@sjcrh/proteinpaint-client 2.166.0 → 2.167.0

package/dist/chunk-YUL2RO7I.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/barchart.js", "../plots/barchart.events.js"],
+  "sourcesContent": ["import { getCompInit, copyMerge, deepEqual } from '../rx'\nimport getHandlers from './barchart.events'\nimport barsRenderer from './bars.renderer'\nimport { rendererSettings, plotLength } from './bars.settings'\nimport { htmlLegend, /** svgLegend, */ renderTable, DownloadMenu } from '#dom'\nimport { select } from 'd3-selection'\nimport { rgb } from 'd3-color'\nimport { controlsInit, term0_term2_defaultQ, renderTerm1Label } from './controls'\n// import { to_svg } from '../src/client'\nimport { fillTermWrapper } from '#termsetting'\nimport { getColors, mclass, plotColor } from '#shared/common.js'\nimport { isNumericTerm } from '#shared/terms.js'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport { getCombinedTermFilter } from '#filter'\nimport { PlotBase, defaultUiLabels } from '#plots/PlotBase.js'\nimport { rebaseGroupFilter } from '../mass/groups.js'\n\nexport class Barchart extends PlotBase {\n\tstatic type = 'barchart'\n\n\tconfigTermKeys = ['term', 'term0', 'term2']\n\n\tconstructor(opts) {\n\t\t// rx.getComponentInit() will set this.app, this.id, this.opts\n\t\tsuper(opts)\n\t\tthis.type = Barchart.type\n\t}\n\t//freeze the api of this class. don't want embedder functions to modify it.\n\tpreApiFreeze(api) {\n\t\tapi.download = this.download\n\t\tapi.getChartImages = () => this.getChartImages()\n\t}\n\n\tasync init(appState) {\n\t\tconst opts = this.opts\n\t\tconst controls = this.opts.controls ? null : opts.holder.append('div')\n\t\tconst holder = opts.controls ? opts.holder : opts.holder.append('div')\n\t\tthis.dom = {\n\t\t\tloadingDiv: holder.append('div').style('display', 'none').style('padding', '24px').html('Loading ...'),\n\t\t\theader: opts.header,\n\t\t\tcontrols,\n\t\t\tholder,\n\t\t\tbanner: holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.style('padding', '24px')\n\t\t\t\t.style('font-size', '16px')\n\t\t\t\t.style('color', '#aaa'),\n\t\t\tbarDiv: holder\n\t\t\t\t.append('div')\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: holder.append('div').style('margin', '5px 5px 15px 5px')\n\t\t}\n\t\tif (this.dom.header) this.dom.header.html('Barchart')\n\t\tthis.settings = JSON.parse(rendererSettings)\n\n\t\tsetRenderers(this)\n\t\tsetInteractivity(this)\n\n\t\tthis.renderers = {}\n\t\tthis.legendRenderer = htmlLegend(\n\t\t\tthis.dom.legendDiv,\n\t\t\t{\n\t\t\t\tsettings: {\n\t\t\t\t\tlegendOrientation: 'vertical'\n\t\t\t\t},\n\t\t\t\thandlers: this.handlers\n\t\t\t},\n\t\t\tthis.dom.barDiv\n\t\t)\n\t\tthis.controls = {}\n\t\tthis.term2toColor = {}\n\n\t\tif (this.opts.bar_click_override) {\n\t\t\t// will use this as callback to bar click\n\t\t\t// and will not set up bar click menu\n\t\t} else if (!this.opts.bar_click_opts) {\n\t\t\tthis.opts.bar_click_opts = ['hide_bar']\n\t\t\tif (this.app.getState().nav.header_mode === 'with_tabs') this.opts.bar_click_opts.push('add_filter', 'add_group')\n\t\t}\n\t}\n\n\tasync setControls() {\n\t\tconst state = this.state\n\t\tconst controlLabels = state.config.controlLabels\n\t\tif (!controlLabels) throw 'controls labels not found'\n\t\tthis.dom.controls.selectAll('*').remove()\n\t\tif (this.opts.controls) {\n\t\t\tthis.opts.controls.on('downloadClick.barchart', 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\t\t\t//.style('margin-left', '10px')\n\n\t\t\tconst inputs = [\n\t\t\t\t{\n\t\t\t\t\ttype: 'term',\n\t\t\t\t\tconfigKey: 'term',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tusecase: { target: 'barchart', detail: 'term' },\n\t\t\t\t\tlabel: controlLabels.term1?.label || renderTerm1Label,\n\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\tmenuOptions: 'edit',\n\t\t\t\t\tdefaultQ4fillTW: { geneVariant: { type: 'custom-groupset' } },\n\t\t\t\t\tgetBodyParams: () => {\n\t\t\t\t\t\tconst tw = this.config['term']\n\t\t\t\t\t\tif (!tw) return { skip_categories: true }\n\t\t\t\t\t\tif (tw.term.categories) return { categories: tw.term.categories }\n\t\t\t\t\t\treturn {}\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\ttype: 'term',\n\t\t\t\t\tconfigKey: 'term2',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tusecase: { target: 'barchart', detail: 'term2' },\n\t\t\t\t\ttitle: controlLabels.term2.title || controlLabels.term2.label,\n\t\t\t\t\tlabel: controlLabels.term2.label,\n\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\tnumericEditMenuVersion: this.opts.numericEditMenuVersion,\n\t\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ,\n\t\t\t\t\t// overlay option should always be visible, but must convert unit from log to abs\n\t\t\t\t\t// when an overlay is added\n\t\t\t\t\t//getDisplayStyle: () => (this.settings.unit == 'log' ? 'none' : ''),\n\t\t\t\t\tprocessConfig: config => {\n\t\t\t\t\t\t//config.settings not usually passed for logic check below\n\t\t\t\t\t\tconst s = this.state.config.settings.barchart\n\t\t\t\t\t\tif (!config.settings) config.settings = { barchart: {} }\n\t\t\t\t\t\t//Prevent showing Log option when overlay is selected\n\t\t\t\t\t\tif (config.term2 && s.unit == 'log') config.settings.barchart.unit = 'abs'\n\t\t\t\t\t\t//Revert back to Linear radio when Proportion is selected\n\t\t\t\t\t\t//but the overlay term is removed\n\t\t\t\t\t\tif (!config.term2 && s.unit == 'pct') config.settings.barchart.unit = 'abs'\n\t\t\t\t\t},\n\t\t\t\t\tgetBodyParams: () => {\n\t\t\t\t\t\tconst tw = this.config['term2']\n\t\t\t\t\t\tif (!tw) return { skip_categories: true }\n\t\t\t\t\t\tif (tw.term.categories) return { categories: tw.term.categories }\n\t\t\t\t\t\treturn {}\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\ttype: 'term',\n\t\t\t\t\tconfigKey: 'term0',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tusecase: { target: 'barchart', detail: 'term0' },\n\t\t\t\t\ttitle: controlLabels.term0.title || controlLabels.term0.label,\n\t\t\t\t\tlabel: controlLabels.term0.label,\n\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\tnumericEditMenuVersion: this.opts.numericEditMenuVersion,\n\t\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ,\n\t\t\t\t\tgetBodyParams: () => {\n\t\t\t\t\t\tconst tw = this.config['term0']\n\t\t\t\t\t\tif (!tw) return { skip_categories: true }\n\t\t\t\t\t\tif (tw.term.categories) return { categories: tw.term.categories }\n\t\t\t\t\t\treturn {}\n\t\t\t\t\t}\n\t\t\t\t},\n\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Bar orientation',\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'orientation',\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{ label: 'Vertical', value: 'vertical' },\n\t\t\t\t\t\t{ label: 'Horizontal', value: 'horizontal' }\n\t\t\t\t\t]\n\t\t\t\t},\n\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Scale',\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'unit',\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{ label: 'Linear', value: 'abs' },\n\t\t\t\t\t\t/** Option not available when term2 is present:\n\t\t\t\t\t\t * 1. The scale for the plot renders incorrectly\n\t\t\t\t\t\t * 2. The bars do not appear to be rendering correctly as a result\n\t\t\t\t\t\t * TODOs: Investigate the cause of the rendering issue\n\t\t\t\t\t\t */\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Log',\n\t\t\t\t\t\t\tvalue: 'log',\n\t\t\t\t\t\t\tgetDisplayStyle: (plot, computedDisplay = 'inline-block') => (plot.term2 ? 'none' : computedDisplay)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Proportion',\n\t\t\t\t\t\t\tvalue: 'pct',\n\t\t\t\t\t\t\tgetDisplayStyle: (plot, computedDisplay = 'inline-block') => (plot.term2 ? computedDisplay : 'none')\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Multicolor bars',\n\t\t\t\t\ttitle: 'Color bars',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'colorBars',\n\t\t\t\t\tboxLabel: 'Yes',\n\t\t\t\t\tgetDisplayStyle: plot => (plot.term2 ? 'none' : 'table-row')\n\t\t\t\t},\n\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Deduplicate',\n\t\t\t\t\ttitle: 'Use separate bars samples that has multiple values or belong to multiple groups',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'dedup',\n\t\t\t\t\tboxLabel: 'Yes',\n\t\t\t\t\tgetDisplayStyle: plot =>\n\t\t\t\t\t\tthis.chartsData?.charts.find(\n\t\t\t\t\t\t\tc =>\n\t\t\t\t\t\t\t\tc.dedupedSerieses?.length &&\n\t\t\t\t\t\t\t\t!deepEqual(\n\t\t\t\t\t\t\t\t\tc.serieses.map(s => s.seriesId),\n\t\t\t\t\t\t\t\t\tc.dedupedSerieses.map(s => s.seriesId)\n\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t)\n\t\t\t\t\t\t\t? 'table-row'\n\t\t\t\t\t\t\t: 'none'\n\t\t\t\t}\n\t\t\t]\n\t\t\tif (isNumericTerm(this.config.term.term))\n\t\t\t\tinputs.push({\n\t\t\t\t\tlabel: 'Show stats',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'showStats',\n\t\t\t\t\tboxLabel: 'Yes'\n\t\t\t\t})\n\t\t\tif (!this.config.term2)\n\t\t\t\tinputs.push({\n\t\t\t\t\tlabel: 'Show percent',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'showPercent',\n\t\t\t\t\tboxLabel: 'Yes'\n\t\t\t\t})\n\t\t\telse\n\t\t\t\tinputs.push({\n\t\t\t\t\tlabel: 'Show association tests',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'showAssociationTests',\n\t\t\t\t\tboxLabel: 'Yes'\n\t\t\t\t})\n\t\t\tif (state.config.settings.barchart.colorBars && (state.config.term2 || state.config.term0))\n\t\t\t\tinputs.splice(7, 0, {\n\t\t\t\t\tlabel: 'Assign colors to',\n\t\t\t\t\ttitle: `Colors bars either considering all the categories or the present categories. If there are many categories and only few are present the present choice will provide more contrast.`,\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'colorUsing',\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{ label: 'All values', value: 'all' },\n\t\t\t\t\t\t{ label: 'Present values', value: 'present' }\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\telse if (!state.config.settings.barchart.colorBars)\n\t\t\t\tinputs.splice(6, 0, {\n\t\t\t\t\tlabel: 'Default color',\n\t\t\t\t\ttitle: 'Default color for bars when there is no overlay',\n\t\t\t\t\ttype: 'color',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'defaultColor'\n\t\t\t\t\t//getDisplayStyle: plot => (plot.settings.barchart.colorBars || plot.term2 ? 'none' : 'table-row')\n\t\t\t\t})\n\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Plot length',\n\t\t\t\ttitle: `Set the plot length in pixels between 200 and 800.`,\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'barchart',\n\t\t\t\tsettingsKey: 'plotLength',\n\t\t\t\tmin: 200,\n\t\t\t\tmax: 800,\n\t\t\t\tstep: 10\n\t\t\t})\n\n\t\t\tconst multipleTestingCorrection = this.app.getState().termdbConfig.multipleTestingCorrection\n\t\t\tif (multipleTestingCorrection) {\n\t\t\t\t// a checkbox to allow users to show or hide asterisks on bars\n\t\t\t\tinputs.push({\n\t\t\t\t\tlabel: 'Asterisks',\n\t\t\t\t\tboxLabel: 'Visible',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'asterisksVisible',\n\t\t\t\t\ttitle: 'Display the asterisks'\n\t\t\t\t})\n\t\t\t\tconst mtcMethod = multipleTestingCorrection.method\n\t\t\t\tif (!mtcMethod) throw 'no multiple testing correction method specified'\n\t\t\t\tinputs.push({\n\t\t\t\t\tlabel: `Multiple testing correction (${mtcMethod == 'bon' ? 'Bonferroni' : mtcMethod})`,\n\t\t\t\t\tboxLabel: '',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'multiTestingCorr',\n\t\t\t\t\ttitle: `Perform multiple testing correction (${mtcMethod == 'bon' ? 