@sjcrh/proteinpaint-client 2.193.0 → 2.195.0

package/dist/geneRanking-ODKGLJX2.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/geneRanking.ts"],
+  "sourcesContent": ["import { renderTable, sayerror, icons } from '#dom'\nimport { dofetch3 } from '#common/dofetch'\nimport { getCompInit, copyMerge } from '#rx'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport { PlotBase } from '#plots/PlotBase.js'\nimport { scaleLinear } from 'd3-scale'\n\nconst Integrative_rank_COLUMN = 'Integrative rank'\n\nconst MISSING_COLOR = '#d9d9d9'\n// sequential scale for per-column min-max-scaled rank: low (top rank) = dark, high = light\nconst SEQ_COLOR_LOW = '#08306b'\nconst SEQ_COLOR_HIGH = '#f7fbff'\n\nclass GeneRanking extends PlotBase {\n\tstatic type = 'geneRanking'\n\n\tloadingDiv: any\n\terrDiv: any\n\ttableDiv: any\n\ttype: string\n\tstate: any\n\tconfig: any\n\tdataKey?: string\n\tcachedData?: { columns: string[]; rows: (string | number | null)[][] }\n\tsortIdx: number = -1\n\tsortAsc: boolean = true\n\tpageSize: number = 10\n\tcurrentPage: number = 1\n\tsearchQuery: string = ''\n\ttoolbarDiv: any\n\tnoteDiv: any\n\tsearchInput: any\n\theatmapSection: any\n\theatmapControls: any\n\theatmapDiv: any\n\theatmapStatus: any\n\theatmapOrder: 'clustered' | 'rank' = 'clustered'\n\tminAssays: number = 3\n\tminAssaysSelect: any\n\t/** identity-tag of the data the current heatmap was rendered for; used to abort stale responses */\n\theatmapRenderKey: string = ''\n\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.type = GeneRanking.type\n\t\tconst main = opts.holder.append('div').style('padding', '12px').style('max-width', '95vw')\n\t\tthis.errDiv = main.append('div').style('color', 'red').style('display', 'none').style('padding', '8px')\n\t\tthis.loadingDiv = main.append('div').style('padding', '8px').text('Loading...')\n\t\tthis.toolbarDiv = main\n\t\t\t.append('div')\n\t\t\t.style('display', 'none')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('justify-content', 'space-between')\n\t\t\t.style('flex-wrap', 'wrap')\n\t\t\t.style('gap', '8px')\n\t\t\t.style('margin-bottom', '6px')\n\t\t\t.style('font-size', '12px')\n\t\tconst leftBar = this.toolbarDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '6px')\n\t\tconst dlBtn = leftBar\n\t\t\t.append('button')\n\t\t\t.style('display', 'inline-flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '6px')\n\t\t\t.style('padding', '4px 10px')\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.on('click', () => this.downloadAll())\n\t\ticons['download'](dlBtn.append('span').style('display', 'inline-flex').style('align-items', 'center'), {\n\t\t\twidth: 14,\n\t\t\theight: 14,\n\t\t\ttitle: 'Download data as TSV'\n\t\t})\n\t\tdlBtn.append('span').text('Download data')\n\t\tconst rightBar = this.toolbarDiv.append('div')\n\t\trightBar.append('span').text('Search: ').style('margin-right', '4px')\n\t\tthis.searchInput = rightBar\n\t\t\t.append('input')\n\t\t\t.attr('type', 'search')\n\t\t\t.attr('placeholder', 'gene name')\n\t\t\t.style('padding', '3px 6px')\n\t\t\t.on('input', (event: any) => {\n\t\t\t\tthis.searchQuery = (event.target.value || '').trim().toLowerCase()\n\t\t\t\tthis.currentPage = 1\n\t\t\t\tthis.renderTable()\n\t\t\t})\n\t\tthis.noteDiv = main\n\t\t\t.append('div')\n\t\t\t.style('display', 'none')\n\t\t\t.style('font-size', '0.85em')\n\t\t\t.style('color', '#555')\n\t\t\t.style('margin-bottom', '10px')\n\t\t\t.style('line-height', '1.4')\n\t\t\t.style('white-space', 'normal')\n\t\t\t.style('word-break', 'normal')\n\t\t\t.style('overflow-wrap', 'break-word')\n\t\tthis.tableDiv = main.append('div').attr('data-testid', 'sjpp-geneRanking-table').style('font-size', '12px')\n\n\t\tthis.heatmapSection = main\n\t\t\t.append('div')\n\t\t\t.style('display', 'none')\n\t\t\t.style('margin-top', '24px')\n\t\t\t.attr('data-testid', 'sjpp-geneRanking-heatmap')\n\t\tconst hmHeader = this.heatmapSection\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '12px')\n\t\t\t.style('margin-bottom', '8px')\n\t\thmHeader.append('div').style('font-weight', 'bold').text('Heatmap of the current page')\n\t\tthis.heatmapControls = hmHeader\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '6px')\n\t\tthis.heatmapControls.append('span').style('font-size', '0.85em').style('color', '#555').text('Row order:')\n\t\tconst orderSelect = this.heatmapControls\n\t\t\t.append('select')\n\t\t\t.style('padding', '2px 4px')\n\t\t\t.on('change', (event: any) => {\n\t\t\t\tthis.heatmapOrder = event.target.value\n\t\t\t\tthis.renderHeatmap()\n\t\t\t})\n\t\torderSelect.append('option').attr('value', 'clustered').text('Clustered').property('selected', true)\n\t\torderSelect.append('option').attr('value', 'rank').text('Ranking score')\n\t\t// min-assays selector wrapper, hidden when order is \"rank\"\n\t\tconst minAssaysWrap = this.heatmapControls\n\t\t\t.append('span')\n\t\t\t.attr('class', 'sjpp-mr-min-assays-wrap')\n\t\t\t.style('display', 'inline-flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '6px')\n\t\tminAssaysWrap.append('span').style('font-size', '0.85em').style('color', '#555').text('Min assays:')\n\t\tthis.minAssaysSelect = minAssaysWrap\n\t\t\t.append('select')\n\t\t\t.style('padding', '2px 4px')\n\t\t\t.on('change', (event: any) => {\n\t\t\t\tthis.minAssays = Number(event.target.value)\n\t\t\t\tthis.renderHeatmap()\n\t\t\t})\n\t\t// options are populated dynamically in renderHeatmap based on available modalities\n\t\tthis.heatmapStatus = this.heatmapSection\n\t\t\t.append('div')\n\t\t\t.style('font-size', '0.85em')\n\t\t\t.style('color', '#777')\n\t\t\t.style('margin-bottom', '6px')\n\t\tthis.heatmapDiv = this.heatmapSection.append('div').style('overflow-x', 'auto')\n\n\t\tthis.dom = {\n\t\t\tholder: main,\n\t\t\theader: opts.header,\n\t\t\terrDiv: this.errDiv,\n\t\t\tloadingDiv: this.loadingDiv,\n\t\t\ttoolbarDiv: this.toolbarDiv,\n\t\t\tnoteDiv: this.noteDiv,\n\t\t\ttableDiv: this.tableDiv\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='${this.id}' found`\n\t\treturn { config, vocab: appState.vocab, termdbConfig: appState.termdbConfig }\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.startsWith('plot_')) return action.id === this.id\n\t\treturn false\n\t}\n\n\tasync main() {\n\t\tthis.config = structuredClone(this.state.config)\n\t\tconst key = this.config.rankingKey\n\t\tif (!key) {\n\t\t\tthis.loadingDiv.style('display', 'none')\n\t\t\tthis.errDiv.style('display', 'block').text('No ranking key selected')\n\t\t\treturn\n\t\t}\n\t\tif (this.dom.header)\n\t\t\tthis.dom.header.html(`${key} <span style=\"font-size:.8em;opacity:.7\">MULTIOMIC RANKINGS</span>`)\n\n\t\tif (this.dataKey !== key) {\n\t\t\tthis.loadingDiv.style('display', 'block')\n\t\t\tthis.tableDiv.selectAll('*').remove()\n\t\t\ttry {\n\t\t\t\tconst resp = await dofetch3('termdb/geneRanking', {\n\t\t\t\t\tbody: {\n\t\t\t\t\t\tgenome: this.state.vocab.genome,\n\t\t\t\t\t\tdslabel: this.state.vocab.dslabel,\n\t\t\t\t\t\tkey\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\tif (resp.error) throw resp.error\n\t\t\t\tthis.cachedData = { columns: resp.columns, rows: resp.rows }\n\t\t\t\tthis.dataKey = key\n\t\t\t\t// default sort: Integrative rank ascending\n\t\t\t\tconst integrativeRankIdx = resp.columns.indexOf(Integrative_rank_COLUMN)\n\t\t\t\tthis.sortIdx = integrativeRankIdx >= 0 ? integrativeRankIdx : -1\n\t\t\t\tthis.sortAsc = true\n\t\t\t\tthis.currentPage = 1\n\t\t\t\tthis.searchQuery = ''\n\t\t\t\tif (this.searchInput) this.searchInput.node().value = ''\n\t\t\t} catch (e: any) {\n\t\t\t\tthis.loadingDiv.style('display', 'none')\n\t\t\t\tsayerror(this.errDiv.style('display', 'block'), e.message || e)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tthis.loadingDiv.style('display', 'none')\n\t\t}\n\t\tthis.toolbarDiv.style('display', 'flex')\n\t\tconst desc = this.state.termdbConfig?.queries?.geneRanking?.description\n\t\tthis.noteDiv.style('display', desc ? 'block' : 'none').text(desc || '')\n\t\tthis.renderTable()\n\t}\n\n\tdownloadAll() {\n\t\tif (!this.cachedData) return\n\t\tconst { columns, rows } = this.cachedData\n\t\tconst filtered = this.searchQuery\n\t\t\t? rows.filter(r => {\n\t\t\t\t\tconst gene = r[0]\n\t\t\t\t\treturn typeof gene === 'string' && gene.toLowerCase().includes(this.searchQuery)\n\t\t\t  })\n\t\t\t: rows\n\t\tconst sorted = this.sortIdx >= 0 ? sortRows(filtered, this.sortIdx, this.sortAsc) : filtered\n\t\tconst lines = [columns.join('\\t')]\n\t\tfor (const row of sorted) {\n\t\t\tlines.push(row.map(v => (v == null ? 'NA' : String(v))).join('\\t'))\n\t\t}\n\t\tconst blob = new Blob([lines.join('\\n')], { type: 'text/tab-separated-values' })\n\t\tconst url = URL.createObjectURL(blob)\n\t\tconst a = document.createElement('a')\n\t\tconst slug = (this.dataKey || 'geneRanking').replace(/[^A-Za-z0-9_-]+/g, '_')\n\t\ta.href = url\n\t\ta.download = `${slug}.tsv`\n\t\tdocument.body.appendChild(a)\n\t\ta.click()\n\t\tdocument.body.removeChild(a)\n\t\tURL.revokeObjectURL(url)\n\t}\n\n\trenderTable() {\n\t\tif (!this.cachedData) return\n\t\tconst { columns, rows } = this.cachedData\n\n\t\tconst filtered = this.searchQuery\n\t\t\t? rows.filter(r => {\n\t\t\t\t\tconst gene = r[0]\n\t\t\t\t\treturn typeof gene === 'string' && gene.toLowerCase().includes(this.searchQuery)\n\t\t\t  })\n\t\t\t: rows\n\n\t\tconst sortedRows = this.sortIdx >= 0 ? sortRows(filtered, this.sortIdx, this.sortAsc) : filtered\n\n\t\tconst cols = columns.map((label, i) => ({\n\t\t\tlabel,\n\t\t\tsortable: true,\n\t\t\talign: i === 0 ? 