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Create script to post reports to Stager #870

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cklamann opened this issue Oct 12, 2021 · 1 comment · May be fixed by #902
Closed

Create script to post reports to Stager #870

cklamann opened this issue Oct 12, 2021 · 1 comment · May be fixed by #902
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@cklamann
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cklamann commented Oct 12, 2021

Depends on #869

The script should take a report csv path and an analysis ID (?) as input and do the following:

  • transform report into long format and separate into separate 'reports' for each participant (see Create script to post reports to PhenoTips variant store #869)
  • break up each participant-level 'report' into json that corresponds to the appropriate Stager data models (i.e., separate data that belongs in the variant table from data that belongs in the genotype table).
  • fetch an API token from Stager using a client key and secret
  • post the data to Stager (we might want to write an endpoint like api/analysis/{id}/report that wraps both inserts in a transaction).

This script should go in the same repo as #869.

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