npm - @sjcrh/proteinpaint-client - Versions diffs - 2.193.0 → 2.194.0 - Mend

@sjcrh/proteinpaint-client 2.193.0 → 2.194.0

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Files changed (540) hide show

package/dist/chunk-SDMOLIEU.js.map DELETED Viewed

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/survival/survival.ts"],
-  "sourcesContent": ["import { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase, defaultUiLabels } from '#plots/PlotBase.ts'\nimport { controlsInit, term0_term2_defaultQ } from '#plots/controls.js'\nimport { select } from 'd3-selection'\nimport { scaleLinear, scaleOrdinal } from 'd3-scale'\nimport { schemeCategory10 } from 'd3-scale-chromatic'\nimport { schemeCategory20 } from '#common/legacy-d3-polyfill'\nimport { axisLeft, axisBottom } from 'd3-axis'\nimport { line, area, curveStepAfter } from 'd3-shape'\nimport { rgb } from 'd3-color'\nimport htmlLegend from '#dom/html.legend'\nimport Partjson from 'partjson'\nimport { rgb2hex } from '#src/client'\nimport { fillTermWrapper } from '#termsetting'\nimport { Menu } from '#dom/menu'\nimport { getSeriesTip } from '#dom/svgSeriesTips'\nimport { renderAtRiskG } from '#dom/renderAtRisk'\nimport { renderPvalues } from '#dom/renderPvalueTable'\nimport { downloadChart } from '#common/svg.download'\nimport { getCombinedTermFilter } from '#filter'\nimport { DownloadMenu } from '#dom/downloadMenu'\nimport { isNumericTerm } from '#shared/terms.js'\n\nexport const t0_t2_defaultQ = structuredClone(term0_term2_defaultQ)\nObject.assign(t0_t2_defaultQ, {\n\tnumeric: {\n\t\tmode: 'discrete',\n\t\ttype: 'custom-bin',\n\t\tpreferredBins: 'median'\n\t},\n\tgeneExpression: {\n\t\tmode: 'discrete',\n\t\ttype: 'custom-bin',\n\t\tpreferredBins: 'median'\n\t}\n})\n\nclass TdbSurvival extends PlotBase implements RxComponent {\n\tstatic type = 'survival'\n\n\t// expected RxComponent props, some are already declared/set in PlotBase\n\ttype: string\n\tparentId?: string\n\tdom!: {\n\t\t[index: string]: any\n\t}\n\tcomponents: { [name: string]: ComponentApi } = {}\n\n\t// expected class-specific props\n\tconfigTermKeys = ['term', 'term0', 'term2']\n\tsettings: any\n\tlineFxn: any\n\tpj: any\n\tactiveMenu = false\n\tlegendRenderer: any\n\thiddenRenderer: any\n\tlegendClick = (_, __, ___) => {}\n\tdownload: () => void = () => {}\n\tgetChartImages = () => this.getChartImages()\n\tloadingWait = 0\n\n\tcolorScale: any\n\n\trefs: any\n\tmsg?: string\n\tsymbol: any\n\tserverData?: any\n\tcurrData?: any\n\tlegendData?: any\n\tlegendOrder: any[] = []\n\thiddenData?: any\n\ttests?: { [name: string]: any }\n\tterm2toColor: { [name: string]: { orig: string; rgb: any; adjusted: string; hex: string } } = {}\n\n\tuniqueSeriesIds: Set<any> = new Set()\n\n\t// TODO: migrate to this.view method\n\trender = () => {}\n\tgetSymbol = (_: number) => {\n\t\treturn ''\n\t}\n\n\tconstructor(opts, api) {\n\t\tsuper(opts, api)\n\t\tthis.type = TdbSurvival.type\n\t\tthis.settings = Object.assign({}, opts.settings)\n\t\tthis.dom = this.getDom()\n\t\tthis.pj = getPj(this)\n\n\t\tthis.lineFxn = line()\n\t\t\t.curve(curveStepAfter)\n\t\t\t.x(c => (c as any).scaledX)\n\t\t\t.y(c => (c as any).scaledY)\n\n\t\tthis.legendRenderer = htmlLegend(this.dom.legendDiv, {\n\t\t\tsettings: {\n\t\t\t\tlegendOrientation: 'vertical'\n\t\t\t},\n\t\t\thandlers: {\n\t\t\t\tlegend: {\n\t\t\t\t\tclick: e => this.legendClick(e.target.__data__, e.clientX, e.clientY)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\tthis.hiddenRenderer = htmlLegend(this.dom.hiddenDiv, {\n\t\t\tsettings: {\n\t\t\t\tlegendOrientation: 'vertical'\n\t\t\t},\n\t\t\thandlers: {\n\t\t\t\tlegend: {\n\t\t\t\t\tclick: e => this.legendClick(e.target.__data__, e.clientX, e.clientY)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tgetDom() {\n\t\tconst opts = this.opts\n\t\tconst holder = opts.controls ? opts.holder : opts.holder.append('div')\n\t\tconst { controls, errdiv, loadingDiv, renderedData, charts, legendDiv } = this.getStandardDomLayout(holder, opts)\n\t\tconst dom = {\n\t\t\tloadingDiv,\n\t\t\theader: opts.header?.html('Survival Plot'),\n\t\t\tcontrols,\n\t\t\tholder,\n\t\t\terrdiv,\n\t\t\trenderedData,\n\t\t\tchartsDiv: charts\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.style('display', 'flex')\n\t\t\t\t.style('flex-direction', 'row')\n\t\t\t\t.style('flex-wrap', 'wrap')\n\t\t\t\t.style('max-width', '100vw'),\n\t\t\tlegendDiv: legendDiv.style('margin', '5px 5px 15px 5px'),\n\t\t\thiddenDiv: renderedData.append('div').style('margin', '5px 5px 15px 5px'),\n\t\t\ttip: new Menu({ padding: '5px' }),\n\t\t\tlegendTip: new Menu({ padding: '5px' })\n\t\t}\n\n\t\tdom.tip.onHide = () => {\n\t\t\tthis.activeMenu = false\n\t\t}\n\n\t\treturn dom\n\t}\n\n\tasync init() {\n\t\tsetInteractivity(this)\n\t\tsetRenderers(this)\n\t\tawait this.setControls()\n\t}\n\n\tasync setControls() {\n\t\tconst state = this.getState(this.app.getState())\n\t\tconst controlLabels = state.config.controlLabels\n\t\tif (!controlLabels) throw 'controls labels not found'\n\t\t// public/unauthenticated views disable stratification to limit inference from aggregated data; admin/user are unaffected\n\t\tconst stratDisabledMsg = this.app.vocabApi.termdbConfig?.survival?.stratificationDisabledMessage\n\t\tif (this.opts.controls) {\n\t\t\tthis.opts.controls.on('downloadClick.survival', this.download)\n\t\t} else {\n\t\t\tthis.dom.holder.attr('class', 'pp-termdb-plot-viz').style('display', 'inline-block').style('min-width', '300px')\n\n\t\t\tthis.components = {\n\t\t\t\tcontrols: await controlsInit({\n\t\t\t\t\tapp: this.app,\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tholder: this.dom.controls.style('display', 'inline-block'),\n\t\t\t\t\tinputs: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'term',\n\t\t\t\t\t\t\tconfigKey: 'term2',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tusecase: { target: 'survival', detail: 'term2' },\n\t\t\t\t\t\t\ttitle: controlLabels.term2.title || controlLabels.term2.label,\n\t\t\t\t\t\t\tlabel: controlLabels.term2.label,\n\t\t\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\t\t\t\t\tdefaultQ4fillTW: t0_t2_defaultQ,\n\t\t\t\t\t\t\tdisabledMessage: stratDisabledMsg\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'term',\n\t\t\t\t\t\t\tconfigKey: 'term0',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tusecase: { target: 'survival', detail: 'term0' },\n\t\t\t\t\t\t\ttitle: controlLabels.term0.title || controlLabels.term0.label,\n\t\t\t\t\t\t\tlabel: controlLabels.term0.label,\n\t\t\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\t\t\t\t\tdefaultQ4fillTW: t0_t2_defaultQ,\n\t\t\t\t\t\t\tdisabledMessage: stratDisabledMsg\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Chart width',\n\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'svgw',\n\t\t\t\t\t\t\ttitle: 'The internal width of the chart plot'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Chart height',\n\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'svgh',\n\t\t\t\t\t\t\ttitle: 'The internal height of the chart plot'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: '95% Confidence Interval',\n\t\t\t\t\t\t\tboxLabel: 'Visible',\n\t\t\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'ciVisible',\n\t\t\t\t\t\t\ttitle: 'Display the 95% confidence interval'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Median Survival',\n\t\t\t\t\t\t\tboxLabel: 'Visible',\n\t\t\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'medianSurvivalVisible',\n\t\t\t\t\t\t\ttitle: 'Display dashed lines indicating the median survival time (50% probability)'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Censored Symbol',\n\t\t\t\t\t\t\ttype: 'radio',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'symbol',\n\t\t\t\t\t\t\toptions: [\n\t\t\t\t\t\t\t\t{ label: 'Tick', value: 'vtick' },\n\t\t\t\t\t\t\t\t{ label: 'X', value: 'x' }\n\t\t\t\t\t\t\t],\n\t\t\t\t\t\t\ttitle: 'Symbol for displaying censored samples'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Survival Time Visualized',\n\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'maxTimeToEvent',\n\t\t\t\t\t\t\ttitle:\n\t\t\t\t\t\t\t\t'The maximum time-to-event to be displayed in the survival plot, affects only the visual representation and does not impact other analyses. All available data is still used to compute p-values. If this value is left empty or set to 0, no cutoff will be applied.'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Time Unit',\n\t\t\t\t\t\t\ttype: 'radio',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'timeUnit',\n\t\t\t\t\t\t\toptions: [\n\t\t\t\t\t\t\t\t{ label: 'years', value: 'years' },\n\t\t\t\t\t\t\t\t{ label: 'months', value: 'months' },\n\t\t\t\t\t\t\t\t{ label: 'weeks', value: 'weeks' },\n\t\t\t\t\t\t\t\t{ label: 'days', value: 'days' }\n\t\t\t\t\t\t\t],\n\t\t\t\t\t\t\ttitle: `The unit to display in the x-axis title, like 'years'`\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'X-axis ticks',\n\t\t\t\t\t\t\ttype: 'text',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'xTickValues',\n\t\t\t\t\t\t\ttitle: `Option to customize the x-axis tick values, enter as comma-separated values. Will be ignored if empty`,\n\t\t\t\t\t\t\tprocessInput: value => (value ? value.split(',').map(Number) : [])\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'At-risk counts',\n\t\t\t\t\t\t\tboxLabel: 'Visible',\n\t\t\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'atRiskVisible',\n\t\t\t\t\t\t\ttitle: 'Display the at-risk counts'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t//{label: 'At-risk label offset', type: 'numeric', chartType: 'survival', settingsKey: 'atRiskLabelOffset'},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Default color',\n\t\t\t\t\t\t\ttype: 'color',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'defaultColor',\n\t\t\t\t\t\t\ttitle: 'Default plot color'\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t}\n\t\t\tthis.components.controls.on('downloadClick.survival', this.download)\n\t\t}\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\n\t\treturn {\n\t\t\tisVisible: config.term.term.type == 'survival' || config.term2?.term.type == 'survival',\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tactiveCohort: appState.activeCohort,\n\t\t\ttermfilter,\n\n\t\t\tconfig: {\n\t\t\t\t// NOTE: will create mutable copies of tw terms in async main() below\n\t\t\t\tterm: config.term,\n\t\t\t\tterm0: config.term0 || null,\n\t\t\t\tterm2: config.term2 || null,\n\t\t\t\tcontrolLabels: config.controlLabels,\n\t\t\t\tsettings: config.settings.survival\n\t\t\t},\n\t\t\ttermdbConfig: appState.termdbConfig\n\t\t}\n\t}\n\n\tasync main() {\n\t\tif (!this.state.isVisible) {\n\t\t\tthis.dom.holder.style('display', 'none')\n\t\t\treturn\n\t\t}\n\n\t\tlet data\n\t\ttry {\n\t\t\tthis.state.config = await this.getMutableConfig()\n\t\t\tthis.maySetSandboxHeader()\n\t\t\tthis.toggleLoadingDiv()\n\n\t\t\tObject.assign(this.settings, this.state.config.settings)\n\t\t\tthis.settings.defaultHidden = this.getDefaultHidden()\n\t\t\tthis.settings.hidden = this.settings.customHidden || this.settings.defaultHidden\n\t\t\tthis.settings.xTitleLabel = this.getXtitleLabel()\n\t\t\tconst reqOpts = this.getDataRequestOpts()\n\t\t\t// do not directly set this.serverData to response, since it could be an error\n\t\t\tdata = await this.app.vocabApi.getNestedChartSeriesData(reqOpts, this.api?.getAbortSignal())\n\t\t} catch (e) {\n\t\t\tif (this.app.isAbortError(e)) return\n\t\t\tthis.toggleLoadingDiv('none', 'none')\n\t\t\tthrow e\n\t\t}\n\t\tthis.serverData = data\n\t\tthis.toggleLoadingDiv('none')\n\t\tthis.app.vocabApi.syncTermData(this.state.config, data)\n\t\tthis.currData = this.processData(data)\n\t\tthis.refs = data.refs\n\t\tthis.pj.refresh({ data: this.currData })\n\t\tthis.setTerm2Color(this.pj.tree.charts)\n\t\tthis.symbol = this.getSymbol(7) // hardcode the symbol size for now\n\t\tthis.render()\n\t}\n\n\tmaySetSandboxHeader() {\n\t\tif (!this.dom.header) return\n\t\tconst { term, term2 } = this.state.config\n\t\tconst mainTerm = term.term.name\n\t\tif (term2?.type) {\n\t\t\tthis.dom.header.html(`${term2.getTitleText?.