@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/SC-RCZT5BRP.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/sc/model/SCModel.ts", "../plots/sc/viewModel/SCViewModel.ts", "../plots/sc/interactions/SCInteractions.ts", "../plots/sc/view/SampleTableRenderer.ts", "../plots/sc/view/PlotButtons.ts", "../plots/sc/view/SectionRenderer.ts", "../plots/sc/settings/Settings.ts", "../plots/sc/view/SCViewRenderer.ts", "../plots/sc/settings/defaults.ts", "../plots/sc/subplots/DynamicSubplot.ts", "../plots/sc/subplots/SubplotManager.ts", "../plots/sc/SC.ts"],
+  "sourcesContent": ["import type { AppApi } from '#rx'\nimport type { SCFormattedState } from '../SCTypes'\nimport { dofetch3 } from '#common/dofetch'\nimport type { SCViewer } from '../SC'\nimport { getNormalRoot } from '#filter/filter.utils'\n\n/** Fetches data for sc app */\nexport class SCModel {\n\tsc: SCViewer\n\tapp: AppApi\n\tid?: string\n\tstate: SCFormattedState\n\n\tconstructor(sc: SCViewer) {\n\t\tthis.sc = sc\n\t\tthis.app = sc.app\n\t\tthis.id = sc.id\n\t\tthis.state = sc.app.getState()\n\t}\n\n\t/********** All Single Cell SAMPLES for rendering the sample table ******** */\n\tasync getAllSampleData(state) {\n\t\tconst body = {\n\t\t\tgenome: state.vocab.genome,\n\t\t\tdslabel: state.vocab.dslabel,\n\t\t\tfilter: getNormalRoot(state.termfilter.filter),\n\t\t\tfilter0: state.termfilter.filter0\n\t\t}\n\t\treturn await dofetch3('termdb/singlecellSamples', { body, signal: this.sc.api?.getAbortSignal() })\n\t}\n\n\t//Fetches optional name for ds defined columns\n\tasync getColumnLabels(dsScSamples: { [key: string]: any }) {\n\t\tif (!dsScSamples || !dsScSamples.sampleColumns) return\n\t\tconst colsCopy = structuredClone(dsScSamples.sampleColumns)\n\t\tfor (const col of colsCopy) {\n\t\t\tlet label = col.termid\n\t\t\ttry {\n\t\t\t\tlabel = (await this.app.vocabApi.getterm(col.termid)).name\n\t\t\t} catch (e: any) {\n\t\t\t\tif (e.message) {\n\t\t\t\t\t//Ignore. if statement to prevent tsc error.\n\t\t\t\t}\n\t\t\t\t/** Ignore errors and use the termid as the column header.\n\t\t\t\t * this is due to practical constrain that gdc needs to supply\n\t\t\t\t * analysis.workflow_type as 'Library', but this is not a term\n\t\t\t\t * in gdc dictionary */\n\t\t\t}\n\t\t\tcol.label = label\n\t\t}\n\t\treturn colsCopy\n\t}\n\n\t/********** Single Cell DATA for rendering plots ********\n\t * This is for the plot buttons. Returns an array plots with found files or\n\t * available data. */\n\tasync getSampleData() { \n\t\tconst body = this.getDataRequestOpts()\n\t\tif (!body) return\n\t\treturn await dofetch3('termdb/singlecellData', { body, signal: this.sc.api?.getAbortSignal() })\n\t}\n\n\t/** May provide active plots to the request and return plot data when\n\t * checkPlotAvailability is false. When checkPlotAvailability is true,\n\t * only returns which plots are available but not the actual data. */\n\tgetDataRequestOpts(_plots: any[] = [], checkPlotAvailability = true) {\n\t\tconst state = this.app.getState()\n\t\tconst singleCellTermdbConfig = state.termdbConfig?.queries?.singleCell\n\t\tif (!singleCellTermdbConfig?.data) throw new Error('No singleCell.data defined in termdbConfig.queries')\n\n\t\tconst config = state.plots.find((p: any) => p.id === this.id)\n\t\tif (!config.settings.sc.item) return\n\n\t\tconst plots = _plots?.length ? _plots : singleCellTermdbConfig.data.plots.map(p => p.name)\n\n\t\treturn {\n\t\t\tgenome: this.state.vocab.genome,\n\t\t\tdslabel: this.state.vocab.dslabel,\n\t\t\t// if true, only return available plot names, but not actual plot data\n\t\t\tcheckPlotAvailability,\n\t\t\tplots,\n\t\t\tsample: {\n\t\t\t\teID: config.settings.sc.item.eID,\n\t\t\t\tsID: config.settings.sc.item.sID\n\t\t\t}\n\t\t}\n\t}\n\n\t/** Essentially for the GDC. Maybe applied to other ds in the future. */\n\tasync getCategories(_plots: any[]): Promise<string[] | undefined> {\n\t\tconst body = this.getDataRequestOpts(_plots, false)\n\t\tif (!body) return\n\n\t\tlet res\n\t\ttry {\n\t\t\tres = await dofetch3('termdb/singlecellData', { body, signal: this.sc.api?.getAbortSignal() })\n\t\t} catch (e: any) {\n\t\t\tif (e instanceof Error) console.error(`${e.message || e}`)\n\t\t}\n\n\t\treturn this.formatCategories(res)\n\t}\n\n\tformatCategories(res: any): string[] {\n\t\tconst plot = structuredClone(res.plots[0])\n\n\t\tplot.cells = [...plot.noExpCells, ...plot.expCells]\n\t\tconst clusters: Set<string> = new Set(plot.cells.map(c => c.category))\n\n\t\t/** Clean up list into an descending array */\n\t\tconst sortedClusters: string[] = Array.from(clusters).sort((a: any, b: any) => {\n\t\t\tconst num1 = parseInt(a.split(' ')[1])\n\t\t\tconst num2 = parseInt(b.split(' ')[1])\n\t\t\treturn num1 - num2\n\t\t})\n\t\treturn sortedClusters\n\t}\n}\n", "import type { AppApi } from '#rx'\nimport type { TableColumn, TableRow } from '#dom'\nimport type { SCConfig, SCFormattedState, SampleColumn, SCTableData } from '../SCTypes'\nimport type { SingleCellSample } from '#types'\n\nexport class SCViewModel {\n\tapp: AppApi\n\tstate: SCFormattedState\n\ttableData!: SCTableData\n\tsampleColumns: SampleColumn[]\n\tmetaResultIds: Set<string>\n\n\tconstructor(app: AppApi, sampleColumns?: SampleColumn[]) {\n\t\tthis.app = app\n\t\tthis.state = this.app.getState()\n\t\tthis.sampleColumns = sampleColumns || []\n\t\tthis.metaResultIds = new Set()\n\t}\n\n\tprocessData(config: SCConfig, _items: SingleCellSample[]) {\n\t\t//Sort meta analysis results to show at the beginning of the table.\n\t\t//Prevents breaking the logic for selected rows after formating the table data.\n\t\tconst items = _items.sort((a, b) => (b.isMetaResult === a.isMetaResult ? 0 : b.isMetaResult ? 1 : -1))\n\n\t\tconst [rows, columns, sampleColIdx] = this.getTabelData(config, items, this.sampleColumns)\n\t\tconst selectedRows: number[] = []\n\t\tconst sID = config.settings.sc.item?.sID\n\t\tconst i = sID\n\t\t\t? items.findIndex(item => item.sample === sID || item.experiments?.some(e => e.sampleName === sID))\n\t\t\t: -1\n\t\tif (i != -1) selectedRows.push(i)\n\n\t\t/** Returning this data separately from the eventual\n\t\t * viewData because it's static. */\n\t\tthis.tableData = {\n\t\t\trows: rows as any,\n\t\t\tcolumns: columns as any,\n\t\t\tselectedRows,\n\t\t\tsampleColIdx\n\t\t}\n\t}\n\n\tgetTabelData(\n\t\tplotConfig: SCConfig,\n\t\titems: SingleCellSample[],\n\t\tsampleColumns?: SampleColumn[]\n\t): [TableRow[], TableColumn[], number] {\n\t\tconst rows: TableRow[] = []\n\t\tconst hasExperiments = items.some(i => i.experiments)\n\t\tlet sampleColIdx = -1\n\n\t\t/** First column may either be a list of samples or mix of samples, meta, and/or pseudobulk.