Dannon Baker
a165e1d9b6
Fix path insertion vs appending of <galaxy>/lib for galaxy/main.py.
2015-02-12 10:36:10 -05:00
Dannon Baker
6a46ea7d50
Fix at least one error with zipfile downloads and file permissions not being set correctly.
2015-02-12 07:57:51 -05:00
Dannon Baker
2822b64d3e
pep8 in eggs module while trying to fix eggnotfetchable bugs
2015-02-12 07:55:52 -05:00
Daniel Blankenberg
19ffbf7a4f
When resetting repository metadata in the toolshed, don't overwrite the already set relative_install_dir.
2015-02-11 17:36:05 -05:00
Daniel Blankenberg
c05931024f
Always add sample file info to metadata, not only during initial creation..
2015-02-11 17:31:49 -05:00
Daniel Blankenberg
d3759a475b
Fix for resetting repository metadata in the toolshed via UI (pass resetting_all_metadata_on_repository=True flag).
2015-02-11 16:50:25 -05:00
Aysam Guerler
0af3cac85c
ToolForm: Modify refresh cycle
2015-02-11 16:06:45 -05:00
Daniel Blankenberg
4086a68347
Fix for parsing Tool Data Table columns that are defined as individual xml elements.
2015-02-11 12:40:33 -05:00
Daniel Blankenberg
6ef811478e
Fix for TabularToolDataTable.get_named_fields_list() when a data line has extra columns.
2015-02-11 12:37:59 -05:00
Daniel Blankenberg
808bfc7efe
Fix for Data Tables persisting when .loc file doesn't exist.
2015-02-11 12:33:49 -05:00
Aysam Guerler
783660ff59
ToolForm: Place requirements into pulldown menu, add toolshed link, remove spaces
2015-02-10 22:13:42 -05:00
Dannon Baker
8accba13c7
Add reminder for why imports are done this way in s3objectstore for the next time I forget.
2015-02-10 15:06:12 -05:00
Dannon Baker
fb8d280528
Merge.
2015-02-10 14:42:26 -05:00
Dannon Baker
bdeded4f1f
Correctly use log.exception where appropriate in s3objectstore
2015-02-10 14:42:02 -05:00
Dannon Baker
a483d76f8c
Correct old reference to the wrong get_filename in s3objectstore.
2015-02-10 14:38:58 -05:00
Dannon Baker
1880f94c26
Style standardization in s3objectstore, a couple fixes.
2015-02-10 14:38:01 -05:00
Dannon Baker
863704d850
Followup to PR https://bitbucket.org/galaxy/galaxy-central/pull-request/658/ , only continue restarting in the case of a 1 return code from stop_daemon
2015-02-10 14:07:01 -05:00
Dannon Baker
d2c7f3fa47
Merged in jmchilton/galaxy-central-fork-1 (pull request #665 )
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Add major version to Galaxy, expose via API.
2015-02-10 13:46:38 -05:00
Dannon Baker
663ada2d0b
Merged in nsoranzo/galaxy-central (pull request #658 )
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Don't abort restart if stop_daemon() failed.
2015-02-10 13:14:21 -05:00
John Chilton
5850683634
Change version format to YY.MM.
2015-02-10 10:04:19 -05:00
Dannon Baker
61b64b6f26
Merge.
2015-02-10 09:51:33 -05:00
John Chilton
944905898b
Add major version to Galaxy, expose via API.
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I suspect there are better ways to do this - but I thought I would put something out there we can argue about and hopefully get something in before the next release.
2015-02-10 09:50:13 -05:00
Dannon Baker
ec0c3be798
Merged in charles_hsu/galaxy-central/fix-multipart-upload-in-swift-backend (pull request #648 )
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Fixed multipart-upload issue while use swift as object storage backend
2015-02-10 09:49:01 -05:00
Dannon Baker
51f32c8fc9
Actually use reduced redundancy only when specified.
2015-02-10 09:48:46 -05:00
Dannon Baker
27022833db
Merge.
2015-02-09 16:51:55 -05:00
Dannon Baker
18981016c6
Enable session timeout for tool_shed application (off by default, as with Galaxy).
