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19,736 Commits 63 Branches 243 Tags
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Commit Graph
1693 Commits
Author SHA1 Message Date
Nicola Soranzo a8bc874736 Remove test broken after #786. 2015-10-02 15:34:46 +01:00
John Chilton 49740caaa2 Add documentation for running casperjs tests through run_tests.sh. 
Add option to run a specific test. Verified xunit reports work and --dockerize works for casperjs tests.
 2015-10-01 13:45:37 +01:00
guerler 6d00f38f0a Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_003 
Conflicts:
	client/galaxy/scripts/mvc/tools/tools-form.js
	static/maps/mvc/tools/tools-form.js.map
	static/scripts/mvc/tools/tools-form.js
 2015-09-29 15:55:59 -04:00
John Chilton ac18cbe978 Improved "special" tool loading. 
Instead of writing out the tools on startup (a more expensive operation than reading), just read the existing files in. Add new abstraction to the tool panel to reduce some otherwise duplicated code.

Testing:

The following two API tests should cover the modified behavior, they verify that metadata is still detectable and that history import and export still works.

```
./run_tests.sh -api test/api/test_histories.py:HistoriesApiTestCase.test_import_export
./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_rdata_not_decompressed
```
 2015-09-29 13:57:15 +01:00
John Chilton 5ff102507b Add regression test for issue in #798. 2015-09-25 14:29:05 +01:00
Nicola Soranzo ac8b5eae02 Fix errors when starting "./run_tests.sh -with_framework_test_tools -api" 2015-09-25 17:51:21 +01:00
Dannon Baker a5610d6845 Merge pull request #797 from jmchilton/java_opts_doc 
Fix unit tests broken with f935d27bdf.
 2015-09-25 11:07:52 -04:00
John Chilton 86c4263b34 Fix unit tests broken with f935d27bdf. 2015-09-25 11:04:12 +01:00
John Chilton fa0c3a4bbc Implement failing workflow test case. 
For galaxyproject/galaxy#776.
 2015-09-24 15:40:52 +01:00
guerler 57f023529a Remove tool form mako 
Fix new-line
 2015-09-23 16:10:56 -04:00
carlfeberhard a90a4fceba Merge pull request #755 from jmchilton/hdca_structure_state_tracking 
Improved state tracking of HDCA in history panel.
 2015-09-23 12:05:59 -04:00
John Chilton 684be5f6a5 Functional test to verify RData is not decompressed in upload process. 2015-09-23 13:56:14 +01:00
Nicola Soranzo 248ce3075b Merge pull request #765 from jmchilton/multi_min_max 
Implement min/max for multiple data input parameters.
 2015-09-22 14:52:47 +01:00
Nicola Soranzo 5e419197d1 Merge pull request #764 from jmchilton/format_discover 
Allow discover_datasets tag to use format attribute (instead of ext).
 2015-09-21 19:44:07 +01:00
John Chilton 87d5063a0d Implement min/max for multiple data input parameters. 2015-09-21 15:51:58 +01:00
John Chilton 07dd69edd5 Allow discover_datasets tag to use format attribute (instead of ext). 
https://github.com/TGAC/tgac-galaxytools/commit/93514438cb50fab48d0e211f1e1869b0f591ed66#commitcomment-13349396.
 2015-09-21 14:24:24 +01:00
John Chilton 311100ff9e Bugfix in test error reporting handling code. 
The code for showing status of histories in error would fail if there are collections in the history. This fixes that and skips over collections.
 2015-09-21 09:22:52 +01:00
Eric Rasche 1f1eed0e05 Merge pull request #759 from jmchilton/dockerize_test 
Updates and fixes for dockerized Galaxy testing.
 2015-09-19 17:12:56 -05:00
Martin Cech 2e55eb11e5 Merge pull request #758 from jmchilton/framework_tests 
API Test Fixes
 2015-09-19 15:03:28 -04:00
John Chilton 134c985f90 Updates and fixes for dockerized Galaxy testing. 2015-09-19 16:52:48 +01:00
Martin Cech c7d7736472 Merge pull request #757 from jmchilton/framework_tests 
Fix failing framework tests.
 2015-09-19 10:34:07 -04:00
John Chilton 45d5e29c1d Extend test_map_over_two_collections timeout. 
May be the cause of intermittent test failure on jenkins (https://jenkins.galaxyproject.org/job/G-API/lastCompletedBuild/default/testReport/api.test_tools/ToolsTestCase/test_map_over_two_collections/).
 2015-09-19 11:55:12 +01:00
John Chilton c6be0bc12c Remove compare_bam_as_sam.xml test. 
It never passed, it was originally used by me to test failing tests compared output of bams as sam files. Now that we want all these tests to pass we need to rethink how to test that aspect of the testing framework.
 2015-09-19 10:29:23 +01:00
John Chilton 2b02677e85 Workaround for metadata_bam.xml failure. 2015-09-19 10:27:09 +01:00
Nicola Soranzo 92a152d89c Uniform and slight increase the default timeout of API tests. 2015-09-18 17:48:59 +01:00
Nicola Soranzo 989191d3ce Fix output_format framework test. 2015-09-18 17:48:59 +01:00
John Chilton ef23abc6df WIP: Improved state tracking of HDCA in history panel. 
For tools which dynamically discover datasets for an output collection, keep the collection yellow until the structure of the HDCA has been fully defined. HDCAs still have the problem that they will always be green even if datasets contained within are in error, running, or queued states - but at least the structure is now reflected in the color.
 2015-09-18 16:28:22 +01:00
John Chilton bd55650f06 Add testing environment variable GALAXY_TEST_LOGGING_CONFIG. 
Unifies logging through the testing process. Requires adding a Galaxy option to disable its own attempts to configure a different root logger.
 2015-09-16 16:24:53 +01:00
Nicola Soranzo 3fafbb5e34 Fix more MissingToolException when running "./run_tests.sh -api" without "-with_framework_test_tools". 2015-09-15 16:47:40 +01:00
Nicola Soranzo c01cf85d45 Use __file__ when adding paths to sys.path instead of os.getcwd() . 
Also insert additional paths in position 1 unless strictly necessary.
 2015-09-11 19:05:37 +01:00
Nicola Soranzo 65519718b3 Fix "KeyError: name" error when running "./run_tests.sh -api". 
Example traceback for test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_run_dynamic_output_collections :

