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846 Commits
Author SHA1 Message Date
mvdbeek d5b31ee55a Fix tool id not getting updated on tool update 2022-01-19 14:46:31 +01:00
mvdbeek fc8fb85530 Set collection update_time when replacing failed elements 
That allows the new history to update the collection.
 2022-01-14 12:59:36 +01:00
mvdbeek 855e9f9f2f Fix re-run with rerun_remap_job_id hiding collection 
Fixes https://github.com/galaxyproject/galaxy/issues/13052
 2022-01-12 20:10:08 +01:00
Marius van den BeekandNicola Soranzo 2086ce9a01 Check response status code 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-01-08 08:51:46 +01:00
mvdbeek a2ede0331e Fix history import for datasets with tags 
and tag dataset used for history import/export tests
 2022-01-07 17:16:45 +01:00
davelopez d364d8b775 Add API test for private histories 2021-12-13 19:09:09 +01:00
mvdbeek 483e5658c0 Use HDCA dataset instance hid to skip unnecesary new HDAs 2021-12-02 18:05:27 +01:00
mvdbeek dd806f0993 Copy HDCA member items to new history when copying history 2021-12-02 16:22:15 +01:00
John Chilton fa8c1a5fdc Merge pull request #12815 from mvdbeek/fix_object_store_datasets_not_purged 
[21.09] Fix remote object store datasets not purged
 2021-11-01 09:56:22 -04:00
John Chilton 483631ec31 Merge pull request #12817 from mvdbeek/allow_anon_delete 
[21.09] Allow dataset and dataset collection deletion for anonymous users
 2021-11-01 09:53:44 -04:00
Simon Bray 1a968952cc add missing tool_ids to workflow invocation failure message 2021-11-01 12:04:02 +01:00
mvdbeek 28000701d7 Allow dataset / collection deletion for anonymous users 
Fixes https://github.com/galaxyproject/galaxy/issues/12442
 2021-10-31 19:40:17 +01:00
mvdbeek 673e068358 Add test case that verifies various object store cache operations 2021-10-30 16:41:41 +02:00
mvdbeek 0736e8f834 Merge branch 'release_21.05' into release_21.09 2021-10-29 16:02:53 +02:00
mvdbeek 629ababe42 Disable library uploads using master API key 
and cleanup some of the parameter validation.
 2021-10-29 10:42:04 +02:00
Nicola Soranzo 511d52fb9a Merge branch 'release_21.05' into release_21.09 2021-10-28 11:09:20 +01:00
Marius van den Beek b6762490d6 Merge pull request #12795 from mvdbeek/fix_api_dataset_permission_error_handling 
[21.09] Drop legacy_expose_api from api/datasets
 2021-10-27 19:56:50 +02:00
davelopez d779b61258 Raise Bad Request when bootstrap admin try to run/create workflows 2021-10-27 18:42:58 +02:00
davelopez b9f7a61d97 Raise Bad Request when bootstrap admins try to run jobs/tools 2021-10-27 17:57:49 +02:00
mvdbeek c92fcb91d7 Drop legacy_expose_api from api/datasets 
We raise MessageException inside the security checks, and these are not
handled in legacy_expose_api.
Fixes
```
MessageException: You are not allowed to access this dataset
  File "galaxy/web/framework/decorators.py", line 184, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/api/datasets.py", line 134, in show
    dataset = self.get_hda_or_ldda(trans, hda_ldda=hda_ldda, dataset_id=id)
  File "galaxy/webapps/base/controller.py", line 987, in get_hda_or_ldda
    return self.get_hda(trans, dataset_id, check_ownership=False, check_accessible=True)
  File "galaxy/webapps/base/controller.py", line 1023, in get_hda
    error("You are not allowed to access this dataset")
  File "galaxy/web/framework/decorators.py", line 32, in error
    raise MessageException(message, type='error')
```
(https://sentry.galaxyproject.org/organizations/galaxy/issues/6012/?project=3&query=is%3Aunresolved).
 2021-10-27 17:29:37 +02:00
mvdbeek 5b8a0e2dd6 Fix test_fetch_nested_elements_from test 
The order within which datasets and dataset collection are added to the
history is different between extended metadata and directory/legacy
metadata collection. To fix the test we just check for the last dataset
collection in the history.
 2021-10-27 09:23:55 +02:00
John Chilton 5cd46c3d5e Various show page PDF bug fixes. 
- In FastAPI mode GET /api/pages/{id}.pdf was being masked by /api/pages/{id} and the tested 400 was an invalid ID error.
- trans.response was being used in the service layer and was unavailable under FastAPI - moved setting response type back up into the controller.
