Timeline



Dec 19, 2008:

2:55 PM Changeset [4712] by Nicklas Nordborg
References #1190: API and interface for creating biomaterial lists …
11:48 AM Ticket #1223 (News visible only for a selected group of users/groups/project) created by Jari Häkkinen
It would be nice to be able to create news items only visible for …

Dec 18, 2008:

7:39 PM Ticket #1221 (Error creating a direcotory) closed by Nicklas Nordborg
invalid: The error happens because the directory already exists.
7:25 PM Ticket #1222 (Document the nice batch import of raw data through experiment import button) created by Jari Häkkinen
http://base.thep.lu.se/chrome/site/doc/test/roles/index.html#user
4:54 PM Ticket #1221 (Error creating a direcotory) created by base
I get the below stacktrace when I create a directory. However, the …
9:22 AM Changeset [4711] by Nicklas Nordborg
Merged patch release 2.9.1 to the trunk.
9:05 AM Milestone BASE 2.9.1 completed
Bug fixes for 2.9. Revision Log: log:branches/2.9-stable@4667:4709
9:05 AM DownloadPage edited by Nicklas Nordborg
Releasing BASE 2.9.1 (diff)
9:01 AM Changeset [4710] by Nicklas Nordborg
Changes for future release 2.9.2
8:43 AM Changeset [4709] by Nicklas Nordborg
Tagging version 2.9.1
8:42 AM Changeset [4708] by Nicklas Nordborg
Preparing release 2.9.1

Dec 17, 2008:

10:33 PM Ticket #1220 (NullPointerException in Experiment overview if an extract is missing a ...) closed by Nicklas Nordborg
fixed: (In [4707]) Fixes #1220: NullPointerException? in Experiment overview …
10:33 PM Changeset [4707] by Nicklas Nordborg
Fixes #1220: NullPointerException? in Experiment overview if an extract …
10:28 PM Ticket #1217 (Unexpected error viewing Project Summary in shared project) closed by Nicklas Nordborg
duplicate: Replaced by #1220.
10:27 PM Ticket #1220 (NullPointerException in Experiment overview if an extract is missing a ...) created by Nicklas Nordborg
The original error was reported in #1217. Below is the relevant stack …
8:35 PM Changeset [4706] by Nicklas Nordborg
Fixes #1219: Deleting the active project results in …
8:35 PM Ticket #1219 (Deleting the active project results in ItemNotFoundException in ...) closed by Nicklas Nordborg
fixed: (In [4706]) Fixes #1219: Deleting the active project results in …
8:15 PM Ticket #1219 (Deleting the active project results in ItemNotFoundException in ...) reopened by Nicklas Nordborg
I think the active project info should be reset if the project is deleted.
8:03 PM Ticket #1219 (Deleting the active project results in ItemNotFoundException in ...) closed by Jari Häkkinen
invalid: You are right. I have now successfully removed the share icon from the …
5:24 PM Ticket #1219 (Deleting the active project results in ItemNotFoundException in ...) created by Jari Häkkinen
I get the below stacktrace. I cannot share the items at all now. Also, …
1:08 PM Ticket #1218 (Unexpected error viewing Project Summary in shared project) closed by Nicklas Nordborg
duplicate: Duplicate of #1217.
1:01 PM Ticket #1218 (Unexpected error viewing Project Summary in shared project) created by base
Hi, I have created a number of projects called 'development', …
1:01 PM Ticket #1217 (Unexpected error viewing Project Summary in shared project) created by base
Hi, I have created a number of projects called 'development', …
1:01 AM Ticket #1216 (Annotation importer selects "wrong" configuration) created by Jari Häkkinen
I have two configurations for the annotation importer. One matches my …

Dec 16, 2008:

9:17 PM Ticket #1215 (Batch importer does not update parent in some cases) created by Jari Häkkinen
This may not be a bug. If it is not, then consider it as an …
2:29 PM Ticket #1191 (Biomaterial lists manager API and interface) closed by Nicklas Nordborg
fixed: (In [4705]) Fixes #1191: Biomaterial lists manager API and interface
2:29 PM Changeset [4705] by Nicklas Nordborg
Fixes #1191: Biomaterial lists manager API and interface

Dec 11, 2008:

4:27 PM Changeset [4704] by Martin Svensson
References #979 First commit of bioplates-support in the webbinterface.
2:27 PM Ticket #1214 (PathInfo support in extension servlets) closed by Nicklas Nordborg
fixed: (In [4703]) Fixes #1214: PathInfo? support in extension servlets
2:27 PM Changeset [4703] by Nicklas Nordborg
Fixes #1214: PathInfo? support in extension servlets
2:23 PM Changeset [4702] by Nicklas Nordborg
References #1166: Store creation date for items Fixed invalid xml in …
1:14 PM Ticket #1214 (PathInfo support in extension servlets) created by Nicklas Nordborg
Extensions that which to use servlets are currently required to follow …
11:31 AM Changeset [4701] by Nicklas Nordborg
Fixes #1180: Quota usage viewing should be possible for standard users
11:31 AM Ticket #1180 (Quota usage viewing should be possible for standard users) closed by Nicklas Nordborg
fixed: (In [4701]) Fixes #1180: Quota usage viewing should be possible for …
9:40 AM Ticket #1213 (Inconsistent behavior of strict equal (==) filter when filter value ...) closed by Nicklas Nordborg
fixed: (In [4700]) Fixes #1213: Inconsistent behavior of strict equal (==) …
9:40 AM Changeset [4700] by Nicklas Nordborg
Fixes #1213: Inconsistent behavior of strict equal (==) filter when …
9:25 AM Ticket #1213 (Inconsistent behavior of strict equal (==) filter when filter value ...) created by Nicklas Nordborg
1. Go to any list page. 2. Filter on a string column with strict …
9:16 AM Changeset [4699] by Nicklas Nordborg
Fixes #1212: NullPointerException? when trying to find dates that has a …
9:16 AM Ticket #1212 (NullPointerException when trying to find dates that has a null value) closed by Nicklas Nordborg
fixed: (In [4699]) Fixes #1212: NullPointerException? when trying to find …
8:56 AM Ticket #1212 (NullPointerException when trying to find dates that has a null value) created by Nicklas Nordborg
1. Go to any list page that has at least one date column. For example, …

Dec 10, 2008:

5:27 PM Ticket #1211 (allow use of configurations with array slide importer) closed by Nicklas Nordborg
worksforme: You can!
4:54 PM Ticket #1211 (allow use of configurations with array slide importer) created by base
The array slide importer as it is in version 2.9.0 is great but it …
2:59 PM Ticket #1174 (Show creation date for items in web interface) closed by Nicklas Nordborg
fixed: (In [4698]) Fixes #1174: Show creation date for items in web interface
2:59 PM Changeset [4698] by Nicklas Nordborg
Fixes #1174: Show creation date for items in web interface
12:12 PM Ticket #1210 (Document the behaviour of underscore character '_' when filtering) created by Jari Häkkinen
The '_' character matches like the '.' character in regular …
11:44 AM Changeset [4697] by Nicklas Nordborg
References #1166: Store creation date for items Increse schema …

Dec 9, 2008:

2:55 PM Ticket #1166 (Store creation date for items) closed by Nicklas Nordborg
fixed: (In [4696]) Fixes #1166: Store creation date for items
2:55 PM Changeset [4696] by Nicklas Nordborg
Fixes #1166: Store creation date for items
2:26 PM Changeset [4695] by Martin Svensson
References #1200 The biomaterial submenu-items are now moved to a …
11:13 AM Ticket #1209 ("Share new files and sub- directories automatically" should have a ...) created by Jari Häkkinen
The problem: People works in projects and share a common project …
11:08 AM Changeset [4694] by Nicklas Nordborg
Fixes #1204: Unknown column 'pos.reporter_id' in 'field list' when …
11:08 AM Ticket #1204 (Unknown column 'pos.reporter_id' in 'field list' when using 'merge on ...) closed by Nicklas Nordborg
fixed: (In [4694]) Fixes #1204: Unknown column 'pos.reporter_id' in 'field …
10:25 AM Ticket #1205 (Serious problem filtering on annotations where one whishes to exlude a ...) reopened by Jari Häkkinen
I still claim that there is a problem with the filtering. If one wants …
9:39 AM Ticket #1206 (= and <> operators have been switched when used on annotations and ...) closed by Nicklas Nordborg
fixed: (In [4693]) Fixes #1206: = and <> operators have been switched when …
9:39 AM Changeset [4693] by Nicklas Nordborg
Fixes #1206: = and <> operators have been switched when used on …
9:27 AM Changeset [4692] by Nicklas Nordborg
Fixes #1207: Using empty filters (= or <>) on an annotation column …
9:27 AM Ticket #1207 (Using empty filters (= or <>) on an annotation column with units ...) closed by Nicklas Nordborg
fixed: (In [4692]) Fixes #1207: Using empty filters (= or <>) on an …

