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31169 Commits
Author SHA1 Message Date
Marius van den Beek ad873032b8 Merge pull request #12604 from bernt-matthias/topic/yaml-extensions 
Check prefix before complete loading when checking yaml and cwl tools
 2022-05-25 15:54:18 +02:00
Marius van den Beek 7cb3f76c6e Merge pull request #12232 from bernt-matthias/topic/drilldown 
fix `drill_down` parameters
 2022-05-25 15:52:50 +02:00
Marius van den Beek aa33272d21 Merge pull request #12533 from jmchilton/deferred_data 
Add DEFERRED datasets to Galaxy.
 2022-05-25 15:50:33 +02:00
Dannon 570b30e9d7 Merge pull request #13848 from ahmedhamidawan/Show_only_name_tags_#13747 
Display name tags only in dataset items
 2022-05-25 06:42:05 -07:00
Marius van den Beek 574a0d42ea Merge pull request #13893 from jmchilton/jobs_grid_tweaks 
Jobs Index and Grid Improvements
 2022-05-25 15:36:12 +02:00
Marius van den Beek ac510bc8dc Merge pull request #7894 from bernt-matthias/topic/count-pairs-correctly 
Fix docs for `expect_num_outputs` and add `count` attribute for test `output` and `element` tags
 2022-05-25 15:23:10 +02:00
Ahmed Awan 08933ee497 stateless tags replace nametags, clicking tag emits filterText 2022-05-24 13:59:58 -04:00
dependabot[bot] 1f8f39664c Bump tensorflow from 2.5.3 to 2.6.4 in /lib/galaxy/dependencies 
Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 2.5.3 to 2.6.4.
- [Release notes](https://github.com/tensorflow/tensorflow/releases)
- [Changelog](https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md)
- [Commits](https://github.com/tensorflow/tensorflow/compare/v2.5.3...v2.6.4)

---
updated-dependencies:
- dependency-name: tensorflow
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
 2022-05-24 17:27:49 +00:00
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
John Chilton d2204b656b Task status API for celery. 2022-05-23 19:19:18 -04:00
John Chilton c796dec0f2 Rework galaxy.model.store.discover to not require unique paths for incoming files. 2022-05-23 18:54:19 -04:00
John Chilton 5790f62855 Document certain job query parameters as admin only. 2022-05-23 09:58:43 -04:00
John Chilton da865c74b3 Use proper typing to handle encoding/decoding IDs in job index API. 
Marius is brilliant.
 2022-05-23 09:58:43 -04:00
John Chilton c137e9bccb Push more job index logic from service into manager layer. 2022-05-23 09:58:43 -04:00
John Chilton c784768a8e More expansive filters on job index search. 
With docs and such.
 2022-05-23 09:49:13 -04:00
John Chilton 3819593602 Move show and index jobs implementation into service layer. 2022-05-23 09:49:13 -04:00
John Chilton 96b88575ce Implement job index search. 2022-05-23 09:49:13 -04:00
John Chilton b9c9284cb2 Small touch-ups to the jobs index API. 2022-05-23 09:49:13 -04:00
John Chilton 4bedf2fa92 Allow base64:// URIs to generate test cases without requiring external resources. 2022-05-21 17:22:41 -04:00
John Chilton 37892dcabc Refactor sniff.stream_url_to_file to galaxy.files.uris. 
The value of this can be seen for instance in unpack_tar_gz_archive - which should have nothing to do with datatypes and now doesn't need to load the whole datatypes module.