() || term2.term.name}  vs ${mainTerm}`)\n\t\t} else {\n\t\t\tthis.dom.header.html(`${mainTerm} plot`)\n\t\t}\n\t}\n\n\t// creates an opts object for the vocabApi.getNestedChartsData()\n\tgetDataRequestOpts() {\n\t\tconst c = this.state.config\n\t\tconst opts: any = {\n\t\t\tchartType: 'survival',\n\t\t\tterm: c.term,\n\t\t\tfilter: this.state.termfilter.filter,\n\t\t\tfilter0: this.state.termfilter.filter0\n\t\t}\n\t\tif (c.term2) {\n\t\t\topts.term2 = c.term2\n\t\t}\n\t\tif (c.term0) opts.term0 = c.term0\n\t\treturn opts\n\t}\n\n\tgetDefaultHidden() {\n\t\tconst hidden: any[] = []\n\t\tconst term2 = this.state.config.term2\n\t\tif (!term2) return hidden\n\t\tconst hiddenValues = term2.q.hiddenValues\n\t\tif (hiddenValues && Object.keys(hiddenValues).length) {\n\t\t\t// term2 has default hidden values\n\t\t\tfor (const k in hiddenValues) {\n\t\t\t\thidden.push(term2.term.values[k].label)\n\t\t\t}\n\t\t}\n\t\treturn hidden\n\t}\n\n\tgetXtitleLabel() {\n\t\tconst termNum = this.state.config.term.term.type == 'survival' ? 'term' : 'term2'\n\t\tconst xUnit = this.settings.timeUnit ? this.settings.timeUnit : this.state.config[termNum].term.unit\n\t\tconst xTitleLabel = `Time to Event (${xUnit})`\n\t\treturn xTitleLabel\n\t}\n\n\tprocessData(data) {\n\t\tthis.uniqueSeriesIds = new Set()\n\t\tthis.msg = ''\n\n\t\tconst rows: any[] = []\n\t\tconst estKeys = ['survival', 'lower', 'upper']\n\t\tfor (const d of data.case) {\n\t\t\tconst obj: { [name: string]: any } = {}\n\t\t\tdata.keys.forEach((k, i) => {\n\t\t\t\tobj[k] = estKeys.includes(k) ? Number(d[i]) : d[i]\n\t\t\t})\n\t\t\tobj.time = obj.time * this.getTimeFactor()\n\t\t\trows.push(obj)\n\t\t\tthis.uniqueSeriesIds.add(obj.seriesId)\n\t\t}\n\n\t\t// process statistical tests\n\t\tthis.tests = {}\n\t\tif (data.tests) {\n\t\t\tfor (const chartId in data.tests) {\n\t\t\t\tconst chartTests = data.tests[chartId]\n\t\t\t\tthis.tests[chartId] = []\n\t\t\t\tfor (const test of chartTests) {\n\t\t\t\t\tif (this.settings.hidden.includes(test.series1) || this.settings.hidden.includes(test.series2)) continue // hide tests that contain hidden series\n\t\t\t\t\tthis.tests[chartId].push({\n\t\t\t\t\t\tpvalue: { id: 'pvalue', text: test.pvalue },\n\t\t\t\t\t\tseries1: { id: test.series1 },\n\t\t\t\t\t\tseries2: { id: test.series2 }\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tif (!this.tests[chartId].length) delete this.tests[chartId]\n\t\t\t}\n\t\t}\n\n\t\t// process refs\n\t\tif (data.refs.byTermId) {\n\t\t\tconst byTermId = data.refs.byTermId\n\t\t\tconst msg = byTermId[this.state.config.term.term.id]?.survMsg\n\t\t\tif (msg) {\n\t\t\t\t// message to be displayed in survival plot\n\t\t\t\t// will be rendered in .pp-survival-chartLegends of each chart\n\t\t\t\tthis.msg = msg\n\t\t\t}\n\t\t}\n\n\t\treturn rows\n\t}\n\n\t// time factor that converts survival data from default time unit to the current time unit.\n\tgetTimeFactor() {\n\t\tconst numUnitInOneYear = this.settings.numUnitInOneYear || 1\n\t\tconst timeUnit = this.settings.timeUnit || 'years'\n\t\tswitch (timeUnit) {\n\t\t\tcase 'years':\n\t\t\t\treturn (1 / numUnitInOneYear) * 1\n\t\t\tcase 'months':\n\t\t\t\treturn (1 / numUnitInOneYear) * 12\n\t\t\tcase 'weeks':\n\t\t\t\treturn (1 / numUnitInOneYear) * 52\n\t\t\tcase 'days':\n\t\t\t\treturn (1 / numUnitInOneYear) * 365.25\n\t\t\tdefault:\n\t\t\t\tthrow 'unknown time Unit for survival data'\n\t\t}\n\t}\n\n\tsetTerm2Color(charts) {\n\t\tif (!charts) return\n\t\tconst config = this.state.config\n\t\t// color override via legend clicks is saved in term2.values, not by directly editing term2.term.values\n\t\tconst t2values = copyMerge({}, config.term2?.term?.values || {}, config.term2?.values || {})\n\t\tconst values = (this.refs.bins[2] && [this.refs.bins[2]]) || Object.values(t2values)\n\t\tlet t2groups\n\t\tif (config.term2?.q.type == 'predefined-groupset' || config.term2?.q.type == 'custom-groupset') {\n\t\t\tconst groupset =\n\t\t\t\tconfig.term2.q.type == 'predefined-groupset'\n\t\t\t\t\t? config.term2.term.groupsetting.lst[config.term2.q.predefined_groupset_idx]\n\t\t\t\t\t: config.term2.q.customset\n\t\t\tif (!groupset) throw 'groupset is missing'\n\t\t\tt2groups = groupset.groups\n\t\t}\n\t\tthis.term2toColor = {}\n\t\tthis.colorScale = this.uniqueSeriesIds.size < 11 ? scaleOrdinal(schemeCategory10) : scaleOrdinal(schemeCategory20)\n\t\tconst legendItems: any[] = []\n\t\tfor (const chart of charts) {\n\t\t\tfor (const series of chart.serieses) {\n\t\t\t\tlet color\n\t\t\t\t// color override via legend clicks is saved in t2values, does not edit term.values or group.color directly\n\t\t\t\tconst v = values.find(\n\t\t\t\t\tv =>\n\t\t\t\t\t\tv.seriesId === series.seriesId ||\n\t\t\t\t\t\tv.key === series.seriesId ||\n\t\t\t\t\t\tv.name === series.seriesId ||\n\t\t\t\t\t\tv.label === series.seriesId\n\t\t\t\t)\n\t\t\t\tcolor = v?.color\n\t\t\t\tif (!color && t2groups?.length) {\n\t\t\t\t\tconst group = t2groups.find(g => g.name == series.seriesId)\n\t\t\t\t\tcolor = group?.color\n\t\t\t\t\t// quick fix to make WT gray darker to pass Section 508 contrast requirement;\n\t\t\t\t\t// doing this in common.js makes this gray in all tools darker and conflicts\n\t\t\t\t\t// with other mclass colors like in-frame insertion, also visually overwhelming\n\t\t\t\t\t// in GDC oncomatrix\n\t\t\t\t\tif (color === '#D3D3D3' && group?.filter?.lst?.find(f => f?.type === 'tvs' && f.tvs.genotype == 'wt'))\n\t\t\t\t\t\tcolor = 'rgb(105,105,105)'\n\t\t\t\t}\n\t\t\t\tconst orig = color || (series.seriesId == '' ? this.settings.defaultColor : this.colorScale(series.seriesId))\n\t\t\t\tconst _rgb = rgb(orig)\n\t\t\t\tconst adjusted = _rgb.toString()\n\t\t\t\tconst c = { orig, rgb: _rgb, adjusted, hex: rgb2hex(adjusted) }\n\t\t\t\tthis.term2toColor[series.seriesId] = c\n\n\t\t\t\tif (!legendItems.find(d => d.seriesId == series.seriesId)) {\n\t\t\t\t\tlegendItems.push({\n\t\t\t\t\t\tkey: series.seriesId,\n\t\t\t\t\t\tseriesId: series.seriesId,\n\t\t\t\t\t\ttext: series.seriesLabel,\n\t\t\t\t\t\tcolor: this.term2toColor[series.seriesId].adjusted,\n\t\t\t\t\t\tisHidden: this.settings.hidden.includes(series.seriesId)\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (this.refs.orderedKeys) {\n\t\t\tconst s = this.refs.orderedKeys.series\n\t\t\tlegendItems.sort((a, b) => s.indexOf(a.seriesId) - s.indexOf(b.seriesId))\n\t\t}\n\n\t\tif (!this.legendOrder.length) {\n\t\t\tthis.legendOrder = legendItems.map(item => item.seriesId)\n\t\t} else {\n\t\t\tlegendItems.sort((a, b) => this.legendOrder.indexOf(a.seriesId) - this.legendOrder.indexOf(b.seriesId))\n\t\t}\n\n\t\tif ((config.term.term.type == 'survival' || config.term2) && legendItems.length) {\n\t\t\tconst termNum = config.term.term.type == 'survival' && config.term2 ? 'term2' : 'term'\n\t\t\tthis.legendData = [\n\t\t\t\t{\n\t\t\t\t\tname: config[termNum].term.name,\n\t\t\t\t\titems: legendItems.filter(s => !s.isHidden)\n\t\t\t\t}\n\t\t\t]\n\n\t\t\tthis.hiddenData = [\n\t\t\t\t{\n\t\t\t\t\tname: `<span style='color:#aaa; font-weight:400'><span>Hidden categories</span><span style='font-size:0.8rem'> CLICK TO SHOW</span></span>`,\n\t\t\t\t\titems: legendItems.filter(s => s.isHidden).map(item => Object.assign({}, item, { isHidden: false }))\n\t\t\t\t}\n\t\t\t]\n\t\t} else {\n\t\t\tthis.legendData = []\n\t\t}\n\t\tfor (const chartId in this.tests) {\n\t\t\tconst chartTests = this.tests[chartId]\n\t\t\tfor (const test of chartTests) {\n\t\t\t\tfor (const key in test) {\n\t\t\t\t\tif (key == 'pvalue') {\n\t\t\t\t\t\t// p-value of test\n\t\t\t\t\t\ttest[key].color = '#000'\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// series of test\n\t\t\t\t\t\tconst item = legendItems.find(item => item.seriesId == test[key].id)\n\t\t\t\t\t\ttest[key].color = item.color\n\t\t\t\t\t\ttest[key].text = item.text\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport const survivalInit = getCompInit(TdbSurvival)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = survivalInit\n\nfunction setRenderers(self) {\n\tself.render = function () {\n\t\tconst data = self.pj.tree.charts || [{ chartId: 'No survival data' }]\n\t\tconst chartDivs = self.dom.chartsDiv.selectAll('.pp-survival-chart').data(data, d => d.chartId)\n\t\tchartDivs.exit().remove()\n\t\tchartDivs.each(self.updateCharts)\n\t\tchartDivs.enter().each(self.addCharts)\n\n\t\tself.dom.holder.style('display', 'inline-block')\n\t\tself.dom.chartsDiv.on('mouseover', self.mouseover).on('mouseout', self.mouseout)\n\n\t\tself.legendRenderer(self.settings.atRiskVisible ? [] : self.legendData)\n\t\tif (!self.hiddenData?.[0]?.items.length) self.dom.hiddenDiv.style('display', 'none')\n\t\telse {\n\t\t\tself.dom.hiddenDiv.style('display', '')\n\t\t\tself.hiddenRenderer(self.hiddenData)\n\t\t}\n\t}\n\n\tconst updateHiddenPvalues = hiddenPvalues => {\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.id,\n\t\t\tconfig: {\n\t\t\t\tsettings: {\n\t\t\t\t\tsurvival: {\n\t\t\t\t\t\thiddenPvalues\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tconst setActiveMenu = bool => (self.activeMenu = bool)\n\n\tself.addCharts = function (chart) {\n\t\tconst s = self.settings\n\t\tsetVisibleSerieses(chart, s)\n\n\t\tconst div = select(this)\n\t\t\t.append('div')\n\t\t\t.attr('class', 'pp-survival-chart')\n\t\t\t.style('opacity', chart.serieses ? 0 : 1) // if the data can be plotted, slowly reveal plot\n\t\t\t.style('width', 'fit-content')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('margin', s.chartMargin + 'px')\n\t\t\t.style('padding', '10px')\n\t\t\t.style('top', 0)\n\t\t\t.style('left', 0)\n\t\t\t.style('text-align', 'left')\n\t\t\t.style('vertical-align', 'top')\n\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.style('width', s.svgw + 50 + 'px')\n\t\t\t.style('height', s.chartTitleDivHt + 'px')\n\t\t\t.style('text-align', 'center')\n\t\t\t.style('font-weight', '600')\n\t\t\t.style('margin', '5px')\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sjpp-survival-title')\n\t\t\t.attr('data-testid', 'sjpp-survival-plotTitle')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('width', 'fit-content')\n\t\t\t.datum(chart)\n\t\t\t.html(chart => chart.chartId)\n\n\t\tif (chart.serieses) {\n\t\t\tconst svg = div.append('svg').attr('class', 'pp-survival-svg')\n\t\t\trenderSVG(svg, chart, s, 0)\n\n\t\t\tdiv.transition().duration(s.duration).style('opacity', 1)\n\n\t\t\t// div for chart-specific legends\n\t\t\tdiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'pp-survival-chartLegends')\n\t\t\t\t.style('vertical-align', 'top')\n\t\t\t\t.style('margin', '10px 10px 10px 10px')\n\t\t\t\t.style('display', 'none')\n\n\t\t\t// p-values legend\n\t\t\tif (self.tests && chart.rawChartId in self.tests) {\n\t\t\t\tconst holder = div\n\t\t\t\t\t.select('.pp-survival-chartLegends')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('margin-bottom', '30px')\n\t\t\t\trenderPvalues({\n\t\t\t\t\ttitle: 'Group comparisons (log-rank test)',\n\t\t\t\t\tholder,\n\t\t\t\t\tplot: 'survival',\n\t\t\t\t\ttests: self.tests[chart.rawChartId],\n\t\t\t\t\ts,\n\t\t\t\t\tbins: self.refs.bins,\n\t\t\t\t\ttip: self.app.tip,\n\t\t\t\t\tsetActiveMenu,\n\t\t\t\t\tupdateHiddenPvalues\n\t\t\t\t})\n\t\t\t}\n\n\t\t\t// message\n\t\t\tif (self.msg) {\n\t\t\t\tconst fontSize = s.axisTitleFontSize ? s.axisTitleFontSize - 2 : 15\n\t\t\t\tconst holder = div.select('.pp-survival-chartLegends').style('display', 'inline-block').append('div')\n\t\t\t\tholder\n\t\t\t\t\t.style('font-size', fontSize + 'px')\n\t\t\t\t\t.style('font-style', 'italic')\n\t\t\t\t\t.text(self.msg)\n\t\t\t}\n\t\t}\n\t}\n\n\tfunction setVisibleSerieses(chart, s) {\n\t\tchart.visibleSerieses = chart.serieses?.filter(series => !s.hidden.includes(series.seriesId)) || []\n\t\tconst maxSeriesLabelLen = chart.visibleSerieses.reduce(\n\t\t\t(maxlen, a) => (a.seriesLabel && a.seriesLabel.length > maxlen ? a.seriesLabel.length : maxlen),\n\t\t\t0\n\t\t)\n\t\t// When there's no overlay term (maxSeriesLabelLen is 0), add extra padding to prevent\n\t\t// \"Number at risk\" text from overlapping with the config menu\n\t\tconst extraPaddingForNoOverlay = maxSeriesLabelLen === 0 ? s.atRiskNoOverlayExtraPadding : 0\n\t\tchart.atRiskLabelWidth = s.atRiskVisible\n\t\t\t? maxSeriesLabelLen * (s.axisTitleFontSize - 2) * 0.4 + s.atRiskLabelOffset + extraPaddingForNoOverlay\n\t\t\t: 0\n\t}\n\n\tself.updateCharts = function (chart) {\n\t\tif (!chart.serieses) return\n\t\tconst s = self.settings\n\t\tsetVisibleSerieses(chart, s)\n\n\t\tconst div = select(this)\n\t\tdiv.transition().duration(s.duration).style('width', 'fit-content')\n\n\t\tdiv\n\t\t\t.select('.sjpp-survival-title')\n\t\t\t.style('width', s.svgw + 50)\n\t\t\t.style('height', s.chartTitleDivHt + 'px')\n\t\t\t.datum(chart.chartId)\n\t\t\t.html(chart.chartId)\n\n\t\tdiv.selectAll('.sjpp-lock-icon').style('display', s.scale == 'byChart' ? 