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Account for different HLA-B variants #684

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23 tasks done
tamslo opened this issue Dec 11, 2023 · 0 comments
Closed
23 tasks done

Account for different HLA-B variants #684

tamslo opened this issue Dec 11, 2023 · 0 comments
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P: App Project: App Study: Must have T: Change Type: Changes

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@tamslo
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tamslo commented Dec 11, 2023

One tile per positive/negative variant.

Could change this in the source data, but then we would probably also need to adapt how lookups are made; therefore it might be cleaner to handle in the app:

  • Adapt test data to include multiple HLA-B variants
  • Rename Diplotype to GeneResult
  • Rename CpicPhenotype to CpicLookup
  • Make GeneResult and CpicLookup inherit from abstract class Genotype
  • Move PhenotypeInformation to own file (not really required for this ticket but should do this when already refactoring) ➡️ added to Refactor User Data #680
  • Fix fetching lookups
    • Somehow, the .fromJson factory is only called later, but at this time the json was already adapted in place at that point
    • Fix by not changing json in place but passing new object to internal FromJson constructor
  • Rename CpicLookup to LookupInformation
  • Refactor to not write gene results and lookups into map with gene as key; need get all information not by gene but gene plus variant / genotypeKey either change to list or adapt keys of map
    • Instead of LookupInformation store GenotypeResults (implements Genotype; stores relevant information from GeneResult; stores lookupkey) as genotypeResults in Map with genotypeKey
    • Rename GeneResult to LabResult and geneResults to labData
    • Better name for GenotypeResults, e.g., something PGx-related? GenotypeResult is pretty accurate
    • Use genotype key as title and only "positive" or "negative" as phenotype / genotype
  • GenotypeResult should have extension to easily get overwritten lookup; possible to include or combine with PhenotypeInformation? (moved to Refactor User Data #680)
  • Test that everything works
    • Linking to gene detail page
      • Non-unique gene
      • Unique gene
      • Not tested
    • Filtering drugs
      • Non-unique gene
      • Unique gene
      • Not tested
    • Lookup matching to guidelines (including source URLs)
      • Non-unique gene
      • Unique gene
      • Not tested
    • Inhibitors working
  • Fix that phenotype shows on guideline card multiple times
@tamslo tamslo added P: App Project: App Study: Must have T: Change Type: Changes labels Dec 11, 2023
tamslo added a commit that referenced this issue Feb 7, 2024
tamslo added a commit that referenced this issue Feb 12, 2024
tamslo added a commit that referenced this issue Feb 12, 2024
@tamslo tamslo closed this as completed Feb 13, 2024
@github-project-automation github-project-automation bot moved this from Todo to Done (last 14 days) in PharMe Study Preparation Feb 13, 2024
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Labels
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