Nicola Soranzo
962def5bb8
Merge branch 'release_22.05' into dev
2022-11-28 15:22:49 +00:00
Nicola Soranzo
9980ebebab
Merge pull request #15039 from mvdbeek/fix_tmpdir_mounting
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[22.05] Mount ``$TMPDIR``, ``$TMP`` and ``$TEMP`` into container
2022-11-28 13:09:06 +00:00
mvdbeek
702bdc0ec9
Test that tempdir creation is possible
2022-11-21 11:44:24 +01:00
mvdbeek
b6117ee3df
Fix metadata setting for discovered datasets with extended metadata
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Fixes https://github.com/galaxyproject/galaxy/issues/15036
2022-11-20 16:02:15 +01:00
mvdbeek
c01e6b8797
Install conda for framework tests
2022-11-20 08:58:33 +01:00
mvdbeek
f24eaa581a
Use APITestCase class to run framework tool tests
2022-11-18 18:35:15 +01:00
mvdbeek
b627762a76
Add more test scenarios
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Test collection black hole
2022-11-08 22:16:20 +01:00
Marius van den Beek
e3a91ab217
Merge pull request #14863 from jmchilton/puslar_extended_metadata_fixes
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Various Pulsar extended metadata fixes
2022-11-08 11:51:59 +01:00
John Chilton
89394bd8b9
Progress toward fixing extended metadata with Pulsar
2022-11-02 08:59:12 -04:00
mvdbeek
ba593057c2
Use `galaxy_driver_class` to create tool shed driver
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Use ``autouse`` fixture to configure test driver
2022-11-01 18:45:07 +00:00
Nicola Soranzo
5ca0aea54a
Drop nose
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It's deprecated and unmaintained, and is broken under Python 3.10 .
2022-11-01 18:45:07 +00:00
Marius van den Beek
cda2aea10c
Merge pull request #12999 from simonbray/dupl-collection
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Add duplicate_file_to_collection tool
2022-10-17 12:01:41 +02:00
Nicola Soranzo
b3bbef0496
Use loc file that actually exists in the param validators of test tool
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Previously, the ``validation_dataset_metadata_in_file`` test tool was failing
to load and was not tested at all during framework tests on GitHub Actions.
2022-09-30 01:19:43 +01:00
Nicola Soranzo
ea4461751c
Use loc file that actually exists in the param validators of test tool
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Previously, the ``validation_dataset_metadata_in_file`` test tool was failing
to load and was not tested at all during framework tests on GitHub Actions.
2022-09-29 01:50:33 +01:00
Nicola Soranzo
fe83c7f99b
Merge branch 'release_22.05' into dev
2022-09-06 12:31:22 +01:00
Nicola Soranzo
70b2ea429c
Merge branch 'release_22.01' into release_22.05
2022-09-06 12:12:21 +01:00
Nicola Soranzo
9f1d8d053b
Merge branch 'release_21.09' into release_22.01
2022-09-06 11:36:36 +01:00
Nicola Soranzo
06baa27d05
Merge branch 'release_21.05' into release_21.09
2022-09-06 11:24:20 +01:00
Nicola Soranzo
8069584d0f
Merge branch 'release_21.01' into release_21.05
2022-09-06 11:12:59 +01:00
mvdbeek
b43dfa2613
Merge branch 'release_22.05' into dev
2022-08-30 20:37:56 +02:00
Matthias Bernt
59f77048ce
test case showing failing set_meta
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broke in https://github.com/galaxyproject/galaxy/commit/7d0ec29fa06ae6f04c0ae6fc193a390bc11cddcd
2022-08-25 16:45:26 +02:00
mvdbeek
94c75a083c
Fix setting metadata elements in conditional tool action
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Fixes https://github.com/galaxyproject/galaxy/issues/14509
2022-08-25 14:27:44 +02:00
mvdbeek
2e22b9e1f8
Merge branch 'release_22.05' into dev
2022-08-22 19:17:35 +02:00
Nicola Soranzo
b5a75cac27
Merge branch 'release_22.01' into release_22.05
2022-08-19 15:28:58 +01:00
Matthias Bernt
8ef9ef4383
fix test
2022-08-18 14:28:55 +02:00
Marius van den Beek
f53edd1f18
Merge pull request #14314 from bernt-matthias/topic/cond_out_action_bool
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Extend docs and tests for conditional output actions
2022-08-11 16:53:41 +02:00
mvdbeek
a351bd1ce9
Merge branch 'release_22.05' into dev
2022-08-09 15:12:15 +02:00
Nicola Soranzo
e383e593e0
Merge branch 'release_22.01' into release_22.05
2022-07-27 15:38:19 +01:00
Matthias Bernt
fe06eea75d
fix test output
2022-07-15 10:49:12 +02:00
M Bernt and Nicola Soranzo
d7272cc987
Update test/functional/tools/options_from_metadata_file.xml
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2022-07-14 23:30:11 +02:00
Matthias Bernt
d642ce34c8
fix startswith attribute of <options>
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as documented in the xsd
in addition fix https://github.com/galaxyproject/galaxy/issues/14324 ,
i.e. document the `separator` attribute of options
also doc that only 1MB is used and lines starting with `#` are always
ignored
2022-07-14 14:19:40 +02:00
Matthias Bernt
85ec7832ba
extend docs and tests for conditional output actions
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for the case that a boolean is referred.
