react-mutation-mapper 0.8.25 → 0.8.29
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/component/column/Annotation.d.ts +2 -0
- package/dist/component/oncokb/AnnotationIcon.d.ts +4 -1
- package/dist/component/oncokb/CompactAnnotationIcon.d.ts +8 -0
- package/dist/component/oncokb/OncoKB.d.ts +4 -0
- package/dist/component/oncokb/OncoKbCard.d.ts +1 -0
- package/dist/component/oncokb/OncoKbCardBody.d.ts +1 -0
- package/dist/index.es.js +322 -130
- package/dist/index.es.js.map +1 -1
- package/dist/index.js +321 -129
- package/dist/index.js.map +1 -1
- package/dist/util/OncoKbUtils.d.ts +4 -1
- package/package.json +6 -6
package/dist/index.js
CHANGED
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@@ -14,10 +14,10 @@ var cbioportalFrontendCommons = require('cbioportal-frontend-commons');
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14
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var cbioportalUtils = require('cbioportal-utils');
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var classnames = _interopDefault(require('classnames'));
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var autobind = _interopDefault(require('autobind-decorator'));
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-
var reactCollapse = require('react-collapse');
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var reactBootstrap = require('react-bootstrap');
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var
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var reactCollapse = require('react-collapse');
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var ReactTable = _interopDefault(require('react-table'));
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var reactIf = require('react-if');
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var genomeNexusTsApiClient = require('genome-nexus-ts-api-client');
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var oncokbTsApiClient = require('oncokb-ts-api-client');
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var Select = require('react-select');
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@@ -413,6 +413,12 @@ function normalizeLevel(level) {
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return null;
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}
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}
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416
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function normalizeOncogenicity(oncogenicity) {
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417
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return (oncogenicity || 'unknown')
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418
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.trim()
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419
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.toLowerCase()
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420
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.replace(/\s/, '-');
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421
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}
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function levelIconClassNames(level) {
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if (level) {
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return "oncokb icon level-" + level;
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@@ -420,13 +426,32 @@ function levelIconClassNames(level) {
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return '';
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}
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function oncogenicityIconClassNames(oncogenicity) {
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423
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-
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-
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return "oncokb icon " + normalizeOncogenicity(oncogenicity);
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430
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}
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function annotationIconClassNames(type, highestLevel, indicator) {
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return type === cbioportalUtils.OncoKbCardDataType.BIOLOGICAL
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433
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? oncogenicityIconClassNames((indicator === null || indicator === void 0 ? void 0 : indicator.oncogenic) || '')
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: levelIconClassNames(normalizeLevel(highestLevel) || '');
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}
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function calcHighestIndicatorLevel(type, indicator) {
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var highestLevel = '';
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if (indicator) {
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switch (type) {
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case cbioportalUtils.OncoKbCardDataType.TXS:
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highestLevel = indicator.highestSensitiveLevel;
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break;
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case cbioportalUtils.OncoKbCardDataType.TXR:
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highestLevel = indicator.highestResistanceLevel;
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break;
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case cbioportalUtils.OncoKbCardDataType.DX:
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highestLevel = indicator.highestDiagnosticImplicationLevel;
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break;
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case cbioportalUtils.OncoKbCardDataType.PX:
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highestLevel = indicator.highestPrognosticImplicationLevel;
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break;
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}
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}
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-
return
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.trim()
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.toLowerCase()
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.replace(/\s/, '-');
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return highestLevel;
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}
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function calcOncogenicScore(oncogenic) {
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return ONCOGENIC_SCORE[oncogenic] || 0;
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@@ -616,6 +641,125 @@ var MyCancerGenome = /** @class */ (function (_super) {
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return MyCancerGenome;
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}(React.Component));
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function hideArrow$1(tooltipEl) {
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var arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
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arrowEl.style.display = 'none';
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}
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var AnnotationIcon = function (props) {
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if (props.availableDataTypes !== undefined &&
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!props.availableDataTypes.includes(props.type)) {
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return null;
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}
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var highestLevel = calcHighestIndicatorLevel(props.type, props.indicator);
