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3869 Commits
Author SHA1 Message Date
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 f6e54b49db Add job configuration test for resource groups and handler plugins. 2019-05-01 15:09:24 -04:00
Nicola Soranzo d545e88703 Add test case and use assertRaises() 
Also remove temporary directory.
 2019-04-12 12:41:48 +01:00
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
Martin Cech adfb7e65b3 Merge pull request #7682 from mvdbeek/fix_format_source_impicit_conversion 
[19.01] Fix format_source for implicit conversion inputs and fasta.gz upload
 2019-04-08 10:13:26 -04:00
mvdbeek 966cad890e Fix fasta.gz uploads 
This looks like it may probably broke with https://github.com/galaxyproject/galaxy/commit/fce2dd3ae801cd13a542388746b84f9cca2a4c48
 2019-04-07 23:15:35 +02:00
mvdbeek 5f578d4108 Add double conversion test 2019-04-07 23:15:35 +02:00
mvdbeek 3e3d15a84b Add test that verifies ftype is being set correctly 2019-04-07 23:15:35 +02:00
Sveinung Gundersen 28cd9948b7 Fixed bug when removing other tags than the first from a dataset. A space was erroneously added in front of these tags. 2019-04-06 03:52:35 +02:00
Dannon bb76daf754 Merge pull request #7633 from mvdbeek/fix_early_run 
[19.01] Delay workflow step execution for discovered & mapped-over input
 2019-04-01 17:00:58 -04:00
mvdbeek 8db8ce5de4 Fix float to int casting 
Fixes https://github.com/galaxyproject/galaxy/issues/998
 2019-03-31 17:15:46 +02:00
mvdbeek e8ea08dd61 Add testcase for mapped over discovered dataset consumption 2019-03-31 13:56:42 +02:00
Nicola Soranzo 2b13dd779d Encode content before writing to temp file 2019-03-29 03:02:51 +00:00
mvdbeek 0aac0a1dc6 Use correct tools in skip_without_tool decorator 2019-03-21 20:26:02 +01:00
mvdbeek db0c39370f Test that switching parameters results in filtered outputs 2019-03-21 20:25:43 +01:00
mvdbeek 3056fbbf12 Simple filter_output 
This obviously doesn't work (yet) with filters that work
on the input dataset, but this already removes a lot of
outputs that arent' going to be produced based on static
options. Since exceptions default to priduing the dataset
this isn't much harm.
 2019-03-21 20:25:43 +01:00
mvdbeek df8a4dcf16 Fix ChangeDatatypeAction for collections 2019-03-11 21:48:10 +01:00
mvdbeek dc23227378 Add tests for delete_intermediate and change_datatype PJAs 
`change_datatype` wasn't part of gxformat2, so this also requires
a new release of gxformat2 with https://github.com/jmchilton/gxformat2/pull/7
 2019-03-11 21:48:09 +01:00
mvdbeek 88fd52a4bb Test PJA actions 
The rename action works, the hide action fails.
Building this to fix
https://github.com/galaxyproject/galaxy/issues/7473.
 2019-03-11 21:48:09 +01:00
mvdbeek 76be1263ca Test that workflows with hidden params can be run 2019-03-04 18:41:51 +01:00
John Chilton 8f7263a1dc Merge pull request #7301 from bgruening/hdf5_tests 
Add new test syntax specific for HDF5 files
 2019-02-07 14:49:33 -05:00
Bjoern Gruening d36cf51f6b change "name" to "key" 2019-02-06 16:31:15 +01:00
mvdbeek a36b56e694 Drop redundant wait for history 
wait_for_invocation_and_jobs does that already, thx @nsoranzo.
 2019-02-05 15:39:42 +01:00
John Chilton 2a97f726cc Tweaks to hdf5 testing. 
- This is in galaxy-lib so h5py import should probably be conditional.
- Namespace very generic test functions a bit by adding h5 into the names.
- Stricter validation of XSD (the other assertions don't have this but that is problematic on their part), I'm not sure if the docs will render unevenly now though - we may want to revisit that and do this for all the assertions.
 2019-02-05 08:45:46 -05:00
mvdbeek cf68cbe907 Verify that list:list will be reduced to list in multi data input 2019-02-05 14:11:27 +01:00
Bjoern Gruening d4420b7566 register new test tool 2019-02-05 04:22:15 +01:00
Bjoern Gruening db2987b2b2 add test tool for new assertions 2019-02-05 04:21:02 +01:00
Nicola Soranzo f9ca90a228 Merge branch 'release_18.09' into release_19.01 2019-01-24 11:57:39 +00:00
mvdbeek 31c71fbd6f strip() text when loading xml 
Should fix https://github.com/galaxyproject/galaxy/issues/7250.
 2019-01-22 11:30:49 +01:00
Nicola Soranzo 7a9422600c Fix `GalaxyInteractorBackwardCompatTestCase.test_local_test_data_download` API test 
Broken in commit bf851269c3 .
 2019-01-17 16:39:48 +01:00
mvdbeek 4b920afba2 Make interactor changes backwards compatible 2019-01-10 14:44:14 +01:00
Nicola Soranzo d16a2348c5 Merge branch 'release_18.09' into release_19.01 2019-01-09 19:09:51 +00:00
Martin Cech f6b978be8c prevent XSS on toolshed when browsing repo changeset 
fix invalid changeset ts test, fix flake8

