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Author SHA1 Message Date
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
Nicola Soranzo 0bfebb4e84 Merge branch 'release_18.09' into release_19.01 2019-04-12 14:35:03 +01:00
Nicola Soranzo 177a2a1cf3 Merge branch 'release_18.05' into release_18.09 2019-04-12 13:02:12 +01:00
Nicola Soranzo d545e88703 Add test case and use assertRaises() 
Also remove temporary directory.
 2019-04-12 12:41:48 +01:00
Marius van den Beek 5d1df57f7f Merge pull request #7725 from nsoranzo/release_18.05_more_ci_backports 
[18.05] Backport other CI config changes
 2019-04-12 09:51:28 +02:00
Nicola Soranzo 9bf4a0fdb9 Fix check on links in `CompressedFile.safemembers()` 
Reported by @curtisecombsjr

Fix the following traceback when installing https://toolshed.g2.bx.psu.edu/view/iuc/package_openssl_1_0/ :

```
  File "lib/tool_shed/galaxy_install/install_manager.py", line 121, in install_and_build_package_via_fabric
    tool_dependency = self.install_and_build_package(install_environment, tool_dependency, actions_dict)
  File "lib/tool_shed/galaxy_install/install_manager.py", line 79, in install_and_build_package
    initial_download=True)
  File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step
    initial_download=initial_download)
  File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 548, in execute_step
    dir = self.url_download(work_dir, downloaded_filename, url, extract=True, checksums=checksums)
  File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 77, in url_download
    extraction_path = archive.extract(install_dir)
  File "lib/galaxy/util/compression_utils.py", line 111, in extract
    self.archive.extractall(extraction_path, members=self.safemembers())
  File "/usr/lib64/python2.7/tarfile.py", line 2041, in extractall
    for tarinfo in members:
  File "lib/galaxy/util/compression_utils.py", line 135, in safemembers
    raise Exception(finfo.name + " is blocked.")

openssl-1.0.2d/apps/md4.c is blocked.
```
 2019-04-11 23:21:07 +01:00
Nicola Soranzo d4030757f9 Backport other CI config changes 
`py35-unit` and `py35-first_startup` jobs were green on CircleCI, but doing
nothing.
Remove duplicated jobs from TravisCI.
 2019-04-11 20:04:26 +01:00
John Chilton 716b8886da Merge pull request #7711 from mvdbeek/fix_workflow_invocations_inaccessible 
[19.01] Restrict workflow invocation index to current user
 2019-04-10 09:50:33 -04:00
mvdbeek 4c9e4118f5 Restrict workflow invocation index to current user 
If the user is not an admin.
Fixes https://github.com/galaxyproject/galaxy/issues/7710

An alternative would be to skip Accessibility / Ownership
exceptions, but given that we can just restrict the query
this seems like the better approach to me.
 2019-04-10 11:13:59 +02:00
Björn Grüning 78ad61506f Merge pull request #7699 from mvdbeek/fix_sort_tool_too_stringent 
[19.01] Only check for exit code on actual sort command
 2019-04-10 10:33:36 +02:00
Nicola Soranzo aa008a650b Restore check_call for sed 2019-04-09 20:26:27 +01:00
Martin Cech 22c3895bf4 Merge pull request #7705 from dannon/backport-genomespace-fix 
[19.01] Backport GenomeSpace Exporter fix
 2019-04-09 14:08:02 -04:00
Dannon Baker c521decf32 Specify profile and look for exit codes for genomespace tool -- warnings cause failures otherwise 2019-04-09 13:34:06 -04:00
mvdbeek 68423aa361 Cleanup sorter.py 
Feed open output file to Popen instead of using stdout redirection in
command string.
 2019-04-09 15:35:21 +02:00
mvdbeek 45a0ff6173 Only check for exit code on actual sort command 2019-04-09 14:02:10 +02:00
Dannon Baker 3ec5547ec6 Add unique identifier to run workflow button, style explicitly instead of on the fly 2019-04-08 14:28:44 -04:00