react-mutation-mapper 0.8.59 → 0.8.61
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/ptm/PtmReferenceList.d.ts +1 -0
- package/dist/index.d.ts +0 -12
- package/dist/index.es.js +179 -1840
- package/dist/index.es.js.map +1 -1
- package/dist/index.js +190 -1875
- package/dist/index.js.map +1 -1
- package/dist/styles.css +0 -229
- package/package.json +5 -4
- package/dist/component/oncokb/ArticleAbstractItem.d.ts +0 -5
- package/dist/component/oncokb/OncoKB.d.ts +0 -33
- package/dist/component/oncokb/OncoKB.spec.d.ts +0 -1
- package/dist/component/oncokb/OncoKBSuggestAnnotationLinkout.d.ts +0 -6
- package/dist/component/oncokb/OncoKbCard.d.ts +0 -20
- package/dist/component/oncokb/OncoKbCardBody.d.ts +0 -15
- package/dist/component/oncokb/OncoKbCardLevelsOfEvidenceDropdown.d.ts +0 -15
- package/dist/component/oncokb/OncoKbCardTitle.d.ts +0 -8
- package/dist/component/oncokb/OncoKbFeedback.d.ts +0 -12
- package/dist/component/oncokb/OncoKbHelper.d.ts +0 -33
- package/dist/component/oncokb/OncoKbSummaryTable.d.ts +0 -31
- package/dist/component/oncokb/OncoKbTooltip.d.ts +0 -21
- package/dist/component/oncokb/OncoKbTreatmentTable.d.ts +0 -86
- package/dist/component/oncokb/PmidItem.d.ts +0 -12
- package/dist/component/oncokb/RefComponent.d.ts +0 -9
- package/dist/component/oncokb/ReferenceList.d.ts +0 -13
- package/dist/component/oncokb/SummaryWithRefs.d.ts +0 -11
- package/dist/component/oncokb/constants.d.ts +0 -10
- package/dist/component/oncokb/icon/AnnotationIcon.d.ts +0 -13
- package/dist/component/oncokb/icon/CompactAnnotationIcon.d.ts +0 -8
- package/dist/component/oncokb/icon/LevelIcon.d.ts +0 -6
- package/dist/component/oncokb/icon/OncogenicIcon.d.ts +0 -6
- package/dist/component/oncokb/oncokbCard/BiologicalContent.d.ts +0 -8
- package/dist/component/oncokb/oncokbCard/EvidenceReferenceContent.d.ts +0 -9
- package/dist/component/oncokb/oncokbCard/ImplicationContent.d.ts +0 -11
- package/dist/util/OncoKbUtils.d.ts +0 -40
- package/dist/util/OncoKbUtils.spec.d.ts +0 -1
package/dist/index.js
CHANGED
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@@ -8,23 +8,22 @@ var mobx = require('mobx');
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var mobxReact = require('mobx-react');
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var React = require('react');
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var cbioportalFrontendCommons = require('cbioportal-frontend-commons');
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var classNames = require('classnames');
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var cbioportalUtils = require('cbioportal-utils');
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var
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var autobind = require('autobind-decorator');
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var oncoKbLogoImgSrc = require('oncokb-styles/dist/images/logo/oncokb.svg');
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var reactBootstrap = require('react-bootstrap');
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var reactCollapse = require('react-collapse');
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var ReactTable = require('react-table');
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var reactIf = require('react-if');
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require('oncokb-styles/dist/oncokb.css');
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var oncokbFrontendCommons = require('oncokb-frontend-commons');
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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 autobind = require('autobind-decorator');
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var ReactTable = require('react-table');
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require('rc-tooltip/assets/bootstrap_white.css');
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var Select = require('react-select');
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var $ = require('jquery');
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var reactCollapse = require('react-collapse');
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var Slider = require('react-rangeslider');
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require('react-rangeslider/lib/index.css');
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var oncoKbImg = require('oncokb-styles/dist/images/oncogenic.svg');
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require('oncokb-frontend-commons/dist/styles.css');
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var reactBootstrap = require('react-bootstrap');
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var request = require('superagent');
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var memoize = require('memoize-weak-decorator');
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var mobxpromise = require('mobxpromise');
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@@ -52,10 +51,8 @@ function _interopNamespace(e) {
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var ___default = /*#__PURE__*/_interopDefaultLegacy(_);
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var ___namespace = /*#__PURE__*/_interopNamespace(_);
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var React__namespace = /*#__PURE__*/_interopNamespace(React);
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var
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var classnames__default = /*#__PURE__*/_interopDefaultLegacy(classnames);
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var classNames__default = /*#__PURE__*/_interopDefaultLegacy(classNames);
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var autobind__default = /*#__PURE__*/_interopDefaultLegacy(autobind);
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var oncoKbLogoImgSrc__default = /*#__PURE__*/_interopDefaultLegacy(oncoKbLogoImgSrc);
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var ReactTable__default = /*#__PURE__*/_interopDefaultLegacy(ReactTable);
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var Select__default = /*#__PURE__*/_interopDefaultLegacy(Select);
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var $__default = /*#__PURE__*/_interopDefaultLegacy($);
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@@ -67,7 +64,7 @@ var memoize__default = /*#__PURE__*/_interopDefaultLegacy(memoize);
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var annotationStyles = {"annotation-item-load":"annotation-module_annotation-item-load__1pDN0","annotation-item-text":"annotation-module_annotation-item-text__Gy_Jv","annotation-item-error":"annotation-module_annotation-item-error__5BhTo","annotation-item":"annotation-module_annotation-item__2EgnB"};
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function loaderIcon(className) {
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return (React__namespace.createElement("span", { className:
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return (React__namespace.createElement("span", { className: classNames__default["default"]("" + annotationStyles['annotation-item'], "" + annotationStyles['annotation-item-load'], className) },
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React__namespace.createElement("i", { className: "fa fa-spinner fa-pulse" })));
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}
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function errorIcon(errorMessage) {
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@@ -164,1607 +161,58 @@ var CivicCard = /** @class */ (function (_super) {
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React__namespace.createElement("p", null,
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React__namespace.createElement("span", { className: "civic-card-gene-name" },
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React__namespace.createElement("a", { href: this.props.geneUrl, target: "_blank" },
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React__namespace.createElement("b", null, this.props.geneName))),
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' ',
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"- ",
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this.props.geneDescription)),
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React__namespace.createElement("div", { className: "col s12" },
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React__namespace.createElement("ul", null, this.generateVariants(this.props.variants))),
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React__namespace.createElement("div", { className: "item disclaimer" },
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React__namespace.createElement("span", null, "Disclaimer: This resource is intended for purely research purposes. It should not be used for emergencies or medical or professional advice.")))),
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React__namespace.createElement("div", { className: "item footer" },
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React__namespace.createElement("a", { href: this.props.geneUrl, target: "_blank" },
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React__namespace.createElement("img", { src: img$5, className: "civic-logo", alt: "CIViC" })))));
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}
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});
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return CivicCard;
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}(React__namespace.Component));
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var img$4 = "data:image/png;base64,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";
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185
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var img$3 = "data:image/png;base64,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";
|
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186
|
-
|
|
187
|
-
function hideArrow$1(tooltipEl) {
|
|
188
|
-
var arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
|
|
189
|
-
arrowEl.style.display = 'none';
|
|
190
|
-
}
|
|
191
|
-
function sortValue$8(civicEntry) {
|
|
192
|
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var score = 0;
|
|
193
|
-
if (civicEntry) {
|
|
194
|
-
score = 1;
|
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195
|
-
}
|
|
196
|
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return score;
|
|
197
|
-
}
|
|
198
|
-
function download$7(civicEntry) {
|
|
199
|
-
if (!civicEntry) {
|
|
200
|
-
return cbioportalUtils.CIVIC_NA_VALUE;
|
|
201
|
-
}
|
|
202
|
-
var variants = ___default["default"].values(civicEntry.variants);
|
|
203
|
-
var values = [];
|
|
204
|
-
if (variants && variants.length > 0 && variants[0].evidenceCounts) {
|
|
205
|
-
___default["default"].forEach(variants[0].evidenceCounts, function (value, key) {
|
|
206
|
-
values.push(key + ": " + value);
|
|
207
|
-
});
|
|
208
|
-
}
|
|
209
|
-
// this indicates that we have an entry but the evidence is empty
|
|
210
|
-
if (values.length === 0) {
|
|
211
|
-
return cbioportalUtils.CIVIC_NA_VALUE;
|
|
212
|
-
}
|
|
213
|
-
return values.join(', ');
|
|
214
|
-
}
|
|
215
|
-
var Civic = /** @class */ (function (_super) {
|
|
216
|
-
tslib.__extends(Civic, _super);
|
|
217
|
-
function Civic(props) {
|
|
218
|
-
var _this = _super.call(this, props) || this;
|
|
219
|
-
Object.defineProperty(_this, "tooltipDataLoadComplete", {
|
|
220
|
-
enumerable: true,
|
|
221
|
-
configurable: true,
|
|
222
|
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writable: true,
|
|
223
|
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value: false
|
|
224
|
-
});
|
|
225
|
-
mobx.makeObservable(_this);
|
|
226
|
-
_this.cardContent = _this.cardContent.bind(_this);
|
|
227
|
-
return _this;
|
|
228
|
-
}
|
|
229
|
-
Object.defineProperty(Civic.prototype, "render", {
|
|
230
|
-
enumerable: false,
|
|
231
|
-
configurable: true,
|
|
232
|
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writable: true,
|
|
233
|
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value: function () {
|
|
234
|
-
var civicContent = (React__namespace.createElement("span", { className: "" + annotationStyles['annotation-item'] }));
|
|
235
|
-
var civicImgWidth = 14;
|
|
236
|
-
var civicImgHeight = 14;
|
|
237
|
-
var civicImgSrc = !this.props.hasCivicVariants
|
|
238
|
-
? img$3
|
|
239
|
-
: img$4;
|
|
240
|
-
if (this.props.civicStatus == 'error') {
|
|
241
|
-
civicContent = errorIcon('Error fetching Civic data');
|
|
242
|
-
}
|
|
243
|
-
else if (this.props.civicEntry !== undefined) {
|
|
244
|
-
if (this.props.civicEntry !== null &&
|
|
245
|
-
this.props.civicStatus == 'complete') {
|
|
246
|
-
civicContent = (React__namespace.createElement("span", { className: "" + annotationStyles['annotation-item'] },
|
|
247
|
-
React__namespace.createElement("img", { width: civicImgWidth, height: civicImgHeight, src: civicImgSrc, alt: "Civic Variant Entry" })));
|
|
248
|
-
civicContent = (React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlay: this.cardContent.bind(this, this.props.civicEntry), placement: "right", trigger: ['hover', 'focus'], onPopupAlign: hideArrow$1, destroyTooltipOnHide: false }, civicContent));
|
|
249
|
-
}
|
|
250
|
-
}
|
|
251
|
-
else {
|
|
252
|
-
// It's still unknown (undefined) if the current gene has a Civic entry or not.
|
|
253
|
-
civicContent = loaderIcon('pull-left');
|
|
254
|
-
}
|
|
255
|
-
return civicContent;
|
|
256
|
-
}
|
|
257
|
-
});
|
|
258
|
-
Object.defineProperty(Civic.prototype, "cardContent", {
|
|
259
|
-
enumerable: false,
|
|
260
|
-
configurable: true,
|
|
261
|
-
writable: true,
|
|
262
|
-
value: function (civicEntry) {
|
|
263
|
-
return (React__namespace.createElement(CivicCard, { title: "CIViC Variants", geneName: civicEntry.name, geneDescription: civicEntry.description, geneUrl: civicEntry.url, variants: civicEntry.variants }));
|
|
264
|
-
}
|
|
265
|
-
});
|
|
266
|
-
tslib.__decorate([
|
|
267
|
-
mobx.observable
|
|
268
|
-
], Civic.prototype, "tooltipDataLoadComplete", void 0);
|
|
269
|
-
Civic = tslib.__decorate([
|
|
270
|
-
mobxReact.observer
|
|
271
|
-
], Civic);
|
|
272
|
-
return Civic;
|
|
273
|
-
}(React__namespace.Component));
|
|
274
|
-
|
|
275
|
-
var NoClinvarData = function () {
|
|
276
|
-
return (React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { placement: "topLeft", overlay: React__namespace.createElement("span", null, "Variant has no ClinVar data.") },
|
|
277
|
-
React__namespace.createElement("span", { style: {
|
|
278
|
-
height: '100%',
|
|
279
|
-
width: '100%',
|
|
280
|
-
display: 'block',
|
|
281
|
-
overflow: 'hidden',
|
|
282
|
-
} }, "\u00A0")));
|
|
283
|
-
};
|
|
284
|
-
var ClinvarSummary = function (props) {
|
|
285
|
-
if (!props.clinvar) {
|
|
286
|
-
return React__namespace.createElement(NoClinvarData, null);
|
|
287
|
-
}
|
|
288
|
-
else {
|
|
289
|
-
var clinvarId = props.clinvar.clinvarId;
|
|
290
|
-
var clinvarLink = "https://www.ncbi.nlm.nih.gov/clinvar/variation/" + clinvarId + "/";
|
|
291
|
-
var clinicalSignificance = props.clinvar.clinicalSignificance;
|
|
292
|
-
var conflictingClinicalSignificance = props.clinvar.conflictingClinicalSignificance;
|
|
293
|
-
return (React__namespace.createElement(cbioportalFrontendCommons.TruncatedText, { maxLength: 30, text: clinicalSignificance, addTooltip: "always", tooltip: React__namespace.createElement("div", { style: { maxWidth: 300 } },
|
|
294
|
-
React__namespace.createElement("div", null, clinicalSignificance),
|
|
295
|
-
conflictingClinicalSignificance && (React__namespace.createElement("div", null, conflictingClinicalSignificance)),
|
|
296
|
-
React__namespace.createElement("div", null,
|
|
297
|
-
"(ClinVar ID:",
|
|
298
|
-
' ',
|
|
299
|
-
React__namespace.createElement("a", { href: clinvarLink, target: "_blank" }, clinvarId),
|
|
300
|
-
")")) }));
|
|
301
|
-
}
|
|
302
|
-
};
|
|
303
|
-
|
|
304
|
-
// oncogenic value => score
|
|
305
|
-
// (used for sorting purposes)
|
|
306
|
-
var ONCOGENIC_SCORE = {
|
|
307
|
-
Unknown: 0,
|
|
308
|
-
Inconclusive: 0,
|
|
309
|
-
'Likely Neutral': 0,
|
|
310
|
-
Resistance: 5,
|
|
311
|
-
'Likely Oncogenic': 5,
|
|
312
|
-
Oncogenic: 5,
|
|
313
|
-
};
|
|
314
|
-
// sensitivity level => score
|
|
315
|
-
// (used for sorting purposes)
|
|
316
|
-
var SENSITIVITY_LEVEL_SCORE = {
|
|
317
|
-
'4': 1,
|
|
318
|
-
'3B': 2,
|
|
319
|
-
'3A': 3,
|
|
320
|
-
'2': 5,
|
|
321
|
-
'1': 6,
|
|
322
|
-
};
|
|
323
|
-
// resistance level <-> score
|
|
324
|
-
// (used for sorting purposes)
|
|
325
|
-
var RESISTANCE_LEVEL_SCORE = {
|
|
326
|
-
R3: 1,
|
|
327
|
-
R2: 2,
|
|
328
|
-
R1: 3,
|
|
329
|
-
};
|
|
330
|
-
// diagnostic level <-> score
|
|
331
|
-
// (used for sorting purposes)
|
|
332
|
-
var DIAGNOSTIC_LEVEL_SCORE = {
|
|
333
|
-
Dx3: 1,
|
|
334
|
-
Dx2: 2,
|
|
335
|
-
Dx1: 3,
|
|
336
|
-
};
|
|
337
|
-
// prognostic level <-> score
|
|
338
|
-
// (used for sorting purposes)
|
|
339
|
-
var PROGNOSTIC_LEVEL_SCORE = {
|
|
340
|
-
Px3: 1,
|
|
341
|
-
Px2: 2,
|
|
342
|
-
Px1: 3,
|
|
343
|
-
};
|
|
344
|
-
function normalizeLevel(level) {
|
|
345
|
-
if (level) {
|
|
346
|
-
var matchArray = level.match(/LEVEL_(.*)/);
|
|
347
|
-
if (matchArray && matchArray.length >= 2) {
|
|
348
|
-
return matchArray[1];
|
|
349
|
-
}
|
|
350
|
-
else {
|
|
351
|
-
return level;
|
|
352
|
-
}
|
|
353
|
-
}
|
|
354
|
-
else {
|
|
355
|
-
return null;
|
|
356
|
-
}
|
|
357
|
-
}
|
|
358
|
-
function normalizeOncogenicity(oncogenicity) {
|
|
359
|
-
return (oncogenicity || 'unknown')
|
|
360
|
-
.trim()
|
|
361
|
-
.toLowerCase()
|
|
362
|
-
.replace(/\s/, '-');
|
|
363
|
-
}
|
|
364
|
-
function levelIconClassNames(level) {
|
|
365
|
-
if (level) {
|
|
366
|
-
return "oncokb icon level-" + level;
|
|
367
|
-
}
|
|
368
|
-
return '';
|
|
369
|
-
}
|
|
370
|
-
function oncogenicityIconClassNames(oncogenicity) {
|
|
371
|
-
return "oncokb icon " + normalizeOncogenicity(oncogenicity);
|
|
372
|
-
}
|
|
373
|
-
function annotationIconClassNames(type, highestLevel, indicator) {
|
|
374
|
-
return type === cbioportalUtils.OncoKbCardDataType.BIOLOGICAL
|
|
375
|
-
? oncogenicityIconClassNames((indicator === null || indicator === void 0 ? void 0 : indicator.oncogenic) || '')
|
|
376
|
-
: levelIconClassNames(normalizeLevel(highestLevel) || '');
|
|
377
|
-
}
|
|
378
|
-
function calcHighestIndicatorLevel(type, indicator) {
|
|
379
|
-
var highestLevel = '';
|
|
380
|
-
if (indicator) {
|
|
381
|
-
switch (type) {
|
|
382
|
-
case cbioportalUtils.OncoKbCardDataType.TXS:
|
|
383
|
-
highestLevel = indicator.highestSensitiveLevel;
|
|
384
|
-
break;
|
|
385
|
-
case cbioportalUtils.OncoKbCardDataType.TXR:
|
|
386
|
-
highestLevel = indicator.highestResistanceLevel;
|
|
387
|
-
break;
|
|
388
|
-
case cbioportalUtils.OncoKbCardDataType.DX:
|
|
389
|
-
highestLevel = indicator.highestDiagnosticImplicationLevel;
|
|
390
|
-
break;
|
|
391
|
-
case cbioportalUtils.OncoKbCardDataType.PX:
|
|
392
|
-
highestLevel = indicator.highestPrognosticImplicationLevel;
|
|
393
|
-
break;
|
|
394
|
-
}
|
|
395
|
-
}
|
|
396
|
-
return highestLevel;
|
|
397
|
-
}
|
|
398
|
-
function calcOncogenicScore(oncogenic) {
|
|
399
|
-
return ONCOGENIC_SCORE[oncogenic] || 0;
|
|
400
|
-
}
|
|
401
|
-
function calcSensitivityLevelScore(level) {
|
|
402
|
-
return SENSITIVITY_LEVEL_SCORE[normalizeLevel(level) || ''] || 0;
|
|
403
|
-
}
|
|
404
|
-
function calcResistanceLevelScore(level) {
|
|
405
|
-
return RESISTANCE_LEVEL_SCORE[normalizeLevel(level) || ''] || 0;
|
|
406
|
-
}
|
|
407
|
-
function calcDiagnosticLevelScore(level) {
|
|
408
|
-
return DIAGNOSTIC_LEVEL_SCORE[normalizeLevel(level) || ''] || 0;
|
|
409
|
-
}
|
|
410
|
-
function calcPrognosticLevelScore(level) {
|
|
411
|
-
return PROGNOSTIC_LEVEL_SCORE[normalizeLevel(level) || ''] || 0;
|
|
412
|
-
}
|
|
413
|
-
/**
|
|
414
|
-
* Return combined alterations name, separated by comma.
