react-mutation-mapper 0.8.47 → 0.8.50

package/dist/component/column/MutationStatus.d.ts

@@ -11,7 +11,7 @@ declare type MutationStatusProps = {
         [mutationStatus: string]: React.CSSProperties;
     };
 };
-export default class MutationStatus extends React.Component<MutationStatusProps, {}> {
+export declare class MutationStatus extends React.Component<MutationStatusProps, {}> {
     static defaultProps: Partial<MutationStatusProps>;
     render(): JSX.Element;
 }

package/dist/index.d.ts

@@ -12,7 +12,7 @@ export { default as MyCancerGenome, download as myCancerGenomeDownload, sortValu
 export { default as Hgvsc, download as hgvscDownload, sortValue as hgvscSortValue, } from './component/column/Hgvsc';
 export { default as Hgvsg } from './component/column/Hgvsg';
 export * from './component/column/HgvsHelper';
-export { default as MutationStatus } from './component/column/MutationStatus';
+export { MutationStatus } from './component/column/MutationStatus';
 export { default as ProteinChange, proteinChangeSortMethod, } from './component/column/ProteinChange';
 export { default as Signal, getSignalData, getSortValue as signalSortValue, download as signalDownload, getSingleSignalValue, SignalTable, } from './component/column/Signal';
 export { default as DropdownSelector, DropdownSelectorProps, } from './component/filter/DropdownSelector';