\n\t\t * Only use 'Sample' or config setting if everything is a sample. */\n\t\tlet firstColLabel = plotConfig.settings.sc.columns.sample\n\t\tif (items[0]?.isMetaResult) firstColLabel = ''\n\t\tconst columns: TableColumn[] = [{ label: firstColLabel, sortable: true }]\n\t\tif (hasExperiments) {\n\t\t\tcolumns.push({ label: 'Sample', sortable: true }) //add after the case column\n\t\t\tsampleColIdx = 1\n\t\t} else sampleColIdx = 0\n\t\tcolumns.push({ label: 'Shown plots' }) //Empty column for plot buttons\n\n\t\t// add in optional sample columns\n\t\tfor (const col of sampleColumns || []) {\n\t\t\tcolumns.push({\n\t\t\t\tlabel: col.label,\n\t\t\t\twidth: '14vw',\n\t\t\t\tsortable: true\n\t\t\t})\n\t\t}\n\n\t\t// if samples are using experiments, add the hardcoded experiment column at the end\n\t\tif (hasExperiments) columns.push({ label: 'Experiment', sortable: true }) // corresponds to this.samples[].experiments[].experimentID\n\n\t\tfor (const item of items) {\n\t\t\tif (item.isMetaResult) this.metaResultIds.add(item.sample)\n\t\t\tif (hasExperiments)\n\t\t\t\t//GDC\n\t\t\t\tfor (const exp of item.experiments!) {\n\t\t\t\t\t// first cell is always sample name. sneak in experiment object to be accessed in click callback\n\t\t\t\t\t//TODO: Consider removing the experimentID as it is no longer needed.\n\t\t\t\t\tconst row: { [index: string]: any }[] = [{ value: item.sample, __experimentID: exp.experimentID }]\n\t\t\t\t\t// hardcode to expect exp.sampleName and add this as a column\n\t\t\t\t\trow.push({ value: exp.sampleName })\n\t\t\t\t\trow.push({ value: '' }) //Empty cell for shown plot buttons\n\t\t\t\t\t// optional sample and experiment columns\n\t\t\t\t\tfor (const col of sampleColumns || []) {\n\t\t\t\t\t\trow.push({ value: item[col.termid] })\n\t\t\t\t\t}\n\n\t\t\t\t\t// hardcode to always add in experiment id column. link out only if the ds declares a\n\t\t\t\t\t// url template for it (as singleCellPlot.js does)\n\t\t\t\t\tconst urlTemp = this.state.termdbConfig?.urlTemplates?.scrnaExperimentId\n\t\t\t\t\tif (urlTemp) row.push({ value: exp.experimentID, url: `${urlTemp.base}${exp.experimentID}` })\n\t\t\t\t\telse row.push({ value: exp.experimentID })\n\t\t\t\t\trows.push(row)\n\t\t\t\t}\n\t\t\telse {\n\t\t\t\t// sample does not use experiment\n\t\t\t\t// first cell is sample name\n\t\t\t\tconst row: { [index: string]: any }[] = item.isMetaResult\n\t\t\t\t\t? [{ html: item.sample.replace(/_/g, ' '), value: item.sample, elemId: 'isMetaResult' }]\n\t\t\t\t\t: [{ value: item.sample }]\n\t\t\t\t//Empty cell for shown plot buttons\n\t\t\t\trow.push({ value: '' })\n\t\t\t\t// optional sample columns\n\t\t\t\tfor (const col of sampleColumns || []) {\n\t\t\t\t\tconst value = item[col.termid]\n\t\t\t\t\tif (value == null && item.isMetaResult) row.push({ value: 'All' })\n\t\t\t\t\telse row.push({ value: item[col.termid] })\n\t\t\t\t}\n\t\t\t\trows.push(row)\n\t\t\t}\n\t\t}\n\t\treturn [rows, columns, sampleColIdx]\n\t}\n}\n", "import type { AppApi } from '#rx'\nimport type { SCModel } from '../model/SCModel.ts'\nimport type { SCViewer } from '../SC.ts'\nimport type { SCViewModel } from '../viewModel/SCViewModel.ts'\n\n/** Handles the interactivity from the view */\nexport class SCInteractions {\n\tapp: AppApi\n\tid: string\n\tmodel: SCModel\n\tviewModel: SCViewModel\n\n\tconstructor(sc: SCViewer) {\n\t\tthis.app = sc.app\n\t\tthis.id = sc.id\n\t\tthis.model = sc.model\n\t\tthis.viewModel = sc.viewModel\n\t}\n\n\t/** Add the plot to the state.plots array with .parentId. Adding\n\t * .parentId prevents the plot from launching in a new sandbox outside SC.\n\t * Pass the .parentId to both the plotConfig and the action.\n\t * this.getState() in SC.ts will find all the subplots with the parentId==this.id\n\t * SC.main() initializes the subplots as components in chartsDiv */\n\tasync createSubplot(config) {\n\t\tconst c = Object.assign({}, config, { parentId: this.id })\n\t\tawait this.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tparentId: this.id,\n\t\t\tconfig: c\n\t\t})\n\t}\n\n\t/** Updates the selected item in the plot settings */\n\tasync updateItem(item) {\n\t\titem.isMetaResult = this.viewModel.metaResultIds.has(item.sID)\n\t\tawait this.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { settings: { sc: { item } } }\n\t\t})\n\t}\n\n\tasync getDropDownOptions(plot): Promise<string[] | undefined> {\n\t\treturn this.model.getCategories(plot)\n\t}\n}\n", "import type { SCDom, SCSampleSandbox, SCTableData } from '../SCTypes'\nimport type { TableCell } from '#dom'\nimport { renderTable } from '#dom'\nimport type { SCInteractions } from '../interactions/SCInteractions'\n\n/** Renders the sample table for selection on SC app init()\n * On selecting a sample, the plot buttons will appear and\n * the user can select a plot to render in the dashboard. */\nexport class SampleTableRenderer {\n\tdom: SCDom\n\tinteractions: SCInteractions\n\ttableData: SCTableData\n\tactiveSandboxes: Map<string, SCSampleSandbox[]> = new Map()\n\t/** Tracks rendered btns per sample to avoid unnecessary destroy/recreate pattern. */\n\trendered: Map<string, { cell: any; plotIds: string }> = new Map()\n\n\tconstructor(dom: SCDom, interactions: SCInteractions, tableData: SCTableData) {\n\t\tthis.dom = dom\n\t\tthis.interactions = interactions\n\t\tthis.tableData = tableData\n\t\tthis.renderSamplesTable(tableData)\n\t}\n\n\t/** Users select one item at a time to render the plot buttons\n\t * to init() plots in the dashboard.*/\n\trenderSamplesTable(tableData: SCTableData) {\n\t\tthis.dom.tableDiv.selectAll('*').remove()\n\n\t\trenderTable({\n\t\t\trows: tableData.rows,\n\t\t\tcolumns: tableData.columns,\n\t\t\tdiv: this.dom.tableDiv,\n\t\t\tsingleMode: true,\n\t\t\t// maxWidth: tableData.columns.length > 3 ? '95vw' : 'auto',\n\t\t\tmaxHeight: '30vh',\n\t\t\theader: {\n\t\t\t\tallowSort: true,\n\t\t\t\tstyle: { 'text-transform': 'capitalize' }\n\t\t\t},\n\t\t\tstriped: true,\n\t\t\tselectedRows: tableData.selectedRows,\n\t\t\tafterRender: () => {\n\t\t\t\tthis.reapplyAllPlotButtons()\n\t\t\t},\n\t\t\tnoButtonCallback: index => {\n\t\t\t\tconst item = this.buildItemFromRow(tableData, index)\n\t\t\t\tthis.interactions.updateItem(item)\n\t\t\t\tthis.dom.plotsBtnsDiv.style('display', 'block')\n\t\t\t}\n\t\t})\n\t}\n\n\t/** Builds an item object from a table row, mapping column labels to keys.