react-mutation-mapper 0.8.81 → 0.8.83

package/dist/index.js

@@ -52,6 +52,7 @@ function _interopNamespace(e) {
 var ___default = /*#__PURE__*/_interopDefaultLegacy(_);
 var ___namespace = /*#__PURE__*/_interopNamespace(_);
 var React__namespace = /*#__PURE__*/_interopNamespace(React);
+var React__default = /*#__PURE__*/_interopDefaultLegacy(React);
 var classNames__default = /*#__PURE__*/_interopDefaultLegacy(classNames);
 var autobind__default = /*#__PURE__*/_interopDefaultLegacy(autobind);
 var ReactTable__default = /*#__PURE__*/_interopDefaultLegacy(ReactTable);
@@ -187,7 +188,7 @@ function hideArrow(tooltipEl) {
     var arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
     arrowEl.style.display = 'none';
 }
-function sortValue$7(civicEntry) {
+function sortValue$8(civicEntry) {
     var score = 0;
     if (civicEntry) {
         score = 1;
@@ -308,7 +309,7 @@ function placeArrow$1(tooltipEl) {
     var arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
     arrowEl.style.left = '10px';
 }
-function sortValue$6(links) {
+function sortValue$7(links) {
     return links.length > 0 ? 1 : 0;
 }
 function download$5(links) {
@@ -432,7 +433,7 @@ var img$1 = "data:image/svg+xml,%3c%3fxml version='1.0' encoding='utf-8'%3f%3e%3
 
 var img = "data:image/svg+xml,%3c%3fxml version='1.0' encoding='utf-8'%3f%3e%3c!-- Generator: Adobe Illustrator 16.0.4%2c SVG Export Plug-In . SVG Version: 6.00 Build 0) --%3e%3c!DOCTYPE svg PUBLIC '-//W3C//DTD SVG 1.1//EN' 'http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd'%3e%3csvg version='1.1' id='Layer_1' xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' x='0px' y='0px' width='24.263px' height='36.366px' viewBox='0 0 24.263 36.366' enable-background='new 0 0 24.263 36.366' xml:space='preserve'%3e%3cg%3e %3cpath fill='%23FF9900' d='M6.828%2c27.947c-1.859-3.872-0.869-6.094%2c0.564-8.184c1.565-2.296%2c1.968-4.558%2c1.968-4.558 s1.231%2c1.6%2c0.742%2c4.104c2.181-2.423%2c2.591-6.286%2c2.256-7.764c4.921%2c3.436%2c7.027%2c10.889%2c4.19%2c16.401 C31.627%2c19.419%2c20.3%2c6.66%2c18.326%2c5.221c0.656%2c1.439%2c0.783%2c3.873-0.546%2c5.053C15.536%2c1.75%2c9.98%2c0%2c9.98%2c0 c0.657%2c4.397-2.388%2c9.208-5.316%2c12.8C4.56%2c11.046%2c4.451%2c9.831%2c3.53%2c8.155c-0.201%2c3.183-2.636%2c5.785-3.298%2c8.974 C-0.659%2c21.445%2c0.9%2c24.61%2c6.828%2c27.947L6.828%2c27.947z'/%3e %3ctext transform='matrix(0.583 0 0 0.583 3.7324 36.1963)' fill='black' font-family='Arial-BoldItalicMT' font-size='20.6802'%3e3D%3c/text%3e%3c/g%3e%3c/svg%3e";
 
-function sortValue$5(isHotspot, is3dHotspot) {
+function sortValue$6(isHotspot, is3dHotspot) {
     var score = 0;
     if (isHotspot) {
         score += 1;
@@ -593,6 +594,42 @@ function initOncoKbClient(oncoKbUrl, cachePostMethods, apiCacheLimit) {
     return client;
 }
 
+var RevueTooltipContent = function (props) {
+    return (React__default["default"].createElement("div", null,
+        props.vue.comment,
+        ' ',
+        React__default["default"].createElement("a", { href: "https://pubmed.ncbi.nlm.nih.gov/" + props.vue.pubmedIds[0] + "/", rel: "noopener noreferrer", target: "_blank" },
+            "(",
+            props.vue.referenceText,
+            ")"),
+        React__default["default"].createElement("ul", null,
+            React__default["default"].createElement("li", null,
+                "Predicted Effect: ",
+                React__default["default"].createElement("strong", null, props.vue.defaultEffect)),
+            React__default["default"].createElement("li", null,
+                "Experimentally Validated Effect:",
+                ' ',
+                React__default["default"].createElement("strong", null, props.vue.variantClassification)),
+            React__default["default"].createElement("li", null,
+                "Revised Protein Effect:",
+                ' ',
+                React__default["default"].createElement("strong", null, props.vue.revisedProteinEffect))),
+        React__default["default"].createElement("div", null,
+            "Source:",
+            ' ',