'Bonferroni' : mtcMethod})`\n\t\t\t\t})\n\t\t\t}\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})\n\t\t\t}\n\n\t\t\tthis.components.controls.on('downloadClick.barchart', this.download)\n\t\t}\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\treturn (\n\t\t\t\t(action.id === this.id || action.id == this.parentId) &&\n\t\t\t\t(!action.config?.childType || action.config?.childType == this.type)\n\t\t\t)\n\t\t}\n\t\treturn true\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 = this.parentId && appState.plots.find(p => p.id === this.parentId)\n\t\t// TODO: may need to combine parentConfig.filter with local config.filter\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\t\treturn {\n\t\t\tnav: {\n\t\t\t\theader_mode: appState.nav.header_mode\n\t\t\t},\n\t\t\ttermfilter,\n\t\t\tconfig: Object.assign({}, config, {\n\t\t\t\tsettings: {\n\t\t\t\t\tbarchart: config.settings.barchart,\n\t\t\t\t\tcommon: config.settings.common\n\t\t\t\t},\n\t\t\t\tdisplaySampleIds: appState.termdbConfig.displaySampleIds && this.app.vocabApi.hasVerifiedToken()\n\t\t\t}),\n\t\t\tmultipleTestingCorrection: appState.termdbConfig.multipleTestingCorrection,\n\t\t\tbar_click_menu: appState.bar_click_menu || {},\n\t\t\tgroups: rebaseGroupFilter(appState)\n\t\t}\n\t}\n\n\tasync main() {\n\t\tconst c = this.state.config\n\t\tif (c.chartType != this.type && c.childType != this.type) return\n\t\ttry {\n\t\t\tthis.config = await this.getMutableConfig(c)\n\t\t\tif (!this.currServerData) this.dom.barDiv.style('max-width', window.innerWidth + 'px')\n\t\t\tthis.prevConfig = this.config || {}\n\t\t\tif (this.dom.header)\n\t\t\t\tthis.dom.header.html(\n\t\t\t\t\tthis.config.term.term.name + ` <span style=\"opacity:.6;font-size:.7em;margin-left:10px;\">BARCHART</span>`\n\t\t\t\t)\n\n\t\t\tthis.toggleLoadingDiv()\n\n\t\t\tconst reqOpts = this.getDataRequestOpts()\n\t\t\tawait this.getDescrStats()\n\t\t\tawait this.setControls() //needs to be called after getDescrStats() to set hasStats\n\t\t\tconst results = await this.app.vocabApi.getNestedChartSeriesData(reqOpts, this.api.getAbortSignal())\n\t\t\tif (results.error) throw results\n\t\t\tconst data = results.data\n\t\t\tthis.charts = data.charts\n\t\t\tthis.sampleType = results.sampleType\n\t\t\tthis.bins = results.bins\n\t\t\tif (results.chartid2dtterm) this.chartid2dtterm = results.chartid2dtterm\n\t\t\tthis.toggleLoadingDiv('none')\n\t\t\tthis.app.vocabApi.syncTermData(this.config, data, this.prevConfig)\n\t\t\tthis.currServerData = data\n\t\t\tif (this.currServerData.refs && this.currServerData.refs.q) {\n\t\t\t\tfor (const q of this.currServerData.refs.q) {\n\t\t\t\t\tif (q.error) throw q.error\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tthis.term1toColor = {}\n\t\t\tthis.term2toColor = {} // forget any assigned overlay colors when refreshing a barchart\n\t\t\tthis.updateSettings(this.config)\n\t\t\tfor (const chart of data.charts) {\n\t\t\t\tconst categoriesPerSerie = chart.serieses.map(s => s.data.length)\n\t\t\t\tconst numColors = this.config.term2 ? Math.max(...categoriesPerSerie) : chart.serieses.length\n\t\t\t\tchart.colorScale = getColors(numColors)\n\t\t\t}\n\t\t\tthis.chartsData = this.processData(this.currServerData)\n\t\t\tthis.render()\n\t\t\tthis.dom.barDiv.style('display', 'flex')\n\t\t} catch (e) {\n\t\t\tif (this.app.isAbortError(e)) return\n\t\t\tthis.toggleLoadingDiv('none')\n\t\t\tthis.dom.barDiv.style('display', 'none')\n\t\t\tthrow e\n\t\t}\n\t}\n\n\t// creates an opts object for the vocabApi.getNestedChartsData()\n\tgetDataRequestOpts() {\n\t\tconst c = this.config\n\t\tconst opts = { term: c.term, filter: this.state.termfilter.filter }\n\t\tif (this.state.termfilter.filter0) opts.filter0 = this.state.termfilter.filter0\n\t\tif (c.term2) opts.term2 = c.term2\n\t\tif (c.term0) opts.term0 = c.term0\n\t\treturn opts\n\t}\n\n\tasync getDescrStats() {\n\t\t// get descriptive statistics for numerical terms\n\t\tconst terms = [this.config.term]\n\t\tif (this.config.term2) terms.push(this.config.term2)\n\t\tif (this.config.term0) terms.push(this.config.term0)\n\n\t\tfor (const t of terms) {\n\t\t\tif (isNumericTerm(t.term)) {\n\t\t\t\tconst data = await this.app.vocabApi.getDescrStats(t, this.state.termfilter)\n\t\t\t\tif (data.error) throw data.error\n\t\t\t\tt.q.descrStats = data\n\t\t\t}\n\t\t}\n\t}\n\n\tupdateSettings(config) {\n\t\tif (!config) return\n\t\t// translate relevant config keys to barchart settings keys\n\t\tconst obj = this.state\n\t\tconst settings = {\n\t\t\tterm0: config.term0 ? config.term0.term.id : '', // convenient reference to the term id\n\t\t\tterm1: config.term.term.id, // convenient reference to the term2 id\n\t\t\tterm2: config.term2 ? config.term2.term.id : '',\n\t\t\tunit: config.settings.barchart.unit,\n\t\t\torientation: config.settings.barchart.orientation,\n\t\t\tasterisksVisible: config.settings.barchart.asterisksVisible,\n\t\t\tmultiTestingCorr: config.settings.barchart.multiTestingCorr,\n\t\t\tdefaultColor: config.settings.barchart.defaultColor,\n\t\t\tcolorBars: config.settings.barchart.colorBars,\n\t\t\tdedup: config.settings.barchart.dedup,\n\t\t\tplotLength: config.settings.barchart.plotLength,\n\t\t\t// normalize bar thickness regardless of orientation\n\t\t\tcolw: config.settings.barchart.barwidth,\n\t\t\trowh: config.settings.barchart.barwidth,\n\t\t\tcolspace: config.settings.barchart.barspace,\n\t\t\trowspace: config.settings.barchart.barspace,\n\t\t\tcolorUsing: config.settings.barchart.colorUsing,\n\t\t\tshowStats: config.settings.barchart.showStats,\n\t\t\tshowAssociationTests: config.settings.barchart.showAssociationTests\n\t\t}\n\n\t\t/* mayResetHidden() was added before to prevent showing empty chart due to automatic hiding uncomputable categories\n\t\tthis has following problems:\n\t\t1. when term1=diaggrp and term2=hrtavg, uncomputable categories from term2 can show up by default.\n\t\t2. inconsistent behavior: when term1=agedx, term2=hrtavg the uncomputable categories are hidden by default\n\n\t\tside effect of disabling this function can cause empty chart, but seems to be minor given above\n\t\t*/\n\t\t//this.mayResetHidden(this.config.term, this.config.term2, this.config.term0)\n\n\t\tthis.setExclude(this.config.term, this.config.term2)\n\t\tObject.assign(this.settings, settings, this.currServerData.refs || {}, {\n\t\t\texclude: this.settings.exclude\n\t\t})\n\n\t\tthis.settings.cols = this.settings.dedup ? this.currServerData.refs.dedupCols : this.currServerData.refs.cols\n\t\tthis.settings.numCharts = this.currServerData.charts ? this.currServerData.charts.length : 0\n\t\tif (!config.term2 && this.settings.unit == 'pct') {\n\t\t\tthis.settings.unit = 'abs'\n\t\t}\n\t}\n\n\tmayResetHidden(term, term2, term0) {\n\t\tconst combinedTermIds = (term && term.term.id) + ';;' + (term2 && term2.term.id) + ';;' + (term0 && term0.term.id)\n\t\tif (combinedTermIds === this.currCombinedTermIds) return\n\t\t// only reset hidden if terms have changed\n\t\tfor (const chart of this.currServerData.charts) {\n\t\t\tif (term.q && term.q.hiddenValues) {\n\t\t\t\tthis.mayEditHiddenValues(term, chart.serieses.length, 'term')\n\t\t\t}\n\t\t\tif (term2 && term2.q && term2.q.hiddenValues) {\n\t\t\t\tfor (const series of chart.serieses) {\n\t\t\t\t\tthis.mayEditHiddenValues(term2, series.data.length, 'term2')\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tthis.currCombinedTermIds = combinedTermIds\n\t}\n\n\tmayEditHiddenValues(term, numAvailable, termNum) {\n\t\tconst numHidden = Object.keys(term.q.hiddenValues).filter(key => term.q.hiddenValues[key]).length\n\t\tif (numHidden < numAvailable) return\n\t\t/*\n\t\t\tif all the serieses are assigned to be hidden on first render,\n\t\t\tshow the usually hidden values instead to avoid confusion\n\t\t\twith an empty plot\n\t\t*/\n\t\tfor (const key in term.q.hiddenValues) {\n\t\t\tif (!term.q.hiddenValues[key]) return\n\t\t\tdelete term.q.hiddenValues[key]\n\t\t}\n\t\t// since config.[term | term2 | term0] are copies of appState,\n\t\t// must save the changes to q.hiddenValues in the stored state\n\t\t// for consistent behavior in later app.dispatch or barchart updates\n\t\tthis.app.save({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: {\n\t\t\t\t[termNum]: term\n\t\t\t}\n\t\t})\n\t}\n\n\tsetExclude(term, term2) {\n\t\t// a non-numeric term.id is used directly as seriesId or dataId\n\t\tthis.settings.exclude.cols = Object.keys(term.q?.hiddenValues || {})\n\t\t\t.filter(id => term.q.hiddenValues[id])\n\t\t\t.map(id => {\n\t\t\t\treturn term.term.type == 'categorical'\n\t\t\t\t\t? id\n\t\t\t\t\t: this.settings.cols?.includes(id)\n\t\t\t\t\t? id\n\t\t\t\t\t: term.term.values[id]?.label\n\t\t\t\t\t? term.term.values[id].label\n\t\t\t\t\t: id\n\t\t\t})\n\n\t\tthis.settings.exclude.rows = !term2?.q?.hiddenValues\n\t\t\t? []\n\t\t\t: Object.keys(term2.q.hiddenValues)\n\t\t\t\t\t.filter(id => term2.q.hiddenValues[id])\n\t\t\t\t\t.map(id =>\n\t\t\t\t\t\tterm2.term.type == 'categorical'\n\t\t\t\t\t\t\t? id\n\t\t\t\t\t\t\t: this.settings.rows?.includes(id)\n\t\t\t\t\t\t\t? id\n\t\t\t\t\t\t\t: term2.term.values[id]?.label\n\t\t\t\t\t\t\t? term2.term.values[id].label\n\t\t\t\t\t\t\t: id\n\t\t\t\t\t)\n\t}\n\n\tprocessData(chartsData) {\n\t\tthis.seriesOrder = this.setMaxVisibleTotals(chartsData)\n\t\tif (!chartsData.charts.length) {\n\t\t\tthis.seriesOrder = []\n\t\t} else if (chartsData.refs.useColOrder) {\n\t\t\tthis.seriesOrder = this.settings.cols\n\t\t}\n\n\t\tconst rows = chartsData.refs.rows\n\n\t\tthis.barSorter = (a, b) => this.seriesOrder.indexOf(a) - this.seriesOrder.indexOf(b)\n\t\tthis.overlaySorter = chartsData.refs.useRowOrder\n\t\t\t? (a, b) => rows.indexOf(a.dataId) - rows.indexOf(b.dataId)\n\t\t\t: (a, b) =>\n\t\t\t\t\tthis.totalsByDataId[b.dataId] > this.totalsByDataId[a.dataId]\n\t\t\t\t\t\t? 1\n\t\t\t\t\t\t: this.totalsByDataId[b.dataId] < this.totalsByDataId[a.dataId]\n\t\t\t\t\t\t? -1\n\t\t\t\t\t\t: a.dataId < b.dataId\n\t\t\t\t\t\t? -1\n\t\t\t\t\t\t: 1\n\n\t\tthis.visibleCharts = chartsData.charts.filter(chart => chart.visibleSerieses.length)\n\n\t\tconst t1 = this.config.term\n\t\tconst t2 = this.config.term2\n\t\tconst chartsTests = chartsData.tests\n\n\t\t//get term1 and term2 labels\n\t\tfor (const chartId in chartsTests) {\n\t\t\tconst chartTests = chartsTests[chartId]\n\t\t\tfor (const t1c of chartTests) {\n\t\t\t\tconst t1label =\n\t\t\t\t\tt1.term.values && t1c.term1comparison in t1.term.values\n\t\t\t\t\t\t? t1.term.values[t1c.term1comparison].label\n\t\t\t\t\t\t: t1c.term1comparison\n\t\t\t\tt1c.term1Label = t1label\n\n\t\t\t\tfor (const t2t of t1c.term2tests) {\n\t\t\t\t\tconst t2label =\n\t\t\t\t\t\tt2.term.values && t2t.term2id in t2.term.values ? t2.term.values[t2t.term2id].label : t2t.term2id\n\t\t\t\t\tt2t.term2Label = t2label\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn chartsData\n\t}\n\n\tsetMaxVisibleTotals(chartsData) {\n\t\t// chartsData = this.currServerData\n\t\tthis.totalsByDataId = {}\n\t\tconst t1 = this.config.term\n\t\tconst t2 = this.config.term2\n\t\t// this will prioritize sorting series totals in the first chart,\n\t\t// then serieses in the subsequent chart that are not already in the first chart, and so on\n\t\tconst visibleTotalsByChartSeriesId = {}\n\t\tlet maxVisibleAcrossCharts = 0\n\t\tfor (const chart of chartsData.charts) {\n\t\t\tif (!chart.settings) chart.settings = JSON.parse(rendererSettings)\n\t\t\tObject.assign(chart.settings, this.settings)\n\t\t\tchart.visibleTotal = 0\n\t\t\tconst serieses = this.settings.dedup ? chart.dedupedSerieses : chart.serieses\n\t\t\tchart.visibleSerieses = serieses.filter(series => {\n\t\t\t\tif (chart.settings.exclude.cols.includes(series.seriesId)) return false\n\t\t\t\tseries.visibleData = series.data.filter(d => !chart.settings.exclude.rows.includes(d.dataId))\n\t\t\t\tseries.visibleTotal = series.visibleData.reduce((sum, a) => sum + a.total, 0)\n\t\t\t\tif (!series.visibleTotal) return false\n\t\t\t\tchart.visibleTotal += series.visibleTotal\n\t\t\t\tif (!