 20:47:05 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl54D011734@pub.open-bio.org> kawas Tue Dec 14 15:47:04 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/Adaptor/moby/queryapi Removed Files: mysql.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi mysql.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Adaptor/moby/queryapi/RCS/mysql.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 20:47:05 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl5HZ011764@pub.open-bio.org> kawas Tue Dec 14 15:47:05 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/Client Removed Files: Central.pm CollectionArticle.pm OntologyServer.pm Registration.pm SecondaryArticle.pm Service.pm ServiceInstance.pm SimpleArticle.pm SimpleInput.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/Client Central.pm,1.1,NONE CollectionArticle.pm,1.1,NONE OntologyServer.pm,1.1,NONE Registration.pm,1.1,NONE SecondaryArticle.pm,1.1,NONE Service.pm,1.1,NONE ServiceInstance.pm,1.1,NONE SimpleArticle.pm,1.1,NONE SimpleInput.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/Central.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/CollectionArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/OntologyServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/Registration.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/SecondaryArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/Service.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/ServiceInstance.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/SimpleArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/Client/RCS/SimpleInput.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 20:47:05 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:47:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142047.iBEKl5td011783@pub.open-bio.org> kawas Tue Dec 14 15:47:05 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv11595/MOBY/RDF Removed Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: erase /MOBY/MOBY in /MOBY moby-live/Perl/MOBY/MOBY/RDF InOutArticlesRDF.pm,1.1,NONE ServiceInstanceRDF.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/InOutArticlesRDF.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/MOBY/RDF/RCS/ServiceInstanceRDF.pm,v: No such file or directory From kawas at pub.open-bio.org Tue Dec 14 20:55:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 15:55:11 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142055.iBEKtBYf011949@pub.open-bio.org> kawas Tue Dec 14 15:55:11 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv11923 Modified Files: Central.pm Log Message: fix type in get_node moby-live/Perl/MOBY Central.pm,1.145,1.146 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.145 retrieving revision 1.146 diff -u -r1.145 -r1.146 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/12/14 20:47:04 1.145 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/12/14 20:55:11 1.146 @@ -2431,7 +2431,7 @@ my $SECONDARY = $doc->getElementsByTagName( "Output" ); my $SecondaryXML = ""; if ( $SECONDARY->get_node( 1 ) ) { - $SecondaryXML = $SECONDARY->get_Node( 1 )->toString; + $SecondaryXML = $SECONDARY->get_node( 1 )->toString; } return ( $authURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML ); } From kawas at pub.open-bio.org Tue Dec 14 22:31:30 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 17:31:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412142231.iBEMVUnp012494@pub.open-bio.org> kawas Tue Dec 14 17:31:30 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv12457/MOBY/Client Modified Files: Central.pm CollectionArticle.pm SimpleArticle.pm SecondaryArticle.pm Log Message: updated the check for dom to check for libxml moby-live/Perl/MOBY/Client Central.pm,1.84,1.85 CollectionArticle.pm,1.10,1.11 SimpleArticle.pm,1.6,1.7 SecondaryArticle.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.84 retrieving revision 1.85 diff -u -r1.84 -r1.85 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/14 20:47:04 1.84 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/14 22:31:30 1.85 @@ -847,6 +847,7 @@ $message .= "\n"; } my ( $type, $Namespaces ) = @{$objectdef}; + $type ||=""; $message .= "$type\n"; unless ( ref( $Namespaces ) =~ /array/i ) { return $self->errorRegXML( =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2004/11/18 17:41:16 1.10 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2004/12/14 22:31:30 1.11 @@ -255,7 +255,7 @@ } if ( $self->XML && ref( $self->XML ) ) { return 0; - } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /dom/i ) ) { + } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /libxml/i ) ) { return 0; } $self->createFromXML if ( $self->XML ); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm 2004/11/18 17:41:16 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm 2004/12/14 22:31:30 1.7 @@ -225,7 +225,7 @@ } if ( $self->XML && ref( $self->XML ) ) { return 0; - } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /dom/i ) ) { + } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /libxml/i ) ) { return 0; } $self->createFromXML if ( $self->XML ); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/11/18 17:41:16 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/12/14 22:31:30 1.6 @@ -201,7 +201,7 @@ $self->{enum} = [] unless $self->enum; if ( $self->XML && ref( $self->XML ) ) { return 0; - } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /dom/i ) ) { + } elsif ( $self->XML_DOM && !( ref( $self->XML_DOM ) =~ /libxml/i ) ) { return 0; } $self->createFromXML if ( $self->XML ); From kawas at pub.open-bio.org Wed Dec 15 04:13:47 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 14 Dec 2004 23:13:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412150413.iBF4DlbY013910@pub.open-bio.org> kawas Tue Dec 14 23:13:47 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv13883/MOBY/Client Modified Files: Central.pm Log Message: checked for CDATA and tried to excise it - eddie moby-live/Perl/MOBY/Client Central.pm,1.85,1.86 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.85 retrieving revision 1.86 diff -u -r1.85 -r1.86 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/14 22:31:30 1.85 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/15 04:13:47 1.86 @@ -3,7 +3,6 @@ use SOAP::Lite; #use SOAP::Lite + trace; # for debugging - use strict; use Carp; use XML::LibXML; @@ -377,7 +376,7 @@ $term ||= ""; my $desc = $a{'description'}; $desc ||= ""; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } my $contactEmail = $a{'contactEmail'}; @@ -507,15 +506,17 @@ my $Object = $doc->getDocumentElement(); my $obj = $Object->nodeName; return undef unless ( $obj eq 'retrieveObjectDefinition' ); - my $term = &_nodeTextContent( $Object, "objectType" ); - my $desc = &_nodeCDATAContent( $Object, "Description" ); + my $term = &_nodeTextContent( $Object, "objectType" ); + my $desc = &_nodeCDATAContent( $Object, "Description" ); + if ( $desc =~ /[^\]]+))\]\]>/ ) { + $desc = $1; + } my $authURI = &_nodeTextContent( $Object, "authURI" ); my $email = &_nodeTextContent( $Object, "contactEmail" ); my %att_value; my %relationships; my $x = $doc->getElementsByTagName( "Relationship" ); my $no_relationships = $x->size(); - for ( my $n = 1 ; $n <= $no_relationships ; ++$n ) { #get_node starts at one my $relationshipType = $x->get_node( $n )->getAttributeNode( 'relationshipType' ) @@ -569,7 +570,7 @@ my $type = $a{'serviceType'}; $type ||= ""; my $desc = $a{'description'}; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } $desc ||= ""; @@ -652,7 +653,7 @@ my $authURI = $a{'authURI'}; $authURI ||= ""; my $desc = $a{'description'}; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } $desc ||= ""; @@ -768,7 +769,8 @@ $URL ||= ""; my $desc = $a{description}; $desc ||= ""; - if ($desc =~ /[^\]]+))\]\]>/) { + + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } my $signatureURL = $a{signatureURL}; @@ -847,7 +849,7 @@ $message .= "\n"; } my ( $type, $Namespaces ) = @{$objectdef}; - $type ||=""; + $type ||= ""; $message .