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41888 Commits
Author SHA1 Message Date
marius-mather 3e81fc1663 mypy fixes 2025-07-04 13:27:31 +10:00
marius-mather 27f701b7c2 Fix type for UserAuthnzToken.extra_data - returned as a dict 2025-07-04 13:26:59 +10:00
marius-mather cc44513482 Lint fixes 2025-07-04 12:53:24 +10:00
marius-mather fe6bc946b5 Pass app config directly to PSAAuthnz instead of going through AuthnzManager 2025-07-04 11:59:27 +10:00
marius-mather e067b75837 Style/lint fixes 2025-07-04 11:51:03 +10:00
marius-mather 7446b5442d Make decoding errors warnings 2025-07-04 11:41:29 +10:00
marius-mather be6fa6cc2b Add decode_access_token step to auth_pipeline only if configured 2025-07-04 11:40:56 +10:00
marius-mather 953414c638 Add a config flag for decoding the OIDC access token 2025-07-04 11:40:00 +10:00
marius-mather e37855d84c Add a try/except around access token decoding to catch decode errors 2025-07-01 12:01:20 +10:00
marius-mather 22a646feaa Linting fixes 2025-06-27 11:48:32 +10:00
marius-mather 5a42326238 Add debug access token step for testing the auth pipeline 2025-06-27 10:58:15 +10:00
marius-mather c5c3b4830c Pass auth pipeline config through to PSA 2025-06-26 09:55:41 +10:00
marius-mather 2c2be1fd82 Add oidc_auth_pipeline option to galaxy.yml 2025-06-25 15:17:52 +10:00
marius-mather 0585050b80 Check if access token is decodable before trying to decode 2025-06-25 10:22:03 +10:00
marius-mather 9180eaea0a Set accepted_audiences from config 2025-06-24 14:46:10 +10:00
marius-mather 640554710b Add decode_access_token to auth pipeline 2025-06-24 14:45:36 +10:00
marius-mather 83901969fa Merge remote-tracking branch 'upstream/dev' into psa-access-token 2025-06-24 10:38:15 +10:00
Nicola Soranzo 99e352a3d0 Merge branch 'release_25.0' into dev 2025-06-22 15:26:46 +01:00
Marius van den Beek 6fe8a7bf6d Merge pull request #20464 from mvdbeek/drop_num_unique_values 
[25.0] Remove ``num_unique_values`` tiff metadata element
 2025-06-22 08:32:30 +02:00
Nate Coraor 751b52f1ec Start work on 25.0.2.dev0 2025-06-20 16:37:11 -04:00
Nate Coraor 5915a88342 Create version 25.0.1 2025-06-20 16:37:07 -04:00
Nate Coraor 96523d4570 Merge remote-tracking branch 'upstream/release_25.0' into dev 2025-06-20 16:18:47 -04:00
Marius van den Beek e3337f8579 Merge pull request #20528 from jmchilton/import_invocation_to_new_history 
Fixes for invocation import.
 2025-06-20 18:29:04 +02:00
Nate Coraor 7899dfbfbc Bump Gravity to 1.1.1 2025-06-20 11:44:22 -04:00
John Chilton af3660ca0d Allow importing invocations into a new history (new default). 2025-06-20 10:53:57 -04:00
Nicola Soranzo cc26ab7834 Merge branch 'release_24.2' into release_25.0 2025-06-20 13:00:45 +01:00
Nicola Soranzo 36ef67be1f Merge branch 'release_24.1' into release_24.2 2025-06-20 13:00:05 +01:00
Nicola Soranzo c96792693c Merge branch 'release_24.0' into release_24.1 2025-06-20 12:55:50 +01:00
Marius van den Beek a55b61c5b4 Merge pull request #20524 from bernt-matthias/users 
[24.2] Do not expose user info to non authenticated users
 2025-06-20 12:21:33 +02:00
Marius van den Beek 94ed4a6a9b Merge pull request #20531 from natefoo/config-script-fixes 
[25.0] Fix `galaxy-config` script, move install to `galaxy-dependencies` in app package
 2025-06-20 09:46:11 +02:00
Marius van den Beek a594358d91 Merge pull request #20527 from natefoo/isa-rwval-0.10.11 
[25.0] Pin isa-rwval 0.10.11, drop conditional import handling
 2025-06-20 09:43:07 +02:00
John Chilton 2bee911ce4 Add max length to pydantic models - not sure this makes sense. 2025-06-19 22:55:54 -04:00
John Chilton 85d634ae9f Implement fetch workbooks. 2025-06-19 22:54:56 -04:00
John Chilton 7efe923b4c Sharper exception handling in apply rules test. 2025-06-19 22:54:55 -04:00
John Chilton 05ecc12d96 Test case for rule builder backend errors. 2025-06-19 22:54:55 -04:00
John Chilton a776836dba Update rule builder to allow list:paired_or_unpaired creation. 2025-06-19 22:54:55 -04:00
Nate Coraor 6a887e0aff Fix galaxy-config script, move install to galaxy-dependencies in app package 2025-06-19 16:58:43 -04:00
Marius van den Beek cb4d73917b Merge pull request #20529 from nsoranzo/release_25.0_fix_tool-util_pkg 
[25.0] Fix import of ``galaxy.tool_util.cwl`` module
 2025-06-19 22:45:28 +02:00
Nicola Soranzo 0764567b21 Fix import of `galaxy.tool_util.cwl` module 
when cwltool is not installed.

