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Load data erroneously requires cache directory to exist. #16

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grosscol opened this issue Sep 21, 2022 · 0 comments
Open

Load data erroneously requires cache directory to exist. #16

grosscol opened this issue Sep 21, 2022 · 0 comments
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bug Something isn't working

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@grosscol
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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.

@grosscol grosscol added the bug Something isn't working label Sep 21, 2022
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