(series.seriesId in visibleTotalsByChartSeriesId))\n\t\t\t\t\tvisibleTotalsByChartSeriesId[series.seriesId] = series.visibleTotal\n\t\t\t\tfor (const data of series.data) {\n\t\t\t\t\tdata.seriesId = series.seriesId\n\t\t\t\t\tif (\n\t\t\t\t\t\t(t1.term.type == 'geneVariant' && t1.q.type == 'values') ||\n\t\t\t\t\t\t(t2?.term.type == 'geneVariant' && t2?.q.type == 'values')\n\t\t\t\t\t) {\n\t\t\t\t\t\t// term1 or term2 is a geneVariant term not using groupsetting\n\t\t\t\t\t\t// need specialized processing\n\t\t\t\t\t\tif (!(data.dataId in this.totalsByDataId)) {\n\t\t\t\t\t\t\tthis.totalsByDataId[data.dataId] = {}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthis.totalsByDataId[data.dataId][chart.chartId] = this.totalsByDataId[data.dataId][chart.chartId]\n\t\t\t\t\t\t\t? this.totalsByDataId[data.dataId][chart.chartId] + data.total\n\t\t\t\t\t\t\t: 0 + data.total\n\t\t\t\t\t} else {\n\t\t\t\t\t\tif (!(data.dataId in this.totalsByDataId)) {\n\t\t\t\t\t\t\tthis.totalsByDataId[data.dataId] = 0\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthis.totalsByDataId[data.dataId] += data.total\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\treturn true\n\t\t\t})\n\t\t\tchart.settings.colLabels = chart.visibleSerieses.map(series => {\n\t\t\t\tconst id = series.seriesId\n\t\t\t\tconst label = t1.term.values && id in t1.term.values ? t1.term.values[id].label : id\n\t\t\t\tconst af = series && 'AF' in series ? ', AF=' + series.AF : ''\n\t\t\t\tconst ntotal =\n\t\t\t\t\tt2 && t2.term.type == 'condition' && t2.q.value_by_computable_grade ? '' : `, n=${series.visibleTotal}`\n\t\t\t\treturn {\n\t\t\t\t\tid,\n\t\t\t\t\tlabel: label + af + ntotal\n\t\t\t\t}\n\t\t\t})\n\t\t\tchart.maxVisibleSeriesTotal = chart.visibleSerieses.reduce((max, series) => {\n\t\t\t\treturn series.visibleTotal > max ? series.visibleTotal : max\n\t\t\t}, 0)\n\t\t\tif (chart.maxVisibleSeriesTotal > maxVisibleAcrossCharts) {\n\t\t\t\tmaxVisibleAcrossCharts = chart.maxVisibleSeriesTotal\n\t\t\t}\n\t\t}\n\t\tfor (const chart of chartsData.charts) {\n\t\t\tchart.maxVisibleAcrossCharts = maxVisibleAcrossCharts\n\t\t}\n\n\t\treturn Object.keys(visibleTotalsByChartSeriesId).sort(\n\t\t\t(a, b) => visibleTotalsByChartSeriesId[b] - visibleTotalsByChartSeriesId[a]\n\t\t)\n\t}\n\n\tsortStacking(series, chart, chartsData) {\n\t\tthis.term1toColor[series.seriesId] = this.settings.colorBars\n\t\t\t? this.getColor(chart, this.config.term, series.seriesId, this.bins?.[1])\n\t\t\t: this.settings.defaultColor\n\n\t\tseries.visibleData.sort(this.overlaySorter)\n\t\tlet seriesLogTotal = 0\n\t\tfor (const result of series.visibleData) {\n\t\t\tresult.colgrp = '-'\n\t\t\tresult.rowgrp = '-'\n\t\t\tresult.chartId = chart.chartId\n\t\t\tresult.seriesId = series.seriesId\n\t\t\tif (chartsData.tests) {\n\t\t\t\t// statistical tests result exist\n\t\t\t\t// put the pvalues corresponding to series.seriesId to result.groupPvalues\n\t\t\t\tresult.groupPvalues = chartsData.tests[chart.chartId].find(x => x.term1comparison === series.seriesId)\n\t\t\t}\n\t\t\tresult.seriesTotal = series.total\n\t\t\tresult.chartTotal = chart.visibleTotal\n\t\t\tresult.logTotal = Math.log10(result.total)\n\t\t\tseriesLogTotal += result.logTotal\n\t\t\tthis.setTerm2Color(chart, result)\n\t\t\tresult.color = this.term2toColor[result.dataId] || this.term1toColor[series.seriesId]\n\t\t}\n\t\tif (seriesLogTotal > chart.maxSeriesLogTotal) {\n\t\t\tchart.maxSeriesLogTotal = seriesLogTotal\n\t\t}\n\t\t// assign color to hidden data for use in legend\n\t\tfor (const result of series.data) {\n\t\t\tif (result.color) continue\n\t\t\tthis.setTerm2Color(chart, result)\n\t\t\tresult.color = this.term2toColor[result.dataId] || this.term1toColor[series.seriesId]\n\t\t}\n\t}\n\n\tsetTerm2Color(chart, result) {\n\t\tif (!this.config.term2) return\n\t\tthis.term2toColor[result.dataId] = this.getColor(chart, this.config.term2, result.dataId, this.bins?.[2])\n\t}\n\n\tgetColor(chart, t, label, bins) {\n\t\tif (!t.term) return\n\t\tif (t.q.type == 'predefined-groupset' || t.q.type == 'custom-groupset') {\n\t\t\tconst groupset =\n\t\t\t\tt.q.type == 'predefined-groupset' ? t.term.groupsetting.lst[t.q.predefined_groupset_idx] : t.q.customset\n\t\t\tif (!groupset) throw 'groupset is missing'\n\t\t\tconst group = groupset.groups.find(g => g.name == label)\n\t\t\tif (group?.color) return group.color\n\t\t}\n\t\t//use predefined colors unless colorBars is set to true.\n\t\t// Assigning colors to bars uses a better color scale as the scale considers the categories present, not in all the categories\n\t\tif (t.term.values && this.settings.colorUsing == 'all') {\n\t\t\tfor (const [key, v] of Object.entries(t.term.values)) {\n\t\t\t\tif (!v.color) continue\n\t\t\t\tif (key === label) return v.color\n\t\t\t\tif (v.label === label) return v.color\n\t\t\t}\n\t\t}\n\t\tconst bin = bins?.find(bin => bin.label == label)\n\t\tif (bin?.color) return bin.color\n\n\t\tif (t.term.type == 'geneVariant' && t.q.type == 'values') return this.getMutationColor(label)\n\t\treturn rgb(chart.colorScale(label)).toString()\n\t}\n\n\t// should move this outside of setTerm2Color(),\n\t// otherwise it will get *** recreated on every call *** to setTerm2Color()\n\tgetMutationColor(label) {\n\t\t// for (const [key, mc] of Object.entries(mclass)) if (mc.label == label) return mc.color\n\n\t\t// key is not used in loop above, can do this instead\n\t\tfor (const mc of Object.values(mclass)) if (mc.label === label && mc.color) return mc.color\n\n\t\t// can loop on the object directly\n\t\tfor (const key in mclass) {\n\t\t\tif (mclass[key].label === label && mclass[key].color) return mclass[key].color\n\t\t}\n\t}\n\n\t/*\n\t  when term1 or term2 is a geneVariant term, return legendGrps: \n\t\t[ \n\t\t\t[\n\t\t\t\t{\n\t\t\t\t\tname: \"...\", \n\t\t\t\t\titems: [...]\n\t\t\t\t},\n\t\t\t\t...\n\t\t\t],\n\t\t\t... \n\t\t]\n\t*/\n\tgetLegendGrps() {\n\t\tconst t1 = this.config.term\n\t\tconst t2 = this.config.term2\n\t\tif (\n\t\t\t(t1.term.type == 'geneVariant' && t1.q.type == 'values') ||\n\t\t\t(t2?.term.type == 'geneVariant' && t2?.q.type == 'values')\n\t\t) {\n\t\t\tconst legendGrps = []\n\t\t\tfor (const chart of this.chartsData.charts) {\n\t\t\t\tlegendGrps.push(this.getOneLegendGrps(chart))\n\t\t\t}\n\t\t\treturn legendGrps\n\t\t}\n\t\treturn this.getOneLegendGrps()\n\t}\n\n\t//Used by getLegendGrps to get one legendGrps\n\tgetOneLegendGrps(chart) {\n\t\tconst legendGrps = []\n\t\tconst s = this.settings\n\t\tconst t1 = this.config.term\n\t\tconst t2 = this.config.term2\n\t\tconst headingStyle = 'color: #aaa; font-weight: 400'\n\n\t\t// descriptive statistics\n\t\tif (t1.q.descrStats && s.showStats) {\n\t\t\t// term1 has descriptive stats\n\t\t\tconst items = Object.values(t1.q.descrStats).map(stat => {\n\t\t\t\treturn {\n\t\t\t\t\ttext: `${stat.label}: ${stat.value}`,\n\t\t\t\t\tnoIcon: true\n\t\t\t\t}\n\t\t\t})\n\t\t\t// title of descriptive stats should include the term1 name if term2 is present\n\t\t\tconst title = t2 ? `Descriptive statistics: ${t1.term.name}` : 'Descriptive statistics'\n\t\t\tconst name = `<span style=\"${headingStyle}\">${title}</span>`\n\t\t\tlegendGrps.push({ name, items })\n\t\t}\n\t\tif (t2?.q.descrStats && s.showAssociationTests) {\n\t\t\t// term2 has descriptive stats\n\t\t\tconst items = Object.values(t2.q.descrStats).map(stat => {\n\t\t\t\treturn {\n\t\t\t\t\ttext: `${stat.label}: ${stat.value}`,\n\t\t\t\t\tnoIcon: true\n\t\t\t\t}\n\t\t\t})\n\t\t\t// title of descriptive stats will include the term2 name\n\t\t\t// because two terms are present\n\t\t\tconst title = `Descriptive statistics: ${t2.term.name}`\n\t\t\tconst name = `<span style=\"${headingStyle}\">${title}</span>`\n\t\t\tlegendGrps.push({ name, items })\n\t\t}\n\n\t\tif (s.cols && s.exclude.cols.length) {\n\t\t\tconst reducer = (sum, b) => sum + b.total\n\t\t\tconst items = s.exclude.cols\n\t\t\t\t.filter(collabel => s.cols.includes(collabel)) // && (!t1.term.values || collabel in t1.term.values))\n\t\t\t\t.flatMap(collabel => {\n\t\t\t\t\tconst filter = c => c.seriesId == collabel\n\t\t\t\t\tconst total =\n\t\t\t\t\t\tt2?.term?.type == 'condition'\n\t\t\t\t\t\t\t? 0\n\t\t\t\t\t\t\t: (t1.term.type == 'geneVariant' && t1.q.type == 'values') ||\n\t\t\t\t\t\t\t  (t2?.term.type == 'geneVariant' && t2?.q.type == 'values')\n\t\t\t\t\t\t\t? chart.serieses.filter(filter).reduce(reducer, 0)\n\t\t\t\t\t\t\t: this.currServerData.charts.reduce((sum, chart) => {\n\t\t\t\t\t\t\t\t\treturn sum + chart.serieses.filter(filter).reduce(reducer, 0)\n\t\t\t\t\t\t\t  }, 0)\n\t\t\t\t\tif (!total && !t2?.term?.type) return []\n\t\t\t\t\tconst label = t1.term.values && collabel in t1.term.values ? t1.term.values[collabel].label : collabel\n\t\t\t\t\tconst ntotal = total ? ', n=' + total : ''\n\t\t\t\t\treturn [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tid: collabel,\n\t\t\t\t\t\t\ttext: label + ntotal,\n\t\t\t\t\t\t\tcolor: '#fff',\n\t\t\t\t\t\t\ttextColor: '#000',\n\t\t\t\t\t\t\tborder: '1px solid #333',\n\t\t\t\t\t\t\t//inset: total ? \"n=\"+total : '',\n\t\t\t\t\t\t\tnoIcon: true,\n\t\t\t\t\t\t\ttype: 'col',\n\t\t\t\t\t\t\tisHidden: true,\n\t\t\t\t\t\t\thiddenOpacity: 1\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t\t.sort(this.barSorter)\n\n\t\t\tif (items.length) {\n\t\t\t\tconst name = t2 ? t1.term.name : 'Other categories'\n\t\t\t\tlegendGrps.push({\n\t\t\t\t\tname: `<span style=\"${headingStyle}\">${name}</span>`,\n\t\t\t\t\titems\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (s.rows /*&& s.rows.length > 1*/ && !s.hidelegend && t2 && this.term2toColor) {\n\t\t\tconst value_by_label =\n\t\t\t\tt2.term.type != 'condition' || !t2.q\n\t\t\t\t\t? ''\n\t\t\t\t\t: t2.q.value_by_max_grade\n\t\t\t\t\t? 'max. grade'\n\t\t\t\t\t: t2.q.value_by_most_recent\n\t\t\t\t\t? 'most recent'\n\t\t\t\t\t: ''\n\t\t\tlegendGrps.push({\n\t\t\t\tname:\n\t\t\t\t\t`<span style=\"${headingStyle}\">` +\n\t\t\t\t\t(t2.term.type == 'geneVariant' ? '' : t2.term.name) +\n\t\t\t\t\t(value_by_label ? ', ' + value_by_label : '') +\n\t\t\t\t\t'</span>',\n\t\t\t\titems: s.rows\n\t\t\t\t\t.flatMap(d => {\n\t\t\t\t\t\tconst total = chart ? this.totalsByDataId[d]?.