@sjcrh/proteinpaint-client 2.216.0 → 2.217.0

package/dist/swimmer-VPKSBV6V.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/swimmer.ts"],
+  "sourcesContent": ["import { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase } from '#plots/PlotBase.ts'\nimport { controlsInit } from './controls'\nimport { dofetch3 } from '#common/dofetch'\nimport { Menu, DownloadMenu, axisstyle, shapes, shapeSelector } from '#dom'\nimport { rgb } from 'd3-color'\nimport { getCombinedTermFilter } from '#filter'\nimport { getColors } from '#shared/common.js'\nimport { scaleLinear } from 'd3-scale'\nimport { axisBottom } from 'd3-axis'\nimport type { SwimmerLane, SwimmerLegendItem, SwimmerPoint, SwimmerRequest, SwimmerResponse } from '#types'\nimport { getTermValue } from './sampleView.ts'\nimport { getT0T2defaultQ } from './summaryQ.ts'\nimport { fillTermWrapper } from '#termsetting'\n\n/*\nswimmer plot: one horizontal lane per patient. the light base bar spans from\ntime 0 to the lane end (the terminal event, e.g. death, else the latest event or interval end);\ncolored segments mark treatment intervals; dots mark clinical events.\n*/\n\ntype LegendEntry = {\n\tkey: string\n\tlabel: string\n\tcolor: string\n\tshape: string\n\tsampleTerms?: string[]\n\t/** hidden by the user in the legend: its segments or markers are not drawn */\n\thidden: boolean\n}\n\n/** user changes to one legend item, overriding the ds config */\ntype LegendOverride = { color?: string; shape?: string; hidden?: boolean }\n\n/** legend overrides by legend label (items of several keys merged under one label change together).\nhidden is stored as false rather than deleted, since plot_edit merges settings and cannot remove keys */\ntype LegendOverrides = {\n\tcategories: { [label: string]: LegendOverride }\n\tevents: { [label: string]: LegendOverride }\n\t/** categories of the \"mark by\" term on linked points (e.g. ctDNA status of CSF dots) */\n\tpointCategories: { [label: string]: LegendOverride }\n}\n\n/** linked points (with a point sample) that have no value for the \"mark by\" term */\nconst noValueCategory = 'No value'\n\n/** pixel width of the legend column, right of the lanes */\nconst legendWidth = 190\n\n/** bounding box of each shape path within its 16x16 icon box, measured once per shape. the icons fill\nthat box unevenly (e.g. the cross spans 12px, the circle 16px), so sizing by the box would give markers\nof different heights */\nconst shapeBBox = new Map<string, { x: number; y: number; width: number; height: number }>()\n\n/** draw an event marker centered at (cx, cy) inside holder, scaled so the visible shape is `height` px tall.\nthe shape is a key of the shared #dom shapes. a transparent\nrect keeps thin shapes (e.g. a cross) easy to hover */\nfunction drawMarker(holder, shapeKey: string, cx: number, cy: number, height: number, color: string) {\n\tconst key = shapes[shapeKey] ? shapeKey : 'filledCircle'\n\tconst shape = shapes[key]\n\tconst g = holder.append('g').attr('transform', `translate(${cx},${cy})`)\n\tg.append('rect')\n\t\t.attr('x', -height / 2)\n\t\t.attr('y', -height / 2)\n\t\t.attr('width', height)\n\t\t.attr('height', height)\n\t\t.attr('fill', 'transparent')\n\tconst path = g.append('path').attr('d', shape.path).attr('fill', color)\n\tlet box = shapeBBox.get(key)\n\tif (!box) {\n\t\tconst b = path.node().getBBox()\n\t\t// getBBox() is all zeros while the svg is hidden; fall back to the icon box without caching\n\t\tif (b.width && b.height) {\n\t\t\tbox = { x: b.x, y: b.y, width: b.width, height: b.height }\n\t\t\tshapeBBox.set(key, box)\n\t\t}\n\t}\n\tconst bb = box || { x: 0, y: 0, width: 16, height: 16 }\n\t// solid shapes get a thin white halo; line shapes (cross, outlines) are thin filled paths, so a\n\t// same-colored stroke thickens them to stay legible. the stroke (px) is subtracted from the height\n\tconst strokePx = shape.isFilled ? 0.5 : Math.max(1, height * 0.08)\n\tconst scale = Math.max(0.1, height - strokePx) / bb.height\n\tpath\n\t\t.attr('transform', `scale(${scale}) translate(${-(bb.x + bb.width / 2)},${-(bb.y + bb.height / 2)})`)\n\t\t.attr('stroke', shape.isFilled ? 'white' : color)\n\t\t.attr('stroke-width', strokePx / scale)\n\t\t.attr('stroke-linejoin', 'round')\n\treturn g\n}\n\ntype SwimmerSettings = {\n\t/** pixel height of one lane, including spacing */\n\trowHeight: number\n\t/** pixel width of the lane area, excluding sample names and legend */\n\tplotWidth: number\n\t/** 'end': longest lane first; 'sample': by lane (patient) name */\n\tsortBy: 'end' | 'sample'\n\tshowSampleNames: boolean\n\tlegend: LegendOverrides\n}\n\nclass Swimmer extends PlotBase implements RxComponent {\n\tstatic type = 'swimmer'\n\n\ttype: string\n\tcomponents: { controls: any }\n\tdom!: {\n\t\tholder: any\n\t\tcontrolsHolder: any\n\t\terrdiv: any\n\t\tloadingDiv: any\n\t\tplotDiv: any\n\t\tnoteDiv: any\n\t\ttip: Menu\n\t}\n\trenderer!: SwimmerRenderer\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = Swimmer.type\n\t\tthis.components = { controls: {} }\n\t\tif (this.opts.header) {\n\t\t\tthis.opts.header.style('padding-left', '7px').style('color', 'rgb(85, 85, 85)').html('Swimmer Plot')\n\t\t}\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn {\n\t\t\tconfig,\n\t\t\t// global mass filter combined with this plot's local filter (config.filter, set by the plot wrapper's filter UI)\n\t\t\ttermfilter: getCombinedTermFilter(appState, config.filter),\n\t\t\tgenome: appState.vocab.genome,\n\t\t\tdslabel: appState.vocab.dslabel,\n\t\t\tswimmer: appState.termdbConfig?.queries?.swimmer || {}\n\t\t}\n\t}\n\n\tasync init() {\n\t\tconst holder = this.opts.holder.append('div').attr('data-testid', 'sjpp-swimmer-holder')\n\t\tconst controlsHolder = holder.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\t\tconst rightDiv = holder.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\tcontrolsHolder,\n\t\t\terrdiv: rightDiv.append('div').attr('class', 'sja_errorbar').style('display', 'none'),\n\t\t\tloadingDiv: rightDiv.append('div').style('display', 'none').style('padding', '24px').text('Loading ...'),\n\t\t\tplotDiv: rightDiv.append('div').attr('data-testid', 'sjpp-swimmer-plot').style('padding', '10px'),\n\t\t\tnoteDiv: rightDiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('padding', '0 10px 10px 10px')\n\t\t\t\t.style('font-size', '.9em')\n\t\t\t\t.style('opacity', 0.7),\n\t\t\ttip: new Menu({ padding: '5px' })\n\t\t}\n\t\tthis.renderer = new SwimmerRenderer(this.app, this.dom, settings =>\n\t\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config: { settings: { swimmer: settings } } })\n\t\t)\n\t\tconst laneName = this.renderer.laneType?.name || 'sample'\n\t\tthis.components = {\n\t\t\tcontrols: await controlsInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tholder: controlsHolder,\n\t\t\t\tinputs: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttype: 'term',\n\t\t\t\t\t\tconfigKey: 'term0',\n\t\t\t\t\t\tchartType: 'swimmer',\n\t\t\t\t\t\tusecase: { target: 'swimmer', detail: 'term0' },\n\t\t\t\t\t\tlabel: 'Divide by',\n\t\t\t\t\t\ttitle: 'Split lanes into one panel per category',\n\t\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\t\t\t\tdefaultQ4fillTW: getT0T2defaultQ()\n\t\t\t\t\t},\n\t\t\t\t\t...this.getPointTermInputs(),\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Sort