@sjcrh/proteinpaint-client 2.220.0 → 2.222.0

package/dist/chunk-R55JRVX7.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/sunburst/sunburst.data.ts", "../plots/sunburst/SunburstChart.ts", "../plots/sunburst/sunburst.ts"],
+  "sourcesContent": ["import type { Filter, SunburstResponse, SunburstNode, SunburstCategory } from '#types'\nimport type { SunNode } from './SunburstRenderer'\n\n/*\nData helpers of the term-based sunburst, without any DOM code: the termdb/sunburst response as a renderer \ntree, and selected wedges as a group filter. Kept apart from sunburst.ts so they can be unit-tested directly.\n*/\n\n/** a wedge of the term sunburst. `id` names it by its path of [ring $id, key] pairs, as JSON so that no\n *  category key can make two paths alike, and a selection can survive a re-fetch; `ring`, `key` and\n *  `category` say which ring category it is */\nexport type TermSunNode = SunNode & {\n\tid: string\n\tring: number\n\tkey: string\n\tcategory: SunburstCategory\n\t/** samples under the wedge (SunNode.value is only those that end here) */\n\tcount: number\n\tchildren?: TermSunNode[]\n}\n\ntype TermSunRoot = SunNode & { children: TermSunNode[]; count: number }\n\n/** the response as a renderer tree; first-ring colours from the dataset (keyed by category key) win\n *  over the term's own */\nexport function buildTermTree(\n\tres: SunburstResponse,\n\ttwLst: any[],\n\trootName: string,\n\tcolors?: { [key: string]: string }\n): TermSunRoot {\n\tconst convert = (n: SunburstNode, ring: number, parentPath: string[][]): TermSunNode => {\n\t\tconst tw = twLst[ring]\n\t\tconst category = res.rings[ring].categories[n.key] || { label: n.key }\n\t\tconst path = [...parentPath, [tw.$id, n.key]]\n\t\tconst children = (n.children || []).map(c => convert(c, ring + 1, path))\n\t\tconst node: TermSunNode = {\n\t\t\tname: category.label,\n\t\t\tlevel: tw.term.name,\n\t\t\t// d3 adds the children to a node's own value, so it holds only the samples that end here\n\t\t\tvalue: n.count - children.reduce((s, c) => s + c.count, 0),\n\t\t\tcount: n.count,\n\t\t\tid: JSON.stringify(path),\n\t\t\tring,\n\t\t\tkey: n.key,\n\t\t\tcategory\n\t\t}\n\t\tconst color = (ring == 0 && colors?.[n.key]) || category.color\n\t\tif (color) node.color = color\n\t\tif (children.length) node.children = children\n\t\treturn node\n\t}\n\treturn { name: rootName, value: 0, count: res.total, children: res.nodes.map(n => convert(n, 0, [])) }\n}\n\n/** one ring category as a filter entry: the tvs of the ring's term, or a filter group's own filter */\nexport function categoryFilterItem(tw: any, category: SunburstCategory): any {\n\tif (category.filter) return structuredClone(category.filter)\n\tif (!category.tvs) throw `no filter for category '${category.label}' of ${tw.term.name}`\n\treturn { type: 'tvs', tvs: { term: tw.term, ...structuredClone(category.tvs) } }\n}\n\n/** the samples of one wedge: its categories along the path from the first ring, joined by \"and\" */\nexport function wedgeFilter(path: TermSunNode[], twLst: any[]): Filter {\n\tconst lst = path.map(n => categoryFilterItem(twLst[n.ring], n.category))\n\treturn { type: 'tvslst', in: true, join: lst.length > 1 ? 'and' : '', lst }\n}\n\n/** the samples of any of the selected wedges, each given as its path from the first ring. One wedge\n *  is just its own filter; several are joined by \"or\" */\nexport function selectionFilter(paths: TermSunNode[][], twLst: any[]): Filter {\n\tif (!paths.length) throw 'no wedge selected'\n\tif (paths.length == 1) return wedgeFilter(paths[0], twLst)\n\treturn { type: 'tvslst', in: true, join: 'or', lst: paths.map(p => wedgeFilter(p, twLst)) }\n}\n\n/** a readable name for a selection: the path of one wedge (e.g. \"BCP-ALL \u203A Hyperdiploid\"), or the\n *  wedge names joined when several are selected */\nexport function selectionName(paths: TermSunNode[][], maxLen = 60): string {\n\tconst names =\n\t\tpaths.length == 1 ? paths[0].map(n => n.name).join(' \u203A ') : paths.map(p => p[p.length - 1].name).join(' or ')\n\treturn names.length > maxLen ? names.slice(0, maxLen - 1) + '\u2026' : names\n}\n\n/** the sample types a new or replacing ring may have, given the other rings: the line of descent through\n *  the deepest of their sample types (its ancestors, itself and its descendants), since no value maps\n *  between sibling types such as primary and PDX samples. Undefined (any type) when the dataset has one\n *  sample type or no other ring is below the top level. `sampleTypes` is termdbConfig.sampleTypes */\nexport function allowedSampleTypes(otherTwLst: any[], sampleTypes?: { [id: string]: any }): string[] | undefined {\n\tif (!sampleTypes || Object.keys(sampleTypes).length < 2) return\n\tconst parent = (t: string) => {\n\t\tconst p = sampleTypes[t]?.parent_id\n\t\treturn p === null || p === undefined ? undefined : String(p)\n\t}\n\tconst ancestors = (t: string) => {\n\t\tconst lst: string[] = []\n\t\tfor (let p = parent(t); p !== undefined && !lst.includes(p); p = parent(p)) lst.push(p)\n\t\treturn lst\n\t}\n\tconst types = otherTwLst\n\t\t.map(tw => tw.term?.sample_type)\n\t\t.filter(t => t !== null && t !== undefined && sampleTypes[t])\n\t\t.map(String)\n\tconst below = types.filter(t => parent(t) !== undefined)\n\tif (!below.length) return\n\tconst deepest = below.reduce((a, b) => (ancestors(b).length > ancestors(a).length ? b : a))\n\tconst descendants = Object.keys(sampleTypes).filter(t => ancestors(t).includes(deepest))\n\treturn [...ancestors(deepest), deepest, ...descendants]\n}\n", "import { dofetch3 } from '#common/dofetch'\nimport { select } from 'd3-selection'\nimport { escapeHtml, capitalizeFirstLetter } from '#dom'\nimport { getNormalRoot, filterJoin } from '#filter'\nimport { addNewGroup, getGroupFilterOfConditions } from '#mass/groups'\nimport { availabilitySections, fetchDataAvailability, type AvailabilityRow } from '#mass/groupDataAvailability'\nimport { TermTypes } from '#types'\nimport { getActiveCohortStr } from '#mass/charts'\nimport type { Filter, SunburstRequest, SunburstResponse } from '#types'\nimport {\n\tSunburstRenderer,\n\tcard,\n\tbadge,\n\tpill,\n\tSIZE,\n\tTEXT_DARK,\n\tTEXT_MUTED,\n\tLINK,\n\tRULE,\n\tSELECT_STROKE,\n\ticon,\n\ttype Card,\n\ttype HNode\n} from './SunburstRenderer'\nimport { buildTermTree, selectionFilter, selectionName, type TermSunNode } from './sunburst.data'\n\n/*\nThe term-based sunburst without its rx plot component: fetches the counts of the given rings, draws them,\nand keeps the wedge selection, one sample group. Below the selected wedges, \"Show available data\" lists how\nmany of the selected samples have each kind of data of the dataset (termdb/dataAvailability); a kind with a\nplot of its own opens that plot of the selected samples, which have the selection as the plot's filter. The\nselection can also become one sample group in the GROUPS tab. Used by the sunburst\nplot (sunburst.ts), which fills the Rings box with term pills, and by the About tab (about.ts), which\nlists the dataset's default rings.