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statgen / bravo_api

Server side data processing and retrieval endpoints for BRAVO
MIT License
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Load data erroneously requires cache directory to exist. #16

Open grosscol opened 2 years ago

grosscol commented 2 years ago

Describe the bug CLI commands to load data fail if CRAM cache path does not exist.

To Reproduce Steps to reproduce the behavior:

  1. Run 
    api/venv/bin/flask load-genes canonical_transcripts.tsv.gz \
  omim_ensembl_refs.tsv.gz \
  hgcn_genenames.tsv.gz \
  gencode.v38.annotation.gtf.gz
  2. Wait for execution to halt with error Exception: Provided CRAM cache path does not exist.

Expected behavior Gene collections to be loaded into mongo db from given inputs.

Desktop (please complete the following information):

Distributor ID: Ubuntu
Description:    Ubuntu 20.04.5 LTS
Release:        20.04
Codename:       focal

Additional context Loading backing data post data_prep processing.