mvdbeek
5fa648aa92
Ensure we copy the cached jobs' extension
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The cached job might be skipped and null, in which case we should not
override the `expression.json` extension, because in that case the
dataset would not be considered as a null.
2025-04-10 15:43:04 +02:00
mvdbeek
fd3d3dbc5b
Fix cache for skipped jobs
2025-04-10 12:20:24 +02:00
mvdbeek
7a8ea3e165
Only pick up cached jobs in OK and skipped states
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It's absolutely feasible to include all types of non-terminal jobs,
but we're missing a bit of test coverage to make sure the jobs always
progress to the same terminal state that the original jobs do.
Also likely fixes https://github.com/galaxyproject/galaxy/pull/19976#discussion_r2036836846
2025-04-10 11:27:53 +02:00
Marius van den Beek
3e62662be0
Merge pull request #19968 from dannon/fix-redirect-cookie-handling
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[24.2] bugfix in psa-authnz redirect handling
2025-04-07 18:36:48 +02:00
Dannon Baker
c417229723
Fix issue where a literal string 'None' is getting set for a login redirect url, which breaks default redirect resolution in authnz
2025-04-07 10:51:54 -04:00
José Manuel Domínguez
0024c84dd3
Renew OIDC access tokens using valid refresh tokens
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Method `OIDCAuthnzBase.refresh()` from custos_authnz.py is supposed to not attempt to use refresh tokens that are already expired. However, the comparison of the token's expiration time with the current time is wrong. Fix the comparison so that it works as intended.
2025-04-07 14:02:07 +02:00
mvdbeek
492fd293f8
Sort intersected options
2025-04-03 09:55:56 +02:00
Marius van den Beek
297ebf7bb7
Merge pull request #19948 from mvdbeek/fix_intersection_in_attempt_value_restriction
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[24.2] Fix attempt restriction on multiple connections
2025-04-03 09:31:49 +02:00
mvdbeek
b240f9e427
Fix attempt restriction on multiple connections
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Broken by the extra elements in the ParameterOption named tuple
introduced in https://github.com/galaxyproject/galaxy/pull/19659 .
2025-04-02 18:13:58 +02:00
mvdbeek
0fdfc13ca5
Use make_fast_zipfile directly
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`make_archive` is not thread-safe and may change the cwd, which can
break history exports.
2025-04-02 17:30:58 +02:00
Nicola Soranzo
a7dc613fbf
Merge pull request #19945 from mvdbeek/job_cache_query_improvement
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[24.2] Drop unnecessary job cache job subquery
2025-04-02 11:16:20 +01:00
mvdbeek
fcadab4b10
Drop unnecessary job cache job subquery
2025-04-02 09:49:04 +02:00
Marius van den Beek
b5ead3b558
Merge pull request #19942 from mvdbeek/better_interactive_tool_entry_point_query
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[24.2] Better interactive tool entry point query
2025-04-02 09:07:54 +02:00
mvdbeek
ab1b36c26d
Better interactive tool entry point query
2025-04-01 21:37:25 +02:00
mvdbeek
5180c13aae
Merge branch 'release_24.1' into release_24.2
2025-03-31 16:59:14 +02:00
davelopez
4f6c4a0a2d
Fix file download logic in InvenioRepositoryInteractor
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Improve download reliability by using always the client route since the API route only works with certain Invenio storage configurations and servers.
2025-03-31 11:50:01 +02:00
Nicola Soranzo
cd11d22129
Merge branch 'release_24.1' into release_24.2
2025-03-28 17:55:45 +00:00
Marius van den Beek
40fc61c847
Merge pull request #19928 from bernt-matthias/linter-error-test-case-validation
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[24.2] Report TestCaseValidation as linter error for 24.2 and above
2025-03-28 18:23:44 +01:00
M Bernt and Nicola Soranzo
f43486a58b
Update lib/galaxy/tool_util/linters/tests.py
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2025-03-28 16:25:25 +01:00
Nicola Soranzo
b10c957646
Add type annotations to `calculate_user_disk_usage_statements()`
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and related code.
