fix(variant): generates cascades of variants synchronously to avoid timeout dead locks

[laurent-laporte-pro]

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[commit-lint]

Chore

• typing: simplify typing in pytest fixture (da13c45)
• variant-study-service: correct the timeout parameter to use a default value (1e2e617)
• improve log message readability by adding prominent emojis (eb87bb8)

Features

• repository: add a method to update a task status to TIMEOUT in database (38addea)
• variant-generation: improve error handling for timeout tasks (979ac6a)
• tasks: add timeout parameter to control task completion wait time (0cac11c)
• variant-study-repo: add the get_ancestor_or_self_ids to retrieve all ancestor IDs of a variant study (8262e14)
• permission: add the assert_permission_on_studies to check user permission of several studies (ea69c38)
• db: add methods to check the variant study snapshot status (e4f7756)
• variant: add the SnapshotGenerator class (70595c9)
• variant: use the SnapshotGenerator class in the VariantStudyService (be805dc)

Bug Fixes

• task-job-service: update the task status to TIMEOUT if the processing is too long (ff357bc)

Code Refactoring

• variant-study-service: improve implementation of safe generation (959b2c0)
• variant-study-repo: optionally use a user-defined SqlAlchemy session instead of the global db.session and improve the documentation (cd15eec)

Tests

• variant-generation: add a unit test to check that the variant generation is not blocking the main thread (0ba6320)
• hydro: improves testing of hydraulic allocation variants (21823ba)
• variant: correct the test_variant_model unit test to use fixtures (340881e)

Styles

• db: add type hints in database model classes (4c9c081)
• correct return type of the get task endpoint (7dff31a)
• correct variable naming (8d42c1b)

Documentation

• cache: add the documentation of cache constants (94d3cdb)

Performance Improvements

• db: improved study query performance using owner and groups preloading (16cf54f)

Contributors

laurent-laporte-pro

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