\n\t * Converts 'sample' -> 'sID' and 'experiment' -> 'eID'.\n\t * Extracted out from noButtonCallback for testing.  */\n\tbuildItemFromRow(tableData: SCTableData, index: number) {\n\t\tconst item = {} as { sID: string; eID: string; [key: string]: any }\n\t\ttableData.rows[index].forEach((r: TableCell, idx: number) => {\n\t\t\tif (!r.value) return\n\t\t\tlet key = tableData.columns[idx].label.toLowerCase()\n\t\t\t/** Convert the column labels into the required sample structure keys.\n\t\t\t * Maintains the sample obj used throughout the app whilst allowing for\n\t\t\t * dynamic column labels based on the config. */\n\t\t\tkey = key === 'sample' || key === '' ? 'sID' : key === 'experiment' ? 'eID' : key\n\t\t\titem[key] = r.value\n\t\t})\n\t\tif (!item.sID) throw new Error('Selected item must have sID property')\n\t\treturn item\n\t}\n\n\tupdateTable(tableData: SCTableData) {\n\t\tthis.tableData = tableData\n\t\tthis.dom.tableDiv.selectAll('*').remove()\n\t\tthis.renderSamplesTable(tableData)\n\t}\n\n\tupdatePlotBtns(activeSandboxes: Map<string, SCSampleSandbox[]>) {\n\t\tthis.activeSandboxes = activeSandboxes\n\t\tthis.reapplyAllPlotButtons()\n\t}\n\n\t/** Called by afterRender to re-apply buttons for all samples with subplots.\n\t * Also called in updateTable when the active sandboxes (i.e. subplots) change.*/\n\treapplyAllPlotButtons() {\n\t\t/** Check btns still apply to active sandboxes. If not delete\n\t\t * from table and tracker. */\n\t\tfor (const sampleId of this.rendered.keys()) {\n\t\t\tif (!this.activeSandboxes.has(sampleId)) {\n\t\t\t\tthis.deleteBtns(sampleId)\n\t\t\t}\n\t\t}\n\t\tfor (const sampleId of this.activeSandboxes.keys()) {\n\t\t\tthis.applyButtonsForSample(sampleId)\n\t\t}\n\t}\n\n\tdeleteBtns(sampleId: string) {\n\t\tconst cached = this.rendered.get(sampleId)\n\t\tif (cached) {\n\t\t\tcached.cell.selectAll('.sjpp-sc-table-plot-btn').remove()\n\t\t\tthis.rendered.delete(sampleId)\n\t\t}\n\t}\n\n\t/** Applies buttons for a single sample. Skips DOM work if cell and plots are unchanged. */\n\tapplyButtonsForSample(sampleId: string) {\n\t\tconst sampleIdx = this.tableData.sampleColIdx\n\n\t\t/** Rows array mutates on sort. Find the row by matching sampleId.*/\n\t\tconst row = this.tableData.rows.find(r => r[sampleIdx].value === sampleId)\n\t\tif (!row) return\n\n\t\tconst cell = row[sampleIdx + 1].__td\n\t\tconst sampleSandboxes = this.activeSandboxes.get(sampleId)\n\t\tif (!sampleSandboxes || sampleSandboxes.length === 0) return\n\n\t\tconst plotIds = sampleSandboxes.map(s => s.plotId).join(',')\n\t\tconst cached = this.rendered.get(sampleId)\n\t\t/** Guard against rerendering btns */\n\t\tif (cached && cached.cell === cell && cached.plotIds === plotIds) return\n\n\t\tcell.selectAll('.sjpp-sc-table-plot-btn').remove()\n\t\tthis.rendered.set(sampleId, { cell, plotIds })\n\t\tfor (const { div, plotName } of sampleSandboxes) {\n\t\t\tthis.appendPlotBtn(cell, div, plotName, sampleId)\n\t\t}\n\t}\n\n\tappendPlotBtn(cell: any, sandboxDiv: any, plotName: string, sampleId: string) {\n\t\tconst text = plotName.length > 25 ? plotName.slice(0, 12) + '...' : plotName\n\t\tconst label = `Scroll