|
|
415
|
-
* Same location variant will be truncated into AALocationAllele e.g. V600E/K
|
|
416
|
-
*
|
|
417
|
-
* @param {Array} alterations - List of alterations
|
|
418
|
-
* @return {string} - Truncated alteration name
|
|
419
|
-
*/
|
|
420
|
-
function mergeAlterations(alterations) {
|
|
421
|
-
var positions = {};
|
|
422
|
-
var regular = [];
|
|
423
|
-
var regExp = new RegExp('^([A-Z])([0-9]+)([A-Z]$)');
|
|
424
|
-
if (___default["default"].isString(alterations)) {
|
|
425
|
-
return alterations;
|
|
426
|
-
}
|
|
427
|
-
___default["default"].each(alterations, function (alteration) {
|
|
428
|
-
var result = regExp.exec(alteration);
|
|
429
|
-
if (___default["default"].isArray(result) && result.length === 4) {
|
|
430
|
-
if (!positions.hasOwnProperty(result[2])) {
|
|
431
|
-
positions[result[2]] = {};
|
|
432
|
-
}
|
|
433
|
-
if (!positions[result[2]].hasOwnProperty(result[1])) {
|
|
434
|
-
// Avoid duplication, use object instead of array
|
|
435
|
-
positions[result[2]][result[1]] = {};
|
|
436
|
-
}
|
|
437
|
-
positions[result[2]][result[1]][result[3]] = 1;
|
|
438
|
-
}
|
|
439
|
-
else {
|
|
440
|
-
regular.push(alteration);
|
|
441
|
-
}
|
|
442
|
-
});
|
|
443
|
-
___default["default"].each(___default["default"].keys(positions)
|
|
444
|
-
.map(function (e) {
|
|
445
|
-
return Number(e);
|
|
446
|
-
})
|
|
447
|
-
.sort(), function (position) {
|
|
448
|
-
___default["default"].each(___default["default"].keys(positions[position]).sort(), function (aa) {
|
|
449
|
-
regular.push(aa +
|
|
450
|
-
position +
|
|
451
|
-
___default["default"].keys(positions[position][aa])
|
|
452
|
-
.sort()
|
|
453
|
-
.join('/'));
|
|
454
|
-
});
|
|
455
|
-
});
|
|
456
|
-
return regular.join(', ');
|
|
457
|
-
}
|
|
458
|
-
/**
|
|
459
|
-
* Return the positional variant of the missense mutation
|
|
460
|
-
* @param alteration The missense mutation
|
|
461
|
-
*/
|
|
462
|
-
function getPositionalVariant(alteration) {
|
|
463
|
-
var regExp = new RegExp('^([A-Z]+)([0-9]+)([A-Z]*)$');
|
|
464
|
-
var result = regExp.exec(alteration);
|
|
465
|
-
// Only if the alteration is missense mutation or positional variant
|
|
466
|
-
// result[0]: matched alteration
|
|
467
|
-
// result[1]: reference alleles (there could be multiple reference alleles, we only return the first allele)
|
|
468
|
-
// result[2]: position(protein start/end)
|
|
469
|
-
// result[3]: variant alleles (empty if the alteration is positional variant already)
|
|
470
|
-
if (___default["default"].isArray(result) &&
|
|
471
|
-
result.length === 4 &&
|
|
472
|
-
(!result[3] || result[1].length === result[3].length)) {
|
|
473
|
-
return "" + result[1][0] + result[2];
|
|
474
|
-
}
|
|
475
|
-
return undefined;
|
|
476
|
-
}
|
|
477
|
-
function getTumorTypeName(tumorType) {
|
|
478
|
-
if (!tumorType) {
|
|
479
|
-
return '';
|
|
480
|
-
}
|
|
481
|
-
else if (tumorType.name) {
|
|
482
|
-
return tumorType.name;
|
|
483
|
-
}
|
|
484
|
-
else if (tumorType.mainType) {
|
|
485
|
-
return tumorType.mainType.name;
|
|
486
|
-
}
|
|
487
|
-
else {
|
|
488
|
-
return '';
|
|
489
|
-
}
|
|
490
|
-
}
|
|
491
|
-
function getTumorTypeNameWithExclusionInfo(tumorType, excludedTumorTypes) {
|
|
492
|
-
var name = getTumorTypeName(tumorType);
|
|
493
|
-
if (!___default["default"].isEmpty(excludedTumorTypes)) {
|
|
494
|
-
name = name + " (excluding " + excludedTumorTypes
|
|
495
|
-
.map(function (ett) { return getTumorTypeName(ett); })
|
|
496
|
-
.join(', ') + ")";
|
|
497
|
-
}
|
|
498
|
-
return name;
|
|
499
|
-
}
|
|
500
|
-
function groupOncoKbIndicatorDataByMutations(mutationsByPosition, oncoKbData, getTumorType, getEntrezGeneId, filter) {
|
|
501
|
-
var indicatorMap = {};
|
|
502
|
-
___default["default"].keys(mutationsByPosition).forEach(function (key) {
|
|
503
|
-
var position = Number(key);
|
|
504
|
-
var indicators = mutationsByPosition[position]
|
|
505
|
-
.map(function (mutation) {
|
|
506
|
-
return getIndicatorData(mutation, oncoKbData, getTumorType, getEntrezGeneId);
|
|
507
|
-
})
|
|
508
|
-
.filter(function (indicator) {
|
|
509
|
-
return indicator !== undefined && (!filter || filter(indicator));
|
|
510
|
-
});
|
|
511
|
-
if (position > 0 && indicators.length > 0) {
|
|
512
|
-
indicatorMap[position] = indicators;
|
|
513
|
-
}
|
|
514
|
-
});
|
|
515
|
-
return indicatorMap;
|
|
516
|
-
}
|
|
517
|
-
function getIndicatorData(mutation, oncoKbData, getTumorType, getEntrezGeneId) {
|
|
518
|
-
if (oncoKbData.indicatorMap === null) {
|
|
519
|
-
return undefined;
|
|
520
|
-
}
|
|
521
|
-
var id = '';
|
|
522
|
-
// @ts-ignore
|
|
523
|
-
var sv = mutation.structuralVariant;
|
|
524
|
-
if (sv) {
|
|
525
|
-
var structuralVariantType = cbioportalUtils.deriveStructuralVariantType(sv);
|
|
526
|
-
id = cbioportalUtils.generateQueryStructuralVariantId(sv.site1EntrezGeneId, sv.site2EntrezGeneId, getTumorType(mutation), structuralVariantType);
|
|
527
|
-
}
|
|
528
|
-
else {
|
|
529
|
-
id = cbioportalUtils.generateQueryVariantId(getEntrezGeneId(mutation), getTumorType(mutation), mutation.proteinChange, mutation.mutationType);
|
|
530
|
-
}
|
|
531
|
-
return oncoKbData.indicatorMap[id];
|
|
532
|
-
}
|
|
533
|
-
function defaultOncoKbIndicatorFilter(indicator) {
|
|
534
|
-
return indicator.oncogenic
|
|
535
|
-
.toLowerCase()
|
|
536
|
-
.trim()
|
|
537
|
-
.includes('oncogenic');
|
|
538
|
-
}
|
|
539
|
-
function defaultOncoKbFilter(mutation, oncoKbData, getTumorType, getEntrezGeneId) {
|
|
540
|
-
var filter = true;
|
|
541
|
-
if (oncoKbData && getTumorType && getEntrezGeneId) {
|
|
542
|
-
var indicatorData = getIndicatorData(mutation, oncoKbData, getTumorType, getEntrezGeneId);
|
|
543
|
-
filter = indicatorData
|
|
544
|
-
? defaultOncoKbIndicatorFilter(indicatorData)
|
|
545
|
-
: false;
|
|
546
|
-
}
|
|
547
|
-
return filter;
|
|
548
|
-
}
|
|
549
|
-
|
|
550
|
-
var img$2 = "data:image/png;base64,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";
|
|
551
|
-
|
|
552
|
-
var mcgStyles = {"link-list":"myCancerGenome-module_link-list__2wFhH"};
|
|
553
|
-
|
|
554
|
-
function placeArrow$1(tooltipEl) {
|
|
555
|
-
var arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
|
|
556
|
-
arrowEl.style.left = '10px';
|
|
557
|
-
}
|
|
558
|
-
function sortValue$7(links) {
|
|
559
|
-
return links.length > 0 ? 1 : 0;
|
|
560
|
-
}
|
|
561
|
-
function download$6(links) {
|
|
562
|
-
return links.length > 0 ? 'present' : 'not present';
|
|
563
|
-
}
|
|
564
|
-
function myCancerGenomeLinks(linksHTML) {
|
|
565
|
-
var links = [];
|
|
566
|
-
___default["default"].each(linksHTML, function (link, index) {
|
|
567
|
-
// TODO this is a workaround, ideally we should fix the data itself
|
|
568
|
-
// parse the data as an HTML dom element, since it is formatted as an HTML link.
|
|
569
|
-
var myCancerGenomeLink = cbioportalUtils.parseMyCancerGenomeLink(link);
|
|
570
|
-
if (myCancerGenomeLink) {
|
|
571
|
-
links.push(React__namespace.createElement("li", { key: index },
|
|
572
|
-
React__namespace.createElement("a", { href: myCancerGenomeLink.url, target: "_blank" }, myCancerGenomeLink.text)));
|
|
573
|
-
}
|
|
574
|
-
});
|
|
575
|
-
return (React__namespace.createElement("span", null,
|
|
576
|
-
React__namespace.createElement("b", null, "My Cancer Genome links:"),
|
|
577
|
-
React__namespace.createElement("br", null),
|
|
578
|
-
React__namespace.createElement("ul", { className: mcgStyles['link-list'] }, links)));
|
|
579
|
-
}
|
|
580
|
-
var MyCancerGenome = /** @class */ (function (_super) {
|
|
581
|
-
tslib.__extends(MyCancerGenome, _super);
|
|
582
|
-
function MyCancerGenome() {
|
|
583
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
584
|
-
}
|
|
585
|
-
Object.defineProperty(MyCancerGenome.prototype, "render", {
|
|
586
|
-
enumerable: false,
|
|
587
|
-
configurable: true,
|
|
588
|
-
writable: true,
|
|
589
|
-
value: function () {
|
|
590
|
-
var myCancerGenomeContent = (React__namespace.createElement("span", { className: "" + annotationStyles['annotation-item'] }));
|
|
591
|
-
if (this.props.linksHTML.length > 0) {
|
|
592
|
-
var arrowContent = React__namespace.createElement("div", { className: "rc-tooltip-arrow-inner" });
|
|
593
|
-
var tooltipContent = myCancerGenomeLinks(this.props.linksHTML);
|
|
594
|
-
myCancerGenomeContent = (React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlay: tooltipContent, placement: "topLeft", trigger: ['hover', 'focus'], arrowContent: arrowContent, onPopupAlign: placeArrow$1 },
|
|
595
|
-
React__namespace.createElement("span", { className: annotationStyles['annotation-item'] + " mcg" },
|
|
596
|
-
React__namespace.createElement("img", { width: "14", height: "14", src: img$2, alt: "My Cancer Genome Symbol" }))));
|
|
597
|
-
}
|
|
598
|
-
return myCancerGenomeContent;
|
|
599
|
-
}
|
|
600
|
-
});
|
|
601
|
-
return MyCancerGenome;
|
|
602
|
-
}(React__namespace.Component));
|
|
603
|
-
|
|
604
|
-
function hideArrow(tooltipEl) {
|
|
605
|
-
var arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
|
|
606
|
-
arrowEl.style.display = 'none';
|
|
607
|
-
}
|
|
608
|
-
var AnnotationIcon = function (props) {
|
|
609
|
-
if (props.availableDataTypes !== undefined &&
|
|
610
|
-
!props.availableDataTypes.includes(props.type)) {
|
|
611
|
-
return null;
|
|
612
|
-
}
|
|
613
|
-
var highestLevel = calcHighestIndicatorLevel(props.type, props.indicator);
|
|
614
|
-
return (React__default["default"].createElement(AnnotationIconWithTooltip, { tooltipOverlay: props.tooltipOverlay, icon: React__default["default"].createElement("i", { className: annotationIconClassNames(props.type, highestLevel, props.indicator), "data-test": "oncogenic-icon-image" }) }));
|
|
615
|
-
};
|
|
616
|
-
var AnnotationIconWithTooltip = function (props) {
|
|
617
|
-
if (props.icon) {
|
|
618
|
-
return (React__default["default"].createElement(cbioportalFrontendCommons.DefaultTooltip, { overlayClassName: "oncokb-tooltip", overlay: function () {
|
|
619
|
-
return props.tooltipOverlay ? props.tooltipOverlay : null;
|
|
620
|
-
}, placement: "right", trigger: ['hover', 'focus'], onPopupAlign: hideArrow, destroyTooltipOnHide: true },
|
|
621
|
-
React__default["default"].createElement("span", { className: "" + annotationStyles['annotation-item'] }, props.icon)));
|
|
622
|
-
}
|
|
623
|
-
else {
|
|
624
|
-
return null;
|
|
625
|
-
}
|
|
626
|
-
};
|
|
627
|
-
|
|
628
|
-
var BIOLOGICAL_COLOR_MAP = {
|
|
629
|
-
oncogenic: '#0968C3',
|
|
630
|
-
'likely-oncogenic': '#0968C3',
|
|
631
|
-
resistance: '#0968C3',
|
|
632
|
-
neutral: '#696969',
|
|
633
|
-
'likely-neutral': '#696969',
|
|
634
|
-
inconclusive: '#AAAAAA',
|
|
635
|
-
vus: '#696969',
|
|
636
|
-
unknown: '#CCCCCC',
|
|
637
|
-
};
|
|
638
|
-
var LEVEL_COLOR_MAP = {
|
|
639
|
-
'1': '#33A02C',
|
|
640
|
-
'2': '#1F78B4',
|
|
641
|
-
'3': '#984EA3',
|
|
642
|
-
'3A': '#984EA3',
|
|
643
|
-
'3B': '#BE98CE',
|
|
644
|
-
'4': '#424242',
|
|
645
|
-
R1: '#EE3424',
|
|
646
|
-
R2: '#F79A92',
|
|
647
|
-
R3: '#FCD6D3',
|
|
648
|
-
Dx1: '#33A02C',
|
|
649
|
-
Dx2: '#1F78B4',
|
|
650
|
-
Dx3: '#984EA3',
|
|
651
|
-
Px1: '#33A02C',
|
|
652
|
-
Px2: '#1F78B4',
|
|
653
|
-
Px3: '#984EA3',
|
|
654
|
-
};
|
|
655
|
-
function getLevelColor(highestLevel, defaultColor) {
|
|
656
|
-
if (defaultColor === void 0) { defaultColor = '#CCCCCC'; }
|
|
657
|
-
var level = normalizeLevel(highestLevel || null) || '';
|
|
658
|
-
return LEVEL_COLOR_MAP[level] || defaultColor;
|
|
659
|
-
}
|
|
660
|
-
function shouldDrawShape(type, level, availableDataTypes) {
|
|
661
|
-
return (level &&
|
|
662
|
-
availableDataTypes !== undefined &&
|
|
663
|
-
availableDataTypes.includes(type));
|
|
664
|
-
}
|
|
665
|
-
function getOncogenicShape(indicator) {
|
|
666
|
-
var oncogenicity = normalizeOncogenicity((indicator === null || indicator === void 0 ? void 0 : indicator.oncogenic) || '');
|
|
667
|
-
var color = BIOLOGICAL_COLOR_MAP[oncogenicity] || '#CCCCCC';
|
|
668
|
-
return (React__default["default"].createElement("g", { transform: "translate(9, 9)" },
|
|
669
|
-
React__default["default"].createElement("circle", { r: "6", fill: "none", strokeWidth: "2", stroke: color }),
|
|
670
|
-
oncogenicity !== 'vus' && oncogenicity !== 'unknown' && (React__default["default"].createElement("g", null,
|
|
671
|
-
React__default["default"].createElement("circle", { r: "3", fill: "none", strokeWidth: "2", stroke: color }),
|
|
672
|
-
React__default["default"].createElement("circle", { r: "1.5", fill: color, stroke: "none" })))));
|
|
673
|
-
}
|
|
674
|
-
function getTherapeuticSensitivityShape(indicator, availableDataTypes) {
|
|
675
|
-
var highestLevel = indicator === null || indicator === void 0 ? void 0 : indicator.highestSensitiveLevel;
|
|
676
|
-
if (!shouldDrawShape(cbioportalUtils.OncoKbCardDataType.TXS, highestLevel, availableDataTypes)) {
|
|
677
|
-
return null;
|
|
678
|
-
}
|
|
679
|
-
var fillColor = getLevelColor(highestLevel, '#33A02C');
|
|
680
|
-
return (React__default["default"].createElement("g", { transform: "translate(14.5, 3.5)" },
|
|
681
|
-
React__default["default"].createElement("circle", { r: "4", fill: fillColor, stroke: "#ffffff", strokeWidth: "1" })));
|
|
682
|
-
}
|
|
683
|
-
function getTherapeuticResistanceShape(indicator, availableDataTypes) {
|
|
684
|
-
var highestLevel = indicator === null || indicator === void 0 ? void 0 : indicator.highestResistanceLevel;
|
|
685
|
-
if (!shouldDrawShape(cbioportalUtils.OncoKbCardDataType.TXR, highestLevel, availableDataTypes)) {
|
|
686
|
-
return null;
|
|
687
|
-
}
|
|
688
|
-
var fillColor = getLevelColor(highestLevel, '#EE3424');
|
|
689
|
-
return (React__default["default"].createElement("g", { transform: "translate(14.5, 14.5)" },
|
|
690
|
-
React__default["default"].createElement("circle", { r: "4", fill: fillColor, stroke: "#ffffff", strokeWidth: "1" })));
|
|
691
|
-
}
|
|
692
|
-
function getDiagnosticShape(indicator, availableDataTypes) {
|
|
693
|
-
var highestLevel = indicator === null || indicator === void 0 ? void 0 : indicator.highestDiagnosticImplicationLevel;
|
|
694
|
-
if (!shouldDrawShape(cbioportalUtils.OncoKbCardDataType.DX, highestLevel, availableDataTypes)) {
|
|
695
|
-
return null;
|
|
696
|
-
}
|
|
697
|
-
var fillColor = getLevelColor(highestLevel, '#33A02C');
|
|
698
|
-
return (React__default["default"].createElement("g", { transform: "translate(-0.5, -0.5)" },
|
|
699
|
-
React__default["default"].createElement("rect", { width: "7", height: "7", fill: fillColor, stroke: "#ffffff", strokeWidth: "1" })));
|
|
700
|
-
}
|
|
701
|
-
function getPrognosticShape(indicator, availableDataTypes) {
|
|
702
|
-
var highestLevel = indicator === null || indicator === void 0 ? void 0 : indicator.highestPrognosticImplicationLevel;
|
|
703
|
-
if (!shouldDrawShape(cbioportalUtils.OncoKbCardDataType.PX, highestLevel, availableDataTypes)) {
|
|
704
|
-
return null;
|
|
705
|
-
}
|
|
706
|
-
var fillColor = getLevelColor(highestLevel, '#33A02C');
|
|
707
|
-
return (React__default["default"].createElement("g", { transform: "translate(0, 10.5)" },
|
|
708
|
-
React__default["default"].createElement("polygon", { points: "3.5 0, 8 8, -1 8", fill: fillColor, stroke: "#ffffff", strokeWidth: "1" })));
|
|
709
|
-
}
|
|
710
|
-
var CompactAnnotationIcon = function (props) {
|
|
711
|
-
var indicatorForLevelIcons = props.usingPublicOncoKbInstance
|
|
712
|
-
? undefined
|
|
713
|
-
: props.indicator;
|
|
714
|
-
return (React__default["default"].createElement("svg", { version: "1.1", width: "18", height: "18", "data-test": "oncogenic-icon-image" },
|
|
715
|
-
getOncogenicShape(props.indicator),
|
|
716
|
-
getTherapeuticSensitivityShape(indicatorForLevelIcons, props.availableDataTypes),
|
|
717
|
-
getTherapeuticResistanceShape(indicatorForLevelIcons, props.availableDataTypes),
|
|
718
|
-
getDiagnosticShape(indicatorForLevelIcons, props.availableDataTypes),
|
|
719
|
-
getPrognosticShape(indicatorForLevelIcons, props.availableDataTypes)));
|
|
720
|
-
};
|
|
721
|
-
|
|
722
|
-
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"};
|
|
723
|
-
|
|
724
|
-
var _a$4;
|
|
725
|
-
exports.OtherBiomarkersQueryType = void 0;
|
|
726
|
-
(function (OtherBiomarkersQueryType) {
|
|
727
|
-
OtherBiomarkersQueryType["MSIH"] = "MSIH";
|
|
728
|
-
OtherBiomarkersQueryType["TMBH"] = "TMBI";
|
|
729
|
-
})(exports.OtherBiomarkersQueryType || (exports.OtherBiomarkersQueryType = {}));
|
|
730
|
-
var OTHER_BIOMARKER_HUGO_SYMBOL = 'Other Biomarkers';
|
|
731
|
-
var MSI_H_NAME = 'MSI-H';
|
|
732
|
-
var TMB_H_NAME = 'TMB-H';
|
|
733
|
-
var OTHER_BIOMARKER_NAME = (_a$4 = {},
|
|
734
|
-
_a$4[exports.OtherBiomarkersQueryType.MSIH] = MSI_H_NAME,
|
|
735
|
-
_a$4[exports.OtherBiomarkersQueryType.TMBH] = TMB_H_NAME,
|
|
736
|
-
_a$4);
|
|
737
|
-
|
|
738
|
-
var OncoKbCardTitle = function (props) {
|
|
739
|
-
var titleContent = [];
|
|
740
|
-
if (props.hugoSymbol &&
|
|
741
|
-
props.hugoSymbol !== OTHER_BIOMARKER_HUGO_SYMBOL &&
|
|
742
|
-
(!props.variant || !props.variant.includes(props.hugoSymbol))) {
|
|
743
|
-
titleContent.push(props.hugoSymbol);
|
|
744
|
-
}
|
|
745
|
-
if (props.variant) {
|
|
746
|
-
titleContent.push(props.variant);
|
|
747
|
-
}
|
|
748
|
-
if (props.tumorType) {
|
|
749
|
-
if (titleContent.length > 0) {
|
|
750
|
-
titleContent.push('in');
|
|
751
|
-
}
|
|
752
|
-
titleContent.push(props.tumorType);
|
|
753
|
-
}
|
|
754
|
-
return (React__namespace.createElement("div", { className: mainStyles['title'], "data-test": "oncokb-card-title" }, React__namespace.createElement("span", null, titleContent.join(' '))));
|
|
755
|
-
};
|
|
756
|
-
|
|
757
|
-
var levelStyles = {"levels":"level-module_levels__2ZL1B","levels-li":"level-module_levels-li__1tgCC"};
|
|
758
|
-
|
|
759
|
-
var collapsibleStyles = {"collapsible-header":"collapsible-module_collapsible-header__3nZtU","levels-collapse":"collapsible-module_levels-collapse__2GBRW"};
|
|
760
|
-
|
|
761
|
-
var OncoKbCardLevelsOfEvidenceDropdown = /** @class */ (function (_super) {
|
|
762
|
-
tslib.__extends(OncoKbCardLevelsOfEvidenceDropdown, _super);
|
|
763
|
-
function OncoKbCardLevelsOfEvidenceDropdown(props) {
|
|
764
|
-
var _this = _super.call(this, props) || this;
|
|
765
|
-
Object.defineProperty(_this, "levelsCollapsed", {
|
|
766
|
-
enumerable: true,
|
|
767
|
-
configurable: true,
|
|
768
|
-
writable: true,
|
|
769
|
-
value: true
|
|
770
|
-
});
|
|
771
|
-
mobx.makeObservable(_this);
|
|
772
|
-
return _this;
|
|
773
|
-
}
|
|
774
|
-
Object.defineProperty(OncoKbCardLevelsOfEvidenceDropdown.prototype, "levelListItem", {
|
|
775
|
-
enumerable: false,
|
|
776
|
-
configurable: true,
|
|
777
|
-
writable: true,
|
|
778
|
-
value: function (level, levelDes) {
|
|
779
|
-
return (React__default["default"].createElement("li", { key: level, className: levelStyles['levels-li'] },
|
|
780
|
-
React__default["default"].createElement("i", { className: levelIconClassNames(level) }),
|
|
781
|
-
levelDes));
|
|
782
|
-
}
|
|
783
|
-
});
|
|
784
|
-
Object.defineProperty(OncoKbCardLevelsOfEvidenceDropdown.prototype, "generateLevelRows", {
