react-mutation-mapper 0.8.60 → 0.8.62

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.
Files changed (35) hide show
  1. package/dist/component/ptm/PtmReferenceList.d.ts +1 -0
  2. package/dist/index.d.ts +0 -12
  3. package/dist/index.es.js +182 -1843
  4. package/dist/index.es.js.map +1 -1
  5. package/dist/index.js +194 -1878
  6. package/dist/index.js.map +1 -1
  7. package/dist/styles.css +0 -229
  8. package/package.json +5 -4
  9. package/dist/component/oncokb/ArticleAbstractItem.d.ts +0 -5
  10. package/dist/component/oncokb/OncoKB.d.ts +0 -33
  11. package/dist/component/oncokb/OncoKB.spec.d.ts +0 -1
  12. package/dist/component/oncokb/OncoKBSuggestAnnotationLinkout.d.ts +0 -6
  13. package/dist/component/oncokb/OncoKbCard.d.ts +0 -20
  14. package/dist/component/oncokb/OncoKbCardBody.d.ts +0 -15
  15. package/dist/component/oncokb/OncoKbCardLevelsOfEvidenceDropdown.d.ts +0 -15
  16. package/dist/component/oncokb/OncoKbCardTitle.d.ts +0 -8
  17. package/dist/component/oncokb/OncoKbFeedback.d.ts +0 -12
  18. package/dist/component/oncokb/OncoKbHelper.d.ts +0 -33
  19. package/dist/component/oncokb/OncoKbSummaryTable.d.ts +0 -31
  20. package/dist/component/oncokb/OncoKbTooltip.d.ts +0 -21
  21. package/dist/component/oncokb/OncoKbTreatmentTable.d.ts +0 -86
  22. package/dist/component/oncokb/PmidItem.d.ts +0 -12
  23. package/dist/component/oncokb/RefComponent.d.ts +0 -9
  24. package/dist/component/oncokb/ReferenceList.d.ts +0 -13
  25. package/dist/component/oncokb/SummaryWithRefs.d.ts +0 -11
  26. package/dist/component/oncokb/constants.d.ts +0 -10
  27. package/dist/component/oncokb/icon/AnnotationIcon.d.ts +0 -13
  28. package/dist/component/oncokb/icon/CompactAnnotationIcon.d.ts +0 -8
  29. package/dist/component/oncokb/icon/LevelIcon.d.ts +0 -6
  30. package/dist/component/oncokb/icon/OncogenicIcon.d.ts +0 -6
  31. package/dist/component/oncokb/oncokbCard/BiologicalContent.d.ts +0 -8
  32. package/dist/component/oncokb/oncokbCard/EvidenceReferenceContent.d.ts +0 -9
  33. package/dist/component/oncokb/oncokbCard/ImplicationContent.d.ts +0 -11
  34. package/dist/util/OncoKbUtils.d.ts +0 -40
  35. package/dist/util/OncoKbUtils.spec.d.ts +0 -1
package/dist/index.js CHANGED
@@ -8,23 +8,23 @@ 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 classnames = require('classnames');
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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 numeral = require('numeral');
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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');
@@ -52,13 +52,12 @@ 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 React__default = /*#__PURE__*/_interopDefaultLegacy(React);
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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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+ var numeral__default = /*#__PURE__*/_interopDefaultLegacy(numeral);
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  var Slider__default = /*#__PURE__*/_interopDefaultLegacy(Slider);
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  var oncoKbImg__default = /*#__PURE__*/_interopDefaultLegacy(oncoKbImg);
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  var request__default = /*#__PURE__*/_interopDefaultLegacy(request);
@@ -67,7 +66,7 @@ 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: classnames__default["default"]("" + annotationStyles['annotation-item'], "" + annotationStyles['annotation-item-load'], 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) {
@@ -164,1607 +163,58 @@ 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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-
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- var img$4 = "data:image/png;base64,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";
184
-
185
- var img$3 = "data:image/png;base64,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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
- var score = 0;
193
- if (civicEntry) {
194
- score = 1;
195
- }
196
- 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
- writable: true,
223
- 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
- writable: true,
233
- 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;
166
+ React__namespace.createElement("b", null, this.props.geneName))),
167
+ ' ',
168
+ "- ",
169
+ this.props.geneDescription)),
170
+ React__namespace.createElement("div", { className: "col s12" },
171
+ React__namespace.createElement("ul", null, this.generateVariants(this.props.variants))),
172
+ React__namespace.createElement("div", { className: "item disclaimer" },
173
+ 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.")))),
174
+ React__namespace.createElement("div", { className: "item footer" },
175
+ React__namespace.createElement("a", { href: this.props.geneUrl, target: "_blank" },
176
+ React__namespace.createElement("img", { src: img$5, className: "civic-logo", alt: "CIViC" })))));
1669
177
  }
1670
178
  });
1671
- OncoKbTooltip = tslib.__decorate([
1672
- mobxReact.observer
1673
- ], OncoKbTooltip);
1674
- return OncoKbTooltip;
179
+ return CivicCard;
1675
180
  }(React__namespace.Component));
1676
181
 
1677
- var OncoKbFeedback = /** @class */ (function (_super) {
1678
- tslib.__extends(OncoKbFeedback, _super);
1679
- function OncoKbFeedback() {
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));
182
+ var img$4 = "data:image/png;base64,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";
183
+
184
+ var img$3 = "data:image/png;base64,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";
1709
185
 
1710
- function sortValue$6(indicator) {
1711
- var values = [0, 0, 0];
1712
- if (indicator) {
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;
186
+ function hideArrow(tooltipEl) {
187
+ var arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
188
+ arrowEl.style.display = 'none';
1720
189
  }
1721
- function download$5(indicator) {
1722
- var _a, _b;
