Timeline



Oct 6, 2006:

9:52 PM Ticket #385 (Make sure that the distribution packaging script creates directories ...) created by Jari Häkkinen
In the case of base-2.0.1.tar.gz the directory created in extracting …
9:49 PM Ticket #384 (Script files (.sh) do not have the proper file permission in linux) created by Jari Häkkinen
This applies for the binary package. Check if the source package is ok.
9:44 PM Changeset [2718] by Jari Häkkinen
Finalized information about publishing a new release.
9:42 PM Changeset [2717] by Jari Häkkinen
Removed obsolete branch. Superseded by source:/branches/2.0.1
9:23 PM Ticket #383 (Should more docs be shipped with the binary package?) created by Jari Häkkinen
As it is now only installation.html is shipped. Should we include …
9:02 PM Ticket #382 (A very minimal extended-properties.xml creates null pointer exceptions.) created by Jari Häkkinen
The bare minimum …
8:32 PM Ticket #381 (User with administrator rights cannot share items (files) to group Everyone) created by Jari Häkkinen
The Everyone group does not show up as an option when sharing files. …
2:26 PM Ticket #377 (hasData() flag not set on creation of new RawBioAssay, prevents ...) closed by Nicklas Nordborg
worksforme
10:46 AM Ticket #220 (Plugin permissions) reopened by Nicklas Nordborg
Reopened because the current solution with permission per thread …
8:05 AM Ticket #380 (Bug in Lowess) created by David Waring <dwaring@…>
There is a bug in the Lowess plugin. Looping through the blocks …
1:44 AM Changeset [2716] by Jari Häkkinen
Fixed typos.
1:41 AM Changeset [2715] by Jari Häkkinen
First steps toward user documentation.
1:23 AM Changeset [2714] by Jari Häkkinen
Added section heading for howto change extended properties.
1:20 AM Changeset [2713] by Jari Häkkinen
Added documentation about extended-properties.xml.
12:29 AM Changeset [2712] by Jari Häkkinen
Fixed spelling.
12:27 AM Changeset [2711] by Jari Häkkinen
Fixed links and added mysql/innodb tuning info.

Oct 5, 2006:

2:56 PM Changeset [2710] by Johan Enell
Merge commands has been added
2:36 PM Ticket #318 (Plugin configuration values are not stored for a job) closed by Nicklas Nordborg
fixed: (In [2709]) Fixes #318: Plugin configuration values are not stored for …
2:36 PM Changeset [2709] by Nicklas Nordborg
Fixes #318: Plugin configuration values are not stored for a job And …
8:38 AM Changeset [2708] by Nicklas Nordborg
Fixed bug with linking if item.type is empty

Oct 4, 2006:

11:12 PM Changeset [2707] by Jari Häkkinen
Spell checked.
10:25 PM Changeset [2706] by Jari Häkkinen
Creating sample extended-properties.xml files.
10:09 PM Ticket #379 (BASE2: Fails to display Raw data from a RawBioassay imported from ...) closed by Nicklas Nordborg
duplicate: This is a duplicate of ticket #99. A workaround is described in the …
5:43 PM Ticket #379 (BASE2: Fails to display Raw data from a RawBioassay imported from ...) created by simon.foote@…
I've done a migration from 1.2.17 to base 2.0. No glaring errors were …
4:46 PM Changeset [2705] by Jari Häkkinen
Removed references to RC2.
4:09 PM Changeset [2704] by Nicklas Nordborg
Fixes #343: Plot tool should be able to use other annotations than bioassay
4:09 PM Ticket #343 (Plot tool should be able to use other annotations than bioassay) closed by Nicklas Nordborg
fixed: (In [2704]) Fixes #343: Plot tool should be able to use other …
2:01 PM Changeset [2703] by Nicklas Nordborg
Fixed some threading problems with Keyring and plugin permissions.
1:59 PM Changeset [2702] by Nicklas Nordborg
Fixed unclosed DbControl?.
1:59 PM Changeset [2701] by Nicklas Nordborg
Deny access if role permission has DENIED flag set.
1:58 PM Changeset [2700] by Nicklas Nordborg
PluginRequest?.doInvoke() and SessionControl?.setActivePlugin() should …
1:55 PM Changeset [2699] by Nicklas Nordborg
Fixed unclosed DbControl? in case of an exception while updating the …
9:59 AM Changeset [2698] by Nicklas Nordborg
Fixed NoSuchElementException? bug when iterating over more than one …
9:14 AM Ticket #378 (Creation of configurations for plug-ins that do not need configs are ...) created by Jari Häkkinen
Many plug-ins do not need configurations and in consequence these …
8:43 AM Changeset [2697] by Nicklas Nordborg
References #368: Migration should migrate plugin settings for BASE 1 …

