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August 2016
- 2 participants
- 160 discussions
24 Aug '16
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: 8b67ddfa37f82081791bcca5330983a2dd1301f9
https://github.com/galaxyproject/galaxy/commit/8b67ddfa37f82081791bcca53309…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Acquire lock before attempting to install conda
Commit: a2f234d5661f88263e1e6c5e8edef1e521b55359
https://github.com/galaxyproject/galaxy/commit/a2f234d5661f88263e1e6c5e8ede…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Create default tool_dependency dir if it doesn't exist
Commit: e9d81500caa3526200b204270aca175839f36f56
https://github.com/galaxyproject/galaxy/commit/e9d81500caa3526200b204270aca…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
shorten Conda environment names
Commit: fad13d50c344112c8ab637e3c568e43d863730bd
https://github.com/galaxyproject/galaxy/commit/fad13d50c344112c8ab637e3c568…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #2851 from martenson/backport_2794_2826
[16.07] Backport conda fixes
Compare: https://github.com/galaxyproject/galaxy/compare/3248b679ac91...fad13d50c344
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ffef288e4fd85261d4bd4c3e8c3abd3450fca859
https://github.com/galaxyproject/galaxy/commit/ffef288e4fd85261d4bd4c3e8c3a…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-08-16 (Tue, 16 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
shorten Conda environment names
Commit: 7ac7e48ca86c8869fc3db7361fedd1fedd1c03ca
https://github.com/galaxyproject/galaxy/commit/7ac7e48ca86c8869fc3db7361fed…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Merge pull request #2794 from bgruening/shorten_conda_envs
shorten Conda environment names
Compare: https://github.com/galaxyproject/galaxy/compare/57937933fb97...7ac7e48ca86c
1
0
24 Aug '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: af948913607b400c6b58dee701a8a23815601b81
https://github.com/galaxyproject/galaxy/commit/af948913607b400c6b58dee701a8…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Acquire lock before attempting to install conda
Commit: 84f309a03dd8c20076d81b6137acacc515be7721
https://github.com/galaxyproject/galaxy/commit/84f309a03dd8c20076d81b6137ac…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Create default tool_dependency dir if it doesn't exist
Commit: 57937933fb97e17beee0711d69040e7d0efad180
https://github.com/galaxyproject/galaxy/commit/57937933fb97e17beee0711d6904…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #2826 from mvdbeek/lock_conda
Acquire lock before attempting to install conda
Compare: https://github.com/galaxyproject/galaxy/compare/2a92a7de86a7...57937933fb97
1
0
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: 7326498335804560d0376c555524b096c69720ce
https://github.com/galaxyproject/galaxy/commit/7326498335804560d0376c555524…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
improve conda doc to include TOC
Commit: 3248b679ac91fbb2275fd3cd47d2fb2ea96e5a2e
https://github.com/galaxyproject/galaxy/commit/3248b679ac91fbb2275fd3cd47d2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Merge pull request #2850 from martenson/docs_conda
[16.07] conda docs - add TOC
Compare: https://github.com/galaxyproject/galaxy/compare/df47bd200736...3248b679ac91
1
0
24 Aug '16
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: f47ea88c236be2414d40ef933dd3ee3c5aa2cbcb
https://github.com/galaxyproject/galaxy/commit/f47ea88c236be2414d40ef933dd3…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-19 (Fri, 19 Aug 2016)
Changed paths:
A doc/source/releases/16.07.rst
M doc/source/releases/16.07_announce.rst
A doc/source/releases/16.10_announce.rst
Log Message:
-----------
initial curated release notes for 16.07
Commit: 53570e471e087fc92e0ef4befdd965703e4aeb14
https://github.com/galaxyproject/galaxy/commit/53570e471e087fc92e0ef4befdd9…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M doc/source/releases/16.07.rst
Log Message:
-----------
Merge some entries, rephrasing and fixes
Commit: 96bdde85bf259c2c821a7bbacc1c4aef60c3f3b7
https://github.com/galaxyproject/galaxy/commit/96bdde85bf259c2c821a7bbacc1c…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M doc/source/releases/16.07_announce.rst
Log Message:
-----------
add a highlight, update git commands
Commit: 113999e5d574b29e1c197bcfe1bdef1777c5c507
https://github.com/galaxyproject/galaxy/commit/113999e5d574b29e1c197bcfe1bd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M doc/source/releases/16.07.rst
Log Message:
-----------
Tweaks to language of many of enhancements in 16.07 release notes.
Commit: c82719f22d3d8971055fc9b833dc7fd2519fad22
https://github.com/galaxyproject/galaxy/commit/c82719f22d3d8971055fc9b833dc…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M doc/source/releases/16.07.rst
M doc/source/releases/16.07_announce.rst
Log Message:
-----------
drop subheaders, reorder, tweak to wording
Commit: 9b96d9dbfa875375bc172451fb9c7e6993c62f41
https://github.com/galaxyproject/galaxy/commit/9b96d9dbfa875375bc172451fb9c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M doc/source/releases/16.07.rst
Log Message:
-----------
More user-focused language in release notes.
Commit: e1060bd18fcf1bc69e5cd41f44adde37ba55ae1d
https://github.com/galaxyproject/galaxy/commit/e1060bd18fcf1bc69e5cd41f44ad…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M doc/source/releases/16.07.rst
Log Message:
-----------
Spelling fix thanks to @nsoranzo.
Commit: 04370845451da1cf839d75366d131325105698fe
https://github.com/galaxyproject/galaxy/commit/04370845451da1cf839d75366d13…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M doc/source/releases/16.07.rst
Log Message:
-----------
Another spelling fix thanks to @nsoranzo.
Commit: 8f571bae7129b4ce07739ab8e4d9ddcef020af5e
https://github.com/galaxyproject/galaxy/commit/8f571bae7129b4ce07739ab8e4d9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M doc/source/releases/16.07.rst
Log Message:
-----------
Wording fix thanks to @nsoranzo.
Commit: f0ffa9c5947674d8e8731f36f00eb82b757b6558
https://github.com/galaxyproject/galaxy/commit/f0ffa9c5947674d8e8731f36f00e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M doc/source/releases/16.07.rst
Log Message:
-----------
drop GRT reference
Commit: 3d4300e5429b2b09b92cf5d9f55541643a0ff62b
https://github.com/galaxyproject/galaxy/commit/3d4300e5429b2b09b92cf5d9f555…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M doc/source/releases/16.07.rst
Log Message:
-----------
tweak wording of notes
Commit: 26ceef668c57c0ef44f4072d3550472ff9582e29
https://github.com/galaxyproject/galaxy/commit/26ceef668c57c0ef44f4072d3550…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M doc/source/releases/16.07_announce.rst
Log Message:
-----------
announce conda as beta, link the IUC doc, link DTD wiki
Commit: 08b2bda13bd4622d9e492aaa256d7c9bba5790aa
https://github.com/galaxyproject/galaxy/commit/08b2bda13bd4622d9e492aaa256d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M doc/source/releases/16.07_announce.rst
Log Message:
-----------
change links to target official docs
Commit: df47bd2007365f22921375fd0eb757f0ec749473
https://github.com/galaxyproject/galaxy/commit/df47bd2007365f22921375fd0eb7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
A doc/source/releases/16.07.rst
M doc/source/releases/16.07_announce.rst
A doc/source/releases/16.10_announce.rst
Log Message:
-----------
Merge pull request #2821 from martenson/16.07_release_notes
[16.07] curated release notes for 16.07
Compare: https://github.com/galaxyproject/galaxy/compare/124d546be6e7...df47bd200736
1
0
[galaxyproject/galaxy] 91de2d: Remove enable_beta_tool_command_isolation config o...
by GitHub 24 Aug '16
by GitHub 24 Aug '16
24 Aug '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 91de2d3681c38bc6d02180bac6d6b7ccd06482af
https://github.com/galaxyproject/galaxy/commit/91de2d3681c38bc6d02180bac6d6…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Remove enable_beta_tool_command_isolation config option
Also fix import order and Python3 compatibility for lib/galaxy/jobs/__init__.py
Commit: 7b65a6c41082c4a0160dba97406f9f8ae2f5edf4
https://github.com/galaxyproject/galaxy/commit/7b65a6c41082c4a0160dba97406f…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Fix typos in config/galaxy.ini.sample
Commit: 2a92a7de86a7e8afc94eaea582dfa5f298e3ce02
https://github.com/galaxyproject/galaxy/commit/2a92a7de86a7e8afc94eaea582df…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Merge pull request #2830 from nsoranzo/remove_enable_beta_tool_command_isolation
Remove enable_beta_tool_command_isolation config option
Compare: https://github.com/galaxyproject/galaxy/compare/52e6c9ac3073...2a92a7de86a7
1
0
[galaxyproject/galaxy] aa41a7: Fix tabular renderer display when total_cols > lin...
by GitHub 24 Aug '16
by GitHub 24 Aug '16
24 Aug '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: aa41a70011dfcda6cf778346dbf698ded8f827c6
https://github.com/galaxyproject/galaxy/commit/aa41a70011dfcda6cf778346dbf6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-23 (Tue, 23 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/data.js
M static/maps/mvc/dataset/data.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/data.js
Log Message:
-----------
Fix tabular renderer display when total_cols > line_cols > 1
Commit: 52e6c9ac307370e0d37681a2a50a2faba3d14103
https://github.com/galaxyproject/galaxy/commit/52e6c9ac307370e0d37681a2a50a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/data.js
M static/maps/mvc/dataset/data.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/data.js
Log Message:
-----------
Merge pull request #2845 from dannon/tabular_dataset_render
Fix tabular renderer display when total_cols > line_cols > 1
Compare: https://github.com/galaxyproject/galaxy/compare/93e74ca51d6b...52e6c9ac3073
1
0
[galaxyproject/galaxy] 4d1975: add conda docs converted and modified from IUC goo...