= "$type\n"; unless ( ref( $Namespaces ) =~ /array/i ) { return $self->errorRegXML( @@ -1209,18 +1211,16 @@ my @child = $de->childNodes; my $content; foreach ( @child ) { - $debug && &_LOG( getNodeTypeName($_), "\t", $_->toString, "\n" ); + $debug && &_LOG( getNodeTypeName( $_ ), "\t", $_->toString, "\n" ); if ( $_->nodeType == TEXT_NODE ) { - if ($_->nodeValue=~ /[^\]]+))\]\]>/) { - $content .= $1; - } else { - $content .= $_->nodeValue; #else try $_->textContent - } + $content .= $_->nodeValue; #else try $_->textContent } else { $content .= $_->toString; } } $content =~ s/^\n//gs; + $content =~ s/[^\]]+))\]\]>/$1/gs; + return $content; } @@ -1323,10 +1323,11 @@ $types->get_node( $x )->getElementsByTagName( 'Description' ) ) { $desc = $elem->firstChild->toString; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } } + $desc =~ s/[^\]]+))\]\]>/$1/gs; $servicetypes{$type} = $desc; } return \%servicetypes; @@ -1365,10 +1366,11 @@ $obnames->get_node( $x )->getElementsByTagName( 'Description' ) ) { $desc = $elem->firstChild->toString; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } } + $desc =~ s/[^\]]+))\]\]>/$1/gs; $objectnames{$name} = $desc; } return \%objectnames; @@ -1407,10 +1409,11 @@ { $desc = $elem->firstChild; $desc = $desc ? $desc->toString : ""; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } } + $desc =~ s/[^\]]+))\]\]>/$1/gs; $namespaces{$ns} = $desc; } return \%namespaces; @@ -1456,10 +1459,11 @@ $objects->get_node( $x )->getElementsByTagName( 'Schema' ) ) { $desc = $elem->firstChild->nodeValue; - if ($desc =~ /[^\]]+))\]\]>/) { + if ( $desc =~ /[^\]]+))\]\]>/ ) { $desc = $1; } } + $desc =~ s/[^\]]+))\]\]>/$1/gs; $objects{$name} = $desc; } return \%objects; @@ -1659,7 +1663,8 @@ #my $Output = &_nodeTextContent($Service, 'outputObject'); my $Description = &_nodeCDATAContent( $Service, 'Description' ); - my $cat = &_nodeTextContent( $Service, 'Category' ); + $Description =~ s/[^\]]+))\]\]>/$1/gs; + my $cat = &_nodeTextContent( $Service, 'Category' ); my @INPUTS; my @OUTPUTS; foreach my $inout ( "Input", "Output" ) { @@ -1821,10 +1826,10 @@ my $Object = $doc->getDocumentElement(); my $obj = $Object->nodeName; return undef unless ( $obj eq 'MOBYRegistration' ); - my $id = &_nodeTextContent( $Object, 'id' ); - my $success = &_nodeTextContent( $Object, 'success' ); + my $id = &_nodeTextContent( $Object, 'id' ); + my $success = &_nodeTextContent( $Object, 'success' ); my $message = &_nodeCDATAContent( $Object, 'message' ); - my $RDF = &_nodeRawContent( $Object, 'RDF' ); + my $RDF = &_nodeRawContent( $Object, 'RDF' ); my $reg = MOBY::Client::Registration->new( success => $success, message => $message, @@ -1844,7 +1849,9 @@ ); return $reg; } + sub _nodeCDATAContent { + # will get text of **all** child $node from the given $DOM # regardless of their depth!! my ( $DOM, $node ) = @_; @@ -1853,16 +1860,15 @@ my @child = $x->get_node( 1 )->childNodes; my $content; foreach ( @child ) { + #print getNodeTypeName($_), "\t", $_->toString,"\n"; next unless $_->nodeType == TEXT_NODE; $content = $_->toString; - if ($content =~ /[^\]]+))\]\]>/) { - $content = $1; - return $content; - } } + $content =~ s/[^\]]+))\]\]>/$1/gs; return $content; } + sub _nodeTextContent { # will get text of **all** child $node from the given $DOM @@ -1873,6 +1879,7 @@ my @child = $x->get_node( 1 )->childNodes; my $content; foreach ( @child ) { + #print getNodeTypeName($_), "\t", $_->toString,"\n"; next unless $_->nodeType == TEXT_NODE; $content = $_->toString; From kawas at pub.open-bio.org Wed Dec 15 17:49:44 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 15 Dec 2004 12:49:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412151749.iBFHniXc016480@pub.open-bio.org> kawas Wed Dec 15 12:49:44 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv16454/MOBY Modified Files: CommonSubs.pm Log Message: fixed typo -> getNodeValue :-> nodeValue - eddie moby-live/Perl/MOBY CommonSubs.pm,1.57,1.58 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.57 retrieving revision 1.58 diff -u -r1.57 -r1.58 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/12/14 20:47:04 1.57 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/12/15 17:49:44 1.58 @@ -1456,7 +1456,7 @@ foreach my $response_component ( $resp->childNodes ) { # $content .= $response_component->toString; - $content .= $response_component->getNodeValue + $content .= $response_component->nodeValue if ( $response_component->nodeType == TEXT_NODE ); } } From mwilkinson at pub.open-bio.org Wed Dec 15 19:37:12 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 15 Dec 2004 14:37:12 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412151937.iBFJbCc5016846@pub.open-bio.org> mwilkinson Wed Dec 15 14:37:12 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv16827 Modified Files: Central.pm Log Message: one more uninitialized value moby-live/Perl/MOBY/Client Central.pm,1.86,1.87 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.86 retrieving revision 1.87 diff -u -r1.86 -r1.87 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/15 04:13:47 1.86 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/12/15 19:37:12 1.87 @@ -1865,6 +1865,7 @@ next unless $_->nodeType == TEXT_NODE; $content = $_->toString; } + $content ||=""; $content =~ s/[^\]]+))\]\]>/$1/gs; return $content; } From kawas at pub.open-bio.org Sat Dec 18 18:33:44 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat, 18 Dec 2004 13:33:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181833.iBIIXiGm030170@pub.open-bio.org> kawas Sat Dec 18 13:33:43 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv30145/org/biomoby/client/gui/util Modified Files: REGEXP.java Log Message: fixed the uri regular expression so that it handles uris like: illuminae.com, and not just www.illuminae.com moby-live/Java/src/main/org/biomoby/client/gui/util REGEXP.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/11/22 17:48:45 1.4 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/12/18 18:33:43 1.5 @@ -21,7 +21,7 @@ private final static String URI = //"(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|www\\.|http:\\/\\/|HTTP:\\/\\/)?[\\w]+\\.[\\w].*\\w$)"; //"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\\?([^#]*))?(#(.*))?"; // as per rfc 2396 appendix a. - "^([\\w]+\\.[\\w]+(\\.[\\w]+)+)$"; + "^([\\w]+\\.[\\w]+(\\.[\\w]+)*)$"; private final static String URL = "(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|http:\\/\\/|HTTP:\\/\\/)[\\w]+\\.[\\w].*(\\/\\w+(\\.{1}\\w+)*)$)"; From kawas at pub.open-bio.org Sat Dec 18 18:48:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat, 18 Dec 2004 13:48:26 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181848.iBIImQxQ030233@pub.open-bio.org> kawas Sat Dec 18 13:48:26 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv30212/org/biomoby/client/gui/util Added Files: ObjectXMLWriter.java Log Message: a class that helps retrieve xml information on moby datatypes. used when we want to display the xml format of an object. requires the file /usr/local/apache2/cgi-bin/applets/retrieveObjectXML.cgi moby-live/Java/src/main/org/biomoby/client/gui/util ObjectXMLWriter.java,NONE,1.1 From kawas at pub.open-bio.org Sat Dec 18 18:51:27 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat, 18 Dec 2004 13:51:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181851.iBIIpRcD030279@pub.open-bio.org> kawas Sat Dec 18 13:51:27 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv30254/org/biomoby/client/gui/serviceInstanceCreationTool Modified Files: ServiceInstancePanelFactory.java Log Message: fixed the edit details page so that it is more consistent with the applet. Other small revisions made. moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool ServiceInstancePanelFactory.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/11/17 17:15:26 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/18 18:51:27 1.3 @@ -629,7 +629,6 @@ // ButtonBeautifier.enhanceButton(done, 11, tool.getClass()); JButton add = new JButton(" Add Data Type To The Collection "); - //TODO press this and ask to choose another object or to add the // collection to the service add.setActionCommand("addDataType"); add.setName("addDataType"); // adds the data type @@ -1059,7 +1058,6 @@ + "of allowable values." + "Once you have inputted all of the appropriate details, click on the button

