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Create script to post reports to PhenoTips variant store #869

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cklamann opened this issue Oct 12, 2021 · 2 comments
Closed

Create script to post reports to PhenoTips variant store #869

cklamann opened this issue Oct 12, 2021 · 2 comments
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@cklamann
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cklamann commented Oct 12, 2021

The script should take a report csv path as input and do the following:

  • transform report into long format and separate into separate 'reports' for each participant
  • fetch an API token from PT using a client key and secret
  • post each participant-level report to the PT variant store endpoint

NB: We currently don't have the specific endpoint for the token or post request that we'll be using, but the script should be written in such a way that we can drop them in when they're available.

This code should go into a new repository, as it's not part of the Stager application, though we'll be tracking progress here for convenience.

@delvinso
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Preliminary steps/notes:

  • barebones script should take a report path as an arg and convert it into long format wrt participant codenames, possibly saving each participant-wise report as a csv -> can potentially apply the wrangling used in variant migration for consistency between reports as the reports have changed over time

@delvinso
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Consolidated into #1021

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