by GitHub 24 Aug '16
by GitHub 24 Aug '16
24 Aug '16
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: 4d19755c1313e8a014f873f1b011baf4f8d59310
https://github.com/galaxyproject/galaxy/commit/4d19755c1313e8a014f873f1b011…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-23 (Tue, 23 Aug 2016)
Changed paths:
A doc/source/admin/conda_faq.rst
M doc/source/admin/index.rst
Log Message:
-----------
add conda docs converted and modified from IUC googledoc
Commit: 01a24f6560be2d6cc9c6aef43e9665f140fc3640
https://github.com/galaxyproject/galaxy/commit/01a24f6560be2d6cc9c6aef43e96…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-23 (Tue, 23 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
rst problems
Commit: 04f22b70a4ecd127e7990982c09db7278bf1cf98
https://github.com/galaxyproject/galaxy/commit/04f22b70a4ecd127e7990982c09d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-23 (Tue, 23 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
fix plural, split lines to prevent indentation
Commit: e33f8fe5b623d38ec7b27c90279713a18807ee48
https://github.com/galaxyproject/galaxy/commit/e33f8fe5b623d38ec7b27c902797…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-23 (Tue, 23 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
replace apostrophes
Commit: 453c98d8ad572b7d9154430f5f61123d7ca5fbc4
https://github.com/galaxyproject/galaxy/commit/453c98d8ad572b7d9154430f5f61…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-23 (Tue, 23 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
this one is even weirder than the ones before
Commit: aedfdffafedd35a1ed52aec85dd373c76b7c3135
https://github.com/galaxyproject/galaxy/commit/aedfdffafedd35a1ed52aec85dd3…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-23 (Tue, 23 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
add more literal includes
Commit: e52dbde3e481a30c5980f1e0171b720c557ee72d
https://github.com/galaxyproject/galaxy/commit/e52dbde3e481a30c5980f1e0171b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-23 (Tue, 23 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Conda/conda standardization
Commit: b4495c1a8bb3e184bf35a9ebc4e795b7da3aadbb
https://github.com/galaxyproject/galaxy/commit/b4495c1a8bb3e184bf35a9ebc4e7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-23 (Tue, 23 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Merge pull request #17 from dannon/docs_conda
Conda/conda standardization
Commit: 3d0bf645ab03585e316d673cd6b073e706fb616d
https://github.com/galaxyproject/galaxy/commit/3d0bf645ab03585e316d673cd6b0…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
fix tiny things in docs
Commit: 779c357dcac2940f9bdaacf8de5259fe632ada1c
https://github.com/galaxyproject/galaxy/commit/779c357dcac2940f9bdaacf8de52…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Merge branch 'docs_conda' of https://github.com/martenson/galaxy into docs_conda
Commit: 124d546be6e789a288f19c21adb229e149e9d7d2
https://github.com/galaxyproject/galaxy/commit/124d546be6e789a288f19c21adb2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
A doc/source/admin/conda_faq.rst
M doc/source/admin/index.rst
Log Message:
-----------
Merge pull request #2844 from martenson/docs_conda
[16.07] add conda docs converted and modified from IUC googledoc
Compare: https://github.com/galaxyproject/galaxy/compare/a1b2ec386e32...124d546be6e7
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: eafa71fb8e84e5a795c15edc4f4204928fd2e47c
https://github.com/galaxyproject/galaxy/commit/eafa71fb8e84e5a795c15edc4f42…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-23 (Tue, 23 Aug 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/batch.py
Log Message:
-----------
Belated typo fixes for 1768
Commit: 93e74ca51d6b5f03b3d1c00e9754548ce4467cb3
https://github.com/galaxyproject/galaxy/commit/93e74ca51d6b5f03b3d1c00e9754…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/batch.py
Log Message:
-----------
Merge pull request #2848 from dannon/typo_branch_230981
Belated typo fixes for 1768
Compare: https://github.com/galaxyproject/galaxy/compare/9de06e1594e8...93e74ca51d6b
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 35b7c7788ac439f6ff3ae383aa910545c7ee85ae
https://github.com/galaxyproject/galaxy/commit/35b7c7788ac439f6ff3ae383aa91…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-04-21 (Tue, 21 Apr 2015)
Changed paths:
M lib/galaxy/web/framework/base.py
A lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/webapps/galaxy/buildapp.py
A test/api/test_api_batch.py
A test/casperjs/api-batch-tests.js
Log Message:
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API, batch: initial commit
Commit: 5dcc4e8e3a071e979503a0172543876f11984a17
https://github.com/galaxyproject/galaxy/commit/5dcc4e8e3a071e979503a0172543…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-04-22 (Wed, 22 Apr 2015)
Changed paths:
M lib/galaxy/web/framework/middleware/batch.py
M test/api/test_api_batch.py
M test/casperjs/api-batch-tests.js
Log Message:
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API, batch: handle bad routes
Commit: 09bcb7441c62c890abf799a93411aa9c3b79891e
https://github.com/galaxyproject/galaxy/commit/09bcb7441c62c890abf799a93411…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-04-22 (Wed, 22 Apr 2015)
Changed paths:
M lib/galaxy/web/framework/middleware/batch.py
Log Message:
-----------
API, batch: properly import paste
Commit: 8fb10a5c9a5316552ed3f8f83ecc58592f44b052
https://github.com/galaxyproject/galaxy/commit/8fb10a5c9a5316552ed3f8f83ecc…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-04-22 (Wed, 22 Apr 2015)
Changed paths:
M lib/galaxy/web/framework/middleware/batch.py
M test/api/test_api_batch.py
M test/casperjs/api-batch-tests.js
Log Message:
-----------
API, batch: test errored calls
Commit: 1dc0876cdd8a5674cdcea0df506ecc65dc02a5eb
https://github.com/galaxyproject/galaxy/commit/1dc0876cdd8a5674cdcea0df506e…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-07-31 (Fri, 31 Jul 2015)
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A CONTRIBUTORS.md
M LICENSE.txt
M README.rst
M client/GruntFile.js
M client/README.md
M client/bower.json
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.masthead.js
R client/galaxy/scripts/galaxy.workflow_editor.canvas.js
R client/galaxy/scripts/galaxy.workflows.js
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/handlebars.runtime.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-choice.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-panel-annotated.js
M client/galaxy/scripts/mvc/history/history-panel-edit.js
M client/galaxy/scripts/mvc/history/history-panel.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/list/list-panel.js
M client/galaxy/scripts/mvc/tools.js
M client/galaxy/scripts/mvc/tools/tools-form-base.js
M client/galaxy/scripts/mvc/tools/tools-form-workflow.js
M client/galaxy/scripts/mvc/tools/tools-template.js
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M client/galaxy/scripts/templates/compiled/tool_search.js
A client/galaxy/scripts/ui/hoverhighlight.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
A client/galaxy/style/blue_colors.ini
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A client/galaxy/style/less/bootstrap/dropdowns.less
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A client/galaxy/style/less/bootstrap/navbar.less
A client/galaxy/style/less/bootstrap/navs.less
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A client/galaxy/style/less/bootstrap/responsive-utilities.less
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A client/galaxy/style/less/bootstrap/theme.less
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A client/galaxy/style/less/bootstrap/tooltip.less
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A client/galaxy/style/less/bootstrap/utilities.less
A client/galaxy/style/less/bootstrap/variables.less
A client/galaxy/style/less/bootstrap/wells.less
A client/galaxy/style/less/circster.less
A client/galaxy/style/less/collections.less
A client/galaxy/style/less/embed_item.less
A client/galaxy/style/less/fontawesome/bordered-pulled.less
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A client/galaxy/style/less/fontawesome/list.less
A client/galaxy/style/less/fontawesome/mixins.less
A client/galaxy/style/less/fontawesome/path.less
A client/galaxy/style/less/fontawesome/rotated-flipped.less
A client/galaxy/style/less/fontawesome/spinning.less
A client/galaxy/style/less/fontawesome/stacked.less
A client/galaxy/style/less/fontawesome/variables.less
A client/galaxy/style/less/frame.less
A client/galaxy/style/less/galaxy_bootstrap.less
A client/galaxy/style/less/galaxy_bootstrap/overrides.less
A client/galaxy/style/less/galaxy_bootstrap/variables.less
A client/galaxy/style/less/galaxy_variables.less
A client/galaxy/style/less/history.less
A client/galaxy/style/less/iconic_stroke.less
A client/galaxy/style/less/iphone.less
A client/galaxy/style/less/job.less
A client/galaxy/style/less/jstree.less
A client/galaxy/style/less/library.less
A client/galaxy/style/less/list-item.less
A client/galaxy/style/less/masthead.less
A client/galaxy/style/less/select2.less
A client/galaxy/style/less/theme/blue.less
A client/galaxy/style/less/toastr.less
A client/galaxy/style/less/trackster.less
A client/galaxy/style/less/ui.less
A client/galaxy/style/less/ui/dataset-choice.less
A client/galaxy/style/less/ui/icon-btn.less
A client/galaxy/style/less/ui/pagination.less
A client/galaxy/style/less/ui/paired-collection-creator.less
A client/galaxy/style/less/ui/peek-column-selector.less
A client/galaxy/style/less/ui/search-input.less
A client/galaxy/style/less/upload.less
A client/galaxy/style/source_material/circle.py
A client/galaxy/style/source_material/galaxy_icons.svg
A client/galaxy/style/source_material/galaxy_spinner.fla
A client/grunt-tasks/install-libs.js
A client/grunt-tasks/scripts.js
A client/grunt-tasks/style.js
A client/grunt-tasks/templates.js
M client/package.json
A client/toolshed/scripts/mvc/groups/group-detail-view.js
A client/toolshed/scripts/mvc/groups/group-list-view.js
A client/toolshed/scripts/mvc/groups/group-listrow-view.js
A client/toolshed/scripts/mvc/groups/group-model.js
A client/toolshed/scripts/toolshed.groups.js
M config/auth_conf.xml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/object_store_conf.xml.sample
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/ipython/config/ipython.ini.sample
M config/plugins/interactive_environments/ipython/config/ipython.xml
M config/plugins/interactive_environments/ipython/templates/ipython.mako
M config/plugins/interactive_environments/ipython/templates/notebook.ipynb
A config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
A config/plugins/interactive_environments/rstudio/config/rstudio.xml
A config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/jsbn.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/prng4.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rng.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rsa.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.min.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/jsbn.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/prng4.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rng.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rsa.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/jsbn.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/prng4.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/rng.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/rsa.js
A config/plugins/interactive_environments/rstudio/static/js/rstudio.js
A config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/visualizations/README.txt
M config/plugins/visualizations/charts/config/charts.xml
M config/plugins/visualizations/charts/static/build-app.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
M config/plugins/visualizations/circster/config/circster.xml
A config/plugins/visualizations/common/templates/script_entry_point.mako
M config/plugins/visualizations/common/templates/visualization_base.mako
M config/plugins/visualizations/graphview/config/graphview.xml
M config/plugins/visualizations/phyloviz/config/phyloviz.xml
M config/plugins/visualizations/scatterplot/config/scatterplot.xml
M config/plugins/visualizations/scatterplot/src/scatterplot-display.js
M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js
M config/plugins/visualizations/sweepster/config/sweepster.xml
M config/plugins/visualizations/trackster/config/trackster.xml
M config/plugins/visualizations/visualization.dtd
M config/tool_conf.xml.sample
M config/tool_shed.ini.sample
M contrib/nagios/check_galaxy.py
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M display_applications/ensembl/ensembl_bam.xml
M display_applications/ensembl/ensembl_gff.xml
M display_applications/ensembl/ensembl_interval_as_bed.xml
M display_applications/gbrowse/gbrowse_gff.xml
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M display_applications/gbrowse/gbrowse_wig.xml
M display_applications/igb/bam.xml
M display_applications/igb/bb.xml
M display_applications/igb/bed.xml
M display_applications/igb/bedgraph.xml
M display_applications/igb/bigwig.xml
M display_applications/igb/gtf.xml
M display_applications/igb/wig.xml
M display_applications/igv/bam.xml
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M doc/source/lib/galaxy.datatypes.util.rst
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M doc/source/lib/galaxy.external_services.result_handlers.rst
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M doc/source/lib/galaxy.managers.rst
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M doc/source/lib/galaxy.openid.rst
M doc/source/lib/galaxy.quota.rst
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M doc/source/lib/galaxy.sample_tracking.rst
M doc/source/lib/galaxy.security.rst
M doc/source/lib/galaxy.tags.rst
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M doc/source/lib/galaxy.web.base.controllers.rst
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A doc/source/lib/pulsar.client.transport.rst
A doc/source/lib/pulsar.rst
A doc/source/lib/tool_shed.capsule.rst
A doc/source/lib/tool_shed.dependencies.repository.rst
A doc/source/lib/tool_shed.dependencies.rst
A doc/source/lib/tool_shed.dependencies.tool.rst
A doc/source/lib/tool_shed.galaxy_install.datatypes.rst
M doc/source/lib/tool_shed.galaxy_install.grids.rst
A doc/source/lib/tool_shed.galaxy_install.metadata.rst
M doc/source/lib/tool_shed.galaxy_install.migrate.rst
A doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst
M doc/source/lib/tool_shed.galaxy_install.rst
A doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst
M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst
A doc/source/lib/tool_shed.galaxy_install.tools.rst
A doc/source/lib/tool_shed.galaxy_install.utility_containers.rst
M doc/source/lib/tool_shed.grids.rst
A doc/source/lib/tool_shed.managers.rst
A doc/source/lib/tool_shed.metadata.rst
A doc/source/lib/tool_shed.repository_types.rst
M doc/source/lib/tool_shed.rst
A doc/source/lib/tool_shed.tools.rst
M doc/source/lib/tool_shed.util.rst
A doc/source/lib/tool_shed.utility_containers.rst
A doc/source/project/organization.rst
A doc/source/releases/13.01_announce.rst
A doc/source/releases/13.02_announce.rst
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A doc/source/releases/13.06_announce.rst
