react-mutation-mapper 0.8.29 → 0.8.34

package/dist/index.js

@@ -24,7 +24,8 @@ var Select = require('react-select');
 var Select__default = _interopDefault(Select);
 var $ = _interopDefault(require('jquery'));
 var Slider = _interopDefault(require('react-rangeslider'));
-var request = _interopDefault(require('superagent'));
+var request = require('superagent');
+var request__default = _interopDefault(request);
 var memoize = _interopDefault(require('memoize-weak-decorator'));
 var mobxpromise = require('mobxpromise');
 
@@ -1867,17 +1868,11 @@ 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 +2300,9 @@ 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 +3161,9 @@ 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 +3171,37 @@ 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 +3209,29 @@ 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 +3272,11 @@ 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 +5220,7 @@ 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 +5290,7 @@ 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;
             }
@@ -8446,8 +8471,24 @@ var ExonTrack = /** @class */ (function (_super) {
         enumerable: false,
         configurable: true
     });
+    Object.defineProperty(ExonTrack.prototype, "chromosome", {
+        get: function () {
+            var _a, _b;
+            return (_b = (_a = this.props.store.ensemblTranscriptLookUp.result) === null || _a === void 0 ? void 0 : _a.body) === null || _b === void 0 ? void 0 : _b.seq_region_name;
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(ExonTrack.prototype, "genomeBuild", {
+        get: function () {
+            return this.props.store.genomeBuild;
+        },
+        enumerable: false,
+        configurable: true
+    });
     Object.defineProperty(ExonTrack.prototype, "exonSpecs", {
         get: function () {
+            var _this = this;
             if (!this.transcriptId || !this.transcript) {
                 return [];
             }
@@ -8461,10 +8502,15 @@ var ExonTrack = /** @class */ (function (_super) {
                 ? exonInfo.map(function (exon, index) {
                     var startCodon = exon.start;
                     var endCodon = exon.start + exon.length;
-                    var exonLength = exon.length;
-                    var stringStart = cbioportalUtils.formatExonLocation(startCodon);
-                    var stringEnd = cbioportalUtils.formatExonLocation(endCodon);
-                    var stringLength = cbioportalUtils.formatExonLocation(exonLength);
+                    var exonStartLocation = cbioportalUtils.formatExonLocation(startCodon, index);
+                    var exonEndLocation = cbioportalUtils.formatExonLocation(endCodon);
+                    var exonLength = cbioportalUtils.formatExonLength(exon.length);
+                    var link = _this.chromosome
+                        ? "https://igv.org/app/?locus=chr" + _this.chromosome + ":" + exon.genomicLocationStart + "-" + exon.genomicLocationEnd + "&genome=" + _this.genomeBuild
+                        : 'https://igv.org';
+                    var linkText = _this.chromosome
+                        ? _this.genomeBuild + ":chr" + _this.chromosome + ":" + exon.genomicLocationStart + " - " + exon.genomicLocationEnd
+                        : exon.genomicLocationStart + " - " + exon.genomicLocationEnd;
                     return {
                         color: altColors[index % 2],
                         startCodon: startCodon,
@@ -8476,14 +8522,41 @@ var ExonTrack = /** @class */ (function (_super) {
                                 " Exon ",
                                 exon.rank,
                                 " "),
-                            "Start: ",
-                            stringStart,
+                            "Start: Nucleotide",
+                            ' ',
+                            React.createElement("strong", null, exonStartLocation.nucleotideLocation),
+                            ' ',
+                            "of amino acid",
+                            ' ',
+                            React.createElement("strong", null, exonStartLocation.aminoAcidLocation),
                             React.createElement("br", null),
-                            "End: ",
-                            stringEnd,
+                            "End: Nucleotide",
+                            ' ',
+                            React.createElement("strong", null, exonEndLocation.nucleotideLocation),
+                            ' ',
+                            "of amino acid",
+                            ' ',
+                            React.createElement("strong", null, exonEndLocation.aminoAcidLocation),
+                            React.createElement("br", null),
+                            "Length:",
+                            ' ',
+                            React.createElement("strong", null, exonLength.aminoAcidLength),
+                            ' ',
+                            "amino acids",
+                            ' ',
+                            exonLength.nucleotideLength && (React.createElement(React.Fragment, null,
+                                ' ',
+                                "and",
+                                ' ',
+                                React.createElement("strong", null, exonLength.nucleotideLength),
+                                ' ',
+                                "nucleotides")),
                             React.createElement("br", null),
-                            "Length: ",
-                            stringLength)),
+                            "Genomic location:", " ",
+                            React.createElement("a", { target: "_blank", href: link, rel: "noopener noreferrer" },
+                                React.createElement(React.Fragment, null,
+                                    linkText, " ",
+                                    React.createElement("i", { className: "fa fa-external-link" }))))),
                     };
                 })
                 : [];
@@ -8514,6 +8587,12 @@ var ExonTrack = /** @class */ (function (_super) {
     __decorate([
         mobx.computed
     ], ExonTrack.prototype, "transcript", null);
+    __decorate([
+        mobx.computed
+    ], ExonTrack.prototype, "chromosome", null);
+    __decorate([
+        mobx.computed
+    ], ExonTrack.prototype, "genomeBuild", null);
     __decorate([
         mobx.computed
     ], ExonTrack.prototype, "exonSpecs", null);
@@ -10134,7 +10213,7 @@ var DefaultPubMedCache = /** @class */ (function (_super) {
                     switch (_a.label) {
                         case 0: return [4 /*yield*/, new Promise(function (resolve, reject) {
                                 // TODO duplicate code from cbioportal-frontend
-                                request
+                                request__default
                                     .post('https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json')
                                     .type('form')
                                     .send({ id: query })
@@ -10168,7 +10247,7 @@ var DefaultPubMedCache = /** @class */ (function (_super) {
 