'block' : 'none')\n\n\t\tdiv.selectAll('.sjpp-unlock-icon').style('display', s.scale == 'byChart' ? 'none' : 'block')\n\n\t\trenderSVG(div.select('svg'), chart, s, s.duration)\n\n\t\t// div for chart-specific legends\n\t\tdiv.select('.pp-survival-chartLegends').style('display', 'none').selectAll('*').remove()\n\n\t\t// p-values legend\n\t\tif (self.tests && chart.rawChartId in self.tests) {\n\t\t\tconst holder = div\n\t\t\t\t.select('.pp-survival-chartLegends')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin-bottom', '30px')\n\t\t\trenderPvalues({\n\t\t\t\ttitle: 'Group comparisons (log-rank test)',\n\t\t\t\tholder,\n\t\t\t\tplot: 'survival',\n\t\t\t\ttests: self.tests[chart.rawChartId],\n\t\t\t\ts,\n\t\t\t\tbins: self.refs.bins,\n\t\t\t\ttip: self.app.tip,\n\t\t\t\tsetActiveMenu,\n\t\t\t\tupdateHiddenPvalues\n\t\t\t})\n\t\t}\n\n\t\t// message\n\t\tif (self.msg) {\n\t\t\tconst fontSize = s.axisTitleFontSize ? s.axisTitleFontSize - 2 : 15\n\t\t\tconst holder = div.select('.pp-survival-chartLegends').style('display', 'inline-block').append('div')\n\t\t\tholder\n\t\t\t\t.style('font-size', fontSize + 'px')\n\t\t\t\t.style('font-style', 'italic')\n\t\t\t\t.text(self.msg)\n\t\t}\n\t}\n\n\tfunction renderSVG(svg, chart, s, duration) {\n\t\tchart.svg = svg\n\t\tconst extraHeight = s.atRiskVisible\n\t\t\t? s.axisTitleFontSize + 4 + chart.visibleSerieses.length * 2 * (s.axisTitleFontSize + 4)\n\t\t\t: 0\n\n\t\tsvg\n\t\t\t.transition()\n\t\t\t.duration(duration)\n\t\t\t.attr('width', s.svgw + chart.atRiskLabelWidth)\n\t\t\t.attr('height', s.svgh + extraHeight)\n\t\t\t.style('overflow', 'visible')\n\t\t\t.style('padding-left', '5px')\n\n\t\t/* eslint-disable */\n\t\tconst [mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect, medianSurvivalG] =\n\t\t\tgetSvgSubElems(svg)\n\t\t/* eslint-enable */\n\t\tconst xOffset = chart.atRiskLabelWidth + s.svgPadding.left + 10 //adding 10 avoids clipping of the svg when downloading\n\t\tmainG.attr('transform', 'translate(' + xOffset + ',' + s.svgPadding.top + ')')\n\n\t\tconst serieses = seriesesG\n\t\t\t.selectAll('.sjpp-survival-series')\n\t\t\t.data(chart.visibleSerieses, d => (d && d[0] ? d[0].seriesId : ''))\n\n\t\tserieses.exit().remove()\n\t\tserieses.each(function (this: HTMLElement, series, i) {\n\t\t\trenderSeries(select(this), chart, series, i, s)\n\t\t})\n\t\tserieses\n\t\t\t.enter()\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-survival-series')\n\t\t\t.each(function (this: HTMLElement, series, i) {\n\t\t\t\trenderSeries(select(this), chart, series, i, s)\n\t\t\t})\n\n\t\trenderAxes(xAxis, xTitle, yAxis, yTitle, s, chart)\n\t\trenderMedianSurvival(medianSurvivalG, chart, s)\n\t\trenderAtRiskG({\n\t\t\tg: atRiskG,\n\t\t\ts,\n\t\t\tchart,\n\t\t\torder: self.legendOrder,\n\t\t\tterm2toColor: self.term2toColor,\n\t\t\tonSerieClick: self.legendClick\n\t\t})\n\n\t\tplotRect\n\t\t\t.attr('x', 0) //s.svgPadding.left) //s.svgh - s.svgPadding.top - s.svgPadding.bottom + 5)\n\t\t\t.attr('width', s.svgw - s.svgPadding.left - s.svgPadding.right)\n\t\t\t.attr('y', 0) //s.svgPadding.top) // - s.svgPadding.bottom + 5)\n\t\t\t.attr('height', s.svgh - s.svgPadding.top - s.svgPadding.bottom + s.xAxisOffset)\n\n\t\tsvg.seriesTip.update({\n\t\t\txScale: chart.xScale,\n\t\t\txTitleLabel: s.xTitleLabel,\n\t\t\tdecimals: s.seriesTipDecimals,\n\t\t\tserieses: chart.visibleSerieses.map(s => {\n\t\t\t\tconst seriesLabel = `${s.seriesLabel || 'Probability'}:`\n\t\t\t\tconst color = self.term2toColor[s.seriesId].adjusted || '#000'\n\t\t\t\treturn {\n\t\t\t\t\tdata: s.data.map(d => {\n\t\t\t\t\t\treturn {\n\t\t\t\t\t\t\tx: d.x,\n\t\t\t\t\t\t\thtml:\n\t\t\t\t\t\t\t\t`<span style='color: ${color}'>` +\n\t\t\t\t\t\t\t\t`${seriesLabel} ${(100 * d.y).toFixed(2)}% (${(100 * d.lower).toFixed(2)} - ${(100 * d.upper).toFixed(\n\t\t\t\t\t\t\t\t\t2\n\t\t\t\t\t\t\t\t)})` +\n\t\t\t\t\t\t\t\t`</span>`\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\t})\n\t}\n\n\tfunction getSvgSubElems(svg) {\n\t\tlet mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect, line, medianSurvivalG\n\t\tif (!svg.select('.sjpp-survival-mainG').size()) {\n\t\t\tmainG = svg.append('g').attr('class', 'sjpp-survival-mainG')\n\t\t\tseriesesG = mainG.append('g').attr('class', 'sjpcb-survival-seriesesG')\n\t\t\tmedianSurvivalG = mainG.append('g').attr('class', 'sjpp-survival-median')\n\t\t\taxisG = mainG.append('g').attr('class', 'sjpp-survival-axis')\n\t\t\txAxis = axisG.append('g').attr('class', 'sjpp-survival-x-axis')\n\t\t\tyAxis = axisG.append('g').attr('class', 'sjpp-survival-y-axis')\n\t\t\txTitle = axisG.append('g').attr('class', 'sjpp-survival-x-title')\n\t\t\tyTitle = axisG.append('g').attr('class', 'sjpp-survival-y-title')\n\t\t\tatRiskG = mainG.append('g').attr('class', 'sjpp-survival-atrisk')\n\t\t\tline = mainG\n\t\t\t\t.append('line')\n\t\t\t\t.attr('class', 'sjpcb-plot-tip-line')\n\t\t\t\t.attr('stroke', '#000')\n\t\t\t\t.attr('stroke-width', '1px')\n\t\t\tplotRect = mainG.append('rect').attr('class', 'sjpcb-plot-tip-rect').style('fill', 'transparent')\n\t\t} else {\n\t\t\tmainG = svg.select('.sjpp-survival-mainG')\n\t\t\tseriesesG = mainG.select('.sjpcb-survival-seriesesG')\n\t\t\tmedianSurvivalG = mainG.select('.sjpp-survival-median')\n\t\t\taxisG = mainG.select('.sjpp-survival-axis')\n\t\t\txAxis = axisG.select('.sjpp-survival-x-axis')\n\t\t\tyAxis = axisG.select('.sjpp-survival-y-axis')\n\t\t\txTitle = axisG.select('.sjpp-survival-x-title')\n\t\t\tyTitle = axisG.select('.sjpp-survival-y-title')\n\t\t\tatRiskG = mainG.select('.sjpp-survival-atrisk')\n\t\t\tplotRect = mainG.select('.sjpcb-plot-tip-rect')\n\t\t\tline = mainG.select('.sjpcb-plot-tip-line')\n\t\t}\n\n\t\tif (!svg.seriesTip) {\n\t\t\tsvg.seriesTip = getSeriesTip(line, plotRect, self.dom.tip)\n\t\t}\n\n\t\treturn [mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect, medianSurvivalG]\n\t}\n\n\tfunction renderSeries(g, chart, series, i, s) {\n\t\t// do not show samples with time to event larger than maxTimeToEvent\n\t\tlet processedData = series.data\n\t\tif (s.maxTimeToEvent) {\n\t\t\tprocessedData = series.data.filter(d => d.x <= s.maxTimeToEvent)\n\t\t}\n\t\t// todo: allow update of exiting path instead of replacing\n\t\tg.selectAll('path').remove()\n\t\tg.append('path')\n\t\t\t.attr(\n\t\t\t\t'd',\n\t\t\t\tarea()\n\t\t\t\t\t.curve(curveStepAfter)\n\t\t\t\t\t.x(c => (c as any).scaledX)\n\t\t\t\t\t.y0(c => (c as any).scaledY[1])\n\t\t\t\t\t.y1(c => (c as any).scaledY[2])(processedData)\n\t\t\t)\n\t\t\t.style('display', s.ciVisible ? '' : 'none')\n\t\t\t.style('fill', self.term2toColor[series.seriesId].adjusted)\n\t\t\t.style('opacity', '0.15')\n\t\t\t.style('stroke', 'none')\n\n\t\trenderSubseries(\n\t\t\ts,\n\t\t\tg,\n\t\t\tprocessedData.map(d => {\n\t\t\t\treturn {\n\t\t\t\t\tseriesId: d.seriesId,\n\t\t\t\t\tx: d.x,\n\t\t\t\t\ty: d.y,\n\t\t\t\t\tscaledX: d.scaledX,\n\t\t\t\t\tscaledY: d.scaledY[0],\n\t\t\t\t\tseriesName: 'survival',\n\t\t\t\t\tseriesLabel: series.seriesLabel,\n\t\t\t\t\tnevent: d.nevent,\n\t\t\t\t\tncensor: d.ncensor,\n\t\t\t\t\tnrisk: d.nrisk\n\t\t\t\t}\n\t\t\t})\n\t\t)\n\n\t\trenderSubseries(\n\t\t\ts,\n\t\t\tg.append('g'),\n\t\t\tprocessedData.map(d => {\n\t\t\t\treturn {\n\t\t\t\t\tseriesId: d.seriesId,\n\t\t\t\t\tx: d.x,\n\t\t\t\t\ty: d.lower,\n\t\t\t\t\tscaledX: d.scaledX,\n\t\t\t\t\tscaledY: d.scaledY[1],\n\t\t\t\t\tseriesName: 'lower',\n\t\t\t\t\tseriesLabel: series.seriesLabel,\n\t\t\t\t\tnevent: d.nevent,\n\t\t\t\t\tncensor: 0, // no censor marks for lower CI\n\t\t\t\t\tnrisk: d.nrisk\n\t\t\t\t}\n\t\t\t})\n\t\t)\n\n\t\trenderSubseries(\n\t\t\ts,\n\t\t\tg.append('g'),\n\t\t\tprocessedData.map(d => {\n\t\t\t\treturn {\n\t\t\t\t\tseriesId: d.seriesId,\n\t\t\t\t\tx: d.x,\n\t\t\t\t\ty: d.upper,\n\t\t\t\t\tscaledX: d.scaledX,\n\t\t\t\t\tscaledY: d.scaledY[2],\n\t\t\t\t\tseriesName: 'upper', // no censor marks for upper CI\n\t\t\t\t\tseriesLabel: series.seriesLabel,\n\t\t\t\t\tnevent: d.nevent,\n\t\t\t\t\tncensor: 0,\n\t\t\t\t\tnrisk: d.nrisk\n\t\t\t\t}\n\t\t\t})\n\t\t)\n\t}\n\n\tfunction renderSubseries(s, g, data) {\n\t\t// todo: allow update of exiting g's instead of replacing\n\t\tg.selectAll('g').remove()\n\n\t\tconst lineData = data.filter((d, i) => i === 0 || d.nevent || i === data.length - 1)\n\t\tconst censoredData = data.filter(d => d.ncensor)\n\n\t\tconst seriesName = data[0].seriesName\n\t\tconst color = self.term2toColor[data[0].seriesId].adjusted\n\t\tif (seriesName == 'survival') {\n\t\t\tg.append('path')\n\t\t\t\t.attr('d', self.lineFxn(lineData))\n\t\t\t\t.style('fill', 'none')\n\t\t\t\t.style('stroke', color)\n\t\t\t\t.style('opacity', 1)\n\t\t\t\t.style('stroke-opacity', 1)\n\t\t}\n\n\t\tconst subg1 = g.append('g').attr('class', 'sjpp-survival-censored')\n\t\tconst censored = subg1.selectAll('.sjpp-survival-censored-x').data(censoredData, d => d.x)\n\n\t\tcensored.exit().remove()\n\n\t\tcensored\n\t\t\t.attr('transform', c => `translate(${c.scaledX},${c.scaledY})`)\n\t\t\t.style('stroke', color)\n\t\t\t.style('display', '')\n\n\t\tcensored\n\t\t\t.enter()\n\t\t\t.append('path')\n\t\t\t.attr('class', 'sjpp-survival-censored-x')\n\t\t\t.attr('transform', c => `translate(${c.scaledX},${c.scaledY})`)\n\t\t\t.attr('d', self.symbol)\n\t\t\t.style('fill', 'transparent')\n\t\t\t.style('fill-opacity', s.fillOpacity)\n\t\t\t.style('stroke', color)\n\t\t\t.style('display', '')\n\t}\n\n\tfunction renderAxes(xAxis, xTitle, yAxis, yTitle, s, chart) {\n\t\tlet xTicks\n\t\tif (s.xTickValues?.length) {\n\t\t\t// xTicksValues should not be larger than maxTimeToEvent\n\t\t\tchart.xTickValues = s.xTickValues.filter(\n\t\t\t\tv => v === 0 || (v >= chart.xMin && v <= Math.min(s.maxTimeToEvent || chart.xMax, chart.xMax))\n\t\t\t)\n\t\t\txTicks = axisBottom(chart.xScale).tickValues(chart.xTickValues)\n\t\t} else {\n\t\t\tchart.xTickValues = []\n\t\t\txTicks = axisBottom(chart.xScale)\n\t\t\t\t.ticks(4)\n\t\t\t\t.tickFormat((xval: any) => {\n\t\t\t\t\tchart.xTickValues.push(xval)\n\t\t\t\t\treturn xval\n\t\t\t\t})\n\t\t}\n\n\t\t// without