    " + "labelled 'Add to Service' to add the secondary input to your service."); - //TODO String[] theLabels = { "Secondary Input Name REQUIRED :", // required @@ -1101,7 +1099,7 @@ // goes back to the input/output radio panel done.addActionListener(ioal); - JButton cancel = new JButton(" Cancel "); //TODO + JButton cancel = new JButton(" Cancel "); ButtonBeautifier.enhanceButton(cancel, 6, tool.getClass()); cancel.setActionCommand("back"); cancel.setName("back"); // goes back to the input/output radio panel @@ -1244,22 +1242,63 @@ JLabel signatureUrlLabel = new JLabel( "Signature URL (Optional)"); - JLabel serviceNameLabel2 = new JLabel( - " Must be in valid XML format"); - JLabel authorityLabel2 = new JLabel( - " Must be a valid URI - e.g. www.biomoby.org"); - JLabel emailLabel2 = new JLabel( - " Must be a valid email address"); - JLabel descriptionLabel2 = new JLabel( - ""); - JLabel authoritativeLabel2 = new JLabel( - ""); - JLabel typeLabel2 = new JLabel( - ""); - JLabel urlLabel2 = new JLabel( - " Must be a valid URL - e.g. http://some.domain/something"); - JLabel signatureUrlLabel2 = new JLabel( - " Must be a valid URL - e.g. http://some.domain/something"); + JButton serviceNameLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(serviceNameLabel2, 14, tool.getClass()); + serviceNameLabel2 + .setToolTipText(" Name cannot contain spaces nor start with special characters "); + serviceNameLabel2.setActionCommand("1"); + serviceNameLabel2.addActionListener(hal); + + JButton authorityLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(authorityLabel2, 14, tool.getClass()); + authorityLabel2 + .setToolTipText(" Must be a valid URI "); + authorityLabel2.setActionCommand("2"); + authorityLabel2.addActionListener(hal); + + JButton emailLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(emailLabel2, 14, tool.getClass()); + emailLabel2 + .setToolTipText(" Must be a valid email address "); + emailLabel2.setActionCommand("3"); + emailLabel2.addActionListener(hal); + + JButton descriptionLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(descriptionLabel2, 14, tool.getClass()); + descriptionLabel2 + .setToolTipText("Please provide a comprehensive description "); + descriptionLabel2.setActionCommand("4"); + descriptionLabel2.addActionListener(hal); + + JButton authoritativeLabel2 = new JButton(""); + ButtonBeautifier + .enhanceButton(authoritativeLabel2, 14, tool.getClass()); + authoritativeLabel2 + .setToolTipText("Is your service authoritative?"); + authoritativeLabel2.setActionCommand("5"); + authoritativeLabel2.addActionListener(hal); + + JButton typeLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(typeLabel2, 14, tool.getClass()); + typeLabel2 + .setToolTipText("What type of service instance are you creating?"); + typeLabel2.setActionCommand("6"); + typeLabel2.addActionListener(hal); + + JButton urlLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(urlLabel2, 14, tool.getClass()); + urlLabel2 + .setToolTipText(" Must be a valid URL "); + urlLabel2.setActionCommand("7"); + urlLabel2.addActionListener(hal); + + JButton signatureUrlLabel2 = new JButton(""); + ButtonBeautifier.enhanceButton(signatureUrlLabel2, 14, tool.getClass()); + signatureUrlLabel2 + .setToolTipText(" Must be a valid URL "); + signatureUrlLabel2.setActionCommand("8"); + signatureUrlLabel2.addActionListener(hal); + // check if we need to fill in the service fields Service s = tool.getService(); @@ -1316,33 +1355,67 @@ else authoritativeComboBox.setSelectedIndex(1); - // add the items to a panel with 2 columns +// add the items to a panel with 2 columns JPanel itemPanel = null; itemPanel = initPanel(itemPanel, "itemPanel", 3); itemPanel.add(serviceNameLabel); itemPanel.add(serviceNameField); - itemPanel.add(serviceNameLabel2); + // the help1 panels ensure that the button is fitted + JPanel help1 = null; + help1 = initPanel(help1, "", -1); + help1.add(serviceNameLabel2,BorderLayout.LINE_START); + itemPanel.add(help1); + + itemPanel.add(descriptionLabel); itemPanel.add(descriptionField); - itemPanel.add(descriptionLabel2); + JPanel help2 = null; + help2 = initPanel(help1, "", -1); + help2.add(descriptionLabel2,BorderLayout.LINE_START); + itemPanel.add(help2); + itemPanel.add(emailLabel); itemPanel.add(emailField); - itemPanel.add(emailLabel2); + JPanel help3 = null; + help3 = initPanel(help3, "", -1); + help3.add(emailLabel2,BorderLayout.LINE_START); + itemPanel.add(help3); + itemPanel.add(urlLabel); itemPanel.add(urlField); - itemPanel.add(urlLabel2); + JPanel help4 = null; + help4 = initPanel(help1, "", -1); + help4.add(urlLabel2,BorderLayout.LINE_START); + itemPanel.add(help4); + + itemPanel.add(authoritativeLabel); itemPanel.add(authoritativeComboBox); - itemPanel.add(authoritativeLabel2); + JPanel help5 = null; + help5 = initPanel(help1, "", -1); + help5.add(authoritativeLabel2,BorderLayout.LINE_START); + itemPanel.add(help5); + itemPanel.add(typeLabel); itemPanel.add(categoryComboBox); - itemPanel.add(typeLabel2); + JPanel help6 = null; + help6 = initPanel(help1, "", -1); + help6.add(typeLabel2,BorderLayout.LINE_START); + itemPanel.add(help6); + itemPanel.add(authorityLabel); itemPanel.add(authorityField); - itemPanel.add(authorityLabel2); + JPanel help7 = null; + help7 = initPanel(help1, "", -1); + help7.add(authorityLabel2,BorderLayout.LINE_START); + itemPanel.add(help7); + itemPanel.add(signatureUrlLabel); itemPanel.add(sigUrlField); - itemPanel.add(signatureUrlLabel2); + JPanel help8 = null; + help8 = initPanel(help1, "", -1); + help8.add(signatureUrlLabel2,BorderLayout.LINE_START); + itemPanel.add(help8); JButton next = new JButton(" Go Back To (In/Out)put Selection "); next.setActionCommand("backFromEdit"); From kawas at pub.open-bio.org Sat Dec 18 18:52:31 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat, 18 Dec 2004 13:52:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181852.iBIIqVYQ030327@pub.open-bio.org> kawas Sat Dec 18 13:52:30 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv30302/org/biomoby/client/gui/serviceInstanceCreationTool Modified Files: MobyInputOutputData.java Log Message: added the code to display an objects details when requested. moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyInputOutputData.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyInputOutputData.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyInputOutputData.java 2004/09/27 21:29:15 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyInputOutputData.java 2004/12/18 18:52:30 1.2 @@ -7,6 +7,7 @@ import java.util.Enumeration; import org.biomoby.client.CentralImpl; +import org.biomoby.client.gui.util.ObjectXMLWriter; import org.biomoby.shared.Central; import org.biomoby.shared.MobyDataType; import org.biomoby.shared.MobyException; @@ -36,6 +37,7 @@ "http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl"; static final String NAMESPACE = "http://mobycentral.cbr.nrc.ca:8080/MOBY/Central"; + private static String _URL = "http://mobycentral.cbr.nrc.ca/cgi-bin/applets/retrieveObjectXML.cgi?name="; /** * @@ -187,14 +189,15 @@ } /** - * NOT YET IMPLEMENTED

