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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
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jprocter [Tue, 29 Nov 2005 16:21:37 +0000 (16:21 +0000)]
small updates.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@99
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jprocter [Tue, 29 Nov 2005 14:20:41 +0000 (14:20 +0000)]
untested vamsasArchive class with additional method for transferring data between session files.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@98
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jprocter [Wed, 23 Nov 2005 15:35:22 +0000 (15:35 +0000)]
basic logging configs.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@97
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jprocter [Wed, 23 Nov 2005 15:34:21 +0000 (15:34 +0000)]
using commons-logging for hierarchial control of logger.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@96
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jprocter [Wed, 23 Nov 2005 15:23:01 +0000 (15:23 +0000)]
use SessionFile constructor and added todo about java.nio file locking.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@95
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jprocter [Mon, 21 Nov 2005 17:49:19 +0000 (17:49 +0000)]
reorganising vamsasArchive (write to temp file, rather than write to original filename)
Added File constructor for sessionFile for convenience.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@94
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jprocter [Fri, 11 Nov 2005 18:12:50 +0000 (18:12 +0000)]
lost from new schema
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@93
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jprocter [Fri, 11 Nov 2005 18:07:39 +0000 (18:07 +0000)]
basics of arhiveWriter
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@92
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jprocter [Fri, 11 Nov 2005 18:05:29 +0000 (18:05 +0000)]
access for vamsas.xml style vamsas archive
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@91
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jprocter [Fri, 11 Nov 2005 18:03:57 +0000 (18:03 +0000)]
extended report of archive contents.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@90
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jprocter [Thu, 10 Nov 2005 11:23:30 +0000 (11:23 +0000)]
synchronized with last schema revision.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@89
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jprocter [Thu, 10 Nov 2005 11:22:12 +0000 (11:22 +0000)]
synchronized with last schema revision.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@88
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jprocter [Thu, 3 Nov 2005 14:10:01 +0000 (14:10 +0000)]
Vamsas Archive Reader and simple test class.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@87
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amwaterhouse [Thu, 3 Nov 2005 11:12:28 +0000 (11:12 +0000)]
Application data has choice of data or dataRef
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@86
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jprocter [Wed, 2 Nov 2005 16:11:46 +0000 (16:11 +0000)]
refactored common locked IO methods from ClientsFile to SessionFile
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@85
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jprocter [Wed, 2 Nov 2005 15:31:53 +0000 (15:31 +0000)]
doc comment about lock holding across session client processes.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@84
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jprocter [Wed, 2 Nov 2005 15:21:39 +0000 (15:21 +0000)]
propagate changes from schema update.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@83
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jprocter [Tue, 1 Nov 2005 17:42:25 +0000 (17:42 +0000)]
creates and holds all the watcher/io objects for a session.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@82
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jprocter [Tue, 1 Nov 2005 17:41:36 +0000 (17:41 +0000)]
partially updated comments (and repurposing of class).
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@81
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jprocter [Fri, 28 Oct 2005 16:03:13 +0000 (16:03 +0000)]
refactored documentHandler to VamsasFile to indicate similarity with ClientFile handler class.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@80
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amwaterhouse [Fri, 28 Oct 2005 12:50:10 +0000 (12:50 +0000)]
DatasetAnnotations begin and end set as integers
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@79
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jprocter [Thu, 27 Oct 2005 17:03:51 +0000 (17:03 +0000)]
javadoc typo
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@78
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jprocter [Tue, 25 Oct 2005 13:28:45 +0000 (13:28 +0000)]
added more extantLock methods and test for clientList monitoring (using FileWatcher.setState())
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@77
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jprocter [Mon, 24 Oct 2005 16:01:07 +0000 (16:01 +0000)]
typo fix.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@76
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jprocter [Mon, 24 Oct 2005 13:32:28 +0000 (13:32 +0000)]
new fileWatcher method passes lock for changed file back to the caller.
ClientsFile methods extended to take an existing lock as a parameter.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@75
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jprocter [Mon, 24 Oct 2005 13:31:23 +0000 (13:31 +0000)]
added automatic channel closure for failed locks. (suggest this class becomes a singleton?)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@74
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jprocter [Mon, 24 Oct 2005 10:10:02 +0000 (10:10 +0000)]
forgot to release a trial lock that failed.