lanes by',\n\t\t\t\t\t\ttype: 'radio',\n\t\t\t\t\t\tchartType: 'swimmer',\n\t\t\t\t\t\tsettingsKey: 'sortBy',\n\t\t\t\t\t\toptions: [\n\t\t\t\t\t\t\t{ label: 'Lane length', value: 'end' },\n\t\t\t\t\t\t\t{ label: `${laneName[0].toUpperCase()}${laneName.slice(1)} name`, value: 'sample' }\n\t\t\t\t\t\t]\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: `Show ${laneName} names`,\n\t\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\t\tchartType: 'swimmer',\n\t\t\t\t\t\tsettingsKey: 'showSampleNames',\n\t\t\t\t\t\tboxLabel: 'Yes'\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Row height',\n\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\tchartType: 'swimmer',\n\t\t\t\t\t\tsettingsKey: 'rowHeight',\n\t\t\t\t\t\tmin: 6,\n\t\t\t\t\t\tmax: 50\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Plot width',\n\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\tchartType: 'swimmer',\n\t\t\t\t\t\tsettingsKey: 'plotWidth',\n\t\t\t\t\t\tmin: 200,\n\t\t\t\t\t\tmax: 3000\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t})\n\t\t}\n\t\tthis.components.controls.on('downloadClick.swimmer', event => {\n\t\t\tconst svg = this.renderer.dom.svg\n\t\t\tif (!svg) return\n\t\t\tnew DownloadMenu([{ name: 'Swimmer plot', svg }], 'swimmer_plot').show(event.clientX, event.clientY, event.target)\n\t\t})\n\t}\n\n\t/** \"Mark <event> by\" term input, only when the ds has points linked to samples (e.g. CSF dots). the\n\tterm picker lists only terms of those samples' types */\n\tgetPointTermInputs() {\n\t\tconst sw = this.app.vocabApi.termdbConfig?.queries?.swimmer\n\t\tif (!sw?.pointSampleTypes?.length) return []\n\t\tconst events = (sw.pointSampleEvents || []).map(k => sw.events?.[k]?.label || k)\n\t\tconst what = [...new Set(events)].join(' / ') || 'linked samples'\n\t\treturn [\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'pointTerm',\n\t\t\t\tchartType: 'swimmer',\n\t\t\t\tusecase: { target: 'swimmer', detail: 'pointTerm', sampleTypes: sw.pointSampleTypes },\n\t\t\t\tlabel: `Mark ${what} by`,\n\t\t\t\ttitle: `Color the ${what} markers by a variable of their own samples`,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\t\tdefaultQ4fillTW: getT0T2defaultQ()\n\t\t\t}\n\t\t]\n\t}\n\n\tasync main() {\n\t\ttry {\n\t\t\tthis.toggleLoadingDiv()\n\t\t\tthis.dom.errdiv.style('display', 'none')\n\t\t\tconst result = await this.fetchLanes()\n\t\t\tthis.toggleLoadingDiv('none')\n\t\t\tthis.renderer.update({\n\t\t\t\tswimmer: this.state.swimmer,\n\t\t\t\tsettings: this.state.config.settings.swimmer,\n\t\t\t\tlanes: result.lanes,\n\t\t\t\tdivideByOrder: result.divideByOrder,\n\t\t\t\tterm0: this.state.config.term0,\n\t\t\t\tpointTerm: this.state.config.pointTerm,\n\t\t\t\tpointCategoryOrder: result.pointCategoryOrder\n\t\t\t})\n\t\t} catch (e: any) {\n\t\t\tthis.toggleLoadingDiv('none')\n\t\t\tthis.printError(e)\n\t\t}\n\t}\n\n\tdestroy() {\n\t\tthis.renderer?.destroy()\n\t}\n\n\tasync fetchLanes(): Promise<SwimmerResponse> {\n\t\tconst body: any = {\n\t\t\tgenome: this.state.genome,\n\t\t\tdslabel: this.state.dslabel,\n\t\t\tfilter: this.state.termfilter?.filter\n\t\t}\n\t\tif (this.state.config.term0) body.term0 = this.state.config.term0\n\t\tif (this.state.config.pointTerm) body.pointTerm = this.state.config.pointTerm\n\t\treturn await fetchSwimmerLanes(body)\n\t}\n}\n\n/** draws swimmer lanes, divide-by panels and the legend into dom.plotDiv, with notes in dom.noteDiv. used by\nthe swimmer chart and by sample view, which shows the lane of the viewed patient */\nexport class SwimmerRenderer {\n\tapp: any\n\t/** client copy of ds.queries.swimmer: timeLabel, categories, events, terminalEvent, pointSampleTypes,\n\tpointSampleEvents */\n\tswimmer: any = {}\n\tsettings!: SwimmerSettings\n\t/** divide-by tw, lanes are then split into one panel per category */\n\tterm0?: any\n\tlanes: SwimmerLane[] = []\n\t/** divide-by category order from the server, only with term0 */\n\tdivideByOrder: string[] = []\n\t/** \"mark by\" tw of the linked points (e.g. a CSF term); their markers are then colored by point.category */\n\tpointTerm?: any\n\t/** point category order from the server, only with pointTerm */\n\tpointCategoryOrder: string[] = []\n\tdom: { plotDiv: any; noteDiv: any; tip: Menu; svg?: any }\n\t/** sample type of the lanes, which are patients: the root sample type when the db has exactly one, e.g.\n\t{name:'patient', plural_name:'patients'}, to name lanes in messages and controls. */\n\tlaneType?: { name: string; plural_name: string }\n\t/** annotations of point samples (e.g. CSF) shown on hover, fetched once per sample id */\n\tpointSampleAnno = new Map<string, Promise<{ label: string; value: string }[]>>()\n\t/** menu to edit a legend entry, reused across legend clicks */\n\tlegendMenu?: Menu\n\n\t/** called with changed settings (e.g. legend edits); without it the renderer keeps the change itself and\n\tredraws, as in sample view where the lane has no plot config to save it to */\n\tonSettingsChange?: (settings: Partial<SwimmerSettings>) => void\n\n\tconstructor(\n\t\tapp: any,\n\t\tdom: { plotDiv: any; noteDiv: any; tip: Menu },\n\t\tonSettingsChange?: (settings: Partial<SwimmerSettings>) => void\n\t) {\n\t\tthis.app = app\n\t\tthis.dom = dom\n\t\tthis.onSettingsChange = onSettingsChange\n\t\tconst roots = Object.values(app.vocabApi?.termdbConfig?.sampleTypes || {}).filter((t: any) => t.parent_id == null)\n\t\tif (roots.length == 1) this.laneType = roots[0] as { name: string; plural_name: string }\n\t}\n\n\tupdate(d: {\n\t\tswimmer: any\n\t\tsettings: SwimmerSettings\n\t\tlanes: SwimmerLane[]\n\t\tdivideByOrder?: string[]\n\t\tterm0?: any\n\t\tpointTerm?: any\n\t\tpointCategoryOrder?: string[]\n\t}) {\n\t\tthis.swimmer = d.swimmer || {}\n\t\tthis.settings = d.settings\n\t\tthis.lanes = d.lanes\n\t\tthis.divideByOrder = d.divideByOrder || []\n\t\tthis.term0 = d.term0\n\t\tthis.pointTerm = d.pointTerm\n\t\tthis.pointCategoryOrder = d.pointCategoryOrder || []\n\t\tthis.render()\n\t}\n\n\t/** whether a point is colored by the \"mark by\" term: a linked point of a markBy event */\n\tisMarkedPoint(p: SwimmerPoint): boolean {\n\t\treturn !!this.pointTerm && p.sampleId !== undefined && !!this.swimmer.pointSampleEvents?.includes(p.event)\n\t}\n\n\t/** with pointTerm: legend of the marked points' categories, in server order, then \"No value\" when some\n\tmarked point lacks a value. colors come from term.values when set there, else a default palette; the shape\n\tis that of the point's event. user overrides apply as for the other legend sections */\n\tgetPointLegend(events: { byKey: Map<string, LegendEntry> }) {\n\t\tif (!this.pointTerm) return { byKey: new Map<string, LegendEntry>(), entries: [] as LegendEntry[] }\n\t\tlet hasNoValue = false\n\t\tlet shape: string | undefined\n\t\tfor (const lane of this.lanes) {\n\t\t\tfor (const p of lane.points) {\n\t\t\t\tif (!this.isMarkedPoint(p)) continue\n\t\t\t\tshape ||= events.byKey.get(p.event)?.shape\n\t\t\t\tif (!p.category) hasNoValue = true\n\t\t\t}\n\t\t}\n\t\tconst termColors = new Map<string, string>()\n\t\tfor (const [k, v] of Object.entries((this.pointTerm.term?.values || {}) as { [k: string]: any }))\n\t\t\tif (v.color) termColors.set(v.label || k, v.color)\n\t\tconst labels = [...this.pointCategoryOrder, ...