react-mutation-mapper 0.8.33 → 0.8.36

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');
 
@@ -8470,8 +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 [];
             }
@@ -8485,10 +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, index);
-                    var stringEnd = cbioportalUtils.formatExonLocation(endCodon);
-                    var stringLength = cbioportalUtils.formatExonLength(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,
@@ -8500,14 +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: Nucleotide",
+                            ' ',
+                            React.createElement("strong", null, exonEndLocation.nucleotideLocation),
+                            ' ',
+                            "of amino acid",
+                            ' ',
+                            React.createElement("strong", null, exonEndLocation.aminoAcidLocation),
                             React.createElement("br", null),
-                            "End: ",
-                            stringEnd,
+                            "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" }))))),
                     };
                 })
                 : [];
@@ -8538,6 +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);
@@ -10158,7 +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 })
@@ -10192,7 +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');
 }
@@ -10568,7 +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']];
@@ -10586,7 +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();
@@ -10744,7 +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);
@@ -11727,6 +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", {
@@ -12036,6 +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);
@@ -12106,6 +12190,9 @@ var DefaultMutationMapperStore = /** @class */ (function () {
     __decorate([
         autobind
     ], DefaultMutationMapperStore.prototype, "getDefaultEntrezGeneId", null);
+    __decorate([
+        mobx.computed
+    ], DefaultMutationMapperStore.prototype, "genomeBuild", null);
     return DefaultMutationMapperStore;
 }());