Timeline



Oct 4, 2008:

12:28 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)

Oct 3, 2008:

8:03 AM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)

Oct 1, 2008:

4:57 PM PluginDownload edited by Jari Häkkinen
(diff)
4:55 PM PluginDownload edited by Jari Häkkinen
Releasing MergeBioAssay 2.1 (diff)
4:51 PM se.lu.onk.MergeBioAssay edited by Jari Häkkinen
(diff)
4:51 PM se.lu.onk.MergeBioAssay edited by Jari Häkkinen
Releasing MergeBioAssay 2.1 (diff)
4:47 PM MergeBioAssay-2.1.tgz.MD5 attached to se.lu.onk.MergeBioAssay by Jari Häkkinen
4:46 PM MergeBioAssay-2.1.tgz attached to se.lu.onk.MergeBioAssay by Jari Häkkinen
4:46 PM Changeset [806] by Jari Häkkinen
Setting pre tag to trunk version of MergeBioAssay.
4:45 PM Changeset [805] by Jari Häkkinen
Fixes #137. Releasing MergeBioAssay 2.1
4:45 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) closed by Jari Häkkinen
fixed: (In [805]) Fixes #137. Releasing MergeBioAssay 2.1
4:44 PM Changeset [804] by Jari Häkkinen
Addresses #137. Preparing release 2.1 of MergeBioAssay package.
4:44 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by Jari Häkkinen
(In [804]) Addresses #137. Preparing release 2.1 of MergeBioAssay package.
4:39 PM Changeset [803] by Jari Häkkinen
Setting pre tag to trunk version of ReplicateError.
4:35 PM PluginDownload edited by Jari Häkkinen
Releasing ReplicateError 1.3 (diff)
4:31 PM se.lu.onk.ReplicateError edited by Jari Häkkinen
Releasing ReplicateError 1.3 (diff)
4:28 PM ReplicateError-1.3.tgz.MD5 attached to se.lu.onk.ReplicateError by Jari Häkkinen
4:28 PM ReplicateError-1.3.tgz attached to se.lu.onk.ReplicateError by Jari Häkkinen
4:27 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) closed by Jari Häkkinen
fixed: (In [802]) Fixes #129. Releasing ReplicateError 1.3
4:27 PM Changeset [802] by Jari Häkkinen
Fixes #129. Releasing ReplicateError 1.3
4:25 PM Changeset [801] by Jari Häkkinen
Addresses #129. Preparing release of ReplicateError 1.3
4:25 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [801]) Addresses #129. Preparing release of ReplicateError 1.3
4:16 PM Changeset [800] by Jari Häkkinen
References #129
4:16 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [800]) References #129
4:09 PM Changeset [799] by Jari Häkkinen
Setting pre tag to trunk version of BaseFile.
4:06 PM PluginDownload edited by Jari Häkkinen
Added link to BaseFile 1.0 package (diff)
4:02 PM se.lu.onk.BaseFile edited by Jari Häkkinen
Uploaded BaseFile 1.0 package. (diff)
3:54 PM BaseFile-1.0.tgz.MD5 attached to se.lu.onk.BaseFile by Jari Häkkinen
3:54 PM BaseFile-1.0.tgz attached to se.lu.onk.BaseFile by Jari Häkkinen
3:53 PM PluginDownload edited by Jari Häkkinen
Added BaseFile version information. (diff)
3:44 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) closed by Jari Häkkinen
fixed: (In [798]) Fixes #131. Releasing BaseFile 1.0
3:44 PM Changeset [798] by Jari Häkkinen
Fixes #131. Releasing BaseFile 1.0
3:41 PM Changeset [797] by Jari Häkkinen
Addresses #131. Preparing release BaseFile 1.0
3:41 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by Jari Häkkinen
(In [797]) Addresses #131. Preparing release BaseFile 1.0
3:09 PM Changeset [796] by Jari Häkkinen
References #129. Improved table footnote.
3:09 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [796]) References #129. Improved table footnote.
2:41 PM Changeset [795] by Jari Häkkinen
Fixes #83. Also shifted code lines to align the WA and AA class …
2:41 PM Ticket #83 (ReplicateError: Error in ReplicateError) closed by Jari Häkkinen
fixed: (In [795]) Fixes #83. Also shifted code lines to align the WA and AA …

Sep 28, 2008:

10:44 AM Changeset [794] by Jari Häkkinen
References #129. Added note about different numbers in table and …
10:44 AM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [794]) References #129. Added note about different numbers in …

Sep 25, 2008:

10:37 AM Changeset [793] by Jari Häkkinen
References #129. No need to generate group information for within …
10:37 AM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [793]) References #129. No need to generate group information for …

Sep 24, 2008:

9:52 PM Changeset [792] by Jari Häkkinen
Fixes #132. Spot object seems to never get more than one position, but …
9:52 PM Ticket #132 (ReplicateError: In witihn assays only one position of accepted ...) closed by Jari Häkkinen
fixed: (In [792]) Fixes #132. Spot object seems to never get more than one …
9:16 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [791]) References #129. Removed unused code, moved common code to …
9:16 PM Changeset [791] by Jari Häkkinen
References #129. Removed unused code, moved common code to super …

Sep 23, 2008:

11:12 AM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)

Sep 21, 2008:

10:42 AM Ticket #139 (ReplciateError: A few data files are created that are always deleted ...) closed by Jari Häkkinen
invalid
10:42 AM Ticket #139 (ReplciateError: A few data files are created that are always deleted ...) reopened by Jari Häkkinen
10:34 AM Ticket #139 (ReplciateError: A few data files are created that are always deleted ...) closed by Jari Häkkinen
wontfix
10:34 AM Ticket #139 (ReplciateError: A few data files are created that are always deleted ...) updated by Jari Häkkinen
These should of course be kept since the R script uses them to create …

Sep 19, 2008:

2:31 PM se.lu.onk.BAFsegmentation edited by markus
(diff)
1:37 PM Ticket #139 (ReplciateError: A few data files are created that are always deleted ...) updated by Jari Häkkinen
Status changed
1:37 PM Ticket #139 (ReplciateError: A few data files are created that are always deleted ...) created by Jari Häkkinen
We should maybe stop creating these files.
11:24 AM Changeset [790] by Jari Häkkinen
Addresses #129. Added proper publication figure references for the algos.
11:24 AM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [790]) Addresses #129. Added proper publication figure references …
10:22 AM Ticket #138 (Importing data for multiple raw bioassays in one step) created by Jari Häkkinen
See http://base.thep.lu.se/ticket/1135 and …

Sep 18, 2008:

11:16 PM Changeset [789] by Jari Häkkinen
Changed stray double space characters to single tab characters.
11:02 PM Changeset [788] by Jari Häkkinen
Addresses #137. Added documentation.
11:02 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by Jari Häkkinen
(In [788]) Addresses #137. Added documentation.
11:01 PM Changeset [787] by Jari Häkkinen
Forgot one copyright line.
11:01 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [786]) Addresses #129. Added reference to paper which this plug-in …
11:00 PM Changeset [786] by Jari Häkkinen
Addresses #129. Added reference to paper which this plug-in is based on.
10:59 PM Changeset [785] by Jari Häkkinen
Removed trailing space character.
9:53 PM Changeset [784] by Jari Häkkinen
Addresses #129. Changing to GPL3.
9:53 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [784]) Addresses #129. Changing to GPL3.
9:28 PM Changeset [783] by Jari Häkkinen
Addresses #137. Changing to GPL3.
9:28 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by Jari Häkkinen
(In [783]) Addresses #137. Changing to GPL3.
9:27 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by Jari Häkkinen
Description changed
9:13 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
Description changed
9:11 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by Jari Häkkinen
(In [782]) Addresses #131. Changing to GPL3.
9:11 PM Changeset [782] by Jari Häkkinen
Addresses #131. Changing to GPL3.
9:11 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by Jari Häkkinen
Description changed
8:28 PM Changeset [781] by Jari Häkkinen
Fixing svn properties.
8:25 PM Changeset [780] by Jari Häkkinen
References #131. Fixing clean up.
8:25 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by Jari Häkkinen
(In [780]) References #131. Fixing clean up.
8:09 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by Jari Häkkinen
(In [779]) References #137. run should be chmod and fixed class path.
8:09 PM Changeset [779] by Jari Häkkinen
References #137. run should be chmod and fixed class path.
7:31 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by Jari Häkkinen
Description changed
7:30 PM Changeset [778] by Jari Häkkinen
Fixing svn properties.
7:27 PM Changeset [777] by Jari Häkkinen
Addresses #137. README replaces doc/INSTALL.txt
7:27 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by Jari Häkkinen
(In [777]) Addresses #137. README replaces doc/INSTALL.txt
7:21 PM Changeset [776] by Jari Häkkinen
Addresses #137.
7:21 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by Jari Häkkinen
(In [776]) Addresses #137.
7:18 PM Changeset [775] by Jari Häkkinen
References #131.
7:18 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by Jari Häkkinen
(In [775]) References #131.
7:16 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [774]) References #129.
7:16 PM Changeset [774] by Jari Häkkinen
References #129.
4:37 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [773]) References #129.
4:37 PM Changeset [773] by Jari Häkkinen
References #129.
3:39 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by Jari Häkkinen
Status changed
3:25 PM Changeset [772] by Jari Häkkinen
References #129.
3:25 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [772]) References #129.
3:18 PM Ticket #132 (ReplicateError: In witihn assays only one position of accepted ...) updated by Jari Häkkinen
Status changed
2:51 PM Ticket #136 (ReplicateError: Make version info to propagate automatically during ...) closed by Jari Häkkinen
fixed: (In [771]) Fixes #136. Version is propagated.
2:51 PM Changeset [771] by Jari Häkkinen
Fixes #136. Version is propagated.
2:38 PM Ticket #135 (ReplicateError: deprecated functionality is used, get rid of it) closed by Jari Häkkinen
wontfix: The new BASEFile<R,S> construct is undocumented and my Java skills are …
2:37 PM Changeset [770] by Jari Häkkinen
Addresses #131. Added information on how to create a package.
2:37 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by Jari Häkkinen
(In [770]) Addresses #131. Added information on how to create a package.
2:12 PM Ticket #135 (ReplicateError: deprecated functionality is used, get rid of it) updated by Jari Häkkinen
Status changed
2:01 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
Summary changed
2:01 PM Ticket #83 (ReplicateError: Error in ReplicateError) updated by Jari Häkkinen
Description, Summary changed
1:01 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by Jari Häkkinen
Owner, Component, Description changed
12:58 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) created by Jari Häkkinen
The onk.lu.se ticket will be split into several stand-alone packages …
12:04 PM Ticket #136 (ReplicateError: Make version info to propagate automatically during ...) updated by Jari Häkkinen
Status, Owner, Component changed
12:04 PM Ticket #135 (ReplicateError: deprecated functionality is used, get rid of it) updated by Jari Häkkinen
Owner, Component changed
12:03 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by Jari Häkkinen
Component changed
12:03 PM Ticket #130 (Base1PluginExecuter/ReplicateError: errors are not catched properly ...) updated by Jari Häkkinen
Owner, Component changed
12:03 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
Component changed
12:02 PM Ticket #83 (ReplicateError: Error in ReplicateError) updated by Jari Häkkinen
Component changed
12:02 PM Ticket #132 (ReplicateError: In witihn assays only one position of accepted ...) updated by Jari Häkkinen
Owner, Component changed
11:49 AM se.lu.onk.BAFsegmentation edited by markus
(diff)

