Trailblazer

Refactor update jobs (237)

Added

- Tests

Changed

- Split update_jobs into two new functions to remove side effects. Move end refactor new functions.
- Add DeleteHandler

Refactor sql analysis (238)

Added

- General filter module for Analysis
- Tests

Changed

- Refactor sql analysis and migrate it ReadHandler



15
Added

- SLURM module: models.py and api.py
- get_squeue_result for reading squeue output into Pydantic models
- get_current_analysis_status for getting the analysis status based on job status distribution
- SqueueResult and SqueueJob Pydantic models
- Constants:
- SlurmJobStatus
- HOURS_IN_DAY
- MINUTES_PER_HOUR
- SCALE_SECONDS_TO_MINUTES
- SlurmSqueueHeader
- Pipeline
- CSV file extension and file format
- Header to squeue output to enable CSV dict stream parsing and aliasing in Pydantic model
- Reading CSV str stream into list of dicts
- Tests

Refactor reading squeue output (241)

Changed

- Lock Pydantic version to 1.10.9
- Remove Pandas
- TrailblazerStatus to be a str based enum, enabling removal of ".value" accessing
- Decode bytes to string in subprocessing squeue output
- Refactored sacct test fixtures into squeue csv files
- All parsing oof squeue output is done when initializing Squeue Pydantic models

quick fix: unsupported tower status in job table (240)

Fixed

- Temporary fix for non-supported tower status in job table. Cancelled and Aborted status in tower are set as Failed.

Refactor add pending analysis (234)

Added

- Tests

Changed

- Moved `add_pending_analysis` to CreateHandler and refactored it
- Renamed `sample_store` to `analysis_store`

fix(TowerWorkflow) null status returned when job is cached (236) (patch)

Fixed

- Null status returned when job has been cached in TowerWorkflow

Refactor sql aggregate failed (232)

Added

- Filter functions for Jobs
- Tests
- Date utility function

Changed

- Refactored and moved aggregate_failed function