2025-03-28 14:56:51 +00:00
M Bernt and Nicola Soranzo
09269c19fa
Apply suggestions from code review
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2025-03-28 13:43:20 +01:00
Matthias Bernt
8c92cee846
report TestCaseValidation as error for 24.2 and above
2025-03-28 13:17:23 +01:00
Marius van den Beek
64648e36b5
Merge pull request #19917 from mvdbeek/index_with_extra_threads
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[24.2] Let pysam use extra threads available in job
2025-03-27 18:47:50 +01:00
mvdbeek
45790b3fe7
Let pysam use extra threads available in job
2025-03-27 17:27:51 +01:00
John Chilton
7186563e5c
Merge pull request #19895 from mvdbeek/skip_data_meta_filter_run_form_restriction
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[24.2] Skip ``data_meta`` filter in run form
2025-03-27 09:18:37 -04:00
davelopez
041fa02f09
Skip implicit HDA conversions in DataToolParameter options
2025-03-26 17:33:46 +01:00
Marius van den Beek
50b62acca6
Merge pull request #19903 from ahmedhamidawan/fix_accepted_formats_duplicate
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[24.2] Fix duplicate extensions for data inputs
2025-03-26 10:02:43 +01:00
Marius van den Beek
1761e48055
Merge pull request #19853 from jdavcs/24.2_admin_ordering
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[24.2] Fix default ordering of items sorted by name
2025-03-26 10:00:42 +01:00
mvdbeek
648239a31f
Merge branch 'release_24.1' into release_24.2
2025-03-26 09:48:18 +01:00
mvdbeek
953a972349
Merge branch 'release_24.0' into release_24.1
2025-03-26 09:44:07 +01:00
Nicola Soranzo
8f0e11b929
Use `best_search_result()` function instead of parsing anaconda.org web pages
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Fix the following mulled unit test:
```
FAILED test/unit/tool_util/mulled/test_get_tests.py::test_hashed_test_search - AssertionError: assert ['samtools --help'] == ['bamtools --help', 'samtools --help']
At index 0 diff: 'samtools --help' != 'bamtools --help'
Right contains one more item: 'samtools --help'
Full diff:
- ['bamtools --help', 'samtools --help']
+ ['samtools --help']
```
that started not finding bamtools-2.4.0 inside
https://anaconda.org/bioconda/bamtools/files any more.
Also:
- Add type annotation to `CondaInDockerContext` and fix ensuing issues.
2025-03-25 19:45:07 +00:00
Ahmed Awan
7fbba6f54d
[24.2] Fix duplicate extensions for data inputs
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Fixes https://github.com/galaxyproject/galaxy/issues/19535
Fixes https://github.com/galaxyproject/galaxy/issues/19778
2025-03-25 14:23:37 -05:00
mvdbeek
4f1509c01a
Add API test that shows data_meta filter ignored in workflow run form
2025-03-25 18:36:40 +01:00
mvdbeek
0f72943993
Skip data_meta filter in run form
2025-03-25 18:35:09 +01:00
mvdbeek
cd640339d0
Fix output state update
2025-03-25 09:28:57 +01:00
Nate Coraor
ecc4b47804
Merge pull request #19824 from mvdbeek/fix_limit_bypass
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[24.2] Fix various job concurrency limit issues
2025-03-24 17:37:26 -04:00
Nicola Soranzo
6f607c4dea
Merge branch 'release_24.1' into release_24.2
2025-03-24 11:54:22 +00:00
Nicola Soranzo
1032fa4703
Merge branch 'release_24.0' into release_24.1
2025-03-24 11:53:30 +00:00
John Davis
e1f35c0077
Check if index exists before creating
2025-03-21 21:41:46 -04:00
John Chilton
bf47f53a6b
Merge pull request #19868 from mvdbeek/fix_double_push_of_unnamed_outputs
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[24.2] Don't collect unnamed outputs twice in extended metadata mode
2025-03-21 09:56:50 -04:00
mvdbeek
d78e0be049
Don't collect twice
2025-03-21 10:46:35 +01:00
John Chilton
ff011fbe01
Handle directories with percents in export_remote.xml.
2025-03-20 16:25:09 -04:00
John Davis
b588b27449
Fix default ordering for admin UI
2025-03-19 20:17:06 -04:00
John Davis
bb5a6a7b91
Try to recover from recurring activation link error
2025-03-18 19:05:43 -04:00
Dannon Baker
3598a2a014
Remove unused client route for standalone wizard interface
2025-03-18 12:22:28 -04:00
mvdbeek
c088f9c08a
Rebuild caches after clearing cache
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and before incrementing in-memory structures.
2025-03-18 14:10:10 +01:00
mvdbeek
1628fffb64
Don't bypass limits in slurm resubmission
2025-03-18 14:10:10 +01:00
mvdbeek
0b302d27f1
Drop redundant queued state in pulsar
2025-03-18 14:10:10 +01:00
mvdbeek
3e767c940e
Add unit tests for queue_with_limit
2025-03-18 14:10:09 +01:00
Martin Cech
078979362d
Merge pull request #19823 from mvdbeek/max_peek_size_50
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[24.2] Bump up max_peek_size to 50MB
2025-03-18 08:51:59 +01:00
mvdbeek