1723
- if (!indicator) {
1724
- return 'NA';
190
+ function sortValue$7(civicEntry) {
191
+ var score = 0;
192
+ if (civicEntry) {
193
+ score = 1;
1725
194
  }
1726
- var oncogenic = indicator.oncogenic ? indicator.oncogenic : 'Unknown';
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;
195
+ return score;
1730
196
  }
1731
- function findDefaultDataTypeForTooltip(usingPublicOncoKbInstance, indicator, availableDataTypes) {
1732
- if (usingPublicOncoKbInstance || !indicator) {
1733
- return cbioportalUtils.OncoKbCardDataType.BIOLOGICAL;
1734
- }
1735
- // priority is in this order: Tx > Dx > Px > Biological
1736
- if (indicator.highestSensitiveLevel &&
1737
- availableDataTypes &&
1738
- availableDataTypes.includes(cbioportalUtils.OncoKbCardDataType.TXS)) {
1739
- return cbioportalUtils.OncoKbCardDataType.TXS;
1740
- }
1741
- else if (indicator.highestResistanceLevel &&
1742
- availableDataTypes &&
1743
- availableDataTypes.includes(cbioportalUtils.OncoKbCardDataType.TXR)) {
1744
- return cbioportalUtils.OncoKbCardDataType.TXR;
1745
- }
1746
- else if (indicator.highestDiagnosticImplicationLevel &&
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;
197
+ function download$6(civicEntry) {
198
+ if (!civicEntry) {
199
+ return cbioportalUtils.CIVIC_NA_VALUE;
200
+ }
201
+ var variants = ___default["default"].values(civicEntry.variants);
202
+ var values = [];
203
+ if (variants && variants.length > 0 && variants[0].evidenceCounts) {
204
+ ___default["default"].forEach(variants[0].evidenceCounts, function (value, key) {
205
+ values.push(key + ": " + value);
206
+ });
207
+ }
208
+ // this indicates that we have an entry but the evidence is empty
209
+ if (values.length === 0) {
210
+ return cbioportalUtils.CIVIC_NA_VALUE;
211
+ }
212
+ return values.join(', ');
1757
213
  }
1758
- var OncoKB = /** @class */ (function (_super) {
1759
- tslib.__extends(OncoKB, _super);
1760
- function OncoKB(props) {
214
+ var Civic = /** @class */ (function (_super) {
215
+ tslib.__extends(Civic, _super);
216
+ function Civic(props) {
1761
217
  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
218
  Object.defineProperty(_this, "tooltipDataLoadComplete", {
1769
219
  enumerable: true,
1770
220
  configurable: true,
@@ -1772,125 +222,136 @@ var OncoKB = /** @class */ (function (_super) {
1772
222
  value: false
1773
223
  });
1774
224
  mobx.makeObservable(_this);
225
+ _this.cardContent = _this.cardContent.bind(_this);
1775
226
  return _this;
1776
227
  }
1777
- Object.defineProperty(OncoKB.prototype, "render", {
228
+ Object.defineProperty(Civic.prototype, "render", {
1778
229
  enumerable: false,
1779
230
  configurable: true,
1780
231
  writable: true,
1781
232
  value: function () {
1782
- var oncoKbContent;
1783
- if (this.props.status === 'error') {
1784
- oncoKbContent = errorIcon('Error fetching OncoKB data');
1785
- }
1786
- else if (this.props.status === 'pending') {
1787
- oncoKbContent = loaderIcon('pull-left');
233
+ var civicContent = (React__namespace.createElement("span", { className: "" + annotationStyles['annotation-item'] }));
234
+ var civicImgWidth = 14;
235
+ var civicImgHeight = 14;
236
+ var civicImgSrc = !this.props.hasCivicVariants
237
+ ? img$3
238
+ : img$4;
239
+ if (this.props.civicStatus == 'error') {
240
+ civicContent = errorIcon('Error fetching Civic data');
1788
241
  }
1789
- else {
1790
- oncoKbContent = this.props.mergeAnnotationIcons
1791
- ? this.singleAnnotationIcon()
1792
- : this.multiAnnotationIcon();
1793
- if (!this.props.disableFeedback && this.showFeedback) {
1794
- oncoKbContent = (React__namespace.createElement("span", null,
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 })));
242
+ else if (this.props.civicEntry !== undefined) {
243
+ if (this.props.civicEntry !== null &&
244
+ this.props.civicStatus == 'complete') {
245
+ civicContent = (React__namespace.createElement("span", { className: "" + annotationStyles['annotation-item'] },
246
+ React__namespace.createElement("img", { width: civicImgWidth, height: civicImgHeight, src: civicImgSrc, alt: "Civic Variant Entry" })));
247
+ 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
248
  }
1800
249
  }
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
250
  else {
1832
- // workaround: use content padding value to draw an empty icon when there is no indicator data.
1833
- // this is to keep the icon alignment consistent with the rest of the column.
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 } });
251
+ // It's still unknown (undefined) if the current gene has a Civic entry or not.
252
+ civicContent = loaderIcon('pull-left');
1837
253
  }
254
+ return civicContent;
1838
255
  }
1839
256
  });
1840
- Object.defineProperty(OncoKB.prototype, "singleAnnotationIcon", {
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", {
257
+ Object.defineProperty(Civic.prototype, "cardContent", {
1850
258
  enumerable: false,
1851
259
  configurable: true,
1852
260
  writable: true,
1853
- value: function (type) {
1854
- return (React__namespace.createElement(OncoKbTooltip, { type: type, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance, hugoSymbol: this.props.hugoGeneSymbol, geneNotExist: this.props.geneNotExist, isCancerGene: this.props.isCancerGene, indicator: this.props.indicator || undefined, pubMedCache: this.props.pubMedCache, handleFeedbackOpen: this.props.disableFeedback
1855
- ? undefined
1856
- : this.handleFeedbackOpen }));
261
+ value: function (civicEntry) {
262
+ return (React__namespace.createElement(CivicCard, { title: "CIViC Variants", geneName: civicEntry.name, geneDescription: civicEntry.description, geneUrl: civicEntry.url, variants: civicEntry.variants }));
1857
263
  }
1858
264
  });
1859
- Object.defineProperty(OncoKB.prototype, "handleFeedbackOpen", {
1860
- enumerable: false,
1861
- configurable: true,
1862
- writable: true,
1863
- value: function () {
1864
- this.showFeedback = true;
265
+ tslib.__decorate([
266
+ mobx.observable
267