this pixel offset, the axes and data are slightly misaligned\n\t\t// this could be because the axes have a 0.5 offset in their path,\n\t\t// for example: <path class=\"domain\" stroke=\"#000\" d=\"M0.5,6V0.5H325.5V6\"></path>\n\t\tconst pixelOffset = -0.5\n\n\t\txAxis\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\t`translate(${pixelOffset}, ${s.svgh - s.svgPadding.top - s.svgPadding.bottom + s.xAxisOffset + pixelOffset})`\n\t\t\t)\n\t\t\t.call(xTicks)\n\n\t\tyAxis\n\t\t\t.attr('transform', `translate(${s.yAxisOffset + pixelOffset}, ${pixelOffset})`)\n\t\t\t.call(axisLeft(scaleLinear().domain(chart.yScale.domain()).range(chart.yScale.range())).ticks(5))\n\n\t\txTitle.select('text, title').remove()\n\t\txTitle\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\t'translate(' +\n\t\t\t\t\t(s.svgw - s.svgPadding.left - s.svgPadding.right) / 2 +\n\t\t\t\t\t',' +\n\t\t\t\t\t(s.svgh - s.axisTitleFontSize - 4) +\n\t\t\t\t\t')'\n\t\t\t)\n\t\t\t.append('text')\n\t\t\t.style('text-anchor', 'middle')\n\t\t\t.style('font-size', s.axisTitleFontSize + 'px')\n\t\t\t.text(s.xTitleLabel)\n\n\t\tconst yTitleLabel = 'Probability of Survival'\n\t\tyTitle.select('text, title').remove()\n\t\tyTitle\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\t'translate(' +\n\t\t\t\t\t(-s.svgPadding.left / 2 - s.axisTitleFontSize) +\n\t\t\t\t\t',' +\n\t\t\t\t\t(s.svgh - s.svgPadding.top - s.svgPadding.bottom) / 2 +\n\t\t\t\t\t')rotate(-90)'\n\t\t\t)\n\t\t\t.append('text')\n\t\t\t.style('text-anchor', 'middle')\n\t\t\t.style('font-size', s.axisTitleFontSize + 'px')\n\t\t\t.text(yTitleLabel)\n\t}\n\n\tfunction renderMedianSurvival(g, chart, s) {\n\t\tg.selectAll('*').remove()\n\t\tif (!s.medianSurvivalVisible) return\n\n\t\tconst yMid = chart.yScale(0.5)\n\t\tconst yBottom = chart.yScale(0)\n\n\t\t// Find the first data point where survival <= 0.5 (median) for a series\n\t\tconst getMedianPoint = (series: any) => {\n\t\t\tconst data = s.maxTimeToEvent ? series.data.filter((d: any) => d.x <= s.maxTimeToEvent) : series.data\n\t\t\treturn (data as any[]).find((d: any) => d.y <= 0.5)\n\t\t}\n\n\t\t// Collect scaled x positions for all visible series that have a median\n\t\tconst medianScaledXs: number[] = []\n\t\tfor (const series of chart.visibleSerieses) {\n\t\t\tconst medianPoint = getMedianPoint(series)\n\t\t\tif (medianPoint) medianScaledXs.push(chart.xScale(medianPoint.x))\n\t\t}\n\n\t\tif (!medianScaledXs.length) return\n\n\t\t// Horizontal dashed line at 50% survival from y-axis to the rightmost median time\n\t\tg.append('line')\n\t\t\t.attr('x1', 0)\n\t\t\t.attr('y1', yMid)\n\t\t\t.attr('x2', Math.max(...medianScaledXs))\n\t\t\t.attr('y2', yMid)\n\t\t\t.attr('stroke', '#000')\n\t\t\t.attr('stroke-width', 1)\n\t\t\t.attr('stroke-dasharray', '4,4')\n\n\t\t// Vertical dashed line from 50% down to x-axis for each series with a median\n\t\tfor (const scaledX of medianScaledXs) {\n\t\t\tg.append('line')\n\t\t\t\t.attr('x1', scaledX)\n\t\t\t\t.attr('y1', yMid)\n\t\t\t\t.attr('x2', scaledX)\n\t\t\t\t.attr('y2', yBottom)\n\t\t\t\t.attr('stroke', '#000')\n\t\t\t\t.attr('stroke-width', 1)\n\t\t\t\t.attr('stroke-dasharray', '4,4')\n\t\t}\n\t}\n\n\tself.getSymbol = function (size) {\n\t\tconst s = size,\n\t\t\th = s / 2\n\n\t\tswitch (self.settings.symbol) {\n\t\t\tcase 'x':\n\t\t\t\treturn `M -${h},-${h} l ${s},${s} M ${h},-${h} l -${s},${s}`\n\n\t\t\tcase 'vtick':\n\t\t\t\treturn `M 0,-${h} L 0,${h}`\n\n\t\t\tdefault:\n\t\t\t\tthrow `Unrecognized survival plot symbol='${self.settings.symbol}'`\n\t\t}\n\t}\n}\n\nfunction setInteractivity(self) {\n\tself.download = function (event) {\n\t\tconst charts = self.getChartImages()\n\t\tconst menu = new DownloadMenu(charts, self.state.config.term.term.name)\n\t\tmenu.show(event.clientX, event.clientY, event.target)\n\t}\n\n\tself.getChartImages = function () {\n\t\tconst charts: any[] = []\n\t\tif (!self.pj.tree.charts) return charts // no charts to download\n\t\tfor (const chart of self.pj.tree.charts) {\n\t\t\tcharts.push({ name: chart.chartId, svg: chart.svg })\n\t\t}\n\t\treturn charts\n\t}\n\n\t// The logic is replaced by the downloadMenu SVG option\n\t// self.download = function () {\n\t// \tif (!self.state) return\n\t// \tdownloadChart(\n\t// \t\tself.dom.chartsDiv.selectAll('.sjpp-survival-mainG'),\n\t// \t\t'Survival_Plot',\n\t// \t\tself.dom.chartsDiv.select('.pp-survival-chart').node()\n\t// \t)\n\t// }\n\n\tself.mouseover = function () {}\n\n\tself.mouseout = function () {\n\t\tif (self.activeMenu) return\n\t\tself.app.tip.hide()\n\t}\n\n\tself.legendClick = function (d, x, y) {\n\t\tif (d === undefined) return\n\t\tconst hidden = self.settings.hidden.slice()\n\t\tconst i = hidden.indexOf(d.seriesId)\n\t\tif (i == -1) {\n\t\t\thidden.push(d.seriesId) // this setting data will be dispatched after clicking on the Hide menu option\n\t\t\tself.showLegendItemMenu(d, hidden, x, y)\n\t\t} else {\n\t\t\thidden.splice(i, 1)\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: self.id,\n\t\t\t\tconfig: {\n\t\t\t\t\tsettings: {\n\t\t\t\t\t\tsurvival: {\n\t\t\t\t\t\t\tcustomHidden: hidden\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\n\tself.showLegendItemMenu = function (d, hidden, x, y) {\n\t\tconst term2 = self.state.config.term2?.term || null\n\t\tconst seriesLabel = term2?.values?.[d.seriesId]?.label || d.seriesId\n\n\t\tconst header = `<div style='padding-bottom:8px'><b>${seriesLabel}</b></div>`\n\t\tconst data = d.seriesId || d.seriesId === 0 ? d : { seriesId: d.id, dataId: d.dataId }\n\t\tif (!data.seriesId && !data.dataId) {\n\t\t\tif (!term2) {\n\t\t\t\tconst label = self.dom.legendTip.clear().d.append('div').html('Edit color: ')\n\t\t\t\tconst input = label\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'color')\n\t\t\t\t\t.attr('value', self.settings.defaultColor)\n\t\t\t\t\t.on('change', () => self.adjustColor(input.property('value'), d))\n\t\t\t\tself.dom.legendTip.show(x, y)\n\t\t\t}\n\t\t\treturn\n\t\t}\n\n\t\tconst options: any[] = []\n\t\toptions.push({\n\t\t\tlabel: 'Hide',\n\t\t\tcallback: () => {\n\t\t\t\tmenu.hide()\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\tsurvival: {\n\t\t\t\t\t\t\t\tcustomHidden: hidden\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\n\t\tif (self.legendData[0]?.items.length > 1) {\n\t\t\toptions.push({\n\t\t\t\tlabel: 'Move&nbsp;',\n\t\t\t\tsetInput: holder => {\n\t\t\t\t\tconst legendIndex = self.legendOrder.indexOf(d.seriesId)\n\t\t\t\t\tif (legendIndex != 0)\n\t\t\t\t\t\tholder\n\t\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t\t.html('up')\n\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t\t\t\tself.adjustLegendOrder(d, -1)\n\t\t\t\t\t\t\t})\n\t\t\t\t\tif (legendIndex < self.legendData[0]?.items.length - 1)\n\t\t\t\t\t\tholder\n\t\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t\t.html('down')\n\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t\t\t\tself.adjustLegendOrder(d, 1)\n\t\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\toptions.push({\n\t\t\t//label: 'Color',\n\t\t\t//callback: d => {}\n\t\t\tsetInput: holder => {\n\t\t\t\tconst label = holder.append('div')\n\t\t\t\tlabel.html('Edit color: ')\n\t\t\t\tconst input = label\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'color')\n\t\t\t\t\t.attr('value', self.term2toColor[d.seriesId].hex)\n\t\t\t\t\t.on('change', () => self.adjustColor(input.property('value'), d))\n\t\t\t}\n\t\t})\n\n\t\tif (!options.length) return\n\t\tconst menu = self.dom.legendTip.clear()\n\t\tmenu.d.append('div').html(header)\n\t\tmenu.d\n\t\t\t.append('div')\n\t\t\t.selectAll('div')\n\t\t\t.data(options)\n\t\t\t.enter()\n\t\t\t.append('div')\n\t\t\t.attr('class', d => (d.label == 'Hide' ? 'sja_menuoption' : 'sja_menuoption_not_interactive'))\n\t\t\t.on('click', (event, c) => {\n\t\t\t\tif (c.setInput) return\n\t\t\t\tself.app.tip.hide()\n\t\t\t\tc.callback(d)\n\t\t\t})\n\n\t\t\t.each(function (this: HTMLElement, d) {\n\t\t\t\tconst div = select(this)\n\t\t\t\tif (d.label) div.append('div').style('display', 'inline-block').html(d.label)\n\t\t\t\tif (d.setInput)\n\t\t\t\t\td.setInput(\n\t\t\t\t\t\tdiv.append('div').style('display', 'inline-block')\n\t\t\t\t\t\t//.style('margin-left', '10px')\n\t\t\t\t\t)\n\t\t\t})\n\n\t\tmenu.show(x, y)\n\t}\n\n\tself.adjustLegendOrder = (d, increment) => {\n\t\tconst oldIndex = self.legendOrder.indexOf(d.seriesId)\n\t\tif (oldIndex == -1) return\n\t\tlet newIndex = oldIndex + increment\n\t\t// clamp to array bounds\n\t\tnewIndex = Math.max(0, Math.min(self.legendOrder.length - 1, newIndex))\n\t\t// remove item\n\t\tself.legendOrder.splice(oldIndex, 1)\n\t\t// insert at new index\n\t\tself.legendOrder.splice(newIndex, 0, d.seriesId)\n\t\tself.app.dispatch({\n\t\t\ttype: 'app_refresh'\n\t\t})\n\t\tself.app.tip.hide()\n\t}\n\n\tself.adjustColor = (value, d) => {\n\t\tconst color = rgb(value).formatHex()\n\t\tconst t2 = self.state.config.term2\n\t\tif (!t2) {\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: self.id,\n\t\t\t\tconfig: { settings: { survival: { defaultColor: color } } }\n\t\t\t})\n\t\t} else {\n\t\t\t// this is the overlay termwrapper\n\t\t\tconst term2 = structuredClone(t2)\n\t\t\t// do not replace term2.term.values directly, will set term2.values to use as overrides\n\t\t\tif (!term2.values) term2.values = {}\n\t\t\tconst values = term2.values\n\t\t\tif (!values[d.seriesId]) values[d.seriesId] = {}\n\t\t\tif (!('key' in values[d.seriesId])) values[d.seriesId].key = d.seriesId\n\t\t\tvalues[d.seriesId].color = color\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: self.id,\n\t\t\t\tconfig: {\n\t\t\t\t\tterm2\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\tself.app.tip.hide()\n\t}\n\n\t// disabled as a click handler for now, need to review\n\t// before completely removing this code\n\tself.showMenuForSelectedChart = function () {\n\t\tself.dom.tip.clear()\n\t\tself.activeMenu = true\n\t\tself.dom.tip\n\t\t\t.showunder(this)\n\t\t\t.d.append('button')\n\t\t\t.html('Download SVG')\n\t\t\t.on('click', () => {\n\t\t\t\tif (!self.state) return\n\t\t\t\tconst chartDiv = select(this.closest('.pp-survival-chart'))\n\t\t\t\tdownloadChart(\n\t\t\t\t\tchartDiv.select('.sjpp-survival-mainG'),\n\t\t\t\t\t'Survival_Plot',\n\t\t\t\t\tchartDiv.node() // use to get computed styles\n\t\t\t\t)\n\t\t\t})\n\t}\n}\n\nexport async function getPlotConfig(opts, app) {\n\tif (!opts.term) throw 'survival getPlotConfig: opts.term{} missing'\n\ttry {\n\t\tawait fillTermWrapper(opts.term, app.vocabApi)\n\t\t// supply t0_t2_defaultQ if opts.term0/2.bins/q is undefined\n\t\t// so that t0_t2_defaultQ does not override bins or q from user\n\t\tif (opts.term2)\n\t\t\tawait fillTermWrapper(opts.term2, app.vocabApi, opts.term2.bins || opts.term2.q ? undefined : t0_t2_defaultQ)\n\t\tif (opts.term0)\n\t\t\tawait fillTermWrapper(opts.term0, app.vocabApi, opts.term0.bins || opts.term0.q ? undefined : t0_t2_defaultQ)\n\t} catch (e) {\n\t\tthrow `${e} [survival getPlotConfig()]`\n\t}\n\n\tconst config = {\n\t\tcontrolLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),\n\t\tsettings: {\n\t\t\tcontrols: {\n\t\t\t\tterm2: null, // the previous overlay value may be displayed as a convenience for toggling\n\t\t\t\tterm0: null\n\t\t\t},\n\t\t\tsurvival: {\n\t\t\t\tradius: 5,\n\t\t\t\tciVisible: true,\n\t\t\t\tmedianSurvivalVisible: false,\n\t\t\t\tfill: '#fff',\n\t\t\t\tstroke: '#000',\n\t\t\t\tsymbol: 'vtick', // 'x', 'vtick'\n\t\t\t\tfillOpacity: 0,\n\t\t\t\tchartMargin: 10,\n\t\t\t\tsvgw: 400,\n\t\t\t\tsvgh: 300,\n\t\t\t\tnumUnitInOneYear: 1,\n\t\t\t\ttimeUnit: 'years',\n\t\t\t\tatRiskVisible: true,\n\t\t\t\tatRiskLabelOffset: -20,\n\t\t\t\tatRiskNoOverlayExtraPadding: 30, // Extra padding when there's no overlay term to prevent \"Number at risk\" text overlap\n\t\t\t\txTickValues: [], // if undefined or empty, will be ignored\n\t\t\t\tseriesTipDecimals: 1,\n\t\t\t\tsvgPadding: {\n\t\t\t\t\ttop: 20,\n\t\t\t\t\tleft: 55,\n\t\t\t\t\tright: 20,\n\t\t\t\t\tbottom: 50\n\t\t\t\t},\n\t\t\t\taxisTitleFontSize: 16,\n\t\t\t\txAxisOffset: 5,\n\t\t\t\tyAxisOffset: -5,\n\t\t\t\thiddenPvalues: [],\n\t\t\t\tdefaultColor: '#2077b4'\n\t\t\t}\n\t\t}\n\t}\n\n\t// default survival settings will be overwritten by the survival settings defined in dataset\n\tconst overrides = app.vocabApi.termdbConfig.survival || {}\n\tcopyMerge(config.settings.survival, overrides.settings)\n\n\t// may apply term-specific changes to the default object\n\treturn copyMerge(config, opts)\n}\n\nfunction getPj(self) {\n\tconst pj = new Partjson({\n\t\ttemplate: {\n\t\t\tyMin: '>=yMin()',\n\t\t\tyMax: '<=yMax()',\n\t\t\tcharts: [\n\t\t\t\t{\n\t\t\t\t\tchartId: '@key',\n\t\t\t\t\trawChartId: '$chartId',\n\t\t\t\t\txMin: '>$time',\n\t\t\t\t\txMax: '<$time',\n\t\t\t\t\t'__:xScale': '=xScale()',\n\t\t\t\t\t'__:yScale': '=yScale()',\n\t\t\t\t\tyMin: '>=yMin()',\n\t\t\t\t\tyMax: '<=yMax()',\n\t\t\t\t\tserieses: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tchartId: '@parent.