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7006 Commits
Author SHA1 Message Date
Marius van den Beek ce26561b33 Merge pull request #14708 from jdavcs/dev_celery_config 
Enable fine-grained celery configuration
 2022-10-17 10:37:24 +02:00
Marius van den Beek 934369aa3a Merge pull request #14792 from jdavcs/dev_sqlalchemy_engine_options 
Make connect_args for SQLAlchemy's engine configurable
 2022-10-17 10:30:44 +02:00
John Chilton 5a3069d283 Pulsar infrastructure improvements for TES execution and MQ-less Kubernetes. 
Updating the Pulsar job runner/client for https://github.com/galaxyproject/pulsar/pull/302 and as described in the new docs at https://pulsar.readthedocs.io/en/latest/containers.html.
 2022-10-16 09:56:58 +02:00
John Davis 243cad2f24 Fix config error in tests 2022-10-14 19:28:17 -04:00
John Davis 0063d1dd7e Add basic celery unit tests 
Rename periodic tasks to match galaxy task naming convention
(galaxy.celery.tasks.foo >> galaxy.foo)
 2022-10-14 19:28:17 -04:00
Björn Grüning 93e47e485d Merge pull request #14489 from itisAliRH/api-key-Enhancement 
API key enhancements
 2022-10-14 22:05:23 +02:00
Björn Grüning 424fc9c8a9 Merge pull request #14620 from jmchilton/bco_rewrite 
Bring BioCompute exports under invocation export framework
 2022-10-14 21:36:21 +02:00
John Davis d957e143ea Engine options are never null 2022-10-14 15:27:20 -04:00
John Davis 7578edbd00 Fix mypy error 2022-10-14 13:31:54 -04:00
John Davis da87ca9209 Allow to set connect_args for SQLAlchemy's engine in config 2022-10-14 13:17:42 -04:00
davelopez c776c8169a Validate BioCompute Objects against schema in tests 2022-10-14 12:20:24 +02:00
davelopez 8aebe9079e Fix some BCO fields 
- Pass the workflow url for the execution_domain instead of a fixed galaxy url
- Fix step annotations in PipelineStep description
- Use API url for downloading collections in InputSubdomainItem
 2022-10-14 12:20:24 +02:00
davelopez 0950722c7c Exclude null values when serializing BCO 
+ fix typo
 2022-10-14 12:20:24 +02:00
davelopez 2140df7eed Add basic BCO export integration tests 2022-10-14 12:20:24 +02:00
John Chilton 61b9e57c7f Implement Workflow Invocation -> BCO export. 2022-10-14 12:20:24 +02:00
Nicola Soranzo 0764183792 Fix `test_get_alternative_versions` unit test 
Fix the following error:

```
>       assert versions == ["recipes/bamtools/2.3.0/meta.yaml"]
E       AssertionError: assert [] == ['recipes/bam....0/meta.yaml']
E         Right contains one more item: 'recipes/bamtools/2.3.0/meta.yaml'
E         Full diff:
E         - ['recipes/bamtools/2.3.0/meta.yaml']
E         + []

test/unit/tool_util/mulled/test_get_tests.py:80: AssertionError
```

due to the removal of the `recipes/bamtools/2.3.0/meta.yaml` file in

https://github.com/bioconda/bioconda-recipes/commit/b94d1bd9a146dcf0ddcf4224ffd265f17ff0a489#diff-d7df16f707f82264802dbbed7b281cb9a3d9053c21cd9bd79f3c8e56612bdc81
 2022-10-14 11:01:11 +01:00
John Davis 66ceff374a Ignore type error in test: wrong value is intentional 2022-10-13 13:42:00 -04:00
John Davis 4818c8dadf Add get_from_env utility + tests 2022-10-13 13:17:15 -04:00
Alireza Heidari aa842df560 Merge branch 'dev' into api-key-Enhancement 2022-10-13 14:38:08 +02:00
Nicola Soranzo c9e5a89c15 Skip unit tests requiring bio.tools if it's down 2022-10-12 18:13:47 +01:00
David López f733734299 Merge pull request #14736 from jmchilton/ts_service_models_2 
Migrate index and show tool shed repositories endpoints to Pydantic and FastAPI
 2022-10-12 18:25:14 +02:00
John Chilton 84005605c8 Extend tool shed install testing to include index API. 2022-10-10 11:19:18 -04:00
John Davis 48d54f57f5 Do not patch config file 2022-10-06 02:54:27 -04:00
John Chilton 94c8218d48 setup service and fastapi layer for tool shed APIs... 2022-10-01 09:14:03 -04:00
davelopez 0356c2e01f Add unit test for api_keys.deleted column 2022-09-30 16:39:12 +02:00
John Chilton 9bc6c1815b Merge pull request #14695 from natefoo/tailscale-container-monitor 
Configurable get IP method for container monitor
 2022-09-29 14:05:32 -04:00
Nicola Soranzo ea4461751c Use loc file that actually exists in the param validators of test tool 
Previously, the ``validation_dataset_metadata_in_file`` test tool was failing
to load and was not tested at all during framework tests on GitHub Actions.
