Timeline



May 19, 2008:

2:48 PM Ticket #987 (NullPointerException in "Test with file" function if no "data header ...) closed by Martin Svensson
fixed: (In [4303]) Fixes #987 NullPointerException? in "Test with file" …
2:48 PM Changeset [4303] by Martin Svensson
Fixes #987 NullPointerException? in "Test with file" function if no …
2:07 PM Changeset [4302] by Nicklas Nordborg
References #1016: Filter table using a reporter list I think this …

May 16, 2008:

11:40 AM Changeset [4301] by Nicklas Nordborg
References #1019: Reporter list manager - Create reporter list using …
11:17 AM Changeset [4300] by Martin Svensson
Removed debug-code

May 15, 2008:

11:31 AM Ticket #978 (Unzipped files never inherit file type specified during upload) closed by Jari Häkkinen
wontfix
11:30 AM Ticket #975 (Experimental overview – error/erroneous warning – Duplicate sub-array index) closed by Jari Häkkinen
worksforme
11:30 AM Ticket #975 (Experimental overview – error/erroneous warning – Duplicate sub-array index) reopened by Jari Häkkinen
11:30 AM Ticket #975 (Experimental overview – error/erroneous warning – Duplicate sub-array index) closed by Jari Häkkinen
wontfix: We'll close this ticket for now since we cannot reproduce the problem.
11:16 AM Ticket #897 (Potential temporary directory clash for plugins running through job agents) closed by Jari Häkkinen
wontfix: This issue is something that the administrator and plugin programmer …
11:00 AM Ticket #1029 (Write specification for support of files in analysis tree (ie not ...) created by Jari Häkkinen
Read the attached file for details. Things to do: - Generate sample …
10:52 AM Ticket #1028 (Plug-in for batch upload/modification of items) created by Jari Häkkinen
References to the latest versions of files (please keep this list up …

May 14, 2008:

10:40 AM Ticket #1020 (A reporter list should hold the number of reporters in it) closed by Nicklas Nordborg
fixed: (In [4299]) Fixes #1020: A reporter list should hold the number of …
10:40 AM Changeset [4299] by Nicklas Nordborg
Fixes #1020: A reporter list should hold the number of reporters in it

May 13, 2008:

11:44 AM ReleaseProcedure edited by Nicklas Nordborg
Fixed example links for revision logs (diff)
11:29 AM Milestone BASE 2.7 completed
Major features in this milestone: * Extension system for the web …
11:26 AM Changeset [4298] by Nicklas Nordborg
Merged pre-2.7-release to the trunk.
11:04 AM ReleaseProcedure edited by Nicklas Nordborg
New (temporary) procedure for generating documentation (diff)
10:49 AM DownloadPage edited by Nicklas Nordborg
Releasing 2.7.0 (diff)
9:54 AM ReleaseProcedure edited by Nicklas Nordborg
Fixed item numbering (diff)
9:49 AM Changeset [4297] by Nicklas Nordborg
Changes for future release 2.7.1
9:44 AM Changeset [4296] by Nicklas Nordborg
Tagging version 2.7
9:44 AM Changeset [4295] by Nicklas Nordborg
Preparing relese 2.7

May 12, 2008:

8:20 PM Changeset [4294] by Nicklas Nordborg
References #932: Convert the MeV launcher to an extension Removed MeV …
2:03 PM ReleaseProcedure edited by Nicklas Nordborg
Added instruction to upload BASE2*.jar files (diff)
12:54 PM Changeset [4293] by Nicklas Nordborg
References #932: Convert the MeV launcher to an extension Updated …
11:46 AM Changeset [4292] by Nicklas Nordborg
Fixes #997: Read and update installation/upgrade instructions
11:46 AM Ticket #997 (Read and update installation/upgrade instructions) closed by Nicklas Nordborg
fixed: (In [4292]) Fixes #997: Read and update installation/upgrade instructions
9:49 AM Ticket #1027 (Annotation importer should be able to remove annotations) created by Nicklas Nordborg
If the new value for an annotation is empty(=null) there should be an …
9:31 AM Changeset [4291] by Nicklas Nordborg
Some minor changes to test procedures

May 9, 2008:

2:24 PM Changeset [4290] by Nicklas Nordborg
References #1011: Select multiple alternatives for a filter with a …
12:49 PM Changeset [4289] by Nicklas Nordborg
References #933: Create extension points for some selected places in …
12:18 PM Changeset [4288] by Nicklas Nordborg
Fixes #1026: Test programs that need the extended test data should …
12:18 PM Ticket #1026 (Test programs that need the extended test data should check that it ...) closed by Nicklas Nordborg
fixed: (In [4288]) Fixes #1026: Test programs that need the extended test …
11:17 AM Ticket #1026 (Test programs that need the extended test data should check that it ...) created by Nicklas Nordborg
The test data we are referring to is described here …
9:35 AM Changeset [4287] by Nicklas Nordborg
Deleting obsolete branches
8:47 AM Changeset [4286] by Nicklas Nordborg
Changes for future release 2.8
8:46 AM Changeset [4285] by Nicklas Nordborg
Forking new minor version 2.7 branch
8:44 AM Changeset [4284] by Nicklas Nordborg
Merged patch release 2.6.3 to the trunk. Delta: tags/2.6.3 - tags/2.6.2
8:33 AM DownloadPage edited by Nicklas Nordborg
Releasing 2.6.3 (diff)
8:13 AM Milestone BASE 2.6.3 completed
Bug fixes for 2.6.2: Revision log: log:branches/2.6-stable@4230:4283
8:10 AM Changeset [4283] by Nicklas Nordborg
Tagging version 2.6.3
8:08 AM Changeset [4282] by Nicklas Nordborg
Preparing release 2.6.3

May 8, 2008:

10:33 PM Changeset [4281] by Jari Häkkinen
Removed potentially dangerous static declaration.
4:37 PM Ticket #1017 (Make MedianRatioNormalization to normalize 1-channel data) closed by Jari Häkkinen
fixed: (In [4280]) Fixes #1017. 1-channel median normalizarion added.
4:37 PM Changeset [4280] by Jari Häkkinen
Fixes #1017. 1-channel median normalizarion added.
1:46 PM Changeset [4279] by Nicklas Nordborg
Updating credits.txt before 2.7.0 release.
1:00 PM Ticket #773 (Filter reporter table using array design) closed by Nicklas Nordborg
wontfix: This should be possible when #1015 and #1016 becomes fixed. Eg. first …
12:57 PM Ticket #1007 (Add reference to the Illumina plugin in BASE doc Appendix B) closed by Nicklas Nordborg
wontfix: I think the existing link is enough.
12:52 PM Ticket #933 (Create extension points for some selected places in the web client) closed by Nicklas Nordborg
fixed: Nothing more to do.
12:51 PM Ticket #1011 (Select multiple alternatives for a filter with a specified list of options) closed by Nicklas Nordborg
fixed: (In [4278]) Fixes #1011: Select multiple alternatives for a filter …
12:51 PM Changeset [4278] by Nicklas Nordborg
Fixes #1011: Select multiple alternatives for a filter with a …
12:51 PM Changeset [4277] by Nicklas Nordborg
Fixes #1025: Add Hql.size() expression
12:51 PM Ticket #1025 (Add Hql.size() expression) closed by Nicklas Nordborg
fixed: (In [4277]) Fixes #1025: Add Hql.size() expression
12:50 PM Ticket #1025 (Add Hql.size() expression) created by Nicklas Nordborg
This is a HQL expression that creates a size(collection) expression. …
11:49 AM Changeset [4276] by Nicklas Nordborg
References #988: Add support for servlets in extensions Fixed …
10:48 AM Changeset [4275] by Nicklas Nordborg
References #1011: Allow to select multiple alternatives for a filter …
9:39 AM Changeset [4274] by Martin Svensson
References #1021 Correct value is now returned by the pathCanBeUsed-method
9:29 AM Ticket #1024 (Allow users to select a specific job-agent when creating a new job) created by Nicklas Nordborg
When job agents are used to execute jobs there is limited way to …
9:12 AM Ticket #1023 (Add support for using regular expressions when filtering lists) created by Nicklas Nordborg
This depends on #1022. We could use '~' and '!~' as the operator prefixes.
9:09 AM Ticket #1022 (Add support for using regular expressions in queries) created by Nicklas Nordborg
This is not in the SQL standard, but both Postgres and MySQL have an …
9:05 AM Changeset [4273] by Martin Svensson
Fixes #1021 Unclosed DbControl?
9:05 AM Ticket #1021 (Unclosed DbControler) closed by Martin Svensson
fixed: (In [4273]) Fixes #1021 Unclosed DbControl?
8:36 AM Ticket #1021 (Unclosed DbControler) created by Martin Svensson
[…]
8:30 AM Changeset [4272] by Nicklas Nordborg
Fixes #1018: Make it possible to filter on null at the same time as a …
8:30 AM Ticket #1018 (Make it possible to filter on null at the same time as a real value) closed by Nicklas Nordborg
fixed: (In [4272]) Fixes #1018: Make it possible to filter on null at the …
8:05 AM Ticket #1018 (Make it possible to filter on null at the same time as a real value) reopened by Nicklas Nordborg
Hmm... something strange has happened... The code that was checked in …

