react-mutation-mapper 0.8.28 → 0.8.33

package/dist/index.js

@@ -1867,17 +1867,11 @@ var OncoKB = /** @class */ (function (_super) {
                 ].map(function (dataType) { return (React.createElement(AnnotationIcon, { type: dataType, tooltipOverlay: _this.tooltipContent(dataType), indicator: _this.props.indicator, availableDataTypes: _this.props.availableDataTypes })); })));
             }
             else {
-                // TODO This doesn't always work, in some cases it adds unnecessary empty icons, we need a better solution.
-                // we still need to draw empty icons even if there is no indicator data.
-                // this is to keep the icon alignment consistent with the rest of the column
-                // return (
-                //     <>
-                //         {this.props.availableDataTypes?.map(() => (
-                //             <AnnotationIconWithTooltip icon={<i />} />
-                //         ))}
-                //     </>
-                // );
-                return null;
+                // workaround: use content padding value to draw an empty icon when there is no indicator data.
+                // this is to keep the icon alignment consistent with the rest of the column.
+                // ideally we should implement grouped columns to avoid these kind of workarounds
+                // (see https://github.com/cBioPortal/cbioportal/issues/8723)
+                return React.createElement("i", { style: { paddingRight: this.props.contentPadding } });
             }
         }
     });
@@ -2305,9 +2299,9 @@ function sortValue$4(annotation) {
     ]);
 }
 function GenericAnnotation(props) {
-    var annotation = props.annotation, enableCivic = props.enableCivic, enableHotspot = props.enableHotspot, enableMyCancerGenome = props.enableMyCancerGenome, enableOncoKb = props.enableOncoKb, pubMedCache = props.pubMedCache, userEmailAddress = props.userEmailAddress, mergeOncoKbIcons = props.mergeOncoKbIcons;
+    var annotation = props.annotation, enableCivic = props.enableCivic, enableHotspot = props.enableHotspot, enableMyCancerGenome = props.enableMyCancerGenome, enableOncoKb = props.enableOncoKb, pubMedCache = props.pubMedCache, userEmailAddress = props.userEmailAddress, mergeOncoKbIcons = props.mergeOncoKbIcons, oncoKbContentPadding = props.oncoKbContentPadding;
     return (React.createElement("span", { style: { display: 'flex', minWidth: 100 } },
-        enableOncoKb && (React.createElement(OncoKB, { usingPublicOncoKbInstance: annotation.usingPublicOncoKbInstance, hugoGeneSymbol: annotation.hugoGeneSymbol, geneNotExist: !annotation.oncoKbGeneExist, isCancerGene: annotation.isOncoKbCancerGene, status: annotation.oncoKbStatus, indicator: annotation.oncoKbIndicator, availableDataTypes: annotation.oncoKbAvailableDataTypes, mergeAnnotationIcons: mergeOncoKbIcons, pubMedCache: pubMedCache, userEmailAddress: userEmailAddress })),
+        enableOncoKb && (React.createElement(OncoKB, { usingPublicOncoKbInstance: annotation.usingPublicOncoKbInstance, hugoGeneSymbol: annotation.hugoGeneSymbol, geneNotExist: !annotation.oncoKbGeneExist, isCancerGene: annotation.isOncoKbCancerGene, status: annotation.oncoKbStatus, indicator: annotation.oncoKbIndicator, availableDataTypes: annotation.oncoKbAvailableDataTypes, mergeAnnotationIcons: mergeOncoKbIcons, pubMedCache: pubMedCache, userEmailAddress: userEmailAddress, contentPadding: oncoKbContentPadding })),
         enableCivic && (React.createElement(Civic, { civicEntry: annotation.civicEntry, civicStatus: annotation.civicStatus, hasCivicVariants: annotation.hasCivicVariants })),
         enableMyCancerGenome && (React.createElement(MyCancerGenome, { linksHTML: annotation.myCancerGenomeLinks })),
         enableHotspot && (React.createElement(HotspotAnnotation, { isHotspot: annotation.isHotspot, is3dHotspot: annotation.is3dHotspot, status: annotation.hotspotStatus }))));
@@ -3166,8 +3160,9 @@ var ProteinChange = /** @class */ (function (_super) {
     return ProteinChange;
 }(React.Component));
 
-function getSignalData(mutation, indexedVariantAnnotations) {
-    var signalData = {};
+function getSignalData(mutation, indexedVariantAnnotations, mutationType // mutationType could be "germline", "somatic", or "undefined" which means both
+) {
+    var signalData = [];
     var variantAnnotation = indexedVariantAnnotations
         ? cbioportalUtils.getVariantAnnotation(mutation, indexedVariantAnnotations.result)
         : undefined;
