Matthias Bernt
db7395b423
Create version 24.1.4
2024-12-11 10:47:48 +01:00
Nicola Soranzo
58496b913e
Merge branch 'release_24.0' into release_24.1
2024-12-10 21:16:00 +00:00
Björn Grüning
3f3fd82df3
Merge pull request #19300 from bernt-matthias/lint_from_url
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[24.0] Linter: allow dynamic option definition by from_url
2024-12-10 21:01:14 +01:00
Matthias Bernt
3ca72f0fc1
linter: allow dynamic option definition by from_url
2024-12-10 18:22:32 +01:00
Marius van den Beek
45f315d91f
Merge pull request #19297 from nsoranzo/release_24.1_fix_merge
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[24.1] Fix bad merge conflict resolution
2024-12-10 12:52:27 +01:00
Nicola Soranzo
c843938e70
Fix bad merge conflict resolution
2024-12-10 11:37:56 +00:00
Nicola Soranzo
e5f0a8c4eb
Merge branch 'release_24.0' into release_24.1
2024-12-10 10:51:03 +00:00
Nicola Soranzo
b39c3b2514
Merge pull request #19295 from bgruening/flip_mamba
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[24.1] flip default value for use_mamba to false
2024-12-10 10:30:25 +00:00
Bjoern Gruening
285bdf4fba
flip default value for use_mamba to false
2024-12-09 22:08:39 +01:00
Marius van den Beek
ee5f8076cf
Merge pull request #19222 from wm75/fix-harmonize
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[24.0] Create harmonized collections from correct tool outputs
2024-12-02 16:38:40 +01:00
John Chilton
1e6a5c09c9
Merge pull request #19215 from mvdbeek/24_0_fix_various_invocation_export_issues
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[24.0] Fix various invocation export issues
2024-11-29 11:45:42 -05:00
Wolfgang Maier
891d7aa0bf
Try to fix tool test
2024-11-29 16:59:11 +01:00
Wolfgang Maier
129b8a2125
Fix test file type
2024-11-29 16:59:11 +01:00
Wolfgang Maier
a42d7f30a7
Create harmonized collections from correct tool outputs
2024-11-29 16:59:11 +01:00
Martin Cech
f4ab432ad6
Merge pull request #19195 from arash77/pr-title-update-change-base
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[24.0] Update PR title handling for changing base ref
2024-11-29 13:08:06 +01:00
mvdbeek
e301ec99c7
Fix up action_arguments for workflows converted by gxformat2 < 0.20.0
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Fixes https://github.com/galaxyproject/galaxy/issues/18995
2024-11-28 15:16:49 +01:00
mvdbeek
91fc1d80c7
Only allow admin users to sync workflows to filesystem
2024-11-27 19:04:39 +01:00
mvdbeek
f631f62669
Don't store workflow_path when importing invocation
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It's a temporary path and probably doesn't make much sense in the
context of an imported invocation.
2024-11-27 19:04:39 +01:00
mvdbeek
2d7667d958
Add regression test for #18927
2024-11-27 18:34:41 +01:00
mvdbeek
b265c2bda9
Don't duplicate exported collections if they're references multiple times
2024-11-27 18:34:41 +01:00
mvdbeek
28ce456292
Prevent assigning opied_from_history_dataset_collection_association if hdca points to self
2024-11-27 18:34:40 +01:00
mvdbeek
e57201e92d
Drop unused copied_to_history_dataset_collection_association relationship
2024-11-27 18:34:40 +01:00
mvdbeek
e9194d7028
Fix exporting of jobs that set copied_from_history_dataset_association
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Without this change jobs like `__EXTRACT_DATASET__` would not be
included in a history or invocation export`.
2024-11-27 18:34:40 +01:00
mvdbeek
137dc4eea1
Fix workflow_invocation_step not being added to session
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if the step is not a job step. This broke in https://github.com/galaxyproject/galaxy/commit/ab2f76c94d89fd9419b1dc0bc5ea606834cdbe2b
where
```
# Safeguard: imported_invocation_step was implicitly merged into this Session prior to SQLAlchemy 2.0.
self.sa_session.add(imported_invocation_step)
```
was replaced with
```
ensure_object_added_to_session(imported_invocation, session=self.sa_session)
```
which seems like a small typo-like bug.
