Timeline



Dec 20, 2006:

5:37 PM Ticket #146 (Add help text to the web gui) updated by Martin Svensson
(In [3046]) References #146 Added one more edit tool for links
5:37 PM Changeset [3046] by Martin Svensson
References #146 Added one more edit tool for links
3:37 PM Tickets #262,​340 batch updated by Nicklas Nordborg
(In [3045]) References #262 and #340. The overview and validation is …
3:37 PM Changeset [3045] by Nicklas Nordborg
References #262 and #340. The overview and validation is now complete. …
1:52 PM Changeset [3044] by Nicklas Nordborg
Return each inherited annotation only once
8:26 AM Ticket #459 (Better error message if plugin jar can't be found) updated by Nicklas Nordborg
Description changed
8:26 AM Ticket #459 (Better error message if plugin jar can't be found) created by Nicklas Nordborg
The stacktrace that is shown when a trying to install a plugin and the …

Dec 19, 2006:

6:54 PM Changeset [3043] by dominic
4:18 PM Changeset [3042] by dominic
tab2mage export with the systen out messages revoved

Dec 18, 2006:

3:59 PM Changeset [3041] by Martin Svensson
Misspelt style name
3:53 PM Ticket #146 (Add help text to the web gui) updated by Martin Svensson
(In [3040]) References #146 Finished with making the help-text writing …
3:53 PM Changeset [3040] by Martin Svensson
References #146 Finished with making the help-text writing more easy. …
9:58 AM Changeset [3039] by Nicklas Nordborg
Added web services for listing projects and experiments

Dec 15, 2006:

7:33 PM Changeset [3038] by dominic
7:25 PM Changeset [3037] by dominic
4:38 PM Changeset [3036] by Martin Svensson
Reference #146 Beginning of tools to make it more easy editing the …
4:38 PM Ticket #439 (Base file export) updated by Johan Enell
Merge on reporter needs to be done.
4:37 PM Changeset [3035] by Johan Enell
References #439
4:37 PM Ticket #439 (Base file export) updated by Johan Enell
(In [3035]) References #439
4:36 PM Ticket #439 (Base file export) updated by Johan Enell
Milestone, Version changed
3:37 PM Changeset [3034] by Nicklas Nordborg
Reverted last change since it appears that Eclipse messed with this …
3:30 PM Tickets #262,​340 batch updated by Nicklas Nordborg
(In [3033]) References #262, #340: First prototype for experiment …
3:30 PM Changeset [3033] by Nicklas Nordborg
References #262, #340: First prototype for experiment overview. Reads …

Dec 14, 2006:

3:49 PM Changeset [3032] by Johan Enell
The header regexp was mixed up between genepix cy3/cy5 and genepix cy5/cy3
12:33 PM Changeset [3031] by dominic
9:41 AM Changeset [3030] by Nicklas Nordborg
Fixed some problems with loading array slide and hybiridization in one …
9:23 AM Ticket #412 (Fix build.xml to make it more developer-friendly) updated by Nicklas Nordborg
(In [3029]) References #412: Fix build.xml to make it more …
9:23 AM Changeset [3029] by Nicklas Nordborg
References #412: Fix build.xml to make it more developer-friendly …
8:50 AM Changeset [3028] by Nicklas Nordborg
Fixed number parsing problems with int/long and double/float

Dec 13, 2006:

5:18 PM Ticket #458 (Edit session) closed by Nicklas Nordborg
wontfix: Sessions are read-only.
4:21 PM Ticket #458 (Edit session) created by Johan Enell
It could be useful for an admin to be able to edit a session. I've …

Dec 12, 2006:

