John Chilton
518fa136d9
[WIP] Implement records - heterogenous dataset collections.
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Existing dataset colleciton types are meant to be homogenous - all datasets of the same time. This introduces CWL-style record dataset collections.
2025-05-09 16:38:19 -04:00
Ahmed Hamid Awan
d7fa1d19ce
Merge pull request #19054 from jmchilton/tool_markdown
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Implement tool markdown reports.
2025-05-06 20:49:30 +05:00
Marius van den Beek
79638b883a
Merge pull request #19753 from bernt-matthias/env-fix-24.1
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Fix setting env and tags on resubmission
2025-05-06 17:23:45 +02:00
Marius van den Beek
507719beb5
Merge pull request #20162 from mvdbeek/yaml_parser_fixes_part2
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Yaml parser fixes part2
2025-05-06 09:13:11 +02:00
John Chilton
4e4017c1be
Merge pull request #20152 from jmchilton/collection_cleanup_2
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Fix certain cases of collection parameter handling during workflow execution.
2025-05-05 15:45:36 -04:00
mvdbeek
7ed247059a
Fix conditional parsing
2025-05-05 20:37:17 +02:00
mvdbeek
fa3c19c2a4
Merge branch 'release_24.2' into dev
2025-05-05 16:52:31 +02:00
mvdbeek
a53b4125aa
Skip `param_value` filter if ref value is runtime value
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Fixes https://github.com/galaxyproject/galaxy/issues/20136
2025-05-04 16:48:33 +02:00
John Chilton
9b0fb38a76
More workflow mapping test cases.
2025-05-03 10:21:17 -04:00
John Chilton
f9e1022360
Test case for bug where workflow collection mapping interprets collection at wrong rank.
2025-05-03 10:21:17 -04:00
John Chilton
1f95f421c9
Tool markdown reports.
2025-05-02 11:25:21 -04:00
Marius van den Beek
01e36311a4
Merge pull request #19954 from bernt-matthias/ext-lower
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Use lower case extension for setting datatype in data discovery
2025-04-16 12:52:23 +02:00
mvdbeek
29d3c23cf2
Merge branch 'release_24.2' into dev
2025-04-15 17:53:08 +02:00
Marius van den Beek
a8cf438ec5
Merge pull request #19763 from jmchilton/missing_functional_tool
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Add missing test file.
2025-04-15 15:09:42 +02:00
Marius van den Beek and M Bernt
e2647616c5
Fix typo
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Co-authored-by: M Bernt <m.bernt@ufz.de >
2025-04-15 15:09:32 +02:00
Marius van den Beek
7a1ea09e9c
Merge pull request #19949 from jmchilton/parameter_model_fixes_0
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[24.2] Fix various parameter validation issues.
2025-04-15 15:08:28 +02:00
mvdbeek
6edab86870
Merge branch 'release_24.2' into dev
2025-04-10 18:54:17 +02:00
mvdbeek
4f9180604f
Make dbkey_filter_input more realistic, regression test for https://github.com/galaxyproject/galaxy/issues/19975
2025-04-10 16:59:09 +02:00
Matthias Bernt
e612db1680
extend tests
2025-04-03 10:32:50 +02:00
John Chilton
f37075c1a5
Fix various parameter validation issues.
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I previously failed to include a bunch of validation checks I assumed had been covered so fixed that first and got a bunch of new issues detected. Also added a parameter specification test case for https://github.com/galaxyproject/galaxy/issues/19908 and fixed that.
2025-04-02 12:49:09 -04:00
Matthias Bernt
0c186b227e
fix test
2025-03-26 18:07:57 +01:00
Matthias Bernt
ef72ecbb66
remove tool test assertions
2025-03-26 17:37:17 +01:00
Matthias Bernt
5b017b240f
fix test
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tool fails with no env var set
failing tool tests allow no output
2025-03-26 13:52:29 +01:00
Matthias Bernt
0247be1866
fix test tool test
2025-03-26 13:52:22 +01:00
Matthias Bernt
70bfcc44dc
fix resubmission integration test
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the test `test/integration/test_job_resubmission.py::TestJobResubmissionToolDetectedErrorResubmitsIntegration`
resubmits with:
```
<destination id="local_resubmit" runner="local">
<env id="GX_TARGET_EXIT_CODE">4</env>
<resubmit condition="tool_detected_failure" destination="local_good" />
</destination>
<destination id="local_good" runner="local">
<env id="GX_TARGET_EXIT_CODE">0</env>
</destination>
```
since env variables are lost on resubmission the current test
was still evaluated successful (because `${GX_TARGET_EXIT_CODE:-0}`).