\n\nClick a wedge to zoom into it; a wedge without rings beneath it, a shift-click, or SELECT above the\nchart (for the wedge at the centre) selects it. Selecting a wedge drops its selected descendants, which\nit already contains.\n\nA sample with no value for a ring, or a value the ring hides (tw.q.hiddenValues, e.g. set in the dataset's\ndefault rings), ends at the previous ring, leaving a gap in the outer ring of its wedge; samples with no\nor a hidden value for the first ring are not in the chart.\n*/\n\n// stat box keys; their titles follow the unit\nconst STAT_SAMPLES = 'Samples'\nconst STAT_SELECTED = 'Selected samples'\n/** indent per ring in the Rings box, so the rings read as a path from the first to the last */\nconst RING_STEP = 6\nconst RING_LINE = '#cbd5e1'\n\nexport type SunburstChartOpts = {\n\tholder: any\n\t/** the mass app, for the term pickers and the created groups */\n\tapp: any\n\t/** px between the chart and its side columns (SunburstRendererOpts.gap) */\n\tgap?: number\n\t/** called before a plot of the selection is created, e.g. to show the plots tab */\n\tbeforeLaunch?: () => Promise<any> | void\n}\n\nexport type SunburstUpdateArg = {\n\tgenome: string\n\tdslabel: string\n\t/** ring term wrappers, inside out, filled */\n\ttwLst: any[]\n\t/** the filter the counts are of: the global filter, joined with the plot's own if any */\n\ttermfilter?: { filter?: Filter; filter0?: any }\n\t/** the plot's own filter, which a created group also has; the global filter is joined where the\n\t *  group is used */\n\tgroupFilter?: Filter\n\t/** first-ring colours from the dataset, keyed by category key */\n\tcolors?: { [key: string]: string }\n}\n\nexport class SunburstChart {\n\tapp: any\n\tdom: {\n\t\terrdiv: any\n\t\tloadingDiv: any\n\t\tnoteDiv: any\n\t\t/** the rings, left of the chart; filled by the caller (ringRow) */\n\t\trings: Card\n\t\t/** the selected wedges, with the create-group action */\n\t\tsel: Card\n\t\t/** selects the wedge at the centre, in the toolbar above the chart */\n\t\tselectFocus: any\n\t}\n\trenderer: SunburstRenderer\n\ttwLst: any[] = []\n\tgroupFilter?: Filter\n\t/** selected wedges by node id, in selection order */\n\tselected: Map<string, HNode> = new Map()\n\t/** note shown in the selection card after a group is created */\n\tcreatedNote = ''\n\t/** the counted unit, from the server */\n\tunit = { one: 'sample', many: 'samples' }\n\t/** number of the latest update(), so that the response of an earlier one that arrives later is dropped */\n\tupdateId = 0\n\tbeforeLaunch?: () => Promise<any> | void\n\t/** whether the available data of the selection is shown; a change of the selection hides it */\n\tdataShown = false\n\t/** number of the latest renderData(), so that the response of an earlier one is dropped */\n\tdataId = 0\n\n\tconstructor(opts: SunburstChartOpts) {\n\t\tthis.app = opts.app\n\t\tthis.beforeLaunch = opts.beforeLaunch\n\t\tconst holder = opts.holder\n\t\tconst errdiv = holder.append('div').attr('class', 'sja_errorbar').style('display', 'none')\n\t\tconst loadingDiv = holder.append('div').style('display', 'none').style('padding', '24px').text('Loading ...')\n\t\tconst noteDiv = holder\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.85em')\n\t\t\t.style('color', TEXT_MUTED)\n\t\t\t.style('margin-bottom', '6px')\n\t\tconst chartHolder = holder.append('div').attr('data-testid', 'sjpp-sunburst-chart')\n\t\tthis.renderer = new SunburstRenderer({\n\t\t\tholder: chartHolder,\n\t\t\tunit: this.unit,\n\t\t\trootName: 'All samples',\n\t\t\tstatLabels: [STAT_SAMPLES, STAT_SELECTED],\n\t\t\tpathCard: false,\n\t\t\tgap: opts.gap,\n\t\t\thooks: {\n\t\t\t\tonClick: (d: HNode, event: any) => this.onWedgeClick(d, event),\n\t\t\t\tisSelected: (d: HNode) => this.selected.has(d.data.id),\n\t\t\t\tcursor: (d: HNode) => (d.children ? 'zoom-in' : 'pointer'),\n\t\t\t\ttooltip: (d: HNode, box: any) => this.tooltip(d, box),\n\t\t\t\tonFocus: () => {\n\t\t\t\t\tthis.renderStats()\n\t\t\t\t\tthis.renderSidebar()\n\t\t\t\t\tthis.renderSelectFocus()\n\t\t\t\t\tthis.markShownRings()\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t\tconst rings = card(this.renderer.dom.left, 'Rings')\n\t\trings.body.attr('data-testid', 'sjpp-sunburst-rings')\n\t\tconst selectFocus = this.renderer\n\t\t\t.addControl()\n\t\t\t.attr('data-testid', 'sjpp-sunburst-select-focus')\n\t\t\t.on('click', () => {\n\t\t\t\tconst f = this.renderer.focus\n\t\t\t\tif (f?.depth && !this.selectedAncestor(f)) this.toggle(f)\n\t\t\t})\n\t\tthis.dom = {\n\t\t\terrdiv,\n\t\t\tloadingDiv,\n\t\t\tnoteDiv,\n\t\t\trings,\n\t\t\tsel: card(this.renderer.dom.right, 'Selected wedges'),\n\t\t\tselectFocus\n\t\t}\n\t}\n\n\t/** fetch and draw the counts of the rings; with no rings, an empty chart and `emptyNote`. Resolves true\n\t *  when drawn, false when the request failed (the error is shown), and undefined when a later update\n\t *  replaced this one, which then has its own outcome */\n\tasync update(arg: SunburstUpdateArg, emptyNote = ''): Promise<boolean | undefined> {\n\t\tconst id = ++this.updateId\n\t\tthis.twLst = arg.twLst\n\t\tthis.groupFilter = arg.groupFilter\n\t\tthis.dom.errdiv.style('display', 'none')\n\t\tthis.dom.noteDiv.text('')\n\t\tif (!this.twLst.length) {\n\t\t\t// an earlier update may still be loading; its response is dropped\n\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t\tthis.selected.clear()\n\t\t\tthis.renderer.setTree({ name: this.renderer.opts.rootName, children: [] })\n\t\t\tthis.dom.noteDiv.text(emptyNote)\n\t\t\treturn true\n\t\t}\n\t\ttry {\n\t\t\tthis.dom.loadingDiv.style('display', '')\n\t\t\tconst res = await fetchSunburst({\n\t\t\t\tgenome: arg.genome,\n\t\t\t\tdslabel: arg.dslabel,\n\t\t\t\ttwLst: this.twLst,\n\t\t\t\tfilter: getNormalRoot(arg.termfilter?.filter),\n\t\t\t\tfilter0: arg.termfilter?.filter0\n\t\t\t})\n\t\t\tif (id != this.updateId) return\n\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t\tthis.render(res, arg.colors)\n\t\t\treturn true\n\t\t} catch (e: any) {\n\t\t\tif (id != this.updateId) return\n\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t\tthis.dom.errdiv.style('display', '').text(e?.message || String(e))\n\t\t\tif (e instanceof Error) console.error(e)\n\t\t\treturn false\n\t\t}\n\t}\n\n\trender(res: SunburstResponse, colors?: { [key: string]: string }) {\n\t\tthis.setUnit(res.unit || { one: 'sample', many: 'samples' })\n\t\tif (res.noFirstRingValue) {\n\t\t\tconst n = res.noFirstRingValue\n\t\t\tthis.dom.noteDiv.text(\n\t\t\t\t`${n.toLocaleString()} ${n == 1 ? this.unit.one : this.unit.many} with ${noValue(this.twLst[0])} ${\n\t\t\t\t\tn == 1 ? 'is' : 'are'\n\t\t\t\t} not shown.