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A doc/source/releases/_header.rst
A doc/source/releases/_thanks.rst
A doc/source/releases/index.rst
A doc/source/releases/older_releases.rst
M eggs.ini
M lib/galaxy/__init__.py
M lib/galaxy/actions/admin.py
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/__init__.py
M lib/galaxy/auth/providers/alwaysreject.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/localdb.py
A lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/subcollections.py
M lib/galaxy/dataset_collections/types/__init__.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/chrominfo.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/coverage.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/__init__.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/chunk.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/exceptions.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/display_applications/util.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/metadata.py
A lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
A lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
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M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
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M lib/galaxy/eggs/dist.py
M lib/galaxy/eggs/scramble.py
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M lib/galaxy/external_services/__init__.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/__init__.py
M lib/galaxy/external_services/result_handlers/basic.py
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M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/lwr.py
M lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/state_handler_factory.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/jobs/splitters/basic.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/main.py
M lib/galaxy/managers/annotatable.py
M lib/galaxy/managers/base.py
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M lib/galaxy/managers/containers.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
A lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/orm/__init__.py
M lib/galaxy/model/orm/logging_connection_proxy.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/model/search.py
M lib/galaxy/model/tool_shed_install/mapping.py
M lib/galaxy/model/tool_shed_install/migrate/check.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/openid/providers.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/quota/__init__.py
M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/data_manager.py
M lib/galaxy/tools/actions/data_source.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/brew_util.py
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M lib/galaxy/tools/deps/resolvers/modules.py
A lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/linters/citations.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/input_translation.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
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M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/aliaspickler.py
M lib/galaxy/util/backports/importlib/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/dbkeys.py
M lib/galaxy/util/debugging.py
M lib/galaxy/util/dictobj.py
M lib/galaxy/util/expressions.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/inflection.py
M lib/galaxy/util/jstree.py
M lib/galaxy/util/log/__init__.py
M lib/galaxy/util/log/fluent_log.py
M lib/galaxy/util/lrucache.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/odict.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/specs.py
M lib/galaxy/util/sqlite.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/template.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/validation.py
A lib/galaxy/util/xml_macros.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/basic.py
M lib/galaxy/visualization/data_providers/cigar.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/__init__.py
M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
M lib/galaxy/visualization/data_providers/registry.py
M lib/galaxy/visualization/genomes.py
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A lib/galaxy/visualization/plugins/registry.py
A lib/galaxy/visualization/plugins/resource_parser.py
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R lib/galaxy/visualization/registry.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
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M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/profile.py
M lib/galaxy/web/framework/middleware/request_id.py
M lib/galaxy/web/framework/middleware/sentry.py
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M lib/galaxy/web/framework/middleware/translogger.py
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M lib/galaxy/web/framework/webapp.py
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M lib/galaxy/webapps/galaxy/api/group_users.py
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M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/item_tags.py
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M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/request_types.py
M lib/galaxy/webapps/galaxy/api/requests.py
M lib/galaxy/webapps/galaxy/api/roles.py
M lib/galaxy/webapps/galaxy/api/samples.py
M lib/galaxy/webapps/galaxy/api/tool_data.py
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M lib/galaxy/webapps/galaxy/api/users.py
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M lib/galaxy/webapps/galaxy/controllers/biostar.py
M lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
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M lib/galaxy/webapps/galaxy/controllers/page.py
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M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
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M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/reports/config.py
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M lib/galaxy/webapps/reports/controllers/root.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/system.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/reports/controllers/workflows.py
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A lib/galaxy/webapps/tool_shed/api/groups.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
R lib/galaxy/webapps/tool_shed/api/search.py
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M lib/galaxy/webapps/tool_shed/controllers/admin.py
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M lib/galaxy/webapps/tool_shed/controllers/hg.py
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M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
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M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py
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M lib/galaxy/workflow/steps.py
M lib/galaxy_ext/metadata/__init__.py
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M lib/tool_shed/capsule/capsule_manager.py
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M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
A lib/tool_shed/managers/__init__.py
A lib/tool_shed/managers/groups.py
A lib/tool_shed/managers/repositories.py
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M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/scripts/api/common.py
M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
M lib/tool_shed/scripts/check_repositories_for_functional_tests.py
M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/review_util.py
M lib/tool_shed/util/search_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_dependency_util.py
M lib/tool_shed/util/web_util.py
M lib/tool_shed/util/workflow_util.py
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A scripts/auth/pam_auth_helper.py
A scripts/bootstrap_history.py
M scripts/build_toolbox.py
M scripts/build_universe_config.py
M scripts/check_eggs.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/db_shell.py
M scripts/dist-scramble.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
A scripts/edam_mapping.py
M scripts/egg_packager_template.py
M scripts/external_chown_script.py
M scripts/extract_dataset_part.py
M scripts/extract_toolbox_sections.py
M scripts/fetch_eggs.py
M scripts/functional_tests.py
M scripts/get_platforms.py
M scripts/helper.py
M scripts/make_egg_packager.py
M scripts/metagenomics/convert_title.py
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M scripts/migrate_tools/migrate_tools.py
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A scripts/runtime_stats.py
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M scripts/scramble/lib/scramble_lib.py
M scripts/scramble/scripts/DRMAA_python-macosx.py
M scripts/scramble/scripts/DRMAA_python-solaris.py
M scripts/scramble/scripts/DRMAA_python.py
M scripts/scramble/scripts/MySQL_python-solaris.py
M scripts/scramble/scripts/MySQL_python.py
M scripts/scramble/scripts/PyRods.py
M scripts/scramble/scripts/bx_python-solaris.py
M scripts/scramble/scripts/generic.py
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M scripts/scramble/scripts/psycopg2-linux.py
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M scripts/scramble/scripts/psycopg2-solaris.py
M scripts/scramble/scripts/psycopg2.py
M scripts/scramble/scripts/pysam-solaris.py
M scripts/scramble/scripts/pysqlite.py
M scripts/set_dataset_sizes.py
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M scripts/summarize_timings.py
M scripts/sync_reports_config.py
M scripts/test_dist_egg.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M setup.cfg
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M static/images/galaxyIcon_noText.png
M static/maps/galaxy.interactive_environments.js.map
M static/maps/galaxy.masthead.js.map
R static/maps/galaxy.workflow_editor.canvas.js.map
M static/maps/galaxy.workflows.js.map
M static/maps/libs/d3.js.map
M static/maps/libs/handlebars.runtime.js.map
M static/maps/libs/jquery/jquery.js.map
M static/maps/libs/require.js.map
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M static/maps/mvc/collection/list-collection-creator.js.map
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M static/maps/mvc/form/form-view.js.map
A static/maps/mvc/groups/group-detail-view.js.map
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M static/scripts/galaxy.workflows.js
M static/scripts/libs/d3.js
M static/scripts/libs/handlebars.runtime.js
M static/scripts/libs/jquery/jquery.js
M static/scripts/libs/raven.js
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M static/scripts/mvc/collection/list-collection-creator.js
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M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/history-content-model.js
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M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
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M static/scripts/mvc/tools.js
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M static/scripts/mvc/ui/ui-select-default.js
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M static/scripts/templates/compiled/tool_form.js
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R static/scripts/templates/tool_link.handlebars
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M static/scripts/utils/config.js
M static/scripts/utils/utils.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
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R static/style/Makefile
R static/style/README
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M static/style/blue/base.css
M static/style/blue/circster.css
M static/style/blue/embed_item.css
M static/style/blue/iphone.css
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R static/style/src/less/bootstrap/badges.less
R static/style/src/less/bootstrap/bootstrap.less
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M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/users_last_access_date.mako
M templates/webapps/reports/users_user_disk_usage.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_user_per_month.mako
M templates/webapps/tool_shed/base_panels.mako
A templates/webapps/tool_shed/group/index.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M templates/webapps/tool_shed/repository/view_repository.mako
A test-data/bcf_index_metadata_test.bcf
A test-data/bcf_index_metadata_test.txt
M test/api/test_dataset_collections.py
M test/api/test_datasets.py
M test/api/test_histories.py
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/api/yaml_to_workflow.py
M test/base/test_db_util.py
M test/base/twilltestcase.py
M test/casperjs/api-anon-history-permission-tests.js
M test/casperjs/api-history-permission-tests.js
M test/casperjs/hda-state-tests.js
M test/casperjs/modules/historypanel.js
M test/casperjs/modules/user.js
M test/casperjs/registration-tests.js
M test/functional/test_admin_features.py
M test/functional/test_data_managers.py
M test/functional/test_data_security.py
M test/functional/test_get_data.py
M test/functional/test_library_features.py
M test/functional/test_library_security.py
M test/functional/test_library_templates.py
M test/functional/test_metadata_editing.py
M test/functional/test_sample_tracking.py
M test/functional/test_toolbox.py
M test/functional/test_ucsc_table_browser.py
M test/functional/test_user_info.py
A test/functional/tools/boolean_conditional.xml
M test/functional/tools/code_file.py
A test/functional/tools/environment_variables.xml
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A test/functional/tools/metadata_bcf.xml
A test/functional/tools/output_auto_format.xml
A test/functional/tools/output_collection_filter.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/simple_constructs.xml
M test/functional/workflow.py
M test/install_and_test_tool_shed_repositories/base/test_db_util.py
M test/install_and_test_tool_shed_repositories/base/util.py
M test/qunit/README.txt
M test/qunit/test-common.js
M test/qunit/tests/hda-base.js
M test/qunit/tests/history_contents_model_tests.js
M test/qunit/tests/job-dag.js
A test/qunit/tests/list-of-pairs-collection-creator.html
A test/qunit/tests/list-of-pairs-collection-creator.js
M test/qunit/tests/metrics-logger.js
R test/qunit/tests/paired-collection-creator.html
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M test/qunit/tests/workflow_editor_tests.js
M test/tool_shed/base/test_db_util.py
M test/tool_shed/base/twilltestcase.py
M test/tool_shed/functional/test_0000_basic_repository_features.py
M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
M test/tool_shed/functional/test_0400_repository_component_reviews.py
M test/tool_shed/functional/test_0410_repository_component_review_access_control.py
M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
M test/tool_shed/functional/test_0430_browse_utilities.py
M test/tool_shed/functional/test_0450_skip_tool_tests.py
M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_rules/20_instance.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_objectstore.py
M test/unit/test_routes.py
M test/unit/test_sockets.py
M test/unit/tool_shed_unit_tests/test_fabric_util.py
M test/unit/tool_shed_unit_tests/test_td_common_util.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/utility.py
A test/unit/visualizations/plugins/__init__.py
A test/unit/visualizations/plugins/test_VisualizationPlugin.py
