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2113 Commits
Author SHA1 Message Date
Dannon Baker ab05091379 Merge pull request #2328 from carlfeberhard/client.libs-update 
Client library updates
 2016-05-12 09:55:49 -04:00
guerler 468f17418e Fix collection test 2016-05-11 12:56:43 -04:00
guerler 6e5aea08c4 Remove unnecessary MockStorage from Metrics test 2016-05-10 22:19:02 -04:00
Dannon Baker 74a53c4ebd QUnit can't be shim/init'd since it's a proper AMD module including a define. 2016-05-10 21:16:02 -04:00
guerler b7dc5cdf8f Fix page test 2016-05-10 21:12:09 -04:00
guerler 7e63ae66cd Update qunit and sinon 2016-05-10 20:40:39 -04:00
carlfeberhard 7afb7616ff Tests: send empty obj to qunit/form_tests 
`null` caused a script error in require.
 2016-05-09 14:49:59 -04:00
guerler cfb0ddb2dd Revise options, add test cases 2016-05-05 13:09:27 -04:00
guerler bd22456c41 Revise selectors, add test cases 2016-05-04 15:57:31 -04:00
John Chilton af7d7de596 More fixes from downstream projects. 
- Fixes a bug in lib/galaxy/tools/linters/general.py found through galaxy-lib.
 - Brings in docstring and import order linting fixes from the gxformat2 project (https://github.com/jmchilton/gxformat2).
 2016-05-02 22:44:23 -04:00
John Chilton 80e6971d5a Fix encoding issues in test/unit/test_objectstore.py. 
Without fix this test fails in Python 3.
 2016-05-02 02:14:13 -04:00
Björn Grüning 9242847a4f Merge pull request #2249 from davebx/remove_ttr 
Cleanup of the install and test framework.
 2016-04-27 23:01:52 +02:00
guerler faa2e69ec7 Add test cases 2016-04-25 16:15:06 -04:00
Dave Bouvier 65a3a6dcf6 Cleanup of the install and test framework. 
The system to install and test repositories has been deprecated, and this commit removes the parts that would display the results.
 2016-04-25 15:34:00 -04:00
Aysam Guerler 18a6393010 Merge pull request #2233 from jmchilton/repeat_multidata 
[16.04] Multi-data collection reductions in repeat blocks are broken.
 2016-04-23 14:08:12 -04:00
John Chilton c2b091d207 Tests demonstrating multi-data params in repeats are broken. 
A test cases and a tool that can be tested directory.
 2016-04-22 10:10:06 -04:00
Martin Cech c79d057ca4 Merge pull request #2079 from davebx/api_install_bugfixes 
Attempted fix for server error on repo preview.
 2016-04-20 10:32:05 -04:00
Nate Coraor 78f35bfe84 Merge branch 'release_16.04' into dev 2016-04-19 10:44:19 -04:00
Martin Cech db805184f5 Merge pull request #2184 from jmchilton/pulsar_fixes_more_v2_updated_even_more_revised_2 
[16.04] More Pulsar fixes.
 2016-04-18 16:02:11 -04:00
Martin Cech 1fd326855d improve on refactoring of the test 2016-04-18 12:42:39 -04:00
Martin Cech a85b5ee762 remove unused import 2016-04-18 12:42:33 -04:00
Martin Cech 76386b5eab remove unwanted check 2016-04-18 12:42:24 -04:00
Martin Cech 7ad55b7eb8 try pushing again when we get unexpected exception... 2016-04-18 12:42:19 -04:00
John Chilton 49a7328186 More Pulsar fixes. 
- Fix working directory outputs for a2e3140375 (giving tools clean working directories).
 - Fix copy action when target directory doesn't already exist (https://github.com/galaxyproject/pulsar/pull/107 thanks to @natefoo).
 - Fix handling of Pulsar jobs that fail during submission (https://github.com/galaxyproject/pulsar/pull/103 thanks to @mvdbeek).
 - Fix PBS status reporting (https://github.com/galaxyproject/pulsar/pull/102 thanks to @mvdbeek).
 - Fix for JetStream that allows setting staging directories on a per-manager basis (https://github.com/galaxyproject/pulsar/commit/7d4030412d1aa58d0c3daa86d0ad7113c79fee81).