`\n\t\t\t)\n\t\t}\n\t\tconst focusId = this.renderer.focus?.data.id\n\t\tconst selectedIds = [...this.selected.keys()]\n\t\tthis.renderer.setTree(buildTermTree(res, this.twLst, this.renderer.opts.rootName, colors))\n\t\t// keep the selection and the centre of a re-fetch (e.g. after a filter change) where their\n\t\t// wedges still exist\n\t\tconst byId = new Map(this.renderer.root.descendants().map((d: HNode) => [d.data.id, d]))\n\t\tthis.selected = new Map(selectedIds.filter(id => byId.has(id)).map(id => [id, byId.get(id)]))\n\t\tthis.renderer.refresh()\n\t\tconst focus = focusId && byId.get(focusId)\n\t\tif (focus?.children) this.renderer.zoomTo(focus)\n\t\telse this.renderSidebar()\n\t}\n\n\t/** wording of the counted unit: centre, stat box titles, tooltip and the create-group action */\n\tsetUnit(unit: { one: string; many: string }) {\n\t\tthis.unit = unit\n\t\tthis.renderer.opts.unit = unit\n\t\tthis.renderer.opts.rootName = `All ${unit.many}`\n\t\tthis.renderer.setStatTitle(STAT_SAMPLES, capitalizeFirstLetter(unit.many))\n\t\tthis.renderer.setStatTitle(STAT_SELECTED, `Selected ${unit.many}`)\n\t}\n\n\t/** SELECT above the chart, for the wedge at the centre (which cannot be clicked) */\n\trenderSelectFocus() {\n\t\tconst f = this.renderer.focus\n\t\tconst el = this.dom.selectFocus\n\t\tif (!f?.depth) {\n\t\t\tel.style('display', 'none')\n\t\t\treturn\n\t\t}\n\t\tconst anc = this.selectedAncestor(f)\n\t\tconst on = this.selected.has(f.data.id)\n\t\tel.style('display', '')\n\t\t\t.style('opacity', anc ? 0.35 : 1)\n\t\t\t.style('cursor', anc ? 'default' : 'pointer')\n\t\t\t.style('color', on ? SELECT_STROKE : TEXT_MUTED)\n\t\t\t.attr('title', anc ? `Included in the selected ${anc.data.name}` : null)\n\t\t\t.html(\n\t\t\t\ton\n\t\t\t\t\t? `${icon('<polyline points=\"5 12 10 17 19 7\"/>')}SELECTED \u00B7 ${escapeHtml(f.data.name.toUpperCase())}`\n\t\t\t\t\t: `${icon('<circle cx=\"12\" cy=\"12\" r=\"9\"/><path d=\"M12 8v8M8 12h8\"/>')}SELECT ${escapeHtml(\n\t\t\t\t\t\t\tf.data.name.toUpperCase()\n\t\t\t\t\t  )}`\n\t\t\t)\n\t}\n\n\t/************ rings box ************/\n\n\t/** a line of the Rings box, indented by its ring, with an elbow from the line above */\n\tringRow(level: number) {\n\t\tconst row = this.dom.rings.body\n\t\t\t.append('div')\n\t\t\t.style('position', 'relative')\n\t\t\t.style('margin', '2px 0')\n\t\t\t.style('margin-left', `${level * RING_STEP}px`)\n\t\tif (level) {\n\t\t\trow\n\t\t\t\t.append('div')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('left', `${-RING_STEP + 4}px`)\n\t\t\t\t.style('top', '-6px')\n\t\t\t\t.style('width', `${RING_STEP - 6}px`)\n\t\t\t\t.style('height', '18px')\n\t\t\t\t.style('border-left', `1px solid ${RING_LINE}`)\n\t\t\t\t.style('border-bottom', `1px solid ${RING_LINE}`)\n\t\t\t\t.style('border-bottom-left-radius', '4px')\n\t\t}\n\t\treturn row\n\t}\n\n\t/** the line of ring i: its number, which is marked while the ring is in the chart (markShownRings),\n\t *  then a slot for the caller's term pill or name */\n\tringLine(i: number) {\n\t\tconst row = this.ringRow(i)\n\t\t\t.attr('class', 'sjpp-sunburst-ring')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '4px')\n\t\trow\n\t\t\t.append('span')\n\t\t\t.attr('class', 'sjpp-sunburst-ringnum')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.style('width', '14px')\n\t\t\t.style('flex', '0 0 auto')\n\t\t\t.style('padding-left', '4px')\n\t\t\t.style('border-left', '3px solid transparent')\n\t\t\t.style('border-radius', '2px')\n\t\t\t.text(i + 1)\n\t\treturn row\n\t}\n\n\t/** mark the two rings around the current centre: a bar beside the ring number, which is bold */\n\tmarkShownRings() {\n\t\tconst first = this.renderer.focus?.depth || 0\n\t\tconst shown = (i: number) => i == first || i == first + 1\n\t\tthis.dom.rings.body\n\t\t\t.selectAll('.sjpp-sunburst-ring')\n\t\t\t.attr('title', (_: any, i: number) => (shown(i) ? 'Shown in the chart' : null))\n\t\t\t.select('.sjpp-sunburst-ringnum')\n\t\t\t.style('border-left-color', (_: any, i: number) => (shown(i) ? LINK : 'transparent'))\n\t\t\t.style('color', (_: any, i: number) => (shown(i) ? TEXT_DARK : TEXT_MUTED))\n\t\t\t.style('font-weight', (_: any, i: number) => (shown(i) ? 'bold' : 'normal'))\n\t}\n\n\t/************ selection ************/\n\n\t/** the selected ancestor that already contains a wedge, if any */\n\tselectedAncestor(d: HNode): HNode | undefined {\n\t\tfor (let a = d.parent; a?.depth; a = a.parent) if (this.selected.has(a.data.id)) return a\n\t}\n\n\ttoggle(d: HNode) {\n\t\tif (!d.depth) return\n\t\tconst id = d.data.id\n\t\tthis.createdNote = ''\n\t\tif (this.selected.has(id)) this.selected.delete(id)\n\t\telse {\n\t\t\tif (this.selectedAncestor(d)) return // already in the selection; the tooltip says so\n\t\t\t// a selected wedge contains its descendants, so drop any that were selected\n\t\t\tfor (const [k, n] of this.selected) if (n.ancestors().includes(d)) this.selected.delete(k)\n\t\t\tthis.selected.set(id, d)\n\t\t}\n\t\tthis.refreshSelection()\n\t}\n\n\trefreshSelection() {\n\t\tthis.dataShown = false\n\t\tthis.renderer.refresh()\n\t\tthis.renderStats()\n\t\tthis.renderSidebar()\n\t\tthis.renderSelectFocus()\n\t}\n\n\t/** wedge paths from the first ring, in selection order */\n\tselectedPaths(): TermSunNode[][] {\n\t\treturn [...this.selected.values()].map(\n\t\t\t(d: HNode) =>\n\t\t\t\td\n\t\t\t\t\t.ancestors()\n\t\t\t\t\t.reverse()\n\t\t\t\t\t.slice(1)\n\t\t\t\t\t.map((a: HNode) => a.data) as TermSunNode[]\n\t\t)\n\t}\n\n\tselectedCount(): number {\n\t\tlet n = 0\n\t\tfor (const d of this.selected.values()) n += d.value || 0\n\t\treturn n\n\t}\n\n\trenderStats() {\n\t\tconst r = this.renderer\n\t\tr.setStats(\n\t\t\tnew Map([\n\t\t\t\t[STAT_SAMPLES, r.focus.value || 0],\n\t\t\t\t[STAT_SELECTED, this.selectedCount()]\n\t\t\t])\n\t\t)\n\t}\n\n\t/************ interaction ************/\n\n\tonWedgeClick(d: HNode, event: any) {\n\t\tif (event?.shiftKey || !d.children) this.toggle(d)\n\t\telse this.renderer.zoomTo(d)\n\t}\n\n\ttooltip(d: HNode, box: any) {\n\t\tconst line = (text: string, color = '#6b7280') => box.append('div').style('color', color).text(text)\n\t\tline(d.data.level)\n\t\tconst total = this.renderer.root.value || 0\n\t\tconst pct = total ? ` (${((100 * (d.value || 0)) / total).toFixed(1)}%)` : ''\n\t\tconst s = box.append('div').style('color', '#374151')\n\t\ts.append('span').text(`${capitalizeFirstLetter(this.unit.many)}: `)\n\t\ts.append('b').text((d.value || 0).toLocaleString())\n\t\ts.append('span').text(pct)\n\t\tconst ended = d.data.value || 0\n\t\tconst next = this.twLst[d.data.ring + 1]\n\t\tif (d.children && ended && next) line(`${ended.toLocaleString()} with ${noValue(next)}`)\n\t\tconst note = (text: string, color: string) =>\n\t\t\tbox.append('div').style('margin-top', '4px').style('color', color).text(text)\n\t\tconst anc = this.selectedAncestor(d)\n\t\tif (anc) note(`Included in the selected ${anc.data.name}`, TEXT_MUTED)\n\t\telse if (this.selected.has(d.data.id))\n\t\t\tnote(d.children ? 