3:12 PM Ticket #457 (Update install instructions for release 2.2) created by Jari Häkkinen
3:03 PM Changeset [3027] by Nicklas Nordborg
References #412: Fix build.xml to make it more developer-friendly …
3:03 PM Ticket #412 (Fix build.xml to make it more developer-friendly) updated by Nicklas Nordborg
(In [3027]) References #412: Fix build.xml to make it more …
2:33 PM Changeset [3026] by Jari Häkkinen
Changed src install instructions to use 'ant package.bin'
2:30 PM Changeset [3025] by Jari Häkkinen
Changed src install instructions to use 'ant package.bin'
1:55 PM Tickets #262,​340 batch updated by Nicklas Nordborg
(In [3024]) References #262 and #340. Added draft specification
1:54 PM Changeset [3024] by Nicklas Nordborg
References #262 and #340. Added draft specification
1:32 PM Changeset [3023] by Nicklas Nordborg
Fixes #311: Allow parsing of numbers with different locale settings
1:32 PM Ticket #311 (Allow parsing of numbers with different locale settings) closed by Nicklas Nordborg
fixed: (In [3023]) Fixes #311: Allow parsing of numbers with different locale …
10:57 AM Changeset [3022] by dominic
10:35 AM Ticket #311 (Allow parsing of numbers with different locale settings) updated by Nicklas Nordborg
Status changed
10:00 AM Changeset [3021] by Martin Svensson
Replaced 'Most recent' in the menu bar with an icon
9:37 AM Changeset [3020] by Nicklas Nordborg
Yet another stylesheet fix
9:36 AM Changeset [3019] by Nicklas Nordborg
More fixes to menu stylesheet
8:57 AM Changeset [3018] by Nicklas Nordborg
Fixed menubar height since the images didn't fit.
8:13 AM Ticket #456 (Mass edit) updated by Nicklas Nordborg
Milestone changed
There are some mass edit functions already. For example for sharing …

Dec 11, 2006:

5:06 PM Ticket #456 (Mass edit) created by Johan Enell
A function to apply the same changes on many items at once can be very …
4:59 PM Changeset [3017] by Martin Svensson
Added a 'refresh-page'- button to the menu bar.
12:51 PM Ticket #418 (Propagate the build number to the source package.) updated by base
Hi, To avoid the error pasted below, I would need to do % ant …
12:39 PM Changeset [3016] by Nicklas Nordborg
Removed 'bin' from ignore properties and added 'testdata'
12:35 PM Ticket #405 (Highlight function in plot tool) closed by Nicklas Nordborg
fixed: (In [3015]) Fixes #405: Highlight function in plot tool
12:35 PM Changeset [3015] by Nicklas Nordborg
Fixes #405: Highlight function in plot tool
8:49 AM Ticket #405 (Highlight function in plot tool) updated by Nicklas Nordborg
Status, Owner changed
8:10 AM Changeset [3014] by Nicklas Nordborg
Fixed problem with aborting a file upload

Dec 8, 2006:

3:26 PM Ticket #98 ("Excluded" items are still included if a list is exported) closed by Martin Svensson
fixed: (In [3013]) Fixes #98 "Excluded" items are still included if a list is …
3:26 PM Changeset [3013] by Martin Svensson
Fixes #98 "Excluded" items are still included if a list is exported
2:32 PM Ticket #444 (Plugins should check that they are allowed to create/overwrite files ...) updated by Martin Svensson
(In [3012]) References #444.Added the check of existing path for this …
2:32 PM Changeset [3012] by Martin Svensson
References #444.Added the check of existing path for this plugin too.
2:09 PM Ticket #262 (Overview of an experiment) updated by Nicklas Nordborg
Status changed
2:08 PM Ticket #340 (Experiment validation tool) updated by Nicklas Nordborg
Status changed
1:08 PM Ticket #98 ("Excluded" items are still included if a list is exported) updated by Martin Svensson
Status changed
1:04 PM Ticket #444 (Plugins should check that they are allowed to create/overwrite files ...) closed by Martin Svensson
fixed: (In [3011]) Fixes #444 Plugins should check that they are allowed to …
1:04 PM Changeset [3011] by Martin Svensson
Fixes #444 Plugins should check that they are allowed to …
11:59 AM Ticket #454 (File upload times out) updated by Nicklas Nordborg
(In [3010]) References #454: File upload times out Use Ajax for …
11:58 AM Changeset [3010] by Nicklas Nordborg
References #454: File upload times out Use Ajax for updating the …
10:47 AM Changeset [3009] by dominic

Dec 7, 2006:

3:34 PM Ticket #437 (build from source doesn't include misc/sql/*.sql) closed by Nicklas Nordborg
fixed: Fixed by ticket #412: Fix build.xml to make it more developer-friendly
2:52 PM Changeset [3008] by Nicklas Nordborg
References #454: File upload times out Changed the way progress …
2:50 PM Changeset [3007] by Nicklas Nordborg
Fixed bug in DbControl.rollback() method when disconnected from the …
10:47 AM Changeset [3006] by Nicklas Nordborg
First go at a webservices framework.
10:31 AM Ticket #444 (Plugins should check that they are allowed to create/overwrite files ...) updated by Martin Svensson
Owner, Status changed
9:25 AM Ticket #455 (Empty date field is not accepted at several places) closed by Martin Svensson
fixed: (In [3005]) Fixes #455 Empty date field is not accepted at several places.
9:25 AM Changeset [3005] by Martin Svensson
Fixes #455 Empty date field is not accepted at several places.

