Timeline



Nov 6, 2009:

2:34 PM Ticket #1432 (TableWriter should provide support for escaping data) created by Nicklas Nordborg
The TableWriter class is, for example, used by when creating …
11:12 AM Changeset [5187] by Nicklas Nordborg
References #1422: More user-configurable job parameters for …
9:39 AM Ticket #1397 (Function to inherit annotations for all experimental factors in the ...) closed by Nicklas Nordborg
fixed: (In [5186]) Fixes #1397: Function to inherit annotations for all …
9:39 AM Changeset [5186] by Nicklas Nordborg
Fixes #1397: Function to inherit annotations for all experimental …

Nov 5, 2009:

10:45 AM Ticket #1431 (Describe extra values. What are they? How are they created?) created by Jari Häkkinen
10:40 AM Changeset [5185] by Nicklas Nordborg
Merged patch release 2.14.1 to the trunk
9:33 AM Milestone BASE 2.14.1 completed
Bug fixes for 2.14. Revision Log: log:branches/2.14-stable@5154:5183
9:31 AM DownloadPage edited by Nicklas Nordborg
Releasing 2.14.1 (diff)
9:28 AM Changeset [5184] by Nicklas Nordborg
Changes for future release 2.14.2
9:18 AM Changeset [5183] by Nicklas Nordborg
Tagging version 2.14.1
9:17 AM Changeset [5182] by Nicklas Nordborg
Preparing release 2.14.1
9:16 AM Changeset [5181] by Nicklas Nordborg
References #1416: Base1PluginExecuter doesn't set the plug-in …

Nov 4, 2009:

2:32 PM Changeset [5180] by Nicklas Nordborg
Fixes #1430: Removing an annotation from an item may cause "Item not …
2:32 PM Ticket #1430 (Removing an annotation from an item may cause "Item not found" error ...) closed by Nicklas Nordborg
fixed: (In [5180]) Fixes #1430: Removing an annotation from an item may cause …
2:10 PM Ticket #1430 (Removing an annotation from an item may cause "Item not found" error ...) created by Nicklas Nordborg
This requires several steps to reproduce. 1. Create two items, one …
1:04 PM Changeset [5179] by Nicklas Nordborg
Fixes #1414: Search function that searches all directories for a …
1:04 PM Ticket #1414 (Search function that searches all directories for a file/directory) closed by Nicklas Nordborg
fixed: (In [5179]) Fixes #1414: Search function that searches all directories …
10:01 AM Ticket #1429 (Document BASEfile exporter plug-in) created by Jari Häkkinen
Maybe we should explain the consequences of what happens when average …

Nov 3, 2009:

2:49 PM Ticket #1420 (Round values imported using Manual transform) closed by Nicklas Nordborg
invalid

Nov 2, 2009:

3:55 PM Ticket #1428 (Write "Formulas" section) created by Jari Häkkinen
The Formulas dialogue is not described in the reference manual.
3:47 PM Changeset [5178] by Jari Häkkinen
Restructured Base1PluginExecuter configuration and BASE1 plug-in …
10:52 AM Changeset [5177] by Nicklas Nordborg
Fixes #1427: Raw data type lookup by name in rawbioassay batch importer
10:52 AM Ticket #1427 (Raw data type lookup by name in rawbioassay batch importer) closed by Nicklas Nordborg
fixed: (In [5177]) Fixes #1427: Raw data type lookup by name in rawbioassay …

Oct 30, 2009:

8:09 PM Ticket #1398 (File tree filter) closed by Nicklas Nordborg
wontfix: I think #1413 solves the issue more in a better way. It is a lot …
5:53 PM Ticket #1398 (File tree filter) reopened by base
Replying to nicklas: > Wouldn't this just move the problem …
5:46 PM Ticket #1427 (Raw data type lookup by name in rawbioassay batch importer) created by base
Plugin batchimporting rawbioassays is using raw data type ID to find …
5:40 PM Ticket #1426 (Problem viewing/downloading file with special characters in ...) created by base
It is possible to create folder with '+' in the name. When trying to …
11:25 AM Changeset [5176] by Nicklas Nordborg
References #1397: Function to inherit annotations for all experimental …
8:40 AM Changeset [5175] by Nicklas Nordborg
Removing unused imports.
8:39 AM Changeset [5174] by Nicklas Nordborg
Fixes #1425: Cached experiment explorer information should be …
8:39 AM Ticket #1425 (Cached experiment explorer information should be distributed into ...) closed by Nicklas Nordborg
fixed: (In [5174]) Fixes #1425: Cached experiment explorer information should …
8:33 AM Ticket #1425 (Cached experiment explorer information should be distributed into ...) created by Nicklas Nordborg
This is the same as #1423, but for the data that is cached by the …
8:32 AM Changeset [5173] by Nicklas Nordborg
Fixes #1424: Cached plots should be distributed into subdirectories
8:32 AM Ticket #1424 (Cached plots should be distributed into subdirectories) closed by Nicklas Nordborg
fixed: (In [5173]) Fixes #1424: Cached plots should be distributed into …
8:20 AM Ticket #1424 (Cached plots should be distributed into subdirectories) created by Nicklas Nordborg
This is the same as #1423, but for the overview plots that are cached …
8:19 AM Changeset [5172] by Nicklas Nordborg
Fixes #1423: Cached annotations should be distributed into subdirectories
8:19 AM Ticket #1423 (Cached annotations should be distributed into subdirectories) closed by Nicklas Nordborg
fixed: (In [5172]) Fixes #1423: Cached annotations should be distributed into …
7:56 AM Ticket #1423 (Cached annotations should be distributed into subdirectories) created by Nicklas Nordborg
The annotation cache implemented in #1374 saves the data in files in …

Oct 29, 2009:

2:19 PM Changeset [5171] by Nicklas Nordborg
Fixes #1422: More user-configurable job parameters for Base1PluginExecuter
2:19 PM Ticket #1422 (More user-configurable job parameters for Base1PluginExecuter) closed by Nicklas Nordborg
fixed: (In [5171]) Fixes #1422: More user-configurable job parameters for …
12:47 PM Ticket #1422 (More user-configurable job parameters for Base1PluginExecuter) created by Nicklas Nordborg
While working with #1376 and #1378 I noticed that testing the …
12:39 PM Changeset [5170] by Nicklas Nordborg
Fixes #1378: Base1PluginExecuter should link the result directory with …
12:39 PM Ticket #1378 (Base1PluginExecuter should link the result directory with the ...) closed by Nicklas Nordborg
fixed: (In [5170]) Fixes #1378: Base1PluginExecuter should link the result …
12:15 PM Changeset [5169] by Nicklas Nordborg
Fixes #1376: Remove the working directory (in the BASE file system) …
12:15 PM Ticket #1376 (Remove the working directory (in the BASE file system) that ...) closed by Nicklas Nordborg
fixed: (In [5169]) Fixes #1376: Remove the working directory (in the BASE …
11:02 AM Changeset [5168] by Nicklas Nordborg
Fixes #1421: Filter on the 'name', 'description' and other columns in …
11:02 AM Ticket #1421 (Filter on the 'name', 'description' and other columns in "Project ...) closed by Nicklas Nordborg
fixed: (In [5168]) Fixes #1421: Filter on the 'name', 'description' and other …

Oct 28, 2009:

2:18 PM Ticket #1421 (Filter on the 'name', 'description' and other columns in "Project ...) created by Nicklas Nordborg
This should now be possible building on the work done in #1377 --> …
2:16 PM Changeset [5167] by Nicklas Nordborg
Fixes #1377: Filter item lists on the 'Shared to' column The "Project …
2:16 PM Ticket #1377 (Filter item lists on the 'Shared to' column) closed by Nicklas Nordborg
fixed: (In [5167]) Fixes #1377: Filter item lists on the 'Shared to' column …
2:07 PM Changeset [5166] by Jari Häkkinen
Removed branch that was never used.
11:04 AM Changeset [5165] by Nicklas Nordborg
References #1377: Filter item lists on the 'Shared to' column All …

Oct 27, 2009:

2:37 PM Changeset [5164] by Nicklas Nordborg
References #1377: Filter item lists on the 'Shared to' column The …
10:06 AM Ticket #1420 (Round values imported using Manual transform) created by Johan Vallon-Christersson
When using Manual transform to import spot data (Ch 1 values) …

Oct 26, 2009:

10:59 AM Changeset [5163] by Nicklas Nordborg
Fixes #1418: List of inherited annotations may include annotations …
10:59 AM Ticket #1418 (List of inherited annotations may include annotations that are not ...) closed by Nicklas Nordborg
fixed: (In [5163]) Fixes #1418: List of inherited annotations may include …
8:23 AM Ticket #1419 (Missing query, SET_INTENSITYTRANSFORM_ON_BIOASSAYSETS, in ...) closed by Nicklas Nordborg
fixed: (In [5162]) Fixes #1419: Missing query, …
8:23 AM Changeset [5162] by Nicklas Nordborg
Fixes #1419: Missing query, SET_INTENSITYTRANSFORM_ON_BIOASSAYSETS, in …
8:14 AM Ticket #1419 (Missing query, SET_INTENSITYTRANSFORM_ON_BIOASSAYSETS, in ...) created by Nicklas Nordborg
This query is needed to update from BASE 2.11 to BASE 2.12 and was …