'left' : 'right',\n\t\t\tnowrap: i === 0\n\t\t}))\n\n\t\tconst tableRows = sortedRows.map(row =>\n\t\t\trow.map(v => {\n\t\t\t\tif (v === null || v === undefined) return { value: '' }\n\t\t\t\tif (typeof v === 'number') return { value: roundValueAuto(v) }\n\t\t\t\treturn { value: v }\n\t\t\t})\n\t\t)\n\n\t\t// onSort hook: when caller-controlled sort is needed across pages, we\n\t\t// rebind by re-rendering the table with our own sort state. Use header\n\t\t// click overlay since renderTable's built-in sort only orders the\n\t\t// current `rows` reference passed in (which is fine here because we\n\t\t// pre-sort the full dataset before passing it in).\n\t\tthis.tableDiv.selectAll('*').remove()\n\n\t\t// Custom sort headers: we wrap renderTable but disable its built-in\n\t\t// sort buttons, intercepting header clicks ourselves to keep sort\n\t\t// applied across all pages.\n\t\trenderTable({\n\t\t\tcolumns: cols,\n\t\t\trows: tableRows,\n\t\t\tdiv: this.tableDiv,\n\t\t\tshowLines: true,\n\t\t\tstriped: true,\n\t\t\tshowHeader: true,\n\t\t\theader: { allowSort: false },\n\t\t\tmaxWidth: '95vw',\n\t\t\tmaxHeight: '70vh',\n\t\t\tpagination: {\n\t\t\t\tpageSize: this.pageSize,\n\t\t\t\tpageSizeOptions: [10, 25, 50, 100],\n\t\t\t\tcurrentPage: this.currentPage,\n\t\t\t\tonChange: ({ currentPage, pageSize }) => {\n\t\t\t\t\tthis.currentPage = currentPage\n\t\t\t\t\tthis.pageSize = pageSize\n\t\t\t\t\tthis.renderHeatmap()\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\t// Make the column headers clickable to sort across the full dataset\n\t\tconst ths = this.tableDiv.selectAll('thead th')\n\t\tths.each((_d, i, nodes) => {\n\t\t\tconst th = nodes[i] as HTMLElement\n\t\t\tth.style.cursor = 'pointer'\n\t\t\tth.style.userSelect = 'none'\n\t\t\tth.style.whiteSpace = 'nowrap'\n\t\t\tth.style.color = '#000'\n\t\t\tth.style.fontWeight = 'bold'\n\t\t\tth.style.opacity = '1'\n\t\t\tconst colIdx = i\n\t\t\tconst label = columns[colIdx]\n\t\t\tif (!label) return\n\t\t\tconst active = this.sortIdx === colIdx\n\t\t\tconst upColor = active && this.sortAsc ? '#000' : '#ccc'\n\t\t\tconst downColor = active && !this.sortAsc ? '#000' : '#ccc'\n\t\t\tth.innerHTML =\n\t\t\t\t`<span>${escapeHtml(label)}</span>` +\n\t\t\t\t`<span style=\"display:inline-flex;flex-direction:column;line-height:0.6em;margin-left:4px;vertical-align:middle;font-size:0.7em;\">` +\n\t\t\t\t`<span style=\"color:${upColor}\">\\u25B2</span>` +\n\t\t\t\t`<span style=\"color:${downColor}\">\\u25BC</span>` +\n\t\t\t\t`</span>`\n\t\t\tth.onclick = () => {\n\t\t\t\tif (this.sortIdx === colIdx) this.sortAsc = !this.sortAsc\n\t\t\t\telse {\n\t\t\t\t\tthis.sortIdx = colIdx\n\t\t\t\t\tthis.sortAsc = true\n\t\t\t\t}\n\t\t\t\tthis.currentPage = 1\n\t\t\t\tthis.renderTable()\n\t\t\t}\n\t\t})\n\n\t\t// match toolbar + note width to the rendered table width\n\t\trequestAnimationFrame(() => {\n\t\t\t// the inline-block wrapper that renderTable creates around the <table>\n\t\t\tconst wrapper = this.tableDiv.select(':scope > div').node() as HTMLElement | null\n\t\t\tconst measured = wrapper || (this.tableDiv.select('table').node() as HTMLElement | null)\n\t\t\tif (!measured) return\n\t\t\tconst w = measured.getBoundingClientRect().width\n\t\t\tif (w > 0) {\n\t\t\t\tconst px = `${Math.ceil(w)}px`\n\t\t\t\tthis.toolbarDiv.style('width', px).style('box-sizing', 'border-box')\n\t\t\t\tthis.noteDiv.style('width', px).style('box-sizing', 'border-box')\n\t\t\t}\n\t\t})\n\t\tthis.renderHeatmap()\n\t}\n\n\t/** rows displayed on the current page after filter + sort + pagination */\n\tprivate getVisibleRows(): (string | number | null)[][] {\n\t\tif (!this.cachedData) return []\n\t\tconst { rows } = this.cachedData\n\t\tconst filtered = this.searchQuery\n\t\t\t? rows.filter(r => {\n\t\t\t\t\tconst gene = r[0]\n\t\t\t\t\treturn typeof gene === 'string' && gene.toLowerCase().includes(this.searchQuery)\n\t\t\t  })\n\t\t\t: rows\n\t\tconst sorted = this.sortIdx >= 0 ? sortRows(filtered, this.sortIdx, this.sortAsc) : filtered\n\t\tconst start = (this.currentPage - 1) * this.pageSize\n\t\treturn sorted.slice(start, start + this.pageSize)\n\t}\n\n\tasync renderHeatmap() {\n\t\tif (!this.cachedData) {\n\t\t\tthis.heatmapSection.style('display', 'none')\n\t\t\treturn\n\t\t}\n\t\tconst { columns } = this.cachedData\n\n\t\t// modality columns available in this dataset, intersected with biological order\n\t\tconst colNameToIdx = new Map(columns.map((c, i) => [c, i]))\n\t\tconst modalities: string[] = this.state.termdbConfig?.queries?.geneRanking?.modalities || []\n\t\tconst usedCols = modalities.filter(m => colNameToIdx.has(m))\n\t\tif (usedCols.length < 2) {\n\t\t\tthis.heatmapSection.style('display', 'none')\n\t\t\treturn\n\t\t}\n\t\tthis.heatmapSection.style('display', 'block')\n\n\t\t// (re)populate min-assays options based on the available modality count\n\t\tif (this.minAssays > usedCols.length) this.minAssays = usedCols.length\n\t\tif (this.minAssays < 2) this.minAssays = 2\n\t\tconst optionVals = this.minAssaysSelect\n\t\t\t.selectAll('option')\n\t\t\t.nodes()\n\t\t\t.map((o: HTMLOptionElement) => Number(o.value))\n\t\tconst want = Array.from({ length: usedCols.length - 1 }, (_, i) => i + 2)\n\t\tif (optionVals.length !