Timeline



Nov 2, 2007:

12:01 PM Changeset [3904] by Nicklas Nordborg
References #746:Transfer existing UML diagrams to latest MagicDraw?

Nov 1, 2007:

2:50 PM WikiStart edited by Jari Häkkinen
Clarified GPL license version. (diff)
2:46 PM Changeset [3903] by Nicklas Nordborg
Recommend Postgres users to use at least 8.2
1:09 PM Changeset [3902] by Nicklas Nordborg
Added svndigest:ignore to testdata directory
11:33 AM Changeset [3901] by Nicklas Nordborg
References #746: Transfer existing UML diagrams to latest MagicDraw?
11:33 AM Changeset [3900] by Nicklas Nordborg
Fixes #612: Add checks in the core so that unsaved objects are not …
11:33 AM Ticket #612 (Add checks in the core so that unsaved objects are not used in queries.) closed by Nicklas Nordborg
fixed: (In [3900]) Fixes #612: Add checks in the core so that unsaved objects …
11:17 AM Changeset [3899] by Nicklas Nordborg
References #721: Store data in files instead of in the database …
9:20 AM WikiStart edited by Jari Häkkinen
Clarified GPL license version. (diff)
8:15 AM Changeset [3898] by Nicklas Nordborg
References #806: Experimental factor values display on Experiment page …

Oct 31, 2007:

3:59 PM Changeset [3897] by Martin Svensson
References #809 Described available services and describe how to …
2:12 PM Changeset [3896] by Nicklas Nordborg
References #746: Transfer existing UML diagrams to latest MagicDraw?
1:34 PM DownloadPage edited by Jari Häkkinen
Releasing 2.4.5 (diff)
1:01 PM Changeset [3895] by Jari Häkkinen
Changes for future release 2.4.6
12:52 PM Changeset [3894] by Jari Häkkinen
Tagging version 2.4.5
12:52 PM Milestone BASE 2.4.5 completed
Revision Log: log:branches/2.4-stable@3856:3893
12:51 PM Changeset [3893] by Jari Häkkinen
Preparing release 2.4.5

Oct 30, 2007:

2:33 PM Ticket #524 (Read "Overview of user documentation" section) closed by Nicklas Nordborg
fixed: (In [3892]) Fixes #524: Read "Overview of user documentation" section
2:33 PM Changeset [3892] by Nicklas Nordborg
Fixes #524: Read "Overview of user documentation" section
1:58 PM Changeset [3891] by Nicklas Nordborg
References #746: Transfer existing UML diagrams to latest MagicDraw?
10:49 AM Changeset [3890] by Nicklas Nordborg
Fixes #707: Can't unlink items that have been put in the trashcan
10:49 AM Ticket #707 (Can't unlink items that have been put in the trashcan) closed by Nicklas Nordborg
fixed: (In [3890]) Fixes #707: Can't unlink items that have been put in the …

Oct 29, 2007:

2:08 PM Ticket #810 (Implement query options for Include.ANNOTATED and Include.NOT_ANNOTATED) created by Nicklas Nordborg
The core already defines the two query options, …
2:03 PM Changeset [3889] by Nicklas Nordborg
References #411: Extending compressed file support and storage …
2:00 PM Changeset [3888] by Nicklas Nordborg
References #707: Can't unlink items that have been put in the trashcan …
9:45 AM Changeset [3887] by Nicklas Nordborg
References #797: Enhance performance for LOWESS and Median-ratio …
8:36 AM Changeset [3886] by Martin Svensson
Replaced old jar-file and updated classpaths

Oct 27, 2007:

4:37 PM Changeset [3885] by Martin Svensson
References #809

Oct 26, 2007:

4:20 PM Changeset [3884] by Martin Svensson
References #809 Documentation of base web services has begun. …
1:40 PM Ticket #809 (Read Web services documentation) created by Martin Svensson
Read documentation about BASE web services …
1:29 PM Changeset [3883] by Nicklas Nordborg
Fixes #808: Remove Thread.sleep() from HibernateUtil?.loadIterator
1:29 PM Ticket #808 (Remove Thread.sleep() from HibernateUtil.loadIterator) closed by Nicklas Nordborg
fixed: (In [3883]) Fixes #808: Remove Thread.sleep() from …
1:21 PM Changeset [3882] by Nicklas Nordborg
References #808: Remove Thread.sleep() from HibernateUtil?.loadIterator …
1:19 PM Ticket #808 (Remove Thread.sleep() from HibernateUtil.loadIterator) created by Nicklas Nordborg
http://base.thep.lu.se/browser/tags/2.4.4/src/core/net/sf/basedb/core/H
12:41 PM Changeset [3881] by Martin Svensson
References #492 WSDL files are now generated when running ant-target …
11:08 AM Changeset [3880] by Nicklas Nordborg
Added column to Jobs list that displays running time (in minutes and …
11:01 AM Ticket #797 (Enhance performance for LOWESS and Medin-ratio plug-ins) closed by Nicklas Nordborg
fixed: (In [3879]) Fixes #797: Enhance performance for LOWESS and Medin-ratio …
11:01 AM Changeset [3879] by Nicklas Nordborg
Fixes #797: Enhance performance for LOWESS and Medin-ratio plug-ins

Oct 25, 2007:

11:57 AM Changeset [3878] by Nicklas Nordborg
References #797: Enhance performance for LOWESS and Median-ratio …
9:57 AM Changeset [3877] by Nicklas Nordborg
References #797: Enhance performance for LOWESS and Medin-ratio …

Oct 24, 2007:

4:58 PM Changeset [3876] by Martin Svensson
References #492 Tests for webservices completed. Fixed the bugs that …
12:53 PM Ticket #806 (Experimental factor values display on Experiment page can only display ...) closed by Nicklas Nordborg
fixed: (In [3875]) Fixes #806: Experimental factor values display on …
12:53 PM Changeset [3875] by Nicklas Nordborg
Fixes #806: Experimental factor values display on Experiment page can …

Oct 23, 2007:

4:48 PM Changeset [3874] by Martin Svensson
References #492 Creating tests for webservices
2:15 PM Changeset [3873] by Nicklas Nordborg
References #721, fixes #789: Extended test program to include more …
2:15 PM Ticket #789 (Extend "Experiment overview" to check for problems related to platform ...) closed by Nicklas Nordborg
fixed: (In [3873]) References #721, fixes #789: Extended test program to …
9:54 AM Changeset [3872] by Nicklas Nordborg
References #807: Doc is now read for reading

Oct 22, 2007:

2:27 PM Ticket #591 (Add option to stop a plug-in from beeing executed by the internal job queue) closed by Nicklas Nordborg
fixed
2:21 PM Changeset [3871] by Nicklas Nordborg
Fixes #595: Add option to stop a plug-in from beeing executed by the …

Oct 20, 2007:

3:30 AM WikiStart edited by Peter Johansson
typo (diff)

Oct 19, 2007:

4:25 PM Changeset [3870] by Nicklas Nordborg
Added section about class loading issues in plug-in developer section.
3:01 PM Changeset [3869] by Nicklas Nordborg
References #807 Added documentation for plug-in developers.
2:59 PM Ticket #807 (Read documentation related to ticket #721: Store data in files instead ...) created by Nicklas Nordborg
This affects several sections: * User documentation about platforms: …
1:10 PM Changeset [3868] by Nicklas Nordborg
References #360: Make subsections on view pages hideable * Added …
11:49 AM Changeset [3867] by Nicklas Nordborg
References #721: Store data in files instead of in the database * …
9:28 AM Changeset [3866] by Nicklas Nordborg
References #364: Support for automatic install of non-core plugins …
9:20 AM Changeset [3865] by Nicklas Nordborg
References #721: Create doc/html/userdoc/platforms directory to make …
8:06 AM Changeset [3864] by Nicklas Nordborg
References #805: Add syntax coloring to code examples in docbook Fix …

Oct 18, 2007:

5:18 PM Changeset [3863] by Jari Häkkinen
Fixing link to baseplugins web site.
5:18 PM Changeset [3862] by Jari Häkkinen
Fixing link to baseplugins web site.
4:33 PM Changeset [3861] by Martin Svensson
References #492 Added Services for RawBioAssay? and ArrayDesign?. Each …
2:59 PM Changeset [3860] by Nicklas Nordborg
References #721: Started to update the docbook documentation with …
12:03 PM Changeset [3859] by Nicklas Nordborg
References #789: Extend "Experiment overview" to check for problems …
9:40 AM WikiStart edited by Nicklas Nordborg
Changed link to BASE plug-ins web site (diff)

Oct 17, 2007:

7:15 PM Changeset [3858] by Nicklas Nordborg
References #794: Additional fix needed in trunk due to API changes in …
1:39 PM Ticket #806 (Experimental factor values display on Experiment page can only display ...) created by Nicklas Nordborg
Problem was posted on the mailing list: >> >> We are trying to …
12:41 PM Changeset [3857] by Jari Häkkinen
Merged patch release 2.4.4 to the trunk. Delta 2.4.4 - 2.4.3
11:58 AM DownloadPage edited by Jari Häkkinen
Releasing 2.4.4 (diff)
11:30 AM Changeset [3856] by Jari Häkkinen
Changes for future release 2.4.5
11:27 AM Changeset [3855] by Jari Häkkinen
Tagging version 2.4.4
11:27 AM Milestone BASE 2.4.4 completed
Revision Log: log:branches/2.4-stable@3788:3854
11:20 AM Changeset [3854] by Jari Häkkinen
Preparing release 2.4.4
11:18 AM Ticket #796 (Don't create indexes on primary key columns for tables in the dynamic ...) closed by Jari Häkkinen
fixed: The tests shows that the fixes improve performance, i.e., creation of …
11:14 AM Ticket #751 (Fail to delete item from table view) closed by Nicklas Nordborg
invalid: Seems to have been caused by Tomcat being overloaded.
11:09 AM Ticket #737 (Script that fixes copyright text may also add extra new line to end of ...) closed by Jari Häkkinen
invalid: This was an issue here for the affected files, but the problem belongs …
11:04 AM Ticket #748 (MeV application fail to load data) closed by Jari Häkkinen
worksforme
10:25 AM Changeset [3853] by Jari Häkkinen
Fixes #768.
10:25 AM Ticket #768 (Add information about running reporter update after migration if needed) closed by Jari Häkkinen
fixed: (In [3853]) Fixes #768.
9:58 AM Changeset [3852] by Nicklas Nordborg
References #721: Auto-detect function is now aware of FileStoreEnabled?
8:56 AM Changeset [3851] by Nicklas Nordborg
References #721: Filter on file extension when selecting platform data …
8:45 AM Changeset [3850] by Nicklas Nordborg
References #788: Select project default platforms / variant The …
8:29 AM Changeset [3849] by Martin Svensson
References #492 Updating license information and 3rd party components
8:17 AM Changeset [3848] by Nicklas Nordborg
References #721: Can now edit raw bioassays, array designs and …
7:52 AM Ticket #788 (Select project default platforms / variant) closed by Nicklas Nordborg
fixed: (In [3847]) Fixes #788: Select project default platforms / variant
7:52 AM Changeset [3847] by Nicklas Nordborg
Fixes #788: Select project default platforms / variant

Oct 16, 2007:

10:23 PM Ticket #804 (Add links to example code in the Plugins section of the documentation) closed by Nicklas Nordborg
worksforme: It is section 23.7: …
4:52 PM Changeset [3846] by Martin Svensson
References #492 Copying webservices into trunk
3:18 PM Changeset [3845] by Martin Svensson
References #492 Copying webservices into trunk
3:12 PM Changeset [3844] by Martin Svensson
References #492 Copying webservices into trunk
2:51 PM Changeset [3843] by Martin Svensson
References #492 Copying webservices into trunk
2:50 PM Changeset [3842] by Martin Svensson
References #492 Copying webservices into trunk
2:44 PM Changeset [3841] by Martin Svensson
References #492 Copying webservices into trunk
1:50 PM Changeset [3840] by Jari Häkkinen
Fixes #667.
1:50 PM Ticket #667 (Move ch. 7 to a lower level) closed by Jari Häkkinen
fixed: (In [3840]) Fixes #667.
1:41 PM Changeset [3839] by Martin Svensson
References #492 Updated javadoc
1:38 PM Changeset [3838] by Nicklas Nordborg
Fixes #805: Add syntax coloring to code examples in docbook
1:38 PM Ticket #805 (Add syntax coloring to code examples in docbook) closed by Nicklas Nordborg
fixed: (In [3838]) Fixes #805: Add syntax coloring to code examples in docbook
1:38 PM Ticket #805 (Add syntax coloring to code examples in docbook) created by Nicklas Nordborg
10:43 AM Ticket #804 (Add links to example code in the Plugins section of the documentation) created by Jari Häkkinen
It may already exist but this needs t be checked.
10:40 AM Ticket #730 (Documentation figures should be centered by default) closed by Jari Häkkinen
worksforme