A test/unit/visualizations/plugins/test_VisualizationsRegistry.py
R test/unit/visualizations/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/workflows/test_extract_summary.py
M tool-data/shared/gbrowse/gbrowse_build_sites.txt
M tool_list.py
M tools/data_source/bed_convert.xml
M tools/data_source/data_source.py
M tools/data_source/fly_modencode.xml
M tools/data_source/genbank.xml
M tools/data_source/import.xml
M tools/data_source/microbial_import.xml
M tools/data_source/ucsc_tablebrowser_archaea.xml
M tools/data_source/ucsc_tablebrowser_test.xml
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/data_source/worm_modencode.xml
M tools/evolution/codingSnps.xml
M tools/evolution/codingSnps_filter.py
M tools/extract/liftOver_wrapper.xml
M tools/filters/axt_to_lav.xml
M tools/filters/axt_to_lav_code.py
M tools/filters/catWrapper.xml
M tools/filters/changeCase.xml
M tools/filters/condense_characters.xml
M tools/filters/cutWrapper.xml
M tools/filters/gff/extract_GFF_Features.xml
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.xml
M tools/filters/gff/gtf_filter_by_attribute_values_list.xml
M tools/filters/headWrapper.xml
M tools/filters/joiner2.xml
M tools/filters/lav_to_bed.py
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M tools/filters/lav_to_bed_code.py
M tools/filters/pasteWrapper.xml
M tools/filters/remove_beginning.xml
M tools/filters/tailWrapper.xml
M tools/filters/ucsc_gene_table_to_intervals.xml
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_exporter.xml
M tools/maf/genebed_maf_to_fasta.xml
M tools/maf/interval2maf.xml
M tools/maf/interval2maf_pairwise.xml
M tools/maf/interval_maf_to_merged_fasta.xml
M tools/maf/maf_by_block_number.xml
M tools/maf/maf_filter.py
M tools/maf/maf_filter.xml
M tools/maf/maf_limit_size.xml
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_reverse_complement.xml
M tools/maf/maf_split_by_species.xml
M tools/maf/maf_stats.xml
M tools/maf/maf_to_fasta.xml
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/plotting/bar_chart.xml
M tools/plotting/boxplot.xml
M tools/solid_tools/maq_cs_wrapper_code.py
M tools/stats/filtering.xml
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/stats/gsummary.xml
M tools/stats/gsummary.xml.groups
M tools/visualization/LAJ.xml
M tools/visualization/LAJ_code.py
A tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into api.batch
Commit: 0b6397ec5c69d73b8b1e6be6e1518b88915e5103
https://github.com/galaxyproject/galaxy/commit/0b6397ec5c69d73b8b1e6be6e151…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
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A .ci/check_mako.sh
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A .ci/flake8_py3_wrapper.sh
M .ci/flake8_wrapper.sh
A .ci/py3_sources.txt
M .gitignore
A CODE_OF_CONDUCT.md
M CONTRIBUTING.md
M CONTRIBUTORS.md
A Makefile
M README.rst
A client/.docker-build.sh
A client/Dockerfile
M client/GruntFile.js
M client/README.md
M client/bower.json
A client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/apps/history-panel.js
A client/galaxy/scripts/apps/login.js
A client/galaxy/scripts/apps/tool-panel.js
R client/galaxy/scripts/base.js
R client/galaxy/scripts/galaxy-app-base.js
R client/galaxy/scripts/galaxy.autocom_tagging.js
R client/galaxy/scripts/galaxy.base.js
R client/galaxy/scripts/galaxy.frame.js
A client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.library.js
R client/galaxy/scripts/galaxy.masthead.js
R client/galaxy/scripts/galaxy.menu.js
M client/galaxy/scripts/galaxy.pages.js
R client/galaxy/scripts/galaxy.panels.js
R client/galaxy/scripts/galaxy.tools.js
R client/galaxy/scripts/galaxy.ui.scrollPanel.js
A client/galaxy/scripts/layout/masthead.js
A client/galaxy/scripts/layout/menu.js
A client/galaxy/scripts/layout/modal.js
A client/galaxy/scripts/layout/page.js
A client/galaxy/scripts/layout/panel.js
A client/galaxy/scripts/layout/scratchbook.js
R client/galaxy/scripts/libs/IE/IE7.js
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R client/galaxy/scripts/libs/IE/ie7-recalc.js
A client/galaxy/scripts/libs/backbone.js
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M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/farbtastic.js
A client/galaxy/scripts/libs/jquery.sparklines.js
M client/galaxy/scripts/libs/jquery/jqtouch.js
M client/galaxy/scripts/libs/jquery/jquery.dynatree.js
M client/galaxy/scripts/libs/jquery/select2.js
M client/galaxy/scripts/libs/raven.js
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M client/galaxy/scripts/libs/tracekit.js
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M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
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M client/galaxy/scripts/mvc/dataset/dataset-choice.js
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M client/galaxy/scripts/mvc/dataset/dataset-model.js
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M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-select-content.js
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M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
A client/galaxy/scripts/mvc/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/hda-li-edit.js
M client/galaxy/scripts/mvc/history/hda-model.js
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R client/galaxy/scripts/mvc/history/history-panel-edit-current.js
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A client/galaxy/scripts/mvc/history/history-view-edit-current.js
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M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/job/job-li.js
M client/galaxy/scripts/mvc/job/job-model.js
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M client/galaxy/scripts/mvc/library/library-folder-view.js
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M client/galaxy/scripts/mvc/library/library-library-view.js
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A client/galaxy/scripts/mvc/tool/tool-form-workflow.js
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A client/galaxy/scripts/mvc/ui/ui-buttons.js
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M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-select-ftp.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
A client/galaxy/scripts/mvc/upload/composite/composite-row.js
A client/galaxy/scripts/mvc/upload/composite/composite-view.js
A client/galaxy/scripts/mvc/upload/default/default-row.js
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M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-model.js
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M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/workflow/workflow-connector.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/nls/zh/locale.js
A client/galaxy/scripts/onload.js
A client/galaxy/scripts/polyfills.js
A client/galaxy/scripts/reports_webapp/run_stats.js
R client/galaxy/scripts/rgenetics/checkbox_and_radiobutton.js
R client/galaxy/scripts/rgenetics/helper_functions.js
R client/galaxy/scripts/rgenetics/timer.js
M client/galaxy/scripts/templates/compiled/panel_section.js
M client/galaxy/scripts/templates/compiled/tool_form.js
M client/galaxy/scripts/templates/compiled/tool_link.js
M client/galaxy/scripts/templates/compiled/tool_search.js
M client/galaxy/scripts/templates/tool_link.handlebars
R client/galaxy/scripts/tools/rgenetics/checkbox_and_radiobutton.js
R client/galaxy/scripts/tools/rgenetics/helper_functions.js
R client/galaxy/scripts/tools/rgenetics/timer.js
A client/galaxy/scripts/ui/autocom_tagging.js
A client/galaxy/scripts/ui/editable-text.js
A client/galaxy/scripts/ui/popupmenu.js
A client/galaxy/scripts/ui/scroll-panel.js
M client/galaxy/scripts/utils/add-logging.js
M client/galaxy/scripts/utils/ajax-queue.js
A client/galaxy/scripts/utils/async-save-text.js
M client/galaxy/scripts/utils/deferred.js
M client/galaxy/scripts/utils/localization.js
M client/galaxy/scripts/utils/metrics-logger.js
A client/galaxy/scripts/utils/query-string-parsing.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/trackster/util.js
M client/galaxy/scripts/viz/visualization.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/bootstrap.less
M client/galaxy/style/less/galaxy_bootstrap/variables.less
M client/galaxy/style/less/history.less
M client/galaxy/style/less/library.less
M client/galaxy/style/less/list-item.less
A client/galaxy/style/less/reports.less
M client/galaxy/style/less/trackster.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M client/grunt-tasks/install-libs.js
M client/grunt-tasks/scripts.js
M client/grunt-tasks/style.js
M client/grunt-tasks/templates.js
M client/package.json
M client/toolshed/scripts/mvc/groups/group-detail-view.js
M client/toolshed/scripts/mvc/groups/group-listrow-view.js
A client/webpack.config.js
M config/auth_conf.xml.sample
M config/datatypes_conf.xml.sample
A config/dependency_resolvers_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml
A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/ipython/config/ipython.ini.sample
M config/plugins/interactive_environments/ipython/static/js/ipython.js
M config/plugins/interactive_environments/ipython/templates/ipython.mako
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/visualizations/charts/static/build-app.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
M config/plugins/visualizations/charts/static/charts/tools.js
M config/plugins/visualizations/charts/static/library/ui-table-form.js
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M config/plugins/visualizations/charts/static/views/group.js
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M config/plugins/visualizations/charts/templates/charts.mako
A config/plugins/visualizations/csg/config/csg.xml
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A config/plugins/visualizations/csg/static/PLYLoader.js
A config/plugins/visualizations/csg/static/VTKLoader.js
A config/plugins/visualizations/csg/static/dat.gui.min.js
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A config/plugins/visualizations/csg/templates/csg.mako
A config/plugins/visualizations/graphviz/README.md
A config/plugins/visualizations/graphviz/config/graphviz.xml
A config/plugins/visualizations/graphviz/static/css/style.css
A config/plugins/visualizations/graphviz/static/img/15xvbd5.png
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A config/plugins/visualizations/graphviz/static/js/graphVis.js
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M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
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M lib/galaxy/util/plugin_config.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/template.py
M lib/galaxy/util/topsort.py
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M lib/galaxy/visualization/data_providers/genome.py
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M lib/galaxy/webapps/galaxy/api/histories.py
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M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
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M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
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M lib/galaxy/webapps/galaxy/controllers/dataset.py
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M lib/galaxy/webapps/galaxy/controllers/history.py
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M lib/galaxy/webapps/galaxy/controllers/page.py
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M lib/galaxy/webapps/galaxy/controllers/requests.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
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M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
R lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py
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M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
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M lib/galaxy/webapps/reports/buildapp.py
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M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/query.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
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A lib/galaxy/webapps/tool_shed/api/configuration.py
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M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/app.py
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M lib/galaxy/webapps/tool_shed/controllers/hg.py
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M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/webapps/tool_shed/model/migrate/check.py
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M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py
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M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py
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M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py
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M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
M lib/galaxy/webapps/tool_shed/search/repo_search.py
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M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy_ext/metadata/set_metadata.py
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R lib/pkg_resources.py
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M lib/pulsar/client/amqp_exchange_factory.py
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M lib/tool_shed/capsule/capsule_manager.py
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M lib/tool_shed/dependencies/repository/relation_builder.py
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M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
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M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py
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M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py
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M lib/tool_shed/metadata/repository_metadata_manager.py
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A static/scripts/bundled/libs.bundled.js
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R static/scripts/galaxy.menu.js
M static/scripts/galaxy.pages.js
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R static/scripts/galaxy.tools.js
R static/scripts/galaxy.ui.scrollPanel.js
R static/scripts/galaxy.workflows.js
A static/scripts/layout/masthead.js
A static/scripts/layout/menu.js
A static/scripts/layout/modal.js
A static/scripts/layout/page.js
A static/scripts/layout/panel.js
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A static/scripts/libs/common-libs.js
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M static/scripts/libs/jquery/select2.js
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M templates/webapps/galaxy/visualization/sweepster.mako
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M test/casperjs/anon-history-tests.js
M test/casperjs/api-anon-history-permission-tests.js
M test/casperjs/api-anon-history-tests.js
M test/casperjs/api-hda-tests.js
M test/casperjs/api-history-permission-tests.js
M test/casperjs/api-history-tests.js
R test/casperjs/api-workflow-tests.js
M test/casperjs/casperjs_runner.py
M test/casperjs/hda-state-tests.js
M test/casperjs/history-panel-tests.js
M test/casperjs/modules/historypanel.js
M test/casperjs/server_env.py
M test/casperjs/spaceghost.js
M test/docker/README.md