@parent.@key',\n\t\t\t\t\t\t\tseriesId: '@key',\n\t\t\t\t\t\t\t'__:seriesLabel': '=seriesLabel()',\n\t\t\t\t\t\t\tdata: [\n\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t'__:seriesId': '@parent.@parent.seriesId',\n\t\t\t\t\t\t\t\t\t//color: \"$color\",\n\t\t\t\t\t\t\t\t\tx: '$time',\n\t\t\t\t\t\t\t\t\ty: '$survival',\n\t\t\t\t\t\t\t\t\tlower: '$lower',\n\t\t\t\t\t\t\t\t\tupper: '$upper',\n\t\t\t\t\t\t\t\t\t'_1:scaledX': '=scaledX()',\n\t\t\t\t\t\t\t\t\t'_1:scaledY': '=scaledY()',\n\t\t\t\t\t\t\t\t\tnevent: '$nevent',\n\t\t\t\t\t\t\t\t\tncensor: '$ncensor',\n\t\t\t\t\t\t\t\t\tnrisk: '$nrisk'\n\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t'=timeCensored()'\n\t\t\t\t\t\t\t]\n\t\t\t\t\t\t},\n\t\t\t\t\t\t'$seriesId'\n\t\t\t\t\t],\n\t\t\t\t\t'@done()': '=sortSerieses()'\n\t\t\t\t},\n\t\t\t\t'=chartTitle()'\n\t\t\t],\n\t\t\t'@done()': '=sortCharts()'\n\t\t},\n\t\t'=': {\n\t\t\tchartTitle(row) {\n\t\t\t\tif (!row.chartId || row.chartId == '-') {\n\t\t\t\t\tconst termNum = self.state.config.term.term.type == 'survival' ? 'term' : 'term2'\n\t\t\t\t\treturn self.state.config[termNum].term.name\n\t\t\t\t}\n\t\t\t\tconst t0 = self.state.config.term0\n\t\t\t\tif (!t0 || !t0.term.values) return row.chartId\n\t\t\t\tif (t0.q?.type == 'predefined-groupset' || t0.q?.type == 'custom-groupset') return row.chartId\n\t\t\t\tconst value = self.state.config.term0.term.values[row.chartId]\n\t\t\t\treturn value && value.label ? value.label : row.chartId\n\t\t\t},\n\t\t\tseriesLabel(row, context) {\n\t\t\t\tconst t2 = self.state.config.term2\n\t\t\t\tif (!t2) return\n\t\t\t\tconst seriesId = context.self.seriesId\n\t\t\t\tif (t2?.q?.type == 'predefined-groupset' || t2?.q?.type == 'custom-groupset') return seriesId\n\t\t\t\tif (t2 && t2.term.values && seriesId in t2.term.values) return t2.term.values[seriesId].label\n\t\t\t\tif (isNumericTerm(t2.term)) {\n\t\t\t\t\t// numeric term\n\t\t\t\t\t// seriesId on its own (e.g. \"<5\") will be vague,\n\t\t\t\t\t// so include term name in series label\n\t\t\t\t\treturn t2.term.name + ' ' + seriesId\n\t\t\t\t}\n\t\t\t\treturn seriesId\n\t\t\t},\n\t\t\ttimeCensored(row) {\n\t\t\t\treturn row.time + '-' + row.ncensor\n\t\t\t},\n\t\t\ty(row, context) {\n\t\t\t\tconst seriesId = context.context.parent.seriesId\n\t\t\t\treturn seriesId == 'CI' ? [row.lower, row.upper] : row[seriesId]\n\t\t\t},\n\t\t\tyMin(row) {\n\t\t\t\treturn row.lower\n\t\t\t},\n\t\t\tyMax(row) {\n\t\t\t\treturn row.upper\n\t\t\t},\n\t\t\txScale(_, context) {\n\t\t\t\tconst s = self.settings\n\t\t\t\treturn (\n\t\t\t\t\tscaleLinear()\n\t\t\t\t\t\t// force x to start at 0 because first data point will always\n\t\t\t\t\t\t// be at x=0 (see survival.R)\n\t\t\t\t\t\t.domain([0, Math.min(s.maxTimeToEvent || context.self.xMax, context.self.xMax)])\n\t\t\t\t\t\t.range([0, s.svgw - s.svgPadding.left - s.svgPadding.right])\n\t\t\t\t)\n\t\t\t},\n\t\t\tscaledX(_, context) {\n\t\t\t\treturn context.context.context.context.parent.xScale(context.self.x)\n\t\t\t},\n\t\t\tscaledY(_, context) {\n\t\t\t\tconst yScale = context.context.context.context.parent.yScale\n\t\t\t\tconst s = context.self\n\t\t\t\treturn [yScale(s.y), yScale(s.lower), yScale(s.upper)]\n\t\t\t},\n\t\t\tyScale() {\n\t\t\t\tconst s = self.settings\n\t\t\t\tconst domain = [1.05, 0]\n\t\t\t\treturn scaleLinear()\n\t\t\t\t\t.domain(domain)\n\t\t\t\t\t.range([0, s.svgh - s.svgPadding.top - s.svgPadding.bottom])\n\t\t\t},\n\t\t\tsortSerieses(result) {\n\t\t\t\tfor (const series of result.serieses) {\n\t\t\t\t\tseries.data.sort((a, b) => (a.x < b.x ? -1 : 1))\n\t\t\t\t}\n\t\t\t\tif (self.refs.orderedKeys) {\n\t\t\t\t\tconst s = self.refs.orderedKeys.series\n\t\t\t\t\tresult.serieses.sort((a, b) => s.indexOf(a.seriesId) - s.indexOf(b.seriesId))\n\t\t\t\t}\n\t\t\t\tif (self.refs.bins) {\n\t\t\t\t\tconst labelOrder = self.refs.bins.map(b => b.label)\n\t\t\t\t\tresult.serieses.sort((a, b) => labelOrder.indexOf(a.seriesId) - labelOrder.indexOf(b.seriesId))\n\t\t\t\t}\n\t\t\t},\n\t\t\tsortCharts(result) {\n\t\t\t\tif (!self.refs.orderedKeys) return\n\t\t\t\tconst c = self.refs.orderedKeys.chart\n\t\t\t\tresult.charts.sort(\n\t\t\t\t\t(a, b) =>\n\t\t\t\t\t\t(c.indexOf(a.chartId) == -1 ? c.indexOf(a.rawChartId) : c.indexOf(a.chartId)) -\n\t\t\t\t\t\t(c.indexOf(b.chartId) == -1 ? c.indexOf(b.rawChartId) : c.indexOf(b.chartId))\n\t\t\t\t)\n\t\t\t}\n\t\t}\n\t})\n\n\treturn pj\n}\n"],
-  "mappings": 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-  "names": ["v", "item", "chart", "s", "d", "Partjson"]
-}

package/dist/chunk-Y45JIQ5Y.js.map DELETED Viewed

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../src/app.mdsjson.js", "../gdc/launch.ts", "../src/app.parseurl.js"],
-  "sourcesContent": ["import * as client from './client'\n\n/*\n********************** EXPORTED\ninit_mdsjson\nvalidate_mdsjson\nget_json_tk\nget_scatterplot_data\n*/\n\nexport async function init_mdsjson(file_str, url_str) {\n\tlet json_files = [],\n\t\tjson_urls = []\n\n\tif (file_str && file_str.includes(',')) json_files = file_str.split(',')\n\telse if (file_str) json_files.push(file_str)\n\telse if (url_str && url_str.includes(',')) json_urls = url_str.split(',')\n\telse if (url_str) json_urls.push(url_str)\n\n\tconst tklst = []\n\tif (json_files.length) {\n\t\tconst json_url = undefined\n\t\tfor (const json_file of json_files) {\n\t\t\ttklst.push(await tklst_pipeline(json_file, json_url))\n\t\t}\n\t} else if (json_urls.length) {\n\t\tconst json_file = undefined\n\t\tfor (const json_url of json_urls) {\n\t\t\ttklst.push(await tklst_pipeline(json_file, json_url))\n\t\t}\n\t}\n\n\treturn tklst\n}\n\nasync function tklst_pipeline(json_file, json_url) {\n\tconst obj = await mdsjson_parse(json_file, json_url)\n\tvalidate_mdsjson(obj)\n\tconst tk = get_json_tk(obj)\n\treturn tk\n}\n\nasync function mdsjson_parse(json_file, json_url) {\n\tif (json_file !== undefined && json_file == '') throw '.jsonfile missing'\n\tif (json_url !== undefined && json_url == '') throw '.jsonurl missing'\n\n\tlet tmp\n\tif (json_file !== undefined) tmp = await client.dofetch('textfile', { file: json_file })\n\telse if (json_url !== undefined) tmp = await client.dofetch('urltextfile', { url: json_url })\n\tif (tmp.error) {\n\t\tthrow tmp.error\n\t}\n\treturn JSON.parse(tmp.text)\n}\n\nexport function validate_mdsjson(obj) {\n\tif (!obj) throw 'file is missing'\n\tif (!obj.type) throw 'dataset type is missing'\n\tconst svcnvfile = obj.svcnvfile || obj.svcnvurl\n\tconst vcffile = obj.vcffile || obj.vcfurl\n\tif (!svcnvfile && !vcffile) throw 'vcf or cnv file/url is required'\n\tif (Object.keys(obj).filter(x => x.includes('expression')).length) {\n\t\tif (!obj.expressionfile && !obj.expressionurl) throw 'expression file/url is missing'\n\t}\n\tif (Object.keys(obj).filter(x => x.includes('rnabam')).length) {\n\t\tif (!obj.rnabamfile && !obj.rnabamurl) throw 'rnabam file/url is missing'\n\t}\n\tif (obj.sampleset) {\n\t\tfor (const sample of obj.sampleset) {\n\t\t\tif (obj.sampleset.length != 1 && !sample.name) throw 'sampleset name is missing'\n\t\t\tif (!sample.samples) throw 'sampleset samples[] is missing'\n\t\t}\n\t}\n\tif (obj.sample2assaytrack) {\n\t\tfor (const [sample, assaylst] of Object.entries(obj.sample2assaytrack)) {\n\t\t\tif (!assaylst.length) throw 'assay[] missing for ' + sample\n\t\t\tfor (const assay of assaylst) {\n\t\t\t\tif (!assay.name) throw 'assay name is missing for ' + sample\n\t\t\t\tif (!assay.type) throw 'assay type is missing for ' + sample\n\t\t\t}\n\t\t}\n\t}\n\n\tif (obj.groupsamplebyattr) {\n\t\tif (!obj.groupsamplebyattr.attrlst) return '.attrlst[] missing from groupsamplebyattr'\n\t\tif (obj.groupsamplebyattr.attrlst.length == 0) return 'groupsamplebyattr.attrlst[] empty array'\n\n\t\tfor (const attr of obj.groupsamplebyattr.attrlst) {\n\t\t\tif (!attr.k) return 'k missing from one of groupsamplebyattr.attrlst[]'\n\t\t}\n\n\t\tif (obj.groupsamplebyattr.sortgroupby) {\n\t\t\tif (!obj.groupsamplebyattr.sortgroupby.key) return '.key missing from .sortgroupby'\n\t\t\tif (!obj.groupsamplebyattr.sortgroupby.order) return '.order[] missing from .sortgroupby'\n\t\t\tif (!Array.isArray(obj.groupsamplebyattr.sortgroupby.order)) return '.order must be an array'\n\t\t\t// values of order[] is not validated\n\t\t}\n\t\tif (!obj.groupsamplebyattr.attrnamespacer) obj.groupsamplebyattr.attrnamespacer = ', '\n\t}\n\n\tif (obj.fixedgeneexpression) {\n\t\tfor (const gene of obj.fixedgeneexpression) {\n\t\t\tif (!gene.gene) throw 'gene missing in fixedgeneexpression array'\n\t\t}\n\t}\n\n\t// hidden classes for vcf file\n\tif (obj.vcf) {\n\t\tif (!obj.vcf.hiddenclass) throw 'hiddenclasses[] missing from .vcf'\n\t}\n}\n\nexport function get_json_tk(tkobj) {\n\tconst track = {\n\t\ttype: tkobj.type,\n\t\tname: tkobj.name\n\t}\n\n\t// dense or full\n\tif (tkobj.isdense == 'true' || tkobj.isdense == true || tkobj.isfull === false) track.isdense = true\n\telse if (tkobj.isfull) track.isfull = true\n\n\t// svcnv file\n\tif (tkobj.svcnvfile) track.file = tkobj.svcnvfile\n\telse if (tkobj.svcnvurl) track.url = tkobj.svcnvurl\n\n\t// expressionrank\n\tif (Object.keys(tkobj).filter(x => x.includes('expression')).length) {\n\t\ttrack.checkexpressionrank = {\n\t\t\tfile: tkobj.expressionfile,\n\t\t\turl: tkobj.expressionurl\n\t\t}\n\t}\n\n\t// vcf\n\tif (Object.keys(tkobj).filter(x => x.includes('vcf')).length) {\n\t\ttrack.checkvcf = {\n\t\t\tfile: tkobj.vcffile,\n\t\t\turl: tkobj.vcfurl\n\t\t}\n\t}\n\n\t// hidden mutation classes\n\tif (tkobj.vcf) {\n\t\tif (tkobj.vcf.hiddenclass) {\n\t\t\ttrack.vcf = []\n\t\t\ttrack.vcf.hiddenclass = tkobj.vcf.hiddenclass\n\t\t}\n\t}\n\n\t// rna bam\n\tif (Object.keys(tkobj).filter(x => x.includes('rnabam')).length) {\n\t\ttrack.checkrnabam = {\n\t\t\tfile: tkobj.rnabamfile,\n\t\t\turl: tkobj.rnabamurl\n\t\t}\n\t}\n\n\t// sampleset\n\tif (tkobj.sampleset) {\n\t\ttrack.sampleset = tkobj.sampleset\n\t}\n\n\t// SampleAssayTrack\n\tif (tkobj.sample2assaytrack) {\n\t\ttrack.sample2assaytrack = tkobj.sample2assaytrack\n\t}\n\n\tif (tkobj.groupsamplebyattr) {\n\t\ttrack.groupsamplebyattr = tkobj.groupsamplebyattr\n\t}\n\n\t// fixed panel of gene expression\n\ttrack.fixedgeneexpression = tkobj.fixedgeneexpression\n\t// show all samples\n\ttrack.getallsamples = tkobj.getallsamples\n\n\t// cnv cutoff settings\n\ttrack.valueCutoff = tkobj.cnvValueCutoff !