vamsas.git
18 years agomore fixes for clientdocument/simpleclient. Testign the vamsasArchive reader and...
jprocter [Wed, 22 Mar 2006 17:04:50 +0000 (17:04 +0000)]
more fixes for clientdocument/simpleclient. Testign the vamsasArchive reader and sessionfile mechanism (windows patches)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@199 be28352e-c001-0410-b1a7-c7978e42abec

18 years agofinished the Appdata/ClientDocument update mechanism. Untested!
jprocter [Wed, 22 Mar 2006 14:12:54 +0000 (14:12 +0000)]
finished the Appdata/ClientDocument update mechanism. Untested!

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@198 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded new method for writing an AppData jar entry directly from an InputStream.
jprocter [Wed, 22 Mar 2006 14:12:12 +0000 (14:12 +0000)]
added new method for writing an AppData jar entry directly from an InputStream.
Also reprioritised some TODOs and made comments

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@197 be28352e-c001-0410-b1a7-c7978e42abec

18 years agointermediate cjeckin - nfs woes!
jprocter [Tue, 21 Mar 2006 17:18:41 +0000 (17:18 +0000)]
intermediate cjeckin - nfs woes!

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@196 be28352e-c001-0410-b1a7-c7978e42abec

18 years agorearranged some todos and preparing to implement SimpleClient and ClientDocument...
jprocter [Tue, 21 Mar 2006 11:59:49 +0000 (11:59 +0000)]
rearranged some todos and preparing to implement SimpleClient and ClientDocument IO stuff.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@195 be28352e-c001-0410-b1a7-c7978e42abec

18 years agorefactored generally useful higher level document IO methods to base class.
jprocter [Tue, 21 Mar 2006 11:58:54 +0000 (11:58 +0000)]
refactored generally useful higher level document IO methods to base class.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@194 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoSimpleClientAppdata implemented but untested.
jprocter [Mon, 20 Mar 2006 22:57:05 +0000 (22:57 +0000)]
SimpleClientAppdata implemented but untested.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@193 be28352e-c001-0410-b1a7-c7978e42abec

18 years agohalf implemented the SimpleClientAppdata interface.
jprocter [Mon, 20 Mar 2006 17:11:43 +0000 (17:11 +0000)]
half implemented the SimpleClientAppdata interface.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@192 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded for completeness, but may not be necessary.
jprocter [Mon, 20 Mar 2006 15:58:47 +0000 (15:58 +0000)]
added for completeness, but may not be necessary.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@191 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoAdd object casting for instrospection methods
pmarguerite [Mon, 20 Mar 2006 13:51:27 +0000 (13:51 +0000)]
Add object casting for instrospection methods

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@190 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoRemove local file Jim local file path for the current working directory.
pmarguerite [Mon, 20 Mar 2006 13:43:07 +0000 (13:43 +0000)]
Remove local file Jim local file path for the current working directory.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@189 be28352e-c001-0410-b1a7-c7978e42abec

18 years agodebugging the org.vamsas.client.SessionUrn selection mechanism (also partial bits...
jprocter [Mon, 20 Mar 2006 13:03:34 +0000 (13:03 +0000)]
debugging the org.vamsas.client.SessionUrn selection mechanism (also partial bits for simpleclientDocument stuff)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@188 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoremoved todo
jprocter [Sun, 19 Mar 2006 18:01:33 +0000 (18:01 +0000)]
removed todo

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@187 be28352e-c001-0410-b1a7-c7978e42abec

18 years agorenamed base class for all vamsas document objects (now org.vamsas.client.Vobject)
jprocter [Fri, 17 Mar 2006 09:27:31 +0000 (09:27 +0000)]
renamed base class for all vamsas document objects (now org.vamsas.client.Vobject)
there may be some incorrectly modified javadocs in unrelated files.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@186 be28352e-c001-0410-b1a7-c7978e42abec

18 years agochanged semaphore implementation and session modified flag.
jprocter [Thu, 16 Mar 2006 18:02:21 +0000 (18:02 +0000)]
changed semaphore implementation and session modified flag.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@185 be28352e-c001-0410-b1a7-c7978e42abec

