Timeline



Mar 4, 2008:

8:14 PM WikiStart edited by Peter Johansson
fixing broken links (diff)
2:50 PM Changeset [4169] by Nicklas Nordborg
References #436: Create extension system for the web application …
2:49 PM Changeset [4168] by Nicklas Nordborg
References #436: Create extension system for the web application …
1:09 PM ReleaseProcedure edited by Nicklas Nordborg
Change links to subversion repository (diff)
1:05 PM DownloadPage edited by Nicklas Nordborg
Change links to subversion repository (diff)
1:01 PM WikiStart edited by Nicklas Nordborg
Change image urls (diff)

Mar 3, 2008:

9:20 AM Ticket #941 (SQLException when exporting "merged on reporters" with BioAssaySet ...) closed by Nicklas Nordborg
fixed: (In [4167]) Fixes #941: SQLException when exporting "merged on …
9:20 AM Changeset [4167] by Nicklas Nordborg
Fixes #941: SQLException when exporting "merged on reporters" with …
8:43 AM Changeset [4166] by Nicklas Nordborg
Fixes #938: BioAssaySetExporter?: last line can have missing columns
8:43 AM Ticket #938 (BioAssaySetExporter: last line can have missing columns) closed by Nicklas Nordborg
fixed: (In [4166]) Fixes #938: BioAssaySetExporter?: last line can have …
8:33 AM Ticket #942 (BioAssaySetExporter should export ratio values instead of log-ratio ...) closed by Nicklas Nordborg
fixed: (In [4165]) Fixes #942: BioAssaySetExporter? should export ratio values …
8:33 AM Changeset [4165] by Nicklas Nordborg
Fixes #942: BioAssaySetExporter? should export ratio values instead of …
8:09 AM Ticket #942 (BioAssaySetExporter should export ratio values instead of log-ratio ...) created by Nicklas Nordborg
MeV expects ratio-values. Using the "Launch MeV" tool in BASE loads …

Feb 29, 2008:

1:48 PM Ticket #941 (SQLException when exporting "merged on reporters" with BioAssaySet ...) created by Nicklas Nordborg
This may be related to #939, but I am not sure. In any case, here is …
8:18 AM Ticket #940 (Can't generate web services wsdl files with ant 1.7) closed by Nicklas Nordborg
fixed: (In [4164]) Fixes #940: Can't generate web services wsdl files with ant 1.7
8:18 AM Changeset [4164] by Nicklas Nordborg
Fixes #940: Can't generate web services wsdl files with ant 1.7

Feb 28, 2008:

8:16 PM Ticket #940 (Can't generate web services wsdl files with ant 1.7) created by Nicklas Nordborg
Compiling BASE with ant 1.7.0 fails when generating wsdl files. The …
5:09 PM Ticket #939 (BioAssaySetExporter doesn't export BASEfiles for multiple array ...) created by base
I am finding problems with BASEfile export, averaged over reporter or …
2:33 PM Ticket #938 (BioAssaySetExporter: last line can have missing columns) created by base
This little bug was preventing base1 hierarchical clustering (due to …
10:54 AM Changeset [4163] by Nicklas Nordborg
References #436: Create extension system for the web application The …

Feb 26, 2008:

7:54 PM Changeset [4162] by Nicklas Nordborg
References #937: Spelling of method name: Xml --> XML
1:28 PM Changeset [4161] by Nicklas Nordborg
Merged log:trunk#4159:4160 into extensions branch
1:21 PM Changeset [4160] by Nicklas Nordborg
Fixes #937: Extend XMLUtil with methods that can validate an XML file …
1:21 PM Ticket #937 (Extend XMLUtil with methods that can validate an XML file agains a ...) closed by Nicklas Nordborg
fixed: (In [4160]) Fixes #937: Extend XMLUtil with methods that can validate …
11:55 AM Ticket #937 (Extend XMLUtil with methods that can validate an XML file agains a ...) created by Nicklas Nordborg
This is needed for the the xml files used by the Extensions API (see …
10:59 AM ReleaseProcedure edited by Jari Häkkinen
Added document generation note for trac. (diff)

Feb 25, 2008:

5:56 PM Ticket #935 (jobagent status) closed by Johan Enell
invalid: Because I was testing my script on a server that was to old…
12:01 PM Ticket #936 (Clearer exception from jobagent) closed by Nicklas Nordborg
worksforme: This is probably because the log4j has been configured to print log …
11:40 AM Ticket #936 (Clearer exception from jobagent) created by Johan Enell
When doing a 'jobagent.sh info' on a jobagent I get a ConnectException?
11:32 AM Ticket #935 (jobagent status) created by Johan Enell
The documentation about jobagent.sh describes the command status but …
11:01 AM Changeset [4159] by Johan Enell
Changes for future release 2.6.1
10:54 AM Milestone BASE 2.6 completed
The major aim with this milestone is to fix all issues related to …
10:54 AM DownloadPage edited by Johan Enell
(diff)
10:52 AM DownloadPage edited by Johan Enell
(diff)
10:52 AM DownloadPage edited by Johan Enell
added the .0 (diff)
10:50 AM DownloadPage edited by Johan Enell
added 2.6 release (diff)