== undefined ? tkobj.cnvValueCutoff : undefined\n\ttrack.bplengthUpperLimit = tkobj.cnvLengthUpperLimit !== undefined ? tkobj.cnvLengthUpperLimit : undefined\n\n\t// loh cutoff settings\n\ttrack.segmeanValueCutoff = tkobj.segmeanValueCutoff !== undefined ? tkobj.segmeanValueCutoff : undefined\n\ttrack.lohLengthUpperLimit = tkobj.lohLengthUpperLimit !== undefined ? tkobj.lohLengthUpperLimit : undefined\n\n\t// multihide labels\n\ttrack.multihidelabel_vcf = tkobj.multihidelabel_vcf !== undefined ? tkobj.multihidelabel_vcf : undefined\n\ttrack.multihidelabel_fusion = tkobj.multihidelabel_fusion !== undefined ? tkobj.multihidelabel_fusion : undefined\n\ttrack.multihidelabel_sv = tkobj.multihidelabel_sv !== undefined ? tkobj.multihidelabel_sv : undefined\n\n\ttrack.legend_vorigin = tkobj.legend_vorigin\n\n\treturn track\n}\n\nexport async function get_scatterplot_data(json_file, json_url) {\n\tlet data = {}\n\tconst obj = await mdsjson_parse(json_file, json_url)\n\tdata.mdssamplescatterplot = obj\n\treturn data\n}\n", "/* launch from runpp() call. GDC react wrappers in the GFF repo use this method, to launch apps in gdc portal\non matching with a flag, imports corresponding plot script, and returns api object to runpp()\nwhen no flags are matched, returns undefined\n*/\nexport async function mayLaunchGdcPlotFromRunpp(arg, app) {\n\tif (arg.geneSearch4GDCmds3) {\n\t\tconst _ = await import('./lollipop.js')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcGb) {\n\t\tconst _ = await import('./gb.ts')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcMatrix) {\n\t\tconst _ = await import('./oncomatrix.js')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcHierCluster) {\n\t\tconst _ = await import('./geneExpClustering.js')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcMaf) {\n\t\tconst _ = await import('./maf.js')\n\t\treturn await _.gdcMAFui(arg, app.holder0)\n\t}\n\tif (arg.launchGdcGrin2) {\n\t\tconst _ = await import('./grin2.ts')\n\t\treturn await _.gdcGRIN2ui(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcScRNAseq) {\n\t\tconst _ = await import('./singlecell.ts')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcScApp) {\n\t\tconst _ = await import('./sc.ts')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcCorrelation) {\n\t\tconst _ = await import('./correlation.ts')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcDE) {\n\t\tconst _ = await import('./DE.ts')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.gdcbamslice) {\n\t\tconst _ = await import('./bam.js')\n\t\targ.gdcbamslice.filter0 = arg.filter0\n\t\treturn await _.bamsliceui(arg.gdcbamslice, app.holder0, app.genomes)\n\t}\n}\n\n/* launch from url param; this is for local testing and not used in gdc portal\nreturns true for a match\n*/\nexport async function mayLaunchGdcPlotFromUrlparam(urlp, arg) {\n\tif (urlp.has('gdcbamslice')) {\n\t\t// for local testing, not used in gdc portal\n\t\tconst _ = await import('./bam.js')\n\t\t_.bamsliceui(\n\t\t\t{\n\t\t\t\tdebugmode: arg.debugmode,\n\t\t\t\tstream2download: urlp.has('stream2download') // for testing only, launch the app in \"download mode\", will not visualize\n\t\t\t} as any,\n\t\t\targ.holder,\n\t\t\targ.genomes\n\t\t)\n\t\treturn true\n\t}\n\tif (urlp.has('gdcmaf')) {\n\t\t// for local testing, not used in gdc portal\n\t\tconst _ = await import('./maf.js')\n\t\tconst p: any = {\n\t\t\tdebugmode: arg.debugmode\n\t\t}\n\t\tif (urlp.has('filter0')) p.filter0 = urlp.get('filter0')\n\t\t_.gdcMAFui(p, arg.holder)\n\t\treturn true\n\t}\n\tif (urlp.has('gdcgrin2')) {\n\t\t// for local testing, not used in gdc portal\n\t\tconst _ = await import('./grin2.ts')\n\t\tconst p: any = {\n\t\t\tdebugmode: arg.debugmode\n\t\t}\n\t\tif (urlp.has('filter0')) p.filter0 = urlp.get('filter0')\n\t\t_.gdcGRIN2ui(p, arg.holder, arg.genomes)\n\t\treturn true\n\t}\n\tif (urlp.has('gdccorrelation')) {\n\t\t// for local testing, not used in gdc portal\n\t\tconst _ = await import('./correlation.ts')\n\t\tconst p: any = {\n\t\t\tdebugmode: arg.debugmode\n\t\t}\n\t\tif (urlp.has('filter0')) p.filter0 = urlp.get('filter0')\n\t\t_.init(p, arg.holder, arg.genomes)\n\t\treturn true\n\t}\n}\n", "import blockinit from './block.init'\nimport * as client from './client'\nimport { loadstudycohort } from './tp.init'\nimport { string2pos } from './coord'\nimport * as mdsjson from './app.mdsjson'\nimport { getSavedToken } from '#common/dofetch'\nimport urlmap from '#common/urlmap'\nimport { first_genetrack_tolist } from '#common/1stGenetk'\nimport { parentCorsMessage, childCorsMessage } from '#common/embedder-helpers'\nimport { sayerror } from '#dom'\nimport { copyMerge } from '#rx'\nimport { mayLaunchGdcPlotFromUrlparam } from '../gdc/launch.ts'\n/*\n********************** EXPORTED\nparse()\nget_tklst()\n*/\n\nexport async function parse(arg) {\n\t/*\narg\n\t.jwt\n\t.genomes{}\n\t.hostURL\n\t.variantPageCall_snv\n\t.samplecart\n\t.holder\n\t.debugmode\n\nupon error, throw err message as a string\n*/\n\tconst urlp = urlmap()\n\tconst features = JSON.parse(sessionStorage.getItem('optionalFeatures'))\n\n\tif (urlp.has('appcard')) {\n\t\tconst ad = await import('../appdrawer/adSandbox')\n\t\tconst cardJsonFile = urlp.get('appcard')\n\t\tconst example = urlp.get('example')\n\t\tconst re = await client.dofetch2('/cards/index.json')\n\t\targ.app.drawer.opts.genomes = arg.genomes\n\t\targ.app.drawer.opts.fromApp = true\n\t\t//Quick fix to launch the sandbox within the current openSandbox code\n\t\targ.app.drawer.opts.app = {\n\t\t\tcardsPath: 'cards'\n\t\t}\n\t\tconst element = re.elements.findIndex(\n\t\t\tt =>\n\t\t\t\tt.sandboxJson == cardJsonFile ||\n\t\t\t\tt.sandboxHtml == cardJsonFile ||\n\t\t\t\tt.name.toUpperCase().includes(cardJsonFile.toUpperCase())\n\t\t)\n\n\t\t//Check if track/app can be shown on this server\n\t\t//If not show error message\n\t\tif (re.elements[element]?.configFeature) {\n\t\t\tif (!features[re.elements[element].configFeature]) {\n\t\t\t\tsayerror(arg.holder, `This track or app is not enabled on this site.`)\n\t\t\t\treturn\n\t\t\t}\n\t\t}\n\n\t\tif (example) {\n\t\t\targ.app.drawer.opts.example = example\n\t\t}\n\n\t\tif (element <= 0) {\n\t\t\tconst nestedCards = [...re.elements.filter(e => e.type == 'nestedCard')]\n\t\t\tlet element, c\n\t\t\tnestedCards.findIndex(t => {\n\t\t\t\tfor (const [i, child] of t.children.entries()) {\n\t\t\t\t\tif (\n\t\t\t\t\t\tchild.sandboxJson == cardJsonFile ||\n\t\t\t\t\t\tchild.sandboxHtml == cardJsonFile ||\n\t\t\t\t\t\tchild.name.toUpperCase().includes(cardJsonFile.toUpperCase())\n\t\t\t\t\t) {\n\t\t\t\t\t\telement = t\n\t\t\t\t\t\tc = i\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t})\n\t\t\tif (!element) {\n\t\t\t\tsayerror(arg.holder, `Invalid app card.`)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tad.openSandbox(element.children[c], arg.app.drawer.opts)\n\t\t} else {\n\t\t\tad.openSandbox(re.elements[element], arg.app.drawer.opts)\n\t\t}\n\t\treturn\n\t}\n\n\tif (await mayLaunchGdcPlotFromUrlparam(urlp, arg)) return // gdc plot launched\n\n\tif (urlp.has('termdb')) {\n\t\tconst value = urlp.get('termdb')\n\t\tconst state = typeof value === 'string' ? JSON.parse(value) : value\n\t\tconst opts = {\n\t\t\tholder: arg.holder,\n\t\t\tstate: copyMerge(state, arg.state || {})\n\t\t}\n\t\tconst _ = await import('../termdb/app')\n\t\tconst subapp = _.appInit(opts)\n\t\treturn subapp\n\t}\n\n\tif (urlp.has('massnative')) {\n\t\t/* ?massnative=hg38-test,TermdbTest\n\t\talternative url for mass={\"genome\":\"hg38-test\",\"dslabel\":\"TermdbTest\"}\n\t\ttidier to include in manuscript\n\t\tno customization supported, though later additional fields may be appended to customize something\n\t\tit is intended that the dataset should carry essential customizations so the link opens mass ui with expected customizations\n\t\t*/\n\t\tconst value = urlp.get('massnative')\n\t\tconst [genomename, dslabel] = value.split(',')\n\t\tif (!genomename || !dslabel) throw 'value is not \"genome,dslabel\"'\n\t\tconst opts = {\n\t\t\tholder: arg.holder,\n\t\t\tgenome: arg.genomes[genomename],\n\t\t\tstate: copyMerge(\n\t\t\t\t{\n\t\t\t\t\tgenome: genomename,\n\t\t\t\t\tdslabel\n\t\t\t\t},\n\t\t\t\targ.state || {}\n\t\t\t),\n\t\t\tpkgver: arg.app.pkgver,\n\t\t\tlaunchDate: arg.app.launchDate\n\t\t}\n\t\tif (!opts.genome) throw 'invalid genome'\n\t\tchildCorsMessage(opts)\n\n\t\tconst _ = await import('../mass/app')\n\t\tconst subapp = await _.appInit(opts)\n\t\treturn subapp\n\t}\n\n\tif (urlp.has('mass')) {\n\t\tconst value = urlp.get('mass')\n\t\tconst state = typeof value === 'string' ? JSON.parse(value) : value\n\t\tconst opts = {\n\t\t\tdebug: arg.app.debugmode,\n\t\t\tholder: arg.holder,\n\t\t\tstate: copyMerge(state, arg.state || {}),\n\t\t\tpkgver: arg.app.pkgver,\n\t\t\tlaunchDate: arg.app.launchDate\n\t\t}\n\t\tif (state.genome) {\n\t\t\topts.genome = arg.genomes[state.genome]\n\t\t} else if (state?.vocab?.genome) {\n\t\t\topts.genome = arg.genomes[state.vocab.genome]\n\t\t}\n\t\tchildCorsMessage(opts)\n\n\t\tconst _ = await import('../mass/app')\n\t\tconst subapp = await _.appInit(opts)\n\t\treturn subapp\n\t}\n\n\tif (urlp.has('mass-session-file') || urlp.has('mass-session-url')) {\n\t\tlet opts\n\t\tif (urlp.has('mass-session-file')) {\n\t\t\tconst file = urlp.get('mass-session-file')\n\t\t\tconst d = await client.dofetch3(`/textfile`, {\n\t\t\t\tmethod: 'POST',\n\t\t\t\tbody: JSON.stringify({ file })\n\t\t\t})\n\t\t\tif (typeof d != 'object') throw 'data not object'\n\t\t\tif (d.error) throw d.error\n\t\t\tif (!d.text) throw 'data.text missing'\n\t\t\tconst state = JSON.parse(d.text)\n\n\t\t\tif (features.overrideEmbedderHostInMassSession) {\n\t\t\t\t// on local dev, set this to override \"embedder{}\" setting in session file\n\t\t\t\t// to prevent redirecting to portal site and test the session with local pp\n\t\t\t\tstate.embedder.host = features.overrideEmbedderHostInMassSession\n\t\t\t\tstate.embedder.origin = 'http://' + features.overrideEmbedderHostInMassSession\n\t\t\t\tstate.embedder.href = `http://${features.overrideEmbedderHostInMassSession}/`\n\t\t\t}\n\n\t\t\tif (state.embedder?.origin && state.embedder.origin != window.location.origin) {\n\t\t\t\tparentCorsMessage({ state })\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\topts = {\n\t\t\t\tdebug: arg.app.debugmode,\n\t\t\t\tholder: arg.holder,\n\t\t\t\tstate,\n\t\t\t\tgenome: arg.genomes[state.vocab.genome],\n\t\t\t\tpkgver: arg.app.pkgver,\n\t\t\t\tlaunchDate: arg.app.launchDate\n\t\t\t}\n\t\t} else if (urlp.has('mass-session-url')) {\n\t\t\tconst url = urlp.get('mass-session-url')\n\t\t\tconst d = await client.dofetch3('/urltextfile', {\n\t\t\t\tmethod: 'POST',\n\t\t\t\tbody: JSON.stringify({ url })\n\t\t\t})\n\t\t\tif (typeof d != 'object') throw 'data not object'\n\t\t\tif (d.error) throw d.error\n\t\t\tif (!d.text) throw 'data.text missing'\n\t\t\tconst state = JSON.parse(d.text)\n\n\t\t\tif (state.embedder?.origin && state.embedder.origin != window.location.origin) {\n\t\t\t\tparentCorsMessage({ state })\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\topts = {\n\t\t\t\tdebug: arg.app.debugmode,\n\t\t\t\tholder: arg.holder,\n\t\t\t\tstate: copyMerge(state, arg.state || {}),\n\t\t\t\tgenome: arg.genomes[state.vocab.genome],\n\t\t\t\tpkgver: arg.app.pkgver,\n\t\t\t\tlaunchDate: arg.app.launchDate\n\t\t\t}\n\t\t}\n\t\tconst _ = await import('../mass/app')\n\t\tconst subapp = _.appInit(opts)\n\t\treturn subapp\n\t}\n\n\tif (urlp.has('mass-session-id')) {\n\t\tconst id = urlp.get('mass-session-id')\n\t\tconst src = urlp.get('src')\n\t\tlet res\n\t\tif (src == 'browser') {\n\t\t\tconst json = localStorage.getItem('savedMassSessions')\n\t\t\tconst savedSessions = JSON.parse(json)\n\t\t\tres = { state: savedSessions[id] }\n\t\t} else {\n\t\t\tconst fetchOpts = { headers: {}, body: { id } }\n\t\t\tif (src == 'cred') {\n\t\t\t\tconst dslabel = urlp.get('dslabel')\n\t\t\t\tconst route = urlp.get('route')\n\t\t\t\tfetchOpts.body.dslabel = dslabel\n\t\t\t\tfetchOpts.body.route = route\n\t\t\t\tfetchOpts.body.route = route\n\t\t\t\tconst jwt = getSavedToken(dslabel, route)\n\t\t\t\tif (jwt) fetchOpts.headers.authorization = `Bearer ${btoa(jwt)}`\n\t\t\t}\n\t\t\tres = await client.dofetch3(`/massSession`, fetchOpts)\n\t\t\tif (res.error) throw res.error\n\t\t}\n\t\tconst embedder = res.state?.embedder\n\t\tif (embedder?.origin && embedder.origin != window.location.origin) {\n\t\t\tparentCorsMessage(res)\n\t\t\treturn\n\t\t}\n\t\tconst opts = {\n\t\t\tdebug: arg.app.debugmode,\n\t\t\tholder: arg.holder,\n\t\t\tstate: copyMerge(res.state, arg.state || {}),\n\t\t\tgenome: arg.genomes[res.state.vocab.genome],\n\t\t\tsessionDaysLeft: res.sessionDaysLeft,\n\t\t\tsessionId: id,\n\t\t\tpkgver: arg.app.pkgver,\n\t\t\tlaunchDate: arg.app.launchDate\n\t\t}\n\t\tconst _ = await import('../mass/app')\n\t\tconst subapp = _.appInit(opts)\n\t\treturn subapp\n\t}\n\n\tif (urlp.has('genome') && arg.selectgenome) {\n\t\tconst n = urlp.get('genome')\n\t\tconst genome_options = [...arg.selectgenome.node().childNodes]\n\t\tconst selectedIndex = genome_options.findIndex(d => d.value == n)\n\t\tif (selectedIndex == -1) {\n\t\t\tsayerror(\n\t\t\t\targ.holder,\n\t\t\t\t`Invalid genome: ${n}. Please provide an available genome from this list: ${genome_options\n\t\t\t\t\t.map(d => d.value)\n\t\t\t\t\t.join(', ')\n\t\t\t\t\t.replace(/,(?