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16011 Commits
Author SHA1 Message Date
Dannon Baker ce4584956b Merge pull request #5050 from erasche/fix-ufr-7036 
Safely handle possible None value encountered in processing and execution of post-job action arguments
 2017-11-21 13:19:52 -05:00
E Rasche 070ab533bd Address comments 2017-11-21 17:21:41 +01:00
E Rasche ddfbf2c3f0 Handle None v 2017-11-21 15:58:07 +01:00
John Chilton efd762e18c Cleanup SA objects between workflow invocation scheduling attempts. 
This would seem to be a fairly serious memory leak in the abstract but I don't have data that it fixes anything. None the less if it gets into dev and the tests seem to pass I'll open a PR to backport it to at least 17.05 and maybe back even more.
 2017-11-20 10:54:14 -05:00
John Chilton 3e2e149325 Merge pull request #5023 from bgruening/cooler 
add cool datatype
 2017-11-19 20:42:02 -05:00
John Chilton db2c3a43e2 Merge pull request #5018 from martenson/api-for-admin-decode 
add API that allows admins to decode galaxy objects' ids
 2017-11-19 20:40:34 -05:00
Björn Grüning 83e9e07bd5 Merge pull request #5016 from natefoo/memory-mb-metric 
Add metric to the core plugin to collect $GALAXY_MEMORY_MB
 2017-11-17 08:50:53 +01:00
Martin Cech b5864ad4f7 Merge pull request #5004 from jmchilton/collection_copy_api 
More HDCA copying tests, add option to copy HDAs into new history.
 2017-11-16 14:37:56 -05:00
Bjoern Gruening 1718f8dc8e add test file 2017-11-16 12:58:19 +01:00
Bjoern Gruening 32a7dfc20b add cooler file format binary class 2017-11-16 12:41:10 +01:00
Martin Cech 7157600f85 fix few stray wiki links 2017-11-15 16:39:26 -05:00
Martin Cech 8a35b940de add API that allows admins to decode galaxy objects' ids 2017-11-15 14:09:01 -05:00
John Chilton 5c28618a27 Merge pull request #5015 from nsoranzo/fix_parse_interpreter 
parse_interpreter: log a warning only if interpreter is set
 2017-11-15 14:04:40 -05:00
Nate Coraor d5aa2595aa Add metric to the core plugin to collect $GALAXY_MEMORY_MB 2017-11-15 13:02:29 -05:00
John Chilton 38c620c62b Merge pull request #4998 from martenson/lib-to-colllection 
enhance hdca creation API endpoint to accept lddas
 2017-11-15 12:49:56 -05:00
Nicola Soranzo d5390350b8 parse_interpreter: log a warning only if interpreter is set 
Also return None instead of False if there is no `<command>`.
Fix typo in warning.
 2017-11-15 17:10:25 +00:00
Nicola Soranzo 7bede53bef Merge branch 'release_17.09' into dev 
Conflicts:
	lib/galaxy/dependencies/pinned-requirements.txt
	lib/galaxy/dependencies/requirements.txt
 2017-11-15 15:09:33 +00:00
Dannon Baker e27a16953d Merge pull request #4961 from jmchilton/job_delete_api 
Add DELETE /api/jobs/<job_id> as a job cancellation API endpoint.
 2017-11-15 08:12:19 -05:00
Nicola Soranzo bbd96c435b Merge pull request #4903 from jmchilton/dev_at_same_time 
Install dev and regular dependencies at the same time.
 2017-11-15 11:47:40 +00:00
Dannon Baker 18467e9b2c Merge pull request #5000 from nsoranzo/release_17.09_add_ipaddress_requirement 
[17.09] Add missing ipaddress requirement
 2017-11-15 06:31:25 -05:00
John Chilton 4773765974 Merge remote-tracking branch 'jmchilton/dev' into lib-to-colllection 2017-11-14 22:26:10 -05:00
John Chilton 39bd5c6a19 Merge branch 'release_17.09' into dev 2017-11-14 20:32:35 -05:00
John Chilton b25de8b003 Merge remote-tracking branch 'upstream/release_17.05' into HEAD 2017-11-14 20:30:49 -05:00
John Chilton eab30c9652 Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 2017-11-14 20:27:25 -05:00
John Chilton 54b9b09fb2 Merge remote-tracking branch 'upstream/release_16.10' into HEAD 2017-11-14 20:25:38 -05:00
John Chilton 4a2814227c Merge remote-tracking branch 'upstream/release_16.07' into HEAD 2017-11-14 20:23:44 -05:00
Nicola Soranzo 2cd95c48f6 Fix import order everywhere 
- Add flake8-import-order to flake8 Pipfile and remove py27-lint-imports
  and py27-lint-imports-include-list tox envs
- Fix most E201 and E202 errors reported by flake8-import-order v0.15,
  but pin flake8-import-order to v0.14.3 until
  https://github.com/PyCQA/flake8-import-order/issues/123
  is fixed

This let us drop 2 jobs on Travis per each job.
