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145 Commits
Author SHA1 Message Date
Ramkrishna Chakrabarty 299f8dd97f Removed print stmts in listener 2009-09-21 15:40:58 -04:00
Ramkrishna Chakrabarty 50345092f4 added psycopg2 import stmt in galaxy_interface.py 2009-09-21 12:41:39 -04:00
Ramkrishna Chakrabarty f99863cfd3 Galaxy AMQP messaging now uses amqp & sqlalchemy eggs 2009-09-21 12:06:33 -04:00
Ramkrishna Chakrabarty c7d575208c Fixed a bug in creating requests as an admin 2009-09-21 10:49:17 -04:00
Ramkrishna Chakrabarty 6b92bf6eb8 Galaxy AMQP Listener, first pass 
Added a check for testing completed requests in Requests functional tests
 2009-09-18 15:18:57 -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 460fd53bb7 Provide datatypes registry location when setting metadata externally. 2009-08-03 15:45:26 -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
Nate Coraor a6cc479643 Fix history deletion method in Galaxy check script 2009-05-05 13:03:23 -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
Nate Coraor 8b0dcb7e4d Fixes for native Leopard Python eggs 2009-04-22 14:43:54 -04:00
Nate Coraor f1304c73e6 Merged from central 2009-04-15 15:45:28 -04:00
Nate Coraor 187a2e25fa Add database versioning support 2009-04-15 15:43:26 -04:00
James Taylor adeef24ce9 Adding workflow tests using Selenium. These actually drive the web browser to test the Javascript UI effectively. Currently can't run under buildbot. 2009-03-27 18:55:00 -04:00
Greg Von Kuster 05c2d4222b merging from central 2009-03-20 03:06:40 -04:00
Greg Von Kuster 354d0447df Fixes for i18n support - all charsets set to utf-8, now able to paste multi-byte chars in upload form, templates use utf-8 as output_charset, other miscellaneous fixes. 2009-03-20 02:49:30 -04:00
Greg Von Kuster da476a3f3a merging from central 2009-03-17 23:57:08 -04:00
Greg Von Kuster 69e383d6a8 Integrating i18n support provided by Mitsuteru Nakao, Takashi Hatakeyama, and Hideyuki Morita. 2009-03-17 22:46:47 -04:00
Daniel Blankenberg 34a4a1f4d5 Fix for setting metadata externally when outputs_to_working_directory = True. 2009-03-06 12:32:31 -05:00
Daniel Blankenberg 50e385d4a5 Use JSON instead of pickle for setting metadata externally, except for DatasetInstance objects. 2009-03-05 12:53:57 -05:00
Daniel Blankenberg df82f3e163 Add the ability for metadata to be set in an external process, this requires set_metadata_externally = True in universe_wsgi.ini. 
Currently this is supported in the local runner (long running set_meta() can now be canceled the same as with jobs) and in the non-staging PBS runner.

There is a slight change to how new Metadata FileParameters are to be created in datatype.set_meta(), see the MAF datatype.

TODO:
Prevent editing of metadata on a running job when metadata is to be set externally.
Have datasets which were copied before job completion use the metadata from the original output dataset; currently .set_meta() is called locally on these.
 2009-03-03 12:54:06 -05:00
Daniel Blankenberg dd8a3c6605 Make history.activatable_datasets return a list. 
Fix update_database_with_security_libraries.py script so that it works again.
 2009-02-26 14:06:11 -05:00
James Taylor cb592fa20b Updating the packed versions of all javascripts. 2009-02-25 14:24:46 -05:00
Greg Von Kuster 19d61ff4cf Make activatable_datasets a property of the History object, eliminating the problematic mapper. 2009-02-23 12:31:15 -05:00
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.. 
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