+            React__default["default"].createElement("a", { href: "https://cancerrevue.org", target: "_blank", rel: "noopener noreferrer" },
+                "reVUE ",
+                React__default["default"].createElement("i", { className: "fa fa-external-link" })))));
+};
+function sortValue$5(vue) {
+    return vue ? 1 : 0;
+}
+var RevueCell = function (props) {
+    return (React__default["default"].createElement(cbioportalFrontendCommons.DefaultTooltip, { placement: "bottom", overlay: React__default["default"].createElement(RevueTooltipContent, { vue: props.vue }) },
+        React__default["default"].createElement("span", { className: "" + annotationStyles['annotation-item'], style: { display: 'inline-flex' } },
+            React__default["default"].createElement("img", { src: '../../images/vue_logo.png', alt: "reVUE logo", width: 14, height: 14 }))));
+};
+
 var DEFAULT_ANNOTATION_DATA = {
     oncoKbStatus: 'complete',
     oncoKbGeneExist: false,
@@ -614,18 +651,15 @@ function getDefaultTumorType() {
     return '';
 }
 var memoized = new Map();
-function getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, myCancerGenomeData, oncoKbData, usingPublicOncoKbInstance, civicGenes, civicVariants, resolveTumorType, resolveEntrezGeneId) {
+function getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, myCancerGenomeData, oncoKbData, usingPublicOncoKbInstance, civicGenes, civicVariants, indexedVariantAnnotations, resolveTumorType, resolveEntrezGeneId) {
+    var _a, _b;
     if (resolveTumorType === void 0) { resolveTumorType = getDefaultTumorType; }
     if (resolveEntrezGeneId === void 0) { resolveEntrezGeneId = getDefaultEntrezGeneId; }
     var value;
     if (mutation) {
         var key = '';
-        var memoize = !!oncoKbCancerGenes && (oncoKbCancerGenes === null || oncoKbCancerGenes === void 0 ? void 0 : oncoKbCancerGenes.isComplete) &&
-            !!hotspotData && (hotspotData === null || hotspotData === void 0 ? void 0 : hotspotData.isComplete) &&
-            !!myCancerGenomeData &&
-            !!oncoKbData && (oncoKbData === null || oncoKbData === void 0 ? void 0 : oncoKbData.isComplete) &&
-            !!civicGenes && (civicGenes === null || civicGenes === void 0 ? void 0 : civicGenes.isComplete) &&
-            !!civicVariants && (civicVariants === null || civicVariants === void 0 ? void 0 : civicVariants.isComplete);
+        var memoize = (oncoKbCancerGenes === null || oncoKbCancerGenes === void 0 ? void 0 : oncoKbCancerGenes.isComplete) && (hotspotData === null || hotspotData === void 0 ? void 0 : hotspotData.isComplete) &&
+            !!myCancerGenomeData && (oncoKbData === null || oncoKbData === void 0 ? void 0 : oncoKbData.isComplete) && (civicGenes === null || civicGenes === void 0 ? void 0 : civicGenes.isComplete) && (civicVariants === null || civicVariants === void 0 ? void 0 : civicVariants.isComplete) && (indexedVariantAnnotations === null || indexedVariantAnnotations === void 0 ? void 0 : indexedVariantAnnotations.isComplete);
         if (memoize) {
             key = JSON.stringify(mutation) + !!usingPublicOncoKbInstance;
             var val = memoized.get(key);
@@ -675,17 +709,16 @@ function getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, myCancerGen
             myCancerGenomeLinks: myCancerGenomeData
                 ? cbioportalUtils.getMyCancerGenomeLinks(mutation, myCancerGenomeData)
                 : [],
-            isHotspot: hotspotData &&
-                hotspotData.result &&
-                hotspotData.status === 'complete'
+            isHotspot: (hotspotData === null || hotspotData === void 0 ? void 0 : hotspotData.isComplete) && hotspotData.result
                 ? cbioportalUtils.isLinearClusterHotspot(mutation, hotspotData.result)
                 : false,
-            is3dHotspot: hotspotData &&
-                hotspotData.result &&
-                hotspotData.status === 'complete'
+            is3dHotspot: (hotspotData === null || hotspotData === void 0 ? void 0 : hotspotData.isComplete) && hotspotData.result
                 ? cbioportalUtils.is3dHotspot(mutation, hotspotData.result)