== want.length || optionVals.some((v, i) => v !== want[i])) {\n\t\t\tthis.minAssaysSelect.selectAll('option').remove()\n\t\t\tfor (const n of want) {\n\t\t\t\tthis.minAssaysSelect\n\t\t\t\t\t.append('option')\n\t\t\t\t\t.attr('value', n)\n\t\t\t\t\t.text(String(n))\n\t\t\t\t\t.property('selected', n === this.minAssays)\n\t\t\t}\n\t\t}\n\n\t\tconst visible = this.getVisibleRows()\n\t\tconst geneNames = visible.map(r => String(r[0]))\n\t\tconst matrix: (number | null)[][] = visible.map(r =>\n\t\t\tusedCols.map(c => {\n\t\t\t\tconst v = r[colNameToIdx.get(c)!]\n\t\t\t\treturn typeof v === 'number' && Number.isFinite(v) ? v : null\n\t\t\t})\n\t\t)\n\n\t\t// per-column stats over the FULL dataset \u2014 the file values are already ranks,\n\t\t// so use them as-is and normalize for color by each column's full-data min/max.\n\t\tconst fullStats = computeColStats(\n\t\t\tthis.cachedData.rows,\n\t\t\tusedCols.map(c => colNameToIdx.get(c)!)\n\t\t)\n\t\tconst toPct = (val: number | null, c: number): number | null => {\n\t\t\tif (val === null || !Number.isFinite(val as number)) return null\n\t\t\tconst lo = fullStats.min[c]\n\t\t\tconst hi = fullStats.max[c]\n\t\t\tif (!Number.isFinite(lo) || !Number.isFinite(hi) || hi === lo) return 0\n\t\t\treturn ((val as number) - lo) / (hi - lo)\n\t\t}\n\t\tconst buildPct = (raw: (number | null)[][]) => raw.map(row => row.map((v, c) => toPct(v, c)))\n\n\t\t// fingerprint of the data so a late-arriving response from a previous\n\t\t// render doesn't overwrite the current one\n\t\tconst renderKey = `${this.dataKey}|${this.heatmapOrder}|${this.minAssays}|${this.currentPage}|${this.pageSize}|${\n\t\t\tthis.searchQuery\n\t\t}|${this.sortIdx}|${this.sortAsc}|${geneNames.join(',')}`\n\t\tthis.heatmapRenderKey = renderKey\n\t\tthis.heatmapDiv.selectAll('*').remove()\n\t\tthis.heatmapStatus.text('Computing heatmap\u2026')\n\n\t\t// show/hide min-assays selector based on order mode\n\t\tthis.heatmapControls\n\t\t\t.select('.sjpp-mr-min-assays-wrap')\n\t\t\t.style('display', this.heatmapOrder === 'clustered' ? 'inline-flex' : 'none')\n\n\t\t// ranking-score order: keep all rows on the page, no clustering\n\t\tif (this.heatmapOrder === 'rank') {\n\t\t\tif (geneNames.length < 1) {\n\t\t\t\tthis.heatmapStatus.text('No rows to display.')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tthis.heatmapStatus.text(\n\t\t\t\t`${geneNames.length} rows in current page order. Missing values shown in gray; cells colored by rank within the full dataset per column (lower = better).`\n\t\t\t)\n\t\t\tthis.drawHeatmap({\n\t\t\t\trowNames: geneNames,\n\t\t\t\tcolNames: usedCols,\n\t\t\t\tmatrix: buildPct(matrix),\n\t\t\t\trankMatrix: matrix,\n\t\t\t\ttotals: fullStats.n,\n\t\t\t\tdendrogram: null\n\t\t\t})\n\t\t\treturn\n\t\t}\n\n\t\ttry {\n\t\t\tconst resp = await dofetch3('termdb/geneRanking', {\n\t\t\t\tbody: {\n\t\t\t\t\tfor: 'cluster',\n\t\t\t\t\tmatrix,\n\t\t\t\t\trow_names: geneNames,\n\t\t\t\t\tcol_names: usedCols,\n\t\t\t\t\tminAssays: this.minAssays\n\t\t\t\t}\n\t\t\t})\n\t\t\tif (renderKey !== this.heatmapRenderKey) return // stale\n\t\t\tif (resp.error) throw resp.error\n\t\t\tconst keptCount = resp.usedRowNames?.length ?? 0\n\t\t\tthis.heatmapStatus.text(\n\t\t\t\t`${keptCount} of ${visible.length} rows shown (proteins with \u2265${this.minAssays} assays). Missing values shown in gray; cells colored by rank within the full dataset per column (lower = better).`\n\t\t\t)\n\t\t\tconst nameToIdx = new Map(geneNames.map((n, i) => [n, i]))\n\t\t\tconst keptRawMatrix = (resp.usedRowNames as string[]).map(n => matrix[nameToIdx.get(n)!])\n\t\t\tconst keptNameToIdx = new Map((resp.usedRowNames as string[]).map((n, i) => [n, i]))\n\t\t\tconst orderedRowNames = resp.row.order.map((o: { name: string }) => o.name)\n\t\t\tconst orderedRank = orderedRowNames.map((name: string) => keptRawMatrix[keptNameToIdx.get(name)!])\n\t\t\tconst orderedPct = buildPct(orderedRank)\n\t\t\tthis.drawHeatmap({\n\t\t\t\trowNames: orderedRowNames,\n\t\t\t\tcolNames: resp.usedColNames,\n\t\t\t\tmatrix: orderedPct,\n\t\t\t\trankMatrix: orderedRank,\n\t\t\t\ttotals: fullStats.n,\n\t\t\t\tdendrogram: resp.row\n\t\t\t})\n\t\t} catch (e: any) {\n\t\t\tif (renderKey !== this.heatmapRenderKey) return\n\t\t\tthis.heatmapStatus.text(`Heatmap error: ${e?.message || e}`)\n\t\t}\n\t}\n\n\tprivate drawHeatmap(opts: {\n\t\trowNames: string[]\n\t\tcolNames: string[]\n\t\tmatrix: (number | null)[][]\n\t\trankMatrix: (number | null)[][]\n\t\ttotals: number[]\n\t\tdendrogram: null | {\n\t\t\tmerge: { n1: number; n2: number }[]\n\t\t\theight: { height: number }[]\n\t\t\torder: { name: string }[]\n\t\t\tinputOrder: string[]\n\t\t}\n\t}) {\n\t\tconst { rowNames, colNames, matrix, rankMatrix, totals, dendrogram } = opts\n\t\tconst cellW = 44\n\t\tconst cellH = 22\n\t\tconst dendroW = dendrogram ? 