2015-02-09 16:51:43 -05:00
Martin Cech
b78858e0f9
load param as bool
2015-02-09 16:39:11 -05:00
Martin Cech
e7f754c2d5
minor adjustments to toolshed search
2015-02-09 16:29:31 -05:00
Dannon Baker
0f12fbdba5
Fix toolshed config/session timeout bug.
2015-02-09 16:17:47 -05:00
Dannon Baker
1319fe5f58
More adjustments to queue kickoff to force webapps to initialize the connection prior to models; this (at least seems to, so far) fixes the concurrent mapper initialization race condition sqlalchemy issue.
2015-02-09 16:14:55 -05:00
Dannon Baker
8215f03082
Merge.
2015-02-09 14:50:00 -05:00
Dannon Baker
b901d64866
Prevent last_action column from being populated with time.now() in the entire database and function correctly with null values here. Related bugfixes.
2015-02-09 14:49:35 -05:00
John Chilton
c26c8a86cb
When copying individual collections via the GUI - copy HDAs by default also.
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We may want to be able to turn this off someday in certain scenarios - but usually this will result in less confusion for the user.
Doing this for whole histories also needs to be done - but it is a bit trickier (don't want the HDA copied twice). Might be better on the other side of eliminating the nessecity that these things have HIDs.
2015-02-09 13:29:45 -05:00
John Chilton
a6ed01ced8
Do not import argparse unconditionally in lib/galaxy/tools/deps/brew_exts.py.
2015-02-09 12:22:22 -05:00
Dannon Baker
fd2f5dce47
Merge.
2015-02-09 12:16:01 -05:00
Carl Eberhard
0e37a931ce
API, configuration: doc and clean up
2015-02-09 11:49:49 -05:00
Nate Coraor
19ce7033d3
Fix warning causing tool failure:
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FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
2015-02-09 11:43:26 -05:00
Dannon Baker
022143ecfb
Merge.
2015-02-09 11:36:45 -05:00
Carl Eberhard
7abdea1eaa
Managers, users: add tags_used and requests to user serializer to match info bootstrapped in galaxy.masthead.mako and galaxy_client_app.mako
2015-02-09 11:34:47 -05:00
Nate Coraor
2e9a80b5e2
Remove escaping of quotes in the slurm cli status checks, I don't think they should be there (the format args should in fact be quoted).
2015-02-09 09:59:36 -06:00
Carl Eberhard
b1ecf26c5a
Dataproviders, column: allow filtering data by parsed column values (numeric, list, and string)
2015-02-09 10:36:43 -05:00
Nate Coraor
440d623ffd
Add a _future_expose_api_raw_anonymous_and_sessionless to restore functionality
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that was previously available with _future_expose_api_raw_anonymous.
2015-02-09 09:17:53 -06:00
Aysam Guerler
3ece75b4fa
Parameters: Fix initial value for drill downs, Workflow/ToolForm: Move module building to api
2015-02-08 23:49:24 -05:00
Dannon Baker
c74448cd57
Allow specifying connection at launch of GalaxyQueueWorker.
2015-02-08 18:02:26 -05:00
Dannon Baker
a831c6e148
Minor formatting, spelling in workflow scheduling_manager.
2015-02-08 11:21:42 -05:00
Dannon Baker
4dc04e1472
Fix a few instances of incorrect (deprecated) use of value instead of identity testing in xml parsing.
2015-02-08 11:16:14 -05:00
John Chilton
0e582719fe
Fix running tool tests for recent control reworking.
2015-02-07 19:32:16 -05:00
John Chilton
9e0d530c0c
Rework control queue setup to work in non-web contexts.
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Namely in the new lib/galaxy/main.py. I think this break down of the code makes more sense also since control queues aren't inheriently something web-y so lib/galaxy/app.py makes more sense for configuring them. Dannon feel free to reorganize if you dislike this particular organization - I just wanted to make sure lib/galaxy/main.py could share in the new stuff.
2015-02-07 19:32:16 -05:00
Carl Eberhard
0547725d03
Fix to 8c71422: add the file
2015-02-06 13:56:31 -05:00
Carl Eberhard
242f2634cf
API, configuration: expand exposed settings to include those needed by the masthead in galaxy.masthead.mako, add serializers for config
2015-02-06 13:38:53 -05:00
Dannon Baker