Sep 17, 2008:

3:57 PM Ticket #136 (ReplicateError: Make version info to propagate automatically during ...) created by Jari Häkkinen
configurationfiles should have version updated.
1:31 PM se.lu.onk.BAFsegmentation edited by markus
(diff)
1:29 PM se.lu.onk.BAFsegmentation edited by markus
(diff)
12:50 PM se.lu.onk.BAFsegmentation edited by markus
(diff)
12:06 PM se.lu.onk.BAFsegmentation edited by markus
(diff)
11:40 AM se.lu.onk.BAFsegmentation edited by markus
(diff)
11:38 AM se.lu.onk.BAFsegmentation edited by markus
(diff)
11:19 AM se.lu.onk.BAFsegmentation edited by markus
(diff)

Sep 16, 2008:

9:08 PM Changeset [769] by Jari Häkkinen
Fixes #133. Read comment made to the ticket.
9:08 PM Ticket #133 (ReplicateError: The plug-in adds new entries to the stdout.txt for ...) closed by Jari Häkkinen
fixed: (In [769]) Fixes #133. Read comment made to the ticket.
9:07 PM Ticket #133 (ReplicateError: The plug-in adds new entries to the stdout.txt for ...) updated by Jari Häkkinen
Status, Owner, Description changed
Now I have a better understanding of the issue. The problem is that in …
9:01 PM Ticket #134 (BaseFile: public void resetDataPosition(BASEFileSection section) ...) closed by Jari Häkkinen
fixed
9:00 PM Ticket #134 (BaseFile: public void resetDataPosition(BASEFileSection section) ...) updated by Jari Häkkinen
This was fixed in changeset:768
8:59 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) reopened by Jari Häkkinen
This is not done yet. changeset:768 fixes ticket:134
6:36 PM Ticket #135 (ReplicateError: deprecated functionality is used, get rid of it) created by Jari Häkkinen
[…]
4:24 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) closed by Jari Häkkinen
fixed: (In [768]) Fixes #131.
4:24 PM Changeset [768] by Jari Häkkinen
Fixes #131.
4:15 PM Changeset [767] by Jari Häkkinen
Addresses #56. Making sure that this tree does not compile.
4:15 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by Jari Häkkinen
(In [767]) Addresses #56. Making sure that this tree does not compile.
3:53 PM Ticket #134 (BaseFile: public void resetDataPosition(BASEFileSection section) ...) updated by Jari Häkkinen
Status, Owner changed
3:53 PM Ticket #134 (BaseFile: public void resetDataPosition(BASEFileSection section) ...) created by Jari Häkkinen
After the call to the function the file pointer will be position to …
2:11 PM se.lu.onk.BAFsegmentation edited by markus
(diff)
11:22 AM Changeset [766] by Jari Häkkinen
Addresses #129. Updated configuration files, reworked html result …
11:22 AM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [766]) Addresses #129. Updated configuration files, reworked html …
11:20 AM Changeset [765] by Jari Häkkinen
Addresses #131.
11:20 AM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by Jari Häkkinen
(In [765]) Addresses #131.
11:16 AM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
11:11 AM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [764]) Addresses #129. Added version info, not distributing …
11:11 AM Changeset [764] by Jari Häkkinen
Addresses #129. Added version info, not distributing source, …
11:07 AM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
11:07 AM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
10:30 AM se.lu.onk.BAFsegmentation edited by markus
(diff)
10:28 AM se.lu.onk.BAFsegmentation edited by markus
(diff)
10:06 AM Ticket #133 (ReplicateError: The plug-in adds new entries to the stdout.txt for ...) created by Jari Häkkinen
This causes Base1PluginExecurter to import these reporters with null …

