Timeline



Aug 30, 2007:

11:07 PM Ticket #737 (Script that fixes copyright text may also add extra new line to end of ...) created by Nicklas Nordborg
I am not sure if the extra new line at the end of …
10:58 PM Ticket #736 (Incorrect error message is displayed if a file upload fails) created by Nicklas Nordborg
The JSP page that should take care of the error and display it has a …
3:59 PM Changeset [3706] by Martin Svensson
References #364 Started updating the GUI to support auto installation …
3:59 PM Ticket #364 (Support for automatic install of non-core plugins) updated by Martin Svensson
(In [3706]) References #364 Started updating the GUI to support auto …

Aug 29, 2007:

8:50 PM Changeset [3705] by Peter Johansson
refs #639
8:50 PM Ticket #639 (exportPureMatrix method) updated by Peter Johansson
(In [3705]) refs #639

Aug 28, 2007:

4:42 PM Ticket #364 (Support for automatic install of non-core plugins) updated by Martin Svensson
(In [3704]) References #364 Moved the PluginInfo class to another …
4:42 PM Changeset [3704] by Martin Svensson
References #364 Moved the PluginInfo class to another package, added a …
4:21 PM Ticket #735 (PermissionDeniedException on array design list view) updated by base
yes that fixed it (sharing the cdf file to Everyone).
4:20 PM Ticket #735 (PermissionDeniedException on array design list view) created by base
As a normal user, another blank list view with the following in …
3:37 PM Ticket #734 (Un-caught NullPointerException in plugin configurations list view.) created by base
As an admin user I can create and view plugin configurations fine. As …
3:29 PM Ticket #733 (Add support to select plugin configurations that should be imported) updated by Martin Svensson
Description changed

Aug 27, 2007:

12:56 PM Ticket #733 (Add support to select plugin configurations that should be imported) updated by Martin Svensson
Description, Status, Milestone changed
12:53 PM Ticket #733 (Add support to select plugin configurations that should be imported) created by Martin Svensson
The plugin-configuration-importer plugin should offer a possibility …
10:03 AM Changeset [3703] by Martin Svensson
Fixes the problem with '+' before the exponent (when its 0). The '+' …

Aug 24, 2007:

3:39 PM Ticket #706 (Averagemethod on raw data types) updated by Jari Häkkinen
Summary changed
3:39 PM Ticket #667 (Move ch. 7 to a lower level) updated by Jari Häkkinen
Owner, Status changed
3:38 PM Ticket #593 (Write "Appendix: Core plug-ins shipped with BASE") updated by Jari Häkkinen
Owner, Status changed
3:37 PM Ticket #732 (Link to basehacks has disappeard) updated by Jari Häkkinen
(In [3702]) Addresses #732. Fixing broken basehacks link.
3:37 PM Changeset [3702] by Jari Häkkinen
Addresses #732. Fixing broken basehacks link.
3:36 PM Changeset [3701] by Jari Häkkinen
Addresses #732. Fixing broken basehacks link.
3:36 PM Ticket #732 (Link to basehacks has disappeard) updated by Jari Häkkinen
(In [3701]) Addresses #732. Fixing broken basehacks link.
1:53 PM Ticket #732 (Link to basehacks has disappeard) created by Jari Häkkinen
We need to keep a link to http://trac.thep.lu.se/trac/basehacks
10:44 AM Ticket #731 (Extend mapping in Base1PluginExecuter) created by Johan Enell
The mapping in the executer should be extended. For instance …

Aug 23, 2007:

1:42 PM Changeset [3700] by Martin Svensson
References #364 The main functions in core is now done for this. A …
1:42 PM Ticket #364 (Support for automatic install of non-core plugins) updated by Martin Svensson
(In [3700]) References #364 The main functions in core is now done for …

Aug 22, 2007:

12:42 PM Changeset [3699] by Jari Häkkinen
URL to demo server change
11:11 AM WikiStart edited by Jari Häkkinen
URL to demo server change (diff)

Aug 21, 2007:

4:17 PM Changeset [3698] by Martin Svensson
References #364 Automatic install non-core plugins. First check-in, …
4:17 PM Ticket #364 (Support for automatic install of non-core plugins) updated by Martin Svensson
(In [3698]) References #364 Automatic install non-core plugins. First …
3:59 PM Changeset [3697] by Jari Häkkinen
Removed 'reference reference' repeat.
3:14 PM Ticket #730 (Documentation figures should be centered by default) created by Jari Häkkinen
It would also be nice to be able to have figures with text next to it …
2:08 PM Changeset [3696] by Jari Häkkinen
Removing obsolete branch. Superseeded by …
11:58 AM Changeset [3695] by Jari Häkkinen
Merged log:trunk#3650:3691 into the webservices branch.

