davelopez and mvdbeek
6248086ea0
Let the job queue handle the jobs deletion
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Co-authored-by: mvdbeek <m.vandenbeek@gmail.com >
2024-02-01 12:11:56 +01:00
davelopez
ffe354a523
Add API test for cancelling jobs for deleted users
2024-02-01 12:11:56 +01:00
davelopez
bd79ab453e
Cancel all active jobs when the user is deleted
2024-02-01 12:11:56 +01:00
David López
29290dea0c
Merge pull request #17391 from nsoranzo/black_2024
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Update to black 2024 stable style
2024-01-31 13:45:01 +01:00
Marius van den Beek
fa670f8f13
Merge pull request #17381 from nsoranzo/17367_followup
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More specific type annotation for ``BaseJobExec.parse_status()``
2024-01-31 10:54:49 +01:00
Aysam Guerler
da12de9702
Merge pull request #17282 from guerler/grids_batchoperation
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Adds delete, purge and undelete batch operations to History Grid
2024-01-30 15:56:53 -05:00
Nicola Soranzo
e975ca3754
Update to black 2024 stable style
2024-01-30 18:09:51 +00:00
Marius van den Beek and Nicola Soranzo
d08044c50b
Define variables
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2024-01-30 17:32:49 +01:00
Aysam Guerler and David López
4407ef981c
Update lib/galaxy/webapps/galaxy/api/histories.py
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Co-authored-by: David López <46503462+davelopez@users.noreply.github.com >
2024-01-30 10:45:21 -05:00
mvdbeek
e9d7b18d41
Adapt to upstream FileResponse logic
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The ``send_header_only`` attribute has been removed in starlette
(https://github.com/encode/starlette/pull/2366 ), and replaced with
`scope["method"].upper() == "HEAD"`
2024-01-30 16:39:22 +01:00
galaxybot
0c0da9c821
Update Python dependencies
2024-01-30 16:39:21 +01:00
Nuwan Goonasekera
431429c749
Merge pull request #17385 from ahmedhamidawan/minor_oidc_backends_comment_bug
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Fix minor oidc_backends_config comment bug
2024-01-30 12:56:17 +05:30
Aysam Guerler and David López
494c2e6d11
Update lib/galaxy/webapps/galaxy/api/histories.py
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Co-authored-by: David López <46503462+davelopez@users.noreply.github.com >
2024-01-29 15:33:00 -05:00
Ahmed Awan
409d8a42ae
Fix minor oidc_backends_config comment bug
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The comment for `<accepted_audiences>` in `oidc_backend_config` causes an error when starting Galaxy.
2024-01-29 13:08:48 -06:00
John Davis
e134e8b633
Merge branch 'release_23.2' into 'release_23.3'
2024-01-29 13:27:15 -05:00
John Davis
a1088bc0e2
Update version to 23.2.1.dev0
2024-01-29 13:27:14 -05:00
John Davis
9c593cd0ce
Update version to 23.2.
2024-01-29 13:27:13 -05:00
Nicola Soranzo
dad746eeed
More specific type annotation for `BaseJobExec.parse_status()`
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Add type annotation to ``BaseJobExec.parse_single_status()``
Follow-up on https://github.com/galaxyproject/galaxy/pull/17367#discussion_r1469748812 .
Needed to add ``TypeAlias`` to ``model.Job.states`` to fix:
```
lib/galaxy/jobs/runners/util/cli/job/__init__.py:67: error: Variable "galaxy.jobs.runners.util.cli.job.job_states" is not valid as a type [valid-type]
def parse_status(self, status: str, job_ids: List[str]) -> Dict[str, job_states]:
^
```
See https://mypy.readthedocs.io/en/stable/common_issues.html#variables-vs-type-aliases :
> You should always use ``TypeAlias`` to define a type alias in a class body
> or inside a function.
2024-01-29 18:04:41 +00:00
Marius van den Beek
5c6dd8eb4b
Merge pull request #17367 from nsoranzo/lxml-stubs
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Fix type annotation of code using XML etree
2024-01-29 16:19:16 +01:00
Nicola Soranzo
9a682d4373
Add assertion message
2024-01-29 14:14:14 +00:00
Nicola Soranzo
237626edc0
Fix type annotation of `BaseJobExec.parse_status()`
2024-01-29 13:49:35 +00:00
mvdbeek
e4147f78f1
Add explicit cache_ok attribute to JSONType subclass
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As for the other JSONType subclasses this is safe.
