vamsas.git
17 years agorefactoring org to uk - never use f**ng eclipse
jprocter [Thu, 14 Dec 2006 18:49:07 +0000 (18:49 +0000)]
refactoring org to uk - never use f**ng eclipse

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@292 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:48:08 +0000 (18:48 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@291 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:47:51 +0000 (18:47 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@290 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:47:18 +0000 (18:47 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@289 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:43:00 +0000 (18:43 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@288 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:42:43 +0000 (18:42 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@287 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:41:20 +0000 (18:41 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@286 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:40:16 +0000 (18:40 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@285 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:39:48 +0000 (18:39 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@284 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:27:53 +0000 (18:27 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@283 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:27:16 +0000 (18:27 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@282 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:26:15 +0000 (18:26 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@281 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:20:51 +0000 (18:20 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@280 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:18:43 +0000 (18:18 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@279 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:18:26 +0000 (18:18 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@278 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactoring org to uk
jprocter [Thu, 14 Dec 2006 18:17:24 +0000 (18:17 +0000)]
refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@277 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored org to uk
jprocter [Thu, 14 Dec 2006 18:16:54 +0000 (18:16 +0000)]
refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@276 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored org to uk
jprocter [Thu, 14 Dec 2006 18:16:15 +0000 (18:16 +0000)]
refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@275 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored org to uk
jprocter [Thu, 14 Dec 2006 18:16:14 +0000 (18:16 +0000)]
refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@274 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored org to uk
jprocter [Thu, 14 Dec 2006 18:08:11 +0000 (18:08 +0000)]
refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@273 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored org to uk
jprocter [Thu, 14 Dec 2006 18:05:40 +0000 (18:05 +0000)]
refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@272 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored org to uk
jprocter [Thu, 14 Dec 2006 17:54:15 +0000 (17:54 +0000)]
refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@271 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored org to uk
jprocter [Thu, 14 Dec 2006 17:52:40 +0000 (17:52 +0000)]
refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@270 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored org to uk
jprocter [Thu, 14 Dec 2006 17:52:15 +0000 (17:52 +0000)]
refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@269 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored org to uk
jprocter [Thu, 14 Dec 2006 17:51:17 +0000 (17:51 +0000)]
refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@268 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored org to uk
jprocter [Thu, 14 Dec 2006 17:50:39 +0000 (17:50 +0000)]
refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@267 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored org to uk
jprocter [Thu, 14 Dec 2006 17:50:38 +0000 (17:50 +0000)]
refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@266 be28352e-c001-0410-b1a7-c7978e42abec

17 years agobroken refactoring
jprocter [Thu, 14 Dec 2006 17:44:21 +0000 (17:44 +0000)]
broken refactoring

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@265 be28352e-c001-0410-b1a7-c7978e42abec

17 years agobacktrack
jprocter [Thu, 14 Dec 2006 17:42:54 +0000 (17:42 +0000)]
backtrack

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@264 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored from org.vamsas to uk.ac.vamsas
jprocter [Thu, 14 Dec 2006 17:15:29 +0000 (17:15 +0000)]
refactored from org.vamsas to uk.ac.vamsas

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@263 be28352e-c001-0410-b1a7-c7978e42abec

17 years agogit-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@262 be28352e-c001...
jprocter [Thu, 14 Dec 2006 17:11:07 +0000 (17:11 +0000)]
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@262 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored from org.vamsas to uk.ac.vamsas
jprocter [Thu, 14 Dec 2006 17:08:32 +0000 (17:08 +0000)]
refactored from org.vamsas to uk.ac.vamsas

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@261 be28352e-c001-0410-b1a7-c7978e42abec

17 years agoremove old ebi packages
jprocter [Thu, 14 Dec 2006 16:40:55 +0000 (16:40 +0000)]
remove old ebi packages

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@260 be28352e-c001-0410-b1a7-c7978e42abec

17 years agoquick commit before refactoring
jprocter [Thu, 14 Dec 2006 16:21:49 +0000 (16:21 +0000)]
quick commit before refactoring