|
|
785
|
-
enumerable: false,
|
|
786
|
-
configurable: true,
|
|
787
|
-
writable: true,
|
|
788
|
-
value: function () {
|
|
789
|
-
var _this = this;
|
|
790
|
-
var rows = [];
|
|
791
|
-
this.props.levels.forEach(function (level) {
|
|
792
|
-
rows.push(_this.levelListItem(level, _this.props.levelDes[level]));
|
|
793
|
-
});
|
|
794
|
-
return rows;
|
|
795
|
-
}
|
|
796
|
-
});
|
|
797
|
-
Object.defineProperty(OncoKbCardLevelsOfEvidenceDropdown.prototype, "handleLevelCollapse", {
|
|
798
|
-
enumerable: false,
|
|
799
|
-
configurable: true,
|
|
800
|
-
writable: true,
|
|
801
|
-
value: function () {
|
|
802
|
-
this.levelsCollapsed = !this.levelsCollapsed;
|
|
803
|
-
}
|
|
804
|
-
});
|
|
805
|
-
Object.defineProperty(OncoKbCardLevelsOfEvidenceDropdown.prototype, "render", {
|
|
806
|
-
enumerable: false,
|
|
807
|
-
configurable: true,
|
|
808
|
-
writable: true,
|
|
809
|
-
value: function () {
|
|
810
|
-
return (React__default["default"].createElement("div", null,
|
|
811
|
-
React__default["default"].createElement("div", { "data-test": "oncokb-card-levels-of-evidence-dropdown-header", className: collapsibleStyles['collapsible-header'], onClick: this.handleLevelCollapse },
|
|
812
|
-
"Levels of Evidence",
|
|
813
|
-
React__default["default"].createElement("span", { style: { float: 'right' } }, this.levelsCollapsed ? (React__default["default"].createElement("i", { className: classnames__default["default"]('fa fa-chevron-down', mainStyles['blue-icon']) })) : (React__default["default"].createElement("i", { className: classnames__default["default"]('fa fa-chevron-up', mainStyles['blue-icon']) })))),
|
|
814
|
-
React__default["default"].createElement(reactCollapse.Collapse, { isOpened: !this.levelsCollapsed },
|
|
815
|
-
React__default["default"].createElement("div", { className: classnames__default["default"](levelStyles.levels, collapsibleStyles['levels-collapse']) },
|
|
816
|
-
React__default["default"].createElement("ul", { style: {
|
|
817
|
-
lineHeight: 8,
|
|
818
|
-
padding: 0,
|
|
819
|
-
} }, this.generateLevelRows())))));
|
|
820
|
-
}
|
|
821
|
-
});
|
|
822
|
-
tslib.__decorate([
|
|
823
|
-
mobx.observable
|
|
824
|
-
], OncoKbCardLevelsOfEvidenceDropdown.prototype, "levelsCollapsed", void 0);
|
|
825
|
-
tslib.__decorate([
|
|
826
|
-
mobx.action.bound
|
|
827
|
-
], OncoKbCardLevelsOfEvidenceDropdown.prototype, "handleLevelCollapse", null);
|
|
828
|
-
OncoKbCardLevelsOfEvidenceDropdown = tslib.__decorate([
|
|
829
|
-
mobxReact.observer
|
|
830
|
-
], OncoKbCardLevelsOfEvidenceDropdown);
|
|
831
|
-
return OncoKbCardLevelsOfEvidenceDropdown;
|
|
832
|
-
}(React__default["default"].Component));
|
|
833
|
-
|
|
834
|
-
var OncoKBSuggestAnnotationLinkout = /** @class */ (function (_super) {
|
|
835
|
-
tslib.__extends(OncoKBSuggestAnnotationLinkout, _super);
|
|
836
|
-
function OncoKBSuggestAnnotationLinkout() {
|
|
837
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
838
|
-
}
|
|
839
|
-
Object.defineProperty(OncoKBSuggestAnnotationLinkout.prototype, "render", {
|
|
840
|
-
enumerable: false,
|
|
841
|
-
configurable: true,
|
|
842
|
-
writable: true,
|
|
843
|
-
value: function () {
|
|
844
|
-
return (React__namespace.createElement("div", null,
|
|
845
|
-
React__namespace.createElement("span", null, "The gene is listed under "),
|
|
846
|
-
React__namespace.createElement("a", { href: "https://www.oncokb.org/cancerGenes", target: "_blank" }, "OncoKB Cancer Gene List"),
|
|
847
|
-
React__namespace.createElement("span", null, " but hasn't been curated yet. Please feel free to "),
|
|
848
|
-
React__namespace.createElement("a", { target: "_blank", href: "mailto:contact@oncokb.org?subject=Annotation suggestion for " + this.props.gene + "&&body=Thank you for using OncoKB\u2122.%0APlease provide the following information for " + this.props.gene + " curation:%0A%0AEvidence:%0APMIDs:%0AAbstracts:", title: "suggest to annotate this gene" }, "suggest the team annotate the gene"),
|
|
849
|
-
"."));
|
|
850
|
-
}
|
|
851
|
-
});
|
|
852
|
-
return OncoKBSuggestAnnotationLinkout;
|
|
853
|
-
}(React__namespace.Component));
|
|
854
|
-
|
|
855
|
-
var levelTooltipContent = function (level) {
|
|
856
|
-
return (React__namespace.createElement("div", { style: { maxWidth: '200px' } }, OncoKbHelper.LEVEL_DESC[level]));
|
|
857
|
-
};
|
|
858
|
-
var LevelIcon = function (props) {
|
|
859
|
-
return (React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlay: levelTooltipContent(props.level), placement: "left", disabled: !props.showDescription, trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
|
|
860
|
-
React__namespace.createElement("i", { className: levelIconClassNames(props.level) })));
|
|
861
|
-
};
|
|
862
|
-
|
|
863
|
-
var OncoKbHelper = /** @class */ (function () {
|
|
864
|
-
function OncoKbHelper() {
|
|
865
|
-
}
|
|
866
|
-
Object.defineProperty(OncoKbHelper, "TX_LEVELS", {
|
|
867
|
-
get: function () {
|
|
868
|
-
return ['1', '2', '3A', '3B', '4', 'R1', 'R2'];
|
|
869
|
-
},
|
|
870
|
-
enumerable: false,
|
|
871
|
-
configurable: true
|
|
872
|
-
});
|
|
873
|
-
Object.defineProperty(OncoKbHelper, "DX_LEVELS", {
|
|
874
|
-
get: function () {
|
|
875
|
-
return ['Dx1', 'Dx2', 'Dx3'];
|
|
876
|
-
},
|
|
877
|
-
enumerable: false,
|
|
878
|
-
configurable: true
|
|
879
|
-
});
|
|
880
|
-
Object.defineProperty(OncoKbHelper, "PX_LEVELS", {
|
|
881
|
-
get: function () {
|
|
882
|
-
return ['Px1', 'Px2', 'Px3'];
|
|
883
|
-
},
|
|
884
|
-
enumerable: false,
|
|
885
|
-
configurable: true
|
|
886
|
-
});
|
|
887
|
-
Object.defineProperty(OncoKbHelper, "LEVELS", {
|
|
888
|
-
get: function () {
|
|
889
|
-
return tslib.__spreadArrays(this.TX_LEVELS, this.DX_LEVELS, this.PX_LEVELS);
|
|
890
|
-
},
|
|
891
|
-
enumerable: false,
|
|
892
|
-
configurable: true
|
|
893
|
-
});
|
|
894
|
-
Object.defineProperty(OncoKbHelper, "getLevelsDesc", {
|
|
895
|
-
enumerable: false,
|
|
896
|
-
configurable: true,
|
|
897
|
-
writable: true,
|
|
898
|
-
value: function (dataType) {
|
|
899
|
-
switch (dataType) {
|
|
900
|
-
case cbioportalUtils.OncoKbCardDataType.TXS:
|
|
901
|
-
case cbioportalUtils.OncoKbCardDataType.TXR:
|
|
902
|
-
return ___default["default"].pick(this.LEVEL_DESC, this.TX_LEVELS);
|
|
903
|
-
case cbioportalUtils.OncoKbCardDataType.DX:
|
|
904
|
-
return ___default["default"].pick(this.LEVEL_DESC, this.DX_LEVELS);
|
|
905
|
-
case cbioportalUtils.OncoKbCardDataType.PX:
|
|
906
|
-
return ___default["default"].pick(this.LEVEL_DESC, this.PX_LEVELS);
|
|
907
|
-
default:
|
|
908
|
-
return {};
|
|
909
|
-
}
|
|
910
|
-
}
|
|
911
|
-
});
|
|
912
|
-
Object.defineProperty(OncoKbHelper, "LEVEL_DESC", {
|
|
913
|
-
get: function () {
|
|
914
|
-
return {
|
|
915
|
-
'1': (React__namespace.createElement("span", null,
|
|
916
|
-
React__namespace.createElement("b", null, "FDA-recognized"),
|
|
917
|
-
" biomarker predictive of response to an",
|
|
918
|
-
' ',
|
|
919
|
-
React__namespace.createElement("b", null, "FDA-approved drug"),
|
|
920
|
-
" in this indication")),
|
|
921
|
-
'2': (React__namespace.createElement("span", null,
|
|
922
|
-
React__namespace.createElement("b", null, "Standard care"),
|
|
923
|
-
" biomarker recommended by the NCCN or other expert panels predictive of response to an",
|
|
924
|
-
' ',
|
|
925
|
-
React__namespace.createElement("b", null, "FDA-approved drug"),
|
|
926
|
-
" in this indication")),
|
|
927
|
-
'3A': (React__namespace.createElement("span", null,
|
|
928
|
-
React__namespace.createElement("b", null, "Compelling clinical evidence"),
|
|
929
|
-
" supports the biomarker as being predictive of response to a drug in this indication")),
|
|
930
|
-
'3B': (React__namespace.createElement("span", null,
|
|
931
|
-
React__namespace.createElement("b", null, "Standard care"),
|
|
932
|
-
" or ",
|
|
933
|
-
React__namespace.createElement("b", null, "investigational"),
|
|
934
|
-
" biomarker",
|
|
935
|
-
' ',
|
|
936
|
-
"predictive of response to an ",
|
|
937
|
-
React__namespace.createElement("b", null, "FDA-approved"),
|
|
938
|
-
" or",
|
|
939
|
-
' ',
|
|
940
|
-
React__namespace.createElement("b", null, "investigational"),
|
|
941
|
-
" drug in another indication")),
|
|
942
|
-
'4': (React__namespace.createElement("span", null,
|
|
943
|
-
React__namespace.createElement("b", null, "Compelling biological evidence"),
|
|
944
|
-
" supports the biomarker as being predictive of response to a drug")),
|
|
945
|
-
R1: (React__namespace.createElement("span", null,
|
|
946
|
-
React__namespace.createElement("b", null, "Standard care"),
|
|
947
|
-
" biomarker predictive of",
|
|
948
|
-
' ',
|
|
949
|
-
React__namespace.createElement("b", null, "resistance"),
|
|
950
|
-
" to an ",
|
|
951
|
-
React__namespace.createElement("b", null, "FDA-approved"),
|
|
952
|
-
" drug",
|
|
953
|
-
' ',
|
|
954
|
-
React__namespace.createElement("b", null, "in this indication"))),
|
|
955
|
-
R2: (React__namespace.createElement("span", null,
|
|
956
|
-
React__namespace.createElement("b", null, "Compelling clinical evidence"),
|
|
957
|
-
" supports the biomarker as being predictive of ",
|
|
958
|
-
React__namespace.createElement("b", null, "resistance"),
|
|
959
|
-
" to a drug")),
|
|
960
|
-
Dx1: (React__namespace.createElement("span", null,
|
|
961
|
-
React__namespace.createElement("b", null, "FDA and/or professional guideline-recognized"),
|
|
962
|
-
' ',
|
|
963
|
-
"biomarker required for diagnosis in this indication")),
|
|
964
|
-
Dx2: (React__namespace.createElement("span", null,
|
|
965
|
-
React__namespace.createElement("b", null, "FDA and/or professional guideline-recognized"),
|
|
966
|
-
' ',
|
|
967
|
-
"biomarker that supports diagnosis in this indication")),
|
|
968
|
-
Dx3: (React__namespace.createElement("span", null,
|
|
969
|
-
"Biomarker that ",
|
|
970
|
-
React__namespace.createElement("b", null, "may assist disease diagnosis"),
|
|
971
|
-
" in this indication based on ",
|
|
972
|
-
React__namespace.createElement("b", null, "clinical evidence"))),
|
|
973
|
-
Px1: (React__namespace.createElement("span", null,
|
|
974
|
-
React__namespace.createElement("b", null, "FDA and/or professional guideline-recognized"),
|
|
975
|
-
' ',
|
|
976
|
-
"biomarker prognostic in this indication based on",
|
|
977
|
-
' ',
|
|
978
|
-
React__namespace.createElement("b", null, "well-powered studie(s)"))),
|
|
979
|
-
Px2: (React__namespace.createElement("span", null,
|
|
980
|
-
React__namespace.createElement("b", null, "FDA and/or professional guideline-recognized"),
|
|
981
|
-
' ',
|
|
982
|
-
"biomarker prognostic in this indication based on",
|
|
983
|
-
' ',
|
|
984
|
-
React__namespace.createElement("b", null, "a single or multiple small studies"))),
|
|
985
|
-
Px3: (React__namespace.createElement("span", null,
|
|
986
|
-
"Biomarker is prognostic in this indication based on",
|
|
987
|
-
' ',
|
|
988
|
-
React__namespace.createElement("b", null, "clinical evidence"),
|
|
989
|
-
" in ",
|
|
990
|
-
React__namespace.createElement("b", null, "well-powered studies"))),
|
|
991
|
-
};
|
|
992
|
-
},
|
|
993
|
-
enumerable: false,
|
|
994
|
-
configurable: true
|
|
995
|
-
});
|
|
996
|
-
Object.defineProperty(OncoKbHelper, "getDefaultColumnDefinition", {
|
|
997
|
-
enumerable: false,
|
|
998
|
-
configurable: true,
|
|
999
|
-
writable: true,
|
|
1000
|
-
value: function (columnKey) {
|
|
1001
|
-
switch (columnKey) {
|
|
1002
|
-
case 'level':
|
|
1003
|
-
return {
|
|
1004
|
-
id: 'level',
|
|
1005
|
-
Header: React__namespace.createElement("div", { style: { textAlign: 'center' } }, "Level"),
|
|
1006
|
-
accessor: 'level',
|
|
1007
|
-
maxWidth: 45,
|
|
1008
|
-
sortMethod: function (a, b) {
|
|
1009
|
-
return cbioportalUtils.defaultSortMethod(cbioportalUtils.LEVELS.all.indexOf(normalizeLevel(a) || ''), cbioportalUtils.LEVELS.all.indexOf(normalizeLevel(b) || ''));
|
|
1010
|
-
},
|
|
1011
|
-
Cell: function (props) {
|
|
1012
|
-
var normalizedLevel = normalizeLevel(props.value) || '';
|
|
1013
|
-
return (React__namespace.createElement(LevelIcon, { level: normalizedLevel, showDescription: true }));
|
|
1014
|
-
},
|
|
1015
|
-
};
|
|
1016
|
-
case 'alterations':
|
|
1017
|
-
return {
|
|
1018
|
-
id: 'alterations',
|
|
1019
|
-
Header: React__namespace.createElement("span", null, "Alteration(s)"),
|
|
1020
|
-
accessor: 'alterations',
|
|
1021
|
-
minWidth: 80,
|
|
1022
|
-
sortMethod: function (a, b) {
|
|
1023
|
-
return cbioportalUtils.defaultArraySortMethod(a, b);
|
|
1024
|
-
},
|
|
1025
|
-
};
|
|
1026
|
-
}
|
|
1027
|
-
}
|
|
1028
|
-
});
|
|
1029
|
-
Object.defineProperty(OncoKbHelper, "getAlterationsColumnCell", {
|
|
1030
|
-
enumerable: true,
|
|
1031
|
-
configurable: true,
|
|
1032
|
-
writable: true,
|
|
1033
|
-
value: function (alterations, variant) {
|
|
1034
|
-
var mergedAlteration = mergeAlterations(alterations);
|
|
1035
|
-
var content = React__namespace.createElement("span", null, mergedAlteration);
|
|
1036
|
-
if (alterations.length > 5) {
|
|
1037
|
-
var lowerCasedQueryVariant_1 = variant.toLowerCase();
|
|
1038
|
-
var matchedAlteration = ___default["default"].find(alterations, function (alteration) {
|
|
1039
|
-
return alteration.toLocaleLowerCase() === lowerCasedQueryVariant_1;
|
|
1040
|
-
});
|
|
1041
|
-
if (!matchedAlteration) {
|
|
1042
|
-
matchedAlteration = getPositionalVariant(variant);
|
|
1043
|
-
}
|
|
1044
|
-
var pickedAlteration = matchedAlteration === undefined
|
|
1045
|
-
? alterations[0]
|
|
1046
|
-
: matchedAlteration;
|
|
1047
|
-
content = (React__namespace.createElement("span", null,
|
|
1048
|
-
pickedAlteration,
|
|
1049
|
-
" and",
|
|
1050
|
-
' ',
|
|
1051
|
-
React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlay: React__namespace.createElement("div", { style: { maxWidth: '400px' } }, mergedAlteration), placement: "right", destroyTooltipOnHide: true },
|
|
1052
|
-
React__namespace.createElement("a", null,
|
|
1053
|
-
alterations.length - 1,
|
|
1054
|
-
" other alterations"))));
|
|
1055
|
-
}
|
|
1056
|
-
return (React__namespace.createElement("div", { style: { whiteSpace: 'normal', lineHeight: '1rem' } }, content));
|
|
1057
|
-
}
|
|
1058
|
-
});
|
|
1059
|
-
return OncoKbHelper;
|
|
1060
|
-
}());
|
|
1061
|
-
|
|
1062
|
-
var styles$a = {"list-group-item":"listGroupItem-module_list-group-item__1Y5zb","list-group-item-title":"listGroupItem-module_list-group-item-title__3diZg","list-group-item-content":"listGroupItem-module_list-group-item-content__Sspft","no-style-ul":"listGroupItem-module_no-style-ul__2Rf8i"};
|
|
1063
|
-
|
|
1064
|
-
var ArticleAbstractItem = /** @class */ (function (_super) {
|
|
1065
|
-
tslib.__extends(ArticleAbstractItem, _super);
|
|
1066
|
-
function ArticleAbstractItem() {
|
|
1067
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
1068
|
-
}
|
|
1069
|
-
Object.defineProperty(ArticleAbstractItem.prototype, "render", {
|
|
1070
|
-
enumerable: false,
|
|
1071
|
-
configurable: true,
|
|
1072
|
-
writable: true,
|
|
1073
|
-
value: function () {
|
|
1074
|
-
var content = React__namespace.createElement("span", null, this.props.abstract);
|
|
1075
|
-
if (this.props.link) {
|
|
1076
|
-
content = (React__namespace.createElement("a", { href: this.props.link, target: "_blank" }, content));
|
|
1077
|
-
}
|
|
1078
|
-
return (React__namespace.createElement("li", { key: "abstract_" + this.props.abstract, className: styles$a['list-group-item'] },
|
|
1079
|
-
React__namespace.createElement("span", { className: styles$a['list-group-item-title'] }, content)));
|
|
1080
|
-
}
|
|
1081
|
-
});
|
|
1082
|
-
return ArticleAbstractItem;
|
|
1083
|
-
}(React__namespace.Component));
|
|
1084
|
-
|
|
1085
|
-
var PmidItem = /** @class */ (function (_super) {
|
|
1086
|
-
tslib.__extends(PmidItem, _super);
|
|
1087
|
-
function PmidItem() {
|
|
1088
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
1089
|
-
}
|
|
1090
|
-
Object.defineProperty(PmidItem.prototype, "render", {
|
|
1091
|
-
enumerable: false,
|
|
1092
|
-
configurable: true,
|
|
1093
|
-
writable: true,
|
|
1094
|
-
value: function () {
|
|
1095
|
-
return (React__namespace.createElement("li", { key: this.props.pmid, className: styles$a['list-group-item'] },
|
|
1096
|
-
React__namespace.createElement("a", { className: styles$a['list-group-item-title'], href: cbioportalFrontendCommons.getNCBIlink("/pubmed/" + this.props.pmid), target: "_blank" },
|
|
1097
|
-
React__namespace.createElement("span", null, cbioportalFrontendCommons.trimOffHtmlTagEntities(this.props.title))),
|
|
1098
|
-
React__namespace.createElement("div", { className: styles$a['list-group-item-content'] },
|
|
1099
|
-
React__namespace.createElement("span", null,
|
|
1100
|
-
this.props.author,
|
|
1101
|
-
" ",
|
|
1102
|
-
this.props.source,
|
|
1103
|
-
".",
|
|
1104
|
-
' ',
|
|
1105
|
-
this.props.date),
|
|
1106
|
-
React__namespace.createElement("span", null,
|
|
1107
|
-
"PMID: ",
|
|
1108
|
-
this.props.pmid))));
|
|
1109
|
-
}
|
|
1110
|
-
});
|
|
1111
|
-
return PmidItem;
|
|
1112
|
-
}(React__namespace.Component));
|
|
1113
|
-
|
|
1114
|
-
var ReferenceList = /** @class */ (function (_super) {
|
|
1115
|
-
tslib.__extends(ReferenceList, _super);
|
|
1116
|
-
function ReferenceList() {
|
|
1117
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
1118
|
-
}
|
|
1119
|
-
Object.defineProperty(ReferenceList.prototype, "isLoading", {
|
|
1120
|
-
get: function () {
|
|
1121
|
-
var _this = this;
|
|
1122
|
-
if (this.props.pmidData && this.props.pmids) {
|
|
1123
|
-
var loadingItems = ___default["default"].filter(this.props.pmids, function (uid) {
|
|
1124
|
-
var cacheData = _this.props.pmidData[uid.toString()];
|
|
1125
|
-
// when the cacheData is undefined, the pmidData will fetch the uid info later which eventually results to an object with a status
|
|
1126
|
-
return !cacheData || cacheData.status === 'pending';
|
|
1127
|
-
});
|
|
1128
|
-
return loadingItems.length > 0;
|
|
1129
|
-
}
|
|
1130
|
-
else {
|
|
1131
|
-
return false;
|
|
1132
|
-
}
|
|
1133
|
-
},
|
|
1134
|
-
enumerable: false,
|
|
1135
|
-
configurable: true
|
|
1136
|
-
});
|
|
1137
|
-
Object.defineProperty(ReferenceList.prototype, "render", {
|
|
1138
|
-
enumerable: false,
|
|
1139
|
-
configurable: true,
|
|
1140
|
-
writable: true,
|
|
1141
|
-
value: function () {
|
|
1142
|
-
var _this = this;
|
|
1143
|
-
if (this.isLoading) {
|
|
1144
|
-
return React__namespace.createElement("i", { className: "fa fa-spinner fa-pulse fa-2x" });
|
|
1145
|
-
}
|
|
1146
|
-
var list = [];
|
|
1147
|
-
if (this.props.pmidData) {
|
|
1148
|
-
this.props.pmids.forEach(function (uid) {
|
|
1149
|
-
var cacheData = _this.props.pmidData[uid.toString()];
|
|
1150
|
-
var articleContent = cacheData ? cacheData.data : null;
|
|
1151
|
-
if (articleContent) {
|
|
1152
|
-
list.push(React__namespace.createElement(PmidItem, { title: articleContent.title, author: ___default["default"].isArray(articleContent.authors) &&
|
|
1153
|
-
articleContent.authors.length > 0
|
|
1154
|
-
? articleContent.authors[0].name + ' et al.'