18 years agosimplification of some events and clarification.
jprocter [Thu, 16 Mar 2006 18:00:51 +0000 (18:00 +0000)]
simplification of some events and clarification.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@184 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded simple semaphore file mechanism for session directory.
jprocter [Thu, 16 Mar 2006 12:16:43 +0000 (12:16 +0000)]
added simple semaphore file mechanism for session directory.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@183 be28352e-c001-0410-b1a7-c7978e42abec

18 years agonull sessionUrn parameter to create a new session
jprocter [Thu, 16 Mar 2006 11:18:02 +0000 (11:18 +0000)]
null sessionUrn parameter to create a new session

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@182 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadding various state flags for events
jprocter [Wed, 15 Mar 2006 19:35:11 +0000 (19:35 +0000)]
adding various state flags for events

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@181 be28352e-c001-0410-b1a7-c7978e42abec

18 years agopartly finished analysis of vamsas client session events.
jprocter [Tue, 14 Mar 2006 19:24:40 +0000 (19:24 +0000)]
partly finished analysis of vamsas client session events.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@180 be28352e-c001-0410-b1a7-c7978e42abec

18 years agopartly finished analysis of vamsas client session events.
jprocter [Tue, 14 Mar 2006 19:24:39 +0000 (19:24 +0000)]
partly finished analysis of vamsas client session events.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@179 be28352e-c001-0410-b1a7-c7978e42abec

18 years agotrivial typo
jprocter [Tue, 14 Mar 2006 18:47:43 +0000 (18:47 +0000)]
trivial typo

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@178 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoextended clientfactory interface for session discovery and default session connection
jprocter [Tue, 14 Mar 2006 18:25:13 +0000 (18:25 +0000)]
extended clientfactory interface for session discovery and default session connection

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@177 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoreprioritising TODOs and LATERs and fixing documentation typos.
jprocter [Tue, 14 Mar 2006 17:59:32 +0000 (17:59 +0000)]
reprioritising TODOs and LATERs and fixing documentation typos.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@176 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoremoved unnecessary createdummyVamsasDocument private method.
jprocter [Tue, 24 Jan 2006 19:34:48 +0000 (19:34 +0000)]
removed unnecessary createdummyVamsasDocument private method.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@175 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoinitial org.vamsas.client.IClientAppData implementation phase.
jprocter [Tue, 24 Jan 2006 19:31:49 +0000 (19:31 +0000)]
initial org.vamsas.client.IClientAppData implementation phase.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@174 be28352e-c001-0410-b1a7-c7978e42abec

18 years agofixed a slight bug in AppData entry searching, and introduced generic AppData entry...
jprocter [Tue, 24 Jan 2006 19:31:24 +0000 (19:31 +0000)]
fixed a slight bug in AppData entry searching, and introduced generic AppData entry searching methods.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@173 be28352e-c001-0410-b1a7-c7978e42abec

18 years agointroduced org.vamsas.client.IClientAppData interface to get and set app-global and...
jprocter [Tue, 24 Jan 2006 19:23:12 +0000 (19:23 +0000)]
introduced org.vamsas.client.IClientAppData interface to get and set app-global and user-specific appdata chunks.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@172 be28352e-c001-0410-b1a7-c7978e42abec

18 years agofixed probable bug
jprocter [Tue, 24 Jan 2006 16:40:47 +0000 (16:40 +0000)]
fixed probable bug

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@171 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoupdated example application to handle IClient.getDocument() exceptions and ensured...
jprocter [Tue, 24 Jan 2006 16:29:56 +0000 (16:29 +0000)]
updated example application to handle IClient.getDocument() exceptions and ensured IVorbaIdFactory actually has object reference for the object it is registering.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@170 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoparameterised the default empty document construction
jprocter [Tue, 24 Jan 2006 15:16:26 +0000 (15:16 +0000)]
parameterised the default empty document construction

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@169 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoSimpleClient creates dummy documents.
jprocter [Tue, 24 Jan 2006 14:56:22 +0000 (14:56 +0000)]
SimpleClient creates dummy documents.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@168 be28352e-c001-0410-b1a7-c7978e42abec