Aug 20, 2007:

4:14 PM WikiStart edited by Jari Häkkinen
Added feature list. (diff)
4:02 PM Milestone BASE 2.4 completed
The aim is to fix various outstanding issues. Major features such as …
4:02 PM Ticket #729 (./jobagent.sh should accept command `status`) created by Jari Häkkinen
status should return if the agent is running or not. Needed for …
3:59 PM Ticket #728 (./jobagent.sh start does not work) created by Jari Häkkinen
The response is: […] Issuing `./jobagent.sh -c …
3:55 PM Ticket #659 (Add wiki page describing BASE features) closed by Jari Häkkinen
fixed: First version added as http://base.thep.lu.se/wiki/Features
3:32 PM Features edited by Jari Häkkinen
More features. (diff)
3:28 PM Features created by Jari Häkkinen
First list of features.
3:22 PM ReleaseProcedure edited by Jari Häkkinen
More fixes to the release procedures. (diff)
2:58 PM ReleaseProcedure edited by Jari Häkkinen
Added link to announcement mail (diff)
2:51 PM DownloadPage edited by Jari Häkkinen
(diff)
2:49 PM ReleaseProcedure edited by Jari Häkkinen
(diff)
2:49 PM DownloadPage edited by Jari Häkkinen
Releasing 2.4 (diff)
2:22 PM Changeset [3694] by Jari Häkkinen
Changes for future release 2.4.1
2:18 PM ReleaseProcedure edited by Jari Häkkinen
(diff)
2:04 PM Changeset [3693] by Jari Häkkinen
Tagging version 2.4
1:56 PM Changeset [3692] by Jari Häkkinen
Preparing release 2.4
1:50 PM Changeset [3691] by Jari Häkkinen
Changes for future release 2.5
1:49 PM Changeset [3690] by Jari Häkkinen
Forking new minor version 2.4 branch.
1:42 PM ReleaseProcedure edited by Jari Häkkinen
Improving procedure. (diff)
12:04 PM Changeset [3689] by Jari Häkkinen
Fixes #615.
12:04 PM Ticket #615 (Write 'Installing job agents' section) closed by Jari Häkkinen
fixed: (In [3689]) Fixes #615.
12:03 PM Changeset [3688] by Jari Häkkinen
Updated link to release procedures.
12:02 PM Changeset [3687] by Jari Häkkinen
Removed links to deleted files.
9:34 AM Changeset [3686] by Jari Häkkinen
Refs #615 and fixed spelling.
9:34 AM Ticket #615 (Write 'Installing job agents' section) updated by Jari Häkkinen
(In [3686]) Refs #615 and fixed spelling.
9:33 AM Changeset [3685] by Jari Häkkinen
Removed obsolete files.

Aug 17, 2007:

4:56 PM Ticket #664 (Remove chapter 6.1.3) closed by Jari Häkkinen
fixed: (In [3684]) Fixes #664
4:56 PM Changeset [3684] by Jari Häkkinen
Fixes #664
4:28 PM Changeset [3683] by Jari Häkkinen
Spelling.
3:45 PM Changeset [3682] by Jari Häkkinen
Added Peter Johansson.
1:59 PM Ticket #721 (Store data in files instead of in the database) updated by Nicklas Nordborg
Description changed
1:56 PM Ticket #721 (Store data in files instead of in the database) updated by Nicklas Nordborg
(In [3681]) References #721: Store data in files instead of in the …
1:56 PM Changeset [3681] by Nicklas Nordborg
References #721: Store data in files instead of in the database First …
1:20 PM Ticket #721 (Store data in files instead of in the database) updated by Nicklas Nordborg
Description changed
1:00 PM Ticket #653 (Implement DbControl.flush() method) updated by Nicklas Nordborg
Milestone changed
1:00 PM Ticket #185 (Refactor the Item class and DbControl and more...) updated by Nicklas Nordborg
Milestone changed
12:04 PM Ticket #727 (Add presentations and publications to the wiki) created by Jari Häkkinen
11:43 AM Ticket #726 (Add nice screen shots to the documentation section in the wiki.) created by Jari Häkkinen
This is for the marketing department.
11:26 AM Changeset [3680] by Nicklas Nordborg
Removed explicit call to System.gc(). Better command line parameters …
11:26 AM Ticket #364 (Support for automatic install of non-core plugins) updated by Martin Svensson
Owner, Status changed
11:09 AM Ticket #725 (Transfer all old documentation to the new wiki system.) updated by Jari Häkkinen
Status changed
11:09 AM Ticket #725 (Transfer all old documentation to the new wiki system.) created by Jari Häkkinen
11:04 AM Ticket #695 (implement run method in AbstractPlugin??) closed by Jari Häkkinen
wontfix
11:02 AM Ticket #689 (Increase 99 hits per page limit (list views)) updated by Jari Häkkinen
Milestone changed
11:00 AM Ticket #683 (Holding down SHIFT, CTRL or ALT when creating a new item should ...) updated by Jari Häkkinen
Milestone changed
10:59 AM Ticket #668 (Displaying icons in the text) updated by Jari Häkkinen
Milestone changed
10:58 AM Ticket #667 (Move ch. 7 to a lower level) updated by Jari Häkkinen
Milestone changed
10:58 AM Ticket #666 (Image in chapter 6.2.3) updated by Jari Häkkinen
Milestone changed
10:57 AM Ticket #665 (Links in the documentation) updated by Jari Häkkinen
Milestone changed
10:57 AM Ticket #664 (Remove chapter 6.1.3) updated by Jari Häkkinen
Milestone, Status, Owner changed
10:56 AM Ticket #664 (Remove chapter 6.1.3) updated by Jari Häkkinen
Milestone changed
10:55 AM Ticket #585 (Make the BASE file system pluggable) updated by Jari Häkkinen
Milestone changed
10:53 AM Ticket #560 (Deleting reporters) updated by Jari Häkkinen
Milestone changed
10:52 AM Ticket #608 (Delete 'removed' items directly from list views) updated by Jari Häkkinen
Milestone changed
10:51 AM Ticket #608 (Delete 'removed' items directly from list views) updated by Jari Häkkinen
Milestone changed
10:50 AM Ticket #425 (Store the character encoding for text files) updated by Jari Häkkinen
Milestone changed
10:48 AM Ticket #376 (Better system for checking which plugins that can be executed in a ...) updated by Jari Häkkinen
Milestone changed
10:37 AM Ticket #706 (Averagemethod on raw data types) updated by Jari Häkkinen
Owner changed
10:35 AM Ticket #636 (Kill a running job) updated by Jari Häkkinen
Summary, Milestone changed
10:30 AM Ticket #591 (Add option to stop a plug-in from beeing executed by the internal job queue) updated by Jari Häkkinen
Priority changed
10:20 AM Ticket #450 (Plugin for importing Imagene raw data) updated by Jari Häkkinen
Description changed
Send a request to the mailing lists asking for test data. If no one is …
10:04 AM Ticket #294 (Performance testing: Plugin-in execution time) updated by Jari Häkkinen
Milestone changed
9:18 AM Changeset [3679] by Jari Häkkinen
Changing the pesky "a (ä) character to a.
9:12 AM ReleaseProcedure edited by Jari Häkkinen
Added a warning about breaking UTF-8 character encoding. (diff)
8:29 AM Changeset [3678] by Nicklas Nordborg
Require DTD files to be encoded in ISO-8859-1