In this case the python string value of the parameter value
needs to be used as the value for the when tag which might be a
bit confusing.
The test is also extended such that:
- multiple (two) conditional actions are used in one output
- referring parameters in sections
2022-07-12 14:51:38 +02:00
Nicola Soranzo
a382eacc58
Fix B023 warnings from flake8-bugbear 22.7.1
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The new flake8-bugbear 22.7.1 warns if a function defined inside a loop uses
a variable redefined in the loop, due to the late-binding closure gotcha:
https://docs.python-guide.org/writing/gotchas/#late-binding-closures
When possible/sensible, I've moved the function definition before the loop
(adding the variable(s) as parameters) which is clearly also a speed-up.
Most other cases are false alarms, e.g. if the function is used and
discarded within the loop iteration that defines it. In such cases, I've
annotated the offending lines with a `# noqa: B023`.
The only file where I've applied the suggested workaround of immediately
binding arguments is in `lib/galaxy/visualization/plugins/config_parser.py`
Also:
- Small refactorings, in particular to `scripts/apply_tags.py`
2022-07-05 12:28:37 +01:00
Nicola Soranzo
b111384289
Merge branch 'release_22.05' into dev
2022-06-27 10:55:24 +01:00
mvdbeek
df6551da78
Test that metadata validators work
2022-06-25 12:55:51 +02:00
Nicola Soranzo
d3b4ef81d0
Merge branch 'release_21.09' into release_22.01
2022-06-23 14:30:57 +01:00
Nicola Soranzo
14b1730eb2
Combine "as" imports with other "from" imports
2022-06-20 20:06:30 +01:00
Dannon
155c1c6e48
Merge pull request #5378 from jmchilton/resource_requirements
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Allow specification of resource requirements in tools.
2022-06-20 14:11:35 -04:00
mvdbeek
1df9646747
Add <resource/> tag set to schema, add tool
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I think this leaves us more room to write expressions without having to
escape everything.
2022-06-15 13:53:58 +02:00
mvdbeek
55ecc382e7
Add selenium test for ucsc table browser data source
2022-06-13 11:03:13 +02:00
mvdbeek
5ea0a53538
Add selenium test for ucsc table browser data source
2022-06-09 15:03:45 +02:00
Marius van den Beek
7cb3f76c6e
Merge pull request #12232 from bernt-matthias/topic/drilldown
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fix `drill_down` parameters
2022-05-25 15:52:50 +02:00
Marius van den Beek
ac510bc8dc
Merge pull request #7894 from bernt-matthias/topic/count-pairs-correctly
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Fix docs for `expect_num_outputs` and add `count` attribute for test `output` and `element` tags
2022-05-25 15:23:10 +02:00
mvdbeek
704af8fc59
Fix collection_creates_dynamic_list_of_pairs test
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The upload1 tool would have created a dataset in the history that would
have become auto-selected ... which is of course a bug when running
tools via the API, xref
https://github.com/galaxyproject/galaxy/issues/13799 .
2022-04-23 12:16:42 +02:00
M Bernt and Marius van den Beek
803b9a5a5b
Apply suggestions from code review
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-04-22 12:05:56 +02:00
M Bernt
228d07a9cc
Merge branch 'dev' into topic/count-pairs-correctly
2022-04-21 13:03:59 +02:00
Matthias Bernt
ad70b9bc4a
fix config file generation
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always create the config file in `job_directory/configs/` and
if `filename` is given create a symlink to the actual config file
fixes https://github.com/galaxyproject/galaxy/issues/13586
2022-04-21 11:15:07 +02:00
John Chilton
c247b38b3d
Fixup simple_constructs.yml...
2022-04-19 11:23:44 -04:00
Nicola Soranzo
8adc7ec870
Merge branch 'release_21.09' into release_22.01
2022-04-11 19:03:41 +01:00
Matthias Bernt
4bc560383f
add test for correct sorting on recursive discovery
2022-04-08 19:38:50 +02:00
Nicola Soranzo