                 : false,
             hotspotStatus: hotspotData ? hotspotData.status : 'pending',
+            vue: (indexedVariantAnnotations === null || indexedVariantAnnotations === void 0 ? void 0 : indexedVariantAnnotations.isComplete) &&
+                indexedVariantAnnotations.result
+                ? (_b = (_a = cbioportalUtils.getVariantAnnotation(mutation, indexedVariantAnnotations.result)) === null || _a === void 0 ? void 0 : _a.annotation_summary) === null || _b === void 0 ? void 0 : _b.vues : undefined,
         };
         // oncoKbData may exist but it might be an instance of Error, in that case we flag the status as error
         if (oncoKbData && oncoKbData.result instanceof Error) {
@@ -730,16 +763,18 @@ function annotationSortMethod(a, b) {
 function sortValue$4(annotation) {
     return ___default["default"].flatten([
         oncokbFrontendCommons.oncoKbAnnotationSortValue(annotation.oncoKbIndicator),
-        sortValue$7(annotation.civicEntry),
-        sortValue$6(annotation.myCancerGenomeLinks),
-        sortValue$5(annotation.isHotspot, annotation.is3dHotspot),
+        sortValue$8(annotation.civicEntry),
+        sortValue$7(annotation.myCancerGenomeLinks),
+        sortValue$6(annotation.isHotspot, annotation.is3dHotspot),
+        sortValue$5(annotation.vue),
         annotation.isOncoKbCancerGene ? 1 : 0,
     ]);
 }
 function GenericAnnotation(props) {
-    var annotation = props.annotation, enableCivic = props.enableCivic, enableHotspot = props.enableHotspot, enableMyCancerGenome = props.enableMyCancerGenome, enableOncoKb = props.enableOncoKb; props.pubMedCache; var userDisplayName = props.userDisplayName, mergeOncoKbIcons = props.mergeOncoKbIcons, oncoKbContentPadding = props.oncoKbContentPadding;
+    var annotation = props.annotation, enableCivic = props.enableCivic, enableHotspot = props.enableHotspot, enableMyCancerGenome = props.enableMyCancerGenome, enableOncoKb = props.enableOncoKb, enableRevue = props.enableRevue; props.pubMedCache; var userDisplayName = props.userDisplayName, mergeOncoKbIcons = props.mergeOncoKbIcons, oncoKbContentPadding = props.oncoKbContentPadding;
     return (React__namespace.createElement("span", { style: { display: 'flex', minWidth: 100 } },
         enableOncoKb && (React__namespace.createElement(oncokbFrontendCommons.OncoKB, { usingPublicOncoKbInstance: annotation.usingPublicOncoKbInstance, hugoGeneSymbol: annotation.hugoGeneSymbol, geneNotExist: !annotation.oncoKbGeneExist, isCancerGene: annotation.isOncoKbCancerGene, status: annotation.oncoKbStatus, indicator: annotation.oncoKbIndicator, availableDataTypes: annotation.oncoKbAvailableDataTypes, mergeAnnotationIcons: mergeOncoKbIcons, userDisplayName: userDisplayName, contentPadding: oncoKbContentPadding })),
+        enableRevue && annotation.vue ? (React__namespace.createElement(RevueCell, { vue: annotation.vue })) : (React__namespace.createElement("span", { className: "" + annotationStyles['annotation-item'] })),
         enableCivic && (React__namespace.createElement(Civic, { civicEntry: annotation.civicEntry, civicStatus: annotation.civicStatus, hasCivicVariants: annotation.hasCivicVariants })),
         enableMyCancerGenome && (React__namespace.createElement(MyCancerGenome, { linksHTML: annotation.myCancerGenomeLinks })),
         enableHotspot && (React__namespace.createElement(HotspotAnnotation, { isHotspot: annotation.isHotspot, is3dHotspot: annotation.is3dHotspot, status: annotation.hotspotStatus }))));
@@ -763,8 +798,8 @@ var Annotation = /** @class */ (function (_super) {
         configurable: true,
         writable: true,
         value: function (props) {
-            var mutation = props.mutation, oncoKbCancerGenes = props.oncoKbCancerGenes, hotspotData = props.hotspotData, myCancerGenomeData = props.myCancerGenomeData, oncoKbData = props.oncoKbData, usingPublicOncoKbInstance = props.usingPublicOncoKbInstance, resolveEntrezGeneId = props.resolveEntrezGeneId, resolveTumorType = props.resolveTumorType, civicGenes = props.civicGenes, civicVariants = props.civicVariants;