+ ], Civic.prototype, "tooltipDataLoadComplete", void 0);
268
+ Civic = tslib.__decorate([
269
+ mobxReact.observer
270
+ ], Civic);
271
+ return Civic;
272
+ }(React__namespace.Component));
273
+
274
+ var NoClinvarData = function () {
275
+ return (React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { placement: "topLeft", overlay: React__namespace.createElement("span", null, "Variant has no ClinVar data.") },
276
+ React__namespace.createElement("span", { style: {
277
+ height: '100%',
278
+ width: '100%',
279
+ display: 'block',
280
+ overflow: 'hidden',
281
+ } }, "\u00A0")));
282
+ };
283
+ var ClinvarSummary = function (props) {
284
+ if (!props.clinvar) {
285
+ return React__namespace.createElement(NoClinvarData, null);
286
+ }
287
+ else {
288
+ var clinvarId = props.clinvar.clinvarId;
289
+ var clinvarLink = "https://www.ncbi.nlm.nih.gov/clinvar/variation/" + clinvarId + "/";
290
+ var clinicalSignificance = props.clinvar.clinicalSignificance;
291
+ var conflictingClinicalSignificance = props.clinvar.conflictingClinicalSignificance;
292
+ return (React__namespace.createElement(cbioportalFrontendCommons.TruncatedText, { maxLength: 30, text: clinicalSignificance, addTooltip: "always", tooltip: React__namespace.createElement("div", { style: { maxWidth: 300 } },
293
+ React__namespace.createElement("div", null, clinicalSignificance),
294
+ conflictingClinicalSignificance && (React__namespace.createElement("div", null, conflictingClinicalSignificance)),
295
+ React__namespace.createElement("div", null,
296
+ "(ClinVar ID:",
297
+ ' ',
298
+ React__namespace.createElement("a", { href: clinvarLink, target: "_blank" }, clinvarId),
299
+ ")")) }));
300
+ }
301
+ };
302
+
303
+ var img$2 = "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAIsAAACACAYAAAA73po8AAAACXBIWXMAAAsTAAALEwEAmpwYAAAKT2lDQ1BQaG90b3Nob3AgSUNDIHByb2ZpbGUAAHjanVNnVFPpFj333vRCS4iAlEtvUhUIIFJCi4AUkSYqIQkQSoghodkVUcERRUUEG8igiAOOjoCMFVEsDIoK2AfkIaKOg6OIisr74Xuja9a89+bN/rXXPues852zzwfACAyWSDNRNYAMqUIeEeCDx8TG4eQuQIEKJHAAEAizZCFz/SMBAPh+PDwrIsAHvgABeNMLCADATZvAMByH/w/qQplcAYCEAcB0kThLCIAUAEB6jkKmAEBGAYCdmCZTAKAEAGDLY2LjAFAtAGAnf+bTAICd+Jl7AQBblCEVAaCRACATZYhEAGg7AKzPVopFAFgwABRmS8Q5ANgtADBJV2ZIALC3AMDOEAuyAAgMADBRiIUpAAR7AGDIIyN4AISZABRG8lc88SuuEOcqAAB4mbI8uSQ5RYFbCC1xB1dXLh4ozkkXKxQ2YQJhmkAuwnmZGTKBNA/g88wAAKCRFRHgg/P9eM4Ors7ONo62Dl8t6r8G/yJiYuP+5c+rcEAAAOF0ftH+LC+zGoA7BoBt/qIl7gRoXgugdfeLZrIPQLUAoOnaV/Nw+H48PEWhkLnZ2eXk5NhKxEJbYcpXff5nwl/AV/1s+X48/Pf14L7iJIEyXYFHBPjgwsz0TKUcz5IJhGLc5o9H/LcL//wd0yLESWK5WCoU41EScY5EmozzMqUiiUKSKcUl0v9k4t8s+wM+3zUAsGo+AXuRLahdYwP2SycQWHTA4vcAAPK7b8HUKAgDgGiD4c93/+8//UegJQCAZkmScQAAXkQkLlTKsz/HCAAARKCBKrBBG/TBGCzABhzBBdzBC/xgNoRCJMTCQhBCCmSAHHJgKayCQiiGzbAdKmAv1EAdNMBRaIaTcA4uwlW4Dj1wD/phCJ7BKLyBCQRByAgTYSHaiAFiilgjjggXmYX4IcFIBBKLJCDJiBRRIkuRNUgxUopUIFVIHfI9cgI5h1xGupE7yAAygvyGvEcxlIGyUT3UDLVDuag3GoRGogvQZHQxmo8WoJvQcrQaPYw2oefQq2gP2o8+Q8cwwOgYBzPEbDAuxsNCsTgsCZNjy7EirAyrxhqwVqwDu4n1Y8+xdwQSgUXACTYEd0IgYR5BSFhMWE7YSKggHCQ0EdoJNwkDhFHCJyKTqEu0JroR+cQYYjIxh1hILCPWEo8TLxB7iEPENyQSiUMyJ7mQAkmxpFTSEtJG0m5SI+ksqZs0SBojk8naZGuyBzmULCAryIXkneTD5DPkG+Qh8lsKnWJAcaT4U+IoUspqShnlEOU05QZlmDJBVaOaUt2ooVQRNY9aQq2htlKvUYeoEzR1mjnNgxZJS6WtopXTGmgXaPdpr+h0uhHdlR5Ol9BX0svpR+iX6AP0dwwNhhWDx4hnKBmbGAcYZxl3GK+YTKYZ04sZx1QwNzHrmOeZD5lvVVgqtip8FZHKCpVKlSaVGyovVKmqpqreqgtV81XLVI+pXlN9rkZVM1PjqQnUlqtVqp1Q61MbU2epO6iHqmeob1Q/pH5Z/YkGWcNMw09DpFGgsV/jvMYgC2MZs3gsIWsNq4Z1gTXEJrHN2Xx2KruY/R27iz2qqaE5QzNKM1ezUvOUZj8H45hx+Jx0TgnnKKeX836K3hTvKeIpG6Y0TLkxZVxrqpaXllirSKtRq0frvTau7aedpr1Fu1n7gQ5Bx0onXCdHZ4/OBZ3nU9lT3acKpxZNPTr1ri6qa6UbobtEd79up+6Ynr5egJ5Mb6feeb3n+hx9L/1U/W36p/VHDFgGswwkBtsMzhg8xTVxbzwdL8fb8VFDXcNAQ6VhlWGX4YSRudE8o9VGjUYPjGnGXOMk423GbcajJgYmISZLTepN7ppSTbmmKaY7TDtMx83MzaLN1pk1mz0x1zLnm+eb15vft2BaeFostqi2uGVJsuRaplnutrxuhVo5WaVYVVpds0atna0l1rutu6cRp7lOk06rntZnw7Dxtsm2qbcZsOXYBtuutm22fWFnYhdnt8Wuw+6TvZN9un2N/T0HDYfZDqsdWh1+c7RyFDpWOt6azpzuP33F9JbpL2dYzxDP2DPjthPLKcRpnVOb00dnF2e5c4PziIuJS4LLLpc+Lpsbxt3IveRKdPVxXeF60vWdm7Obwu2o26/uNu5p7ofcn8w0nymeWTNz0MPIQ+BR5dE/C5+VMGvfrH5PQ0+BZ7XnIy9jL5FXrdewt6V3qvdh7xc+9j5yn+M+4zw33jLeWV/MN8C3yLfLT8Nvnl+F30N/I/9k/3r/0QCngCUBZwOJgUGBWwL7+Hp8Ib+OPzrbZfay2e1BjKC5QRVBj4KtguXBrSFoyOyQrSH355jOkc5pDoVQfujW0Adh5mGLw34MJ4WHhVeGP45wiFga0TGXNXfR3ENz30T6RJZE3ptnMU85ry1KNSo+qi5qPNo3ujS6P8YuZlnM1VidWElsSxw5LiquNm5svt/87fOH4p3iC+N7F5gvyF1weaHOwvSFpxapLhIsOpZATIhOOJTwQRAqqBaMJfITdyWOCnnCHcJnIi/RNtGI2ENcKh5O8kgqTXqS7JG8NXkkxTOlLOW5hCepkLxMDUzdmzqeFpp2IG0yPTq9MYOSkZBxQqohTZO2Z+pn5mZ2y6xlhbL+xW6Lty8elQfJa7OQrAVZLQq2QqboVFoo1yoHsmdlV2a/zYnKOZarnivN7cyzytuQN5zvn//tEsIS4ZK2pYZLVy0dWOa9rGo5sjxxedsK4xUFK4ZWBqw8uIq2Km3VT6vtV5eufr0mek1rgV7ByoLBtQFr6wtVCuWFfevc1+1dT1gvWd+1YfqGnRs+FYmKrhTbF5cVf9go3HjlG4dvyr+Z3JS0qavEuWTPZtJm6ebeLZ5bDpaql+aXDm4N2dq0Dd9WtO319kXbL5fNKNu7g7ZDuaO/PLi8ZafJzs07P1SkVPRU+lQ27tLdtWHX+G7R7ht7vPY07NXbW7z3/T7JvttVAVVN1WbVZftJ+7P3P66Jqun4lvttXa1ObXHtxwPSA/0HIw6217nU1R3SPVRSj9Yr60cOxx++/p3vdy0NNg1VjZzG4iNwRHnk6fcJ3/ceDTradox7rOEH0x92HWcdL2pCmvKaRptTmvtbYlu6T8w+0dbq3nr8R9sfD5w0PFl5SvNUyWna6YLTk2fyz4ydlZ19fi753GDborZ752PO32oPb++6EHTh0kX/i+c7vDvOXPK4dPKy2+UTV7hXmq86X23qdOo8/pPTT8e7nLuarrlca7nuer21e2b36RueN87d9L158Rb/1tWeOT3dvfN6b/fF9/XfFt1+cif9zsu72Xcn7q28T7xf9EDtQdlD3YfVP1v+3Njv3H9qwHeg89HcR/cGhYPP/pH1jw9DBY+Zj8uGDYbrnjg+OTniP3L96fynQ89kzyaeF/6i/suuFxYvfvjV69fO0ZjRoZfyl5O/bXyl/erA6xmv28bCxh6+yXgzMV70VvvtwXfcdx3vo98PT+R8IH8o/2j5sfVT0Kf7kxmTk/8EA5jz/GMzLdsAAAAgY0hSTQAAeiUAAICDAAD5/wAAgOkAAHUwAADqYAAAOpgAABdvkl/FRgAADvNJREFUeNrsXT1y4koXPaacj94KPnkFIwfEI0eEg1dgWIFNkVJFu4qUwrMCMyswExIZxwTWrMB6Kxi9FfAFuhq3Zf20Wt2tFuJWuZ7rDZaa1tG95/722eFwQCJnZ2fogvSn2yEAj/tfm/1yEGi4jwvAB+AC+EL3fKF/3gEI9stB1IY9OxwOOOsSWPrTrQfgiR5eWnYAJipA059uRwBuU4DMkzWAn/vlYHcCi13a5Engo+P9crCWuL4D4I5A4kgscU1gjU5gaV6jPFd4iMKAIVMzBzBSsNQQwLUOk3gCizhYnok7iEoE4KroofWnW59A4itebum9T2DRBxSftIrMW37JmwUyNUMCiatx2RGAC5tM0uFwwHkHnJ+55N+5AFb96XZCAPmmyNSIiEP86sqmjbRCsxD5/M65mem3LKCff8nd3Ale1wXwJrmsgDykkSRhVSHX++Vgc9Is8cNMvAe35C3zeW7Qn24TMxFS3CIEEGaA6FbQ3IR5YOxPty+CXpQurbjptGYh7+RRMA4ha/MTbfRfKpbyFyT75SAUXO+K3OIm5NIGstsIwZVwY6UBs18O/lG47leN4C6Mv+yXg7ENYOlZHu+otcmq+QNpLNMytMUM9QwCJWH4psjiD5UXI5M1aeAZOeQAdAcsBmITvGxE+UhFwKw1aCwRuekMWMiFNUkQf2q89oSIs1FTRJq5E5rl1uB3CnXGJiiqOm6Avwy7AhaTX/SH7huQK2vaQ7k9erCQB+Qa/E5GOAVpL5OA8cicH7VmMQoUk8k3IrxXBk3S7bGDxTP4fe5NbyClBi4Nkd5RV1xnE1olbOLG++Ug3C8HlwRWnVrGoZLNowXLNwP3iNBMwCwNGkZaRidvmjf1/bTnhiSq1GTEmlQ+971d4hgjqI9aj/fLwZoKu5Da3x0qJElFxUgisT/dvmkmuQ/75WACi4VMxzcKIcgAJyJOFCIuo/gqEI7YQVG3gkmwHDTzlDFaJBRKSMIJXzPA88KBI8p72BVeQqluBeNgoRD1nxNQtIDOh3htce2aGBMlCt4JKFpddlGepoQUt9F1vu86UHgTI+iqD9sAFpVeUIi4n4bZ9sQYW3iMLTzT9+WSmqJcqROa5YHs7s7S9b0CeGVs8dgAYDa0P2Xi2A6WugG5HeJmK2t7gBlb8A9hxNhi1IRpRnm6obYLrdsb+iOB6IiI231T4XsJwKS/5yVjs8DkGkrqm2sXr2vtG6LFO4LgCOjnxbZIrKBs8DHJ94g47G/SHAX96XaM7B4nJXt6rgkoLsfAd5wa/A/vTV1hWzSHgPxKgcVjbHHH2OzBMGA2BJg0d1JSZlrbDJEGuUEcU+G1SadiIRmmKGRsdtHEWvrT7SMH3nC/HNReR62gXH+69Snk/Iq4GNtPbdZLx2Ie6XJOl7GF28RC6CVdc+RXifQkgTIiMuWW2PEuyQM+B8jcphZDgNngY8uuWbBQw1NZPGHTlsF66szQLEJcYrkh0EQw3zKSFg/Ak6o2ksqcRTDbqSTTeZJavMXHe6IxQBz9ln6BK7vOgpX60TGbIOIhiacXMDbbWbrU25SGeetPt7XGj1U1QyLq7NhN0Ir7eWZs8cbYYmiZVuEBzT+7V5qJY47gVvQKjk1+Z5DYJ8YWzFKt8gns/en2WYbHVAVLmcYIbBzLqcHryfqO86Zc5ZRWcVDeMuKTWfK1gYWAEHVYq6S9nipvtCkZCdIFB8AzTbXSZobyABF2xQNibBYxNrtGXEsSpoikzSYoS+760+2rSGusDFgecrTLPTomjM3WiBOGY9DBDQ2boCHkAoEekd9C8yWVG8qYg68k/3CS2mB5Qv0SysycnnRuiMoI1l3WKhYCxYGaWtsRJSLVuc6EvgDA7hSttUJ8hdcaZcVj6sZZ7nHE2eW4JsV8IbakqF7nKk1664JlDuBWReW4pXKDuBD7tQWg+arhmh/MkXSlXH+6ZRyaHynvELVQe3jkbvrkSQQA7hmbbRDPvk2GJa9g2cELKXF0mLb+dOsmFY3nkkDx8LHLzSMUXtd8cAzAF8ZmE4HPOogDUN9oo14Ym7EK93JozcMMdf4E4IyxWcjY4oKA8m/HzFAit6BxJjIlCg69bVn+/GS/HDzUAEsynmPN2Gxc8Lm8Wfr/UIRVBCjPRRvM2KxVhy9pHEAQ7JeDS1nXuahCblWTvyQPelTSsHVX8+3ySj67OTlXn/e0VxG9Iid5PNeozOJTCTINW6rcxx+MLVzyhpyuoyXxinoV/uAOYgPwHEiez0OFRAGvqSpmcv+XY3ZcxhZ+6j4h95Ed4iDjGMAF/XtEfMhvyTMNNV7bFSa4FN5fVXnD+9Mtk2xin+C9HNDhCVZqY9y8L5UhrwAcxhaTpJenrE2DuM91ixRACM0F4j0BoHgoL9DOjMHI8Bd6q3clPOSnYY+gDaItbJEMJOgJeD51jn1ZSf7dhPvyLxmAYsjO8Oat8xLAlekOQcPyWzcIyzRLWW+QiDmqbPOpqfwCcToh7wFnHhbFcxPueqHFhdXKXFxN1/27b+c1PR8RuYFEoxNxBlbw7yFji2vIndl8jKLrZfiV/JIZlMuoV6kr/+hKBZB7/ciB6KyraNFwjuPfUR1FQbmV4u8x1LVBVK2WzFZ7QLdF9aFcH+qUPmkWKq1TPe5qs18OrnES3ZrFhfyh5584EJ1HgCLN8l3D9/Db/BAYW6wYWzzb1kyW4eKGirhLhIwYU5Zm0ZWQurSxp4ixRdK7vcP7uPOIfvfwOYp7JeNZccnPCHGidKJJu/gKSP9VetjjJ80i4+ZWENdyBeIjTmfMibM90e/pPbmVAIqH9+SnA+BO12RLesh1tMs4bypo2gw5Gh+GZylIqpJCGVOU5QmOsmJCBC6HsQWrkcSU1VrronrqXkseqE55QLWAloQJmoU595gXvFhz2fAFmfuqgNmVjXUzOTT5m41Ioe7CpFEsrGpOqYzhQATYr6jB/JKsul9yzSLAPEC8LieAQNL0POOtmXdQuyTxmjU9nHmBB+cytrijvRpyHManh7sBMM6o2NsgO341RHF86LYGBxkTuL0SEzkWCZr2BGxr10CzY2x2hbg4O888rRCXPcwzeN4wi9eQKcqSm6w11ORIiXaJUH4YhPCAn16Gres8YLgHJmL3A8QFU2fcTx5JzAKMl0NkN5yp82sApoi/VDrprFe0SMUSthAz3wWAclWgNUTJcZaZ+KXQnV7j8yGfm6rF9ec5RGykYeP/tV+bfHiD+dhIEVCqaOJ70b1lbLZmbDGHovjUfjkYc0fuJeapkvQ0BHVaqVkolP/M/awUAyXhLQ8518uSawA7hbU411UIrajrLHpCVhUJLFcsnsBnItIOlYHCAWbCmYQwx3NKPhsQ2VZljkK8pzUqS26TmeLsc+0jTAxolqLzpzcAfhUQ11YIlzcKUHEubuEcXDpkGooAs2vBXkap3zeI6383slrEQplzWrRyu/F5GYsmwKxQL2/0swUbOUFc9BwhzgofVQiBLAWvOYf96fauikck1OvMtYN4Euu0YoQYNy3h9zGCQQAsWWP0I8THCpbuhXCv8345SKqmHiTWacu40yG5rSsAb5YNOTbBVbJccKdKmKTqHNwJclowCniALaQwTG3SnJJ/TgfwUpTvu9ECFgLMBnHTlghptWmOf9Z6fajtYrBRq3goLmv1tIEl8df3y8EVyqdUWjPFkgJimYChksdjFWVTv2vVs1Dj+1WOWdpZeGBmnld2VydZZ7FWcaCwDad28ROlBy7wOUJr3WxcCqrlAfjxCPnLUCDkERoDCwEmIg2z5tzlnaUbmJdAc1GcOGyjiJBX4RiY8hPjqUf6xeZBylTptsrx3i6OIQYj2HD2oZGsSGod1VsgL4hn4zr2gmX2kOPSOzieovUyDrZBxVGtOsBySxv+bDlgxnjPrgcEnqsjGs3xvSCEcL1fDq6rhjWUmqGMbrhOnRpvielxSUPO6UV44UASyMa9Kp++KkGoRv3pNqLIbxPcxCHSGra9vIB7GXlTmbTXeBlej/IxJ6o1y58cV62Rc55TRLZwELPFmmJIJsWv8KfCxLWKZulpQH1mDKOhwyD4GMKIwNMKDUIHTb0R2P2Klwh0rEslwXVL/v2pAcK7w8fo8nfbNUl/uk1qgIc1LvW77WBxoX5IUJnHE+Fja4trMVAYaRJfweWs1ywiCxzSvDqTYvWRfKRNku5GVRIdA1gS/mLMHFG2eZ3BYWzxblQPDYSuoUk9hQsMIVbj4pg2R3gfwhxYBJQRcRMHLRHVrrNXYQOuRJONpImSty+UKX2ID3uYhRYBRdcLs6NaI6VyOBy0JBI9xNVnZWTyQyF3KuD0Be+BJq/ALgeII5QBVfC1wS0eQm91XnvAwmmCEbKDSSH340BdcU7i+fyyFTgVNa+saEmxaAOLBeo4BHBvW5mEhgnYmd6f5NE9pWDpNbl59DB18AiXvK63Blz1ojiKZ+BWka4L9yzYR51xEBdx5Pg5faC16VgKzI1fC44ZLBvonzblA3htUMscxZy+RjkL9+Y9Qs8AoSwxmgEnsv/HoGnX8hAb5yycmGxxfSRibUpM3ivQeXErwELh6fBIAXNr8Hvtjh4sJKbHcmivsSGOZJJY/+gKWNYN3FN3jc2Nyf3T3QFqDVjoiwaGb+tCU46GK4k0IREMlGLYpFlME91Ehv3p9q7lxHZioq/cNrBsGrrvSgN/MUVs16ZCAVaBhVoX1g3dXllRFnlajoE135vsyzqHffLLsApPxENcST8uAIFPvyb//ZoDijDFIb5BbWtsiIITx3SJFRHcjIfyhuaKq8c0pdMnUHylh1xlPRd5HILMnUvXrHrtEA1l0xsvUSiJTzQxvisk3lSH8EoVH3FDAt2Uxnohb2fX5IGk1oKFNu/JkOuZAORn8jD60+2qBmDGNo8bOVawOIiryjxNt9gRQNY595cpVLJi5q8usPRsXRw3TUq16l0jLha/KtEAVUa4/tUqOGKxVrOkNMwT6nXqJS75jyrBq4o1sw9NTYvovBnKiV1UPawpcWGl5/EKdisc/RyaVoElBZqkayAvxrGDwip/0m53iBODPGgCcmU3OHJpJVgyHiJPQgPdE7256UqBRdPDzYPlJCcpkv8PAHSv/QtFBkyYAAAAAElFTkSuQmCC";
304
+
305
+ var mcgStyles = {"link-list":"myCancerGenome-module_link-list__2wFhH"};
306
+
307
+ function placeArrow$1(tooltipEl) {
308
+ var arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
309
+ arrowEl.style.left = '10px';
310
+ }
311
+ function sortValue$6(links) {
312
+ return links.length > 0 ? 1 : 0;
313
+ }
314
+ function download$5(links) {
315
+ return links.length > 0 ? 'present' : 'not present';
316
+ }
317
+ function myCancerGenomeLinks(linksHTML) {
318
+ var links = [];
319
+ ___default["default"].each(linksHTML, function (link, index) {
320
+ // TODO this is a workaround, ideally we should fix the data itself
321
+ // parse the data as an HTML dom element, since it is formatted as an HTML link.
322
+ var myCancerGenomeLink = cbioportalUtils.parseMyCancerGenomeLink(link);
323
+ if (myCancerGenomeLink) {
324
+ links.push(React__namespace.createElement("li", { key: index },
325
+ React__namespace.createElement("a", { href: myCancerGenomeLink.url, target: "_blank" }, myCancerGenomeLink.text)));
1865
326
  }
1866
327
  });
1867
- Object.defineProperty(OncoKB.prototype, "handleFeedbackClose", {
328
+ return (React__namespace.createElement("span", null,
329
+ React__namespace.createElement("b", null, "My Cancer Genome links:"),
330
+ React__namespace.createElement("br", null),
331
+ React__namespace.createElement("ul", { className: mcgStyles['link-list'] }, links)));
332
+ }
333
+ var MyCancerGenome = /** @class */ (function (_super) {
