Merge pull request #1081 from zhx828/master

Linkout to categorical alteration page if the alteration starts with the categorical alteration

src/main/webapp/app/config/constants.tsx

@@ -616,6 +616,14 @@ export const GAIN_OF_FUNCTION_MUTATIONS = 'Gain-of-function Mutations';
 export const LOSS_OF_FUNCTION_MUTATIONS = 'Loss-of-function Mutations';
 export const SWITCH_OF_FUNCTION_MUTATIONS = 'Switch-of-function Mutations';
 
+export const CATEGORICAL_ALTERATIONS = [
+  ONCOGENIC_MUTATIONS,
+  FUSIONS,
+  TRUNCATING_MUTATIONS,
+  GAIN_OF_FUNCTION_MUTATIONS,
+  LOSS_OF_FUNCTION_MUTATIONS,
+  SWITCH_OF_FUNCTION_MUTATIONS,
+];
 export enum SEARCH_QUERY_KEY {
   REFERENCE_GENOME = 'refGenome',
 }

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

@@ -11,6 +11,7 @@ import {
 import {
   encodeSlash,
   getAlterationName,
+  getCategoricalAlteration,
   getYouTubeLink,
   IAlteration,
 } from 'app/shared/utils/Utils';
@@ -73,17 +74,19 @@ export const getAlterationPageLink = (props: {
   searchQueries?: AlterationPageSearchQueries;
   hashQueries?: AlterationPageHashQueries;
 }): string => {
-  let pageLink = `${PAGE_ROUTE.GENE_HEADER}/${props.hugoSymbol}/${
+  const linkoutAltName = getCategoricalAlteration(
     typeof props.alteration === 'string'
       ? props.alteration
       : props.alteration.name
-  }`;
+  );
+
+  let pageLink = `${PAGE_ROUTE.GENE_HEADER}/${props.hugoSymbol}/${linkoutAltName}`;
   if (props.cancerType) {
     pageLink = `${pageLink}/${encodeSlash(props.cancerType)}`;
   }
   const sq = props.searchQueries || {};
 
-  // Prop alterationRefGenomes is just a convinient way to process reference genomes when it's a list.
+  // Prop alterationRefGenomes is just a convenient way to process reference genomes when it's a list.
   if (!sq.refGenome && props.alterationRefGenomes) {
     if (!props.alterationRefGenomes.includes(DEFAULT_REFERENCE_GENOME)) {
       sq.refGenome = props.alterationRefGenomes[0];

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

@@ -10,6 +10,7 @@ import {
   APP_LOCAL_DATE_FORMAT,
   APP_LOCAL_DATETIME_FORMAT_Z,
   APP_TIMESTAMP_FORMAT,
+  CATEGORICAL_ALTERATIONS,
   DELETION,
   FUSIONS,
   GAIN_OF_FUNCTION_MUTATIONS,
@@ -756,22 +757,24 @@ export interface IAlteration {
 }
 
 export const isCategoricalAlteration = (alteration: string) => {
-  const categoricalAlterations = [
-    ONCOGENIC_MUTATIONS,
-    FUSIONS,
-    TRUNCATING_MUTATIONS,
-    GAIN_OF_FUNCTION_MUTATIONS,
-    LOSS_OF_FUNCTION_MUTATIONS,
-    SWITCH_OF_FUNCTION_MUTATIONS,
-  ];
   return (
     alteration &&
-    categoricalAlterations.filter(alt =>
+    CATEGORICAL_ALTERATIONS.filter(alt =>
       alteration.toLowerCase().startsWith(alt.toLowerCase())
     ).length > 0
   );
 };
 
+export const getCategoricalAlteration = (alteration: string) => {
+  if (isCategoricalAlteration(alteration)) {
+    const matched = CATEGORICAL_ALTERATIONS.filter(categoricalAlt => {
+      return alteration.toLowerCase().startsWith(categoricalAlt.toLowerCase());
+    });
+    return matched.pop();
+  }
+  return alteration;
+};
+
 /**
  *
  * @param alteration Alteration, either in string or in IAlteration
@@ -856,7 +859,7 @@ export const getCategoricalAlterationDescription = (
     default:
       break;
   }
-  if (alteration.startsWith(ONCOGENIC_MUTATIONS)) {
+  if (ONCOGENIC_MUTATIONS.toLowerCase() === alteration.toLowerCase()) {
     let prefix =
       'Defined as point mutations, rearrangements/fusions or copy number alterations within';
     if (oncogene && !tsg) {
@@ -869,8 +872,8 @@ export const getCategoricalAlterationDescription = (
       <span>
         {prefix} {geneLink} considered "oncogenic", "likely oncogenic" or
         "resistance" as defined by{' '}
-        <SopPageLink version={2.2}>
-          {ONCOKB_TM} Curation Standard Operating Protocol v2.2, Chapter 2,
+        <SopPageLink>
+          {ONCOKB_TM} Curation Standard Operating Protocol, Chapter 1,
           Sub-Protocol 2.5
         </SopPageLink>
         .