Timeline



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 …

Sep 6, 2006:

4:09 PM Changeset [2625] by Nicklas Nordborg
Added JobAgent? to UML diagram

Sep 5, 2006:

5:02 PM Changeset [2624] by Martin Svensson
Updated the documentation with information about plugin permissions.
1:04 PM DeveloperInformation edited by Nicklas Nordborg
Changed link for development plan to roadmap (diff)
1:01 PM Changeset [2623] by Nicklas Nordborg
Removed links to the very old development status pages. Fixed redirect …
12:01 PM Changeset [2622] by Nicklas Nordborg
References #332: Fix bugs in migration program This should fix most …
11:20 AM Ticket #358 (Better info from Migration tool) created by Nicklas Nordborg
The output of the migration tool is somewhat sporadic and not very …

Sep 1, 2006:

4:49 PM Changeset [2621] by Johan Enell
Merge file added
4:31 PM Tickets #355,​356,​357 batch updated by Johan Enell
fixed: (In [2620]) fixes #355 #356 #357
4:31 PM Changeset [2620] by Johan Enell
fixes #355 #356 #357
4:24 PM Ticket #357 (Importing datamatrix) created by Johan Enell
The Base1PluginExecuter cant import a matrix base file
4:23 PM Ticket #356 (Nullpointer in Base1PluginExecuter) created by Johan Enell
When exporting a hidden string the Base1PluginExecuter is throwing a …
4:21 PM Ticket #355 (Log2ratio is calculated wrong in base1executer) created by Johan Enell
The log2ratio is wrong when exporting data in Base1PluginExecuter
3:44 PM Changeset [2619] by Jari Häkkinen
Removed RC2.

Aug 31, 2006:

2:32 PM Milestone BASE 2.0 completed
This milestone includes * Affymetrix support (delayed from RC2, will …
2:32 PM WikiStart edited by Jari Häkkinen
2.0 released. (diff)
2:23 PM DownloadPage edited by Jari Häkkinen
(diff)
2:21 PM DownloadPage edited by Jari Häkkinen
(diff)
1:38 PM Changeset [2618] by Nicklas Nordborg
Create bugfix branch for 2.0
1:37 PM Changeset [2617] by Nicklas Nordborg
Releasing 2.0
1:23 PM Changeset [2616] by Nicklas Nordborg
Oracle JDBC driver is not needed
1:17 PM Changeset [2615] by Nicklas Nordborg
Added info about debug parameter for the migration.
1:13 PM Changeset [2614] by Nicklas Nordborg
References #332: Base 1 ID lookup is unstable Should fix the original …
1:10 PM Changeset [2613] by Nicklas Nordborg
Fixes incorrect plate mappings installed by previous releases.

Aug 30, 2006:

10:01 PM Changeset [2612] by Nicklas Nordborg
Fixed batch files for running test programs in windows.
4:35 PM Ticket #264 (Base1 plug-in executer enhancements) closed by Johan Enell
fixed
4:34 PM Changeset [2611] by Johan Enell
Fixex #264
4:23 PM Changeset [2610] by Martin Svensson
Filled up some javaDocs
4:06 PM Changeset [2609] by Jari Häkkinen
Added people to credits list.
1:48 PM Changeset [2608] by Jari Häkkinen
Added information about the broken migration tool.
10:23 AM Changeset [2607] by Nicklas Nordborg
Fixed NullPointerException? in configure() method
8:03 AM Changeset [2606] by Nicklas Nordborg
Removed non-existing email address from plugins.
7:57 AM Changeset [2605] by Nicklas Nordborg
Changed text about Type.ITEM to not talk about lists any more.