334
+ tslib.__extends(MyCancerGenome, _super);
335
+ function MyCancerGenome() {
336
+ return _super !== null && _super.apply(this, arguments) || this;
337
+ }
338
+ Object.defineProperty(MyCancerGenome.prototype, "render", {
1868
339
  enumerable: false,
1869
340
  configurable: true,
1870
341
  writable: true,
1871
342
  value: function () {
1872
- this.showFeedback = false;
343
+ var myCancerGenomeContent = (React__namespace.createElement("span", { className: "" + annotationStyles['annotation-item'] }));
344
+ if (this.props.linksHTML.length > 0) {
345
+ var arrowContent = React__namespace.createElement("div", { className: "rc-tooltip-arrow-inner" });
346
+ var tooltipContent = myCancerGenomeLinks(this.props.linksHTML);
347
+ myCancerGenomeContent = (React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, { overlay: tooltipContent, placement: "topLeft", trigger: ['hover', 'focus'], arrowContent: arrowContent, onPopupAlign: placeArrow$1 },
348
+ React__namespace.createElement("span", { className: annotationStyles['annotation-item'] + " mcg" },
349
+ React__namespace.createElement("img", { width: "14", height: "14", src: img$2, alt: "My Cancer Genome Symbol" }))));
350
+ }
351
+ return myCancerGenomeContent;
1873
352
  }
1874
353
  });
1875
- tslib.__decorate([
1876
- mobx.observable
1877
- ], 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;
354
+ return MyCancerGenome;
1894
355
  }(React__namespace.Component));
1895
356
 
1896
357
  var hotspotStyles = {"hotspot-info":"hotspotInfo-module_hotspot-info__S24fX"};
@@ -2242,8 +703,8 @@ function getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, myCancerGen
2242
703
  oncoKbData.result &&
2243
704
  !(oncoKbData.result instanceof Error) &&
2244
705
  oncoKbData.status === 'complete') {
2245
- oncoKbIndicator = getIndicatorData(mutation, oncoKbData.result, resolveTumorType, resolveEntrezGeneId);
2246
- oncoKbAvailableDataTypes = ___default["default"].uniq(tslib.__spreadArrays(oncoKbAvailableDataTypes, cbioportalUtils.calculateOncoKbAvailableDataType(___default["default"].values(oncoKbData.result.indicatorMap))));
706
+ oncoKbIndicator = oncokbFrontendCommons.getIndicatorData(mutation, oncoKbData.result, resolveTumorType, resolveEntrezGeneId);
707
+ oncoKbAvailableDataTypes = ___default["default"].uniq(tslib.__spreadArrays(oncoKbAvailableDataTypes, oncokbFrontendCommons.calculateOncoKbAvailableDataType(___default["default"].values(oncoKbData.result.indicatorMap))));
2247
708
  }
2248
709
  value = tslib.__assign(tslib.__assign({}, value), { oncoKbStatus: oncoKbData ? oncoKbData.status : 'pending', oncoKbIndicator: oncoKbIndicator,
2249
710
  oncoKbAvailableDataTypes: oncoKbAvailableDataTypes });
@@ -2268,17 +729,17 @@ function annotationSortMethod(a, b) {
2268
729
  }
2269
730
  function sortValue$4(annotation) {
2270
731
  return ___default["default"].flatten([
2271
- sortValue$6(annotation.oncoKbIndicator),
2272
- sortValue$8(annotation.civicEntry),
2273
- sortValue$7(annotation.myCancerGenomeLinks),
732
+ oncokbFrontendCommons.oncoKbAnnotationSortValue(annotation.oncoKbIndicator),
733
+ sortValue$7(annotation.civicEntry),
734
+ sortValue$6(annotation.myCancerGenomeLinks),
2274
735
  sortValue$5(annotation.isHotspot, annotation.is3dHotspot),
2275
736
  annotation.isOncoKbCancerGene ? 1 : 0,
2276
737
  ]);
2277
738
  }
2278
739
  function GenericAnnotation(props) {
2279
- var annotation = props.annotation, enableCivic = props.enableCivic, enableHotspot = props.enableHotspot, enableMyCancerGenome = props.enableMyCancerGenome, enableOncoKb = props.enableOncoKb, pubMedCache = props.pubMedCache, userEmailAddress = props.userEmailAddress, mergeOncoKbIcons = props.mergeOncoKbIcons, oncoKbContentPadding = props.oncoKbContentPadding;
740
+ 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
741
  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, pubMedCache: pubMedCache, userEmailAddress: userEmailAddress, contentPadding: oncoKbContentPadding })),
742
+ 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
743
  enableCivic && (React__namespace.createElement(Civic, { civicEntry: annotation.civicEntry, civicStatus: annotation.civicStatus, hasCivicVariants: annotation.hasCivicVariants })),
2283
744
  enableMyCancerGenome && (React__namespace.createElement(MyCancerGenome, { linksHTML: annotation.myCancerGenomeLinks })),
2284
745
  enableHotspot && (React__namespace.createElement(HotspotAnnotation, { isHotspot: annotation.isHotspot, is3dHotspot: annotation.is3dHotspot, status: annotation.hotspotStatus }))));
@@ -3344,7 +1805,7 @@ var DropdownSelector = /** @class */ (function (_super) {
3344
1805
  var _a;
3345
1806
  var allValuesSelected = this.allValues.length === this.selectedValues.length;
3346
1807
  var classes = this.props.selectionIndicatorClassNames;
3347
- return classnames__default["default"](classes.base, (_a = {},
1808
+ return classNames__default["default"](classes.base, (_a = {},
3348
1809
  _a[classes.allSelected] = allValuesSelected,
3349
1810
  _a[classes.partiallySelected] = !allValuesSelected,
3350
1811
  _a));
@@ -4086,8 +2547,8 @@ var FilterResetPanel = /** @class */ (function (_super) {
4086
2547
  writable: true,
4087
2548
  value: {
4088
2549
  buttonText: 'Show all',
4089
- buttonClass: classnames__default["default"]('btn', 'btn-secondary', 'btn-sm'),
4090
- className: classnames__default["default"]('alert', 'alert-success', styles$7.filterResetPanel),
2550
+ buttonClass: classNames__default["default"]('btn', 'btn-secondary', 'btn-sm'),
2551
+ className: classNames__default["default"]('alert', 'alert-success', styles$7.filterResetPanel),
4091
2552
  }
4092
2553
  });
4093
2554
  FilterResetPanel = tslib.__decorate([
@@ -4502,7 +2963,7 @@ var DataTable = /** @class */ (function (_super) {
4502
2963
  value: function () {
4503
2964
  return (React__namespace.createElement("div", { className: "cbioportal-frontend" },
4504
2965