 function fetchMutationAlignerLink(pfamDomainId, mutationAlignerUrlTemplate) {
     if (mutationAlignerUrlTemplate === void 0) { mutationAlignerUrlTemplate = DEFAULT_MUTATION_ALIGNER_PROXY_URL_TEMPLATE; }
-    return request
+    return request__default
         .get(getUrl(mutationAlignerUrlTemplate, { pfamDomainId: pfamDomainId }))
         .accept('application/json');
 }
@@ -10544,7 +10623,7 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
                 var myGeneData;
                 return __generator(this, function (_a) {
                     switch (_a.label) {
-                        case 0: return [4 /*yield*/, request.get(getUrl(this.config.myGeneUrlTemplate || DEFAULT_MY_GENE_URL_TEMPLATE, { entrezGeneId: entrezGeneId }))];
+                        case 0: return [4 /*yield*/, request__default.get(getUrl(this.config.myGeneUrlTemplate || DEFAULT_MY_GENE_URL_TEMPLATE, { entrezGeneId: entrezGeneId }))];
                         case 1:
                             myGeneData = _a.sent();
                             return [2 /*return*/, JSON.parse(myGeneData.text).uniprot['Swiss-Prot']];
@@ -10562,7 +10641,7 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
                 var uniprotData;
                 return __generator(this, function (_a) {
                     switch (_a.label) {
-                        case 0: return [4 /*yield*/, request.get(getUrl(this.config.uniprotIdUrlTemplate ||
+                        case 0: return [4 /*yield*/, request__default.get(getUrl(this.config.uniprotIdUrlTemplate ||
                                 DEFAULT_UNIPROT_ID_URL_TEMPLATE, { swissProtAccession: swissProtAccession }))];
                         case 1:
                             uniprotData = _a.sent();
@@ -10720,7 +10799,7 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
                     switch (_a.label) {
                         case 0:
                             if (!swissProtId) return [3 /*break*/, 2];
-                            return [4 /*yield*/, request.get(getUrl("https://www.ebi.ac.uk/proteins/api/features/<%= uniprotAccession %>?categories=" + category.join(','), { uniprotAccession: swissProtId }))];
+                            return [4 /*yield*/, request__default.get(getUrl("https://www.ebi.ac.uk/proteins/api/features/<%= uniprotAccession %>?categories=" + category.join(','), { uniprotAccession: swissProtId }))];
                         case 1:
                             uniprotData = _a.sent();
                             featureList = JSON.parse(uniprotData.text);
@@ -11703,6 +11782,28 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                 },
             })
         });
+        Object.defineProperty(this, "ensemblTranscriptLookUp", {
+            enumerable: true,
+            configurable: true,
+            writable: true,
+            value: cbioportalFrontendCommons.remoteData({
+                await: function () { return [_this.activeTranscript]; },
+                invoke: function () { return __awaiter(_this, void 0, void 0, function () {
+                    var ensemblTranscriptLookUpLink;
+                    return __generator(this, function (_a) {
+                        ensemblTranscriptLookUpLink = this.genomeBuild === 'hg19'
+                            ? "https://grch37.rest.ensembl.org/lookup/id/" + this.activeTranscript.result + "?content-type=application/json"
+                            : "https://rest.ensembl.org/lookup/id/" + this.activeTranscript.result + "?content-type=application/json";
+                        return [2 /*return*/, this.activeTranscript.result
+                                ? request.get(ensemblTranscriptLookUpLink)
+                                : undefined];
+                    });
+                }); },
+                onError: function () {
+                    // fail silently, leave the error handling responsibility to the data consumer
+                },
+            })
+        });
         mobx.makeObservable(this);
     }
     Object.defineProperty(DefaultMutationMapperStore.prototype, "selectedTranscript", {
@@ -12012,6 +12113,13 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                 0);
         }
     });
+    Object.defineProperty(DefaultMutationMapperStore.prototype, "genomeBuild", {
+        get: function () {
+            return this.config.genomeBuild || 'hg19';
+        },
+        enumerable: false,
+        configurable: true
+    });
     __decorate([
         mobx.observable
     ], DefaultMutationMapperStore.prototype, "_selectedTranscript", void 0);
@@ -12082,6 +12190,9 @@ var DefaultMutationMapperStore = /** @class */ (function () {
     __decorate([
         autobind
     ], DefaultMutationMapperStore.prototype, "getDefaultEntrezGeneId", null);
+    __decorate([
+        mobx.computed
+    ], DefaultMutationMapperStore.prototype, "genomeBuild", null);
     return DefaultMutationMapperStore;
 }());
 
@@ -12895,7 +13006,7 @@ 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;