2024-01-29 10:31:20 +01:00
Nicola Soranzo
37116c39a0
Fix type annotation of code using XML etree
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by adding lxml-stubs to our typecheck requirements.
2024-01-26 18:41:09 +00:00
Matthias Bernt
7530fb4dc2
Revert "Escape pipe character"
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This reverts commit 4152c350db
2024-01-26 18:40:13 +01:00
John Davis
6f7f8b0d2a
Merge pull request #17361 from mvdbeek/drop_unused_wildcard_replacement
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Remove unused statements in job search function
2024-01-26 09:32:54 -05:00
mvdbeek
a0f69c5375
Remove unused statements in job search function
2024-01-26 11:51:09 +01:00
Cameron Hyde
4152c350db
Escape pipe character
2024-01-26 10:38:36 +10:00
Nate Coraor
add8b28efa
Write to a temp filename in posix file source plugin
2024-01-24 15:08:18 -05:00
John Davis
568480f923
Merge branch 'release_23.2' into dev_merge_23.2
2024-01-24 16:28:01 +00:00
mvdbeek
a3e70c6eb6
Only switch out compressor if deflate requested
2024-01-23 11:46:59 +01:00
mvdbeek
a4b14be89e
Work around no unused ignores
2024-01-23 11:35:14 +01:00
mvdbeek
7e9c02b75c
Use python-isal for fast zip deflate compression in rocrate export
2024-01-23 11:16:26 +01:00
Nicola Soranzo
12ad482d66
Fix B038 errors reported by flake8-bugbear 24.1.17
2024-01-22 20:33:47 +00:00
Nicola Soranzo
fd5102dd1d
Fix B036 errors reported by flake8-bugbear 24.1.17
2024-01-22 20:33:46 +00:00
Nicola Soranzo
a11f77d4be
Merge pull request #17335 from davelopez/fix_quotas_id_encoding
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Fix quotas ID encoding
2024-01-22 18:34:38 +00:00
davelopez
0b4df0f37b
Fix quotas id encoding
2024-01-22 12:23:56 +01:00
Ubuntu
6860c9a0fb
Add support for Python 3.12
2024-01-21 11:57:59 +00:00
Nicola Soranzo
30a6aab6c9
Workaround `ImportError for importlib.resources.Anchor`
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xref: https://github.com/python/cpython/issues/113238
2024-01-21 10:31:16 +00:00
Nicola Soranzo
76e566d1e1
Fix E231 flake8 error in f-string
2024-01-21 10:31:16 +00:00
Ubuntu
cc878ba75f
Update comments
2024-01-20 22:12:06 +00:00
Björn Grüning
5f25a48ac9
Merge pull request #17311 from bgruening/s3fs-templating
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[23.2] fix s3fs templating
2024-01-20 10:56:38 +01:00
nuwang
000246826e
Also pop bucket name during get and write to filesource
2024-01-19 22:50:07 +05:30
Marius van den Beek
f12984bf37
Merge pull request #17324 from pcm32/patch-13
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Enable job resubmissions in k8s runner
2024-01-18 14:59:45 +01:00
mvdbeek
e02a765b7b
Merge branch 'release_23.2' into dev
2024-01-18 12:23:00 +01:00
Bjoern Gruening
29d7820cb3
fix linting
2024-01-18 11:42:17 +01:00
Bjoern Gruening
a75422d9c8
ls() can not handle the bucket in its arguments
2024-01-18 11:38:59 +01:00
nuwang
7392c6b70d
Move _bucket initializer to open_fs, following GoogleCloudStorageFilesSource
2024-01-18 11:36:30 +01:00
Björn Grüning
625ae9700f
bucket needs special handling
2024-01-18 11:36:30 +01:00
Björn Grüning
488d2838e9
Update s3fs.py
2024-01-18 11:36:30 +01:00
Björn Grüning
89f02ff060
fix s3fs templating
2024-01-18 11:36:30 +01:00
