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70 Commits
Author SHA1 Message Date
Lance Parsons b4c9f2fb10 Added pkg_resources to load required Mako package 2014-12-03 14:50:56 -05:00
Nate Coraor acd078a65c merge. 2014-09-15 16:57:28 -04:00
Nate Coraor 8fadc6392b Rename universe_wsgi.ini -> galaxy.ini everywhere. 2014-09-15 16:43:51 -04:00
Nate Coraor 4306560237 Remove unused "Main" versions of cleanup convenienence wrappers. 2014-09-15 15:34:03 -04:00
Dannon Baker 038f6dc6d5 Switch to_json_string/from_json_string in galaxy/scripts. 2014-09-09 10:04:28 -04:00
Kyle Ellrott 47f0f822f0 Refactoring work to add in Workflow UUIDs 2014-08-20 14:10:43 -07:00
Dave Bouvier 5bdb75aa82 Correct usage of "it's" versus "its". 2014-04-17 15:49:32 -04:00
Kyle Ellrott e4f45e04e3 Adding script to generate UUIDs for datasets where the value is null. This is to backfill previously generated records (from now on UUID will be generated during creation) 2014-03-04 15:46:10 -08:00
Nate Coraor 5a8c6457b9 Fix username argument to PostgreSQL connection in pgcleanup.py 2014-01-09 10:46:01 -05:00
Dannon Baker eed1f76001 Merged in lance_parsons/galaxy-central-pull-requests/dataset-cleanup (pull request #158) 
Basic administrative dataset cleanup script
 2013-09-10 13:14:10 -04:00
Lance Parsons 91ba836a00 Fix unicode issue when printing history names in cleanup_datasets.py script 2013-07-22 14:24:13 -04:00
Nate Coraor c1fb32d7c6 Update pgcleanup.py for dialect name change. 2013-05-29 16:16:11 -04:00
Lance Parsons d37fabc834 Fix admin_cleanup_datasets.py for copied datasets 2013-04-18 15:43:00 -04:00
Lance Parsons bd8cd477bc Basic administrative dataset cleanup script 2013-04-18 11:24:09 -04:00
Nate Coraor 1e2256fe0e pgcleanup: Print a useful message if no options are given. 2012-10-01 13:45:37 -04:00
Nate Coraor 8193489dda pgcleanup/set_user_disk_usage: set usage to 0, not null, when the user has no active data. 2012-09-28 16:11:38 -04:00
Nate Coraor 459d3a2c1d More pgcleanup.py fixes and addition of cleanup event tables for library items. 2012-09-17 12:51:17 -04:00
Nate Coraor 71d7f7c132 Distributed object store fixes for pgcleanup.py. 2012-09-11 12:22:03 -04:00
Nate Coraor 0e1b041cde Bug fixes for pgcleanup.py 2012-09-10 16:59:33 -04:00
Nate Coraor c8e49cdd6d Bugfix for pgcleanup.py 2012-09-10 14:07:05 -04:00
Nate Coraor e19092e9c5 Add a dataset cleanup script that's optimized for (and compatible only with) PostgreSQL 9.1+. Also add a bunch of tables for logging all cleanup events, which makes reversing such events trivial. 2012-09-10 12:03:23 -04:00
Nate Coraor 35dd4e1ef9 Fix for cleanup_datasets.py when database_connection is the uncommented default in the config file. 2012-04-16 10:07:10 -04:00
Nate Coraor 9aed5a36d8 Fix for dataset cleanup scripts and object store. 2012-01-31 14:07:14 -05:00
Nate Coraor 3a1526ac8a Decrease user disk usage when files are removed from disk by the cleanup_datasets.py. 2011-08-22 16:19:49 -04:00
Greg Von Kuster 581c3d9c67 Another patch from Assaf Gordon for the cleanup_datasets.py script. 
This patch adds messages for the "purge histories" step:
1. A message is printed when processing a new history (so that the user can tell to which history the following dataset/hda messages belong).
2. in "info_only" mode, a message is printed about each deleted history
3. in "info_only" mode, a message is printed for each HDA that is checked
4. The message for HDA is changed to include the associated dataset id.
 2011-07-14 15:58:06 -04:00
Greg Von Kuster 8eb0033904 Add patch from Assaf Gordon to the cleanup_datasets.py script. The changes are: 
1. If a dataset is skipped (because it's shared/cloned and was already process), no message is printed at all.
2. If a dataset can not be deleted because it is shared, and one instance is not marked as "deleted", a proper message is printed.