Dec 6, 2006:

4:34 PM Ticket #455 (Empty date field is not accepted at several places) updated by Martin Svensson
Status changed
4:34 PM Ticket #455 (Empty date field is not accepted at several places) created by Martin Svensson
Trying to save an item with no date specified(where date is not a …
4:06 PM Changeset [3004] by Martin Svensson
Fixes #374 Restoring a Bioassayset or Transformation restores all …
4:06 PM Ticket #374 (Restoring a Bioassayset or Transformation restores all child bioassay ...) closed by Martin Svensson
fixed: (In [3004]) Fixes #374 Restoring a Bioassayset or Transformation …
12:25 PM Changeset [3003] by Nicklas Nordborg
References #454: File upload times out Possible fix but have to be …
12:25 PM Ticket #454 (File upload times out) updated by Nicklas Nordborg
(In [3003]) References #454: File upload times out Possible fix but …
11:06 AM Ticket #454 (File upload times out) updated by Nicklas Nordborg
Status changed
I have now investigated this a bit more by delving in the Tomcat code …

Dec 5, 2006:

9:28 PM Ticket #454 (File upload times out) updated by Nicklas Nordborg
I have testet this from my home which has a very slow connection. None …
12:44 PM Changeset [3002] by dominic
10:53 AM Changeset [3001] by Jari Häkkinen
Creating a new branch for web services development.
10:47 AM Changeset [3000] by Jari Häkkinen
Creating a new branch for tab2mage development.

Dec 4, 2006:

3:25 PM Ticket #374 (Restoring a Bioassayset or Transformation restores all child bioassay ...) updated by Martin Svensson
Status, Owner changed
12:57 PM Ticket #453 (End date is not allowed to be empty) closed by Nicklas Nordborg
fixed: (In [2999]) Fixes #453: End date is not allowed to be empty
12:56 PM Changeset [2999] by Nicklas Nordborg
Fixes #453: End date is not allowed to be empty
11:35 AM Ticket #454 (File upload times out) created by Nicklas Nordborg
The file upload may randomly get a timeout exception: […] * It …
10:46 AM Ticket #440 (Update to latest versions of 3rd-party software) updated by Nicklas Nordborg
The second option turned out to be a bit unsafe, since the loss of …
10:28 AM Ticket #215 (Incorrect use of DynamicSpotQuery in table view, plot function, filter ...) updated by Nicklas Nordborg
(In [2998]) References #215: Incorrect use of DynamicSpotQuery... …
10:28 AM Changeset [2998] by Nicklas Nordborg
References #215: Incorrect use of DynamicSpotQuery... Fixed problem …
10:11 AM Ticket #453 (End date is not allowed to be empty) created by Jari Häkkinen
BASE complains with a popup: Invalid data On page …
12:45 AM WikiStart edited by Jari Häkkinen
Changed demo server location (diff)
12:00 AM Ticket #452 (Add BASEfile to the list of supported formats for BioAssaySetExporter ...) created by Jari Häkkinen

Dec 1, 2006:

6:06 PM Milestone BASE 2.1.1 completed
Issues assigned to this milestone will be fixed ASAP.
6:05 PM Changeset [2997] by Jari Häkkinen
Removing obsolete branch.
6:04 PM DownloadPage edited by Jari Häkkinen
2.1.1 released. (diff)
4:15 PM Changeset [2996] by Jari Häkkinen
Deleting outdated branch.
4:11 PM Changeset [2995] by Jari Häkkinen
Bumped version to 2.1.2pre
3:41 PM Changeset [2994] by Nicklas Nordborg
Fixed bug when web.xml wansn't found in config/local
3:34 PM Ticket #215 (Incorrect use of DynamicSpotQuery in table view, plot function, filter ...) closed by Nicklas Nordborg
fixed: (In [2993]) Fixes #215: Incorrect use of DynamicSpotQuery in table …
3:34 PM Changeset [2993] by Nicklas Nordborg
Fixes #215: Incorrect use of DynamicSpotQuery in table view, plot …
3:00 PM Changeset [2992] by Johan Enell
Merged log:branches/2.1#2846:2990 trunk.
12:34 PM Changeset [2991] by Jari Häkkinen
New bug fix branch for 2.1
12:33 PM Changeset [2990] by Jari Häkkinen
Tagging version 2.1.1
12:32 PM Changeset [2989] by Jari Häkkinen
Set version to 2.1.1
12:11 PM Ticket #439 (Base file export) updated by Johan Enell
Milestone changed
11:53 AM Changeset [2988] by Johan Enell
Fixes #433
11:53 AM Ticket #433 (Base1PluginExecutor doesn't set MIME type on files) closed by Johan Enell
fixed: (In [2988]) Fixes #433
11:34 AM Ticket #429 (Add BASEfile export to the bioassayset exporter.) closed by Johan Enell
fixed: (In [2987]) Fixes #429 BioAssaySetExporter can export a serial …
11:34 AM Changeset [2987] by Johan Enell
Fixes #429 BioAssaySetExporter can export a serial basefile not merged …
11:30 AM Changeset [2986] by Johan Enell
Added jep function for spot position
11:27 AM Changeset [2985] by Johan Enell
Implements to methods to sort the enumeration on keys or values
8:45 AM Ticket #215 (Incorrect use of DynamicSpotQuery in table view, plot function, filter ...) updated by Nicklas Nordborg
This will be fixed as follows: Each bioassayset/datacube will keep a …

Nov 30, 2006:

12:50 PM Changeset [2984] by Nicklas Nordborg
Use the default error handling when nothing else has been specified
12:13 PM Changeset [2983] by Nicklas Nordborg
Fixed incorrect generation of build.xml in source distribution
10:51 AM Changeset [2982] by Nicklas Nordborg
Fixed compilation error
10:50 AM Ticket #447 (Fix javadoc warnings) closed by Nicklas Nordborg
fixed: (In [2981]) Fixes #447: Fix javadoc warnings
10:50 AM Changeset [2981] by Nicklas Nordborg
Fixes #447: Fix javadoc warnings
9:58 AM Changeset [2980] by Johan Enell
addded nullcheck
8:53 AM Ticket #215 (Incorrect use of DynamicSpotQuery in table view, plot function, filter ...) updated by Nicklas Nordborg
Status changed
8:37 AM Changeset [2979] by Nicklas Nordborg
Need to generate hibernate mappings for test programs
8:27 AM Changeset [2978] by Nicklas Nordborg
Added session="false" to all jsp pages so we no longer generate …

Nov 29, 2006:

2:51 PM Ticket #383 (Should more docs be shipped with the binary package?) closed by Nicklas Nordborg
fixed
2:50 PM Changeset [2977] by Nicklas Nordborg
Fixes #138: Write documentation: 5c) Authentication plug-ins
2:50 PM Ticket #138 (Write documentation: 5c) Authentication plug-ins) closed by Nicklas Nordborg
fixed: (In [2977]) Fixes #138: Write documentation: 5c) Authentication plug-ins
2:49 PM Changeset [2976] by Nicklas Nordborg
Fixed some spelling errors and added links to Javadoc
1:01 PM Ticket #326 (Mass annotation plug-in) updated by Nicklas Nordborg
Milestone changed
1:00 PM Ticket #435 (A check for reporter information is needed when adding/using ...) updated by Nicklas Nordborg
Milestone changed
12:28 PM Ticket #451 (Zipped download) created by Nicklas Nordborg
Create a plugin that allows a user to select one or more …
12:14 PM Changeset [2975] by Nicklas Nordborg
Updated configuration files with correct column mappings.
12:11 PM Changeset [2974] by Nicklas Nordborg
Fixed issues with incorrect column mappings and swithced channels in …
10:24 AM Ticket #449 (Innherit BASE 1 sample annotations to BASE 2 RawBioAssays during migration) closed by Nicklas Nordborg
fixed: (In [2973]) Fixes #449: Innherit BASE 1 sample annotations to BASE 2 …
10:24 AM Changeset [2973] by Nicklas Nordborg
Fixes #449: Innherit BASE 1 sample annotations to BASE 2 RawBioAssays
9:02 AM Ticket #449 (Innherit BASE 1 sample annotations to BASE 2 RawBioAssays during migration) updated by Nicklas Nordborg
Status, Milestone changed
8:59 AM Tickets #383,​412 batch updated by Nicklas Nordborg
(In [2972]) References #383 and #412. Include some files from the misc …
8:59 AM Changeset [2972] by Nicklas Nordborg
References #383 and #412. Include some files from the misc directory …
8:35 AM Ticket #440 (Update to latest versions of 3rd-party software) reopened by Nicklas Nordborg
It turns out that there is a connection leak in the c3p0 connection …
8:28 AM Changeset [2971] by Nicklas Nordborg
Added svn.ignore
8:24 AM Ticket #450 (Plugin for importing Imagene raw data) created by Nicklas Nordborg
Imagene raw data comes in two files. One for the cy3 channel and one …

