Nate Coraor
bb6a16d1f4
Fix MySQL_python static egg on OS X
2010-02-19 14:34:25 -05:00
Ramkrishna Chakrabarty
2da3981679
LIMS: using threads for data transfer. first pass
2010-02-12 16:59:57 -05:00
Ramkrishna Chakrabarty
1e3bcd5d7c
LIMS data transfer:
...
- Fixed some config variable issues
- Now for the time being, Galaxy can transfer one dataset at a time.
2010-02-12 14:01:45 -05:00
Ramkrishna Chakrabarty
453092bf74
fixed the 0037_sample_library migration script to work with sqlite
2010-02-11 09:25:29 -05:00
Ramkrishna Chakrabarty
ebe405446a
LIMS: replaced os.system with subprocess to spawn the data transfer daemon process
2010-02-09 11:21:53 -05:00
Ramkrishna Chakrabarty
5747633a06
LIMS data acquisition: now the data transfer user logs out after the transfer is complete
2010-02-04 17:00:46 -05:00
Ramkrishna Chakrabarty
cea3324bbb
Sequencer data acquisition for LIMS
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- Add a data transfer script which fetches datasets from the sequencer
- transfer_datasets.ini for setting up the separate user to login to Galaxy programmatically to add datasets to the data libraries.
- Added a dataset transfer page which includes remote file browser to select files for transfer
Removed library & folder foreign keys from the request table and added them to the sample table. Also the sample table now has a dataset_files column to store the datatsets and the their transfer status.
Add an egg for pexpect which is used in the remote file browser.
The request_type table has a new column datatx_info which stores all the login info for the sequencer machine
2010-02-04 11:01:45 -05:00
Nate Coraor
eace604562
require pysqlite in functional_tests to work around a bug in nose
2010-01-28 14:52:02 -05:00
Nate Coraor
96a4144bc3
Fix another exception error (only in 2.4) with check_python.py
2010-01-28 13:37:53 -05:00
Nate Coraor
ae12fd7d5b
Prevent sys.exit() from being caught by the try-except block in check_galaxy.py (since sys.exit() actually raises an exception, but one not derived from Exception).
2010-01-05 15:17:10 -05:00
Nate Coraor
1f5e079a3a
python run from virtualenv sets up site.py to pull things from the real python's lib directory, so 'python -S' breaks it. To fix this, have the check_python.py script check for virtualenv and output the arguments that should be used to start python ('python -E' for virtualenv, 'python -ES' for real), then use these arguments anywhere 'python -ES' was used in the past.
2010-01-04 12:51:34 -05:00
Nate Coraor
a3aaa1e780
Fix libdrmaa runtime link path on OS X
2009-12-09 10:15:15 -05:00
Ramkrishna Chakrabarty
ec1aac46e4
AMQP listener now updates request_event table when all samples have finished processing
2009-12-07 14:45:09 -05:00
Ramkrishna Chakrabarty
8ff7f8f853
AMQP listener config file bug fix
2009-12-04 14:50:00 -05:00
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.
...
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
...
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
Nate Coraor