to ${plotName}`\n\t\tcell\n\t\t\t.append('button')\n\t\t\t.attr('class', 'sjpp-sc-table-plot-btn')\n\t\t\t.attr('data-testid', `sjpp-sc-table-${sampleId}-${plotName}-btn`)\n\t\t\t.style('padding', '2px 5px')\n\t\t\t.style('margin-left', '4px')\n\t\t\t.style('font-size', '0.8em')\n\t\t\t.style('border-radius', '20px')\n\t\t\t.style('border', '0.5px solid black')\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.text(text)\n\t\t\t.attr('aria-label', label)\n\t\t\t.attr('title', label)\n\t\t\t.attr('tabindex', 0)\n\t\t\t.on('click', () => {\n\t\t\t\tsandboxDiv.node().scrollIntoView({ behavior: 'smooth', block: 'start' })\n\t\t\t})\n\t}\n}\n", "import type { Div, Elem } from '../../../types/d3'\nimport type { SCInteractions } from '../interactions/SCInteractions'\nimport { Menu } from '#dom'\nimport { digestMessage } from '#termsetting'\nimport { TermTypeGroups } from '#shared/terms.js'\nimport { SINGLECELL_CELLTYPE, SINGLECELL_GENE_EXPRESSION } from '#types'\nimport type { SCSample } from '../SCTypes'\nimport type { Settings } from '../settings/Settings'\n\n/** Rendering for the plot buttons that appear below the item\n * table. Plot buttons are rendered based on the available plots\n * for the selected sample, and the config defined in\n * termdbConfig.queries.singleCell.data.plots. Each plot config\n * in termdbConfig should define a name that matches the plot\n * names returned from the server, and can optionally define\n * colorColumns which will be used to apply color to the plot\n * if those columns are present in the data.\n *\n * Notes:\n *  - The hierarchical clustering limits to the first 100 genes.\n * */\nexport class PlotButtons {\n\tplotBtnsDom: {\n\t\tholder: Div\n\t\tpromptDiv: Div\n\t\tselectPrompt: Elem\n\t\tbtnsDiv: Div\n\t\ttip: Menu\n\t}\n\tdata?: any\n\titem?: SCSample\n\tinteractions: SCInteractions\n\tscTermdbConfig: any\n\tsettings!: Settings\n\tscctTerms?: any[]\n\tavailablePlots!: Set<string>\n\n\t/** scctTerms and the scTermdbConfig are created on server init and will not change. */\n\tconstructor(interactions: SCInteractions, holder: Div, termdbConfig) {\n\t\tholder.style('padding', '10px')\n\t\tconst promptDiv = holder.append('div').style('padding', '10px 0').text('Select data from')\n\t\tthis.plotBtnsDom = {\n\t\t\tholder,\n\t\t\tpromptDiv,\n\t\t\tselectPrompt: promptDiv.append('span'),\n\t\t\tbtnsDiv: holder.append('div'),\n\t\t\ttip: new Menu({ padding: '' })\n\t\t}\n\t\tthis.interactions = interactions\n\t\tthis.scctTerms = termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_CELLTYPE]\n\t\tthis.scTermdbConfig = termdbConfig.queries.singleCell\n\t}\n\n\tupdate(settings: Settings, data) {\n\t\t/** If the user has not selected a item yet but clicks\n\t\t * the select item/plots btn above the table, the prompt appears\n\t\t * unnecessarily */\n\t\tconst item = settings.sc.item\n\t\tthis.plotBtnsDom.holder.style('display', !item ? 'none' : 'block')\n\t\tif (!item) return\n\t\tif (data != null && data.plots) this.data = data\n\t\t//Show buttons for plots with found data files (see note above).