Aug 16, 2007:

8:13 PM Changeset [3677] by Jari Häkkinen
Added copyright statement.
6:36 PM Changeset [3676] by Jari Häkkinen
Trying to fix illegal character problem.
4:47 PM WikiStart edited by Jari Häkkinen
Added link to svndigest output. (diff)
4:16 PM Changeset [3675] by Jari Häkkinen
Fixing copyright statements. Fixing svn properties.
2:52 PM ReleaseProcedure edited by Jari Häkkinen
(diff)
2:45 PM ReleaseProcedure edited by Jari Häkkinen
Packages moved to http://base2.thep.lu.se (diff)
2:42 PM Ticket #721 (Store data in files instead of in the database) updated by Nicklas Nordborg
Owner, Status changed
2:40 PM DownloadPage edited by Jari Häkkinen
Moved all downloadable packages to http://base2.thep.lu.se (diff)
11:43 AM Changeset [3674] by Jari Häkkinen
Added Dominic to .svndigest config.
11:27 AM Changeset [3673] by Jari Häkkinen
Updated .svndigest config.
11:21 AM ReleaseProcedure edited by Jari Häkkinen
svndigest information related fixes. (diff)
11:01 AM Changeset [3672] by Jari Häkkinen
Removed obsolete links and information.
10:07 AM Ticket #656 (Update release procedure) closed by Jari Häkkinen
fixed: (In [3671]) Fixes #656. New release procedures are added to …
10:07 AM Changeset [3671] by Jari Häkkinen
Fixes #656. New release procedures are added to wiki:ReleaseProcedure.
10:04 AM ReleaseProcedure edited by Jari Häkkinen
Working on ticket:656. This is the last draft before actually trying … (diff)
9:33 AM ReleaseProcedure edited by Jari Häkkinen
Working on ticket:656 (diff)
9:30 AM DownloadPage edited by Jari Häkkinen
Typo, changed svndigest to base. (diff)
9:21 AM ReleaseProcedure edited by Jari Häkkinen
Working on ticket:656 (diff)
9:02 AM DownloadPage edited by Jari Häkkinen
Restructurred the download page. (diff)

Aug 15, 2007:

12:37 PM ReleaseProcedure edited by Jari Häkkinen
Working on the release procedure. Refs ticket:656 (diff)
12:02 PM Changeset [3670] by Nicklas Nordborg
Included numbers with scientific notation in the test.
11:50 AM Changeset [3669] by Jari Häkkinen
Removing obsolete file.
11:01 AM Ticket #724 (Nullpointer exception when 'overwrite' is not set in export-plugin ...) closed by Martin Svensson
fixed: (In [3668]) Fixes #724 Nullpointer exception when 'overwrite' is not …
11:01 AM Changeset [3668] by Martin Svensson
Fixes #724 Nullpointer exception when 'overwrite' is not set in …
10:57 AM Changeset [3667] by Nicklas Nordborg
Display free memory before AND after System.gc().
10:52 AM ReleaseProcedure created by Jari Häkkinen
Creating release procedure page. This version is stolen from …
10:51 AM DeveloperInformation edited by Jari Häkkinen
Adding release procedures, refs ticket:656 (diff)
9:46 AM Ticket #337 (Tab2Mage export plugin) closed by Jari Häkkinen
fixed: This plugin is developed and distributed through …
9:43 AM Ticket #338 (Tab2Mage import plugin) closed by Jari Häkkinen
fixed: This plugin is developed and distributed through …
9:33 AM Ticket #724 (Nullpointer exception when 'overwrite' is not set in export-plugin ...) updated by Martin Svensson
Status changed
9:31 AM Ticket #724 (Nullpointer exception when 'overwrite' is not set in export-plugin ...) created by Martin Svensson
This appear in the configuration process when no value has been …

Aug 14, 2007:

7:46 PM Ticket #469 (Improve error handling of invalid values in import plugins) updated by Nicklas Nordborg
(In [3666]) References #469: Added negative numbers to test case with …
7:46 PM Changeset [3666] by Nicklas Nordborg
References #469: Added negative numbers to test case with dirty data
4:55 PM WikiStart edited by Jari Häkkinen
Fixed sponsor links and images. (diff)
4:05 PM Ticket #723 (Update list with core plugins) closed by Martin Svensson
duplicate: This will be done when the core-plugin page is re-written into current …
2:53 PM Ticket #514 (Change permissions in Power User) closed by Martin Svensson
fixed: (In [3665]) Fixes #514 Change permissions in Power User
2:53 PM Changeset [3665] by Martin Svensson
Fixes #514 Change permissions in Power User
2:50 PM Changeset [3664] by Nicklas Nordborg
Fixes #722: Create DynamicReporterQuery
2:50 PM Ticket #722 (Create DynamicReporterQuery) closed by Nicklas Nordborg
fixed: (In [3664]) Fixes #722: Create DynamicReporterQuery
2:05 PM Ticket #723 (Update list with core plugins) created by Martin Svensson
The list with core plugins needs to be updated with configurations to …
12:47 PM Ticket #722 (Create DynamicReporterQuery) updated by Nicklas Nordborg
Owner, Status changed
12:47 PM Ticket #722 (Create DynamicReporterQuery) created by Nicklas Nordborg
This will allow programs to load exactly the needed reporter …
12:01 PM Ticket #514 (Change permissions in Power User) updated by Martin Svensson
Status changed
11:23 AM Ticket #514 (Change permissions in Power User) updated by Jari Häkkinen
Status, Priority, Owner, Type changed
After deep consideration we have decided to remove the create and …
9:25 AM Ticket #364 (Support for automatic install of non-core plugins) updated by Nicklas Nordborg
Milestone changed
9:21 AM Ticket #721 (Store data in files instead of in the database) created by Nicklas Nordborg
As I see it there are four basic problems: 1. Make it possible to …
9:09 AM Changeset [3663] by Nicklas Nordborg
Measure performance for reporter migration.
8:54 AM Changeset [3662] by Martin Svensson
Fixes #551 Read "Plugin developer" section
8:54 AM Ticket #551 (Read "Plugin developer" section) closed by Martin Svensson
fixed: (In [3662]) Fixes #551 Read "Plugin developer" section
8:16 AM Ticket #720 (Progress reporter when emptying trashcan) updated by Nicklas Nordborg
(In [3661]) References #720: Progress reporter when emptying trashcan …
8:15 AM Changeset [3661] by Nicklas Nordborg
References #720: Progress reporter when emptying trashcan Progress …

Aug 13, 2007:

1:25 PM Ticket #294 (Performance testing: Plugin-in execution time) updated by Nicklas Nordborg
Owner, Status changed
1:09 PM Ticket #595 (Read "Appendix: extended-properties.xml reference") closed by Martin Svensson
fixed: (In [3660]) Fixes #595 Read "Appendix: extended-properties.xml reference"
1:09 PM Changeset [3660] by Martin Svensson
Fixes #595 Read "Appendix: extended-properties.xml reference"
12:57 PM Ticket #294 (Performance testing: Plugin-in execution time) updated by Nicklas Nordborg
Milestone changed
12:55 PM Ticket #294 (Performance testing: Plugin-in execution time) updated by Nicklas Nordborg
(In [3659]) References #294: Performance testing Added framework for …
12:55 PM Changeset [3659] by Nicklas Nordborg
References #294: Performance testing Added framework for testing BASE …
12:51 PM Ticket #595 (Read "Appendix: extended-properties.xml reference") updated by Martin Svensson
Owner, Status changed
11:44 AM Changeset [3658] by Nicklas Nordborg
Show stacktrace when a plug-in reports an error
11:26 AM Changeset [3657] by Nicklas Nordborg
Migrate reporters first.
10:57 AM Ticket #686 (Make it possible for core analysis plug-ins to work on a subset of ...) closed by Jari Häkkinen
wontfix
10:49 AM Ticket #523 (Write "Overview of BASE" section in Overview part) updated by Jari Häkkinen
Milestone changed
10:49 AM Ticket #522 (Write "Why use BASE" section) updated by Jari Häkkinen
Milestone changed
10:48 AM Ticket #445 (Plug-in writers should check that the plug-in has the proper ...) closed by Jari Häkkinen
wontfix: Plug-ins should check that it has proper credential before it starts …
8:03 AM Ticket #719 (Add support for JEP if() function) closed by Nicklas Nordborg
fixed: (In [3656]) Fixes #719: Add support for JEP if() function
8:03 AM Changeset [3656] by Nicklas Nordborg
Fixes #719: Add support for JEP if() function

Aug 10, 2007:

2:50 PM Ticket #719 (Add support for JEP if() function) updated by Nicklas Nordborg
Status, Owner changed
2:22 PM Ticket #720 (Progress reporter when emptying trashcan) closed by Nicklas Nordborg
fixed: (In [3655]) Fixes #720: Progress reporter when emptying trashcan
2:22 PM Changeset [3655] by Nicklas Nordborg
Fixes #720: Progress reporter when emptying trashcan
1:26 PM Changeset [3654] by Jari Häkkinen
Copying another missing file from trunk.
12:59 PM Changeset [3653] by Jari Häkkinen
Merged log:trunk#3581:3649 into the wwebservices branch.
12:53 PM Changeset [3652] by Jari Häkkinen
Adding missing files. These files exist in trunk but was not included …
12:17 PM Changeset [3651] by Jari Häkkinen
Fixed svn properties issues.
11:46 AM Changeset [3650] by Nicklas Nordborg
Fixed performance problem with reporter migration. Added support for …
9:10 AM Changeset [3649] by Nicklas Nordborg
Make sure list of formulas get loaded to avoid …
8:48 AM Ticket #720 (Progress reporter when emptying trashcan) updated by Nicklas Nordborg
Status, Owner changed
8:48 AM Ticket #720 (Progress reporter when emptying trashcan) created by Nicklas Nordborg
Emptying the trashcan can take a very long time. Right now it is hard …