Oct 3, 2006:

5:00 PM Changeset [2696] by Martin Svensson
References #335 Export plugin for plugin configurations. Saves the …
3:47 PM Changeset [2695] by Nicklas Nordborg
Installation now installs Base1PluginExecuter plugin.
3:44 PM Tickets #201,​370,​371 batch updated by Nicklas Nordborg
fixed: (In [2694]) Fixes #201, #370 and #371 * Experiment directory * …
3:44 PM Changeset [2694] by Nicklas Nordborg
Fixes #201, #370 and #371 * Experiment directory * Hyperlink to …
3:41 PM Ticket #377 (hasData() flag not set on creation of new RawBioAssay, prevents ...) created by micha.bayer@…
When a new RawBioAssay? has been created and data have been imported …
1:44 PM Changeset [2693] by Nicklas Nordborg
Fixes #368: Migration should migrate plugin settings for BASE 1 plugins
1:44 PM Ticket #368 (Migration should migrate plugin settings for BASE 1 plugins) closed by Nicklas Nordborg
fixed: (In [2693]) Fixes #368: Migration should migrate plugin settings for …
1:30 PM Changeset [2692] by Martin Svensson
Fixes #220 Plugin permissions.
1:30 PM Ticket #220 (Plugin permissions) closed by Martin Svensson
fixed: (In [2692]) Fixes #220 Plugin permissions.
1:21 PM Ticket #220 (Plugin permissions) reopened by Martin Svensson
The plugin should ignore the owner- and project/shared permissions for …
9:35 AM Ticket #366 (Batch upload using zip-files) closed by Nicklas Nordborg
fixed: (In [2691]) Fixes #366: Batch upload using zip-files
9:35 AM Changeset [2691] by Nicklas Nordborg
Fixes #366: Batch upload using zip-files
8:28 AM Ticket #376 (Better system for checking which plugins that can be executed in a ...) created by Nicklas Nordborg
The current implementation leads to lots of situation where you think …

Oct 2, 2006:

4:44 PM Changeset [2690] by Johan Enell
Merged log:branches/2.0#2618:2688 from branch 2.0 to trunk.
4:04 PM Changeset [2689] by Nicklas Nordborg
References #366: Batch upload using zip-files Added plugin for zip …
3:00 PM Changeset [2688] by Nicklas Nordborg
Added AbsoluteProgressReporter? and two simple implementations.
2:05 PM Changeset [2687] by Johan Enell
extra values added to pluginexecuter
1:24 PM Milestone BASE 2.0.1 completed
Problems and bugs found in 2.0. These will be fixed ASAP. The next …
1:23 PM Ticket #332 (Fix bugs in migration program) closed by Jari Häkkinen
fixed: The known issues are fixed and we have made extensive manual testing …
12:43 PM Changeset [2686] by Jari Häkkinen
Added information on what to do when publishing a new release of BASE.
12:35 PM Changeset [2685] by Jari Häkkinen
New bug fix branch for 2.0.1.
12:29 PM DownloadPage edited by Jari Häkkinen
Added version information to the download table. (diff)
12:27 PM DownloadPage edited by Jari Häkkinen
Removed obsolete packages. (diff)
12:26 PM DownloadPage edited by Jari Häkkinen
Version 2.0.1 released. (diff)
11:44 AM Changeset [2684] by Jari Häkkinen
Tagging version 2.0.1
11:40 AM Changeset [2683] by Jari Häkkinen
Bumped version number. Added disclaimer text to migration.
10:50 AM Changeset [2682] by Jari Häkkinen
Spell checked.

