Nate Coraor
bf606c99f8
merge
2009-01-30 11:39:39 -05:00
Nate Coraor
f8ce6fc19d
merge
2009-01-30 11:39:29 -05:00
Nate Coraor
dd2ba78f45
Add fetch_eggs option to pull for other platforms (e.g. cluster nodes)
2009-01-30 11:37:18 -05:00
Greg Von Kuster
cfde4c4015
Normalize the model supporting the new library features. This rev assumes all current Library tables will be dropped so they are re-created at server start-up ( all library data will be lost ). Normalized objects are as follows:
...
1. ActionDatasetRoleAssociation -> DatasetPermissions ( renamed )
2. LibraryFolderDatasetAssociation -> LibraryDatasetDatasetAssociation ( renamed )
3. ActionLibraryItemRoleAssociation -> LibraryPermissions, LibraryFolderPermissions, LibraryDatasetPermissions, LibraryDatasetDatasetPermissions, LibraryItemInfoPermissions, LibraryItemInfoTemplatePermissions
4. LibraryItemInfoAssociation -> LibraryInfoAssociation, LibraryFolderInfoAssociation, LibraryDatasetInfoAssociation, LibraryDatasetDatasetInfoAssociation
5. LibraryItemInfoTemplateAssociation -> LibraryInfoTemplateAssociation, LibraryFolderInfoTemplateAssociation, LibraryDatasetInfoTemplateAssociation, LibraryDatasetDatasetInfoTemplateAssociation
2009-01-28 16:29:30 -05:00
Nate Coraor
5506ec8d3b
merging heads
2008-12-23 13:28:43 -05:00
Nate Coraor
80f42e4199
Since tempfiles seem to occasionally be left behind, allow logging of
...
open tempfiles, including a traceback (to determine callers) if
LOG_TEMPFILES is set in the environment when Galaxy starts. This
should be considered temporary and will be removed when it's determined
where/how this happens.
2008-12-23 13:28:27 -05:00
Nate Coraor
8fdd73aaed
merging heads
2008-12-23 13:28:24 -05:00
Greg Von Kuster
6a3f5a925e
Eagerload active_datasets for a history rather than activatable_datasets since it throws exceptions in the migration script.
2008-12-23 10:25:54 -05:00
Greg Von Kuster
61951c59e1
More optimization, code cleanup in migration script.
2008-12-23 09:29:58 -05:00
Greg Von Kuster
1cf912260d
Bug fixes for my last commit.
2008-12-22 17:12:20 -05:00
Greg Von Kuster
6d9db00839
Speed up script for migrating central to security.
2008-12-22 16:39:36 -05:00
Guruprasad Anada
0eb6e8d521
Pushing changes from central to security..
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G: Enter commit message. Lines beginning with 'HG:' are removed.
2008-12-22 13:38:00 -05:00
Guruprasad Anada
54dc919413
Script to enumerate GOPS JOIN jobs that could have returned an incorrect result before the issue with minimum overlap was fixed last week.
2008-12-22 13:35:01 -05:00
Guruprasad Anada
14e8c4fcad
speed enhancement for incorrect_gops_jobs script.
2008-12-17 12:13:38 -05:00
Guruprasad Anada
25cd5b63f5
central to security
2008-12-17 12:13:32 -05:00
Guruprasad Anada
6e266a9deb
Central to security
2008-12-17 11:26:32 -05:00
Guruprasad Anada
42263dd8b2
Fix for a minor bug in my previous commit.
2008-12-17 11:25:35 -05:00
Guruprasad Anada
8bd7ce669b
Commiting changes from central to security:
2008-12-17 11:03:27 -05:00
Guruprasad Anada
b84c1cb2ab
Enhancing incorrect_Gops_job script to output only those jobs whose output has changed since the BitSetSafeReaderWrapper was fixed.
2008-12-17 11:01:57 -05:00
Daniel Blankenberg
2c05491514
A script to update a pre-security/library Galaxy database with necessary schema changes and set default roles/permissions for users and their histories and datasets.
...
It will reset permissions on histories and datasets if they are already set (i.e. script was run on a database which already has security/library tables).
This has been tested with Postgres, SQLite, and MySQL databases.
Due to limitations of SQLite this script is unable to add foreign keys to existing SQLite tables (fks are ignored anyway).
*** Remember to backup your database before running. ***
2008-12-11 14:10:11 -05:00
Daniel Blankenberg
f1b591f3be
Some Fixes for setting permisions on the current history when users login, and some preparation for the database update script.
2008-12-03 17:16:40 -05:00
Greg Von Kuster
4015f31eff
Refix cleanup_dataset.py script.
