Trailblazer

Add config model (272) (major)


Added

- ANALYSIS_HOST to dockerfile to enable setting it at runtime
- Add and use Pydantic Config model for CLI input
- Tests

Changed

- Use `trailblazer_db` instead of ´trailblazer` in click.context
- Remove `database` from click.context as it was not used
- Remove `database` CLI option
- Refactor `database` in config to `database_url`
- Require config option on CLI
- Use ANALYSIS_HOST when using SSH

Refactor cancel slurm job (273)

Changed

- Refactor and migrate`cancel_slurm_job` to SLURM API
- Removed `cancel_slurm_job` from Mockstore

Refactor mark analyses deleted (269)

Added

- Tests
- Added `get_analyses_for_case` function

Changed

- Refactored and migrated `mark_analyses_deleted` into CRUD modules.
- Refactored `case_name` to `case_id`

feat(refactor): query_slurm function (266)

Changed

- New utility function to return reformatted SLURM job ids
- New utility function to update analysis status from SLURM run
- Migrate and refactor query_slurm to slurm/api.py
- Extract method from update_analysis_from_slurm_run_status into CRUD
- Remove query_slurm from MockStore
- Add new test fixtures

patch(analysis) Make get_latest_analysis_for_case return the latest case (267)(patch)

Fixed

- `get_latest_analysis_for_case` now returns the latest analysis

Refactor get latest analysis (264)

Added

- Tests

Changed

- Refactor `get_latest_analysis` and migrate to CRUD.
- Refactor tests
- Rename case_id fixtures to case_name