Fix uniprot PTM crash when centain fields are missing in uniprot data

cBioPortal · Nov 10, 2021 · 2b516fe · 2b516fe
1 parent 2878f05
commit 2b516fe
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Showing 5 changed files with 82 additions and 37 deletions.
diff --git a/packages/cbioportal-utils/src/model/Uniprot.ts b/packages/cbioportal-utils/src/model/Uniprot.ts
@@ -23,17 +23,17 @@ export interface UniprotFeatureEvidence {
 export interface UniprotFeature {
     type: string; // "MOD_RES"
     category: string; // "PTM"
-    description: string; // "Phosphoserine; by HIPK4"
+    description?: string; // "Phosphoserine; by HIPK4"
     begin: string; // "9"
     end: string; // "9"
-    molecule: string;
-    evidences: UniprotFeatureEvidence[];
+    molecule?: string;
+    evidences?: UniprotFeatureEvidence[];
 }
 
 export interface UniprotTopology {
     type: string; // TOPO_DOM
     startPosition: number; // 25
     endPosition: number; // 645
-    description: string; // Extracellular
-    evidence: UniprotFeatureEvidence[]; // ECO:0000255
+    description?: string; // Extracellular
+    evidence?: UniprotFeatureEvidence[]; // ECO:0000255
 }
diff --git a/packages/cbioportal-utils/src/ptm/PtmUtils.spec.ts b/packages/cbioportal-utils/src/ptm/PtmUtils.spec.ts
@@ -5,6 +5,8 @@ import {
     compareByPtmTypePriority,
     convertDbPtmToPtm,
     convertUniprotFeatureToPtm,
+    getPtmTypeFromUniprotFeature,
+    getPubmedIdsFromUniprotFeature,
     groupPtmDataByPosition,
     groupPtmDataByTypeAndPosition,
     ptmColor,
@@ -197,6 +199,15 @@ describe('PtmUtils', () => {
         },
     ];
 
+    const partialUniprotPtm = [
+        {
+            type: 'MOD_RES',
+            category: 'PTM',
+            begin: '2',
+            end: '2',
+        },
+    ];
+
     describe('convertToPtmData', () => {
         it('identically converts residues for both dbPTM and uniprotPTM data', () => {
             assert.deepEqual(
@@ -341,4 +352,20 @@ describe('PtmUtils', () => {
             );
         });
     });
+    describe('partial Uniprot data', () => {
+        it('uses default ptm type when description is empty', () => {
+            assert.equal(
+                getPtmTypeFromUniprotFeature(partialUniprotPtm[0]),
+                'Other',
+                'Type should be "Other" if no "description" in data'
+            );
+        });
+        it('returns no pubmed ids when evidence is empty', () => {
+            assert.equal(
+                getPubmedIdsFromUniprotFeature(partialUniprotPtm[0]).length,
+                0,
+                'No pubmed ids could be found if no "evidence" in data'
+            );
+        });
+    });
 });
diff --git a/packages/cbioportal-utils/src/ptm/PtmUtils.ts b/packages/cbioportal-utils/src/ptm/PtmUtils.ts
@@ -268,9 +268,12 @@ export function groupPtmDataByTypeAndPosition(
 export function ptmColor(ptms: PostTranslationalModification[]) {
     let color = PTM_COLORS.default;
     const uniqueTypes = _.uniq((ptms || []).map(ptm => ptm.type));
-
     if (uniqueTypes.length === 1) {
-        color = PTM_COLORS[uniqueTypes[0]] || PTM_COLORS.default;
+        if (uniqueTypes[0]) {
+            return PTM_COLORS[uniqueTypes[0]] || PTM_COLORS.default;
+        } else {
+            return PTM_COLORS.default;
+        }
     } else if (uniqueTypes.length > 1) {
         color = PTM_COLORS.multiType;
     }
@@ -304,25 +307,29 @@ function getResiduesFromUniprotFeature(ptm: UniprotFeature) {
 