18 years agonote about making default provenance entries at same time as ensuring all Vorba Ids...
jprocter [Tue, 24 Jan 2006 14:49:18 +0000 (14:49 +0000)]
note about making default provenance entries at same time as ensuring all Vorba Ids are made.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@167 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoimplementing minimal set : SimpleClientFactory createSession method -> SimpleClient...
jprocter [Mon, 23 Jan 2006 19:10:43 +0000 (19:10 +0000)]
implementing minimal set : SimpleClientFactory createSession method -> SimpleClient -> SimpleDocument + events.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@166 be28352e-c001-0410-b1a7-c7978e42abec

18 years agobeginning refactoring of locked IO for lists.
jprocter [Mon, 23 Jan 2006 14:14:59 +0000 (14:14 +0000)]
beginning refactoring of locked IO for lists.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@165 be28352e-c001-0410-b1a7-c7978e42abec

18 years agobeginning refactoring of locked IO for lists.
jprocter [Mon, 23 Jan 2006 14:14:45 +0000 (14:14 +0000)]
beginning refactoring of locked IO for lists.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@164 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoclarified the getSessionUrn function and added new importDocument method
jprocter [Mon, 23 Jan 2006 10:54:24 +0000 (10:54 +0000)]
clarified the getSessionUrn function and added new importDocument method

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@163 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded some more comments about event types/implementation
jprocter [Mon, 23 Jan 2006 10:53:19 +0000 (10:53 +0000)]
added some more comments about event types/implementation

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@162 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded asFile method to get urn path as a file object.
jprocter [Mon, 23 Jan 2006 10:52:24 +0000 (10:52 +0000)]
added asFile method to get urn path as a file object.
Need to fix this to deal with local/non local urns.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@161 be28352e-c001-0410-b1a7-c7978e42abec

18 years agourn classes for different kinds of vamsas object.
jprocter [Mon, 23 Jan 2006 10:34:06 +0000 (10:34 +0000)]
urn classes for different kinds of vamsas object.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@160 be28352e-c001-0410-b1a7-c7978e42abec

18 years agourn classes for different kinds of vamsas object.
jprocter [Mon, 23 Jan 2006 10:13:23 +0000 (10:13 +0000)]
urn classes for different kinds of vamsas object.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@159 be28352e-c001-0410-b1a7-c7978e42abec

18 years agopartially implemented simpleclient.EventGenerator
jprocter [Fri, 20 Jan 2006 18:03:29 +0000 (18:03 +0000)]
partially implemented simpleclient.EventGenerator

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@158 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded Appender for the VAMSAS session.
jprocter [Fri, 20 Jan 2006 18:01:37 +0000 (18:01 +0000)]
added Appender for the VAMSAS session.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@157 be28352e-c001-0410-b1a7-c7978e42abec

18 years agocomments and removed spurious todo:
jprocter [Fri, 20 Jan 2006 16:19:45 +0000 (16:19 +0000)]
comments and removed spurious todo:

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@156 be28352e-c001-0410-b1a7-c7978e42abec

18 years agotidying IO.
jprocter [Fri, 20 Jan 2006 15:22:15 +0000 (15:22 +0000)]
tidying IO.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@155 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded overwrite flag to VamsasArchive writer class (avoids loss of locks on file...
jprocter [Fri, 20 Jan 2006 12:00:23 +0000 (12:00 +0000)]
added overwrite flag to VamsasArchive writer class (avoids loss of locks on file deletion)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@154 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoVamsasArchive tested. Locked IO routines to be implemented in ArchiveFile
jprocter [Fri, 20 Jan 2006 11:05:28 +0000 (11:05 +0000)]
VamsasArchive tested. Locked IO routines to be implemented in ArchiveFile

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@153 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoremoved after schema modification,
jprocter [Fri, 20 Jan 2006 09:57:33 +0000 (09:57 +0000)]
removed after schema modification,

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@152 be28352e-c001-0410-b1a7-c7978e42abec

18 years agomore locked IO performance tests.
jprocter [Fri, 20 Jan 2006 08:50:30 +0000 (08:50 +0000)]
more locked IO performance tests.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@151 be28352e-c001-0410-b1a7-c7978e42abec

18 years agointroduced locked IO testing for Archive IO
jprocter [Thu, 19 Jan 2006 18:17:31 +0000 (18:17 +0000)]
introduced locked IO testing for Archive IO

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@150 be28352e-c001-0410-b1a7-c7978e42abec