May 7, 2008:

11:07 PM Ticket #1020 (A reporter list should hold the number of reporters in it) created by Nicklas Nordborg
I think this would be useful information once #1019 is implemented and …
4:41 PM Ticket #1019 (Reporter list manager - Create reporter list using combinations of ...) created by Johan Vallon-Christersson
Added functionality to manage reporter lists and create new reporter …
4:14 PM Ticket #1008 (Error in API doc for class `SpotExtraValueBatcher<I>`) closed by Martin Svensson
fixed: (In [4271]) Fixes #1008 Updated documentation
4:14 PM Changeset [4271] by Martin Svensson
Fixes #1008 Updated documentation
3:01 PM Changeset [4270] by Nicklas Nordborg
Fixes #1018: Make it possible to filter on null at the same time as a …
3:01 PM Ticket #1018 (Make it possible to filter on null at the same time as a real value) closed by Nicklas Nordborg
fixed: (In [4270]) Fixes #1018: Make it possible to filter on null at the …
1:38 PM Ticket #1018 (Make it possible to filter on null at the same time as a real value) created by Nicklas Nordborg
In the web client it is possible to filter on two values by giving a …
9:26 AM Ticket #1017 (Make MedianRatioNormalization to normalize 1-channel data) created by Jari Häkkinen
The summary says it all. Remember to change the information on core …

May 6, 2008:

7:30 PM Ticket #1016 (Filter table using a reporter list) created by Johan Vallon-Christersson
For a table that lists reporters/reporter info it would be useful to …
7:11 PM Ticket #1015 (Add reporter list from tables that list reporters/reporter info.) created by Johan Vallon-Christersson
Currently, the functionality to create reporter lists is only …
1:51 PM Ticket #954 (Array slides – Creating array slides using import plugin) closed by Nicklas Nordborg
wontfix: This will be probably be implemented as a more generic import plug-in …
9:23 AM Changeset [4269] by Nicklas Nordborg
Fixes #1013: Sharing of items to other users and/or groups fails This …
9:23 AM Ticket #1013 (Sharing of items to other users and/or groups fails) closed by Nicklas Nordborg
fixed: (In [4269]) Fixes #1013: Sharing of items to other users and/or groups …
9:08 AM Ticket #1014 (Issues listing data after removing items) created by Jari Häkkinen
In some cases listing of spot data fails for me. After deleting …
8:47 AM Ticket #1013 (Sharing of items to other users and/or groups fails) created by Jari Häkkinen
A user with role 'User' cannot share items to other users nor groups. …
8:41 AM Ticket #1012 (Information on 'read' access to users needs clarification) created by Jari Häkkinen
In …
8:25 AM Changeset [4268] by Jari Häkkinen
Minor change in web client doc.

May 5, 2008:

10:05 PM Changeset [4267] by Nicklas Nordborg
References #974. Revert accidental renaming of method in [4256]
3:02 PM Ticket #964 (Support preset filter list with null/not null values) closed by Nicklas Nordborg
duplicate: Replaced by #1011
3:02 PM Ticket #962 (Filtering the list – ”not equal to” operator for selection list options) closed by Nicklas Nordborg
duplicate: Replaced by #1011
3:01 PM Ticket #1011 (Select multiple alternatives for a filter with a specified list of options) created by Nicklas Nordborg
This ticket replaces #962 and #964. A property of an item that can …
1:24 PM Changeset [4266] by Nicklas Nordborg
Fixes #943: Base1PluginExecuter should import reporterlists
1:24 PM Ticket #943 (Base1PluginExecuter should import reporterlists) closed by Nicklas Nordborg
fixed: (In [4266]) Fixes #943: Base1PluginExecuter should import reporterlists
9:37 AM Ticket #1001 (Plug-ins that use the 'execute immediately' option can't be aborted) closed by Nicklas Nordborg
fixed: (In [4265]) Fixes #1001: Plug-ins that use the 'execute immediately' …
9:37 AM Changeset [4265] by Nicklas Nordborg
Fixes #1001: Plug-ins that use the 'execute immediately' option can't …
9:36 AM Ticket #1010 (Display progress reporter for plug-ins that are executing with the ...) created by Nicklas Nordborg
In the current implementation a window with the message `Do not close …

Apr 30, 2008:

12:40 PM Changeset [4264] by Nicklas Nordborg
References #436: Create extension system for the web application …
12:39 PM Changeset [4263] by Nicklas Nordborg
References #933: Create extension points for some selected places in …
9:54 AM Changeset [4262] by Nicklas Nordborg
References #933: Create extension points for some selected places in …

Apr 29, 2008:

1:58 PM Ticket #1009 (Link from array design to job that imported the features) closed by Nicklas Nordborg
fixed: (In [4261]) Fixes #1009: Link from array design to job that imported …
1:58 PM Changeset [4261] by Nicklas Nordborg
Fixes #1009: Link from array design to job that imported the features
1:58 PM Changeset [4260] by Nicklas Nordborg
References #974. Don't display import information for file-only data sets
1:47 PM Changeset [4259] by Nicklas Nordborg
References #974. Changed label on 'import date' column
1:42 PM Changeset [4258] by Nicklas Nordborg
Fixes #974: Link from raw bioassay to job that imported the raw data
1:42 PM Ticket #974 (Link from raw bioassay to job that imported the raw data) closed by Nicklas Nordborg
fixed: (In [4258]) Fixes #974: Link from raw bioassay to job that imported …
12:59 PM Changeset [4257] by Nicklas Nordborg
References #1009: Link from array design to job that imported the …
11:39 AM Changeset [4256] by Nicklas Nordborg
References #974: Link from raw bioassay to job that imported the raw …
8:26 AM Ticket #1009 (Link from array design to job that imported the features) created by Nicklas Nordborg
This is the same thing for array designs as #974 is for raw bioassays

Apr 28, 2008:

11:16 PM Ticket #1008 (Error in API doc for class `SpotExtraValueBatcher<I>`) created by Jari Häkkinen
In javadoc section for Class SpotExtraValueBatcher<I> there should …
8:29 PM Ticket #1007 (Add reference to the Illumina plugin in BASE doc Appendix B) created by Jari Häkkinen
The listing of core plugins should reference to baseplugins.thep.lu.se …
3:44 PM Changeset [4255] by Jari Häkkinen
Typo.
3:00 PM Changeset [4254] by Nicklas Nordborg
Fixes #972: Assign job to experiment when the job is created The …
3:00 PM Ticket #972 (Assign job to experiment when the job is created) closed by Nicklas Nordborg
fixed: (In [4254]) Fixes #972: Assign job to experiment when the job is …
12:25 PM Changeset [4253] by Nicklas Nordborg
Undo changes made in [4250] to this file. The code was related to …
12:19 PM Ticket #1006 (Make it possible to search for missing annotations) closed by Nicklas Nordborg
fixed: (In [4252]) Fixes #1006: Make it possible to search for missing annotations
12:19 PM Changeset [4252] by Nicklas Nordborg
Fixes #1006: Make it possible to search for missing annotations
10:54 AM Ticket #1006 (Make it possible to search for missing annotations) created by Nicklas Nordborg
There is an issue that manifests itself when filtering lists of items …
10:48 AM Changeset [4251] by Nicklas Nordborg
Fixes #965: Filtering the list – selection list vs. input box for …
10:48 AM Ticket #965 (Filtering the list – selection list vs. input box for enumeration type ...) closed by Nicklas Nordborg
fixed: (In [4251]) Fixes #965: Filtering the list ?\226?\128?\147 selection …

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. …
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