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/provision.yml
M test/docker/base/run_test_wrapper.sh
M test/docker/base/start_mysql.sh
M test/functional/test_metadata_editing.py
M test/functional/test_toolbox.py
A test/functional/tool-data/fasta_indexes.loc
M test/functional/tool-data/sample_tool_data_tables.xml
A test/functional/tools/cheetah_problem_syntax_error.xml
A test/functional/tools/cheetah_problem_unbound_var.xml
A test/functional/tools/cheetah_problem_unbound_var_input.xml
A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml
A test/functional/tools/collection_creates_dynamic_nested.xml
A test/functional/tools/collection_creates_list_of_pairs.xml
A test/functional/tools/collection_type_source.xml
R test/functional/tools/compare_bam_as_sam.xml
A test/functional/tools/create_10.xml
A test/functional/tools/dbkey_filter_input.xml
A test/functional/tools/dbkey_filter_multi_input.xml
M test/functional/tools/disambiguate_cond.xml
A test/functional/tools/maxseconds.xml
M test/functional/tools/metadata_bam.xml
M test/functional/tools/min_repeat.xml
M test/functional/tools/multi_data_param.xml
M test/functional/tools/multi_output_configured.xml
M test/functional/tools/output_format.xml
A test/functional/tools/output_format_collection.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/simple_constructs.yml
A test/functional/tools/unicode_stream.xml
M test/functional/tools/validation_repeat.xml
M test/install_and_test_tool_shed_repositories/base/test_db_util.py
M test/install_and_test_tool_shed_repositories/base/twilltestcase.py
M test/install_and_test_tool_shed_repositories/base/util.py
M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py
M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
M test/manual/workflows_scaling.py
M test/qunit/README.txt
M test/qunit/package.json
A test/qunit/test-app.js
M test/qunit/test-common.js
A test/qunit/test-data/bootstrapped.js
A test/qunit/test-data/fakeserver.js
M test/qunit/tests/galaxy-app-base.js
A test/qunit/tests/upload_dialog_tests.html
A test/qunit/tests/upload_dialog_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/tool_shed/base/test_db_util.py
M test/tool_shed/base/twilltestcase.py
M test/tool_shed/functional/test_0000_basic_repository_features.py
M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_0020_basic_repository_dependencies.py
M test/tool_shed/functional/test_0030_repository_dependency_revisions.py
M test/tool_shed/functional/test_0040_repository_circular_dependencies.py
M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_0060_workflows.py
M test/tool_shed/functional/test_0070_invalid_tool.py
M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py
M test/tool_shed/functional/test_0090_tool_search.py
M test/tool_shed/functional/test_0100_complex_repository_dependencies.py
M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py
M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
M test/tool_shed/functional/test_0130_datatype_converters.py
M test/tool_shed/functional/test_0140_tool_help_images.py
M test/tool_shed/functional/test_0150_prior_installation_required.py
M test/tool_shed/functional/test_0160_circular_prior_installation_required.py
M test/tool_shed/functional/test_0170_complex_prior_installation_required.py
M test/tool_shed/functional/test_0300_reset_all_metadata.py
M test/tool_shed/functional/test_0310_hg_push_from_api.py
M test/tool_shed/functional/test_0400_repository_component_reviews.py
M test/tool_shed/functional/test_0410_repository_component_review_access_control.py
M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
M test/tool_shed/functional/test_0430_browse_utilities.py
M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py
M test/tool_shed/functional/test_0450_skip_tool_tests.py
M test/tool_shed/functional/test_0460_upload_to_repository.py
M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py
M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py
M test/tool_shed/functional/test_0490_export_import_repositories.py
M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
M test/tool_shed/functional/test_0530_repository_admin_feature.py
M test/tool_shed/functional/test_1000_install_basic_repository.py
M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_1060_install_repository_with_workflow.py
M test/tool_shed/functional/test_1070_invalid_tool.py
M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py
M test/tool_shed/functional/test_1085_repository_dependency_handling.py
M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py
M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py
M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py
M test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py
M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py
M test/tool_shed/functional/test_1130_datatype_converters.py
M test/tool_shed/functional/test_1140_tool_help_images.py
M test/tool_shed/functional/test_1150_prior_installation_required.py
M test/tool_shed/functional/test_1160_circular_prior_installation_required.py
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M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
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M test/tool_shed/functional/test_1300_reset_all_metadata.py
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M test/tool_shed/functional/test_1430_repair_installed_repository.py
M test/tool_shed/functional/test_1440_missing_env_sh_files.py
M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py
M test/tool_shed/functional/test_1460_data_managers.py
M test/tool_shed/functional/test_1470_updating_installed_repositories.py
M test/tool_shed/functional_tests.py
M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml
M test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_objectstore.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/unittest_utils/utility.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_render.py
M test/unit/workflows/test_run_parameters.py
A test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
M tool-data/all_fasta.loc.sample
M tool-data/faseq.loc.sample
R tool-data/fastx_clipper_sequences.txt
M tool-data/liftOver.loc.sample
M tool-data/mosaik_index.loc.sample
M tool-data/ngs_sim_fasta.loc.sample
M tool-data/perm_base_index.loc.sample
M tool-data/perm_color_index.loc.sample
M tool-data/picard_index.loc.sample
M tool-data/regions.loc.sample
R tool-data/shared/ucsc/manual_builds.txt
A tool-data/shared/ucsc/manual_builds.txt.sample
M tool-data/srma_index.loc.sample
M tools/data_source/biomart.xml
M tools/data_source/biomart_test.xml
M tools/data_source/data_source.py
R tools/data_source/echo.py
R tools/data_source/echo.xml
R tools/data_source/ucsc_archaea.xml
R tools/data_source/ucsc_filter.py
R tools/data_source/ucsc_proxy.py
R tools/data_source/ucsc_proxy.xml
M tools/data_source/ucsc_tablebrowser.xml
M tools/data_source/ucsc_tablebrowser_archaea.xml
M tools/data_source/ucsc_tablebrowser_test.xml
R tools/data_source/ucsc_testproxy.xml
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.py
M tools/extract/liftOver_wrapper.xml
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/catWrapper.py
M tools/filters/cutWrapper.xml
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/sort_gtf.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/lav_to_bed.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/wig_to_bigwig.xml
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_file_browser_dev.xml
M tools/genomespace/genomespace_file_browser_prod.xml
M tools/genomespace/genomespace_file_browser_test.xml
M tools/genomespace/genomespace_importer.py
M tools/genomespace/genomespace_importer.xml
M tools/maf/interval2maf.py
M tools/maf/interval2maf.xml
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/sr_mapping/bfast_wrapper.xml
M tools/sr_mapping/fastq_statistics.xml
M tools/sr_mapping/mosaik.xml
M tools/sr_mapping/srma_wrapper.xml
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ.xml
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'origin/dev' into api.batch
Commit: 69de8d58deda7e1a627e21581e7f14a39e114847
https://github.com/galaxyproject/galaxy/commit/69de8d58deda7e1a627e21581e7f…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-02-10 (Wed, 10 Feb 2016)
Changed paths:
A .ci/first_startup.sh
M .gitignore
M .travis.yml
M Makefile
M client/GruntFile.js
M client/README.md
M client/bower.json
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/scratchbook.js
A client/galaxy/scripts/libs/bootstrap-tour.js
R client/galaxy/scripts/libs/handlebars.runtime.js
M client/galaxy/scripts/mvc/base-mvc.js
M client/galaxy/scripts/mvc/collection/collection-li-edit.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-choice.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/dataset/dataset-list.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/dataset/states.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/hda-li-edit.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hda-model.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-structure-view.js
M client/galaxy/scripts/mvc/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/job-dag.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/list/list-item.js
M client/galaxy/scripts/mvc/list/list-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-template.js
M client/galaxy/scripts/mvc/tool/tools.js
A client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/onload.js
R client/galaxy/scripts/templates/compiled/panel_section.js
R client/galaxy/scripts/templates/compiled/tool_form.js
R client/galaxy/scripts/templates/compiled/tool_link.js
R client/galaxy/scripts/templates/compiled/tool_search.js
R client/galaxy/scripts/templates/panel_section.handlebars
R client/galaxy/scripts/templates/tool_form.handlebars
R client/galaxy/scripts/templates/tool_link.handlebars
R client/galaxy/scripts/templates/tool_search.handlebars
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/frame.less
M client/galaxy/style/less/library.less
R client/galaxy/style/less/masthead.less
A client/galaxy/style/less/tour.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M client/grunt-tasks/install-libs.js
M client/grunt-tasks/style.js
R client/grunt-tasks/templates.js
A client/grunt-tasks/webpack.js
M client/package.json
M client/webpack.config.js
M config/datatypes_conf.xml.sample
M config/dependency_resolvers_conf.xml.sample
M config/galaxy.ini.sample
R config/plugins/interactive_environments/ipython/config/ipython.ini.sample
R config/plugins/interactive_environments/ipython/config/ipython.xml
R config/plugins/interactive_environments/ipython/static/js/ipython.js
R config/plugins/interactive_environments/ipython/templates/ipython.mako
R config/plugins/interactive_environments/ipython/templates/notebook.ipynb
A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
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A config/plugins/interactive_environments/phinch/config/phinch.ini.sample
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A config/plugins/interactive_environments/phinch/static/js/phinch.js
A config/plugins/interactive_environments/phinch/templates/phinch.mako
A config/plugins/tours/core.galaxy_ui.yaml
A config/plugins/tours/core.history.yaml
A config/plugins/tours/core.scratchbook.yaml
M config/plugins/visualizations/charts/Gruntfile.js
R config/plugins/visualizations/charts/static/build-app.js
M config/plugins/visualizations/charts/templates/charts.mako
M config/plugins/visualizations/scatterplot/Gruntfile.js
M config/plugins/visualizations/scatterplot/package.json
R config/plugins/visualizations/scatterplot/src/handlebars/chartcontrol.handlebars
R config/plugins/visualizations/scatterplot/src/handlebars/datacontrol.handlebars
R config/plugins/visualizations/scatterplot/src/handlebars/editor.handlebars
M config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js
M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
M config/tool_conf.xml.sample
M doc/source/admin/dependency_resolvers.rst
A doc/source/admin/framework_dependencies.rst
M doc/source/admin/index.rst
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M doc/source/project/issues.rst
A doc/source/releases/16.01.rst
M doc/source/releases/16.01_announce.rst
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M lib/galaxy/config.py
M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/chrominfo.py
A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py
A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml
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A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/metadata.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
A lib/galaxy/dependencies/conda-environment.txt
A lib/galaxy/dependencies/pinned-hashed-requirements.txt
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M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/histories.py
A lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/managers/workflows.py
R lib/galaxy/metadata
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
A lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/pulsar.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/upload_common.py
A lib/galaxy/tools/cwl/__init__.py
A lib/galaxy/tools/cwl/cwltool_deps.py
A lib/galaxy/tools/cwl/parser.py
A lib/galaxy/tools/cwl/representation.py
A lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
A lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/resolvers/__init__.py
A lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
A lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/history_query.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
A lib/galaxy/tools/parameters/wrapped_json.py
A lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/special_tools.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
A lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/panel.py
A lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/wrappers.py
A lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/directory_hash.py
M lib/galaxy/util/expressions.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/json.py
M lib/galaxy/util/multi_byte.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/odict.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/topsort.py
A lib/galaxy/util/ucsc.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/js/lib/proxy.js
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
A lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
A lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/work/context.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/pulsar/client/amqp_exchange.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/scripts/check_repositories_for_functional_tests.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M requirements.txt
M run.sh
M run_tests.sh
M scripts/binary_compatibility.py
M scripts/bootstrap_history.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/common_startup.sh
R scripts/set_metadata.py
R set_metadata.sh
A static/maps/galaxy.menu.js.map
M static/maps/layout/masthead.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/maps/layout/scratchbook.js.map
R static/maps/libs/backbone/backbone.js.map
A static/maps/libs/bootstrap-tour.js.map
R static/maps/libs/handlebars.runtime.js.map
M static/maps/mvc/base-mvc.js.map
M static/maps/mvc/collection/collection-li-edit.js.map