Now the test fails if `GX_TARGET_EXIT_CODE` is not set.
2025-03-26 13:52:08 +01:00
mvdbeek
3c6b6c5971
Merge branch 'release_24.2' into dev
2025-03-26 09:51:08 +01:00
mvdbeek
3c12acb270
Assert column_types
2025-03-25 10:29:01 +01:00
mvdbeek
8622dfa237
Merge branch 'release_24.2' into dev
2025-03-14 09:32:27 +01:00
mvdbeek
858593a8ba
Fix transfer of $_TOOL_DIRECTORY subdirectories
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Goes together with https://github.com/galaxyproject/pulsar/pull/385
2025-03-13 16:19:10 +01:00
mvdbeek
eb1709fcbb
Merge branch 'release_24.2' into dev
2025-03-08 11:20:03 +01:00
Marius van den Beek
54de00e2cf
Merge pull request #19694 from mvdbeek/bwa_index_directory_datatype
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[24.2] Add bwa_mem2_index directory datatype, framework enhancements for testing directories
2025-03-08 11:14:52 +01:00
John Chilton
cc14cb4719
Missing test file.
2025-03-07 10:14:50 -05:00
mvdbeek
ab2f7c3b57
Merge branch 'release_24.2' into dev
2025-02-28 12:34:02 +01:00
Marius van den Beek and Björn Grüning
e6b27a32b2
Adjust test tool and datatype config to best practices
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Co-authored-by: Björn Grüning <bjoern@gruenings.eu >
2025-02-26 13:18:25 +01:00
mvdbeek
07a4a7c058
Fix directory uploads, use `__FETCH_DATA__` api
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for tool tests, which were still using upload1.
2025-02-25 18:10:10 +01:00
John Chilton
387ce7dd37
Add failing test case for #19678
2025-02-25 11:39:58 -05:00
mvdbeek
6512b4c366
Add bwa_mem2_index datatype
2025-02-19 17:26:09 +01:00
John Davis
5cf48dc995
Merge remote-tracking branch 'upstream/release_24.2' into dev
2025-02-14 17:05:07 -05:00
mvdbeek
871a6901be
Test sanitization
2025-02-11 14:36:20 +01:00
mvdbeek
2e6841680c
Merge branch 'release_24.1' into release_24.2
2025-01-28 15:55:05 +01:00
mvdbeek
6006816033
Add regression test for https://github.com/galaxyproject/galaxy/issues/19245
2025-01-27 15:35:42 +01:00
mvdbeek
f65b754dd0
Add regression test for https://github.com/galaxyproject/galaxy/issues/19245
2025-01-10 18:55:08 +02:00
mvdbeek
b88a792b93
Merge branch 'release_24.2' into dev
2024-12-20 11:19:56 +01:00
mvdbeek
962839d68d
Merge branch 'release_24.1' into release_24.2
2024-12-20 11:19:12 +01:00
Marius van den Beek and Nicola Soranzo
d66555ec1e
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2024-12-19 16:54:03 +01:00
Marius van den Beek
5c2a471afa
Fix branch reference
2024-12-19 15:47:09 +01:00
mvdbeek
02492685cc
Use select_from_url test data from github, not usegalaxy.org
2024-12-19 14:14:05 +01:00
Nicola Soranzo
26a4e146e0
Fix UP031 errors
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reported by ruff 0.8.0 .
2024-11-24 21:35:23 +00:00
Marius van den Beek
363ab5342f
Merge pull request #12941 from bernt-matthias/topic/data-table-filter
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Dynamic options: add data table filter
2024-11-22 17:53:40 +01:00
M Bernt and Marius van den Beek
f2100cc3f9
Update test/functional/tools/filter_data_table.xml
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2024-11-21 17:36:36 +01:00
John Chilton