Timeline



Feb 16, 2007:

9:10 AM Changeset [3135] by Jari Häkkinen
Added missing import statement.
9:04 AM Changeset [3134] by Jari Häkkinen
Changed to also get shared projects.
8:58 AM Changeset [3133] by Jari Häkkinen
Merged log:trunk#3001:3128 into this branch.

Feb 15, 2007:

3:11 PM Ticket #497 (Floating point numbers with leading zeroes in the decimal part are not ...) created by base
Version BASE 2.3.0pre (build #3130; schema #29) Web server Apache …
9:56 AM Ticket #496 (Minor Display Glitch on 'Annotation & Parameter' Tab on all Item View) created by base
Version BASE 2.3.0pre (build #3130; schema #29) Web server Apache …
9:50 AM Ticket #495 (Pb when creating Hybs from Labeled Extracts View Page) created by base
Version BASE 2.3.0pre (build #3130; schema #29) Web server Apache …
9:40 AM Ticket #494 (Unexpected Error on JSP for Experiment Overview) created by base
I have loaded 2 experiments, one gives me the following problem …

Feb 13, 2007:

9:45 AM Ticket #493 (Trashcan display item owned by other users in some cases) created by Nicklas Nordborg
If logged in as a user with admin permissions this user is able to see …
2:05 AM Changeset [3132] by Jari Häkkinen
Removed stray carriage return characters.
2:03 AM Changeset [3131] by Jari Häkkinen
Removed stray carriage return characters.
1:42 AM Changeset [3130] by Jari Häkkinen
Fixed Id tag.

Feb 12, 2007:

1:31 PM Ticket #489 (Build #0 is reported after upgrade to 2.2 and 2.2.1) closed by Nicklas Nordborg
fixed: (In [3129]) Fixes #489: Build #0 is reported after upgrade to 2.2 and …
1:31 PM Changeset [3129] by Nicklas Nordborg
Fixes #489: Build #0 is reported after upgrade to 2.2 and 2.2.1 …
11:59 AM Ticket #490 (BASE demo server issue) closed by Jari Häkkinen
fixed
11:32 AM Ticket #349 (Callback for events to plugins) closed by Jari Häkkinen
wontfix
11:26 AM Ticket #212 (Array slide import plugin) closed by Jari Häkkinen
wontfix
11:20 AM Ticket #23 (Apply button in popup windows?) closed by Jari Häkkinen
wontfix
11:16 AM Ticket #492 (Web services) created by Jari Häkkinen
The outline for the web services implementation: 1. We are going to …

Feb 9, 2007:

10:26 PM WikiStart edited by Jari Häkkinen
Replaced 2.0 with 2. Also removed ref to old demo server. (diff)
4:39 PM Changeset [3128] by Johan Enell
Added javadoc
12:22 PM Ticket #491 (MeV plugin shows tag 'ExperimentalFactor' for genes in 'Display' menu) created by Jari Häkkinen
which it should not do. The ExperimentalFactors tag is an internal …
1:57 AM Ticket #490 (BASE demo server issue) created by base
[…]

Feb 8, 2007:

4:04 PM Milestone BASE 2.2.1 completed
Bug fixes for the 2.2 release.
4:04 PM Changeset [3127] by Jari Häkkinen
Removed obsolete branch 2.2.1.
3:57 PM Changeset [3126] by Johan Enell
Merged log:branches/2.2.1#3119:3123 trunk.
2:39 PM Ticket #489 (Build #0 is reported after upgrade to 2.2 and 2.2.1) created by Jari Häkkinen
2:35 PM DownloadPage edited by Jari Häkkinen
2.2.1 released. (diff)
2:28 PM Changeset [3125] by Jari Häkkinen
New bug six branch for 2.2
2:18 PM Changeset [3124] by Jari Häkkinen
Tagging version 2.2.1
2:17 PM Changeset [3123] by Jari Häkkinen
Bumped version to 2.2.1
2:04 PM Ticket #488 (Upgrade 2.1.1 to 2.2 fails) closed by Jari Häkkinen
fixed: This issue is returned to the original ticket:466. The upgrade problem …
1:53 PM Ticket #466 (Remaining Quantity not display in extracts) reopened by Jari Häkkinen
Reopened since the previous upgrade failed.
12:11 PM Ticket #487 (Update script must check the schema version before trying to update) closed by Martin Svensson
fixed: (In [3122]) Fixes #487. Update script must check the schema version …
12:11 PM Changeset [3122] by Martin Svensson
Fixes #487. Update script must check the schema version before trying …
11:47 AM Changeset [3121] by Johan Enell
References #488. Update schema version without validating the measured …
10:38 AM Changeset [3120] by Martin Svensson
References #488. Update schema version without validating the measured …
10:10 AM DownloadPage edited by Jari Häkkinen
(diff)