    - * @param datatype - * @return should return the MobyData type in xml format. - *

    TODO implement this! - */ - public static String ObjectInXML(String datatype) { // TODO - create an xml view of the data type - String str = - "looking for a way to get the xml from a cgi script?\n is there one already?"; - return str; + * @param datatype - the name of the datatype to retrieve informationon. + * @return if we are able to retrieve information on the datatype, then we return the MobyData type in xml format. + */ + public static String ObjectInXML(String datatype) { + String content = null; + content = ObjectXMLWriter.generatePrettyXML(_URL+datatype); + if (content.equals("")) { + content = "Couldn't retrieve object details in xml format."; + } + return content; } } From kawas at pub.open-bio.org Sat Dec 18 19:00:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Sat, 18 Dec 2004 14:00:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412181900.iBIJ0t3l030373@pub.open-bio.org> kawas Sat Dec 18 14:00:55 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv30348/org/biomoby/client/gui/serviceInstanceCreationTool Modified Files: ServiceInstancePanelFactory.java Log Message: fixed bug where MOBY, CGI, WSDL appearred when in 'edit service details' view. moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool ServiceInstancePanelFactory.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/18 18:51:27 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/18 19:00:55 1.4 @@ -892,10 +892,9 @@ // create the text area to display the service info JTextArea area = new JTextArea(); - area.setText(/* tool.getService().getObjectString(name) */ - MobyInputOutputData.ObjectInXML(name)); + area.setText(MobyInputOutputData.ObjectInXML(name)); area.setCaretPosition(0); - + JScrollPane scrollableTextArea = new JScrollPane(area); // create a back button JButton back = new JButton(" Go Back "); back.setActionCommand("back2Object"); @@ -909,7 +908,7 @@ button.add(back); // add everything to the panel - panel.add(area, BorderLayout.CENTER); + panel.add(scrollableTextArea, BorderLayout.CENTER); panel.add(button, BorderLayout.PAGE_END); return panel; } @@ -1337,7 +1336,7 @@ if (SET) sigUrlField.setText(s.getSignatureURL()); // Create comboboxes - String[] typeItems = { "Moby", "CGI", "WSDL" }; + String[] typeItems = { "Moby"/*, "CGI", "WSDL" */}; JComboBox categoryComboBox = new JComboBox(typeItems); categoryComboBox.setName("category"); categoryComboBox.setActionCommand("category"); From kawas at pub.open-bio.org Mon Dec 20 17:13:06 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 20 Dec 2004 12:13:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412201713.iBKHD6ul013123@pub.open-bio.org> kawas Mon Dec 20 12:13:06 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv13098/org/biomoby/client/gui/util Modified Files: ObjectXMLWriter.java Log Message: Added/Modified documentation moby-live/Java/src/main/org/biomoby/client/gui/util ObjectXMLWriter.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/ObjectXMLWriter.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/ObjectXMLWriter.java 2004/12/18 18:48:26 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/ObjectXMLWriter.java 2004/12/20 17:13:06 1.2 @@ -6,8 +6,7 @@ /** * @author Eddie Kawas - *

    Created for - *

    This class was created to ... + *

    This class was created to query mobycentral in order to return the xml representation of a moby object. *

    For questions, comments, or bugs *

    email me at edward.kawas at gmail.com */ @@ -19,6 +18,13 @@ import org.jdom.output.XMLOutputter; public class ObjectXMLWriter { + /** + * + * PRE:unformattedXML is valid XML.

    + * POST:Pretty, i.e. tabbed, spaced, etc, XML is returned.

