Timeline



Jul 6, 2007:

4:53 PM Changeset [3552] by Martin Svensson
References #375. Only wants to do a commit before the weekend.
2:03 PM Ticket #671 (Exporting basefiles - the last line of the bioassay set is absent) created by base
Greetings! I've discovered a problem with exporting BASEfiles. I …

Jul 5, 2007:

4:20 PM Changeset [3551] by Martin Svensson
References #375. Added column with projects, groups, users that an …
1:18 PM Ticket #611 (Improvements of Trashcan) closed by Martin Svensson
fixed: (In [3550]) Fixes #611 Improvements of Trashcan. Changed confusing …
1:18 PM Changeset [3550] by Martin Svensson
Fixes #611 Improvements of Trashcan. Changed confusing button …

Jul 4, 2007:

2:59 PM Changeset [3549] by Martin Svensson
References #611. Added new icon and text on the delete button in …
11:36 AM Changeset [3548] by Martin Svensson
References #375.Missed one view-page in the last commit

Jul 3, 2007:

11:41 AM Changeset [3547] by Martin Svensson
References #375. The first part is done, listing which …
11:26 AM Ticket #470 (Improve batch upload to support tar:ed files) reopened by Jari Häkkinen
Section 8.2.1 Uploading a new file. Update the information on …
11:17 AM Ticket #670 (Update doc on formulas and extravalues) created by Johan Enell
Depends on #669, #546 Update documentation on formulas and …
11:12 AM Ticket #669 (Add possibility to set average method to fomulas and extravalues from ...) created by Johan Enell
Depends on #648
10:53 AM Ticket #668 (Displaying icons in the text) created by Johan Enell
Icons are displayed in different ways in the text. …
10:39 AM Ticket #667 (Move ch. 7 to a lower level) created by Johan Enell
I think the that …
10:29 AM Ticket #666 (Image in chapter 6.2.3) created by Johan Enell
I think an image on single-item view for a project should be added to …
10:05 AM Ticket #665 (Links in the documentation) created by Johan Enell
I think we should discuss how the links are used in the documentations …
9:46 AM Ticket #664 (Remove chapter 6.1.3) created by Johan Enell
I think that the section 6.1.3 Share an item to other users should be …

Jul 2, 2007:

5:54 PM Ticket #663 (TOC is to big) created by Johan Enell
The table of contents of the documentations is getting big. Maybe its …
3:51 PM Milestone BASE 2.3.2 completed
3:50 PM Changeset [3546] by Jari Häkkinen
Removing obsolete branch.
3:45 PM Changeset [3545] by Johan Enell
Merged log:branches/2.3.2#3537:3542 to trunk.
9:41 AM Ticket #191 (Mobile number field in user info?) closed by Martin Svensson
fixed: (In [3544]) Fixes #191. Updating schema version and added …
9:41 AM Changeset [3544] by Martin Svensson
Fixes #191. Updating schema version and added since(javadoc) to new methods

Jun 30, 2007:

1:02 AM RobotsTxt edited by Jari Häkkinen
(diff)
12:24 AM DownloadPage edited by Jari Häkkinen
2.3.2 released. (diff)
12:11 AM Changeset [3543] by Jari Häkkinen
Tagging version 2.3.2

Jun 29, 2007:

11:31 PM Changeset [3542] by Jari Häkkinen
Bumping version number.
11:29 PM Ticket #191 (Mobile number field in user info?) reopened by Nicklas Nordborg
I think the schema version should be updated as well. The extended …
4:46 PM Tickets #661,​662 batch updated by Johan Enell
fixed: (In [3541]) Fixes #661, #662
4:46 PM Changeset [3541] by Johan Enell
Fixes #661, #662
2:39 PM Changeset [3540] by Peter Johansson
corrected address to BASE-hacks trac site
2:35 PM Ticket #191 (Mobile number field in user info?) closed by Martin Svensson
fixed: (In [3539]) Fixes #191 Mobile number field in user info?
2:35 PM Changeset [3539] by Martin Svensson
Fixes #191 Mobile number field in user info?
2:30 PM Ticket #660 (Parameters should be sorted on position) closed by Johan Enell
fixed: (In [3538]) Fixes #660 Added permission delete for File and read for Job
2:30 PM Changeset [3538] by Johan Enell
Fixes #660 Added permission delete for File and read for Job
9:54 AM Ticket #662 (Print 'section\tsettings') created by Johan Enell
If the first parameter isn't section, 'section\tsettings' should be …
9:50 AM Ticket #661 (Print parameters in correct order) created by Johan Enell
The parameters sent to BioAssaySetExporter?.exportBaseFile should be …
9:45 AM Ticket #660 (Parameters should be sorted on position) created by Johan Enell
The job parameters that the Base1PluginExecuter sends to …
9:36 AM Changeset [3537] by Jari Häkkinen
New patch release branch for 2.3
9:09 AM Changeset [3536] by Martin Svensson
References #625. This will correct the issue related to #657

Jun 28, 2007:

7:10 PM Ticket #657 (Plug-in wizard may selects wrong plug-in if only one of several ...) closed by Nicklas Nordborg
duplicate: Should be fixed as part of #625.
7:09 PM Ticket #657 (Plug-in wizard may selects wrong plug-in if only one of several ...) reopened by Nicklas Nordborg
The checked in changes fixes the problem, but it also destroys the fix …
5:43 PM Changeset [3535] by Martin Svensson
References #191
4:13 PM Ticket #658 (Invalid request ID: Data in your configuration wizard has become ...) closed by Martin Svensson
worksforme
3:40 PM Ticket #657 (Plug-in wizard may selects wrong plug-in if only one of several ...) closed by Martin Svensson
fixed
2:53 PM Changeset [3534] by Martin Svensson
References #657
1:46 PM Ticket #659 (Add wiki page describing BASE features) created by Johan Enell
A features list could useful from the fist page in the wiki. …
1:21 AM Ticket #658 (Invalid request ID: Data in your configuration wizard has become ...) created by Jari Häkkinen
I am trying to start RMAExpress/Plier, but after selecting bioassays …
12:22 AM Ticket #657 (Plug-in wizard may selects wrong plug-in if only one of several ...) created by Jari Häkkinen
the affymetrix INTENSITY plug-ins are not recognized. When "New root …

Jun 27, 2007:

11:22 PM Changeset [3533] by Jari Häkkinen
Merged log:trunk#3433:3532 into the webservices branch.
10:33 PM Ticket #656 (Update release procedure) created by Jari Häkkinen
4:35 PM Ticket #358 (Better info from Migration tool) closed by Martin Svensson
fixed: (In [3532]) Fixes #358 Better info from migration tool
4:35 PM Changeset [3532] by Martin Svensson
Fixes #358 Better info from migration tool

Jun 26, 2007:

1:12 PM Changeset [3531] by Martin Svensson
References #358. Some changes on the log statements

Jun 25, 2007:

10:05 AM Ticket #655 (Plugins -> defintions fails with 'illegal attempt to dereference ...) created by Jari Häkkinen
illegal attempt to dereference collection …

Jun 23, 2007:

8:31 PM Ticket #654 (Batch deletion of reporters) created by Nicklas Nordborg
From a mail exchange with Phillippe: >> Just a note regarding deleting …

Jun 22, 2007:

11:22 AM Changeset [3530] by Johan Enell
some admin changes

Jun 21, 2007:

5:16 PM Changeset [3529] by Martin Svensson
References #358. Use log4j properly in migration. Updated more …
4:20 PM Ticket #648 (Average method for formulas and extra values) closed by Johan Enell
fixed: (In [3528]) AverageMethod? added Fixes #648
4:20 PM Changeset [3528] by Johan Enell
AverageMethod? added Fixes #648
1:19 PM Ticket #642 (Add method that finds an enumerated annotation value that can ignore ...) closed by Nicklas Nordborg
fixed: (In [3527]) Fixes #642: Add method that finds an enumerated annotation …
1:19 PM Changeset [3527] by Nicklas Nordborg
Fixes #642: Add method that finds an enumerated annotation value that …
12:50 PM Ticket #252 (Make the trashcan smarter when deleting items) closed by Nicklas Nordborg
fixed: (In [3526]) Fixes #252: Make the trashcan smarter when deleting items
12:50 PM Changeset [3526] by Nicklas Nordborg
Fixes #252: Make the trashcan smarter when deleting items
8:22 AM Ticket #653 (Implement DbControl.flush() method) created by Nicklas Nordborg
This method should flush queued changes to the database in the same …