Aug 9, 2007:

4:31 PM Ticket #639 (exportPureMatrix method) updated by Peter Johansson
Milestone changed
The interface of this method is not mature enough to be included in …
4:28 PM Ticket #639 (exportPureMatrix method) updated by Peter Johansson
(In [3648]) refs #639 removing the exportPlainMatrix method.
4:28 PM Changeset [3648] by Peter Johansson
refs #639 removing the exportPlainMatrix method.
3:03 PM Ticket #719 (Add support for JEP if() function) created by Nicklas Nordborg
JEP supports an if() function with the following syntax: …
11:11 AM Changeset [3647] by Nicklas Nordborg
Fixes #718: BioAssaySet tries to calculate number of spots and …
11:11 AM Ticket #718 (BioAssaySet tries to calculate number of spots and reporter on ...) closed by Nicklas Nordborg
fixed: (In [3647]) Fixes #718: BioAssaySet tries to calculate number of spots …
9:47 AM Ticket #718 (BioAssaySet tries to calculate number of spots and reporter on ...) updated by Nicklas Nordborg
Owner, Status changed
9:46 AM Ticket #451 (Zipped download) updated by Nicklas Nordborg
(In [3646]) References #451: Zipped download Fixed test program and …
9:46 AM Changeset [3646] by Nicklas Nordborg
References #451: Zipped download Fixed test program and added it to …

Aug 8, 2007:

7:43 PM Ticket #718 (BioAssaySet tries to calculate number of spots and reporter on ...) created by Nicklas Nordborg
Stop with the following stack trace: […] The …
7:28 PM Ticket #639 (exportPureMatrix method) updated by Peter Johansson
(In [3645]) refs #639 stupid version of exportPureMatrix method that …
7:28 PM Changeset [3645] by Peter Johansson
refs #639 stupid version of exportPureMatrix method that simply …
2:52 PM Ticket #294 (Performance testing: Plugin-in execution time) updated by Nicklas Nordborg
Owner, Status changed
I will start to create a BASE 2 test framework that can be used to: …
2:45 PM Ticket #716 (Plugin configuration import should be able ot set the permission on ...) closed by Nicklas Nordborg
fixed: (In [3644]) Fixes #716: Plugin configuration import should be able ot …
2:45 PM Changeset [3644] by Nicklas Nordborg
Fixes #716: Plugin configuration import should be able ot set the …
2:32 PM Changeset [3643] by Nicklas Nordborg
Fixes #451: Zipped download Added user and plug-in developer documentation
2:32 PM Ticket #451 (Zipped download) closed by Nicklas Nordborg
fixed: (In [3643]) Fixes #451: Zipped download Added user and plug-in …
1:42 PM Changeset [3642] by Nicklas Nordborg
Fixes #715: Install should set same permission on plugin …
1:42 PM Ticket #715 (Install should set same permission on plugin configurations as on the ...) closed by Nicklas Nordborg
fixed: (In [3642]) Fixes #715: Install should set same permission on plugin …
1:38 PM Ticket #717 (Make initdb, updatedb and other scripts accept a username) created by Nicklas Nordborg
The current implementation forces the root user account to be named …
1:32 PM Ticket #451 (Zipped download) updated by Nicklas Nordborg
(In [3641]) References #451: Zipped download Major redesign of the …
1:32 PM Changeset [3641] by Nicklas Nordborg
References #451: Zipped download Major redesign of the packing …
12:59 PM Ticket #716 (Plugin configuration import should be able ot set the permission on ...) created by Nicklas Nordborg
This should probably be an option in the wizard. See also ticket #715.
12:57 PM Ticket #715 (Install should set same permission on plugin configurations as on the ...) created by Nicklas Nordborg

Aug 7, 2007:

5:20 PM Changeset [3640] by Johan Enell
a plugin can have no parameters
3:44 PM Ticket #714 (Base1PluginExecutor.JobParameter.toString() may generate incorrect XML) closed by Johan Enell
fixed: (In [3639]) Fixes #714
3:44 PM Changeset [3639] by Johan Enell
Fixes #714
1:40 PM Ticket #714 (Base1PluginExecutor.JobParameter.toString() may generate incorrect XML) updated by Johan Enell
Milestone, Status, Owner changed
12:49 PM Ticket #451 (Zipped download) updated by Nicklas Nordborg
Status changed
12:49 PM Ticket #451 (Zipped download) updated by Nicklas Nordborg
Owner, Status changed
12:09 PM Ticket #625 (Improve error/warning message display when selecting plug-ins) closed by Nicklas Nordborg
fixed
12:08 PM Ticket #698 (Fix Javadoc warnings) closed by Nicklas Nordborg
fixed
12:07 PM Ticket #663 (TOC is to big) closed by Nicklas Nordborg
wontfix
12:06 PM Ticket #504 (Use different icon for inherited annotations in the tree in Experiment ...) closed by Nicklas Nordborg
wontfix
11:35 AM Ticket #714 (Base1PluginExecutor.JobParameter.toString() may generate incorrect XML) created by Nicklas Nordborg
The Base1PluginExecutor.JobParameter.toString() method is used to …
11:30 AM Ticket #713 (Differences in the configuration file from base1) closed by Nicklas Nordborg
fixed: (In [3638]) Fixes #713: Differences in the configuration file from base1
11:30 AM Changeset [3638] by Nicklas Nordborg
Fixes #713: Differences in the configuration file from base1
11:17 AM Ticket #710 (Allow subclasses to AbstractFlatFileParser to participate in ...) closed by Nicklas Nordborg
fixed: (In [3637]) Fixes #710: Allow subclasses to AbstractFlatFileParser to …
11:17 AM Changeset [3637] by Nicklas Nordborg
Fixes #710: Allow subclasses to AbstractFlatFileParser to participate …
11:13 AM Ticket #486 (Import raw data from the Illumina platform) updated by Nicklas Nordborg
(In [3636]) References #486: Added Jeremy Davis-Turak to credits.txt …
11:13 AM Changeset [3636] by Nicklas Nordborg
References #486: Added Jeremy Davis-Turak to credits.txt for helping …
8:10 AM Ticket #710 (Allow subclasses to AbstractFlatFileParser to participate in ...) updated by Nicklas Nordborg
Owner, Milestone, Status changed