(hasNoValue ? [noValueCategory] : [])]\n\t\tconst palette = getColors(Math.max(labels.length, 1))\n\t\tconst configured = {}\n\t\tfor (const label of labels)\n\t\t\tconfigured[label] = {\n\t\t\t\tlabel,\n\t\t\t\tcolor: label == noValueCategory ? '#aaa' : termColors.get(label) || palette(label),\n\t\t\t\tshape\n\t\t\t}\n\t\treturn this.getLegend(configured, new Set(labels), this.settings.legend?.pointCategories)\n\t}\n\n\t/** lanes split by divide-by category, in server order. without term0 there is one unlabeled group.\n\ta patient with several categories (a multivalue term, or samples in different categories) is in each\n\tof its groups; lanes without a value are left out and counted in the note below the plot */\n\tgetGroups<T extends { lane: SwimmerLane }>(lanes: T[]): { label?: string; lanes: T[] }[] {\n\t\tif (!this.term0) return [{ lanes }]\n\t\tconst byLabel = new Map<string, T[]>(this.divideByOrder.map(c => [c, []]))\n\t\tlet noValue = 0\n\t\tfor (const l of lanes) {\n\t\t\tif (!l.lane.divideBy?.length) {\n\t\t\t\tnoValue++\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tfor (const c of l.lane.divideBy) {\n\t\t\t\tif (!byLabel.has(c)) byLabel.set(c, [])\n\t\t\t\tbyLabel.get(c)!.push(l)\n\t\t\t}\n\t\t}\n\t\tif (noValue) {\n\t\t\tconst name = this.term0.term?.name || 'the divide-by variable'\n\t\t\tconst noun = noValue > 1 ? this.laneType?.plural_name || 'samples' : this.laneType?.name || 'sample'\n\t\t\tthis.dom.noteDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-swimmer-novalue-note')\n\t\t\t\t.text(`${noValue} ${noun} without a value for ${name} not shown`)\n\t\t}\n\t\treturn [...byLabel].filter(([, l]) => l.length).map(([label, l]) => ({ label, lanes: l }))\n\t}\n\n\t/** lane end: the terminal event time when present, else the latest event or interval time */\n\tgetLaneEnd(lane: SwimmerLane): number {\n\t\tconst terminal = this.swimmer.terminalEvent\n\t\tif (terminal) {\n\t\t\tconst t = lane.points.find(p => p.event == terminal)\n\t\t\tif (t) return t.time\n\t\t}\n\t\tlet end = 0\n\t\tfor (const p of lane.points) end = Math.max(end, p.time)\n\t\tfor (const r of lane.ranges) end = Math.max(end, r.start, r.end ?? 0)\n\t\treturn end\n\t}\n\n\t/** legend entries for interval categories or events: configured items first (in config order,\n\tmerged by label), then any key found in the data that the ds did not configure, with a default color.\n\tuser overrides (by label) take precedence over the ds config */\n\tgetLegend(\n\t\tconfigured: { [key: string]: SwimmerLegendItem } | undefined,\n\t\tdataKeys: Set<string>,\n\t\toverrides: { [label: string]: LegendOverride } = {}\n\t) {\n\t\tconst byKey = new Map<string, LegendEntry>()\n\t\tconst entries: LegendEntry[] = []\n\t\tconst seenLabels = new Set<string>()\n\t\tconst unconfigured = [...dataKeys].filter(k => !configured?.[k])\n\t\tconst fallback = getColors(Math.max(unconfigured.length, 1))\n\t\tconst add = (key: string, item: SwimmerLegendItem) => {\n\t\t\tconst label = item.label || key\n\t\t\tconst o = overrides[label] || {}\n\t\t\tconst e: LegendEntry = {\n\t\t\t\tkey,\n\t\t\t\tlabel,\n\t\t\t\tcolor: o.color || item.color || fallback(key),\n\t\t\t\tshape: o.shape || item.shape || 'filledCircle',\n\t\t\t\tsampleTerms: item.sampleTerms,\n\t\t\t\thidden: !!o.hidden\n\t\t\t}\n\t\t\tbyKey.set(key, e)\n\t\t\tif (!seenLabels.has(e.label)) {\n\t\t\t\tseenLabels.add(e.label)\n\t\t\t\tentries.push(e)\n\t\t\t}\n\t\t}\n\t\tfor (const [key, item] of Object.entries(configured || {})) add(key, item)\n\t\tfor (const key of unconfigured) add(key, {})\n\t\treturn { byKey, entries }\n\t}\n\n\trender() {\n\t\tconst s = this.settings\n\t\tconst plotDiv = this.dom.plotDiv\n\t\tplotDiv.selectAll('*').remove()\n\t\tthis.dom.noteDiv.selectAll('*').remove()\n\t\tdelete this.dom.svg\n\n\t\tif (!this.lanes.length) {\n\t\t\tplotDiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('opacity', 0.6)\n\t\t\t\t.text(`No ${this.laneType?.plural_name || 'samples'} with timeline data match the current filter`)\n\t\t\treturn\n\t\t}\n\n\t\tconst lanes = this.lanes.map(lane => ({ lane, end: this.getLaneEnd(lane) }))\n\t\tif (s.sortBy == 'sample') lanes.sort((a, b) => a.lane.sample.localeCompare(b.lane.sample))\n\t\telse lanes.sort((a, b) => b.end - a.end)\n\n\t\tconst categoryKeys = new Set<string>()\n\t\tconst eventKeys = new Set<string>()\n\t\tfor (const { lane } of lanes) {\n\t\t\tfor (const r of lane.ranges) categoryKeys.add(r.category)\n\t\t\tfor (const p of lane.points) eventKeys.add(p.event)\n\t\t}\n\t\tconst categories = this.getLegend(this.swimmer.categories, categoryKeys, s.legend?.categories)\n\t\tconst events = this.getLegend(this.swimmer.events, eventKeys, s.legend?.events)\n\t\tconst pointCategories = this.getPointLegend(events)\n\n\t\tconst fontSize = Math.min(12, Math.max(7, s.rowHeight - 3))\n\t\tconst axisHeight = 45\n\t\tconst topPad = 10\n\t\tconst rightPad = 20\n\t\t// lanes are separated by a thin fixed gap so the bar fills most of the row; segments and\n\t\t// event dots scale with the bar rather than the row\n\t\tconst laneGap = Math.max(1, Math.round(s.rowHeight * 0.1))\n\t\tconst barH = Math.max(2, s.rowHeight - laneGap)\n\t\tconst segH = Math.max(1, barH * 0.6)\n\t\t// event markers are 70% of the bar height, all shapes the same height\n\t\tconst markerH = Math.max(4, barH * 0.7)\n\n\t\tconst svg = plotDiv.append('svg').attr('data-testid', 'sjpp-swimmer-svg')\n\t\tthis.dom.svg = svg\n\t\tconst labelWidth = s.showSampleNames\n\t\t\t? getMaxTextWidth(\n\t\t\t\t\tsvg,\n\t\t\t\t\tlanes.map(l => l.lane.sample),\n\t\t\t\t\tfontSize\n\t\t\t  ) + 12\n\t\t\t: 10\n\n\t\t// one shared time scale for all divide-by panels, so they can be compared\n\t\tconst maxEnd = Math.max(...lanes.map(l => l.end), 1)\n\t\t// events before the time origin (e.g. a CSF sample collected before treatment start) have\n\t\t// negative times; extend the axis left so they do not overlap the sample names\n\t\tlet minTime = 0\n\t\tfor (const { lane } of lanes) {\n\t\t\tfor (const p of lane.points) minTime = Math.min(minTime, p.time)\n\t\t\tfor (const r of lane.ranges) minTime = Math.min(minTime, r.start)\n\t\t}\n\t\tconst x = scaleLinear()\n\t\t\t.domain([minTime < 0 ? minTime - (maxEnd - minTime) * 0.01 : 0, maxEnd * 1.02])\n\t\t\t.range([0, s.plotWidth])\n\t\tconst ticks = x.ticks(Math.max(2, Math.floor(s.plotWidth / 90)))\n\n\t\tconst tip = this.dom.tip\n\t\tconst timeLabel = this.swimmer.timeLabel || 'Time'\n\t\tconst fmt = (d: number) => (Number.isInteger(d) ? String(d) : d.toFixed(1))\n\n\t\tconst groups = this.getGroups(lanes)\n\t\tif (!groups.length) {\n\t\t\tsvg.remove()\n\t\t\tdelete this.dom.svg\n\t\t\tplotDiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('opacity', 0.6)\n\t\t\t\t.text(`No ${this.laneType?.plural_name || 'samples'} have a value for the divide-by variable`)\n\t\t\treturn\n\t\t}\n\t\tconst titleH = groups[0].label !== undefined ? 24 : 0\n\t\tconst groupGap = 16\n\t\tlet yOffset = topPad\n\t\tfor (const group of groups) {\n\t\t\tif (group.label !