react-mutation-mapper 0.8.48 → 0.8.51

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/component/oncokb/OncoKbHelper.d.ts

@@ -11,7 +11,6 @@ export default class OncoKbHelper {
     static get LEVEL_DESC(): {
         [level: string]: JSX.Element;
     };
-    static levelTooltipContent: (level: string) => JSX.Element;
     static getDefaultColumnDefinition(columnKey: 'level' | 'alterations'): {
         id: string;
         Header: JSX.Element;

package/dist/component/oncokb/icon/LevelIcon.d.ts

@@ -0,0 +1,6 @@
+import * as React from 'react';
+declare const LevelIcon: React.FunctionComponent<{
+    level: string;
+    showDescription?: boolean;
+}>;
+export default LevelIcon;

package/dist/component/oncokb/icon/OncogenicIcon.d.ts

@@ -0,0 +1,6 @@
+import * as React from 'react';
+declare const OncogenicIcon: React.FunctionComponent<{
+    oncogenicity: string;
+    showDescription?: boolean;
+}>;
+export default OncogenicIcon;

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) {
@@ -797,6 +806,14 @@ var OncoKBSuggestAnnotationLinkout = /** @class */ (function (_super) {
     return OncoKBSuggestAnnotationLinkout;
 }(React.Component));
 
+var levelTooltipContent = function (level) {
+    return (React.createElement("div", { style: { maxWidth: '200px' } }, OncoKbHelper.LEVEL_DESC[level]));
+};
+var LevelIcon = function (props) {
+    return (React.createElement(DefaultTooltip, { overlay: levelTooltipContent(props.level), placement: "left", disabled: !props.showDescription, trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
+        React.createElement("i", { className: levelIconClassNames(props.level) })));
+};
+
 var OncoKbHelper = /** @class */ (function () {
     function OncoKbHelper() {
     }
@@ -935,7 +952,6 @@ var OncoKbHelper = /** @class */ (function () {
         configurable: true,
         writable: true,
         value: function (columnKey) {
-            var _this = this;
             switch (columnKey) {
                 case 'level':
                     return {
@@ -948,8 +964,7 @@ var OncoKbHelper = /** @class */ (function () {
                         },
                         Cell: function (props) {
                             var normalizedLevel = normalizeLevel(props.value) || '';
-                            return (React.createElement(DefaultTooltip, { overlay: _this.levelTooltipContent(normalizedLevel), placement: "left", trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
-                                React.createElement("i", { className: levelIconClassNames(normalizedLevel), style: { margin: 'auto' } })));
+                            return (React.createElement(LevelIcon, { level: normalizedLevel, showDescription: true }));
                         },
                     };
                 case 'alterations':
@@ -965,14 +980,6 @@ var OncoKbHelper = /** @class */ (function () {
             }
         }
     });
-    Object.defineProperty(OncoKbHelper, "levelTooltipContent", {
-        enumerable: true,
-        configurable: true,
-        writable: true,
-        value: function (level) {
-            return (React.createElement("div", { style: { maxWidth: '200px' } }, OncoKbHelper.LEVEL_DESC[level]));
-        }
-    });
     Object.defineProperty(OncoKbHelper, "getAlterationsColumnCell", {
         enumerable: true,
         configurable: true,
@@ -1338,6 +1345,11 @@ var ImplicationContent = function (props) {
 
 var tabsStyles = {"tabs-wrapper":"tabs-module_tabs-wrapper__XKjzo","tabs":"tabs-module_tabs__2I3mz","tab":"tabs-module_tab__3MoDA","tab-pane":"tabs-module_tab-pane__sGd85","tab-title-a":"tabs-module_tab-title-a__2WTNA","tab-title":"tabs-module_tab-title__2z9-D","tab-subtitle":"tabs-module_tab-subtitle__1P8B_"};
 