Fix:

```
Traceback (most recent call last):
  File "/home/conda/feedstock_root/build_artifacts/galaxy-tool-util_1750355530639/test_tmp/run_test.py", line 11, in <module>
    import galaxy.tool_util.cwl
  File "/home/conda/feedstock_root/build_artifacts/galaxy-tool-util_1750355530639/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.9/site-packages/galaxy/tool_util/cwl/__init__.py", line 2, in <module>
    from .parser import (
  File "/home/conda/feedstock_root/build_artifacts/galaxy-tool-util_1750355530639/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.9/site-packages/galaxy/tool_util/cwl/parser.py", line 122, in <module>
    class ToolProxy(metaclass=ABCMeta):
  File "/home/conda/feedstock_root/build_artifacts/galaxy-tool-util_1750355530639/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.9/site-packages/galaxy/tool_util/cwl/parser.py", line 127, in ToolProxy
    tool: process.Process,
AttributeError: 'NoneType' object has no attribute 'Process'
```
 2025-06-19 20:32:43 +01:00
Nicola Soranzo fdf931b954 Fix new `test_index_anon` API test 2025-06-19 20:01:47 +01:00
Nate Coraor fd41e726e1 Pin isa-rwval 0.10.11, drop conditional import handling 2025-06-19 14:12:25 -04:00
Matthias Bernt 98ddca1e11 fixup 2025-06-19 19:34:52 +02:00
Matthias Bernt 79d08a4d2f Merge branch 'users' of https://github.com/bernt-matthias/galaxy into users 2025-06-19 19:09:02 +02:00
Matthias Bernt b71eaaf437 try to add test 2025-06-19 18:58:01 +02:00
M BerntandNicola Soranzo 14ab0e22b8 Raise exception for unauthenicated users 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-06-19 18:27:34 +02:00
Matthias Bernt 4b7afea7da never exopose user info to non authenticated users 
fixes https://github.com/galaxyproject/galaxy/issues/20505

should be fine is non-authenticated users can't share anything
(not sure about this)
 2025-06-19 16:21:35 +02:00
Nicola Soranzo f4b5e74c91 Merge pull request #20520 from mvdbeek/gravity_1_1_0 
[25.0] Bump gravity dependency to 1.1.0
 2025-06-19 15:07:02 +01:00
Marius van den Beek e95a55907f Merge pull request #20516 from natefoo/web-client-static-fixes 
[25.0] Fixes for static handling and the web_client package
 2025-06-19 11:18:23 +02:00
Marius van den Beek e839cb7cd5 Merge pull request #20509 from jmchilton/input_by_url_to_conversion 
Test case for using URL-based workflow inputs with implicit conversions.
 2025-06-19 10:41:11 +02:00
mvdbeek d95d07b059 Bump gravity dependency to 1.1.0 
So that the next package release will use
https://github.com/galaxyproject/gravity/releases/tag/v1.1.0.
I want to use this in planemo.
 2025-06-19 10:29:09 +02:00