biocore / biocore/LabControl

Move definition of number of lanes per sequencer into database from SequencingProcess

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#266 6 comments 0 reactions 0 assignees View on GitHub
code refactor priority:low scope:medium
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Python
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Description

It appears that currently the number of lanes for each kind of sequencer is hard-coded into the labman.db.process.SequencingProcess class at

https://github.com/jdereus/labman/blob/3cd014c1039a65542bce0f7e127d7db65699a66d/labman/db/process.py#L2408-L2410

I believe the kind names here are (a subset of the) values from the description field of the qiita.equipment_type table, which is populated in labman.db.support_files.db_patch_manual.sql, lines 39-45:

```
-- Populate the equipment type table
INSERT INTO qiita.equipment_type (description) VALUES
('echo'), ('mosquito'), ('EpMotion'), ('King Fisher'),
('tm 1000 8 channel pipette head'), ('tm 300 8 channel pipette head'),
('tm 50 8 channel pipette head'), ('HiSeq4000'), ('MiniSeq'), ('NextSeq'),
('HiSeq3000'), ('HiSeq2500'), ('HiSeq1500'), ('MiSeq'), ('NovaSeq'),
('Not applicable');
```

I worry that in the future, someone will add a new sequencer to the equipment table but forget to update the hardcoded lane values.

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