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Author SHA1 Message Date
Björn Grüning 08fb160b38 Merge pull request #2481 from martenson/fix-html-sharing 
[16.04] fix markup for button links on sharing template
 2016-06-10 21:47:07 +02:00
Nicola Soranzo 14844e48eb Merge branch 'release_16.01' into release_16.04 
Conflicts:
	lib/galaxy/jobs/runners/drmaa.py
 2016-06-10 17:31:10 +01:00
Martin Cech dbbf1edef3 Merge pull request #2484 from nsoranzo/release_16.01_fix_for_4a024b882f504aded1db32f1ed056f7c9109d218 
[16.01] Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries
 2016-06-10 12:06:41 -04:00
Nicola Soranzo 933f42619e Log all failed job status checks 2016-06-10 12:34:48 +01:00
Nicola Soranzo 7c40c85034 Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries 2016-06-10 12:31:00 +01:00
Martin Cech 7610f82a42 fix markup for button links on sharing template 
(ff would fail to generate images)
turn of autocomplete
 2016-06-09 15:38:57 -04:00
Nicola Soranzo 04863c833b Merge pull request #2473 from martenson/port-value-to-display 
[16.04] Avoid empty strings when converting values to display text
 2016-06-08 20:48:39 +01:00
guerler 4cd2af860f Avoid empty strings when converting values to display text 2016-06-08 15:17:15 -04:00
Martin Cech befe35456a Merge pull request #2471 from guerler/fix_workflow_display 
[16.04] Prevent missing display to text values in workflow preview
 2016-06-08 15:13:55 -04:00
guerler d2be9dc98d Prevent missing display to text values in workflow preview 2016-06-08 14:20:58 -04:00
Martin Cech 8983e43040 Merge pull request #2466 from nsoranzo/release_16.04_fix_for_2463 
[16.04] Delay import of DrmaaSessionFactory after runner initialization
 2016-06-08 10:44:25 -04:00
Nicola Soranzo 9e5419f58c Delay import of DrmaaSessionFactory after runner initialization 
Fix issue #2463, i.e. the regression introduced in #2102 by which Galaxy
no longer respects <param id="drmaa_library_path"> in config/job_conf.xml ,
preventing the use of multiple drmaa runners.
 2016-06-08 13:46:56 +01:00
John Chilton 10a3f23de2 Merge pull request #2459 from blankenberg/metadata-id-fix 
[16.04] Do not encode dict items that start with 'metadata_' in return value of api/tools/create.
 2016-06-07 15:35:13 -04:00
Martin Cech 37a4915992 Merge pull request #2458 from guerler/fix_process_data 
[16.04] Filter missing inputs when processing data
 2016-06-07 13:27:41 -04:00
Daniel Blankenberg 42739c88c8 Add test for failing handling of BIOM1 metadata. 2016-06-07 12:02:09 -04:00
Daniel Blankenberg edca79a0cf Do not encode dict items that start with 'metadata_' in return value of api/tools/create. 
Resolves #2423, #2137, and https://github.com/galaxyproject/tools-iuc/pull/770. However, this whole act of encoding by key.endswith('_id') is very messy.
 2016-06-06 16:12:32 -04:00
guerler b97c796445 Filter missing inputs when processing data 2016-06-06 13:23:56 -04:00
Dannon Baker 58f3f5c7dd Merge pull request #2447 from nsoranzo/release_16.04_fix_for_2432 
[16.04] Overwrite the correct part of stderr
 2016-06-02 11:05:27 -04:00
Nicola Soranzo 7cb527ac59 Overwrite the correct part of stderr 
- Skip partial line
- Seek back to the correct position after readlines()
- Use the same approach in __check_memory_limit()
 2016-06-02 15:32:36 +01:00
Dannon Baker ceb825bea8 Merge pull request #2432 from natefoo/job-output-memory-fix 
[16.04] Only scan the last 16 MB of a job's stderr for slurm memory warning messages
 2016-05-31 12:46:24 -04:00
Nate Coraor dcb28e0950 Fix linting error 2016-05-31 11:58:57 -04:00
Nate Coraor 214e757d81 Only scan the last 16 MB of a job's stderr for slurm memory warning 
messages.
 2016-05-31 11:42:36 -04:00
John Chilton 6094990e43 Merge pull request #2424 from martenson/port-exceptionwrap-16.04 
[16.04] wrap bare str exceptions
 2016-05-26 18:59:43 -04:00
Martin Cech fe64a8198b fix the mess made with mass edit 2016-05-26 16:45:36 -04:00
Martin Cech a27e86786a wrap bare str raises with generic Exception() 
as Pyton 2.7 does not support bare str
 2016-05-26 16:45:31 -04:00
Dannon Baker c63bf911bc Merge pull request #2389 from jmchilton/checkers_restore 
[16.04] Provide backward compatible galaxy.datatypes.checkers module...
