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2245 Commits
Author SHA1 Message Date
E Rasche e4518ff3e3 Rebase hardening commits from dev 2017-10-12 17:04:55 -04:00
Nicola Soranzo 0ff61d9ffc Fix Registry.get_datatype_by_extension() to return None if ext is unknown 
Without this fix, the Cheetah expression:

$dataset.is_of_type('unknown_ext')

in a tool command would be equivalent to:

$dataset.is_of_type('txt')

meaning that if the dataset datatype is a subclass of Text, the expression
would evaluate to True without any warning.

xref. https://github.com/galaxyproject/tools-iuc/issues/1373

Also add missing `xml` datatype to
`test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test
tools.
 2017-06-26 13:44:36 +01:00
John Chilton c3687114d6 Set metadata on HDAs from dynamically discovered collections. 
With test case that previously failed.

Fixes #3267.
 2017-01-05 14:48:53 -05:00
Nicola Soranzo 3b3e2e3358 Merge branch 'release_16.04' into release_16.07 
Conflicts:
	lib/galaxy/webapps/tool_shed/controllers/repository.py
	lib/galaxy/webapps/tool_shed/model/__init__.py
 2016-09-23 17:52:54 +01:00
Martin Cech 5e7ee28e0d bump freebayes in test (since it was updated) 2016-09-22 17:48:20 -04:00
carlfeberhard e5f4f2fab6 Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 2016-09-14 13:24:52 -04:00
carlfeberhard b50d07d5bf Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 2016-09-14 13:23:41 -04:00
carlfeberhard e7cb0ac2a1 Datasets: test for anon deserialization 2016-09-13 13:10:42 -04:00
carlfeberhard 9636ea1b6c Datasets: test for anon access/manage 2016-09-13 13:09:11 -04:00
carlfeberhard fc3dcf3b87 Permissions, datasets: allow admin in RBAC 
- Admin are considered permitted when calling
  ** dataset_manager.permssions.access and
  ** dataset_manager.permissions.manage
- Update bad test
- Add admin test to other permission checks
 2016-09-13 13:00:58 -04:00
carlfeberhard b88035955d Datasets: confirm admin ability to set permissions 
The power was inside you all along.
 2016-09-12 11:04:39 -04:00
carlfeberhard 91a190c6eb Datasets: allow admin to serialize permissions 
And updates tests.
 2016-09-12 10:50:57 -04:00
Nicola Soranzo f4806e9dd4 Merge branch 'release_16.04' into release_16.07 2016-08-18 15:49:30 +01:00
John Chilton 0110d5a05a Add a test case to dbkey_output_action.xml. 
Per @nsoranzo's template and suggestion.
 2016-08-16 14:08:38 -04:00
John Chilton 510290feea Add example of regressed 16.04 behavior related to dbkey output actions. 2016-08-16 10:34:57 -04:00
Marius van den Beek b0bd9a3326 Adjust test for new GalaxyPackageDependency signature 2016-08-08 16:41:35 +02:00
Nicola Soranzo f06c895d61 Update INDETERMINATE_DEPENDENCY to NullDependency 
Fix unit test broken in https://github.com/galaxyproject/galaxy/pull/2554
 2016-07-29 19:38:06 +01:00
Dannon Baker fed3665fcf Merge pull request #2680 from mvdbeek/toolshed_test_fixes 
Fix broken toolshed tests with #2554
 2016-07-28 07:44:21 -04:00
Marius van den Beek 12a789f3e1 Adjust tests for 8cca7be 2016-07-28 14:05:09 +03:00
Daniel Blankenberg a731ce2e22 Merge pull request #2554 from bxlab/install_via_conda 
Fix bugs in post.
 2016-07-27 15:38:58 -04:00
Dannon Baker f0024d64e1 Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it) 2016-07-26 16:42:40 -04:00
Marius van den Beek 645a891706 Remove reference to /tmp 2016-07-26 20:35:16 +03:00
Marius van den Beek 9917512f8f Revert svgwrite import, fixed in #2656 2016-07-26 20:35:08 +03:00
Martin Cech 9607e528be Merge pull request #2656 from jmchilton/pyparsing_testing 