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return (React__default.createElement(AnnotationIconWithTooltip, { tooltipOverlay: props.tooltipOverlay, icon: React__default.createElement("i", { className: annotationIconClassNames(props.type, highestLevel, props.indicator), "data-test": "oncogenic-icon-image" }) }));
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};
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var AnnotationIconWithTooltip = function (props) {
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if (props.icon) {
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return (React__default.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlayClassName: "oncokb-tooltip", overlay: function () {
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return props.tooltipOverlay ? props.tooltipOverlay : null;
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}, placement: "right", trigger: ['hover', 'focus'], onPopupAlign: hideArrow$1, destroyTooltipOnHide: true },
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React__default.createElement("span", { className: "" + annotationStyles['annotation-item'] }, props.icon)));
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}
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else {
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return null;
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}
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};
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var BIOLOGICAL_COLOR_MAP = {
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oncogenic: '#0968C3',
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'likely-oncogenic': '#0968C3',
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'predicted-oncogenic': '#0968C3',
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resistance: '#0968C3',
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neutral: '#696969',
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'likely-neutral': '#696969',
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inconclusive: '#AAAAAA',
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vus: '#696969',
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unknown: '#CCCCCC',
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};
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var LEVEL_COLOR_MAP = {
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'1': '#33A02C',
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'2': '#1F78B4',
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'3': '#984EA3',
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'3A': '#984EA3',
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'3B': '#BE98CE',
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'4': '#424242',
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R1: '#EE3424',
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R2: '#F79A92',
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R3: '#FCD6D3',
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Dx1: '#33A02C',
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Dx2: '#1F78B4',
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Dx3: '#984EA3',
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Px1: '#33A02C',
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Px2: '#1F78B4',
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Px3: '#984EA3',
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};
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function getLevelColor(highestLevel, defaultColor) {
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if (defaultColor === void 0) { defaultColor = '#CCCCCC'; }
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var level = normalizeLevel(highestLevel || null) || '';
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return LEVEL_COLOR_MAP[level] || defaultColor;
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}
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function shouldDrawShape(type, level, availableDataTypes) {
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return (level &&
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availableDataTypes !== undefined &&
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availableDataTypes.includes(type));
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}
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function getOncogenicShape(indicator) {
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var oncogenicity = normalizeOncogenicity((indicator === null || indicator === void 0 ? void 0 : indicator.oncogenic) || '');
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708
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var color = BIOLOGICAL_COLOR_MAP[oncogenicity] || '#CCCCCC';
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return (React__default.createElement("g", { transform: "translate(9, 9)" },
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React__default.createElement("circle", { r: "6", fill: "none", strokeWidth: "2", stroke: color }),
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oncogenicity !== 'vus' && oncogenicity !== 'unknown' && (React__default.createElement("g", null,
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React__default.createElement("circle", { r: "3", fill: "none", strokeWidth: "2", stroke: color }),
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React__default.createElement("circle", { r: "1.5", fill: color, stroke: "none" })))));
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}
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function getTherapeuticSensitivityShape(indicator, availableDataTypes) {
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var highestLevel = indicator === null || indicator === void 0 ? void 0 : indicator.highestSensitiveLevel;
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717
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if (!shouldDrawShape(cbioportalUtils.OncoKbCardDataType.TXS, highestLevel, availableDataTypes)) {
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718
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return null;
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719
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}
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var fillColor = getLevelColor(highestLevel, '#33A02C');
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return (React__default.createElement("g", { transform: "translate(14.5, 3.5)" },
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React__default.createElement("circle", { r: "4", fill: fillColor, stroke: "#ffffff", strokeWidth: "1" })));
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}
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function getTherapeuticResistanceShape(indicator, availableDataTypes) {
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var highestLevel = indicator === null || indicator === void 0 ? void 0 : indicator.highestResistanceLevel;
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if (!shouldDrawShape(cbioportalUtils.OncoKbCardDataType.TXR, highestLevel, availableDataTypes)) {
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return null;
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}
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var fillColor = getLevelColor(highestLevel, '#EE3424');
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return (React__default.createElement("g", { transform: "translate(14.5, 14.5)" },
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React__default.createElement("circle", { r: "4", fill: fillColor, stroke: "#ffffff", strokeWidth: "1" })));
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}
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function getDiagnosticShape(indicator, availableDataTypes) {
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734
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var highestLevel = indicator === null || indicator === void 0 ? void 0 : indicator.highestDiagnosticImplicationLevel;