galaxy.web.framework.decorators: ERROR: Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "/opt/galaxy/lib/galaxy/web/framework/decorators.py", line 260, in decorator
    rval = func( self, trans, *args, **kwargs)
  File "/opt/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 182, in create
    return self.__api_import_new_workflow( trans, payload, **kwd )
  File "/opt/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 374, in __api_import_new_workflow
    workflow, missing_tool_tups = self._workflow_from_dict( trans, data, **from_dict_kwds )
  File "/opt/galaxy/lib/galaxy/web/base/controller.py", line 1111, in _workflow_from_dict
    publish=publish
  File "/opt/galaxy/lib/galaxy/managers/workflows.py", line 165, in build_workflow_from_dict
    missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] )
KeyError: 'name'
 2015-09-11 19:05:37 +01:00
Nicola Soranzo 760899f9c0 Fix MissingToolException when running "./run_tests.sh -api" without "-with_framework_test_tools". 2015-09-11 19:05:37 +01:00
Nicola Soranzo 63a715f27c Fix Tool Shed test broken with PR #706. 2015-09-11 19:05:37 +01:00
John Chilton 9711a60b82 Merge pull request #640 from carlfeberhard/managers 
Allow deserializing dataset permissions
 2015-08-27 18:08:20 +01:00
Nicola Soranzo e958041255 Merge branch 'master' into dev 
Conflicts:
	lib/tool_shed/metadata/metadata_generator.py
 2015-08-27 17:13:45 +01:00
Björn Grüning 949b3de568 Merge pull request #653 from nsoranzo/dev 
Finish flake8 of test/ .
 2015-08-27 17:10:51 +02:00
Dannon Baker dc7f7f2e3b Fix mock_trans to provide a user_is_admin member 2015-08-26 15:11:13 -04:00
Nicola Soranzo 93716ec08a Suggest to install grunt-cli globally to have grunt in PATH. 2015-08-26 20:08:15 +01:00
Nicola Soranzo 6f1e1cea82 Add mandatory "version" field to package.json . 2015-08-26 20:08:15 +01:00
Nicola Soranzo 2fccd0c11f Finish flake8 of test/ . 2015-08-26 20:08:09 +01:00
Nicola Soranzo fc2861ce78 Fix 3 failing functional tests in test/tool_shed/ . 2015-08-26 10:54:11 +01:00
Nicola Soranzo 11870a96f4 Remove from proteomics_datatypes.tar test data the datatypes that have been added to Galaxy datatypes. 
Fix tests in test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py .
 2015-08-26 10:54:11 +01:00
Nicola Soranzo 5701934e65 Fix broken test_0025_install_matplotlib_repository test. 2015-08-26 10:54:11 +01:00
Nicola Soranzo bc3ecbbae8 flake8 test/tool_shed/ . 2015-08-26 10:54:11 +01:00
Eric Rasche 71125326f8 Merge pull request #649 from jmchilton/yield_at_top_level 
[15.07] Fix yield statements at the top level of macros.
 2015-08-25 17:39:02 -05:00
John Chilton dc6700eec5 Fix yield statements at the top level of macros. 
Fixes #647.
 2015-08-25 16:51:59 +01:00
guerler 8be164f92c Fix tests 2015-08-20 16:00:19 -04:00
Nicola Soranzo 0f883ef776 Merge branch 'release_15.07' into dev 
Conflicts:
	lib/galaxy/model/__init__.py
 2015-08-20 14:12:27 +01:00
Nicola Soranzo a34f13a9f6 Merge branch 'release_15.05' into release_15.07 2015-08-20 14:07:09 +01:00
John Chilton a9827fae31 Fix failing tests for 238d908cce. 2015-08-20 06:45:11 +01:00