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Author SHA1 Message Date
John Chilton 70cd2e252e Fix bug in testcase code for fetching drivers. 2022-04-08 10:43:07 -04:00
John Chilton 637036ebd5 Merge pull request #13688 from bernt-matthias/test/collection_order 
Fix sorting of recursively discovered datasets
 2022-04-08 10:28:19 -04:00
mvdbeek 6f3bdd39d9 Merge branch 'release_22.01' into dev 2022-04-08 10:13:24 +02:00
John Chilton 308db49301 Merge pull request #13681 from davelopez/use_datasets_api_link_for_download 
Use API link to download datasets
 2022-04-07 08:53:33 -04:00
John Chilton 8cf850b7fc Merge pull request #13682 from mvdbeek/doc_fixes_tusd 
Fix apache upload config, update gunicorn_extra_args
 2022-04-07 08:50:03 -04:00
Matthias Bernt 0626e45b3c add test for correct sorting on recursive discovery 2022-04-07 14:42:19 +02:00
Matthias Bernt 297f7e51ef refactor: do not store intermediate lists 2022-04-07 14:42:19 +02:00
Matthias Bernt 52be5c9cc7 fix sorting for recursively discovered datasets 
files in subdirectories were not subject to sort
 2022-04-07 12:25:18 +02:00
Matthias Bernt 72be35fa8a fix error message on collection order 
by using the correct variable
 2022-04-07 12:24:12 +02:00
Matthias Bernt 4ac6c9f2e9 fix profile of multi_output_recurse 
feature was merged in july 21
 2022-04-07 12:24:12 +02:00
Marius van den Beek 5935182af8 Merge pull request #13685 from nsoranzo/respect_GRAVITY_STATE_DIR 
Respect ``GRAVITY_STATE_DIR`` when activating venv
 2022-04-07 12:00:34 +02:00
Marius van den Beek 77d5fe25de Merge pull request #13686 from nsoranzo/fix_22.01_release_notes 
[22.01] Re-add ``announce_start`` label to 22.01 release notes
 2022-04-07 11:31:43 +02:00
Nicola Soranzo 4a8b4d01fe Re-add `announce_start` label to 22.01 release notes 
Removed by mistake in commit 4ecd09e427 ,
without it the list of PRs is not shown at
https://docs.galaxyproject.org/en/master/releases/22.01_announce.html#release-notes
 2022-04-07 00:34:20 +01:00
Nicola Soranzo 6d53620a52 Respect GRAVITY_STATE_DIR when activating venv 
So that:

export GRAVITY_STATE_DIR=/srv/galaxy/gravity
./run.sh

writes gravity state/log files to the right place.
 2022-04-06 23:48:18 +01:00
mvdbeek e08d0c2c99 Fix gunicorn_extra_args, this is just extra_args nows 2022-04-06 20:37:17 +02:00
mvdbeek 9abb53a2c8 Fix apache config for uploads 2022-04-06 20:37:15 +02:00
Nicola Soranzo 4c3844895d Merge pull request #13670 from jmchilton/disable_implicit_cascade 
Disable implicitly attaching HDAs to histories.
 2022-04-06 19:25:59 +01:00
davelopez a04763ade2 Replace dataset download link with API link 2022-04-06 18:58:33 +02:00
davelopez 4cb3300efd Add API alias for dataset display 
Since the `history_id` is really only used for consistency with other history contents routes, we can make it optional and create a route alias for the datasets API
 2022-04-06 18:44:00 +02:00
John Chilton 96f55574b4 Disable implicitly attaching HDAs to histories. 
This is bad and we should be explicit about it... if we want it to happen gotta make sure it has an HID and such.
 2022-04-06 11:36:47 -04:00
Marius van den Beek 4c858252af Merge pull request #13648 from shivani-sangwan/dev 
Porting undocumented API: '/api/groups/{encoded_group_id}/users' to FastAPI
 2022-04-06 17:12:20 +02:00
Dannon 333df8f5b2 Merge pull request #13680 from davelopez/update_precommit_sample_config 
Use authenticated git protocol in pre-commit repo
 2022-04-06 09:41:13 -04:00
davelopez ca7442dbc8 Use authenticated git protocol in pre-commit repo 2022-04-06 15:05:08 +02:00
Dannon 1e986f41f7 Merge pull request #13580 from mvdbeek/pre-commit-config 
Add pre-commit config
 2022-04-06 07:09:24 -04:00
Marius van den Beek f8e434dda2 Merge pull request #13676 from nsoranzo/misc_fixes 
Misc fixes
 2022-04-06 12:47:37 +02:00
Shivani Sangwan be633f8ac5 Porting /api/groups/{encoded_group_id}/users to FastAPI 2022-04-06 15:01:51 +05:30
Nicola Soranzo 85068ffb92 Fix exception message 2022-04-05 19:24:09 +01:00
Nicola Soranzo 7ecd7f0cb8 Remove --wait startup option 
Follow-up on https://github.com/galaxyproject/galaxy/pull/13071 .
 2022-04-05 19:15:23 +01:00
Nicola Soranzo 528f847d13 Remove file added by mistake 
in commit 9690680ec7 .
 2022-04-05 18:16:53 +01:00
Nicola Soranzo ad195966cf Fix error message for RegexValidator 
Fix `TypeError` that would be raised when interpolating `message` in
`Validator.validate()` if `expression` contains a `%`.
 2022-04-05 18:15:29 +01:00
Nicola Soranzo 9cb00b625c More type annotations for CwlPopulator 2022-04-05 18:02:49 +01:00
Nicola Soranzo 4dbd955dd2 Replace use of deprecated API endpoint in BaseWorkflowPopulator.wait_for_invocation() 2022-04-05 17:20:58 +01:00
Nicola Soranzo 5542ad0356 Fix typo 2022-04-05 17:19:44 +01:00
Nicola Soranzo 02da697c79 Replace invoke_workflow() call with invoke_workflow_and_assert_ok() 
Follow-up on commit 18891f3791 .