  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: classnames__default["default"](this.props.className, 'cbioportal-frontend', 'default-data-table') },
2966
+ React__namespace.createElement("div", { className: classNames__default["default"](this.props.className, 'cbioportal-frontend', 'default-data-table') },
4506
2967
  React__namespace.createElement(ReactTable__default["default"], tslib.__assign({ data: this.tableData, columns: this.columns, getTrProps: this.needToCustomizeRowStyle
4507
2968
  ? this.getTrProps
4508
2969
  : 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)))));
@@ -5748,8 +4209,8 @@ function calcYMaxInput(yMaxInput, yMaxStep, countRange, oppositeCountRange, yAxi
5748
4209
  var input = yMaxInput;
5749
4210
  if (input === undefined) {
5750
4211
  input = yAxisSameScale
5751
- ? getCommonYAxisMaxSliderValue(yMaxStep, countRange, oppositeCountRange)
5752
- : getYAxisMaxSliderValue(yMaxStep, countRange);
4212
+ ? numeral__default["default"](numeral__default["default"](getCommonYAxisMaxSliderValue(yMaxStep, countRange, oppositeCountRange)).format(String(yMaxStep))).value()
4213
+ : numeral__default["default"](numeral__default["default"](getYAxisMaxSliderValue(yMaxStep, countRange)).format(String(yMaxStep))).value();
5753
4214
  }
5754
4215
  return input;
5755
4216
  }
@@ -5779,7 +4240,9 @@ function calcCountRange(lollipops, defaultMax, defaultMin) {
5779
4240
  for (var _i = 0, lollipops_1 = lollipops; _i < lollipops_1.length; _i++) {
5780
4241
  var lollipop = lollipops_1[_i];
5781
4242
  max = Math.max(max, lollipop.count);
5782
- min = Math.min(min, lollipop.count);
4243
+ min = Number.isInteger(lollipop.count)
4244
+ ? Math.min(min, lollipop.count)
4245
+ : Math.min(0.1, lollipop.count);
5783
4246
  }
5784
4247
  return [min, Math.max(min, max)];
5785
4248
  }
@@ -7371,7 +5834,7 @@ var LollipopMutationPlotControls = /** @class */ (function (_super) {
7371
5834
  });
7372
5835
  Object.defineProperty(LollipopMutationPlotControls.prototype, "trackSelector", {
7373
5836
  get: function () {
7374
- return (React__namespace.createElement("div", { className: classnames__default["default"]('annotation-track-selector', 'small'), style: { width: 180, marginRight: 7 } },
5837
+ return (React__namespace.createElement("div", { className: classNames__default["default"]('annotation-track-selector', 'small'), style: { width: 180, marginRight: 7 } },
7375
5838
  React__namespace.createElement(TrackSelector, { tracks: this.props.tracks, trackVisibility: this.props.trackVisibility, trackDataStatus: this.props.trackDataStatus, onChange: this.props.onTrackVisibilityChange })));
7376
5839
  },
7377
5840
  enumerable: false,
@@ -7398,7 +5861,7 @@ var LollipopMutationPlotControls = /** @class */ (function (_super) {
7398
5861
  configurable: true,
7399
5862
  writable: true,
7400
5863
  value: function () {
7401
- return (React__namespace.createElement("div", { className: classnames__default["default"]('lollipop_mutation_plot__controls', this.props.showControls
5864
+ return (React__namespace.createElement("div", { className: classNames__default["default"]('lollipop_mutation_plot__controls', this.props.showControls
7402
5865
  ? styles$5['fade-in']
7403
5866
  : styles$5['fade-out']) },
7404
5867
  React__namespace.createElement("div", { style: { display: 'flex', alignItems: 'center' } },
@@ -8011,7 +6474,7 @@ var Track = /** @class */ (function (_super) {
8011
6474
  position: 'relative',
8012
6475
  display: 'flex',
8013
6476
  } },
8014
- React__namespace.createElement("span", { className: classnames__default["default"](styles$4.trackTitle, 'small', (this.props.isSubTrack ? 'subtrack-' : '') + "trackTitle") }, this.props.trackTitle),
6477
+ React__namespace.createElement("span", { className: classNames__default["default"](styles$4.trackTitle, 'small', (this.props.isSubTrack ? 'subtrack-' : '') + "trackTitle") }, this.props.trackTitle),
8015
6478
  React__namespace.createElement("span", null,
8016
6479
  React__namespace.createElement(cbioportalFrontendCommons.DefaultTooltip, tslib.__assign({ placement: this.getOverlayPlacement(), overlay: this.getOverlay, onVisibleChange: this.onTooltipVisibleChange, destroyTooltipOnHide: true }, this.tooltipVisibleProps), this.hitZone),
8017
6480
  React__namespace.createElement("span", { style: { marginLeft: this.props.xOffset }, onMouseOver: this.onMouseOver },
@@ -8171,130 +6634,6 @@ var OncoKbFilterValue;
8171
6634
  OncoKbFilterValue["Oncogenic"] = "ONCOGENIC";
8172
6635
  })(OncoKbFilterValue || (OncoKbFilterValue = {}));
8173
6636
 
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
6637
  function oncoKbTooltip(usingPublicOncoKbInstance, indicatorData) {
8299
6638
  var sampleCount = indicatorData.length;
8300
6639
  // generate info
@@ -8343,7 +6682,7 @@ function oncoKbTooltip(usingPublicOncoKbInstance, indicatorData) {
8343
6682
  oncogenicInfo,
8344
6683
  ' ',
8345
6684
  "mutations.",
8346
- React__namespace.createElement(OncoKbSummaryTable, { usingPublicOncoKbInstance: usingPublicOncoKbInstance, data: tableData })));
6685
+ React__namespace.createElement(oncokbFrontendCommons.OncoKbSummaryTable, { usingPublicOncoKbInstance: usingPublicOncoKbInstance, data: tableData })));
8347
6686
  }
8348
6687
  function generateLevelData(indicatorData) {
8349
6688
  var levels = {};
@@ -8352,12 +6691,12 @@ function generateLevelData(indicatorData) {
8352
6691
  var parts = treatment.level.split('_');
8353
6692
  var level = parts.length === 2 ? parts[1] : treatment.level;
8354
6693
  levels[level] = levels[level] || [];
8355
- levels[level].push(getTumorTypeNameWithExclusionInfo(treatment.levelAssociatedCancerType, treatment.levelExcludedCancerTypes));
6694
+ levels[level].push(oncokbFrontendCommons.getTumorTypeNameWithExclusionInfo(treatment.levelAssociatedCancerType, treatment.levelExcludedCancerTypes));
8356
6695
  });
8357
6696
  });
8358
6697
  return ___default["default"].keys(levels)
8359
6698
  .sort(function (a, b) {
8360
- return cbioportalUtils.LEVELS.all.indexOf(a) > cbioportalUtils.LEVELS.all.indexOf(b) ? -1 : 1;