18 years agostarted on ClientDocument implementation and Locked IO tests for VamsasArchive
jprocter [Thu, 19 Jan 2006 18:17:04 +0000 (18:17 +0000)]
started on ClientDocument implementation and Locked IO tests for VamsasArchive

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@149 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded skeleton class for vorbaId methods and comments
jprocter [Thu, 19 Jan 2006 18:15:51 +0000 (18:15 +0000)]
added skeleton class for vorbaId methods and comments

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@148 be28352e-c001-0410-b1a7-c7978e42abec

18 years agotodo
jprocter [Thu, 19 Jan 2006 13:32:33 +0000 (13:32 +0000)]
todo

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@147 be28352e-c001-0410-b1a7-c7978e42abec

18 years agomoved IClientDocument implementation into the simpleclient package.
jprocter [Thu, 19 Jan 2006 12:12:42 +0000 (12:12 +0000)]
moved IClientDocument implementation into the simpleclient package.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@146 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoset correct get/Set VamsasRoots type, added addVamsasRoot, and some more TODOs
jprocter [Thu, 19 Jan 2006 12:12:04 +0000 (12:12 +0000)]
set correct get/Set VamsasRoots type, added addVamsasRoot, and some more TODOs

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@145 be28352e-c001-0410-b1a7-c7978e42abec

18 years agogeneralised ArchiveReports functions to output on any stream.
jprocter [Thu, 19 Jan 2006 11:51:36 +0000 (11:51 +0000)]
generalised ArchiveReports functions to output on any stream.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@144 be28352e-c001-0410-b1a7-c7978e42abec

18 years agocomments - explanation of bad heuristic that has to be fixed.
jprocter [Thu, 19 Jan 2006 11:31:56 +0000 (11:31 +0000)]
comments - explanation of bad heuristic that has to be fixed.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@143 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded and tested simple document handling and update with test.ArchiveWriter.
jprocter [Tue, 17 Jan 2006 16:41:34 +0000 (16:41 +0000)]
added and tested simple document handling and update with test.ArchiveWriter.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@142 be28352e-c001-0410-b1a7-c7978e42abec

18 years agodebugged VamsasArchive and rationalised debugging messages.
jprocter [Tue, 17 Jan 2006 12:17:30 +0000 (12:17 +0000)]
debugged VamsasArchive and rationalised debugging messages.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@141 be28352e-c001-0410-b1a7-c7978e42abec

18 years agofixed the User element and the form of the ApplicationData dataType.xsd definition.
jprocter [Tue, 17 Jan 2006 10:37:39 +0000 (10:37 +0000)]
fixed the User element and the form of the ApplicationData dataType.xsd definition.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@140 be28352e-c001-0410-b1a7-c7978e42abec

18 years agofound cyclic dependency problems in schema and in VorbaId mechanism.
jprocter [Mon, 16 Jan 2006 20:25:49 +0000 (20:25 +0000)]
found cyclic dependency problems in schema and in VorbaId mechanism.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@139 be28352e-c001-0410-b1a7-c7978e42abec

18 years agominimally debugged idFactory and vorbaId mechanism. Inelegant!
jprocter [Mon, 16 Jan 2006 20:05:03 +0000 (20:05 +0000)]
minimally debugged idFactory and vorbaId mechanism. Inelegant!

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@138 be28352e-c001-0410-b1a7-c7978e42abec

18 years agotypo
jprocter [Mon, 16 Jan 2006 11:19:16 +0000 (11:19 +0000)]
typo

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@137 be28352e-c001-0410-b1a7-c7978e42abec

18 years agochanged textual references for Class.class initializer for commons-logger
jprocter [Mon, 16 Jan 2006 10:25:52 +0000 (10:25 +0000)]
changed textual references for Class.class initializer for commons-logger

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@136 be28352e-c001-0410-b1a7-c7978e42abec

18 years agorefactored - Vorba object binding machinery and interfaces live in org.vamsas.client...
jprocter [Mon, 16 Jan 2006 10:14:00 +0000 (10:14 +0000)]
refactored - Vorba object binding machinery and interfaces live in org.vamsas.client, specific clients now live in their own package.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@135 be28352e-c001-0410-b1a7-c7978e42abec

18 years agodebug as far as test marshalling - a vorbaIdFactory is now required.
jprocter [Mon, 16 Jan 2006 09:37:30 +0000 (09:37 +0000)]
debug as far as test marshalling - a vorbaIdFactory is now required.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@134 be28352e-c001-0410-b1a7-c7978e42abec