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if (!shouldDrawShape(cbioportalUtils.OncoKbCardDataType.DX, highestLevel, availableDataTypes)) {
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return null;
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}
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var fillColor = getLevelColor(highestLevel, '#33A02C');
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return (React__default.createElement("g", { transform: "translate(-0.5, -0.5)" },
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React__default.createElement("rect", { width: "7", height: "7", fill: fillColor, stroke: "#ffffff", strokeWidth: "1" })));
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}
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function getPrognosticShape(indicator, availableDataTypes) {
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743
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var highestLevel = indicator === null || indicator === void 0 ? void 0 : indicator.highestPrognosticImplicationLevel;
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744
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if (!shouldDrawShape(cbioportalUtils.OncoKbCardDataType.PX, highestLevel, availableDataTypes)) {
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return null;
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746
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}
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747
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var fillColor = getLevelColor(highestLevel, '#33A02C');
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return (React__default.createElement("g", { transform: "translate(0, 10.5)" },
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React__default.createElement("polygon", { points: "3.5 0, 8 8, -1 8", fill: fillColor, stroke: "#ffffff", strokeWidth: "1" })));
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}
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var CompactAnnotationIcon = function (props) {
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752
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var indicatorForLevelIcons = props.usingPublicOncoKbInstance
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753
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? undefined
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754
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: props.indicator;
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return (React__default.createElement("svg", { version: "1.1", width: "18", height: "18", "data-test": "oncogenic-icon-image" },
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getOncogenicShape(props.indicator),
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757
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getTherapeuticSensitivityShape(indicatorForLevelIcons, props.availableDataTypes),
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getTherapeuticResistanceShape(indicatorForLevelIcons, props.availableDataTypes),
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getDiagnosticShape(indicatorForLevelIcons, props.availableDataTypes),
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760
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getPrognosticShape(indicatorForLevelIcons, props.availableDataTypes)));
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};
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var oncoKbLogoImgSrc = "data:image/svg+xml,%3Csvg%20width%3D%22138%22%20height%3D%2226%22%20viewBox%3D%220%200%20138%2026%22%20fill%3D%22none%22%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%3E%20%20%3Cpath%20d%3D%22M13.3232%2026C21.0801%2026%2026.7182%2020.1464%2026.7182%2013V12.9282C26.7182%205.78177%2021.1519%200%2013.395%200C5.63812%200%200%205.85359%200%2013V13.0718C0%2020.2182%205.5663%2026%2013.3232%2026ZM13.395%2020.9006C8.94199%2020.9006%205.78177%2017.3094%205.78177%2013V12.9282C5.78177%208.61878%208.87016%205.09945%2013.3232%205.09945C17.7762%205.09945%2020.9365%208.69061%2020.9365%2013V13.0718C20.9365%2017.3812%2017.8481%2020.9006%2013.395%2020.9006Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20d%3D%22M29.9722%2025.5691H35.4307V14.8315C35.4307%2012.2459%2036.7594%2010.9171%2038.8423%2010.9171C40.9252%2010.9171%2042.1462%2012.2459%2042.1462%2014.8315V25.5691H47.6048V13.1077C47.6048%208.69061%2045.1987%205.96133%2041.0688%205.96133C38.3036%205.96133%2036.6876%207.4337%2035.4307%209.04972V6.32044H29.9722V25.5691Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20d%3D%22M60.3551%2026C64.1976%2026%2066.3523%2024.5276%2068.2197%2022.4807L65.0236%2019.2486C63.6948%2020.5055%2062.4379%2021.2956%2060.6064%2021.2956C57.6258%2021.2956%2055.7225%2018.9254%2055.7225%2015.9807V15.9088C55.7225%2013.0718%2057.6617%2010.6657%2060.391%2010.6657C62.3302%2010.6657%2063.5512%2011.4917%2064.7722%2012.7845L68.112%209.19337C66.3164%207.18232%2064.054%205.96133%2060.4269%205.96133C54.5374%205.96133%2050.3357%2010.4862%2050.3357%2015.9807V16.0525C50.3357%2021.547%2054.5733%2026%2060.3551%2026Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20d%3D%22M91.3584%2025.5691H96.8888V17.884L99.7977%2014.8674L107.59%2025.5691H114.234L103.532%2011.0967L113.803%200.430938H107.016L96.8888%2011.4199V0.430938H91.3584V25.5691Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20d%3D%22M116.182%2025.5691H128.14C133.814%2025.5691%20137.549%2023.2707%20137.549%2018.674V18.6022C137.549%2015.2265%20135.754%2013.5387%20132.845%2012.4254C134.64%2011.4199%20136.149%209.83978%20136.149%207.00276V6.93094C136.149%205.20718%20135.574%203.80663%20134.425%202.65746C132.989%201.22099%20130.726%200.430938%20127.853%200.430938H116.182V25.5691ZM130.654%207.93646C130.654%209.80387%20129.11%2010.5939%20126.668%2010.5939H121.569V5.27901H127.027C129.361%205.27901%20130.654%206.21271%20130.654%207.86464V7.93646ZM132.055%2017.9199V17.9917C132.055%2019.8591%20130.582%2020.721%20128.14%2020.721H121.569V15.1906H127.961C130.798%2015.1906%20132.055%2016.232%20132.055%2017.9199Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20fill-rule%3D%22evenodd%22%20clip-rule%3D%22evenodd%22%20d%3D%22M78.8032%2023.5C82.9454%2023.5%2086.3032%2020.1421%2086.3032%2016C86.3032%2011.8579%2082.9454%208.5%2078.8032%208.5C74.6611%208.5%2071.3032%2011.8579%2071.3032%2016C71.3032%2020.1421%2074.6611%2023.5%2078.8032%2023.5ZM78.8032%2026C84.3261%2026%2088.8032%2021.5228%2088.8032%2016C88.8032%2010.4772%2084.3261%206%2078.8032%206C73.2804%206%2068.8032%2010.4772%2068.8032%2016C68.8032%2021.5228%2073.2804%2026%2078.8032%2026Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20fill-rule%3D%22evenodd%22%20clip-rule%3D%22evenodd%22%20d%3D%22M78.8032%2019.5C80.7362%2019.5%2082.3032%2017.933%2082.3032%2016C82.3032%2014.067%2080.7362%2012.5%2078.8032%2012.5C76.8702%2012.5%2075.3032%2014.067%2075.3032%2016C75.3032%2017.933%2076.8702%2019.5%2078.8032%2019.5ZM78.8032%2022C82.1169%2022%2084.8032%2019.3137%2084.8032%2016C84.8032%2012.6863%2082.1169%2010%2078.8032%2010C75.4895%2010%2072.8032%2012.6863%2072.8032%2016C72.8032%2019.3137%2075.4895%2022%2078.8032%2022Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20fill-rule%3D%22evenodd%22%20clip-rule%3D%22evenodd%22%20d%3D%22M78.8032%2018C79.9078%2018%2080.8032%2017.1046%2080.8032%2016C80.8032%2014.8954%2079.9078%2014%2078.8032%2014C77.6987%2014%2076.8032%2014.8954%2076.8032%2016C76.8032%2017.1046%2077.6987%2018%2078.8032%2018Z%22%20fill%3D%22%230968C3%22%2F%3E%3C%2Fsvg%3E";
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var mainStyles = {"oncokb-card":"main-module_oncokb-card__32DzD","tab-content":"main-module_tab-content__8nUyf","tooltip-refs":"main-module_tooltip-refs__SpA4W","disclaimer":"main-module_disclaimer__3CLlM","blue-icon":"main-module_blue-icon__2Hs-v","footer":"main-module_footer__2dc-8","oncokb-logo":"main-module_oncokb-logo__3RVg7","title":"main-module_title__2kT-n","additional-info":"main-module_additional-info__1nXTm","biological-info":"main-module_biological-info__2efDC","ellipsis-text-wrapper":"main-module_ellipsis-text-wrapper__18dny"};