+var OncogenicIcon = function (props) {
+    return (React.createElement(DefaultTooltip, { overlay: React.createElement("span", null, props.oncogenicity), placement: "left", trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
+        React.createElement("i", { className: oncogenicityIconClassNames(props.oncogenicity) })));
+};
+
 var _a$3;
 var OncoKbMedicalDisclaimer = (React__default.createElement("p", { className: mainStyles.disclaimer }, "The information above is intended for research purposes only and should not be used as a substitute for professional diagnosis and treatment."));
 var ONCOKB_DATA_ACCESS_PAGE_LINK = 'https://docs.cbioportal.org/2.4-integration-with-other-webservices/oncokb-data-access';
@@ -1359,8 +1371,9 @@ var TabContentWrapper = function (props) {
     return React__default.createElement("div", { className: mainStyles['tab-content'] }, props.children);
 };
 var TabTitle = function (props) {
+    var _a;
     var title = DATA_TYPE_TO_TITLE[props.type];
-    var icon = props.displayHighestLevelInTabTitle ? (React__default.createElement("i", { className: annotationIconClassNames(props.type, calcHighestIndicatorLevel(props.type, props.indicator), props.indicator) })) : null;
+    var icon = props.displayHighestLevelInTabTitle ? (props.type === OncoKbCardDataType.BIOLOGICAL ? (React__default.createElement(OncogenicIcon, { oncogenicity: ((_a = props.indicator) === null || _a === void 0 ? void 0 : _a.oncogenic) || '', showDescription: true })) : (React__default.createElement(LevelIcon, { level: normalizeLevel(calcHighestIndicatorLevel(props.type, props.indicator)) || '', showDescription: true }))) : null;
     return icon ? (React__default.createElement("span", { style: { display: 'flex' } },
         icon,
         " ",
@@ -1967,7 +1980,7 @@ 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/';
@@ -2091,7 +2104,7 @@ function getDefaultEntrezGeneId(mutation) {
     return (mutation.gene && mutation.gene.entrezGeneId) || 0;
 }
 function getDefaultTumorType() {
-    return 'Unknown';
+    return '';
 }
 var memoized = new Map();
 function getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, myCancerGenomeData, oncoKbData, usingPublicOncoKbInstance, civicGenes, civicVariants, resolveTumorType, resolveEntrezGeneId) {
@@ -8167,9 +8180,7 @@ var OncoKbSummaryTable = /** @class */ (function (_super) {
                             overflow: 'hidden',
                             textOverflow: 'ellipsis',
                         } },
-                        React.createElement("i", { className: levelIconClassNames(level.level), style: {
-                                verticalAlign: 'text-bottom',
-                            } }),
+                        React.createElement(LevelIcon, { level: level.level, showDescription: true }),
                         React.createElement("span", { style: {
                                 paddingRight: 3,
                             } }, ":"),
@@ -8289,7 +8300,7 @@ function generateLevelData(indicatorData) {
             var parts = treatment.level.split('_');
             var level = parts.length === 2 ? parts[1] : treatment.level;
             levels[level] = levels[level] || [];
-            levels[level].push(indicator.query.tumorType);
+            levels[level].push(getTumorTypeName(treatment.levelAssociatedCancerType));
         });
     });
     return ___default.keys(levels)
@@ -9799,7 +9810,7 @@ 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", {
@@ -10597,7 +10608,7 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
         writable: true,
         value: function (mutations, fields, isoformOverrideSource, client) {
             if (fields === void 0) { fields = ['annotation_summary']; }
-            if (isoformOverrideSource === void 0) { isoformOverrideSource = 'uniprot'; }
+            if (isoformOverrideSource === void 0) { isoformOverrideSource = 'mskcc'; }
             if (client === void 0) { client = this.genomeNexusClient; }
             return __awaiter(this, void 0, void 0, function () {
                 return __generator(this, function (_a) {
@@ -10827,7 +10838,9 @@ 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 = [];
@@ -12021,7 +12034,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
         value: function (mutation) {
             return this.config.getTumorType
                 ? this.config.getTumorType(mutation)
-                : 'Unknown';
+                : '';
         }
     });
     Object.defineProperty(DefaultMutationMapperStore.prototype, "getDefaultEntrezGeneId", {
@@ -12303,7 +12316,7 @@ 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,