source.jalview.org Git - vamsas.git/log

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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jprocter [Mon, 16 Jan 2006 11:19:16 +0000 (11:19 +0000)]

typo

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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

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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

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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

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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

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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

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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

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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

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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

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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

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jprocter [Fri, 13 Jan 2006 18:14:40 +0000 (18:14 +0000)]

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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

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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

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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

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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

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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

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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

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jprocter [Fri, 13 Jan 2006 16:05:24 +0000 (16:05 +0000)]

added command line definition

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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

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

trivial

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jprocter [Fri, 13 Jan 2006 15:33:21 +0000 (15:33 +0000)]

trivial doc

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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

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jprocter [Fri, 13 Jan 2006 15:24:25 +0000 (15:24 +0000)]

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jprocter [Fri, 13 Jan 2006 15:23:24 +0000 (15:23 +0000)]

some test data

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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

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jprocter [Fri, 13 Jan 2006 15:05:08 +0000 (15:05 +0000)]

schema update

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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

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jprocter [Fri, 13 Jan 2006 14:53:54 +0000 (14:53 +0000)]

added getOriginalRoots() method for current archive.

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jprocter [Fri, 13 Jan 2006 14:53:22 +0000 (14:53 +0000)]

synchronizing commit

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jprocter [Fri, 13 Jan 2006 14:06:39 +0000 (14:06 +0000)]

refactored standard static 'ArchiveReports' into their own class.

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jprocter [Fri, 13 Jan 2006 14:06:10 +0000 (14:06 +0000)]

extracted serial command processing for use by other test classes

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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.

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jprocter [Fri, 13 Jan 2006 12:36:40 +0000 (12:36 +0000)]

added a couple of TODO: entries.

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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

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jprocter [Wed, 30 Nov 2005 18:06:50 +0000 (18:06 +0000)]

added OriginalArchiveReader access method and helper method for updating archives.

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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.

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jprocter [Wed, 30 Nov 2005 14:44:54 +0000 (14:44 +0000)]

Switched xs:base64encoded and xs:String for type of AppData and AppDataReference.

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jprocter [Tue, 29 Nov 2005 16:33:04 +0000 (16:33 +0000)]

probably deprecating this class.

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jprocter [Tue, 29 Nov 2005 16:21:37 +0000 (16:21 +0000)]

small updates.

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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.

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jprocter [Wed, 23 Nov 2005 15:35:22 +0000 (15:35 +0000)]

basic logging configs.

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jprocter [Wed, 23 Nov 2005 15:34:21 +0000 (15:34 +0000)]

using commons-logging for hierarchial control of logger.

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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.

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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.

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jprocter [Fri, 11 Nov 2005 18:12:50 +0000 (18:12 +0000)]

lost from new schema

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jprocter [Fri, 11 Nov 2005 18:07:39 +0000 (18:07 +0000)]

basics of arhiveWriter

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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 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 11 Nov 2005 18:03:57 +0000 (18:03 +0000)]

extended report of archive contents.

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jprocter [Thu, 10 Nov 2005 11:23:30 +0000 (11:23 +0000)]

synchronized with last schema revision.

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jprocter [Thu, 10 Nov 2005 11:22:12 +0000 (11:22 +0000)]

synchronized with last schema revision.

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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 be28352e-c001-0410-b1a7-c7978e42abec

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amwaterhouse [Thu, 3 Nov 2005 11:12:28 +0000 (11:12 +0000)]

Application data has choice of data or dataRef

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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 be28352e-c001-0410-b1a7-c7978e42abec

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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.

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jprocter [Wed, 2 Nov 2005 15:21:39 +0000 (15:21 +0000)]

propagate changes from schema update.

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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.

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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 be28352e-c001-0410-b1a7-c7978e42abec

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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 be28352e-c001-0410-b1a7-c7978e42abec

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amwaterhouse [Fri, 28 Oct 2005 12:50:10 +0000 (12:50 +0000)]

DatasetAnnotations begin and end set as integers

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jprocter [Thu, 27 Oct 2005 17:03:51 +0000 (17:03 +0000)]

javadoc typo

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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 be28352e-c001-0410-b1a7-c7978e42abec

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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 be28352e-c001-0410-b1a7-c7978e42abec