[chart.chartId] : this.totalsByDataId[d]\n\t\t\t\t\t\tif (!total) return []\n\t\t\t\t\t\tconst ntotal = total ? ', n=' + total : ''\n\t\t\t\t\t\tconst label = t2.term.values && d in t2.term.values ? t2.term.values[d].label : d\n\t\t\t\t\t\treturn [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tdataId: d,\n\t\t\t\t\t\t\t\ttext: label + ntotal,\n\t\t\t\t\t\t\t\tcolor: this.term2toColor[d],\n\t\t\t\t\t\t\t\ttype: 'row',\n\t\t\t\t\t\t\t\tisHidden: s.exclude.rows.includes(d)\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\t.sort(this.overlaySorter)\n\t\t\t})\n\t\t}\n\t\tif (t2 && this.state.multipleTestingCorrection) {\n\t\t\t// the dataset requires multiple testing correction and therefore needs to show this legend of Statistical Significance\n\t\t\t// calculate total number of unskipped tests\n\t\t\tlet testNum = 0\n\t\t\tfor (const chartId in this.chartsData.tests) {\n\t\t\t\ttestNum += this.chartsData.tests[chartId].reduce((a, b) => a + b.term2tests.filter(a => !a.skipped).length, 0)\n\t\t\t}\n\t\t\tconst items =\n\t\t\t\ttestNum > 1 && this.state.config.settings.barchart.multiTestingCorr\n\t\t\t\t\t? [{ text: `* p-value < (0.05 / ${testNum} tests)`, noEditColor: true }]\n\t\t\t\t\t: [{ text: `* p-value < 0.05`, noEditColor: true }]\n\t\t\tlegendGrps.push({\n\t\t\t\tname: `<span style=\"${headingStyle}\">&nbsp;</span>`,\n\t\t\t\titems\n\t\t\t})\n\t\t}\n\n\t\treturn legendGrps\n\t}\n\n\t// helper so that 'Loading...' does not flash when not needed\n\ttoggleLoadingDiv(display = '') {\n\t\tif (display != 'none') {\n\t\t\tthis.dom.loadingDiv\n\t\t\t\t.style('opacity', 0)\n\t\t\t\t.style('display', display)\n\t\t\t\t.transition()\n\t\t\t\t.duration('loadingWait' in this ? this.loadingWait : 0)\n\t\t\t\t.style('opacity', 1)\n\t\t} else {\n\t\t\tthis.dom.loadingDiv.style('display', display)\n\t\t}\n\t\t// do not transition on initial chart load\n\t\tthis.loadingWait = 1000\n\t}\n}\n\nexport const barInit = getCompInit(Barchart)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = barInit\n\nfunction setRenderers(self) {\n\tself.render = function () {\n\t\tconst charts = self.dom.barDiv.selectAll('.pp-sbar-div').data(self.visibleCharts, chart => chart.chartId)\n\n\t\tcharts.exit().each(self.exitChart)\n\t\tcharts.each(self.updateChart)\n\t\tcharts.enter().append('div').each(self.addChart)\n\n\t\tself.dom.holder.selectAll('.pp-chart-title').style('display', self.visibleCharts.length < 2 ? 'none' : 'block')\n\t\tconst grps = self.getLegendGrps()\n\t\tself.legendRenderer(grps)\n\n\t\tif (!self.visibleCharts.length) {\n\t\t\tconst clickLegendMessage =\n\t\t\t\tself.settings.exclude.cols.length || self.settings.exclude.rows.length\n\t\t\t\t\t? `<br/><span>click on a legend label below to display the barchart</span>`\n\t\t\t\t\t: ''\n\t\t\tself.dom.banner\n\t\t\t\t.html(`<span>No visible barchart data to render</span>${clickLegendMessage}`)\n\t\t\t\t.style('display', 'block')\n\t\t\tself.dom.legendDiv.selectAll('*').remove()\n\t\t} else {\n\t\t\tself.dom.banner.text('').style('display', 'none')\n\t\t}\n\t}\n\n\tself.exitChart = function (chart) {\n\t\tdelete self.renderers[chart.chartId]\n\t\tselect(this).remove()\n\t}\n\n\tself.updateChart = function (chart) {\n\t\t// this.dom.legendDiv.remove(\"*\")\n\t\tchart.settings.cols.sort(self.barSorter)\n\t\tchart.maxAcrossCharts = self.chartsData.maxAcrossCharts\n\t\tchart.handlers = self.handlers\n\t\tchart.maxSeriesLogTotal = 0\n\t\tchart.visibleSerieses.forEach(series => self.sortStacking(series, chart, self.chartsData))\n\t\tself.renderers[chart.chartId] = barsRenderer(self, select(this)) //rerender as settings may have changed\n\t\tself.renderers[chart.chartId](chart)\n\n\t\tconst div = select(this)\n\t\tdiv.style('display', 'inline-block')\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'pp-sbar-div-chartLengends')\n\t\t\t.attr('data-testid', 'sjpcb-bars-chartLengends')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('margin', '10px 10px 10px 30px')\n\t\t\t.style('display', 'none')\n\t\tif (\n\t\t\tself.chartsData.tests &&\n\t\t\tself.chartsData.tests[chart.chartId] &&\n\t\t\tself.config.settings.barchart.showAssociationTests\n\t\t) {\n\t\t\t//chart has pvalues\n\t\t\tgeneratePvalueTable(chart, div)\n\t\t}\n\t}\n\n\tself.addChart = function (chart, i) {\n\t\tconst div = select(this)\n\t\t\t.attr('class', 'pp-sbar-div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', '20px')\n\t\t\t.style('vertical-align', 'top')\n\t\tself.renderers[chart.chartId] = barsRenderer(self, select(this))\n\t\t//self.updateChart.call(this, chart)\n\t\tchart.settings.cols.sort(self.barSorter)\n\t\tchart.maxAcrossCharts = self.chartsData.maxAcrossCharts\n\t\tchart.handlers = self.handlers\n\t\tchart.maxSeriesLogTotal = 0\n\t\tchart.visibleSerieses.forEach(series => self.sortStacking(series, chart, self.chartsData))\n\t\tself.renderers[chart.chartId](chart)\n\n\t\t// div for chart-specific legends\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'pp-sbar-div-chartLengends')\n\t\t\t.attr('data-testid', 'sjpcb-bars-chartLengends')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('margin', '10px 10px 10px 30px')\n\t\t\t.style('display', 'none')\n\t\tif (\n\t\t\tself.chartsData.tests &&\n\t\t\tself.chartsData.tests[chart.chartId] &&\n\t\t\tself.config.settings.barchart.showAssociationTests\n\t\t) {\n\t\t\t//chart has pvalues\n\t\t\tgeneratePvalueTable(chart, div)\n\t\t}\n\t}\n\n\t/*\n\tA function to generate a p-value table for Chi-squared/Fisher's exact tests\n\t*/\n\tfunction generatePvalueTable(chart, div) {\n\t\tconst holder = div\n\t\t\t.select('.pp-sbar-div-chartLengends')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('text-align', 'center')\n\t\t\t.append('div')\n\t\t// sort term1 categories based on self.chartsData.refs.cols\n\t\t// const cols = self.settings.dedup ?  self.chartsData.refs.cols\n\t\tself.chartsData.tests[chart.chartId].sort(function (a, b) {\n\t\t\treturn self.settings.cols.indexOf(a.term1comparison) - self.settings.cols.indexOf(b.term1comparison)\n\t\t})\n\n\t\t// sort term2 categories based on self.chartsData.refs.rows\n\t\tfor (const t1c of self.chartsData.tests[chart.chartId]) {\n\t\t\tt1c.term2tests.sort(function (a, b) {\n\t\t\t\treturn self.chartsData.refs.rows.indexOf(a.term2id) - self.chartsData.refs.rows.indexOf(b.term2id)\n\t\t\t})\n\t\t}\n\t\tconst columns = [\n\t\t\t{ label: 'Row 1' },\n\t\t\t{ label: 'Row 2' },\n\t\t\t{ label: 'Column 1' },\n\t\t\t{ label: 'Column 2' },\n\t\t\t{ label: 'P-value' }\n\t\t]\n\t\tconst noSkipped = self.chartsData.tests[chart.chartId].every(term1 =>\n\t\t\tterm1.term2tests.every(term2 => !term2.skipped)\n\t\t)\n\t\tconst rows = []\n\n\t\tconst visibleTests = self.chartsData.tests[chart.chartId].filter(term1Data =>\n\t\t\tchart.visibleSerieses.some(visibleTerm1 => visibleTerm1.seriesId === term1Data.term1comparison)\n\t\t)\n\t\tfor (const [index, term1] of visibleTests.entries()) {\n\t\t\tif (visibleTests.length == 2 && index == 1) {\n\t\t\t\t// when term1 has only 2 categories, then only a single category needs to be tested in the\n\t\t\t\t// association test (because the other category will get tested in that same test).\n\t\t\t\tbreak\n\t\t\t}\n\t\t\tconst visibleTerm1Data = chart.visibleSerieses.find(\n\t\t\t\tvisibleTerm1 => visibleTerm1.seriesId === term1.term1comparison\n\t\t\t)\n\t\t\tconst visibleTerm2Data = term1.term2tests.filter(term2Data =>\n\t\t\t\tvisibleTerm1Data.visibleData.some(visibleTerm2 => visibleTerm2.dataId === term2Data.term2id)\n\t\t\t)\n\t\t\tfor (const [index2, term2] of visibleTerm2Data.entries()) {\n\t\t\t\tif (chart.settings.rows.length - chart.settings.exclude.rows.length == 2 && index2 == 1) {\n\t\t\t\t\t// when term2 has only 2 visible categories, then only a single category needs to be tested in the\n\t\t\t\t\t// association test (because the other category will get tested in that same test).\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tlet negateTerm2Label = negateTermLabel(term2.term2Label)\n\t\t\t\tif (chart.settings.rows.length - chart.settings.exclude.rows.length == 2) {\n\t\t\t\t\t// when term2 has only 2 visible categories, Col2 would be the other category instead of \"not Col1\"\n\t\t\t\t\tconst visibleTerm2CatsKeys = chart.settings.rows.filter(row => !chart.settings.exclude.rows.includes(row))\n\t\t\t\t\tconst visibleTerm2Labels = visibleTerm2CatsKeys\n\t\t\t\t\t\t.map(catK => self.config.term2?.term?.values?.[catK]?.label)\n\t\t\t\t\t\t.filter(x => x != undefined)\n\t\t\t\t\tif (visibleTerm2Labels?.length == 2)\n\t\t\t\t\t\tnegateTerm2Label = visibleTerm2Labels[0] == term2.term2Label ? visibleTerm2Labels[1] : visibleTerm2Labels[0]\n\t\t\t\t}\n\n\t\t\t\trows.push([\n\t\t\t\t\t{ value: `${term1.term1Label}` },\n\t\t\t\t\t// when term1 has only 2 categories, Row2 would be the other category instead of \"not Row1\"\n\t\t\t\t\t{ value: visibleTests.length == 2 ? visibleTests[1].term1Label : negateTermLabel(term1.term1Label) },\n\t\t\t\t\t{ value: term2.term2Label },\n\t\t\t\t\t{ value: negateTerm2Label },\n\t\t\t\t\t//if both chi-square and Fisher's exact tests were used. for the tests computed by Fisher's exact test, add a superscript letter 'a' after the pvalue.\n\t\t\t\t\t{\n\t\t\t\t\t\thtml: term2.skipped\n\t\t\t\t\t\t\t? 'N/A'\n\t\t\t\t\t\t\t: term2.pvalue > 1e-4\n\t\t\t\t\t\t\t? roundValueAuto(Number(term2.pvalue))\n\t\t\t\t\t\t\t: roundValueAuto(Number(term2.pvalue))\n\t\t\t\t\t}\n\t\t\t\t])\n\t\t\t}\n\t\t}\n\t\t//adding a title for the pvalue table\n\t\t//title is \"Group comparisons (Fisher's exact test)\" if all tests are Fisher's exact test, otherwise title is 'Group comparisons (Chi-square test)'\n\t\tconst title = holder\n\t\t\t.append('div')\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.style('padding-bottom', '0.5em')\n\t\t\t.html(\"2x2 Association test (Fisher's exact test)\")\n\t\t\t.style('font-size', '0.9em')\n\n\t\tconst table = holder.append('div').style('font-size', '0.9em')\n\t\trenderTable({\n\t\t\tcolumns,\n\t\t\trows,\n\t\t\tdiv: table,\n\t\t\tshowLines: false,\n\t\t\tmaxWidth: '70vw',\n\t\t\tmaxHeight: `${chart.svgh - 100}px`,\n\t\t\tresize: true\n\t\t})\n\n\t\t//footnote: superscript letter 'a' indicates the pvalue was computed by Fisher's exact test\n\t\ttable\n\t\t\t.append('div')\n\t\t\t.style('margin-top', '10px')\n\t\t\t.style('text-align', 'left')\n\t\t\t.style('font-size', '10px')\n\t\t\t.style('font-weight', 'normal')\n\t\t\t.html(noSkipped ? '' : 'N/A: association test skipped because of limited sample size <br>')\n\t}\n}\n\nfunction setInteractivity(self) {\n\tself.handlers = getHandlers(self)\n\n\tself.getChartImages = function () {\n\t\tconst charts = []\n\n\t\tfor (const chart of self.charts) {\n\t\t\tconst name = `${this.config.term.term.name}  ${chart.name ? chart.name : ''}`\n\t\t\tcharts.push({ name, svg: chart.svg })\n\t\t}\n\t\treturn charts\n\t}\n\n\tself.download = function (event) {\n\t\tconst charts = self.getChartImages()\n\t\tconst dm = new DownloadMenu(charts, self.config.term.term.name)\n\t\tdm.show(event.clientX, event.clientY)\n\t}\n\n\t/** Downloads all charts as a single svg image, including the legend for each barchart, needs review as it\n\t * has some glitches. The legend rendering may be moved to the same svg and then it will be included in the download or a callback may be provided\n\t * to the downloadMenu to use this download when generating a single svg, once it works well\n\t */\n\t// self.download = function () {\n\t// \tif (!self.state) return\n\t// \t// has to be able to handle multichart view\n\t// \tconst mainGs = []\n\t// \tconst translate = { x: undefined, y: undefined }\n\t// \tconst titles = []\n\t// \tlet maxw = 0,\n\t// \t\tmaxh = 0,\n\t// \t\ttboxh = 0\n\t// \tlet prevY = 0,\n\t// \t\tnumChartsPerRow = 0\n\n\t// \tself.dom.barDiv.selectAll('.sjpcb-bars-mainG').each(function () {\n\t// \t\tmainGs.push(this)\n\t// \t\tconst bbox = this.getBBox()\n\t// \t\tif (bbox.width > maxw) maxw = bbox.width\n\t// \t\tif (bbox.height > maxh) maxh = bbox.height\n\t// \t\tconst divY = Math.round(this.parentNode.parentNode.getBoundingClientRect().y)\n\t// \t\tif (!numChartsPerRow) {\n\t// \t\t\tprevY = divY\n\t// \t\t\tnumChartsPerRow++\n\t// \t\t} else if (Math.abs(divY - prevY) < 5) {\n\t// \t\t\tnumChartsPerRow++\n\t// \t\t}\n\t// \t\tconst xy = select(this)\n\t// \t\t\t.attr('transform')\n\t// \t\t\t.split('translate(')[1]\n\t// \t\t\t.split(')')[0]\n\t// \t\t\t.split(',')\n\t// \t\t\t.map(d => +d.trim())\n\t// \t\tif (translate.x === undefined || xy[0] > translate.x) translate.x = +xy[0]\n\t// \t\tif (translate.y === undefined || xy[1] > translate.y) translate.y = +xy[1]\n\n\t// \t\tconst title = this.parentNode.parentNode.firstChild\n\t// \t\tconst tbox = title.getBoundingClientRect()\n\t// \t\tif (tbox.width > maxw) maxw = tbox.width\n\t// \t\tif (tbox.height > tboxh) tboxh = tbox.height\n\t// \t\ttitles.push({ text: title.innerText, styles: window.getComputedStyle(title) })\n\t// \t})\n\n\t// \t// add padding between charts\n\t// \tmaxw += 30\n\t// \tmaxh += 30\n\n\t// \tconst svg = document.createElementNS('http://www.w3.org/2000/svg', 'svg')\n\n\t// \tconst svgSel = select(svg)\n\t// \t\t.style('display', 'block')\n\t// \t\t.style('opacity', 1)\n\t// \t\t.attr('width', numChartsPerRow * maxw)\n\t// \t\t.attr('height', Math.floor(mainGs.length / numChartsPerRow) * maxh)\n\n\t// \tconst svgStyles = window.getComputedStyle(document.querySelector('.pp-bars-svg'))\n\t// \tfor (const prop of svgStyles) {\n\t// \t\tif (prop.startsWith('font')) svgSel.style(prop, svgStyles.getPropertyValue(prop))\n\t// \t}\n\n\t// \tmainGs.forEach((g, i) => {\n\t// \t\tconst mainG = g.cloneNode(true)\n\t// \t\tconst colNum = i % numChartsPerRow\n\t// \t\tconst rowNum = Math.floor(i / numChartsPerRow)\n\t// \t\tconst corner = { x: colNum * maxw + translate.x, y: rowNum * maxh + translate.y }\n\t// \t\tconst title = select(svg)\n\t// \t\t\t.append('text')\n\t// \t\t\t.attr('transform', 'translate(' + corner.x + ',' + corner.y + ')')\n\t// \t\t\t.text(titles[i].text)\n\t// \t\tfor (const prop of titles[i].styles) {\n\t// \t\t\tif (prop.startsWith('font')) title.style(prop, titles[i].styles.getPropertyValue(prop))\n\t// \t\t}\n\n\t// \t\tselect(mainG).attr('transform', 'translate(' + corner.x + ',' + (corner.y + tboxh) + ')')\n\t// \t\tsvg.appendChild(mainG)\n\t// \t})\n\n\t// \t// svg + legend must be attached to DOM in order for getBBox() to work within svgLegendRenderer\n\t// \tconst hiddenDiv = select('body').append('div').style('opacity', 0)\n\t// \thiddenDiv.node().appendChild(svg)\n\n\t// \tself.svgLegendRenderer = svgLegend({\n\t// \t\tholder: svgSel.append('g'),\n\t// \t\trectFillFxn: d => d.color,\n\t// \t\ticonStroke: '#aaa'\n\t// \t})\n\n\t// \tconst s = self.settings\n\t// \tconst svg0 = self.dom.barDiv.select('svg').node().getBoundingClientRect()\n\t// \tlet data = self.getLegendGrps()\n\t// \tdata.forEach(d => {\n\t// \t\td.name = d.name.replace(/<[^>]*>?/gm, '')\n\t// \t\tif (d.items) d.items = d.items.filter(c => !c.isHidden)\n\t// \t})\n\t// \tdata = data.filter(d => d.items.length && !d.name.includes('tatistic'))\n\t// \tconst fontsize = 14\n\t// \tself.svgLegendRenderer(data, {\n\t// \t\tsettings: Object.assign(\n\t// \t\t\t{\n\t// \t\t\t\tontop: false,\n\t// \t\t\t\tlineh: 25,\n\t// \t\t\t\tpadx: 5,\n\t// \t\t\t\tpadleft: 0, //150,\n\t// \t\t\t\tpadright: 20,\n\t// \t\t\t\tpadbtm: 30,\n\t// \t\t\t\tfontsize,\n\t// \t\t\t\ticonh: fontsize - 2,\n\t// \t\t\t\ticonw: fontsize - 2,\n\t// \t\t\t\thangleft: 1,\n\t// \t\t\t\tlinesep: false\n\t// \t\t\t},\n\t// \t\t\t{\n\t// \t\t\t\tsvgw: self.visibleCharts.length * svg0.width,\n\t// \t\t\t\tsvgh: svg0.height,\n\t// \t\t\t\tdimensions: {\n\t// \t\t\t\t\txOffset: 50\n\t// \t\t\t\t},\n\t// \t\t\t\tpadleft: 50\n\t// \t\t\t}\n\t// \t\t)\n\t// \t})\n\n\t// \tconst box = self.dom.legendDiv.node().getBoundingClientRect()\n\t// \tselect(svg).attr('height', svg0.height + box.height + 30)\n\t// \tif (box.width > svg0.width) select(svg).attr('width', box.width)\n\t// \thiddenDiv.remove()\n\n\t// \tconst svg_name = self.config.term.term.name + ' barchart'\n\t// \tto_svg(svg, svg_name, { apply_dom_styles: true })\n\t// }\n}\n\nexport function getDefaultBarSettings(app) {\n\treturn {\n\t\tbarspace: 2,\n\t\tbarwidth: 20,\n\t\tplotLength,\n\t\torientation: 'horizontal',\n\t\tunit: 'abs',\n\t\toverlay: 'none',\n\t\tdivideBy: 'none',\n\t\trowlabelw: 250,\n\t\tasterisksVisible: app?.getState()?.termdbConfig?.multipleTestingCorrection ? true : false,\n\t\tmultiTestingCorr: app?.getState()?.termdbConfig?.multipleTestingCorrection?.applyByDefault ? true : false,\n\t\tdefaultColor: plotColor,\n\t\tcolorBars: false,\n\t\tcolorUsing: 'all',\n\t\tdedup: false,\n\t\tshowStats: true,\n\t\tshowAssociationTests: true,\n\t\tshowPercent: false\n\t}\n}\n\nexport async function getPlotConfig(opts, app) {\n\tif (!opts.term) throw 'barchart getPlotConfig: opts.term{} missing'\n\ttry {\n\t\topts.tw = await fillTermWrapper(opts.term, app.vocabApi)\n\t\tif (opts.term2) opts.term2 = await fillTermWrapper(opts.term2, app.vocabApi)\n\t\tif (opts.term0) opts.term0 = await fillTermWrapper(opts.term0, app.vocabApi)\n\t} catch (e) {\n\t\tconsole.log('Error reading config: ' + JSON.stringify(opts))\n\t\tconsole.error(e)\n\t\tthrow `${e} [barchart getPlotConfig()]`\n\t}\n\n\tconst config = {\n\t\tid: opts.term.term.id,\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\tcommon: {\n\t\t\t\tuse_logscale: false, // flag for y-axis scale type, 0=linear, 1=log\n\t\t\t\tuse_percentage: false\n\t\t\t\t// Moved to barchart settings\n\t\t\t\t// barheight: 300, // maximum bar length\n\t\t\t\t// barwidth: 20, // bar thickness\n\t\t\t\t// barspace: 2 // space between two bars\n\t\t\t},\n\t\t\tbarchart: getDefaultBarSettings(app)\n\t\t}\n\t}\n\n\t// may apply term-specific changes to the default object\n\treturn copyMerge(config, opts)\n}\n\n// a function used by generatePvalueTable to negate a term label\n// TODO: add more conditions for better negation than \"not termLable\"\nexport function negateTermLabel(termLabel) {\n\tconst termLabelStr = String(termLabel)\n\tif (termLabelStr.toUpperCase().startsWith('NOT ')) {\n\t\treturn termLabelStr.substring(4) // Remove the \"not\" prefix\n\t} else {\n\t\treturn 'not ' + termLabelStr // Otherwise, add \"not\" prefix\n\t}\n}\n", "import { Menu, renderTable } from '#dom'\nimport { dofetch3 } from '../common/dofetch'\nimport { mclass, dt2label } from '#shared/common.js'\nimport { newpane, export_data } from '../src/client'\nimport { filterJoin, getFilterItemByTag, getNormalRoot, findItemByTermId, normalizeProps } from '#filter'\nimport { rgb } from 'd3-color'\nimport { create } from 'd3-selection'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport { isNumericTerm } from '#shared/terms.js'\nimport { negateTermLabel } from './barchart'\nimport { getSamplelstFilter, getSamplelstTW, getFilter, addNewGroup } from '../mass/groups.js'\n\nexport default function getHandlers(self) {\n\tconst tip = new Menu({ padding: '5px' })\n\tself.dom.tip = tip\n\tconst s = self.settings\n\n\treturn {\n\t\tchart: {\n\t\t\ttitle(chart) {\n\t\t\t\tif (!self.config.term0) return chart.chartId\n\t\t\t\treturn self.config.term0.term.values && chart.chartId in self.config.term0.term.values\n\t\t\t\t\t? self.config.term0.term.values[chart.chartId].label\n\t\t\t\t\t: chart.chartId\n\t\t\t}\n\t\t},\n\t\tsvg: {\n\t\t\tmouseout: () => {\n\t\t\t\ttip.hide()\n\t\t\t}\n\t\t},\n\t\tseries: {\n\t\t\tmouseover(event, d) {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\tlet percent = self.config.term2 ? (d.total / d.seriesTotal) * 100 : (d.seriesTotal / d.chartTotal) * 100\n\t\t\t\tpercent = percent.toFixed(1)\n\t\t\t\tconst t1 = self.config.term.term\n\t\t\t\tconst t2 = self.config.term2 && self.config.term2.term\n\t\t\t\tconst term1unit = t1.unit\n\t\t\t\tconst seriesLabel =\n\t\t\t\t\t(t1.values && d.seriesId in t1.values ? t1.values[d.seriesId].label : d.seriesId) +\n\t\t\t\t\t(t1.unit ? ' ' + t1.unit : '')\n\t\t\t\tconst dataLabel =\n\t\t\t\t\t(t2 && t2.values && d.dataId in t2.values ? t2.values[d.dataId].label : d.dataId) +\n\t\t\t\t\t(t2 && t2.unit ? ' ' + t2.unit : '')\n\t\t\t\tconst icon = !t2\n\t\t\t\t\t? ''\n\t\t\t\t\t: \"<div style='display:inline-block; width:14px; height:14px; margin: 2px 3px; vertical-align:top; background:\" +\n\t\t\t\t\t  d.color +\n\t\t\t\t\t  \"'>&nbsp;</div>\"\n\t\t\t\tconst rows = [`<tr><td colspan=2 style='padding:3px; text-align:center'>${seriesLabel}</td></tr>`]\n\t\t\t\tif (t2) {\n\t\t\t\t\trows.push(\n\t\t\t\t\t\t`<tr><td colspan=2 style='padding:3px; text-align:center'>${icon} <span>${dataLabel}</span></td></tr>`\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\trows.push(\n\t\t\t\t\t`<tr><td style='padding:3px; color:#aaa'>#Individuals</td><td style='padding:3px; text-align:center'>${d.total}</td></tr>`,\n\t\t\t\t\t`<tr><td style='padding:3px; color:#aaa'>percent</td><td style='padding:3px; text-align:center'>${percent}%</td></tr>`\n\t\t\t\t)\n\n\t\t\t\t//mouse-over p-value and 2x2 table\n\t\t\t\tif (t2) {\n\t\t\t\t\tconst pvalue = d.groupPvalues?.term2tests?.find(x => x.term2id === d.dataId).pvalue\n\t\t\t\t\tconst term1Label = d.groupPvalues.term1Label\n\t\t\t\t\tconst term2Label = d.groupPvalues.term2tests.find(x => x.term2id === d.dataId).term2Label\n\t\t\t\t\tconst tableValues = d.groupPvalues.term2tests.find(x => x.term2id === d.dataId).tableValues\n\t\t\t\t\tconst skipped = d.groupPvalues.term2tests.find(x => x.term2id === d.dataId).skipped\n\n\t\t\t\t\t// when term1 has only 2 categories, Row2 would be the other category instead of \"not Row1\"\n\t\t\t\t\tconst negateTerm1Label = !(\n\t\t\t\t\t\tself.settings.cols.length - self.settings.exclude.cols.length == 2 &&\n\t\t\t\t\t\tself.chartsData.tests[d.chartId].length == 2\n\t\t\t\t\t)\n\t\t\t\t\t\t? negateTermLabel(term1Label)\n\t\t\t\t\t\t: self.chartsData.tests[d.chartId][0].term1Label == term1Label\n\t\t\t\t\t\t? self.chartsData.tests[d.chartId][1].term1Label\n\t\t\t\t\t\t: self.chartsData.tests[d.chartId][0].term1Label\n\n\t\t\t\t\tlet negateTerm2Label = negateTermLabel(term2Label)\n\t\t\t\t\tif (self.settings.rows.length - self.settings.exclude.rows.length == 2) {\n\t\t\t\t\t\t// when term2 has only 2 visible categories, Col2 would be the other category instead of \"not Col1\"\n\t\t\t\t\t\tconst visibleTerm2CatsKeys = self.settings.rows.filter(row => !self.settings.exclude.rows.includes(row))\n\t\t\t\t\t\tconst visibleTerm2Labels = visibleTerm2CatsKeys\n\t\t\t\t\t\t\t.map(catK => self.config.term2?.term?.values?.[catK]?.label)\n\t\t\t\t\t\t\t.filter(x => x != undefined)\n\t\t\t\t\t\tif (visibleTerm2Labels?.length == 2)\n\t\t\t\t\t\t\tnegateTerm2Label = visibleTerm2Labels[0] == term2Label ? visibleTerm2Labels[1] : visibleTerm2Labels[0]\n\t\t\t\t\t}\n\n\t\t\t\t\t//Only show the p-value and 2x2 table in tooltip\n\t\t\t\t\t//when the user enabled association tests\n\t\t\t\t\t//from control panel\n\t\t\t\t\tif (self.settings.showAssociationTests) {\n\t\t\t\t\t\trows.push(\n\t\t\t\t\t\t\t`<tr>\n\t\t\t\t\t\t\t<td style='padding:3px; color:#aaa'>p-value</td>\n\t\t\t\t\t\t\t<td style='padding:3px; text-align:center'>${\n\t\t\t\t\t\t\t\tskipped ? 