Aug 29, 2006:

3:59 PM Changeset [2604] by dominic
Removed category duplication
2:59 PM Changeset [2603] by Johan Enell
added some html.javaScriptEncode lines
1:41 PM Ticket #354 (Copy transformation) created by Johan Enell
A copy action for transformations. Create a new transformation from …
12:12 PM Changeset [2602] by dominic
Removed category duplication
11:32 AM Changeset [2601] by Martin Svensson
Updated Javadoc and added missing imports for javadoc ref.
10:00 AM Ticket #353 (Create connectivity from R/BioConductor to BASE) created by Jari Häkkinen
As a part of our effort in an EU project http://www.eu-acgt.org we …
9:58 AM Ticket #352 (Connect parts of the TM4 software suite to BASE) created by Jari Häkkinen
We are going to connect parts of the TM4 suite (http://www.tm4.org) to …

Aug 28, 2006:

3:26 PM Ticket #351 (External job server usage) created by Jari Häkkinen
Add possibility to run jobs in other JVMs that the server.
3:05 PM Ticket #308 (Firefox unresponsive script warning when uploading files) closed by Jari Häkkinen
worksforme
1:56 PM Changeset [2600] by Nicklas Nordborg
Updated About and exception dialog with jdbc driver version, java …
1:06 PM Ticket #350 (Switch to another user functionality) created by Nicklas Nordborg
For users with the "Act as another user" permission it should be …
1:04 PM Changeset [2599] by Nicklas Nordborg
Delete, Restore, Share and Export buttons now works in popup windows …
12:58 PM Ticket #349 (Callback for events to plugins) created by Nicklas Nordborg
Make it possible to catch onChange event for plugin parameters and …
11:42 AM Ticket #348 (Take ownership of items) created by Nicklas Nordborg
Implement interface for taking the ownership of an item, given that …
11:40 AM Ticket #347 (Give administrators access to other users trashcans) created by Nicklas Nordborg
11:39 AM Ticket #346 (If an item is used, get information about the items that are using it) created by Nicklas Nordborg
A used item can't be deleted and it is annoying to not know what is …
11:37 AM Ticket #345 (List all items owned by a user) created by Nicklas Nordborg
11:18 AM Ticket #344 (Display extra values in data tables and other places) created by Nicklas Nordborg
In the current implementation it is not possible to display extra …
11:15 AM Ticket #343 (Plot tool should be able to use other annotations than bioassay) created by Nicklas Nordborg
In the current implementation you can only annotate the plots with the …
11:13 AM Ticket #342 (Plot tool should be able to use extra values) created by Nicklas Nordborg
The current implementation cannot plot extra values.
10:57 AM Ticket #341 (Raw data type conversion plugin) created by Nicklas Nordborg
Develop one or more plugins that can convert raw data of one type to …
10:55 AM Ticket #340 (Experiment validation tool) created by Nicklas Nordborg
The core is very loose when it comes to checking the structure of …
10:50 AM Ticket #339 (Protocol parameters) created by Nicklas Nordborg
Make it possible to specify parameters for a protocol. Then, when that …
10:49 AM Ticket #338 (Tab2Mage import plugin) created by Nicklas Nordborg
Create a plugin that can import Tab2Mage files.
10:48 AM Ticket #337 (Tab2Mage export plugin) created by Nicklas Nordborg
Create a plugin that can export an experiment in Tab2Mage format
10:47 AM Ticket #336 (Install common file formats with main installation) created by Nicklas Nordborg
Plugin configurations for some common file formats could probably be …
10:46 AM Ticket #335 (Plugins for importing/exporting plugin configurations) created by Nicklas Nordborg
Configuring a plugin is a tedious task that sometimes requires …
10:44 AM Ticket #334 (Project default items) created by Nicklas Nordborg
Make is possible to specify default items (protocols, scanner, …
10:42 AM Ticket #333 (Administrator documentation) created by Nicklas Nordborg
Write documentation for the Base 2 server administrator. Base 2 has a …
10:37 AM Ticket #300 (Fields in Properties display mis-aligned) closed by Nicklas Nordborg
fixed: Has probably been fixed by one of the style sheet changes some time ago.
9:09 AM Ticket #332 (Fix bugs in migration program) created by Nicklas Nordborg
The migration tool is not stable if it encounters a Base 1 …
9:04 AM Ticket #331 (Remember the last used item when creating new items) closed by Nicklas Nordborg
fixed: (In [2598]) Fixes #331: Remember the last used item when creating new items
9:04 AM Changeset [2598] by Nicklas Nordborg
Fixes #331: Remember the last used item when creating new items
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