Oct 23, 2009:

4:40 PM Ticket #1418 (List of inherited annotations may include annotations that are not ...) created by Jari Häkkinen
I have two different symptoms on the problem. The problem is found in …
1:48 PM Changeset [5161] by Nicklas Nordborg
Fixes #1417: SessionControl?.updateLastAccess() should not check if it …
1:48 PM Ticket #1417 (SessionControl.updateLastAccess() should not check if it is closed or not) closed by Nicklas Nordborg
fixed: (In [5161]) Fixes #1417: SessionControl?.updateLastAccess() should not …
1:47 PM Ticket #1417 (SessionControl.updateLastAccess() should not check if it is closed or not) created by Nicklas Nordborg
This can result in some cleanup issues. Eg. calling logout() should …
1:44 PM Ticket #1416 (Base1PluginExecuter doesn't set the plug-in configuration description ...) closed by Nicklas Nordborg
fixed: (In [5160]) Fixes #1416: Base1PluginExecuter doesn't set the plug-in …
1:44 PM Changeset [5160] by Nicklas Nordborg
Fixes #1416: Base1PluginExecuter doesn't set the plug-in configuration …
1:25 PM Ticket #1405 (Use 'description' as help text for job parameters if the plug-in ...) closed by Nicklas Nordborg
fixed: (In [5159]) Fixes #1405: Use 'description' as help text for job …
1:25 PM Changeset [5159] by Nicklas Nordborg
Fixes #1405: Use 'description' as help text for job parameters if the …
12:58 PM Ticket #1416 (Base1PluginExecuter doesn't set the plug-in configuration description ...) created by Nicklas Nordborg
When a BASE 1 plug-in is configured with the help of a plug-in …
11:33 AM Changeset [5158] by Nicklas Nordborg
Fixes #1413: Make the directory icon clickable in the Files and …
11:33 AM Ticket #1413 (Make the directory icon clickable in the Files and directories view) closed by Nicklas Nordborg
fixed: (In [5158]) Fixes #1413: Make the directory icon clickable in the …
11:28 AM Changeset [5157] by Nicklas Nordborg
Fixes #1415: Lazy directory loading doesn't work with Internet Explorer
11:28 AM Ticket #1415 (Lazy directory loading doesn't work with Internet Explorer) closed by Nicklas Nordborg
fixed: (In [5157]) Fixes #1415: Lazy directory loading doesn't work with …
10:47 AM Ticket #1415 (Lazy directory loading doesn't work with Internet Explorer) created by Nicklas Nordborg
Using Internet explorer 8. 1. Go to View -> Files. 2. Try expand …

Oct 22, 2009:

5:36 PM Ticket #1414 (Search function that searches all directories for a file/directory) created by Nicklas Nordborg
If you are looking for a file but doesn't know in which directory it …
3:24 PM Ticket #1398 (File tree filter) closed by Nicklas Nordborg
wontfix: Replaced by #1413 which is probably a better solution.
3:22 PM Ticket #1413 (Make the directory icon clickable in the Files and directories view) created by Nicklas Nordborg
When the icon is clicked, the same thing should happen as if the user …
1:45 PM Ticket #1349 (Select button does not work in IE7.0 + XP Home SP3) closed by Nicklas Nordborg
worksforme
9:10 AM Milestone BASE 2.14 completed
The main feature of this release: * Major performance enhancements …
9:09 AM Changeset [5156] by Nicklas Nordborg
Merged pre-2.14-releases to the trunk
8:52 AM DownloadPage edited by Nicklas Nordborg
Releasing 2.14 (diff)
8:40 AM Changeset [5155] by Nicklas Nordborg
Changes for future release 2.14.1
8:29 AM Changeset [5154] by Nicklas Nordborg
Tagging version 2.14
8:28 AM Changeset [5153] by Nicklas Nordborg
Preparing release 2.14

Oct 21, 2009:

2:39 PM Ticket #1412 (The selected unit for an annotation type should not be remembered when ...) closed by Nicklas Nordborg
fixed: (In [5152]) Fixes #1412: The selected unit for an annotation type …
2:39 PM Changeset [5152] by Nicklas Nordborg
Fixes #1412: The selected unit for an annotation type should not be …
9:46 AM Ticket #1412 (The selected unit for an annotation type should not be remembered when ...) created by Nicklas Nordborg
To reproduce: 1. Create a numerical annotation type. Select any …