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@259 be28352e-c001-0410-b1a7-c7978e42abec

17 years agoadded SimpleClientFactory implementation and new class SessionsFile to deal with...
pmarguerite [Thu, 14 Dec 2006 16:19:27 +0000 (16:19 +0000)]
added SimpleClientFactory implementation  and new class SessionsFile to deal with the list of active sessions

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@258 be28352e-c001-0410-b1a7-c7978e42abec

17 years agoUpdated docs and logging for the picking api.
imilne [Thu, 14 Dec 2006 16:15:36 +0000 (16:15 +0000)]
Updated docs and logging for the picking api.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@257 be28352e-c001-0410-b1a7-c7978e42abec

17 years agomodifiable attribute is now a string rather than a boolean. See 'locks' type document...
jprocter [Thu, 14 Dec 2006 12:26:59 +0000 (12:26 +0000)]
modifiable attribute is now a string rather than a boolean. See 'locks' type documentation in vamsas.xsd

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@256 be28352e-c001-0410-b1a7-c7978e42abec

17 years agoPicking code updated with full basic implementation of message sending and server...
imilne [Thu, 14 Dec 2006 11:56:17 +0000 (11:56 +0000)]
Picking code updated with full basic implementation of message sending and server restart code.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@255 be28352e-c001-0410-b1a7-c7978e42abec

17 years agorefactored mapping to mapList type in both DbRef and SeqType object.
jprocter [Thu, 14 Dec 2006 10:25:25 +0000 (10:25 +0000)]
refactored mapping to mapList type in both DbRef and SeqType object.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@254 be28352e-c001-0410-b1a7-c7978e42abec

17 years agoFirst check-in of the picking api.
imilne [Wed, 13 Dec 2006 17:03:37 +0000 (17:03 +0000)]
First check-in of the picking api.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@253 be28352e-c001-0410-b1a7-c7978e42abec

17 years agoIObjectUpdate interface introduction.
jprocter [Wed, 13 Dec 2006 16:45:02 +0000 (16:45 +0000)]
IObjectUpdate interface introduction.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@252 be28352e-c001-0410-b1a7-c7978e42abec

17 years agoMapping element added
amwaterhouse [Wed, 13 Dec 2006 16:32:21 +0000 (16:32 +0000)]
Mapping element added

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@251 be28352e-c001-0410-b1a7-c7978e42abec

17 years agofirst round of todos for codefest
jprocter [Tue, 12 Dec 2006 23:52:36 +0000 (23:52 +0000)]
first round of todos for codefest

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@250 be28352e-c001-0410-b1a7-c7978e42abec

17 years agobasic ideas for per-object update interface
jprocter [Tue, 12 Dec 2006 23:49:50 +0000 (23:49 +0000)]
basic ideas for per-object update interface

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@249 be28352e-c001-0410-b1a7-c7978e42abec

17 years agoadded todo for making library automatically construct the user handle
jprocter [Tue, 12 Dec 2006 23:43:21 +0000 (23:43 +0000)]
added todo for making library automatically construct the user handle

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@248 be28352e-c001-0410-b1a7-c7978e42abec

17 years agonew stuff for vamsas hack.
jprocter [Tue, 12 Dec 2006 11:02:13 +0000 (11:02 +0000)]
new stuff for vamsas hack.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@247 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoshow vamsasId for aligments.
jprocter [Sun, 17 Sep 2006 14:42:32 +0000 (14:42 +0000)]
show vamsasId for aligments.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@246 be28352e-c001-0410-b1a7-c7978e42abec

18 years agotidier file locks - lock file is removed on JVM exit.
jprocter [Sun, 17 Sep 2006 14:42:13 +0000 (14:42 +0000)]
tidier file locks - lock file is removed on JVM exit.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@245 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoensured that hash binding vorbaIds is passed to client document object for vorba...
jprocter [Sun, 17 Sep 2006 14:41:31 +0000 (14:41 +0000)]
ensured that hash binding vorbaIds is passed to client document object for vorba object lookup methods.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@244 be28352e-c001-0410-b1a7-c7978e42abec

