Nate Coraor
8c872c16e7
Add numpy egg, update bx_python egg (now with 100% more numpy) and include code that allows scrambling to depend on other eggs existing and being importable.
2010-03-15 14:35:35 -04:00
Daniel Blankenberg
2223606101
Add a helper script that will re.escape files; useful for creating files valid for re_match and re_match_multiline comparisons in tool tests.
2010-03-09 15:25:23 -05:00
Nate Coraor
b10c2324f5
Update psycopg2 to 2.0.13/postgresql 8.4.2
2010-03-09 14:13:05 -05:00
Nate Coraor
4a0c9b3175
I am having a bad day
2010-03-02 12:10:43 -05:00
Nate Coraor
1b8bcabd1e
pbs_python 2.9.8 doesn't work
2010-03-02 12:08:01 -05:00
Nate Coraor
9b912184d0
Scratch that, just upgrade pbs_python instead
2010-03-02 11:52:16 -05:00
Nate Coraor
a0bd85dbb3
Use the old method for fixing pbs_python's version
2010-03-02 11:37:55 -05:00
Nate Coraor
9a8c5f6711
psycopg2 scramble fix
2010-03-02 00:38:57 -05:00
James Taylor
31a4f80604
[mq] workflow-invocation: Track workflow invocations in database, provide a view of the history grouped by workflow and job
2010-02-11 00:17:04 -05:00
Nate Coraor
006716f53a
Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES
2010-03-01 15:41:30 -05:00
Nate Coraor
6e9996f89a
Fix for set metadata tests when setting metadata externally
2010-02-24 15:54:52 -05:00
Ramkrishna Chakrabarty
6b45a2c1f9
lims:
...
- code cleanup
- cleanup tmp files after data transfer
2010-02-24 10:42:36 -05:00
Ramkrishna Chakrabarty
dd4757f20a
lims:
...
- added error msg when dataset transfer is started for samples with no library
- fixed typos
- now dataset transfer does not affect sample state
- request completion logic restored.
2010-02-24 10:04:03 -05:00
Nate Coraor
5e34e82e5c
Modify functional_tests.py to allow for testing of an environment nearly identical to Galaxy Test/Main via buildbot
2010-02-23 15:14:28 -05:00
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
...
- 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