react-mutation-mapper 0.8.50 → 0.8.53

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

@@ -68,7 +68,7 @@ export * from './util/DataFetcherUtils';
 export * from './util/FilterUtils';
 export { calculateGnomadAlleleFrequency, getGnomadData, } from './util/GnomadUtils';
 export { MUTATION_TYPE_PRIORITY, mutationTypeSort, getColorForProteinImpactType, DEFAULT_PROTEIN_IMPACT_TYPE_COLORS, } from './util/MutationTypeUtils';
-export { defaultOncoKbFilter, groupOncoKbIndicatorDataByMutations, oncogenicityIconClassNames, normalizeLevel, levelIconClassNames, } from './util/OncoKbUtils';
+export { defaultOncoKbFilter, groupOncoKbIndicatorDataByMutations, oncogenicityIconClassNames, normalizeLevel, levelIconClassNames, getTumorTypeNameWithExclusionInfo, } from './util/OncoKbUtils';
 export * from './util/SelectorUtils';
 export * from './util/TrackUtils';
 export { default as DefaultMutationMapperDataFetcher } from './store/DefaultMutationMapperDataFetcher';

package/dist/index.es.js

@@ -451,6 +451,15 @@ function getTumorTypeName(tumorType) {
         return '';
     }
 }
+function getTumorTypeNameWithExclusionInfo(tumorType, excludedTumorTypes) {
+    var name = getTumorTypeName(tumorType);
+    if (!___default.isEmpty(excludedTumorTypes)) {
+        name = name + " (excluding " + excludedTumorTypes
+            .map(function (ett) { return getTumorTypeName(ett); })
+            .join(', ') + ")";
+    }
+    return name;
+}
 function groupOncoKbIndicatorDataByMutations(mutationsByPosition, oncoKbData, getTumorType, getEntrezGeneId, filter) {
     var indicatorMap = {};
     ___default.keys(mutationsByPosition).forEach(function (key) {
@@ -806,6 +815,14 @@ 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() {
     }
@@ -944,7 +961,6 @@ var OncoKbHelper = /** @class */ (function () {
         configurable: true,
         writable: true,
         value: function (columnKey) {
-            var _this = this;
             switch (columnKey) {
                 case 'level':
                     return {
@@ -957,8 +973,7 @@ 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':
@@ -974,14 +989,6 @@ 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,
@@ -1284,7 +1291,7 @@ var OncoKbTreatmentTable = /** @class */ (function (_super) {
                         "cancer type(s)")),
                     accessor: 'levelAssociatedCancerType',
                     minWidth: 120,
-                    Cell: function (props) { return (React.createElement("div", { style: { whiteSpace: 'normal', lineHeight: '1rem' } }, getTumorTypeName(props.original.levelAssociatedCancerType))); },
+                    Cell: function (props) { return (React.createElement("div", { style: { whiteSpace: 'normal', lineHeight: '1rem' } }, getTumorTypeNameWithExclusionInfo(props.original.levelAssociatedCancerType, props.original.levelExcludedCancerTypes))); },
                 },
                 {
                     id: 'referenceList',
@@ -1347,6 +1354,11 @@ 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';
@@ -1368,8 +1380,9 @@ 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,
         " ",
@@ -2100,7 +2113,7 @@ 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) {
@@ -8176,9 +8189,7 @@ 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,
                             } }, ":"),
@@ -8298,7 +8309,7 @@ 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(getTumorTypeNameWithExclusionInfo(treatment.levelAssociatedCancerType, treatment.levelExcludedCancerTypes));
         });
     });
     return ___default.keys(levels)
@@ -10606,7 +10617,7 @@ 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) {
@@ -12032,7 +12043,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
         value: function (mutation) {
             return this.config.getTumorType
                 ? this.config.getTumorType(mutation)
-                : 'Unknown';
+                : '';
         }
     });
     Object.defineProperty(DefaultMutationMapperStore.prototype, "getDefaultEntrezGeneId", {
@@ -12832,5 +12843,5 @@ var MutationMapper = /** @class */ (function (_super) {
     return MutationMapper;
 }(React.Component));
 