Oct 1, 2006:

9:34 PM Ticket #375 (Shared items: the shareness of items should be listed in the ...) created by Jari Häkkinen
As it is now the properties view will tell the user that the item is …

Sep 29, 2006:

9:58 AM Changeset [2681] by Nicklas Nordborg
References #366: Batch upload using zip-files Added utility class and …

Sep 28, 2006:

4:33 PM Changeset [2680] by Martin Svensson
References #335 A beginning of a PluginConfigurationExporter?.
2:01 PM Changeset [2679] by Nicklas Nordborg
The AbstractFlatFileImporter?.requiresConfiguration() now returns true …
1:52 PM Ticket #361 (Export of bioassaysets) closed by Nicklas Nordborg
fixed: (In [2678]) Fixes #361: Export of bioassaysets
1:52 PM Changeset [2678] by Nicklas Nordborg
Fixes #361: Export of bioassaysets
11:54 AM Changeset [2677] by Nicklas Nordborg
Remember recently used files and other items when importing and …
11:06 AM Changeset [2676] by Nicklas Nordborg
Added image to Abort button in file upload. Added image for Browse buttons.
10:58 AM Changeset [2675] by Martin Svensson
Displaying permissions for a plugindefinition on it's view page.
10:03 AM Changeset [2674] by Nicklas Nordborg
Removed debug code
10:01 AM Ticket #169 (Use formulas for creating extra values) closed by Nicklas Nordborg
fixed: (In [2673]) Fixes #169: Use formulas for creating extra values Also …
10:01 AM Changeset [2673] by Nicklas Nordborg
Fixes #169: Use formulas for creating extra values Also added plugin …
9:49 AM Changeset [2672] by Martin Svensson
Corrupt page when open creating a new plugindefinition is fixed
8:06 AM DownloadPage edited by Nicklas Nordborg
(diff)
7:58 AM DownloadPage edited by Nicklas Nordborg
(diff)

Sep 27, 2006:

4:08 PM Ticket #220 (Plugin permissions) closed by Martin Svensson
fixed: (In [2671]) Fixes #220 Plugin permissions
4:08 PM Changeset [2671] by Martin Svensson
Fixes #220 Plugin permissions
3:47 PM Changeset [2670] by Nicklas Nordborg
Added "Add" and "Remove" images to default images.
1:44 PM Tickets #342,​344 batch updated by Nicklas Nordborg
fixed: (In [2669]) Fixes #342 and #344: Display extra values in plot tool and …
1:44 PM Changeset [2669] by Nicklas Nordborg
Fixes #342 and #344: Display extra values in plot tool and tables, etc.
11:58 AM Changeset [2668] by Nicklas Nordborg
Fixed problem in formatNumber method that displayed an extra minus …

Sep 26, 2006:

4:07 PM Changeset [2667] by Nicklas Nordborg
Added QueryElement?.getChildren() method.
2:59 PM Changeset [2666] by Nicklas Nordborg
Can now use the externalId in extra value expression with JEP.
1:36 PM Changeset [2665] by Nicklas Nordborg
Added a note about warning for an unclosed DbControl?
1:28 PM Changeset [2664] by Nicklas Nordborg
References #342, #344 and #169 Extra values are now displayed in a …
1:08 PM Changeset [2663] by Nicklas Nordborg
Added createJepExpression method
1:06 PM Changeset [2662] by Nicklas Nordborg
Added storeValue() method
1:00 PM Changeset [2661] by Nicklas Nordborg
Create copy of list of values to avoid external manipulation after the …
9:18 AM Ticket #374 (Restoring a Bioassayset or Transformation restores all child bioassay ...) created by Nicklas Nordborg
If you for example have marked one part of the analysis for deletion …