 2017-11-14 19:42:39 +00:00
Nicola Soranzo fb78cb6be3 Merge pull request #4994 from natefoo/non-mule-changes 
Changes made while working on uWSGI mules that don't belong in the mules PR
 2017-11-14 19:34:26 +00:00
Martin Cech 63f039b66f remove the default override 
since it is wrong and ignores the access permissions
 2017-11-14 14:15:22 -05:00
John Chilton a0643e0385 More HDCA copying tests, add option to copy HDAs into new history. 2017-11-14 11:09:57 -05:00
John Chilton 8a41921b49 Respect permissions when creating HDAs/HDCAs from LDDAs. 2017-11-14 09:30:26 -05:00
Nicola Soranzo 0a6c297420 Add missing ipaddress requirement 
Broken in https://github.com/galaxyproject/galaxy/pull/4289 .

Fix https://github.com/galaxyproject/galaxy/issues/4999 .
 2017-11-14 11:15:21 +00:00
Nate Coraor eed12ad15c Docstring fixes 2017-11-13 17:12:53 -05:00
Martin Cech 08eb9859f2 enhance hdca creation endpoint to accept lddas 
by implementing automatic conversion of any such elements
 2017-11-13 16:29:31 -05:00
Martin Cech 95c297c556 Merge pull request #4986 from mvdbeek/remove_galaxy_set_tool_versions 
Remove unused galaxy-side set_tool_version code
 2017-11-13 15:40:23 -05:00
Nate Coraor f5ee540df1 To avoid duplication, move common utilities used by external scripts to 
galaxy.util.script. Update one such script to use the new module.
 2017-11-13 12:18:09 -05:00
John Chilton 9d9c323f73 Merge pull request #4989 from nsoranzo/fix_allow-register 
Fix allow-register option in auth module
 2017-11-13 12:17:43 -05:00
Nate Coraor f8e59b922a Improve util.listify documentation and allow it to accept tuples 2017-11-13 12:16:48 -05:00
Nate Coraor ae720d6f4c Log a more useful error message when tool loading fails due to 
IOError/OSError or a nonexistent tool config.
 2017-11-13 12:15:35 -05:00
Nate Coraor c0a3e6c12a Update imports for galaxy.util.path moves 2017-11-13 12:14:25 -05:00
Dannon Baker c83a8260fd Merge branch 'release_17.09' into dev 2017-11-13 11:36:25 -05:00
Dannon Baker 1a412bfb1b Merge branch 'release_17.05' into release_17.09 2017-11-13 11:36:02 -05:00
Dannon Baker e5587dcb64 Merge pull request #4984 from mvdbeek/fix_crash_when_creating_collection_from_datasets_with_tags 
[17.05][BUG] Specify TagAssociation class when copying a tag
 2017-11-13 11:35:34 -05:00
Martin Cech 15852fcbf8 Merge branch 'dev' into remove_old_library 2017-11-13 11:21:42 -05:00
Martin Cech 7d8dd63957 Merge pull request #4962 from jmchilton/job_cleanup_local 
Kill off processes when stopping the local job runner.
 2017-11-13 11:03:31 -05:00
Martin Cech 3b52326055 Merge pull request #4988 from jmchilton/revert_export_to_file 
[17.09] Revert export to file
 2017-11-13 10:21:37 -05:00
Dannon Baker e78efe16f4 Merge branch 'release_17.09' into dev 2017-11-13 09:44:48 -05:00
Dannon Baker 577d57a69c Merge branch 'release_17.05' into release_17.09 2017-11-13 09:44:20 -05:00
John Chilton a18835b516 Merge pull request #4958 from natefoo/memory-env-var 
Create the $GALAXY_MEMORY_MB tool job environment variable
 2017-11-13 09:39:19 -05:00
John Chilton 0799e511c4 Merge pull request #4979 from nsoranzo/hg_clone 
Run `hg clone` in a subprocess instead of using Mercurial API
 2017-11-13 09:28:44 -05:00