|
|
1155
|
-
: 'Unknown', source: articleContent.source, date: new Date(articleContent.pubdate)
|
|
1156
|
-
.getFullYear()
|
|
1157
|
-
.toString(), pmid: articleContent.uid }));
|
|
1158
|
-
}
|
|
1159
|
-
});
|
|
1160
|
-
}
|
|
1161
|
-
this.props.abstracts.forEach(function (abstract) {
|
|
1162
|
-
list.push(React__namespace.createElement(ArticleAbstractItem, { abstract: abstract.abstract, link: abstract.link }));
|
|
1163
|
-
});
|
|
1164
|
-
return React__namespace.createElement("ul", { className: styles$a['no-style-ul'] }, list);
|
|
1165
|
-
}
|
|
1166
|
-
});
|
|
1167
|
-
tslib.__decorate([
|
|
1168
|
-
mobx.computed
|
|
1169
|
-
], ReferenceList.prototype, "isLoading", null);
|
|
1170
|
-
ReferenceList = tslib.__decorate([
|
|
1171
|
-
mobxReact.observer
|
|
1172
|
-
], ReferenceList);
|
|
1173
|
-
return ReferenceList;
|
|
1174
|
-
}(React__namespace.Component));
|
|
1175
|
-
|
|
1176
|
-
var RefComponent = /** @class */ (function (_super) {
|
|
1177
|
-
tslib.__extends(RefComponent, _super);
|
|
1178
|
-
function RefComponent() {
|
|
1179
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
1180
|
-
}
|
|
1181
|
-
Object.defineProperty(RefComponent.prototype, "render", {
|
|
1182
|
-
enumerable: false,
|
|
1183
|
-
configurable: true,
|
|
1184
|
-
writable: true,
|
|
1185
|
-
value: function () {
|
|
1186
|
-
var _this = this;
|
|
1187
|
-
var parts = this.props.content.split(/pmid|nct/i);
|
|
1188
|
-
if (parts.length < 2) {
|
|
1189
|
-
return React__namespace.createElement("span", null, this.props.content);
|
|
1190
|
-
}
|
|
1191
|
-
var ids = parts[1].match(/[0-9]+/g);
|
|
1192
|
-
if (!ids) {
|
|
1193
|
-
return React__namespace.createElement("span", null, this.props.content);
|
|
1194
|
-
}
|
|
1195
|
-
var prefix;
|
|
1196
|
-
if (this.props.content.toLowerCase().indexOf('pmid') >= 0) {
|
|
1197
|
-
prefix = 'PMID: ';
|
|
1198
|
-
}
|
|
1199
|
-
else if (this.props.content.toLowerCase().indexOf('nct') >= 0) {
|
|
1200
|
-
prefix = 'NCT';
|
|
1201
|
-
}
|
|
1202
|
-
var link;
|
|
1203
|
-
if (prefix) {
|
|
1204
|
-
link = (React__namespace.createElement("a", { target: "_blank", href: cbioportalFrontendCommons.getNCBIlink("/pubmed/" + ids.join(',')) }, "" + prefix + ids.join(',')));
|
|
1205
|
-
}
|
|
1206
|
-
if (this.props.componentType === 'tooltip') {
|
|
1207
|
-
var tooltipContent = function () { return (React__namespace.createElement("div", { className: mainStyles['tooltip-refs'] },
|
|
1208
|
-
React__namespace.createElement(ReferenceList, { pmids: ids.map(function (id) { return parseInt(id); }), pmidData: _this.props.pmidData, abstracts: [] }))); };
|
|
1209
|
-
return (React__namespace.createElement("span", { key: this.props.content },
|
|
1210
|
-
parts[0],
|
|
1211
|
-
React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlay: tooltipContent, placement: "right", trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
|
|
1212
|
-
React__namespace.createElement("i", { className: "fa fa-book", style: { color: 'black' } })), ")"));
|
|
1213
|
-
}
|
|
1214
|
-
else if (link) {
|
|
1215
|
-
return (React__namespace.createElement("span", { key: this.props.content },
|
|
1216
|
-
parts[0],
|
|
1217
|
-
link, ")"));
|
|
1218
|
-
}
|
|
1219
|
-
else {
|
|
1220
|
-
return React__namespace.createElement("span", null, this.props.content);
|
|
1221
|
-
}
|
|
1222
|
-
}
|
|
1223
|
-
});
|
|
1224
|
-
return RefComponent;
|
|
1225
|
-
}(React__namespace.Component));
|
|
1226
|
-
|
|
1227
|
-
var SummaryWithRefs = /** @class */ (function (_super) {
|
|
1228
|
-
tslib.__extends(SummaryWithRefs, _super);
|
|
1229
|
-
function SummaryWithRefs() {
|
|
1230
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
1231
|
-
}
|
|
1232
|
-
Object.defineProperty(SummaryWithRefs.prototype, "render", {
|
|
1233
|
-
enumerable: false,
|
|
1234
|
-
configurable: true,
|
|
1235
|
-
writable: true,
|
|
1236
|
-
value: function () {
|
|
1237
|
-
var _this = this;
|
|
1238
|
-
if (!this.props.content) {
|
|
1239
|
-
return React__namespace.createElement("span", null);
|
|
1240
|
-
}
|
|
1241
|
-
var content = [];
|
|
1242
|
-
// example delimiters:
|
|
1243
|
-
// (PMID: 11900253)
|
|
1244
|
-
// (PMID: 11753428, 16007150, 21467160)
|
|
1245
|
-
// (cBioPortal, MSKCC, May 2015, PMID: 24718888)
|
|
1246
|
-
// (NCT1234567)
|
|
1247
|
-
var regex = /(\(.*?[PMID|NCT].*?\))/i;
|
|
1248
|
-
// split the string with delimiters included
|
|
1249
|
-
var parts = this.props.content.split(regex);
|
|
1250
|
-
parts.forEach(function (part) {
|
|
1251
|
-
// if delimiter convert to a JSX component
|
|
1252
|
-
if (part.match(regex)) {
|
|
1253
|
-
content.push(React__namespace.createElement(RefComponent, { pmidData: _this.props.pmidData, componentType: _this.props.type, content: part }));
|
|
1254
|
-
}
|
|
1255
|
-
else {
|
|
1256
|
-
content.push(React__namespace.createElement("span", null, part));
|
|
1257
|
-
}
|
|
1258
|
-
});
|
|
1259
|
-
return React__namespace.createElement("span", null, content);
|
|
1260
|
-
}
|
|
1261
|
-
});
|
|
1262
|
-
return SummaryWithRefs;
|
|
1263
|
-
}(React__namespace.Component));
|
|
1264
|
-
|
|
1265
|
-
var EvidenceReferenceContent = function (props) {
|
|
1266
|
-
return (React__default["default"].createElement(reactIf.If, { condition: !!props.description },
|
|
1267
|
-
React__default["default"].createElement(reactIf.Then, null,
|
|
1268
|
-
React__default["default"].createElement(SummaryWithRefs, { content: props.description, type: 'tooltip', pmidData: props.pmidData })),
|
|
1269
|
-
React__default["default"].createElement(reactIf.Else, null,
|
|
1270
|
-
React__default["default"].createElement(reactIf.If, { condition: props.citations != undefined &&
|
|
1271
|
-
(props.citations.abstracts.length > 0 ||
|
|
1272
|
-
props.citations.pmids.length > 0) },
|
|
1273
|
-
React__default["default"].createElement(reactIf.Then, null,
|
|
1274
|
-
React__default["default"].createElement(ReferenceList, { pmidData: props.pmidData, pmids: props.citations.pmids.map(function (pmid) {
|
|
1275
|
-
return Number(pmid);
|
|
1276
|
-
}), abstracts: props.citations.abstracts })),
|
|
1277
|
-
React__default["default"].createElement(reactIf.Else, null, props.noInfoDisclaimer
|
|
1278
|
-
? props.noInfoDisclaimer
|
|
1279
|
-
: 'Information is not available.')))));
|
|
1280
|
-
};
|
|
1281
|
-
|
|
1282
|
-
var OncoKbTreatmentTable = /** @class */ (function (_super) {
|
|
1283
|
-
tslib.__extends(OncoKbTreatmentTable, _super);
|
|
1284
|
-
function OncoKbTreatmentTable() {
|
|
1285
|
-
var _this = _super !== null && _super.apply(this, arguments) || this;
|
|
1286
|
-
Object.defineProperty(_this, "levelTooltipContent", {
|
|
1287
|
-
enumerable: true,
|
|
1288
|
-
configurable: true,
|
|
1289
|
-
writable: true,
|
|
1290
|
-
value: function (level) {
|
|
1291
|
-
return (React__namespace.createElement("div", { style: { maxWidth: '200px' } }, OncoKbHelper.LEVEL_DESC[level]));
|
|
1292
|
-
}
|
|
1293
|
-
});
|
|
1294
|
-
Object.defineProperty(_this, "treatmentTooltipContent", {
|
|
1295
|
-
enumerable: true,
|
|
1296
|
-
configurable: true,
|
|
1297
|
-
writable: true,
|
|
1298
|
-
value: function (abstracts, pmids, pmidData, description) {
|
|
1299
|
-
return abstracts.length > 0 || pmids.length > 0 ? (function () { return (React__namespace.createElement("div", { className: mainStyles['tooltip-refs'] },
|
|
1300
|
-
React__namespace.createElement(EvidenceReferenceContent, { description: description, citations: {
|
|
1301
|
-
pmids: pmids.map(function (pmid) { return pmid.toString(); }),
|
|
1302
|
-
abstracts: abstracts,
|
|
1303
|
-
}, pmidData: pmidData, noInfoDisclaimer: 'Mutation effect information is not available.' }))); }) : (React__namespace.createElement("span", null));
|
|
1304
|
-
}
|
|
1305
|
-
});
|
|
1306
|
-
Object.defineProperty(_this, "columns", {
|
|
1307
|
-
enumerable: true,
|
|
1308
|
-
configurable: true,
|
|
1309
|
-
writable: true,
|
|
1310
|
-
value: [
|
|
1311
|
-
OncoKbHelper.getDefaultColumnDefinition('level'),
|
|
1312
|
-
tslib.__assign(tslib.__assign({}, OncoKbHelper.getDefaultColumnDefinition('alterations')), { Cell: function (props) {
|
|
1313
|
-
return OncoKbHelper.getAlterationsColumnCell(props.value, _this.props.variant);
|
|
1314
|
-
} }),
|
|
1315
|
-
{
|
|
1316
|
-
id: 'treatment',
|
|
1317
|
-
Header: React__namespace.createElement("span", null, "Drug(s)"),
|
|
1318
|
-
accessor: 'drugs',
|
|
1319
|
-
Cell: function (props) { return (React__namespace.createElement("div", { style: { whiteSpace: 'normal', lineHeight: '1rem' } }, props.original.drugs
|
|
1320
|
-
.map(function (drug) { return drug.drugName; })
|
|
1321
|
-
.join(' + '))); },
|
|
1322
|
-
},
|
|
1323
|
-
{
|
|
1324
|
-
id: 'cancerType',
|
|
1325
|
-
Header: (React__namespace.createElement("span", null,
|
|
1326
|
-
"Level-associated",
|
|
1327
|
-
React__namespace.createElement("br", null),
|
|
1328
|
-
"cancer type(s)")),
|
|
1329
|
-
accessor: 'levelAssociatedCancerType',
|
|
1330
|
-
minWidth: 120,
|
|
1331
|
-
Cell: function (props) { return (React__namespace.createElement("div", { style: { whiteSpace: 'normal', lineHeight: '1rem' } }, getTumorTypeNameWithExclusionInfo(props.original.levelAssociatedCancerType, props.original.levelExcludedCancerTypes))); },
|
|
1332
|
-
},
|
|
1333
|
-
{
|
|
1334
|
-
id: 'referenceList',
|
|
1335
|
-
Header: React__namespace.createElement("span", null),
|
|
1336
|
-
sortable: false,
|
|
1337
|
-
maxWidth: 25,
|
|
1338
|
-
Cell: function (props) {
|
|
1339
|
-
return (props.original.abstracts.length > 0 ||
|
|
1340
|
-
props.original.pmids.length > 0) && (React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlay: _this.treatmentTooltipContent(props.original.abstracts, props.original.pmids.map(function (pmid) { return Number(pmid); }), _this.props.pmidData, props.original.description), placement: "right", trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
|
|
1341
|
-
React__namespace.createElement("i", { className: "fa fa-book" })));
|
|
1342
|
-
},
|
|
1343
|
-
},
|
|
1344
|
-
]
|
|
1345
|
-
});
|
|
1346
|
-
return _this;
|
|
1347
|
-
}
|
|
1348
|
-
Object.defineProperty(OncoKbTreatmentTable.prototype, "render", {
|
|
1349
|
-
enumerable: false,
|
|
1350
|
-
configurable: true,
|
|
1351
|
-
writable: true,
|
|
1352
|
-
value: function () {
|
|
1353
|
-
return (React__namespace.createElement("div", { className: "oncokb-treatment-table" },
|
|
1354
|
-
React__namespace.createElement(ReactTable__default["default"], { data: this.props.treatments, columns: this.columns, showPagination: false, pageSize: this.props.treatments.length, className: "-striped -highlight" })));
|
|
1355
|
-
}
|
|
1356
|
-
});
|
|
1357
|
-
OncoKbTreatmentTable = tslib.__decorate([
|
|
1358
|
-
mobxReact.observer
|
|
1359
|
-
], OncoKbTreatmentTable);
|
|
1360
|
-
return OncoKbTreatmentTable;
|
|
1361
|
-
}(React__namespace.Component));
|
|
1362
|
-
|
|
1363
|
-
var BiologicalContent = function (props) {
|
|
1364
|
-
return (React__default["default"].createElement(EvidenceReferenceContent, { description: props.biologicalSummary, citations: props.mutationEffectCitations, pmidData: props.pmidData, noInfoDisclaimer: 'Mutation effect information is not available.' }));
|
|
1365
|
-
};
|
|
1366
|
-
|
|
1367
|
-
var ImplicationContent = function (props) {
|
|
1368
|
-
var columns = [
|
|
1369
|
-
tslib.__assign(tslib.__assign({}, OncoKbHelper.getDefaultColumnDefinition('level')), { accessor: 'levelOfEvidence', maxWidth: 100 }),
|
|
1370
|
-
tslib.__assign(tslib.__assign({}, OncoKbHelper.getDefaultColumnDefinition('alterations')), { Cell: function (cellProps) {
|
|
1371
|
-
return OncoKbHelper.getAlterationsColumnCell(cellProps.value, props.variant);
|
|
1372
|
-
} }),
|
|
1373
|
-
{
|
|
1374
|
-
id: 'referenceList',
|
|
1375
|
-
Header: React__namespace.createElement("span", null),
|
|
1376
|
-
sortable: false,
|
|
1377
|
-
maxWidth: 50,
|
|
1378
|
-
Cell: function (cellProps) { return (React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlay: function () { return (React__namespace.createElement("div", { className: mainStyles['tooltip-refs'] },
|
|
1379
|
-
React__namespace.createElement(EvidenceReferenceContent, { description: cellProps.original.description, citations: {
|
|
1380
|
-
pmids: cellProps.original.pmids,
|
|
1381
|
-
abstracts: cellProps.original.abstracts,
|
|
1382
|
-
}, pmidData: props.pmidData, noInfoDisclaimer: 'Mutation effect information is not available.' }))); }, placement: "right", trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
|
|
1383
|
-
React__namespace.createElement("i", { className: "fa fa-book" }))); },
|
|
1384
|
-
},
|
|
1385
|
-
];
|
|
1386
|
-
return (React__namespace.createElement("div", null,
|
|
1387
|
-
React__namespace.createElement("p", null, props.summary),
|
|
1388
|
-
React__namespace.createElement("div", null,
|
|
1389
|
-
React__namespace.createElement(ReactTable__default["default"], { data: props.implications, columns: columns, showPagination: false, pageSize: props.implications.length, className: "-striped -highlight" }))));
|
|
1390
|
-
};
|
|
1391
|
-
|
|
1392
|
-
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_"};
|
|
1393
|
-
|
|
1394
|
-
var OncogenicIcon = function (props) {
|
|
1395
|
-
return (React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlay: React__namespace.createElement("span", null, props.oncogenicity), placement: "left", trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
|
|
1396
|
-
React__namespace.createElement("i", { className: oncogenicityIconClassNames(props.oncogenicity) })));
|
|
1397
|
-
};
|
|
1398
|
-
|
|
1399
|
-
var _a$3;
|
|
1400
|
-
var OncoKbMedicalDisclaimer = (React__default["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."));
|
|
1401
|
-
var ONCOKB_DATA_ACCESS_PAGE_LINK = 'https://docs.cbioportal.org/2.4-integration-with-other-webservices/oncokb-data-access';
|
|
1402
|
-
var publicInstanceDisclaimerOverLay = (React__default["default"].createElement("div", null,
|
|
1403
|
-
React__default["default"].createElement("p", null,
|
|
1404
|
-
"This cBioPortal instance is not linked to an OncoKB\u2122 license, and therefore some OncoKB content is not available including therapeutic, diagnostic and prognostic implications. To obtain a license, please follow",
|
|
1405
|
-
' ',
|
|
1406
|
-
React__default["default"].createElement("a", { href: ONCOKB_DATA_ACCESS_PAGE_LINK, target: '_blank' }, "these instructions"),
|
|
1407
|
-
"."),
|
|
1408
|
-
OncoKbMedicalDisclaimer));
|
|
1409
|
-
var DATA_TYPE_TO_TITLE = (_a$3 = {},
|
|
1410
|
-
_a$3[cbioportalUtils.OncoKbCardDataType.BIOLOGICAL] = 'Biological Effect',
|
|
1411
|
-
_a$3[cbioportalUtils.OncoKbCardDataType.TXS] = 'Therapeutic Implications',
|
|
1412
|
-
_a$3[cbioportalUtils.OncoKbCardDataType.TXR] = 'Therapeutic Implications',
|
|
1413
|
-
_a$3[cbioportalUtils.OncoKbCardDataType.DX] = 'Diagnostic Implications',
|
|
1414
|
-
_a$3[cbioportalUtils.OncoKbCardDataType.PX] = 'Prognostic Implications',
|
|
1415
|
-
_a$3);
|
|
1416
|
-
var TabContentWrapper = function (props) {
|
|
1417
|
-
return React__default["default"].createElement("div", { className: mainStyles['tab-content'] }, props.children);
|
|
1418
|
-
};
|
|
1419
|
-
var TabTitle = function (props) {
|
|
1420
|
-
var _a;
|
|
1421
|
-
var title = DATA_TYPE_TO_TITLE[props.type];
|
|
1422
|
-
var icon = props.displayHighestLevelInTabTitle ? (props.type === cbioportalUtils.OncoKbCardDataType.BIOLOGICAL ? (React__default["default"].createElement(OncogenicIcon, { oncogenicity: ((_a = props.indicator) === null || _a === void 0 ? void 0 : _a.oncogenic) || '', showDescription: true })) : (React__default["default"].createElement(LevelIcon, { level: normalizeLevel(calcHighestIndicatorLevel(props.type, props.indicator)) || '', showDescription: true }))) : null;
|
|
1423
|
-
return icon ? (React__default["default"].createElement("span", { style: { display: 'flex' } },
|
|
1424
|
-
icon,
|
|
1425
|
-
" ",
|
|
1426
|
-
title)) : (React__default["default"].createElement("span", null, title));
|
|
1427
|
-
};
|
|
1428
|
-
var OncoKbCardBody = function (props) {
|
|
1429
|
-
var defaultTabActiveKey;
|
|
1430
|
-
// Do not assign a default key if the data type specified through the property does not have any content
|
|
1431
|
-
// When the content is not available, we do not render the tab.
