Invalid metadata spreadsheet should be handled

ShawHahnLab / umbra

Python package and executable for Linux for managing Illumina sequencing runs

GNU Affero General Public License v3.0

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Invalid metadata spreadsheet should be handled #65

Closed ressy closed 4 years ago

ressy commented 4 years ago

If an experiment metadata CSV file is malformed it will crash IlluminaProcessor. Instead this should be caught and logged.

ressy commented 4 years ago

I think the appropriate place would be project.ProjectData.from_alignment, as already done with FileNotFoundError except with more complaining via LOGGER.error or similar. Then the processor's _proc_new_alignment callback will receive an empty set of projects and and will continue from there.