== undefined) {\n\t\t\t\tsvg\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.attr('data-testid', 'sjpp-swimmer-group-title')\n\t\t\t\t\t.attr('x', labelWidth)\n\t\t\t\t\t.attr('y', yOffset + 15)\n\t\t\t\t\t.attr('font-size', 14)\n\t\t\t\t\t.attr('font-weight', 600)\n\t\t\t\t\t.attr('fill', '#333')\n\t\t\t\t\t.text(`${group.label} (n=${group.lanes.length})`)\n\t\t\t\tyOffset += titleH\n\t\t\t}\n\t\t\tconst plotHeight = group.lanes.length * s.rowHeight\n\t\t\tconst mainG = svg.append('g').attr('transform', `translate(${labelWidth},${yOffset})`)\n\n\t\t\t// vertical grid lines behind the lanes\n\t\t\tmainG\n\t\t\t\t.append('g')\n\t\t\t\t.selectAll('line')\n\t\t\t\t.data(ticks)\n\t\t\t\t.enter()\n\t\t\t\t.append('line')\n\t\t\t\t.attr('x1', d => x(d))\n\t\t\t\t.attr('x2', d => x(d))\n\t\t\t\t.attr('y1', 0)\n\t\t\t\t.attr('y2', plotHeight)\n\t\t\t\t.attr('stroke', '#e6e6e6')\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\n\t\t\tfor (const [i, { lane, end }] of group.lanes.entries()) {\n\t\t\t\tconst y = i * s.rowHeight\n\t\t\t\tconst g = mainG.append('g').attr('transform', `translate(0,${y})`)\n\n\t\t\t\t// base bar\n\t\t\t\tg.append('rect')\n\t\t\t\t\t.attr('x', x(0))\n\t\t\t\t\t.attr('y', (s.rowHeight - barH) / 2)\n\t\t\t\t\t.attr('width', Math.max(0, x(end) - x(0)))\n\t\t\t\t\t.attr('height', barH)\n\t\t\t\t\t.attr('fill', '#f7f7f7')\n\t\t\t\t\t.attr('stroke', '#999')\n\t\t\t\t\t.attr('stroke-width', 0.5)\n\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\ttip.clear().show(event.clientX, event.clientY)\n\t\t\t\t\t\ttip.d.append('div').style('font-weight', 'bold').text(lane.sample)\n\t\t\t\t\t\ttip.d.append('div').text(`Lane end: ${fmt(end)} (${timeLabel.toLowerCase()})`)\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => tip.hide())\n\n\t\t\t\t// interval segments. one without an end (blank or NA in the file) is ongoing: drawn up to the lane\n\t\t\t\t// end, with an arrowhead\n\t\t\t\tfor (const r of lane.ranges) {\n\t\t\t\t\tconst entry = categories.byKey.get(r.category)!\n\t\t\t\t\tif (entry.hidden) continue\n\t\t\t\t\tconst segEnd = r.end ?? Math.max(end, r.start)\n\t\t\t\t\tconst segTop = (s.rowHeight - segH) / 2\n\t\t\t\t\tconst seg = g.append('g').on('mouseout', () => tip.hide())\n\t\t\t\t\tseg\n\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t.attr('x', x(r.start))\n\t\t\t\t\t\t.attr('y', segTop)\n\t\t\t\t\t\t.attr('width', Math.max(1, x(segEnd) - x(r.start)))\n\t\t\t\t\t\t.attr('height', segH)\n\t\t\t\t\t\t.attr('fill', entry.color)\n\t\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\tif (r.end == null) {\n\t\t\t\t\t\tconst xe = x(r.start) + Math.max(1, x(segEnd) - x(r.start))\n\t\t\t\t\t\tseg\n\t\t\t\t\t\t\t.append('path')\n\t\t\t\t\t\t\t.attr(\n\t\t\t\t\t\t\t\t'd',\n\t\t\t\t\t\t\t\t`M${xe},${segTop - segH / 3}L${xe + segH * 0.8},${s.rowHeight / 2}L${xe},${segTop + segH * 1.33}Z`\n\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t.attr('fill', entry.color)\n\t\t\t\t\t}\n\t\t\t\t\tseg.on('mouseover', event => {\n\t\t\t\t\t\ttip.clear().show(event.clientX, event.clientY)\n\t\t\t\t\t\ttip.d.append('div').style('font-weight', 'bold').text(lane.sample)\n\t\t\t\t\t\ttip.d.append('div').text(`${entry.label}${entry.label != r.category ? ` (${r.category})` : ''}`)\n\t\t\t\t\t\ttip.d\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.text(\n\t\t\t\t\t\t\t\tr.end == null\n\t\t\t\t\t\t\t\t\t? `From ${fmt(r.start)}, ongoing (${timeLabel.toLowerCase()})`\n\t\t\t\t\t\t\t\t\t: `${fmt(r.start)} to ${fmt(r.end)} (${timeLabel.toLowerCase()})`\n\t\t\t\t\t\t\t)\n\t\t\t\t\t})\n\t\t\t\t}\n\n\t\t\t\t// events\n\t\t\t\tfor (const p of lane.points) {\n\t\t\t\t\tconst entry = events.byKey.get(p.event)!\n\t\t\t\t\tif (entry.hidden) continue\n\t\t\t\t\t// a marked point is drawn by its \"mark by\" category\n\t\t\t\t\tconst mark = this.isMarkedPoint(p) ? pointCategories.byKey.get(p.category || noValueCategory) : undefined\n\t\t\t\t\tif (mark?.hidden) continue\n\t\t\t\t\tconst dot = drawMarker(\n\t\t\t\t\t\tg,\n\t\t\t\t\t\tmark?.shape || entry.shape,\n\t\t\t\t\t\tx(p.time),\n\t\t\t\t\t\ts.rowHeight / 2,\n\t\t\t\t\t\tmarkerH,\n\t\t\t\t\t\tmark?.color || entry.color\n\t\t\t\t\t)\n\t\t\t\t\t\t.attr('data-event', p.event)\n\t\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\t\ttip.clear().show(event.clientX, event.clientY)\n\t\t\t\t\t\t\ttip.d.append('div').style('font-weight', 'bold').text(lane.sample)\n\t\t\t\t\t\t\ttip.d.append('div').text(`${entry.label}: ${fmt(p.time)} (${timeLabel.toLowerCase()})`)\n\t\t\t\t\t\t\tif (mark) tip.d.append('div').text(`${this.pointTerm.term?.name}: ${mark.label}`)\n\t\t\t\t\t\t\tif (p.sample) {\n\t\t\t\t\t\t\t\ttip.d.append('div').text(`Sample: ${p.sample}`)\n\t\t\t\t\t\t\t\tif (p.sampleId !== undefined && entry.sampleTerms?.length)\n\t\t\t\t\t\t\t\t\tthis.showPointSampleAnno(tip, p.sampleId, entry.sampleTerms)\n\t\t\t\t\t\t\t\ttip.d.append('div').style('font-size', '0.8em').style('opacity', 0.7).text('Click to open sample view')\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('mouseout', () => tip.hide())\n\t\t\t\t\tif (p.sample && p.sampleId !== undefined) {\n\t\t\t\t\t\tconst sample = { sampleId: p.sampleId, sampleName: p.sample }\n\t\t\t\t\t\tdot\n\t\t\t\t\t\t\t.attr('data-testid', 'sjpp-swimmer-linked-point')\n\t\t\t\t\t\t\t.attr('role', 'button')\n\t\t\t\t\t\t\t.attr('tabindex', 0)\n\t\t\t\t\t\t\t.attr('aria-label', `Open sample view of ${p.sample}`)\n\t\t\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t\t\tthis.openSampleView(sample)\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t.on('keydown', (event: KeyboardEvent) => {\n\t\t\t\t\t\t\t\tif (event.key === 'Enter' || event.key === ' ') {\n\t\t\t\t\t\t\t\t\tevent.preventDefault()\n\t\t\t\t\t\t\t\t\tthis.openSampleView(sample)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tif (s.showSampleNames) {\n\t\t\t\t\tg.append('text')\n\t\t\t\t\t\t.attr('x', -6)\n\t\t\t\t\t\t.attr('y', s.rowHeight / 2)\n\t\t\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t\t.attr('font-size', fontSize)\n\t\t\t\t\t\t.attr('fill', '#333')\n\t\t\t\t\t\t.attr('role', 'button')\n\t\t\t\t\t\t.attr('tabindex', 0)\n\t\t\t\t\t\t.attr('aria-label', `Open sample view of ${lane.sample}`)\n\t\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t\t.text(lane.sample)\n\t\t\t\t\t\t.on('click', () => this.openSampleView({ sampleId: lane.sampleId, sampleName: lane.sample }, true))\n\t\t\t\t\t\t.on('keydown', (event: KeyboardEvent) => {\n\t\t\t\t\t\t\tif (event.key === 'Enter' || event.key === ' ') {\n\t\t\t\t\t\t\t\tevent.preventDefault()\n\t\t\t\t\t\t\t\tthis.openSampleView({ sampleId: lane.sampleId, sampleName: lane.sample }, true)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\t\ttip.clear().show(event.clientX, event.clientY)\n\t\t\t\t\t\t\ttip.d.append('div').text('Click to open sample view')\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('mouseout', () => tip.hide())\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// x axis\n\t\t\tconst axisG = mainG.append('g').attr('transform', `translate(0,${plotHeight + 2})`)\n\t\t\taxisG.call(axisBottom(x).tickValues(ticks))\n\t\t\taxisstyle({ axis: axisG, showline: true, fontsize: 11 })\n\t\t\taxisG\n\t\t\t\t.append('text')\n\t\t\t\t.attr('x', s.plotWidth / 2)\n\t\t\t\t.attr('y', 34)\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('font-size', 12)\n\t\t\t\t.attr('fill', '#333')\n\t\t\t\t.text(timeLabel)\n\t\t\tyOffset += plotHeight + axisHeight + groupGap\n\t\t}\n\t\tconst