'click to zoom in \u00B7 shift-click to deselect' : 'click to deselect', LINK)\n\t\telse note(d.children ? 'click to zoom in \u00B7 shift-click to select' : 'click to select', LINK)\n\t}\n\n\t/** the selected-wedges card: one line per wedge with its path and count, and the create-group\n\t *  action as the footer */\n\trenderSidebar() {\n\t\tconst sel = this.dom.sel\n\t\tconst { title, headRight, body } = sel\n\t\theadRight.selectAll('*').remove()\n\t\tbody.selectAll('*').remove()\n\t\theadRight.style('margin-bottom', '8px')\n\t\tconst n = this.selected.size\n\t\ttitle.text(n ? 'Selected wedges' : 'No wedges selected')\n\t\tif (n) {\n\t\t\tpill(headRight).text(n)\n\t\t\theadRight\n\t\t\t\t.append('span')\n\t\t\t\t.style('font-size', '11px')\n\t\t\t\t.style('color', LINK)\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.text('Clear')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tthis.selected.clear()\n\t\t\t\t\tthis.refreshSelection()\n\t\t\t\t})\n\t\t}\n\t\tconst list = body\n\t\t\t.append('div')\n\t\t\t.style('max-height', `${SIZE - 200}px`)\n\t\t\t.style('overflow-y', 'auto')\n\t\tif (!n) {\n\t\t\tlist\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '0.85em')\n\t\t\t\t.style('color', TEXT_MUTED)\n\t\t\t\t.style('padding', '4px 0')\n\t\t\t\t.text('Shift-click a wedge, click an outermost one, or zoom into one and click SELECT above the chart.')\n\t\t}\n\t\tfor (const [id, d] of this.selected) {\n\t\t\tconst path = d\n\t\t\t\t.ancestors()\n\t\t\t\t.reverse()\n\t\t\t\t.slice(1)\n\t\t\t\t.map((a: HNode) => a.data.name)\n\t\t\tconst row = list\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'flex')\n\t\t\t\t.style('align-items', 'center')\n\t\t\t\t.style('gap', '8px')\n\t\t\t\t.style('padding', '3px 6px')\n\t\t\t\t.style('margin', '2px 0')\n\t\t\t\t.style('border-radius', '6px')\n\t\t\t\t.on('mouseenter', (event: any) => {\n\t\t\t\t\tselect(event.currentTarget).style('background', '#f3f4f6').select('.sjpp-sunburst-remove').style('opacity', 1)\n\t\t\t\t})\n\t\t\t\t.on('mouseleave', (event: any) => {\n\t\t\t\t\tselect(event.currentTarget)\n\t\t\t\t\t\t.style('background', 'transparent')\n\t\t\t\t\t\t.select('.sjpp-sunburst-remove')\n\t\t\t\t\t\t.style('opacity', 0)\n\t\t\t\t})\n\t\t\tbadge(row, d.data.name, this.renderer.color(d), 24)\n\t\t\tconst text = row.append('div').style('flex', '1 1 auto').style('min-width', '0').style('line-height', '1.2')\n\t\t\ttext\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '0.9em')\n\t\t\t\t.style('color', TEXT_DARK)\n\t\t\t\t.style('overflow', 'hidden')\n\t\t\t\t.style('text-overflow', 'ellipsis')\n\t\t\t\t.style('white-space', 'nowrap')\n\t\t\t\t.attr('title', path.join(' \u203A '))\n\t\t\t\t.text(path.join(' \u203A '))\n\t\t\ttext\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '0.7em')\n\t\t\t\t.style('color', '#6b7280')\n\t\t\t\t.text(this.renderer.unitText(d.value || 0))\n\t\t\trow\n\t\t\t\t.append('span')\n\t\t\t\t.attr('class', 'sjpp-sunburst-remove')\n\t\t\t\t.style('opacity', 0)\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('color', '#9ca3af')\n\t\t\t\t.style('font-size', '0.85em')\n\t\t\t\t.attr('title', 'Remove')\n\t\t\t\t.text('\u2715')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tthis.selected.delete(id)\n\t\t\t\t\tthis.refreshSelection()\n\t\t\t\t})\n\t\t}\n\n\t\tconst count = this.selectedCount()\n\t\tif (n) void this.renderData(body, count)\n\n\t\tconst footer = body\n\t\t\t.append('div')\n\t\t\t.style('margin-top', '10px')\n\t\t\t.style('padding-top', '10px')\n\t\t\t.style('border-top', `1px solid ${RULE}`)\n\t\tpill(footer, { button: true })\n\t\t\t.attr('data-testid', 'sjpp-sunburst-create-group')\n\t\t\t.property('disabled', n === 0)\n\t\t\t.style('opacity', n ? 1 : 0.3)\n\t\t\t.style('cursor', n ? 'pointer' : 'default')\n\t\t\t.text(n ? `Create group of ${this.renderer.unitText(count)}` : 'Create group')\n\t\t\t.on('click', () => this.createGroup())\n\t\tif (this.createdNote) {\n\t\t\tfooter\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '0.8em')\n\t\t\t\t.style('color', TEXT_MUTED)\n\t\t\t\t.style('margin-top', '6px')\n\t\t\t\t.text(this.createdNote)\n\t\t}\n\t}\n\n\t/** \"Show available data\", then how many of the selected samples have each kind of data of the dataset;\n\t *  a kind with a plot of the selected samples opens it */\n\tasync renderData(body: any, count: number) {\n\t\tconst div = body\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-sunburst-group-data')\n\t\t\t.style('margin-top', '10px')\n\t\t\t.style('padding-top', '10px')\n\t\t\t.style('border-top', `1px solid ${RULE}`)\n\t\tif (!this.dataShown) {\n\t\t\tpill(div, { button: true })\n\t\t\t\t.attr('data-testid', 'sjpp-sunburst-show-data')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.text('Show available data')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tthis.dataShown = true\n\t\t\t\t\tthis.renderSidebar()\n\t\t\t\t})\n\t\t\treturn\n\t\t}\n\t\tconst id = ++this.dataId\n\t\tconst head = div\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('justify-content', 'space-between')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '8px')\n\t\t\t.style('margin-bottom', '6px')\n\t\thead\n\t\t\t.append('span')\n\t\t\t.attr('data-testid', 'sjpp-sunburst-data-title')\n\t\t\t.style('white-space', 'nowrap')\n\t\t\t.style('font-size', '0.95em')\n\t\t\t.style('font-weight', 600)\n\t\t\t.style('color', TEXT_DARK)\n\t\t\t.text(capitalizeFirstLetter(this.renderer.unitText(count)))\n\t\t// back to the button\n\t\thead\n\t\t\t.append('button')\n\t\t\t.attr('data-testid', 'sjpp-sunburst-hide-data')\n\t\t\t.style('flex', '0 0 auto')\n\t\t\t.style('font-size', '11px')\n\t\t\t.style('padding', '1px 10px')\n\t\t\t.style('border', `1px solid ${RULE}`)\n\t\t\t.style('border-radius', '10px')\n\t\t\t.style('background', 'white')\n\t\t\t.style('color', LINK)\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.text('Hide \u25B4')\n\t\t\t.on('click', () => this.hideData())\n\t\tconst list = div.append('div').text('Loading ...').style('font-size', '0.85em').style('color', TEXT_MUTED)\n\t\ttry {\n\t\t\tconst appState = this.app.getState()\n\t\t\tconst termfilter = appState.termfilter || {}\n\t\t\tconst filter = filterJoin([this.plotFilter(), termfilter.filter].filter(f => f?.lst?.length))\n\t\t\tconst groups = [{ name: 'selection', filter }]\n\t\t\tconst res = await fetchDataAvailability(\n\t\t\t\tthis.app.vocabApi,\n\t\t\t\tgroups,\n\t\t\t\ttermfilter.filter0,\n\t\t\t\tgetActiveCohortStr(appState)\n\t\t\t)\n\t\t\tif (id != this.dataId) return\n\t\t\tlist.text('').style('color', null)\n\t\t\t// differential expression compares groups, and the selection is one\n\t\t\tconst sections = availabilitySections(res, ['rnaseqGeneCount'])\n\t\t\tif (!sections.length) {\n\t\t\t\tlist.style('color', TEXT_MUTED).text(`No data for these ${this.unit.many}`)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tfor (const section of sections) {\n\t\t\t\tif (section.title) {\n\t\t\t\t\tlist\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('data-testid', `sjpp-sunburst-section-${section.key}`)\n\t\t\t\t\t\t.style('margin', '8px 0 2px 0')\n\t\t\t\t\t\t.style('padding', '0 6px')\n\t\t\t\t\t\t.style('font-size', '10px')\n\t\t\t\t\t\t.style('font-weight', 600)\n\t\t\t\t\t\t.style('letter-spacing', '.06em')\n\t\t\t\t\t\t.style('text-transform', 'uppercase')\n\t\t\t\t\t\t.style('color', TEXT_MUTED)\n\t\t\t\t\t\t.text(section.title)\n\t\t\t\t}\n\t\t\t\tfor (const row of section.rows) {\n\t\t\t\t\tconst launch = this.dataPlot(row)\n\t\t\t\t\tthis.dataRow(list, row, !!section.title, launch)\n\t\t\t\t}\n\t\t\t}\n\t\t} catch (e: any) {\n\t\t\tif (id != this.dataId) return\n\t\t\tlist.attr('class', 'sja_errorbar').text(e?.message || String(e))\n\t\t}\n\t}\n\n\thideData() {\n\t\tthis.dataShown = false\n\t\t// a response still on its way is not drawn\n\t\tthis.dataId++\n\t\tthis.renderSidebar()\n\t}\n\n\t/** a line of the available data: the kind of data and its count, which opens `launch`, a plot_create config,\n\t *  when given; a row of a section is indented under the section's title */\n\tdataRow(list: any, row: AvailabilityRow, inSection: boolean, launch?: any) {\n\t\tconst n = row.counts[0] || 0\n\t\tconst div = list\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', `sjpp-sunburst-data-${row.kind == 'data' ? '' : row.kind + '-'}${row.key}`)\n\t\t\t.style('display', 'flex')\n\t\t\t.style('justify-content', 'space-between')\n\t\t\t.style('gap', '8px')\n\t\t\t.style('padding', `3px 6px 3px ${inSection ? 16 : 6}px`)\n\t\t\t.style('margin', '1px 0')\n\t\t\t.style('border-radius', '6px')\n\t\t\t.style('color', TEXT_DARK)\n\t\tdiv.append('span').text(row.label)\n\t\tdiv\n\t\t\t.append('span')\n\t\t\t.style('white-space', 'nowrap')\n\t\t\t.style('color', launch ? LINK : null)\n\t\t\t.text(`${n.toLocaleString()}${row.unit ? ' ' + row.unit : ''}${launch ? ' \u203A' : ''}`)\n\t\tif (!launch) return\n\t\tdiv\n\t\t\t.attr('role', 'button')\n\t\t\t.attr('tabindex', 0)\n\t\t\t.attr('title', `Open the ${row.label} of these ${this.unit.many}`)\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.on('mouseenter', (event: any) => select(event.currentTarget).style('background', '#f3f4f6'))\n\t\t\t.on('mouseleave', (event: any) => select(event.currentTarget).style('background', 'transparent'))\n\t\t\t.on('click', () => this.launchPlot(launch))\n\t\t\t.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\tthis.launchPlot(launch)\n\t\t\t\t}\n\t\t\t})\n\t}\n\n\t/** the filter of the selected samples: the selection with the plot's own filter. A plot that is given it as\n\t *  its own filter joins the global filter to it */\n\tplotFilter(): Filter {\n\t\tconst filters = [selectionFilter(this.selectedPaths(), this.twLst), this.groupFilter]\n\t\treturn filterJoin(filters.filter(f => f?.lst?.length)) as Filter\n\t}\n\n\t/** the plot of the selected samples for a row of the available data, as a plot_create config; undefined\n\t *  when the row has no plot of its own */\n\tdataPlot(row: AvailabilityRow): any {\n\t\tconst filter = this.plotFilter()\n\t\tconst q = this.app.vocabApi.termdbConfig?.queries || {}\n\t\t// the mutations of the selected samples, in the genome browser after a gene is entered\n\t\tif (row.kind == 'assay')\n\t\t\treturn q.snvindel || q.svfusion || q.cnv\n\t\t\t\t? {\n\t\t\t\t\t\tchartType: 'genomeBrowser',\n\t\t\t\t\t\tfilter,\n\t\t\t\t\t\t/* the mutation track shown, which the genome browser hides by default when the dataset also has\n\t\t\t\t\t\ttrackLst. The query is copied as the browser's config replaces it, not merged */\n\t\t\t\t\t\t...(q.snvindel ? { snvindel: { ...structuredClone(q.snvindel), shown: true } } : {})\n\t\t\t\t  }\n\t\t\t\t: undefined\n\t\t// the survival curve of the selected samples\n\t\tif (row.kind == 'survival') return { chartType: 'survival', term: { id: row.key }, filter }\n\t\t// the input form of expression plots; each plot it opens has the filter\n\t\tif (row.key == 'geneExpression')\n\t\t\treturn { chartType: 'GeneExpInput', termType: TermTypes.GENE_EXPRESSION, spawnConfig: { filter } }\n\t\t// the term search, whose DNA methylation tab lists methylation terms; a term opens its summary with the filter\n\t\tif (row.key == 'dnaMethylation') return { chartType: 'dictionary', spawnConfig: { filter } }\n\t\t// the table of the imaging samples that pass the filter, to render on a brain template\n\t\tif (row.key == 'NIdata') return { chartType: 'brainImaging', filter }\n\t\t// the lanes of the patients of the selected samples\n\t\tif (row.key == 'longitudinal') return { chartType: 'swimmer', filter }\n\t}\n\n\tasync launchPlot(config: any) {\n\t\ttry {\n\t\t\tawait this.beforeLaunch?.()\n\t\t\tawait this.app.dispatch({ type: 'plot_create', config })\n\t\t} catch (e: any) {\n\t\t\tthis.dom.errdiv.style('display', '').text(e?.message || String(e))\n\t\t}\n\t}\n\n\t/** one group of the union of the selected wedges, added to the GROUPS tab; the group also has the\n\t *  plot's own filter, which the counts are of. The global filter is joined where the group is used */\n\tcreateGroup() {\n\t\tconst paths = this.selectedPaths()\n\t\tif (!paths.length) return\n\t\ttry {\n\t\t\tconst name = selectionName(paths)\n\t\t\tconst groups = this.app.getState().groups || []\n\t\t\tconst filter = getGroupFilterOfConditions([this.groupFilter, selectionFilter(paths, this.twLst)])\n\t\t\taddNewGroup(this.app, filter, groups, name)\n\t\t\tthis.selected.clear()\n\t\t\tthis.createdNote = `Group \"${name}\" added; find it in the GROUPS tab.`\n\t\t\tthis.refreshSelection()\n\t\t} catch (e: any) {\n\t\t\tthis.dom.errdiv.style('display', '').text(e?.message || String(e))\n\t\t}\n\t}\n\n\tdestroy() {\n\t\tthis.renderer?.destroy()\n\t}\n}\n\n/** why a sample is not in a ring: \"no X value\", or \"no or a hidden X value\" when the ring hides some\n *  categories (tw.q.hiddenValues), which the server treats as missing. The term's uncomputable values,\n *  which fillTermWrapper puts in hiddenValues by default, are missing values anyway, so they do not count */\nfunction noValue(tw: any): string {\n\tconst values = tw.term.values || {}\n\tconst hidden = Object.keys(tw.q?.hiddenValues || {}).some(k => !values[k]?.uncomputable)\n\treturn `no ${hidden ? 'or a hidden ' : ''}${tw.term.name} value`\n}\n\n/** termdb/sunburst request; errors are thrown */\nasync function fetchSunburst(body: SunburstRequest): Promise<SunburstResponse> {\n\tconst res: any = await dofetch3('termdb/sunburst', { body })\n\tif (res?.error) throw res.error\n\tif (!res?.nodes) throw 'invalid response from termdb/sunburst'\n\treturn res\n}\n", "import { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase } from '#plots/PlotBase.ts'\nimport { getCombinedTermFilter } from '#filter'\nimport { fillTermWrapper, termsettingInit } from '#termsetting'\nimport { SunburstChart } from './SunburstChart'\nimport { allowedSampleTypes } from './sunburst.data'\n\n/*\nSunburst of nested sample counts, one dictionary term per ring (categorical, or numeric binned),\ninside out. The dataset sets the default rings (termdb.sunburst.twLst); the Rings box left of the\nchart switches, edits, adds and removes them (from each term pill's menu). Counts follow the\nglobal and plot filters.