110 : 0\n\t\tconst dendroPad = dendrogram ? 8 : 0\n\t\tconst colLabelH = 110\n\t\tconst rowLabelW = 130\n\t\tconst legendBlockW = 110 // space reserved to the right of row labels for the vertical legend\n\t\tconst gridW = colNames.length * cellW\n\t\tconst gridH = rowNames.length * cellH\n\t\t// legend dims (must match values used below when drawing)\n\t\tconst legendGradH = Math.max(120, Math.min(gridH, 240))\n\t\tconst missingSwatchExtra = 18 + 12 // gap + swatch height\n\t\tconst totalW = dendroW + dendroPad + gridW + 8 + rowLabelW + legendBlockW\n\t\tconst totalH = colLabelH + Math.max(gridH, legendGradH + missingSwatchExtra) + 16\n\n\t\tthis.heatmapDiv.selectAll('*').remove()\n\t\tconst svg = this.heatmapDiv\n\t\t\t.append('svg')\n\t\t\t.attr('width', totalW)\n\t\t\t.attr('height', totalH)\n\t\t\t.attr('font-family', 'sans-serif')\n\n\t\t// sequential color scale on min-max-scaled rank in [0,1]: low (best rank) = dark, high = light\n\t\tconst seq = scaleLinear<string>().domain([0, 1]).range([SEQ_COLOR_LOW, SEQ_COLOR_HIGH]).clamp(true)\n\t\tconst color = (v: number) => seq(v)\n\n\t\t// row dendrogram (left)\n\t\tif (dendrogram) {\n\t\t\tconst g = svg.append('g').attr('transform', `translate(0,${colLabelH})`)\n\t\t\tdrawRowDendrogram(g, dendrogram, dendroW, gridH, cellH)\n\t\t}\n\n\t\t// column labels (rotated)\n\t\tconst gridX = dendroW + dendroPad\n\t\tconst labelsG = svg.append('g').attr('transform', `translate(${gridX},${colLabelH - 4})`)\n\t\tlabelsG\n\t\t\t.selectAll('text')\n\t\t\t.data(colNames)\n\t\t\t.enter()\n\t\t\t.append('text')\n\t\t\t.attr('x', (_d, i) => i * cellW + cellW / 2)\n\t\t\t.attr('y', 0)\n\t\t\t.attr('transform', (_d, i) => `rotate(-45,${i * cellW + cellW / 2},0)`)\n\t\t\t.attr('text-anchor', 'start')\n\t\t\t.attr('font-size', '13px')\n\t\t\t.attr('fill', '#000')\n\t\t\t.text(d => d)\n\n\t\t// cells\n\t\tconst cellsG = svg.append('g').attr('transform', `translate(${gridX},${colLabelH})`)\n\t\tconst cellData: { x: number; y: number; v: number | null; row: number; col: number }[] = []\n\t\tfor (let r = 0; r < matrix.length; r++) {\n\t\t\tfor (let c = 0; c < matrix[r].length; c++) {\n\t\t\t\tcellData.push({ x: c * cellW, y: r * cellH, v: matrix[r][c], row: r, col: c })\n\t\t\t}\n\t\t}\n\t\tcellsG\n\t\t\t.selectAll('rect')\n\t\t\t.data(cellData)\n\t\t\t.enter()\n\t\t\t.append('rect')\n\t\t\t.attr('x', d => d.x)\n\t\t\t.attr('y', d => d.y)\n\t\t\t.attr('width', cellW)\n\t\t\t.attr('height', cellH)\n\t\t\t.attr('fill', d => (d.v === null || !Number.isFinite(d.v) ? MISSING_COLOR : color(d.v as number)))\n\t\t\t.attr('stroke', '#fff')\n\t\t\t.attr('stroke-width', 0.5)\n\t\t\t.append('title')\n\t\t\t.text(d => {\n\t\t\t\tif (d.v === null || !Number.isFinite(d.v)) return `${rowNames[d.row]} \u2014 ${colNames[d.col]}\\nmissing`\n\t\t\t\tconst r = rankMatrix[d.row][d.col] as number\n\t\t\t\tconst n = totals[d.col]\n\t\t\t\tconst rStr = Number.isInteger(r) ? String(r) : r.toFixed(1)\n\t\t\t\treturn `${rowNames[d.row]} \u2014 ${colNames[d.col]}\\nrank: ${rStr} of ${n}\\nscaled rank: ${(d.v as number).toFixed(\n\t\t\t\t\t3\n\t\t\t\t)}`\n\t\t\t})\n\n\t\t// rank number overlay on each non-null cell\n\t\tcellsG\n\t\t\t.selectAll('text.sjpp-mr-rank')\n\t\t\t.data(cellData.filter(d => d.v !== null && Number.isFinite(d.v)))\n\t\t\t.enter()\n\t\t\t.append('text')\n\t\t\t.attr('class', 'sjpp-mr-rank')\n\t\t\t.attr('x', d => d.x + cellW / 2)\n\t\t\t.attr('y', d => d.y + cellH / 2 + 3)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('font-size', '9px')\n\t\t\t.attr('font-weight', 300)\n\t\t\t.attr('pointer-events', 'none')\n\t\t\t.attr('fill', d => ((d.v as number) < 0.5 ? 'rgba(255,255,255,0.85)' : 'rgba(40,40,40,0.7)'))\n\t\t\t.text(d => {\n\t\t\t\tconst r = rankMatrix[d.row][d.col] as number\n\t\t\t\treturn Number.isInteger(r) ? String(r) : r.toFixed(1)\n\t\t\t})\n\n\t\t// row labels (gene names) on the right\n\t\tconst rowLabelsG = svg.append('g').attr('transform', `translate(${gridX + gridW + 6},${colLabelH})`)\n\t\trowLabelsG\n\t\t\t.selectAll('text')\n\t\t\t.data(rowNames)\n\t\t\t.enter()\n\t\t\t.append('text')\n\t\t\t.attr('x', 0)\n\t\t\t.attr('y', (_d, i) => i * cellH + cellH / 2 + 4)\n\t\t\t.attr('font-size', '13px')\n\t\t\t.attr('fill', '#000')\n\t\t\t.text(d => d)\n\n\t\t// vertical color legend (placed to the right of the row labels)\n\t\tconst legendGradW = 16\n\t\tconst legendX = gridX + gridW + 8 + rowLabelW + 8\n\t\tconst legendY = colLabelH\n\t\tconst legendG = svg.append('g').attr('transform', `translate(${legendX},${legendY})`)\n\t\t// title rotated alongside the