- API tests should skip if the Galaxy configuration is invalid - it wasn't doing this.

While I was in there I also tweaked the exception handling a bit to indicate that this is not a USER FORBIDDEN (403) operation so much as an optional SERVER configuration NOT IMPLEMENTED (501).
 2021-10-16 15:00:59 -04:00
guerler a8701a3402 Consolidate render wait calls in workflow editor tests 2021-10-14 06:50:40 -04:00
guerler 88dcba87af Adjust selenium and jest tests 2021-10-14 06:32:18 -04:00
Nicola Soranzo dbb91a05db Merge branch 'release_21.05' into release_21.09 2021-10-05 12:59:56 +01:00
Nicola Soranzo 6c3a4ad535 Fix id encoding in datasets API show method 
Follow-up on https://github.com/galaxyproject/galaxy/pull/12616
Fix https://github.com/galaxyproject/galaxy/issues/12610

Also:
- Add API test
- Some refactoring in `LibraryPopulator`
- Add `test_` to `ServerDirectoryValidUsageTestCase.link_data_only()`
  method name so it actually gets tested
 2021-10-04 23:19:18 +01:00
mvdbeek a1b263d1fe Test that remapped job output is not visible 2021-10-04 14:23:57 +02:00
mvdbeek 77b7012d11 Use collection_type instead of type to define test_data collection type 
It was a TODO and simplifies load_data_dict.
 2021-10-04 14:23:56 +02:00
mvdbeek 5b7cb2257d Add testcase 2021-10-02 20:27:03 +02:00
mvdbeek 97c5bd8771 Merge API GalaxyInteractorTestCase into integration test 
This seems more appropraite as an integration test.
 2021-09-23 19:05:30 +02:00
mvdbeek 66fd430763 Include tool_version in API requests for test-data 
Should fix https://github.com/galaxyproject/ephemeris/issues/179.
 2021-09-23 19:05:30 +02:00
Marius van den Beek 03ff774f23 Merge pull request #11701 from OlegZharkov/share-to-users 
Refactor Sharing
 2021-09-20 19:46:54 +02:00
Marius van den Beek 9538c18deb Merge pull request #11309 from bernt-matthias/topic/build-collection-identifiers 
build list: list identifiers
 2021-09-20 16:19:25 +02:00
mvdbeek ed9f46f757 Add two versions of build_list tool 2021-09-20 14:17:14 +02:00
John Chilton 97f019e51b Fix bug when restarting Galaxy in selenium integration tests. 2021-09-17 11:57:19 -04:00
Oleg Zharkov 7001c9f8a5 fix HistorySharingTestCase::test_unsharing 2021-09-17 10:18:38 +02:00
Oleg Zharkov bd157ead1d fix selenium test_sharing_valid_by_id 2021-09-17 10:18:38 +02:00
davelopez d98f3346de Use unique resource name in tests 2021-09-17 10:18:37 +02:00
davelopez c724f6ba93 Remove test assert no longer applicable 2021-09-17 10:18:37 +02:00
davelopez 13235d4981 Rename set_sharing_with_users to share_with_users 
- Fix legacy routes in buildapp.py
 2021-09-17 10:18:37 +02:00
davelopez cf1fa74ce5 Merge share and unshare in the same request 
Instead of having two different requests for adding or removing users from a shared resource now a simple list of users is sent in the request.
The resource will be shared with new users and unshared with users that are no more on that list.
 2021-09-17 10:18:37 +02:00
davelopez 6d224447c9 Adapt tests to use JSON payload 
See https://github.com/galaxyproject/galaxy/pull/12152
 2021-09-17 10:18:37 +02:00
davelopez 0227f96cd2 Fix is_history_shared_with query + test multiple shares with same user 2021-09-17 10:18:37 +02:00
davelopez c6af9a80b2 Avoid sharing with duplicated users in the same request 2021-09-17 10:18:37 +02:00
Oleg Zharkov e7b9152f7e fix remaining selenium 2021-09-17 10:18:37 +02:00
Oleg Zharkov 1d79a4f661 fix selenium test 2021-09-17 10:18:37 +02:00
davelopez 373a1a21a2 Do not send extra field when sharing with no_changes + update tests 2021-09-17 10:18:36 +02:00
davelopez 4b4abcf3ab Add more history sharing tests and move them to SharingHistoryTestCase 2021-09-17 10:18:36 +02:00
davelopez 8f888adc60 Add tests for sharing restricted histories 2021-09-17 10:18:36 +02:00
davelopez f122205413 Rename share and unshare actions 
This is to emphasize that the action requires a target user or list of users
 2021-09-17 10:18:36 +02:00