6699
+ return oncokbFrontendCommons.LEVELS.all.indexOf(a) > oncokbFrontendCommons.LEVELS.all.indexOf(b) ? -1 : 1;
8361
6700
  })
8362
6701
  .map(function (level) { return ({ level: level, tumorTypes: ___default["default"].uniq(levels[level]) }); });
8363
6702
  }
@@ -8614,9 +6953,9 @@ var PtmReferenceList = /** @class */ (function (_super) {
8614
6953
  maxHeight: 400,
8615
6954
  overflowY: 'auto',
8616
6955
  } },
8617
- React__namespace.createElement(ReferenceList, { pmids: this.props.pubmedIds
6956
+ React__namespace.createElement(oncokbFrontendCommons.ReferenceList, { pmids: this.props.pubmedIds
8618
6957
  .map(function (id) { return extractNumericalPart(id); })
8619
- .filter(function (id) { return id !== undefined; }), pmidData: this.props.pmidData, abstracts: [] })), destroyTooltipOnHide: true },
6958
+ .filter(function (id) { return id !== undefined; }), abstracts: [] })), destroyTooltipOnHide: true },
8620
6959
  React__namespace.createElement("div", { style: { textAlign: 'right' } },
8621
6960
  React__namespace.createElement("i", { className: "fa fa-book", style: { color: 'black' } }))));
8622
6961
  }
@@ -8741,7 +7080,7 @@ var PtmAnnotationTable = /** @class */ (function (_super) {
8741
7080
  var showPagination = data.length >
8742
7081
  (this.props.initialItemsPerPage ||
8743
7082
  PtmAnnotationTable_1.defaultProps.initialItemsPerPage);
8744
- return (React__namespace.createElement("div", { className: classnames__default["default"]('cbioportal-frontend', 'default-track-tooltip-table') },
7083
+ return (React__namespace.createElement("div", { className: classNames__default["default"]('cbioportal-frontend', 'default-track-tooltip-table') },
8745
7084
  React__namespace.createElement(ReactTable__default["default"], { data: data, columns: this.columns, defaultSorted: [
8746
7085
  {
8747
7086
  id: initialSortColumn ||
@@ -10165,7 +8504,7 @@ var AxisScaleSwitch = /** @class */ (function (_super) {
10165
8504
  configurable: true,
10166
8505
  writable: true,
10167
8506
  value: function (scale, onClick) {
10168
- return (React__namespace.createElement("button", { className: classnames__default["default"]({
8507
+ return (React__namespace.createElement("button", { className: classNames__default["default"]({
10169
8508
  'btn-secondary': this.props.selectedScale === scale,
10170
8509
  'btn-outline-secondary': this.props.selectedScale !== scale,
10171
8510
  }, 'btn', 'btn-sm', 'btn-axis-switch'), style: {
@@ -11008,14 +9347,14 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
11008
9347
  switch (_c.label) {
11009
9348
  case 0:
11010
9349
  mutationQueryVariants = ___default["default"].uniqBy(___default["default"].map(queryVariants.filter(function (mutation) { return mutation.mutationType !== 'Fusion'; }), function (mutation) {
11011
- return cbioportalUtils.generateProteinChangeQuery(getEntrezGeneId(mutation), getTumorType(mutation), mutation.proteinChange, mutation.mutationType, mutation.proteinPosStart, mutation.proteinPosEnd, evidenceTypes);
9350
+ return oncokbFrontendCommons.generateProteinChangeQuery(getEntrezGeneId(mutation), getTumorType(mutation), mutation.proteinChange, mutation.mutationType, mutation.proteinPosStart, mutation.proteinPosEnd, evidenceTypes);
11012
9351
  }), 'id');
11013
9352
  structuralQueryVariants = ___default["default"].uniqBy(___default["default"].map(queryVariants.filter(function (mutation) {
11014
9353
  var _a;
11015
9354
  return ((_a = mutation.mutationType) === null || _a === void 0 ? void 0 : _a.toUpperCase()) ===
11016
- cbioportalUtils.StructuralVariantType.FUSION;
9355
+ oncokbFrontendCommons.StructuralVariantType.FUSION;
11017
9356
  }), function (mutation) {
11018
- return cbioportalUtils.generateAnnotateStructuralVariantQuery(
9357
+ return oncokbFrontendCommons.generateAnnotateStructuralVariantQuery(
11019
9358
  /* @ts-ignore */
11020
9359
  mutation.structuralVariant, getTumorType(mutation), evidenceTypes);
11021
9360
  }), 'id');
@@ -11121,7 +9460,7 @@ var DefaultMutationMapperFilterApplier = /** @class */ (function () {
11121
9460
  return (!filter.values ||
11122
9461
  !this.oncoKbData.result ||
11123
9462
  this.oncoKbData.result instanceof Error ||
11124
- defaultOncoKbFilter(mutation, this.oncoKbData.result, this.getDefaultTumorType, this.getDefaultEntrezGeneId));
9463
+ oncokbFrontendCommons.defaultOncoKbFilter(mutation, this.oncoKbData.result, this.getDefaultTumorType, this.getDefaultEntrezGeneId));
11125
9464
  }
11126
9465
  });
11127
9466
  Object.defineProperty(DefaultMutationMapperFilterApplier.prototype, "applyHostpotFilter", {
@@ -12177,7 +10516,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
12177
10516
  get: function () {
12178
10517
  if (this.oncoKbData.result &&
12179
10518
  !(this.oncoKbData.result instanceof Error)) {
12180
- return groupOncoKbIndicatorDataByMutations(this.mutationsByPosition, this.oncoKbData.result, this.getDefaultTumorType, this.getDefaultEntrezGeneId, defaultOncoKbIndicatorFilter);
10519
+ return oncokbFrontendCommons.groupOncoKbIndicatorDataByMutations(this.mutationsByPosition, this.oncoKbData.result, this.getDefaultTumorType, this.getDefaultEntrezGeneId, oncokbFrontendCommons.defaultOncoKbIndicatorFilter);
12181
10520
  }
12182
10521
  else {
12183
10522
  return {};
@@ -12370,7 +10709,7 @@ var TranscriptDropdown = /** @class */ (function (_super) {
12370
10709
  canonicalTranscriptId &&
12371
10710
  transcriptsWithAnnotations.result &&
12372
10711
  transcriptsWithAnnotations.result.length > 0;
12373
- return (React__namespace.createElement("div", { className: classnames__default["default"]('small', styles$1.dropDown) },
10712
+ return (React__namespace.createElement("div", { className: classNames__default["default"]('small', styles$1.dropDown) },
12374
10713
  this.loadingIndicator(isLoading),
12375
10714
  !isLoading &&
12376
10715
  requiredData &&
@@ -12383,7 +10722,7 @@ var TranscriptDropdown = /** @class */ (function (_super) {