Aug 6, 2007:

2:49 PM Changeset [3635] by Nicklas Nordborg
References #358: Better info from Migration tool Show log message …
2:49 PM Ticket #358 (Better info from Migration tool) updated by Nicklas Nordborg
(In [3635]) References #358: Better info from Migration tool Show log …
2:48 PM Ticket #573 (Trim whitespace when checking for unique values) closed by Nicklas Nordborg
fixed: (In [3634]) Fixes #573: Trim whitespace when checking for unique values
2:48 PM Changeset [3634] by Nicklas Nordborg
Fixes #573: Trim whitespace when checking for unique values
12:35 PM Ticket #573 (Trim whitespace when checking for unique values) reopened by Nicklas Nordborg
As it turns out, BASE 1 only removed trailing white spaces...not …
9:36 AM Ticket #574 (Handle database differences with case sensitivity) updated by Nicklas Nordborg
(In [3633]) References #574. Test program didn't report error properly
9:36 AM Changeset [3633] by Nicklas Nordborg
References #574. Test program didn't report error properly

Aug 3, 2007:

4:53 PM Ticket #713 (Differences in the configuration file from base1) reopened by Nicklas Nordborg
new Integer(options) exists in several other places in the …
4:10 PM Changeset [3632] by Johan Enell
Fixes #713
4:10 PM Ticket #713 (Differences in the configuration file from base1) closed by Johan Enell
fixed: (In [3632]) Fixes #713
4:02 PM Ticket #713 (Differences in the configuration file from base1) created by Johan Enell
The options value for the enumeration parameter can be empty. The …
3:09 PM Ticket #701 (JarClassLoader should be able to auto-reload based on timestamp) closed by Nicklas Nordborg
fixed: (In [3631]) Fixes #701: JarClassLoader should be able to auto-reload …
3:09 PM Changeset [3631] by Nicklas Nordborg
Fixes #701: JarClassLoader should be able to auto-reload based on timestamp
2:32 PM Ticket #701 (JarClassLoader should be able to auto-reload based on timestamp) updated by Nicklas Nordborg
Status, Milestone, Owner changed
2:10 PM illumina-raw-data.xml attached to Ticket #486 by Nicklas Nordborg
This replaces the older raw-data-types.xml. It incorrectly set one …
2:02 PM Changeset [3630] by Nicklas Nordborg
Fixes #704: Make sure DbControl is closed from www/common/import/index.jsp
2:02 PM Ticket #704 (Make sure DbControl is closed from www/common/import/index.jsp) closed by Nicklas Nordborg
fixed: (In [3630]) Fixes #704: Make sure DbControl is closed from …
1:58 PM Ticket #704 (Make sure DbControl is closed from www/common/import/index.jsp) updated by Nicklas Nordborg
Status, Owner changed
1:53 PM Tickets #711,​712 batch updated by Nicklas Nordborg
fixed: (In [3629]) Fixes #712, References #711
1:53 PM Changeset [3629] by Nicklas Nordborg
Fixes #712, References #711
1:51 PM Ticket #711 (Deleting a bioassayset doesn't decrease used quota as much as expected) updated by Nicklas Nordborg
The good news is that the problem with the experiment beeing updated …
1:48 PM Ticket #711 (Deleting a bioassayset doesn't decrease used quota as much as expected) closed by Nicklas Nordborg
duplicate: Duplicate of #712
1:47 PM Ticket #712 (DbControl.commit() may call onBeforeCommit() multiple times for the ...) created by Nicklas Nordborg
See ticket #711 for a symptom of this defect. The …
1:09 PM Ticket #711 (Deleting a bioassayset doesn't decrease used quota as much as expected) updated by Nicklas Nordborg
Priority, Status, Owner changed
I have made some initial checks and the problem seems to be unrelated …
12:07 PM Ticket #711 (Deleting a bioassayset doesn't decrease used quota as much as expected) created by Nicklas Nordborg
1. I started out with a new fresh experiment. It used 0 bytes. 2. A …
12:00 PM Changeset [3628] by Nicklas Nordborg
References #625: PrintMapFlatFileImporter.isInContext now checks if …
12:00 PM Ticket #625 (Improve error/warning message display when selecting plug-ins) updated by Nicklas Nordborg
(In [3628]) References #625: PrintMapFlatFileImporter.isInContext now …
11:49 AM Ticket #710 (Allow subclasses to AbstractFlatFileParser to participate in ...) created by Nicklas Nordborg
This is currently an affair for the AbstractFlatFileParser only. The …
11:39 AM Ticket #709 (Install should install missing plug-in configurations when updating) updated by Nicklas Nordborg
(In [3627]) References #709: Forgot to add predefined query
11:39 AM Changeset [3627] by Nicklas Nordborg
References #709: Forgot to add predefined query
11:38 AM Ticket #486 (Import raw data from the Illumina platform) closed by Nicklas Nordborg
fixed: (In [3626]) Fixes #486: Import raw data from the Illumina platform
11:38 AM Changeset [3626] by Nicklas Nordborg
Fixes #486: Import raw data from the Illumina platform
11:24 AM Changeset [3625] by Nicklas Nordborg
Fixes #709: Install should install missing plug-in configurations when …
11:24 AM Ticket #709 (Install should install missing plug-in configurations when updating) closed by Nicklas Nordborg
fixed: (In [3625]) Fixes #709: Install should install missing plug-in …
10:58 AM Ticket #709 (Install should install missing plug-in configurations when updating) updated by Nicklas Nordborg
Status changed
10:58 AM Ticket #709 (Install should install missing plug-in configurations when updating) created by Nicklas Nordborg
Currently, plug-in configurations are only installed if it is a new …
9:42 AM Changeset [3624] by Nicklas Nordborg
Fixes #708: "NaN" and "Infinity" values in files causes SqlException
9:42 AM Ticket #708 ("NaN" and "Infinity" values in files causes SqlException) closed by Nicklas Nordborg
fixed: (In [3624]) Fixes #708: "NaN" and "Infinity" values in files causes …
9:42 AM Ticket #708 ("NaN" and "Infinity" values in files causes SqlException) updated by Nicklas Nordborg
Summary changed
9:06 AM Ticket #708 ("NaN" and "Infinity" values in files causes SqlException) updated by Nicklas Nordborg
Owner, Status changed
9:06 AM Ticket #708 ("NaN" and "Infinity" values in files causes SqlException) updated by Nicklas Nordborg
Doing it at the batcher level turned out to a bad idea. The reason is …
8:42 AM Ticket #708 ("NaN" and "Infinity" values in files causes SqlException) created by Nicklas Nordborg
The string "NaN" when parsed by Java is seen as a valid numeric value …
7:44 AM Ticket #707 (Can't unlink items that have been put in the trashcan) updated by Nicklas Nordborg
Milestone, Summary, Description, Priority changed

