Timeline



Apr 25, 2008:

3:41 PM Changeset [4250] by Nicklas Nordborg
References #965: Filtering the list – selection list vs. input box for …

Apr 24, 2008:

1:30 PM Changeset [4249] by Nicklas Nordborg
Fixes #1005: Test programs should print out server information just …
1:30 PM Ticket #1005 (Test programs should print out server information just like the initdb ...) closed by Nicklas Nordborg
fixed: (In [4249]) Fixes #1005: Test programs should print out server …
1:08 PM Changeset [4248] by Nicklas Nordborg
Fixes #1004: Upgrade Postgres JDBC driver to 8.3.603
1:08 PM Ticket #1004 (Upgrade Postgres JDBC driver to 8.3.603) closed by Nicklas Nordborg
fixed: (In [4248]) Fixes #1004: Upgrade Postgres JDBC driver to 8.3.603
1:07 PM Ticket #1005 (Test programs should print out server information just like the initdb ...) created by Nicklas Nordborg
This is very useful to know and make sure that the test programs run …
12:55 PM Changeset [4247] by Nicklas Nordborg
Fixes #1003: Illumina raw data importer – Enhance feature mismatch …
12:55 PM Ticket #1003 (Illumina raw data importer – Enhance feature mismatch error handling) closed by Nicklas Nordborg
fixed: (In [4247]) Fixes #1003: Illumina raw data importer ?\226?\128?\147 …
12:11 PM Ticket #1004 (Upgrade Postgres JDBC driver to 8.3.603) created by Nicklas Nordborg
We currently have 8.2.506. The documentation on their web page …
11:39 AM Changeset [4246] by Nicklas Nordborg
Fixes #968: Raw data importer – Enhance feature mismatch error handling
11:39 AM Ticket #968 (Raw data importer – Enhance feature mismatch error handling) closed by Nicklas Nordborg
fixed: (In [4246]) Fixes #968: Raw data importer ?\226?\128?\147 Enhance …
10:48 AM Ticket #1003 (Illumina raw data importer – Enhance feature mismatch error handling) created by Nicklas Nordborg
Do the same things with this importer as for the flat file raw data …
8:00 AM Changeset [4245] by Nicklas Nordborg
Fixes #1002: Possible PermissionDeniedException? when listing …
8:00 AM Ticket #1002 (Possible PermissionDeniedException when listing rawbioassay through ...) closed by Nicklas Nordborg
fixed: (In [4245]) Fixes #1002: Possible PermissionDeniedException? when …
7:44 AM Ticket #1002 (Possible PermissionDeniedException when listing rawbioassay through ...) created by Nicklas Nordborg
This happens if one of the raw bioassays the user has access to is …

Apr 23, 2008:

3:04 PM Changeset [4244] by Nicklas Nordborg
Fixes #993: Paste multiple barcodes in the Multiple slides wizard
3:04 PM Ticket #993 (Paste multiple barcodes in the Multiple slides wizard) closed by Nicklas Nordborg
fixed: (In [4244]) Fixes #993: Paste multiple barcodes in the Multiple slides …
1:51 PM Changeset [4243] by Nicklas Nordborg
Fixes #920: Add support for aborting queries using a StatlessSession?
1:51 PM Ticket #920 (Add support for aborting queries using a StatlessSession) closed by Nicklas Nordborg
fixed: (In [4243]) Fixes #920: Add support for aborting queries using a …
1:50 PM Ticket #1001 (Plug-ins that use the 'execute immediately' option can't be aborted) created by Nicklas Nordborg
This is true for all plug-ins even those that implements the …
1:44 PM Changeset [4242] by Nicklas Nordborg
Fixes #1000: SimpleExport? count items twice
1:44 PM Ticket #1000 (SimpleExport count items twice) closed by Nicklas Nordborg
fixed: (In [4242]) Fixes #1000: SimpleExport? count items twice
1:40 PM Ticket #1000 (SimpleExport count items twice) created by Nicklas Nordborg
The SimpleExport is the plug-in that is used for all table-like …

Apr 22, 2008:

2:07 PM Changeset [4241] by Nicklas Nordborg
Fixes #994: Create GAL export plug-in for array designs
2:07 PM Ticket #994 (Create GAL export plug-in for array designs) closed by Nicklas Nordborg
fixed: (In [4241]) Fixes #994: Create GAL export plug-in for array designs
2:06 PM Changeset [4240] by Nicklas Nordborg
Fixes #999: PrintMapImporter? should import feature diameter from TAM …
2:06 PM Ticket #999 (PrintMapImporter should import feature diameter from TAM and MWBR files) closed by Nicklas Nordborg
fixed: (In [4240]) Fixes #999: PrintMapImporter? should import feature …
11:48 AM Changeset [4239] by Nicklas Nordborg
References #994: Create GAL export plug-in for array designs Added …
11:36 AM Ticket #999 (PrintMapImporter should import feature diameter from TAM and MWBR files) created by Nicklas Nordborg
We need a new column in the ArrayDesignBlock table for this. The …

Apr 21, 2008:

10:50 AM Ticket #989 (Add support for using extension classes in custom JSP pages) closed by Nicklas Nordborg
fixed
10:50 AM Ticket #988 (Add support for servlets in extensions) closed by Nicklas Nordborg
fixed
10:49 AM Ticket #436 (Create extension system for the web application) closed by Nicklas Nordborg
fixed
10:00 AM Changeset [4238] by Nicklas Nordborg
Fixes #998: Decimal numbers may be incorrectly rounded
10:00 AM Ticket #998 (Decimal numbers may be incorrectly rounded) closed by Nicklas Nordborg
fixed: (In [4238]) Fixes #998: Decimal numbers may be incorrectly rounded

Apr 19, 2008:

3:26 PM Ticket #998 (Decimal numbers may be incorrectly rounded) created by Johan Vallon-Christersson
Numbers are not sorted correctly. Bioassay, Spots data, Sort Ch1. …

Apr 18, 2008:

2:41 PM Ticket #997 (Read and update installation/upgrade instructions) created by Nicklas Nordborg
The installation and upgrade instructions are becoming a bit old. We …
2:08 PM Changeset [4237] by Nicklas Nordborg
References #436: Create extension system for the web application …
1:06 PM Changeset [4236] by Nicklas Nordborg
References #436: Create extension system for the web application …
11:51 AM Changeset [4235] by Nicklas Nordborg
Fixes #996: MEV can't open data files that has a missing value in the …
11:51 AM Ticket #996 (MEV can't open data files that has a missing value in the last column) closed by Nicklas Nordborg
fixed: (In [4235]) Fixes #996: MEV can't open data files that has a missing …
11:31 AM Ticket #932 (Convert the MeV launcher to an extension) closed by Nicklas Nordborg
fixed: (In [4234]) Fixes #932: Convert the MeV launcher to an extension …
11:31 AM Changeset [4234] by Nicklas Nordborg
Fixes #932: Convert the MeV launcher to an extension MEV-related code …
11:16 AM Ticket #996 (MEV can't open data files that has a missing value in the last column) created by Nicklas Nordborg
The BioAssaySetExporter? can export data in MEV format. The export …

Apr 17, 2008:

3:05 PM Changeset [4233] by Nicklas Nordborg
References #436: Create extension system for the web application …
2:25 PM Ticket #995 (Add link to closed tickets for each milestone on DownloadPage) closed by Nicklas Nordborg
fixed
2:25 PM DownloadPage edited by Nicklas Nordborg
Fixes #995 (diff)
2:06 PM Changeset [4232] by Nicklas Nordborg
Merged patch release 2.6.2 to the trunk. Delta 2.6.2 - 2.6.1
1:53 PM Ticket #995 (Add link to closed tickets for each milestone on DownloadPage) created by Nicklas Nordborg
It is a bit difficult to get to know what has been fixed for each …
1:38 PM Milestone BASE 2.6.2 completed
Bug fixes for 2.6.1. Revision log: log:branches/2.6-stable@4191:4230
1:37 PM DownloadPage edited by Nicklas Nordborg
Releasing 2.6.2 (diff)
1:31 PM Changeset [4231] by Nicklas Nordborg
Changes for future release 2.6.3
1:19 PM Changeset [4230] by Nicklas Nordborg
Tagging version 2.6.2
1:19 PM Changeset [4229] by Nicklas Nordborg
Preparing release 2.6.2
1:18 PM Changeset [4228] by Nicklas Nordborg
References #957: Base1PluginExecuter doesn't import plug-in generated …
12:30 PM Tickets #990,​991 batch updated by Nicklas Nordborg
fixed: (In [4227]) Fixes #990 and #991: Change default create date... and …
12:30 PM Changeset [4227] by Nicklas Nordborg
Fixes #990 and #991: Change default create date... and Created date - …
12:17 PM Changeset [4226] by Nicklas Nordborg
Fixes #961: Expand the maximum number of characters accepted by filter …
12:17 PM Ticket #961 (Expand the maximum number of characters accepted by filter input box) closed by Nicklas Nordborg
fixed: (In [4226]) Fixes #961: Expand the maximum number of characters …

