opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 12:13:33 +08:00
Code Issues Packages Projects Releases Wiki Activity
61,861 Commits 63 Branches 243 Tags
v22.05
Commit Graph
132 Commits
Author SHA1 Message Date
mvdbeek 0eff482466 Pass --cleanenv by default to singularity command 2022-08-10 16:52:59 +02:00
Nicola Soranzo d4d3485b72 Fix mypy reexport error for testfixtures 
Fix this mypy error for the galaxy-app package:

```
tests/app/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py:5: error:
Module "testfixtures" does not explicitly export attribute "log_capture";
implicit reexport disabled  [attr-defined]
    from testfixtures import log_capture
    ^
```
 2022-07-08 02:33:28 +01:00
mvdbeek f139d29f19 Drop custom fail_job method in pbs/chronos/pulsar 2022-06-23 10:38:54 +02:00
mvdbeek 1b4bbe090c Test that files are not created in system tmpdir 2022-06-20 08:25:29 +02:00
Nuwan Goonasekera 1be6b1583b Update tpv rule module name and constrain version 2022-06-15 00:34:55 +05:30
Nicola Soranzo fd8826904b Merge branch 'release_22.01' into dev 2022-06-13 22:46:38 +01:00
Marius van den BeekandNicola Soranzo 3db96f4096 Use single quote to refer to tool_stdout / tool_stderr path in command line 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-06-13 19:03:51 +02:00
mvdbeek 5448144669 Only `stream` stdout/stderr on kubernetes 2022-06-13 18:13:16 +02:00
Dannon 4644922783 Merge pull request #13655 from mvdbeek/metadata_embed 
Create data_fetch and set_metadata celery tasks
 2022-06-07 10:27:06 -04:00
Nicola Soranzo fa7a20ed19 Merge pull request #14017 from nuwang/misc_typo_fixes_and_cleanup 2022-06-07 01:10:11 +02:00
Nicola Soranzo 27b2ee0e9e Merge branch 'release_22.01' into dev 2022-06-06 19:18:55 +01:00
Nuwan Goonasekera c3521dc542 Fix some minor typos in docs 2022-06-04 19:55:08 +05:30
Nicola Soranzo 493db8669c Remove Python 2 support 2022-06-02 16:17:56 +01:00
mvdbeek 4ac1ff1034 Fix up unit tests 2022-05-27 13:48:42 +02:00
Sergey Golitsynskiy 8dd58897a9 Fix linting 2022-05-26 15:34:28 -04:00
Nate Coraor 37edbaf74c Trim spaces from around email addresses and usernames when registering. 
Additionally, include a stricter email address validation.
 2022-05-26 14:55:27 -04:00
Enis Afgan e977f8289c Merge pull request #13636 from nuwang/add_tpv_optional 
Add optional dependency on total-perspective-vortex
 2022-05-25 22:15:36 +00:00
mvdbeek 899393f108 Use metadata_strategy to run set_meta in celery 2022-05-25 19:46:05 +02:00
Nuwan Goonasekera 76de85c7f3 Change sample file for TPV 2022-05-25 11:11:23 +05:30
Nuwan Goonasekera 268235e512 Added conditional requirement on TPV 2022-05-25 11:11:21 +05:30
John Chilton c5bf63bc91 Add DEFERRED datasets to Galaxy 
- Improves options and display around discarded datasets.
- Adds new APIs for importing model stores.
- Adds support to model store layer for importing/exporting workflow invocations and APIs and tests to support this.
- Add new DEFERRED dataset state - with APIs for materializing them or the option to defer them on the worker node if using tool_evaluation_strategy=remote on the job destination.
- UI and API options for uploading deferred datasets individually or into collections.
