react-mutation-mapper 0.8.49 → 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) {
@@ -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 = [];