18 years agojalview'esque vamsas session example for org.vamsas.test.simpleclient.ArchiveClient...
jprocter [Wed, 13 Sep 2006 14:25:32 +0000 (14:25 +0000)]
jalview'esque vamsas session example for org.vamsas.test.simpleclient.ArchiveClient test model.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@243 be28352e-c001-0410-b1a7-c7978e42abec

18 years agobug fix to ensure valid and vorbaIds are generated and stored in vamsas object model
jprocter [Wed, 13 Sep 2006 14:24:57 +0000 (14:24 +0000)]
bug fix to ensure valid and vorbaIds are generated and stored in vamsas object model

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@242 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoobjects regenerated with valid schema (without excess id field cancelled in previous...
jprocter [Tue, 12 Sep 2006 10:20:55 +0000 (10:20 +0000)]
objects regenerated with valid schema (without excess id field cancelled in previous commit)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@241 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoremoved excess id field (cancels previous commit)
jprocter [Tue, 12 Sep 2006 10:19:48 +0000 (10:19 +0000)]
removed excess id field (cancels previous commit)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@240 be28352e-c001-0410-b1a7-c7978e42abec

18 years agobugfixed org.vamsas.test.simpleclient.ArchiveClient and made VorbaId mechanism more...
jprocter [Tue, 12 Sep 2006 10:07:11 +0000 (10:07 +0000)]
bugfixed org.vamsas.test.simpleclient.ArchiveClient and made VorbaId mechanism more rigorous.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@239 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded id for RangeAnnotation types.
jprocter [Tue, 12 Sep 2006 10:04:04 +0000 (10:04 +0000)]
added id for RangeAnnotation types.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@238 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoAdded a javadoc Ant build task.
imilne [Fri, 8 Sep 2006 12:12:01 +0000 (12:12 +0000)]
Added a javadoc Ant build task.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@237 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded V_parent reference to parent object in document.
jprocter [Wed, 6 Sep 2006 13:43:37 +0000 (13:43 +0000)]
added V_parent reference to parent object in document.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@236 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoenum constants for Glyph types.
jprocter [Tue, 5 Sep 2006 09:50:42 +0000 (09:50 +0000)]
enum constants for Glyph types.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@235 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoupdated test cases for spring 2006 schema, and major debug of locking system
jprocter [Fri, 1 Sep 2006 17:02:21 +0000 (17:02 +0000)]
updated test cases for spring 2006 schema, and major debug of locking system

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@234 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded some example logging configs
jprocter [Fri, 1 Sep 2006 17:01:10 +0000 (17:01 +0000)]
added some example logging configs

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@233 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoupdated binding with castor-1.0.2
jprocter [Fri, 1 Sep 2006 17:00:47 +0000 (17:00 +0000)]
updated binding with castor-1.0.2

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@232 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoJava binding for new document schema (from 1st hinxton vamsas Meeting)
jprocter [Fri, 1 Sep 2006 16:57:38 +0000 (16:57 +0000)]
Java binding for new document schema (from 1st hinxton vamsas Meeting)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@231 be28352e-c001-0410-b1a7-c7978e42abec

18 years agointroducing Lock File based locking (for portability) - part implemented.
jprocter [Wed, 24 May 2006 13:32:33 +0000 (13:32 +0000)]
introducing Lock File based locking (for portability) - part implemented.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@230 be28352e-c001-0410-b1a7-c7978e42abec

18 years agochanges propagated from Provenance.App entry.
jprocter [Wed, 24 May 2006 13:30:43 +0000 (13:30 +0000)]
changes propagated from Provenance.App entry.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@229 be28352e-c001-0410-b1a7-c7978e42abec

18 years agochanges propagated from Provenance.App entry.
jprocter [Wed, 24 May 2006 13:30:25 +0000 (13:30 +0000)]
changes propagated from Provenance.App entry.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@228 be28352e-c001-0410-b1a7-c7978e42abec