 2022-05-23 19:48:47 -04:00
Björn Grüning 4e8819e793 use -f instead of /dev/null in the tests 2022-05-13 16:18:58 +02:00
Björn Grüning 1c65352354 Update test_command_factory.py 2022-05-13 11:35:43 +02:00
Björn Grüning e9d890a7a3 add test 2022-05-13 10:24:45 +02:00
Nicola Soranzo 4160a90ef8 Merge branch 'release_22.01' into dev 2022-05-11 20:23:02 +01:00
mvdbeek 853ef69d02 Redirect stderr of trap cleanup 
Prevents
```
rm: cannot remove '/data/jwd/main/046/709/46709070/tmp/out.471762': No such file or directory
rm: cannot remove '/data/jwd/main/046/709/46709070/tmp/err.471762': No such file or directory
```
reported in https://github.com/galaxyproject/galaxy/issues/13902.

I don't think this is what fails the job, there is likely something else
wrong on top of this.
 2022-05-11 10:52:39 +02:00
Dannon b7793780db Merge pull request #13683 from gecage952/oidc-pkce-param-support 
Add OIDC PKCE parameter support
 2022-05-09 11:28:00 -07:00
Nicola Soranzo 6ab35f4817 Fix error message from `ExpressionValidator` 
when the expression could not be evaluated. Previously the message
would be:
```
Validator '<code object <module> at 0x7fcfdf6737c0, file "<string>", line 1>' could not be evaluated on '%s'
```

Also, move doc tests to unit tests.
 2022-05-06 13:29:13 +01:00
Dannon Baker 2569f09316 Skip unittest when pkce not available 2022-05-02 22:08:02 -04:00
Dannon Baker bf82bf37fd Update custos_authnz test for pkce dep 2022-05-02 19:32:56 -04:00
John Chilton 758f47343c Improved typing for output collect and its ilk... 2022-05-02 11:17:22 -04:00
Matthias Bernt cfc2043e00 fix black formatting 2022-04-21 16:58:58 +02:00
M Bernt 4243ae86ad Merge branch 'dev' into topic/min-length 2022-04-21 11:26:51 +02:00
Gregory Cage 4d72180956 Fix more code styling issues with black and isort 2022-04-12 14:13:23 -04:00
Nicola Soranzo bf1a23eb38 Merge branch 'release_22.01' into dev 2022-04-11 19:13:06 +01:00
Gregory Cage 26e785fc48 Add unit test for OIDC PKCE parameters 2022-04-06 11:14:09 -04:00
davelopez 0d272ba256 Allow admins to run tools on private datasets 2022-04-06 10:32:00 +02:00
davelopez 356ef0fae3 Allow JSON boolean when parsing query filters 
This will avoid having to explicitly transform booleans in the client when building the query
 2022-04-05 17:26:11 +02:00
Nicola Soranzo a4053dc199 Merge branch 'release_22.01' into dev 2022-03-28 23:16:34 +01:00
mvdbeek 3818f50af5 Drop interactive environments 2022-03-23 15:43:24 +01:00
mvdbeek 6bfa842314 Replace container kill trap if present 2022-03-19 14:54:00 +01:00
mvdbeek cd2716f259 Fix stdout/stderr capture for container commands 
By pulling `capture_stdout_stderr` to the outer scope the capture
runs on the "host" instead of the container.
 2022-03-19 14:54:00 +01:00
mvdbeek 2e61fccb1c Extend kubernetes logs to check that job logs are properly recorded 2022-03-19 12:11:41 +01:00
Nicola Soranzo 6189032838 Fix test_callback_nonce_validation_with_bad_nonce unit test 
Broken in PR #13572.
 2022-03-19 02:20:05 +00:00
mvdbeek dab6237bbc Fix tee pattern for stdout/stderr streaming 2022-03-18 17:26:10 +01:00
mvdbeek f8c39d5289 Unit test for named pipe capture 2022-03-18 16:50:40 +01:00
Nicola Soranzo 13d0f92fc0 Merge pull request #13071 from mvdbeek/drop_wsgi_mode 2022-03-18 13:41:33 +00:00
mvdbeek 434991101f One more f-string 2022-03-18 13:03:05 +01:00
Marius van den BeekandNicola Soranzo a43458e764 One more string formatting 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-03-17 19:58:02 +01:00
Marius van den BeekandNicola Soranzo aa13988023 Use string formatting instead of concatenation 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-03-17 19:57:32 +01:00