    + * @param unformattedXML - a string of xml that will be to look orderly. + * @return an XML string outputted neatly. + */ public static String generatePrettyXML(String unformattedXML) { try { ByteArrayOutputStream buf = new ByteArrayOutputStream(); From kawas at pub.open-bio.org Mon Dec 20 17:13:34 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 20 Dec 2004 12:13:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412201713.iBKHDYes013173@pub.open-bio.org> kawas Mon Dec 20 12:13:34 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv13136/org/biomoby/client/gui/serviceInstanceCreationTool Modified Files: TreeListener.java ServiceInstancePanelFactory.java NamespaceTree.java ServiceTypeTree.java Log Message: Added/Modified documentation moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool TreeListener.java,1.1,1.2 ServiceInstancePanelFactory.java,1.4,1.5 NamespaceTree.java,1.1,1.2 ServiceTypeTree.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/TreeListener.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/TreeListener.java 2004/09/27 21:29:15 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/TreeListener.java 2004/12/20 17:13:34 1.2 @@ -36,7 +36,7 @@ * POST: the tree listener is initialized. *

    * - * @param tool + * @param tool - the ServiceCreationTool that registered this listener. */ public TreeListener(ServiceCreationTool tool) { this.tool = tool; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/18 19:00:55 1.4 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2004/12/20 17:13:34 1.5 @@ -92,9 +92,6 @@ } }; worker.start(); - // before doing anything, load the service tree in a - // separate thread to increase performance - // also download the object tree for use final TreeLoaderThread workerTree = new TreeLoaderThread() { public Object construct() { mobyTree = new MobyTree(false, @@ -106,10 +103,6 @@ } }; workerTree.start(); - - // before doing anything, load the service tree in a - // separate thread to increase performance - // also download the object tree for use final TreeLoaderThread workerNamespace = new TreeLoaderThread() { public Object construct() { namespaceTree = new NamespaceTree(false, @@ -123,6 +116,12 @@ workerNamespace.start(); } + /** + * + * PRE:None.

    + * POST:The starting panel for the applet is returned.

    + * @return - the starting panel for the applet is returned. + */ public JPanel createStartingPanel() { /* all tabs go to the center of this panel */ @@ -372,6 +371,12 @@ return pan; } + /** + * + * PRE:None.

    + * POST:The add inputs/outputs panel is created for the applet.

    + * @return - a JPanel representing the input/output chooser for the applet. + */ public JPanel createChoosingPanel() { /* all tabs go to the center of this panel */ JPanel pan = null; @@ -447,6 +452,14 @@ return pan; } + /** + * + * PRE:Top and bottom are valid JPanels.

    + * POST:a JSplitPane is created with top placed at the top of the panel and bottom placed at the bottom

    + * @param top - a JPanel that will be the top component of the split pane. + * @param bottom - a JPanel that will be the bottom component of the split pane. + * @return - a JSplitPane with the top and bottom components initialized to top and bottom. + */ public JSplitPane createSplitePane(JPanel top, JPanel bottom) { JSplitPane vpane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, top, bottom); @@ -455,6 +468,11 @@ return vpane; } + /** + * PRE:None.

    + * POST:A JPanel containing the service type tree is returned.

    + * @return - a JPanel containing the service type tree. + */ public JPanel createServiceTypeChooserPanel() { JPanel panel = null; panel = initPanel(panel, "Choose the Service Type", @@ -489,6 +507,14 @@ return panel; } + /** + * + * PRE:dataTypeName is found in the mobycentral object ontology.

    + * POST:A JPanel containing the information of the recently chosen datatype, along with a namespace tree so that user can choose appropriate namespaces for their input/output.

    + * @param dataTypeName - a string name of a valid object in the moby object ontology. + * @param isInput - if isInput is true, then datatype is a primary input. Otherwise the datatype is an output. + * @return - a JPanel containing information on the datatype, as well as other widgets that aid in the supplementing of the input/output object. + */ public JPanel createSimplePrimaryPanel(String dataTypeName, boolean isInput) { JPanel panel = null; panel = initPanel(panel, "" @@ -609,6 +635,15 @@ return panel; } + /** + * + * PRE:datatype name is found in the moby object ontology.

    + * POST:a JPanel is returned that allows the user to add more information on the object contained in their collection

    + * @param dataTypeName - a valid object name found in the moby object ontology. + * @param isInput - if true, then collection (and object contained in collection) is an input, otherwise the collection is an output. + * @param collectionName - the name of the collection. + * @return - a JPanel with widgets that allow for the user to supplement the information on the collection. + */ public JPanel createCollectionPrimaryPanel(String dataTypeName, boolean isInput, String collectionName) { JPanel panel = null; @@ -764,6 +799,12 @@ return panel; } + /** + * + * PRE:None.

    + * POST:a JPanel containing an object tree that allows for object additions to the users current collection is returned

    + * @return - JPanel with an object tree allowing for the addition of the selected object to the users collection. + */ public JPanel createObjectTreePanelForAddingToCollections() { JPanel panel = null; panel = initPanel( @@ -850,6 +891,12 @@ return p; } + /** + * + * PRE:None.

    + * POST:An empty JPanel is returned.

    + * @return - a JPanel with nothing contained within. + */ public JPanel createEmptyPanel() { JPanel p = null; p = initPanel(p, "empty", -1); @@ -857,6 +904,12 @@ return p; } + /** + * + * PRE:None

    + * POST:A JPanel containing information about the users service is shown.

    + * @return - JPanel with information on the users service. + */ public JPanel createServiceViewPanel() { JPanel panel = null; panel = initPanel(panel, "Service View", -1); @@ -884,6 +937,12 @@ return panel; } + /** + * + * PRE:An object is selected in the object tree.

    + * POST:Information about the selected object is returned.

    + * @return - JPanel with information on the selected moby object. + */ public JPanel createObjectViewPanel() { String name = objectTreeListener.getSelectedNode(); JPanel panel = null; @@ -913,6 +972,12 @@ return panel; } + /** + * + * PRE:None.

    + * POST:JPanel with information and widgets that allow the user to supplement their collection is returned.

    + * @return - JPanel with information fields and widgets that allow the user to supplement their collection. + */ public JPanel createObjectViewPanelForCollection() { String name = objectTreeListener.getSelectedNode(); JPanel panel = null; @@ -942,6 +1007,12 @@ return panel; } + /** + * + * PRE:None.

    + * POST:JPanel displaying a tree of the moby object ontology is returned that aids in the addition of objects to the service.