Jun 20, 2007:

5:33 PM Ticket #577 (exception while emptying trash (experiment and raw bioassays)) closed by Nicklas Nordborg
duplicate: I have now been able to reproduce this problem. It is triggered when a …
4:56 PM Changeset [3525] by Martin Svensson
References #358. Use log4j properly in migration. Updated more files…
3:01 PM Changeset [3524] by Nicklas Nordborg
References #583: Send message at job completion only if user has …
2:32 PM Ticket #583 (Allow changing the array design of a raw bioasay when it has raw data) closed by Nicklas Nordborg
fixed: (In [3523]) Fixes #583: Allow changing the array design of a raw …
2:32 PM Changeset [3523] by Nicklas Nordborg
Fixes #583: Allow changing the array design of a raw bioasay when it …
1:28 PM Changeset [3522] by Johan Enell
Fixes #650 added some info to the geometricMean method
1:28 PM Ticket #650 (Geometric mean) closed by Johan Enell
fixed: (In [3522]) Fixes #650 added some info to the geometricMean method
10:44 AM Changeset [3521] by Nicklas Nordborg
Fixes #556: Add a favicon.ico
10:44 AM Ticket #556 (Add a favicon.ico) closed by Nicklas Nordborg
fixed: (In [3521]) Fixes #556: Add a favicon.ico
9:36 AM Ticket #652 (Experiment explorer throws exception when showing average values and ...) closed by Nicklas Nordborg
fixed: (In [3520]) Fixes #652: Experiment explorer throws exception when …
9:36 AM Changeset [3520] by Nicklas Nordborg
Fixes #652: Experiment explorer throws exception when showing average …
9:20 AM Ticket #652 (Experiment explorer throws exception when showing average values and ...) created by Nicklas Nordborg
Go to the Experiment explorer for an experiment. 1. Display more …
9:00 AM Changeset [3519] by Nicklas Nordborg
References #625. Fixed ClassCastException? when using auto-detect and …
8:48 AM Ticket #637 (Multiple plugin configurations gets mixed up.) closed by Nicklas Nordborg
fixed: (In [3518]) Fixes #637
8:48 AM Changeset [3518] by Nicklas Nordborg
Fixes #637

Jun 19, 2007:

4:20 PM Changeset [3517] by Johan Enell
References #650 Creates Ql and String from the parts already made in …
3:38 PM Ticket #650 (Geometric mean) reopened by Nicklas Nordborg
The LN() and EXP() functions have different names in different …
2:10 PM Changeset [3516] by Jari Häkkinen
Removing obsolete branch.
1:05 PM Changeset [3515] by Nicklas Nordborg
Fixes #503: We now display annotation and protocol parameter values …
1:05 PM Ticket #503 (Display more info about items in Experiment overview) closed by Nicklas Nordborg
fixed: (In [3515]) Fixes #503: We now display annotation and protocol …
1:05 PM Ticket #650 (Geometric mean) closed by Johan Enell
fixed: (In [3514]) Fixes #650
1:05 PM Changeset [3514] by Johan Enell
Fixes #650
11:58 AM Changeset [3513] by Nicklas Nordborg
Fixes #651
11:58 AM Ticket #651 (Experiment overview doesn't find missing annotations if an item ...) closed by Nicklas Nordborg
fixed: (In [3513]) Fixes #651
11:47 AM Ticket #651 (Experiment overview doesn't find missing annotations if an item ...) created by Nicklas Nordborg
The experiment overview has options for validating that an item has …
11:34 AM Ticket #650 (Geometric mean) created by Johan Enell
Create an geometric mean expression in the query package. Use the …
11:31 AM Ticket #649 (Use correct avgerage method in Experiment Explorer) created by Johan Enell
Refs. #648 and #674 When formulas and raw data have specific average …
11:30 AM Changeset [3512] by Nicklas Nordborg
References #512. Exception should sometimes hide the menubar
11:29 AM Ticket #648 (Average method for formulas and extra values) created by Johan Enell
A user should be able to specify which average method to use. When you …
9:06 AM Changeset [3511] by Nicklas Nordborg
References #470. Updated doc
8:56 AM Ticket #470 (Improve batch upload to support tar:ed files) closed by Nicklas Nordborg
fixed: (In [3510]) Fixes #470
8:56 AM Changeset [3510] by Nicklas Nordborg
Fixes #470

