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Commit Graph
32455 Commits
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
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
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
galaxybot 873cdfc30c Update Python dependencies 2022-10-15 03:57:24 +00:00
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
John Davis d957e143ea Engine options are never null 2022-10-14 15:27:20 -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
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
John Davis c8a1581e06 Assign values from env using new utility function 
Also, fix error: don't break out early as both values should be
assigned.
 2022-10-13 13:17:33 -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
Marius van den Beek 5f30153180 Merge pull request #14784 from jmchilton/sync_job_script 
Synchronize job script module with Pulsar fixes.
 2022-10-13 10:19:32 +02:00
John Chilton 5dde30a9db Synchronize job script module with Pulsar fixes. 
- Allows memory_statement.log to be written to a better location than the working directory.
- Allow Pulsar to handle home directory outside the command_factory abstraction.
 2022-10-12 14:36:57 -04:00
Nicola Soranzo 847946a887 Move `skip_if_site_down` test decorator to be reusable in unit tests 
Also:
- Add type annotations
 2022-10-12 18:13:46 +01:00
Nicola Soranzo c810ebf9e1 Make 2 test decorators usable on both functions and methods 2022-10-12 18:13:45 +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
Nicola Soranzo a81d680cca Merge branch 'release_22.05' into dev 2022-10-11 21:34:31 +01:00
Nicola Soranzo b31e2f02f2 Merge branch 'release_22.01' into release_22.05 2022-10-11 13:28:32 +01:00
Nicola Soranzo bb3006df87 Fix dataset provenance API when `follow=False` 2022-10-11 00:45:37 +01:00
Martin Cech 11ac6cd7c6 Merge pull request #14755 from jdavcs/dev_config_file 
Do not load sample config file; assign correct config paths
 2022-10-10 20:29:10 +02:00
John Chilton 552f0cfd61 Migrate index and show install repository endpoints to Pydantic+FastAPI. 2022-10-10 11:19:18 -04:00