=[^,]*$)/, ', or')}`\n\t\t\t)\n\t\t\treturn\n\t\t}\n\t\targ.selectgenome.node().selectedIndex = selectedIndex\n\t\targ.selectgenome.node().dispatchEvent(new Event('change'))\n\t}\n\n\tif (urlp.has('hicfile') || urlp.has('hicurl')) {\n\t\t// whole-genome view\n\t\tlet file, url, name\n\t\tif (urlp.has('hicfile')) {\n\t\t\tfile = urlp.get('hicfile')\n\t\t\tname = file.split('/').pop()\n\t\t} else {\n\t\t\turl = urlp.get('hicurl')\n\t\t\tname = url.split('/').pop()\n\t\t}\n\t\tconst gn = urlp.get('genome')\n\t\tif (!gn) throw 'genome is required for hic'\n\t\tconst genome = arg.genomes[gn]\n\t\tif (!genome) throw 'invalid genome'\n\t\tconst hic = {\n\t\t\tgenome,\n\t\t\tfile,\n\t\t\turl,\n\t\t\tname, //.basename(file || url),\n\t\t\thostURL: arg.hostURL,\n\t\t\tenzyme: urlp.get('enzyme'),\n\t\t\tholder: arg.holder\n\t\t}\n\t\tconst _ = await import('../tracks/hic/HicApp')\n\t\tawait _.hicInit(hic)\n\t\treturn\n\t}\n\n\t//////////// legacy, may be replaced by sampleScatter, kept for existing views on vizcom\n\tif (urlp.has('singlecell')) {\n\t\tif (!urlp.has('genome')) throw '\"genome\" is required for \"singlecell\"'\n\t\tconst genomename = urlp.get('genome')\n\t\tconst genomeobj = arg.genomes[genomename]\n\t\tif (!genomeobj) throw 'invalid genome: ' + genomename\n\n\t\tconst _ = await import('./singlecell')\n\t\t_.init(\n\t\t\t{\n\t\t\t\tgenome: genomeobj,\n\t\t\t\tjsonfile: urlp.get('singlecell')\n\t\t\t},\n\t\t\targ.holder\n\t\t)\n\t\treturn\n\t}\n\n\tif (urlp.has('mavbfile')) {\n\t\tif (!urlp.has('genome')) throw '\"genome\" is required for \"mavb\"'\n\t\tconst genomename = urlp.get('genome')\n\t\tconst genome = arg.genomes[genomename]\n\t\tif (!genome) throw 'invalid genome: ' + genomename\n\t\tconst _ = await import('./mavb')\n\t\t_.mavbparseinput(\n\t\t\t{\n\t\t\t\tgenome,\n\t\t\t\thostURL: arg.hostURL,\n\t\t\t\tfile: urlp.get('mavbfile')\n\t\t\t},\n\t\t\t() => {},\n\t\t\targ.holder,\n\t\t\targ.jwt\n\t\t)\n\t\treturn\n\t}\n\n\tif (urlp.has('mavburl')) {\n\t\tif (!urlp.has('genome')) throw '\"genome\" is required for \"mavb\"'\n\t\tconst genomename = urlp.get('genome')\n\t\tconst genome = arg.genomes[genomename]\n\t\tif (!genome) throw 'invalid genome: ' + genomename\n\t\tconst _ = await import('./mavb')\n\t\t_.mavbparseinput(\n\t\t\t{\n\t\t\t\tgenome,\n\t\t\t\thostURL: arg.hostURL,\n\t\t\t\turl: urlp.get('mavburl')\n\t\t\t},\n\t\t\t() => {},\n\t\t\targ.holder,\n\t\t\targ.jwt\n\t\t)\n\t\treturn\n\t}\n\n\t//////////// legacy, replaced by sampleScatter (just need to support adhoc data), kept for existing views on vizcom\n\tif (urlp.has('scatterplot')) {\n\t\tif (!urlp.has('genome')) throw '\"genome\" is required for \"scatterplot\"'\n\t\tconst genomename = urlp.get('genome')\n\t\tconst genome = arg.genomes[genomename]\n\t\tif (!genome) throw 'invalid genome: ' + genomename\n\n\t\tlet plot_data\n\t\tif (urlp.has('mdsjson') || urlp.has('mdsjsonurl')) {\n\t\t\tconst url_str = urlp.get('mdsjsonurl')\n\t\t\tconst file_str = urlp.get('mdsjson')\n\t\t\tplot_data = await mdsjson.get_scatterplot_data(file_str, url_str)\n\t\t}\n\t\tif (urlp.has('tsnejson')) {\n\t\t\tconst file_str = urlp.get('tsnejson')\n\t\t\tconst data = await client.dofetch('textfile', { file: file_str })\n\t\t\tif (data.error) throw data.error\n\t\t\telse if (data.text) {\n\t\t\t\tplot_data = {\n\t\t\t\t\tmdssamplescatterplot: {\n\t\t\t\t\t\tanalysisdata: JSON.parse(data.text)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t// if genome is defined in url, pass it to samplescatterplot\n\t\tplot_data.mdssamplescatterplot.genome = genome\n\t\tconst _ = await import('./mds.samplescatterplot')\n\t\t_.init(plot_data.mdssamplescatterplot, arg.holder, false)\n\t\treturn\n\t}\n\n\tif (urlp.has('block')) {\n\t\tif (!urlp.has('genome')) throw 'missing genome for block'\n\t\tconst genomename = urlp.get('genome')\n\t\tconst genomeobj = arg.genomes[genomename]\n\t\tif (!genomeobj) throw 'invalid genome: ' + genomename\n\n\t\tconst par = {\n\t\t\tnobox: 1,\n\t\t\thostURL: arg.hostURL,\n\t\t\tjwt: arg.jwt,\n\t\t\tholder: arg.holder,\n\t\t\tgenome: genomeobj,\n\t\t\tdogtag: genomename,\n\t\t\tdebugmode: arg.debugmode\n\t\t}\n\n\t\tlet position = null\n\t\tlet rglst = null\n\n\t\tif (urlp.has('position')) {\n\t\t\t// can be multiple regions joined by ;\n\t\t\t// first region is main panel, rest of regions are subpanels\n\n\t\t\tconst lst = urlp.get('position').split(';')\n\t\t\tif (lst[0]) {\n\t\t\t\t// if first region is blank, do not parse; it will be assigned with defaultcoord\n\t\t\t\tconst tmp = lst[0].split(/[:-]/)\n\t\t\t\tconst chr = tmp[0]\n\t\t\t\tconst start = Number.parseInt(tmp[1])\n\t\t\t\tconst stop = Number.parseInt(tmp[2])\n\t\t\t\tif (!chr) throw 'chr missing'\n\t\t\t\tif (Number.isNaN(start) || Number.isNaN(stop)) throw 'Invalid start/stop value in position'\n\t\t\t\t// valid position\n\t\t\t\tposition = { chr, start, stop }\n\t\t\t}\n\n\t\t\tconst subpanels = [] // collect rest of regions into this array\n\t\t\tfor (let i = 1; i < lst.length; i++) {\n\t\t\t\tif (!lst[i]) continue // skip blank string\n\t\t\t\tconst tmp = lst[i].split(/[:-]/)\n\t\t\t\tconst chr = tmp[0]\n\t\t\t\tconst start = Number.parseInt(tmp[1])\n\t\t\t\tconst stop = Number.parseInt(tmp[2])\n\t\t\t\tif (!chr) throw 'subpanel chr missing'\n\t\t\t\tif (Number.isNaN(start) || Number.isNaN(stop)) throw 'Invalid start/stop value in subpanel position'\n\t\t\t\t// valid pos\n\t\t\t\tsubpanels.push({\n\t\t\t\t\tchr,\n\t\t\t\t\tstart,\n\t\t\t\t\tstop,\n\t\t\t\t\twidth: 600,\n\t\t\t\t\tleftborder: 'rgba(200,0,0,.1)',\n\t\t\t\t\tleftpad: 5\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (subpanels.length) {\n\t\t\t\t// has valid subpanels\n\t\t\t\tpar.subpanels = subpanels\n\t\t\t}\n\t\t}\n\n\t\tif (urlp.has('regions')) {\n\t\t\t// for a different purpose than \"position=\"\n\t\t\t// all regions here are shown in one view and scroll together, as in gmmode. it does not introduce subpanels\n\t\t\trglst = []\n\t\t\tfor (const s of urlp.get('regions').split(',')) {\n\t\t\t\tconst l = s.split(/[:-]/)\n\t\t\t\tconst chr = l[0]\n\t\t\t\tconst start = Number.parseInt(l[1])\n\t\t\t\tconst stop = Number.parseInt(l[2])\n\t\t\t\tif (Number.isNaN(start) || Number.isNaN(stop)) throw 'Invalid start/stop value in regions'\n\t\t\t\trglst.push({ chr: l[0], start: start, stop: stop })\n\t\t\t}\n\t\t}\n\n\t\tif (!position && !rglst) {\n\t\t\t// no position given, use default\n\t\t\tif (genomeobj.defaultcoord) {\n\t\t\t\tposition = {\n\t\t\t\t\tchr: genomeobj.defaultcoord.chr,\n\t\t\t\t\tstart: genomeobj.defaultcoord.start,\n\t\t\t\t\tstop: genomeobj.defaultcoord.stop\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (position) {\n\t\t\tpar.chr = position.chr\n\t\t\tpar.start = position.start\n\t\t\tpar.stop = position.stop\n\t\t} else if (rglst) {\n\t\t\tpar.rglst = rglst\n\t\t}\n\n\t\tif (urlp.has('hlregion')) {\n\t\t\tconst lst = []\n\t\t\tfor (const t of urlp.get('hlregion').split(',')) {\n\t\t\t\tconst pos = string2pos(t, genomeobj, true)\n\t\t\t\tif (pos) lst.push(pos)\n\t\t\t}\n\t\t\tif (lst.length) par.hlregions = lst\n\t\t}\n\n\t\tpar.datasetqueries = may_get_officialmds(urlp)\n\n\t\tpar.tklst = await get_tklst(urlp, genomeobj)\n\n\t\tfirst_genetrack_tolist(arg.genomes[genomename], par.tklst)\n\n\t\tmayAddBedjfilterbyname(urlp, par.tklst)\n\t\tconst b = await import('./block')\n\t\tnew b.Block(par)\n\t\treturn\n\t}\n\n\tif (urlp.has('gene')) {\n\t\tconst str = urlp.get('gene')\n\t\tif (str.length == 0) throw 'zero length query string'\n\t\tconst par = {\n\t\t\thostURL: arg.hostURL,\n\t\t\tquery: str,\n\t\t\tholder: arg.holder,\n\t\t\tvariantPageCall_snv: arg.variantPageCall_snv,\n\t\t\tsamplecart: arg.samplecart,\n\t\t\tdebugmode: arg.debugmode\n\t\t}\n\t\t{\n\t\t\tlet genomename\n\t\t\tfor (let n in arg.genomes) {\n\t\t\t\tif (arg.genomes[n].isdefault) {\n\t\t\t\t\tgenomename = n\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (urlp.has('genome')) {\n\t\t\t\tgenomename = urlp.get('genome')\n\t\t\t}\n\t\t\tif (!genomename) throw 'No genome, and none set as default'\n\t\t\tpar.genome = arg.genomes[genomename]\n\t\t\tif (!par.genome) throw 'invalid genome: ' + genomename\n\t\t}\n\t\tlet ds = null\n\t\tif (urlp.has('dataset')) {\n\t\t\tpar.dataset = urlp.get('dataset').split(',')\n\t\t}\n\t\tif (urlp.has('hlaachange')) {\n\t\t\tpar.hlaachange = new Map()\n\t\t\tfor (const s of urlp.get('hlaachange').split(',')) {\n\t\t\t\tpar.hlaachange.set(s, false)\n\t\t\t}\n\t\t}\n\t\tif (urlp.has('hlregion')) {\n\t\t\tconst lst = []\n\t\t\tfor (const t of urlp.get('hlregion').split(',')) {\n\t\t\t\tconst pos = string2pos(t, par.genome, true)\n\t\t\t\tif (pos) lst.push(pos)\n\t\t\t}\n\t\t\tif (lst.length) par.hlregions = lst\n\t\t}\n\t\tif (urlp.has('aarange')) {\n\t\t\tconst [a, b] = urlp.get('aarange').split(',').map(Number)\n\t\t\tif (Number.isInteger(a) && Number.isInteger(b) && a > 0 && b > a) {\n\t\t\t\tpar.aarange = [a, b]\n\t\t\t} else {\n\t\t\t\tthrow 'invalid aarange'\n\t\t\t}\n\t\t}\n\n\t\tpar.tklst = await get_tklst(urlp, par.genome)\n\n\t\tmayAddBedjfilterbyname(urlp, par.tklst)\n\n\t\tpar.datasetqueries = may_get_officialmds(urlp)\n\t\tawait blockinit(par)\n\t\treturn\n\t}\n\n\tif (urlp.has('disco')) {\n\t\t// a direct link to make manual testing easy\n\t\tconst genomeName = urlp.get('genome')\n\t\tconst genome = arg.genomes[genomeName]\n\t\tif (!genome) throw 'genome missing'\n\t\tconst dslabel = urlp.get('dslabel')\n\t\tif (!dslabel) throw 'dslabel missing'\n\t\tconst sample_id = urlp.get('sample')\n\t\tif (!sample_id) throw 'sample_id missing'\n\t\tconst vocabApi = (await import('#termdb/vocabulary')).vocabInit({ state: { genome: genomeName, dslabel } })\n\t\tconst termdbConfig = await vocabApi.getTermdbConfig()\n\t\tawait (await import('#plots/plot.disco.js')).default(termdbConfig, dslabel, { sample_id }, arg.holder, genome)\n\t\treturn\n\t}\n\n\t///////////// legacy, totally replaced by mass. kept for some views on vizcom\n\tif (urlp.has('study')) {\n\t\tconst v = urlp.get('study')\n\t\tif (v != '') {\n\t\t\tloadstudycohort(\n\t\t\t\targ.genomes,\n\t\t\t\tv,\n\t\t\t\targ.holder,\n\t\t\t\targ.hostURL,\n\t\t\t\tundefined, // jwt\n\t\t\t\tfalse, // no show\n\t\t\t\targ.app || {\n\t\t\t\t\tdebugmode: arg.debugmode,\n\t\t\t\t\tinstanceTracker: arg.instanceTracker || {},\n\t\t\t\t\tcallbacks: arg.callbacks || {}\n\t\t\t\t}\n\t\t\t)\n\t\t}\n\t}\n}\n\nfunction may_get_officialmds(urlp) {\n\tif (!urlp.has('mds')) return\n\tconst tmp = urlp.get('mds').split(',')\n\tif (tmp[0] && tmp[1]) {\n\t\tconst dataset = { dataset: tmp[0], querykey: tmp[1] }\n\t\tif (urlp.has('sample')) {\n\t\t\tdataset.singlesample = { name: urlp.get('sample') }\n\t\t\t// quick fix!!