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Author SHA1 Message Date
Oleg Zharkov ccfceebcb0 Merge pull request #12428 from dannon/prettier-finally-bracket-sameline 
Vue component dangling bracket style fix (prettier upgrade)
 2021-11-29 19:31:32 +01:00
John Chilton 089b0b59b7 Merge pull request #12974 from bernt-matthias/topic/lint-input-redundant-name 
lint for inputs with redundant name
 2021-11-29 12:59:39 -05:00
John Chilton 965f579c39 Merge pull request #13000 from mvdbeek/separate_celery_tasks 
Move ``galaxy_tasks`` decorator to ``galaxy.celery``
 2021-11-29 11:41:55 -05:00
Dannon d3a73bc6c6 Merge pull request #12984 from OlegZharkov/formOnChangefix 
Fix Rerun in the new form
 2021-11-29 08:20:11 -05:00
mvdbeek 0091d37469 Add interactive shell for celery tasks 
That's pretty useful for developing new tasks or just running one-off
tasks.
 2021-11-29 10:34:01 +01:00
mvdbeek 6036a234c1 Move galaxy_tasks decorator to galaxy.celery 
That means we can import additional tasks that use `galaxy_task` in
galaxy.celery.tasks without circular imports.
 2021-11-29 10:34:01 +01:00
guerler adedd9ac2b Add debug statements to tool loader 2021-11-27 12:21:59 -05:00
guerler ecea7d2966 Properly sync output section data in workflow editor 2021-11-27 12:08:00 -05:00
Nicola Soranzo 9140d95621 Merge pull request #12994 from nsoranzo/run_tool_raw 
Split `run_tool_raw()` out of `BaseDatasetPopulator.run_tool()`
 2021-11-27 11:21:45 +00:00
Björn Grüning 3456ccc6bf Merge pull request #12960 from bernt-matthias/topic/lint-test-expect-failure-outputs 
Linting: check for test expecting failure with outputs
 2021-11-27 11:47:36 +01:00
Björn Grüning 621ed6696e Merge pull request #12990 from gmauro/patch-6 
Update interactivetool_pyiron.xml
 2021-11-27 11:46:32 +01:00
John Chilton 8d8e89e840 Merge pull request #12983 from mvdbeek/create_explicit_select_statement 
Create select() construct explicitly
 2021-11-26 22:30:40 -05:00
John Chilton 5e35b6aeec Merge pull request #12991 from mvdbeek/evaluator_cleanup 
Remove unused dataset conversion code
 2021-11-26 22:28:59 -05:00
Nicola Soranzo 6a6abf37ef Split run_tool_raw() out of BaseDatasetPopulator.run_tool() 
so that the former always returns a `Response` object while the latter
returns the response content.

Also:
- In `CwlPopulator.run_cwl_job()` wait for the run only if `assert_ok`
  is True; if the `wait()` call fails, summarize history also for
  workflow runs.
 2021-11-27 03:14:52 +00:00
Nicola Soranzo 1ff3802ebc Merge pull request #12993 from nsoranzo/misc_fixes_v3 
Misc fixes - round 3
 2021-11-26 22:59:23 +00:00
Nicola Soranzo 38c0a5aa50 Remove tests that are now passing from RED_TESTS 2021-11-26 18:21:58 +00:00
mvdbeek a7c80bc5b6 Remove seemingly dead conversion code 
We seem to setup implicit conversions just fine without this.