Should consider automatically closing/releasing if lock fails.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@73
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jprocter [Sat, 22 Oct 2005 21:58:11 +0000 (21:58 +0000)]
debugged fileWatcher logic and Lock release function.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@72
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jprocter [Thu, 20 Oct 2005 16:51:28 +0000 (16:51 +0000)]
better time delay in command execution.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@71
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jprocter [Thu, 20 Oct 2005 10:16:16 +0000 (10:16 +0000)]
fixed change test.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@70
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jprocter [Thu, 20 Oct 2005 10:06:36 +0000 (10:06 +0000)]
better builder
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@69
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jprocter [Thu, 20 Oct 2005 10:00:35 +0000 (10:00 +0000)]
added better check for file change (length + last modified)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@68
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jprocter [Thu, 20 Oct 2005 09:58:13 +0000 (09:58 +0000)]
slackened lock_release success requirement.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@67
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amwaterhouse [Fri, 14 Oct 2005 15:45:59 +0000 (15:45 +0000)]
Dataset should not contain gaps
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@66
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jprocter [Wed, 12 Oct 2005 15:41:53 +0000 (15:41 +0000)]
franks data and topali analysis
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@65
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jprocter [Wed, 12 Oct 2005 15:36:46 +0000 (15:36 +0000)]
updated core objects from latest schema (dbRef)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@64
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amwaterhouse [Wed, 12 Oct 2005 10:57:01 +0000 (10:57 +0000)]
Dbref attributes are of type string
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@63
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jprocter [Wed, 12 Oct 2005 10:46:59 +0000 (10:46 +0000)]
modified FileWatcher to only register file change after a lock release (incurs a momentary file lock).
tested multi-process watching.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@62
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jprocter [Tue, 11 Oct 2005 21:15:55 +0000 (21:15 +0000)]
ClientsFileTest debugged and verified.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@61
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jprocter [Tue, 11 Oct 2005 17:35:29 +0000 (17:35 +0000)]
added test config for eclipse
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@60
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jprocter [Tue, 11 Oct 2005 17:34:09 +0000 (17:34 +0000)]
test clientsFile handlers.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@59
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jprocter [Tue, 11 Oct 2005 09:57:51 +0000 (09:57 +0000)]
quick update
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@58
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jprocter [Tue, 11 Oct 2005 09:57:32 +0000 (09:57 +0000)]
quick update
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@57
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jprocter [Sat, 8 Oct 2005 09:22:45 +0000 (09:22 +0000)]
accidental deletion of vamsas Client build config (now renamed)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@56
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jprocter [Fri, 7 Oct 2005 15:14:53 +0000 (15:14 +0000)]
random bits and pieces whilst in hamburg - beginnings of file handliongimpmementation.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@55
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amwaterhouse [Thu, 6 Oct 2005 15:54:00 +0000 (15:54 +0000)]
Provenance must contain 1 entry, Alignment may have multiple AlignmentAnnotations
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@54
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jprocter [Sun, 25 Sep 2005 19:02:11 +0000 (19:02 +0000)]
implemented state flags and automatic call to VorbaIdFactory for unregistered (but registerable) vamsas objects.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@53
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jprocter [Fri, 23 Sep 2005 17:43:17 +0000 (17:43 +0000)]
refactored schema (SequenceSet to DataSet and SequenceSetAnnotation to DataSetAnnotation).
More client implementation.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@52
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jprocter [Fri, 23 Sep 2005 09:19:39 +0000 (09:19 +0000)]
added a pollUpdate method to kick the vamsas Document watcher thread when the application wants to be immediatly informed of a document update.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@51
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jprocter [Thu, 22 Sep 2005 22:07:22 +0000 (22:07 +0000)]
event handler.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@50
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jprocter [Thu, 22 Sep 2005 21:58:56 +0000 (21:58 +0000)]
refactored Client to simpleClient. Implemented many housekeeping functions.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@49
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jprocter [Thu, 22 Sep 2005 16:17:33 +0000 (16:17 +0000)]
part implementation of simpleClient and refactoring of ClientDocument.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@48
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jprocter [Thu, 22 Sep 2005 09:56:36 +0000 (09:56 +0000)]
added sourcegen entry for the vamsasDocument.xsd objects.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@47
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jprocter [Thu, 22 Sep 2005 09:56:04 +0000 (09:56 +0000)]
created new schema to define the document XML file. Added two well formed schema examples.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@46
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jprocter [Tue, 20 Sep 2005 19:12:04 +0000 (19:12 +0000)]
made vamsas a proper root element in schema and added example document.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@45
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amwaterhouse [Tue, 20 Sep 2005 16:53:30 +0000 (16:53 +0000)]
Optional instead of min/max
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@44
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jprocter [Tue, 20 Sep 2005 16:41:10 +0000 (16:41 +0000)]
builder for eclipse
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@43
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jprocter [Tue, 20 Sep 2005 16:40:43 +0000 (16:40 +0000)]
changed vamsas.xsd filename.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@42
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jprocter [Tue, 20 Sep 2005 16:40:23 +0000 (16:40 +0000)]
transient file.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@41
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jprocter [Tue, 20 Sep 2005 16:38:27 +0000 (16:38 +0000)]