\n\nThe chart itself, its wedge selection and the sample group made from it are in SunburstChart.ts, which\nthe About tab also uses.\n\nIn a dataset with a sample hierarchy, the rings are patient terms and the terms of one sample type (no\nvalue maps between sibling types such as primary and PDX samples): once a ring is of a sample type, the\npickers offer only terms of its line of descent. The server returns the counted unit (e.g. patients,\nprimary samples), which the chart's wording follows.\n*/\n\nclass Sunburst extends PlotBase implements RxComponent {\n\tstatic type = 'sunburst'\n\ttype: string\n\tchart!: SunburstChart\n\ttwLst: any[] = []\n\t/** the rings the Rings box shows, to rebuild its pills only when they change */\n\tringsShown = ''\n\t/** the Rings box pills and their main() argument without the filter, which follows the state */\n\tringPills: { pill: any; arg: any }[] = []\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = Sunburst.type\n\t\tif (this.opts.header)\n\t\t\tthis.opts.header.style('padding-left', '7px').style('color', 'rgb(85, 85, 85)').html('Sunburst')\n\t}\n\n\tgetState(appState: any) {\n\t\tconst config = appState.plots.find((p: any) => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn {\n\t\t\tconfig,\n\t\t\t// global mass filter combined with this plot's local filter\n\t\t\ttermfilter: getCombinedTermFilter(appState, config.filter),\n\t\t\tgenome: appState.vocab.genome,\n\t\t\tdslabel: appState.vocab.dslabel,\n\t\t\tsunburst: appState.termdbConfig?.sunburst || {}\n\t\t}\n\t}\n\n\tasync init() {\n\t\t// the plot holder inherits nowrap from the sandbox; the cards need their text to wrap\n\t\tconst holder = this.opts.holder\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-sunburst-holder')\n\t\t\t.style('white-space', 'normal')\n\t\t\t.style('padding', '10px')\n\t\tthis.chart = new SunburstChart({ holder, app: this.app })\n\t\t// a ring pill is only the term: termsetting's info button (its holder's 4th child) is hidden\n\t\tthis.chart.dom.rings.box\n\t\t\t.append('style')\n\t\t\t.text('.sjpp-sunburst-ringpill > div:nth-child(4) { display: none !important; }')\n\t}\n\n\tasync main() {\n\t\tconst config = this.state.config\n\t\tthis.twLst = config.twLst || []\n\t\tawait this.renderRings()\n\t\tawait this.chart.update(\n\t\t\t{\n\t\t\t\tgenome: this.state.genome,\n\t\t\t\tdslabel: this.state.dslabel,\n\t\t\t\ttwLst: this.twLst,\n\t\t\t\ttermfilter: this.state.termfilter,\n\t\t\t\tgroupFilter: config.filter,\n\t\t\t\tcolors: this.state.sunburst.colors\n\t\t\t},\n\t\t\t'Add a ring in the Rings box to draw the sunburst.'\n\t\t)\n\t}\n\n\t/************ rings box ************/\n\n\t/** one line per ring: its number and a term pill, whose menu switches, edits or removes the\n\t *  term; then + Add ring. Rebuilt only when the rings change; otherwise the pills get the current\n\t *  filter, which their term pickers use */\n\tasync renderRings() {\n\t\tconst twLst = this.twLst\n\t\tconst filter = this.state.termfilter?.filter\n\t\tconst sig = JSON.stringify(twLst.map(tw => [tw.$id, tw.q]))\n\t\tif (sig == this.ringsShown) {\n\t\t\tawait Promise.all(this.ringPills.map(({ pill, arg }) => pill.main({ ...arg, filter })))\n\t\t\treturn\n\t\t}\n\t\tthis.ringsShown = sig\n\t\tthis.ringPills = []\n\t\tthis.chart.dom.rings.body.selectAll('*').remove()\n\t\tconst disable_terms = twLst.map(tw => tw.term)\n\t\tconst sampleTypes = this.app.vocabApi.termdbConfig?.sampleTypes\n\t\tconst edit = (lst: any[]) => this.app.dispatch({ type: 'plot_edit', id: this.id, config: { twLst: lst } })\n\t\tfor (const [i, tw] of twLst.entries()) {\n\t\t\tconst pillDiv = this.chart\n\t\t\t\t.ringLine(i)\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-sunburst-ringpill')\n\t\t\t\t.style('min-width', '0')\n\t\t\t\t.style('overflow', 'hidden')\n\t\t\t\t.style('white-space', 'nowrap')\n\t\t\t\t.style('font-size', '.9em')\n\t\t\t\t.style('text-overflow', 'ellipsis')\n\t\t\t\t.attr('title', tw.term.name)\n\t\t\tconst others = twLst.filter((_, j) => j != i)\n\t\t\tconst p = await this.ringPill(\n\t\t\t\tpillDiv,\n\t\t\t\tnewTw => {\n\t\t\t\t\tconst lst = twLst.slice()\n\t\t\t\t\tif (newTw?.term) lst[i] = newTw\n\t\t\t\t\telse lst.splice(i, 1)\n\t\t\t\t\tedit(lst)\n\t\t\t\t},\n\t\t\t\tallowedSampleTypes(others, sampleTypes)\n\t\t\t)\n\t\t\tthis.ringPills.push({ pill: p, arg: { term: tw.term, q: tw.q, $id: tw.$id, disable_terms } })\n\t\t}\n\t\tconst addDiv = this.chart\n\t\t\t.ringRow(twLst.length)\n\t\t\t.style('margin-top', '6px')\n\t\t\t.append('div')\n\t\t\t.style('margin-left', '21px')\n\t\tconst add = await this.ringPill(\n\t\t\taddDiv,\n\t\t\tnewTw => {\n\t\t\t\tif (newTw?.term) edit([...twLst, newTw])\n\t\t\t},\n\t\t\tallowedSampleTypes(twLst, sampleTypes),\n\t\t\t'+ Add ring'\n\t\t)\n\t\tthis.ringPills.push({ pill: add, arg: { term: null, q: null, disable_terms } })\n\t\tawait Promise.all(this.ringPills.map(({ pill, arg }) => pill.main({ ...arg, filter })))\n\t\tthis.chart.markShownRings()\n\t}\n\n\t/** a ring term pill; `sampleTypes` limits the terms it offers (see allowedSampleTypes) */\n\tasync ringPill(holder: any, callback: (tw: any) => void, sampleTypes?: string[], placeholder?: string) {\n\t\treturn await termsettingInit({\n\t\t\tholder,\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tusecase: { target: 'sunburst', ...(sampleTypes ? { sampleTypes } : {}) },\n\t\t\t// the full term name; a name too long for the box is clipped, with the name as its tooltip\n\t\t\tabbrCutoff: 1000,\n\t\t\tmenuOptions: '*',\n\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\tdefaultQ4fillTW: { numeric: { mode: 'discrete' } },\n\t\t\t...(placeholder ? { placeholder } : {}),\n\t\t\tdebug: this.app.opts.debug,\n\t\t\tcallback\n\t\t})\n\t}\n\n\tdestroy() {\n\t\tthis.chart?.destroy()\n\t}\n}\n\n/** the plot config, with the dataset's default rings unless `opts` gives its own; also used by the\n *  About tab for the same rings */\nexport async function getPlotConfig(opts: any, app: any) {\n\tconst config: any = {\n\t\tchartType: 'sunburst',\n\t\tsettings: {}\n\t}\n\tcopyMerge(config, opts)\n\t// default rings from the dataset; a saved session or another chart may give its own\n\tif (!config.twLst) config.twLst = structuredClone(app.vocabApi.termdbConfig?.sunburst?.twLst || [])\n\tconfig.twLst = await Promise.all(\n\t\tconfig.twLst.map((tw: any) => fillTermWrapper(tw, app.vocabApi, { numeric: { mode: 'discrete' } } as any))\n\t)\n\treturn config\n}\n\nexport const sunburstInit = getCompInit(Sunburst)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = sunburstInit\n"],