 2021-11-26 17:02:45 +01:00
guerler bba68c5271 Fix test cases, move inital value emission to helper 2021-11-26 10:57:51 -05:00
Nicola Soranzo 529579b608 Handle $graph packed documents in guess_artifact_type() 2021-11-26 15:30:47 +00:00
Nicola Soranzo b9b0046621 Remove unnecessary checks for Python version 2021-11-26 15:30:09 +00:00
mvdbeek 6e01abe4b2 Bump version and add profile 2021-11-26 16:18:31 +01:00
Gianmauro Cuccuru 0cf0b82959 Update interactivetool_pyiron.xml 2021-11-26 15:57:34 +01:00
Sergey Golitsynskiy 72870468f7 Merge pull request #12951 from ic4f/dev_cleanup_mapping 
Assorted mapping cleanup
 2021-11-25 13:22:00 -05:00
oleg c2370d3d1a populate change event on mounted 2021-11-25 19:14:14 +01:00
mvdbeek d8c5af582e Create select() construct explicitly 
Silences
```
/opt/galaxy/server/lib/galaxy/jobs/handler.py:360: SAWarning: Coercing
Subquery object into a select() for use in IN(); please pass a select()
construct explicitly
```
Fixes #12981
 2021-11-25 18:08:39 +01:00
Nicola Soranzo a37bdfd42f Merge branch 'release_21.09' into dev 2021-11-25 16:30:56 +00:00
Nicola Soranzo 1b53f0cfd8 Merge pull request #12982 from nsoranzo/misc_fixes_v2 2021-11-25 16:25:56 +00:00
Marius van den Beek e204c7dc75 Merge pull request #12956 from davelopez/remove_response_from_datatypes 
Avoid setting response headers through `trans` in datatypes
 2021-11-25 16:27:28 +01:00
Marius van den Beek 22991365a6 Merge pull request #12929 from davelopez/add_response_wrapper 
FastAPI: Add response wrapper for `SessionRequestContext`
 2021-11-25 15:55:07 +01:00
Marius van den Beek 760e77b5f7 Merge pull request #12973 from IslamHeggy/release_21.09 
[21.09] BugFix: Update social-auth-core library version to fix OIDC problem
 2021-11-25 15:50:35 +01:00
Marius van den Beek 37fa6a3af6 Merge branch 'dev' into dev_cleanup_mapping 2021-11-25 15:40:20 +01:00
David López 1e481a4937 Merge pull request #12980 from davelopez/fix_flaky_legacy_api_tests 
Fix flaky legacy API tests (hopefully)
 2021-11-25 15:21:00 +01:00
Nicola Soranzo 26fe8497c3 Fix handling of artifact and job paths in run_cwl_job() 2021-11-25 13:37:45 +00:00
Nicola Soranzo eeb8a4e6bd Fix path handling in imported conformance tests 2021-11-25 13:37:44 +00:00
Michael R. Crusoe 59c5b59e70 Upgrade to cwl-utils 0.13 2021-11-25 13:37:44 +00:00
Nicola Soranzo 4f66b6411e Fix abs_path_or_uri() not returning an absolute path 2021-11-25 13:37:43 +00:00
Nicola Soranzo 7564325ac4 Better type annotation of optional string parameters 2021-11-25 13:37:43 +00:00
Nicola Soranzo fe0f6e48e1 Use f-strings instead of string interpolation 2021-11-25 13:37:42 +00:00
Marius van den Beek 181cc319c4 Merge pull request #12977 from natefoo/celery-outside-root 
Support running celery when cwd is not galaxy_root by setting $GALAXY_ROOT_DIR
 2021-11-25 13:09:03 +01:00
David López 36474fd7c9 Merge pull request #12976 from mvdbeek/job_handler_type_hints 
Add type hints to JobHandlerQueue
 2021-11-25 13:02:59 +01:00
davelopez ed1d53888c Remove json=True in POST from flaky legacy tests 2021-11-25 10:23:07 +01:00
Nicola Soranzo 8045ee5b61 Update social-auth-core library also in requirements files 2021-11-24 17:46:09 +00:00
Nate Coraor 4abfa9a427 Set galaxy_root config kwarg for celery entrypoint if GALAXY_ROOT_DIR is set. 2021-11-24 11:39:13 -05:00
Nate Coraor afec0833c6 Attempt to load config schema from galaxy_root if it does not exist at 
cwd.
 2021-11-24 11:38:07 -05:00
mvdbeek e4fa19bdb9 Add JobConfiguration to MinimalManagerApp 2021-11-24 13:38:22 +01:00
mvdbeek 4947218383 Add type hints to JobHandlerQueue 2021-11-24 13:13:21 +01:00
Matthias Bernt bc4e8d71d5 lint for inputs with redundant name 
fixes: https://github.com/galaxyproject/galaxy-language-server/issues/85
 2021-11-24 11:02:55 +01:00
davelopez a31d1a305f Fix unit test 
To explicitly state the behavior of using `trans.response.set_content_type` when returning the default implicit response
 2021-11-24 10:04:28 +01:00
Nicola Soranzo 38a69b19b5 Merge pull request #12972 from nsoranzo/misc_fixes 2021-11-24 03:18:09 +00:00
Islam Heggy cde79eef33 Update social-auth-core library version to fix OIDC problem 2021-11-24 05:00:28 +02:00