'N/A' : pvalue > 1e-4 ? Number(pvalue.toFixed(4)) : roundValueAuto(Number(pvalue))\n\t\t\t\t\t\t\t}</td>\n\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t<table style=\"margin: 5px; text-align:left; font-size: 0.8em; border-spacing: 5px; border-collapse: separate;\"\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td style='color:#aaa'></td>\n\t\t\t\t\t\t\t\t<td style='color:#aaa'>${term2Label}</td>\n\t\t\t\t\t\t\t\t<td style='color:#aaa'>${negateTerm2Label}</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td style='color:#aaa'>${term1Label}</td>\n\t\t\t\t\t\t\t\t<td>${tableValues.R1C1}</td>\n\t\t\t\t\t\t\t\t<td>${tableValues.R1C2}</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td style='color:#aaa'>${negateTerm1Label}</td>\n\t\t\t\t\t\t\t\t<td>${tableValues.R2C1}</td>\n\t\t\t\t\t\t\t\t<td>${tableValues.R2C2}</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t</table>`\n\t\t\t\t\t\t)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (!t1.type == 'condition' && (!t2 || !t2.type == 'condition')) {\n\t\t\t\t\trows.push(\n\t\t\t\t\t\t`<tr><td style='padding:3px; color:#aaa'>Percentage</td><td style='padding:3px; text-align:center'>${(\n\t\t\t\t\t\t\t(100 * d.total) /\n\t\t\t\t\t\t\t(t2 ? d.seriesTotal : d.chartTotal)\n\t\t\t\t\t\t).toFixed(1)}%</td></tr>`\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\ttip.show(event.clientX, event.clientY).d.html(`<table class='sja_simpletable'>${rows.join('\\n')}</table>`)\n\t\t\t},\n\t\t\tmouseout: () => {\n\t\t\t\ttip.hide()\n\t\t\t},\n\t\t\trectFill(d) {\n\t\t\t\treturn d.color\n\t\t\t},\n\t\t\tstrokeFill(d) {\n\t\t\t\tconst rgbColor = rgb(d.color)\n\t\t\t\tconst stroke = rgbColor.toString() == rgb('white').toString() ? rgbColor.darker() : rgbColor\n\t\t\t\treturn stroke\n\t\t\t},\n\t\t\tclick: self.opts.bar_click_override\n\t\t\t\t? (event, d) => self.opts.bar_click_override(getTermValues(d, self))\n\t\t\t\t: (event, d) => handle_click(event, self, d)\n\t\t},\n\t\tbarLabel: {\n\t\t\ttext: d => {\n\t\t\t\treturn 'label' in d\n\t\t\t\t\t? d.label\n\t\t\t\t\t: self.config.term.values && 'id' in d && d.id in self.config.term.values\n\t\t\t\t\t? self.config.term.values[d.id].label\n\t\t\t\t\t: d\n\t\t\t},\n\t\t\tclick: self.opts.bar_click_override\n\t\t\t\t? (event, d) => self.opts.bar_click_override(getTermValues(d, self))\n\t\t\t\t: (event, d) => handle_click(event, self, d),\n\t\t\tmouseover: event => {\n\t\t\t\tevent.stopPropagation()\n\t\t\t},\n\t\t\tmouseout: () => {\n\t\t\t\ttip.hide()\n\t\t\t}\n\t\t},\n\t\tlegend: {\n\t\t\tonColorClick: e => handleLegendClick(e.target, self),\n\t\t\tclick: e => handleLegendClick(e.target, self),\n\t\t\tmouseover: event => {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\tconst d = event.target.__data__\n\t\t\t\tif (d === undefined) return\n\t\t\t\tif (d.isHidden) tip.show(event.clientX, event.clientY).d.html('Click to unhide bar')\n\t\t\t},\n\t\t\tmouseout: () => {\n\t\t\t\ttip.hide()\n\t\t\t}\n\t\t},\n\t\tyAxis: {\n\t\t\ttext: visibleTotal => {\n\t\t\t\tconst type = self.sampleType?.plural_name || 'samples'\n\t\t\t\tconst term = self.config.term\n\t\t\t\tif (s.orientation == 'vertical') {\n\t\t\t\t\t// Do not show the sum of serieses as (n=...) when serieses are 'Sub-condition', 'Most recent grade' or 'Any grade'\n\t\t\t\t\t// because a patient could have multiple 'Sub-condition', 'Most recent grade' or 'Any grade', and as a result could\n\t\t\t\t\t// be counted multiple times.\n\t\t\t\t\treturn s.unit == 'pct'\n\t\t\t\t\t\t? `% of ${type}`\n\t\t\t\t\t\t: `# of ${type} ` +\n\t\t\t\t\t\t\t\t(term.q.bar_by_children || term.q.value_by_most_recent || term.q.value_by_computable_grade\n\t\t\t\t\t\t\t\t\t? ''\n\t\t\t\t\t\t\t\t\t: `(n=${visibleTotal})`)\n\t\t\t\t} else {\n\t\t\t\t\treturn term.q.bar_by_children\n\t\t\t\t\t\t? 'Sub-condition'\n\t\t\t\t\t\t: term.q.value_by_max_grade\n\t\t\t\t\t\t? 'Maximum grade'\n\t\t\t\t\t\t: term.q.value_by_most_recent\n\t\t\t\t\t\t? 'Most recent grade'\n\t\t\t\t\t\t: term.q.value_by_computable_grade\n\t\t\t\t\t\t? 'Any grade'\n\t\t\t\t\t\t: term.type == 'categorical' || !term.unit\n\t\t\t\t\t\t? ''\n\t\t\t\t\t\t: term.unit\n\t\t\t\t}\n\t\t\t}\n\t\t},\n\t\txAxis: {\n\t\t\ttext: visibleTotal => {\n\t\t\t\tconst type = self.sampleType?.plural_name || 'samples'\n\t\t\t\tconst term = self.config.term\n\t\t\t\tif (s.orientation == 'vertical') {\n\t\t\t\t\treturn term.q.bar_by_children\n\t\t\t\t\t\t? 'Sub-condition'\n\t\t\t\t\t\t: term.q.value_by_max_grade\n\t\t\t\t\t\t? 'Maximum grade'\n\t\t\t\t\t\t: term.q.value_by_most_recent\n\t\t\t\t\t\t? 'Most recent grade'\n\t\t\t\t\t\t: term.q.value_by_computable_grade\n\t\t\t\t\t\t? 'Any grade'\n\t\t\t\t\t\t: term.type == 'categorical' || !term.unit\n\t\t\t\t\t\t? ''\n\t\t\t\t\t\t: term.unit\n\t\t\t\t} else {\n\t\t\t\t\t// Do not show the sum of serieses as (n=...) when serieses are 'Sub-condition', 'Most recent grade' or 'Any grade'\n\t\t\t\t\t// because a patient could have multiple 'Sub-condition', 'Most recent grade' or 'Any grade', and as a result could\n\t\t\t\t\t// be counted multiple times.\n\t\t\t\t\treturn s.unit == 'pct'\n\t\t\t\t\t\t? `% of ${type}`\n\t\t\t\t\t\t: `# of ${type} ` +\n\t\t\t\t\t\t\t\t(term.q.bar_by_children || term.q.value_by_most_recent || term.q.value_by_computable_grade\n\t\t\t\t\t\t\t\t\t? ''\n\t\t\t\t\t\t\t\t\t: `(n=${visibleTotal})`)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n\nfunction handleColorClick(d, self, color) {\n\tconst termNum = d.type == 'col' ? 'term' : 'term2'\n\tconst term = self.config[termNum]\n\tlet dataId = d.dataId\n\tif (term.term.values && !term.term.values?.[dataId])\n\t\tfor (const [key, value] of Object.entries(term.term.values)) if (value.label == d.dataId) dataId = key\n\tif (term.term.values?.[dataId]) term.term.values[dataId].color = color\n\tif (term.term.type == 'geneVariant') {\n\t\tlet groupset\n\t\tif (term.q.type == 'predefined-groupset') {\n\t\t\tgroupset = term.term.groupsetting.lst[term.q.predefined_groupset_idx]\n\t\t} else if (term.q.type == 'custom-groupset') {\n\t\t\tgroupset = term.q.customset\n\t\t} else {\n\t\t\tthrow 'unexpected q.type'\n\t\t}\n\t\tconst group = groupset.groups.find(g => g.name == d.dataId)\n\t\tif (!group) throw 'group not found'\n\t\tgroup.color = color\n\t}\n\tlet binColored = null\n\tif (self.bins[2].length > 0) {\n\t\t//term index: term0: 0, term: 1, term2: 2\n\t\tconst binMatched = self.bins[2].find(bin => bin.label == d.dataId)\n\t\tif (binMatched) {\n\t\t\tbinMatched.color = color\n\t\t\tbinColored = self.bins[2]\n\t\t}\n\t}\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: {\n\t\t\t[termNum]: {\n\t\t\t\t$id: term.$id,\n\t\t\t\tid: term.id,\n\t\t\t\tisAtomic: true,\n\t\t\t\tterm: term.term,\n\t\t\t\tq: getUpdatedQfromClick(d, term, d.isHidden, binColored)\n\t\t\t}\n\t\t}\n\t})\n}\n\nfunction handleLegendClick(target, self) {\n\tconst d = target.__data__\n\tif (d === undefined) return\n\tif (!('type' in d)) return\n\tconst termNum = d.type == 'col' ? 'term' : 'term2'\n\tconst term = self.config[termNum]\n\tconst isHidden =\n\t\t'isHidden' in d\n\t\t\t? !d.isHidden\n\t\t\t: !(term.q && term.q.hiddenValues && term.q.hiddenValues['dataId' in d ? d.dataId : d.id])\n\tconst tip = self.app.tip\n\tconst menu = tip.clear()\n\tmenu.showunder(target)\n\tconst div = menu.d.append('div')\n\tdiv\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t.text(!isHidden ? 'Show' : 'Hide')\n\t\t.on('click', () => {\n\t\t\tmenu.hide()\n\t\t\thideCategory(d, self, isHidden)\n\t\t})\n\tif (term.q.hiddenValues && Object.keys(term.q.hiddenValues).length > 1)\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text('Show all')\n\t\t\t.on('click', () => {\n\t\t\t\tmenu.hide()\n\t\t\t\tconst config = {}\n\t\t\t\tconst tw = structuredClone(term)\n\t\t\t\tdelete tw.q.hiddenValues\n\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: { [termNum]: tw }\n\t\t\t\t})\n\t\t\t})\n\tconst color = rgb(d.color).formatHex()\n\tif (color != '#ffffff') {\n\t\tconst input = div\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t.style('padding', '0px 10px')\n\t\t\t.text('Color:')\n\t\t\t.append('input')\n\t\t\t.attr('type', 'color')\n\t\t\t.attr('value', color)\n\t\t\t.on('change', () => {\n\t\t\t\thandleColorClick(d, self, input.node().value)\n\t\t\t\tmenu.hide()\n\t\t\t})\n\t}\n}\n\nexport function hideCategory(d, self, isHidden) {\n\tconst termNum = d.type == 'col' ? 'term' : 'term2'\n\tconst term = self.config[termNum]\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: {\n\t\t\t[termNum]: {\n\t\t\t\t//Fix for list samples options not working\n\t\t\t\t//after hiding a category\n\t\t\t\t$id: term?.$id,\n\t\t\t\tid: term.id,\n\n\t\t\t\tisAtomic: true,\n\t\t\t\tterm: term.term,\n\t\t\t\tq: getUpdatedQfromClick(d, term, isHidden)\n\t\t\t}\n\t\t}\n\t})\n}\n\nfunction getUpdatedQfromClick(d, term, isHidden = false, binColored = null) {\n\tconst label = 'id' in d ? d.id : d.type == 'col' ? d.seriesId : d.dataId\n\tconst valueId = term.term.values && Object.keys(term.term.values).find(id => term.term.values[id].label === label)\n\tconst id = !valueId ? label : valueId\n\tconst q = JSON.parse(JSON.stringify(term.q))\n\tif (!q.hiddenValues) q.hiddenValues = {}\n\tif (isHidden) q.hiddenValues[id] = 1\n\telse delete q.hiddenValues[id]\n\tif (binColored) q.binColored = binColored\n\treturn q\n}\n\nfunction handle_click(event, self, chart) {\n\tconst d = event.target.__data__ || event.target.parentNode.__data__\n\t// bar label data only has {id,label},\n\t// while bar data has all required data including seriesId\n\tconst term1 = self.config.term.term\n\tconst term2 = self.config.term2 ? self.config.term2.term : null\n\tconst uncomp_term1 = term1.values ? Object.values(term1.values).map(v => v.label) : []\n\tconst uncomp_term2 = term2 && term2.values ? Object.values(term2.values).map(v => v.label) : []\n\tconst term1unit = term1.unit && !uncomp_term1.includes(d.seriesId || d.id) ? ' ' + term1.unit : ''\n\tconst term2unit = term2 && term2.unit && !uncomp_term2.includes(d.dataId || d.id) ? ' ' + term2.unit : ''\n\tconst seriesLabel =\n\t\t(term1.values && d.seriesId in term1.values ? term1.values[d.seriesId].label : d.seriesId ? d.seriesId : d.id) +\n\t\tterm1unit\n\tconst dataLabel =\n\t\t(term2 && term2.values && d.dataId in term2.values ? term2.values[d.dataId].label : d.dataId ? d.dataId : d.id) +\n\t\tterm2unit\n\tconst icon = !term2\n\t\t? ''\n\t\t: \"<div style='display:inline-block; width:14px; height:14px; margin: 2px 3px; vertical-align:top; background:\" +\n\t\t  d.color +\n\t\t  \"'>&nbsp;</div>\"\n\tconst header =\n\t\t`<div style='padding:2px'><b>${term1.name}</b>: ${seriesLabel}</div>` +\n\t\t(d.seriesId && term2 ? `<div style='padding:2px'><b>${term2.name}</b>: ${dataLabel} ${icon}</div>` : '')\n\n\tconst data = d.seriesId || d.seriesId === 0 ? d : { seriesId: d.id, dataId: d.dataId }\n\n\tconst options = []\n\tif (self.opts.bar_click_opts.includes('hide_bar')) {\n\t\toptions.push({\n\t\t\tlabel: data.seriesId ? 'Hide \"' + seriesLabel + '\"' : 'Hide',\n\t\t\tcallback: () => {\n\t\t\t\tconst term = self.config.term\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t$id: term.$id,\n\t\t\t\t\t\t\tid: term.id,\n\t\t\t\t\t\t\tisAtomic: true,\n\t\t\t\t\t\t\tterm: term.term,\n\t\t\t\t\t\t\tq: getUpdatedQfromClick({ id: data.seriesId, type: 'col' }, term, true)\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 (data.dataId || data.dataId === 0) {\n\t\t\toptions.push({\n\t\t\t\tlabel: 'Hide \"' + dataLabel + '\" ' + icon,\n\t\t\t\tcallback: () => {\n\t\t\t\t\tconst term2 = self.config.term2\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\tisAtomic: true,\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: self.