3. If a dataset has metadata files, the message is changed depending on "info_only" and "remove_from_disk" flags.
4. The final summary message is slightly changed.
 2011-07-13 09:39:02 -04:00
Greg Von Kuster 40d02d1e7b Add patch from Assaf Gordon to fix the cleanup_dataset.py script, correcting the behavior of setting the info_only flag to True when running delete_datasets.sh and purge_datasets.sh. 2011-07-06 09:52:28 -04:00
Ross Lazarus d53c3e984f Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository 
This is a backout of commit 5765
 2011-07-06 09:44:56 +10:00
Ross Lazarus 86b55bb0c0 branch merge 2011-07-05 12:40:43 +10:00
Greg Von Kuster b0b5df4e93 Add a purged column to the LibraryDataset table - a LibraryDataset is marked purged when all associated LibraryDatasetDatasetAssociations are marked deleted. Fix the cleanup_datasets.py script to more correclty handle the lifecycle of LibraryDatasets. 2011-02-09 15:42:09 -05:00
Kanwei Li 7736a34123 Add default file_path to cleanup_datasets.py script. Closes #376 2010-10-07 14:15:19 -04:00
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
Greg Von Kuster 8f6e8213a0 Fix most of the db flushes to be compatibel with sqlalchemy 05. Add the _monkeypatch_query_method() back into assignmapper due to a single object.get() method in the MetadataCollection class since Metadata has no current hook into mapping.context ( the sqlalchemy session ). There a 4 flushes in metadata,py and 20 flushes in model.__init__.py that still use the _monkeypatch_session_method in assignmapper due to the same issue, but all other flushes are fixed. 2009-11-11 15:59:41 -05:00
Greg Von Kuster 1c4070ea92 Eliminate printing PYTHONPATH to stderr in the cleanup_datasets.py script. 2009-11-04 13:09:37 -05:00
Greg Von Kuster da149187b4 Bug fix for cleanup_datasets.py - use app.sa_session instead of self.sa_session. 2009-11-02 09:54:18 -05:00
Greg Von Kuster 29b55b8707 Make sqlalchemy queries use sa_session.query( object ) rather than object.query(). This eliminates the need for the _monkeypatch_query_method() in assignmapper.py. Also eliminate the need for the _monkeypatch_session_method() for everything except object.flush() - I just ran out of time and will handle flush() asap. I also eliminated the .all() call on several queries where it was not necessary - should improve performance. I fixed several bugs I found as well. 2009-10-22 23:02:28 -04:00
Greg Von Kuster 18c95bb622 Improve logging for cleanup_datasets.py script. 2009-09-24 21:17:32 -04:00
Greg Von Kuster 947491b270 More improvement in cleanup_datasets script - will take significantly less disk, and may be faster. 2009-09-24 16:52:15 -04:00
Greg Von Kuster a40bf886f1 Performance improvements in delete_datasets method in cleanup_datasets script ( hopefully enough ). 2009-09-24 12:21:41 -04:00
Nate Coraor 2abf463a95 More fixes for cleanup_datasets.py 2009-09-15 12:57:17 -04:00
Nate Coraor f11dcd9781 Fix path mangling in cleanup_datasets.py 2009-09-14 12:23:16 -04:00
Greg Von Kuster 5665f1dbaf Fix for cleanup_datasets.py script. 2009-09-11 11:26:26 -04:00
Daniel Blankenberg 52d1bc065a Enable the cleanup_datasets script to purge Dataset Instances (HDAs, LDDAs) and mark base datasets as deleted without requiring the container (history, library/folder) to be deleted. 2009-08-10 11:53:28 -04:00
Daniel Blankenberg f4a7dbc436 Add a new flag -f/--force_retry to cleanup_datasets.py. This flag will cause the script to attempt to perform the requestion action on objects regardless if it has been performed before. 
This is useful, i.e. if purge_datasets was called with out using --remove_from_disk, but it is later decided to remove these files: the purge_datasets script should be called with both -r and -f.
 2009-07-30 12:56:16 -04:00
Greg Von Kuster 0090622f59 Add ability to share histories with multiple users, along with bug fixes and more functional test coverage for history features. 2009-06-05 11:15:25 -04:00
Nate Coraor 9113ceb29f Fix the cleanup_datasets script 2009-05-28 15:18:49 -04:00
Daniel Blankenberg da52bd848a Add ability for admins to delete and undelete library items. 
Modify cleanup_datasets.py script and include a database migration script.
 2009-04-23 12:42:05 -04:00
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
Greg Von Kuster 2dd60568fc merging from central 2008-12-01 14:07:33 -05:00
Greg Von Kuster 4015f31eff Refix cleanup_dataset.py script. 2008-12-01 14:07:36 -05:00