Timeline



Sep 7, 2006:

2:23 PM Changeset [2628] by Jari Häkkinen
Added svndigest:ignore property on test data files.
11:20 AM Ticket #351 (External job server usage) updated by Nicklas Nordborg
(In [2627]) References #351: External job server usage Added data …
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 …
12:47 PM Ticket #351 (External job server usage) updated by Nicklas Nordborg
Status changed
12:01 PM Ticket #332 (Fix bugs in migration program) updated by Nicklas Nordborg
(In [2622]) References #332: Fix bugs in migration program This …
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) updated by Nicklas Nordborg
Component changed
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 4, 2006:

4:36 PM Ticket #220 (Plugin permissions) updated by Martin Svensson
Status changed
3:49 PM Ticket #294 (Performance testing: Plugin-in execution time) updated by Martin Svensson
Owner changed
3:49 PM Ticket #220 (Plugin permissions) updated by Martin Svensson
Owner changed
3:47 PM Ticket #336 (Install common file formats with main installation) updated by Martin Svensson
Owner changed
3:47 PM Ticket #335 (Plugins for importing/exporting plugin configurations) updated by Martin Svensson
Owner changed
3:47 PM Ticket #344 (Display extra values in data tables and other places) updated by Martin Svensson
Owner changed
11:18 AM Ticket #332 (Fix bugs in migration program) updated by Martin Svensson
Also:: Protocol is not connected with Hybridization

Sep 1, 2006:

4:49 PM Changeset [2621] by Johan Enell
Merge file added
4:39 PM Ticket #332 (Fix bugs in migration program) updated by Martin Svensson
* One more issue found. Original and remaining quantity for extracts …
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.
2:04 PM Ticket #10 (Analysis: Hierarchical clustering) updated by Jari Häkkinen
Milestone changed
2:00 PM Ticket #332 (Fix bugs in migration program) updated by Jari Häkkinen
Milestone changed
1:21 PM Ticket #332 (Fix bugs in migration program) updated by Nicklas Nordborg
Summary changed
Here are some more issues that I have found: * BASE 1 permissions …

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 Ticket #332 (Fix bugs in migration program) updated by Nicklas Nordborg
(In [2614]) References #332: Base 1 ID lookup is unstable Should fix …
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.
11:32 AM Ticket #354 (Copy transformation) updated by Martin Svensson
Status, Owner changed

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
2:11 PM Ticket #354 (Copy transformation) updated by Johan Enell
Description changed
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.
10:01 AM Ticket #352 (Connect parts of the TM4 software suite to BASE) updated by Jari Häkkinen
Owner, Component changed
10:01 AM Ticket #353 (Create connectivity from R/BioConductor to BASE) updated by Jari Häkkinen
Component changed
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) updated by Jari Häkkinen
Type changed
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 …
8:20 AM Ticket #332 (Fix bugs in migration program) updated by Nicklas Nordborg
Status changed
8:17 AM Ticket #340 (Experiment validation tool) updated by Nicklas Nordborg
Priority changed
8:16 AM Ticket #311 (Allow parsing of numbers with different locale settings) updated by Nicklas Nordborg
Priority changed
8:16 AM Ticket #317 (Display and enter dates in different formats) updated by Nicklas Nordborg
Priority changed
8:15 AM Ticket #333 (Administrator documentation) updated by Nicklas Nordborg
Priority changed
8:15 AM Ticket #337 (Tab2Mage export plugin) updated by Nicklas Nordborg
Priority changed
8:06 AM Ticket #169 (Use formulas for creating extra values) updated by Nicklas Nordborg
Priority changed
8:05 AM Ticket #313 (Error handling in import plugins) updated by Nicklas Nordborg
Priority changed
8:04 AM Ticket #349 (Callback for events to plugins) updated by Nicklas Nordborg
Priority changed
8:04 AM Ticket #351 (External job server usage) updated by Nicklas Nordborg
Type changed
8:03 AM Ticket #318 (Plugin configuration values are not stored for a job) updated by Nicklas Nordborg
Priority changed

Aug 28, 2006:

4:06 PM Ticket #332 (Fix bugs in migration program) updated by Jari Häkkinen
Version changed
4:06 PM Ticket #10 (Analysis: Hierarchical clustering) updated by Jari Häkkinen
Version changed
3:27 PM Ticket #332 (Fix bugs in migration program) updated by Jari Häkkinen
Priority changed
3:27 PM Ticket #10 (Analysis: Hierarchical clustering) updated by Jari Häkkinen
Priority changed
3:26 PM Ticket #351 (External job server usage) created by Jari Häkkinen
Add possibility to run jobs in other JVMs that the server.
3:24 PM Ticket #350 (Switch to another user functionality) updated by Jari Häkkinen
Milestone changed
3:23 PM Ticket #349 (Callback for events to plugins) updated by Jari Häkkinen
Milestone changed
3:22 PM Ticket #348 (Take ownership of items) updated by Jari Häkkinen
Milestone changed
3:21 PM Ticket #347 (Give administrators access to other users trashcans) updated by Jari Häkkinen
Milestone changed
3:21 PM Ticket #346 (If an item is used, get information about the items that are using it) updated by Jari Häkkinen
Milestone changed
3:21 PM Ticket #345 (List all items owned by a user) updated by Jari Häkkinen
Milestone changed
3:21 PM Ticket #344 (Display extra values in data tables and other places) updated by Jari Häkkinen
Milestone changed
3:20 PM Ticket #343 (Plot tool should be able to use other annotations than bioassay) updated by Jari Häkkinen
Milestone changed
3:20 PM Ticket #342 (Plot tool should be able to use extra values) updated by Jari Häkkinen
Milestone changed
3:19 PM Ticket #340 (Experiment validation tool) updated by Jari Häkkinen
Milestone changed
3:18 PM Ticket #339 (Protocol parameters) updated by Jari Häkkinen
Milestone changed
3:17 PM Ticket #337 (Tab2Mage export plugin) updated by Jari Häkkinen
Milestone changed
3:17 PM Ticket #336 (Install common file formats with main installation) updated by Jari Häkkinen
Milestone changed
3:16 PM Ticket #335 (Plugins for importing/exporting plugin configurations) updated by Jari Häkkinen
Milestone changed
3:16 PM Ticket #334 (Project default items) updated by Jari Häkkinen
Milestone changed
3:15 PM Ticket #333 (Administrator documentation) updated by Jari Häkkinen
Milestone changed
3:14 PM Ticket #332 (Fix bugs in migration program) updated by Jari Häkkinen
Milestone changed
3:10 PM Ticket #326 (Mass annotation plug-in) updated by Jari Häkkinen
Version, Milestone changed
3:09 PM Ticket #318 (Plugin configuration values are not stored for a job) updated by Jari Häkkinen
Version, Milestone changed
3:08 PM Ticket #317 (Display and enter dates in different formats) updated by Jari Häkkinen
Version, Milestone changed
3:07 PM Ticket #316 (Add support for color coding in data tables) updated by Jari Häkkinen
Version, Milestone changed
3:07 PM Ticket #313 (Error handling in import plugins) updated by Jari Häkkinen
Milestone changed
3:07 PM Ticket #312 (ReporterType import) updated by Jari Häkkinen
Milestone changed
3:06 PM Ticket #311 (Allow parsing of numbers with different locale settings) updated by Jari Häkkinen
Version, Milestone changed
3:05 PM Ticket #308 (Firefox unresponsive script warning when uploading files) closed by Jari Häkkinen
worksforme
3:04 PM Ticket #301 (Better GUI for defining file formats) updated by Jari Häkkinen
Version, Milestone changed
3:04 PM Ticket #298 (Add administrator page for viewing disk usage statistics) updated by Jari Häkkinen
Version, Milestone changed
3:04 PM Ticket #295 (Filter on selected bioassays) updated by Jari Häkkinen
Milestone changed
3:04 PM Ticket #294 (Performance testing: Plugin-in execution time) updated by Jari Häkkinen
Milestone changed
3:03 PM Ticket #293 (allow queuing of uploads) updated by Jari Häkkinen
Milestone, Version changed
3:01 PM Ticket #262 (Overview of an experiment) updated by Jari Häkkinen
Version, Milestone changed
3:00 PM Ticket #257 (Fix the Jep.nodeToExpression method) updated by Jari Häkkinen
Version, Milestone changed
3:00 PM Ticket #252 (Make the trashcan smarter when deleting items) updated by Jari Häkkinen
Version, Milestone changed
2:59 PM Ticket #241 (Files that have been used for parameters to a job can't be deleted properly) updated by Jari Häkkinen
Milestone changed
2:57 PM Ticket #220 (Plugin permissions) updated by Jari Häkkinen
Milestone changed
2:55 PM Ticket #212 (Array slide import plugin) updated by Jari Häkkinen
Version, Milestone changed
2:52 PM Ticket #201 (Experiment directory) updated by Jari Häkkinen
Milestone changed
2:51 PM Ticket #189 (Allow export plugins to send download immediately to client) updated by Jari Häkkinen
Milestone changed
2:51 PM Ticket #172 (Add externalId property to annotation type) updated by Jari Häkkinen
Milestone changed
2:50 PM Ticket #169 (Use formulas for creating extra values) updated by Jari Häkkinen
Milestone changed
2:50 PM Ticket #153 (More progress from importer plug-ins) updated by Jari Häkkinen
Milestone changed
2:49 PM Ticket #146 (Add help text to the web gui) updated by Jari Häkkinen
Milestone changed
2:49 PM Ticket #140 (Write documentation: 5e) Secondary file storage) updated by Jari Häkkinen
Milestone changed
2:49 PM Ticket #138 (Write documentation: 5c) Authentication plug-ins) updated by Jari Häkkinen
Milestone changed
2:48 PM Ticket #108 (Logging the change history of an item) updated by Jari Häkkinen
Milestone changed
2:46 PM Ticket #10 (Analysis: Hierarchical clustering) updated by Jari Häkkinen
Milestone changed
2:05 PM Ticket #10 (Analysis: Hierarchical clustering) updated by Jari Häkkinen
Milestone changed
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 …
11:44 AM Ticket #347 (Give administrators access to other users trashcans) updated by Nicklas Nordborg
When the root user deletes an item owner by another user, it ends up …
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 …
10:56 AM Ticket #262 (Overview of an experiment) updated by Nicklas Nordborg
Description, Milestone changed
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