18 years agodebugging.
jprocter [Sun, 15 Jan 2006 17:58:35 +0000 (17:58 +0000)]
debugging.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@133 be28352e-c001-0410-b1a7-c7978e42abec

18 years agodebugging.
jprocter [Sun, 15 Jan 2006 17:58:15 +0000 (17:58 +0000)]
debugging.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@132 be28352e-c001-0410-b1a7-c7978e42abec

18 years agominimal log.info output for commons-logging (commented out the specific org.vamsas...
jprocter [Sun, 15 Jan 2006 16:04:22 +0000 (16:04 +0000)]
minimal log.info output for commons-logging (commented out the specific org.vamsas logger so root logger takes precedence only)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@131 be28352e-c001-0410-b1a7-c7978e42abec

18 years agomore verbose reports and demo VamsasDocument testing
jprocter [Sun, 15 Jan 2006 13:18:21 +0000 (13:18 +0000)]
more verbose reports and demo VamsasDocument testing

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@130 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoControlled versionString vocabulary, newVamsasDocument construction methods and newAl...
jprocter [Sun, 15 Jan 2006 13:17:45 +0000 (13:17 +0000)]
Controlled versionString vocabulary, newVamsasDocument construction methods and newAlignmentSequence methods

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@129 be28352e-c001-0410-b1a7-c7978e42abec

18 years agosave on nasty svn conflicts.
jprocter [Fri, 13 Jan 2006 18:21:29 +0000 (18:21 +0000)]
save on nasty svn conflicts.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@128 be28352e-c001-0410-b1a7-c7978e42abec

18 years agogit-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@127 be28352e-c001...
jprocter [Fri, 13 Jan 2006 18:14:40 +0000 (18:14 +0000)]
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@127 be28352e-c001-0410-b1a7-c7978e42abec

18 years agowhere packaged build will go
jprocter [Fri, 13 Jan 2006 18:14:04 +0000 (18:14 +0000)]
where packaged build will go

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@126 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoeclipse builder
jprocter [Fri, 13 Jan 2006 18:13:30 +0000 (18:13 +0000)]
eclipse builder

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@125 be28352e-c001-0410-b1a7-c7978e42abec

18 years agorefactored and incorporated basic io routines from vamsas web services stack.
jprocter [Fri, 13 Jan 2006 17:36:29 +0000 (17:36 +0000)]
refactored and incorporated basic io routines from vamsas web services stack.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@124 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoimported from the old vamsas webservices datatypes and adapted for new
jprocter [Fri, 13 Jan 2006 16:35:54 +0000 (16:35 +0000)]
imported from the old vamsas webservices datatypes and adapted for new

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@123 be28352e-c001-0410-b1a7-c7978e42abec

18 years agobasic class defining symbol dictionaries
jprocter [Fri, 13 Jan 2006 16:35:09 +0000 (16:35 +0000)]
basic class defining symbol dictionaries

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@122 be28352e-c001-0410-b1a7-c7978e42abec

18 years agomore plus added VAMAS: tag for a policy decision
jprocter [Fri, 13 Jan 2006 16:09:34 +0000 (16:09 +0000)]
more plus added VAMAS: tag for a policy decision

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@121 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded command line definition
jprocter [Fri, 13 Jan 2006 16:05:24 +0000 (16:05 +0000)]
added command line definition

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@120 be28352e-c001-0410-b1a7-c7978e42abec

18 years agocomments
jprocter [Fri, 13 Jan 2006 15:52:34 +0000 (15:52 +0000)]
comments

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@119 be28352e-c001-0410-b1a7-c7978e42abec

18 years agotrivial
jprocter [Fri, 13 Jan 2006 15:50:56 +0000 (15:50 +0000)]
trivial

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@118 be28352e-c001-0410-b1a7-c7978e42abec

18 years agotrivial doc
jprocter [Fri, 13 Jan 2006 15:33:21 +0000 (15:33 +0000)]
trivial doc

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@117 be28352e-c001-0410-b1a7-c7978e42abec

18 years agopackage for testing the core objects and their helper classes
jprocter [Fri, 13 Jan 2006 15:26:52 +0000 (15:26 +0000)]
package for testing the core objects and their helper classes