    + * @return JPanel containing a tree representation of the moby object ontology. + */ public JPanel createObjectTreePanel() { JPanel panel = null; panel = initPanel(panel, "Choose an Object", -1); @@ -980,72 +1051,81 @@ } /** - * @return + * @return true if a radio button is selected, false otherwise. */ public boolean isRADIO_SELECTED() { return RADIO_SELECTED; } /** - * @param b + * @param b - set whether or not the radio button is selected. */ public void setRADIO_SELECTED(boolean b) { RADIO_SELECTED = b; } /** - * @return + * @return - return the service type tree. */ public ServiceTypeTree getTree() { return tree; } /** - * @param tree + * @param tree - the tree to set the service type tree to. */ public void setTree(ServiceTypeTree tree) { this.tree = tree; } /** - * @return + * @return - the TreeListener registered to this tool */ public TreeListener getMouseTreeListener() { return mtl; } /** - * @return + * @return - the moby tree registered to this tool. */ public MobyTree getMobyTree() { return mobyTree; } /** - * @return + * @return - the namespace tree. */ public NamespaceTree getNamespaceTree() { return namespaceTree; } /** - * @return + * @return - the listener associated with the namespace tree registered with this tool. */ public NamespaceListener getNamespaceListener() { return ntl; } /** - * @return + * @return - DefaultListModel for the namespace dropdown list. */ public DefaultListModel getNamespaceDropdownListModel() { return model; } + /** + * @return - the size of the namespace dropdown list. + */ public int getNamespaceDropdownListSize() { return namespaceDropdownList.getModel().getSize(); } + /** + * + * PRE:None.

    + * POST:JPanel with widgets required to add secondary input to the service instance is returned.

    + * @return - JPanel with various widgets that allow for the addition of secondary inputs to the service instance. + */ public JPanel createSecondaryPanel() { JPanel panel = null; panel = initPanel(panel, "Secondary Input Entry", -1); @@ -1138,6 +1218,9 @@ return panel; } + /** + * @return - an Enumeration of secondary data valid inputs + */ public Enumeration getSecondaryInputEnumeration() { Vector vec = new Vector(); StringTokenizer st = new StringTokenizer(InputOutputFocusListener @@ -1153,14 +1236,26 @@ return vec.elements(); } + /** + * @return - the secondary input datatype - Can be INTEGER, STRING, DATETIME or FLOAT + */ public static String getSecondaryDataType() { return ServiceInstancePanelFactory.datatype; } + /** + * @param datatype - the secondary input datatype - INTEGER, STRING, DATETIME, or FLOAT + */ public static void setSecondaryDataType(String datatype) { ServiceInstancePanelFactory.datatype = datatype; } + /** + * + * PRE:None.

    + * POST:JPanel that displays the service instance is returned.

    + * @return - JPanel that initiates submission of the service instance. + */ public JPanel createSubmissionPanel() { JPanel panel = null; panel = initPanel( @@ -1200,12 +1295,18 @@ } /** - * @return + * @return - the submit JButton. */ public JButton getSubmit() { return submit; } + /** + * + * PRE:None.

    + * POST:JPanel with various widgets for editing the details of the service instance is returned.

    + * @return - JPanel is returned that aids in the editing of the service instance details. + */ public JPanel createDetailEditingPanel() { /* all tabs go to the center of this panel */ @@ -1438,7 +1539,7 @@ } /** - * @return + * @return - the edit JButton */ public JButton getEdit() { return edit; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/NamespaceTree.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/NamespaceTree.java 2004/09/27 21:29:15 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/NamespaceTree.java 2004/12/20 17:13:34 1.2 @@ -40,9 +40,9 @@ private String rdf = ""; /** * PRE: None

    - * POST: A moby tree is constructed with the root node labeled as 'Service'

    + * POST: A moby tree is constructed with the root node labeled as 'Namespace'

    * and the material for the tree taken from the RDF located at - * @link http://biomoby.org/RESOURCES/MOBY-S/Service + * @link http://biomoby.org/RESOURCES/MOBY-S/Namespace * @param canEdit, if true, then the nodes are editable, else they are not. */ public NamespaceTree(boolean canEdit, String rdf) { @@ -84,7 +84,7 @@ /** * PRE: None.

    - * POST: The MobyTree object contains an empty tree with a single node labeled 'Object' + * POST: The MobyTree Namespace contains an empty tree with a single node labeled 'Namespace' * @return - none. * */ @@ -294,6 +294,12 @@ return tree; } + /** + * + * PRE:None.

    + * POST:THe Namespace tree is refreshed.

    + * + */ public void reload() { hashmap = new Construct(rdf).createHomes(); makeObjectTree(); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceTypeTree.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceTypeTree.java 2004/09/27 21:29:15 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/ServiceTypeTree.java 2004/12/20 17:13:34 1.2 @@ -298,6 +298,12 @@ return tree; } + /** + * + * PRE:None.

    + * POST:The Service Type tree for this tool is refreshed.

    + * + */ public void reload() { hashmap = new Construct(rdf).createHomes(); makeObjectTree(); From kawas at pub.open-bio.org Wed Dec 22 14:33:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 09:33:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221433.iBMEXatx001964@pub.open-bio.org> kawas Wed Dec 22 09:33:36 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv1939/org/biomoby/client/gui/objectCreationTool Modified Files: MobyTree.java Log Message: Revised MobyTree.java moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool MobyTree.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/MobyTree.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/MobyTree.java 2004/09/27 22:15:13 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/MobyTree.java 2004/12/22 14:33:36 1.2 @@ -66,7 +66,17 @@ tree.setEditable(canEdit); tree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION); tree.setShowsRootHandles(true); - + } + + /** + * + * PRE:tree is a valid JTree.

    + * POST:JTree is collapsed at root node.