@@ -3175,12 +3170,37 @@ function getSignalData(mutation, indexedVariantAnnotations) {
         variantAnnotation.signalAnnotation &&
         variantAnnotation.signalAnnotation.annotation &&
         variantAnnotation.signalAnnotation.annotation.length > 0) {
-        variantAnnotation.signalAnnotation.annotation.forEach(function (annotation) {
-            // only have one germline annotation
-            if (annotation.mutationStatus.includes('germline')) {
-                signalData = cbioportalUtils.extendMutations([annotation])[0];
+        // if mutation is somatic OR germline, get annotation depending on mutationType
+        if (variantAnnotation.signalAnnotation.annotation.length === 1) {
+            if ((mutationType === cbioportalUtils.Pathogenicity.GERMLINE &&
+                variantAnnotation.signalAnnotation.annotation[0].mutationStatus.includes('germline')) ||
+                (mutationType === cbioportalUtils.Pathogenicity.SOMATIC &&
+                    variantAnnotation.signalAnnotation.annotation[0].mutationStatus.includes('somatic'))) {
+                signalData = cbioportalUtils.extendMutations([
+                    variantAnnotation.signalAnnotation.annotation[0],
+                ]);
+            }
+        }
+        // if mutation is both somatic AND germline, get annotation for both or get one of them depending on mutationType
+        else {
+            // if mutationType is undefined, get annotation for both somatic and germline
+            if (mutationType === undefined) {
+                signalData = cbioportalUtils.extendMutations(variantAnnotation.signalAnnotation.annotation);
             }
-        });
+            // if mutationType is defined, get annotation depending on mutationType
+            else {
+                variantAnnotation.signalAnnotation.annotation.forEach(function (annotation) {
+                    if (mutationType === cbioportalUtils.Pathogenicity.GERMLINE &&
+                        annotation.mutationStatus.includes('germline')) {
+                        signalData = cbioportalUtils.extendMutations([annotation]);
+                    }
+                    else if (mutationType === cbioportalUtils.Pathogenicity.SOMATIC &&
+                        annotation.mutationStatus.includes('somatic')) {
+                        signalData = cbioportalUtils.extendMutations([annotation]);
+                    }
+                });
+            }
+        }
     }
     return signalData;
 }
@@ -3188,25 +3208,29 @@ function signalSortMethod(a, b) {
     return cbioportalUtils.defaultSortMethod(getSortValue(a), getSortValue(b));
 }
 function getSortValue(signalData) {
-    return signalData.germlineFrequency || null;
+    return signalData ? signalData.germlineFrequency || null : null;
 }
-function download$7(signalData) {
-    return signalData.germlineFrequency != null
+function download$7(signalData, mutationType) {
+    return signalData && signalData.germlineFrequency !== null
         ? "" + cbioportalUtils.formatNumberValueInSignificantDigits(signalData.germlineFrequency, 2)
         : '';
 }
-function getSignalValue(mutation, indexedVariantAnnotations, significantDigits) {
-    var signalData = getSignalData(mutation, indexedVariantAnnotations);
-    if (signalData.tumorTypeDecomposition) {
-        return cbioportalUtils.formatNumberValueInSignificantDigits(signalData.germlineFrequency, significantDigits || 2);
+// Get germline OR somatic frequency value
+function getSingleSignalValue(mutation, mutationType, indexedVariantAnnotations, significantDigits) {
+    var signalData = getSignalData(mutation, indexedVariantAnnotations, mutationType);
+    if (signalData &&
+        signalData.length === 1 &&
+        signalData[0].tumorTypeDecomposition) {
+        return cbioportalUtils.formatNumberValueInSignificantDigits(signalData[0].germlineFrequency || signalData[0].somaticFrequency, significantDigits || 2);
     }
     else {
         return null;
     }
 }
 var SignalTable = function (props) {
-    var signalData = getSignalData(props.mutation, props.indexedVariantAnnotations);
-    if (getSignalValue(props.mutation, props.indexedVariantAnnotations) !== null) {
+    // signal data should be either germline or somatic, so should be only one element
+    var signalData = getSignalData(props.mutation, props.indexedVariantAnnotations, props.mutationType)[0];
+    if (getSingleSignalValue(props.mutation, props.mutationType || cbioportalUtils.Pathogenicity.GERMLINE, props.indexedVariantAnnotations) !== null) {