Jun 18, 2007:

5:52 PM Changeset [3509] by Peter Johansson
References #639. First non-tested non-generic version of the matrix …
5:01 PM Changeset [3508] by Martin Svensson
References #358. Use log4j properly in migration.
1:51 PM Changeset [3507] by Nicklas Nordborg
References #470. Upload form can now handle file names with double …
1:31 PM Changeset [3506] by Nicklas Nordborg
Show more characters from the name of recently used items
1:29 PM Tickets #622,​632,​643,​644,​645,​646,​647 batch updated by Nicklas Nordborg
fixed: (In [3505]) Fixes #632, #622, #643, #644, #645, #646, #647
1:29 PM Changeset [3505] by Nicklas Nordborg
Fixes #632, #622, #643, #644, #645, #646, #647
12:20 PM Ticket #647 (Base1PluginExecter fails when importing data) created by Nicklas Nordborg
Used the Base1NullPlugin for testing. Get the following stacktrace …
11:19 AM Ticket #622 (After restarting a job that has crashed an 'Item already exists' error ...) reopened by Nicklas Nordborg
The problem is not fixed: […]
11:03 AM Ticket #646 (Base1PluginExecuter fails with ConnectionClosedException) created by Nicklas Nordborg
Trying to run a BASE 1 plugin on an experiment which has experimental …
10:48 AM Ticket #645 (Base1PluginExecuter fails with NumberFormatException) created by Nicklas Nordborg
I created a new configuration for the Base1PluginExecutor with the …
10:43 AM Ticket #644 (Base1PluginExecuter doesn't have permission to read some items) created by Nicklas Nordborg
The plug-in lacks permission on lots of items. Found so far: * Extra …
8:42 AM Ticket #643 (BioAssaySetExporter doesn't have permission to extra values) created by Nicklas Nordborg
Trying to export data in BASEfile format from a bioassayset which has …

Jun 15, 2007:

1:21 PM Changeset [3504] by Nicklas Nordborg
Fixes #512
1:21 PM Ticket #512 (Feature request: switch user stays on same page if possible) closed by Nicklas Nordborg
fixed: (In [3504]) Fixes #512
11:41 AM Changeset [3503] by Nicklas Nordborg
Fixes #628
11:41 AM Ticket #628 (Create update script that fixes incorrect file sizes) closed by Nicklas Nordborg
fixed: (In [3503]) Fixes #628
11:41 AM Changeset [3502] by Nicklas Nordborg
References #518. Fixed compilation warning from Hibernate. Added …
11:38 AM Ticket #642 (Add method that finds an enumerated annotation value that can ignore ...) created by Nicklas Nordborg
Dominic Oyeniran wrote: > Having an annotation type cell type with …
11:16 AM Changeset [3501] by Johan Enell
Merged log:branches/2.3.1#3431:3486 trunk.
9:47 AM Ticket #353 (Create connectivity from R/BioConductor to BASE) closed by Jari Häkkinen
worksforme: The R/BASE connectivity is accomplished as one of the clients at …
9:47 AM Changeset [3500] by Nicklas Nordborg
References #578. Changed to load the names of items by default
9:42 AM Changeset [3499] by Nicklas Nordborg
Fixes #640
9:42 AM Ticket #640 (The HTML code for the "Recent items" meny is outputted before the ...) closed by Nicklas Nordborg
fixed: (In [3499]) Fixes #640
9:40 AM Changeset [3498] by Nicklas Nordborg
Fixes #369
9:40 AM Ticket #369 (Display of ExperimentalFactor and associated Values from Experiment Page) closed by Nicklas Nordborg
fixed: (In [3498]) Fixes #369
9:39 AM Ticket #641 (Link to non-existing image in annotate.jsp) closed by Nicklas Nordborg
fixed: (In [3497]) Fixes #641
9:39 AM Changeset [3497] by Nicklas Nordborg
Fixes #641
9:38 AM Ticket #641 (Link to non-existing image in annotate.jsp) created by Nicklas Nordborg
There is a link to /images/annotation.gif which doesn't exists. The …
9:20 AM Ticket #640 (The HTML code for the "Recent items" meny is outputted before the ...) created by Nicklas Nordborg
Go to any page and check "View source...". The code for the recent …