Use this in workflows API to allow downloading workflow files from configured URIs.
 2022-05-21 17:22:41 -04:00
John Chilton ec2f121f0b Refactor stream_to_file out of galaxy.datatypes.sniff. 
Doesn't do anything datatype specific, can be pushed into a lower package. galaxy.files.uris is better I think.
 2022-05-21 17:22:41 -04:00
John Chilton ace06f4286 Apply URI access checks more uniformly. 
This doesn't resolve explicit security problems I can imagine a way to take advantage of - but if we have these checks we should apply them uniformly - not just for file uploads.
 2022-05-21 17:22:41 -04:00
John Chilton 805ded7b9c Improvements to valdiating IP address access during uploads. 
Move to a lower level in package hierarchy, add types, add unit tests.
 2022-05-21 17:22:41 -04:00
Matthias Bernt 686db90d96 Merge branch 'dev' into topic/yaml-extensions 2022-05-21 11:19:37 +02:00
galaxybot 54a9d57ffa Update Python dependencies 2022-05-21 03:18:49 +00:00
John Chilton 82f63e67d8 Small fixes to galaxy.model.stores. 2022-05-20 10:47:28 -04:00
David López f6273636b7 Merge pull request #13934 from jmchilton/search_by_user_in_workflow_api 
API workflow index allow 'searching' by owner.
 2022-05-20 16:30:10 +02:00
David López 5423ad3377 Merge pull request #13932 from jmchilton/deferred_typing 
Assorted Python typing.
 2022-05-20 16:28:47 +02:00
John Chilton 9adb2a9b03 Merge pull request #13935 from davelopez/bulk_operations_fixes 
Bulk operations: more API tests & fixes
 2022-05-20 09:57:24 -04:00
Nicola Soranzo f12ee5ce6d Merge pull request #13925 from bernt-matthias/fix-mulled-respect-conda-channels 
fix two bugs in mulled container building
 2022-05-19 17:22:18 +02:00
John Chilton 9c09327477 API workflow index allow 'searching' by owner. 2022-05-19 10:48:30 -04:00
John Chilton 87c29cba99 Typing plugin_config.py. 2022-05-19 10:35:06 -04:00
John Chilton d86edfda2c More typing in galaxy.files... 2022-05-19 10:32:56 -04:00
davelopez 7c809c73e8 Add API test only owner can apply bulk operation 2022-05-19 15:22:21 +02:00
davelopez 41956d80ad Purge dataset collections contents in bulk 
First step, reusing what is used in the old history `DatasetCollectionManager.delete` probably needs a celery task version.
 2022-05-19 15:22:21 +02:00
davelopez 303fc4530f Avoid undeleting purged datasets in bulk operations 2022-05-19 15:22:21 +02:00
davelopez 82f5794944 Ensure purging marks datasets as deleted 
It does, just stating it in the tests
 2022-05-19 15:22:21 +02:00
Matthias Bernt 92edf4fa71 fix a logging error message 2022-05-19 01:37:00 +02:00
Matthias Bernt 7967096faf fix two bugs in mulled container building 
respecting conda channels on disk: follow up on https://github.com/galaxyproject/galaxy/pull/13755

- CondaInDockerContext needs the list of channels and not the joined str
- get_file_from_recipe should use local data
 2022-05-18 15:34:16 +02:00
galaxybot d60a1492fd Update Python dependencies 2022-05-17 10:21:28 +02:00
Nicola Soranzo f6275fb0d0 Fix typo in `StagingInterface` class name 
without breaking Planemo.
 2022-05-12 16:38:13 +01:00
Nicola Soranzo 4160a90ef8 Merge branch 'release_22.01' into dev 2022-05-11 20:23:02 +01:00
Björn Grüning 0ac6f411d8 Merge pull request #13905 from mvdbeek/suppress_trap_failure 
[22.01] Redirect stderr of trap cleanup
 2022-05-11 19:42:40 +02:00
John Chilton 60d4b85bc6 Fix typing for unpinned request dependency. 2022-05-11 10:56:35 -04:00
mvdbeek 8f903c9e44 Set default celery app for all threads 2022-05-11 13:11:25 +02:00
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
John Chilton a313cf3f5e Improved index filtering input for workflow list. 2022-05-09 18:41:21 -04:00
John Chilton 4e92f96d68 Selenium workflow management tests - improved assertion. 2022-05-09 18:41:21 -04:00
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
Dannon 71ec553098 Merge pull request #13829 from ahmedhamidawan/Custos_login_enh 
Custos Login Ambiguity enhancement
 2022-05-09 06:23:38 -07:00