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WIP: Filter irrelevant pubmed references

Tor Solli-Nowlan requested to merge 1355-filter-irrelevant-pubmed-references into dev

Description

References from ClinVar include a number of reports that are not directly relevant to the variants in question, e.g. describing procedures or guidelines. These show up recurrently for a lot of variants and results in unnecessary work dismissing them.

Closes issues: LA-1355

Related issues:

[SUMMARY] As discussed, a new entry was created in usergroups.json to hold the list of IDs to filter. The key is interpretation.removePubmedReferences and is expected to be an array of ints.

While the fetching/display of reference info happens in getReferences.js, just filtering there made it look like there was missing reference data. The underlying function for accessing reference data was getReferencesIdsForAllele. I modified it to accept a filter list as a parameter, since it cannot access the user config directly.

Notes to reviewer

You can test that the filter is working correctly by adding {"interpretation": { "removePubmedReferences": [ 17453335 ] } } to usergroups.json. This removes the reference listed on the BRCA2 c.10G>T allele. NB: usergroups.json is stored in the DB and does not reload automatically on change like the js.

Type of change

Application (affects UI or general functionality):

  • New feature
  • Bug fix
  • Improvement

Ops / admin / CI related only (not impacting users):

  • New feature
  • Bug fix
  • Improvement

Tests

General

  • Tests have been added that prove my fix is effective or that my feature works
  • Related tests have been modified/removed

Hypothesis testing:

  • Soak testing has been done
  • Distribution between positive / negative cases has been checked

Database

  • Includes changes to database schema
  • Includes necessary database migrations

Configuration

  • Includes changes to configuration
  • Includes configuration migration instructions in documentation

Merge checklist

  • Self-review of code performed
  • Feature review against specification (if applicable)
  • Need for documentation has been evaluated and, if necessary, updated
  • Code and implementation is reviewed by other core developer (all changes, inc. changes based on initial review)

Closes #1355

Edited by Tor Solli-Nowlan

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