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
Matthias Bernt
3ca72f0fc1
linter: allow dynamic option definition by from_url
2024-12-10 18:22:32 +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
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
...
[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
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
...
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
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
...
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
...
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
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
davelopez
f96111a4ae
Add PatchGenericPickle to fix pickle issue in celery notifications
2024-11-20 18:23:41 +01:00
mvdbeek
29da6fec23
Add selenium test for optional runtime parameter submission
2024-11-19 17:35:04 +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
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
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
Ahmed Hamid Awan
1042d386cb
Merge pull request #19068 from mvdbeek/fix_slow_workflow_count
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[24.1] Fix very slow workflow editor loading
2024-10-29 15:45:17 -04:00
mvdbeek
84b05313c1
Fix very slow workflow editor loading
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Loading the editor for my usegalaxy.org account takes 20 seconds. I've
narrowed this down to the unnecessary join against the workflow table
and loading all steps. I'm also returning the needed columns directly.
2024-10-28 16:22:29 +01:00
Matthias Bernt
17056521bd
Start work on 24.1.4.dev0
2024-10-25 12:51:08 +02:00
Matthias Bernt
71f5048e52
Create version 24.1.3
2024-10-25 12:51:02 +02:00
Matthias Bernt
56fae9bc6e
reset default channels
2024-10-21 21:32:34 +02:00
M Bernt and Nicola Soranzo
57b36669bb
also add home for default return
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2024-10-21 21:31:56 +02:00
Matthias Bernt
b99e3c8244
add miniforge3 to prefix search
2024-10-21 21:31:56 +02:00
Nicola Soranzo
af9b9efdd6
Remove conda defaults channel from more places
2024-10-21 21:31:56 +02:00
Matthias Bernt
14f382e9f0
deprecate 32bit conda installation option
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can be installed manually by affected users
2024-10-21 21:31:56 +02:00
Matthias Bernt
4e81a78c61
remove defaults channel for conda
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https://www.theregister.com/2024/08/08/anaconda_puts_the_squeeze_on/
According to the FAQs on https://repo.anaconda.com/pkgs/ this includes
`pkgs/main`, `pkgs/r`, and `pkgs/msys2`.
Seems also to be a good idea because for `mulled_channels` we apparently never used it (consistency).
2024-10-21 21:31:56 +02:00
John Chilton
666ab5e084
Merge pull request #19011 from jmchilton/fix_extra_call_to_test_data_path
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[24.1] Fix extra call to test_data_path that requires an admin key
2024-10-16 18:43:51 -07:00
John Chilton
d1d846f2e4
Merge pull request #19012 from mvdbeek/dont_recover_cached_jobs_on_startup
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[24.1] Put cached jobs back into queue on handler restart
2024-10-16 11:20:35 -07:00
mvdbeek
d772cbc620
Merge branch 'release_24.0' into release_24.1
2024-10-16 19:05:45 +02:00
mvdbeek
e1c0c08939
Put cached jobs back into queue on handler restart
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and don't recover job wrapper, which will fail since we don't actually
create a job working directory for cached jobs.
2024-10-16 18:38:41 +02:00
John Chilton
569eeb3086
Fix extra call to test_data_path that requires an admin key
2024-10-16 12:08:56 -04:00
mvdbeek
ced634a287
Fix job search statement building
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Broke in
https://github.com/galaxyproject/galaxy/commit/9a4ccbc58d861c74d11271736fc311834f0073c2 .
This gets worse the more inputs there are.
2024-10-16 17:17:44 +02:00
Nicola Soranzo
ceef7caad2
Merge branch 'release_24.0' into release_24.1
2024-10-16 11:03:57 +01:00
Nicola Soranzo
cfc31bcb40
Merge branch 'release_23.2' into release_24.0
2024-10-16 11:03:03 +01:00
Matthias Bernt