 2022-09-29 01:50:33 +01:00
Nicola Soranzo d4afe4d10b Make `metadata_name` a required attribute of certain validators 2022-09-29 01:50:13 +01:00
Nicola Soranzo aa7c6ea895 Fix typos 2022-09-29 00:53:20 +01:00
Nicola Soranzo c35d8f2a06 Replace `unittest.TestCase` with pytest-based partial re-implementation 
Also:
- Rename `FooBarTestCase` test classes as `TestFooBar`. These were collected
  by pytest only because they were `unittest.TestCase` derived, but normally
  pytest collects only test classes whose name starts with `Test`, see
  https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes
 2022-09-27 03:34:58 +01:00
Nicola Soranzo 215beecece Replace conditional `self.fail()` method calls with asserts 2022-09-27 03:34:57 +01:00
Nicola Soranzo 7646d9eb7b Workaround for abstract test classes 2022-09-27 03:34:56 +01:00
Nicola Soranzo 30d8d2ba66 Remove unused function 2022-09-27 03:34:56 +01:00
Nicola Soranzo 3091737ab9 Misc test fixes 2022-09-27 03:34:55 +01:00
Marius van den Beek 955815ca11 Merge pull request #14688 from mvdbeek/dev 
Merge 22.05 into dev
 2022-09-26 15:19:53 +02:00
mvdbeek cbd38554f1 Merge branch 'release_22.05' into dev 2022-09-26 15:15:19 +02:00
John Chilton 156977f65a Merge pull request #14691 from jmchilton/tool_util_testing_3 
More typing and unit testing for tool test verification functions
 2022-09-24 08:41:04 -04:00
Björn Grüning e4636cead0 Merge pull request #14682 from jmchilton/galaxy_install_typing 
More typing for tool shed install and relevant utility code.
 2022-09-23 21:56:06 +02:00
Nate Coraor 44cd326157 Generalize to allowing any command for the container monitor 2022-09-23 13:46:06 -04:00
John Chilton fc491434ab Merge pull request #14673 from natefoo/container-monitor-relocate 
Packaging and configurability for the container monitor script
 2022-09-23 09:17:23 -04:00
John Chilton 550d29493f Merge pull request #14683 from mvdbeek/type_annotation_workflow_run 
Add type hints for galaxy.workflow.{run, run_request}
 2022-09-23 09:14:46 -04:00
John Chilton 19aba1807e Initial unit test for copying test data. 2022-09-23 09:11:40 -04:00
John Chilton 2684cdb908 Refactor mock tool test interactor for reuse. 2022-09-23 09:06:15 -04:00
mvdbeek 81b2f3e1e1 Add ModuleInjector, avoids test type mismatch 2022-09-23 10:19:02 +02:00
mvdbeek 48c654d1b2 Add type hint for galaxy.workflow.{run, run_request} 
Trying out https://github.com/dropbox/pyannotate here.
It's still a lot of work even with pyannotate, but I think this fixes
some minor oddities, like assigning non-mapped attributes to
WorkflowInvocation instances.
 2022-09-23 09:33:47 +02:00
John Chilton ace1e13da3 Merge pull request #14641 from mvdbeek/fix_optional_data_input_submission_expanded_tool_form 
[22.05] Fix delayed optional data input handling
 2022-09-22 18:08:58 -04:00
John Chilton 357a2ee954 Improved assertion in error in failing test. 2022-09-22 18:05:33 -04:00
John Chilton ba9df94510 Merge pull request #14674 from nsoranzo/replace_self.assert_methods 
Replace ``self.assert*()`` method calls with plain asserts
 2022-09-22 11:20:29 -04:00
John Davis 06c9475683 Merge pull request #14537 from jdavcs/dev_managedb_cli 
A replacement for manage_db.sh + rewrite of migration system documentation
 2022-09-22 10:06:45 -04:00
Nicola Soranzo a5c41adb96 Remove unused `get_suite()` functions 2022-09-22 02:21:12 +01:00