Oct 15, 2007:

7:43 PM Changeset [3837] by Nicklas Nordborg
No longer implement the FilenameFilter? interface since it couldn't be …
2:58 PM Changeset [3836] by Martin Svensson
References #492 A BioAssaySet? can now be downloaded in MeV-format …
2:26 PM Changeset [3835] by Nicklas Nordborg
References #721. Updated documentation.
1:55 PM Changeset [3834] by Martin Svensson
Export methods that take an OutputStream? as a parameter are now public …
9:36 AM Changeset [3833] by Nicklas Nordborg
Updated "Development ideas" with information about already implemented …
9:25 AM Changeset [3832] by Nicklas Nordborg
References #364. * Test program now looks for the test plug-ins: …
8:27 AM Changeset [3831] by Martin Svensson
References #492 Updated copyright statement

Oct 13, 2007:

12:48 AM Changeset [3830] by Jari Häkkinen
Adding files that was not merged from trunk previously.

Oct 12, 2007:

11:08 PM Changeset [3829] by Jari Häkkinen
Fixing copyright statement.
11:07 PM Changeset [3828] by Jari Häkkinen
Fixing svn properties and eol characters.
9:04 PM Changeset [3827] by Jari Häkkinen
Merged log:trunk#3795:3824 into webservices branch.
4:09 PM Changeset [3826] by Martin Svensson
References #492 Extended the services for bioassaysets. A download …
3:06 PM Changeset [3825] by Nicklas Nordborg
Fixes #803: Experiment overview is broken if protocols with …
3:06 PM Ticket #803 (Experiment overview is broken if protocols with non-predefined ...) closed by Nicklas Nordborg
fixed: (In [3825]) Fixes #803: Experiment overview is broken if protocols …
2:57 PM Ticket #803 (Experiment overview is broken if protocols with non-predefined ...) created by Nicklas Nordborg
A predefined protocol type is a protocol type which has a system ID. …
2:47 PM Changeset [3824] by Nicklas Nordborg
Fixes #802: Migration should attach data files to array design and raw …
2:47 PM Ticket #802 (Migration should attach data files to array design and raw bioassays) closed by Nicklas Nordborg
fixed: (In [3824]) Fixes #802: Migration should attach data files to array …
1:46 PM Changeset [3823] by Jari Häkkinen
Fixed spelling on the word 'everything'.
12:27 PM Changeset [3822] by Nicklas Nordborg
Fixes #801: Code for the "Recently viewed items" menu is unstable when …
12:27 PM Ticket #801 (Code for the "Recently viewed items" menu is unstable when data is in ...) closed by Nicklas Nordborg
fixed: (In [3822]) Fixes #801: Code for the "Recently viewed items" menu is …
12:10 PM Ticket #802 (Migration should attach data files to array design and raw bioassays) created by Nicklas Nordborg
Depends on #721. This information has not been possible to transfer to …
12:04 PM Changeset [3821] by Nicklas Nordborg
Delete filedb branch since it has now been merged into the trunk
12:03 PM Changeset [3820] by Nicklas Nordborg
Merged branches/filedb into trunk.
11:30 AM Changeset [3819] by Nicklas Nordborg
Merged log:trunk#3795:3815 into filedb branch
11:14 AM Changeset [3818] by Nicklas Nordborg
References #721: Store data in files instead of in the database * …

Oct 11, 2007:

7:32 PM Ticket #801 (Code for the "Recently viewed items" menu is unstable when data is in ...) created by Nicklas Nordborg
I have the following setup: […] Without changing anything, today …
3:38 PM Changeset [3817] by Nicklas Nordborg
References #721: Store data in files instead of in the database * …

Oct 10, 2007:

5:32 PM Ticket #800 (Make the Illumina importer accept tab as data delimiter and comma as ...) created by base
My Illumina files are not comma separted but tab separeted. Can you …
4:48 PM Changeset [3816] by Martin Svensson
References #492 Start working on services for BioAssaySets? and added a …
2:58 PM Changeset [3815] by Martin Svensson
Fixes #799. The same bug was found when BASE tries to look in the …
2:58 PM Ticket #799 (External plugin installer fails when jars don't have base-plugin.xml) closed by Martin Svensson
fixed: (In [3815]) Fixes #799. The same bug was found when BASE tries to look …
2:57 PM Changeset [3814] by Nicklas Nordborg
References #721: Store data in files instead of in the database * …
2:30 PM Ticket #799 (External plugin installer fails when jars don't have base-plugin.xml) created by Martin Svensson
1:44 PM Changeset [3813] by Martin Svensson
References #492 -Made it possible to send restrictions and …
11:46 AM Changeset [3812] by Nicklas Nordborg
References #721: Store data in files instead of in the database * …

Oct 9, 2007:

7:13 PM Ticket #798 (Stopping job agent should stop jobs gracefully and set status killed ...) closed by Nicklas Nordborg
duplicate: Duplicate of #636.
4:21 PM Ticket #798 (Stopping job agent should stop jobs gracefully and set status killed ...) created by Jari Häkkinen
2:15 PM Changeset [3811] by Nicklas Nordborg
References #796: Don't create indexes on primary key columns for …
12:06 PM Changeset [3810] by Nicklas Nordborg
References #796: Don't create indexes on primary key columns for …
9:47 AM Ticket #797 (Enhance performance for LOWESS and Medin-ratio plug-ins) created by Nicklas Nordborg
The performance tests (#294) shows that the LOWESS plug-in has bad …
9:38 AM Ticket #796 (Don't create indexes on primary key columns for tables in the dynamic ...) created by Nicklas Nordborg
The performance testing (#294) discovered that a lot of indexes are …

Oct 8, 2007:

12:17 PM Changeset [3809] by Nicklas Nordborg
Fixes #793: Job agent get logged out when waiting for a job to finish …
12:17 PM Ticket #793 (Job agent get logged out when waiting for a job to finish) closed by Nicklas Nordborg
fixed: (In [3809]) Fixes #793: Job agent get logged out when waiting for a …
11:25 AM Ticket #794 (Long query may cause session to timeout) closed by Nicklas Nordborg
fixed: (In [3808]) Fixes #794: Long query may cause session to timeout
11:25 AM Changeset [3808] by Nicklas Nordborg
Fixes #794: Long query may cause session to timeout
7:49 AM Ticket #795 (Base1PluginExecuter throw PermissionDeniedException: Data cube has ...) created by Nicklas Nordborg
I'm running base-2.4.2 on tomcat 6.0.14. I'm running a base1 plugin. …
3:50 AM ReleaseProcedure edited by Peter Johansson
fixed typo (diff)

Oct 5, 2007:

3:36 PM Changeset [3807] by Nicklas Nordborg
References #721: Most things for attaching files to rw bioassays are …
1:12 PM Changeset [3806] by Jari Häkkinen
Fixed typo.

Oct 4, 2007:

4:33 PM Changeset [3805] by Martin Svensson
References #492 Added a basic support for includes in queries and …
2:25 PM Changeset [3804] by Nicklas Nordborg
References #721: Most things for attaching files to array designs are …

Oct 3, 2007:

4:33 PM Changeset [3803] by Martin Svensson
References #492 Updated Axis2 from 1.1 to 1.3
1:58 PM Changeset [3802] by Nicklas Nordborg
References #721: File validation is now in place. More robust code for …
8:46 AM Ticket #794 (Long query may cause session to timeout) created by Nicklas Nordborg
If a client application executes a query that takes a long time …
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