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/dataset/dataset-choice.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/dataset/dataset-list.js.map
M static/maps/mvc/dataset/dataset-model.js.map
M static/maps/mvc/dataset/states.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/copy-dialog.js.map
M static/maps/mvc/history/hda-li-edit.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hda-model.js.map
M static/maps/mvc/history/hdca-li-edit.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/hdca-model.js.map
M static/maps/mvc/history/history-content-model.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-structure-view.js.map
M static/maps/mvc/history/history-view-annotated.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/job-dag.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-libraryrow-view.js.map
M static/maps/mvc/list/list-item.js.map
M static/maps/mvc/list/list-view.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-template.js.map
M static/maps/mvc/tool/tools.js.map
A static/maps/mvc/tours.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/maps/mvc/ui/ui-list.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-popover.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-settings.js.map
M static/maps/mvc/user/user-model.js.map
M static/maps/mvc/user/user-quotameter.js.map
M static/maps/mvc/visualization/visualization-model.js.map
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/onload.js.map
M static/maps/utils/uploadbox.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
A static/scripts/galaxy.menu.js
M static/scripts/layout/masthead.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/layout/scratchbook.js
R static/scripts/libs/backbone/backbone.js
A static/scripts/libs/bootstrap-tour.js
R static/scripts/libs/handlebars.runtime.js
M static/scripts/mvc/base-mvc.js
M static/scripts/mvc/collection/collection-li-edit.js
M static/scripts/mvc/collection/collection-li.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/dataset/dataset-choice.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/dataset/dataset-list.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/dataset/states.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/hda-li-edit.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hda-model.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-content-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-structure-view.js
M static/scripts/mvc/history/history-view-annotated.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/job-dag.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/mvc/list/list-item.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-template.js
M static/scripts/mvc/tool/tools.js
A static/scripts/mvc/tours.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/mvc/ui/ui-list.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-settings.js
M static/scripts/mvc/user/user-model.js
M static/scripts/mvc/user/user-quotameter.js
M static/scripts/mvc/visualization/visualization-model.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/onload.js
R static/scripts/templates/compiled/panel_section.js
R static/scripts/templates/compiled/tool_form.js
R static/scripts/templates/compiled/tool_link.js
R static/scripts/templates/compiled/tool_search.js
M static/scripts/utils/uploadbox.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
A static/style/blue/bootstrap-tour.css
M static/style/blue/library.css
M static/style/blue/masthead.css
M templates/admin/reload_tool.mako
M templates/admin/tool_shed_repository/manage_repository.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/grid_base.mako
M templates/js-app.mako
M templates/show_params.mako
M templates/user/info.mako
M templates/user/username.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/history/embed.mako
M templates/webapps/galaxy/visualization/sweepster.mako
M templates/webapps/galaxy/workflow/editor_tool_form.mako
M templates/webapps/galaxy/workflow/run.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/users_last_access_date.mako
M templates/webapps/reports/users_user_disk_usage.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
M templates/webapps/reports/workflows_user_per_month.mako
M templates/webapps/tool_shed/base_panels.mako
M templates/webapps/tool_shed/repository/common.mako
M test-data/3.bam
M test/api/helpers.py
M test/api/test_tools.py
A test/api/test_tours.py
A test/api/test_workflow_missing_tool.ga
M test/api/test_workflows.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/interface.py
M test/api/workflows_format_2/main.py
M test/casperjs/api-tool-tests.js
M test/casperjs/casperjs_runner.py
M test/casperjs/modules/historyoptions.js
M test/casperjs/modules/user.js
M test/casperjs/registration-tests.js
M test/casperjs/spaceghost.js
M test/docker/base/run_test_wrapper.sh
M test/functional/test_toolbox.py
A test/functional/tools/for_workflows/1.bam
A test/functional/tools/for_workflows/mapper.xml
A test/functional/tools/for_workflows/pileup.xml
A test/functional/tools/inputs_as_json.xml
M test/functional/tools/output_action_change_format.xml
A test/functional/tools/paths_as_file.xml
M test/functional/tools/samples_tool_conf.xml
M test/qunit/test-app.js
A test/qunit/tests/masthead_tests.html
A test/qunit/tests/masthead_tests.js
A test/qunit/tests/modal_tests.html
A test/qunit/tests/modal_tests.js
A test/qunit/tests/popover_tests.html
A test/qunit/tests/popover_tests.js
A test/qunit/tests/ui_tests.html
A test/qunit/tests/ui_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/tool_shed/base/twilltestcase.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_runner_local.py
A test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/test_objectstore.py
M test/unit/test_routes.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
A test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
A test/unit/web/framework/__init__.py
A test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M tools/data_source/data_source.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/phenotype_association/linkToDavid.xml
M tools/stats/aggregate_scores_in_intervals.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into api.batch
Commit: 50b065a50adb4403ecf46f367e8b6960c586777d
https://github.com/galaxyproject/galaxy/commit/50b065a50adb4403ecf46f367e8b…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-02-17 (Wed, 17 Feb 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M config/tool_conf.xml.sample
M lib/galaxy/datatypes/text.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdas.py
A lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/workflow/modules.py
M templates/show_params.mako
A test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/import.py
M tools/data_source/microbial_import.py
M tools/data_source/microbial_import_code.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/convert_characters.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/sff_extract.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/plotting/bar_chart.py
R tools/plotting/plot_filter.py
R tools/plotting/plotter.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/sr_mapping/srma_wrapper.xml
R tools/validation/fix_errors.py
R tools/validation/fix_errors.xml
R tools/validation/fix_errors_code.py
R tools/validation/validate.py
M tools/visualization/LAJ.py
M tools/visualization/LAJ_code.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into api.batch
Commit: 7e8537b4697fd6f8b459e3ffe7f6a25ebdddb912
https://github.com/galaxyproject/galaxy/commit/7e8537b4697fd6f8b459e3ffe7f6…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-02-17 (Wed, 17 Feb 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/batch.py
Log Message:
-----------
API, batch: update for newer webob
Commit: b9744906aa4eb020ce84896a735983856d05b482
https://github.com/galaxyproject/galaxy/commit/b9744906aa4eb020ce84896a7359…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-03-07 (Mon, 07 Mar 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/api/test_api_batch.py
Log Message:
-----------
API, batch: remove simplejson refs, fix linting errors
Commit: 60936120fb27b1e6242551e55a868bf57793f3f8
https://github.com/galaxyproject/galaxy/commit/60936120fb27b1e6242551e55a86…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-03-07 (Mon, 07 Mar 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/py3_sources.txt
M .travis.yml
M Makefile
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/popup-menu.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/onload.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/fontawesome/core.less
M client/galaxy/style/less/library.less
M client/galaxy/style/less/ui/icon-btn.less
M client/grunt-tasks/style.js
M client/package.json
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/tool_conf.xml.main
M create_db.sh
M doc/source/project/organization.rst
M doc/source/releases/16.01.rst
M doc/source/releases/16.01_announce.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.json
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/search.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/dbkeys.py
M lib/galaxy/util/json.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/visualization/data_providers/basic.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/registry.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/galaxy/workflow/run.py
M lib/galaxy_utils/sequence/fasta.py
M lib/galaxy_utils/sequence/fastq.py
M lib/pulsar/client/interface.py
M lib/pulsar/client/manager.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/encoding_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_content_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/workflow_util.py
M manage_db.sh
M manage_tools.sh
M run_reports.sh
M run_tool_shed.sh
M scripts/api/common.py
M scripts/api/copy_hda_to_library_folder.py
M scripts/api/create.py
M scripts/api/data_manager_example_execute.py
M scripts/api/delete.py
M scripts/api/display.py
M scripts/api/example_watch_folder.py
M scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
M scripts/api/history_delete_history.py
M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/install_tool_shed_repositories.py
M scripts/api/library_create_folder.py
M scripts/api/library_create_library.py
M scripts/api/library_upload_dir.py
M scripts/api/library_upload_from_import_dir.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/request_type_create_from_xml.py
M scripts/api/requests_update_state.py
M scripts/api/reset_metadata_on_installed_repositories.py
M scripts/api/sample_dataset_update_status.py
M scripts/api/sample_update_state.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/update.py
M scripts/api/upload_to_history.py
M scripts/api/workflow_delete.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_execute_parameters.py
M scripts/api/workflow_import.py
M scripts/api/workflow_import_from_file_rpark.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/create_db.py
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/db_shell.py
M scripts/edam_mapping.py
M scripts/extract_dataset_part.py
M scripts/functional_tests.py
M scripts/galaxy-main
M scripts/get_platforms.py
M scripts/helper.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/manage_db.py
M scripts/manage_tools.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/create_nib_seq_loc_file.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/microbes/ncbi_to_ucsc.py
M scripts/microbes/util.py
M scripts/migrate_tools/migrate_tools.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/paster.py
A scripts/patch.sh
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tools/maf/check_loc_file.py
M scripts/tools/re_escape_output.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M static/maps/galaxy.library.js.map
M static/maps/layout/masthead.js.map
M static/maps/layout/menu.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tours.js.map
M static/maps/mvc/ui/popup-menu.js.map
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/maps/mvc/workflow/workflow-view-node.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/onload.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/galaxy.library.js
M static/scripts/layout/masthead.js
M static/scripts/layout/menu.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/ui/popup-menu.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view-node.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/onload.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
M static/style/blue/library.css
R templates/admin/requests/select_datasets_to_transfer.mako
M templates/admin/tool_shed_repository/common.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/requests/common/common.mako
M templates/webapps/galaxy/requests/common/view_request_history.mako
M templates/webapps/galaxy/requests/common/view_sample_datasets.mako
M templates/webapps/galaxy/workflow/run.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/view_repository.mako
M test/api/test_tools.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/twilltestcase.py
M test/docker/base/Dockerfile
M test/docker/base/run_test_wrapper.sh
M test/functional/test_admin_features.py
M test/functional/test_data_security.py
M test/functional/test_dataset_features.py
M test/functional/test_get_data.py
M test/functional/test_library_features.py
M test/functional/test_library_security.py
M test/functional/test_library_templates.py
M test/functional/test_metadata_editing.py
M test/functional/test_sample_tracking.py
M test/functional/test_tags.py
M test/functional/test_ucsc_table_browser.py
M test/functional/test_user_info.py
A test/functional/tools/empty_output.xml
M test/functional/tools/output_format.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/strict_shell.xml
A test/functional/tools/strict_shell_default_off.xml
A test/functional/tools/validation_empty_dataset.xml
M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
M test/qunit/tests/masthead_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/tool_shed/base/twilltestcase.py
M test/tool_shed/functional/test_0000_basic_repository_features.py
M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_0020_basic_repository_dependencies.py
M test/tool_shed/functional/test_0030_repository_dependency_revisions.py
M test/tool_shed/functional/test_0040_repository_circular_dependencies.py
M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_0060_workflows.py
M test/tool_shed/functional/test_0070_invalid_tool.py
M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py
M test/tool_shed/functional/test_0090_tool_search.py
M test/tool_shed/functional/test_0100_complex_repository_dependencies.py
M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py
M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
M test/tool_shed/functional/test_0130_datatype_converters.py
M test/tool_shed/functional/test_0140_tool_help_images.py
M test/tool_shed/functional/test_0150_prior_installation_required.py
M test/tool_shed/functional/test_0160_circular_prior_installation_required.py
M test/tool_shed/functional/test_0170_complex_prior_installation_required.py
M test/tool_shed/functional/test_0300_reset_all_metadata.py
M test/tool_shed/functional/test_0310_hg_push_from_api.py
M test/tool_shed/functional/test_0400_repository_component_reviews.py
M test/tool_shed/functional/test_0410_repository_component_review_access_control.py
M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