Apr 16, 2008:

8:15 AM Changeset [4225] by Nicklas Nordborg
References #989: Add support for using extension classes in custom JSP …
8:02 AM Changeset [4224] by Nicklas Nordborg
References #436: Create extension system for the web application Svn …

Apr 15, 2008:

10:09 PM Ticket #927 (Image Macro fails on Feature Trac Page) closed by Johan Vallon-Christersson
fixed
10:06 PM bioassayset_plot.jpg attached to Features by Johan Vallon-Christersson
9:59 PM Features edited by Johan Vallon-Christersson
(diff)
9:58 PM experiment_overview.jpg attached to Features by Johan Vallon-Christersson
9:50 PM bioassayset_histplot.jpg attached to Features by Johan Vallon-Christersson
9:47 PM experiment_explorer.jpg attached to Features by Johan Vallon-Christersson
8:14 PM Changeset [4223] by Nicklas Nordborg
References #989: Add support for using extension classes in custom JSP …
2:24 PM Changeset [4222] by Nicklas Nordborg
References #989: Add support for using extension classes in custom JSP …
12:59 PM dynamic_columns.jpg attached to Features by Johan Vallon-Christersson
12:18 PM Ticket #994 (Create GAL export plug-in for array designs) created by Johan Vallon-Christersson
Add functionality to create/download GAL files from array designs …
10:05 AM Ticket #993 (Paste multiple barcodes in the Multiple slides wizard) created by Johan Vallon-Christersson
In BASE2, multiple array slides can be created using the “Multiple …

Apr 14, 2008:

7:29 PM Ticket #957 (Base1PluginExecuter doesn't import plug-in generated BASEfiles as expected) closed by Nicklas Nordborg
fixed: I am closing this now so we can release 2.6.2. New or remaining bugs …
7:13 PM Ticket #992 (Regular expressions with backslashes trigger "Not allowed to use ...) closed by Nicklas Nordborg
wontfix: This can't be fixed. A column mapping ends as soon as a \ is …
5:34 PM Ticket #992 (Regular expressions with backslashes trigger "Not allowed to use ...) created by base
I have some raw data files with column headings F635 Median and …
2:40 PM Changeset [4221] by Nicklas Nordborg
References #988: Add support for servlets in extensions The main …
7:53 AM Ticket #955 (Array slides – make test for barcode uniqueness) closed by Nicklas Nordborg
fixed: (In [4220]) Fixes #955: Array slides ?\226?\128?\147 make test for …
7:53 AM Changeset [4220] by Nicklas Nordborg
Fixes #955: Array slides – make test for barcode uniqueness

Apr 11, 2008:

5:36 PM Ticket #991 (Created date - auto changed from blank when edit sample) created by Johan Vallon-Christersson
When editing a sample that does not have Creation date defined …
5:32 PM Ticket #990 (Change default create date for samples (and other items).) created by Johan Vallon-Christersson
When adding Samples the Created date is by default set to current …
1:57 PM Ticket #986 (Move example code for web services to the BASE plug-ins site) closed by Nicklas Nordborg
fixed
1:54 PM Changeset [4219] by Nicklas Nordborg
References #986: Move example code for web services to the BASE …
11:49 AM Ticket #898 (Move example code for plug-ins to the BASE plug-ins site) closed by Nicklas Nordborg
fixed
11:46 AM DeveloperInformation edited by Nicklas Nordborg
Changed documentation links (diff)
11:41 AM DeveloperInformation edited by Nicklas Nordborg
Link to new site for examples (diff)
10:58 AM Changeset [4218] by Nicklas Nordborg
References #898: Move example code for plug-ins to the BASE plug-ins …

