Remove mechanism of inheritance conversion to allele state (oncokb#1281)

Author: calvinlu3

src/main/webapp/app/pages/genePage/GenomicIndicatorTable.tsx

@@ -2,19 +2,41 @@ import OncoKBTable, {
   SearchColumn,
 } from 'app/components/oncokbTable/OncoKBTable';
 import {
+  ALLELE_STATE_BIALLELEIC,
+  ALLELE_STATE_CARRIER,
+  ALLELE_STATE_MONOALLELIC,
+  AlleleState,
   LG_TABLE_FIXED_HEIGHT,
   THRESHOLD_TABLE_FIXED_HEIGHT,
 } from 'app/config/constants';
 import React from 'react';
-import {
-  getAlleleStatesFromEvidence,
-  getAlterationName,
-} from 'app/shared/utils/Utils';
+import { getAlterationName } from 'app/shared/utils/Utils';
 import { LongText } from 'app/oncokb-frontend-commons/src/components/LongText';
 import { Evidence } from 'app/shared/api/generated/OncoKbAPI';
 import AlleleStateTag from 'app/components/tag/AlleleStateTag';
 import { genomicIndicatorNameSortMethod } from 'app/shared/utils/ReactTableUtils';
 
+const parseAlleleStateFromIndicatorName = (
+  name: string
+): { displayName: string; alleleState?: AlleleState } => {
+  const alleleStateMap: { [key: string]: AlleleState } = {
+    carrier: ALLELE_STATE_CARRIER,
+    monoallelic: ALLELE_STATE_MONOALLELIC,
+    biallelic: ALLELE_STATE_BIALLELEIC,
+  };
+
+  const match = (name ?? '').match(
+    /\s*\((carrier|monoallelic|biallelic)\)\s*$/i
+  );
+  if (match) {
+    const alleleState = alleleStateMap[match[1].toLowerCase()];
+    const displayName = name.replace(match[0], '').trim();
+    return { displayName, alleleState };
+  }
+
+  return { displayName: name };
+};
+
 export const GenomicIndicatorTable: React.FunctionComponent<{
   data: Evidence[];
   isPending: boolean;
@@ -27,12 +49,14 @@ export const GenomicIndicatorTable: React.FunctionComponent<{
     {
       Header: <span>Genomic Indicator</span>,
       maxWidth: 200,
-      accessor: 'name',
+      id: 'name',
       Cell(row: { original: Evidence }) {
-        const alleleState = getAlleleStatesFromEvidence(row.original);
+        const { displayName, alleleState } = parseAlleleStateFromIndicatorName(
+          row.original.name
+        );
         return (
           <>
-            <div>{row.original.name}</div>
+            <div>{displayName}</div>
             {alleleState && <AlleleStateTag alleleState={alleleState} />}
           </>
         );

src/main/webapp/app/shared/utils/Utils.tsx

@@ -970,38 +970,3 @@ export const getFdaSubmissionNumber = (
     ? `${primaryNumber}/${supplementNumber}`
     : primaryNumber;
 };
-
-const isAlleleState = (str: string): str is AlleleState => {
-  return (
-    str === ALLELE_STATE_MONOALLELIC ||
-    str === ALLELE_STATE_BIALLELEIC ||
-    str === ALLELE_STATE_CARRIER
-  );
-};
-
-export const getAlleleStateFromMechanismOfInheritance = (
-  inheritanceMechanism: InheritanceMechanism
-): AlleleState | undefined => {
-  if (inheritanceMechanism === MECHANISM_OF_INHERITANCE_AUTOSOMAL_DOMINANT) {
-    return ALLELE_STATE_MONOALLELIC;
-  }
-
-  if (inheritanceMechanism === MECHANISM_OF_INHERITANCE_AUTOSOMAL_RECESSIVE) {
-    return ALLELE_STATE_BIALLELEIC;
-  }
-
-  if (inheritanceMechanism === 'Carrier') {
-    return ALLELE_STATE_CARRIER;
-  }
-
-  return undefined;
-};
-
-export const getAlleleStatesFromEvidence = (evidence: Evidence) => {
-  if (!evidence.knownEffect) {
-    return undefined;
-  }
-  const moi = evidence.knownEffect.trim() as InheritanceMechanism;
-  const alleleState = getAlleleStateFromMechanismOfInheritance(moi);
-  return alleleState;
-};