-            return getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, myCancerGenomeData, oncoKbData, usingPublicOncoKbInstance, civicGenes, civicVariants, resolveTumorType, resolveEntrezGeneId);
+            var mutation = props.mutation, oncoKbCancerGenes = props.oncoKbCancerGenes, hotspotData = props.hotspotData, myCancerGenomeData = props.myCancerGenomeData, oncoKbData = props.oncoKbData, usingPublicOncoKbInstance = props.usingPublicOncoKbInstance, resolveEntrezGeneId = props.resolveEntrezGeneId, resolveTumorType = props.resolveTumorType, civicGenes = props.civicGenes, civicVariants = props.civicVariants, indexedVariantAnnotations = props.indexedVariantAnnotations;
+            return getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, myCancerGenomeData, oncoKbData, usingPublicOncoKbInstance, civicGenes, civicVariants, indexedVariantAnnotations, resolveTumorType, resolveEntrezGeneId);
         }
     });
     Annotation = tslib.__decorate([
@@ -3658,7 +3693,7 @@ var DefaultMutationTable = /** @class */ (function (_super) {
             return this.annotationColumnDataStatus === 'pending'
                 ? function () { return undefined; }
                 : function (mutation) {
-                    return getAnnotationData(mutation, _this.props.oncoKbCancerGenes, _this.props.hotspotData, _this.props.myCancerGenomeData, _this.props.oncoKbData, _this.props.usingPublicOncoKbInstance, _this.props.civicGenes, _this.props.civicVariants);
+                    return getAnnotationData(mutation, _this.props.oncoKbCancerGenes, _this.props.hotspotData, _this.props.myCancerGenomeData, _this.props.oncoKbData, _this.props.usingPublicOncoKbInstance, _this.props.civicGenes, _this.props.civicVariants, _this.props.indexedVariantAnnotations);
                 };
         },
         enumerable: false,
@@ -3761,7 +3796,7 @@ var DefaultMutationTable = /** @class */ (function (_super) {
             var _this = this;
             switch (columnKey) {
                 case exports.MutationColumn.ANNOTATION:
-                    return function (column) { return (React__namespace.createElement(Annotation, { mutation: column.original, enableOncoKb: true, enableHotspot: true, enableCivic: _this.props.enableCivic || false, enableMyCancerGenome: true, hotspotData: _this.props.hotspotData, oncoKbData: _this.props.oncoKbData, oncoKbCancerGenes: _this.props.oncoKbCancerGenes, usingPublicOncoKbInstance: _this.props.usingPublicOncoKbInstance, pubMedCache: _this.props.pubMedCache, civicGenes: _this.props.civicGenes, civicVariants: _this.props.civicVariants })); };
+                    return function (column) { return (React__namespace.createElement(Annotation, { mutation: column.original, enableOncoKb: true, enableHotspot: true, enableCivic: _this.props.enableCivic || false, enableMyCancerGenome: true, enableRevue: true, hotspotData: _this.props.hotspotData, oncoKbData: _this.props.oncoKbData, oncoKbCancerGenes: _this.props.oncoKbCancerGenes, usingPublicOncoKbInstance: _this.props.usingPublicOncoKbInstance, pubMedCache: _this.props.pubMedCache, civicGenes: _this.props.civicGenes, civicVariants: _this.props.civicVariants, indexedVariantAnnotations: _this.props.indexedVariantAnnotations })); };
                 case exports.MutationColumn.HGVSG:
                     return function (column) { return React__namespace.createElement(Hgvsg, { mutation: column.original }); };
                 case exports.MutationColumn.HGVSC:
@@ -11016,6 +11051,7 @@ function initDefaultMutationMapperStore(props) {
         oncoKbUrl: props.oncoKbUrl,
         enableCivic: props.enableCivic,
         enableOncoKb: props.enableOncoKb,
+        enableRevue: props.enableRevue,
         cachePostMethodsOnClients: props.cachePostMethodsOnClients,
         apiCacheLimit: props.apiCacheLimit,
         getMutationCount: props.getMutationCount,
@@ -11223,7 +11259,7 @@ var MutationMapper = /** @class */ (function (_super) {
                 if (this.props.mutationTableColumns) {
                     columns = this.props.mutationTableColumns;
                 }
