WIP: Filter irrelevant pubmed references
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):
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New feature -
Bug fix -
Improvement
Ops / admin / CI related only (not impacting users):
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New feature -
Bug fix -
Improvement
Tests
General
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Tests have been added that prove my fix is effective or that my feature works -
Related tests have been modified/removed
Hypothesis testing:
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Soak testing has been done -
Distribution between positive / negative cases has been checked
Database
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Includes changes to database schema -
Includes necessary database migrations
Configuration
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Includes changes to configuration -
Includes configuration migration instructions in documentation
Merge checklist
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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