|
|
@@ -1179,35 +1323,6 @@ var EvidenceReferenceContent = function (props) {
|
|
|
1179
1323
|
: 'Information is not available.')))));
|
|
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|
};
|
|
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|
|
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|
-
var BiologicalContent = function (props) {
|
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|
-
return (React__default.createElement(EvidenceReferenceContent, { description: props.biologicalSummary, citations: props.mutationEffectCitations, pmidData: props.pmidData, noInfoDisclaimer: 'Mutation effect information is not available.' }));
|
|
1184
|
-
};
|
|
1185
|
-
|
|
1186
|
-
var ImplicationContent = function (props) {
|
|
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|
-
var columns = [
|
|
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|
-
__assign(__assign({}, OncoKbHelper.getDefaultColumnDefinition('level')), { accessor: 'levelOfEvidence', maxWidth: 100 }),
|
|
1189
|
-
__assign(__assign({}, OncoKbHelper.getDefaultColumnDefinition('alterations')), { Cell: function (cellProps) {
|
|
1190
|
-
return OncoKbHelper.getAlterationsColumnCell(cellProps.value, props.variant);
|
|
1191
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-
} }),
|
|
1192
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{
|
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1193
|
-
id: 'referenceList',
|
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1194
|
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Header: React.createElement("span", null),
|
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1195
|
-
sortable: false,
|
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1196
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-
maxWidth: 50,
|
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1197
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Cell: function (cellProps) { return (React.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlay: function () { return (React.createElement("div", { className: mainStyles['tooltip-refs'] },
|
|
1198
|
-
React.createElement(EvidenceReferenceContent, { description: cellProps.original.description, citations: {
|
|
1199
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-
pmids: cellProps.original.pmids,
|
|
1200
|
-
abstracts: cellProps.original.abstracts,
|
|
1201
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-
}, pmidData: props.pmidData, noInfoDisclaimer: 'Mutation effect information is not available.' }))); }, placement: "right", trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
|
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1202
|
-
React.createElement("i", { className: "fa fa-book" }))); },
|
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1203
|
-
},
|
|
1204
|
-
];
|
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1205
|
-
return (React.createElement("div", null,
|
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1206
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-
React.createElement("p", null, props.summary),
|
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1207
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-
React.createElement("div", null,
|
|
1208
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-
React.createElement(ReactTable, { data: props.implications, columns: columns, showPagination: false, pageSize: props.implications.length, className: "-striped -highlight" }))));
|
|
1209
|
-
};
|
|
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|
-
|
|
1211
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|
var OncoKbTreatmentTable = /** @class */ (function (_super) {
|
|
1212
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|
__extends(OncoKbTreatmentTable, _super);
|
|
1213
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|
function OncoKbTreatmentTable() {
|
|
@@ -1289,8 +1404,38 @@ var OncoKbTreatmentTable = /** @class */ (function (_super) {
|
|
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1289
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|
return OncoKbTreatmentTable;
|
|
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|
}(React.Component));
|
|
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|
|
|
1407
|
+
var BiologicalContent = function (props) {
|
|
1408
|
+
return (React__default.createElement(EvidenceReferenceContent, { description: props.biologicalSummary, citations: props.mutationEffectCitations, pmidData: props.pmidData, noInfoDisclaimer: 'Mutation effect information is not available.' }));
|
|
1409
|
+
};
|
|
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|
+
|
|
1411
|
+
var ImplicationContent = function (props) {
|
|
1412
|
+
var columns = [
|
|
1413
|
+
__assign(__assign({}, OncoKbHelper.getDefaultColumnDefinition('level')), { accessor: 'levelOfEvidence', maxWidth: 100 }),
|
|
1414
|
+
__assign(__assign({}, OncoKbHelper.getDefaultColumnDefinition('alterations')), { Cell: function (cellProps) {
|
|
1415
|
+
return OncoKbHelper.getAlterationsColumnCell(cellProps.value, props.variant);
|
|
1416
|
+
} }),
|
|
1417
|
+
{
|
|
1418
|
+
id: 'referenceList',
|
|
1419
|
+
Header: React.createElement("span", null),
|
|
1420
|
+
sortable: false,
|
|
1421
|
+
maxWidth: 50,
|
|
1422
|
+
Cell: function (cellProps) { return (React.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlay: function () { return (React.createElement("div", { className: mainStyles['tooltip-refs'] },
|
|
1423
|
+
React.createElement(EvidenceReferenceContent, { description: cellProps.original.description, citations: {
|
|
1424
|
+
pmids: cellProps.original.pmids,
|
|
1425
|
+
abstracts: cellProps.original.abstracts,
|
|
1426
|
+
}, pmidData: props.pmidData, noInfoDisclaimer: 'Mutation effect information is not available.' }))); }, placement: "right", trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
|
|
1427
|
+
React.createElement("i", { className: "fa fa-book" }))); },
|
|
1428
|
+
},
|
|
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|
+
];
|
|
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|
+
return (React.createElement("div", null,
|
|
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|
+
React.createElement("p", null, props.summary),
|
|
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|
+
React.createElement("div", null,
|
|
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|
+
React.createElement(ReactTable, { data: props.implications, columns: columns, showPagination: false, pageSize: props.implications.length, className: "-striped -highlight" }))));
|
|
1434
|
+
};
|
|
1435
|
+
|
|
1292
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|
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_"};
|
|
1293
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|
|
|
1438
|
+
var _a$1;
|
|
1294
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|
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."));
|
|
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|
var ONCOKB_DATA_ACCESS_PAGE_LINK = 'https://docs.cbioportal.org/2.4-integration-with-other-webservices/oncokb-data-access';
|
|
1296
1441
|
var publicInstanceDisclaimerOverLay = (React__default.createElement("div", null,
|
|
@@ -1300,9 +1445,24 @@ var publicInstanceDisclaimerOverLay = (React__default.createElement("div", null,
|
|
|
1300
1445
|
React__default.createElement("a", { href: ONCOKB_DATA_ACCESS_PAGE_LINK, target: '_blank' }, "these instructions"),
|
|
1301
1446
|
"."),
|
|
1302
1447
|
OncoKbMedicalDisclaimer));
|
|
1448
|
+
var DATA_TYPE_TO_TITLE = (_a$1 = {},
|
|
1449
|
+
_a$1[cbioportalUtils.OncoKbCardDataType.BIOLOGICAL] = 'Biological Effect',
|
|
1450
|
+
_a$1[cbioportalUtils.OncoKbCardDataType.TXS] = 'Therapeutic Implications',
|
|
1451
|
+
_a$1[cbioportalUtils.OncoKbCardDataType.TXR] = 'Therapeutic Implications',
|
|
1452
|
+
_a$1[cbioportalUtils.OncoKbCardDataType.DX] = 'Diagnostic Implications',
|
|
1453
|
+
_a$1[cbioportalUtils.OncoKbCardDataType.PX] = 'Prognostic Implications',
|
|
1454
|
+
_a$1);
|
|
1303
1455
|