legendHeight = this.renderLegend(\n\t\t\tsvg.append('g').attr('transform', `translate(${labelWidth + s.plotWidth + rightPad},${topPad})`),\n\t\t\tcategories.entries,\n\t\t\tevents.entries,\n\t\t\tpointCategories.entries\n\t\t)\n\t\t// a few lanes (e.g. one patient in sample view) can be shorter than the legend\n\t\tsvg\n\t\t\t.attr('width', labelWidth + s.plotWidth + rightPad + legendWidth)\n\t\t\t.attr('height', Math.max(yOffset - groupGap, topPad + legendHeight))\n\t}\n\n\t/** returns the legend height. events linked to samples (e.g. \"CSF sample\") are listed last. with a \"mark\n\tby\" term their markers take the term's category colors and shapes, so the event row has no icon and names\n\tthe term, and the term's categories follow, indented:\n\t  Events\n\t    Follow-up\n\t    CSF sample by <term name>\n\t      category1\n\t      category2 */\n\trenderLegend(g, categories: LegendEntry[], events: LegendEntry[], pointCategories: LegendEntry[] = []): number {\n\t\tconst lineH = 18\n\t\tconst indent = 20\n\t\tlet y = 0\n\t\tconst fit = (text: string, max: number) => (text.length > max ? text.slice(0, max - 1) + '\u2026' : text)\n\t\tconst title = (text: string) => {\n\t\t\tg.append('text')\n\t\t\t\t.attr('y', y + 10)\n\t\t\t\t.attr('font-size', 12)\n\t\t\t\t.attr('font-weight', 'bold')\n\t\t\t\t.text(text)\n\t\t\ty += lineH\n\t\t}\n\t\tconst item = (\n\t\t\ttype: keyof LegendOverrides,\n\t\t\te: LegendEntry,\n\t\t\tentries: LegendEntry[],\n\t\t\tdrawIcon: (holder: any, e: LegendEntry) => void,\n\t\t\t/** label: shown instead of e.label */\n\t\t\topts: { x?: number; allowColor?: boolean; allowShape?: boolean; label?: string } = {}\n\t\t) => {\n\t\t\tconst x = opts.x || 0\n\t\t\t// long labels (e.g. a term name, or a free-text note stored as a category) are cut to fit the legend\n\t\t\t// width, with the full text on hover\n\t\t\tconst max = Math.floor((26 * (legendWidth - x)) / legendWidth)\n\t\t\tconst row = g\n\t\t\t\t.append('g')\n\t\t\t\t.attr('transform', `translate(${x},${y})`)\n\t\t\t\t.attr('data-testid', 'sjpp-swimmer-legend-item')\n\t\t\t\t.attr('data-legend-type', type)\n\t\t\t\t.attr('role', 'button')\n\t\t\t\t.attr('tabindex', 0)\n\t\t\t\t.attr('aria-label', `Edit legend item ${opts.label || e.label}`)\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('opacity', e.hidden ? 0.4 : 1)\n\t\t\tconst showMenu = event =>\n\t\t\t\tthis.showLegendMenu(event, type, e, entries, {\n\t\t\t\t\tallowColor: opts.allowColor !== false,\n\t\t\t\t\tallowShape: type != 'categories' && opts.allowShape !== false\n\t\t\t\t})\n\t\t\trow.on('click', showMenu).on('keydown', (event: KeyboardEvent) => {\n\t\t\t\tif (event.key === 'Enter' || event.key === ' ') {\n\t\t\t\t\tevent.preventDefault()\n\t\t\t\t\tshowMenu(event)\n\t\t\t\t}\n\t\t\t})\n\t\t\t// transparent box so the gap between icon and label is clickable too\n\t\t\trow\n\t\t\t\t.append('rect')\n\t\t\t\t.attr('width', legendWidth - 20 - x)\n\t\t\t\t.attr('height', lineH)\n\t\t\t\t.attr('fill', 'transparent')\n\t\t\tdrawIcon(row, e)\n\t\t\trow\n\t\t\t\t.append('text')\n\t\t\t\t.attr('x', 20)\n\t\t\t\t.attr('y', 10)\n\t\t\t\t.attr('font-size', 12)\n\t\t\t\t.attr('fill', '#333')\n\t\t\t\t.style('text-decoration', e.hidden ? 'line-through' : 'none')\n\t\t\t\t.text(fit(opts.label || e.label, max))\n\t\t\tif ((opts.label || e.label).length > max) row.append('title').text(opts.label || e.label)\n\t\t\ty += lineH\n\t\t}\n\t\tconst rect = (row, e: LegendEntry) =>\n\t\t\trow.append('rect').attr('x', 0).attr('y', 3).attr('width', 14).attr('height', 8).attr('fill', e.color)\n\t\tconst marker = (row, e: LegendEntry) => drawMarker(row, e.shape, 7, 7, 12, e.color)\n\n\t\tif (categories.length) {\n\t\t\ttitle('Intervals')\n\t\t\tfor (const e of categories) item('categories', e, categories, rect)\n\t\t\ty += 8\n\t\t}\n\t\tif (events.length) {\n\t\t\tconst linkedKeys = new Set<string>(this.swimmer.pointSampleEvents || [])\n\t\t\tconst linked = events.filter(e => linkedKeys.has(e.key))\n\t\t\tconst ordered = [...events.filter(e => !linkedKeys.has(e.key)), ...linked]\n\t\t\tconst marked = this.pointTerm && pointCategories.length > 0\n\t\t\ttitle('Events')\n\t\t\tfor (const e of ordered) {\n\t\t\t\tif (!marked || !linkedKeys.has(e.key)) {\n\t\t\t\t\titem('events', e, ordered, marker)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\t// markers take the mark-by term's category colors and shapes: no icon, no color or shape option\n\t\t\t\titem('events', e, ordered, () => {}, {\n\t\t\t\t\tallowColor: false,\n\t\t\t\t\tallowShape: false,\n\t\t\t\t\tlabel: `${e.label} by ${this.pointTerm.term?.name || ''}`\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (marked) {\n\t\t\t\tfor (const e of pointCategories) item('pointCategories', e, pointCategories, marker, { x: indent })\n\t\t\t}\n\t\t\ty += 8\n\t\t}\n\t\treturn y\n\t}\n\n\t/** legend item menu, as in the scatter plot legend: hide/show, show only, show all, color, and shape for\n\tevents. \"show only\" and \"show all\" act within the item's own section (intervals, events or mark-by\n\tcategories). color and shape options are left out for an event whose markers are drawn by the mark-by term */\n\tshowLegendMenu(\n\t\tevent,\n\t\ttype: keyof LegendOverrides,\n\t\te: LegendEntry,\n\t\tentries: LegendEntry[],\n\t\topts: { allowColor: boolean; allowShape: boolean }\n\t) {\n\t\tthis.dom.tip.hide()\n\t\tif (!this.legendMenu) this.legendMenu = new Menu({ padding: '0px' })\n\t\tconst menu = this.legendMenu\n\t\tconst div = menu.clear().d.append('div')\n\t\tconst option = (text: string, edit: () => { [label: string]: LegendOverride }) =>\n\t\t\tdiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.text(text)\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tmenu.hide()\n\t\t\t\t\tthis.editLegend(type, edit())\n\t\t\t\t})\n\t\toption(e.hidden ? 'Show' : 'Hide', () => ({ [e.label]: { hidden: !e.hidden } }))\n\t\tif (entries.length > 1)\n\t\t\toption('Show only', () => Object.fromEntries(entries.map(x => [x.label, { hidden: x.label != e.label }])))\n\t\tif (entries.some(x => x.hidden))\n\t\t\toption('Show all', () => Object.fromEntries(entries.map(x => [x.label, { hidden: false }])))\n\t\tif (opts.allowColor)\n\t\t\tdiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('padding', '0px 10px')\n\t\t\t\t.text('Color:')\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'color')\n\t\t\t\t.attr('value', rgb(e.color).formatHex())\n\t\t\t\t.on('change', (ev: Event) => {\n\t\t\t\t\tmenu.hide()\n\t\t\t\t\tthis.editLegend(type, { [e.label]: { color: (ev.target as HTMLInputElement).value } })\n\t\t\t\t})\n\t\tif (opts.allowShape) {\n\t\t\tdiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.text('Change shape')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tdiv.selectAll('*').remove()\n\t\t\t\t\t// shapeSelector lists the shapes in the order of the shapes object\n\t\t\t\t\tshapeSelector(div, (index: number) => {\n\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t\tthis.editLegend(type, { [e.label]: { shape: Object.keys(shapes)[index] } })\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t}\n\t\tmenu.showunder(event.target)\n\t}\n\n\t/** remove the body-mounted menus and their body listeners */\n\tdestroy() {\n\t\tthis.dom.tip.destroy()\n\t\tthis.legendMenu?.destroy()\n\t}\n\n\t/** merge