Feb 22, 2008:

2:47 PM Changeset [4158] by Nicklas Nordborg
References #436: Create extension system for the web application …
2:28 PM Changeset [4157] by Nicklas Nordborg
References #436: Creating branch for prototyping web extensions

Feb 21, 2008:

6:31 PM DownloadPage edited by Jari Häkkinen
Removed links to packages older than 2.5 (diff)
4:28 PM Changeset [4156] by Johan Enell
Tagging version 2.6
2:17 PM Ticket #934 (Move the BASE subversion repository to the new server) created by Nicklas Nordborg
The new URL of the subversion repository is: …
11:09 AM WikiStart edited by Jari Häkkinen
(diff)
10:48 AM Changeset [4155] by Nicklas Nordborg
Preparing release 2.6.0
10:47 AM Changeset [4154] by Nicklas Nordborg
Changes for future release 2.7
10:44 AM Changeset [4153] by Nicklas Nordborg
Forking new minor version 2.6 branch
10:43 AM Changeset [4152] by Nicklas Nordborg
Updated credits.txt before 2.6 release
10:36 AM WikiStart edited by Nicklas Nordborg
Link to correct version of GPL (diff)
9:14 AM Ticket #834 (Trashcan cannot be emptied) closed by Nicklas Nordborg
invalid: Since there is no new information about this, I close this ticket as …
7:44 AM Ticket #933 (Create extension points for some selected places in the web client) created by Nicklas Nordborg
Depends on #436. An extension point is needed in the bioassayset tree …
7:41 AM Ticket #932 (Convert the MeV launcher to an extension) created by Nicklas Nordborg
Depends on #436

Feb 20, 2008:

11:46 AM Changeset [4151] by Martin Svensson
Base-hacks site has been moved to a new location - updated links
11:25 AM Changeset [4150] by Martin Svensson
Base-hacks has been moved to a new location - updated link in documentation
10:49 AM DeveloperInformation edited by Nicklas Nordborg
Location for testdata has changed (diff)

Feb 19, 2008:

12:50 PM Ticket #621 (Write 'Plate' section) closed by Martin Svensson
duplicate: see #617
11:00 AM Changeset [4149] by Martin Svensson
Fixed some typos in the documentation
8:36 AM Ticket #930 (Read 'Server settings' section) closed by Nicklas Nordborg
fixed: (In [4148]) Fixes #930: Read 'Server settings' section
8:36 AM Changeset [4148] by Nicklas Nordborg
Fixes #930: Read 'Server settings' section

Feb 18, 2008:

2:34 PM Ticket #896 (Stop generating too long URL:s) closed by Nicklas Nordborg
fixed: Have now worked through the 'roles' test procedure and not found any …
2:18 PM Changeset [4147] by Nicklas Nordborg
References #868: Support for chips with multiple arrays Fixes broken …
2:15 PM Changeset [4146] by Martin Svensson
Typo
1:16 PM Changeset [4145] by Nicklas Nordborg
References #909: Move some static fields from AbstractFlatFileImporter?
11:33 AM Changeset [4144] by Martin Svensson
References #930 Ready for reading

Feb 15, 2008:

1:41 PM Changeset [4143] by Nicklas Nordborg
References #896: Stop generating too long URL:s The POST is now in …
10:30 AM Ticket #931 (Share items to EVERYONE without SHARE_TO_EVERYONE permission) closed by Nicklas Nordborg
fixed: (In [4142]) Fixes #931: Share items to EVERYONE without …
10:30 AM Changeset [4142] by Nicklas Nordborg
Fixes #931: Share items to EVERYONE without SHARE_TO_EVERYONE permission
9:59 AM Ticket #931 (Share items to EVERYONE without SHARE_TO_EVERYONE permission) created by Nicklas Nordborg
This is somewhat related to ticket #929. It seems like there is …

Feb 13, 2008:

3:10 PM Ticket #889 (Clicking "Help" throws a Python error) closed by Nicklas Nordborg
fixed
1:33 PM Changeset [4141] by Nicklas Nordborg
Fixes #929: An existing share to Everyone may block sharing an item to …
1:33 PM Ticket #929 (An existing share to Everyone may block sharing an item to others if ...) closed by Nicklas Nordborg
fixed: (In [4141]) Fixes #929: An existing share to Everyone may block …
1:19 PM Ticket #930 (Read 'Server settings' section) created by Martin Svensson
The current documentation has no section that covers …
11:32 AM Ticket #889 (Clicking "Help" throws a Python error) reopened by Nicklas Nordborg
I think the fix only works for new installations. It will not update …
11:09 AM Changeset [4140] by Martin Svensson
Fixes #889 Clicking "Help" throws a Python error. Changed an invalid link
11:09 AM Ticket #889 (Clicking "Help" throws a Python error) closed by Martin Svensson
fixed: (In [4140]) Fixes #889 Clicking "Help" throws a Python error. Changed …
9:24 AM Changeset [4139] by Nicklas Nordborg
Fixed Javadoc warnings

Feb 12, 2008:

7:00 PM Ticket #929 (An existing share to Everyone may block sharing an item to others if ...) created by base
If I am a normal user without "share to Everyone" permissions, it is …
6:58 AM Changeset [4138] by Nicklas Nordborg
Fixes #928
6:58 AM Ticket #928 (Can't import feature to an array design which has metadata about ...) closed by Nicklas Nordborg
fixed: (In [4138]) Fixes #928

Feb 11, 2008:

2:01 PM Ticket #928 (Can't import feature to an array design which has metadata about ...) created by Nicklas Nordborg
1. Create an array design and select a platform which has a metadata …
11:56 AM Ticket #909 (Move some static fields from AbstractFlatFileImporter to a separate class) closed by Nicklas Nordborg
fixed
11:44 AM Ticket #924 (FAQ 2 in Chapter 28. Reporters related FAQs is outdated) closed by Nicklas Nordborg
fixed: Fixed in [4137]
11:43 AM Changeset [4137] by Nicklas Nordborg
Fixes #928
11:36 AM Ticket #894 (Support for array designs with other feature identification methods ...) closed by Nicklas Nordborg
fixed: Everything seems to be ok. Test programs run fine.
11:12 AM WikiStart edited by Jari Häkkinen
(diff)
10:53 AM Changeset [4136] by Nicklas Nordborg
Format of progress output was incosistent

Feb 8, 2008:

5:43 PM Ticket #927 (Image Macro fails on Feature Trac Page) created by Peter Johansson
Image macro fails on feature page http://base.thep.lu.se/wiki/Features
5:08 PM MailingLists edited by Jari Häkkinen
(diff)
3:03 PM Changeset [4135] by Nicklas Nordborg
Fixes #868: Support for chips with multiple arrays Found an …
2:48 PM Changeset [4134] by Nicklas Nordborg
Fixes #921: Experiment overview should be updated with support for …
2:48 PM Ticket #921 (Experiment overview should be updated with support for mutli-array slides) closed by Nicklas Nordborg
fixed: (In [4134]) Fixes #921: Experiment overview should be updated with …
11:54 AM Changeset [4133] by Nicklas Nordborg
References #868: Support for chips with multiple arrays Fixed some …
11:18 AM Ticket #926 (Update IlluminaRawDataImporter to set the RawBioAssay.arrayNum property) closed by Nicklas Nordborg
fixed: (In [4132]) Fixes #926: Update IlluminaRawDataImporter? to set the …
11:18 AM Changeset [4132] by Nicklas Nordborg
Fixes #926: Update IlluminaRawDataImporter? to set the …
9:55 AM Changeset [4131] by Nicklas Nordborg
Fixes #868: Support for chips with multiple arrays
9:55 AM Ticket #868 (Support for chips with multiple arrays) closed by Nicklas Nordborg
fixed: (In [4131]) Fixes #868: Support for chips with multiple arrays
8:52 AM Ticket #926 (Update IlluminaRawDataImporter to set the RawBioAssay.arrayNum property) created by Nicklas Nordborg
The last character in the column names the Illumina Beadstudio files …

Feb 7, 2008:

11:56 AM Ticket #922 (Migration should be updated to transfer channel information) closed by Nicklas Nordborg
wontfix: No longer possible with the updated solution for #868.
10:17 AM Ticket #925 (A candidate FAQ to Chapter 28. Reporters related FAQs) created by Jari Häkkinen
This siutation should be covered in the FAQ: In some cases the …
10:13 AM Ticket #924 (FAQ 2 in Chapter 28. Reporters related FAQs is outdated) created by Jari Häkkinen
Reporters can be deleted with a plug-in now, there is no need to fall …
10:08 AM Changeset [4130] by Jari Häkkinen
Added information on how to resolve missing probe set situations.
8:30 AM Changeset [4129] by Nicklas Nordborg
Fixes #923: Possible NullPointerException? in ExperimentOverview?
8:30 AM Ticket #923 (Possible NullPointerException in ExperimentOverview) closed by Nicklas Nordborg
fixed: (In [4129]) Fixes #923: Possible NullPointerException? in ExperimentOverview?
8:29 AM Ticket #923 (Possible NullPointerException in ExperimentOverview) created by Nicklas Nordborg
The method addHybridization() has null check on the 'scan' variable on …

