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Clinical-Genomics / trailblazer / 5783106565
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Build:
DEFAULT BRANCH: master
Ran 07 Aug 2023 09:00AM UTC
Jobs 1
Files 42
Run time 2s
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Refactor reading squeue output (#241) (minor)

### 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

### 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

188 of 188 new or added lines in 12 files covered. (100.0%)

942 of 1250 relevant lines covered (75.36%)

0.75 hits per line

Jobs
ID Job ID Ran Files Coverage
1 5783106565.1 07 Aug 2023 09:00AM UTC 0
75.36
Source Files on build 5783106565
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