Oct 20, 2009:

2:51 PM Changeset [5151] by Nicklas Nordborg
Changes for future release 2.15
2:50 PM Changeset [5150] by Nicklas Nordborg
Forking new minor version 2.14 branch
2:49 PM Ticket #1386 (Plot function in the bioassay table in experiment explorer) closed by Nicklas Nordborg
fixed: (In [5149]) Fixes #1386: Plot function in the bioassay table in …
2:49 PM Changeset [5149] by Nicklas Nordborg
Fixes #1386: Plot function in the bioassay table in experiment …
2:35 PM Changeset [5148] by Martin Svensson
Fixes #1410 Sort problem in EExplorer when Avg
2:35 PM Ticket #1410 (Sort problem in EExplorer when Avg) closed by Martin Svensson
fixed: (In [5148]) Fixes #1410 Sort problem in EExplorer when Avg
12:33 PM Changeset [5147] by Nicklas Nordborg
Fixes #1389: Cache annotation summary groups in experiment explorer …
12:33 PM Ticket #1389 (Cache annotation summary groups in experiment explorer) closed by Nicklas Nordborg
fixed: (In [5147]) Fixes #1389: Cache annotation summary groups in experiment …
10:26 AM Changeset [5146] by Nicklas Nordborg
Fixes #1411: Test programs must empty the static cache before running
10:26 AM Ticket #1411 (Test programs must empty the static cache before running) closed by Nicklas Nordborg
fixed: (In [5146]) Fixes #1411: Test programs must empty the static cache …
8:50 AM Changeset [5145] by Nicklas Nordborg
Fixes #1404: Use cached annotations in "item overview" The tests in …
8:50 AM Ticket #1404 (Use cached annotations in "item overview") closed by Nicklas Nordborg
fixed: (In [5145]) Fixes #1404: Use cached annotations in "item overview" …
8:21 AM Changeset [5144] by Nicklas Nordborg
Fixes #1406: Add a protocol parameter in the 'roles' test case Added …
8:21 AM Ticket #1406 (Add a protocol parameter in the 'roles' test case) closed by Nicklas Nordborg
fixed: (In [5144]) Fixes #1406: Add a protocol parameter in the 'roles' test …
7:51 AM Ticket #1389 (Cache annotation summary groups in experiment explorer) reopened by Nicklas Nordborg
See comment 19+ in ticket 1374

Oct 19, 2009:

3:32 PM Ticket #1411 (Test programs must empty the static cache before running) created by Nicklas Nordborg
If old data from previous executions is still in the cache, the test …
2:54 PM Ticket #1410 (Sort problem in EExplorer when Avg) created by Johan Vallon-Christersson
Noticed that sorting of the bioassay table in EExplorer doesn't work …
1:32 PM Changeset [5143] by Nicklas Nordborg
References #1404: Use cached annotations in "item overview" Fixes a …
11:34 AM Ticket #1385 (Plot function in the annotation summary table in experiment explorer) closed by Nicklas Nordborg
fixed: Everything seems to be ok now.
9:42 AM Ticket #1409 (Annotation summary table displays NaNs) closed by Jari Häkkinen
worksforme: Works for me now as of trunk revision 5142
9:11 AM Changeset [5142] by Nicklas Nordborg
References #1385 and #1386. Plot functions in experiment explorer The …
9:03 AM Changeset [5141] by Nicklas Nordborg
References #1386: Plot function in the bioassay table in experiment …
8:25 AM Changeset [5140] by Nicklas Nordborg
References #1384: Move the annotation summary information table in …
8:22 AM Changeset [5139] by Nicklas Nordborg
References #1388: Display the count for each group in the annotation …

Oct 16, 2009:

4:57 PM Ticket #1408 (Cannot deselect annotation in the annoation summary drop down) closed by Nicklas Nordborg
worksforme: I can.
4:54 PM Ticket #1407 (Functionality of the "No labels" selection in plot function in the ...) closed by Nicklas Nordborg
wontfix: It is not possible. The only way to know the coordinates were to put …
3:58 PM Ticket #1409 (Annotation summary table displays NaNs) created by Jari Häkkinen
The screen dump shows the problem.
3:47 PM Ticket #1408 (Cannot deselect annotation in the annoation summary drop down) created by Jari Häkkinen
Related to ticket:1383 After selecting one annotation (out of one …
3:43 PM Ticket #1407 (Functionality of the "No labels" selection in plot function in the ...) created by Jari Häkkinen
Related to ticket:1386 Checking the No labels box removes all labels …
2:39 PM Ticket #1406 (Add a protocol parameter in the 'roles' test case) created by Nicklas Nordborg
To get some more automatic testing for the 'item overview' …
2:27 PM Changeset [5138] by Nicklas Nordborg
References #1385 and #1386. Plot functions in experiment explorer …