gradient\n\t\tlegendG\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(-6,${legendGradH / 2}) rotate(-90)`)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('font-size', '11px')\n\t\t\t.attr('fill', '#555')\n\t\t\t.text('scaled rank (per column)')\n\t\tconst stops = 32\n\t\tfor (let i = 0; i < stops; i++) {\n\t\t\t// top of legend = 0 (best rank, dark); bottom = 1 (worst rank, light)\n\t\t\tconst v = i / (stops - 1)\n\t\t\tlegendG\n\t\t\t\t.append('rect')\n\t\t\t\t.attr('x', 0)\n\t\t\t\t.attr('y', (i * legendGradH) / stops)\n\t\t\t\t.attr('width', legendGradW)\n\t\t\t\t.attr('height', legendGradH / stops + 0.5)\n\t\t\t\t.attr('fill', color(v))\n\t\t}\n\t\tlegendG\n\t\t\t.append('rect')\n\t\t\t.attr('x', 0)\n\t\t\t.attr('y', 0)\n\t\t\t.attr('width', legendGradW)\n\t\t\t.attr('height', legendGradH)\n\t\t\t.attr('fill', 'none')\n\t\t\t.attr('stroke', '#999')\n\t\t\t.attr('stroke-width', 0.5)\n\t\t// tick labels: show actual ranks (1 = top/best) rather than the scaled [0,1]\n\t\t// value. The gradient is min-max-scaled per column, so the largest rank count\n\t\t// across columns is used as the shared bottom-of-legend value.\n\t\tconst maxRank = totals.reduce((m, t) => (Number.isFinite(t) && t > m ? t : m), 0)\n\t\tconst midRank = Math.round((1 + maxRank) / 2)\n\t\tlegendG\n\t\t\t.append('text')\n\t\t\t.attr('x', legendGradW + 6)\n\t\t\t.attr('y', 4)\n\t\t\t.attr('font-size', '11px')\n\t\t\t.text('1 (top)')\n\t\tlegendG\n\t\t\t.append('text')\n\t\t\t.attr('x', legendGradW + 6)\n\t\t\t.attr('y', legendGradH / 2 + 4)\n\t\t\t.attr('font-size', '11px')\n\t\t\t.text(String(midRank))\n\t\tlegendG\n\t\t\t.append('text')\n\t\t\t.attr('x', legendGradW + 6)\n\t\t\t.attr('y', legendGradH)\n\t\t\t.attr('font-size', '11px')\n\t\t\t.text(`${maxRank} (bottom)`)\n\n\t\t// missing-value swatch below the gradient\n\t\tconst missingG = svg.append('g').attr('transform', `translate(${legendX},${legendY + legendGradH + 18})`)\n\t\tmissingG\n\t\t\t.append('rect')\n\t\t\t.attr('width', legendGradW)\n\t\t\t.attr('height', 12)\n\t\t\t.attr('fill', MISSING_COLOR)\n\t\t\t.attr('stroke', '#999')\n\t\t\t.attr('stroke-width', 0.5)\n\t\tmissingG\n\t\t\t.append('text')\n\t\t\t.attr('x', legendGradW + 6)\n\t\t\t.attr('y', 10)\n\t\t\t.attr('font-size', '11px')\n\t\t\t.attr('fill', '#555')\n\t\t\t.text('missing')\n\t}\n}\n\nfunction escapeHtml(s: string): string {\n\treturn s.replace(/[&<>\"']/g, c => ({ '&': '&amp;', '<': '&lt;', '>': '&gt;', '\"': '&quot;', \"'\": '&#39;' }[c]!))\n}\n\nfunction sortRows(rows: (string | number | null)[][], idx: number, asc: boolean): (string | number | null)[][] {\n\tconst sign = asc ? 1 : -1\n\treturn rows\n\t\t.map((r, i) => ({ r, i }))\n\t\t.sort((a, b) => {\n\t\t\tconst va = a.r[idx]\n\t\t\tconst vb = b.r[idx]\n\t\t\t// nulls always last regardless of direction\n\t\t\tif (va == null && vb == null) return a.i - b.i\n\t\t\tif (va == null) return 1\n\t\t\tif (vb == null) return -1\n\t\t\tif (typeof va === 'number' && typeof vb === 'number') return (va - vb) * sign\n\t\t\treturn String(va).localeCompare(String(vb)) * sign\n\t\t})\n\t\t.map(x => x.r)\n}\n\nfunction computeColStats(\n\tallRows: (string | number | null)[][],\n\tcolIdxs: number[]\n): { min: number[]; max: number[]; n: number[] } {\n\tconst min: number[] = colIdxs.map(() => Infinity)\n\tconst max: number[] = colIdxs.map(() => -Infinity)\n\tconst n: number[] = colIdxs.map(() => 0)\n\tfor (const row of allRows) {\n\t\tfor (let i = 0; i < colIdxs.length; i++) {\n\t\t\tconst v = row[colIdxs[i]]\n\t\t\tif (typeof v === 'number' && Number.isFinite(v)) {\n\t\t\t\tif (v < min[i]) min[i] = v\n\t\t\t\tif (v > max[i]) max[i] = v\n\t\t\t\tn[i]++\n\t\t\t}\n\t\t}\n\t}\n\treturn { min, max, n }\n}\n\n/**\n * Render a row dendrogram from hclust output into the given <g>.\n * Adapted from matrix/hierCluster.renderers.js plotDendrogramHclust:\n * we walk the merge tree, recording each cluster's (x, y) where y is the\n * vertical center of its leaf range and x is its merge height. Branches\n * extend leftward from the heatmap edge so the deepest merges sit at x=0.\n */\nfunction drawRowDendrogram(\n\tg: any,\n\tdend: {\n\t\tmerge: { n1: number; n2: number }[]\n\t\theight: { height: number }[]\n\t\torder: { name: string }[]\n\t\tinputOrder: string[]\n\t},\n\twidth: number,\n\tgridH: number,\n\tcellH: number\n) {\n\tconst heights = dend.height.map(h => h.height)\n\tconst maxH = Math.max(...heights, 1e-9)\n\tconst hToX = scaleLinear().domain([0, maxH]).range([width, 0])\n\n\t// position of each leaf in the dendrogram (y in pixels, leaf order from .order)\n\tconst leafYByName = new Map<string, number>()\n\tdend.order.forEach((leaf, i) => {\n\t\tleafYByName.set(leaf.name, i * cellH + cellH / 2)\n\t})\n\n\t// for each merged cluster, record {x, y}\n\tconst merged = new Map<number, { x: number; y: number }>()\n\tfor (let i = 0; i < dend.merge.length; i++) {\n\t\tconst { n1, n2 } = dend.merge[i]\n\t\tconst pos = (n: number): { x: number; y: number } => {\n\t\t\tif (n < 0) {\n\t\t\t\t// leaf: index in inputOrder is -n-1\n\t\t\t\tconst name = dend.inputOrder[-n - 1]\n\t\t\t\treturn { x: width, y: leafYByName.get(name) ?? 