var TabContentWrapper = function (props) {
|
|
1304
1456
|
return React__default.createElement("div", { className: mainStyles['tab-content'] }, props.children);
|
|
1305
1457
|
};
|
|
1458
|
+
var TabTitle = function (props) {
|
|
1459
|
+
var title = DATA_TYPE_TO_TITLE[props.type];
|
|
1460
|
+
var icon = props.displayHighestLevelInTabTitle ? (React__default.createElement("i", { className: annotationIconClassNames(props.type, calcHighestIndicatorLevel(props.type, props.indicator), props.indicator) })) : null;
|
|
1461
|
+
return icon ? (React__default.createElement("span", { style: { display: 'flex' } },
|
|
1462
|
+
icon,
|
|
1463
|
+
" ",
|
|
1464
|
+
title)) : (React__default.createElement("span", null, title));
|
|
1465
|
+
};
|
|
1306
1466
|
var OncoKbCardBody = function (props) {
|
|
1307
1467
|
var defaultTabActiveKey;
|
|
1308
1468
|
// Do not assign a default key if the data type specified through the property does not have any content
|
|
@@ -1346,13 +1506,13 @@ var OncoKbCardBody = function (props) {
|
|
|
1346
1506
|
function getBody(type, indicator) {
|
|
1347
1507
|
var tabs = [];
|
|
1348
1508
|
if (dataTypeHasContent(cbioportalUtils.OncoKbCardDataType.BIOLOGICAL)) {
|
|
1349
|
-
tabs.push(React__default.createElement(reactBootstrap.Tab, { eventKey: cbioportalUtils.OncoKbCardDataType.BIOLOGICAL, title:
|
|
1509
|
+
tabs.push(React__default.createElement(reactBootstrap.Tab, { eventKey: cbioportalUtils.OncoKbCardDataType.BIOLOGICAL, title: React__default.createElement(TabTitle, { type: cbioportalUtils.OncoKbCardDataType.BIOLOGICAL, indicator: props.indicator, displayHighestLevelInTabTitle: props.displayHighestLevelInTabTitle }) },
|
|
1350
1510
|
React__default.createElement(TabContentWrapper, null,
|
|
1351
1511
|
React__default.createElement(BiologicalContent, { mutationEffectCitations: indicator.mutationEffect.citations, biologicalSummary: indicator.mutationEffect.description, pmidData: props.pmidData }))));
|
|
1352
1512
|
}
|
|
1353
1513
|
if (!props.usingPublicOncoKbInstance &&
|
|
1354
1514
|
dataTypeHasContent(cbioportalUtils.OncoKbCardDataType.TXS)) {
|
|
1355
|
-
tabs.push(React__default.createElement(reactBootstrap.Tab, { eventKey: cbioportalUtils.OncoKbCardDataType.TXS, title:
|
|
1515
|
+
tabs.push(React__default.createElement(reactBootstrap.Tab, { eventKey: cbioportalUtils.OncoKbCardDataType.TXS, title: React__default.createElement(TabTitle, { type: cbioportalUtils.OncoKbCardDataType.TXS, indicator: props.indicator, displayHighestLevelInTabTitle: props.displayHighestLevelInTabTitle }) },
|
|
1356
1516
|
React__default.createElement(TabContentWrapper, null,
|
|
1357
1517
|
React__default.createElement("div", { style: {
|
|
1358
1518
|
marginTop: 10,
|
|
@@ -1361,13 +1521,13 @@ var OncoKbCardBody = function (props) {
|
|
|
1361
1521
|
}
|
|
1362
1522
|
if (!props.usingPublicOncoKbInstance &&
|
|
1363
1523
|
dataTypeHasContent(cbioportalUtils.OncoKbCardDataType.DX)) {
|
|
1364
|
-
tabs.push(React__default.createElement(reactBootstrap.Tab, { eventKey: cbioportalUtils.OncoKbCardDataType.DX, title:
|
|
1524
|
+
tabs.push(React__default.createElement(reactBootstrap.Tab, { eventKey: cbioportalUtils.OncoKbCardDataType.DX, title: React__default.createElement(TabTitle, { type: cbioportalUtils.OncoKbCardDataType.DX, indicator: props.indicator, displayHighestLevelInTabTitle: props.displayHighestLevelInTabTitle }) },
|
|
1365
1525
|
React__default.createElement(TabContentWrapper, null,
|
|
1366
1526
|
React__default.createElement(ImplicationContent, { variant: indicator.query.alteration, summary: indicator.diagnosticSummary, implications: indicator.diagnosticImplications, pmidData: props.pmidData }))));
|
|
1367
1527
|
}
|
|
1368
1528
|
if (!props.usingPublicOncoKbInstance &&
|
|
1369
1529
|
dataTypeHasContent(cbioportalUtils.OncoKbCardDataType.PX)) {
|
|
1370
|
-
tabs.push(React__default.createElement(reactBootstrap.Tab, { eventKey: cbioportalUtils.OncoKbCardDataType.PX, title:
|
|
1530
|
+
tabs.push(React__default.createElement(reactBootstrap.Tab, { eventKey: cbioportalUtils.OncoKbCardDataType.PX, title: React__default.createElement(TabTitle, { type: cbioportalUtils.OncoKbCardDataType.PX, indicator: props.indicator, displayHighestLevelInTabTitle: props.displayHighestLevelInTabTitle }) },
|
|
1371
1531
|
React__default.createElement(TabContentWrapper, null,
|
|
1372
1532
|
React__default.createElement(ImplicationContent, { variant: indicator.query.alteration, summary: indicator.prognosticSummary, implications: indicator.prognosticImplications, pmidData: props.pmidData }))));
|
|
1373
1533
|
}
|
|
@@ -1464,7 +1624,6 @@ var OncoKbCard = /** @class */ (function (_super) {
|
|
|
1464
1624
|
enumerable: false,
|
|
1465
1625
|
configurable: true
|
|
1466
1626
|
});
|
|
1467
|
-
// TODO we should replace the tabs with an actual ReactBootstrap Tab,
|
|
1468
1627
|
Object.defineProperty(OncoKbCard.prototype, "render", {
|
|
1469
1628
|
enumerable: false,
|
|
1470
1629
|
configurable: true,
|
|
@@ -1476,7 +1635,7 @@ var OncoKbCard = /** @class */ (function (_super) {
|
|
|
1476
1635
|
!this.props.geneNotExist && this.props.indicator && (React.createElement(OncoKbCardTitle, { hugoSymbol: this.props.indicator.query.hugoSymbol, variant: this.props.indicator.query.alteration, tumorType: this.props.indicator
|
|
1477
1636
|
? this.props.indicator.query.tumorType
|
|
1478
1637
|
: '' })),
|
|
1479
|
-
React.createElement(OncoKbCardBody, { type: this.props.type, indicator: this.props.indicator, geneNotExist: this.props.geneNotExist, isCancerGene: this.props.isCancerGene, hugoSymbol: this.props.hugoSymbol, pmidData: this.props.pmidData, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance }),
|
|
1638
|
+
React.createElement(OncoKbCardBody, { type: this.props.type, indicator: this.props.indicator, geneNotExist: this.props.geneNotExist, isCancerGene: this.props.isCancerGene, hugoSymbol: this.props.hugoSymbol, pmidData: this.props.pmidData, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance, displayHighestLevelInTabTitle: this.props.displayHighestLevelInTabTitle }),
|
|
1480
1639
|
React.createElement("div", { className: mainStyles.footer },
|
|
1481
1640
|
this.oncokbLinkOut === undefined ? ({ oncokbLogo: oncokbLogo }) : (React.createElement("a", { href: "" + this.oncokbLinkOut, target: "_blank", className: mainStyles['oncokb-logo'] }, oncokbLogo)),
|
|
1482
1641
|
this.props.handleFeedbackOpen && (React.createElement("span", null,
|
|
@@ -1535,14 +1694,14 @@ var OncoKbTooltip = /** @class */ (function (_super) {
|
|
|
1535
1694
|
value: function () {
|
|
1536
1695
|
var tooltipContent = React.createElement("span", null);
|
|
1537
1696
|
if (this.props.geneNotExist) {
|
|
1538
|
-
tooltipContent = (React.createElement(OncoKbCard, { type: this.props.type, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance, hugoSymbol: this.props.hugoSymbol, geneNotExist: this.props.geneNotExist, isCancerGene: this.props.isCancerGene, pmidData: {}, handleFeedbackOpen: this.props.handleFeedbackOpen }));
|
|
1697
|
+
tooltipContent = (React.createElement(OncoKbCard, { type: this.props.type, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance, hugoSymbol: this.props.hugoSymbol, geneNotExist: this.props.geneNotExist, isCancerGene: this.props.isCancerGene, pmidData: {}, handleFeedbackOpen: this.props.handleFeedbackOpen, displayHighestLevelInTabTitle: true }));
|
|
1539
1698
|
}
|
|
1540
1699
|
if (!this.props.indicator) {
|
|
1541
1700
|
return tooltipContent;
|
|
1542
1701
|
}
|
|
1543
1702
|
if (!this.props.geneNotExist) {
|
|
1544
1703
|
var pmidData = this.pmidData;
|
|
1545
|
-
tooltipContent = (React.createElement(OncoKbCard, { type: this.props.type, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance, geneNotExist: this.props.geneNotExist, isCancerGene: this.props.isCancerGene, hugoSymbol: this.props.hugoSymbol, indicator: this.props.indicator, pmidData: pmidData, handleFeedbackOpen: this.props.handleFeedbackOpen }));
|
|
1704
|
+