Feb 7, 2007:

11:14 PM Ticket #488 (Upgrade 2.1.1 to 2.2 fails) created by Nicklas Nordborg
Here is the stacktrace: […] For more info see the mailing list …
11:10 PM Ticket #487 (Update script must check the schema version before trying to update) created by Nicklas Nordborg
If the schema version is higher than expected the update script must …
12:45 PM DownloadPage edited by Jari Häkkinen
(diff)
12:45 PM DownloadPage edited by Jari Häkkinen
(diff)
12:36 PM Milestone BASE 2.2 completed
Doc, help, larger feature changes.
12:36 PM DownloadPage edited by Jari Häkkinen
Releasing v2.2 (diff)
12:21 PM Changeset [3119] by Jari Häkkinen
New bug fix branch for 2.2
12:18 PM Ticket #457 (Update install instructions for release 2.2) closed by Jari Häkkinen
fixed
12:17 PM Changeset [3118] by Jari Häkkinen
Tagging version 2.2
12:15 PM Changeset [3117] by Jari Häkkinen
Changed link to BASE (MeV) hacks site.
11:14 AM Changeset [3116] by Jari Häkkinen
Bumped version number to 2.2.0. Added Micha to contribution list.
9:57 AM Changeset [3115] by Jari Häkkinen
Added text on how to stop unintentional migration.
2:14 AM Changeset [3114] by Jari Häkkinen
Cleaning.
2:13 AM Changeset [3113] by Jari Häkkinen
Updated installation document.
2:13 AM Changeset [3112] by Jari Häkkinen
Removed MeV export of an unneeded reporter column.
12:51 AM Changeset [3111] by Jari Häkkinen
Added MeV to the list of 3rd party components and to the tools list.

Feb 6, 2007:

4:18 PM Ticket #10 (Analysis: Hierarchical clustering) closed by Jari Häkkinen
fixed: Hierarchical clustering is now supported through MeV …
4:17 PM Ticket #352 (Connect parts of the TM4 software suite to BASE) closed by Jari Häkkinen
fixed: MeV is now integrated as a Java Web Start application. It requires …
3:59 PM Ticket #464 (Permission denied when creting AnyToAny) closed by Jari Häkkinen
fixed
3:55 PM Changeset [3110] by Jari Häkkinen
Addresses #10 and #352. Unique temporary filenames used at client side.
3:54 PM Changeset [3109] by Jari Häkkinen
Blank experimental factor labels are propagated properly in MeV export.
3:28 PM Changeset [3108] by Johan Enell
BASE1PluginExecuter uses BioAssaySetExporter? to create basefile
3:26 PM Ticket #439 (Base file export) closed by Johan Enell
fixed: (In [3107]) Fixes #439
3:26 PM Changeset [3107] by Johan Enell
Fixes #439
3:11 PM Changeset [3106] by Jari Häkkinen
Addresses #10 and #352. Removed hard coded indexes for datamatrix …
3:09 PM Changeset [3105] by Jari Häkkinen
Addresses #10 and #352. MeV uses system tmp directory system properties.
11:03 AM Changeset [3104] by Martin Svensson
References #146. Added help texts for view user
11:00 AM Changeset [3103] by Martin Svensson
References #146. Modified the function of the toolbar that is used to …
10:14 AM Ticket #486 (Import raw data from the Illumina platform) created by Nicklas Nordborg
A discussion about importing raw data from the Illumina platform was …

Feb 5, 2007:

11:02 PM Changeset [3102] by Jari Häkkinen
Addresses #10 and #352. MeV jsp uses Servlet API to retrieve server …
9:02 PM Ticket #365 (Use java web start to launch plug-ins) closed by Jari Häkkinen
fixed: Mulit experiment viewer, http://www.tm4.org, is started with web …
8:55 PM Ticket #472 (java.lang.OutOfMemoryError: PermGen space) closed by Jari Häkkinen
fixed: Increasing the MaxPermSize? solves the problem. Our server is still …
8:53 PM Ticket #471 (Filenames with () are not treated well by trac) closed by Jari Häkkinen
fixed: Fixed in changeset:3066
4:43 PM Changeset [3101] by Jari Häkkinen
Addresses #10 and #352. Fixed problem with non-appearing tool icons in MeV.
3:18 PM Ticket #485 (A user's group membership is not listed.) created by Martin Svensson
You have a group, lets say Group A, where some users have been added …
12:19 PM Changeset [3100] by Jari Häkkinen
Addresses #10 and #352. Now actually using the bioassayset used to …
12:03 PM Changeset [3099] by Jari Häkkinen
Moved max heap size tag to correct tag.
11:52 AM Changeset [3098] by Nicklas Nordborg
References #10: Hierarchical clustering Added servlet for downloading …
11:49 AM Changeset [3097] by Nicklas Nordborg
Fixed permission check problem that caused a query to return items the …
11:37 AM Changeset [3096] by Jari Häkkinen
Addresses #10, #352, #365. First checkin for JWS use to launch MeV.
10:58 AM Changeset [3095] by Martin Svensson
Fixed so the list page of plate mappings not are corrupt when user …
8:09 AM Changeset [3094] by Nicklas Nordborg
Fixes #483: Add a direct start icon for export of bioassaysets in …
8:09 AM Ticket #483 (Add a direct start icon for export of bioassaysets in analysis tree) closed by Nicklas Nordborg
fixed: (In [3094]) Fixes #483: Add a direct start icon for export of …
7:42 AM Ticket #484 ('Run plugin' button has misleading label since it only runs analysis ...) created by Nicklas Nordborg
The export plug-in does not show up in the plug-in list for running …

Feb 2, 2007:

11:39 AM Ticket #483 (Add a direct start icon for export of bioassaysets in analysis tree) created by Jari Häkkinen
As it is now the user has to select a specific bioassayset to get a …

Feb 1, 2007:

4:41 PM Changeset [3093] by Martin Svensson
References #146. Added group.edit... helptexts and began at role.edit…

Jan 31, 2007:

10:30 PM Ticket #482 (Check that reporters really exists before using them ....) closed by Nicklas Nordborg
duplicate: Duplicate of #435
8:32 PM Ticket #482 (Check that reporters really exists before using them ....) created by Jari Häkkinen
With Affymetrix it is possible to create an array design and associate …
8:27 PM Ticket #481 (Reporter importer plug-in should report how many reporters were ...) created by Jari Häkkinen
As it is now number of new and updated reporters are reporter. For …
8:12 PM Changeset [3092] by Jari Häkkinen
Added another affymetrix reporter importer configuration.
7:55 PM Ticket #480 (Verify values in extended-properties.xml and raw-data-types.xml) created by Nicklas Nordborg
Empty column names are, for example, passed through and later an error …
3:15 PM Changeset [3091] by Martin Svensson
References #146 Added helptexts for editing user. Set svn:eol-style on …

Jan 30, 2007:

10:26 AM Changeset [3090] by Nicklas Nordborg
References #440: Update to latest versions of 3rd-party software …

Jan 29, 2007:

4:13 PM Changeset [3089] by Martin Svensson
BASE now throws right exception when trying to save a new user with a …
2:52 PM Changeset [3088] by Martin Svensson
Marked the password field to be required when editing a new user.
2:45 PM Changeset [3087] by Nicklas Nordborg
Make sure DbControl? is closed
2:45 PM Changeset [3086] by Nicklas Nordborg
Fixes #466: Remaining Quantity not display in extracts
2:45 PM Ticket #466 (Remaining Quantity not display in extracts) closed by Nicklas Nordborg
fixed: (In [3086]) Fixes #466: Remaining Quantity not display in extracts
1:29 PM RobotsTxt created by Jari Häkkinen
Adding web indexing robot repellent.
1:28 PM DeveloperInformation edited by Jari Häkkinen
Adding web indexing robot repellent. (diff)
10:46 AM Ticket #479 (BioAssaySetExport should allow immediate download.) created by Jari Häkkinen
This relates to the fixed ticket:189. Read the last comment, …
10:42 AM Ticket #440 (Update to latest versions of 3rd-party software) closed by Nicklas Nordborg
fixed: (In [3085]) Fixes #440: Update to latest versions of 3rd-party software
10:42 AM Changeset [3085] by Nicklas Nordborg
Fixes #440: Update to latest versions of 3rd-party software
10:23 AM WikiStart edited by Jari Häkkinen
(diff)