0 }\n\t\t\t}\n\t\t\treturn merged.get(n) || { x: width, y: 0 }\n\t\t}\n\t\tconst a = pos(n1)\n\t\tconst b = pos(n2)\n\t\tconst x = hToX(heights[i])\n\t\tconst y = (a.y + b.y) / 2\n\n\t\t// horizontal segment from each child to the merge x, then a vertical between them\n\t\tg.append('line')\n\t\t\t.attr('x1', a.x)\n\t\t\t.attr('x2', x)\n\t\t\t.attr('y1', a.y)\n\t\t\t.attr('y2', a.y)\n\t\t\t.attr('stroke', '#000')\n\t\t\t.attr('stroke-width', 1)\n\t\tg.append('line')\n\t\t\t.attr('x1', b.x)\n\t\t\t.attr('x2', x)\n\t\t\t.attr('y1', b.y)\n\t\t\t.attr('y2', b.y)\n\t\t\t.attr('stroke', '#000')\n\t\t\t.attr('stroke-width', 1)\n\t\tg.append('line')\n\t\t\t.attr('x1', x)\n\t\t\t.attr('x2', x)\n\t\t\t.attr('y1', a.y)\n\t\t\t.attr('y2', b.y)\n\t\t\t.attr('stroke', '#000')\n\t\t\t.attr('stroke-width', 1)\n\n\t\tmerged.set(i + 1, { x, y })\n\t}\n}\n\nexport async function getPlotConfig(opts) {\n\tconst config = {\n\t\tchartType: GeneRanking.type,\n\t\trankingKey: opts.rankingKey || ''\n\t}\n\treturn copyMerge(config, opts)\n}\n\nexport const componentInit = getCompInit(GeneRanking)\n\nexport function makeChartBtnMenu(holder, chartsInstance) {\n\tchartsInstance.dom.tip.clear()\n\tconst cfg = chartsInstance.state.termdbConfig?.queries?.geneRanking as\n\t\t| { rankings?: Record<string, string> }\n\t\t| undefined\n\tconst rankings = cfg?.rankings\n\n\tif (!rankings || !Object.keys(rankings).length) {\n\t\tholder\n\t\t\t.append('div')\n\t\t\t.style('padding', '8px')\n\t\t\t.style('color', '#888')\n\t\t\t.text('No multiomic rankings available for this dataset.')\n\t\treturn\n\t}\n\n\tfor (const key of Object.keys(rankings)) {\n\t\tholder\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text(key)\n\t\t\t.on('click', () => {\n\t\t\t\tchartsInstance.dom.tip.hide()\n\t\t\t\tchartsInstance.prepPlot({\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tchartType: 'geneRanking',\n\t\t\t\t\t\trankingKey: key\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t})\n\t}\n}\n"],
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+  "names": []
+}

package/dist/geneVariant-QT6E7YZN.js

@@ -0,0 +1,39 @@
+import {
+  getDtsFromGroups,
+  getHandler
+} from "./chunk-LYULXXGR.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-CPMOBFFR.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-B4VBTVVQ.js";
+import "./chunk-IQTEW3SK.js";
+import "./chunk-MNPTPENH.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-UAALI7MC.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  getDtsFromGroups,
+  getHandler
+};
+//# sourceMappingURL=geneVariant-QT6E7YZN.js.map

package/dist/geneVariant-UYQ4XIOQ.js

@@ -0,0 +1,41 @@
+import {
+  SearchHandler,
+  addParentTerm,
+  getChildTerms
+} from "./chunk-LYULXXGR.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-CPMOBFFR.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-B4VBTVVQ.js";
+import "./chunk-IQTEW3SK.js";
+import "./chunk-MNPTPENH.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-UAALI7MC.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  SearchHandler,
+  addParentTerm,
+  getChildTerms
+};
+//# sourceMappingURL=geneVariant-UYQ4XIOQ.js.map

package/dist/geneVariant.integration.spec-HQ5GJ7UM.js

@@ -0,0 +1,198 @@
+import {
+  hg38
+} from "./chunk-7VB2BKXW.js";
+import {
+  sleep
+} from "./chunk-DJQTUDJM.js";
+import {
+  require_tape
+} from "./chunk-TUMA63WX.js";
+import {
+  SearchHandler,
+  vocabInit
+} from "./chunk-LYULXXGR.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-CPMOBFFR.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-B4VBTVVQ.js";
+import "./chunk-IQTEW3SK.js";
+import "./chunk-MNPTPENH.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-UAALI7MC.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// termdb/handlers/test/geneVariant.integration.spec.ts
+var import_tape = __toESM(require_tape(), 1);
+async function getVocabApi() {
+  const vocabApi2 = vocabInit({ state: { vocab: { genome: "hg38-test", dslabel: "TermdbTest" } } });
+  if (!vocabApi2) throw "vocabApi is missing";
+  await vocabApi2.getTermdbConfig();
+  return vocabApi2;
+}
+var vocabApi = await getVocabApi();
+var handler = new SearchHandler();
+function getHolder() {
+  const holder = select_default("body").append("div");
+  return holder;
+}
+async function initializeSearchHandler(opts) {
+  const callback = opts.callback || (() => {
+  });
+  await handler.init({
+    holder: opts.holder,
+    app: { vocabApi },
+    genomeObj: hg38,
+    callback
+  });
+}
