Timeline



Jul 20, 2007:

6:50 PM Ticket #692 (Jobs that are part of an experiment should use permissions from that ...) created by Nicklas Nordborg
In the current situation, only the user that created the job has …
3:45 PM Changeset [3587] by Martin Svensson
References #686 Two more coreplugins are updated …
3:36 PM Ticket #691 (Make LowessNormalization and MedianRatioNormalization extend ...) created by Martin Svensson
These plugins should extend AbstractAnalysisPlugin? instead of …
2:40 PM Changeset [3586] by Nicklas Nordborg
References #326: Mass annotation plug-in Major features in place. …
12:27 PM Ticket #685 (Add plugin parameter asking for bioassays to AbstractAnalysisPlugin) closed by Martin Svensson
fixed: (In [3585]) Fixes #685 The documentation is done
12:27 PM Changeset [3585] by Martin Svensson
Fixes #685 The documentation is done
12:09 PM Changeset [3584] by Martin Svensson
References #686 Updated gui contexts in JepExtraValueCalculator? to …
11:44 AM Changeset [3583] by Martin Svensson
References #686 Jep Formula Filter and JepExtraValueCalculator? can now …
9:29 AM Ticket #685 (Add plugin parameter asking for bioassays to AbstractAnalysisPlugin) reopened by Martin Svensson
How about the documentation…
8:28 AM Changeset [3582] by Jari Häkkinen
Reverting build.xml, accidental last checkin of build.xml
8:23 AM Changeset [3581] by Jari Häkkinen
Merged log:trunk#3533:3580 into the wwebservices branch.
8:02 AM Changeset [3580] by Nicklas Nordborg
Fixes #690: Not allowed to read Extra value type
8:02 AM Ticket #690 (Not allowed to read Extra value type) closed by Nicklas Nordborg
fixed: (In [3580]) Fixes #690: Not allowed to read Extra value type
7:41 AM Ticket #690 (Not allowed to read Extra value type) reopened by Nicklas Nordborg
Found a few more places where there is the same problem

Jul 19, 2007:

11:11 PM Changeset [3579] by Nicklas Nordborg
Fixed incorrect tooltip for "Extra value types" menu item
11:10 PM Ticket #690 (Not allowed to read Extra value type) closed by Nicklas Nordborg
fixed: (In [3578]) Fixes #690: Not allowed to read Extra value type
11:10 PM Changeset [3578] by Nicklas Nordborg
Fixes #690: Not allowed to read Extra value type
6:33 PM Changeset [3577] by Peter Johansson
fixed typo in docs
3:48 PM Changeset [3576] by Martin Svensson
References #451 Avoid null pointer exception
3:42 PM Changeset [3575] by Martin Svensson
Fixes #685 Add plugin parameter asking for bioassays to …
3:42 PM Ticket #685 (Add plugin parameter asking for bioassays to AbstractAnalysisPlugin) closed by Martin Svensson
fixed: (In [3575]) Fixes #685 Add plugin parameter asking for bioassays to …
2:46 PM Ticket #690 (Not allowed to read Extra value type) created by base
I've loaded an experiment as an administrator, all within a project. …
1:01 PM Ticket #689 (Increase 99 hits per page limit (list views)) created by base
I found that sharing via projects isn't exactly what I need (the other …
12:31 PM Changeset [3574] by Nicklas Nordborg
References #658: Compare requestId as strings instead of integers to …
11:48 AM Ticket #688 (Don't use Float.valueOf() or Float.parseString() to parse integer values) created by Nicklas Nordborg
A float doesn't have enough precision to be able to parse with correct …
9:49 AM Changeset [3573] by Nicklas Nordborg
References #680: Fixed a bug that caused the column mapping tab to …
9:16 AM Changeset [3572] by Martin Svensson
Fixes #451 This plugin is now installed with BASE as a core plugin and …
9:16 AM Ticket #451 (Zipped download) closed by Martin Svensson
fixed: (In [3572]) Fixes #451 This plugin is now installed with BASE as a …
8:47 AM Changeset [3571] by Martin Svensson
References #451 Some minor bugs are fixed.
8:45 AM Changeset [3570] by Nicklas Nordborg
References #551. Moved (and updated) documentation about analysis …
8:29 AM Ticket #684 (AbstractAnalysisPlugin should not include [Item.BIOASSAYS, Type.LIST] ...) closed by Nicklas Nordborg
fixed: (In [3569]) Fixes #684: AbstractAnalysisPlugin? should not include …
8:29 AM Changeset [3569] by Nicklas Nordborg
Fixes #684: AbstractAnalysisPlugin? should not include [Item.BIOASSAYS, …
8:23 AM Ticket #687 (Make it possible for other plug-ins than the FormulaFilter to be ...) created by Nicklas Nordborg
To make this work we need to create an interface (say …
8:19 AM Ticket #686 (Make it possible for core analysis plug-ins to work on a subset of ...) created by Nicklas Nordborg
Once ticket #685 is in place it should not be so difficult. The core …
8:15 AM Ticket #685 (Add plugin parameter asking for bioassays to AbstractAnalysisPlugin) created by Nicklas Nordborg
This will make it easier to implement plug-ins that only work on a …
7:42 AM Ticket #684 (AbstractAnalysisPlugin should not include [Item.BIOASSAYS, Type.LIST] ...) created by Nicklas Nordborg
This context is optional and is not supported by all plug-ins.