         return (React.createElement(cbioportalFrontendCommons.MutationTumorTypeFrequencyTable, { data: cbioportalUtils.generateTumorTypeDecomposition(signalData, signalData.countsByTumorType, signalData.biallelicCountsByTumorType, signalData.qcPassCountsByTumorType, signalData.statsByTumorType), columns: [
                 cbioportalFrontendCommons.FREQUENCY_COLUMNS_DEFINITION[cbioportalFrontendCommons.FrequencyTableColumnEnum.TUMOR_TYPE],
                 cbioportalFrontendCommons.FREQUENCY_COLUMNS_DEFINITION[cbioportalFrontendCommons.FrequencyTableColumnEnum.MUTATION_STATUS],
@@ -3247,11 +3271,11 @@ var Signal = /** @class */ (function (_super) {
                 }
                 else {
                     content = React.createElement("div", null);
-                    var signalValue = getSignalValue(this.props.mutation, this.props.indexedVariantAnnotations);
+                    var signalValue = getSingleSignalValue(this.props.mutation, this.props.mutationType || cbioportalUtils.Pathogenicity.GERMLINE, this.props.indexedVariantAnnotations);
                     if (signalValue !== null) {
                         content = (React.createElement(cbioportalFrontendCommons.DefaultTooltip, { placement: "top", overlayStyle: {
                                 width: 800,
-                            }, overlay: React.createElement(SignalTable, { mutation: this.props.mutation, indexedVariantAnnotations: this.props.indexedVariantAnnotations }) },
+                            }, overlay: React.createElement(SignalTable, { mutation: this.props.mutation, indexedVariantAnnotations: this.props.indexedVariantAnnotations, mutationType: this.props.mutationType }) },
                             React.createElement("span", null, signalValue)));
                     }
                 }
@@ -5195,7 +5219,7 @@ var DefaultMutationTable = /** @class */ (function (_super) {
             return this.indexedVariantAnnotationDataStatus === 'pending'
                 ? function () { return undefined; }
                 : function (mutation) {
-                    return getSignalData(mutation, _this.props.indexedVariantAnnotations);
+                    return getSignalData(mutation, _this.props.indexedVariantAnnotations, cbioportalUtils.Pathogenicity.GERMLINE)[0];
                 };
         },
         enumerable: false,
@@ -5265,7 +5289,7 @@ var DefaultMutationTable = /** @class */ (function (_super) {
                 case exports.MutationColumn.DBSNP:
                     return function (column) { return (React.createElement(Dbsnp, { mutation: column.original, indexedMyVariantInfoAnnotations: _this.props.indexedMyVariantInfoAnnotations })); };
                 case exports.MutationColumn.SIGNAL:
-                    return function (column) { return (React.createElement(Signal, { mutation: column.original, indexedVariantAnnotations: _this.props.indexedVariantAnnotations })); };
+                    return function (column) { return (React.createElement(Signal, { mutation: column.original, indexedVariantAnnotations: _this.props.indexedVariantAnnotations, mutationType: cbioportalUtils.Pathogenicity.GERMLINE })); };
                 default:
                     return undefined;
             }
@@ -8462,9 +8486,9 @@ var ExonTrack = /** @class */ (function (_super) {
                     var startCodon = exon.start;
                     var endCodon = exon.start + exon.length;
                     var exonLength = exon.length;
-                    var stringStart = cbioportalUtils.formatExonLocation(startCodon);
+                    var stringStart = cbioportalUtils.formatExonLocation(startCodon, index);
                     var stringEnd = cbioportalUtils.formatExonLocation(endCodon);
-                    var stringLength = cbioportalUtils.formatExonLocation(exonLength);
+                    var stringLength = cbioportalUtils.formatExonLength(exonLength);
                     return {
                         color: altColors[index % 2],
                         startCodon: startCodon,
@@ -12895,7 +12919,7 @@ exports.getProteinImpactTypeBadgeLabel = getProteinImpactTypeBadgeLabel;
 exports.getProteinImpactTypeOptionLabel = getProteinImpactTypeOptionLabel;
 exports.getSelectedOptionValues = getSelectedOptionValues;
 exports.getSignalData = getSignalData;
-exports.getSignalValue = getSignalValue;
+exports.getSingleSignalValue = getSingleSignalValue;
 exports.getUrl = getUrl;
 exports.gnomadDownload = download$5;
 exports.gnomadSortValue = sortValue$7;