 2016-05-25 16:40:33 -04:00
John Chilton 71f9d96216 Remove HTML_CHECK_LINES from checkers export. 
As suggested by @nsoranzo and @dannon, we will restore if and only if someone finds a datatype that uses it.
 2016-05-25 16:29:02 -04:00
Nicola Soranzo 5db5e13958 Merge branch 'release_16.01' into release_16.04 
Conflicts:
	test/unit/managers/test_HistoryManager.py
 2016-05-25 16:23:07 +01:00
Daniel Blankenberg 7dcf850ed5 Merge pull request #2402 from natefoo/slurm-fixes 
[16.04] Catch all exceptions in slurm's _complete_terminal_job() to prevent looping job completion
 2016-05-25 09:51:06 -04:00
John Chilton 47a6516096 Merge pull request #2407 from carlfeberhard/fix.most_recently_used 
[16.01] API, history: fix order in most_recently_used
 2016-05-25 09:41:32 -04:00
carlfeberhard 2a29e92ef9 API, history: fix order in most_recently_used 
- Fix ascending order used in HistoryManager.most_recent to descending
- Slightly update the docs to reflect actual value better
- Add tests
 2016-05-24 17:08:08 -04:00
Nate Coraor b6d65da83d Fix linting error 2016-05-24 15:13:39 -04:00
Nate Coraor 5fbb65e503 Catch all exceptions in slurm's _complete_terminal_job() to prevent 
looping job completion
 2016-05-24 14:03:19 -04:00
John Chilton 66947c20ef Provide backward-compatible galaxy.datatypes.checkers module. 
xref http://dev.list.galaxyproject.org/STACKS-error-td4669428.html
 2016-05-23 10:21:08 -04:00
John Chilton 8d0e1c51df Fix Pulsar remote metadata temp files for https://github.com/galaxyproject/galaxy/pull/1688/commits/a2e31403753c407e7f6966b69b157e32f5f3ef8a 
xref #1688 and https://github.com/galaxyproject/galaxy/commit/2a90811ea37e1361d58538f11500643ff1f537e5
 2016-05-20 10:22:41 -04:00
Nicola Soranzo e194c64e26 Merge pull request #2377 from dannon/stray_print_breaking_sharing 
[16.04] Remove stray print left in workflow sharing which actually throws an …
 2016-05-19 15:37:07 +02:00
Dannon Baker 5f8b9e04ba Remove stray print left in workflow sharing which actually throws an exception and breaks sharing when item_name is unicode. 2016-05-19 08:46:36 -04:00
Dannon Baker d926b3f509 Merge pull request #2373 from martenson/fix=release-docs 
[16.04] remove the comment that breaks toc generation
 2016-05-18 15:01:41 -04:00
Martin Cech ad3a65a688 remove the comment that breaks toc generation 2016-05-18 14:54:48 -04:00
John Chilton 99c8f54a77 Update version to 16.04 v16.04 2016-05-18 07:43:10 -04:00
John Chilton 8195d81739 Merge pull request #2353 from martenson/16.04_release_notes 
[16.04] Release notes for 16.04
 2016-05-18 07:28:01 -04:00
John Chilton f887c059a2 Expand 16.04 highlights... 2016-05-18 07:26:25 -04:00
Martin Cech 9d5bf7b62d minor release notes touch 2016-05-17 15:56:50 -04:00
Martin Cech 50e596fb1b reorder sections, un-quote bitbucket paragraph 2016-05-17 15:51:23 -04:00
Martin Cech afb9027482 final touch of release notes from my side 2016-05-17 15:48:00 -04:00
Martin Cech cc86096c83 Merge pull request #2362 from dannon/slurm_complete_job_fix 
[16.04] Fix for slurm's complete_terminal_job where if unable to inspect the …
 2016-05-16 18:26:46 -04:00
Martin Cech 62b6eaa92a Merge branch '16.04_release_notes' of https://github.com/martenson/galaxy into 16.04_release_notes 2016-05-16 17:08:32 -04:00
Martin Cech 3b7f6cb777 add some highlights, seems tough for this release 2016-05-16 17:07:32 -04:00
Dannon Baker 2390da54ae Fix for slurm's complete_terminal_job where if unable to inspect the failed job with scontrol drmaajobrunner's _complete_terminal_job was called twice. 2016-05-16 11:48:33 -04:00
John Chilton 38209bbbac Merge pull request #2350 from natefoo/fix-ajs-red-herring 
[16.04] Properly handle AsynchronousJobState objects in the job runner work queue
 2016-05-14 15:30:38 -04:00