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+  "names": ["pill"]
+}

package/dist/chunk-RSMASA5S.js

@@ -0,0 +1,340 @@
+import {
+  summaryInit
+} from "./chunk-J5XV35LN.js";
+import {
+  navInit
+} from "./chunk-BVSVFCKB.js";
+import {
+  skipPrevActionAbort,
+  storeInit
+} from "./chunk-LHM4UVYZ.js";
+import {
+  AppBase,
+  downloadSVGsAsPdf,
+  filterRxCompInit,
+  newSandboxDiv,
+  sayerror,
+  vocabInit
+} from "./chunk-4ASBDE27.js";
+import {
+  importPlot
+} from "./chunk-OF6FDDKV.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import {
+  AppApi,
+  getCompInit,
+  multiInit
+} from "./chunk-HBNB5TRH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// mass/plot.js
+var MassPlot = class _MassPlot {
+  static type = "plot";
+  constructor(opts) {
+    this.type = _MassPlot.type;
+    setRenderers(this);
+    this.initUi(opts);
+  }
+  reactsTo(action) {
+    if (action.type.endsWith("_group")) return true;
+    if (action.type.startsWith("plot_")) {
+      return action.id === this.id || action.id == this.parentId || action.config?.parentId === this.id || action.parentId === this.id;
+    }
+    if (action.type.startsWith("filter")) return true;
+    if (action.type.startsWith("cohort")) return true;
+    if (action.type == "app_refresh") return true;
+    if (action.type.endsWith("customTerm")) return true;
+  }
+  // !!! NOTE: This getState() method is reused by the plot-specific recover component.
+  // When logging something within getState, it may have been called by either the plot or recover instance
+  getState(appState) {
+    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 {
+      termfilter: appState.termfilter,
+      config,
+      groups: appState.groups,
+      // quick fix to skip history tracking as needed
+      _scope_: appState._scope_
+    };
+  }
+  async main() {
+    this.dom.errdiv.style("display", "none").style("background-color", "rgba(255,100,100,0.2)").html("");
+    if (!this.components) await this.setComponents(this.opts);
+  }
+  async setComponents(opts) {
+    const _ = await importPlot(opts.chartType);
+    const promises = {
+      // recover: recoverInit({
+      // 	app: this.app,
+      // 	holder: this.dom.localRecoverDiv,
+      // 	getState: appState => this.getState(appState),
+      // 	reactsTo: action =>
+      // 		action.id == this.id &&
+      // 		(action.type == 'plot_edit' || action.type == 'plot_nestedEdits') &&
+      // 		action._track_ != 'none',
+      // 	plot_id: this.id,
+      // 	maxHistoryLen: 10,
+      // 	hideLabel: true
+      // }),
+      chart: _.componentInit({
+        app: this.app,
+        holder: this.dom.viz,
+        header: this.dom.paneTitleDiv,
+        id: this.id,
+        plotDiv: select_default(this.dom.holder.app_div.node().parentNode),
+        /******* reason for passing plotDiv to chart ********
+        				- this plot instance may allow to launch a new plot as a persistent sandbox
+        				  inside mass plotDiv, maintaining the uniform plot appearance despite it's ad-hoc
+        				  the new plot is not a formal mass plot type, and cannot be done via app.dispatch()
+        				  thus the need to directly access plotDiv
+        				- example: mds3 tk from genome browser can launch disco etc
+        				- having access to plotDiv may offer flexibility for the plot to do stuff
+        
+        				since plot.js has no access to mass app .dom.plotDiv in which all apps are shown,
+        				this workarounds gets the parent node of sandbox.app_div which is app.dom.plotDiv
+        				*/
+        getFilterImage: async () => this.components.filter.getFilterImage()
+      })
+    };
+    const plotFilterCfg = this.app.vocabApi.termdbConfig?.plotFilter;
+    if (!this.state.config.hidePlotFilter && !plotFilterCfg?.hide) {
+      const filterDisabledMsg = plotFilterCfg?.disabledMessage;
+      const filterHolder = filterDisabledMsg ? this.dom.filterDiv.append("div").style("pointer-events", "none").style("opacity", 0.5) : this.dom.filterDiv;
+      if (filterDisabledMsg) this.dom.filterDiv.attr("title", filterDisabledMsg).style("cursor", "not-allowed");
+      promises.filter = filterRxCompInit({
+        app: this.app,
+        vocabApi: this.app.vocabApi,
+        parentId: this.id,
+        holder: filterHolder,
+        hideLabel: true,
+        emptyLabel: "+Add new filter",
+        callback: (filter) => {
+          this.app.dispatch({
+            id: this.id,
+            type: "plot_edit",
+            config: { filter }
+          });
+        }
+      });
+    }
+    this.components = await multiInit(promises);
+  }
+  destroy() {
+    this.dom.holder.app_div.selectAll("*").remove();
+    this.dom.holder.app_div.remove();
+    for (const key in this.dom) {
+      delete this.dom[key];
+    }
+  }
+};
+var plotInit = getCompInit(MassPlot);
+function setRenderers(self) {
+  self.initUi = function(opts) {
+    const holder = opts.holder;
+    opts.holder.app_div.attr("data-testid", "sjpp-massplot-sandbox-" + opts.chartType);
+    holder.header.style("padding", 0);
+    try {
+      self.dom = {
+        tip: new Menu({ padding: "0px" }),
+        holder,
+        paneTitleDiv: holder.header.append("div").style("display", "inline-block").style("color", "#555").style("padding-left", "7px").style("vertical-align", "sub"),
+        localRecoverDiv: holder.header.append("div").style("display", "inline-block"),
+        filterDiv: holder.header.append("div").style("display", "inline-block").style("zoom", 0.9),
+        body: holder.body.style("white-space", "nowrap").style("overflow-x", "auto"),
+        // will hold no data notice or the page title in multichart views
+        errdiv: holder.body.append("div").style("display", "none").style("padding", "5px").style("background-color", "rgba(255,100,100,0.2)"),
+        // dom.viz will hold the rendered view
+        viz: holder.body.append("div")
+      };
+    } catch (e) {
+      self.dom.errdiv.style("display", "none").text(e);
+    }
+  };
+}
+
+// mass/app.ts
+var MassApp = class extends AppBase {
+  // expected class-specific props
+  constructor(opts, api) {
+    super(opts);
+    this.components = {};
+    this.wasDestroyed = false;
+    this.api = api;
+    if (opts.addLoginCallback) {
+      opts.addLoginCallback(() => this.api.dispatch({ type: "app_refresh" }));
+    }
+    this.type = "app";
+    this.dom = {
+      holder: opts.holder,
+      // do not modify holder style
+      topbar: opts.holder.append("div"),
+      errdiv: opts.holder.append("div"),
+      plotDiv: opts.holder.append("div")
+    };
+    if (opts.getPlotConfig_mutateSummary) {
+      if (typeof opts.getPlotConfig_mutateSummary != "function")
+        throw new Error("opts.getPlotConfig_mutateSummary is not function");