tooltipContent = (React.createElement(OncoKbCard, { type: this.props.type, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance, geneNotExist: this.props.geneNotExist, isCancerGene: this.props.isCancerGene, hugoSymbol: this.props.hugoSymbol, indicator: this.props.indicator, pmidData: pmidData, handleFeedbackOpen: this.props.handleFeedbackOpen, displayHighestLevelInTabTitle: true }));
|
|
1546
1705
|
}
|
|
1547
1706
|
return tooltipContent;
|
|
1548
1707
|
}
|
|
@@ -1586,44 +1745,6 @@ var OncoKbFeedback = /** @class */ (function (_super) {
|
|
|
1586
1745
|
return OncoKbFeedback;
|
|
1587
1746
|
}(React.Component));
|
|
1588
1747
|
|
|
1589
|
-
function hideArrow$1(tooltipEl) {
|
|
1590
|
-
var arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
|
|
1591
|
-
arrowEl.style.display = 'none';
|
|
1592
|
-
}
|
|
1593
|
-
var AnnotationIcon = function (props) {
|
|
1594
|
-
var _a;
|
|
1595
|
-
if (props.availableDataTypes !== undefined &&
|
|
1596
|
-
!props.availableDataTypes.includes(props.type)) {
|
|
1597
|
-
return null;
|
|
1598
|
-
}
|
|
1599
|
-
var highestLevel = '';
|
|
1600
|
-
if (props.indicator) {
|
|
1601
|
-
switch (props.type) {
|
|
1602
|
-
case cbioportalUtils.OncoKbCardDataType.TXS:
|
|
1603
|
-
highestLevel = props.indicator.highestSensitiveLevel;
|
|
1604
|
-
break;
|
|
1605
|
-
case cbioportalUtils.OncoKbCardDataType.TXR:
|
|
1606
|
-
highestLevel = props.indicator.highestResistanceLevel;
|
|
1607
|
-
break;
|
|
1608
|
-
case cbioportalUtils.OncoKbCardDataType.DX:
|
|
1609
|
-
highestLevel =
|
|
1610
|
-
props.indicator.highestDiagnosticImplicationLevel;
|
|
1611
|
-
break;
|
|
1612
|
-
case cbioportalUtils.OncoKbCardDataType.PX:
|
|
1613
|
-
highestLevel =
|
|
1614
|
-
props.indicator.highestPrognosticImplicationLevel;
|
|
1615
|
-
break;
|
|
1616
|
-
}
|
|
1617
|
-
}
|
|
1618
|
-
return (React__default.createElement("span", { className: "" + annotationStyles['annotation-item'] },
|
|
1619
|
-
React__default.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlayClassName: "oncokb-tooltip", overlay: function () {
|
|
1620
|
-
return props.tooltipOverlay ? props.tooltipOverlay : null;
|
|
1621
|
-
}, placement: "right", trigger: ['hover', 'focus'], onPopupAlign: hideArrow$1, destroyTooltipOnHide: true },
|
|
1622
|
-
React__default.createElement("i", { className: props.type === cbioportalUtils.OncoKbCardDataType.BIOLOGICAL
|
|
1623
|
-
? oncogenicityIconClassNames(((_a = props.indicator) === null || _a === void 0 ? void 0 : _a.oncogenic) || '')
|
|
1624
|
-
: levelIconClassNames(normalizeLevel(highestLevel) || ''), "data-test": "oncogenic-icon-image" }))));
|
|
1625
|
-
};
|
|
1626
|
-
|
|
1627
1748
|
function sortValue$2(indicator) {
|
|
1628
1749
|
var values = [0, 0, 0];
|
|
1629
1750
|
if (indicator) {
|
|
@@ -1645,6 +1766,33 @@ function download$2(indicator) {
|
|
|
1645
1766
|
var resistanceLevel = ((_b = indicator.highestResistanceLevel) === null || _b === void 0 ? void 0 : _b.toLowerCase()) || 'resistance NA';
|
|
1646
1767
|
return oncogenic + ", " + sensitivityLevel + ", " + resistanceLevel;
|
|
1647
1768
|
}
|
|
1769
|
+
function findDefaultDataTypeForTooltip(usingPublicOncoKbInstance, indicator, availableDataTypes) {
|
|
1770
|
+
if (usingPublicOncoKbInstance || !indicator) {
|
|
1771
|
+
return cbioportalUtils.OncoKbCardDataType.BIOLOGICAL;
|
|
1772
|
+
}
|
|
1773
|
+
// priority is in this order: Tx > Dx > Px > Biological
|
|
1774
|
+
if (indicator.highestSensitiveLevel &&
|
|
1775
|
+
availableDataTypes &&
|
|
1776
|
+
availableDataTypes.includes(cbioportalUtils.OncoKbCardDataType.TXS)) {
|
|
1777
|
+
return cbioportalUtils.OncoKbCardDataType.TXS;
|
|
1778
|
+
}
|
|
1779
|
+
else if (indicator.highestResistanceLevel &&
|
|
1780
|
+
availableDataTypes &&
|
|
1781
|
+
availableDataTypes.includes(cbioportalUtils.OncoKbCardDataType.TXR)) {
|
|
1782
|
+
return cbioportalUtils.OncoKbCardDataType.TXR;
|
|
1783
|
+
}
|
|
1784
|
+
else if (indicator.highestDiagnosticImplicationLevel &&
|
|
1785
|
+
availableDataTypes &&
|
|
1786
|
+
availableDataTypes.includes(cbioportalUtils.OncoKbCardDataType.DX)) {
|
|
1787
|
+
return cbioportalUtils.OncoKbCardDataType.DX;
|
|
1788
|
+
}
|
|
1789
|
+
else if (indicator.highestPrognosticImplicationLevel &&
|
|
1790
|
+
availableDataTypes &&
|
|
1791
|
+
availableDataTypes.includes(cbioportalUtils.OncoKbCardDataType.PX)) {
|
|
1792
|
+
return cbioportalUtils.OncoKbCardDataType.PX;
|
|
1793
|
+
}
|
|
1794
|
+
return cbioportalUtils.OncoKbCardDataType.BIOLOGICAL;
|
|
1795
|
+
}
|
|
1648
1796
|
var OncoKB = /** @class */ (function (_super) {
|
|
1649
1797
|
__extends(OncoKB, _super);
|
|
1650
1798
|
function OncoKB(props) {
|
|
@@ -1669,8 +1817,7 @@ var OncoKB = /** @class */ (function (_super) {
|
|
|
1669
1817
|
configurable: true,
|
|
1670
1818
|
writable: true,
|
|
1671
1819
|
value: function () {
|
|
1672
|
-
var
|
|
1673
|
-
var oncoKbContent = (React.createElement("span", { className: "" + annotationStyles['annotation-item'] }));
|
|
1820
|
+
var oncoKbContent;
|
|
1674
1821
|
if (this.props.status === 'error') {
|
|
1675
1822
|
oncoKbContent = errorIcon('Error fetching OncoKB data');
|
|
1676
1823
|
}
|
|
@@ -1678,15 +1825,9 @@ var OncoKB = /** @class */ (function (_super) {
|
|
|
1678
1825
|
oncoKbContent = loaderIcon('pull-left');
|
|
1679
1826
|
}
|
|
1680
1827
|
else {
|
|
1681
|
-
oncoKbContent =
|
|
1682
|
-
|
|
1683
|
-
|
|
1684
|
-
this.props.indicator && (React.createElement(React.Fragment, null, [
|
|
1685
|
-
cbioportalUtils.OncoKbCardDataType.TXS,
|
|
1686
|
-
cbioportalUtils.OncoKbCardDataType.TXR,
|
|
1687
|
-
cbioportalUtils.OncoKbCardDataType.DX,
|
|
1688
|
-
cbioportalUtils.OncoKbCardDataType.PX,
|
|
1689
|
-
].map(function (dataType) { return (React.createElement(AnnotationIcon, { type: dataType, tooltipOverlay: _this.tooltipContent(dataType), indicator: _this.props.indicator, availableDataTypes: _this.props.availableDataTypes })); })))));
|
|
1828
|
+
oncoKbContent = this.props.mergeAnnotationIcons
|
|
1829
|
+
? this.singleAnnotationIcon()
|
|
1830
|
+
: this.multiAnnotationIcon();
|
|
1690
1831
|
if (!this.props.disableFeedback && this.showFeedback) {
|
|
1691
1832
|
oncoKbContent = (React.createElement("span", null,
|
|
1692
1833
|
oncoKbContent,
|
|
@@ -1698,6 +1839,57 @@ var OncoKB = /** @class */ (function (_super) {
|
|
|
1698
1839
|
return oncoKbContent;
|
|
1699
1840
|
}
|
|
1700
1841
|
});
|
|
1842
|
+
Object.defineProperty(OncoKB.prototype, "multiAnnotationIcon", {
|
|
1843
|
+
enumerable: false,
|
|
1844
|
+
configurable: true,
|
|
1845
|
+
writable: true,
|
|
1846
|
+
value: function () {
|
|
1847
|
+
return (React.createElement("span", { className: "oncokb-content", style: { display: 'inline-flex' } },
|
|
1848
|
+
React.createElement(AnnotationIcon, { type: cbioportalUtils.OncoKbCardDataType.BIOLOGICAL, tooltipOverlay: this.tooltipContent(cbioportalUtils.OncoKbCardDataType.BIOLOGICAL), indicator: this.props.indicator, availableDataTypes: this.props.availableDataTypes }),
|
|
1849
|
+
this.levelIcons()));
|
|
1850
|
+
}
|
|
1851
|
+
});
|
|
1852
|
+
Object.defineProperty(OncoKB.prototype, "levelIcons", {
|
|
1853
|
+
enumerable: false,
|
|
1854
|
+
configurable: true,
|
|
1855
|
+
writable: true,
|
|
1856
|
+
value: function () {
|
|
1857
|
+
var _this = this;
|
|
1858
|
+
if (this.props.usingPublicOncoKbInstance) {
|
|
1859
|
+
return null;
|
|
1860
|
+
}
|
|
1861
|
+
if (this.props.indicator) {
|
|
1862
|
+
return (React.createElement(React.Fragment, null, [
|
|
1863
|
+
cbioportalUtils.OncoKbCardDataType.TXS,
|
|
1864
|
+
cbioportalUtils.OncoKbCardDataType.TXR,
|
|
1865
|
+
cbioportalUtils.OncoKbCardDataType.DX,
|
|
1866
|
+
cbioportalUtils.OncoKbCardDataType.PX,
|
|
1867
|
+
].map(function (dataType) { return (React.createElement(AnnotationIcon, { type: dataType, tooltipOverlay: _this.tooltipContent(dataType), indicator: _this.props.indicator, availableDataTypes: _this.props.availableDataTypes })); })));
|
|
1868
|
+
}
|
|
1869
|
+
else {
|
|
1870
|
+
// TODO This doesn't always work, in some cases it adds unnecessary empty icons, we need a better solution.
|
|
1871
|
+
// we still need to draw empty icons even if there is no indicator data.