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- geneVariant search handler -***-");
+  test.end();
+});
+(0, import_tape.default)("Search handler layout", async (test) => {
+  const holder = getHolder();
+  await initializeSearchHandler({ holder });
+  const mutationTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]');
+  test.ok(
+    mutationTypeRadiosDiv.selectAll('input[type="radio"]').size() > 0,
+    "Mutation type radio buttons should be present"
+  );
+  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
+  test.equal(
+    inputTypeRadiosDiv.selectAll('input[type="radio"]').size(),
+    2,
+    "Input type radio buttons should be present"
+  );
+  const searchDiv = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]');
+  test.equal(searchDiv.selectAll('input[type="search"]').size(), 1, "Gene search input should be present");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Single gene input", async (test) => {
+  let tw;
+  const callback = (_tw) => {
+    tw = _tw;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
+  geneSearchInput.value = "TP53";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  test.equal(tw.term.type, "geneVariant", "term.type should be geneVariant");
+  test.equal(tw.q.type, "predefined-groupset", "q.type should be predefined-groupset");
+  test.equal(tw.q.predefined_groupset_idx, 0, "q.predefined_groupset_idx should be 0");
+  test.equal(tw.term.genes.length, 1, "term.genes[] should have length of 1");
+  test.deepEqual(
+    tw.term.genes[0],
+    { kind: "gene", id: "TP53", gene: "TP53", name: "TP53", type: "geneVariant" },
+    "term.genes[0] should have expected structure"
+  );
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Change mutation type", async (test) => {
+  let tw;
+  const callback = (_tw) => {
+    tw = _tw;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const mutationTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]');
+  const mutationTypeRadios = mutationTypeRadiosDiv.selectAll('input[type="radio"]');
+  const thirdRadio = mutationTypeRadios.nodes()[2];
+  thirdRadio.click();
+  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
+  const geneSetDiv = inputTypeRadiosDiv.selectAll("div").filter((d) => d.value == "geneset");
+  test.equal(geneSetDiv.style("display"), "none", "Gene set option should be hidden for CNV");
+  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
+  geneSearchInput.value = "TP53";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  test.equal(tw.q.predefined_groupset_idx, 2, "q.predefined_groupset_idx should be 2 upon selecting third radio button");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Gene set input", async (test) => {
+  let tw;
+  const callback = (_tw) => {
+    tw = _tw;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
+  const inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type="radio"]');
+  const secondRadio = inputTypeRadios.nodes()[1];
+  secondRadio.click();
+  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
+  geneSearchInput.value = "TP53";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  geneSearchInput.value = "KRAS";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  const buttons = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').selectAll("button").nodes();
+  const submitButton = buttons.find((btn) => btn.textContent.trim() === "Submit");
+  await sleep(100);
+  submitButton.click();
+  await sleep(100);
+  test.equal(tw.term.genes.length, 2, "term.genes[] should have length of 2");
+  test.equal(tw.term.name, "TP53, KRAS", "term.name should concatenate gene names");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Gene set input - custom name", async (test) => {
+  let tw;
+  const callback = (_tw) => {
+    tw = _tw;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
+  const inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type="radio"]');
+  const secondRadio = inputTypeRadios.nodes()[1];
+  secondRadio.click();
+  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
+  geneSearchInput.value = "TP53";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  geneSearchInput.value = "KRAS";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  const nameInput = holder.select('[data-testid="sja_genesetinput_name"]').node();
+  nameInput.value = "Test gene set";
+  const buttons = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').selectAll("button").nodes();
+  const submitButton = buttons.find((btn) => btn.textContent.trim() === "Submit");
+  await sleep(100);
+  submitButton.click();
+  await sleep(100);
+  test.equal(tw.term.genes.length, 2, "term.genes[] should have length of 2");
+  test.equal(tw.term.name, "Test gene set", "term.name should be custom name");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+//# sourceMappingURL=geneVariant.integration.spec-HQ5GJ7UM.js.map