M test/tool_shed/functional/test_0430_browse_utilities.py
M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py
M test/tool_shed/functional/test_0450_skip_tool_tests.py
M test/tool_shed/functional/test_0460_upload_to_repository.py
M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py
M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py
M test/tool_shed/functional/test_0490_export_import_repositories.py
M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
M test/tool_shed/functional/test_0530_repository_admin_feature.py
A test/tool_shed/functional/test_0540_get_all_metadata_from_api.py
M test/tool_shed/functional/test_1000_install_basic_repository.py
M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_1060_install_repository_with_workflow.py
M test/tool_shed/functional/test_1070_invalid_tool.py
M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py
R test/tool_shed/functional/test_1085_repository_dependency_handling.py
R test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py
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A test/tool_shed/functional/test_1090_repository_dependency_handling.py
R test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py
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A test/tool_shed/functional/test_1110_install_tool_from_tool_search.py
A test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py
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R test/tool_shed/functional/test_1130_datatype_converters.py
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A test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py
R test/tool_shed/functional/test_1140_tool_help_images.py
A test/tool_shed/functional/test_1150_datatype_converters.py
R test/tool_shed/functional/test_1150_prior_installation_required.py
R test/tool_shed/functional/test_1160_circular_prior_installation_required.py
A test/tool_shed/functional/test_1160_tool_help_images.py
R test/tool_shed/functional/test_1170_complex_prior_installation_required.py
A test/tool_shed/functional/test_1170_prior_installation_required.py
A test/tool_shed/functional/test_1180_circular_prior_installation_required.py
A test/tool_shed/functional/test_1190_complex_prior_installation_required.py
M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1300_reset_all_metadata.py
M test/tool_shed/functional/test_1400_review_migration_stages.py
M test/tool_shed/functional/test_1410_update_manager.py
M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py
M test/tool_shed/functional/test_1430_repair_installed_repository.py
M test/tool_shed/functional/test_1440_missing_env_sh_files.py
M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py
M test/tool_shed/functional/test_1460_data_managers.py
M test/tool_shed/functional/test_1470_updating_installed_repositories.py
A test/tool_shed/test_data/0540_files/column_maker/column_maker.tar
A test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml
A test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar
A test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml
A test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/test_objectstore.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
A test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_parsing.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/workflows/test_render.py
M tools/data_source/upload.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into api.batch
Commit: 7d5cc9373703a522c38009b16844fae4647a8a54
https://github.com/galaxyproject/galaxy/commit/7d5cc9373703a522c38009b16844…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-05-11 (Wed, 11 May 2016)
Changed paths:
M .ci/flake8_wrapper.sh
M .ci/py3_sources.txt
M .gitignore
M CONTRIBUTORS.md
M Makefile
M README.rst
R buildbot_setup.sh
M client/README.md
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/citation/citation-model.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
R client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-drilldown.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
A client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/utils/localization.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/library.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M client/grunt-tasks/scripts.js
M client/grunt-tasks/style.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.scratchbook.yaml
M config/plugins/visualizations/charts/static/views/group.js
R config/plugins/visualizations/graphview/config/graphview.xml
R config/plugins/visualizations/graphview/static/graphview.css
R config/plugins/visualizations/graphview/static/graphview.js
R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js
R config/plugins/visualizations/graphview/templates/graphview.mako
M config/reports.ini.sample
M config/tool_data_table_conf.xml.sample
M config/tool_shed.ini.sample
M contrib/galaxy.debian-init
M contrib/galaxy.fedora-init
A contrib/galaxy_reports.fedora-init
A contrib/galaxy_supervisor.conf
A display_applications/biom/biom_simple.xml
A display_applications/iobio/bam.xml
A display_applications/iobio/vcf.xml
M doc/source/admin/framework_dependencies.rst
M doc/source/lib/modules.rst
R doc/source/lib/pulsar.client.rst
R doc/source/lib/pulsar.client.staging.rst
R doc/source/lib/pulsar.client.transport.rst
R doc/source/lib/pulsar.rst
M doc/source/releases/index.rst
R install_and_test_tool_shed_repositories.sh
M lib/galaxy/app.py
M lib/galaxy/config.py
A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/display_applications/application.py
A lib/galaxy/datatypes/molecules.py
A lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/5e5z.pdb
A lib/galaxy/datatypes/test/drugbank_drugs.cml
A lib/galaxy/datatypes/test/drugbank_drugs.inchi
A lib/galaxy/datatypes/test/drugbank_drugs.mol2
A lib/galaxy/datatypes/test/drugbank_drugs.sdf
A lib/galaxy/datatypes/test/drugbank_drugs.smi
A lib/galaxy/datatypes/test/issue1818.tabular
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist
A lib/galaxy/datatypes/test/q.fps
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py
M lib/galaxy/model/util.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
A lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/__init__.py
M lib/galaxy/tools/linters/citations.py
M lib/galaxy/tools/linters/command.py
A lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/help.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
R lib/galaxy/tools/linters/top_level.py
M lib/galaxy/tools/linters/xml_order.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
R lib/galaxy/util/dictobj.py
M lib/galaxy/util/jstree.py
M lib/galaxy/util/log/fluent_log.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/validation.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/package.json
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/scheduling_manager.py
R lib/pulsar/__init__.py
R lib/pulsar/client/__init__.py
R lib/pulsar/client/action_mapper.py
R lib/pulsar/client/amqp_exchange.py
R lib/pulsar/client/amqp_exchange_factory.py
R lib/pulsar/client/client.py
R lib/pulsar/client/config_util.py
R lib/pulsar/client/decorators.py
R lib/pulsar/client/destination.py
R lib/pulsar/client/interface.py
R lib/pulsar/client/job_directory.py
R lib/pulsar/client/manager.py
R lib/pulsar/client/object_client.py
R lib/pulsar/client/path_mapper.py
R lib/pulsar/client/setup_handler.py
R lib/pulsar/client/staging/__init__.py
R lib/pulsar/client/staging/down.py
R lib/pulsar/client/staging/up.py
R lib/pulsar/client/transport/__init__.py
R lib/pulsar/client/transport/curl.py
R lib/pulsar/client/transport/poster.py
R lib/pulsar/client/transport/requests.py
R lib/pulsar/client/transport/ssh.py
R lib/pulsar/client/transport/standard.py
R lib/pulsar/client/util.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
R lib/tool_shed/scripts/api/add_repository_registry_entry.py
R lib/tool_shed/scripts/api/common.py
R lib/tool_shed/scripts/api/create_categories.py
R lib/tool_shed/scripts/api/create_users.py
R lib/tool_shed/scripts/api/export.py
R lib/tool_shed/scripts/api/get_filtered_repository_revisions.py
R lib/tool_shed/scripts/api/import_capsule.py
R lib/tool_shed/scripts/api/remove_repository_registry_entry.py
R lib/tool_shed/scripts/api/reset_metadata_on_repositories.py
R lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
R lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
R lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh
R lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
R lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py
R lib/tool_shed/scripts/check_repositories_for_functional_tests.py
R lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
R lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
R lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
R lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
R lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M run.sh
M run_reports.sh
M run_tests.sh
M run_tool_shed.sh
M scripts/bootstrap_history.py
M scripts/common_startup.sh
M scripts/functional_tests.py
M scripts/summarize_timings.py
A scripts/tool_shed/api/add_repository_registry_entry.py
A scripts/tool_shed/api/common.py
A scripts/tool_shed/api/create_categories.py
A scripts/tool_shed/api/create_users.py
A scripts/tool_shed/api/export.py
A scripts/tool_shed/api/get_filtered_repository_revisions.py
A scripts/tool_shed/api/import_capsule.py
A scripts/tool_shed/api/remove_repository_registry_entry.py
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R test/tool_shed/functional/test_0060_workflows.py
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R test/tool_shed/functional/test_0490_export_import_repositories.py
R test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
R test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
R test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
R test/tool_shed/functional/test_0530_repository_admin_feature.py
R test/tool_shed/functional/test_0540_get_all_metadata_from_api.py
R test/tool_shed/functional/test_1000_install_basic_repository.py
R test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
R test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
R test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
R test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
R test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
R test/tool_shed/functional/test_1060_install_repository_with_workflow.py
R test/tool_shed/functional/test_1070_invalid_tool.py
R test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py
R test/tool_shed/functional/test_1090_repository_dependency_handling.py
R test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py
R test/tool_shed/functional/test_1110_install_tool_from_tool_search.py
R test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py
R test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py
R test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py
R test/tool_shed/functional/test_1150_datatype_converters.py
R test/tool_shed/functional/test_1160_tool_help_images.py
R test/tool_shed/functional/test_1170_prior_installation_required.py
R test/tool_shed/functional/test_1180_circular_prior_installation_required.py
R test/tool_shed/functional/test_1190_complex_prior_installation_required.py
R test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
R test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
R test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
R test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
R test/tool_shed/functional/test_1300_reset_all_metadata.py
R test/tool_shed/functional/test_1400_review_migration_stages.py
R test/tool_shed/functional/test_1410_update_manager.py
R test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py
R test/tool_shed/functional/test_1430_repair_installed_repository.py
R test/tool_shed/functional/test_1440_missing_env_sh_files.py
R test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py
R test/tool_shed/functional/test_1460_data_managers.py
R test/tool_shed/functional/test_1470_updating_installed_repositories.py
R test/tool_shed/functional_tests.py
R test/tool_shed/test_data/0460_files/repository_dependencies.xml
R test/tool_shed/test_data/0460_files/repository_dependencies_in_root.tar
R test/tool_shed/test_data/0460_files/repository_dependencies_in_subfolder.tar
R test/tool_shed/test_data/0460_files/tool_dependencies.xml
R test/tool_shed/test_data/0460_files/tool_dependencies_in_root.tar
R test/tool_shed/test_data/0460_files/tool_dependencies_in_subfolder.tar
R test/tool_shed/test_data/0480_files/tool_dependencies.xml
R test/tool_shed/test_data/0540_files/column_maker/column_maker.tar
R test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml
R test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar
R test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml
R test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml
R test/tool_shed/test_data/1420_files/binary_tarballs/atlas.tar
R test/tool_shed/test_data/1420_files/binary_tarballs/boost.tar
R test/tool_shed/test_data/1420_files/binary_tarballs/bzlib.tar
R test/tool_shed/test_data/1420_files/binary_tarballs/lapack.tar
R test/tool_shed/test_data/1420_files/binary_tarballs/numpy.tar
R test/tool_shed/test_data/1420_files/binary_tarballs/rdkit.tar
R test/tool_shed/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml
R test/tool_shed/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml
R test/tool_shed/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml
R test/tool_shed/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml
R test/tool_shed/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml
R test/tool_shed/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml
R test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml
R test/tool_shed/test_data/1440_files/dependency_definition/tool_dependencies.xml
R test/tool_shed/test_data/1460_files/data_manager_files/test_data_manager.tar
R test/tool_shed/test_data/bed_to_gff_converter/bed_to_gff_converter.tar
R test/tool_shed/test_data/bismark/bismark.tar
R test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml
R test/tool_shed/test_data/blast/blast_datatypes.tar
R test/tool_shed/test_data/blast/blastxml_to_top_descr.tar
R test/tool_shed/test_data/bwa/bwa_base.tar
R test/tool_shed/test_data/bwa/bwa_color.tar
R test/tool_shed/test_data/bwa/complex/bwa_base.tar
R test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml
R test/tool_shed/test_data/bwa/complex/tool_dependencies.xml
R test/tool_shed/test_data/column_maker/column_maker.tar
R test/tool_shed/test_data/convert_chars/convert_chars.tar
R test/tool_shed/test_data/emboss/0470_files/emboss_complex_dependency.tar
R test/tool_shed/test_data/emboss/0470_files/tool_dependencies.xml
R test/tool_shed/test_data/emboss/datatypes/datatypes_conf.xml
R test/tool_shed/test_data/emboss/emboss.tar
R test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml
R test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml
R test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml
R test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml
R test/tool_shed/test_data/filtering/README
R test/tool_shed/test_data/filtering/filtering_0000.txt
R test/tool_shed/test_data/filtering/filtering_1.1.0.tar
R test/tool_shed/test_data/filtering/filtering_2.2.0.tar
R test/tool_shed/test_data/filtering/filtering_test_data.tar
