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Author SHA1 Message Date
mvdbeek 5fa648aa92 Ensure we copy the cached jobs' extension 
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 
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 
[24.2] bugfix in psa-authnz redirect handling
 2025-04-07 18:36:48 +02:00
Marius van den Beek d244ef708d Merge pull request #19967 from kysrpex/custos_reject_expired_tokens 
[24.2] Renew OIDC access tokens using valid refresh tokens
 2025-04-07 17:28:31 +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 
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
Marius van den Beek 452b93a56a Merge pull request #19953 from mvdbeek/sort_options 
[24.2] Sort intersected options
 2025-04-03 15:05:24 +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 
[24.2] Fix attempt restriction on multiple connections
 2025-04-03 09:31:49 +02:00
Marius van den Beek 4de5ceb85d Merge pull request #19947 from mvdbeek/fix_history_exports 
[24.2] Use ``make_fast_zipfile`` directly
 2025-04-02 18:59:56 +02:00
mvdbeek b240f9e427 Fix attempt restriction on multiple connections 
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 
`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 
[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 
[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
David López 462dc8364f Merge pull request #19930 from davelopez/24.1_fix_invenio_download_reliability 
[24.1] Fix Invenio file source downloads not working with some Invenio instances
 2025-03-31 15:46:16 +02:00
davelopez 4f6c4a0a2d Fix file download logic in InvenioRepositoryInteractor 
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
John Davis b731dde238 Merge pull request #19925 from jdavcs/24.1_19880 
[24.1] Handle special charater in raw SQL
 2025-03-28 13:34:31 -04:00
Marius van den Beek 40fc61c847 Merge pull request #19928 from bernt-matthias/linter-error-test-case-validation 
[24.2] Report TestCaseValidation as linter error for 24.2 and above
 2025-03-28 18:23:44 +01:00
M BerntandNicola Soranzo f43486a58b Update lib/galaxy/tool_util/linters/tests.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-03-28 16:25:25 +01:00
Marius van den Beek 53aa74a0d0 Merge pull request #19913 from davelopez/24.2_fix_duplicate_data_on_drop 
[24.2] Fix duplicate entries when using drag and drop in multiple mode
 2025-03-28 16:20:12 +01:00
John Davis 1bf72997a0 Handle "%" character in raw SQL 
This statement is prepared for SQLAlchemy but executed via psycopg2 in
the `pgcleanup.py` script. For psycopg2, the "%" character should be replaced
with %% (see docs
https://www.psycopg.org/docs/usage.html#passing-parameters-to-sql-queries).
SQLAlchemy already takes care of it automatically.
 2025-03-28 15:08:21 +00:00
Nicola Soranzo b10c957646 Add type annotations to `calculate_user_disk_usage_statements()` 
and related code.
 2025-03-28 14:56:51 +00:00
M BerntandNicola Soranzo 09269c19fa Apply suggestions from code review 
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
davelopez d36e867445 Enhance FormData handling to prevent duplicate entries 2025-03-28 12:21:52 +01:00
davelopez 989a615f60 Refactor handleIncoming function to use toDataOption 
For reusability
 2025-03-28 12:20:29 +01:00
Marius van den Beek 64648e36b5 Merge pull request #19917 from mvdbeek/index_with_extra_threads 
[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 
[24.2] Skip ``data_meta`` filter in run form
 2025-03-27 09:18:37 -04:00
Marius van den Beek 1a2f9ab5df Merge pull request #19911 from davelopez/24.2_skip_implicitly_converted_in_tool_build_options 
[24.2] Skip implicit HDA conversions in DataToolParameter options
 2025-03-27 12:12:32 +01:00
davelopez 19c448adc6 Add containsDataOption function to prevent duplicate entries in FormData 
When drag and dropping the same item
 2025-03-27 10:49:36 +01:00
davelopez cc2ee180d6 Move itemUniqueKey function to types module for reuse 2025-03-26 18:10:32 +01:00
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 
[24.2] Fix duplicate extensions for data inputs
 2025-03-26 10:02:43 +01:00
Marius van den Beek 7bd3e599ad Merge pull request #19837 from jdavcs/24.2_multiselect 
[24.2] Do not reorder options in FormSelect component when multiselect disabled
 2025-03-26 10:01:59 +01:00
Marius van den Beek 1761e48055 Merge pull request #19853 from jdavcs/24.2_admin_ordering 
[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
Marius van den Beek a1418f3f30 Merge pull request #19896 from nsoranzo/release_24.0_drop_alembic-utils 
[24.0] Drop unused alembic-utils from galaxy-data package requirements
 2025-03-26 09:42:35 +01:00
Nicola Soranzo 8f0e11b929 Use `best_search_result()` function instead of parsing anaconda.org web pages 
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 
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
John Chilton b1f401d56d Merge pull request #19797 from mvdbeek/fix_collection_builder_input_restriction 
[24.2] Fix collection builder input states
 2025-03-25 12:00:08 -04:00
Marius van den Beek 68be79f17a Merge pull request #19841 from ahmedhamidawan/fix_directory_form_element_encoding 
[24.2] Decode/encode FormDirectory paths to allow spaces (and other characters)
 2025-03-25 16:50:24 +01:00