changes into the legend overrides, then save them through onSettingsChange or redraw locally */\n\teditLegend(type: keyof LegendOverrides, changes: { [label: string]: LegendOverride }) {\n\t\tconst legend: LegendOverrides = structuredClone(\n\t\t\tthis.settings.legend || { categories: {}, events: {}, pointCategories: {} }\n\t\t)\n\t\tif (!legend[type]) legend[type] = {}\n\t\tfor (const [label, o] of Object.entries(changes)) legend[type][label] = { ...legend[type][label], ...o }\n\t\tif (this.onSettingsChange) this.onSettingsChange({ legend })\n\t\telse {\n\t\t\tthis.settings = { ...this.settings, legend }\n\t\t\tthis.render()\n\t\t}\n\t}\n\n\t/** list annotations of a point's own sample (e.g. a CSF sample) in the open tooltip, using the same\n\tsingle-sample query and value formatting as sample view. termIds comes from the event's sampleTerms in\n\tthe dataset config and sets which terms are shown and in what order. the table fills in only if the\n\ttooltip still shows this point */\n\tasync showPointSampleAnno(tip, sampleId: number, termIds: string[]) {\n\t\tconst holder = tip.d.append('div').attr('data-sampleid', sampleId).style('margin', '4px 0')\n\t\tholder.append('div').style('opacity', 0.6).text('Loading annotations ...')\n\t\tlet rows: { label: string; value: string }[]\n\t\ttry {\n\t\t\trows = await this.getPointSampleAnno(sampleId, termIds)\n\t\t} catch (e: any) {\n\t\t\trows = []\n\t\t\tconsole.warn('swimmer: cannot load sample annotations', e)\n\t\t}\n\t\tif (!holder.node()?.isConnected) return // tooltip moved on to another element\n\t\tholder.selectAll('*').remove()\n\t\tif (!rows.length) return\n\t\tconst table = holder.append('table').style('border-spacing', '0 1px').style('font-size', '0.9em')\n\t\tfor (const r of rows) {\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td').style('padding-right', '8px').style('opacity', 0.7).text(r.label)\n\t\t\ttr.append('td').text(r.value)\n\t\t}\n\t}\n\n\tgetPointSampleAnno(sampleId: number, termIds: string[]) {\n\t\tconst cacheKey = `${sampleId}\\t${termIds.join('\\t')}`\n\t\tlet pr = this.pointSampleAnno.get(cacheKey)\n\t\tif (!pr) {\n\t\t\tpr = (async () => {\n\t\t\t\tconst data = await this.app.vocabApi.getSingleSampleData({ sampleId, term_ids: termIds })\n\t\t\t\tif ('error' in data) throw data.error\n\t\t\t\tconst rows: { label: string; value: string }[] = []\n\t\t\t\t// configured order; a term without a value for this sample is skipped\n\t\t\t\tfor (const id of termIds.filter(id => data[id])) {\n\t\t\t\t\tconst term = data[id].term\n\t\t\t\t\tconst value = getTermValue(term, data)\n\t\t\t\t\tif (value != null) rows.push({ label: term.name, value })\n\t\t\t\t}\n\t\t\t\treturn rows\n\t\t\t})()\n\t\t\t// a failed fetch is not cached, so the next hover retries\n\t\t\tpr.catch(() => this.pointSampleAnno.delete(cacheKey))\n\t\t\tthis.pointSampleAnno.set(cacheKey, pr)\n\t\t}\n\t\treturn pr\n\t}\n\n\t/** withRelated: open the sample with its related samples (e.g. a patient lane shows the patient and\n\tits primary/PDX/CSF samples as columns), as when the sample is picked in the sample view search box;\n\totherwise only this sample (e.g. a CSF dot) */\n\topenSampleView(sample: { sampleId: number; sampleName: string }, withRelated = false) {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig: { chartType: 'sampleView', ...(withRelated ? { sample } : { samples: [sample] }) }\n\t\t})\n\t}\n}\n\n/** termdb/swimmer request. the route sends errors as a plain string, so they are not cached by dofetch3 */\nexport async function fetchSwimmerLanes(body: SwimmerRequest): Promise<SwimmerResponse> {\n\tconst result: SwimmerResponse | string = await dofetch3('termdb/swimmer', { body })\n\tif (typeof result == 'string') throw result\n\tif (!result?.lanes) throw 'invalid response from termdb/swimmer'\n\treturn result\n}\n\n/** default settings of the swimmer chart, reused by sample view */\nexport function getDefaultSwimmerSettings(): SwimmerSettings {\n\treturn {\n\t\trowHeight: 20,\n\t\tplotWidth: 800,\n\t\tsortBy: 'end',\n\t\tshowSampleNames: true,\n\t\tlegend: { categories: {}, events: {}, pointCategories: {} }\n\t}\n}\n\n/** widest rendered label in px at the given font size (px). getBBox() is 0 when the svg is hidden,\nwhich only shrinks the left margin; the plot is visible when render() runs */\nfunction getMaxTextWidth(svg, labels: string[], fontSize: number): number {\n\tlet max = 0\n\tfor (const label of labels) {\n\t\tconst t = svg.append('text').attr('font-size', fontSize).text(label)\n\t\tmax = Math.max(max, t.node().getBBox().width)\n\t\tt.remove()\n\t}\n\treturn max\n}\n\nexport async function getPlotConfig(opts, app) {\n\tconst settings = getDefaultSwimmerSettings()\n\tconst config: any = {\n\t\tchartType: 'swimmer',\n\t\tsettings: {\n\t\t\tcontrols: { isOpen: false },\n\t\t\tswimmer: settings\n\t\t}\n\t}\n\tcopyMerge(config, opts)\n\t// a divide-by or mark-by tw from a saved session or another chart is raw until filled here\n\tif (config.term0) config.term0 = await fillTermWrapper(config.term0, app.vocabApi)\n\tif (config.pointTerm) config.pointTerm = await fillTermWrapper(config.pointTerm, app.vocabApi)\n\treturn config\n}\n\nexport const swimmerInit = getCompInit(Swimmer)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = swimmerInit\n"],
+  "mappings": 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+  "names": ["id"]
+}

package/dist/table-GX3VJLPZ.js

@@ -0,0 +1,192 @@
+import {
+  PlotBase,
+  controlsInit
+} from "./chunk-NNDKYTUV.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-HWNQOADC.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-PLFPXOGX.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-BIJOXCLN.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-L2WOLNZK.js";
+import "./chunk-AMW5LCUB.js";
+import "./chunk-ZPWBYHNE.js";
+import {
+  getCompInit
+} from "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-6XKAOSQE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// plots/table.js
+var TdbTable = class _TdbTable extends PlotBase {
+  static type = "table";
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = _TdbTable.type;
+  }
+  async init() {
+    const opts = this.opts;
+    const controls = opts.controls ? null : opts.holder.append("div");
+    const holder = opts.controls ? opts.holder : opts.holder.append("div");
+    this.dom = {
+      header: opts.header,
+      controls,
+      holder,
+      div: holder.style("margin", "10px 0px").style("display", "none"),
+      inputs: ["term1", "overlay"]
+    };
+    if (this.dom.header) this.dom.header.html("Crosstab");
+    setInteractivity(this);
+    setRenderers(this);
+    await this.setControls();
+  }
+  async setControls() {
+    if (this.opts.controls) {
+      this.opts.controls.on("downloadClick.table", this.download);
+    } else {
+      this.dom.holder.attr("class", "pp-termdb-plot-viz").style("display", "inline-block").style("min-width", "300px").style("margin-left", "50px");
+      this.components = {
+        controls: await controlsInit({
+          app: this.app,
+          id: this.id,
+          holder: this.dom.controls.style("display", "inline-block")
+        })
+      };
+      this.components.controls.on("downloadClick.table", this.download);
+    }