|
|
1872
|
+
// this is to keep the icon alignment consistent with the rest of the column
|
|
1873
|
+
// return (
|
|
1874
|
+
// <>
|
|
1875
|
+
// {this.props.availableDataTypes?.map(() => (
|
|
1876
|
+
// <AnnotationIconWithTooltip icon={<i />} />
|
|
1877
|
+
// ))}
|
|
1878
|
+
// </>
|
|
1879
|
+
// );
|
|
1880
|
+
return null;
|
|
1881
|
+
}
|
|
1882
|
+
}
|
|
1883
|
+
});
|
|
1884
|
+
Object.defineProperty(OncoKB.prototype, "singleAnnotationIcon", {
|
|
1885
|
+
enumerable: false,
|
|
1886
|
+
configurable: true,
|
|
1887
|
+
writable: true,
|
|
1888
|
+
value: function () {
|
|
1889
|
+
return (React.createElement("span", { className: "oncokb-content", style: { display: 'inline-flex' } },
|
|
1890
|
+
React.createElement(AnnotationIconWithTooltip, { tooltipOverlay: this.tooltipContent(findDefaultDataTypeForTooltip(this.props.usingPublicOncoKbInstance, this.props.indicator, this.props.availableDataTypes)), icon: React.createElement(CompactAnnotationIcon, { indicator: this.props.indicator, availableDataTypes: this.props.availableDataTypes, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance }) })));
|
|
1891
|
+
}
|
|
1892
|
+
});
|
|
1701
1893
|
Object.defineProperty(OncoKB.prototype, "tooltipContent", {
|
|
1702
1894
|
enumerable: false,
|
|
1703
1895
|
configurable: true,
|
|
@@ -2113,9 +2305,9 @@ function sortValue$4(annotation) {
|
|
|
2113
2305
|
]);
|
|
2114
2306
|
}
|
|
2115
2307
|
function GenericAnnotation(props) {
|
|
2116
|
-
var annotation = props.annotation, enableCivic = props.enableCivic, enableHotspot = props.enableHotspot, enableMyCancerGenome = props.enableMyCancerGenome, enableOncoKb = props.enableOncoKb, pubMedCache = props.pubMedCache, userEmailAddress = props.userEmailAddress;
|
|
2308
|
+
var annotation = props.annotation, enableCivic = props.enableCivic, enableHotspot = props.enableHotspot, enableMyCancerGenome = props.enableMyCancerGenome, enableOncoKb = props.enableOncoKb, pubMedCache = props.pubMedCache, userEmailAddress = props.userEmailAddress, mergeOncoKbIcons = props.mergeOncoKbIcons;
|
|
2117
2309
|
return (React.createElement("span", { style: { display: 'flex', minWidth: 100 } },
|
|
2118
|
-
enableOncoKb && (React.createElement(OncoKB, { usingPublicOncoKbInstance: annotation.usingPublicOncoKbInstance, hugoGeneSymbol: annotation.hugoGeneSymbol, geneNotExist: !annotation.oncoKbGeneExist, isCancerGene: annotation.isOncoKbCancerGene, status: annotation.oncoKbStatus, indicator: annotation.oncoKbIndicator, availableDataTypes: annotation.oncoKbAvailableDataTypes, pubMedCache: pubMedCache, userEmailAddress: userEmailAddress })),
|
|
2310
|
+
enableOncoKb && (React.createElement(OncoKB, { usingPublicOncoKbInstance: annotation.usingPublicOncoKbInstance, hugoGeneSymbol: annotation.hugoGeneSymbol, geneNotExist: !annotation.oncoKbGeneExist, isCancerGene: annotation.isOncoKbCancerGene, status: annotation.oncoKbStatus, indicator: annotation.oncoKbIndicator, availableDataTypes: annotation.oncoKbAvailableDataTypes, mergeAnnotationIcons: mergeOncoKbIcons, pubMedCache: pubMedCache, userEmailAddress: userEmailAddress })),
|
|
2119
2311
|
enableCivic && (React.createElement(Civic, { civicEntry: annotation.civicEntry, civicStatus: annotation.civicStatus, hasCivicVariants: annotation.hasCivicVariants })),
|
|
2120
2312
|
enableMyCancerGenome && (React.createElement(MyCancerGenome, { linksHTML: annotation.myCancerGenomeLinks })),
|
|
2121
2313
|
enableHotspot && (React.createElement(HotspotAnnotation, { isHotspot: annotation.isHotspot, is3dHotspot: annotation.is3dHotspot, status: annotation.hotspotStatus }))));
|
|
@@ -2497,7 +2689,7 @@ function generateGnomadUrl(chromosome, position, reference, variant) {
|
|
|
2497
2689
|
}
|
|
2498
2690
|
}
|
|
2499
2691
|
|
|
2500
|
-
var _a$
|
|
2692
|
+
var _a$2;
|
|
2501
2693
|
function frequencyOutput(frequency) {
|
|
2502
2694
|
if (frequency === 0) {
|
|
2503
2695
|
return React.createElement("span", null, "0");
|
|
@@ -2511,13 +2703,13 @@ function frequencyOutput(frequency) {
|
|
|
2511
2703
|
}
|
|
2512
2704
|
}
|
|
2513
2705
|
var headerClassName = 'text-wrap font-weight-bold';
|
|
2514
|
-
var HEADERS = (_a$
|
|
2515
|
-
_a$
|
|
2516
|
-
_a$
|
|
2517
|
-
_a$
|
|
2518
|
-
_a$
|
|
2519
|
-
_a$
|
|
2520
|
-
_a$
|
|
2706
|
+
var HEADERS = (_a$2 = {},
|
|
2707
|
+
_a$2[GnomadTableColumnName.population] = (React.createElement(ColumnHeader, { className: headerClassName, headerContent: React.createElement("span", null, "Population") })),
|
|
2708
|
+
_a$2[GnomadTableColumnName.alleleCount] = (React.createElement(ColumnHeader, { className: headerClassName, headerContent: React.createElement("span", null, "Allele Count"), overlay: React.createElement("span", null, "Number of individuals with this allele") })),
|
|
2709
|
+
_a$2[GnomadTableColumnName.alleleNumber] = (React.createElement(ColumnHeader, { className: headerClassName, headerContent: React.createElement("span", null, "Allele Number"), overlay: React.createElement("span", null, "Number of times any allele has been observed at this position in the population") })),
|
|
2710
|
+
_a$2[GnomadTableColumnName.homozygotes] = (React.createElement(ColumnHeader, { className: headerClassName, headerContent: React.createElement("span", null, "Number of Homozygotes"), overlay: React.createElement("span", null, "Number of individuals carrying this allele in both copies") })),
|
|
2711
|
+
_a$2[GnomadTableColumnName.alleleFrequency] = (React.createElement(ColumnHeader, { className: headerClassName, headerContent: React.createElement("span", null, "Allele Frequency"), overlay: React.createElement("span", null, "Proportion of the population with this allele") })),
|
|
2712
|
+
_a$2);
|
|
2521
2713
|
function renderNumericalValue(column) {
|
|
2522
2714
|
return React.createElement("span", { className: "pull-right mr-1" }, column.value);
|
|
2523
2715
|
}
|
|
@@ -4669,7 +4861,7 @@ var MutationType = /** @class */ (function (_super) {
|
|
|
4669
4861
|
return MutationType;
|
|
4670
4862
|
}(React.Component));
|
|
4671
4863
|
|
|
4672
|
-
var _a$
|
|
4864
|
+
var _a$3, _b;
|
|
4673
4865
|
(function (MutationColumn) {
|
|
4674
4866
|
MutationColumn["PROTEIN_CHANGE"] = "proteinChange";
|
|
4675
4867
|
MutationColumn["ANNOTATION"] = "annotation";
|
|
@@ -4707,33 +4899,33 @@ var _a$2, _b;
|
|
|
4707
4899
|
function rightAlignedCell(cellProps) {
|
|
4708
4900
|
return React.createElement("span", { className: "pull-right mr-3" }, cellProps.value);
|
|
4709
4901
|
}
|
|
4710
|
-
var MUTATION_COLUMN_HEADERS = (_a$
|
|
4711
|
-
_a$
|
|
4712
|
-
_a$
|
|
4713
|
-
_a$
|
|
4714
|
-
_a$
|
|
4715
|
-
_a$
|
|
4716
|
-
_a$
|
|
4717
|
-
_a$
|
|
4718
|
-
_a$
|
|
4719
|
-
_a$
|
|
4720
|
-
_a$
|
|
4721
|
-
_a$
|
|
4722
|
-
_a$
|
|
4902
|
+
var MUTATION_COLUMN_HEADERS = (_a$3 = {},
|
|
4903
|
+