|
|
1432
|
-
if (dataTypeHasContent(props.type)) {
|
|
1433
|
-
defaultTabActiveKey = props.type;
|
|
1434
|
-
// Both TXS and TXR are therapeutic implication data type which will be shown in the same tab. We use TXS as the tab key when rendering
|
|
1435
|
-
if ([cbioportalUtils.OncoKbCardDataType.TXS, cbioportalUtils.OncoKbCardDataType.TXR].includes(defaultTabActiveKey)) {
|
|
1436
|
-
defaultTabActiveKey = cbioportalUtils.OncoKbCardDataType.TXS;
|
|
1437
|
-
}
|
|
1438
|
-
}
|
|
1439
|
-
var _a = React.useState(defaultTabActiveKey), activateTabKey = _a[0], setActivateTabKey = _a[1];
|
|
1440
|
-
var _b = React.useState(getLevelsOfEvidence(activateTabKey)), levelsOfEvidence = _b[0], setLevelsOfEvidence = _b[1];
|
|
1441
|
-
function updateActivateTabKey(newKey) {
|
|
1442
|
-
setActivateTabKey(newKey);
|
|
1443
|
-
setLevelsOfEvidence(getLevelsOfEvidence(newKey));
|
|
1444
|
-
}
|
|
1445
|
-
function hasMutationEffectInfo(mutationEffect) {
|
|
1446
|
-
return (mutationEffect &&
|
|
1447
|
-
(mutationEffect.description ||
|
|
1448
|
-
mutationEffect.citations.abstracts.length > 0 ||
|
|
1449
|
-
mutationEffect.citations.pmids.length > 0));
|
|
1450
|
-
}
|
|
1451
|
-
function dataTypeHasContent(type) {
|
|
1452
|
-
var _a, _b, _c, _d, _e;
|
|
1453
|
-
switch (type) {
|
|
1454
|
-
case cbioportalUtils.OncoKbCardDataType.BIOLOGICAL:
|
|
1455
|
-
return hasMutationEffectInfo((_a = props.indicator) === null || _a === void 0 ? void 0 : _a.mutationEffect);
|
|
1456
|
-
case cbioportalUtils.OncoKbCardDataType.TXS:
|
|
1457
|
-
case cbioportalUtils.OncoKbCardDataType.TXR:
|
|
1458
|
-
return (!!((_b = props.indicator) === null || _b === void 0 ? void 0 : _b.highestSensitiveLevel) ||
|
|
1459
|
-
!!((_c = props.indicator) === null || _c === void 0 ? void 0 : _c.highestResistanceLevel));
|
|
1460
|
-
case cbioportalUtils.OncoKbCardDataType.DX:
|
|
1461
|
-
return !!((_d = props.indicator) === null || _d === void 0 ? void 0 : _d.highestDiagnosticImplicationLevel);
|
|
1462
|
-
case cbioportalUtils.OncoKbCardDataType.PX:
|
|
1463
|
-
return !!((_e = props.indicator) === null || _e === void 0 ? void 0 : _e.highestPrognosticImplicationLevel);
|
|
1464
|
-
default:
|
|
1465
|
-
return false;
|
|
1466
|
-
}
|
|
1467
|
-
}
|
|
1468
|
-
function getBody(type, indicator) {
|
|
1469
|
-
var tabs = [];
|
|
1470
|
-
if (dataTypeHasContent(cbioportalUtils.OncoKbCardDataType.BIOLOGICAL)) {
|
|
1471
|
-
tabs.push(React__default["default"].createElement(reactBootstrap.Tab, { eventKey: cbioportalUtils.OncoKbCardDataType.BIOLOGICAL, title: React__default["default"].createElement(TabTitle, { type: cbioportalUtils.OncoKbCardDataType.BIOLOGICAL, indicator: props.indicator, displayHighestLevelInTabTitle: props.displayHighestLevelInTabTitle }) },
|
|
1472
|
-
React__default["default"].createElement(TabContentWrapper, null,
|
|
1473
|
-
React__default["default"].createElement(BiologicalContent, { mutationEffectCitations: indicator.mutationEffect.citations, biologicalSummary: indicator.mutationEffect.description, pmidData: props.pmidData }))));
|
|
1474
|
-
}
|
|
1475
|
-
if (!props.usingPublicOncoKbInstance &&
|
|
1476
|
-
dataTypeHasContent(cbioportalUtils.OncoKbCardDataType.TXS)) {
|
|
1477
|
-
tabs.push(React__default["default"].createElement(reactBootstrap.Tab, { eventKey: cbioportalUtils.OncoKbCardDataType.TXS, title: React__default["default"].createElement(TabTitle, { type: cbioportalUtils.OncoKbCardDataType.TXS, indicator: props.indicator, displayHighestLevelInTabTitle: props.displayHighestLevelInTabTitle }) },
|
|
1478
|
-
React__default["default"].createElement(TabContentWrapper, null,
|
|
1479
|
-
React__default["default"].createElement("div", { style: {
|
|
1480
|
-
marginTop: 10,
|
|
1481
|
-
} },
|
|
1482
|
-
React__default["default"].createElement(OncoKbTreatmentTable, { variant: indicator.query.alteration || '', pmidData: props.pmidData, treatments: indicator.treatments })))));
|
|
1483
|
-
}
|
|
1484
|
-
if (!props.usingPublicOncoKbInstance &&
|
|
1485
|
-
dataTypeHasContent(cbioportalUtils.OncoKbCardDataType.DX)) {
|
|
1486
|
-
tabs.push(React__default["default"].createElement(reactBootstrap.Tab, { eventKey: cbioportalUtils.OncoKbCardDataType.DX, title: React__default["default"].createElement(TabTitle, { type: cbioportalUtils.OncoKbCardDataType.DX, indicator: props.indicator, displayHighestLevelInTabTitle: props.displayHighestLevelInTabTitle }) },
|
|
1487
|
-
React__default["default"].createElement(TabContentWrapper, null,
|
|
1488
|
-
React__default["default"].createElement(ImplicationContent, { variant: indicator.query.alteration, summary: indicator.diagnosticSummary, implications: indicator.diagnosticImplications, pmidData: props.pmidData }))));
|
|
1489
|
-
}
|
|
1490
|
-
if (!props.usingPublicOncoKbInstance &&
|
|
1491
|
-
dataTypeHasContent(cbioportalUtils.OncoKbCardDataType.PX)) {
|
|
1492
|
-
tabs.push(React__default["default"].createElement(reactBootstrap.Tab, { eventKey: cbioportalUtils.OncoKbCardDataType.PX, title: React__default["default"].createElement(TabTitle, { type: cbioportalUtils.OncoKbCardDataType.PX, indicator: props.indicator, displayHighestLevelInTabTitle: props.displayHighestLevelInTabTitle }) },
|
|
1493
|
-
React__default["default"].createElement(TabContentWrapper, null,
|
|
1494
|
-
React__default["default"].createElement(ImplicationContent, { variant: indicator.query.alteration, summary: indicator.prognosticSummary, implications: indicator.prognosticImplications, pmidData: props.pmidData }))));
|
|
1495
|
-
}
|
|
1496
|
-
return (React__default["default"].createElement("div", { style: { padding: '10px' } },
|
|
1497
|
-
React__default["default"].createElement("p", null, indicator.geneSummary),
|
|
1498
|
-
React__default["default"].createElement("p", null, indicator.variantSummary),
|
|
1499
|
-
props.usingPublicOncoKbInstance ? (React__default["default"].createElement("p", { className: mainStyles.disclaimer },
|
|
1500
|
-
"Therapeutic, diagnostic and prognostic implications are not available in this instance of cBioPortal.",
|
|
1501
|
-
' ',
|
|
1502
|
-
React__default["default"].createElement(cbioportalFrontendCommons.DefaultTooltip, { overlayStyle: {
|
|
1503
|
-
maxWidth: 400,
|
|
1504
|
-
}, overlay: publicInstanceDisclaimerOverLay },
|
|
1505
|
-
React__default["default"].createElement("i", { className: 'fa fa-info-circle' })))) : (React__default["default"].createElement("p", null, indicator.tumorTypeSummary)),
|
|
1506
|
-
tabs.length > 0 && (React__default["default"].createElement(reactBootstrap.Tabs, { defaultActiveKey: defaultTabActiveKey, className: classnames__default["default"]('oncokb-card-tabs'), onSelect: updateActivateTabKey }, tabs))));
|
|
1507
|
-
}
|
|
1508
|
-
function getLevelsOfEvidence(activateTabKey) {
|
|
1509
|
-
switch (activateTabKey) {
|
|
1510
|
-
case cbioportalUtils.OncoKbCardDataType.TXS:
|
|
1511
|
-
case cbioportalUtils.OncoKbCardDataType.TXR:
|
|
1512
|
-
return {
|
|
1513
|
-
levels: OncoKbHelper.TX_LEVELS,
|
|
1514
|
-
levelDes: OncoKbHelper.getLevelsDesc(activateTabKey),
|
|
1515
|
-
};
|
|
1516
|
-
case cbioportalUtils.OncoKbCardDataType.DX:
|
|
1517
|
-
return {
|
|
1518
|
-
levels: OncoKbHelper.DX_LEVELS,
|
|
1519
|
-
levelDes: OncoKbHelper.getLevelsDesc(cbioportalUtils.OncoKbCardDataType.DX),
|
|
1520
|
-
};
|
|
1521
|
-
case cbioportalUtils.OncoKbCardDataType.PX:
|
|
1522
|
-
return {
|
|
1523
|
-
levels: OncoKbHelper.PX_LEVELS,
|
|
1524
|
-
levelDes: OncoKbHelper.getLevelsDesc(cbioportalUtils.OncoKbCardDataType.PX),
|
|
1525
|
-
};
|
|
1526
|
-
default:
|
|
1527
|
-
return {
|
|
1528
|
-
levels: [],
|
|
1529
|
-
levelDes: {},
|
|
1530
|
-
};
|
|
1531
|
-
}
|
|
1532
|
-
}
|
|
1533
|
-
var UNKNOWN = 'Unknown';
|
|
1534
|
-
function getOncogenicity() {
|
|
1535
|
-
var _a;
|
|
1536
|
-
var oncogenicity = (_a = props.indicator) === null || _a === void 0 ? void 0 : _a.oncogenic;
|
|
1537
|
-
if (!oncogenicity || oncogenicity === UNKNOWN) {
|
|
1538
|
-
oncogenicity = 'Unknown Oncogenic Effect';
|
|
1539
|
-
}
|
|
1540
|
-
return oncogenicity;
|
|
1541
|
-
}
|
|
1542
|
-
function getMutationEffect() {
|
|
1543
|
-
var _a;
|
|
1544
|
-
var mutationEffect = (_a = props.indicator) === null || _a === void 0 ? void 0 : _a.mutationEffect.knownEffect;
|
|
1545
|
-
if (!mutationEffect || mutationEffect === UNKNOWN) {
|
|
1546
|
-
mutationEffect = 'Unknown Biological Effect';
|
|
1547
|
-
}
|
|
1548
|
-
return mutationEffect;
|
|
1549
|
-
}
|
|
1550
|
-
return (React__default["default"].createElement(React__default["default"].Fragment, null,
|
|
1551
|
-
!props.geneNotExist && (React__default["default"].createElement("div", null,
|
|
1552
|
-
props.indicator && (React__default["default"].createElement(React__default["default"].Fragment, null,
|
|
1553
|
-
React__default["default"].createElement("div", { className: mainStyles['biological-info'] },
|
|
1554
|
-
React__default["default"].createElement("div", { style: { flexGrow: 1 } }, getOncogenicity()),
|
|
1555
|
-
React__default["default"].createElement("div", { style: { flexGrow: 1 } }, getMutationEffect())),
|
|
1556
|
-
React__default["default"].createElement("div", { className: mainStyles['oncokb-card'], "data-test": "oncokb-card" }, getBody(props.type, props.indicator)))),
|
|
1557
|
-
!props.usingPublicOncoKbInstance && (React__default["default"].createElement(React__default["default"].Fragment, null,
|
|
1558
|
-
React__default["default"].createElement("div", { className: tabsStyles['tab-pane'] }, OncoKbMedicalDisclaimer),
|
|
1559
|
-
levelsOfEvidence &&
|
|
1560
|
-
levelsOfEvidence.levels.length > 0 && (React__default["default"].createElement(OncoKbCardLevelsOfEvidenceDropdown, { levels: levelsOfEvidence.levels, levelDes: levelsOfEvidence.levelDes })))))),
|
|
1561
|
-
!props.isCancerGene && (React__default["default"].createElement("div", { className: mainStyles['additional-info'], "data-test": 'oncokb-card-additional-info' }, "There is currently no information about this gene in OncoKB.")),
|
|
1562
|
-
props.geneNotExist && props.isCancerGene && (React__default["default"].createElement("div", { className: mainStyles['additional-info'] },
|
|
1563
|
-
React__default["default"].createElement(OncoKBSuggestAnnotationLinkout, { gene: props.hugoSymbol })))));
|
|
1564
|
-
};
|
|
1565
|
-
|
|
1566
|
-
var OncoKbCard = /** @class */ (function (_super) {
|
|
1567
|
-
tslib.__extends(OncoKbCard, _super);
|
|
1568
|
-
function OncoKbCard(props) {
|
|
1569
|
-
var _this = _super.call(this, props) || this;
|
|
1570
|
-
mobx.makeObservable(_this);
|
|
1571
|
-
return _this;
|
|
1572
|
-
}
|
|
1573
|
-
Object.defineProperty(OncoKbCard.prototype, "oncokbLinkOut", {
|
|
1574
|
-
get: function () {
|
|
1575
|
-
var link = undefined;
|
|
1576
|
-
if (this.props.hugoSymbol) {
|
|
1577
|
-
link = "https://www.oncokb.org/gene/" + this.props.hugoSymbol;
|
|
1578
|
-
if (!this.props.geneNotExist &&
|
|
1579
|
-
this.props.indicator &&
|
|
1580
|
-
this.props.indicator.variantExist) {
|
|
1581
|
-
link = link + "/" + this.props.indicator.query.alteration;
|
|
1582
|
-
}
|
|
1583
|
-
}
|
|
1584
|
-
return link;
|
|
1585
|
-
},
|
|
1586
|
-
enumerable: false,
|
|
1587
|
-
configurable: true
|
|
1588
|
-
});
|
|
1589
|
-
Object.defineProperty(OncoKbCard.prototype, "render", {
|
|
1590
|
-
enumerable: false,
|
|
1591
|
-
configurable: true,
|
|
1592
|
-
writable: true,
|
|
1593
|
-
value: function () {
|
|
1594
|
-
var oncokbLogo = (React__namespace.createElement("img", { src: oncoKbLogoImgSrc__default["default"], className: mainStyles['oncokb-logo'], alt: "OncoKB\u2122" }));
|
|
1595
|
-
return (React__namespace.createElement("div", { className: mainStyles['oncokb-card'], "data-test": "oncokb-card" },
|
|
1596
|
-
React__namespace.createElement("div", null,
|
|
1597
|
-
!this.props.geneNotExist && this.props.indicator && (React__namespace.createElement(OncoKbCardTitle, { hugoSymbol: this.props.indicator.query.hugoSymbol, variant: this.props.indicator.query.alteration, tumorType: this.props.indicator
|
|
1598
|
-
? this.props.indicator.query.tumorType
|
|
1599
|
-
: '' })),
|
|
1600
|
-
React__namespace.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 }),
|
|
1601
|
-
React__namespace.createElement("div", { className: mainStyles.footer },
|
|
1602
|
-
this.oncokbLinkOut === undefined ? ({ oncokbLogo: oncokbLogo }) : (React__namespace.createElement("a", { href: "" + this.oncokbLinkOut, target: "_blank", className: mainStyles['oncokb-logo'] }, oncokbLogo)),
|
|
1603
|
-
this.props.handleFeedbackOpen && (React__namespace.createElement("span", null,
|
|
1604
|
-
React__namespace.createElement("button", { className: "btn btn-default btn-xs", onClick: this.props.handleFeedbackOpen }, "Feedback")))))));
|
|
1605
|
-
}
|
|
1606
|
-
});
|
|
1607
|
-
tslib.__decorate([
|
|
1608
|
-
mobx.computed
|
|
1609
|
-
], OncoKbCard.prototype, "oncokbLinkOut", null);
|
|
1610
|
-
OncoKbCard = tslib.__decorate([
|
|
1611
|
-
mobxReact.observer
|
|
1612
|
-
], OncoKbCard);
|
|
1613
|
-
return OncoKbCard;
|
|
1614
|
-
}(React__namespace.Component));
|
|
1615
|
-
|
|
1616
|
-
/**
|
|
1617
|
-
* @author Selcuk Onur Sumer
|
|
1618
|
-
*/
|
|
1619
|
-
var OncoKbTooltip = /** @class */ (function (_super) {
|
|
1620
|
-
tslib.__extends(OncoKbTooltip, _super);
|
|
1621
|
-
function OncoKbTooltip() {
|
|
1622
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
1623
|
-
}
|
|
1624
|
-
Object.defineProperty(OncoKbTooltip.prototype, "pmidData", {
|
|
1625
|
-
get: function () {
|
|
1626
|
-
if (this.props.pubMedCache) {
|
|
1627
|
-
var allPmids_1 = [];
|
|
1628
|
-
if (this.props.indicator) {
|
|
1629
|
-
if (this.props.indicator.mutationEffect) {
|
|
1630
|
-
allPmids_1 = allPmids_1.concat(this.props.indicator.mutationEffect.citations.pmids);
|
|
1631
|
-
}
|
|
1632
|
-
this.props.indicator.treatments.forEach(function (treatment) {
|
|
1633
|
-
allPmids_1 = allPmids_1.concat(treatment.pmids);
|
|
1634
|
-
});
|
|
1635
|
-
this.props.indicator.diagnosticImplications.forEach(function (implication) {
|
|
1636
|
-
allPmids_1 = allPmids_1.concat(implication.pmids);
|
|
1637
|
-
});
|
|
1638
|
-
this.props.indicator.prognosticImplications.forEach(function (implication) {
|
|
1639
|
-
allPmids_1 = allPmids_1.concat(implication.pmids);
|
|
1640
|
-
});
|
|
1641
|
-
}
|
|
1642
|
-
for (var _i = 0, _a = ___default["default"].uniq(allPmids_1).map(function (pmid) { return Number(pmid); }); _i < _a.length; _i++) {
|
|
1643
|
-
var ref = _a[_i];
|
|
1644
|
-
this.props.pubMedCache.get(ref);
|
|
1645
|
-
}
|
|
1646
|
-
}
|
|
1647
|
-
return (this.props.pubMedCache && this.props.pubMedCache.cache) || {};
|
|
1648
|
-
},
|
|
1649
|
-
enumerable: false,
|
|
1650
|
-
configurable: true
|
|
1651
|
-
});
|
|
1652
|
-
Object.defineProperty(OncoKbTooltip.prototype, "render", {
|
|
1653
|
-
enumerable: false,
|
|
1654
|
-
configurable: true,
|
|
1655
|
-
writable: true,
|
|
1656
|
-
value: function () {
|
|
1657
|
-
var tooltipContent = React__namespace.createElement("span", null);
|
|
1658
|
-
if (this.props.geneNotExist) {
|
|
1659
|
-
tooltipContent = (React__namespace.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 }));