+  }
+  getState(appState, sub) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) {
+      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
+    }
+    return {
+      activeCohort: appState.activeCohort,
+      termfilter: appState.termfilter,
+      config: {
+        term: config.term,
+        term2: config.term2,
+        settings: {
+          common: config.settings.common,
+          table: config.settings.table
+        }
+      }
+    };
+  }
+  async main() {
+    try {
+      this.config = structuredClone(this.state.config);
+      if (!this.config.term2) {
+        this.dom.div.style("display", "none");
+        throw "term2 is required for table view";
+      }
+      const c = this.state.config;
+      if (this.dom.header) this.dom.header.html(c.term.term.name + " vs " + c.term2.term.name);
+      const reqOpts = this.getDataRequestOpts();
+      this.data = await this.vocabApi.getNestedChartSeriesData(reqOpts);
+      this.app.vocabApi.syncTermData(this.state.config, this.data);
+      const [columns, rows] = this.processData(this.data);
+      this.render(columns, rows);
+    } catch (e) {
+      throw e;
+    }
+  }
+  // creates an opts object for the vocabApi.getNestedChartsData()
+  getDataRequestOpts() {
+    const c = this.config;
+    const opts = { term: c.term, filter: this.state.termfilter.filter };
+    if (c.term2) opts.term2 = c.term2;
+    if (c.term0) opts.term0 = c.term0;
+    return opts;
+  }
+  processData(data) {
+    const t2 = this.config.term2.term;
+    const columns = data.refs.rows.map((key) => {
+      const label = t2.values && key in t2.values ? t2.values[key].label : key;
+      return { key, label };
+    });
+    const column_keys = data.refs.rows;
+    const t1 = this.config.term.term;
+    const rows = data.refs.cols.map((v1) => {
+      const series = data.charts[0].serieses.find((d) => d.seriesId == v1);
+      const label = t1.values && v1 in t1.values ? t1.values[v1].label : v1;
+      return {
+        label,
+        lst: !series ? [] : series.data.slice().sort((a, b) => column_keys.indexOf(a.dataId) - column_keys.indexOf(b.dataId)).map((d) => {
+          return {
+            label: d.dataId,
+            value: d.total
+          };
+        })
+      };
+    });
+    return [columns, rows];
+  }
+};
+function setInteractivity(self) {
+  self.download = () => {
+    if (!self.state || !self.state.isVisible) return;
+    const data = [];
+    self.dom.div.selectAll("tr").each(function() {
+      const series = [];
+      select_default(this).selectAll("th, td").each(function() {
+        series.push(select_default(this).text());
+      });
+      data.push(series);
+    });
+    const matrix = data.map((row) => row.join("	")).join("\n");
+    const a = document.createElement("a");
+    document.body.appendChild(a);
+    a.addEventListener(
+      "click",
+      function() {
+        a.download = self.config.term.term.name + " table.txt";
+        a.href = URL.createObjectURL(new Blob([matrix], { type: "text/tab-separated-values" }));
+        document.body.removeChild(a);
+      },
+      false
+    );
+    a.click();
+  };
+}
+function setRenderers(self) {
+  self.render = function render(columns, rows) {
+    self.dom.div.style("display", "inline-block").selectAll("*").remove();
+    const table = self.dom.div.append("table").style("margin-right", "20px").style("border-spacing", "3px").style("border-collapse", "collapse").style("border", "1px solid black");
+    const tr = table.append("tr").style("white-space", "normal").style("background-color", "#ececec");
+    tr.append("td");
+    for (const value of columns) {
+      const label = value.label;
+      tr.append("th").text(label.length > 20 ? label.slice(0, 16) + "..." : label).attr("aria-label", label).style("border", "1px solid black").style("padding", "3px").style("text-align", "center").style("min-width", "80px").style("max-width", "150px").style("word-break", label.length > 12 ? "break-word" : "normal").style("vertical-align", "top");
+    }
+    let i = 0;
+    for (const t1v of rows) {
+      const tr2 = table.append("tr").style("background-color", i++ % 2 == 0 ? "#fff" : "#ececec");
+      tr2.append("th").text(t1v.label.length > 20 ? t1v.label.slice(0, 20) + "..." : t1v.label).attr("aria-label", t1v.label).style("border", "1px solid black").style("padding", "3px").style("word-break", t1v.label.length > 12 ? "break-all" : "normal");
+      const column_keys = columns.map((d) => d.key);
+      for (const t2label of column_keys) {
+        const td = tr2.append("td").style("border", "1px solid black").style("padding", "3px 5px").style("text-align", "center");
+        const v = t1v.lst.find((i2) => i2.label == t2label);
+        if (v) {
+          td.html(v.value);
+        }
+      }
+    }
+  };
+}
+var tableInit = getCompInit(TdbTable);
+export {
+  tableInit
+};
+//# sourceMappingURL=table-GX3VJLPZ.js.map

package/dist/termCollection-QE7U5QBD.js

@@ -0,0 +1,29 @@
+import {
+  SearchHandler
+} from "./chunk-5G6O5RYM.js";
+import "./chunk-NNDKYTUV.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-HWNQOADC.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-PLFPXOGX.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-BIJOXCLN.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-L2WOLNZK.js";
+import "./chunk-AMW5LCUB.js";
+import "./chunk-ZPWBYHNE.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-6XKAOSQE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+export {
+  SearchHandler
+};
+//# sourceMappingURL=termCollection-QE7U5QBD.js.map

package/dist/termCollection-YQ332WKB.js

@@ -0,0 +1,247 @@
+import {
+  HandlerBase,
+  getFractionSelectionError,
+  renderFractionSelection,
+  renderTable
+} from "./chunk-NNDKYTUV.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-HWNQOADC.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-PLFPXOGX.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-BIJOXCLN.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-L2WOLNZK.js";
+import {
+  termItemType
+} from "./chunk-AMW5LCUB.js";
+import "./chunk-ZPWBYHNE.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-6XKAOSQE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// termsetting/handlers/termCollection.ts
+var TermCollectionHandler = class extends HandlerBase {
+  //main menu dom elements before drag and drop divs are added
+  constructor(opts) {
+    super(opts);
+    this.dom = {};
+    this.termsetting = opts.termsetting;
+    this.tw = opts.termsetting.tw;
+    this.dom.holder = opts.holder || this.termsetting.dom.tip.d;
+  }
+  async showEditMenu(div) {
+    const self = this.termsetting;
+    div.selectAll("*").remove();
+    const terms = self.term.termlst;
+    const groupDiv = div.append("div");
+    const callback = this.tw.term.memberType == "numeric" ? self.tw.type === "TermCollectionTWFraction" ? addFractionTable(self, groupDiv, terms) : addNumericTable(self, groupDiv, terms) : addCategoricalTable(self, groupDiv, terms);
+    const buttons = div.append("div").style("padding", "6px 20px");
+    buttons.append("button").attr("data-testid", "sjpp-term-collection-members-apply").text("Apply").on("click", callback);
+  }
+  async showBinsEditMenu(div) {
+    const self = this.termsetting;