Import pyparsing in testing so twill's older version doesn't get loaded.
 2016-07-26 11:49:08 -04:00
John Chilton 93ba35fdd1 Import pyparsing in testing so twill's older version doesn't get loaded. 
There are unintended consequences if not, such as svgwrite not loading properly.
 2016-07-26 11:18:18 -04:00
Marius van den Beek e53a81c40d Fix syntax, return None if dependency not found 2016-07-26 13:32:09 +03:00
Marius van den Beek deef480cad Add more API tests for resolver dependencies 2016-07-26 01:35:52 +03:00
Nicola Soranzo 134f988549 Merge pull request #2650 from dannon/flake8_update_tox_default 
Ignore .tox directory.  Used to be ignored by default w/ flake8 appar…
 2016-07-25 19:18:44 +01:00
Marius van den Beek b5fad4a048 Add api test for conda dependency resolution 2016-07-25 20:32:41 +03:00
Dannon Baker 9f2237905b Remove two #noqas and specify __all__ for those modules. Specify many more #noqas to skip the precise relevant exception. 2016-07-25 11:09:15 -04:00
Dannon Baker 10745f252f Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it) 2016-07-25 10:15:33 -04:00
Marius van den Beek 4ed151a771 Revert mako hack to always display install_tool_dependency button 
- Add resolver checkbox
 - Add possibility to disable resolvers if initialization failed
 2016-07-22 22:01:38 +02:00
guerler 881af45dfe Fix upload dialog test cases 2016-07-22 09:38:53 -04:00
guerler 45038d1399 Merge branch 'dev' into move_workflow_run 2016-07-22 09:24:48 -04:00
Dannon Baker 576e09fe63 Merge branch 'select_performance' into dev 2016-07-22 08:51:37 -04:00
guerler 35ef492e21 Merge branch 'dev' into move_workflow_run 2016-07-21 21:33:38 -04:00
John Chilton 2075af4de8 Merge pull request #2538 from pvanheus/dev 
Make conda autoinstall of packages safer:
 2016-07-21 15:47:31 -04:00
guerler 80d20900ef Adjust icon button, add test cases 2016-07-21 12:50:31 -04:00
guerler 842a981062 Adjust check state button and add test cases 2016-07-21 12:24:25 -04:00
John Chilton f67d3cbe93 Merge pull request #2579 from phac-nml/add-dtd-to-galaxy 
Add DTD to Galaxy
 2016-07-21 11:07:55 -04:00
Nicola Soranzo 47f25f1dc6 Merge pull request #2631 from jmchilton/output_filter_exception 
Add tool test for what happens when output filter throws exception.
 2016-07-21 15:59:43 +01:00
guerler 7b49080dc1 Adjust/fix button link variation, add test cases 2016-07-21 10:13:04 -04:00
guerler 193c27e3db Move execute button and new history form to top of workflow execution form 2016-07-21 09:46:07 -04:00
John Chilton 274ec0f953 Fix typo spotted by @nsoranzo. 2016-07-21 08:55:35 -04:00
Eric Enns 43fccc9887 Moved dtd tests into a different folder 2016-07-20 15:52:04 -05:00
John Chilton d87957e1a2 Ease configuration and add documentation for using DTD syntax for destinations. 
Moving rules also means it won't conflict with other peoples custom dynamic destinations and should prevent Galaxy from reloading the Python repeatedly.
 2016-07-20 15:58:34 -04:00
John Chilton 54b8ae00db Rework test case that fails occasionally on Jenkins. 
Should be a little more robust now.
 2016-07-20 12:08:18 -04:00
John Chilton 30fd1e0e64 Test case for dynamically creating list:list:lists. 
This could check the outputs ideally, but it was failing to simply execute the workflow so this does serve as check that some bugs are fixed.
 2016-07-19 16:20:09 -04:00
Eric Enns 85671bd466 Fixed E302 2016-07-19 14:27:39 -04:00
Eric Enns 09b9339569 Fixed to only line_count not line_count + 1 lines and added in really basic test 2016-07-19 14:27:09 -04:00