12383
10722
  var requiredData = transcriptsWithProteinLength.result &&
12384
10723
  transcriptsWithProteinLength.result.length > 0 &&
12385
10724
  canonicalTranscriptId;
12386
- return (React__namespace.createElement("div", { className: classnames__default["default"]('small', styles$1.dropDown) },
10725
+ return (React__namespace.createElement("div", { className: classNames__default["default"]('small', styles$1.dropDown) },
12387
10726
  this.loadingIndicator(isLoading),
12388
10727
  !isLoading &&
12389
10728
  requiredData &&
@@ -13055,7 +11394,6 @@ exports.LollipopMutationPlot = LollipopMutationPlot;
13055
11394
  exports.LollipopPlot = LollipopPlot;
13056
11395
  exports.LollipopPlotNoTooltip = LollipopPlotNoTooltip;
13057
11396
  exports.LollipopTooltipCountInfo = LollipopTooltipCountInfo;
13058
- exports.MSI_H_NAME = MSI_H_NAME;
13059
11397
  exports.MUTATION_COLUMNS_DEFINITION = MUTATION_COLUMNS_DEFINITION;
13060
11398
  exports.MUTATION_COLUMN_HEADERS = MUTATION_COLUMN_HEADERS;
13061
11399
  exports.MUTATION_STATUS_BADGE_STYLE_OVERRIDE = MUTATION_STATUS_BADGE_STYLE_OVERRIDE;
@@ -13066,26 +11404,14 @@ exports.MutationStatusBadgeSelector = MutationStatusBadgeSelector;
13066
11404
  exports.MyCancerGenome = MyCancerGenome;
13067
11405
  exports.ONCOKB_DEFAULT_DATA = ONCOKB_DEFAULT_DATA;
13068
11406
  exports.ONCOKB_DEFAULT_INFO = ONCOKB_DEFAULT_INFO;
13069
- exports.OTHER_BIOMARKER_HUGO_SYMBOL = OTHER_BIOMARKER_HUGO_SYMBOL;
13070
- exports.OTHER_BIOMARKER_NAME = OTHER_BIOMARKER_NAME;
13071
- exports.OncoKB = OncoKB;
13072
- exports.OncoKBSuggestAnnotationLinkout = OncoKBSuggestAnnotationLinkout;
13073
- exports.OncoKbFeedback = OncoKbFeedback;
13074
- exports.OncoKbHelper = OncoKbHelper;
13075
- exports.OncoKbTooltip = OncoKbTooltip;
13076
- exports.OncoKbTreatmentTable = OncoKbTreatmentTable;
13077
11407
  exports.PercentToggle = PercentToggle;
13078
11408
  exports.ProteinChange = ProteinChange;
13079
11409
  exports.ProteinImpactTypeBadgeSelector = ProteinImpactTypeBadgeSelector;
13080
11410
  exports.ProteinImpactTypeDropdownSelector = ProteinImpactTypeDropdownSelector;
13081
- exports.RefComponent = RefComponent;
13082
- exports.ReferenceList = ReferenceList;
13083
11411
  exports.Sequence = LollipopPlot;
13084
11412
  exports.Signal = Signal;
13085
11413
  exports.SignalTable = SignalTable;
13086
- exports.SummaryWithRefs = SummaryWithRefs;
13087
11414
  exports.TEXT_INPUT_FILTER_ID = TEXT_INPUT_FILTER_ID;
13088
- exports.TMB_H_NAME = TMB_H_NAME;
13089
11415
  exports.TrackSelector = TrackSelector;
13090
11416
  exports.USE_DEFAULT_PUBLIC_INSTANCE_FOR_ONCOKB = USE_DEFAULT_PUBLIC_INSTANCE_FOR_ONCOKB;
13091
11417
  exports.annotationSortValue = sortValue$4;
@@ -13096,14 +11422,12 @@ exports.applyDefaultMutationStatusFilter = applyDefaultMutationStatusFilter;
13096
11422
  exports.applyDefaultPositionFilter = applyDefaultPositionFilter;
13097
11423
  exports.applyDefaultProteinImpactTypeFilter = applyDefaultProteinImpactTypeFilter;
13098
11424
  exports.calculateGnomadAlleleFrequency = calculateGnomadAlleleFrequency;
13099
- exports.civicDownload = download$7;
13100
- exports.civicSortValue = sortValue$8;
11425
+ exports.civicDownload = download$6;
11426
+ exports.civicSortValue = sortValue$7;
13101
11427
  exports.clinvarDownload = download$4;
13102
11428
  exports.clinvarSortValue = sortValue$3;
13103
11429
  exports.dbsnpDownload = download$3;
13104
11430
  exports.dbsnpSortValue = sortValue$2;
13105
- exports.defaultOncoKbFilter = defaultOncoKbFilter;
13106
- exports.errorIcon = errorIcon;
13107
11431
  exports.fetchVariantAnnotationsByMutation = fetchVariantAnnotationsByMutation;
13108
11432
  exports.fetchVariantAnnotationsIndexedByGenomicLocation = fetchVariantAnnotationsIndexedByGenomicLocation;
13109
11433
  exports.findAllUniquePositions = findAllUniquePositions;
@@ -13122,13 +11446,11 @@ exports.getProteinImpactTypeOptionLabel = getProteinImpactTypeOptionLabel;
13122
11446
  exports.getSelectedOptionValues = getSelectedOptionValues;
13123
11447
  exports.getSignalData = getSignalData;
13124
11448
  exports.getSingleSignalValue = getSingleSignalValue;
13125
- exports.getTumorTypeNameWithExclusionInfo = getTumorTypeNameWithExclusionInfo;
13126
11449
  exports.getUrl = getUrl;
13127
11450
  exports.gnomadDownload = download$2;
13128
11451
  exports.gnomadSortValue = sortValue$1;
13129
11452
  exports.groupDataByGroupFilters = groupDataByGroupFilters;
13130
11453
  exports.groupDataByProteinImpactType = groupDataByProteinImpactType;
13131
- exports.groupOncoKbIndicatorDataByMutations = groupOncoKbIndicatorDataByMutations;
13132
11454
  exports.handleOptionSelect = handleOptionSelect;
13133
11455
  exports.hgvscDownload = download$1;
13134
11456
  exports.hgvscSortValue = sortValue;
@@ -13140,17 +11462,11 @@ exports.initDefaultTrackVisibility = initDefaultTrackVisibility;
13140
11462
  exports.initGenomeNexusClient = initGenomeNexusClient;
13141
11463
  exports.initGenomeNexusInternalClient = initGenomeNexusInternalClient;
13142
11464
  exports.initOncoKbClient = initOncoKbClient;
13143
- exports.levelIconClassNames = levelIconClassNames;
13144
- exports.loaderIcon = loaderIcon;
13145
11465
  exports.mergeColumns = mergeColumns;
13146
11466
  exports.mutationTypeSort = mutationTypeSort;
13147
- exports.myCancerGenomeDownload = download$6;
13148
- exports.myCancerGenomeSortValue = sortValue$7;
13149
- exports.normalizeLevel = normalizeLevel;
11467
+ exports.myCancerGenomeDownload = download$5;
11468
+ exports.myCancerGenomeSortValue = sortValue$6;
13150
11469
  exports.onFilterOptionSelect = onFilterOptionSelect;
13151
- exports.oncoKbAnnotationDownload = download$5;
13152
- exports.oncoKbAnnotationSortValue = sortValue$6;
13153
- exports.oncogenicityIconClassNames = oncogenicityIconClassNames;
13154
11470
  exports.proteinChangeSortMethod = proteinChangeSortMethod;
13155
11471
  exports.rightAlignedCell = rightAlignedCell;
13156
11472
  exports.signalDownload = download;