18 years agorefactored uri type to a link element and replaced type references with element refer...
jprocter [Mon, 22 May 2006 16:31:32 +0000 (16:31 +0000)]
refactored uri type to a link element and replaced type references with element references.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@227 be28352e-c001-0410-b1a7-c7978e42abec

18 years agorefactored uri type to a link element and replaced type references with element refer...
jprocter [Mon, 22 May 2006 16:29:12 +0000 (16:29 +0000)]
refactored uri type to a link element and replaced type references with element references.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@226 be28352e-c001-0410-b1a7-c7978e42abec

18 years agofixed loss of plural alignmentannotation in new schema version
jprocter [Mon, 22 May 2006 16:27:33 +0000 (16:27 +0000)]
fixed loss of plural alignmentannotation in new schema version

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@225 be28352e-c001-0410-b1a7-c7978e42abec

18 years agorefactored uri type to a link element and replaced type references with element refer...
jprocter [Mon, 22 May 2006 16:17:30 +0000 (16:17 +0000)]
refactored uri type to a link element and replaced type references with element references.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@224 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoautogenerated java classes for current schema
jprocter [Mon, 22 May 2006 15:59:40 +0000 (15:59 +0000)]
autogenerated java classes for current schema

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@223 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded 'attachment' element example.
jprocter [Mon, 22 May 2006 15:50:38 +0000 (15:50 +0000)]
added 'attachment' element example.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@222 be28352e-c001-0410-b1a7-c7978e42abec

18 years agopost-meeting refinements and commenting.
jprocter [Mon, 22 May 2006 15:50:20 +0000 (15:50 +0000)]
post-meeting refinements and commenting.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@221 be28352e-c001-0410-b1a7-c7978e42abec

18 years agostill refactoring the rangeType and features/annotation elements.
jprocter [Fri, 19 May 2006 16:53:59 +0000 (16:53 +0000)]
still refactoring the rangeType and features/annotation elements.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@220 be28352e-c001-0410-b1a7-c7978e42abec

18 years agocurrent vamsas type document. Still being worked on and refined.
jprocter [Thu, 18 May 2006 17:01:14 +0000 (17:01 +0000)]
current vamsas type document. Still being worked on and refined.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@219 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded registration/object retrieval methods to ClientDoc.
jprocter [Mon, 27 Mar 2006 12:18:18 +0000 (12:18 +0000)]
added registration/object retrieval methods to ClientDoc.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@218 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoIncorrect bounds for Provenance type in Dataset.DatasetAnnotations. (could have an...
jprocter [Mon, 27 Mar 2006 12:17:43 +0000 (12:17 +0000)]
Incorrect bounds for Provenance type in Dataset.DatasetAnnotations. (could have an array of provenance arrays).

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@217 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoIncorrect bounds for Provenance type in Dataset.DatasetAnnotations. (could have an...
jprocter [Mon, 27 Mar 2006 11:46:41 +0000 (11:46 +0000)]
Incorrect bounds for Provenance type in Dataset.DatasetAnnotations. (could have an array of provenance arrays).

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@216 be28352e-c001-0410-b1a7-c7978e42abec

18 years agodebugged the runnable main for ArchiveClient. ClientDoc provides api returned by...
jprocter [Sun, 26 Mar 2006 17:08:41 +0000 (17:08 +0000)]
debugged the runnable main for ArchiveClient. ClientDoc provides api returned by ArchiveClient.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@215 be28352e-c001-0410-b1a7-c7978e42abec

18 years agolatest version is Beta. but we might change this :)
jprocter [Sun, 26 Mar 2006 17:07:33 +0000 (17:07 +0000)]
latest version is Beta. but we might change this :)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@214 be28352e-c001-0410-b1a7-c7978e42abec

18 years agoadded new constructor and File object accessor to make VamsasFile usable with VamsasA...
jprocter [Sun, 26 Mar 2006 17:06:51 +0000 (17:06 +0000)]
added new constructor and File object accessor to make VamsasFile usable with VamsasArchive.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@213 be28352e-c001-0410-b1a7-c7978e42abec

