Timeline



May 14, 2009:

10:49 AM Ticket #554 (Direct link to native search results view) created by Fredrik Levander
Users sometimes want to see the original Mascot or X!Tandem view of …
9:32 AM Changeset [3275] by olle
Refs #553. Refs #537. Refs #491. Class/file gui/formFormFactory.java …
9:17 AM Changeset [3274] by olle
Refs #553. Refs #537. Refs #491. First revision of support for …

May 12, 2009:

4:34 PM Changeset [3273] by Fredrik Levander
Refs #545. Gel import also refactored to use io file validation.
4:24 PM Changeset [3272] by Fredrik Levander
Refs #545. Further refactoring of peak list file validation. Now using …
2:55 PM Changeset [3271] by olle
Refs #537. Refs #491. First revision of support for extended spectrum …
1:59 PM Changeset [3270] by olle
Refs #537. Refs #491. Spectrum interface and class, as well as …

May 11, 2009:

4:32 PM Ticket #553 (Extend spectrum interface with fragmentation type) created by Fredrik Levander
Refs #537. In the case of fragmentation spectra (MS/MS) it would be …

May 7, 2009:

5:02 PM Releases edited by olle
Changed "Direct access" to 3D data to just "Access" since a number of … (diff)
11:50 AM Releases edited by Fredrik Levander
Info about 2.7 edited (diff)
11:43 AM Changeset [3269] by Fredrik Levander
Logging xml validation errors, to enable debugging.
11:42 AM Changeset [3268] by Fredrik Levander
Refs #552. Using spectrum id if it is available. Needs to be …
11:41 AM Ticket #552 (Preferential use of spectrum ids as string) created by Fredrik Levander
Refs #486. Spectra should preferentially be looked up by their string …
11:36 AM Changeset [3267] by Fredrik Levander
Refs #550. Adding option to keep random hits.
11:33 AM Ticket #551 (Filtering of protein report by number of peptides) created by Fredrik Levander
There should be an option for the protein assembly to only keep …
11:29 AM Ticket #550 (Propagation of random hits) created by Fredrik Levander
Currently combined random hits are not kept after generating a …
11:23 AM Changeset [3266] by Fredrik Levander
Refs #545. Refactoring peak list file validation
11:13 AM Changeset [3265] by olle
Refs #537. Refs #491. Spectrum file inspection utility updated to …
11:00 AM Releases edited by Fredrik Levander
(diff)
10:53 AM Changeset [3264] by Gregory Vincic
Bumping minor version to 8
10:52 AM Changeset [3263] by Gregory Vincic
Updated frontpage with rpm and 2.7.0 release
10:23 AM KnownIssuesProteios edited by Fredrik Levander
(diff)
10:13 AM Milestone Proteios SE 2.7 completed
Enhancing - job execution and management - installation procedure …
10:13 AM Ticket #520 (RPM based installation) closed by Gregory Vincic
fixed
9:34 AM Changeset [3262] by Gregory Vincic
Tagging 2.7.0 release
9:22 AM Changeset [3261] by Gregory Vincic
Correcting name of ftp server startup script for rpm based installation

May 6, 2009:

9:34 AM Ticket #549 (Decide policy for plug-in estimated execution time setting) created by olle
After support for several job queues was added in Ticket #517 (job …

May 5, 2009:

5:16 PM Ticket #548 (Integration of MyriMatch search engine) created by Fredrik Levander
The MyriMatch
5:13 PM Ticket #516 (project files showed as shared) closed by Fredrik Levander
fixed: Should have been fixed with ticket #457.
12:30 PM Ticket #539 (Display item id in forms) closed by Gregory Vincic
fixed: Specific form generation methods in the FormFactory? should be …
12:26 PM Changeset [3260] by Gregory Vincic
Removing compile warnings
11:44 AM Changeset [3259] by Gregory Vincic
Refs #539. getForm(Class, Object) displays the itemId as a disabled field.
11:32 AM Changeset [3258] by Gregory Vincic
Added URI to dictionary and removed a debug println statement from File.
11:24 AM Ticket #231 (Rewrite the QuickImport plugin as an extension) closed by Gregory Vincic
wontfix: The plugin will be removed instead.
11:23 AM Changeset [3257] by Gregory Vincic
Fixes #546. Removed concurency problems. Tested with test no. 8
11:23 AM Ticket #546 (Concurrency bug in webservice) closed by Gregory Vincic
fixed: (In [3257]) Fixes #546. Removed concurency problems. Tested with test no. 8
11:06 AM Changeset [3256] by Gregory Vincic
Adding test 7 to target 'all'
11:04 AM Ticket #547 (Select Project list too long) created by Gregory Vincic
All accessible projects are available in the File->Select Project list …
10:58 AM Ticket #444 (Enable uploading of files through webservice PUT method) closed by Gregory Vincic
fixed: This already works, some issues reference the #366 ticket.
10:57 AM Ticket #366 (External file support) closed by Gregory Vincic
fixed: http:// protocol works with and without basic authentication. file://
10:56 AM Changeset [3255] by Gregory Vincic
Refs #366. URI with basic authentication works.
10:52 AM Changeset [3254] by Gregory Vincic
Refs #366. Using hello.txt file in test.
10:17 AM Changeset [3253] by Gregory Vincic
Refs #366. File form displays the URI and downloading a non …
7:44 AM Ticket #515 (Editing of sample and contact info in mzData and mzML files) closed by olle
fixed: Ticket closed as the desired functionality has been added.

May 4, 2009:

11:06 AM Changeset [3252] by olle
Refs #526. Class/file io/OMSSAParameterSetOptionsUtil.java in …
9:35 AM Changeset [3251] by Fredrik Levander
Refs #502. Updated URIs for source files i converters. Updated mzML …
9:34 AM Releases edited by Fredrik Levander
updated links (diff)

Apr 30, 2009:

1:38 PM Ticket #529 (Project directory not shared to project) closed by olle
fixed: Ticket closed, since the implemented solution should solve the most …
12:28 PM Changeset [3250] by olle
Refs #529. Plug-ins modified to check for permission USE instead of …
11:21 AM Changeset [3249] by olle
Refs #536. Class/file io/MzMLFileReader.java in api/core/ updated to …
11:02 AM Changeset [3248] by olle
Refs #536. Class/file io/MzMLFileReader.java in api/core/ updated to …

Apr 29, 2009:

3:36 PM Ticket #517 (job queues) closed by olle
fixed: Ticket closed as the desired functionality has been added.
1:41 PM Changeset [3247] by Fredrik Levander
Refs #545. Allowing retention time lookups in mzML-based search …
12:01 PM Changeset [3246] by olle
Refs #515. Support for editing of sample and contact information in …

Apr 28, 2009:

2:31 PM Changeset [3245] by Gregory Vincic
Refs #366. Fixing test for modifying filename.
2:15 PM Changeset [3244] by Gregory Vincic
Refs #366. Added test for renaming a file.
1:41 PM FollowingAJob edited by olle
Section Name updated by changing header to a class of lower level, as … (diff)
1:12 PM SiteMap edited by olle
SiteMap updated with new entry FollowingAJob under UserGuide (diff)
1:08 PM UserGuide edited by olle
Section Activities updated with link to new wiki page FollowingAJob. (diff)
1:02 PM FollowingAJob created by olle
First revision of wiki page FollowingAJob.
9:23 AM Changeset [3243] by Gregory Vincic
Refs #366. Working test for disallowed protocol file://
8:43 AM Changeset [3242] by Gregory Vincic
Refs #546. File upload test works. Also started on testing the …

Apr 27, 2009:

4:47 PM Changeset [3241] by olle
Refs #515. Support for editing of contact information in mzData …
3:48 PM Changeset [3240] by olle
Refs #515. Support for editing of sample information in mzData …
3:04 PM Changeset [3239] by olle
Refs #515. Support for editing of sample information in mxML spectrum …
2:17 PM Changeset [3238] by Gregory Vincic
Refs #546. Moving getAttributes(...) method out of RequestData?.
2:12 PM Changeset [3237] by Gregory Vincic
Refs #546. Removing method isValidResource() from RequestData?.
2:10 PM Changeset [3236] by Gregory Vincic
Refs #546. Removing wrappermethod getParameter(...) in RequestData?.
2:03 PM Changeset [3235] by Gregory Vincic
Moving parsePath(...) and getClass(...) methods from RequestData?.
1:55 PM Changeset [3234] by Gregory Vincic
Refs #546. Moving home into RequestData?.
1:53 PM Changeset [3233] by Gregory Vincic
Refs #546. Moving activeProject into RequestData?.
1:52 PM Changeset [3232] by Gregory Vincic
Refs #546. Moving item into RequestData?.
1:48 PM Changeset [3231] by Gregory Vincic
Refs #546. Moving ClassDescriptor? into RequestData?.
1:43 PM Changeset [3230] by Gregory Vincic
Refs #546. Moving ItemFactory? into RequestData?.
1:42 PM Changeset [3229] by Gregory Vincic
Refs #546. Moving DbControl? into RequestData?.
1:39 PM Changeset [3228] by Gregory Vincic
Refs #546. Moving SessionControl? into RequestData?
1:33 PM Changeset [3227] by Gregory Vincic
Refs #546. Making user an attribute of RequestData?
1:24 PM Changeset [3226] by Gregory Vincic
Refs #546. Making data a local variable of each method.
1:19 PM Changeset [3225] by Gregory Vincic
Refs #546. Started rewriting webservice. Making RequestData? a value …
1:15 PM Ticket #546 (Concurrency bug in webservice) created by Gregory Vincic
The current implementation of the webservice does not allow for …
1:00 PM Changeset [3224] by olle
Refs #536. Class/file io/MzMLFileReader.java in api/core/ updated to …
12:37 PM Changeset [3223] by Gregory Vincic
Refs #366. Constraining UniformResourceIdentifier? protocol to http:// only

Apr 24, 2009:

3:00 PM Changeset [3222] by olle
Refs #515. Support for editing of contact information in mxML spectrum …
2:36 PM Changeset [3221] by Fredrik Levander
Refs #545. Very basic support for import of mzML-based Tandem searches
2:35 PM Ticket #545 (Allow mzML as source files in Hits report) created by Fredrik Levander
As search engines become capable of using mzML as source files it …
11:53 AM Changeset [3220] by olle
Refs #515. Support for editing of contact information in mzData and …
11:07 AM Changeset [3219] by Gregory Vincic
Refs #366. Initial revision of webservice tests.
9:57 AM Changeset [3218] by olle
Refs #515. Support for editing of sample and contact information in …

Apr 22, 2009:

9:15 AM Changeset [3217] by Gregory Vincic
Icons in PopupLinks? are now aligned to the left when converted to …

Apr 20, 2009:

4:37 PM Changeset [3216] by olle
Refs #517. Refs #287. Support for putting selected jobs into a high …
11:07 AM Ticket #544 (Execute external binaries as a plugin) created by Gregory Vincic
Doing this could solve the problem of killing jobs that have long …

Apr 17, 2009:

2:02 PM MoreAboutProteios edited by Fredrik Levander
(diff)
1:27 PM Changeset [3215] by olle
Refs #526. Class/file io/OMSSAParameterSetOptionsUtil.java in …
9:44 AM Changeset [3214] by olle
Refs #517. Refs #287. Update intended to clarify job queue …

Apr 16, 2009:

4:40 PM Changeset [3213] by olle
Refs #517. Refs #287. Job table page updated to show the number of …
11:21 AM Ticket #518 (Cancel jobs) closed by olle
fixed: Ticket closed as the desired functionality has been added.
11:17 AM Changeset [3212] by olle
Refs #518. Refs #517. Jobs whose execution were stopped by shutdown of …

Apr 14, 2009:

1:33 PM MoreAboutProteios edited by Fredrik Levander
Added references (diff)
11:45 AM Ticket #543 (Mascot Search Results Importer should not throw exception if ...) closed by olle
fixed: Ticket closed as the requested functionality has been added.
11:40 AM Changeset [3211] by olle
Refs #543. Refs #140. Class/file plugins/SearchResultsImporter.java in …
11:22 AM Ticket #543 (Mascot Search Results Importer should not throw exception if ...) created by olle
Mascot Search Results Importer should not throw exception if …
9:28 AM Ticket #542 (List of Proteios Extensions Wiki Pages) closed by olle
fixed: Ticket closed as the desired functionality has been added. …
9:14 AM Ticket #542 (List of Proteios Extensions Wiki Pages) created by olle
To facilitate navigation of Proteios Extensions wiki, a wiki page …
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