    + * + */ + public void collapseMobyTree() { + tree.clearSelection(); + tree.collapseRow(0); } /** From kawas at pub.open-bio.org Wed Dec 22 14:34:58 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 09:34:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221434.iBMEYwdL002035@pub.open-bio.org> kawas Wed Dec 22 09:34:58 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2014/org/biomoby/client/gui/objectCreationTool Added Files: TreeWindow.java PopUpWindow.java TreeMouseListener.java SubmissionWindow.java Log Message: Revised Object Creation Tool - newly updated moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool TreeWindow.java,NONE,1.1 PopUpWindow.java,NONE,1.1 TreeMouseListener.java,NONE,1.1 SubmissionWindow.java,NONE,1.1 From kawas at pub.open-bio.org Wed Dec 22 14:40:50 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 09:40:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221440.iBMEeoVd002108@pub.open-bio.org> kawas Wed Dec 22 09:40:50 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main In directory pub.open-bio.org:/tmp/cvs-serv2087 Added Files: retrieveObjectXML.cgi Log Message: File needed for retrieving xml representations for moby objects. referenced in org\biomoby\client\gui\objectCreationTool\TreeWindow.java moby-live/Java/src/main retrieveObjectXML.cgi,NONE,1.1 From kawas at pub.open-bio.org Wed Dec 22 14:42:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 09:42:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221442.iBMEgaQG002142@pub.open-bio.org> kawas Wed Dec 22 09:42:36 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main In directory pub.open-bio.org:/tmp/cvs-serv2117 Modified Files: retrieveObjectXML.cgi Log Message: added the code to strip CDATA from returned xml moby-live/Java/src/main retrieveObjectXML.cgi,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/retrieveObjectXML.cgi,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/retrieveObjectXML.cgi 2004/12/22 14:40:50 1.1 +++ /home/repository/moby/moby-live/Java/src/main/retrieveObjectXML.cgi 2004/12/22 14:42:36 1.2 @@ -15,4 +15,5 @@ print "Content-type: text/plain\n\n"; my $output = $DEFS->{'XML'}; $output =~ s/retrieveObjectDefinition/objectDetails/g; + $output =~ s/[^\]]+))\]\]>/$1/gs; print $output; From kawas at pub.open-bio.org Wed Dec 22 14:48:43 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 09:48:43 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221448.iBMEmhs2002207@pub.open-bio.org> kawas Wed Dec 22 09:48:43 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2180 Removed Files: ButtonActions.java ButtonBeautifier.java FieldFocusListeners.java FieldKeyListener.java MobyUserPanel.java PanelFactory.java Log Message: removed - no longer necessary moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool ButtonActions.java,1.2,NONE ButtonBeautifier.java,1.1,NONE FieldFocusListeners.java,1.2,NONE FieldKeyListener.java,1.1,NONE MobyUserPanel.java,1.1,NONE PanelFactory.java,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/ButtonActions.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/ButtonBeautifier.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/FieldFocusListeners.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/FieldKeyListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/MobyUserPanel.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/PanelFactory.java,v: No such file or directory From kawas at pub.open-bio.org Wed Dec 22 14:49:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 09:49:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221449.iBMEnaa3002248@pub.open-bio.org> kawas Wed Dec 22 09:49:36 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2226 Removed Files: TreeListener.java Log Message: removed - no longer necessary moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool TreeListener.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/TreeListener.java,v: No such file or directory From kawas at pub.open-bio.org Wed Dec 22 16:01:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 11:01:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221601.iBMG1cvQ002501@pub.open-bio.org> kawas Wed Dec 22 11:01:38 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2460/org/biomoby/client/gui/objectCreationTool Modified Files: TreeWindow.java PopUpWindow.java Registration.java TreeMouseListener.java SubmissionWindow.java Log Message: Added documentation moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool TreeWindow.java,1.1,1.2 PopUpWindow.java,1.1,1.2 Registration.java,1.1,1.2 TreeMouseListener.java,1.1,1.2 SubmissionWindow.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeWindow.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeWindow.java 2004/12/22 14:34:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeWindow.java 2004/12/22 16:01:38 1.2 @@ -16,8 +16,11 @@ import org.biomoby.client.gui.util.ObjectXMLWriter; /** * @author Eddie Kawas - *

    Created for - *

    This class was created to ... + *

    This class was created with the purpose of + * displaying the mobycentral object ontology in + * tree format, as well as providing a way to + * retrieve information about objects from the + * mobycentral object ontology. *

    For questions, comments, or bugs *

    email me at edward.kawas at gmail.com */ =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/PopUpWindow.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/PopUpWindow.java 2004/12/22 14:34:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/PopUpWindow.java 2004/12/22 16:01:38 1.2 @@ -13,8 +13,8 @@ import javax.swing.ImageIcon; /** * @author Eddie Kawas - *

    Created for - *

    This class was created to ... + *

    This class was created to present a convenience class + * that presents modal pop up windows to the user. *

    For questions, comments, or bugs *

    email me at edward.kawas at gmail.com */ =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Registration.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Registration.java 2004/09/27 22:15:13 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Registration.java 2004/12/22 16:01:38 1.2 @@ -20,24 +20,47 @@ static final String ENDPOINT = "http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl"; static final String NAMESPACE = "http://mobycentral.cbr.nrc.ca:8080/MOBY/Central"; - - private static boolean PROTO = false; + /** + * + * Constructor + * @param name - the name of the moby data type + * @param proto - is this object a prototype? + */ public Registration(String name, boolean proto) { super(name); PROTO = proto; } + /** + * + * PRE:None.

    + * POST:The name of the data type is renamed to str.

    + * @param str - the new name of the data type. + */ public void setName(String str) { this.name = str; } - + /** + * + * PRE:Pair p is a well constructed Pair object.

    + * POST:Data from Pair p is added to the data type + * in the form of HASA relationship

    + * @param p - the pair to add to the HASA containment relationship for the data type + */ public void addHASAChildren(Pair p) { //System.out.println("ArticleName: " + p.getArticlename() + " DataType: " + p.getAttribute()); this.addChild(p.getArticlename(), p.getAttribute(), Central.iHASA); } + /** + * + * PRE:Pair p is a well constructed Pair object.

    + * POST:Data from Pair p is added to the data type + * in the form of HAS relationship

    + * @param p - the pair to add to the HAS containment relationship for the data type + */ public void addHASChildren(Pair p) { //System.out.println("ArticleName: " + p.getArticlename() + " DataType: " + p.getAttribute()); this.addChild(p.getArticlename(), p.getAttribute(), Central.iHAS); @@ -45,9 +68,11 @@ } /** - * - * PRE: - *

    POST:

    + * + * PRE:MobyDataType has been properly initialized.

    + * POST:MobyDataType is registered in the mobycentral object + * ontology and a string representing its LSID is returned.

    + * @param tool - the ObjectCreationTool that is registering this new data type. * @return 1 for success, 0 for failure and -1 for 'pending curation' */ public String performRegistration(ObjectCreationTool tool) { @@ -83,12 +108,10 @@ return reg; } + /** - * - * PRE: - *

    POST:

    - * @param name - * @return + * @deprecated - no longer used. + * TODO - remove method from class. */ public String getDataTypeInfo(String name) { String ret = ""; @@ -108,10 +131,19 @@ } + /** + * + * PRE:MobyDataType has been registered.

    + * POST:LSID is returned

    + * @return - the LSID of the moby data type. + */ public String getMobyID() { return this.getId(); } + /** + * TODO - remove from class. Shouldn't have this method. + */ public void setMobyID(String s) { this.setId(s); } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeMouseListener.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeMouseListener.java 2004/12/22 14:34:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeMouseListener.java 2004/12/22 16:01:38 1.2 @@ -10,8 +10,11 @@ import javax.swing.tree.TreePath; /** - * @author Eddie Kawas

    Created for

    This class was created to ...

    For - * questions, comments, or bugs

    email me at edward.kawas at gmail.com + * @author Eddie Kawas + *

    This class was created to implement the Mouselistener interface + * for use with a tree that displays the mobycentral object ontology. + *

    For questions, comments, or bugs + *

    email me at edward.kawas at gmail.com */ public class TreeMouseListener implements MouseListener { @@ -65,10 +68,11 @@ } /** - * PRE:

    POST:

    - * - * @param selected - * @return + * PRE: None.

    + * POST: THe name of the event originator is returned: ISA, HAS, HASA.