Aug 25, 2006:

4:07 PM Ticket #331 (Remember the last used item when creating new items) updated by Nicklas Nordborg
(In [2597]) References #331: Remember the last used item when creating …
4:07 PM Changeset [2597] by Nicklas Nordborg
References #331: Remember the last used item when creating new items …
1:15 PM Ticket #331 (Remember the last used item when creating new items) updated by Nicklas Nordborg
(In [2596]) References #331: Remember the last used item when creating …
1:15 PM Changeset [2596] by Nicklas Nordborg
References #331: Remember the last used item when creating new items …
12:45 PM Changeset [2595] by dominic

Aug 24, 2006:

4:33 PM Changeset [2594] by Martin Svensson
Correct column names in plot types table, chapter 6, §7
4:24 PM Changeset [2593] by Martin Svensson
Added a missing configuration value for the Raw data importer in the …
3:55 PM Ticket #331 (Remember the last used item when creating new items) updated by Nicklas Nordborg
Owner, Status, Milestone changed
3:47 PM Changeset [2592] by Martin Svensson
Made toolbar visible in popupwindows.
3:42 PM Changeset [2591] by Nicklas Nordborg
:Merged trunk changes r2577:2590 into dominic_annotations
2:04 PM Changeset [2590] by Nicklas Nordborg
Create hybridzations from multiple labeled extracts
1:01 PM Changeset [2589] by Nicklas Nordborg
Fixed incorrect link when write permission is missing.
12:54 PM Ticket #330 (Make it possible to inherit annotations for new items) closed by Nicklas Nordborg
fixed: (In [2588]) Fixes #330: Make it possible to inherit annotations for …
12:54 PM Changeset [2588] by Nicklas Nordborg
Fixes #330: Make it possible to inherit annotations for new items
12:53 PM Changeset [2587] by Nicklas Nordborg
Plates now save the annotations
12:52 PM Changeset [2586] by Nicklas Nordborg
Get all annotatable parents
10:47 AM Changeset [2585] by dominic
the category column removed
9:58 AM Changeset [2584] by Nicklas Nordborg
References #330: Make it possible to inherit annotations for new items …
9:58 AM Ticket #330 (Make it possible to inherit annotations for new items) updated by Nicklas Nordborg
(In [2584]) References #330: Make it possible to inherit annotations …
9:20 AM Changeset [2583] by Nicklas Nordborg
Updated documentation about where to find test data
9:06 AM Changeset [2582] by Nicklas Nordborg
8:49 AM Changeset [2581] by Nicklas Nordborg
Replaced fixed array with map. Use printStackTrace() method to always …
7:57 AM Changeset [2580] by Nicklas Nordborg
Changed yellow icon background to grey

Aug 23, 2006:

4:10 PM DeveloperInformation edited by Jari Häkkinen
Added test data repo. (diff)
3:47 PM Ticket #330 (Make it possible to inherit annotations for new items) updated by Nicklas Nordborg
Milestone, Status changed
3:27 PM Ticket #329 (Auto-focus on input field when selecting annotation or plugin parameter) closed by Nicklas Nordborg
fixed: (In [2579]) Fixes #329: Auto-focus on input field when selecting …
3:27 PM Changeset [2579] by Nicklas Nordborg
Fixes #329: Auto-focus on input field when selecting annotation or …
3:20 PM Ticket #329 (Auto-focus on input field when selecting annotation or plugin parameter) updated by Nicklas Nordborg
Status changed
2:13 PM Ticket #331 (Remember the last used item when creating new items) created by Nicklas Nordborg
For example, when you create a new Raw bioassay you may select "Scan", …
1:57 PM Ticket #330 (Make it possible to inherit annotations for new items) created by Nicklas Nordborg
The current implemenation requires that the item is saved before it …
1:32 PM Ticket #329 (Auto-focus on input field when selecting annotation or plugin parameter) created by Nicklas Nordborg
When you click on a plugin parameter or annotation in the left list an …
12:49 PM Changeset [2578] by Nicklas Nordborg
:Fixed compilation errors after merge
12:34 PM Changeset [2577] by Nicklas Nordborg
:Merged trunk changes r2343:2576 into dominic_annotations
10:51 AM Changeset [2576] by Nicklas Nordborg
Test formulas before experiments since formulas are used in the …
10:36 AM Changeset [2575] by Nicklas Nordborg
Copy function for plugin configurations now copy the parameters also.
8:58 AM Changeset [2574] by Nicklas Nordborg
Don't show "Configure plugin" action if the logged in user doesn't …
8:54 AM Changeset [2573] by Nicklas Nordborg
Fixes #328: Enable clicks on the enumeration option when annotating …
8:54 AM Ticket #328 (Enable clicks on the enumeration option when annotating items) closed by Nicklas Nordborg
fixed: (In [2573]) Fixes #328: Enable clicks on the enumeration option when …

Aug 22, 2006:

3:39 PM Ticket #328 (Enable clicks on the enumeration option when annotating items) updated by Nicklas Nordborg
Status changed
2:52 PM Ticket #327 (Not all users are listed as members in a group) closed by Nicklas Nordborg
fixed: (In [2572]) Fixes #327: Not all users are listed as members in a group
2:52 PM Changeset [2572] by Nicklas Nordborg
Fixes #327: Not all users are listed as members in a group
2:48 PM Ticket #327 (Not all users are listed as members in a group) updated by Nicklas Nordborg
Status changed
2:41 PM Changeset [2571] by Nicklas Nordborg
Original quantities are empty by default. Event dates default to …
2:40 PM Changeset [2570] by Nicklas Nordborg
Removed list of labeled extracts from labels view since it is …
2:35 PM Changeset [2569] by Nicklas Nordborg
Use dye-swap labeled extracts for dye-swap hybridizations
2:22 PM Tickets #221,​222 batch updated by Nicklas Nordborg
(In [2568]) Fixes #221: Create enhanced test procedure. References …
2:22 PM Changeset [2568] by Nicklas Nordborg
Fixes #221: Create enhanced test procedure. References #222: Automated …
1:42 PM Ticket #259 (A job's progress doesn't get upadated when a job is executing in ...) closed by Nicklas Nordborg
fixed: (In [2567]) Fixes #259: A job's progress doesn't get upadated when a …
1:42 PM Changeset [2567] by Nicklas Nordborg
Fixes #259: A job's progress doesn't get upadated when a job is …
1:41 PM Ticket #259 (A job's progress doesn't get upadated when a job is executing in ...) updated by Nicklas Nordborg
Milestone, Status changed
1:13 PM Changeset [2566] by Martin Svensson
Fixed an unhandled exception when trying to read the quantity of an …
1:10 PM Changeset [2565] by Nicklas Nordborg
Pad plate names with 0 instead of space since Postgres ignores spaces …
1:08 PM Changeset [2564] by Nicklas Nordborg
Added Application.start(boolean) method that allows an application to …
12:59 PM Changeset [2563] by Nicklas Nordborg
Break after ten iterations to avoid endless loops
11:06 AM Changeset [2562] by Martin Svensson
Fixed an unhandled exception when trying to read the quantity of an …
10:43 AM Changeset [2561] by Nicklas Nordborg
Made some optimizations to the Lowess normalization. Arrays get a size …
8:49 AM Changeset [2560] by Nicklas Nordborg
Removed duplicated formulas
8:46 AM Changeset [2559] by Nicklas Nordborg
Dates are now shown with time information as well
8:42 AM Changeset [2558] by Nicklas Nordborg
No publication date by default

Aug 21, 2006:

3:04 PM Changeset [2557] by Martin Svensson
Fixes #325 Corrupt page when viewing an biomaterial event
3:04 PM Ticket #325 (Corrupt page when viewing an biomaterial event) closed by Martin Svensson
fixed: (In [2557]) Fixes #325 Corrupt page when viewing an biomaterial event
2:43 PM Changeset [2556] by Nicklas Nordborg
Display label of each labeled extract
2:26 PM Ticket #328 (Enable clicks on the enumeration option when annotating items) created by Nicklas Nordborg
When the web interface displays radio buttons or checkboxes for …
2:13 PM Changeset [2555] by Nicklas Nordborg
Fixed ArrayDesignPlate.getQuery() method to create a query that …
1:44 PM Changeset [2554] by Nicklas Nordborg
Fixed incorrect message when no plates are connected with an array design.
1:43 PM Changeset [2553] by Nicklas Nordborg
Removed "New plate" functionality since plates are usually imported …
1:41 PM Changeset [2552] by Nicklas Nordborg
Display times with seconds.
1:05 PM Ticket #327 (Not all users are listed as members in a group) created by Nicklas Nordborg
Users that have been assigned a quota group are not listed as members …
12:14 PM Ticket #326 (Mass annotation plug-in) created by Johan Enell
There should be a plugin for doing anotation of item from a file. The …

Aug 18, 2006:

5:51 PM Changeset [2551] by Johan Enell
corrected a nullpointer in the reader
5:43 PM Changeset [2550] by Johan Enell
made some major design changes looks a little bit better now
4:33 PM Changeset [2549] by Martin Svensson
Creat a copy of an existing plugin configuration is added to the web-gui.

Aug 17, 2006:

3:43 PM Ticket #222 (Automated test program suite for enhanced test procedure) closed by Nicklas Nordborg
fixed: (In [2548]) Fixes #222: Automated test program suite for enhanced test …
3:43 PM Changeset [2548] by Nicklas Nordborg
Fixes #222: Automated test program suite for enhanced test procedure
2:26 PM Ticket #264 (Base1 plug-in executer enhancements) updated by Johan Enell
Annotations are now exported
2:23 PM Changeset [2547] by Johan Enell
exports annotations
2:23 PM Changeset [2546] by Johan Enell
made getIdFromPath public
11:49 AM Changeset [2545] by Nicklas Nordborg
Now handles the case with a null reporter correctly
11:48 AM Changeset [2544] by Nicklas Nordborg
Fixed index problem when linking to plates/wells (use 0-based instead …
11:47 AM Changeset [2543] by Nicklas Nordborg
Let superclass handle error reporting
11:47 AM Changeset [2542] by Nicklas Nordborg
Fixed equals() method to behave as documented
11:45 AM Changeset [2541] by Nicklas Nordborg
Better error reportering which include line number in most error messages
11:44 AM Changeset [2540] by Nicklas Nordborg
Added line number info to FlatFileParser.Line object
11:09 AM Changeset [2539] by Nicklas Nordborg
* FlatFileParse now ignores comment lines within the data section. * …
11:08 AM Changeset [2538] by Nicklas Nordborg
Fixed bad link on Run plugin button
10:53 AM Ticket #325 (Corrupt page when viewing an biomaterial event) updated by Martin Svensson
Status changed
10:39 AM Changeset [2537] by Nicklas Nordborg
Fixes #324: Filter feature on block results in error message
10:39 AM Ticket #324 (Filter feature on block results in error message) closed by Nicklas Nordborg
fixed: (In [2537]) Fixes #324: Filter feature on block results in error message
9:13 AM Ticket #325 (Corrupt page when viewing an biomaterial event) created by Martin Svensson
Logg in with user permissions. View a sample that's shared to you. Go …

Aug 16, 2006:

4:02 PM Ticket #324 (Filter feature on block results in error message) created by Nicklas Nordborg
could not resolve property: block of: …
12:05 PM Changeset [2536] by Nicklas Nordborg
Fixes #197: Submenu onClick
12:05 PM Ticket #197 (Submenu onClick) closed by Nicklas Nordborg
fixed: (In [2536]) Fixes #197: Submenu onClick
12:04 PM Ticket #197 (Submenu onClick) updated by Nicklas Nordborg
Milestone changed
11:49 AM Ticket #319 (Spot images shown in experiment explorer do not seem to correspond to ...) closed by Nicklas Nordborg
fixed: (In [2535]) Fixes #319: Spot images shown in experiment explorer do …
11:49 AM Changeset [2535] by Nicklas Nordborg
Fixes #319: Spot images shown in experiment explorer do not seem to …
11:05 AM Ticket #319 (Spot images shown in experiment explorer do not seem to correspond to ...) updated by Nicklas Nordborg
Status changed
11:01 AM Changeset [2534] by Nicklas Nordborg
Fixes problem with disappearing buttons and page width in Plot tool.
9:46 AM Changeset [2533] by Martin Svensson
Fixes #323 Corrupt link in Samples->'The sample'->Event
9:46 AM Ticket #323 (Corrupt link in Samples->'The sample'->Event) closed by Martin Svensson
fixed: (In [2533]) Fixes #323 Corrupt link in Samples->'The sample'->Event
9:27 AM Changeset [2532] by Nicklas Nordborg
Fixed link to bioassayset tools when viewing a transformation.
9:15 AM Changeset [2531] by Nicklas Nordborg
Experiment explorer can now handle the case with zero matching reporters
9:04 AM Changeset [2530] by Nicklas Nordborg
Added caching for AnnotationTypeCategoryData as specified
9:03 AM Ticket #323 (Corrupt link in Samples->'The sample'->Event) updated by Martin Svensson
Status changed
9:03 AM Ticket #323 (Corrupt link in Samples->'The sample'->Event) created by Martin Svensson
Logged in as a normal user. Link to protocol on view_event_page. …
9:02 AM Ticket #131 (Write documentation 4a) Schematic overview of BASE) closed by Nicklas Nordborg
fixed: (In [2529]) Fixes #131: Write documentation 4a) Schematic overview of BASE
9:02 AM Changeset [2529] by Nicklas Nordborg
Fixes #131: Write documentation 4a) Schematic overview of BASE
9:02 AM Ticket #131 (Write documentation 4a) Schematic overview of BASE) updated by Nicklas Nordborg
Summary changed