+    }
+    this.plotIdToSandboxId = {};
+  }
+  static {
+    this.type = "app";
+  }
+  async preApiFreeze(api) {
+    try {
+      api.tip = new Menu({ padding: "5px" });
+      api.tip.d.on("keyup", (event) => {
+        if (event.key == "Escape") api.tip.hide();
+      });
+      api.printError = (e) => this.printError(e);
+      api.vocabApi = await vocabInit({
+        app: api,
+        state: { vocab: this.opts.state.vocab },
+        fetchOpts: this.opts.fetchOpts,
+        getDatasetAccessToken: this.opts.getDatasetAccessToken
+      });
+      api.hasWebGL = function() {
+        try {
+          const canvas = document.createElement("canvas");
+          return !!(window.WebGLRenderingContext && (canvas.getContext("webgl") || canvas.getContext("experimental-webgl")));
+        } catch (_) {
+          return false;
+        }
+      };
+      this.opts.state.vocab = api.vocabApi.vocab;
+    } catch (e) {
+      console.log(`preApiFreeze error`, e);
+      throw e;
+    }
+  }
+  async init() {
+    try {
+      const debounceInterval = "debounceInterval" in this.opts ? this.opts.debounceInterval : 0;
+      const embeddedSessionState = this.opts.embeddedSessionState;
+      if (embeddedSessionState) {
+        Object.assign(this.opts.state, embeddedSessionState);
+      }
+      this.store = await storeInit({ app: this.api, state: this.opts.state, debounceInterval });
+      this.state = await this.store.copyState();
+      this.components = {};
+      if (this.state.nav.header_mode != "hidden") {
+        this.components.nav = await navInit({
+          app: this.api,
+          holder: this.dom.topbar,
+          header_mode: this.state && this.state.nav && this.state.nav.header_mode,
+          vocab: this.state.vocab,
+          massSessionDuration: this.state.termdbConfig.massSessionDuration,
+          // this.opts.massSessionDuration
+          pkgver: this.opts.pkgver,
+          downloadPlots: () => {
+            this.downloadPlots();
+          }
+        });
+      }
+      this.components.plots = {};
+      if (this.opts.app?.doNotAwaitInitRender) {
+        this.api.dispatch();
+      } else {
+        await this.api.dispatch();
+      }
+    } catch (e) {
+      this.printError(e);
+      throw e;
+    }
+  }
+  async main() {
+    await this.api.vocabApi.main();
+    this.dom.plotDiv?.style(
+      "display",
+      this.state.nav?.header_mode != "hidden" && this.state.nav?.activeTab == 0 ? "none" : "block"
+    );
+    const newPlots = {};
+    let sandbox;
+    for (const plot of this.state.plots) {
+      if (plot.parentId) continue;
+      if (this.components.plots && !(plot.id in this.components.plots)) {
+        sandbox = newSandboxDiv(this.dom.plotDiv, {
+          close: () => {
+            this.api.dispatch({
+              type: "plot_delete",
+              id: plot.id
+            });
+          },
+          plotId: plot.id,
+          beforePlotId: plot.insertBefore || null,
+          style: {
+            width: "98.5%"
+          }
+        });
+        if (plot.chartType == "summary")
+          newPlots[plot.id] = summaryInit(Object.assign({ app: this.api, holder: sandbox }, plot));
+        else newPlots[plot.id] = plotInit(Object.assign({ app: this.api, holder: sandbox }, plot));
+      }
+    }
+    const numNewPlots = Object.keys(newPlots).length;
+    if (numNewPlots) {
+      await Promise.all(Object.values(newPlots));
+      for (const plotId in newPlots) {
+        this.components.plots[plotId] = await newPlots[plotId];
+      }
+    }
+    for (const plotId in this.components.plots) {
+      if (!this.state.plots.find((p) => p.id === plotId)) {
+        this.components.plots[plotId].destroy();
+        delete this.components.plots[plotId];
+      }
+    }
+  }
+  printError(e) {
+    const errdiv = e.errdiv || this.dom.errdiv;
+    if (errdiv) errdiv.style("display", "").html("").style("background-color", "");
+    sayerror(errdiv || this.opts.holder, "Error: " + (e.message || e.error || e));
+    if (e.stack) console.log(e.stack);
+    this.bus.emit("error");
+    if (this.opts?.debug) {
+      console.groupCollapsed("Stack trace from MassApp.printError() call.");
+      console.trace();
+      console.groupEnd();
+    }
+  }
+  skipPrevActionAbort(action) {
+    return skipPrevActionAbort(action);
+  }
+  async downloadPlots() {
+    const chartImagesAll = [];
+    let i = 1;
+    const values = Object.values(this.components.plots);
+    for (const plot of values) {
+      const chart = plot.type == "plot" ? plot.getComponents("chart") : plot;
+      const chartImages = chart.getChartImages ? chart.getChartImages() : null;
+      if (!chartImages) {
+        console.log(`The ${chart.type} does not support downloading images yet`);
+        continue;
+      }
+      for (const chartImage of chartImages) {
+        if (values.length > 1) chartImage.name = `${i}. ${chartImage.name}`;
+        chartImagesAll.push(chartImage);
+      }
+      i++;
+    }
+    if (chartImagesAll.length > 0) {
+      const filters = [];
+      const globalFilterImg = await this.components.nav.getComponents("filter").getFilterImage();
+      if (globalFilterImg) filters.push(globalFilterImg);
+      downloadSVGsAsPdf(chartImagesAll, "plots", "landscape", filters);
+    } else alert("No chart images available for download");
+  }
+};
+var appInit = AppApi.getInitFxn(MassApp);
+
+export {
+  appInit
+};
+//# sourceMappingURL=chunk-RSMASA5S.js.map

package/dist/chunk-S2BMWHFY.js

@@ -0,0 +1,54 @@
+import {
+  addGeneSearchbox
+} from "./chunk-4ASBDE27.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+
+// termdb/handlers/snp.ts
+var SearchHandler = class {
+  init(opts) {
+    this.callback = opts.callback;
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: opts.holder,
+      searchOnly: "snp",
+      allowVariant: true,
+      callback: () => this.selectSnp(geneSearch)
+    });
+  }
+  async selectSnp(geneSearch) {
+    const { chr, ref, alt, fromWhat } = geneSearch;
+    if (!chr || !ref || !alt || !fromWhat) throw "missing chr, ref, alt, or fromWhat of snp";
+    let start, stop;
+    if (!geneSearch.start && !geneSearch.stop) {
+      if (geneSearch.pos) {
+        start = geneSearch.pos - 1;
+        stop = geneSearch.pos;
+      } else {
+        throw "missing coordinate of snp";
+      }
+    } else {
+      start = geneSearch.start;
+      stop = geneSearch.stop;
+    }
+    const term = {
+      id: fromWhat,
+      chr,
+      start,
+      stop,
+      name: fromWhat,
+      ref,
+      alt: typeof alt == "string" ? [alt] : alt,
+      // is string if input to geneSearch was in variant or hgvs format // TODO: update genesearch.ts to parse alternative alleles from any input format into arrays
+      type: "snp"
+    };
+    this.callback(term);
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-S2BMWHFY.js.map