|
|
1660
|
-
}
|
|
1661
|
-
if (!this.props.indicator) {
|
|
1662
|
-
return tooltipContent;
|
|
1663
|
-
}
|
|
1664
|
-
if (!this.props.geneNotExist) {
|
|
1665
|
-
var pmidData = this.pmidData;
|
|
1666
|
-
tooltipContent = (React__namespace.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 }));
|
|
1667
|
-
}
|
|
1668
|
-
return tooltipContent;
|
|
164
|
+
React__namespace.createElement("b", null, this.props.geneName))),
|
|
165
|
+
' ',
|
|
166
|
+
"- ",
|
|
167
|
+
this.props.geneDescription)),
|
|
168
|
+
React__namespace.createElement("div", { className: "col s12" },
|
|
169
|
+
React__namespace.createElement("ul", null, this.generateVariants(this.props.variants))),
|
|
170
|
+
React__namespace.createElement("div", { className: "item disclaimer" },
|
|
171
|
+
React__namespace.createElement("span", null, "Disclaimer: This resource is intended for purely research purposes. It should not be used for emergencies or medical or professional advice.")))),
|
|
172
|
+
React__namespace.createElement("div", { className: "item footer" },
|
|
173
|
+
React__namespace.createElement("a", { href: this.props.geneUrl, target: "_blank" },
|
|
174
|
+
React__namespace.createElement("img", { src: img$5, className: "civic-logo", alt: "CIViC" })))));
|
|
1669
175
|
}
|
|
1670
176
|
});
|
|
1671
|
-
|
|
1672
|
-
mobxReact.observer
|
|
1673
|
-
], OncoKbTooltip);
|
|
1674
|
-
return OncoKbTooltip;
|
|
177
|
+
return CivicCard;
|
|
1675
178
|
}(React__namespace.Component));
|
|
1676
179
|
|
|
1677
|
-
var
|
|
1678
|
-
|
|
1679
|
-
|
|
1680
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
1681
|
-
}
|
|
1682
|
-
Object.defineProperty(OncoKbFeedback.prototype, "render", {
|
|
1683
|
-
enumerable: false,
|
|
1684
|
-
configurable: true,
|
|
1685
|
-
writable: true,
|
|
1686
|
-
value: function () {
|
|
1687
|
-
var url = 'https://docs.google.com/forms/d/1lt6TtecxHrhIE06gAKVF_JW4zKFoowNFzxn6PJv4g7A/viewform';
|
|
1688
|
-
var geneParam = "entry.1744186665=" + (this.props.hugoSymbol || '');
|
|
1689
|
-
var alterationParam = "entry.1671960263=" + (this.props.alteration ||
|
|
1690
|
-
'');
|
|
1691
|
-
var userParam = "entry.1381123986=" + (this.props.userEmailAddress ||
|
|
1692
|
-
'');
|
|
1693
|
-
var uriParam = "entry.1083850662=" + encodeURIComponent(window.location.href);
|
|
1694
|
-
return (React__namespace.createElement(reactBootstrap.Modal, { show: this.props.showFeedback, onHide: this.props.handleFeedbackClose },
|
|
1695
|
-
React__namespace.createElement(reactBootstrap.Modal.Header, { closeButton: true },
|
|
1696
|
-
React__namespace.createElement(reactBootstrap.Modal.Title, null, "OncoKB\u2122 Annotation Feedback")),
|
|
1697
|
-
React__namespace.createElement(reactBootstrap.Modal.Body, null,
|
|
1698
|
-
React__namespace.createElement("iframe", { src: url + "?" + geneParam + "&" + alterationParam + "&entry.118699694&entry.1568641202&" + userParam + "&" + uriParam + "&embedded=true", style: {
|
|
1699
|
-
width: 550,
|
|
1700
|
-
height: 500,
|
|
1701
|
-
border: 'none',
|
|
1702
|
-
marginLeft: '10px',
|
|
1703
|
-
}, marginHeight: 0, marginWidth: 0 },
|
|
1704
|
-
React__namespace.createElement("i", { className: "fa fa-spinner fa-pulse fa-2x" })))));
|
|
1705
|
-
}
|
|
1706
|
-
});
|
|
1707
|
-
return OncoKbFeedback;
|
|
1708
|
-
}(React__namespace.Component));
|
|
180
|
+
var img$4 = "data:image/png;base64,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";
|
|
181
|
+
|
|
182
|
+
var img$3 = "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEAAAABACAQAAAAAYLlVAAAAAmJLR0QA/4ePzL8AAAAJcEhZcwAACxMAAAsTAQCanBgAAAAHdElNRQfhAgILACGBOQbTAAAKjklEQVRo3sWYe4xV1RXGf3ufcx/zwJnh6eBUFOyAKFDFB9WSlooaRZIi9RlrrUpQW6Ik1KTW1CaNmtjal7F/1KYWpYrGlFcMojGiVsRRi1ixcXyL4oPXMHPn3nvO2Y/+cfY999zLzDBjir0398zjnrO+b6+19lrf2vB/fokv+2CeqzK5ybmzaQ2eCHY8VOr9agnc0DZ2a7bTwwAWQ8j+E+57M/xqCGS56cqWlRLjHjaAwdK/dvfi+81XQODmW9t+ZZBIACwWg8FgKbJTPmxHZs0bKfxPpoxba/CQNNGMRCffWDxEueufh9UDl4lOkwU8GhmFoEwfGus+hpDPM/erkViUIyPQOj6DRSCAiBBVtxZJ7qqRWRwhgcY7rHN3QIEQSQNejSNz910qDhuB74vMggoBjULSyBG0IF0yWiyCrHeYCCwSWcGESsZbLB45smTwscl+EPi5ReIwEFgkQFHZ5gaLQROhUChHKi5LWsd3D+/lDxccILJRt+mME84gKGCRlIkcndgzoao8s8b+TzyQXk3xF8qVHYMhpIceCmgHDhB1B3qgJ79kHag3MSo/vphHujooAQ+FduvXaA507n0n/cShvCBHAC8QfUHfKlP9kxxZVxXAAiE97yX/cDaG9oMcJnxitPfaIOU8n0zSESyKQru2B3t2KApymPAJjbLuPV1jk1aSSdWA/t/17Emo1vlhhDkwAHz1Kjo2jzlDIPFoJcPnKCI0JT5rCJWLRe11iGyQI4AX7s3+BWVnXeK5qqDomxnq6j01tIfwghwBfOUj+0v7LrI1Biz9a/d3p6CHTaGmEF0pGinQfzB8vVlR3m4RLvquMG2uCadFuA/u6ijUB8IRaODupjN+MP7HmROD7l33PP3gq716IPjkKpuqSIklkYZK0XAUxnqzx0yff+vXix9/9OT2T+7SKQLLxdK7py535jrb7/nGPf/567037I4GgJeV32xi3b0UMkk8UXO1gDiv44IPW4gwCGbyXeacfklXFBucyC37pi63jqrAoDn+6p+VWzJ18ALpPqI+dwxG192R9hk/nH/Rhx49lAicipr70pM3uhxafcnYVpvatj4eZY7k8l8flP8VGgOkri0ja+Cr9YC5087Y1IfGR+IhkGgO0Pn7B+eAvEWetlpTX3M9ikxbNmVsDbxM4KVJgmwriRi6FiHq3uT9C3cYcmTwHHxspsCsF2/05JyTs9iDqpPF4HPK9TXwJBDSOAq2+qxOLNcQyHpLl7eSIYuPj5eKj0Yy4yQ55sxogPJgsYSMv67GnRUHe1WHVcudVQi8Oi8wo/32V+bcKdzq469IvBYx6tt+0G/RiJoBIZYXAc0TJh/33rt10RdJN06EGIDV+G5IkvG4NKFhwVXzf+MT4LutYFK+NmgU3lF+3zvK5b9M4CNCAhQRZ77w8ddCnQIXyTJqtqHBVk0YRENu3rcuXjuKEO3aFckIU1FPClCfyE92lAidxrdOcJcoo1CUGN26+KFk1ZW1SyTSplQAsbnkjrkn3fXONWsbUYnjZSq0sXAJUfj0via37vmCkBJlihTpp49eikQYSggMHQsv/WmSA5UIe4njnUmLJs6w2dNvW3/TMxNbNSJJuurKY3BNhAFC3tsqH7Bb50UU6XfgfQRoNH1E5Mig6Lzt4tuT1Ys41WySAdpJkWA34vhJy/98y+ZZZxhXTaodySY6WhMRoTBk2F9+q+jDs89OpQ2fjHOUJqSEIpvM/rOWNY9/5Ob+ErEIkAhdkeBYDCX6ysfOmDtvwW0etm7itcn8rNGoBN5ieHqCI3jH0ed+aMjiIdzMY11hj3d7hmYOlP925sefVkKam3DMljySJkrsg57zOauVAbdzrBU0Ck1ESIgiQiF5afHGNY7s0wfOHTPm9MDJa1IVK972HoZm/9SlpR0730fi4XmNrddk0BTxyqcVrs5Pax5YWVmsi7oiIiRyVARv37nm3pRcuEJep5tQrqfWNnbwkQh8sry+4dFf9h3Ay40/+nmJLc8on5Mflx9M71kHXQE3KEIMlu3L1v8plq+iIhSOyl1eymOTTKt8aV3g44TK0c/aJV3P47XvmMT5PSfkxZDwykU9jntEhKDAltnPvVYpIaIqljpbFu/PYNzWkSk1JZO+aski2frIUw/P/8PFk4bS+9blewweU7Eodm7ZdN5HhaqSEWm1NrXtgr3NjoKsCUa1vRsCGmgnV/byQ8Erghpwg2UvL8z+1+uhSUupGk34Vk+p5aIDozA1qtIkAYnz+QjG0QBDwGsiAgeuHfgBtl+6Zf2BsKbl1nsAAWNyC+8/5hKbxJ1kZ1sUGUbTNuRIbZPNptyGtuxn+5Kux3b3u85l0630IAIIX86/7JSVWQzS0bR4GDTNTKBpyHlWERCgMG5kNfTyyrKXH9nT6yrXcAggEMcfc3bX6FaTeEohGcd4skPAawK30zUKMOyl6/pX1+zvdcVwGASoio9R2XkrTrzNRyEp4TOJMfiDwhtC10E1GknE5+Uty7Y/3ldwRwkVMTAsAlSk1eTJ33ngyNl9NDGFljrRUgseuJVrAhS7urfevuOZUgHjmoVJRJCthR+IQI0E9/wpJy9YM6u1EdJKrAY8JHTHE0UKGJ5a8vLjGHdwdEgCQx/RWK13d8+kcYAbLZoyBQqUCFEU+JR9+LQx/ZT29vqxaRhHNPVpGFeitpY/fppHJcJCpIpsvHKNJkOJz2hmNBkUGSzrV2xapYPk8Myk9HudB5KwHl9PABDeXdtGt5Zd8lVsaEICt26FQPBGeXPhBI7zJYb4GH/GOdPmvbux0F8dGw5y4HDOiJb8fOKkfleE4p2kCChRpERIiEWyq7yu5x+8nc8ToMmQIYtEMW32Ld2zph86CIN7QJww6epH+xMlb1xPr1b4DHvLLxaeV1+0Cr9BzSDrk5rcFHlOubbY9f67A698MAKpOXBFd1PeIFKSKnJujxBItvWsU7vzfrOHQagZ5HzrRuKYhsFj5qXm391v1Y5QtTT8weIzZ/LE1jKeE2XGFddYMwl2ffjse7u+mc/naaTPTSIKicHgJ/LZIFi0+ou5L3UN45Ss7uRCnPWYdkUszvggUXMh2zb8duHrTzbkM6mRwbimq5z4MIDEYPnR8+1tg2/KQZLw6IajTixBEvcQ5apcxLoVDy5X5exEz+lFAfh5lS878MgdYWtAosmy9AMhBj45G5RAR7vv5GNsUKMI0BRZdcXWx7AYr0giWiT9b3z0Rnz4ECaDXXx4LwnpyJ86c4QHlcfOrYiJipINUQSs/N6bz1VO62VSliTF11ZfuPH6PRjKlNz6jQOQGOb+fbB9IAdMQXvETOU0rE7qnuKJFR90VUqCCKu3C7wWou0bV87atiEkokSAdeCxSpjQ2dF8SA+k09A02WQd8cazdL+6dZWbNCzWlElNfbaIxfbtW7d005ICAbrmQAV8Oo4eURLqSDkdWylAZd76S6qmWx2lDicgqkyp2zasX9iLJOOmw4qwHTNjoACssYMQKLxRgTeuBpTwW1MDoRVBTXMOkznVvP/i9mXjyLnZuFLdZFs9xhq7xg7sAQs7n4qSKmCcuOy4yW3sysCXWpCIUm3HHtvRTJZMUsY1IaXuevj4538BBXB1HeF6wqkAAAAASUVORK5CYII=";
|
|
1709
183
|
|
|
1710
|
-
function
|
|
1711
|
-
var
|
|
1712
|
-
|
|
1713
|
-
values[0] = calcOncogenicScore(indicator.oncogenic);
|
|
1714
|
-
values[1] = calcSensitivityLevelScore(indicator.highestSensitiveLevel);
|
|
1715
|
-
values[2] = calcResistanceLevelScore(indicator.highestResistanceLevel);
|
|
1716
|
-
values[3] = calcDiagnosticLevelScore(indicator.highestDiagnosticImplicationLevel);
|
|
1717
|
-
values[4] = calcPrognosticLevelScore(indicator.highestPrognosticImplicationLevel);
|
|
1718
|
-
}
|
|
1719
|
-
return values;
|
|
184
|
+
function hideArrow(tooltipEl) {
|
|
185
|
+
var arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
|
|
186
|
+
arrowEl.style.display = 'none';
|
|
1720
187
|
}
|
|
1721
|
-
function
|
|
1722
|
-
var
|
|
1723
|
-
if (
|
|
1724
|
-
|
|
188
|
+
function sortValue$7(civicEntry) {
|
|
189
|
+
var score = 0;
|
|
190
|
+
if (civicEntry) {
|
|
191
|
+
score = 1;
|
|
1725
192
|
}
|
|
1726
|
-
|
|
1727
|
-
var sensitivityLevel = ((_a = indicator.highestSensitiveLevel) === null || _a === void 0 ? void 0 : _a.toLowerCase()) || 'level NA';
|
|
1728
|
-
var resistanceLevel = ((_b = indicator.highestResistanceLevel) === null || _b === void 0 ? void 0 : _b.toLowerCase()) || 'resistance NA';
|
|
1729
|
-
return oncogenic + ", " + sensitivityLevel + ", " + resistanceLevel;
|
|
193
|
+
return score;
|
|
1730
194
|
}
|
|
1731
|
-
function
|
|
1732
|
-
if (
|
|
1733
|
-
return cbioportalUtils.
|
|
1734
|
-
}
|
|
1735
|
-
|
|
1736
|
-
|
|
1737
|
-
|
|
1738
|
-
|
|
1739
|
-
|
|
1740
|
-
|
|
1741
|
-
|
|
1742
|
-
|
|
1743
|
-
|
|
1744
|
-
return cbioportalUtils.
|
|
1745
|
-
}
|
|
1746
|
-
|
|
1747
|
-
availableDataTypes &&
|
|
1748
|
-
availableDataTypes.includes(cbioportalUtils.OncoKbCardDataType.DX)) {
|
|
1749
|
-
return cbioportalUtils.OncoKbCardDataType.DX;
|
|
1750
|
-
}
|
|
1751
|
-
else if (indicator.highestPrognosticImplicationLevel &&
|
|
1752
|
-
availableDataTypes &&
|
|
1753
|
-
availableDataTypes.includes(cbioportalUtils.OncoKbCardDataType.PX)) {
|
|
1754
|
-
return cbioportalUtils.OncoKbCardDataType.PX;
|
|
1755
|
-
}
|
|
1756
|
-
return cbioportalUtils.OncoKbCardDataType.BIOLOGICAL;
|
|
195
|
+
function download$6(civicEntry) {
|
|
196
|
+
if (!civicEntry) {
|
|
197
|
+
return cbioportalUtils.CIVIC_NA_VALUE;
|
|
198
|
+
}
|
|
199
|
+
var variants = ___default["default"].values(civicEntry.variants);
|
|
200
|
+
var values = [];
|
|
201
|
+
if (variants && variants.length > 0 && variants[0].evidenceCounts) {
|
|
202
|
+
___default["default"].forEach(variants[0].evidenceCounts, function (value, key) {
|
|
203
|
+
values.push(key + ": " + value);
|
|
204
|
+
});
|
|
205
|
+
}
|
|
206
|
+
// this indicates that we have an entry but the evidence is empty
|
|
207
|
+
if (values.length === 0) {
|
|
208
|
+
return cbioportalUtils.CIVIC_NA_VALUE;
|
|
209
|
+
}
|
|
210
|
+
return values.join(', ');
|
|
1757
211
|
}
|
|
1758
|
-
var
|
|
1759
|
-
tslib.__extends(
|
|
1760
|
-
function
|
|
212
|
+
var Civic = /** @class */ (function (_super) {
|
|
213
|
+
tslib.__extends(Civic, _super);
|
|
214
|
+
function Civic(props) {
|
|
1761
215
|
var _this = _super.call(this, props) || this;
|
|
1762
|
-
Object.defineProperty(_this, "showFeedback", {
|
|
1763
|
-
enumerable: true,
|
|
1764
|
-
configurable: true,
|
|
1765
|
-
writable: true,
|
|
1766
|
-
value: false
|
|
1767
|
-
});
|
|
1768
216
|
Object.defineProperty(_this, "tooltipDataLoadComplete", {
|
|
1769
217
|
enumerable: true,
|
|
1770
218
|
configurable: true,
|
|
@@ -1772,125 +220,136 @@ var OncoKB = /** @class */ (function (_super) {
|
|
|
1772
220
|
value: false
|
|
1773
221
|
});
|
|
1774
222
|
mobx.makeObservable(_this);
|
|
223
|
+
_this.cardContent = _this.cardContent.bind(_this);
|
|
1775
224
|
return _this;
|
|
1776
225
|
}
|
|
1777
|
-
Object.defineProperty(
|
|
226
|
+
Object.defineProperty(Civic.prototype, "render", {
|
|
1778
227
|
enumerable: false,
|
|
1779
228
|
configurable: true,
|
|
1780
229
|
writable: true,
|
|
1781
230
|
value: function () {
|
|
1782
|
-
var
|
|
1783
|
-
|
|
1784
|
-
|
|
1785
|
-
|
|
1786
|
-
|
|
1787
|
-
|
|
231
|
+
var civicContent = (React__namespace.createElement("span", { className: "" + annotationStyles['annotation-item'] }));
|
|
232
|
+
var civicImgWidth = 14;
|
|
233
|
+
var civicImgHeight = 14;
|
|
234
|
+
var civicImgSrc = !this.props.hasCivicVariants
|
|
235
|
+
? img$3
|
|
236
|
+
: img$4;
|
|
237
|
+
if (this.props.civicStatus == 'error') {
|
|
238
|
+
civicContent = errorIcon('Error fetching Civic data');
|
|
1788
239
|
}
|
|
1789
|
-
else {
|
|
1790
|
-
|
|
1791
|
-
|
|
1792
|
-
|
|
1793
|
-
|
|
1794
|
-
|
|
1795
|
-
oncoKbContent,
|
|
1796
|
-
React__namespace.createElement(OncoKbFeedback, { userEmailAddress: this.props.userEmailAddress, hugoSymbol: this.props.hugoGeneSymbol, alteration: this.props.indicator
|
|
1797
|
-
? this.props.indicator.query.alteration
|
|
1798
|
-
: undefined, showFeedback: this.showFeedback, handleFeedbackClose: this.handleFeedbackClose })));
|
|
240
|
+
else if (this.props.civicEntry !== undefined) {
|
|
241
|
+
if (this.props.civicEntry !== null &&
|
|
242
|
+
this.props.civicStatus == 'complete') {
|
|
243
|
+
civicContent = (React__namespace.createElement("span", { className: "" + annotationStyles['annotation-item'] },
|
|
244
|
+
React__namespace.createElement("img", { width: civicImgWidth, height: civicImgHeight, src: civicImgSrc, alt: "Civic Variant Entry" })));
|
|
245
|
+
civicContent = (React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlay: this.cardContent.bind(this, this.props.civicEntry), placement: "right", trigger: ['hover', 'focus'], onPopupAlign: hideArrow, destroyTooltipOnHide: false }, civicContent));
|
|
1799
246
|
}
|
|
1800
247
|
}
|
|
1801
|
-
return oncoKbContent;
|
|
1802
|
-
}
|
|
1803
|
-
});
|
|
1804
|
-
Object.defineProperty(OncoKB.prototype, "multiAnnotationIcon", {
|
|
1805
|
-
enumerable: false,
|
|
1806
|
-
configurable: true,
|
|
1807
|
-
writable: true,
|
|
1808
|
-
value: function () {
|
|
1809
|
-
return (React__namespace.createElement("span", { className: "oncokb-content", style: { display: 'inline-flex' } },
|
|
1810
|
-
React__namespace.createElement(AnnotationIcon, { type: cbioportalUtils.OncoKbCardDataType.BIOLOGICAL, tooltipOverlay: this.tooltipContent(cbioportalUtils.OncoKbCardDataType.BIOLOGICAL), indicator: this.props.indicator, availableDataTypes: this.props.availableDataTypes }),
|
|
1811
|
-
this.levelIcons()));
|
|
1812
|
-
}
|
|
1813
|
-
});
|
|
1814
|
-
Object.defineProperty(OncoKB.prototype, "levelIcons", {
|
|
1815
|
-
enumerable: false,
|
|
1816
|
-
configurable: true,
|
|
1817
|
-
writable: true,
|
|
1818
|
-
value: function () {
|
|
1819
|
-
var _this = this;
|
|
1820
|
-
if (this.props.usingPublicOncoKbInstance) {
|
|
1821
|
-
return null;
|
|
1822
|
-
}
|
|
1823
|
-
if (this.props.indicator) {
|
|
1824
|
-
return (React__namespace.createElement(React__namespace.Fragment, null, [
|
|
1825
|
-
cbioportalUtils.OncoKbCardDataType.TXS,
|
|
1826
|
-
cbioportalUtils.OncoKbCardDataType.TXR,
|
|
1827
|
-
cbioportalUtils.OncoKbCardDataType.DX,
|
|
1828
|
-
cbioportalUtils.OncoKbCardDataType.PX,
|
|
1829
|
-
].map(function (dataType) { return (React__namespace.createElement(AnnotationIcon, { type: dataType, tooltipOverlay: _this.tooltipContent(dataType), indicator: _this.props.indicator, availableDataTypes: _this.props.availableDataTypes })); })));
|
|
1830
|
-
}
|
|
1831
248
|
else {
|
|
1832
|
-
//
|
|
1833
|
-
|
|
1834
|
-
// ideally we should implement grouped columns to avoid these kind of workarounds
|
|
1835
|
-
// (see https://github.com/cBioPortal/cbioportal/issues/8723)
|
|
1836
|
-
return React__namespace.createElement("i", { style: { paddingRight: this.props.contentPadding } });
|
|
249
|
+
// It's still unknown (undefined) if the current gene has a Civic entry or not.