Jul 18, 2007:

10:58 PM Ticket #683 (Holding down SHIFT, CTRL or ALT when creating a new item should ...) created by Nicklas Nordborg
Bob MacCallum? wrote: > I don't know if this would be dangerous, but …
3:46 PM Changeset [3568] by Martin Svensson
References #451 Packer plugin for zip, tar.gz and tar.bz2 format …
2:43 PM Ticket #655 (Plugins -> defintions fails with 'illegal attempt to dereference ...) closed by Nicklas Nordborg
worksforme: I am not able to reproduce this
2:41 PM Ticket #670 (Update doc on formulas and extravalues) closed by Nicklas Nordborg
invalid: There is no documentation written that can be updated.
2:39 PM Ticket #682 (Object with id: 3 was not of the specified subclass: ...) closed by Nicklas Nordborg
duplicate: Duplicate of #509. This is a problem with MySQL. You have the …
1:54 PM Ticket #682 (Object with id: 3 was not of the specified subclass: ...) created by base
Hi! After BASE2 first start i loaded some plugin for Affy (RMA e …
11:42 AM Changeset [3567] by Nicklas Nordborg
Fixes #681
11:42 AM Ticket #681 (Plug-in configuration wizard may use invalid default value for item ...) closed by Nicklas Nordborg
fixed: (In [3567]) Fixes #681
11:39 AM Ticket #681 (Plug-in configuration wizard may use invalid default value for item ...) created by Nicklas Nordborg
The plug-in/job configuration wizard automatically selects the item …
10:41 AM Tickets #678,​679,​680 batch updated by Nicklas Nordborg
fixed: (In [3566]) Fixes #678, #679, #680
10:41 AM Changeset [3566] by Nicklas Nordborg
Fixes #678, #679, #680
9:48 AM Ticket #680 (The 'Test with file' function tries to map columns, even if the parent ...) created by Nicklas Nordborg
9:44 AM Ticket #679 (The 'Test with file' function should take the file to test from the ...) created by Nicklas Nordborg
Currently, only the regular expressions, and other parser settings are …
9:42 AM Ticket #678 (The 'Test with file' function doesn't clear values from parent form) created by Nicklas Nordborg
1. Enter a plug-in configuration sequence for one of the flat file …

Jul 17, 2007:

1:33 PM Changeset [3565] by Nicklas Nordborg
References #551: Moved doc about import plug-ins from old to new …
11:28 AM Changeset [3564] by Nicklas Nordborg
Fixes #675, #676 and #677
11:28 AM Tickets #675,​676,​677 batch updated by Nicklas Nordborg
fixed: (In [3564]) Fixes #675, #676 and #677
9:56 AM Ticket #677 (The auto detect file format function doesn't use Plugin.isInContext ...) created by Nicklas Nordborg
9:54 AM Ticket #676 (The autodetect file format function doesn't check ...) created by Nicklas Nordborg
9:53 AM Ticket #675 (The autodetect file format function never calls Plugin.done()) created by Nicklas Nordborg

Jul 16, 2007:

2:47 PM Ticket #470 (Improve batch upload to support tar:ed files) closed by Nicklas Nordborg
fixed: (In [3563]) Fixes #470
2:46 PM Changeset [3563] by Nicklas Nordborg
Fixes #470
2:35 PM Tickets #649,​674 batch updated by Nicklas Nordborg
fixed: (In [3562]) Fixes #649 and #674
2:35 PM Changeset [3562] by Nicklas Nordborg
Fixes #649 and #674
2:16 PM Ticket #674 (Add possibility to set average method for extended properties and raw ...) created by Nicklas Nordborg
Relates to #648 and #649
12:04 PM Changeset [3561] by Nicklas Nordborg
Fixes #672: Enable AnnotationRestriction? to be used on joined tables
12:04 PM Ticket #672 (Enable AnnotationRestriction to be used on joined tables) closed by Nicklas Nordborg
fixed: (In [3561]) Fixes #672: Enable AnnotationRestriction? to be used on …
12:02 PM Changeset [3560] by Nicklas Nordborg
References #573. Must also trim annotation values or the filter will …
9:55 AM Changeset [3559] by Nicklas Nordborg
References #625. Use correct plugin configuration.
9:44 AM Changeset [3558] by Nicklas Nordborg
Fixes #669
9:44 AM Ticket #669 (Add possibility to set average method to fomulas and extravalues from ...) closed by Nicklas Nordborg
fixed: (In [3558]) Fixes #669
9:01 AM Changeset [3557] by Nicklas Nordborg
Fixes #648
9:01 AM Ticket #648 (Average method for formulas and extra values) closed by Nicklas Nordborg
fixed: (In [3557]) Fixes #648
8:57 AM Ticket #648 (Average method for formulas and extra values) reopened by Nicklas Nordborg
The update sets the average method to geometric mean for all formulas …
8:43 AM Tickets #650,​648 batch updated by Nicklas Nordborg
fixed: (In [3556]) Fixes #648 and #650
8:43 AM Changeset [3556] by Nicklas Nordborg
Fixes #648 and #650
8:21 AM Ticket #648 (Average method for formulas and extra values) reopened by Nicklas Nordborg
Add @since to javadoc for new methods.
8:18 AM Ticket #650 (Geometric mean) reopened by Nicklas Nordborg
Add correct @version number in javadoc.

Jul 13, 2007:

4:29 PM Changeset [3555] by Martin Svensson
Reference #451 The actual compression is not quite written yet.

Jul 12, 2007:

4:46 PM Ticket #673 (BioAssayExporter basefile: Wrong count in section spots) created by Johan Enell
The header count is wrong in section spots when a matrix is exported. …
4:28 PM Ticket #671 (Exporting basefiles - the last line of the bioassay set is absent) closed by Johan Enell
fixed: (In [3554]) Fixes #671, References #590 Test for BioAssaySetExporter?
4:28 PM Changeset [3554] by Johan Enell
Fixes #671, References #590 Test for BioAssaySetExporter? added which …

Jul 10, 2007:

8:26 PM Ticket #672 (Enable AnnotationRestriction to be used on joined tables) created by Nicklas Nordborg
For example, the query below gives a stracktrace, since annotations …

Jul 9, 2007:

12:45 PM Ticket #375 (Shared items: the shareness of items should be listed in the ...) closed by Martin Svensson
fixed: Decided after a closer look to not change the view-pages.
11:39 AM Changeset [3553] by Martin Svensson
References #375. The list pages is done but the view pages should be …

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 …
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