Dec 8, 2008:

9:29 PM Changeset [4691] by Jari Häkkinen
Fixes #1208.
9:29 PM Ticket #1208 (BioAssaySetExporter produces malformed data for plainMatrix format) closed by Jari Häkkinen
fixed: (In [4691]) Fixes #1208.
9:28 PM Ticket #1208 (BioAssaySetExporter produces malformed data for plainMatrix format) created by Jari Häkkinen
For non-complete data in a bioassayset the resulting file rows has …
7:49 PM Ticket #1207 (Using empty filters (= or <>) on an annotation column with units ...) created by Nicklas Nordborg
1. Create an annotation type for any kind of item. Select any unit and …
7:43 PM Ticket #1206 (= and <> operators have been switched when used on annotations and ...) created by Nicklas Nordborg
1. Create an annotation type for any kind of item 2. Create two items …
7:39 PM Ticket #1205 (Serious problem filtering on annotations where one whishes to exlude a ...) closed by Nicklas Nordborg
invalid: This has nothing to with if you are searching on annotations or not. …
3:55 PM Ticket #1205 (Serious problem filtering on annotations where one whishes to exlude a ...) created by Jari Häkkinen
The problem is that when I use a filter like <>string then all items …
2:53 PM Ticket #1204 (Unknown column 'pos.reporter_id' in 'field list' when using 'merge on ...) created by Nicklas Nordborg
1. From any experiment with data, select a bioassay set and then the …
1:27 PM Changeset [4690] by Nicklas Nordborg
Fixes #1184: Default project sharing level should be setable
1:27 PM Ticket #1184 (Default project sharing level should be setable) closed by Nicklas Nordborg
fixed: (In [4690]) Fixes #1184: Default project sharing level should be setable
9:53 AM Changeset [4689] by Nicklas Nordborg
References #1184: Default project sharing level should be setable …

Dec 5, 2008:

2:51 PM Ticket #1203 (Improve error handling in plug-in auto-installation wizard) closed by Nicklas Nordborg
fixed: (In [4688]) Fixes #1203: Improve error handling in plug-in …
2:51 PM Changeset [4688] by Nicklas Nordborg
Fixes #1203: Improve error handling in plug-in auto-installation wizard
1:15 PM Ticket #1202 (PluginDefinition.loadPluginInformation throws strange error message if ...) closed by Nicklas Nordborg
fixed: (In [4687]) Fixes #1202: PluginDefinition?.loadPluginInformation throws …
1:15 PM Changeset [4687] by Nicklas Nordborg
Fixes #1202: PluginDefinition?.loadPluginInformation throws strange …
11:30 AM Changeset [4686] by Nicklas Nordborg
Fixes #1194: A missing raw data type breaks experiment and raw …
11:30 AM Ticket #1194 (A missing raw data type breaks experiment and raw bioassay views) closed by Nicklas Nordborg
fixed: (In [4686]) Fixes #1194: A missing raw data type breaks experiment and …

Dec 4, 2008:

4:34 PM Changeset [4685] by Martin Svensson
References #979 Added some more comments for javadoc and finished the test.
2:26 PM Changeset [4684] by Nicklas Nordborg
Fixes #1201: JAR path fields are not visible or editable for data file …
2:26 PM Ticket #1201 (JAR path fields are not visible or editable for data file types) closed by Nicklas Nordborg
fixed: (In [4684]) Fixes #1201: JAR path fields are not visible or editable …
1:30 PM Ticket #1199 (NullPointerException when using "Table exporter" to export annotations) closed by Nicklas Nordborg
fixed: (In [4683]) Fixes #1199: NullPointerException? when using "Table …
1:29 PM Changeset [4683] by Nicklas Nordborg
Fixes #1199: NullPointerException? when using "Table exporter" to …
9:53 AM Changeset [4682] by Nicklas Nordborg
References #1175: Biomaterial lists Added role key for biomaterial lists
9:29 AM Ticket #1203 (Improve error handling in plug-in auto-installation wizard) created by Nicklas Nordborg
Error information while installing one or more plug-ins with the …
9:24 AM Ticket #1202 (PluginDefinition.loadPluginInformation throws strange error message if ...) created by Nicklas Nordborg
This is typically child item that takes the permissions from a parent …

Dec 3, 2008:

2:04 PM Changeset [4681] by Nicklas Nordborg
References #1175: Biomaterial lists Basic web interface is now in place.
1:40 PM Ticket #1201 (JAR path fields are not visible or editable for data file types) created by Nicklas Nordborg
A data file type may have a validator and/or meta data reader that are …
1:29 PM Ticket #1200 (Biomaterial LIMS as a top-level menu item) created by Nicklas Nordborg
The menu under "View" is growing large since all new items seems to …

Dec 2, 2008:

4:21 PM Changeset [4680] by Jari Häkkinen
Correcting typo.
1:42 PM Ticket #1199 (NullPointerException when using "Table exporter" to export annotations) created by Nicklas Nordborg
Here is the stacktrace: […] This happens when all of the following …
9:37 AM Changeset [4679] by Nicklas Nordborg
References #1175: Biomaterial lists Core and data layer implemented.
9:08 AM Changeset [4678] by Martin Svensson
References #979 Removed compling error in test-class

Dec 1, 2008:

11:36 AM Changeset [4677] by Martin Svensson
References #979 Updated schema_version, implemented the last methods …

Nov 28, 2008:

1:38 PM Changeset [4676] by Nicklas Nordborg
References #1196: BASE is trying to set a cookie when editing an …
1:35 PM Changeset [4675] by Nicklas Nordborg
Fixes #1196: BASE is trying to set a cookie when editing an …
1:35 PM Ticket #1196 (BASE is trying to set a cookie when editing an annotations) closed by Nicklas Nordborg
fixed: (In [4675]) Fixes #1196: BASE is trying to set a cookie when editing …
1:01 PM Changeset [4674] by Nicklas Nordborg
Fixes #1172: Make it visually clear when a filter is active.
1:01 PM Ticket #1172 (Make it visually clear when a filter is active.) closed by Nicklas Nordborg
fixed: (In [4674]) Fixes #1172: Make it visually clear when a filter is active.
12:52 PM Ticket #1198 (Error: The query has already been executed (Illumina detection P-value ...) closed by Nicklas Nordborg
invalid: Plese report this error on the BASE plugins site: …
12:51 PM Ticket #1197 (Plugin running time unexpected output while executing) closed by Nicklas Nordborg
invalid: This is a server configuration issue. Eg. The job agent has a …
12:47 PM Ticket #1198 (Error: The query has already been executed (Illumina detection P-value ...) created by Johan Vallon-Christersson
When trying to run plugin 'Illumina detection P-value calculation' I …
12:11 PM Ticket #1197 (Plugin running time unexpected output while executing) created by Johan Vallon-Christersson
When running a plugin (Illumina package) the running time reads +6h …
11:16 AM Changeset [4673] by Nicklas Nordborg
Fixes #1186: Column display size should not become too large in …
11:16 AM Ticket #1186 (Column display size should not become too large in listings) closed by Nicklas Nordborg
fixed: (In [4673]) Fixes #1186: Column display size should not become too …

Nov 27, 2008:

10:29 PM Ticket #1196 (BASE is trying to set a cookie when editing an annotations) created by Nicklas Nordborg
1. Create a new item that supports annotations, for example a …
4:39 PM Changeset [4672] by Martin Svensson
References #979 Missed some files in the last commit.
4:33 PM Changeset [4671] by Martin Svensson
References #979 Added keyword to svn-properties
4:24 PM Changeset [4670] by Martin Svensson
References #979 Added data- and item classes needed by BioMaterial?
4:23 PM Ticket #1195 (Problem when importing negative values for annotations with float as ...) created by base
I tried to annotate a number of my extracts using the annotation …
3:58 PM Ticket #1194 (A missing raw data type breaks experiment and raw bioassay views) created by base
Sorting and Filtering in the Experiments List View is not working at …

Nov 26, 2008:

12:06 PM Milestone BASE 2.9 completed
12:05 PM Changeset [4669] by Nicklas Nordborg
Merged 2.9-stable@4643:4666 to trunk.
11:45 AM DownloadPage edited by Nicklas Nordborg
Releasing 2.9.0 (diff)
11:30 AM Changeset [4668] by Nicklas Nordborg
Changes for future release 2.9.1
11:14 AM Changeset [4667] by Nicklas Nordborg
Tagging version 2.9
11:13 AM Changeset [4666] by Nicklas Nordborg
Preparing release 2.9

Nov 25, 2008:

11:42 AM Changeset [4665] by Jari Häkkinen
Updated current BASE team.

