Clinical-Genomics / cg / 15823539042

86%

Build Type

push

github

Committed by web-flow

Commit Message

Fix(Start query) Harmonize cases to start query (#4443)(minor)

## Description
This PR harmonises the logic for getting which cases should be analysed. I removes all the special logic for Balsamic and MIP-DNA and centralises the logic to the database layer.

### Important changes:
- microSALT is now explicitly treated as an exception, and is the only pipeline that will start automatically if allready analysed but new data is added.

- The start-available command no longer performs the SeqeuencingQC check. Instead it just queries the `case.aggregated_sequencing_qc` column in the database. The command `cg sequencing-qc` runs the same logic on a timer, so the will be performed by this command instead.

### Changed

- Sequencing QC removed from start-available
- Sequencing QC added as a query filter in start-available
- Removed special `is_case_ready_for_analysis` from MIP-DNA and Balsamic
- Removed the extra `_is_case_to_be_analyzed` check in read.py

Run Details

20 of 22 new or added lines in 10 files covered. (90.91%)

19 existing lines in 5 files now uncovered.

26674 of 31106 relevant lines covered (85.75%)

0.86 hits per line