Fix tracebacks on CWL conformance tests like:

```
>       self.cwl_populator.run_conformance_test("""v1.0""", """Testing Any type compatibility in outputSource""")

lib/galaxy_test/api/cwl/test_cwl_conformance_v1_0.py:535:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/galaxy_test/base/populators.py:482: in run_conformance_test
    run = self.run_cwl_job(artifact, job_path=job_path)
lib/galaxy_test/base/populators.py:467: in run_cwl_job
    run_object.wait()
lib/galaxy_test/base/populators.py:343: in wait
    self.workflow_populator.wait_for_invocation_and_jobs(self.history_id, self.workflow_id, self.invocation_id)
lib/galaxy_test/base/populators.py:1629: in wait_for_invocation_and_jobs
    state = self.wait_for_invocation(workflow_id, invocation_id)
lib/galaxy_test/base/populators.py:1301: in wait_for_invocation
    return wait_on_state(workflow_state, desc="workflow invocation state", timeout=timeout, assert_ok=assert_ok)
lib/galaxy_test/base/populators.py:2379: in wait_on_state
    return wait_on(get_state, desc=desc, timeout=timeout)
lib/galaxy_test/base/populators.py:2465: in wait_on
    return tool_util_wait_on(function, desc, timeout)
lib/galaxy/tool_util/verify/wait.py:38: in wait_on
    value = function()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

    def get_state():
        response = state_func()
>       assert response.status_code == 200, f"Failed to fetch state update while waiting. [{response.content}]"
E       AssertionError: Failed to fetch state update while waiting. [b'{"err_msg": "Wrong  id ( <Response [200]> ) specified, unable to decode.", "err_code": 400009}']
```
 2022-04-05 17:19:25 +01:00
Dannon e1ed4e5ac5 Merge pull request #13630 from ahmedhamidawan/Scrollwheel_Workflow_#13525 
Feature for #13517: Workflow Editor - Scroll Wheel Zoom feature
 2022-04-05 10:17:12 -04:00
John Chilton 56982bef8e Merge pull request #13674 from mvdbeek/galaxyctl_update 
[22.01] Update supervisor config when starting galaxy via run.sh
 2022-04-05 09:24:45 -04:00
Dannon 4b9b619056 Merge pull request #13649 from guerler/history_revise_navigation_dropdown 
Adjust new history navigation header
 2022-04-05 09:15:49 -04:00
David López 5280599e75 Merge pull request #13675 from nsoranzo/fix_format 
Fix black formatting
 2022-04-05 15:15:31 +02:00
Nicola Soranzo b37a30a1e8 Fix black formatting 
which I broke when merging forward in commit
7c442d63df .
 2022-04-05 11:36:20 +01:00
Nicola Soranzo 7c442d63df Merge branch 'release_22.01' into dev 2022-04-05 10:41:56 +01:00
Marius van den Beek 16f5166d4b Merge pull request #13673 from jmchilton/workflow_link_selenium_tests 
Selenium tests for much of #13600.
 2022-04-05 11:29:18 +02:00
Marius van den Beek 4aa985e16e Merge pull request #13669 from jmchilton/2201_fix_upload_calls 
[22.01] Correct data fetch API call in the client.
 2022-04-05 11:28:00 +02:00
mvdbeek 89e06a06cc Update supervisor config when starting galaxy via run.sh 2022-04-05 11:14:11 +02:00
Dannon 1e7c268826 Merge pull request #13672 from ahmedhamidawan/Focus_cursor_#13354 
Focus cursor in text box after clearing search term
 2022-04-04 21:28:23 -04:00
John Chilton 5104147117 Add integration test for TRS check mark on imported workflows. 
Swap embedded style for scoped style in Dropdown Vue component.
 2022-04-04 20:40:05 -04:00
John Chilton 3e0793e341 Add check for external link icon to workflow upload by URL checks... 2022-04-04 20:19:19 -04:00
John Chilton 630e2f628f Test more simple workflow display/linking options. 
- Test link source.
- Test showing workflow annotation.
 2022-04-04 19:57:27 -04:00
John Chilton fdfa72bf72 Improved workflow show test case - use navigation and less arbitrary DOM element. 2022-04-04 19:43:15 -04:00
Marius van den Beek d4001d1851 Merge pull request #13665 from nsoranzo/release_22.01_update_uvicorn 
[22.01] Update uvicorn from broken 0.17.1
 2022-04-05 01:14:22 +02:00
John Chilton 884cdda722 Merge pull request #13600 from simonbray/trs-ui 
Expose TRS id of imported workflows in the UI
 2022-04-04 19:12:02 -04:00