\n\t\tthis.availablePlots = new Set(this.data?.plots?.map((p: any) => p.name))\n\t\tthis.settings = settings\n\t\tthis.item = item\n\t\tconst name = item.sID\n\t\tthis.plotBtnsDom.selectPrompt.text(` ${name}:`)\n\t\tthis.renderChartBtns()\n\t}\n\n\trenderChartBtns() {\n\t\tthis.plotBtnsDom.btnsDiv.selectAll('*').remove()\n\t\tconst btns = this.getChartBtnOpts()\n\n\t\tthis.plotBtnsDom.btnsDiv\n\t\t\t.selectAll('button')\n\t\t\t.data(btns.filter(b => (b.isVisible ? b.isVisible() : true)))\n\t\t\t.enter()\n\t\t\t.append('button')\n\t\t\t.attr('type', 'button')\n\t\t\t.attr('data-testid', b => `sjpp-sc-plot-btn-${b.label.toLowerCase().replace(/\\s/g, '-')}`)\n\t\t\t.style('padding', '10px 15px')\n\t\t\t.style('border-radius', '20px')\n\t\t\t.style('border-color', 'transparent')\n\t\t\t.style('background-color', '#CFE2F3')\n\t\t\t.style('margin', '0 10px')\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.text(b => b.label)\n\t\t\t.on('click', async (e, plot) => {\n\t\t\t\tif (plot.open) {\n\t\t\t\t\tthis.plotBtnsDom.tip.clear().showunder(e.target)\n\t\t\t\t\tplot.open(plot, this)\n\t\t\t\t} else {\n\t\t\t\t\tif (!plot.getPlotConfig)\n\t\t\t\t\t\tthrow new Error(`No getPlotConfig function defined for this plot button = ${plot.label}`)\n\t\t\t\t\tconst config = await plot.getPlotConfig()\n\t\t\t\t\tawait this.interactions.createSubplot(config)\n\t\t\t\t}\n\t\t\t})\n\t}\n\n\tgetChartBtnOpts() {\n\t\tconst btns: {\n\t\t\tlabel: string\n\t\t\tisVisible: () => boolean\n\t\t\topen?: (plot: any, self: PlotButtons) => void\n\t\t\tgetPlotConfig?: (f?: any) => any\n\t\t}[] = []\n\n\t\tfor (const plot of this.scTermdbConfig?.data?.plots || []) {\n\t\t\tif (!this.availablePlots.has(plot.name)) continue\n\t\t\tbtns.push({\n\t\t\t\tlabel: plot.name,\n\t\t\t\tisVisible: () => true,\n\t\t\t\tgetPlotConfig: async () => {\n\t\t\t\t\treturn await this.getSingleCellConfig(plot.name)\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\tbtns.push(\n\t\t\t{\n\t\t\t\tlabel: 'Summary',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tgetPlotConfig: () => {\n\t\t\t\t\tconst sample = { ...this.item!, plots: Array.from(this.availablePlots) }\n\t\t\t\t\tconst isMeta = sample?.isMetaResult || false\n\t\t\t\t\treturn {\n\t\t\t\t\t\tchartType: 'dictionary',\n\t\t\t\t\t\tsample,\n\t\t\t\t\t\tspawnConfig: {\n\t\t\t\t\t\t\tparentId: this.interactions.id,\n\t\t\t\t\t\t\theaderText: `${isMeta ? '' : 'Sample: '}${this.item!.sID}`,\n\t\t\t\t\t\t\thidePlotFilter: !isMeta,\n\t\t\t\t\t\t\tsample\n\t\t\t\t\t\t},\n\t\t\t\t\t\ttree: {\n\t\t\t\t\t\t\tusecase: {\n\t\t\t\t\t\t\t\ttarget: 'dictionary',\n\t\t\t\t\t\t\t\tspecialCase: {\n\t\t\t\t\t\t\t\t\ttype: 'singleCell',\n\t\t\t\t\t\t\t\t\tconfig: { sample }\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Gene expression',\n\t\t\t\tisVisible: () => this.scTermdbConfig?.geneExpression,\n\t\t\t\tgetPlotConfig: () => {\n\t\t\t\t\tconst sample = this.item!