Kanwei Li
fb00e2b7a2
trackster: load block data incrementally, huge performance gains from drawing smaller tiles
2009-11-19 18:55:35 -05:00
Enis Afgan
4c7e009359
Fixed a bug in cloud store update. Also, added method comments to EC2 cloud provider implementation class.
2009-11-19 12:56:24 -05:00
Nate Coraor
6cf823e1ef
Only fix OS X platform name on 2.5, the only version on which it's broken
2009-11-18 16:18:09 -05:00
Kanwei Li
9efa130e6f
revert to sqlite default in universe.sample
2009-11-18 13:45:53 -05:00
Enis Afgan
bcf8c43069
merge
2009-11-18 13:37:41 -05:00
Enis Afgan
82a7e1d9cc
Fixed table migration bug encountered with PostgreSQL.
2009-11-18 13:36:37 -05:00
Jeremy Goecks
405e679191
Tweaks to grid filter UI: (1) added search image/submit button for initiating search and (2) styled text filter criteria.
2009-11-18 11:51:09 -05:00
James Taylor
1c33863991
Change a few foreign keys, this may change behavior of the cloud stuff, needs to be checked.
2009-11-18 10:57:24 -05:00
James Taylor
5b6aeb3231
Another tweak to cloud table order
2009-11-18 10:47:14 -05:00
James Taylor
d10f6f40be
Change cloud table creation order
2009-11-18 10:43:08 -05:00
Jeremy Goecks
1820348d81
Unicode fix: make it possible to display non-acii characters in dataset name.
2009-11-18 09:52:38 -05:00
Jeremy Goecks
03780db05d
merge
2009-11-17 19:07:19 -05:00
Jeremy Goecks
7519604261
'Insert history link' functionality added to pages. A user can select 1 or more histories and create links that point to a view of each history.
2009-11-17 19:06:42 -05:00
Enis Afgan
9312efac12
Fix cloud execution on startup
2009-11-17 16:39:05 -05:00
Enis Afgan
05fb70f48d
merge
2009-11-17 16:16:26 -05:00
Enis Afgan
1bb086c83d
Moved cloud control flag in universe.ini file to appropriate location.
2009-11-17 16:14:54 -05:00
Enis Afgan
af64c352fd
Completed port to SQLalchemy 0.5. Also, fixed couple of bugs, cleaned up cloud provider code, tested w/ EC2.
2009-11-17 15:51:39 -05:00
Ramkrishna Chakrabarty
c73610de9d
Adding grids to forms, requests & request types pages. Resolves issue #231 .
2009-11-17 14:28:34 -05:00
Nate Coraor
bd171235de
Updated GeneTrack egg
2009-11-17 13:43:34 -05:00
Greg Von Kuster
371e2b9a22
Fix a sqlalchemy session flush bug in the make_library_uploaded_dataset method.
2009-11-17 13:31:56 -05:00
Enis Afgan
535d90f840
Ported DB interaction to be compatible with Sqlalchemy 0.5.6
2009-11-16 20:37:47 -05:00
Nate Coraor
02010b8f58
Job recovery fix for jobs queued but with no runner where track_jobs_in_database=True
2009-11-16 18:38:32 -05:00
Greg Von Kuster
8b29c18868
Enhance history item error reports that are emailed
...
- report form now defaults to include the users email address if they are logged in
- email now includes the id of both the dataset and the history, the hid and hda.display_name(), and a link to the history
- admin users now have "view" access to any history and dataset ( this uses the new ~/history/view?id=... feature )
2009-11-16 16:27:48 -05:00
Jeremy Goecks
5aea142075
Unicode fix: allow non-ascii characters to be displayed in tool help.
2009-11-16 15:06:07 -05:00
Jeremy Goecks
e275657e3d
merge
2009-11-16 14:52:51 -05:00
Jeremy Goecks
8211514a1c
Ajax support for grid operations. Preparations for ajaxing history grid.
2009-11-16 14:52:33 -05:00
Nate Coraor
a3d62f4036
Explicitly check eggs and fetch when starting, instead of relying on automatic in-process fetching. Also contains a fix for pysqlite egg building
2009-11-16 14:42:09 -05:00
Jeremy Goecks
20ac20385f
Fix unicode error in data.display_info(). Fixes #226 .
2009-11-16 11:27:30 -05:00
Daniel Blankenberg
4d7be79a2b
Have Extract Genomic DNA tool copy metadata from input file.
