Timeline



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
2:23 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
10:39 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
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 …
11:01 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) 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

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 …
3:41 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
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
8:32 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 …

Aug 12, 2006:

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:

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 …
12:07 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. …
8:16 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 Changeset [2509] by Martin Svensson
References #39 Handling a string with only blank space in required …
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 - …
2:46 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 …
2:35 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 Changeset [2506] by Nicklas Nordborg
References #170: Categorize annotation types Updated UML diagram
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 Changeset [2503] by Martin Svensson
References #266 Strange mouse-over message in some places. file-, …
1:03 PM Changeset [2502] by Nicklas Nordborg
References #127: Experiment explorer Cleaned up and documented most …
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 …
3:43 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)
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
9:29 AM Changeset [2490] by Nicklas Nordborg
References #127: Experiment explorer * Added annotations, support …

Aug 7, 2006:

3:49 PM Changeset [2489] by Jari Häkkinen
Added PostgreSQL setup information.
12:13 PM Changeset [2488] by Nicklas Nordborg
Fixed sorting problem with always visible columns

Aug 4, 2006:

2:33 PM Changeset [2487] by Nicklas Nordborg
References #127: Experiment explorer First version. A lot of the code …
2:15 PM Ticket #313 (Error handling in import plugins) created by Johan Enell
The reporter importer (and pobably others) fails when there is to long …
1:54 PM Ticket #312 (ReporterType import) created by Johan Enell
ReporterFlatFileImporter? assumes that every reporter in the file has …

Aug 3, 2006:

5:20 PM Changeset [2486] by Martin Svensson
References #173. Possible to attach a hardware to a PlateEvent? in the GUI
1:03 PM Changeset [2485] by Johan Enell
Position batcher added
10:48 AM Ticket #311 (Allow parsing of numbers with different locale settings) created by Nicklas Nordborg
The problem can arise in the FlatFileParser? and it's different Mapper …
8:41 AM Changeset [2484] by Martin Svensson
Refrences #173 A hardware can now be attach to a Hybridization in the GUI.
8:35 AM Ticket #309 (count spots in bioassayset) closed by Nicklas Nordborg
fixed: (In [2483]) Fixes #309: count spots in bioassayset
8:35 AM Changeset [2483] by Nicklas Nordborg
Fixes #309: count spots in bioassayset
7:59 AM Changeset [2482] by Nicklas Nordborg
Fixes #310: Permission denied on raw bioassay
7:59 AM Ticket #310 (Permission denied on raw bioassay) closed by Nicklas Nordborg
fixed: (In [2482]) Fixes #310: Permission denied on raw bioassay

Aug 2, 2006:

2:39 PM Ticket #310 (Permission denied on raw bioassay) created by Johan Enell
I get a permission denied when clicking on a raw bioassay. The owned …
1:59 PM Changeset [2481] by Johan Enell
Base1PluginExecuter can now export data to base1 plug-in and import from it
12:57 PM Ticket #309 (count spots in bioassayset) created by Johan Enell
If a BioAssaySet? only has spot data the spot count is wrong.
11:21 AM Changeset [2480] by Martin Svensson
Updated db schema_version and correct comments in BioMaterialEvent? and …
9:40 AM Changeset [2479] by Martin Svensson
References #173 Made it possible to attach a Hardware item to …
9:11 AM Changeset [2478] by Martin Svensson
Fixed a corrupt link
8:15 AM Ticket #307 (display of annotation type to users from administrate page) closed by Nicklas Nordborg
invalid: In the view/presets dropdown one has to select the 'Shared to me' …

Aug 1, 2006:

7:19 PM Ticket #308 (Firefox unresponsive script warning when uploading files) created by msettles@…
When uploading affymetrix .CEL files, upload process occurs in …
4:13 PM Ticket #307 (display of annotation type to users from administrate page) created by rocca@…
I have noted the following: When creating a new user and setting the …
2:16 PM Changeset [2477] by Martin Svensson
Created an association between BiomaterialEventData?-HardwareData? and …
1:43 PM Ticket #306 (empty trashcan) created by Johan Enell
When you want to empty the trashcan you have to mark every item (max …
1:39 PM Ticket #305 (delete recusively) created by Johan Enell
When items are presented in a tree view (the analyse tree and the file …
8:13 AM Changeset [2476] by Martin Svensson
Fixes #304 An empty list page is viewed when changing the …
8:13 AM Ticket #304 (An empty list page is viewed when changing the view-preferences for ...) closed by Martin Svensson
fixed: (In [2476]) Fixes #304 An empty list page is viewed when changing the …

Jul 31, 2006:

5:59 PM Changeset [2475] by dominic
Fixed issues from feedbacks: code comments and patterns, standards …
3:53 PM Ticket #263 (Update to latest versions of 3rd-party software) closed by Nicklas Nordborg
fixed: (In [2474]) Fixes #263: Update to latest versions of 3rd-party …
3:52 PM Changeset [2474] by Nicklas Nordborg
Fixes #263: Update to latest versions of 3rd-party software * Log4j: …
11:56 AM Ticket #304 (An empty list page is viewed when changing the view-preferences for ...) created by Martin Svensson
Precondition: Viewing items that's "Owned by me" and "Shared to me" …
9:11 AM Ticket #303 (News items are not shown in View -> home page) closed by Nicklas Nordborg
fixed: (In [2473]) Fixes #303: News items are not shown in View -> home page …
9:11 AM Changeset [2473] by Nicklas Nordborg
Fixes #303: News items are not shown in View -> home page Needed a …
8:43 AM Changeset [2472] by Martin Svensson
Added pool button for samples, extracts and labeledextracts.

Jul 26, 2006:

11:59 PM Changeset [2471] by Jari Häkkinen
Creating tab2mage export branch for Dominic.

Jul 22, 2006:

2:26 PM Changeset [2470] by Jari Häkkinen
Fixed spelling for 'successfully'.
11:17 AM Ticket #303 (News items are not shown in View -> home page) created by Jari Häkkinen
7:48 AM Ticket #302 (Running a plugin without a configuration should not be possible ...) created by Jari Häkkinen
and is not. However the behaviour of BASE should be changed in this …
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