Nov 24, 2008:

2:49 PM Changeset [4664] by Martin Svensson
Stylesheet is now included in doc/historical/ when running ant dist.
2:13 PM Historical edited by Martin Svensson
Changed links to historical documents (diff)
11:39 AM Changeset [4663] by Nicklas Nordborg
References #1175: Biomaterial lists Added BioMaterialList? to UML diagram
9:25 AM Ticket #1151 (Create a batch-importer version of the 'roles' test procedure) closed by Martin Svensson
fixed: The file has been added to the test-data repository.
9:17 AM Ticket #1193 (Generic tree-like item overview) created by Nicklas Nordborg
Implement a function that is similar to the "Experiment overview" that …
9:03 AM Ticket #1192 (Use biomaterial lists as filters) created by Nicklas Nordborg
This depends on #1175. On any given list page with biomaterials …
8:59 AM Ticket #1191 (Biomaterial lists manager API and interface) created by Nicklas Nordborg
This depends on #1175. Add support for merging and manipulating …
8:56 AM Ticket #1190 (API and interface for creating biomaterial lists) created by Nicklas Nordborg
This depends on #1175. In the web interface it should be possible to …
8:34 AM Changeset [4662] by Nicklas Nordborg
Fixes #1181: No navigation path to enclosing directory on single file …
8:34 AM Ticket #1181 (No navigation path to enclosing directory on single file view page) closed by Nicklas Nordborg
fixed: (In [4662]) Fixes #1181: No navigation path to enclosing directory on …

Nov 21, 2008:

8:37 PM Ticket #1151 (Create a batch-importer version of the 'roles' test procedure) reopened by Nicklas Nordborg
The 'rawbioassay_out.txt' file is missing in the repository. Running …
2:33 PM Changeset [4661] by Nicklas Nordborg
Fixes #1183: Filtering on file size does not accept units Also fixed …
2:33 PM Ticket #1183 (Filtering on file size does not accept units) closed by Nicklas Nordborg
fixed: (In [4661]) Fixes #1183: Filtering on file size does not accept units …
1:02 PM Changeset [4660] by Nicklas Nordborg
Fixes #1189: Can't import annotation to raw bioassays
1:02 PM Ticket #1189 (Can't import annotation to raw bioassays) closed by Nicklas Nordborg
fixed: (In [4660]) Fixes #1189: Can't import annotation to raw bioassays
12:58 PM Ticket #1189 (Can't import annotation to raw bioassays) created by Nicklas Nordborg
Start a job configuration with the Annotation importer on the 'Raw …
10:31 AM Ticket #1160 (MeV export: Base1 style column headers should be changed to BASE 2 style) closed by Jari Häkkinen
fixed: (In [4659]) Fixes #1160.
10:31 AM Changeset [4659] by Jari Häkkinen
Fixes #1160.
10:25 AM Ticket #1188 (Create a super batch importer?) created by Jari Häkkinen
With the new really nice batch importers available a natural idea …
10:19 AM Ticket #1187 (Can batch importers be made smart enough to import data to several ...) created by Jari Häkkinen
The use case we would like to support is that the laboratory staff …
10:05 AM Ticket #1186 (Column display size should not become too large in listings) created by Jari Häkkinen
In many cases the table listings are hampered by too much information …
9:47 AM Changeset [4658] by Nicklas Nordborg
References #979: Biomaterial LIMS Added BioLIMS to UML diagram.
9:21 AM Ticket #1185 (Manual transform creator) created by Jari Häkkinen
Normally all transforms are created by plug-ins in BASE. However, many …
9:16 AM Ticket #1184 (Default project sharing level should be setable) created by Jari Häkkinen
Currently the sharing level is set but the setting used in the …
9:13 AM Ticket #1183 (Filtering on file size does not accept units) created by Jari Häkkinen
It would be nice to be able to filter on file size using units like kB …
9:06 AM Ticket #727 (Add presentations and publications to the wiki) closed by Jari Häkkinen
wontfix
9:04 AM Changeset [4657] by Jari Häkkinen
Fixing typo.

Nov 20, 2008:

1:36 PM Changeset [4656] by Nicklas Nordborg
References #792: Add support for units to annotation values Test …
1:15 PM Changeset [4655] by Nicklas Nordborg
References #1145 and #1151. Added instructions in the documentation …
1:13 PM Changeset [4654] by Nicklas Nordborg
References #1145: Make the generic raw data importer support batch …
12:42 PM Changeset [4653] by Nicklas Nordborg
References #1145: Make the generic raw data importer support batch …
12:05 PM Changeset [4652] by Nicklas Nordborg
References #1133: Experimental factors - inherit annotations Changed …
11:59 AM Changeset [4651] by Nicklas Nordborg
References #1133: Experimental factors - inherit annotations Closing …
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