2008-12-01 14:07:36 -05:00
Greg Von Kuster
2dd60568fc
merging from central
2008-12-01 14:07:33 -05:00
Greg Von Kuster
5d40b2b545
merging from central
2008-11-30 08:05:04 -05:00
Greg Von Kuster
3748e41924
Fixes, code cleanup in cleanup_datasets.py.
2008-11-30 08:03:21 -05:00
Greg Von Kuster
3fae320495
merging from central
2008-11-12 15:42:51 -05:00
Greg Von Kuster
511510797a
Fix a bug I missed in my last commit.
2008-11-12 15:42:46 -05:00
Greg Von Kuster
6625b0e216
merging from central
2008-11-12 15:20:00 -05:00
Greg Von Kuster
5a17479269
Fixes for the incorrect_gops_jobs script.
2008-11-12 15:19:27 -05:00
Greg Von Kuster
34cda87570
Add ability to manage deleted libraries, requires db schema change, commands are:
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ALTER TABLE library ADD COLUMN purged BOOLEAN DEFAULT FALSE;
CREATE INDEX ix_library_purged ON library USING btree (purged);
ALTER TABLE library_folder ADD COLUMN purged BOOLEAN DEFAULT FALSE;
CREATE INDEX ix_library_folder_purged ON library_folder USING btree (purged);
- Deleting a library will mark all folders and contents ( LibraryFolderDatasetAssociations ) deleted in the db (weakness is that state is not saved for undeleting )
- Undeleting a library will mark all folders and contents as undeleted in the db
- Purging a library will mark the library, all folders, and LibraryFolderDatasetAssociations as purged, datasets will only be marked as deleted - marking as purged and removing the file from disk will be handled by the cleanup_datasets script.
2008-11-12 14:35:07 -05:00
Guruprasad Anada
e5293f8d15
Fixed indentation bug in incorrect_gops_jobs script.
2008-11-12 10:19:55 -05:00
Guruprasad Anada
a2e0908a61
Fixed an indentation bug in incorrect_gops_jobs script.
2008-11-12 10:16:04 -05:00
Guruprasad Anada
1a00974152
updating incorrect_gops_jobs script
2008-11-11 16:21:20 -05:00
Guruprasad Anada
c3403e993c
small modification to incorrect_gops_jobs script to include all HDAs associated with a dataset.
2008-11-11 16:20:12 -05:00
Nate Coraor
3654d294b2
merging heads
2008-11-11 15:33:40 -05:00
Guruprasad Anada
2f5e0c58ae
Script to fetch gops jobs that might have produced incorrect/empty oUtput due to the bug in BitsetSafeReaderWrapper.
2008-11-11 15:20:36 -05:00
Greg Von Kuster
e0df0fa44e
merging from central
2008-11-10 15:30:20 -05:00
Greg Von Kuster
ea7074e280
Fix for purging dataset - add check for pre-history_dataset_association approach to sharing.
2008-11-10 15:30:07 -05:00
Daniel Blankenberg
ec188a33cb
Resolve a bunch of merge conflicts.
2008-10-31 11:28:09 -04:00
Greg Von Kuster
5be8fefaf5
Migrate central repo to alchemy 4.
2008-10-30 16:17:46 -04:00
Nate Coraor
aafccaa367
Use LD_RUN_PATH when building pbs_python
2008-10-30 16:11:44 -04:00
Nate Coraor
7e73b1539a
merging heads
2008-10-29 17:33:49 -04:00
Nate Coraor
32e98de2b7
Fix pbs_python to just use existing torque.
2008-10-29 17:20:54 -04:00
Greg Von Kuster
3b78d585c0
Purge metadata files associated with a purged dataset via the library association.
2008-10-28 14:44:09 -04:00
Greg Von Kuster
1f3494adc3
merging from central
2008-10-28 14:31:36 -04:00
Greg Von Kuster
9a7bc1370d
Purge metadata files associated with a dataset when the dataset is purged. Also remembered log.exception logs the exception, so corrected a few things in jobs.__init__.
2008-10-28 14:31:02 -04:00
Daniel Blankenberg
07d94113a7
Merging heads
2008-09-25 15:05:07 -04:00
Nate Coraor
fbe9d4e4e5
Update check_galaxy for new twill.
2008-09-25 10:19:56 -04:00
Greg Von Kuster
8e17384a79
Upgrade to SQLAlchemy 0.4.7 and correct conflicts in ~/model/__init__.py.
2008-09-18 15:18:12 -04:00
Greg Von Kuster
3de877519e
Migrate cleanup_datasets script to work with new db schema.
2008-07-10 19:54:46 +00:00
Nate Coraor