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tterm2: {\n\t\t\t\t\t\t\t\tisAtomic: true,\n\t\t\t\t\t\t\t\tterm: term2.term,\n\t\t\t\t\t\t\t\tq: getUpdatedQfromClick({ id: data.dataId, type: 'row' }, term2, true)\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\t}\n\n\tif (self.opts.bar_click_opts.includes('add_filter')) {\n\t\tconst item = findItemByTermId(self.state.termfilter.filter, self.config.term.term.id)\n\t\tif (!item) {\n\t\t\toptions.push({\n\t\t\t\tlabel: 'Add as filter',\n\t\t\t\tcallback: async (self, tvslst) => {\n\t\t\t\t\tconst arg = getListSamplesArg(event, self, data.seriesId, data.dataId, chart.chartId)\n\t\t\t\t\tawait menuoption_add_filter(self, tvslst, arg)\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\n\tif (self.opts.bar_click_opts.includes('add_group') && self.config.displaySampleIds) {\n\t\toptions.push({\n\t\t\tlabel: 'Add as group',\n\t\t\tcallback: async () => {\n\t\t\t\tconst arg = getListSamplesArg(event, self, data.seriesId, data.dataId, chart.chartId)\n\t\t\t\tawait addAsGroup(arg)\n\t\t\t}\n\t\t})\n\t}\n\n\t//disable sample listing temporarily\n\tif (self.config.displaySampleIds) {\n\t\toptions.push({\n\t\t\tlabel: 'List samples',\n\t\t\tcallback: async () => {\n\t\t\t\tconst arg = getListSamplesArg(event, self, data.seriesId, data.dataId, chart.chartId)\n\t\t\t\tawait listSamples(arg)\n\t\t\t}\n\t\t})\n\t}\n\n\t// TODO: add to cart\n\t//\n\t// if (self.opts.bar_click_opts.includes('add_to_cart')) {\n\t// \toptions.push({\n\t// \t\tlabel: 'Add group to cart',\n\t// \t\tcallback: menuoption_select_group_add_to_cart\n\t// \t})\n\t// }\n\n\tif (!options.length) return\n\tself.app.tip.clear()\n\tif (header) {\n\t\tself.app.tip.d.append('div').html(header)\n\t}\n\tconst tvslst = getTermValues(data, self)\n\tself.app.tip.d\n\t\t.append('div')\n\t\t.selectAll('div')\n\t\t.data(options)\n\t\t.enter()\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.html(d => d.label)\n\t\t.on('click', async (event, d) => {\n\t\t\tif (event.target._clicked) return\n\t\t\tevent.target._clicked = true\n\t\t\tevent.target.textContent = 'Loading...'\n\t\t\tawait d.callback(self, tvslst)\n\t\t\tself.app.tip.hide()\n\t\t})\n\tself.app.tip.show(event.clientX, event.clientY)\n}\n\nfunction getListSamplesArg(event, self, seriesId, dataId, chartId) {\n\tconst terms = [self.config.term]\n\tconst tvslst = {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin: 'and',\n\t\tlst: []\n\t}\n\tconst geneVariant = {}\n\tconst tvs = getTvs(1, seriesId, self, geneVariant)\n\tif (tvs) tvslst.lst.push(tvs)\n\tif (self.config.term2) {\n\t\tterms.push(self.config.term2)\n\t\tconst tvs = getTvs(2, dataId, self, geneVariant)\n\t\tif (tvs) tvslst.lst.push(tvs)\n\t}\n\tif (self.config.term0) {\n\t\tterms.push(self.config.term0)\n\t\tconst tvs = getTvs(0, chartId, self, geneVariant)\n\t\tif (tvs) tvslst.lst.push(tvs)\n\t}\n\tconst arg = {\n\t\tevent,\n\t\tself,\n\t\tterms,\n\t\ttvslst,\n\t\tgeneVariant\n\t}\n\treturn arg\n}\n\nfunction getTvs(termIndex, value, self, geneVariant) {\n\tif (!value) return\n\tconst term = termIndex == 0 ? self.config.term0 : termIndex == 1 ? self.config.term : self.config.term2\n\tif (term.term.type == 'geneVariant') {\n\t\t// geneVariant filtering will be handled by mayFilterByGeneVariant()\n\t\tgeneVariant[`t${termIndex}value`] = value\n\t\treturn\n\t}\n\tlet tvs = {\n\t\ttype: 'tvs',\n\t\ttvs: {\n\t\t\tterm: term.term,\n\t\t\tvalues: [{ key: value }]\n\t\t}\n\t}\n\tif (term.q.type == 'custom-groupset' || term.q.type == 'predefined-groupset') {\n\t\tconst groupset =\n\t\t\tterm.q.type == 'custom-groupset' ? term.q.customset : term.term.groupsetting.lst[term.q.predefined_groupset_idx]\n\t\tconst group = groupset.groups.find(group => group.name == value)\n\t\tif (!group) throw 'group not found'\n\t\ttvs.tvs.values = group.values\n\t} else if (isNumericTerm(term.term)) {\n\t\tconst bins = self.bins[termIndex]\n\t\ttvs.tvs.ranges = [bins.find(bin => bin.label == value)]\n\t} else if (term.term.type == 'samplelst') {\n\t\tconst list = term.term.values?.[value]?.list || []\n\t\tconst ids = list.map(s => s.sampleId)\n\t\tconst tvslst = getSamplelstFilter(ids)\n\t\ttvs = tvslst.lst[0] // tvslst only has the tvs for the samplelst term\n\t} else if (term.term.type == 'geneVariant' && term.q.type == 'values') {\n\t\tthrow 'no longer supported in barchart'\n\t}\n\treturn tvs\n}\n\nexport async function listSamples(arg) {\n\t// validate arg\n\tfor (const k of Object.keys(arg)) {\n\t\tconst param = arg[k]\n\t\tif (!param) throw `parameter '${k}' is undefined`\n\t}\n\n\t// query sample data\n\tconst { event, self, terms, tvslst, geneVariant, tip } = arg\n\tconst opts = {\n\t\tterms,\n\t\tfilter: filterJoin([self.state.termfilter.filter, tvslst]),\n\t\tfilter0: self.state.termfilter.filter0,\n\t\tisSummary: true\n\t}\n\tconst data = await self.app.vocabApi.getAnnotatedSampleData(opts)\n\n\t// fill table rows with sample data\n\tconst rows = []\n\tconst termIsNumeric = isNumericTerm(self.config.term.term)\n\tconst term2isNumeric = self.config.term2 ? isNumericTerm(self.config.term2.term) : false\n\tconst termIsGv = self.config.term.term.type == 'geneVariant'\n\tconst term2isGv = self.config.term2?.term.type == 'geneVariant'\n\tconst term2isSurv = self.config.term2?.term.type == 'survival'\n\tfor (const sample of data.lst) {\n\t\tconst pass = mayFilterByGeneVariant(sample, self, geneVariant)\n\t\tif (!pass) continue\n\t\tconst sampleName = data.refs.bySampleId[sample.sample].label\n\t\tconst row = [{ value: sampleName }]\n\t\tconst urlTemplate = self.app.vocabApi.termdbConfig?.urlTemplates?.sample\n\t\tif (urlTemplate) {\n\t\t\t// sample url template is defined, use it to format sample name as url\n\t\t\trow[0].url = urlTemplate.base + (sample[urlTemplate.namekey] || sample.sample)\n\t\t}\n\t\tconst t1entry = sample[self.config.term.$id]\n\t\tif (!t1entry) continue\n\t\t/** Don't show hidden values in the results\n\t\t * May not be caught in server request for custom variables\n\t\t * with user supplied keys */\n\t\tif (self.config.term.q?.hiddenValues && self.config.term.q.hiddenValues[t1entry.value]) continue\n\t\tif (termIsNumeric) {\n\t\t\tconst value = t1entry.value\n\t\t\trow.push({ value: roundValueAuto(value) })\n\t\t} else if (termIsGv) {\n\t\t\taddGvRowVals(sample, self.config.term, row)\n\t\t}\n\t\tif (self.config.term2) {\n\t\t\tconst t2entry = sample[self.config.term2.$id]\n\t\t\tif (!t2entry) continue\n\t\t\t//Don't show hidden values in the results\n\t\t\tif (self.config.term2.q?.hiddenValues && self.config.term2.q.hiddenValues[t2entry.value]) continue\n\t\t\tif (term2isNumeric) {\n\t\t\t\tconst value = roundValueAuto(t2entry.value)\n\t\t\t\trow.push({ value })\n\t\t\t} else if (term2isGv) {\n\t\t\t\taddGvRowVals(sample, self.config.term2, row)\n\t\t\t} else if (term2isSurv) {\n\t\t\t\tconst value = self.config.term2.term.values[t2entry.key].label\n\t\t\t\trow.push({ value })\n\t\t\t} else {\n\t\t\t\tconst label = self.config.term2.term.values?.[t2entry.value]?.label\n\t\t\t\tconst value = label || t2entry.value\n\t\t\t\trow.push({ value })\n\t\t\t}\n\t\t}\n\t\trows.push(row)\n\t}\n\n\t// fill table columns with term metadata\n\tconst columns = [{ label: 'Sample' }]\n\tif (termIsNumeric) {\n\t\tcolumns.push({ label: self.config.term.term.name })\n\t} else if (termIsGv) {\n\t\taddGvCols(self.config.term, columns)\n\t}\n\tif (self.config.term2) {\n\t\tif (term2isGv) {\n\t\t\taddGvCols(self.config.term2, columns)\n\t\t} else {\n\t\t\tcolumns.push({ label: self.config.term2.term.name })\n\t\t}\n\t}\n\n\t// render table in div. from now on arg.tip should always be given\n\tlet div\n\tif (tip) {\n\t\tdiv = tip.d\n\t\ttip.clear().show(event.clientX, event.clientY, false)\n\t} else {\n\t\tconst menu = new Menu({ padding: '5px' })\n\t\tmenu.show(event.clientX, event.clientY, false)\n\t\tdiv = menu.d.append('div')\n\t}\n\trenderTable({\n\t\trows,\n\t\tcolumns,\n\t\tdiv,\n\t\tshowLines: true,\n\t\tmaxHeight: '40vh',\n\t\tresize: true,\n\t\tdataTestId: 'sjpp-listsampletable'\n\t})\n}\nasync function getSampleGrp(arg) {\n\t// query sample data\n\tconst { event, self, terms, tvslst, geneVariant, tip } = arg\n\tconst opts = {\n\t\tterms,\n\t\tfilter: filterJoin([self.state.termfilter.filter, tvslst]),\n\t\tfilter0: self.state.termfilter.filter0,\n\t\tisSummary: true\n\t}\n\tconst data = await self.app.vocabApi.getAnnotatedSampleData(opts)\n\tconst samples = []\n\tfor (const sample of data.lst) {\n\t\tconst pass = mayFilterByGeneVariant(sample, self, geneVariant)\n\t\tif (!pass) continue\n\t\tconst t1entry = sample[self.config.term.$id]\n\t\tif (!t1entry) continue\n\t\tif (self.config.term.q?.hiddenValues && self.config.term.q.hiddenValues[t1entry.value]) continue\n\t\tsamples.push({ sampleId: sample.sample })\n\t}\n\n\tconst group = {\n\t\tname: 'Group',\n\t\titems: samples\n\t}\n\treturn group\n}\n\nexport async function addAsGroup(arg) {\n\t// validate arg\n\tfor (const k of Object.keys(arg)) {\n\t\tconst param = arg[k]\n\t\tif (!param) throw `parameter '${k}' is undefined`\n\t}\n\tconst group = await getSampleGrp(arg)\n\tconst tw = getSamplelstTW([group])\n\tconst filter = getFilter(tw)\n\taddNewGroup(arg.self.app, filter, arg.self.state.groups)\n}\n\n// if geneVariant term is present, filter sample by its geneVariant group assignment\nfunction mayFilterByGeneVariant(sample, self, geneVariant) {\n\tif (self.config.term.term.type == 'geneVariant' && geneVariant.t1value) {\n\t\tconst tw = self.config.term\n\t\tif (tw.q.type == 'values') throw 'q.type=values not supported'\n\t\tconst value = sample[tw.$id]?.value\n\t\tif (value != geneVariant.t1value) return false\n\t}\n\tif (self.config.term2?.term.type == 'geneVariant' && geneVariant.t2value) {\n\t\tconst tw = self.config.term2\n\t\tif (tw.q.type == 'values') throw 'q.type=values not supported'\n\t\tconst value = sample[tw.$id]?.value\n\t\tif (value != geneVariant.t2value) return false\n\t}\n\tif (self.config.term0?.term.type == 'geneVariant' && geneVariant.t0value) {\n\t\tconst tw = self.config.term0\n\t\tif (tw.q.type == 'values') throw 'q.type=values not supported'\n\t\tconst value = sample[tw.$id]?.value\n\t\tif (value != geneVariant.t0value) return false\n\t}\n\treturn true\n}\n\n// add geneVariant values to row\nfunction addGvRowVals(sample, tw, row) {\n\tconst mlst = sample[tw.$id]?.values\n\tconst gene2mlst = new Map()\n\t// map each gene to its mutations\n\tfor (const gene of tw.term.genes) {\n\t\tconst mlst_gene = mlst.filter(m => m.gene == gene.id)\n\t\tgene2mlst.set(gene.name, mlst_gene)\n\t}\n\tif (!gene2mlst.size) throw 'gene2mlst is empty'\n\tif (gene2mlst.size == 1) {\n\t\t// single gene, add its mutations to mutation column\n\t\tconst entry = gene2mlst.entries().next().value\n\t\tconst mlst = entry[1]\n\t\tconst htmls = mlst2htmls(mlst)\n\t\trow.push({ html: htmls.join('<br>') })\n\t} else {\n\t\t// multiple genes, add each gene to gene column and its\n\t\t// mutations to mutation column\n\t\tconst genes = []\n\t\tconst htmls = []\n\t\tfor (const [gene, mlst] of gene2mlst) {\n\t\t\tgenes.push(...Array(mlst.length).fill(gene))\n\t\t\thtmls.push(...mlst2htmls(mlst))\n\t\t}\n\t\trow.push({ html: genes.join('<br>') })\n\t\trow.push({ html: htmls.join('<br>') })\n\t}\n}\n\nfunction mlst2htmls(mlst) {\n\tconst htmls = mlst.map(m => {\n\t\tconst mname = m.mname || '' // e.g. aa change\n\t\tconst value = m.value ? roundValueAuto(m.value, false, 3) : '' // e.g. cnv value\n\t\tconst color = mclass[m.class].color\n\t\tconst label = mclass[m.class].label.toUpperCase()\n\n\t\tconst holder = create('div')\n\n\t\tholder.append('span').text(mname || value)\n\n\t\tholder\n\t\t\t.append('span')\n\t\t\t.style('margin-left', mname || value ? '5px' : '0px')\n\t\t\t.style('color', color)\n\t\t\t.style('font-size', '.8em')\n\t\t\t.text(label)\n\n\t\treturn holder.html()\n\t})\n\treturn htmls\n}\n\n// add geneVariant columns\nfunction addGvCols(tw, columns) {\n\tif (tw.term.genes.length == 1) {\n\t\tcolumns.push({ label: tw.term.name })\n\t} else {\n\t\tcolumns.push({ label: 'Gene' })\n\t\tif (tw.q.type == 'predefined-groupset') {\n\t\t\tconst groupset = tw.term.groupsetting.lst[tw.q.predefined_groupset_idx]\n\t\t\tcolumns.push({ label: dt2label[groupset.dt] })\n\t\t} else if (tw.q.type == 'custom-groupset') {\n\t\t\tcolumns.push({ label: 'Genotype' })\n\t\t} else {\n\t\t\tthrow 'unexpected tw.q.type'\n\t\t}\n\t}\n}\n\nasync function menuoption_add_filter(self, tvslst, arg) {\n\t/*\n\tself: the tree object\n\ttvslst: an array of 1 or 2 term-value setting objects\n\t\tthis is to be added to the obj.termfilter.filter[]\n\t\tif barchart is single-term, tvslst will have only one element\n\t\tif barchart is two-term overlay, tvslst will have two elements, one for term1, the other for term2\n\targ: object of parameters used by getSampleGrp to get sample group\n\t\t*/\n\tif (!tvslst) return\n\tif (!self.state.termfilter || self.state.nav?.header_mode !