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Author SHA1 Message Date
Martin Cech cb53c7390e Merge pull request #8085 from dannon/fix-multipanel-history-search 
[19.01] Fix multipanel history search.
 2019-06-05 15:04:58 -04:00
Marius van den Beek 2a19b2151f Merge pull request #8097 from bgruening/fix_macro_backport_19.01 
[19.01] Fix nested macro/token expansion
 2019-06-05 15:48:00 +02:00
Nicola Soranzo fc2bff63b3 Remove recursion from `expand_nested_tokens()` 
Also add test for recursive nested token.
 2019-06-05 13:54:18 +02:00
mvdbeek 574d9ad1f5 Fix nested macro/token expansion on python 3 
I noticed that in multiqc @ESCAPE_IDENTIFIER@ wasn't being replaced.
It's surprising that this didn't cause any issues on python 2,
but might have to do with the iteration order changes.
 2019-06-05 13:44:46 +02:00
Dannon Baker 8edffb118a const, formatting 2019-06-04 11:47:21 -04:00
Dannon Baker b732950c70 Actually search in onfirstsearch of history search in multipanel 2019-06-04 11:46:24 -04:00
Dannon Baker edcce00aab Fix multipanel history search. 2019-06-04 11:46:24 -04:00
Nicola Soranzo fd02b745c3 Merge branch 'release_18.09' into release_19.01 2019-06-03 18:06:45 +01:00
Björn Grüning 2f21e73ff4 [18.09] Backport 8023: Fix ColumnSetAction post job action (#8069) 
[18.09] Backport 8023: Fix ColumnSetAction post job action
 2019-06-01 10:50:02 +02:00
mvdbeek 44256971eb Fix ColumnSetAction post job action 
If columns are specified as integers this would fail currently.
Reported by Peter Briggs on the [mailing list](https://lists.galaxyproject.org/archives/list/galaxy-dev@lists.galaxyproject.org/thread/PXLCVKIZ5LW3MLI6333PFMANYGOCDLD2/)
 2019-05-31 10:44:45 +02:00
Björn Grüning da0f5f290c [19.01] Document the handler max_grab config param (#8060) 
[19.01] Document the handler max_grab config param
 2019-05-30 17:16:06 +02:00
Nate Coraor dfb591caf6 Document the handler max_grab config param 2019-05-30 09:18:42 -04:00
Björn Grüning d25dcc4fe4 [19.01] Fixes for job handler and worklflow scheduler self-assignment grab limits (#8059) 
[19.01] Fixes for job handler and worklflow scheduler self-assignment grab limits
 2019-05-30 09:30:40 +02:00
Nate Coraor c0c39d5969 Default the maximum grab limit for handler database preassignment 
methods to unlimited as intended. Document the config param.
 2019-05-29 15:25:55 -04:00
John Chilton 374526357f Merge pull request #8032 from mvdbeek/backport_param_as_output_fix 
[19.01] Backport #7799 Skip recording workflow outputs for input parameters
 2019-05-24 09:29:41 -04:00
mvdbeek e988fdee87 Skip recording workflow outputs for input parameters 
These can come in as a literal parameter value, or as a dictionary like
{'id': 'encoded_id', 'src': 'hda'}, none of which is quite right.
 2019-05-24 10:45:18 +02:00
Marius van den Beek c60613cb9b Merge pull request #8002 from natefoo/pgcleanup-purge-user-fix 
[19.01] Fix use of pgcleanup's purge_deleted_users when there are no users to purge
 2019-05-18 10:16:25 +02:00
Nate Coraor bd06628a3d Fix use of pgcleanup's purge_deleted_users when there are no users to 
purge
 2019-05-17 16:37:19 -04:00
Marius van den Beek 82052db4db Merge pull request #7999 from natefoo/pgcleanup-work-mem-fix 
[19.01] Fix variable name for work mem in pgcleanup.py
 2019-05-17 19:28:59 +02:00
Nate Coraor fc027182f7 Fix variable name for work mem in pgcleanup.py 2019-05-17 11:30:40 -04:00
Nicola Soranzo 9b9daffd41 Merge pull request #7766 from natefoo/slurmstepd 
[19.01] Catch and filter *all* Slurm cgroup-related messages
 2019-05-07 15:57:31 +01:00
Dannon 7130ae9411 Merge pull request #7824 from tmcgowan/issue_7758 
[19.01] Possible fix for WSGI process issue #7758
 2019-05-07 09:00:37 -04:00
John Chilton ea398cbdfd Merge pull request #7857 from natefoo/fix-job-config-get-default 
[19.01] Fix the job config's shared _get_default() method
 2019-05-04 11:40:41 -04:00
John Chilton b2eb394a7d Merge pull request #7870 from jmchilton/1901_fix_plugin 
[19.01] Fix bug preventing handler runner plugin handling.