\n\t\t\t// tell  mds_load_query_bykey to load assay tracks in this context, but will not do so if launching sample view from main tk\n\t\t\tdataset.getsampletrackquickfix = true\n\t\t}\n\t\treturn [dataset]\n\t}\n\treturn\n}\n\nexport async function get_tklst(urlp, genomeobj) {\n\tconst tklst = []\n\n\tfor (const [key, value] of urlp) {\n\t\tconst tks = await mayGetTkobj(key, value, urlp, genomeobj)\n\t\tif (!tks) continue // no tkobj derived, parameter doesn't match with anything\n\t\tif (Array.isArray(tks)) tklst.push(...tks)\n\t\telse tklst.push(tks)\n\t}\n\n\tfor (const t of tklst) {\n\t\t// uncertain reason why all tk are labeled as custom\n\t\t// the mds3 tk has \"dslabel\" and should be official, do not label as custom, so in block.tk.menu won't show the delete button\n\t\tif (t.type == 'mds3' && t.dslabel) continue\n\t\tt.iscustom = true\n\t}\n\n\t// quick fix to modify behaviors of mds tracks collected through parameters\n\t// if isdense=1, turn to dense\n\t// if sample=..., change to a single sample track\n\tif (urlp.has('isdense')) {\n\t\ttklst\n\t\t\t.filter(t => t.type == client.tkt.mdssvcnv)\n\t\t\t.forEach(t => {\n\t\t\t\tt.isdense = true\n\t\t\t\tt.isfull = false\n\t\t\t})\n\t}\n\tif (urlp.has('sample')) {\n\t\ttklst\n\t\t\t.filter(t => t.type == client.tkt.mdssvcnv)\n\t\t\t.forEach(t => {\n\t\t\t\tt.singlesample = { name: urlp.get('sample') }\n\t\t\t\tt.getsampletrackquickfix = true\n\t\t\t\t// XXX this doesn't work to load assay tracks for a custom mds, can only load for official mds\n\t\t\t\t// for both custom and official, the expression rank track is not loaded.\n\t\t\t})\n\t}\n\treturn tklst\n}\n\n/*\nreturns:\n- object for one successfully parsed track\n- array for multiple track objects, could be empty!\n- null for no tracks\n*/\nexport async function mayGetTkobj(key, value, urlp, genomeobj) {\n\tif (key == 'mds3') {\n\t\t// official mds3 dataset; value is comma-joined dslabels\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (const n of lst) {\n\t\t\tconst tk = {\n\t\t\t\ttype: client.tkt.mds3,\n\t\t\t\tdslabel: n\n\t\t\t}\n\t\t\tif (urlp.has('token')) tk.token = urlp.get('token') // temporary\n\t\t\tif (urlp.has('filterobj')) tk.filterObj = urlp.get('filterobj')\n\t\t\tif (urlp.has('filter0')) tk.filter0 = urlp.get('filter0')\n\t\t\tif (urlp.has('cnvonly')) tk.hardcodeCnvOnly = true // for testing cnv-only mode via url param; in actual use this flag should be set in runpp()\n\t\t\tif (urlp.has('snvindelonly')) tk.snvIndelOnly = true // for testing snvindel-only mode\n\t\t\ttks.push(tk)\n\t\t}\n\t\treturn tks\n\t}\n\n\tif (key == 'mds3bcffile') {\n\t\t// \"name,path\" pairs to server-side vcf files\n\t\tconst [tkname, bcffile] = value.split(',')\n\t\tlet tk\n\t\tif (tkname && bcffile) {\n\t\t\ttk = {\n\t\t\t\ttype: client.tkt.mds3,\n\t\t\t\tname: tkname,\n\t\t\t\tbcf: { file: bcffile }\n\t\t\t}\n\t\t}\n\t\treturn tk\n\t}\n\tif (key == 'mds3bcfurl') {\n\t\t// \"name,url,indexURL\" to remote file. indexURL is optional when the index file is not co-locating with the bcf file\n\t\tconst [tkname, url, indexURL] = value.split(',')\n\t\tlet tk\n\t\tif (tkname && url) {\n\t\t\ttk = {\n\t\t\t\ttype: client.tkt.mds3,\n\t\t\t\tname: tkname,\n\t\t\t\tbcf: { url, indexURL }\n\t\t\t}\n\t\t}\n\t\treturn tk\n\t}\n\n\tif (key == 'arcfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.hicstraw,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tbedfile: lst[i + 1],\n\t\t\t\t\tmode_hm: false,\n\t\t\t\t\tmode_arc: true\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\n\tif (key == 'mdsjson' || key == 'mdsjsonurl') {\n\t\tlet url_str, file_str\n\t\tif (key == 'mdsjson') file_str = value\n\t\telse url_str = value\n\t\treturn await mdsjson.init_mdsjson(file_str, url_str)\n\t}\n\n\tif (key == 'tkjsonfile') {\n\t\tconst re = await client.dofetch('textfile', { file: value })\n\t\tif (re.error) throw re.error\n\t\tif (!re.text) throw '.text missing'\n\t\tconst lst = JSON.parse(re.text)\n\t\tconst tks = []\n\t\tfor (const i of lst) {\n\t\t\tif (i.isfacet) {\n\t\t\t\tif (!genomeobj.tkset) genomeobj.tkset = []\n\t\t\t\tif (!i.tracks) throw '.tracks[] missing from a facet table'\n\t\t\t\tif (!Array.isArray(i.tracks)) throw '.tracks[] not an array from a facet table'\n\t\t\t\ti.tklst = i.tracks\n\t\t\t\tdelete i.tracks\n\t\t\t\tfor (const t of i.tklst) {\n\t\t\t\t\tif (!t.assay) throw '.assay missing from a facet track'\n\t\t\t\t\tif (!t.sample) throw '.sample missing from a facet track'\n\t\t\t\t\t// must assign tkid otherwise the tk buttons from facet table won't work\n\t\t\t\t\tt.tkid = Math.random().toString()\n\t\t\t\t}\n\t\t\t\tgenomeobj.tkset.push(i)\n\t\t\t} else {\n\t\t\t\t// must be a track\n\t\t\t\ttks.push(i)\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\n\tif (key == 'bamfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.bam,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'bamurl') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.bam,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\turl: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'bedjfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.bedj,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'bedjurl') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.bedj,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\turl: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'hictkfile' || key == 'hictkurl') {\n\t\t// name,enzyme,file/url\n\t\tconst isfile = key == 'hictkfile'\n\t\tconst lst = value.split(',')\n\t\tconst norm = urlp.has('hictknorm') ? urlp.get('hictknorm').split(',') : null\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 3) {\n\t\t\tif (lst[i] && lst[i + 1] && lst[i + 2]) {\n\t\t\t\tconst t = {\n\t\t\t\t\ttype: client.tkt.hicstraw,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tenzyme: lst[i + 1],\n\t\t\t\t\tnormalizationmethod: norm ? norm[i / 3] : null\n\t\t\t\t}\n\t\t\t\tif (isfile) {\n\t\t\t\t\tt.file = lst[i + 2]\n\t\t\t\t} else {\n\t\t\t\t\tt.url = lst[i + 2]\n\t\t\t\t}\n\t\t\t\ttks.push(t)\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'ldfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.ld,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'bigwigfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.bigwig,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1],\n\t\t\t\t\tscale: { auto: 1 }\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'bigwigurl') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.bigwig,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\turl: lst[i + 1],\n\t\t\t\t\tscale: { auto: 1 }\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'junctionfile') {\n\t\t// legacy\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.junction,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\ttracks: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'junctionurl') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.junction,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\ttracks: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\turl: lst[i + 1]\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\t/*\n\tif (urlp.has('vcffile')) {\n\t\tconst lst = urlp.get('vcffile').split(',')\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttklst.push({\n\t\t\t\t\ttype: 'vcf',\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n\tif (urlp.has('vcfurl')) {\n\t\tconst lst = urlp.get('vcfurl').split(',')\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttklst.push({\n\t\t\t\t\ttype: 'vcf',\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\turl: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n\t*/\n\tif (key == 'aicheckfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: 'aicheck',\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'bampilefile') {\n\t\tconst lst = value.split(',')\n\t\tlet links = null\n\t\tif (urlp.has('bampilelink')) {\n\t\t\tlinks = urlp.get('bampilelink').split(',').map(decodeURIComponent)\n\t\t}\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\tconst tk = {\n\t\t\t\t\ttype: client.tkt.bampile,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t}\n\t\t\t\tif (links && links[i / 2]) {\n\t\t\t\t\ttk.link = links[i / 2]\n\t\t\t\t}\n\t\t\t\ttks.push(tk)\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'svcnvfpkmurl') {\n\t\tconst lst = value.split(',')\n\t\t// defines a single track, all members using url\n\t\tconst name = lst[0]\n\t\tconst type2url = {}\n\t\tfor (let i = 1; i < lst.length; i += 2) {\n\t\t\ttype2url[lst[i]] = lst[i + 1]\n\t\t}\n\t\tlet tk\n\t\tif (type2url.svcnv || type2url.vcf) {\n\t\t\ttk = {\n\t\t\t\ttype: client.tkt.mdssvcnv,\n\t\t\t\tname: name\n\t\t\t}\n\t\t\tif (type2url.svcnv) {\n\t\t\t\ttk.url = type2url.svcnv\n\t\t\t}\n\t\t\tif (type2url.vcf) {\n\t\t\t\ttk.checkvcf = {\n\t\t\t\t\turl: type2url.vcf,\n\t\t\t\t\tindexURL: type2url.vcfindex\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (type2url.fpkm) {\n\t\t\t\ttk.checkexpressionrank = {\n\t\t\t\t\tdatatype: 'FPKM',\n\t\t\t\t\turl: type2url.fpkm,\n\t\t\t\t\tindexURL: type2url.fpkmindex\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn tk\n\t}\n\tif (key == 'svcnvfpkmfile') {\n\t\tconst lst = value.split(',')\n\t\t// defines a single track, all members using file\n\t\tconst name = lst[0]\n\t\tconst type2file = {}\n\t\tfor (let i = 1; i < lst.length; i += 2) {\n\t\t\ttype2file[lst[i]] = lst[i + 1]\n\t\t}\n\t\tlet tk\n\t\tif (type2file.svcnv || type2file.vcf) {\n\t\t\ttk = {\n\t\t\t\ttype: client.tkt.mdssvcnv,\n\t\t\t\tname: name\n\t\t\t}\n\t\t\tif (type2file.svcnv) {\n\t\t\t\ttk.file = type2file.svcnv\n\t\t\t}\n\t\t\tif (type2file.vcf) {\n\t\t\t\ttk.checkvcf = {\n\t\t\t\t\tfile: type2file.vcf\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (type2file.fpkm) {\n\t\t\t\ttk.checkexpressionrank = {\n\t\t\t\t\tdatatype: 'FPKM',\n\t\t\t\t\tfile: type2file.fpkm\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn tk\n\t}\n\tif (key == 'mdsjunctionfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: 'mdsjunction',\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'junctionmatrix') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: 'mdsjunction',\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile2: lst[i + 1] // quick fix to support new file type\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\n\tif (key == 'junctionrnapeg') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.junction,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\ttracks: [{ rnapegfile: lst[i + 1] }]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n}\n\nfunction mayAddBedjfilterbyname(urlp, tklst) {\n\t/* !! a quick fix !!\n\tthe filter string will be applied to all bedj tracks,\n\trather than specific for a track\n\tmay mess up with other bedj tracks shown at the same time\n\t*/\n\tif (urlp.has('bedjfilterbyname')) {\n\t\tfor (const t of tklst) {\n\t\t\tif (t.type == 'bedj') t.filterByName = urlp.get('bedjfilterbyname')\n\t\t}\n\t}\n}\n"],
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