Jun 14, 2007:

9:01 PM Ticket #639 (exportPureMatrix method) created by Peter Johansson
It would be useful to have a method exporting a BioAssaySet to pure …
4:58 PM Changeset [3496] by Martin Svensson
References #358. Started to implement a log-structure in the migration …
3:35 PM DownloadPage edited by Jari Häkkinen
2.3.1 released. (diff)
3:28 PM DownloadPage edited by Jari Häkkinen
2.3.1 released. (diff)
2:36 PM Changeset [3495] by Nicklas Nordborg
References #625. Major features are now in place. It's a bit tricky to …
2:11 PM Milestone BASE 2.3.1 completed
Bug fixes for the 2.3 release Revision log: log:branches/2.3.1@3431:3494
1:35 PM Changeset [3494] by Jari Häkkinen
Tagging version 2.3.1
12:25 PM Changeset [3493] by Nicklas Nordborg
Fixes #566
12:25 PM Ticket #566 (Plugins using the flat file parser should warn about complex column ...) closed by Nicklas Nordborg
fixed: (In [3493]) Fixes #566
10:44 AM Changeset [3492] by Nicklas Nordborg
Fixes #578
10:44 AM Ticket #578 (Update the History function to remember more than one item of each type) closed by Nicklas Nordborg
fixed: (In [3492]) Fixes #578
10:09 AM Changeset [3491] by Peter Johansson
added Date property
9:54 AM Changeset [3490] by Martin Svensson
References #426 Documentation about setting the user preferences for …

Jun 13, 2007:

8:30 PM Changeset [3489] by Nicklas Nordborg
Removed xref links from web client help text version
8:24 PM Changeset [3488] by Nicklas Nordborg
Create missing directory for appendixes
7:56 PM Changeset [3487] by Peter Johansson
added end-of-line style property and replaced don't and similiar with …
7:16 PM Ticket #638 (Read raw data headers from CEL files) closed by Nicklas Nordborg
fixed: Fixed in [3483]
7:15 PM Ticket #638 (Read raw data headers from CEL files) created by Nicklas Nordborg
3:34 PM Changeset [3486] by Jari Häkkinen
Bumped version number.
3:33 PM Ticket #624 (Update copyright in 'About' button) closed by Jari Häkkinen
fixed: (In [3485]) Fixes #624
3:33 PM Changeset [3485] by Jari Häkkinen
Fixes #624
2:48 PM Ticket #627 (History of used items in the menu bar should be saved between sessions.) closed by Nicklas Nordborg
fixed: (In [3484]) Fixes #627
2:48 PM Changeset [3484] by Nicklas Nordborg
Fixes #627
2:24 PM Changeset [3483] by Nicklas Nordborg
Read raw data headers from CEL file and put in RawBioAssay?
1:54 PM Ticket #435 (A check for reporter information is needed when adding/using ...) closed by Nicklas Nordborg
fixed: (In [3482]) Fixes #435.
1:54 PM Changeset [3482] by Nicklas Nordborg
Fixes #435.
1:41 PM Changeset [3481] by Martin Svensson
Fixes #426 Option to automatically delete a (import/export) job once …
1:41 PM Ticket #426 (Option to automatically delete a (import/export) job once it has been ...) closed by Martin Svensson
fixed: (In [3481]) Fixes #426 Option to automatically delete a …
1:16 PM Ticket #637 (Multiple plugin configurations gets mixed up.) created by base
Scenario: 1) Start a new plugin configuration of …
12:39 PM Changeset [3480] by Martin Svensson
References #426 Option to flag an import/export job to be removed, …