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@116 be28352e-c001-0410-b1a7-c7978e42abec

18 years agogit-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@115 be28352e-c001...
jprocter [Fri, 13 Jan 2006 15:24:25 +0000 (15:24 +0000)]
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@115 be28352e-c001-0410-b1a7-c7978e42abec

18 years agosome test data
jprocter [Fri, 13 Jan 2006 15:23:24 +0000 (15:23 +0000)]
some test data

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@114 be28352e-c001-0410-b1a7-c7978e42abec

18 years agosimple VamsasArchive testing class.
jprocter [Fri, 13 Jan 2006 15:10:15 +0000 (15:10 +0000)]
simple VamsasArchive testing class.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@113 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoschema update
jprocter [Fri, 13 Jan 2006 15:05:08 +0000 (15:05 +0000)]
schema update

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@112 be28352e-c001-0410-b1a7-c7978e42abec

18 years agomethods for making and accessing objects in org.vamsa.objects.core
jprocter [Fri, 13 Jan 2006 15:04:06 +0000 (15:04 +0000)]
methods for making and accessing objects in org.vamsa.objects.core

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@111 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded getOriginalRoots() method for current archive.
jprocter [Fri, 13 Jan 2006 14:53:54 +0000 (14:53 +0000)]
added getOriginalRoots() method for current archive.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@110 be28352e-c001-0410-b1a7-c7978e42abec

18 years agosynchronizing commit
jprocter [Fri, 13 Jan 2006 14:53:22 +0000 (14:53 +0000)]
synchronizing commit

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@109 be28352e-c001-0410-b1a7-c7978e42abec

18 years agorefactored standard static 'ArchiveReports' into their own class.
jprocter [Fri, 13 Jan 2006 14:06:39 +0000 (14:06 +0000)]
refactored standard static 'ArchiveReports' into their own class.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@108 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoextracted serial command processing for use by other test classes
jprocter [Fri, 13 Jan 2006 14:06:10 +0000 (14:06 +0000)]
extracted serial command processing for use by other test classes

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@107 be28352e-c001-0410-b1a7-c7978e42abec

18 years agosynchronized AppData parsing stuff with new AppData entry (embedded/references)
jprocter [Fri, 13 Jan 2006 12:37:21 +0000 (12:37 +0000)]
synchronized AppData parsing stuff with new AppData entry (embedded/references)
 - this is untested at the mo.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@106 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded a couple of TODO: entries.
jprocter [Fri, 13 Jan 2006 12:36:40 +0000 (12:36 +0000)]
added a couple of TODO: entries.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@105 be28352e-c001-0410-b1a7-c7978e42abec

18 years agopartially implemented ArchiveWriter test class (routines will form basis of Get/Set...
jprocter [Fri, 13 Jan 2006 12:34:03 +0000 (12:34 +0000)]
partially implemented ArchiveWriter test class (routines will form basis of Get/Set clientDocument stuff)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@104 be28352e-c001-0410-b1a7-c7978e42abec

19 years agoadded OriginalArchiveReader access method and helper method for updating archives.
jprocter [Wed, 30 Nov 2005 18:06:50 +0000 (18:06 +0000)]
added OriginalArchiveReader access method and helper method for updating archives.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@103 be28352e-c001-0410-b1a7-c7978e42abec

19 years agowrapper class to prevent client from closing JarOutputStream when it closes the AppDa...
jprocter [Wed, 30 Nov 2005 18:06:04 +0000 (18:06 +0000)]
wrapper class to prevent client from closing JarOutputStream when it closes the AppData writing stream.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@102 be28352e-c001-0410-b1a7-c7978e42abec

19 years agoSwitched xs:base64encoded and xs:String for type of AppData and AppDataReference.
jprocter [Wed, 30 Nov 2005 14:44:54 +0000 (14:44 +0000)]
Switched xs:base64encoded and xs:String for type of AppData and AppDataReference.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@101 be28352e-c001-0410-b1a7-c7978e42abec

19 years agoprobably deprecating this class.
jprocter [Tue, 29 Nov 2005 16:33:04 +0000 (16:33 +0000)]
probably deprecating this class.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@100 be28352e-c001-0410-b1a7-c7978e42abec