Timeline



May 28, 2008:

8:21 PM Ticket #408 (Implement FTP server) closed by Nicklas Nordborg
invalid: Moved to http://baseplugins.thep.lu.se/wiki/net.sf.basedb.ftp
8:01 AM Ticket #1039 (link to list of plugins is broken) closed by Martin Svensson
fixed: The link is fixed
8:00 AM WikiStart edited by Martin Svensson
Repaired a broken link (diff)
12:15 AM Ticket #1039 (link to list of plugins is broken) created by Peter Johansson
Link on first page core plug-ins with sample configuration files

May 27, 2008:

12:21 PM Ticket #1038 (Provide manual parameter for 'spotsize' in GAL exporter) created by Nicklas Nordborg
Since the 'spotsize' column wasn't added until BASE 2.7 (#999), many …
11:55 AM Ticket #1037 (Add 'id' column to all list pages) created by Nicklas Nordborg
The internal ID of items is not visible anywhere in the web interface. …
10:16 AM Ticket #639 (exportPureMatrix method) closed by Jari Häkkinen
fixed: changeset:4318 adds functionality to export 2-channel data. ch1/ch2 …
10:08 AM Changeset [4318] by Jari Häkkinen
Addresses #639. Exporting plain matrix for 1 and 2 channel data.
9:36 AM Ticket #1036 (Implement 'service' extension point) created by Nicklas Nordborg
It could be useful to have an extension point that can be used for …
8:44 AM Changeset [4317] by Nicklas Nordborg
Fixes #1022: Add support for using regular expressions in queries
8:44 AM Ticket #1022 (Add support for using regular expressions in queries) closed by Nicklas Nordborg
fixed: (In [4317]) Fixes #1022: Add support for using regular expressions in …
8:17 AM Changeset [4316] by Jari Häkkinen
Removed obsolete/stray code.

May 26, 2008:

2:12 PM Changeset [4315] by Nicklas Nordborg
Fixes #1035: Exception when applying filter on multiple Item type in …
2:12 PM Ticket #1035 (Exception when applying filter on multiple Item type in some list views) closed by Nicklas Nordborg
fixed: (In [4315]) Fixes #1035: Exception when applying filter on multiple …
1:01 PM Ticket #967 (Assign the parent directory permissions to new files/directories) closed by Nicklas Nordborg
fixed: (In [4314]) Fixes #967: Assign the parent directory permissions to new …
1:01 PM Changeset [4314] by Nicklas Nordborg
Fixes #967: Assign the parent directory permissions to new …
11:52 AM Changeset [4313] by Nicklas Nordborg
References #981: Share all subdirectories and files when sharing a …
9:31 AM Changeset [4312] by Nicklas Nordborg
Fixes #981: Share all subdirectories and files when sharing a directory
9:31 AM Ticket #981 (Share all subdirectories and files when sharing a directory) closed by Nicklas Nordborg
fixed: (In [4312]) Fixes #981: Share all subdirectories and files when …

May 23, 2008:

3:12 PM Ticket #1035 (Exception when applying filter on multiple Item type in some list views) created by Johan Vallon-Christersson
Selecting to filter on two Item types in Trashcan table view, e.g., …
2:24 PM Changeset [4311] by Nicklas Nordborg
Fixes #1024: Allow users to select a specific job-agent when creating …
2:24 PM Ticket #1024 (Allow users to select a specific job-agent when creating a new job) closed by Nicklas Nordborg
fixed: (In [4311]) Fixes #1024: Allow users to select a specific job-agent …
2:08 PM Changeset [4310] by Jari Häkkinen
Fixes #1034
2:08 PM Ticket #1034 (Normalization: Lowess. Add information about reporter lists to plug-in ...) closed by Jari Häkkinen
fixed: (In [4310]) Fixes #1034
2:02 PM Ticket #1034 (Normalization: Lowess. Add information about reporter lists to plug-in ...) created by Jari Häkkinen
11:39 AM Ticket #1033 (Mark columns containing unique information in list views) created by Jari Häkkinen
It would be nice if the web interface could highlight information that …
11:33 AM Ticket #1032 (Apache server complains "Request-URI Too Large") created by Jari Häkkinen
In some cases the Apache server complains in the URI size. If one …

May 22, 2008:

3:51 PM Changeset [4309] by Martin Svensson
References #532. Chapter is ready to be read.

May 21, 2008:

10:49 PM Ticket #1030 (Normaliztion: Median ratio for 1-channel data should support scaling ...) closed by Jari Häkkinen
fixed: (In [4308]) Fixes #1030. User selects scaling/subtraction depending on …
10:49 PM Changeset [4308] by Jari Häkkinen
Fixes #1030. User selects scaling/subtraction depending on whether …
5:29 PM Changeset [4307] by Martin Svensson
References #532. Written main part of the Job section
3:39 PM Changeset [4306] by Nicklas Nordborg
References #1015: Add reporter list from tables that list …
1:22 PM Ticket #1031 (Filtering with selection lists) closed by Nicklas Nordborg
invalid: It is intentional and needed if using only a keybord and follows the …
1:13 PM Ticket #1031 (Filtering with selection lists) created by Jari Häkkinen
The selection list filters in list views works if the green check box …
1:11 PM Changeset [4305] by Nicklas Nordborg
References #1015: Add reporter list from tables that list …
8:47 AM Ticket #1027 (Annotation importer should be able to remove annotations) closed by Nicklas Nordborg
fixed: (In [4304]) Fixes #1027: Annotation importer should be able to remove …
8:47 AM Changeset [4304] by Nicklas Nordborg
Fixes #1027: Annotation importer should be able to remove annotations

May 20, 2008:

10:54 AM Ticket #1030 (Normaliztion: Median ratio for 1-channel data should support scaling ...) created by Jari Häkkinen
The current implementation translate the data to zero median for each …

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 …
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