Jan 26, 2007:

4:07 PM Changeset [3084] by Martin Svensson
Added a help text for column configuration

Jan 25, 2007:

8:57 AM Changeset [3083] by Martin Svensson
Correct a parameter in genepix-dyeswap configuration for the …

Jan 24, 2007:

9:10 AM Changeset [3082] by Martin Svensson
Fixes #478 Plate Importer requests more permissions
9:10 AM Ticket #478 (Plate Importer requests more permissions) closed by Martin Svensson
fixed: (In [3082]) Fixes #478 Plate Importer requests more permissions
8:49 AM Ticket #478 (Plate Importer requests more permissions) created by Martin Svensson
The Plate importer plugin requests read permission on plates but has …

Jan 23, 2007:

10:15 AM Ticket #473 (Cannot import a plug-in configuration as administrator (not 'root' user)) closed by Nicklas Nordborg
duplicate: Ok, then it is the same as #476. I am closing this as a duplicate.
9:52 AM Changeset [3081] by Martin Svensson
Remarks added for each configuration in the list.

Jan 22, 2007:

4:40 PM Changeset [3080] by Martin Svensson
Gave the edit-toolbar a proper BASE2-look.
4:02 PM Changeset [3079] by Nicklas Nordborg
References #466: Remaining Quantity not display in extracts Fixed …
2:51 PM Changeset [3078] by Nicklas Nordborg
References #459: Better error message if plugin jar can't be found …
2:15 PM Ticket #431 (Multiple tables from the Table taglib on the same HTML page interfere ...) closed by Nicklas Nordborg
fixed: (In [3077]) Fixes #431: Multiple tables from the Table taglib on the …
2:15 PM Changeset [3077] by Nicklas Nordborg
Fixes #431: Multiple tables from the Table taglib on the same HTML …
1:37 PM Ticket #340 (Experiment validation tool) closed by Nicklas Nordborg
fixed
1:36 PM Ticket #262 (Overview of an experiment) closed by Nicklas Nordborg
fixed
12:20 PM Changeset [3076] by Nicklas Nordborg
Added better log messages to find out where unclosed DbControl:s are …
12:02 PM Ticket #475 (Error running RMAExpress plug-in to create new root bioassay.) closed by Nicklas Nordborg
fixed: (In [3075]) Fixes #475: Error running RMAExpress plug-in to create new …
12:02 PM Changeset [3075] by Nicklas Nordborg
Fixes #475: Error running RMAExpress plug-in to create new root bioassay.
11:16 AM Ticket #476 ("Import" button is not shown even if the user has permission to use an ...) closed by Nicklas Nordborg
fixed: (In [3074]) Fixes #476: "Import" button is not shown even if the user …
11:16 AM Changeset [3074] by Nicklas Nordborg
Fixes #476: "Import" button is not shown even if the user has …
10:57 AM Changeset [3073] by Nicklas Nordborg
Fixes #477: Creating a child item in the same transaction as the …
10:57 AM Ticket #477 (Creating a child item in the same transaction as the parent item gives ...) closed by Nicklas Nordborg
fixed: (In [3073]) Fixes #477: Creating a child item in the same transaction …
9:54 AM Ticket #477 (Creating a child item in the same transaction as the parent item gives ...) created by Nicklas Nordborg
For example: […] Happens because the permission check in …

Jan 21, 2007:

10:23 PM Changeset [3072] by Nicklas Nordborg
Fixed another path problem when running server on Windows
10:15 PM Ticket #476 ("Import" button is not shown even if the user has permission to use an ...) created by Nicklas Nordborg
From a comment in ticket #473: Another problem related to …
8:18 PM Ticket #474 (Creation of new plug-in definition throws an exception if jar is not ...) closed by Nicklas Nordborg
duplicate: Duplicate and fixed by ticket #459.
6:04 PM Ticket #475 (Error running RMAExpress plug-in to create new root bioassay.) created by Jari Häkkinen
I get "Error: Table 'base2dynamic.d1rawparents' doesn't exist" when …
5:34 PM Ticket #474 (Creation of new plug-in definition throws an exception if jar is not ...) created by Jari Häkkinen
but this exception should be caught and a nicer output could returned …
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