== 'with_tabs') {\n\t\t// do not display ui, and do not collect callbacks\n\t\treturn\n\t}\n\t// validate arg\n\tfor (const k of Object.keys(arg)) {\n\t\tconst param = arg[k]\n\t\tif (!param) throw `parameter '${k}' is undefined`\n\t}\n\n\tconst hasGrpSetting = arg.terms.find(t => t.q?.type == 'predefined-groupset' || t.q?.type == 'custom-groupset')\n\tlet samplelstTW\n\tif (hasGrpSetting) {\n\t\t// if any term has group setting, add filter as samplelst\n\t\tconst group = await getSampleGrp(arg)\n\t\tsamplelstTW = getSamplelstTW([group])\n\t}\n\n\tconst filterUiRoot = getFilterItemByTag(self.state.termfilter.filter, 'filterUiRoot')\n\tconst filter = filterJoin([\n\t\tfilterUiRoot,\n\t\tsamplelstTW\n\t\t\t? getFilter(samplelstTW)\n\t\t\t: {\n\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\tin: true,\n\t\t\t\t\tjoin: tvslst.length > 1 ? 'and' : '',\n\t\t\t\t\tlst: [...tvslst.map(wrapTvs)]\n\t\t\t  }\n\t])\n\tfilter.tag = 'filterUiRoot'\n\tself.app.dispatch({\n\t\ttype: 'filter_replace',\n\t\tfilter\n\t})\n}\n\nfunction wrapTvs(tvs) {\n\treturn tvs.type === 'tvs' ? tvs : { type: 'tvs', tvs }\n}\n\n/* \t\t\tTODO: add to cart and gp          */\n\nfunction menuoption_listsamples(self, tvslst) {\n\tconst filterRoot = getNormalRoot({\n\t\ttype: 'tvslst',\n\t\tjoin: 'and',\n\t\tlst: [\n\t\t\tself.state.termfilter.filter,\n\t\t\t// create a copy of tvslst to not mutate the barchart state,\n\t\t\t// such as when deleting tvs.tvs.term.values below\n\t\t\t...tvslst.map(tvs => wrapTvs(JSON.parse(JSON.stringify(tvs))))\n\t\t]\n\t})\n\t///////////// quick fix to delete term.values{} from stringified filter to reduce url length\n\tnormalizeProps(filterRoot, f => {\n\t\tdelete f.tag\n\t\tif (f.type == 'tvs' && f.tvs && f.tvs.term) delete f.tvs.term.values\n\t})\n\tconst arg = [\n\t\t'getsamples=1',\n\t\t'genome=' + self.app.vocabApi.vocab.genome,\n\t\t'dslabel=' + self.app.vocabApi.vocab.dslabel,\n\t\t'filter=' + encodeURIComponent(JSON.stringify(filterRoot))\n\t]\n\n\tdofetch3('termdb?' + arg.join('&')).then(data => {\n\t\texport_data(data.samples.length + ' samples', [{ text: data.samples.join('\\n') }])\n\t})\n}\n\nfunction menuoption_select_group_add_to_cart(self, tvslst) {\n\tif (!tvslst || !tvslst.length) return\n\n\tconst new_group = {}\n\tnew_group.is_termdb = true\n\tnew_group.terms = []\n\n\tfor (const [i, term] of tvslst.entries()) {\n\t\tnew_group.terms.push(term)\n\t}\n\n\tif (!self.selected_groups) {\n\t\tself.selected_groups = []\n\t}\n\n\tself.selected_groups.push(new_group)\n\tself.components.cart.main()\n}\n\nfunction getTermValues(d, self) {\n\t/*\n\td: clicked bar data\n  */\n\tconst termValues = []\n\tif (self.state.nav?.header_mode == 'with_cohortHtmlSelect') {\n\t\t// pass the cohort filter information back to calling app\n\t\t// do not set the renderAs in here since that is decided by the calling app\n\t\tconst cohortFilter = getFilterItemByTag(self.state.termfilter.filter, 'cohortFilter')\n\t\tif (cohortFilter) termValues.push(JSON.parse(JSON.stringify(cohortFilter)))\n\t}\n\n\tconst t1 = self.config.term\n\tconst t1ValKey =\n\t\tt1.term.values && Object.keys(t1.term.values).filter(key => t1.term.values[key].label === d.seriesId)[0]\n\tconst t1ValId = t1.term.values && t1ValKey in t1.term.values ? t1ValKey : d.seriesId\n\tconst t2 = self.config.term2\n\tconst t2ValKey =\n\t\tt2 && t2.term.values && Object.keys(t2.term.values).filter(key => t2.term.values[key].label === d.dataId)[0]\n\tconst t2ValId = t2 && t2.term.values && t2ValKey in t2.term.values ? t2ValKey : d.dataId\n\n\tfor (const term of [t1, t2]) {\n\t\tif (!term) continue\n\t\tconst i = term == t1 ? 1 : 2\n\t\tconst key = term == t1 ? t1ValId : t2ValId\n\t\tif (!key) continue\n\t\t// const q = term ? term.q : {}\n\t\tconst q = term.q //self.currServerData.refs.q[i]\n\t\tconst label = !term || !term.term.values ? key : key in term.term.values ? term.term.values[key].label : key\n\n\t\tif (q.type == 'predefined-groupset' || q.type == 'custom-groupset') {\n\t\t\tconst groupset =\n\t\t\t\tq.type == 'predefined-groupset' ? term.term.groupsetting.lst[q.predefined_groupset_idx] : q.customset\n\t\t\tconst group = groupset.groups.find(g => g.name === key)\n\t\t\tconst tvs = { term: term.term, values: group.values, groupset_label: group.name }\n\t\t\tif (term.term.type == 'condition') {\n\t\t\t\ttvs.bar_by_children = term.q.bar_by_children\n\t\t\t\ttvs.bar_by_grade = term.q.bar_by_grade\n\t\t\t\ttvs.value_by_most_recent = term.q.value_by_most_recent\n\t\t\t\ttvs.value_by_max_grade = term.q.value_by_max_grade\n\t\t\t}\n\t\t\ttermValues.push(tvs)\n\t\t} else if (term.term.type == 'condition') {\n\t\t\tif (!t2 || t1.term.id != t2.term.id) {\n\t\t\t\ttermValues.push(\n\t\t\t\t\tObject.assign(\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tterm: term.term,\n\t\t\t\t\t\t\tvalues: [{ key, label }]\n\t\t\t\t\t\t},\n\t\t\t\t\t\tq\n\t\t\t\t\t)\n\t\t\t\t)\n\t\t\t}\n\n\t\t\tif (term == t1 && t2 && term.term.id == t2.term.id) {\n\t\t\t\tconst q2 = t2.q\n\t\t\t\tconst term2Label =\n\t\t\t\t\tt2.term.values && d.dataId in t2.term.values ? 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+  "names": ["bin", "chart", "a", "id", "term2", "self", "tvslst", "d", "event", "tvs", "group", "mlst", "d"]
+}

package/dist/chunk-ZFFHOEBE.js

@@ -0,0 +1,117 @@
+import {
+  copyMerge,
+  getInitFxn
+} from "./chunk-DDOM4XYV.js";
+
+// termdb/termInfo.js
+var defaultState = { isVisible: false, term: null };
+var TdbTermInfo = class {
+  /*
+  		Will display background information about a term, 
+  		such as rubric, publication source, description, etc
+  
+  		opts{}
+  			.content_holder: required d3-wrapped DOM element
+  				****TODO: Create menu on the fly if content_holder is not supplied****
+  			
+  			.icon_holder: optional, creates information icon for terms
+  			
+  			.vocabApi: 
+  				- for termInfoInit(), required as opts.vocabApi
+  				- for termInfoComp(), required as part of opts.app
+  				- a vocabulary API that has a getTermInfo() method
+  			
+  			.state{} optional, see defaultState value above
+  				.isVisible: boolean, optional
+  				.term: {id, ...} optional (may be supplied with either getState() or main({state}))
+  	*/
+  constructor(opts) {
+    this.vocabApi = opts.vocabApi || opts.app && opts.app.vocabApi;
+    this.state = Object.assign({}, defaultState, opts.state ? opts.state : {});
+    this.api = this;
+    setInteractivity(this);
+    setRenderers(this);
+    this.initUI(opts);
+  }
+  /*
+  	state: replace 1 or more state values by attribute key
+  */
+  async main(state = {}) {
+    copyMerge(this.state, state);
+    this.dom.content_holder.style("display", this.state.isVisible ? "block" : "none");
+    this.dom.icon_holder.style("background-color", this.state.isVisible ? "darkgray" : "transparent").style("color", this.state.isVisible ? "white" : "#797a7a");
+    if (!this.state.isVisible) return;
+    const data = await this.vocabApi.getTermInfo(this.state.term.id);
+    this.render(data);
+  }
+};
+var termInfoInit = getInitFxn(TdbTermInfo);
+function setRenderers(self) {
+  self.initUI = function(opts) {
+    self.dom = {
+      content_holder: opts.content_holder.style("margin-left", "25px").attr("class", "term_info_div").style("display", self.state.isVisible ? "block" : "none").style("white-space", "normal").style("padding-bottom", "20px"),
+      //Term information/description
+      details: opts.content_holder.append("div"),
+      tbody: opts.content_holder.append("table").append("tbody"),
+      //Information icon button div. Term description appears in content_holder
+      icon_holder: opts.icon_holder.style("margin", "1px 0px 1px 5px").style("padding", "2px 5px").style("font-family", "Times New Roman").style("font-size", "14px").style("font-weight", "bold").style("cursor", "pointer").style("background-color", "transparent").style("color", "#797a7a").style("align-items", "center").style("justify-content", "center").style("border", "none").style("border-radius", "3px").attr("aria-label", "Term Information").html("ⓘ").on("mouseenter", () => {
+        if (self.state.isVisible == true) return;
+        self.dom.icon_holder.style("color", "blue");
+      }).on("mouseleave", () => {
+        if (self.state.isVisible == true) return;
+        self.dom.icon_holder.style("color", "#797a7a");
+      }).on("click", self.toggleDescription)
+    };
+  };
+  self.render = function(data) {
+    if (!data?.terminfo) {
+      self.dom.details.append("div").style("margin-top", "10px").text("No definition found.");
+      return;
+    }
+    self.dom.tbody.selectAll("*").remove();
+    if (data.terminfo.src) {
+      for (let s of data.terminfo.src) {
+        const source_td = self.dom.tbody.append("tr").append("td").style("padding", "5px 0");
+        source_td.append("div").style("font-weight", "bold").text("Source");
+        source_td.append("div").style("margin-left", "20px").text(s.pub);
+        source_td.append("div").style("margin-left", "20px").html(s.title + ":&nbsp;<i>" + s.section + "</i>");
+      }
+    }
+    if (data.terminfo.rubric) {
+      const grade_td = self.dom.tbody.append("tr").append("td").style("padding", "5px 0").append("div").style("font-weight", "bold").text("Grading Rubric").append("ol").style("margin", "0px");
+      for (let grade of data.terminfo.rubric) {
+        grade_td.append("li").style("font-weight", "normal").text(grade);
+      }
+    }
+    self.dom.details.selectAll("*").remove();
+    if (data.terminfo.description) {
+      const header = self.dom.details.append("div").style("padding-top", "20px").style("padding-bottom", "10px").style("font-weight", "bold").text("Description");
+      for (const d of data.terminfo.description) {
+        self.renderDetail(d, self.dom.details.append("div").style("padding-bottom", "3px"));
+      }
+    }
+  };
+  self.renderDetail = function(d, div) {
+    if (Array.isArray(d.value)) {
+      div.append("span").html("<i>" + d.label + "</i>");
+      const section = div.append("div").style("padding-left", "20px");
+      for (const v of d.value) {
+        v.label = "- " + v.label;
+        self.renderDetail(v, section.append("div"));
+      }
+    } else {
+      div.html("<i>" + d.label + ":</i>&nbsp;" + d.value);
+    }
+  };
+}
+function setInteractivity(self) {
+  self.toggleDescription = function() {
+    self.state.isVisible = !self.state.isVisible;
+    self.main({ isVisible: self.state.isVisible });
+  };
+}
+
+export {
+  termInfoInit
+};
+//# sourceMappingURL=chunk-ZFFHOEBE.js.map