|
|
250
|
+
civicContent = loaderIcon('pull-left');
|
|
1837
251
|
}
|
|
252
|
+
return civicContent;
|
|
1838
253
|
}
|
|
1839
254
|
});
|
|
1840
|
-
Object.defineProperty(
|
|
1841
|
-
enumerable: false,
|
|
1842
|
-
configurable: true,
|
|
1843
|
-
writable: true,
|
|
1844
|
-
value: function () {
|
|
1845
|
-
return (React__namespace.createElement("span", { className: "oncokb-content", style: { display: 'inline-flex' } },
|
|
1846
|
-
React__namespace.createElement(AnnotationIconWithTooltip, { tooltipOverlay: this.tooltipContent(findDefaultDataTypeForTooltip(this.props.usingPublicOncoKbInstance, this.props.indicator, this.props.availableDataTypes)), icon: React__namespace.createElement(CompactAnnotationIcon, { indicator: this.props.indicator, availableDataTypes: this.props.availableDataTypes, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance }) })));
|
|
1847
|
-
}
|
|
1848
|
-
});
|
|
1849
|
-
Object.defineProperty(OncoKB.prototype, "tooltipContent", {
|
|
255
|
+
Object.defineProperty(Civic.prototype, "cardContent", {
|
|
1850
256
|
enumerable: false,
|
|
1851
257
|
configurable: true,
|
|
1852
258
|
writable: true,
|
|
1853
|
-
value: function (
|
|
1854
|
-
return (React__namespace.createElement(
|
|
1855
|
-
? undefined
|
|
1856
|
-
: this.handleFeedbackOpen }));
|
|
259
|
+
value: function (civicEntry) {
|
|
260
|
+
return (React__namespace.createElement(CivicCard, { title: "CIViC Variants", geneName: civicEntry.name, geneDescription: civicEntry.description, geneUrl: civicEntry.url, variants: civicEntry.variants }));
|
|
1857
261
|
}
|
|
1858
262
|
});
|
|
1859
|
-
|
|
1860
|
-
|
|
1861
|
-
|
|
1862
|
-
|
|
1863
|
-
|
|
1864
|
-
|
|
263
|
+
tslib.__decorate([
|
|
264
|
+
mobx.observable
|
|
265
|
+
], Civic.prototype, "tooltipDataLoadComplete", void 0);
|
|
266
|
+
Civic = tslib.__decorate([
|
|
267
|
+
mobxReact.observer
|
|
268
|
+
], Civic);
|
|
269
|
+
return Civic;
|
|
270
|
+
}(React__namespace.Component));
|
|
271
|
+
|
|
272
|
+
var NoClinvarData = function () {
|
|
273
|
+
return (React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { placement: "topLeft", overlay: React__namespace.createElement("span", null, "Variant has no ClinVar data.") },
|
|
274
|
+
React__namespace.createElement("span", { style: {
|
|
275
|
+
height: '100%',
|
|
276
|
+
width: '100%',
|
|
277
|
+
display: 'block',
|
|
278
|
+
overflow: 'hidden',
|
|
279
|
+
} }, "\u00A0")));
|
|
280
|
+
};
|
|
281
|
+
var ClinvarSummary = function (props) {
|
|
282
|
+
if (!props.clinvar) {
|
|
283
|
+
return React__namespace.createElement(NoClinvarData, null);
|
|
284
|
+
}
|
|
285
|
+
else {
|
|
286
|
+
var clinvarId = props.clinvar.clinvarId;
|
|
287
|
+
var clinvarLink = "https://www.ncbi.nlm.nih.gov/clinvar/variation/" + clinvarId + "/";
|
|
288
|
+
var clinicalSignificance = props.clinvar.clinicalSignificance;
|
|
289
|
+
var conflictingClinicalSignificance = props.clinvar.conflictingClinicalSignificance;
|
|
290
|
+
return (React__namespace.createElement(cbioportalFrontendCommons.TruncatedText, { maxLength: 30, text: clinicalSignificance, addTooltip: "always", tooltip: React__namespace.createElement("div", { style: { maxWidth: 300 } },
|
|
291
|
+
React__namespace.createElement("div", null, clinicalSignificance),
|
|
292
|
+
conflictingClinicalSignificance && (React__namespace.createElement("div", null, conflictingClinicalSignificance)),
|
|
293
|
+
React__namespace.createElement("div", null,
|
|
294
|
+
"(ClinVar ID:",
|
|
295
|
+
' ',
|
|
296
|
+
React__namespace.createElement("a", { href: clinvarLink, target: "_blank" }, clinvarId),
|
|
297
|
+
")")) }));
|
|
298
|
+
}
|
|
299
|
+
};
|
|
300
|
+
|
|
301
|
+
var img$2 = "data:image/png;base64,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";
|
|
302
|
+
|
|
303
|
+
var mcgStyles = {"link-list":"myCancerGenome-module_link-list__2wFhH"};
|
|
304
|
+
|
|
305
|
+
function placeArrow$1(tooltipEl) {
|
|
306
|
+
var arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
|
|
307
|
+
arrowEl.style.left = '10px';
|
|
308
|
+
}
|
|
309
|
+
function sortValue$6(links) {
|
|
310
|
+
return links.length > 0 ? 1 : 0;
|
|
311
|
+
}
|
|
312
|
+
function download$5(links) {
|
|
313
|
+
return links.length > 0 ? 'present' : 'not present';
|
|
314
|
+
}
|
|
315
|
+
function myCancerGenomeLinks(linksHTML) {
|
|
316
|
+
var links = [];
|
|
317
|
+
___default["default"].each(linksHTML, function (link, index) {
|
|
318
|
+
// TODO this is a workaround, ideally we should fix the data itself
|
|
319
|
+
// parse the data as an HTML dom element, since it is formatted as an HTML link.
|
|
320
|
+
var myCancerGenomeLink = cbioportalUtils.parseMyCancerGenomeLink(link);
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|
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if (myCancerGenomeLink) {
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links.push(React__namespace.createElement("li", { key: index },
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React__namespace.createElement("a", { href: myCancerGenomeLink.url, target: "_blank" }, myCancerGenomeLink.text)));
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return (React__namespace.createElement("span", null,
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React__namespace.createElement("b", null, "My Cancer Genome links:"),
|
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React__namespace.createElement("br", null),
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React__namespace.createElement("ul", { className: mcgStyles['link-list'] }, links)));
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}
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var MyCancerGenome = /** @class */ (function (_super) {
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tslib.__extends(MyCancerGenome, _super);
|
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|
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function MyCancerGenome() {
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return _super !== null && _super.apply(this, arguments) || this;
|
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}
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Object.defineProperty(MyCancerGenome.prototype, "render", {
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enumerable: false,
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configurable: true,
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value: function () {
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var myCancerGenomeContent = (React__namespace.createElement("span", { className: "" + annotationStyles['annotation-item'] }));
|
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|
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if (this.props.linksHTML.length > 0) {
|
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var arrowContent = React__namespace.createElement("div", { className: "rc-tooltip-arrow-inner" });
|
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|
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var tooltipContent = myCancerGenomeLinks(this.props.linksHTML);
|
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|
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myCancerGenomeContent = (React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlay: tooltipContent, placement: "topLeft", trigger: ['hover', 'focus'], arrowContent: arrowContent, onPopupAlign: placeArrow$1 },
|
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React__namespace.createElement("span", { className: annotationStyles['annotation-item'] + " mcg" },
|
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+
React__namespace.createElement("img", { width: "14", height: "14", src: img$2, alt: "My Cancer Genome Symbol" }))));
|
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|
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}
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return myCancerGenomeContent;
|
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|
}
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|
});
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|
-
|
|
1876
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-
mobx.observable
|
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|
-
], OncoKB.prototype, "showFeedback", void 0);
|
|
1878
|
-
tslib.__decorate([
|
|
1879
|
-
mobx.observable
|
|
1880
|
-
], OncoKB.prototype, "tooltipDataLoadComplete", void 0);
|
|
1881
|
-
tslib.__decorate([
|
|
1882
|
-
autobind__default["default"]
|
|
1883
|
-
], OncoKB.prototype, "tooltipContent", null);
|
|
1884
|
-
tslib.__decorate([
|
|
1885
|
-
autobind__default["default"]
|
|
1886
|
-
], OncoKB.prototype, "handleFeedbackOpen", null);
|
|
1887
|
-
tslib.__decorate([
|
|
1888
|
-
autobind__default["default"]
|
|
1889
|
-
], OncoKB.prototype, "handleFeedbackClose", null);
|
|
1890
|
-
OncoKB = tslib.__decorate([
|
|
1891
|
-
mobxReact.observer
|
|
1892
|
-
], OncoKB);
|
|
1893
|
-
return OncoKB;
|
|
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|
+
return MyCancerGenome;
|
|
1894
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|
}(React__namespace.Component));
|
|
1895
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|
|
|
1896
355
|
var hotspotStyles = {"hotspot-info":"hotspotInfo-module_hotspot-info__S24fX"};
|
|
@@ -2242,8 +701,8 @@ function getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, myCancerGen
|
|
|
2242
701
|
oncoKbData.result &&
|
|
2243
702
|
!(oncoKbData.result instanceof Error) &&
|
|
2244
703
|
oncoKbData.status === 'complete') {
|
|
2245
|
-
oncoKbIndicator = getIndicatorData(mutation, oncoKbData.result, resolveTumorType, resolveEntrezGeneId);
|
|
2246
|
-
oncoKbAvailableDataTypes = ___default["default"].uniq(tslib.__spreadArrays(oncoKbAvailableDataTypes,
|
|
704
|
+
oncoKbIndicator = oncokbFrontendCommons.getIndicatorData(mutation, oncoKbData.result, resolveTumorType, resolveEntrezGeneId);
|
|
705
|
+
oncoKbAvailableDataTypes = ___default["default"].uniq(tslib.__spreadArrays(oncoKbAvailableDataTypes, oncokbFrontendCommons.calculateOncoKbAvailableDataType(___default["default"].values(oncoKbData.result.indicatorMap))));
|
|
2247
706
|
}
|
|
2248
707
|
value = tslib.__assign(tslib.__assign({}, value), { oncoKbStatus: oncoKbData ? oncoKbData.status : 'pending', oncoKbIndicator: oncoKbIndicator,
|
|
2249
708
|
oncoKbAvailableDataTypes: oncoKbAvailableDataTypes });
|
|
@@ -2268,17 +727,17 @@ function annotationSortMethod(a, b) {
|
|
|
2268
727
|
}
|
|
2269
728
|
function sortValue$4(annotation) {
|
|
2270
729
|
return ___default["default"].flatten([
|
|
2271
|
-
|
|
2272
|
-
sortValue$
|
|
2273
|
-
sortValue$
|
|
730
|
+
oncokbFrontendCommons.oncoKbAnnotationSortValue(annotation.oncoKbIndicator),
|
|
731
|
+
sortValue$7(annotation.civicEntry),
|
|
732
|
+
sortValue$6(annotation.myCancerGenomeLinks),
|
|
2274
733
|
sortValue$5(annotation.isHotspot, annotation.is3dHotspot),
|
|
2275
734
|
annotation.isOncoKbCancerGene ? 1 : 0,
|
|
2276
735
|
]);
|
|
2277
736
|
}
|
|
2278
737
|
function GenericAnnotation(props) {
|
|
2279
|
-
var annotation = props.annotation, enableCivic = props.enableCivic, enableHotspot = props.enableHotspot, enableMyCancerGenome = props.enableMyCancerGenome, enableOncoKb = props.enableOncoKb
|
|
738
|
+
var annotation = props.annotation, enableCivic = props.enableCivic, enableHotspot = props.enableHotspot, enableMyCancerGenome = props.enableMyCancerGenome, enableOncoKb = props.enableOncoKb; props.pubMedCache; var userEmailAddress = props.userEmailAddress, mergeOncoKbIcons = props.mergeOncoKbIcons, oncoKbContentPadding = props.oncoKbContentPadding;
|
|
2280
739
|
return (React__namespace.createElement("span", { style: { display: 'flex', minWidth: 100 } },
|
|
2281
|
-
enableOncoKb && (React__namespace.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,
|
|
740
|
+
enableOncoKb && (React__namespace.createElement(oncokbFrontendCommons.OncoKB, { usingPublicOncoKbInstance: annotation.usingPublicOncoKbInstance, hugoGeneSymbol: annotation.hugoGeneSymbol, geneNotExist: !annotation.oncoKbGeneExist, isCancerGene: annotation.isOncoKbCancerGene, status: annotation.oncoKbStatus, indicator: annotation.oncoKbIndicator, availableDataTypes: annotation.oncoKbAvailableDataTypes, mergeAnnotationIcons: mergeOncoKbIcons, userEmailAddress: userEmailAddress, contentPadding: oncoKbContentPadding })),
|
|
2282
741
|
enableCivic && (React__namespace.createElement(Civic, { civicEntry: annotation.civicEntry, civicStatus: annotation.civicStatus, hasCivicVariants: annotation.hasCivicVariants })),
|
|
2283
742
|
enableMyCancerGenome && (React__namespace.createElement(MyCancerGenome, { linksHTML: annotation.myCancerGenomeLinks })),
|
|
2284
743
|
enableHotspot && (React__namespace.createElement(HotspotAnnotation, { isHotspot: annotation.isHotspot, is3dHotspot: annotation.is3dHotspot, status: annotation.hotspotStatus }))));
|
|
@@ -3344,7 +1803,7 @@ var DropdownSelector = /** @class */ (function (_super) {
|
|
|
3344
1803
|
var _a;
|
|
3345
1804
|
var allValuesSelected = this.allValues.length === this.selectedValues.length;
|
|
3346
1805
|
var classes = this.props.selectionIndicatorClassNames;
|
|
3347
|
-
return
|
|
1806
|
+
return classNames__default["default"](classes.base, (_a = {},
|
|
3348
1807
|
_a[classes.allSelected] = allValuesSelected,
|
|
3349
1808
|
_a[classes.partiallySelected] = !allValuesSelected,
|
|
3350
1809
|
_a));
|
|
@@ -4086,8 +2545,8 @@ var FilterResetPanel = /** @class */ (function (_super) {
|
|
|
4086
2545
|
writable: true,
|
|
4087
2546
|
value: {
|
|
4088
2547
|
buttonText: 'Show all',
|
|
4089
|
-
buttonClass:
|
|
4090
|
-
className:
|
|
2548
|
+
buttonClass: classNames__default["default"]('btn', 'btn-secondary', 'btn-sm'),
|
|
2549
|
+
className: classNames__default["default"]('alert', 'alert-success', styles$7.filterResetPanel),
|
|
4091
2550
|
}
|
|
4092
2551
|
});
|
|
4093
2552
|
FilterResetPanel = tslib.__decorate([
|
|
@@ -4502,7 +2961,7 @@ var DataTable = /** @class */ (function (_super) {
|
|
|
4502
2961
|
value: function () {
|
|
4503
2962
|
return (React__namespace.createElement("div", { className: "cbioportal-frontend" },
|
|
4504
2963
|
React__namespace.createElement(DataTableToolbar, { visibilityToggle: this.onVisibilityToggle, showSearchBox: this.props.showSearchBox, onSearch: this.onSearch, filterInputRef: this.filterInputRef, searchDelay: this.props.searchDelay, searchPlaceHolder: this.props.searchPlaceholder, info: this.props.info, showColumnVisibility: this.props.showColumnVisibility, columnVisibility: this.columnVisibilityDef, columnSelectorProps: this.props.columnSelectorProps }),
|
|
4505
|
-
React__namespace.createElement("div", { className:
|
|
2964
|
+
React__namespace.createElement("div", { className: classNames__default["default"](this.props.className, 'cbioportal-frontend', 'default-data-table') },
|
|
4506
2965
|
React__namespace.createElement(ReactTable__default["default"], tslib.__assign({ data: this.tableData, columns: this.columns, getTrProps: this.needToCustomizeRowStyle
|
|
4507
2966
|
? this.getTrProps
|
|
4508
2967
|
: undefined, defaultSorted: this.defaultSorted, defaultPageSize: this.props.initialItemsPerPage, showPagination: this.showPagination, className: "-striped -highlight", previousText: "<", nextText: ">", expanded: this.expanded, onExpandedChange: this.onExpandedChange, onPageChange: this.resetExpander, onPageSizeChange: this.resetExpander, onSortedChange: this.resetExpander, minRows: 1 }, this.props.reactTableProps)))));
|
|
@@ -7371,7 +5830,7 @@ var LollipopMutationPlotControls = /** @class */ (function (_super) {
|
|
|
7371
5830
|
});
|
|
7372
5831
|
Object.defineProperty(LollipopMutationPlotControls.prototype, "trackSelector", {
|
|
7373
5832
|
get: function () {
|
|
7374
|
-
return (React__namespace.createElement("div", { className:
|
|
5833
|
+
return (React__namespace.createElement("div", { className: classNames__default["default"]('annotation-track-selector', 'small'), style: { width: 180, marginRight: 7 } },
|
|
7375
5834
|
React__namespace.createElement(TrackSelector, { tracks: this.props.tracks, trackVisibility: this.props.trackVisibility, trackDataStatus: this.props.trackDataStatus, onChange: this.props.onTrackVisibilityChange })));
|
|
7376
5835
|
},
|
|
7377
5836
|
enumerable: false,
|
|
@@ -7398,7 +5857,7 @@ var LollipopMutationPlotControls = /** @class */ (function (_super) {
|
|
|
7398
5857
|
configurable: true,
|
|
7399
5858
|
writable: true,
|
|
7400
5859
|
value: function () {
|
|
7401
|
-
return (React__namespace.createElement("div", { className:
|
|
5860
|
+
return (React__namespace.createElement("div", { className: classNames__default["default"]('lollipop_mutation_plot__controls', this.props.showControls
|
|
7402
5861
|
? styles$5['fade-in']
|
|
7403
5862
|
: styles$5['fade-out']) },
|
|
7404
5863
|
React__namespace.createElement("div", { style: { display: 'flex', alignItems: 'center' } },
|
|
@@ -8011,7 +6470,7 @@ var Track = /** @class */ (function (_super) {
|
|
|
8011
6470
|
position: 'relative',
|
|
8012
6471
|
display: 'flex',
|
|
8013
6472
|
} },
|
|
8014
|
-
React__namespace.createElement("span", { className:
|
|
6473
|
+
React__namespace.createElement("span", { className: classNames__default["default"](styles$4.trackTitle, 'small', (this.props.isSubTrack ? 'subtrack-' : '') + "trackTitle") }, this.props.trackTitle),
|
|
8015
6474
|
React__namespace.createElement("span", null,
|
|
8016
6475
|
React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, tslib.__assign({ placement: this.getOverlayPlacement(), overlay: this.getOverlay, onVisibleChange: this.onTooltipVisibleChange, destroyTooltipOnHide: true }, this.tooltipVisibleProps), this.hitZone),
|
|
8017
6476
|
React__namespace.createElement("span", { style: { marginLeft: this.props.xOffset }, onMouseOver: this.onMouseOver },
|
|
@@ -8171,130 +6630,6 @@ var OncoKbFilterValue;
|
|
|
8171
6630
|
OncoKbFilterValue["Oncogenic"] = "ONCOGENIC";
|
|
8172
6631
|
})(OncoKbFilterValue || (OncoKbFilterValue = {}));
|
|
8173
6632
|
|
|
8174
|
-
var OncoKbSummaryTable = /** @class */ (function (_super) {
|
|
8175
|
-
tslib.__extends(OncoKbSummaryTable, _super);
|
|
8176
|
-
function OncoKbSummaryTable(props) {
|
|
8177
|
-
var _this = _super.call(this, props) || this;
|
|
8178
|
-
mobx.makeObservable(_this);
|
|
8179
|
-
_this.state = {};
|
|
8180
|
-
return _this;
|
|
8181
|
-
}
|
|
8182
|
-
OncoKbSummaryTable_1 = OncoKbSummaryTable;
|
|
8183
|
-
Object.defineProperty(OncoKbSummaryTable.prototype, "hasLevelData", {
|
|
8184
|
-
get: function () {
|
|
8185
|
-
return this.props.data.find(function (d) { return d.level.length > 0; }) !== undefined;
|
|
8186
|
-
},
|
|
8187
|
-
enumerable: false,
|
|
8188
|
-
configurable: true
|
|
8189
|
-
});
|
|
8190
|
-
Object.defineProperty(OncoKbSummaryTable.prototype, "columns", {
|
|
8191
|
-
get: function () {
|
|
8192
|
-
var columns = [
|
|
8193