Apr 10, 2008:

9:47 PM Ticket #989 (Add support for using extension classes in custom JSP pages) created by Nicklas Nordborg
An extensions that uses custom JSP pages are currently limited to use …
9:31 PM Ticket #988 (Add support for servlets in extensions) created by Nicklas Nordborg
This is "needed" by the MeV launcher. It currently uses the MevExport?
6:07 PM Ticket #987 (NullPointerException in "Test with file" function if no "data header ...) created by Johan Vallon-Christersson
When using Annotation importer. Input file is small and contains two …
2:34 PM Ticket #986 (Move example code for web services to the BASE plug-ins site) created by Nicklas Nordborg
Was part of #898. Better to have this as it's own ticket.
2:28 PM Changeset [4217] by Nicklas Nordborg
References #436: Create extension system for the web application …
2:23 PM Changeset [4216] by Nicklas Nordborg
Fixes #985: File sizes are not correctly rounded Also fixed so that …
2:23 PM Ticket #985 (File sizes are not correctly rounded) closed by Nicklas Nordborg
fixed: (In [4216]) Fixes #985: File sizes are not correctly rounded Also …
1:58 PM Ticket #985 (File sizes are not correctly rounded) created by Nicklas Nordborg
I uploaded a file which size is 4050 (~3.995Kb) bytes in size. This is …
1:52 PM Changeset [4215] by Nicklas Nordborg
Fixes #984: Bioassays may show up duplicated in list of bioassays The …
1:52 PM Ticket #984 (Bioassays may show up duplicated in list of bioassays) closed by Nicklas Nordborg
fixed: (In [4215]) Fixes #984: Bioassays may show up duplicated in list of …
1:45 PM Ticket #983 (update.sh script doesn't validate parameters) closed by Nicklas Nordborg
fixed: (In [4214]) Fixes #983: update.sh script doesn't validate parameters
1:45 PM Changeset [4214] by Nicklas Nordborg
Fixes #983: update.sh script doesn't validate parameters
1:42 PM Changeset [4213] by Nicklas Nordborg
Fixes #980: Items created by jobs are not shared to the active project.
1:42 PM Ticket #980 (Items created by jobs are not shared to the active project.) closed by Nicklas Nordborg
fixed: (In [4213]) Fixes #980: Items created by jobs are not shared to the …
12:53 PM Changeset [4212] by Nicklas Nordborg
References #957: Base1PluginExecuter doesn't import plug-in generated …
12:18 PM Ticket #984 (Bioassays may show up duplicated in list of bioassays) created by Nicklas Nordborg
I am not really sure why this is happening. Sometimes a bioassay …
12:09 PM Ticket #983 (update.sh script doesn't validate parameters) created by Jari Häkkinen
I am following the Illumina plug-in installation recipe and read that …

Apr 9, 2008:

4:08 PM Ticket #982 (Wrong destination (for shared to user) from link to directory from ...) created by Johan Vallon-Christersson
After running a plugin (that creates directories and files and …
3:16 PM Ticket #981 (Share all subdirectories and files when sharing a directory) created by Johan Vallon-Christersson
When sharing a directory, its subdirectories and files are not shared. …
3:15 PM Ticket #980 (Items created by jobs are not shared to the active project.) created by Johan Vallon-Christersson
The user case: When working in an active project I run a plugin in an …
2:44 PM Ticket #979 (Biomaterial LIMS) created by Johan Vallon-Christersson
Enhancing biomaterial management in BASE by adding Biomaterial LIMS …

Apr 8, 2008:

2:16 PM Ticket #978 (Unzipped files never inherit file type specified during upload) created by base
There should perhaps be an option to unpack an uploaded zip file …

Apr 7, 2008:

2:02 PM Changeset [4211] by Nicklas Nordborg
Fixes #970: PluginConfigurationImporter? doesn't support multi-valued …
2:02 PM Ticket #970 (PluginConfigurationImporter doesn't support multi-valued parameters) closed by Nicklas Nordborg
fixed: (In [4211]) Fixes #970: PluginConfigurationImporter? doesn't support …
1:48 PM Changeset [4210] by Nicklas Nordborg
Fixes #977: ClassCastException? in Experiment overview when clicking on …
1:48 PM Ticket #977 (ClassCastException in Experiment overview when clicking on an ...) closed by Nicklas Nordborg
fixed: (In [4210]) Fixes #977: ClassCastException? in Experiment overview when …
1:24 PM Ticket #977 (ClassCastException in Experiment overview when clicking on an ...) created by Nicklas Nordborg
1. Select an experiment which has at least one experimental factor. …
1:19 PM Changeset [4209] by Nicklas Nordborg
Fixes #976: NullPointerException? in Experiment overview
1:19 PM Ticket #976 (NullPointerException in Experiment overview) closed by Nicklas Nordborg
fixed: (In [4209]) Fixes #976: NullPointerException? in Experiment overview
1:01 PM Changeset [4208] by Nicklas Nordborg
References #436: Create extension system for the web application …
12:19 PM Ticket #976 (NullPointerException in Experiment overview) created by Nicklas Nordborg
The original report is found in #975. I have now been able to …

Apr 4, 2008:

6:36 PM Ticket #975 (Experimental overview – error/erroneous warning – Duplicate sub-array index) created by Johan Vallon-Christersson
Working in an experiment containing 3 raw bioassays, all from the same …
2:44 PM Changeset [4207] by Nicklas Nordborg
References #436: Create extension system for the web application …
8:42 AM Changeset [4206] by Nicklas Nordborg
References #436: Create extension system for the web application …

Apr 3, 2008:

11:34 AM Ticket #974 (Link from raw bioassay to job that imported the raw data) created by Johan Vallon-Christersson
This ticket relates to ticket:750 A user scenario involves going back …

Apr 2, 2008:

8:41 PM Ticket #973 (Add a 'svn.update' target to the build file) closed by Nicklas Nordborg
fixed: (In [4205]) Fixes #973: Add a 'svn.update' target to the build file
8:41 PM Changeset [4205] by Nicklas Nordborg
Fixes #973: Add a 'svn.update' target to the build file
7:54 PM Ticket #973 (Add a 'svn.update' target to the build file) created by Nicklas Nordborg
This would simplify automatic generation of the documentation. After …
5:06 PM Ticket #972 (Assign job to experiment when the job is created) created by Johan Vallon-Christersson
This ticket concerns jobs running in experiments. Typically, a user …
1:46 PM Ticket #971 (Be able to upgrade BASE without restarting Tomcat) closed by Nicklas Nordborg
invalid: This is problem with Tomcat.
1:20 PM Ticket #971 (Be able to upgrade BASE without restarting Tomcat) created by base
I just upgraded our dev server (system info below) […] and found …
12:43 PM Ticket #970 (PluginConfigurationImporter doesn't support multi-valued parameters) created by Nicklas Nordborg
From the mailing list: …
10:44 AM Changeset [4204] by Nicklas Nordborg
Fixes #969: Annotation importer doesn't save "Owned by ..." parameter …
10:44 AM Ticket #969 (Annotation importer doesn't save "Owned by ..." parameter values) closed by Nicklas Nordborg
fixed: (In [4204]) Fixes #969: Annotation importer doesn't save "Owned by …
9:43 AM Ticket #963 (New hybridization... button on labelled extract page doesn't work as ...) closed by Nicklas Nordborg
fixed: (In [4203]) Fixes #963: New hybridization... button on labelled …
9:43 AM Changeset [4203] by Nicklas Nordborg
Fixes #963: New hybridization... button on labelled extract page …

Apr 1, 2008:

7:24 PM Ticket #969 (Annotation importer doesn't save "Owned by ..." parameter values) created by Nicklas Nordborg
It seems like the annotation importer doesn't save which option has …
3:30 PM Ticket #968 (Raw data importer – Enhance feature mismatch error handling) created by Johan Vallon-Christersson
Feature mismatch error handling when importing raw data concerns how …
3:18 PM Ticket #967 (Assign the parent directory permissions to new files/directories) created by base
I made a /home/shared folder and gave it Everyone RU permissions. The …
2:55 PM Changeset [4202] by Nicklas Nordborg
References #436: Create extension system for the web application All …
2:43 PM Ticket #966 (Registered and possibly last updated – add to all/most items) created by Johan Vallon-Christersson
Some items, such as Samples, have a Registered property, i.e., the …
2:25 PM Ticket #965 (Filtering the list – selection list vs. input box for enumeration type ...) created by Johan Vallon-Christersson
This ticket is somewhat related to ticket:962 but more specifically …

Mar 31, 2008:

8:41 PM Ticket #964 (Support preset filter list with null/not null values) created by Nicklas Nordborg
Currently, when a preset filter uses a list of predefined values you …
2:58 PM Ticket #963 (New hybridization... button on labelled extract page doesn't work as ...) created by base
When clicking on the "New hybridization..." action button on a labeled …
12:44 PM Ticket #962 (Filtering the list – ”not equal to” operator for selection list options) created by Johan Vallon-Christersson
When filtering an item list some columns that can only take a few …
12:13 PM Ticket #961 (Expand the maximum number of characters accepted by filter input box) created by Johan Vallon-Christersson
If an item list contains many items you may need to use a filter to be …
10:48 AM Changeset [4201] by Nicklas Nordborg
Fixes #958: Document that the migration program is no longer actively …
10:48 AM Ticket #958 (Document that the migration program is no longer actively tested or ...) closed by Nicklas Nordborg
fixed: (In [4201]) Fixes #958: Document that the migration program is no …
10:00 AM Ticket #960 (Removing a user from a group doesn't work if the user is a quota group ...) closed by Nicklas Nordborg
fixed: (In [4200]) Fixes #960: Removing a user from a group doesn't work if …
10:00 AM Changeset [4200] by Nicklas Nordborg
Fixes #960: Removing a user from a group doesn't work if the user is a …
9:59 AM Ticket #959 (Users may be duplicated in group member list for quota groups) closed by Nicklas Nordborg
fixed: (In [4199]) Fixes #959: Users may be duplicated in group member list …
9:59 AM Changeset [4199] by Nicklas Nordborg
Fixes #959: Users may be duplicated in group member list for quota groups
9:58 AM Ticket #960 (Removing a user from a group doesn't work if the user is a quota group ...) created by Nicklas Nordborg
How to reproduce: 1. Create a group G and assign it some quota 2. …

Mar 28, 2008:

2:52 PM Ticket #959 (Users may be duplicated in group member list for quota groups) created by Nicklas Nordborg
How to reproduce: 1. Create two groups, A and B. Assign quota to one …
2:42 PM Ticket #958 (Document that the migration program is no longer actively tested or ...) created by Nicklas Nordborg
There is a section about the migration in the docbook documentation.
2:41 PM Changeset [4198] by Nicklas Nordborg
References #436: Create extension system for the web application …

Mar 27, 2008:

8:56 AM Ticket #957 (Base1PluginExecuter doesn't import plug-in generated BASEfiles as expected) created by Nicklas Nordborg
The first case was a filtering plug-in which caused the raw data links …
8:36 AM Ticket #956 (Spot image generation throws NullPointerException if a spot has an X ...) closed by Nicklas Nordborg
fixed: (In [4197]) Fixes #956: Spot image generation throws …
8:36 AM Changeset [4197] by Nicklas Nordborg
Fixes #956: Spot image generation throws NullPointerException? if a …
8:02 AM Ticket #956 (Spot image generation throws NullPointerException if a spot has an X ...) created by Nicklas Nordborg
Here is the stacktrace (from BASE 2.4.5): […] See also: …

Mar 26, 2008:

7:12 PM Ticket #955 (Array slides – make test for barcode uniqueness) created by Nicklas Nordborg
As mentioned in the BASE core specifications enforcing array slide …
6:16 PM Ticket #954 (Array slides – Creating array slides using import plugin) created by Johan Vallon-Christersson
In BASE2, array slides can be created one-by-one or by using the …
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