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Commit Graph
1237 Commits
Author SHA1 Message Date
Marcus Christie 0792bcd6c0 Merge remote-tracking branch 'upstream/dev' into idp-logout 2020-01-12 14:07:08 -05:00
Nicola Soranzo 1e4ec5c843 Use @pytest.mark.skipif decorator 2020-01-09 14:40:48 +01:00
mvdbeek 03e7ea25fb Fix tool watcher unit tests; sleep needs to happen after watching the file 2020-01-09 14:40:48 +01:00
mvdbeek d33813c28d Tweak paramiko missing hostkey policies 2020-01-09 14:40:48 +01:00
mvdbeek 4fd536658d Merge branch 'release_19.09' into release_20.01 2019-12-27 20:14:21 +01:00
mvdbeek f12e0844fe Merge branch 'release_19.05' into release_19.09 2019-12-27 20:12:05 +01:00
Marcus Christie 757cf8cd93 FIx py3 compat and add unit test 2019-12-24 11:02:02 -05:00
mvdbeek 9d1cccd14d Cast to None for optional params if not comparing strings 
Proposed by @nsroanzo in https://github.com/galaxyproject/galaxy/pull/9149#discussion_r360225247
 2019-12-21 17:22:34 +01:00
John Chilton a2d14be11f Allow testing command versions in tools - tests, XSD. 2019-12-19 17:34:31 -05:00
John Chilton 738ea0c506 Re-locate version path to a writable directory in containers. 2019-12-19 17:32:40 -05:00
mvdbeek d12f21d62e Add test for unset optional parameters 2019-12-19 17:55:00 +01:00
Dannon 84a0ec271a Merge pull request #8893 from jmchilton/markdown_export 
PDF Export of Galaxy Markdown
 2019-12-19 11:21:09 -05:00
mvdbeek b52b022383 Merge branch 'release_19.09' into dev 2019-12-19 10:36:07 +01:00
mvdbeek 5759160036 Merge branch 'release_19.05' into release_19.09 2019-12-19 10:28:30 +01:00
Nicola Soranzo 21cb3d9d7d Restore returning "None" when casting unselected multiselect param to str 
Broken in commit 7d3b9c53bb .

Before the above-mentioned commit, when a
`<param name="blah" type="select" multiple="true"/>` was left unselected,
its value was `None`, casted to string as `"None"`.
Tool authors would check if the user has selected a value with something
like:

```
 #if str($blah) != 'None':
```

After the above-mentioned commit, the value of the unselected param is `[]`,
casted to string as `""`, which breaks tools using the check above.
This restores the previous behaviour.

Seen in pull request:

https://github.com/galaxyproject/tools-iuc/pull/2691
 2019-12-19 02:21:28 +00:00
John Chilton eca65e9c01 PDF generation for reports. 2019-12-18 17:18:05 -05:00
Marius van den Beek 005c7e0ea1 Merge pull request #9099 from jmchilton/validation_separation 
Separate Markdown Validation into its own module.
 2019-12-17 22:38:59 +02:00
Marius van den Beek c10a434fcc Merge pull request #8512 from jmchilton/page_format 
Markdown-based Galaxy Pages.
 2019-12-17 22:37:21 +02:00
Marius van den Beek 9c46e852b1 Merge pull request #9086 from jmchilton/revise_workflow_inputs_2 
Even Richer Workflow Inputs
 2019-12-17 22:26:08 +02:00
Björn Grüning 850d483bf2 Merge pull request #9116 from mvdbeek/mulled_build_minimal 
Automatically use extended-base-image if necessary
 2019-12-16 20:59:27 +01:00
John Chilton 7a09995b3a Separate markdown parse out into own module for reuse. 2019-12-16 10:13:33 -05:00
John Chilton 5fc7c3b8b2 Implement Markdown pages w/editor toolbar. 2019-12-16 07:25:16 -05:00
mvdbeek fa1c8db202 Use pytest.skipif 2019-12-15 14:25:24 +02:00
mvdbeek 1077475567 Skip test_mulled_build on regular unit tests 
And move commonly used skip_if_environ/external_dependency_management
to test/unit/tool_util/util.py
 2019-12-15 14:09:15 +02:00
mvdbeek 67590388e6 Fix test_hashed_test_search 2019-12-15 14:09:15 +02:00
mvdbeek bcd7c8081b Automatically set destination image to extended image 
If necessary and no explicit destination image is set.
 2019-12-15 14:09:15 +02:00
Nicola Soranzo e9af7ea7be Merge branch 'release_19.09' into dev 2019-12-12 18:30:52 +00:00
John Chilton 26d5150245 Eliminate extensions=['input_collection']. 
The existing hack of extensions=['input'] is bad enough and should work fine for collections. Not sure what past-John was thinking by adding this.
 2019-12-11 12:26:32 -05:00
John Chilton 20d737cd09 Fix unit tests. 2019-12-10 21:21:31 -05:00
mvdbeek 1a46416ebc Fix mulled version comparison 
Mulled tags are composed like this: `<version>--<build_string> where
`<build_string>` ends with `_build_number`.
To get the last build this sorts by build build string, then by build
number and finally by build version.
 2019-12-08 12:26:04 +01:00
Nicola Soranzo 38889c98ae Merge branch 'release_19.09' into dev 2019-12-03 16:37:40 +00:00
Nicola Soranzo ad84cef8f8 Merge branch 'release_19.05' into release_19.09 2019-12-03 16:01:00 +00:00
Nicola Soranzo 8ef252c192 Small refactor of InputValueWrapper comparison methods. 
Add more tests.
 2019-12-02 18:30:29 +00:00
mvdbeek c7312e19be Merge branch 'release_19.09' into dev 2019-12-02 10:21:24 +01:00
mvdbeek d5655d24de Merge branch 'release_19.05' into release_19.09 2019-12-02 10:14:49 +01:00
mvdbeek b6047d4048 Add test for optional value casting 2019-11-30 11:52:47 +01:00
mvdbeek 685b073986 Merge branch 'release_19.09' into dev 2019-11-30 11:00:03 +01:00
mvdbeek c080549053 Merge branch 'release_19.05' into release_19.09 2019-11-30 10:57:32 +01:00
Nicola Soranzo c126a7ac20 Restore casting a boolean param to str when comparing with one 
Broken in https://github.com/galaxyproject/galaxy/pull/9047
 2019-11-29 18:05:41 +00:00
Nicola Soranzo b49acc05f9 Merge branch 'release_19.09' into dev 2019-11-29 15:28:48 +00:00
Nicola Soranzo c3d532572e Merge branch 'release_19.05' into release_19.09 2019-11-29 15:20:45 +00:00
Marius van den BeekandNicola Soranzo 8afe7a1a1d Cleanup test_input_value_wrapper assertions 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-11-29 14:25:00 +01:00
mvdbeek 155660083d Simplify parameter value comparisons 
Cast self instead of other. This fails 5 == '5', which is less magic
(https://github.com/galaxyproject/galaxy/pull/9047#discussion_r352111557)
 2019-11-29 13:43:17 +01:00
mvdbeek 95e3f447c8 Fix input parameter comparisons 
Fixes https://github.com/galaxyproject/tools-iuc/pull/2702#issuecomment-559718768
Broken in https://github.com/galaxyproject/galaxy/pull/7826
Also compares via `float` instead of `int` when other is int,
since that is more reasonable. Otherwise 5.1 > 5 is False.
 2019-11-29 11:02:40 +01:00
Marius van den Beek aaec85e134 Merge pull request #7936 from simonbray/cli-tools 
CLI tools for installing/testing Docker and Singularity containers
 2019-11-29 09:28:30 +01:00
Marius van den Beek 18db389113 Merge pull request #8930 from jmchilton/extended_metadata 
Implement extended job metadata collection
 2019-11-13 12:43:36 +01:00
John Chilton 180d96c540 Refactor tool shed tests into tool shed namespace. 2019-11-12 09:05:07 -05:00
John Chilton 45019c3fbd Move galaxy testing utilities into more sane package structure. 
Split test/base into lib/galaxy_test/base and lib/galaxy_test/driver. Dividing things on whether they import galaxy-app code or not - with the goal of a galaxy-test-base package that doesn't depend on galaxy-app and a galaxy-test-driver package that does.

I've been refactoring around this division for a long time. Certain tests (namely the integration tests) always need to bootstrap Galaxy - but the API tests and the Selenium tests should be installable and runnable without Galaxy in the Python environment. So future galaxy-test-api and galaxy-test-selenium packages should have only an optional dependency on galaxy-test-driver.

Properly sturcturing these namespaces is a precursor for real packages on PyPI, clean separation of the tool shed testing code, and cleans up all the flake8 noqa hacks in test/.
 2019-11-12 09:03:06 -05:00
John Chilton 559b664b07 Refactor tool_shed webapp out of Galaxy. 2019-11-11 12:32:19 -05:00
John Chilton 8a537d6c65 Cleanup random tool_shed imports in Galaxy. 2019-11-11 00:28:49 -05:00