Nov 28, 2006:

3:27 PM Ticket #449 (Innherit BASE 1 sample annotations to BASE 2 RawBioAssays during migration) created by Jari Häkkinen
The migration program should innherit the sample annotation from the …
3:04 PM Changeset [2970] by Nicklas Nordborg
Fixes #440: Update to latest versions of 3rd-party software Verified …
3:04 PM Ticket #440 (Update to latest versions of 3rd-party software) closed by Nicklas Nordborg
fixed: (In [2970]) Fixes #440: Update to latest versions of 3rd-party …
1:40 PM Changeset [2969] by Nicklas Nordborg
Fixes #448: Setting 'Used quantity' for pooled sources of sample, …
1:40 PM Ticket #448 (Setting 'Used quantity' for pooled sources of sample, extracts and ...) closed by Nicklas Nordborg
fixed: (In [2969]) Fixes #448: Setting 'Used quantity' for pooled sources of …
12:49 PM Ticket #448 (Setting 'Used quantity' for pooled sources of sample, extracts and ...) created by Nicklas Nordborg
No error message. The value entered is silently ignored. The problem …
12:41 PM Changeset [2968] by Nicklas Nordborg
Removed unused file
12:40 PM Ticket #440 (Update to latest versions of 3rd-party software) updated by Nicklas Nordborg
(In [2967]) References #440: Update to latest versions of 3rd-party …
12:40 PM Changeset [2967] by Nicklas Nordborg
References #440: Update to latest versions of 3rd-party software …
11:00 AM Ticket #440 (Update to latest versions of 3rd-party software) updated by Nicklas Nordborg
(In [2966]) References #440: Update to latest versions of 3rd-party …
11:00 AM Changeset [2966] by Nicklas Nordborg
References #440: Update to latest versions of 3rd-party software …
8:50 AM Ticket #383 (Should more docs be shipped with the binary package?) updated by Nicklas Nordborg
Owner, Status changed
8:50 AM Ticket #440 (Update to latest versions of 3rd-party software) updated by Nicklas Nordborg
Status changed
8:45 AM Ticket #412 (Fix build.xml to make it more developer-friendly) updated by Nicklas Nordborg
(In [2965]) References #412: Fix build.xml to make it more …
8:45 AM Changeset [2965] by Nicklas Nordborg
References #412: Fix build.xml to make it more developer-friendly …
8:42 AM Ticket #447 (Fix javadoc warnings) created by Nicklas Nordborg

Nov 27, 2006:

3:44 PM Ticket #430 (The MeV bioassay set export should also generate an annotation file ...) closed by Jari Häkkinen
fixed: (In [2964]) Fixes #430. Finalized export ... fixed experimental factor …
3:44 PM Changeset [2964] by Jari Häkkinen
Fixes #430. Finalized export ... fixed experimental factor output. …
3:43 PM Changeset [2963] by Nicklas Nordborg
Added link to BASE web site
3:02 PM Ticket #412 (Fix build.xml to make it more developer-friendly) updated by Nicklas Nordborg
(In [2962]) References #412: Fix build.xml to make it more …
3:02 PM Changeset [2962] by Nicklas Nordborg
References #412: Fix build.xml to make it more developer-friendly …
2:59 PM Ticket #446 (File browser should have a possiblity to show creation/modifcation time) created by Jari Häkkinen
This would be very useful for sorting and checking of file age.
2:32 PM Ticket #429 (Add BASEfile export to the bioassayset exporter.) updated by Johan Enell
(In [2961]) References #429
2:32 PM Changeset [2961] by Johan Enell
References #429
1:40 PM Ticket #412 (Fix build.xml to make it more developer-friendly) updated by Nicklas Nordborg
(In [2960]) References #412: Fix build.xml to make it more …
1:40 PM Changeset [2960] by Nicklas Nordborg
References #412: Fix build.xml to make it more developer-friendly Get …
12:36 PM Ticket #412 (Fix build.xml to make it more developer-friendly) updated by Nicklas Nordborg
(In [2959]) References #412: Fix build.xml to make it more …
12:36 PM Changeset [2959] by Nicklas Nordborg
References #412: Fix build.xml to make it more developer-friendly
12:20 PM Changeset [2958] by Nicklas Nordborg
Fixed permission problem when a plugin tries to access annotation values.
11:20 AM Ticket #445 (Plug-in writers should check that the plug-in has the proper ...) created by Jari Häkkinen
The plug-ins may have own permissions and these are used when the …
11:15 AM Ticket #444 (Plugins should check that they are allowed to create/overwrite files ...) created by Jari Häkkinen
before they are started (i.e., in the plug-in/job creation dialogue). …
8:11 AM Ticket #443 (raw bioassay data not linked to LIMS kills Feature.getWell in ...) closed by Nicklas Nordborg
fixed: (In [2957]) Fixes #443: raw bioassay data not linked to LIMS kills …
8:11 AM Changeset [2957] by Nicklas Nordborg
Fixes #443: raw bioassay data not linked to LIMS kills Feature.getWell …

Nov 26, 2006:

11:33 PM Changeset [2956] by Jari Häkkinen
Addresses #430. Most things fixed for export but experimental factors …
11:33 PM Ticket #430 (The MeV bioassay set export should also generate an annotation file ...) updated by Jari Häkkinen
(In [2956]) Addresses #430. Most things fixed for export but …
11:31 PM Ticket #430 (The MeV bioassay set export should also generate an annotation file ...) updated by Jari Häkkinen
An annotation file will not be created but the annotation information …
11:28 PM Ticket #443 (raw bioassay data not linked to LIMS kills Feature.getWell in ...) updated by Jari Häkkinen
A similar exception occurs when trying to list the features for an …
10:05 PM Changeset [2955] by Jari Häkkinen
Minor clarification for genepix reporter map imports.
9:38 PM Changeset [2954] by Jari Häkkinen
Improved Genepix information in the getting started doc.

Nov 25, 2006:

8:35 AM Changeset [2953] by Jari Häkkinen
Fixed null pointer exception for getting parameter values.
8:33 AM Changeset [2952] by Jari Häkkinen
Closing DbControl.

Nov 24, 2006:

10:03 PM Changeset [2951] by Jari Häkkinen
Moved overwrite of existing file check to job configuration dialogue.
9:51 PM Ticket #412 (Fix build.xml to make it more developer-friendly) updated by Jari Häkkinen
Some of these things have been fixed in the 2.1.1 branch. There is a …
9:45 PM Changeset [2950] by Jari Häkkinen
Fixed typo.
8:18 PM Ticket #443 (raw bioassay data not linked to LIMS kills Feature.getWell in ...) updated by Nicklas Nordborg
Thanks for providing a fix. It is more or less identical to the …
8:16 PM Ticket #443 (raw bioassay data not linked to LIMS kills Feature.getWell in ...) updated by Nicklas Nordborg
Status, Milestone, Version changed
This was fixed in the trunk as part of ticket #189 (changeset …
4:53 PM Ticket #334 (Project default items) closed by Martin Svensson
fixed: (In [2949]) Fixes #334 Project default items
4:53 PM Changeset [2949] by Martin Svensson
Fixes #334 Project default items
3:41 PM Ticket #443 (raw bioassay data not linked to LIMS kills Feature.getWell in ...) created by base
I have migrated data sucessfully from BASE 1.2.x where we did not use …
Note: See TracTimeline for information about the timeline view.