Aug 2, 2007:

2:03 PM Ticket #707 (Can't unlink items that have been put in the trashcan) created by Nicklas Nordborg
Items that have been marked for removal can't be unlinked with other …
12:37 PM Ticket #706 (Averagemethod on raw data types) updated by Johan Enell
(In [3623]) References #706 Added average for genepix.flags
12:37 PM Changeset [3623] by Johan Enell
References #706 Added average for genepix.flags
12:36 PM Tickets #700,​590 batch updated by Johan Enell
fixed: (In [3622]) Fixes #700, #590
12:36 PM Changeset [3622] by Johan Enell
Fixes #700, #590
12:09 PM Ticket #669 (Add possibility to set average method to fomulas and extravalues from ...) closed by Nicklas Nordborg
fixed: (In [3621]) Fixes #669
12:09 PM Changeset [3621] by Nicklas Nordborg
Fixes #669
11:59 AM Ticket #669 (Add possibility to set average method to fomulas and extravalues from ...) reopened by Nicklas Nordborg
NullPointerException when creating a formula type that shouldn't have …
11:40 AM Ticket #706 (Averagemethod on raw data types) created by Johan Enell
Go through the raw-data-types.xml and add appropriate average method …
9:00 AM Ticket #486 (Import raw data from the Illumina platform) updated by Nicklas Nordborg
An example file from the Tab2Mage project …
8:41 AM Ticket #705 (Add preset to "Test with file" for regular expression that can split a ...) updated by Nicklas Nordborg
Description changed
8:40 AM Ticket #705 (Add preset to "Test with file" for regular expression that can split a ...) closed by Nicklas Nordborg
fixed: (In [3620]) Fixes #705: Add preset to "Test with file" for regular …
8:40 AM Changeset [3620] by Nicklas Nordborg
Fixes #705: Add preset to "Test with file" for regular expression that …
8:28 AM Ticket #705 (Add preset to "Test with file" for regular expression that can split a ...) updated by Nicklas Nordborg
Description changed
8:23 AM Ticket #705 (Add preset to "Test with file" for regular expression that can split a ...) updated by Nicklas Nordborg
Owner, Status changed
8:22 AM Ticket #705 (Add preset to "Test with file" for regular expression that can split a ...) created by Nicklas Nordborg
This regexp seems to work: […] Thanks to Raimond Brookman …

Aug 1, 2007:

2:13 PM Ticket #704 (Make sure DbControl is closed from www/common/import/index.jsp) updated by Nicklas Nordborg
Description changed
2:13 PM Ticket #704 (Make sure DbControl is closed from www/common/import/index.jsp) created by Nicklas Nordborg
The following stack trace appears in Tomcat log file: […]
1:36 PM Ticket #486 (Import raw data from the Illumina platform) updated by Nicklas Nordborg
Status changed
1:35 PM Changeset [3619] by Nicklas Nordborg
Include test for selecting a parameter expression in SQL: SELECT …
1:19 PM Ticket #702 (Add lineNum() function(s) to mapping expressions supported by the ...) closed by Nicklas Nordborg
fixed: (In [3618]) Fixes #702: Add lineNum() function(s) to mapping …
1:19 PM Changeset [3618] by Nicklas Nordborg
Fixes #702: Add lineNum() function(s) to mapping expressions supported …
12:06 PM Ticket #702 (Add lineNum() function(s) to mapping expressions supported by the ...) updated by Nicklas Nordborg
Status, Owner changed
12:05 PM Ticket #703 (Error message when loading invalid XML files doesn't include the file name) closed by Nicklas Nordborg
fixed: (In [3617]) Fixes #703: Error message when loading invalid XML files …
12:05 PM Changeset [3617] by Nicklas Nordborg
Fixes #703: Error message when loading invalid XML files doesn't …
11:00 AM Ticket #703 (Error message when loading invalid XML files doesn't include the file name) updated by Nicklas Nordborg
Status, Owner changed
10:40 AM Ticket #703 (Error message when loading invalid XML files doesn't include the file name) created by Nicklas Nordborg
For example: […]
10:06 AM Ticket #486 (Import raw data from the Illumina platform) updated by Nicklas Nordborg
From Jeremy Davis-Turak: Here is a brief summary of what the data …
10:02 AM Ticket #486 (Import raw data from the Illumina platform) updated by Nicklas Nordborg
Description changed
10:02 AM Ticket #702 (Add lineNum() function(s) to mapping expressions supported by the ...) created by Nicklas Nordborg
With this function we can import data and use the current line number …
9:53 AM Ticket #701 (JarClassLoader should be able to auto-reload based on timestamp) created by Nicklas Nordborg
This would simplify plug-in development since you would only have to …
8:49 AM Ticket #698 (Fix Javadoc warnings) updated by Nicklas Nordborg
(In [3616]) References #698: Fix Javadoc warnings Removed all …
8:49 AM Changeset [3616] by Nicklas Nordborg
References #698: Fix Javadoc warnings Removed all existing warnings. …

Jul 31, 2007:

10:28 PM 1401771138_A.sample.txt attached to Ticket #486 by base
Example of a file resulting from the R script. Note that the column …
10:27 PM gene_profile_human_sample.csv attached to Ticket #486 by base
Sample human annotation file. Note the different number of columns …
10:25 PM RatRef_12_v1_11222119_A.sample.csv attached to Ticket #486 by base
Sample rat annotation file.
10:22 PM gene_profile_Rat_sample.2.csv attached to Ticket #486 by base
Sample rat data.
10:21 PM gene_profile_Rat_sample.csv attached to Ticket #486 by base
3:34 PM Ticket #700 (BioAssayExporter basefile: make it use merge on reporter) created by Johan Enell
The exporter should be able to merge on reporter.
3:27 PM Ticket #698 (Fix Javadoc warnings) updated by Nicklas Nordborg
Status, Owner changed
2:45 PM Ticket #691 (Make LowessNormalization and MedianRatioNormalization extend ...) closed by Nicklas Nordborg
fixed: (In [3615]) Fixes #691: Make LowessNormalization and …
2:45 PM Changeset [3615] by Nicklas Nordborg
Fixes #691: Make LowessNormalization and MedianRatioNormalization
2:14 PM Changeset [3614] by Johan Enell
Fixes #699
2:14 PM Ticket #699 (BioAssayExporter basefile: Wrong number of columns) closed by Johan Enell
fixed: (In [3614]) Fixes #699
2:05 PM Ticket #699 (BioAssayExporter basefile: Wrong number of columns) created by Johan Enell
When exporting matrix not merged on reporter there is wrong number of …
1:56 PM Changeset [3613] by Johan Enell
Fixes #673
1:56 PM Ticket #673 (BioAssayExporter basefile: Wrong count in section spots) closed by Johan Enell
fixed: (In [3613]) Fixes #673
1:44 PM Ticket #691 (Make LowessNormalization and MedianRatioNormalization extend ...) updated by Nicklas Nordborg
Status, Owner changed
1:17 PM Ticket #673 (BioAssayExporter basefile: Wrong count in section spots) updated by Johan Enell
Status changed
12:57 PM Ticket #595 (Read "Appendix: extended-properties.xml reference") updated by Nicklas Nordborg
Summary, Priority, Owner, Status changed
12:57 PM Ticket #595 (Read "Appendix: extended-properties.xml reference") updated by Nicklas Nordborg
(In [3612]) References #595: Write "Appendix: extended-properties.xml …
12:57 PM Changeset [3612] by Nicklas Nordborg
References #595: Write "Appendix: extended-properties.xml reference" …
9:55 AM Ticket #595 (Read "Appendix: extended-properties.xml reference") updated by Nicklas Nordborg
Status, Owner changed
9:54 AM Ticket #191 (Mobile number field in user info?) updated by Nicklas Nordborg
(In [3611]) References #191: Added callto: link to skype contact
9:54 AM Changeset [3611] by Nicklas Nordborg
References #191: Added callto: link to skype contact
9:15 AM Ticket #486 (Import raw data from the Illumina platform) updated by Nicklas Nordborg
Description changed
9:07 AM DeveloperInformation edited by Nicklas Nordborg
Example plug-ins download has changed location (diff)
9:03 AM Ticket #653 (Implement DbControl.flush() method) updated by Nicklas Nordborg
Owner, Status, Milestone changed
I had a go to implement this, but it turned out to be a lot more …
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