|
-
{
|
|
8194
|
-
id: 'proteinChange',
|
|
8195
|
-
accessor: 'proteinChange',
|
|
8196
|
-
Header: 'Protein Change',
|
|
8197
|
-
sortMethod: function (a, b) {
|
|
8198
|
-
return cbioportalUtils.defaultSortMethod(cbioportalUtils.calcProteinChangeSortValue(a), cbioportalUtils.calcProteinChangeSortValue(b));
|
|
8199
|
-
},
|
|
8200
|
-
},
|
|
8201
|
-
{
|
|
8202
|
-
id: 'count',
|
|
8203
|
-
accessor: 'count',
|
|
8204
|
-
Header: 'Occurrence',
|
|
8205
|
-
maxWidth: 80,
|
|
8206
|
-
},
|
|
8207
|
-
{
|
|
8208
|
-
id: 'clinicalImplication',
|
|
8209
|
-
accessor: 'clinicalImplication',
|
|
8210
|
-
Header: 'Implication',
|
|
8211
|
-
Cell: function (props) { return (React__namespace.createElement("span", null, props.original.clinicalImplication.join(', '))); },
|
|
8212
|
-
sortMethod: cbioportalUtils.defaultStringArraySortMethod,
|
|
8213
|
-
minWidth: 120,
|
|
8214
|
-
},
|
|
8215
|
-
{
|
|
8216
|
-
id: 'biologicalEffect',
|
|
8217
|
-
accessor: 'biologicalEffect',
|
|
8218
|
-
Header: 'Effect',
|
|
8219
|
-
Cell: function (props) { return (React__namespace.createElement("span", null, props.original.biologicalEffect.join(', '))); },
|
|
8220
|
-
sortMethod: cbioportalUtils.defaultStringArraySortMethod,
|
|
8221
|
-
minWidth: 150,
|
|
8222
|
-
},
|
|
8223
|
-
];
|
|
8224
|
-
if (!this.props.usingPublicOncoKbInstance) {
|
|
8225
|
-
columns.push({
|
|
8226
|
-
id: 'level',
|
|
8227
|
-
accessor: 'level',
|
|
8228
|
-
Header: 'Level',
|
|
8229
|
-
sortable: false,
|
|
8230
|
-
Cell: function (props) { return (React__namespace.createElement(React__namespace.Fragment, null, props.original.level.map(function (level) { return (React__namespace.createElement("div", { key: level.level, style: {
|
|
8231
|
-
display: 'flex',
|
|
8232
|
-
overflow: 'hidden',
|
|
8233
|
-
textOverflow: 'ellipsis',
|
|
8234
|
-
} },
|
|
8235
|
-
React__namespace.createElement(LevelIcon, { level: level.level, showDescription: true }),
|
|
8236
|
-
React__namespace.createElement("span", { style: {
|
|
8237
|
-
paddingRight: 3,
|
|
8238
|
-
} }, ":"),
|
|
8239
|
-
React__namespace.createElement(cbioportalFrontendCommons.EllipsisTextTooltip, { text: level.tumorTypes.join(', '), style: {
|
|
8240
|
-
overflow: 'hidden',
|
|
8241
|
-
whiteSpace: 'nowrap',
|
|
8242
|
-
textOverflow: 'ellipsis',
|
|
8243
|
-
} }))); }))); },
|
|
8244
|
-
minWidth: this.hasLevelData ? 180 : 50,
|
|
8245
|
-
});
|
|
8246
|
-
}
|
|
8247
|
-
return columns;
|
|
8248
|
-
},
|
|
8249
|
-
enumerable: false,
|
|
8250
|
-
configurable: true
|
|
8251
|
-
});
|
|
8252
|
-
Object.defineProperty(OncoKbSummaryTable.prototype, "render", {
|
|
8253
|
-
enumerable: false,
|
|
8254
|
-
configurable: true,
|
|
8255
|
-
writable: true,
|
|
8256
|
-
value: function () {
|
|
8257
|
-
var _a = this.props, data = _a.data, initialSortColumn = _a.initialSortColumn, initialSortDirection = _a.initialSortDirection, initialItemsPerPage = _a.initialItemsPerPage;
|
|
8258
|
-
var showPagination = data.length >
|
|
8259
|
-
(this.props.initialItemsPerPage ||
|
|
8260
|
-
OncoKbSummaryTable_1.defaultProps.initialItemsPerPage);
|
|
8261
|
-
return (React__namespace.createElement("div", { className: classnames__default["default"]('cbioportal-frontend', 'default-track-tooltip-table') },
|
|
8262
|
-
React__namespace.createElement(ReactTable__default["default"], { data: data, columns: this.columns, defaultSorted: [
|
|
8263
|
-
{
|
|
8264
|
-
id: initialSortColumn ||
|
|
8265
|
-
OncoKbSummaryTable_1.defaultProps
|
|
8266
|
-
.initialSortColumn,
|
|
8267
|
-
desc: initialSortDirection === 'desc',
|
|
8268
|
-
},
|
|
8269
|
-
], defaultPageSize: data.length > initialItemsPerPage
|
|
8270
|
-
? initialItemsPerPage
|
|
8271
|
-
: data.length, showPagination: showPagination, showPaginationTop: true, showPaginationBottom: false, className: "-striped -highlight", previousText: "<", nextText: ">" })));
|
|
8272
|
-
}
|
|
8273
|
-
});
|
|
8274
|
-
var OncoKbSummaryTable_1;
|
|
8275
|
-
Object.defineProperty(OncoKbSummaryTable, "defaultProps", {
|
|
8276
|
-
enumerable: true,
|
|
8277
|
-
configurable: true,
|
|
8278
|
-
writable: true,
|
|
8279
|
-
value: {
|
|
8280
|
-
data: [],
|
|
8281
|
-
initialSortColumn: 'count',
|
|
8282
|
-
initialSortDirection: 'desc',
|
|
8283
|
-
initialItemsPerPage: 10,
|
|
8284
|
-
}
|
|
8285
|
-
});
|
|
8286
|
-
tslib.__decorate([
|
|
8287
|
-
mobx.computed
|
|
8288
|
-
], OncoKbSummaryTable.prototype, "hasLevelData", null);
|
|
8289
|
-
tslib.__decorate([
|
|
8290
|
-
mobx.computed
|
|
8291
|
-
], OncoKbSummaryTable.prototype, "columns", null);
|
|
8292
|
-
OncoKbSummaryTable = OncoKbSummaryTable_1 = tslib.__decorate([
|
|
8293
|
-
mobxReact.observer
|
|
8294
|
-
], OncoKbSummaryTable);
|
|
8295
|
-
return OncoKbSummaryTable;
|
|
8296
|
-
}(React__namespace.Component));
|
|
8297
|
-
|
|
8298
6633
|
function oncoKbTooltip(usingPublicOncoKbInstance, indicatorData) {
|
|
8299
6634
|
var sampleCount = indicatorData.length;
|
|
8300
6635
|
// generate info
|
|
@@ -8343,7 +6678,7 @@ function oncoKbTooltip(usingPublicOncoKbInstance, indicatorData) {
|
|
|
8343
6678
|
oncogenicInfo,
|
|
8344
6679
|
' ',
|
|
8345
6680
|
"mutations.",
|
|
8346
|
-
React__namespace.createElement(OncoKbSummaryTable, { usingPublicOncoKbInstance: usingPublicOncoKbInstance, data: tableData })));
|
|
6681
|
+
React__namespace.createElement(oncokbFrontendCommons.OncoKbSummaryTable, { usingPublicOncoKbInstance: usingPublicOncoKbInstance, data: tableData })));
|
|
8347
6682
|
}
|
|
8348
6683
|
function generateLevelData(indicatorData) {
|
|
8349
6684
|
var levels = {};
|
|
@@ -8352,12 +6687,12 @@ function generateLevelData(indicatorData) {
|
|
|
8352
6687
|
var parts = treatment.level.split('_');
|
|
8353
6688
|
var level = parts.length === 2 ? parts[1] : treatment.level;
|
|
8354
6689
|
levels[level] = levels[level] || [];
|
|
8355
|
-
levels[level].push(getTumorTypeNameWithExclusionInfo(treatment.levelAssociatedCancerType, treatment.levelExcludedCancerTypes));
|
|
6690
|
+
levels[level].push(oncokbFrontendCommons.getTumorTypeNameWithExclusionInfo(treatment.levelAssociatedCancerType, treatment.levelExcludedCancerTypes));
|
|
8356
6691
|
});
|
|
8357
6692
|
});
|
|
8358
6693
|
return ___default["default"].keys(levels)
|
|
8359
6694
|
.sort(function (a, b) {
|
|
8360
|
-
return
|
|
6695
|
+
return oncokbFrontendCommons.LEVELS.all.indexOf(a) > oncokbFrontendCommons.LEVELS.all.indexOf(b) ? -1 : 1;
|
|
8361
6696
|
})
|
|
8362
6697
|
.map(function (level) { return ({ level: level, tumorTypes: ___default["default"].uniq(levels[level]) }); });
|
|
8363
6698
|
}
|
|
@@ -8614,9 +6949,9 @@ var PtmReferenceList = /** @class */ (function (_super) {
|
|
|
8614
6949
|
maxHeight: 400,
|
|
8615
6950
|
overflowY: 'auto',
|
|
8616
6951
|
} },
|
|
8617
|
-
React__namespace.createElement(ReferenceList, { pmids: this.props.pubmedIds
|
|
6952
|
+
React__namespace.createElement(oncokbFrontendCommons.ReferenceList, { pmids: this.props.pubmedIds
|
|
8618
6953
|
.map(function (id) { return extractNumericalPart(id); })
|
|
8619
|
-
.filter(function (id) { return id !== undefined; }),
|
|
6954
|
+
.filter(function (id) { return id !== undefined; }), abstracts: [] })), destroyTooltipOnHide: true },
|
|
8620
6955
|
React__namespace.createElement("div", { style: { textAlign: 'right' } },
|
|
8621
6956
|
React__namespace.createElement("i", { className: "fa fa-book", style: { color: 'black' } }))));
|
|
8622
6957
|
}
|
|
@@ -8741,7 +7076,7 @@ var PtmAnnotationTable = /** @class */ (function (_super) {
|
|
|
8741
7076
|
var showPagination = data.length >
|
|
8742
7077
|
(this.props.initialItemsPerPage ||
|
|
8743
7078
|
PtmAnnotationTable_1.defaultProps.initialItemsPerPage);
|
|
8744
|
-
return (React__namespace.createElement("div", { className:
|
|
7079
|
+
return (React__namespace.createElement("div", { className: classNames__default["default"]('cbioportal-frontend', 'default-track-tooltip-table') },
|
|
8745
7080
|
React__namespace.createElement(ReactTable__default["default"], { data: data, columns: this.columns, defaultSorted: [
|
|
8746
7081
|
{
|
|
8747
7082
|
id: initialSortColumn ||
|
|
@@ -10165,7 +8500,7 @@ var AxisScaleSwitch = /** @class */ (function (_super) {
|
|
|
10165
8500
|
configurable: true,
|
|
10166
8501
|
writable: true,
|
|
10167
8502
|
value: function (scale, onClick) {
|
|
10168
|
-
return (React__namespace.createElement("button", { className:
|
|
8503
|
+
return (React__namespace.createElement("button", { className: classNames__default["default"]({
|
|
10169
8504
|
'btn-secondary': this.props.selectedScale === scale,
|
|
10170
8505
|
'btn-outline-secondary': this.props.selectedScale !== scale,
|
|
10171
8506
|
}, 'btn', 'btn-sm', 'btn-axis-switch'), style: {
|
|
@@ -10176,6 +8511,9 @@ var AxisScaleSwitch = /** @class */ (function (_super) {
|
|
|
10176
8511
|
fontWeight: this.props.selectedScale === scale
|
|
10177
8512
|
? 'bolder'
|
|
10178
8513
|
: 'normal',
|
|
8514
|
+
color: this.props.selectedScale === scale ? '#fff' : '#6c757d',
|
|
8515
|
+
backgroundColor: this.props.selectedScale === scale ? '#6c757d' : '#fff',
|
|
8516
|
+
borderColor: '#6c757d',
|
|
10179
8517
|
}, onClick: onClick }, scale));
|
|
10180
8518
|
}
|
|
10181
8519
|
});
|
|
@@ -11005,14 +9343,14 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
|
|
|
11005
9343
|
switch (_c.label) {
|
|
11006
9344
|
case 0:
|
|
11007
9345
|
mutationQueryVariants = ___default["default"].uniqBy(___default["default"].map(queryVariants.filter(function (mutation) { return mutation.mutationType !== 'Fusion'; }), function (mutation) {
|
|
11008
|
-
return
|
|
9346
|
+
return oncokbFrontendCommons.generateProteinChangeQuery(getEntrezGeneId(mutation), getTumorType(mutation), mutation.proteinChange, mutation.mutationType, mutation.proteinPosStart, mutation.proteinPosEnd, evidenceTypes);
|
|
11009
9347
|
}), 'id');
|
|
11010
9348
|
structuralQueryVariants = ___default["default"].uniqBy(___default["default"].map(queryVariants.filter(function (mutation) {
|
|
11011
9349
|
var _a;
|
|
11012
9350
|
return ((_a = mutation.mutationType) === null || _a === void 0 ? void 0 : _a.toUpperCase()) ===
|
|
11013
|
-
|
|
9351
|
+
oncokbFrontendCommons.StructuralVariantType.FUSION;
|
|
11014
9352
|
}), function (mutation) {
|
|
11015
|
-
return
|
|
9353
|
+
return oncokbFrontendCommons.generateAnnotateStructuralVariantQuery(
|
|
11016
9354
|
/* @ts-ignore */
|
|
11017
9355
|
mutation.structuralVariant, getTumorType(mutation), evidenceTypes);
|
|
11018
9356
|
}), 'id');
|
|
@@ -11118,7 +9456,7 @@ var DefaultMutationMapperFilterApplier = /** @class */ (function () {
|
|
|
11118
9456
|
return (!filter.values ||
|
|
11119
9457
|
!this.oncoKbData.result ||
|
|
11120
9458
|
this.oncoKbData.result instanceof Error ||
|
|
11121
|
-
defaultOncoKbFilter(mutation, this.oncoKbData.result, this.getDefaultTumorType, this.getDefaultEntrezGeneId));
|
|
9459
|
+
oncokbFrontendCommons.defaultOncoKbFilter(mutation, this.oncoKbData.result, this.getDefaultTumorType, this.getDefaultEntrezGeneId));
|
|
11122
9460
|
}
|
|
11123
9461
|
});
|
|
11124
9462
|
Object.defineProperty(DefaultMutationMapperFilterApplier.prototype, "applyHostpotFilter", {
|
|
@@ -12174,7 +10512,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
|
|
|
12174
10512
|
get: function () {
|
|
12175
10513
|
if (this.oncoKbData.result &&
|
|
12176
10514
|
!(this.oncoKbData.result instanceof Error)) {
|
|
12177
|
-
return groupOncoKbIndicatorDataByMutations(this.mutationsByPosition, this.oncoKbData.result, this.getDefaultTumorType, this.getDefaultEntrezGeneId, defaultOncoKbIndicatorFilter);
|
|
10515
|
+
return oncokbFrontendCommons.groupOncoKbIndicatorDataByMutations(this.mutationsByPosition, this.oncoKbData.result, this.getDefaultTumorType, this.getDefaultEntrezGeneId, oncokbFrontendCommons.defaultOncoKbIndicatorFilter);
|
|
12178
10516
|
}
|
|
12179
10517
|
else {
|
|
12180
10518
|
return {};
|
|
@@ -12367,7 +10705,7 @@ var TranscriptDropdown = /** @class */ (function (_super) {
|
|
|
12367
10705
|
canonicalTranscriptId &&
|
|
12368
10706
|
transcriptsWithAnnotations.result &&
|
|
12369
10707
|
transcriptsWithAnnotations.result.length > 0;
|
|
12370
|
-
return (React__namespace.createElement("div", { className:
|
|
10708
|
+
return (React__namespace.createElement("div", { className: classNames__default["default"]('small', styles$1.dropDown) },
|
|
12371
10709
|
this.loadingIndicator(isLoading),
|
|
12372
10710
|
!isLoading &&
|
|
12373
10711
|
requiredData &&
|
|
@@ -12380,7 +10718,7 @@ var TranscriptDropdown = /** @class */ (function (_super) {
|
|
|
12380
10718
|
var requiredData = transcriptsWithProteinLength.result &&
|
|
12381
10719
|
transcriptsWithProteinLength.result.length > 0 &&
|
|
12382
10720
|
canonicalTranscriptId;
|
|
12383
|
-
return (React__namespace.createElement("div", { className:
|
|
10721
|
+
return (React__namespace.createElement("div", { className: classNames__default["default"]('small', styles$1.dropDown) },
|
|
12384
10722
|
this.loadingIndicator(isLoading),
|
|
12385
10723
|
!isLoading &&
|
|
12386
10724
|
requiredData &&
|
|
@@ -13052,7 +11390,6 @@ exports.LollipopMutationPlot = LollipopMutationPlot;
|
|
|
13052
11390
|
exports.LollipopPlot = LollipopPlot;
|
|
13053
11391
|
exports.LollipopPlotNoTooltip = LollipopPlotNoTooltip;
|
|
13054
11392
|
exports.LollipopTooltipCountInfo = LollipopTooltipCountInfo;
|
|
13055
|
-
exports.MSI_H_NAME = MSI_H_NAME;
|
|
13056
11393
|
exports.MUTATION_COLUMNS_DEFINITION = MUTATION_COLUMNS_DEFINITION;
|
|
13057
11394
|
exports.MUTATION_COLUMN_HEADERS = MUTATION_COLUMN_HEADERS;
|
|
13058
11395
|
exports.MUTATION_STATUS_BADGE_STYLE_OVERRIDE = MUTATION_STATUS_BADGE_STYLE_OVERRIDE;
|
|
@@ -13063,26 +11400,14 @@ exports.MutationStatusBadgeSelector = MutationStatusBadgeSelector;
|
|
|
13063
11400
|
exports.MyCancerGenome = MyCancerGenome;
|
|
13064
11401
|
exports.ONCOKB_DEFAULT_DATA = ONCOKB_DEFAULT_DATA;
|
|
13065
11402
|
exports.ONCOKB_DEFAULT_INFO = ONCOKB_DEFAULT_INFO;
|
|
13066
|
-
exports.OTHER_BIOMARKER_HUGO_SYMBOL = OTHER_BIOMARKER_HUGO_SYMBOL;
|
|
13067
|
-
exports.OTHER_BIOMARKER_NAME = OTHER_BIOMARKER_NAME;
|
|
13068
|
-
exports.OncoKB = OncoKB;
|
|
13069
|
-
exports.OncoKBSuggestAnnotationLinkout = OncoKBSuggestAnnotationLinkout;
|
|
13070
|
-
exports.OncoKbFeedback = OncoKbFeedback;
|
|
13071
|
-
exports.OncoKbHelper = OncoKbHelper;
|
|
13072
|
-
exports.OncoKbTooltip = OncoKbTooltip;
|
|
13073
|
-
exports.OncoKbTreatmentTable = OncoKbTreatmentTable;
|
|
13074
11403
|
exports.PercentToggle = PercentToggle;
|
|
13075
11404
|
exports.ProteinChange = ProteinChange;
|
|
13076
11405
|
exports.ProteinImpactTypeBadgeSelector = ProteinImpactTypeBadgeSelector;
|
|
13077
11406
|
exports.ProteinImpactTypeDropdownSelector = ProteinImpactTypeDropdownSelector;
|
|
13078
|
-
exports.RefComponent = RefComponent;
|
|
13079
|
-
exports.ReferenceList = ReferenceList;
|
|
13080
11407
|
exports.Sequence = LollipopPlot;
|
|
13081
11408
|
exports.Signal = Signal;
|
|
13082
11409
|
exports.SignalTable = SignalTable;
|
|
13083
|
-
exports.SummaryWithRefs = SummaryWithRefs;
|
|
13084
11410
|
exports.TEXT_INPUT_FILTER_ID = TEXT_INPUT_FILTER_ID;
|
|
13085
|
-
exports.TMB_H_NAME = TMB_H_NAME;
|
|
13086
11411
|
exports.TrackSelector = TrackSelector;
|
|
13087
11412
|
exports.USE_DEFAULT_PUBLIC_INSTANCE_FOR_ONCOKB = USE_DEFAULT_PUBLIC_INSTANCE_FOR_ONCOKB;
|
|
13088
11413
|
exports.annotationSortValue = sortValue$4;
|
|
@@ -13093,14 +11418,12 @@ exports.applyDefaultMutationStatusFilter = applyDefaultMutationStatusFilter;
|
|
|
13093
11418
|
exports.applyDefaultPositionFilter = applyDefaultPositionFilter;
|
|
13094
11419
|
exports.applyDefaultProteinImpactTypeFilter = applyDefaultProteinImpactTypeFilter;
|
|
13095
11420
|
exports.calculateGnomadAlleleFrequency = calculateGnomadAlleleFrequency;
|
|
13096
|
-
exports.civicDownload = download$
|
|
13097
|
-
exports.civicSortValue = sortValue$
|
|
11421
|
+
exports.civicDownload = download$6;
|
|
11422
|
+
exports.civicSortValue = sortValue$7;
|
|
13098
11423
|
exports.clinvarDownload = download$4;
|
|
13099
11424
|
exports.clinvarSortValue = sortValue$3;
|
|
13100
11425
|
exports.dbsnpDownload = download$3;
|
|
13101
11426
|
exports.dbsnpSortValue = sortValue$2;
|
|
13102
|
-
exports.defaultOncoKbFilter = defaultOncoKbFilter;
|
|
13103
|
-
exports.errorIcon = errorIcon;
|
|
13104
11427
|
exports.fetchVariantAnnotationsByMutation = fetchVariantAnnotationsByMutation;
|
|
13105
11428
|
exports.fetchVariantAnnotationsIndexedByGenomicLocation = fetchVariantAnnotationsIndexedByGenomicLocation;
|
|
13106
11429
|
exports.findAllUniquePositions = findAllUniquePositions;
|
|
@@ -13119,13 +11442,11 @@ exports.getProteinImpactTypeOptionLabel = getProteinImpactTypeOptionLabel;
|
|
|
13119
11442
|
exports.getSelectedOptionValues = getSelectedOptionValues;
|
|
13120
11443
|
exports.getSignalData = getSignalData;
|
|
13121
11444
|
exports.getSingleSignalValue = getSingleSignalValue;
|
|
13122
|
-
exports.getTumorTypeNameWithExclusionInfo = getTumorTypeNameWithExclusionInfo;
|
|
13123
11445
|
exports.getUrl = getUrl;
|
|
13124
11446
|
exports.gnomadDownload = download$2;
|
|
13125
11447
|
exports.gnomadSortValue = sortValue$1;
|
|
13126
11448
|
exports.groupDataByGroupFilters = groupDataByGroupFilters;
|
|
13127
11449
|
exports.groupDataByProteinImpactType = groupDataByProteinImpactType;
|
|
13128
|
-
exports.groupOncoKbIndicatorDataByMutations = groupOncoKbIndicatorDataByMutations;
|
|
13129
11450
|
exports.handleOptionSelect = handleOptionSelect;
|
|
13130
11451
|
exports.hgvscDownload = download$1;
|
|
13131
11452
|
exports.hgvscSortValue = sortValue;
|
|
@@ -13137,17 +11458,11 @@ exports.initDefaultTrackVisibility = initDefaultTrackVisibility;
|
|
|
13137
11458
|
exports.initGenomeNexusClient = initGenomeNexusClient;
|
|
13138
11459
|
exports.initGenomeNexusInternalClient = initGenomeNexusInternalClient;
|
|
13139
11460
|
exports.initOncoKbClient = initOncoKbClient;
|
|
13140
|
-
exports.levelIconClassNames = levelIconClassNames;
|
|
13141
|
-
exports.loaderIcon = loaderIcon;
|
|
13142
11461
|
exports.mergeColumns = mergeColumns;
|
|
13143
11462
|
exports.mutationTypeSort = mutationTypeSort;
|
|
13144
|
-
exports.myCancerGenomeDownload = download$
|
|
13145
|
-
exports.myCancerGenomeSortValue = sortValue$
|
|
13146
|
-
exports.normalizeLevel = normalizeLevel;
|
|
11463
|
+
exports.myCancerGenomeDownload = download$5;
|
|
11464
|
+
exports.myCancerGenomeSortValue = sortValue$6;
|
|
13147
11465
|
exports.onFilterOptionSelect = onFilterOptionSelect;
|
|
13148
|
-
exports.oncoKbAnnotationDownload = download$5;
|
|
13149
|
-
exports.oncoKbAnnotationSortValue = sortValue$6;
|
|
13150
|
-
exports.oncogenicityIconClassNames = oncogenicityIconClassNames;
|
|
13151
11466
|
exports.proteinChangeSortMethod = proteinChangeSortMethod;
|
|
13152
11467
|
exports.rightAlignedCell = rightAlignedCell;
|
|
13153
11468
|
exports.signalDownload = download;
|