feat(browser): sort ClinVar by consequence in table

Sort ClinVar terms by their submitted classification, rather than lexicographically

browser/src/ClinvarVariantsTrack/clinvarVariantCategories.ts

@@ -16,7 +16,7 @@ const CLINICAL_SIGNIFICANCE_GROUPS = {
     'Conflicting classifications of pathogenicity',
     'conflicting data from submitters',
   ]),
-  benign: new Set(['Benign', 'Likely benign', 'Benign/Likely benign']),
+  benign: new Set(['Likely benign', 'Benign/Likely benign', 'Benign']),
   other: new Set([
     'other',
     'drug response',
@@ -29,6 +29,22 @@ const CLINICAL_SIGNIFICANCE_GROUPS = {
   ]),
 } as const
 
+const buildPriorityMapping = () => {
+  const mapping: { [key: string]: number } = {}
+  let priority = 1
+
+  for (const category of CLINICAL_SIGNIFICANCE_CATEGORIES) {
+    const group = CLINICAL_SIGNIFICANCE_GROUPS[category as ClinicalSignificance]
+    for (const significance of group) {
+      mapping[significance] = priority++
+    }
+  }
+
+  return mapping
+}
+
+export const CLINICAL_SIGNIFICANCE_SORT_PRIORITY = buildPriorityMapping()
+
 export type ClinicalSignificance = keyof typeof CLINICAL_SIGNIFICANCE_GROUPS
 
 export const clinvarVariantClinicalSignificanceCategory = (variant: any) => {

browser/src/VariantList/sortUtilities.ts

@@ -1,3 +1,5 @@
+import { CLINICAL_SIGNIFICANCE_SORT_PRIORITY } from '../ClinvarVariantsTrack/clinvarVariantCategories'
+
 export const isEmpty = (val: any) => val === undefined || val === null || val === ''
 
 export const makeCompareFunction =
@@ -29,3 +31,11 @@ export const makeStringCompareFunction = (key: any) =>
 
 export const makeNumericCompareFunction = (key: any) =>
   makeCompareFunction(key, (v1: any, v2: any) => v1 - v2)
+
+export const makeClinvarCompareFunction = (key: any) =>
+  makeCompareFunction(key, (v1: string, v2: string) => {
+    return (
+      (CLINICAL_SIGNIFICANCE_SORT_PRIORITY[v1] ?? 999) -
+      (CLINICAL_SIGNIFICANCE_SORT_PRIORITY[v2] ?? 999)
+    )
+  })

browser/src/VariantList/variantTableColumns.tsx

@@ -8,6 +8,7 @@ import { Cell, NumericCell, renderAlleleCountCell, renderAlleleFrequencyCell } f
 import { getCategoryFromConsequence, getLabelForConsequenceTerm } from '../vepConsequences'
 import SampleSourceIcon from './SampleSourceIcon'
 import {
+  makeClinvarCompareFunction,
   makeCompareFunction,
   makeNumericCompareFunction,
   makeStringCompareFunction,
@@ -126,7 +127,7 @@ const variantTableColumns: VariantTableColumn[] = [
     description: 'ClinVar clinical significance',
     grow: 1,
     minWidth: 150,
-    compareFunction: makeStringCompareFunction('clinical_significance'),
+    compareFunction: makeClinvarCompareFunction('clinical_significance'),
     getSearchTerms: (variant: any) => variant.clinical_significance,
     render: (variant: any, _: any, { highlightWords }: any) => (
       <Cell>