Sep 25, 2006:

9:32 AM Changeset [2660] by Martin Svensson
References #220 Store the plugin's keyring information in a local …

Sep 22, 2006:

11:08 PM WikiStart edited by Jari Häkkinen
Minor sponsor fixes. (diff)
11:06 PM WikiStart edited by Jari Häkkinen
Added sponsor logos. (diff)
10:50 PM WikiStart edited by Jari Häkkinen
Removed footer link to title index. (diff)
1:45 PM Changeset [2659] by Nicklas Nordborg
Fixes #373: Wrong character for less then
1:45 PM Ticket #373 (Wrong character for less then) closed by Nicklas Nordborg
fixed: (In [2659]) Fixes #373: Wrong character for less then
1:37 PM Changeset [2658] by Nicklas Nordborg
Refences #169: Use formulas for creating extra values Added admin …
1:34 PM Changeset [2657] by Martin Svensson
References #220 1 Put the handle of plugin permissions into Keyring. …
12:49 PM Changeset [2656] by Nicklas Nordborg
Tab can automatically adjust the height when popup window is beeing …
12:47 PM Ticket #373 (Wrong character for less then) created by Johan Enell
In the expression builder view the greater then or equal(>=) is shown …
9:51 AM Ticket #301 (Better GUI for defining file formats) closed by Nicklas Nordborg
fixed: (In [2655]) Fixes #301: Better GUI for defining file formats
9:51 AM Changeset [2655] by Nicklas Nordborg
Fixes #301: Better GUI for defining file formats

Sep 21, 2006:

2:29 PM Changeset [2654] by Nicklas Nordborg
Log stacktrace in case of an exception
12:49 PM Ticket #372 (Check Affymetrix CEL files vs Affymetrix Array Design during file upload) created by rocca@…
CEL files contains information about the ArrayDesign? used to generated …
12:15 PM Ticket #371 (Add a field Publication Title to the Publication Page in Experiment Section) created by rocca@…
12:13 PM Ticket #370 (Hyperlink to Pubmed if Pubmed id submitted from Publication Page in ...) created by rocca@…
$pubmed_id should be an integer. linking to EBI's Citexplore using …
10:41 AM Ticket #369 (Display of ExperimentalFactor and associated Values from Experiment Page) created by rocca@…
When setting an 'annotationType' as ExperimentalFactor? in a given …
9:25 AM Changeset [2653] by Nicklas Nordborg
Change minor version to 1

Sep 20, 2006:

10:56 AM Ticket #368 (Migration should migrate plugin settings for BASE 1 plugins) created by Nicklas Nordborg
The settings should be stored as different configurations for the …

Sep 19, 2006:

4:01 PM Changeset [2652] by Martin Svensson
References #220. Fixed nullpointerexception when calling invoke() in …
2:46 PM Changeset [2651] by Nicklas Nordborg
The agent should not stop BASE. It may run inside another application.
2:32 PM Changeset [2650] by Nicklas Nordborg
Fixes #363: Updating from RC1 throws NullPointerException?
2:32 PM Ticket #363 (Updating from RC1 throws NullPointerException) closed by Nicklas Nordborg
fixed: (In [2650]) Fixes #363: Updating from RC1 throws NullPointerException?
2:27 PM Changeset [2649] by Nicklas Nordborg
Now uses ant task instead of external program to get the subversion …
1:30 PM Changeset [2648] by Nicklas Nordborg
References #351: External job server usage Most functionality is now …
8:07 AM Ticket #367 (Error on "About" update) closed by Nicklas Nordborg
fixed: (In [2647]) Fixes #367: Error on "About" update
8:07 AM Changeset [2647] by Nicklas Nordborg
Fixes #367: Error on "About" update
8:01 AM DownloadPage edited by Nicklas Nordborg
Added warning about the using the trunk (diff)

Sep 18, 2006:

7:33 PM Ticket #367 (Error on "About" update) created by cgwiita@…
Built from subversion checkout, up to changeset 2622. Build and …
2:41 PM Changeset [2646] by Martin Svensson
References #220 Using the plugin permissions when a plugin is executed.
12:41 PM Changeset [2645] by Jari Häkkinen
Removing branch that has been merged into trunk.
11:19 AM Changeset [2644] by Jari Häkkinen
Removing a never used branch.