Aug 15, 2006:

10:19 PM Ticket #322 (Wrong message when not all item could be restored) closed by Martin Svensson
fixed: (In [2528]) Fixes #322 Wrong message when not all item could be restored
10:19 PM Changeset [2528] by Martin Svensson
Fixes #322 Wrong message when not all item could be restored
4:49 PM Changeset [2527] by Johan Enell
missed a null check
4:35 PM Ticket #305 (delete recusively) closed by Martin Svensson
fixed: (In [2526]) Fixes #305 Delete recursively. Implemented for …
4:35 PM Changeset [2526] by Martin Svensson
Fixes #305 Delete recursively. Implemented for Directories, …
4:12 PM Ticket #322 (Wrong message when not all item could be restored) created by Martin Svensson
If the user doesn't have permission to restore an item the dialog …
3:47 PM Changeset [2525] by Nicklas Nordborg
References #131: Write documentation 3a) Schematic overview of BASE …
3:47 PM Ticket #131 (Write documentation 4a) Schematic overview of BASE) updated by Nicklas Nordborg
(In [2525]) References #131: Write documentation 3a) Schematic …
3:41 PM Changeset [2524] by Nicklas Nordborg
Compile JSP pages with more memeory since we got an OutOfMemoryError
3:40 PM Ticket #321 (Error on filter page: NoSuchMethod) closed by Nicklas Nordborg
fixed: (In [2523]) Fixes #321: Error on filter page: NoSuchMethod And two …
3:40 PM Changeset [2523] by Nicklas Nordborg
Fixes #321: Error on filter page: NoSuchMethod And two other …
2:52 PM Ticket #321 (Error on filter page: NoSuchMethod) created by Johan Enell
When I try the ' java.lang.NoSuchMethodError on page …
1:17 PM Ticket #320 (Nullpointer in experiment explorer) closed by Johan Enell
fixed: (In [2522]) Fixes #320
1:17 PM Changeset [2522] by Johan Enell
Fixes #320
1:07 PM Ticket #320 (Nullpointer in experiment explorer) updated by Johan Enell
Owner, Component changed
12:04 PM Ticket #320 (Nullpointer in experiment explorer) created by Johan Enell
When choosing annotation. Base version 2.0 (build #2517; schema …
11:21 AM Changeset [2521] by Johan Enell
supports annotation parameter
8:39 AM Ticket #131 (Write documentation 4a) Schematic overview of BASE) updated by Nicklas Nordborg
Status changed
8:32 AM Changeset [2520] by Nicklas Nordborg
Updated documentation that contained errors or wasn't up to date with …

Aug 14, 2006:

4:22 PM Changeset [2519] by Johan Enell
will remove stdin/stdout if specified by config
2:30 PM Changeset [2518] by Nicklas Nordborg
Fixes #170: Categorize annotation types
2:30 PM Ticket #170 (Categorize annotation types) closed by Nicklas Nordborg
fixed: (In [2518]) Fixes #170: Categorize annotation types
12:07 PM Changeset [2517] by Nicklas Nordborg
References #170: Install now sets correct permissions for categories
11:52 AM Changeset [2516] by Nicklas Nordborg
References #170: Categorize annotation types Updated UML diagram
11:50 AM Changeset [2515] by Nicklas Nordborg
References #170: Categorize annotation types Most of the core and web …
8:05 AM Ticket #319 (Spot images shown in experiment explorer do not seem to correspond to ...) updated by Nicklas Nordborg
Milestone, Owner changed
There are some info that doesn't make sense to average. Spot images is …