-                return (React__namespace.createElement(DefaultMutationTable, { dataStore: this.store.dataStore, columns: columns, initialSort: this.props.mutationTableInitialSort, initialSortRemoteData: this.props.mutationTableInitialSortRemoteData, reactTableProps: this.props.customMutationTableProps, hotspotData: this.store.indexedHotspotData, oncoKbData: this.store.oncoKbData, usingPublicOncoKbInstance: this.store.usingPublicOncoKbInstance, oncoKbCancerGenes: this.store.oncoKbCancerGenes, myCancerGenomeData: this.store.myCancerGenomeData, enableCivic: this.props.enableCivic, civicGenes: this.store.civicGenes, civicVariants: this.store.civicVariants, indexedMyVariantInfoAnnotations: this.store.indexedMyVariantInfoAnnotations, indexedVariantAnnotations: this.store.indexedVariantAnnotations, selectedTranscriptId: this.store.selectedTranscript, pubMedCache: this.pubMedCache, info: this.mutationTableInfo }));
+                return (React__namespace.createElement(DefaultMutationTable, { dataStore: this.store.dataStore, columns: columns, initialSort: this.props.mutationTableInitialSort, initialSortRemoteData: this.props.mutationTableInitialSortRemoteData, reactTableProps: this.props.customMutationTableProps, hotspotData: this.store.indexedHotspotData, oncoKbData: this.store.oncoKbData, usingPublicOncoKbInstance: this.store.usingPublicOncoKbInstance, oncoKbCancerGenes: this.store.oncoKbCancerGenes, myCancerGenomeData: this.store.myCancerGenomeData, enableCivic: this.props.enableCivic, enableRevue: this.props.enableRevue, civicGenes: this.store.civicGenes, civicVariants: this.store.civicVariants, indexedMyVariantInfoAnnotations: this.store.indexedMyVariantInfoAnnotations, indexedVariantAnnotations: this.store.indexedVariantAnnotations, selectedTranscriptId: this.store.selectedTranscript, pubMedCache: this.pubMedCache, info: this.mutationTableInfo }));
             }
         },
         enumerable: false,
@@ -11425,6 +11461,7 @@ var MutationMapper = /** @class */ (function (_super) {
             showTranscriptDropDown: false,
             enableCivic: true,
             enableOncoKb: true,
+            enableRevue: true,
             filterMutationsBySelectedTranscript: false,
             cachePostMethodsOnClients: true,
         }
@@ -11520,6 +11557,8 @@ exports.PercentToggle = PercentToggle;
 exports.ProteinChange = ProteinChange;
 exports.ProteinImpactTypeBadgeSelector = ProteinImpactTypeBadgeSelector;
 exports.ProteinImpactTypeDropdownSelector = ProteinImpactTypeDropdownSelector;
+exports.RevueCell = RevueCell;
+exports.RevueTooltipContent = RevueTooltipContent;
 exports.Sequence = LollipopPlot;
 exports.Signal = Signal;
 exports.SignalTable = SignalTable;
@@ -11535,7 +11574,7 @@ exports.applyDefaultPositionFilter = applyDefaultPositionFilter;
 exports.applyDefaultProteinImpactTypeFilter = applyDefaultProteinImpactTypeFilter;
 exports.calculateGnomadAlleleFrequency = calculateGnomadAlleleFrequency;
 exports.civicDownload = download$6;
-exports.civicSortValue = sortValue$7;
+exports.civicSortValue = sortValue$8;
 exports.clinvarDownload = download$4;
 exports.clinvarSortValue = sortValue$3;
 exports.dbsnpDownload = download$3;
@@ -11566,7 +11605,7 @@ exports.groupDataByProteinImpactType = groupDataByProteinImpactType;
 exports.handleOptionSelect = handleOptionSelect;
 exports.hgvscDownload = download$1;
 exports.hgvscSortValue = sortValue;
-exports.hotspotAnnotationSortValue = sortValue$5;
+exports.hotspotAnnotationSortValue = sortValue$6;
 exports.includesSearchTextIgnoreCase = includesSearchTextIgnoreCase;
 exports.indexPositions = indexPositions;
 exports.initDefaultMutationMapperStore = initDefaultMutationMapperStore;
@@ -11577,7 +11616,7 @@ exports.initOncoKbClient = initOncoKbClient;
 exports.mergeColumns = mergeColumns;
 exports.mutationTypeSort = mutationTypeSort;
 exports.myCancerGenomeDownload = download$5;
-exports.myCancerGenomeSortValue = sortValue$6;
+exports.myCancerGenomeSortValue = sortValue$7;
 exports.onFilterOptionSelect = onFilterOptionSelect;
 exports.proteinChangeSortMethod = proteinChangeSortMethod;
 exports.rightAlignedCell = rightAlignedCell;