Revert "fix invalid changeset ts test, fix flake8"

This reverts commit 84864fe82a9f3b9ffa1cd5ef272f979e867e2002.

tweak the invalid changeset test and add a new one
 2019-01-08 12:52:28 -05:00
Nicola Soranzo 240633b373 Comment out unused line 2019-01-08 15:09:15 +00:00
John Chilton 3ecb0a1a08 Fix workflow parameter test case? 2019-01-08 09:24:27 -05:00
mvdbeek bed8b54af6 Only run integration tests with --privileged 2019-01-06 15:11:11 +01:00
mvdbeek 06f5abe1bc Install singularity 3.0.1 from source 2019-01-06 15:11:11 +01:00
mvdbeek a03f8bdffd Test singularity exec as Galaxy user 2019-01-06 15:11:10 +01:00
mvdbeek c0b63a18c7 Fix container integration tests 2019-01-06 15:01:31 +01:00
mvdbeek 44d73f72c8 Update Dockefile and run_test_wrapper.sh 
We use the Galaxy users' home dir for HOME.
Otherwise os.environ.get('HOME') would return '/home/galaxy',
but jobs run would see /galaxy.
 2019-01-06 15:01:31 +01:00
mvdbeek 83473f075d Update testing docker image; drop mysql tests, add singularity 2019-01-06 15:01:31 +01:00
mvdbeek fd4b009089 Skip singualrity integration tests if singularity not available 2019-01-06 15:01:31 +01:00
mvdbeek b41d969d68 Add integration test for singularity resolution 2019-01-06 15:01:31 +01:00
mvdbeek 50d8e3079d Add integration test for un/install with resolver_type 2019-01-06 15:01:31 +01:00
John Chilton 1222f80ae9 Merge pull request #7129 from natefoo/serializable-job-assignment 
Perform job assignment using DB serialization techniques
 2019-01-05 20:22:56 -05:00
Nate Coraor df7f8b425d Integration tests for handler assignment methods 2019-01-04 16:46:29 -05:00
Nicola Soranzo b8f445556a Merge pull request #7169 from mvdbeek/fix_process_key_unordered_elements 
Fix process_key test and deal with unordered repeat elements
 2019-01-04 21:01:54 +00:00
Nate Coraor b0691089ea Unit tests for new DB serialization handler assignment methods 2019-01-04 14:18:21 -05:00
mvdbeek 31e5fced00 Fix nesting and test 2019-01-04 19:18:33 +01:00
Nicola Soranzo 403d0a9361 Stricter `process_key` tests 2019-01-04 19:16:43 +01:00