Nicola Soranzo
95c0950ba6
Add type annotations to `JobRunnerMapper` and related code
2024-11-07 15:19:32 +00:00
Marius van den Beek
8a0fbf638b
Merge pull request #19113 from mvdbeek/stage_hashes
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Enable specifying dataset hash in test jobs
2024-11-07 14:16:58 +01:00
mvdbeek
feb3747698
Enable specifying dataset hash in test jobs
2024-11-07 11:50:08 +01:00
Björn Grüning
206b729337
Merge pull request #19048 from mvdbeek/invocation_metrics_api
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Add job metrics per invocation
2024-11-06 20:02:39 +01:00
Marius van den Beek
4251715943
Merge pull request #19047 from jmchilton/toolshed_fixes
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Better search stuff in Tool Shed 2.0.
2024-11-06 17:08:13 +01:00
Marius van den Beek
360b72a82a
Improve user_id description, set email where needed
2024-11-06 11:42:18 +01:00
mvdbeek
3a6fdf24fb
Allow searching jobs in public histories for job cache
2024-11-06 11:42:18 +01:00
mvdbeek
ec6831e14b
Merge branch 'release_24.1' into dev
2024-11-06 11:33:46 +01:00
Nicola Soranzo
6004c814b3
Merge branch 'release_24.0' into release_24.1
2024-11-05 23:02:11 +00:00
John Davis
e5635dc2b7
Merge pull request #19073 from jmchilton/pydantic_model_linting
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Integrate Tool Parameter Modeling into Linting (for Planemo)
2024-11-05 17:52:10 -05:00
Nicola Soranzo
242c533b59
Merge pull request #19109 from nsoranzo/path_upload_check_hashes
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Test hash validation also for upload by path
2024-11-05 22:36:25 +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
Nicola Soranzo
b97ede779c
Add type annotations
2024-11-05 15:28:02 +00:00
Arash
5d9a867dbe
Move is_valid_slug function into SlugBuilder class as classmethod
2024-11-05 16:13:12 +01:00
Arash
4247a5cc44
Assert slug in response
2024-11-05 16:13:11 +01:00
Arash
9acb8a1fd0
order alphabetically
2024-11-05 16:13:10 +01:00
Arash
2740abe4c0
Add types-python-slugify library for mypy type check
2024-11-05 16:08:48 +01:00
Arash
49a22a62d5
remove unused import
2024-11-05 16:04:54 +01:00
Arash
29479cd00a
Refactor slug generation to use slugify library
2024-11-05 16:04:54 +01:00
Arash
17c962a66e
Refactor valid slug to just exclude /:?# characters
2024-11-05 16:04:52 +01:00
Arash
6f91b0f68e
Fix python lint
2024-11-05 16:04:51 +01:00
Arash
217ee881ec
Add test for sharing non-alphanumeric history
2024-11-05 16:04:50 +01:00
Arash
15ad84636a
Fix issue with generating slug for sharing history
2024-11-05 16:04:49 +01:00
John Davis
3523f02f0e
Merge pull request #19094 from jdavcs/dev_purged_no_login
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Prevent purged users from logging in
2024-11-05 09:46:23 -05:00
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
Nicola Soranzo
1fadd2f658
Do not recalculate dependencies when exporting
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Saves a few milliseconds :D
2024-11-05 09:53:16 +00:00
Aysam Guerler
1b4dd45f8d
Merge pull request #19097 from davelopez/support_deferred_datasets_in_visualizations
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Support deferred datasets in visualizations
2024-11-05 01:21:28 +03:00
Björn Grüning
a5aaa1c1be
Merge pull request #19077 from davelopez/allow_deferred_as_uri
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Allow deferred datasets to behave as URIs
2024-11-04 23:09:12 +01:00
mvdbeek
6b94267a88
Enable grouping by workflow step
2024-11-04 17:53:17 +01:00
mvdbeek
e5b300b9c1
Add job metrics per invocation
2024-11-04 17:53:17 +01:00
davelopez
2bdcec0dda
Add test for gx_allow_uri_if_protocol with deferred collections
2024-11-03 12:47:15 +01:00
davelopez
53e8a23747
Refactor deferred source URI handling in DatasetInstance and ToolEvaluator
2024-11-03 12:43:24 +01:00
davelopez
605389f1f2
Expand documentation on allow_uri_if_protocol
2024-11-03 11:06:25 +01:00
davelopez
557e7bed8d
Add is_deferred property to DatasetFilenameWrapper
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For improved handling of deferred data
2024-11-03 10:37:33 +01:00
davelopez
688b08a15a
Add wildcard support for all protocols in visualization checks
2024-11-02 14:02:04 +01:00
davelopez
4be350b8e0
Add support for URI protocols in visualization datatype checks
2024-11-02 13:28:26 +01:00
davelopez
5a35684b28
Refine deferred data source handling in visualization plugins
2024-11-01 10:36:35 +01:00
davelopez
92e1f199a6
Add support for deferred datasets in visualizations
2024-11-01 10:18:14 +01:00
Björn Grüning
3ff384319f
Merge pull request #19030 from jmchilton/fixes_for_21.01
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Fix numerous issues with tool input format "21.01"
2024-11-01 10:05:22 +01:00
Marius van den Beek
9b39ec7ef3
Merge pull request #18996 from martenson/schema-cond
2024-11-01 03:43:13 -04:00
John Davis
f89c1d7185
Prevent purged users from logging in
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Was possible if account was not deleted
2024-10-31 16:49:42 -04:00
Nicola Soranzo
febd6f9413
Use fissix to replace lib2to3 under Python >=3.13
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Add entries to `sys.modules` so that `future`/`past` can find
lib2to3 modules.
2024-10-31 12:09:22 +00:00
Nicola Soranzo
ac480e7df5
Drop use of deprecated imghdr standard library module
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which has been removed in the upcoming Python 3.13 .
2024-10-31 12:09:21 +00:00
Nicola Soranzo
f0420d70a3
Pin minimum package versions for Python 3.13 support
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Also:
- Cheetah3 package on PyPI has been renamed to CT3 since 3.3.0, see
https://cheetahtemplate.org/news.html
2024-10-31 12:09:20 +00:00
davelopez
72735ebf96
Remove redundant check for missing deferred input in ToolEvaluator
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There might be cases with additional deferred inputs outside of the input definitions see test_metadata_validator_on_deferred_input.
2024-10-31 11:57:47 +01:00
davelopez
18fb0a785e
Enhance allow_uri_if_protocol to support wildcard '*' for deferred datasets
2024-10-31 11:49:49 +01:00
Nicola Soranzo
93078d949a
Replace poetry with uv
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for lightning-fast Python dependency updates.
To update all dependencies (as done by the GitHub action):
$ make update-dependencies
To update only one package:
./lib/galaxy/dependencies/update.sh -p <PKG>
2024-10-31 10:22:52 +00:00
davelopez
678caa415f
Add test for allow_uri_if_protocol with deferred input
2024-10-31 11:17:17 +01:00
davelopez
fd14e606e8
Fix handling for missing deferred input in ToolEvaluator
2024-10-31 11:17:17 +01:00
davelopez
305dd2b181
Add has_deferred_data flag to MockDataset and FakeDatasetAssociation
2024-10-31 11:17:16 +01:00
Nicola Soranzo