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4186 Commits
Author SHA1 Message Date
John Chilton 754ca26f92 Fix failing integration test. 
https://jenkins.galaxyproject.org/job/docker-integration/9044/testReport/junit/test.integration.test_job_recovery/JobRecoveryBeforeHandledIntegerationTestCase/test_recovery/

Likely transiently broken with #7874
 2019-05-03 08:38:33 -04:00
John Chilton 5dd92d2421 Merge remote-tracking branch 'upstream/release_19.05' into dev 2019-05-02 14:19:49 -04:00
John Chilton 9bfb08f00c Merge remote-tracking branch 'upstream/release_19.01' into release_19.05 2019-05-02 11:43:51 -04:00
John Chilton 9bc0a0cbe5 Add file missing from #7694 2019-05-02 11:41:44 -04:00
Martin Cech 918db5537e Merge pull request #7874 from jmchilton/cleanup_integration_tests 
Cleanup integration test configuration code.
 2019-05-02 11:32:10 -04:00
Dannon Baker 8b0bbba1a7 Merge remote-tracking branch 'upstream/release_19.05' into dev 2019-05-02 11:20:39 -04:00
John Chilton c6fcd051c8 Cleanup integration test configuration code. 
Remove copy and paste problems, remote excess configuration unrelated to the what is being tested (handler configuration, multiple worker counts, etc..).
 2019-05-02 08:45:11 -04:00
John Chilton faae919af1 Add file missing from #7694 2019-05-02 08:27:04 -04:00
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
Helena Rasche c545aaf4d4 [19.05] Add shapefile datatype (#7819) 
[19.05] Add shapefile datatype
 2019-05-02 10:18:40 +02:00
John Chilton f6e54b49db Add job configuration test for resource groups and handler plugins. 2019-05-01 15:09:24 -04:00
guerler 89cf0a48fc Wait until workflow saving message disappears 2019-04-30 21:31:26 -04:00
guerler 2a0e0e1736 Remove close option from selenium tests 2019-04-30 19:14:25 -04:00
Bjoern Gruening 102b619c43 make tests stricter 2019-04-30 09:47:06 +02:00
Bjoern Gruening bec0d87f4c ordering matters 2019-04-30 00:12:28 +02:00
Bjoern Gruening 1d2126a84e enable input composite data 2019-04-29 19:09:18 +02:00
Nicola Soranzo ed18d34f08 Merge pull request #7838 from mvdbeek/use_getfullargspec_on_python3 
Use getfullargspec on python3
 2019-04-29 13:50:45 +01:00
Björn Grüning 1e2528b754 fixing file names in tests 2019-04-29 14:09:33 +02:00
mvdbeek b68dcb4507 Use getfullargspec on python3 
`getargspec` is marked for deprecation.
 2019-04-29 11:52:33 +02:00
Marius van den Beekandbgruening 977c59fa0a Update test/functional/tools/composite_shapefile.xml 
Co-Authored-By: bgruening <bjoern@gruenings.eu>
 2019-04-29 10:55:12 +02:00
Bjoern Gruening 75c53409a0 add datatype and tool to the tests 2019-04-29 09:50:00 +02:00
Nicola Soranzo 084296c92a Remove recursion from `expand_nested_tokens()` 
Also add test for recursive nested token.
 2019-04-27 00:09:31 +01:00
John Chilton 003cdb83fd Merge pull request #7823 from mvdbeek/fix_token_replacement_py3 
Fix nested macro/token expansion on python 3
 2019-04-26 10:59:38 -04:00
mvdbeek 60d87107ee Fix InputValueWrapper gt/ge/lt/le comparisons 2019-04-25 21:32:47 +02:00
mvdbeek 77ae679746 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.