package/dist/index.es.js

@@ -6,7 +6,7 @@ import { observer } from 'mobx-react';
 import * as React from 'react';
 import React__default, { useState } from 'react';
 import { DefaultTooltip, TruncatedText, getNCBIlink, trimOffHtmlTagEntities, cachePostMethodsOnClient, CanonicalMutationType, MutationTumorTypeFrequencyTable, FREQUENCY_COLUMNS_DEFINITION, FrequencyTableColumnEnum, CheckedSelect, getSelectedValuesMap, Checklist, MUT_COLOR_MISSENSE, MUT_COLOR_MISSENSE_PASSENGER, MUT_COLOR_INFRAME, MUT_COLOR_INFRAME_PASSENGER, MUT_COLOR_TRUNC, MUT_COLOR_TRUNC_PASSENGER, MUT_COLOR_SPLICE, MUT_COLOR_SPLICE_PASSENGER, STRUCTURAL_VARIANT_COLOR, STRUCTURAL_VARIANT_PASSENGER_COLOR, MUT_COLOR_OTHER, getCanonicalMutationType, getProteinImpactTypeFromCanonical, ProteinImpactType, getProteinImpactType, resolveColumnVisibility, resolveColumnVisibilityByColumnDefinition, longestCommonStartingSubstring, getTextWidth, unhoverAllComponents, SVGAxis, getComponentIndex, defaultHitzoneConfig, initHitZoneFromConfig, EditableSpan, DownloadControls, EllipsisTextTooltip, remoteData, WindowWrapper } from 'cbioportal-frontend-commons';
-import { CIVIC_NA_VALUE, generateQueryVariantId, OncoKbCardDataType, parseMyCancerGenomeLink, defaultArraySortMethod, defaultSortMethod, LEVELS, uniqueGenomicLocations, indexAnnotationsByGenomicLocation, getCivicEntry, getRemoteDataGroupStatus, getMyCancerGenomeLinks, isLinearClusterHotspot, is3dHotspot, calculateOncoKbAvailableDataType, getVariantAnnotation, getDbsnpRsId, getMyVariantInfoAnnotation, generateHgvsgByMutation, calcProteinChangeSortValue, Pathogenicity, extendMutations, formatNumberValueInSignificantDigits, generateTumorTypeDecomposition, formatPercentValue, countMutationsByProteinChange, numberOfLeadingDecimalZeros, filterLinearClusterHotspotsByMutations, filter3dHotspotsByMutations, isHotspot, defaultHotspotFilter, defaultStringArraySortMethod, extractExonInformation, formatExonLocation, formatExonLength, ptmColor, compareByPtmTypePriority, UniprotTopologyTrackToColor, UniprotTopologyTypeToTitle, PtmSource, PTM_SOURCE_URL, getMyVariantInfoAnnotationsFromIndexedVariantAnnotations, generateProteinChangeQuery, StructuralVariantType, generateAnnotateStructuralVariantQuery, getMyCancerGenomeData, genomicLocationString, convertUniprotFeatureToPtm, convertDbPtmToPtm, UniprotCategory, convertUniprotFeatureToUniprotTopology, groupPtmDataByPosition, groupPtmDataByTypeAndPosition, groupCancerHotspotDataByPosition, indexHotspotsData, fetchCivicGenes, fetchCivicVariants, getMutationsByTranscriptId, groupMutationsByProteinStartPos, groupHotspotsByMutations } from 'cbioportal-utils';
+import { CIVIC_NA_VALUE, deriveStructuralVariantType, generateQueryStructuralVariantId, generateQueryVariantId, OncoKbCardDataType, parseMyCancerGenomeLink, defaultArraySortMethod, defaultSortMethod, LEVELS, uniqueGenomicLocations, indexAnnotationsByGenomicLocation, getCivicEntry, getRemoteDataGroupStatus, getMyCancerGenomeLinks, isLinearClusterHotspot, is3dHotspot, calculateOncoKbAvailableDataType, getVariantAnnotation, getDbsnpRsId, getMyVariantInfoAnnotation, generateHgvsgByMutation, calcProteinChangeSortValue, Pathogenicity, extendMutations, formatNumberValueInSignificantDigits, generateTumorTypeDecomposition, formatPercentValue, countMutationsByProteinChange, numberOfLeadingDecimalZeros, filterLinearClusterHotspotsByMutations, filter3dHotspotsByMutations, isHotspot, defaultHotspotFilter, defaultStringArraySortMethod, extractExonInformation, formatExonLocation, formatExonLength, ptmColor, compareByPtmTypePriority, UniprotTopologyTrackToColor, UniprotTopologyTypeToTitle, PtmSource, PTM_SOURCE_URL, getMyVariantInfoAnnotationsFromIndexedVariantAnnotations, generateProteinChangeQuery, StructuralVariantType, generateAnnotateStructuralVariantQuery, getMyCancerGenomeData, genomicLocationString, convertUniprotFeatureToPtm, convertDbPtmToPtm, UniprotCategory, convertUniprotFeatureToUniprotTopology, groupPtmDataByPosition, groupPtmDataByTypeAndPosition, groupCancerHotspotDataByPosition, indexHotspotsData, fetchCivicGenes, fetchCivicVariants, getMutationsByTranscriptId, groupMutationsByProteinStartPos, groupHotspotsByMutations } from 'cbioportal-utils';
 import classnames from 'classnames';
 import autobind from 'autobind-decorator';
 import oncoKbLogoImgSrc from 'oncokb-styles/dist/images/logo/oncokb.svg';
@@ -472,7 +472,16 @@ function getIndicatorData(mutation, oncoKbData, getTumorType, getEntrezGeneId) {
     if (oncoKbData.indicatorMap === null) {
         return undefined;
     }
-    var id = generateQueryVariantId(getEntrezGeneId(mutation), getTumorType(mutation), mutation.proteinChange, mutation.mutationType);
+    var id = '';
+    // @ts-ignore
+    var sv = mutation.structuralVariant;
+    if (sv) {
+        var structuralVariantType = deriveStructuralVariantType(sv);
+        id = generateQueryStructuralVariantId(sv.site1EntrezGeneId, sv.site2EntrezGeneId, getTumorType(mutation), structuralVariantType);
+    }
+    else {
+        id = generateQueryVariantId(getEntrezGeneId(mutation), getTumorType(mutation), mutation.proteinChange, mutation.mutationType);
+    }
     return oncoKbData.indicatorMap[id];
 }
 function defaultOncoKbIndicatorFilter(indicator) {
@@ -1910,7 +1919,7 @@ var HotspotInfo = function (props) {
 
