Fix bug in upstream data with letter case in gene name

src/js/gene-cache.js

@@ -82,6 +82,7 @@ function getEnsemblId(ensemblPrefix, slimEnsemblId) {
 /** Parse a gene cache TSV file, return array of useful transforms */
 function parseCache(rawTsv, orgName) {
   const names = [];
+  const nameCaseMap = {};
   const namesById = {};
   const idsByName = {};
   const lociByName = {};
@@ -113,6 +114,7 @@ function parseCache(rawTsv, orgName) {
     const locus = [chromosome, start, stop];
 
     names.push(gene);
+    nameCaseMap[gene.toLowerCase()] = gene;
     namesById[ensemblId] = gene;
     idsByName[gene] = ensemblId;
     lociByName[gene] = locus;
@@ -124,7 +126,10 @@ function parseCache(rawTsv, orgName) {
   const sortedAnnots = parseAnnots(preAnnots);
   perfTimes.parseAnnots = Math.round(performance.now() - t1);
 
-  return [names, namesById, idsByName, lociByName, lociById, sortedAnnots];
+  return [
+    names, nameCaseMap, namesById, idsByName, lociByName, lociById,
+    sortedAnnots
+  ];
 }
 
 /** Get organism's metadata fields */
@@ -181,12 +186,14 @@ export default async function initGeneCache(orgName, ideo, cacheDir=null) {
   perfTimes.fetch = Math.round(fetchEndTime - fetchStartTime);
 
   const [
-    interestingNames, namesById, idsByName, lociByName, lociById, sortedAnnots
+    interestingNames, nameCaseMap, namesById, idsByName,
+    lociByName, lociById, sortedAnnots
   ] = parseCache(data, orgName);
   perfTimes.parseCache = Math.round(performance.now() - fetchEndTime);
 
   ideo.geneCache = {
     interestingNames, // Array ordered by general or scholarly interest
+    nameCaseMap, // Maps of lowercase gene names to proper gene names
     namesById,
     idsByName,
     lociByName, // Object of gene positions, keyed by gene name

src/js/kit/related-genes.js

@@ -105,7 +105,7 @@ function maybeGeneSymbol(ixn, gene) {
 function isInteractionRelevant(rawIxn, gene, nameId, seenNameIds, ideo) {
   let isGeneSymbol;
   if ('geneCache' in ideo && gene.name) {
-    isGeneSymbol = rawIxn in ideo.geneCache.lociByName;
+    isGeneSymbol = rawIxn.toLowerCase() in ideo.geneCache.nameCaseMap;
   } else {
     isGeneSymbol = maybeGeneSymbol(rawIxn, gene);
   }
@@ -263,14 +263,24 @@ function fetchGenesFromCache(names, type, ideo) {
 
   const hits = names.map(name => {
 
-    if (!locusMap[name]) {
+    const nameLc = name.toLowerCase();
+
+    if (!locusMap[name] && !cache.nameCaseMap[nameLc]) {
       if (isSymbol) {
         throwGeneNotFound(name, ideo);
       } else {
         return;
       }
     }
 
+    // Canonicalize name if it is mistaken in upstream data source.
+    // This can sometimes happen in WikiPathways, e.g. when searching
+    // interactions for rat Pten, it includes a result for "PIK3CA".
+    // In that case, this would correct PIK3CA to be Pik3ca.
+    if (isSymbol && !locusMap[name] && cache.nameCaseMap[nameLc]) {
+      name = cache.nameCaseMap[nameLc];
+    }
+
     const locus = locusMap[name];
     const symbol = isSymbol ? name : nameMap[name];
     const ensemblId = isSymbol ? nameMap[name] : name;