Scout: Add synopsis, phenotype_terms and cohorts to load config

Created on 15 Oct 2020  路  5Comments  路  Source: Clinical-Genomics/scout

StarLIMS can now export new fields to the order json files going over to CG. We wish to be able to load these into Scout for new cases:

  • synopsis: list(str)
  • phenotype_terms: list(str)
  • cohorts: list(str)
enhancement Easy

All 5 comments

I'm planning to work on this. Questions:

  • Synopsis is a list of single words or a list of sentences?
  • Phenotype terms are a list of HPO terms like HP:number ?
  • Cohort should be something like ["pedhep", mito", ..], right?

Synopsis is just str I guess

Ah, no, array of str actually: Synopsis becomes a note type in the LIMS, and users could theoretically add multiple such notes in different places on a case..

I've sent you the specs over email @northwestwitch - thanks for picking this one up!

I've sent you the specs over email @northwestwitch - thanks for picking this one up!

Thank you!

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