Jun 12, 2007:

5:23 PM Changeset [3479] by Peter Johansson
fixed some typos and grammar
2:47 PM Ticket #634 (Analysis plug-ins doesn't show up on bioassays list) closed by Nicklas Nordborg
fixed: (In [3478]) Fixes #634
2:47 PM Changeset [3478] by Nicklas Nordborg
Fixes #634
2:16 PM Changeset [3477] by Nicklas Nordborg
Removed call to deprecated method
1:56 PM Ticket #372 (Check Affymetrix CEL files vs Affymetrix Array Design during file upload) closed by Nicklas Nordborg
fixed: (In [3476]) Fixes #372
1:56 PM Changeset [3476] by Nicklas Nordborg
Fixes #372
11:18 AM Changeset [3475] by Martin Svensson
Fixes #635 The exception was thrown from the index.jsp page in …
11:18 AM Ticket #635 (AbstractExporterPlugin throws an exception when finishing an export) closed by Martin Svensson
fixed: (In [3475]) Fixes #635 The exception was thrown from the index.jsp …

Jun 11, 2007:

2:27 PM Ticket #481 (Reporter importer plug-in should report how many reporters were ...) closed by Nicklas Nordborg
fixed: (In [3474]) Fixes #481
2:27 PM Changeset [3474] by Nicklas Nordborg
Fixes #481
2:11 PM Changeset [3473] by Nicklas Nordborg
Removed strange assignment
2:06 PM Ticket #469 (Improve error handling of invalid values in import plugins) closed by Nicklas Nordborg
fixed: (In [3472]) Fixes #469.
2:06 PM Changeset [3472] by Nicklas Nordborg
Fixes #469.
9:44 AM Tickets #573,​574 batch updated by Nicklas Nordborg
fixed: (In [3471]) Fixes #574 and #573.
9:44 AM Changeset [3471] by Nicklas Nordborg
Fixes #574 and #573.
9:34 AM Ticket #636 (Kill a running job) created by Johan Enell
It should be possible for a user to kill a running job. The core sends …
9:23 AM Ticket #479 (BioAssaySetExport should allow immediate download.) closed by Martin Svensson
fixed: (In [3470]) Fixes #479 BioAssaySetExport? should allow immediate download.
9:23 AM Changeset [3470] by Martin Svensson
Fixes #479 BioAssaySetExport? should allow immediate download.
9:21 AM Ticket #635 (AbstractExporterPlugin throws an exception when finishing an export) created by Martin Svensson
The export seems to work and the file is downloaded but there is an …

Jun 8, 2007:

4:54 PM Tickets #606,​622 batch updated by Johan Enell
fixed: (In [3469]) Fixes #606 Fixes #622
4:54 PM Changeset [3469] by Johan Enell
Fixes #606 Fixes #622
2:29 PM Changeset [3468] by Nicklas Nordborg
References #574, #573 and #469. Created a simple test case with dirty …
12:18 PM Ticket #634 (Analysis plug-ins doesn't show up on bioassays list) created by Johan Enell
From the bioassayset view I press the bioassays tab. I click run …
11:29 AM Ticket #81 (SessionControl should be able to assign default groups and roles to ...) closed by Nicklas Nordborg
fixed: (In [3467]) Fixes #81
11:29 AM Changeset [3467] by Nicklas Nordborg
Fixes #81
8:37 AM Ticket #446 (File browser should have a possiblity to show creation/modifcation time) closed by Nicklas Nordborg
fixed: (In [3466]) Fixes #446
8:37 AM Changeset [3466] by Nicklas Nordborg
Fixes #446
Note: See TracTimeline for information about the timeline view.