Feb 6, 2008:

2:34 PM MailingLists edited by Jari Häkkinen
Fixed spelling. (diff)
9:18 AM Ticket #922 (Migration should be updated to transfer channel information) created by Nicklas Nordborg
See #868
9:17 AM Ticket #921 (Experiment overview should be updated with support for mutli-array slides) created by Nicklas Nordborg
See #868

Feb 5, 2008:

12:24 PM Ticket #636 (Kill a running job) closed by Nicklas Nordborg
fixed: Reopen or create new tickets if there are problems or support for …
12:23 PM Changeset [4128] by Nicklas Nordborg
References #636: Kill a running job Support for interruption in some …
11:40 AM Ticket #893 (Add support for setting a job's status to ABORTING) closed by Nicklas Nordborg
fixed: (In [4127]) Fixes #893: Add support for setting a job's status to ABORTING
11:40 AM Changeset [4127] by Nicklas Nordborg
Fixes #893: Add support for setting a job's status to ABORTING
9:33 AM Ticket #892 (Abort long-running queries) closed by Nicklas Nordborg
fixed: DataQuery:s also has the potential of taking long time. This includes …
9:32 AM Ticket #920 (Add support for aborting queries using a StatlessSession) created by Nicklas Nordborg
Many of our performance-sensitive queries use a StatelessSession? since …
8:57 AM Ticket #919 (Long query against dynamic database may cause session to timeout) closed by Nicklas Nordborg
fixed: Fixed in [4126]
8:39 AM Changeset [4126] by Nicklas Nordborg
Fxies #919: Long query against dynamic database may cause session to …
8:06 AM Ticket #919 (Long query against dynamic database may cause session to timeout) created by Nicklas Nordborg
This is the same as #794, but is seems like it was never implemented …

Feb 4, 2008:

8:29 PM Changeset [4125] by Nicklas Nordborg
Fixes #918: Adding multiple new DataFileTypes? to a platform or variant …
8:29 PM Ticket #918 (Adding multiple new DataFileTypes to a platform or variant only saves ...) closed by Nicklas Nordborg
fixed: (In [4125]) Fixes #918: Adding multiple new DataFileTypes? to a …
8:22 PM Ticket #918 (Adding multiple new DataFileTypes to a platform or variant only saves ...) created by Nicklas Nordborg
This happens in the Illumina installation plug-ins (see …
7:20 PM Ticket #913 (Plug-in JAR paths should support paths relative to the plugins.dir ...) closed by Nicklas Nordborg
fixed: Now tested on windows.
2:36 PM Changeset [4124] by Nicklas Nordborg
Fixes #915: NullPointerException? when a raw data type is missing Use …
2:36 PM Ticket #915 (NullPointerException when a raw data type is missing) closed by Nicklas Nordborg
fixed: (In [4124]) Fixes #915: NullPointerException? when a raw data type is …
1:32 PM Changeset [4123] by Nicklas Nordborg
Fixes #917: The progress reporter for a job should update the database …
1:32 PM Ticket #917 (The progress reporter for a job should update the database if the ...) closed by Nicklas Nordborg
fixed: (In [4123]) Fixes #917: The progress reporter for a job should update …
1:26 PM Ticket #917 (The progress reporter for a job should update the database if the ...) created by Nicklas Nordborg
The current rule is that the progress is only updated if at least 5 …
1:14 PM Changeset [4122] by Nicklas Nordborg
References #913: Plug-in JAR paths should support paths relative to …
1:02 PM Ticket #913 (Plug-in JAR paths should support paths relative to the plugins.dir ...) reopened by Nicklas Nordborg
Reopens this ticket because I think the implementation is not …
12:17 PM Changeset [4121] by Nicklas Nordborg
Fixes #916: Base1PluginExecuter commits transaction even in case of a …
12:17 PM Ticket #916 (Base1PluginExecuter commits transaction even in case of a failure) closed by Nicklas Nordborg
fixed: (In [4121]) Fixes #916: Base1PluginExecuter commits transaction even …
12:09 PM Changeset [4120] by Nicklas Nordborg
References #636: Kill a running job All core plug-ins can now be …
12:01 PM Ticket #916 (Base1PluginExecuter commits transaction even in case of a failure) created by Nicklas Nordborg
If there is an error during the execution of a BASE 1 plug-in using …
10:00 AM Ticket #915 (NullPointerException when a raw data type is missing) created by Nicklas Nordborg
If a raw data type is removed from the raw-data-types.xml file and …
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