refactored to vamsas.xsd
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@40
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jprocter [Tue, 20 Sep 2005 16:37:09 +0000 (16:37 +0000)]
renamed.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@39
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jprocter [Tue, 20 Sep 2005 16:33:50 +0000 (16:33 +0000)]
latest schema.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@38
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jprocter [Tue, 20 Sep 2005 10:13:56 +0000 (10:13 +0000)]
objects from refactored schema.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@37
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jprocter [Tue, 20 Sep 2005 10:00:58 +0000 (10:00 +0000)]
move to new eclipse version.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@36
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jprocter [Tue, 20 Sep 2005 09:49:07 +0000 (09:49 +0000)]
updated builders
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@35
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jprocter [Tue, 20 Sep 2005 09:48:35 +0000 (09:48 +0000)]
more comments.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@34
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jprocter [Tue, 20 Sep 2005 09:42:33 +0000 (09:42 +0000)]
refactored tree type to avoid conflicts.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@33
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jprocter [Tue, 20 Sep 2005 09:42:13 +0000 (09:42 +0000)]
added source generator and builder
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@32
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jprocter [Mon, 19 Sep 2005 23:31:25 +0000 (23:31 +0000)]
updated to castor-0.9.9M2 and added some comments
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@31
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jprocter [Mon, 19 Sep 2005 23:26:31 +0000 (23:26 +0000)]
tried to resolve some namespace clashes and add xs:ID attributes where necessary.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@30
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jprocter [Mon, 19 Sep 2005 23:25:22 +0000 (23:25 +0000)]
updated to castor-0.9.9M2
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@29
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jprocter [Mon, 19 Sep 2005 18:16:16 +0000 (18:16 +0000)]
making more relocatable.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@28
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jprocter [Mon, 19 Sep 2005 18:13:52 +0000 (18:13 +0000)]
regenerate core objects
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@27
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jprocter [Mon, 19 Sep 2005 18:08:43 +0000 (18:08 +0000)]
renamed getId to avoid clashes.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@26
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jprocter [Mon, 19 Sep 2005 18:06:07 +0000 (18:06 +0000)]
changed sourcegenerator destination package
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@25
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jprocter [Mon, 19 Sep 2005 18:05:18 +0000 (18:05 +0000)]
refactored core objects and regenerated.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@24
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jprocter [Mon, 19 Sep 2005 16:19:59 +0000 (16:19 +0000)]
needed for castor sourcegenerator.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@23
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jprocter [Mon, 19 Sep 2005 16:19:41 +0000 (16:19 +0000)]
added castor sourcegenerator task.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@22
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jprocter [Mon, 19 Sep 2005 16:19:17 +0000 (16:19 +0000)]
default generation using sourcegen schema.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@21
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jprocter [Mon, 19 Sep 2005 14:19:27 +0000 (14:19 +0000)]
directory for runtime dependencies and non-java class data.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@20
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jprocter [Mon, 19 Sep 2005 14:15:55 +0000 (14:15 +0000)]
ant based sourcegen task
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@19
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jprocter [Mon, 19 Sep 2005 13:24:13 +0000 (13:24 +0000)]
log4j
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@18
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jprocter [Mon, 19 Sep 2005 13:20:36 +0000 (13:20 +0000)]
first attempt at object build.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@17
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jprocter [Mon, 19 Sep 2005 13:15:24 +0000 (13:15 +0000)]
latestish vamsas schema
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@16
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jprocter [Mon, 19 Sep 2005 13:14:58 +0000 (13:14 +0000)]
added a few more dependencies
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@15
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jprocter [Mon, 19 Sep 2005 13:13:07 +0000 (13:13 +0000)]
added comments concerning provenance
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@14
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jprocter [Mon, 19 Sep 2005 13:12:29 +0000 (13:12 +0000)]
added for generation of vamsas classes
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@13
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jprocter [Fri, 16 Sep 2005 15:26:43 +0000 (15:26 +0000)]
basic example application skeleton and SimpleClientFactory .
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@12
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jprocter [Fri, 16 Sep 2005 13:38:28 +0000 (13:38 +0000)]
LGPL from FSF site.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@11
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jprocter [Wed, 14 Sep 2005 16:24:26 +0000 (16:24 +0000)]
separate some interface methods into abstract classes to enforce access control
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@10
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jprocter [Wed, 14 Sep 2005 15:25:38 +0000 (15:25 +0000)]
object registration functions return an Id for the object.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@9
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jprocter [Wed, 14 Sep 2005 13:47:34 +0000 (13:47 +0000)]
renamed Iclient and others.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@8
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jprocter [Wed, 14 Sep 2005 13:41:41 +0000 (13:41 +0000)]
first version sent out to Iain and Pierre
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@7
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jprocter [Mon, 12 Sep 2005 09:36:10 +0000 (09:36 +0000)]
Initial revision
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@2
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jprocter [Mon, 12 Sep 2005 09:36:10 +0000 (09:36 +0000)]
New repository initialized by cvs2svn.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@1
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