Sep 15, 2008:

7:36 PM Changeset [763] by Jari Häkkinen
Moved README.old to lib.
7:34 PM Changeset [762] by Jari Häkkinen
Moved Concept.ps to lib and added a PDF version of the file.
6:59 PM Changeset [761] by Jari Häkkinen
Addresses #129. Added license and moved README to README.old
6:59 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
(In [761]) Addresses #129. Added license and moved README to README.old
6:31 PM Changeset [760] by Jari Häkkinen
Fixed spelling.
3:53 PM Ticket #132 (ReplicateError: In witihn assays only one position of accepted ...) created by Jari Häkkinen
See Johans Test Expression 2 experiment on the production server.
3:19 PM PluginDownload edited by Jari Häkkinen
Addresses ticket:129 (diff)
3:17 PM PluginDownload edited by Jari Häkkinen
Addresses ticket:131 (diff)
2:35 PM se.lu.onk.ReplicateError created by Jari Häkkinen
Addresses ticket:129
2:30 PM Changeset [759] by Jari Häkkinen
Addresses #131. Added version info.
2:30 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by Jari Häkkinen
(In [759]) Addresses #131. Added version info.
2:27 PM se.lu.onk.BaseFile created by Jari Häkkinen
Addresses ticket:131
1:45 PM Changeset [758] by Jari Häkkinen
Addresses #56, #129, #131. Created se.lu.onk.BaseFile and moved …
1:45 PM Tickets #129,​131,​56 batch updated by Jari Häkkinen
(In [758]) Addresses #56, #129, #131. Created se.lu.onk.BaseFile and …
1:43 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by Jari Häkkinen
Status, Owner changed
1:42 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by Jari Häkkinen
Description changed
1:41 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by Jari Häkkinen
Summary changed
1:40 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by Jari Häkkinen
Description changed
1:40 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) created by Jari Häkkinen
Relates to ticket:56 BaseFile should be its own packages. This will …
10:00 AM Ticket #130 (Base1PluginExecuter/ReplicateError: errors are not catched properly ...) created by Jari Häkkinen
If the plug-in fails the job reports done! There is information …

Sep 14, 2008:

7:12 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by Jari Häkkinen
Status, Owner changed
7:12 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by Jari Häkkinen
Description, Summary changed
7:11 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) created by Jari Häkkinen
The onk.lu.se ticket will be split into several stand-alone packages …
7:05 PM Ticket #83 (ReplicateError: Error in ReplicateError) updated by Jari Häkkinen
Status, Owner changed

Sep 11, 2008:

8:50 AM Ticket #128 (Warning when ftp-config.xml is missing) created by Martin Svensson
There should perhaps be a warning when trying to start the BASE …

Sep 8, 2008:

1:32 PM PluginDownload edited by Nicklas Nordborg
Releasing FTP Server 1.0beta (diff)
1:27 PM Ticket #127 (Update to final release of Apache Mina FTP server) created by Nicklas Nordborg
The current beta-release relies on the 1.0-M2 (milestone 2) release of …
1:24 PM Changeset [757] by Nicklas Nordborg
Preparing for future release 1.0
1:19 PM net.sf.basedb.ftp edited by Nicklas Nordborg
Releasing FTP Server 1.0beta (diff)
1:14 PM Ticket #114 (Implement FTP Server) closed by Nicklas Nordborg
fixed
1:14 PM Changeset [756] by Nicklas Nordborg
Tagging 1.0beta
Note: See TracTimeline for information about the timeline view.