Oct 15, 2009:

9:42 AM Changeset [5137] by Nicklas Nordborg
References #1383: Make it possible to select more than one annotation …
8:33 AM Changeset [5136] by Nicklas Nordborg
Merged patch release 2.13.1 to the trunk.
8:18 AM Milestone BASE 2.13.1 completed
Bug fixes for 2.13. Revision Log: log:branches/2.13-stable@5089:5134
8:17 AM DownloadPage edited by Nicklas Nordborg
Releasing BASE 2.13.1 (diff)
8:13 AM Changeset [5135] by Nicklas Nordborg
Changes for future release 2.13.2
8:02 AM Changeset [5134] by Nicklas Nordborg
Tagging version 2.13.1
8:01 AM Changeset [5133] by Nicklas Nordborg
Preparing release 2.13.1 and fixed some incorrect javadoc links.

Oct 14, 2009:

1:55 PM Changeset [5132] by Nicklas Nordborg
References #1404: Use cached annotations in "item overview" This …
9:44 AM Changeset [5131] by Nicklas Nordborg
References #1374 and #1403: Caching of annotations, etc... Made some …

Oct 13, 2009:

2:17 PM Ticket #1405 (Use 'description' as help text for job parameters if the plug-in ...) created by Johan Vallon-Christersson
The 'Run analysis plugin' pop-up dialogue can contain a useful plugin …
12:44 PM Changeset [5130] by Nicklas Nordborg
Fixes #1403: Use cached annotations in experiment explorer, plot …
12:44 PM Ticket #1403 (Use cached annotations in experiment explorer, plot function, BASEfile ...) closed by Nicklas Nordborg
fixed: (In [5130]) Fixes #1403: Use cached annotations in experiment …
11:11 AM WikiStart edited by Jari Häkkinen
Updated how to cite information. (diff)
8:49 AM Ticket #1400 (Store the item id together with annotation sets) closed by Nicklas Nordborg
fixed: (In [5129]) Fixes #1400: Store the item id together with annotation …
8:49 AM Changeset [5129] by Nicklas Nordborg
Fixes #1400: Store the item id together with annotation sets More …
8:29 AM Changeset [5128] by Nicklas Nordborg
Fixes #1374: Caching of experimental factors Removed timing code.
8:29 AM Ticket #1374 (Caching of experimental factors) closed by Nicklas Nordborg
fixed: (In [5128]) Fixes #1374: Caching of experimental factors Removed …
8:26 AM Ticket #1404 (Use cached annotations in "item overview") created by Nicklas Nordborg
Caching was fixed in #1374. It seems to be a major performance enhancement.
8:25 AM Ticket #1403 (Use cached annotations in experiment explorer, plot function, BASEfile ...) created by Nicklas Nordborg
Caching was fixed in #1374. It seems to be a major performance enhancement.

Oct 12, 2009:

2:41 PM Changeset [5127] by Nicklas Nordborg
References #1400: Store the item id together with annotation sets The …
1:00 PM Ticket #1402 (New Affymetrix CEL file support) created by base
New is a "generic" CEL data file format, for which BASE Affy import …

Oct 9, 2009:

2:36 PM Changeset [5126] by Nicklas Nordborg
Fixes #1392: Incorrect warning about non-default platform/variant from …
2:36 PM Ticket #1392 (Incorrect warning about non-default platform/variant from validator) closed by Nicklas Nordborg
fixed: (In [5126]) Fixes #1392: Incorrect warning about non-default …
2:28 PM Changeset [5125] by Nicklas Nordborg
Fixes #1399: Array slide's create multiple puts a wrong number into …
2:28 PM Ticket #1399 (Array slide's create multiple puts a wrong number into batch index field) closed by Nicklas Nordborg
fixed: (In [5125]) Fixes #1399: Array slide's create multiple puts a wrong …
1:20 PM Changeset [5124] by Nicklas Nordborg
References #1374: Caching of experimental factors Implements our own …
12:37 PM Changeset [5123] by Nicklas Nordborg
References #1374: Caching of experimental factors The 'Annotations & …
10:55 AM Changeset [5122] by Nicklas Nordborg
References #1400: Store the item id together with annotation sets …
10:54 AM Changeset [5121] by Nicklas Nordborg
References #1374: Caching of experimental factors This should …
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