 export function getPubmedIdsFromUniprotFeature(ptm: UniprotFeature) {
     return ptm.evidences
-        .filter(
-            e =>
-                e.source &&
-                e.source.name &&
-                e.source.name.toLowerCase().includes('pubmed')
-        )
-        .map(e => e.source!.id);
+        ? ptm.evidences
+              .filter(
+                  e =>
+                      e.source &&
+                      e.source.name &&
+                      e.source.name.toLowerCase().includes('pubmed')
+              )
+              .map(e => e.source!.id)
+        : [];
 }
 
 export function getPtmTypeFromUniprotFeature(ptm: UniprotFeature) {
     // actual `type` field provided by the feature itself (MOD_RES, CROSS_LINK, etc.) is not what we want to display
     // we need specific PTM types (Ubiquitination, Phosphorylation, etc.)
-    const keyword = ptm.description.split(';')[0].trim();
-    let ptmType: PtmType | undefined = KEYWORD_TO_PTM_TYPE[keyword];
+    const keyword = ptm.description?.split(';')[0].trim();
+    let ptmType: PtmType | undefined = keyword
+        ? KEYWORD_TO_PTM_TYPE[keyword]
+        : undefined;
 
     if (!ptmType) {
-        if (ptm.description.toLowerCase().includes('ubiquitin')) {
+        if (ptm.description?.toLowerCase().includes('ubiquitin')) {
             ptmType = PtmType.Ubiquitination;
-        } else if (ptm.description.toLowerCase().includes('sumo')) {
+        } else if (ptm.description?.toLowerCase().includes('sumo')) {
             ptmType = PtmType.Sumoylation;
         } else {
             ptmType = PtmType.Other;

diff --git a/packages/cbioportal-utils/src/uniprot/UniprotUtils.ts b/packages/cbioportal-utils/src/uniprot/UniprotUtils.ts
@@ -6,23 +6,33 @@ export const UniprotCategory = {
     TOPOLOGY: 'TOPOLOGY',
 };
 
+function getTopologyTypeName(type: string, description: string | undefined) {
+    // need to conver TOPO_DOM to detailed type name(e.g. TOPO_DOM_EXTRACELLULAR), keep the same name for TRANSMEM and INTRAMEM
+    if (type === 'TOPO_DOM') {
+        return description
+            ? _.toUpper(`${type}_${description.replace(/\s+/g, '_')}`)
+            : undefined;
+    } else {
+        return type;
+    }
+}
+
 export function convertUniprotFeatureToUniprotTopology(
     uniprotFeature: UniprotFeature
-): UniprotTopology {
-    return {
-        type:
-            uniprotFeature.type === 'TOPO_DOM'
-                ? _.toUpper(
-                      `${
-                          uniprotFeature.type
-                      }_${uniprotFeature.description.replace(/\s+/g, '_')}`
-                  )
-                : uniprotFeature.type,
-        startPosition: Number(uniprotFeature.begin),
-        endPosition: Number(uniprotFeature.end),
-        description: uniprotFeature.description,
-        evidence: uniprotFeature.evidences,
-    };
+): UniprotTopology | undefined {
+    const typeName = getTopologyTypeName(
+        uniprotFeature.type,
+        uniprotFeature.description
+    );
+    return typeName
+        ? {
+              type: typeName,
+              startPosition: Number(uniprotFeature.begin),
+              endPosition: Number(uniprotFeature.end),
+              description: uniprotFeature.description,
+              evidence: uniprotFeature.evidences,
+          }
+        : undefined;
 }
 
 export const UniprotTopologyTypeToTitle: { [type: string]: string } = {

diff --git a/packages/react-mutation-mapper/src/store/DefaultMutationMapperStore.ts b/packages/react-mutation-mapper/src/store/DefaultMutationMapperStore.ts
@@ -802,11 +802,12 @@ class DefaultMutationMapperStore<T extends Mutation>
                         [UniprotCategory.TOPOLOGY]
                     );
                     uniprotFeatures.forEach(uniprotFeature => {
-                        data.push(
-                            convertUniprotFeatureToUniprotTopology(
-                                uniprotFeature
-                            )
+                        let uniprotTopology = convertUniprotFeatureToUniprotTopology(
+                            uniprotFeature
                         );
+                        if (uniprotTopology) {
+                            data.push(uniprotTopology);
+                        }
                     });
                     return data;
                 } else {