+    div.selectAll("*").remove();
+    const { NumericHandler } = await import("./NumericHandler-SEFTQJDM.js");
+    const { NumDiscreteEditor } = await import("./NumDiscreteEditor-IT7NIXTV.js");
+    const numericHandler = new NumericHandler({ termsetting: self });
+    const densityData = { min: 0, max: 1 };
+    numericHandler.density_data = densityData;
+    numericHandler.density.density_data = densityData;
+    numericHandler.density.no_density_data = true;
+    numericHandler.density.showViolin = async (div2) => {
+      div2.selectAll("*").remove();
+      div2.append("div").style("padding", "10px 5px").text("Fraction range is 0 to 1.");
+      return densityData;
+    };
+    numericHandler.density.setBinLines = async () => {
+    };
+    const editor = new NumDiscreteEditor({ termsetting: self }, numericHandler);
+    await editor.showEditMenu(div.append("div"));
+    const buttons = div.append("div").style("margin", "0px 0px 10px 12px");
+    buttons.append("button").attr("data-testid", "sjpp-term-collection-bins-apply").text("Apply").on("click", () => {
+      const editedQ = editor.getEditedQ();
+      self.q = {
+        ...editedQ,
+        denominators: self.q.denominators,
+        numerators: self.q.numerators
+      };
+      self.dom.tip.hide();
+      self.api.runCallback();
+    });
+    buttons.append("button").style("margin-left", "8px").text("Reset").on("click", () => editor.undoEdits());
+  }
+  getPillStatus() {
+    return this.tw.getStatus(this.termsetting.usecase);
+  }
+};
+function addFractionTable(self, div, terms) {
+  const selection = {
+    numerators: self.q.numerators?.slice() || [],
+    denominators: self.q.denominators?.slice() || []
+  };
+  renderFractionSelection({
+    holder: div,
+    termlst: terms,
+    selection,
+    propsByTermId: self.term.propsByTermId
+  });
+  return () => {
+    const error = getFractionSelectionError(selection);
+    if (error) return window.alert(error);
+    const q = self.q;
+    q.denominators = selection.denominators;
+    q.numerators = selection.numerators;
+    self.api.runCallback();
+  };
+}
+function addNumericTable(self, div, terms) {
+  const selectedRows = getSelectedRows(self, terms);
+  const rows = [];
+  for (const [index, term] of terms.entries()) {
+    const selected = selectedRows.includes(index);
+    const checked = selected && self.q.numerators?.includes(term.id) ? "checked" : "";
+    const disabled = selected ? "" : "disabled";
+    rows.push([
+      {},
+      {
+        html: `<input type='checkbox' data-testid='sjpp-term-collection-sort-member' ${checked} ${disabled} />`
+      }
+    ]);
+  }
+  const columns = [getTermNameColumn(self, terms), { label: "Use for sorting" }];
+  const noButtonCallback = () => {
+    for (const tr of div.select("table").select("tbody").node().querySelectorAll("tr")) {
+      const memberCheckbox = tr.querySelector(
+        'input[type="checkbox"]:not([data-testid="sjpp-term-collection-sort-member"])'
+      );
+      const sortingCheckbox = tr.querySelector(
+        '[data-testid="sjpp-term-collection-sort-member"]'
+      );
+      if (!memberCheckbox || !sortingCheckbox) continue;
+      sortingCheckbox.disabled = !memberCheckbox.checked;
+      if (!memberCheckbox.checked) sortingCheckbox.checked = false;
+    }
+  };
+  renderTable({
+    rows,
+    columns,
+    div,
+    maxHeight: "40vh",
+    noButtonCallback,
+    striped: false,
+    showHeader: true,
+    //false,
+    selectedRows,
+    columnButtons: void 0,
+    //Leave until table.js is typed
+    buttons: void 0
+  });
+  return () => {
+    const q = self.q;
+    const trs = div.select("table").select("tbody").node().querySelectorAll("tr");
+    q.lst = getSelectedTermIds(terms, trs);
+    q.numerators = terms.filter((term, i) => {
+      const checked = trs[i].querySelector('[data-testid="sjpp-term-collection-sort-member"]')?.checked;
+      return checked === true;
+    }).map((t) => t.id);
+    self.api.runCallback();
+  };
+}
+function addCategoricalTable(self, div, terms) {
+  const rows = [];
+  for (let i = 0; i < terms.length; i++) {
+    rows.push([{}]);
+  }
+  const selectedRows = getSelectedRows(self, terms);
+  const columns = [getTermNameColumn(self, terms)];
+  renderTable({
+    rows,
+    columns,
+    div: div.append("div").style("margin-top", "10px"),
+    maxWidth: "30vw",
+    maxHeight: "40vh",
+    noButtonCallback: () => {
+    },
+    striped: false,
+    showHeader: true,
+    //false,
+    selectedRows,
+    columnButtons: void 0,
+    //Leave until table.js is typed
+    buttons: void 0
+  });
+  const categoryDiv = div.append("div").style("margin-top", "15px");
+  const values = Object.assign({}, ...self.tw.term.termlst?.map((t) => t.values || {}) ?? []);
+  const categoryTable = categoryDiv.append("div");
+  const ckSource = self.tw.q.categoryKeys || self.tw.term.categoryKeys || [];
+  renderTable({
+    columns: [{ label: "CATEGORIES" }],
+    rows: ckSource.map((ck) => {
+      return [{ value: values[ck.key]?.label ?? ck.key, checked: ck.shown }];
+    }),
+    div: categoryTable,
+    maxWidth: "30vw",
+    maxHeight: "40vh",
+    noButtonCallback: () => {
+    },
+    // FIXME to supply a real callback
+    striped: false,
+    showHeader: true,
+    //false,
+    selectAll: true,
+    columnButtons: void 0,
+    //Leave until table.js is typed
+    buttons: void 0
+  });
+  return () => {
+    const trs = div.select("table").select("tbody").node().querySelectorAll("tr");
+    self.q.lst = getSelectedTermIds(terms, trs);
+    const catTrs = categoryTable.select("table").select("tbody").node().querySelectorAll("tr");
+    self.q.categoryKeys = ckSource.map((ck, i) => {
+      const checked = catTrs[i].querySelectorAll("td")[1].querySelector("input")?.checked;
+      return { key: ck.key, shown: !!checked };
+    });
+    self.api.runCallback();
+  };
+}
+function getSelectedRows(self, terms) {
+  const selectedIds = self.q.lst?.length > 0 ? new Set(self.q.lst) : new Set(self.term.termIds?.length > 0 ? self.term.termIds : terms.map((term) => term.id));
+  return terms.map((term, index) => selectedIds.has(term.id) ? index : -1).filter((index) => index !== -1);
+}
+function getSelectedTermIds(terms, trs) {
+  return terms.filter((_, i) => trs[i].querySelectorAll("td")[1].querySelector("input")?.checked === true).map((term) => term.id);
+}
+function getTermNameColumn(self, terms) {
+  if (!terms?.[0]) throw new Error("terms[0] missing");
+  return {
+    label: termItemType(terms[0]),
+    fillCell(td, index) {
+      const term = terms[index];
+      const color = self.term.propsByTermId?.[term.id]?.color || term.color;
+      if (color) {
+        td.append("span").attr("data-testid", "sjpp-term-collection-member-color").style("display", "inline-block").style("width", "10px").style("height", "10px").style("margin-right", "5px").style("background-color", color);
+      }
+      td.append("span").text(term.name);
+    }
+  };
+}
+function fillTW(tw) {
+  if (!tw.type) tw.type = "termCollection";
+  if (!tw.q) tw.q = { mode: "continuous", type: "compositePercentage" };
+  else tw.q.mode = "continuous";
+  return tw;
+}
+export {
+  TermCollectionHandler,
+  fillTW
+};
+//# sourceMappingURL=termCollection-YQ332WKB.js.map