Aug 12, 2006:

11:38 PM Ticket #10 (Analysis: Hierarchical clustering) updated by Jari Häkkinen
Status, Owner changed
11:37 PM Ticket #150 (Affymetrix support) closed by Jari Häkkinen
fixed: * The resulting expression matrix is still not available as a file and …
11:33 PM DownloadPage edited by Jari Häkkinen
New packaged release (revision 2514). (diff)
12:18 AM Ticket #319 (Spot images shown in experiment explorer do not seem to correspond to ...) created by base
When viewing avg of spots in experiment explorer under reporter view, …

Aug 11, 2006:

2:15 PM Ticket #127 (Experiment explorer) closed by Nicklas Nordborg
fixed: (In [2514]) Fixes #127: Experiment explorer
2:15 PM Changeset [2514] by Nicklas Nordborg
Fixes #127: Experiment explorer
8:15 AM Changeset [2513] by Nicklas Nordborg
Do not show message about configurations for non-configurable plugins. …

Aug 10, 2006:

1:15 PM Ticket #305 (delete recusively) updated by Martin Svensson
Status changed
12:18 PM Ticket #318 (Plugin configuration values are not stored for a job) created by Nicklas Nordborg
Consider the following case: A user selects a plugin and …
12:08 PM Ticket #305 (delete recusively) updated by Nicklas Nordborg
Owner, Milestone changed
12:07 PM Ticket #217 (Delete entire directory structure) closed by Nicklas Nordborg
duplicate: Is part of #305: delete recusively
11:54 AM Ticket #302 (Running a plugin without a configuration should not be possible ...) closed by Nicklas Nordborg
fixed: (In [2512]) Fixes #302: Running a plugin without a configuration …
11:54 AM Changeset [2512] by Nicklas Nordborg
Fixes #302: Running a plugin without a configuration should not be possible
9:36 AM Ticket #39 (Handling a string with only blank space in required fields) closed by Martin Svensson
fixed: (In [2511]) Fixes #39 Handling a string with only blank space in …
9:36 AM Changeset [2511] by Martin Svensson
Fixes #39 Handling a string with only blank space in required fields. …
8:17 AM Ticket #302 (Running a plugin without a configuration should not be possible ...) updated by Nicklas Nordborg
Status changed
8:16 AM Changeset [2510] by Nicklas Nordborg
Fixes #306: empty trashcan
8:16 AM Ticket #306 (empty trashcan) closed by Nicklas Nordborg
fixed: (In [2510]) Fixes #306: empty trashcan

Aug 9, 2006:

4:53 PM Ticket #39 (Handling a string with only blank space in required fields) updated by Martin Svensson
(In [2509]) References #39 Handling a string with only blank space in …
4:53 PM Changeset [2509] by Martin Svensson
References #39 Handling a string with only blank space in required …
4:15 PM Ticket #39 (Handling a string with only blank space in required fields) updated by Martin Svensson
Status, Owner changed
3:54 PM Ticket #306 (empty trashcan) updated by Nicklas Nordborg
Status, Milestone changed
3:48 PM Ticket #302 (Running a plugin without a configuration should not be possible ...) updated by Nicklas Nordborg
Milestone changed
3:30 PM Ticket #317 (Display and enter dates in different formats) updated by Johan Enell
The new format should also include time if possible.
2:59 PM Changeset [2508] by Martin Svensson
Fixes #315 Ctrl + clicking on the name of an images - opens two edit …
2:59 PM Ticket #315 (Ctrl + clicking on the name of an images - opens two edit windows for ...) closed by Martin Svensson
fixed: (In [2508]) Fixes #315 Ctrl + clicking on the name of an images - …
2:54 PM Ticket #315 (Ctrl + clicking on the name of an images - opens two edit windows for ...) updated by Martin Svensson
Status changed
2:46 PM Ticket #317 (Display and enter dates in different formats) created by Nicklas Nordborg
Add support in the web client for displaying and entering dates in …
2:45 PM Ticket #316 (Add support for color coding in data tables) created by Nicklas Nordborg
Base1 has a nice feature where ratios are displayed with a colored …
2:40 PM Ticket #313 (Error handling in import plugins) updated by Nicklas Nordborg
Maybe this should be configurable at the job level. Ie. the user could …
2:35 PM Ticket #266 (Strange mouse-over message in some places) closed by Martin Svensson
fixed: (In [2507]) Fixes #266 Strange mouse-over message in some places. view …
2:35 PM Changeset [2507] by Martin Svensson
Fixes #266 Strange mouse-over message in some places. view pages updated.
2:33 PM Ticket #170 (Categorize annotation types) updated by Nicklas Nordborg
(In [2506]) References #170: Categorize annotation types Updated UML …
2:33 PM Changeset [2506] by Nicklas Nordborg
References #170: Categorize annotation types Updated UML diagram
2:12 PM Ticket #170 (Categorize annotation types) updated by Nicklas Nordborg
Status changed
2:10 PM Changeset [2505] by Johan Enell
plugin parameters removed only job parameters
1:37 PM Ticket #315 (Ctrl + clicking on the name of an images - opens two edit windows for ...) created by Martin Svensson
1:33 PM Changeset [2504] by Nicklas Nordborg
Fixed problem with execution time estimation.
1:20 PM Ticket #266 (Strange mouse-over message in some places) updated by Martin Svensson
(In [2503]) References #266 Strange mouse-over message in some places. …
1:20 PM Changeset [2503] by Martin Svensson
References #266 Strange mouse-over message in some places. file-, …
1:03 PM Ticket #127 (Experiment explorer) updated by Nicklas Nordborg
(In [2502]) References #127: Experiment explorer Cleaned up and …
1:03 PM Changeset [2502] by Nicklas Nordborg
References #127: Experiment explorer Cleaned up and documented most …
11:17 AM Ticket #266 (Strange mouse-over message in some places) updated by Martin Svensson
(In [2501]) References #266 Strange mouse-over message in some places. …
11:17 AM Changeset [2501] by Martin Svensson
References #266 Strange mouse-over message in some places. …
10:36 AM Changeset [2500] by Martin Svensson
References # 266 Strange mouse-over message in some places. …

