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Author SHA1 Message Date
Marius van den Beek 672ed4984f Merge pull request #14694 from sveinugu/dev 
Allow path-based interactive tools using nginx proxy
 2022-10-17 11:24:38 +02:00
Marius van den Beek 241da69672 Merge pull request #12288 from dannon/sorted-tools-in-sections 
Automatically sort tools in sections by name
 2022-10-17 10:49:17 +02:00
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
Marius van den Beek a1fc34b0a8 Merge pull request #14797 from nsoranzo/rename_TestCases 
Rename `FooBarTestCase` test classes as `TestFooBar`
 2022-10-17 10:27:17 +02:00
Marius van den Beek 2650dc87dc Merge pull request #14804 from nsoranzo/no_integrity_check_CWL_relocate_script 
Disable integrity check for CWL relocate script
 2022-10-17 10:26:48 +02:00
Marius van den Beek 58dd8f17b2 Merge pull request #14806 from nsoranzo/gh_wf_updates 
Replace ``set-output`` commands with ``$GITHUB_OUTPUT`` environment file in GitHub workflows
 2022-10-17 10:23:42 +02:00
Nicola Soranzo c5052c7242 Add missing `python-version` to matrix expansion 
Also:
- Simplify some steps
 2022-10-17 03:15:53 +01:00
Nicola Soranzo c1e839c570 Replace `set-output commands with $GITHUB_OUTPUT` environment file 
See https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
 2022-10-17 02:26:39 +01:00
Nicola Soranzo 5fab7ee8bd Use indentation for YAML nested sequences for consistency 2022-10-17 02:17:11 +01:00
Nicola Soranzo 2988127158 Update GitHub action versions 2022-10-17 01:21:12 +01:00
Nicola Soranzo 825dfa4733 Disable integrity check for CWL relocate script 
Also:
- Add type annotation to script writing methods and functions calling
  them.
 2022-10-16 20:48:37 +01:00
Marius van den Beek 5566ddfc71 Merge pull request #14777 from jmchilton/pulsar_container_scheduling 
Pulsar infrastructure improvements for TES execution and MQ-less Kubernetes.
 2022-10-16 13:17:42 +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
Nicola Soranzo 0391cd4b62 Rename FooBarTestCase test classes as TestFooBar in API, framework, performance, Selenium and ToolShed tests 
These are collected by pytest only because they are `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

Also:
- Some type annotations
 2022-10-15 17:54:31 +01:00
Nicola Soranzo 49ecb1bc26 Merge pull request #14800 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2022-10-15 10:13:02 +01:00
galaxybot 873cdfc30c Update Python dependencies 2022-10-15 03:57:24 +00:00
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
John Davis d310635895 Celery config option result_backend is required 2022-10-14 19:28:17 -04:00
John Davis d8e8202c40 Use celery_conf[result_backend] instead of celery_backend 2022-10-14 19:28:17 -04:00
John Davis 9e39e03809 Check for celery_conf, raise appropriate error 2022-10-14 19:28:17 -04:00
John Davis 069c82577f Drop reference to old config property 2022-10-14 19:28:17 -04:00
John Davis d26ad37e97 Remove celery_backend from config_schema, use celery_conf instead 2022-10-14 19:28:17 -04:00
John Davis f9ae790188 Use celery_conf[broker_url] instead of celery_broker 2022-10-14 19:28:17 -04:00
John Davis b6b49897dc Remove celery_broker from config_schema, use celery_conf instead 2022-10-14 19:28:17 -04:00
John Davis 939c8bc2ac Cleanup celery module namespace, refactor 2022-10-14 19:28:17 -04:00
John Davis f27d5e116f Remove unused code (exec celery module as a program) 
(This seems to be a leftover from an initial WIP in #11720)
 2022-10-14 19:28:17 -04:00
John Davis cab2582b0c Do not hardcode queues assignment to tasks 2022-10-14 19:28:17 -04:00
John Davis 48da572c4e Override celery task name generation 2022-10-14 19:28:17 -04:00
John Davis 2de79dd7d1 Add default task routes to config schema 2022-10-14 19:28:17 -04:00
John Davis 535a524e33 Enable celery configuration via galaxy's config 2022-10-14 19:28:17 -04:00
Aysam Guerler eee3cb19fd Merge pull request #14646 from assuntad23/12725/feature/collection-change-datatype 
Adding Bulk Datatype Change to Collection Edit
 2022-10-14 19:10:01 -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 71829ae6af Add more details to setting db engine options to config schema 2022-10-14 13:18:35 -04:00
John Davis da87ca9209 Allow to set connect_args for SQLAlchemy's engine in config 2022-10-14 13:17:42 -04:00
John Chilton c3618f275d Merge pull request #14789 from nsoranzo/fix_test_get_alternative_versions 
Fix ``test_get_alternative_versions`` unit test
 2022-10-14 10:12:15 -04:00
davelopez c776c8169a Validate BioCompute Objects against schema in tests 2022-10-14 12:20:24 +02:00
davelopez ffd29f01b7 Restore temporarily bco API test 2022-10-14 12:20:24 +02:00
davelopez e75923fce3 Restore bco endpoints as deprecated 
Minimal implementation trying to reuse the export store system to keep the old endpoints until they are finally removed.
 2022-10-14 12:20:24 +02:00
davelopezandNicola Soranzo 5dc7dae7c1 Use pydantic[email] instead of email-validator 
Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
 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 70e7600968 Fix some pydantic validation issues 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