    + * @param selected - the integer value representing the event originator + * @see org.biomoby.client.gui.objectCreationTool + * @return String representing the event originator. */ private String getEventOriginatorName(int selected) { String str = null; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/SubmissionWindow.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/SubmissionWindow.java 2004/12/22 14:34:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/SubmissionWindow.java 2004/12/22 16:01:38 1.2 @@ -13,8 +13,9 @@ import javax.swing.ImageIcon; /** * @author Eddie Kawas - *

    Created for - *

    This class was created to ... + *

    This class was created to present a view to the user + * of the tool that displays their newly created object prior + * to registration. *

    For questions, comments, or bugs *

    email me at edward.kawas at gmail.com */ From kawas at pub.open-bio.org Wed Dec 22 16:07:03 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed, 22 Dec 2004 11:07:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200412221607.iBMG73tG002580@pub.open-bio.org> kawas Wed Dec 22 11:07:03 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool In directory pub.open-bio.org:/tmp/cvs-serv2555/org/biomoby/client/gui/serviceTypeCreationTool Modified Files: ServiceTypeApplet.java Log Message: Added documentation moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool ServiceTypeApplet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java 2004/09/27 21:06:17 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java 2004/12/22 16:07:03 1.3 @@ -35,14 +35,13 @@ import org.biomoby.shared.PendingCurationException; /** - * @author Eddie Created for - *

    - * This class was created to ... - *

    - * For questions, comments, or bugs - *

    - * email me at edward.kawas at gmail.com - *

    + * + * @author Eddie Kawas + *

    This class was created to present + * users of moby the chance to create + * new service types quickly and easily. + *

    For questions, comments, or bugs + *

    email me at edward.kawas at gmail.com */ public class ServiceTypeApplet extends JApplet { @@ -125,17 +124,20 @@ return super.getAppletContext(); } - /* - * (non-Javadoc) - *@see java.applet.Applet#getAppletInfo() - */ + /* + * (non-Javadoc) + *@see java.applet.Applet#getAppletInfo() + */ public String getAppletInfo() { - return "Title: Moby Service Type Construction Tool v1.00, 24 September 2004\n" - + "Author: Edward Kawas\n" - + "An interactive way to create Service Types for the MobyCentral Ontology." + - newline + "This is" + ((PROTOTYPE) ? "" : " not " ) + "a prototype!"; - } - + return "Title: Moby Service Type Construction Tool v1.00, 24 September 2004\n" + + "Author: Edward Kawas\n" + + "An interactive way to create Service Types for the MobyCentral Ontology." + + newline + + "This is" + + ((PROTOTYPE) ? "" : " not ") + + "a prototype!"; + } + /* * (non-Javadoc) * @@ -159,17 +161,17 @@ .getLastSelectedPathComponent().toString(); switch (arg0.getClickCount()) { - case 1: - break; - case 2: - //set text box to be this node, and close frame - parentTextField.setText(selected); - frame.dispose(); - frame = null; - break; - default: - // do nothing - break; + case 1: + break; + case 2: + //set text box to be this node, and close frame + parentTextField.setText(selected); + frame.dispose(); + frame = null; + break; + default: + // do nothing + break; } } @@ -229,9 +231,8 @@ title.setFont(new java.awt.Font("Dialog", java.awt.Font.BOLD, 24)); title.setHorizontalAlignment(javax.swing.SwingConstants.CENTER); title.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER); - title - .setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/moby.gif"))); + title.setIcon(new ImageIcon(getClass().getResource( + "/org/biomoby/client/gui/img/moby.gif"))); title.setOpaque(true); backgroundPane.add(title, java.awt.BorderLayout.NORTH); backgroundPane.add(getCenterPane(), java.awt.BorderLayout.CENTER); @@ -313,20 +314,24 @@ registerServiceType.setText("Create New Service Type"); registerServiceType.setCursor(new java.awt.Cursor( java.awt.Cursor.DEFAULT_CURSOR)); - registerServiceType.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/ComposeMail24.gif"))); + registerServiceType + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/ComposeMail24.gif"))); registerServiceType.setActionCommand("register"); registerServiceType .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { - + // check whether inputs is valid /* * data is an array of values: 0.service type name * 1.service type description 2.service type uri * 3.service type parent 4. valid email address */ - String[] data = { getNameTxtField().getText(), + String[] data = { + getNameTxtField().getText(), getDescTxtArea().getText(), getUriTxtField().getText(), getParentTextField().getText(), @@ -351,7 +356,7 @@ createPopUpMsg("Please enter a valid email address."); return; } - + Central worker = null; boolean success = false; String errorMsg = ""; @@ -560,8 +565,11 @@ private JButton getNamehelpBtn() { if (namehelpBtn == null) { namehelpBtn = new JButton(); - namehelpBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); + namehelpBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); namehelpBtn.setOpaque(false); namehelpBtn.setActionCommand("nameHelp"); namehelpBtn.setMaximumSize(new java.awt.Dimension(34, 26)); @@ -592,8 +600,11 @@ descHelpBtn.setMaximumSize(new java.awt.Dimension(34, 26)); descHelpBtn.setMinimumSize(new java.awt.Dimension(34, 26)); descHelpBtn.setOpaque(false); - descHelpBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); + descHelpBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); descHelpBtn.setActionCommand("descHelp"); descHelpBtn.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { @@ -619,8 +630,11 @@ emailHelpBtn.setMaximumSize(new java.awt.Dimension(34, 26)); emailHelpBtn.setMinimumSize(new java.awt.Dimension(34, 26)); emailHelpBtn.setOpaque(false); - emailHelpBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); + emailHelpBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); emailHelpBtn.setActionCommand("emailHelp"); emailHelpBtn.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { @@ -645,8 +659,11 @@ uriHelpBtn.setMaximumSize(new java.awt.Dimension(34, 26)); uriHelpBtn.setMinimumSize(new java.awt.Dimension(34, 26)); uriHelpBtn.setOpaque(false); - uriHelpBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); + uriHelpBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Help24.gif"))); uriHelpBtn.setActionCommand("uriHelp"); uriHelpBtn.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { @@ -686,8 +703,11 @@ chooseParentBtn = new JButton(); chooseParentBtn.setText("Choose Service Type Parent"); chooseParentBtn.setActionCommand("chooseParent"); - chooseParentBtn.setIcon(new ImageIcon(getClass().getResource( - "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Preferences24.gif"))); + chooseParentBtn + .setIcon(new ImageIcon( + getClass() + .getResource( + "/org/biomoby/client/gui/img/toolbarButtonGraphics/general/Preferences24.gif"))); chooseParentBtn.setOpaque(true); chooseParentBtn.setPreferredSize(new java.awt.Dimension(274, 27)); chooseParentBtn.setMinimumSize(new java.awt.Dimension(274, 27)); @@ -708,7 +728,8 @@ return; } frame = new JFrame("Service Type Chooser"); - JScrollPane scrollable = new JScrollPane(tree.getTree()); + JScrollPane scrollable = new JScrollPane(tree + .getTree()); frame.getContentPane().add(scrollable); frame .setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);

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