...
This will allow the tool to keep column assignments when outputing interval format.
2009-11-16 10:57:31 -05:00
Greg Von Kuster
91d97585c1
Fix for cleanup_datasets.py - add app param to the _purge_dataset method signature.
2009-11-14 20:32:41 -05:00
Nate Coraor
bd09952bb6
Support Solaris 10 x86 as well.
2009-11-13 17:19:44 -05:00
Nate Coraor
588ea5e038
Update PySQLite to latest version. This resolves bitbucket issue #101
2009-11-13 17:08:12 -05:00
Nate Coraor
8ad4e0eb95
PBS Upload Tool w/ set_metadata_externally = True fixes
2009-11-13 16:50:56 -05:00
Jeremy Goecks
8278531c29
Merge
2009-11-13 16:35:07 -05:00
Jeremy Goecks
978261b496
Initial AJAX support for grids. AJAX support is not integrated into grids yet, but there are mako templates for AJAXed grids. AJAXed grids can be used for grids that do not use operations.
2009-11-13 16:34:32 -05:00
Jeremy Goecks
d766fd2ad5
Cleaned up messages for delete/undelete history/ies.
2009-11-13 16:32:36 -05:00
Greg Von Kuster
dd32491716
A bit of code cleanup in genetics.py, and add all rgenetics data types to datatypes_conf.xml.sample. Also include the new Sff data type in the upload config help section.
2009-11-13 16:24:00 -05:00
Nate Coraor
cbdcf42aa0
get_display_links fix for GeneTrack
2009-11-13 15:28:22 -05:00
Greg Von Kuster
527e1258f1
Change the version of the liftOver tool due to the application of Brad Chapman's patch in change set 3021.
2009-11-13 14:20:03 -05:00
Greg Von Kuster
e38e78f5e4
Fixes, cleanup and new functional tests for data types and upload:
...
- moved all supported binary data types to the new binary.py
- changed GeneTrack data type to subclass from Text rather than Binary
- added Sff data type to datatypes_conf.xml.sample
- merged test_sniffinad_and_metadata_settings.py test scritp into test_get_data.py
- added several additional functional test for data types to test_get_data.py
- fixed some bugs in upload.py when uploading binary data types
2009-11-13 14:13:03 -05:00
Nate Coraor
531e8043ad
Officially support Python 2.6.
2009-11-13 10:39:15 -05:00
Nate Coraor
5a0041b9e4
Upgrade to an SVN checkout of SQLAlchemy 0.5.x to resolve a race condition in 0.5.6 proper
2009-11-13 10:09:42 -05:00
Kanwei Li
1573a19e1d
Import cloud management module
2009-11-12 16:36:07 -05:00
Enis Afgan
c921a41616
Cleaned up AJAXed UCI state changes on main UI. UCI still does not get automatically removed after from displayed list being deleted by user.
2009-11-12 15:26:10 -05:00
Greg Von Kuster
dc8e7c1039
Eliminate the _monkeypatch_session_method from assignmapper by cleaning up remaining object flushes. The _monkeypatch_query_method remains due to a single object query in ~/datatypes/metadata.py in the FileParameter.wrap() method. The sqlalchemy session is now also passed into the __init__ methods for both HistoryDatasetAssociation and LibraryDatasetDatasetAssociation when the create_dataset param is True to enable methods in the DatasetInstance class to correctly add the created dataset to the sqlalchemy session and flush it.
2009-11-12 15:25:48 -05:00
Enis Afgan
3cab97ba8e
Cleaned up code in main cloud controller.
2009-11-12 14:24:43 -05:00
Ramkrishna Chakrabarty
468a631370
Applied patch provided by Brad Chapman in the liftOver tool to support BED files that contain track or browser lines. Resolves bitbucket issue 201.
2009-11-12 13:20:19 -05:00
Nate Coraor
1561cd8af8
Upgrade Paste/PasteDeploy/PasteScript. Paste can go no further without changing the way we stream templates and tarballs.
2009-11-12 13:12:12 -05:00
Kelly Vincent
803cbc5ef4
Corrected sloppy temp file/directory cleanup in index creation for Bowtie and BWA
2009-11-12 13:02:04 -05:00
Enis Afgan
b335c62c72
Cleaned up code dealing with error reporting in cloud providers (EC2 and Eucalyptus).
2009-11-12 12:42:17 -05:00
Kanwei Li