R test/tool_shed/test_data/filtering/readme.txt
R test/tool_shed/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga
R test/tool_shed/test_data/freebayes/freebayes.tar
R test/tool_shed/test_data/freebayes/freebayes.xml
R test/tool_shed/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml
R test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml
R test/tool_shed/test_data/freebayes/sam_fa_indices.loc.sample
R test/tool_shed/test_data/freebayes/tool_data_table_conf.xml.sample
R test/tool_shed/test_data/freebayes/tool_dependencies.xml
R test/tool_shed/test_data/htseq_count/htseq_count.tar
R test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar
R test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml
R test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar
R test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar
R test/tool_shed/test_data/readme.txt
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R test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz
R test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz
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M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/test_HistoryContentsManager.py
A test/unit/shed_unit/__init__.py
A test/unit/shed_unit/test_fabric_util.py
A test/unit/shed_unit/test_td_common_util.py
A test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_lazy_process.py
M test/unit/test_objectstore.py
R test/unit/tool_shed_unit_tests/__init__.py
R test/unit/tool_shed_unit_tests/test_fabric_util.py
R test/unit/tool_shed_unit_tests/test_td_common_util.py
R test/unit/tool_shed_unit_tests/test_tool_panel_manager.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_select_parameters.py
M test/unit/workflows/test_modules.py
A tool-data/bam_iobio.loc.sample
A tool-data/biom_simple_display.loc.sample
A tool-data/vcf_iobio.loc.sample
M tools/data_source/biomart.xml
M tools/data_source/upload.py
M tools/filters/trimmer.xml
M tools/stats/grouping.py
M tools/stats/grouping.xml
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into api.batch
Commit: 7bfd6410eb8b66a89045e13ca00f6a11572fa9d8
https://github.com/galaxyproject/galaxy/commit/7bfd6410eb8b66a89045e13ca00f…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-06-23 (Thu, 23 Jun 2016)
Changed paths:
M .ci/py3_sources.txt
M Makefile
M README.rst
M client/bower.json
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/libs/backbone.js
M client/galaxy/scripts/libs/bootstrap-tour.js
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/jquery/jquery.migrate.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
R client/galaxy/scripts/libs/tracekit.js
M client/galaxy/scripts/libs/underscore.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
R client/galaxy/scripts/mvc/tool/tool-template.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/popup-menu.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select.js
M client/galaxy/scripts/ui/hoverhighlight.js
M client/galaxy/scripts/ui/loading-indicator.js
M client/galaxy/scripts/ui/mode-button.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.js
M client/galaxy/scripts/utils/metrics-logger.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/frame.less
M client/galaxy/style/less/library.less
M client/galaxy/style/less/ui.less
M client/grunt-tasks/install-libs.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/tool_conf.xml.sample
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M doc/source/dev/faq.rst
M doc/source/releases/16.01.rst
A doc/source/releases/16.04.rst
M doc/source/releases/16.04_announce.rst
A doc/source/releases/16.07_announce.rst
M doc/source/releases/index.rst
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/NuBBE_1_obabel_3D.pdbqt
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
A lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
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M test/shed_functional/functional/test_0170_complex_prior_installation_required.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_0310_hg_api_features.py
M test/shed_functional/functional/test_1000_install_basic_repository.py
M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py
M test/shed_functional/functional/test_1190_complex_prior_installation_required.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py
M test/shed_functional/functional_tests.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_run_parameters.py
M tool_list.py
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/import.py
M tools/data_source/microbial_import.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_concat_fasta.xml
M tools/filters/axt_to_fasta.xml
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav.xml
M tools/filters/bed2gff.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/bed_to_gff_converter.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff2bed.xml
M tools/filters/gff_to_bed_converter.py
M tools/filters/gtf2bedgraph.xml
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/sff_extract.py
M tools/filters/sorter.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/filtering.xml
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/stats/gsummary.xml
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into api.batch
Commit: 6825f4c5f48ebcff0d7ce15e6fc4adc6df5dfc43
https://github.com/galaxyproject/galaxy/commit/6825f4c5f48ebcff0d7ce15e6fc4…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-07-14 (Thu, 14 Jul 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/batch.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M test/api/test_api_batch.py
Log Message:
-----------
API, batch: add allowed_list to narrow use
- only allows processing batch calls to the urls that match the regexs
in allowed_list controlling/decreasing the scope of the middleware
Commit: 15a686e316a3d47bcc120073dedf1ed659eb0cfa
https://github.com/galaxyproject/galaxy/commit/15a686e316a3d47bcc120073dedf…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-07-28 (Thu, 28 Jul 2016)
Changed paths:
M .ci/flake8_blacklist.txt
A .ci/flake8_lint_include_list.txt
A .ci/flake8_wrapper_imports.sh
M .ci/py3_sources.txt
M .gitignore
M .travis.yml
M Makefile
A client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/ui.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/object_store_conf.xml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample
A config/plugins/interactive_environments/neo/config/neo.ini.sample
A config/plugins/interactive_environments/neo/config/neo.xml
A config/plugins/interactive_environments/neo/static/js/neo.js
A config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/library/datasets.js
M config/plugins/visualizations/charts/static/library/jobs.js
M config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/library/ui-table-form.js
M config/plugins/visualizations/charts/static/models/chart.js
M config/plugins/visualizations/charts/static/models/config.js
R config/plugins/visualizations/charts/static/models/group.js
R config/plugins/visualizations/charts/static/models/groups.js
M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
M config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/group.js
A config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/graphviz/config/graphviz.xml
M config/plugins/visualizations/graphviz/static/js/graphVis.js
M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
M config/plugins/visualizations/graphviz/templates/graphviz.mako
M config/tool_data_table_conf.xml.sample
A config/tool_destinations.yml.sample
A display_applications/igv/bigwig.xml
A display_applications/ucsc/trackhub.xml
A doc/source/admin/grt.rst
M doc/source/admin/index.rst
M doc/source/admin/interactive_environments.rst
M doc/source/dev/index.rst
A doc/source/dev/interactive_environments.rst
M doc/source/lib/galaxy.objectstore.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/molecules.py
A lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/actions/post.py
A lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/managers/base.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
A lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/objectstore/__init__.py
A lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
A lib/galaxy/tools/toolbox/requirements.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/js/lib/proxy.js
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
A lib/galaxy/webapps/reports/controllers/history.py
A lib/galaxy/webapps/reports/controllers/tools.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/util/shed_util_common.py
M run_tests.sh
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
M scripts/api/history_delete_history.py
M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/library_create_folder.py
M scripts/api/library_create_library.py
M scripts/api/library_upload_from_import_dir.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/request_type_create_from_xml.py
M scripts/api/requests_update_state.py
M scripts/api/sample_dataset_update_status.py
M scripts/api/sample_update_state.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/upload_to_history.py
M scripts/api/workflow_delete.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_import.py
M scripts/api/workflow_import_from_file_rpark.py
M scripts/bootstrap_history.py
M scripts/build_toolbox.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
A scripts/communication/communication_server.py
A scripts/communication/template/communication.css
A scripts/communication/template/communication.html
A scripts/communication/template/communication.js
M scripts/data_libraries/build_whoosh_index.py
M scripts/db_shell.py
M scripts/drmaa_external_runner.py
M scripts/fetch_eggs.py
A scripts/grt.py
A scripts/grt.yml.sample
M scripts/set_dataset_sizes.py
M setup.cfg
A static/maps/layout/generic-nav-view.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/hdca-li-edit.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/hdca-model.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/tool/tool-template.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
A static/scripts/layout/generic-nav-view.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/mvc/collection/collection-li.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/tool/tool-template.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
A static/style/base.css
M static/style/blue/base.css
M templates/admin/impersonate.mako
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/manage_repository.mako
M templates/admin/tool_shed_repository/preview_repository.mako
M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/ind_share_base.mako
M templates/js-app.mako
M templates/user/change_password.mako
A templates/user/communication_settings.mako
M templates/user/index.mako
M templates/webapps/galaxy/history/grid.mako
A templates/webapps/reports/history_and_dataset_per_user.mako
A templates/webapps/reports/history_and_dataset_type.mako
A templates/webapps/reports/history_per_user.mako
M templates/webapps/reports/index.mako
A templates/webapps/reports/tool_error_messages.mako
A templates/webapps/reports/tool_execution_time.mako
A templates/webapps/reports/tool_execution_time_per_month.mako
A templates/webapps/reports/tools_and_job_state.mako
A templates/webapps/reports/tools_and_job_state_per_month.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/export_repository.mako
A test-data/neostore.zip
M test/api/helpers.py
M test/api/test_datasets.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/base/driver_util.py
M test/base/twilltestcase.py
A test/functional/tools/identifier_collection.xml
A test/functional/tools/output_filter_exception_1.xml
M test/functional/tools/samples_tool_conf.xml
A test/integration/test_resolvers.py
M test/qunit/tests/ui_tests.js
M test/qunit/tests/upload_dialog_tests.js
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/shed_functional/functional_tests.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
A test/unit/datatypes/test_data.py
A test/unit/jobs/dynamic_tool_destination/__init__.py
A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml
A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/data/test.empty
A test/unit/jobs/dynamic_tool_destination/data/test.fasta
A test/unit/jobs/dynamic_tool_destination/data/test1.full
A test/unit/jobs/dynamic_tool_destination/data/test3.full
A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml
A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml
A test/unit/jobs/dynamic_tool_destination/data/test_users.yml
A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
A test/unit/jobs/dynamic_tool_destination/ymltests.py
M test/unit/managers/base.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_toolbox.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/gsummary.xml
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into api.batch
Commit: ff261296673095410eefdcce8c27cf2697c318bc
https://github.com/galaxyproject/galaxy/commit/ff261296673095410eefdcce8c27…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-07-29 (Fri, 29 Jul 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/batch.py
M test/api/test_api_batch.py
Log Message:
-----------
API, batch: update docs and test, cleanup
Commit: 45c95061d3e76c450cfb6a52e85e84f91927b6dc
https://github.com/galaxyproject/galaxy/commit/45c95061d3e76c450cfb6a52e85e…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-07-29 (Fri, 29 Jul 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/jobs.py
Log Message:
-----------
API, jobs: have create return galactic 501
- Uses MessageException version which can be parsed as 501
Commit: e781aaa2aa6f12b949d301957dddc61f7b1751ac
https://github.com/galaxyproject/galaxy/commit/e781aaa2aa6f12b949d301957ddd…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-08-02 (Tue, 02 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M Makefile
M client/bower.json
A client/galaxy/scripts/libs/jquery.complexify.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/style/less/base.less
M client/grunt-tasks/install-libs.js
M client/webpack.config.js
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/version.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M run_tests.sh
M scripts/bootstrap_history.py
M scripts/nosetests.py
A static/maps/libs/jquery.complexify.js.map
M static/maps/libs/jquery/jquery.js.map
M static/maps/libs/raven.js.map
M static/maps/mvc/history/options-menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/libs/jquery.complexify.js
M static/scripts/libs/jquery/jquery.js
M static/scripts/libs/raven.js
M static/scripts/mvc/history/options-menu.js
M static/style/blue/base.css
M templates/user/change_password.mako
M templates/user/register.mako
M test/unit/tools/test_tool_deps.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into api.batch
Commit: 9de06e1594e8ccff37008bd2700ff4dc38b76f56
https://github.com/galaxyproject/galaxy/commit/9de06e1594e8ccff37008bd2700f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-23 (Tue, 23 Aug 2016)
Changed paths:
M lib/galaxy/web/framework/base.py
A lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/buildapp.py
A test/api/test_api_batch.py
A test/casperjs/api-batch-tests.js
Log Message:
-----------
Merge pull request #1768 from carlfeberhard/api.batch
Api batch endpoint
Compare: https://github.com/galaxyproject/galaxy/compare/b16a9403de99...9de06e1594e8
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