 2019-04-25 19:51:25 +02:00
Bjoern Gruening 21a60e3020 add shapefile test 2019-04-25 16:43:06 +02:00
John Chilton 75ec6dba53 Merge pull request #7594 from martenson/workflow-ux 
improve workflow cog menu ux
 2019-04-24 08:28:18 -04:00
Dannon 745ae6d298 Merge pull request #7804 from mvdbeek/nsoranzo-fix_deprecations 
Fix 'postgres' dialect name has been renamed to 'postgresql' deprecat…
 2019-04-24 08:00:37 -04:00
Marius van den Beek 4bd8644b24 Merge pull request #7800 from nsoranzo/fix_deprecations 
Fix various Python deprecations
 2019-04-24 10:52:34 +02:00
mvdbeek 1c38a4a075 Fix 'postgres' dialect name has been renamed to 'postgresql' deprecation warning 2019-04-24 10:49:23 +02:00
Nicola Soranzo d53112aa43 Use `yaml.safe_load() instead of load()` 
See https://msg.pyyaml.org/load
 2019-04-23 16:50:55 +01:00
Nate Coraor 1ce4c5fade Don't clean up jobs when running tests if $GALAXY_TEST_NO_CLEANUP is 
set. `$GALAXY_CONFIG_OVERRIDE_CLEANUP_JOB` can be used to override this
behavior.
 2019-04-23 11:01:08 -04:00
Nicola Soranzo faac99976b Fix deprecated `assertEquals()` 
See https://docs.python.org/2/library/unittest.html#deprecated-aliases
 2019-04-23 12:48:35 +01:00
mvdbeek 6b3aecdcc4 Restrict search to items in owned histories 
This was an oversight in https://github.com/galaxyproject/galaxy/pull/7745.
This is the quick fix, but I think it's feasible to implement the
accessible logic as a query, which means we could push this down to
a Mixin, and treat it as a regular fiter (so admins could for instance
search/sort for the largest datasets, which is already possible in the
reports app).
 2019-04-20 16:27:34 +02:00
John Chilton 32604d9b03 Merge pull request #7745 from mvdbeek/dataset_search_api 
Extend dataset search and add search API endpoint
 2019-04-19 09:00:28 -04:00
mvdbeek e7b0867602 Make sure orm filters operate on correct model 
In practice we use ParsedFiler.filter_type to discriminate
the different filter types. Filters that require the correct
model class for a specific query are now functions that take
a model_class and generate the correct filter.
 2019-04-18 18:55:14 +02:00
mvdbeek 885d9d1766 Fix err_msg assertion 2019-04-17 16:30:24 +02:00
mvdbeek ae5e781edf Make TaggableFilterMixin use orm_filters 
This is way more peformant and also doesn't give
weird results when a limit is used.
 2019-04-17 16:03:27 +02:00
John Chilton 1e731b7c03 Add HDCA support to model persistence script. 2019-04-17 08:51:18 -04:00
John Chilton ca1b1fd854 Fix nested composite files during history import/export. 
Fixes #3628
 2019-04-17 08:49:09 -04:00
mvdbeek 4469b9cbc0 Split up test and test searching by tool id 2019-04-17 12:56:46 +02:00
Martin Cech 93da1fc0bd Merge pull request #7684 from jmchilton/build_objects_script 
Script to populate datasets/libraries directly into an objectstore and model store.
 2019-04-16 22:16:31 -04:00
mvdbeek 48d9eaf78f Add some basic dataset search testing 2019-04-16 19:31:36 +02:00
mvdbeek 95fe0ffcf5 Adjust DatasetsApiTestCase.test_index to status code 200 
And modernize test setup by using DatasetPopulator.
 2019-04-16 19:31:03 +02:00
Martin Cech 51cbf440bf Merge pull request #7755 from jmchilton/job_error_reporting 
Report a couple common errors in dataset/job report.
 2019-04-16 13:30:12 -04:00
John Chilton 44856a3f75 Report a couple common errors in dataset/job report. 
Report if empty inputs were used or if the same input was used more than once, these were identified as common sources of potential errors across many tools. Neither of these are definite problems, but both could be depending on the tool and both happen frequently. Outline a few more ideas as TODOs in the code.
 2019-04-16 10:24:28 -04:00
Marius van den Beek 7c233a9c2d Merge pull request #7754 from jmchilton/fix_for_docker_on_mac_kubernetes_test 
Fix Kubernetes integration tests for Docker on Mac.
 2019-04-16 16:20:53 +02:00
John Chilton 74bf94f445 Fix kubernetes integration tests for Docker on Mac. 2019-04-16 08:28:36 -04:00
John Chilton c33b4d4364 Merge pull request #7724 from mvdbeek/dependent_jobs 
Unpause dependent jobs when resuming jobs
 2019-04-15 14:16:47 -04:00
Nicola Soranzo 1b1f6e9cda Fix comments 2019-04-14 18:02:42 +01:00