2024-11-27 18:34:37 +01:00
Marius van den Beek
616fe39e2e
Merge pull request #19159 from mvdbeek/make_runtime_value_open_legacy_form
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[24.1] Make runtime value in optional parameter open legacy workflow run form
2024-11-26 16:45:02 +01:00
Arash and Nicola Soranzo
afdfa789f1
Refactor version extraction in PR title update workflow for improved accuracy
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Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk >
2024-11-26 12:20:19 +01:00
Arash
f3e65fa1b9
Refactor PR title update workflow to handle version extraction and title formatting more efficiently
2024-11-25 11:39:58 +01:00
John Davis
d59f7a6014
Merge pull request #19183 from nsoranzo/release_24.0_check_base_ref_changed
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[24.0] Update title of edited PRs only if base ref changed
2024-11-22 10:41:37 -05:00
Nicola Soranzo
09d86951b1
Update title of edited PRs only if base ref changed
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Also:
- Update title of reopened PRs too.
- Don't unnecessarily checkout the repo.
2024-11-22 12:16:03 +00:00
Marius van den Beek
7ab0c0918b
Merge pull request #19155 from mvdbeek/fix_aws_file_source_template
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[24.1] Fix production_aws_private_bucket.yml
2024-11-22 10:37:02 +01:00
Marius van den Beek
c290421d6e
Merge pull request #19174 from davelopez/24.1_fix_pickle_issue_in_celery_notifications
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[24.1] Remove the default `Incoming` suffix in `GenericModel` class
2024-11-21 17:02:13 +01:00
davelopez
f96111a4ae
Add PatchGenericPickle to fix pickle issue in celery notifications
2024-11-20 18:23:41 +01:00
Nicola Soranzo
f3823055cf
Merge pull request #19162 from mvdbeek/optimize_converter_order
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[24.1] Prefer auto-decompressed datatype when picking conversion target
2024-11-20 00:00:41 +00:00
mvdbeek
29da6fec23
Add selenium test for optional runtime parameter submission
2024-11-19 17:35:04 +01:00
mvdbeek
1bdd9e7af5
Make runtime value in optional parameter open legacy workflow run form
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We can only accept disconnected optional data inputs, for all other
parameters we need to replace the runtime value placeholder.
2024-11-19 17:35:04 +01:00
mvdbeek
974d7e58bf
Tighten conversion target input
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This way we test that conversion to txt occurs via fasta, not the fasta
to tabular converter.
2024-11-19 17:33:58 +01:00
mvdbeek
f559ced17d
Prefer auto-decompressed datatype when picking conversion target
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Fixes https://github.com/galaxyproject/galaxy/issues/18709
2024-11-19 17:33:58 +01:00
Marius van den Beek
da31407117
Merge pull request #19160 from dannon/cherrypick-phylocanvas-build-fix
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[24.1] Add buffer as a devDependency in phylocanvas package.json
2024-11-19 17:33:47 +01:00
davelopez
d088fe764b
Add buffer as a devDependency in phylocanvas package.json
2024-11-19 09:20:21 -05:00
mvdbeek
e37eba31cb
Fix production_aws_private_bucket.yml
2024-11-18 12:32:48 +01:00
Marius van den Beek
6cc2fec100
Merge pull request #18495 from mvdbeek/dont_call_stop_job_for_new_jobs
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[24.1] Don't call job_runner.stop_job on jobs in new state
2024-11-15 18:55:58 +01:00
Marius van den Beek
2c59753744
Merge pull request #19083 from ahmedhamidawan/use_singular_default_box_in_upload
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[24.1] Persist uploaded data between Regular and Collection upload tabs
2024-11-08 09:22:45 +01:00
Ahmed Awan
d6a5f99cc1
use explicit selector for regular tab start button (upload tour)
2024-11-07 17:22:12 -06:00
Ahmed Awan
b8dbc5236f
fix selectors unable to find upload start or close buttons
2024-11-07 15:00:27 -06:00
Ahmed Awan
6364764c33
fix _perform_upload method to use proper selector
2024-11-06 17:19:02 -06:00
Nicola Soranzo
6004c814b3
Merge branch 'release_24.0' into release_24.1
2024-11-05 23:02:11 +00:00
Nicola Soranzo
46c1dcdc23
Merge pull request #19106 from mvdbeek/sqlite_fix_workflow_test
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[24.0] Optimize/fix sqlite hid update statement
2024-11-05 15:35:06 +00:00
mvdbeek
71e499bb78
Optimize/fix sqlite hid update statement
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`./run_tests.sh --skip-common-startup -api lib/galaxy_test/api -- -s -k
cache` would fail on sqlite with database locked.
Not using a separate connection means that we expire loaded attributes
in the sqlite case, but I don't think we need to be concerned about
performance if you're using sqlite.
2024-11-05 13:58:14 +01:00
mvdbeek
58ff6d20d0
Merge branch 'release_24.0' into release_24.1
2024-10-31 15:18:20 +01:00
Marius van den Beek
2311374cdb
Merge pull request #19079 from ahmedhamidawan/fetch_invocation_id_once_job_info
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[24.0] Fetch invocation id only once on the job info page
2024-10-31 10:16:18 -04:00
Matthias Bernt