 2016-04-18 09:16:28 -04:00
Dave Bouvier afa353b6fd Return current changeset if it is latest. 2016-04-15 10:30:08 -04:00
John Chilton 5ff7f9a19f Fix running tool tests if remote user middleware is enabled. 2016-04-14 20:05:38 -04:00
Dave Bouvier d8b0add9c2 Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_bugfixes 2016-04-14 10:31:34 -04:00
Nicola Soranzo 4797f811a4 Merge pull request #2130 from martenson/try-fix-pushcheck 
try pushing again when we get unexpected exception...
 2016-04-13 17:23:38 +01:00
Martin Cech 26a4c137ce improve on refactoring of the test 2016-04-12 13:33:49 -04:00
Nicola Soranzo 408827e251 Merge branch 'release_16.04' into dev 2016-04-12 14:35:37 +01:00
Martin Cech 3dc46809c4 remove unused import 2016-04-11 15:03:43 -04:00
Martin Cech cd1e1f5e3e remove unwanted check 2016-04-11 13:47:47 -04:00
Martin Cech e5ce5dfe33 try pushing again when we get unexpected exception... 2016-04-11 13:16:14 -04:00
Martin Cech 0ff81d3dcb remove buildbot remnants 2016-04-11 11:19:39 -04:00
John Chilton 84ad9c2ee2 Rev Pulsar to 0.7.0.dev3. 
- Fixes numerous problems mostly notably fixes external metadata generation and job metrics collection for recent Pulsar. This was broken when tools were given clean working directory.
 - Produce a new message if an older Pulsar version is targetted via REST of library (should help with upgrading to Galaxy 16.04).
 - Newer pulsar lib allows more flexible configuration of managers - update documntation to reflect this.
 2016-04-10 23:54:02 -04:00
Dave Bouvier 78e2eef2fc Fix another travis error that escaped my notice. 2016-04-06 09:20:46 -04:00
Dave Bouvier f4993b7826 Fix one more travis error. 2016-04-06 09:19:28 -04:00
Dave Bouvier 8c3f458bca Correct docs and names. 2016-04-06 09:10:03 -04:00
Martin Cech 4138860bfd Merge pull request #2075 from jmchilton/conda_download_fixes 
Fix deps.command.download_command on Mac OS X.
 2016-04-05 16:25:23 -04:00
Nate Coraor 2bd4de2025 Fix things found by @mvdbeek 2016-04-05 14:59:09 -04:00
Dave Bouvier ad929f2310 Add test for server error with updated repository. 2016-04-05 11:05:33 -04:00
John Chilton 7aa2d6840a Implement IntegrationTestCase and EmbeddedPulsarTestCase. 
IntegrationTestCases differ from functional tests in that they start up a Galaxy instance configured on a per test class basis - so this new class of "integration tests" can test configuration modalities of Galaxy that cannot be tested with traditional Galaxy functional tests.
 2016-04-04 20:08:55 -04:00
John Chilton 53f1782964 Allow setting job_conf path for functional tests. 2016-04-04 14:39:17 -04:00
John Chilton 3b31f23eb6 Fix deps.command.download_command on Mac OS X. 
Previously -O- and --recursive would be used together - this doesn't seem to be possible on Mac OS X.

See issue https://github.com/galaxyproject/planemo/issues/431.
 2016-04-04 12:04:01 -04:00
John Chilton e02e97dc79 Merge pull request #2067 from jmchilton/shed_tests 
Adjust testing directories so no python root is ever "tool_shed".
 2016-04-01 22:30:27 -04:00
Dave Bouvier 27f99cdf40 Fix test data path. 2016-04-01 14:50:26 -04:00
Nicola Soranzo 26569c3ec4 Merge pull request #2066 from jmchilton/static_tool_conf 
Allow tool confs with a tool_path to not be interpreted as shed confs.
 2016-04-01 18:03:56 +01:00
John Chilton 4c216f1077 Adjust testing directories so no python root is ever "tool_shed". 
We have a tool_shed directory in lib, so if we enter a test case from some path and test/tool_shed happens to be a valid python top-level module - it blocks out lib/tool_shed and Galaxy doesn't work properly in the test.

A similar problem was encountered with unit tests and fixed with https://github.com/galaxyproject/galaxy/commit/df442a06382f23bdf0401bdd632b9584d3431281 - but I have decided that directory name was a bit log and so this commit unifies the approach to unit and functional test names for tool shed tests.
 2016-04-01 10:09:49 -04:00
John Chilton 34e3b7f1c2 Rename shed_conf attribute to is_shed_conf. 
Per discussion with @nsoranzo.
 2016-04-01 10:01:54 -04:00
Nicola Soranzo 205850586e Use a stricter regexp for microseconds. 2016-04-01 14:46:30 +01:00