 var img$1 = "data:image/svg+xml,%3c%3fxml version='1.0' encoding='utf-8'%3f%3e%3c!-- Generated by IcoMoon.io --%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' xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' width='1024' height='1024' viewBox='0 0 1024 1024'%3e %3cg id='icomoon-ignore'%3e %3c/g%3e %3cpath fill='%23ff9900' d='M321.008 1045.333c-68.245-142.008-31.901-223.379 20.551-300.044 57.44-83.956 72.244-167.065 72.244-167.065s45.153 58.7 27.092 150.508c79.772-88.8 94.824-230.28 82.783-284.464 180.315 126.012 257.376 398.856 153.523 601.065 552.372-312.532 137.399-780.172 65.155-832.851 24.081 52.676 28.648 141.851-20 185.127-82.352-312.276-285.972-376.276-285.972-376.276 24.083 161.044-87.296 337.144-194.696 468.731-3.775-64.216-7.783-108.528-41.549-169.98-7.58 116.656-96.732 211.748-120.873 328.628-32.701 158.287 24.496 274.18 241.748 396.623z'%3e%3c/path%3e%3c/svg%3e";
 
-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";
+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) {
     var score = 0;
@@ -1967,7 +1976,7 @@ var HotspotAnnotation = /** @class */ (function (_super) {
 var DEFAULT_MUTATION_ALIGNER_URL_TEMPLATE = 'http://mutationaligner.org/api/domains/<%= pfamDomainId %>?metadata=true';
 var DEFAULT_MUTATION_ALIGNER_PROXY_URL_TEMPLATE = 'https://www.cbioportal.org/proxy/mutationaligner.org/api/domains/<%= pfamDomainId %>?metadata=true';
 var DEFAULT_MY_GENE_URL_TEMPLATE = 'https://mygene.info/v3/gene/<%= entrezGeneId %>?fields=uniprot';
-var DEFAULT_UNIPROT_ID_URL_TEMPLATE = 'https://www.uniprot.org/uniprot/?query=accession:<%= swissProtAccession %>&format=tab&columns=entry+name';
+var DEFAULT_UNIPROT_ID_URL_TEMPLATE = 'https://rest.uniprot.org/uniprotkb/search?query=accession:<%= swissProtAccession %>&format=tsv&fields=id';
 var DEFAULT_GENOME_NEXUS_URL = 'https://www.genomenexus.org/';
 // The legacy instance does not require an authentication but the data will not be update.
 var DEFAULT_ONCO_KB_URL = 'https://legacy.oncokb.org/';
@@ -9799,7 +9808,7 @@ var LollipopMutationPlot = /** @class */ (function (_super) {
         writable: true,
         value: function () {
             return (React.createElement("div", { style: { maxWidth: 200 } },
-                React.createElement("a", { href: "http://www.uniprot.org/uniprot/" + this.props.store.uniprotId.result, target: "_blank" }, this.props.store.uniprotId.result)));
+                React.createElement("a", { href: "https://www.uniprot.org/uniprot/" + this.props.store.uniprotId.result, target: "_blank" }, this.props.store.uniprotId.result)));
         }
     });
     Object.defineProperty(LollipopMutationPlot.prototype, "sequence", {
@@ -10827,7 +10836,9 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
                                 return ((_a = mutation.mutationType) === null || _a === void 0 ? void 0 : _a.toUpperCase()) ===
                                     StructuralVariantType.FUSION;
                             }), function (mutation) {
-                                return generateAnnotateStructuralVariantQuery(getEntrezGeneId(mutation), getTumorType(mutation), mutation.proteinChange, mutation.mutationType, evidenceTypes);
+                                return generateAnnotateStructuralVariantQuery(
+                                /* @ts-ignore */
+                                mutation.structuralVariant, getTumorType(mutation), evidenceTypes);
                             }), 'id');
                             if (!(mutationQueryVariants.length === 0)) return [3 /*break*/, 1];
                             _a = [];
@@ -12303,7 +12314,7 @@ var GeneSummaryInfo = function (_a) {
                 DATA: ccdsId,
             },
         }), target: "_blank" }, ccdsId)) : ('-');
-    var uniprot = uniprotId ? (React.createElement("a", { href: "http://www.uniprot.org/uniprot/" + uniprotId, target: "_blank" }, uniprotId)) : ('-');
+    var uniprot = uniprotId ? (React.createElement("a", { href: "https://www.uniprot.org/uniprot/" + uniprotId, target: "_blank" }, uniprotId)) : ('-');
     var compactGeneSummaryInfo = (React.createElement("div", null,
         React.createElement("span", { "data-test": "compactGeneSummaryRefSeq" }, refSeq), " | ",
         ensembl,