 2019-05-02 11:39:39 -04:00
Dannon d7b1479314 Merge pull request #7872 from mvdbeek/allow_not_uploading_optional_files 
[19.01] Allow composite upload if all non-optional files are selected
 2019-05-02 11:13:37 -04:00
mvdbeek a52f3f30d8 Allow upload if all non-optional files are selected 
Fixes https://github.com/galaxyproject/galaxy/issues/5326
 2019-05-02 14:13:31 +02:00
Björn Grüningandjmchilton 175865740c Update test/unit/jobs/test_job_configuration.py 
Co-Authored-By: jmchilton <jmchilton@gmail.com>
 2019-05-02 08:08:23 -04:00
John Chilton 98fa693a7c Fix bug preventing handler runner plugin handling. 2019-05-01 15:09:25 -04:00
John Chilton f6e54b49db Add job configuration test for resource groups and handler plugins. 2019-05-01 15:09:24 -04:00
Nate Coraor 1410e8cf93 Fix tests broken by previous commit, also, handler defaults are never 
required (preassign uses all defined handlers if no default is set).
 2019-04-30 15:01:45 -04:00
Nate Coraor 1994c3598f Merge pull request #7855 from mvdbeek/fix_workflow_extraction 
[19.01] Fix workflow extraction for jobs whose JobToDatasetOutputAssociation references a discovered dataset
 2019-04-30 14:48:40 -04:00
Nicola Soranzo 170bd027cd [19.01] Use just the env name when checking `CONDA_DEFAULT_ENV` (#7853) 
[19.01] Use just the env name when checking ``CONDA_DEFAULT_ENV``
 2019-04-30 19:36:06 +01:00
Nate Coraor 7ac30ec590 Fix the job config's shared _get_default() method so it does the correct 
thing for destinations
 2019-04-30 14:14:18 -04:00
Nicola Soranzo 96ed324131 Ensure that also $CONDA_DEFAULT_ENV is just the env name 
That's not the case e.g. for conda 4.1.1 when using `conda_exec` not inside `conda_prefix`.
 2019-04-30 17:49:49 +01:00
mvdbeek 4af1c0a6cc Fix workflow extraction for jobs whose JobToDatasetOutputAssociation references a discovered dataset 
To test this run a tool that generates discovered datsets twice,
with the second run taking the first output as input.
 2019-04-30 18:31:19 +02:00
mvdbeek 8fd0652d76 CONDA_DEFAULT_NAME is just the env name 
This will still write the conda activate part out multiple times,
but fix the check that would otherwise lead to repeated activation
of the conda env. Fixes the slowness reported in https://github.com/galaxyproject/galaxy/issues/7849
 2019-04-30 14:02:42 +02:00
Marius van den Beek 7d8ec2b5fd Merge pull request #7850 from nsoranzo/release_19.01_backport_7696 
[19.01] Backport of #7696
 2019-04-30 10:03:58 +02:00
Aysam Guerler ce6ee86dec Merge pull request #7845 from dannon/fix_trackster_overflow_issue 
[19.01] Fix trackster issue w/ constraining (overflow:non-visible) containers
 2019-04-29 17:39:16 -04:00
Bérénice Batut 3dc68dbe92 Add extra column metadata check for minimal biom1 file 2019-04-29 18:59:25 +01:00
Dannon Baker f09bc22459 Fix trackster issue w/ constraining (overflow:non-visible) containers 2019-04-29 12:00:23 -04:00
Thomas McGowan 966a46c9b4 Removed trailing whitespace 2019-04-25 14:29:31 -05:00
Thomas McGowan d0f07acd2d Processes -> threads to minimize server load 2019-04-25 13:36:43 -05:00
John Chilton 343e6e4cd3 Merge pull request #7786 from natefoo/job-fail-destination-loop 
[19.01] Fix the use of JobMappingException
 2019-04-24 14:00:27 -04:00
John Chilton 166a83b6fe Merge pull request #7783 from natefoo/backport-7667 
[19.01] Fix shutdown for Pulsar MQ Runner
 2019-04-19 16:20:15 -04:00
Nate Coraor 87b7bfd458 Fix the use of JobMappingException 2019-04-19 14:43:30 -04:00
John Chilton ca55cab671 Fix PulsarMQRunner shutdown. 2019-04-19 12:44:53 -04:00
John Chilton b0f0fdc171 Remove unused variable. 2019-04-19 12:44:48 -04:00
Nate Coraor 1ba753ca54 Catch and filter *all* Slurm cgroup-related messages 2019-04-18 12:53:34 -04:00
Dannon 5f65252d4d Merge pull request #7675 from gtrack/workflow_btn_dont_jump 
[19.01] Bugfix: "Run workflow" jumps when clicked
 2019-04-15 14:24:54 -04:00
Björn Grüning a6c531e3c5 Merge pull request #7723 from nsoranzo/release_19.01_fix_safemembers 
[19.01] Fix check on links in ``CompressedFile.safemembers()``
 2019-04-12 22:24:41 +02:00