Aug 8, 2006:

4:09 PM Changeset [2499] by Nicklas Nordborg
Fixed problem with the new update method.
4:01 PM Ticket #314 (Update documentation that shows code examples with ...) closed by Nicklas Nordborg
fixed: (In [2498]) Fixes #314: Update documentation that shows code examples …
4:01 PM Changeset [2498] by Nicklas Nordborg
Fixes #314: Update documentation that shows code examples with …
3:58 PM Ticket #266 (Strange mouse-over message in some places) updated by Martin Svensson
Status changed
3:58 PM Ticket #266 (Strange mouse-over message in some places) updated by Martin Svensson
Owner changed
3:49 PM Ticket #314 (Update documentation that shows code examples with ...) updated by Nicklas Nordborg
Status changed
3:43 PM Changeset [2497] by Nicklas Nordborg
Better performance when creating a root bioassayset by fetching the …
2:55 PM Changeset [2496] by Nicklas Nordborg
Deleted obsolete files related to the removed AffyFeatureData class.
2:52 PM Ticket #173 (Attach Hardware/Software to more items) closed by Martin Svensson
fixed: (In [2495]) Fixes #173 Fully functional to create/delete HardwareType
2:52 PM Changeset [2495] by Martin Svensson
Fixes #173 Fully functional to create/delete HardwareType and attach …
1:35 PM Ticket #314 (Update documentation that shows code examples with ...) created by Nicklas Nordborg
The Transformation.newProduct() method changed because of ticket #196. …
1:20 PM Changeset [2494] by Nicklas Nordborg
* Fixed problem with FlatFileParser skipping every other section. * …
1:13 PM Changeset [2493] by dominic
gui changes and removal of default categories in install.java
12:57 PM Ticket #196 (Transformation.newProduct should create child BioAssays if possible) closed by Nicklas Nordborg
fixed: (In [2492]) Fixes #196: Transformation.newProduct should create child …
12:57 PM Changeset [2492] by Nicklas Nordborg
Fixes #196: Transformation.newProduct should create child BioAssays if …
11:36 AM DownloadPage edited by Jari Häkkinen
Updated demo server to revision 2491 (diff)
11:14 AM Ticket #196 (Transformation.newProduct should create child BioAssays if possible) updated by Nicklas Nordborg
Status changed
9:51 AM Changeset [2491] by Nicklas Nordborg
Fixes #168: Use formulas in table listings of bioassay data
9:51 AM Ticket #168 (Use formulas in table listings of bioassay data) closed by Nicklas Nordborg
fixed: (In [2491]) Fixes #168: Use formulas in table listings of bioassay data
9:31 AM Ticket #127 (Experiment explorer) updated by Nicklas Nordborg
Priority changed
9:30 AM Ticket #168 (Use formulas in table listings of bioassay data) updated by Nicklas Nordborg
Status, Priority changed
9:29 AM Ticket #127 (Experiment explorer) updated by Nicklas Nordborg
(In [2490]) References #127: Experiment explorer * Added …
9:29 AM Changeset [2490] by Nicklas Nordborg
References #127: Experiment explorer * Added annotations, support …
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