Daniel Blankenberg
77bd226f2b
When setting metadata externally, substitute a MetadataTempFile object for all populated metadata FileParameters. Fixes the problem with writting to metadata FileParameter files on cluster nodes with read-only database/files directory.
2009-11-30 14:55:30 -05:00
Kanwei Li
e4a4889524
Fix run.sh --reload by requiring Paste before PasteScript
2009-11-23 17:20:01 -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
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
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
Nate Coraor
531e8043ad
Officially support Python 2.6.
2009-11-13 10:39:15 -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
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
Nate Coraor
56032de2bd
Upgrade to Cheetah 2.2.2
2009-11-10 13:47:34 -05:00
Nate Coraor
d3caedd53b
Add env var to set metadata externally during tests
2009-11-10 11:20:04 -05:00
Daniel Blankenberg
3fdac6ca6b
Fix error message displayed when setting metadata_externally.
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e.g:
Exception exceptions.TypeError: TypeError('<galaxy.datatypes.metadata.MetadataTempFile object at 0x40d9a10> is not JSON serializable',) in <bound method MutableAttrInstanceState._cleanup of <sqlalchemy.orm.state.MutableAttrInstanceState object at 0x40d99d0>> ignored
2009-11-09 15:33:38 -05:00
Nate Coraor
29694cda88
Fix for GeneTrack egg
2009-11-06 14:23:21 -05:00
Nate Coraor
53bda50c19
Run test webserver on a random port between 8000 and 9999 instead of a fixed port, so multiple people can run tests at the same time w/o setting GALAXY_TEST_PORT manually
2009-11-05 10:39:59 -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
Nate Coraor
d0769e236a
Add the GeneTrack egg. Also includes some enhancements and cleanup of the eggs/fetch/scramble code.
2009-11-04 12:58:48 -05:00
Ramkrishna Chakrabarty
f4bedf8e5c
AMQP messaging server and client files.
2009-11-04 10:04:51 -05:00
Nate Coraor
1d4ed96a04
Fix new functional tests script return code (for buildbot)
2009-11-03 11:28:34 -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
Nate Coraor
c9e0e1ea17
A get_platform() monkeypatch for fat versions of python on Mac. Also do more explicit version checking ( >= 2.4, <= 2.5 ) and provide helpful messages if the version is not supported.
2009-10-27 11:36:57 -04:00
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
James Taylor
4cf17c1961
Fix for tool tests. Comment out get_peek test, doesn't appear correct (result is unicode and forced to multiple lines, when did this change?)
2009-10-21 15:45:01 -04:00
Nate Coraor
f77b88322d
Don't unpack dist-eggs
2009-10-21 15:03:09 -04:00
James Taylor
2c1e959a94
New functional test harness. Update to recent nose. No longer rely on nose to manage the embedded web server (this is not done in functional_tests.py). Log page contents to a temporary file on check_page_for_string error.
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[mq]: functional-test-harness
2009-10-20 13:08:29 -04:00
Ross Lazarus
2dc106df97
moved the rgGRR svg scripts to static/scripts/tools/rgenetics and decreased chattiness in genetics.py
2009-10-15 19:01:07 -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
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
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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.
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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.
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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
Daniel Blankenberg