_a$3[exports.MutationColumn.PROTEIN_CHANGE] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-left" }, exports.MutationColumnName.PROTEIN_CHANGE) })),
|
|
4904
|
+
_a$3[exports.MutationColumn.ANNOTATION] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-left" }, exports.MutationColumnName.ANNOTATION) })),
|
|
4905
|
+
_a$3[exports.MutationColumn.MUTATION_STATUS] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-left" }, exports.MutationColumnName.MUTATION_STATUS) })),
|
|
4906
|
+
_a$3[exports.MutationColumn.MUTATION_TYPE] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-left" }, exports.MutationColumnName.MUTATION_TYPE) })),
|
|
4907
|
+
_a$3[exports.MutationColumn.CHROMOSOME] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-right mr-3" }, exports.MutationColumnName.CHROMOSOME) })),
|
|
4908
|
+
_a$3[exports.MutationColumn.START_POSITION] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-right mr-3" }, exports.MutationColumnName.START_POSITION) })),
|
|
4909
|
+
_a$3[exports.MutationColumn.END_POSITION] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-right mr-3" }, exports.MutationColumnName.END_POSITION) })),
|
|
4910
|
+
_a$3[exports.MutationColumn.REFERENCE_ALLELE] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-left" }, exports.MutationColumnName.REFERENCE_ALLELE), overlay: React.createElement("span", null, "Reference Allele") })),
|
|
4911
|
+
_a$3[exports.MutationColumn.VARIANT_ALLELE] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-left" }, exports.MutationColumnName.VARIANT_ALLELE), overlay: React.createElement("span", null, "Variant Allele") })),
|
|
4912
|
+
_a$3[exports.MutationColumn.HGVSG] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-left" }, exports.MutationColumnName.HGVSG) })),
|
|
4913
|
+
_a$3[exports.MutationColumn.HGVSC] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-left" }, exports.MutationColumnName.HGVSC) })),
|
|
4914
|
+
_a$3[exports.MutationColumn.GNOMAD] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-right mr-3" },
|
|
4723
4915
|
exports.MutationColumnName.GNOMAD,
|
|
4724
4916
|
' ',
|
|
4725
4917
|
React.createElement("i", { className: "fa fa-info-circle" })), overlay: React.createElement("span", null,
|
|
4726
4918
|
React.createElement("a", { href: "https://gnomad.broadinstitute.org/", target: "_blank" }, "gnomAD"),
|
|
4727
4919
|
' ',
|
|
4728
4920
|
"population allele frequencies. Overall population allele frequency is shown. Hover over a frequency to see the frequency for each specific population.") })),
|
|
4729
|
-
_a$
|
|
4921
|
+
_a$3[exports.MutationColumn.CLINVAR] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-left" },
|
|
4730
4922
|
exports.MutationColumnName.CLINVAR,
|
|
4731
4923
|
' ',
|
|
4732
4924
|
React.createElement("i", { className: "fa fa-info-circle" })), overlay: React.createElement("span", null,
|
|
4733
4925
|
React.createElement("a", { href: "https://www.ncbi.nlm.nih.gov/clinvar/", target: "_blank" }, "ClinVar"),
|
|
4734
4926
|
' ',
|
|
4735
4927
|
"aggregates information about genomic variation and its relationship to human health.") })),
|
|
4736
|
-
_a$
|
|
4928
|
+
_a$3[exports.MutationColumn.DBSNP] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-right mr-3" },
|
|
4737
4929
|
exports.MutationColumnName.DBSNP,
|
|
4738
4930
|
' ',
|
|
4739
4931
|
React.createElement("i", { className: "fa fa-info-circle" })), overlay: React.createElement("span", null,
|
|
@@ -4742,14 +4934,14 @@ var MUTATION_COLUMN_HEADERS = (_a$2 = {},
|
|
|
4742
4934
|
") is a free public archive for genetic variation within and across different species.",
|
|
4743
4935
|
React.createElement("br", null),
|
|
4744
4936
|
"NOTE: Currently only SNPs, single base deletions and insertions are supported.") })),
|
|
4745
|
-
_a$
|
|
4937
|
+
_a$3[exports.MutationColumn.SIGNAL] = (React.createElement(ColumnHeader, { headerContent: React.createElement("span", { className: "pull-right mr-3" },
|
|
4746
4938
|
exports.MutationColumnName.SIGNAL,
|
|
4747
4939
|
' ',
|
|
4748
4940
|
React.createElement("i", { className: "fa fa-info-circle" })), overlay: React.createElement("span", null,
|
|
4749
4941
|
"Prevalence of germline mutations in cancer patients from",
|
|
4750
4942
|
' ',
|
|
4751
4943
|
React.createElement("a", { href: "https://www.signaldb.org/", target: "_blank" }, "SIGNAL")) })),
|
|
4752
|
-
_a$
|
|
4944
|
+
_a$3);
|
|
4753
4945
|
/**
|
|
4754
4946
|
* These default columns only include static props.
|
|
4755
4947
|
* So, for some columns, like Annotation, no default accessor or Cell (render) properties included.
|
|
@@ -8371,7 +8563,7 @@ var PtmReferenceList = /** @class */ (function (_super) {
|
|
|
8371
8563
|
return PtmReferenceList;
|
|
8372
8564
|
}(React.Component));
|
|
8373
8565
|
|
|
8374
|
-
var _a$
|
|
8566
|
+
var _a$4;
|
|
8375
8567
|
var PtmAnnotationTableColumnId;
|
|
8376
8568
|
(function (PtmAnnotationTableColumnId) {
|
|
8377
8569
|
PtmAnnotationTableColumnId["POSITION"] = "position";
|
|
@@ -8379,33 +8571,33 @@ var PtmAnnotationTableColumnId;
|
|
|
8379
8571
|
PtmAnnotationTableColumnId["DESCRIPTION"] = "description";
|
|
8380
8572
|
PtmAnnotationTableColumnId["PUBMED_IDS"] = "pubmedIds";
|
|
8381
8573
|
})(PtmAnnotationTableColumnId || (PtmAnnotationTableColumnId = {}));
|
|
8382
|
-
var PTM_ANNOTATION_DEFAULT_COLUMNS = (_a$
|
|
8383
|
-
_a$
|
|
8574
|
+
var PTM_ANNOTATION_DEFAULT_COLUMNS = (_a$4 = {},
|
|
8575
|
+
_a$4[PtmAnnotationTableColumnId.POSITION] = {
|
|
8384
8576
|
id: PtmAnnotationTableColumnId.POSITION,
|
|
8385
8577
|
accessor: function (ptm) { return ptm.residue.start; },
|
|
8386
8578
|
Header: 'Residue',
|
|
8387
8579
|
Cell: function (props) { return (React.createElement("div", { style: { textAlign: 'right' } }, getResidue(props.original))); },
|
|
8388
8580
|
maxWidth: 64,
|
|
8389
8581
|
},
|
|
8390
|
-
_a$
|
|
8582
|
+
_a$4[PtmAnnotationTableColumnId.TYPE] = {
|
|
8391
8583
|
id: PtmAnnotationTableColumnId.TYPE,
|
|
8392
8584
|
accessor: function (ptm) { return ptm.type; },
|
|
8393
8585
|
Header: 'Type',
|
|
8394
8586
|
minWidth: 100,
|
|
8395
8587
|
},
|
|
8396
|
-
_a$
|
|
8588
|
+
_a$4[PtmAnnotationTableColumnId.DESCRIPTION] = {
|
|
8397
8589
|
id: PtmAnnotationTableColumnId.DESCRIPTION,
|
|
8398
8590
|
accessor: function (ptm) { return ptm.description; },
|
|
8399
8591
|
Header: 'Description',
|
|
8400
8592
|
minWidth: 180,
|
|
8401
8593
|
},
|
|
8402
|
-
_a$
|
|
8594
|
+
_a$4[PtmAnnotationTableColumnId.PUBMED_IDS] = {
|
|
8403
8595
|
id: PtmAnnotationTableColumnId.PUBMED_IDS,
|
|
8404
8596
|
Header: '',
|
|
8405
8597
|
sortable: false,
|
|
8406
8598
|
maxWidth: 32,
|
|
8407
8599
|
},
|
|
8408
|
-
_a$
|
|
8600
|
+
_a$4);
|
|
8409
8601
|
function getResidue(ptm) {
|
|
8410
8602
|
if (ptm.residue.end && ptm.residue.end > ptm.residue.start) {
|
|
8411
8603
|
return ptm.residue.start + "-" + ptm.residue.end;
|