-export { Annotation, BadgeLabel, BadgeSelector, Civic, ClinvarInterpretation, ClinvarSummary, ColumnHeader, ColumnSelector, ColumnSortDirection, DEFAULT_ANNOTATION_DATA, DEFAULT_GENOME_NEXUS_URL, DEFAULT_MUTATION_ALIGNER_PROXY_URL_TEMPLATE, DEFAULT_MUTATION_ALIGNER_URL_TEMPLATE, DEFAULT_MUTATION_COLUMNS, DEFAULT_MY_GENE_URL_TEMPLATE, DEFAULT_ONCO_KB_URL, DEFAULT_PROTEIN_IMPACT_TYPE_COLORS, DEFAULT_UNIPROT_ID_URL_TEMPLATE, DataFilterType, DataTable, Dbsnp, DbsnpId, DefaultMutationMapperDataFetcher, DefaultMutationMapperDataStore, DefaultMutationMapperFilterApplier, DefaultMutationMapperStore, DefaultMutationTable, Domain, DropdownSelector, FilterResetPanel, GenericAnnotation, Gnomad, GnomadFrequency, GnomadFrequencyBreakdown, GnomadFrequencyTable, GnomadFrequencyValue, Hgvsc, Hgvsg, HotspotAnnotation, HotspotInfo, Lollipop, LollipopMutationPlot, LollipopPlot, LollipopPlotNoTooltip, MSI_H_NAME, MUTATION_COLUMNS_DEFINITION, MUTATION_COLUMN_HEADERS, MUTATION_STATUS_BADGE_STYLE_OVERRIDE, MUTATION_TYPE_PRIORITY, MutationColumn, MutationColumnName, MutationMapper, MutationStatus, MutationStatusBadgeSelector, MyCancerGenome, ONCOKB_DEFAULT_DATA, ONCOKB_DEFAULT_INFO, OTHER_BIOMARKER_HUGO_SYMBOL, OTHER_BIOMARKER_NAME, OncoKB, OncoKBSuggestAnnotationLinkout, OncoKbFeedback, OncoKbHelper, OncoKbTooltip, OncoKbTreatmentTable, OtherBiomarkersQueryType, ProteinChange, ProteinImpactTypeBadgeSelector, ProteinImpactTypeDropdownSelector, RefComponent, ReferenceList, LollipopPlot as Sequence, Signal, SignalTable, SummaryWithRefs, TEXT_INPUT_FILTER_ID, TMB_H_NAME, TrackName, TrackSelector, USE_DEFAULT_PUBLIC_INSTANCE_FOR_ONCOKB, sortValue$4 as annotationSortValue, applyDataFilters, applyDataFiltersOnDatum, applyDefaultMutationFilter, applyDefaultMutationStatusFilter, applyDefaultPositionFilter, applyDefaultProteinImpactTypeFilter, calculateGnomadAlleleFrequency, download$7 as civicDownload, sortValue$8 as civicSortValue, download$4 as clinvarDownload, sortValue$3 as clinvarSortValue, download$3 as dbsnpDownload, sortValue$2 as dbsnpSortValue, defaultOncoKbFilter, errorIcon, fetchVariantAnnotationsByMutation, fetchVariantAnnotationsIndexedByGenomicLocation, findAllUniquePositions, findNonTextInputFilters, findOneMutationFilterValue, findTextInputFilter, getAllOptionValues, getAnnotationData, getClinvarData, getColorForProteinImpactType, getGnomadData, getHgvscColumnData, getHgvsgColumnData, getProteinImpactTypeBadgeLabel, getProteinImpactTypeOptionLabel, getSelectedOptionValues, getSignalData, getSingleSignalValue, getUrl, download$2 as gnomadDownload, sortValue$1 as gnomadSortValue, groupDataByGroupFilters, groupDataByProteinImpactType, groupOncoKbIndicatorDataByMutations, handleOptionSelect, download$1 as hgvscDownload, sortValue as hgvscSortValue, sortValue$5 as hotspotAnnotationSortValue, includesSearchTextIgnoreCase, indexPositions, initDefaultMutationMapperStore, initDefaultTrackVisibility, initGenomeNexusClient, initGenomeNexusInternalClient, initOncoKbClient, levelIconClassNames, loaderIcon, mergeColumns, mutationTypeSort, download$6 as myCancerGenomeDownload, sortValue$7 as myCancerGenomeSortValue, normalizeLevel, onFilterOptionSelect, download$5 as oncoKbAnnotationDownload, sortValue$6 as oncoKbAnnotationSortValue, oncogenicityIconClassNames, proteinChangeSortMethod, rightAlignedCell, download as signalDownload, getSortValue as signalSortValue, updatePositionHighlightFilters, updatePositionRangeHighlightFilters, updatePositionSelectionFilters };