18 years agofixed (hopefully) locking/read problems in test.simpleclient.VamsasArchive/Watcher...
jprocter [Fri, 24 Mar 2006 19:16:26 +0000 (19:16 +0000)]
fixed (hopefully) locking/read problems in test.simpleclient.VamsasArchive/Watcher classes and commented out the RandomAccess based reading/writing for mo.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@212 be28352e-c001-0410-b1a7-c7978e42abec

18 years agofixed leaky lock (answers todo about verifying that channel.close() should be called...
jprocter [Fri, 24 Mar 2006 19:13:22 +0000 (19:13 +0000)]
fixed leaky lock (answers todo about verifying that channel.close() should be called before lock.release())

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@211 be28352e-c001-0410-b1a7-c7978e42abec

18 years agonew target - jar, and added an 'exclude' for Pierre's java5 vamav code (for the moment)
jprocter [Fri, 24 Mar 2006 19:04:20 +0000 (19:04 +0000)]
new target - jar, and added an 'exclude' for Pierre's java5 vamav code (for the moment)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@210 be28352e-c001-0410-b1a7-c7978e42abec

18 years agosimple test of locked IO based on ArchiveWatcher. Extend this to quickly incorporate...
jprocter [Fri, 24 Mar 2006 19:03:00 +0000 (19:03 +0000)]
simple test of locked IO based on ArchiveWatcher. Extend this to quickly incorporate vamsas dataset updates into a program (? really)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@209 be28352e-c001-0410-b1a7-c7978e42abec

18 years agocommented out stream constructor for vamsasArchive.
jprocter [Fri, 24 Mar 2006 19:01:45 +0000 (19:01 +0000)]
commented out stream constructor for vamsasArchive.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@208 be28352e-c001-0410-b1a7-c7978e42abec

18 years agovamsas api example classes - AstexViewer@MSD-EBI
pmarguerite [Fri, 24 Mar 2006 15:40:31 +0000 (15:40 +0000)]
vamsas api example classes - AstexViewer@MSD-EBI

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@207 be28352e-c001-0410-b1a7-c7978e42abec

18 years agodeveloping streamReader tests.
jprocter [Fri, 24 Mar 2006 10:21:36 +0000 (10:21 +0000)]
developing streamReader tests.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@206 be28352e-c001-0410-b1a7-c7978e42abec

18 years agostill dealing with JarInputStream issues.
jprocter [Thu, 23 Mar 2006 19:27:57 +0000 (19:27 +0000)]
still dealing with JarInputStream issues.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@205 be28352e-c001-0410-b1a7-c7978e42abec

18 years agofixed exception when trying to cancel unwritten archives.
jprocter [Thu, 23 Mar 2006 14:13:46 +0000 (14:13 +0000)]
fixed exception when trying to cancel unwritten archives.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@204 be28352e-c001-0410-b1a7-c7978e42abec

18 years agodebug output - just incase strange things are happening when trying to read jars
jprocter [Thu, 23 Mar 2006 14:10:51 +0000 (14:10 +0000)]
debug output - just incase strange things are happening when trying to read jars

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@203 be28352e-c001-0410-b1a7-c7978e42abec

18 years agofix call of the argument parsing - '!' missing
pmarguerite [Thu, 23 Mar 2006 13:48:35 +0000 (13:48 +0000)]
fix call of the argument parsing - '!' missing

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@202 be28352e-c001-0410-b1a7-c7978e42abec

18 years agolocking for windows (XP) partly debugged. ClientsFileTest watchers do not behave...
jprocter [Thu, 23 Mar 2006 11:41:09 +0000 (11:41 +0000)]
locking for windows (XP) partly debugged. ClientsFileTest watchers do not behave perfectly yet.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@201 be28352e-c001-0410-b1a7-c7978e42abec

18 years ago'!' missing for testing if the session directory is readeable.
pmarguerite [Wed, 22 Mar 2006 17:29:00 +0000 (17:29 +0000)]
'!' missing for testing if the session directory is readeable.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@200 be28352e-c001-0410-b1a7-c7978e42abec

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