Sep 15, 2006:

4:45 PM Ticket #366 (Batch upload using zip-files) created by Jari Häkkinen
A way to provide batch upload is to create an upload plug-in that …
4:43 PM Ticket #365 (Use java web start to launch plug-ins) created by Jari Häkkinen
In order to support more powerful visualization plug-ins we should …
4:11 PM Ticket #364 (Support for automatic install of non-core plugins) created by Jari Häkkinen
It would be nice to get an automatic install/update of non-core …
4:08 PM Changeset [2643] by Nicklas Nordborg
References #351: External job server usage In-process job executor is …
3:57 PM Changeset [2642] by Jari Häkkinen
Refs #363. Added information about the RC1 to 2.0 updating problem.
3:47 PM Ticket #363 (Updating from RC1 throws NullPointerException) created by Nicklas Nordborg
[…] The problem is that there is no SchemaVersion? information in …

Sep 14, 2006:

12:17 PM Changeset [2641] by Nicklas Nordborg
References #351: External job server usage The core of the job agent …

Sep 13, 2006:

1:51 PM Changeset [2640] by Martin Svensson
References #220 Improved the handling of permissions in PluginDefinitions?
9:47 AM Changeset [2639] by Nicklas Nordborg
target 'web' now depends on 'main'.
9:43 AM Changeset [2638] by Martin Svensson
Added copyright and license header
9:05 AM Changeset [2637] by Nicklas Nordborg
Deprecated net.sf.basedb.clients.web.util.Values. Use …

Sep 12, 2006:

4:21 PM Changeset [2636] by Martin Svensson
Refereces #220. Separate permissions for plugindefinitions. The use of …
2:48 PM Changeset [2635] by Nicklas Nordborg
Semi-automatic detection if Hibernate mappings needs to be generated or not
2:24 PM Changeset [2634] by Nicklas Nordborg
References #351: External job server usage Communincation with the …
8:21 AM Ticket #362 (Stack trace is output to catalina.out when it shouldn't) closed by Nicklas Nordborg
wontfix: If you wish to do this you have to configure Tomcat differently. The …

Sep 9, 2006:

11:09 PM Ticket #362 (Stack trace is output to catalina.out when it shouldn't) created by Jari Häkkinen
The below exception is thrown when ones tries to run an analysis …
3:48 PM Changeset [2633] by Jari Häkkinen
Added link to http://base.thep.lu.se
2:07 AM Ticket #361 (Export of bioassaysets) created by Jari Häkkinen
A plug-in to export bioassay data is needed as reported at the …

Sep 8, 2006:

4:06 PM Changeset [2632] by Nicklas Nordborg
References #351: External job server usage Started to implement the …
12:17 PM Changeset [2631] by Nicklas Nordborg
References #351: External job server usage Update web pages for …
9:27 AM Ticket #360 (Make subsections on view pages hideable) created by Nicklas Nordborg
Some view pages for items have lots of information on them and they …
9:21 AM Changeset [2630] by Nicklas Nordborg
Fixed compilatio errors in test program after change to JobAgent?
9:17 AM Changeset [2629] by Nicklas Nordborg
References #351: External job server usage Added web pages for …

Sep 7, 2006:

2:23 PM Changeset [2628] by Jari Häkkinen
Added svndigest:ignore property on test data files.
11:20 AM Changeset [2627] by Nicklas Nordborg
References #351: External job server usage Added data layer class, …
11:07 AM Changeset [2626] by Martin Svensson
Updated UML-diagram with entity value for plugin permissions.
9:36 AM Ticket #359 (Sorting on mulitple columns in web tables) created by Nicklas Nordborg
Sometimes you want to sort the results using multiple columns. For …
Note: See TracTimeline for information about the timeline view.