+export { Annotation, BadgeLabel, BadgeSelector, Civic, ClinvarInterpretation, ClinvarSummary, ColumnHeader, ColumnSelector, ColumnSortDirection, DEFAULT_ANNOTATION_DATA, DEFAULT_GENOME_NEXUS_URL, DEFAULT_MUTATION_ALIGNER_PROXY_URL_TEMPLATE, DEFAULT_MUTATION_ALIGNER_URL_TEMPLATE, DEFAULT_MUTATION_COLUMNS, DEFAULT_MY_GENE_URL_TEMPLATE, DEFAULT_ONCO_KB_URL, DEFAULT_PROTEIN_IMPACT_TYPE_COLORS, DEFAULT_UNIPROT_ID_URL_TEMPLATE, DataFilterType, DataTable, Dbsnp, DbsnpId, DefaultMutationMapperDataFetcher, DefaultMutationMapperDataStore, DefaultMutationMapperFilterApplier, DefaultMutationMapperStore, DefaultMutationTable, Domain, DropdownSelector, FilterResetPanel, GenericAnnotation, Gnomad, GnomadFrequency, GnomadFrequencyBreakdown, GnomadFrequencyTable, GnomadFrequencyValue, Hgvsc, Hgvsg, HotspotAnnotation, HotspotInfo, Lollipop, LollipopMutationPlot, LollipopPlot, LollipopPlotNoTooltip, MSI_H_NAME, MUTATION_COLUMNS_DEFINITION, MUTATION_COLUMN_HEADERS, MUTATION_STATUS_BADGE_STYLE_OVERRIDE, MUTATION_TYPE_PRIORITY, MutationColumn, MutationColumnName, MutationMapper, MutationStatus, MutationStatusBadgeSelector, MyCancerGenome, ONCOKB_DEFAULT_DATA, ONCOKB_DEFAULT_INFO, OTHER_BIOMARKER_HUGO_SYMBOL, OTHER_BIOMARKER_NAME, OncoKB, OncoKBSuggestAnnotationLinkout, OncoKbFeedback, OncoKbHelper, OncoKbTooltip, OncoKbTreatmentTable, OtherBiomarkersQueryType, ProteinChange, ProteinImpactTypeBadgeSelector, ProteinImpactTypeDropdownSelector, RefComponent, ReferenceList, LollipopPlot as Sequence, Signal, SignalTable, SummaryWithRefs, TEXT_INPUT_FILTER_ID, TMB_H_NAME, TrackName, TrackSelector, USE_DEFAULT_PUBLIC_INSTANCE_FOR_ONCOKB, sortValue$4 as annotationSortValue, applyDataFilters, applyDataFiltersOnDatum, applyDefaultMutationFilter, applyDefaultMutationStatusFilter, applyDefaultPositionFilter, applyDefaultProteinImpactTypeFilter, calculateGnomadAlleleFrequency, download$7 as civicDownload, sortValue$8 as civicSortValue, download$4 as clinvarDownload, sortValue$3 as clinvarSortValue, download$3 as dbsnpDownload, sortValue$2 as dbsnpSortValue, defaultOncoKbFilter, errorIcon, fetchVariantAnnotationsByMutation, fetchVariantAnnotationsIndexedByGenomicLocation, findAllUniquePositions, findNonTextInputFilters, findOneMutationFilterValue, findTextInputFilter, getAllOptionValues, getAnnotationData, getClinvarData, getColorForProteinImpactType, getGnomadData, getHgvscColumnData, getHgvsgColumnData, getProteinImpactTypeBadgeLabel, getProteinImpactTypeOptionLabel, getSelectedOptionValues, getSignalData, getSingleSignalValue, getTumorTypeNameWithExclusionInfo, getUrl, download$2 as gnomadDownload, sortValue$1 as gnomadSortValue, groupDataByGroupFilters, groupDataByProteinImpactType, groupOncoKbIndicatorDataByMutations, handleOptionSelect, download$1 as hgvscDownload, sortValue as hgvscSortValue, sortValue$5 as hotspotAnnotationSortValue, includesSearchTextIgnoreCase, indexPositions, initDefaultMutationMapperStore, initDefaultTrackVisibility, initGenomeNexusClient, initGenomeNexusInternalClient, initOncoKbClient, levelIconClassNames, loaderIcon, mergeColumns, mutationTypeSort, download$6 as myCancerGenomeDownload, sortValue$7 as myCancerGenomeSortValue, normalizeLevel, onFilterOptionSelect, download$5 as oncoKbAnnotationDownload, sortValue$6 as oncoKbAnnotationSortValue, oncogenicityIconClassNames, proteinChangeSortMethod, rightAlignedCell, download as signalDownload, getSortValue as signalSortValue, updatePositionHighlightFilters, updatePositionRangeHighlightFilters, updatePositionSelectionFilters };
 //# sourceMappingURL=index.es.js.map