\n\t\t\t\t\tconst isMeta = sample?.isMetaResult || false\n\t\t\t\t\tconst headerText = `${isMeta ? '' : 'Sample: '}${this.item!.sID}`\n\n\t\t\t\t\treturn {\n\t\t\t\t\t\tchartType: 'GeneExpInput',\n\t\t\t\t\t\ttermType: SINGLECELL_GENE_EXPRESSION,\n\t\t\t\t\t\theaderText,\n\t\t\t\t\t\ttermProperties: { sample },\n\t\t\t\t\t\tparentId: this.interactions.id,\n\t\t\t\t\t\tsample,\n\t\t\t\t\t\tspawnConfig: {\n\t\t\t\t\t\t\tparentId: this.interactions.id,\n\t\t\t\t\t\t\theaderText,\n\t\t\t\t\t\t\thidePlotFilter: !isMeta,\n\t\t\t\t\t\t\t/** Must pass this to summary config in the event a continuous\n\t\t\t\t\t\t\t * overlay is applied, launching the scatter plot. Without it,\n\t\t\t\t\t\t\t * the single cell model is not used. */\n\t\t\t\t\t\t\tsingleCellPlot: {\n\t\t\t\t\t\t\t\tname: [...this.availablePlots][0],\n\t\t\t\t\t\t\t\tsample\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Differential expression',\n\t\t\t\tisVisible: () => this.scTermdbConfig?.DEgenes,\n\t\t\t\topen: this.termDropdownMenu,\n\t\t\t\tgetPlotConfig: value => {\n\t\t\t\t\tconst isMeta = this.item?.isMetaResult || false\n\t\t\t\t\treturn {\n\t\t\t\t\t\tchartType: 'differentialAnalysis',\n\t\t\t\t\t\ttermType: SINGLECELL_CELLTYPE,\n\t\t\t\t\t\tcategoryName: `${value}`,\n\t\t\t\t\t\theaderText: `${isMeta ? '' : 'Sample: '}${this.item!.sID}, ${this.scTermdbConfig.DEgenes.termId} ${value}`,\n\t\t\t\t\t\ttermId: this.scTermdbConfig.DEgenes.termId,\n\t\t\t\t\t\tsample: this.item!,\n\t\t\t\t\t\tplotName: 'Differential expression'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: this.scTermdbConfig?.images?.label || 'Image',\n\t\t\t\tisVisible: () =>\n\t\t\t\t\tthis.scTermdbConfig?.images && this.availablePlots.has(this.scTermdbConfig.images.label || 'Image'),\n\t\t\t\tgetPlotConfig: () => {\n\t\t\t\t\tconst isMeta = this.item?.isMetaResult || false\n\t\t\t\t\treturn {\n\t\t\t\t\t\tchartType: 'imagePlot',\n\t\t\t\t\t\tsample: this.item!,\n\t\t\t\t\t\timgDir: this.scTermdbConfig?.images,\n\t\t\t\t\t\theaderText: `${isMeta ? '' : 'Sample: '}${this.item!.sID}`,\n\t\t\t\t\t\tsettings: { imagePlot: { width: '', height: 400 } }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t)\n\t\treturn btns\n\t}\n\n\t//********** Btn Menus **********/\n\tasync termDropdownMenu(plot: any, self: PlotButtons) {\n\t\t/** An array of plots is required for the server request.\n\t\t * The data for all scRNA plots is the same. Pick the first one */\n\t\tconst _plot = Array.from(self.availablePlots)[0]\n\t\tconst options: string[] | undefined = await self.interactions.getDropDownOptions([_plot])\n\t\tif (!options?.length) throw new Error('No options found for this plot. Cannot open dropdown menu.')\n\n\t\tself.plotBtnsDom.tip.clear()\n\t\tconst wrapper = self.plotBtnsDom.tip.d.append('div').style('padding', '10px')\n\t\twrapper\n\t\t\t.append('div')\n\t\t\t.style('display', 'block')\n\t\t\t.style('width', '300px')\n\t\t\t.text(`View differentially expressed genes of a ${self.scTermdbConfig.DEgenes.termId} versus rest of the cells:`)\n\n\t\tconst select = wrapper\n\t\t\t.append('select')\n\t\t\t.style('margin', '10px 0')\n\t\t\t.style('width', 'auto')\n\t\t\t.style('padding', '5px')\n\t\t\t.on('change', async function () {\n\t\t\t\tself.plotBtnsDom.tip.hide()\n\t\t\t\tconst value = select.node()!.value\n\t\t\t\tif (value.indexOf('Select') == 0) return //ignore prompt option\n\t\t\t\tconst config = plot.getPlotConfig(value)\n\t\t\t\tawait self.interactions.createSubplot(config)\n\t\t\t})\n\n\t\tconst regex = new RegExp(self.scTermdbConfig.DEgenes.termId, 'gi')\n\t\toptions.unshift(`Select a ${self.scTermdbConfig.DEgenes.termId}...`)\n\t\tfor (const cluster of options) {\n\t\t\tselect.append('option').attr('value', cluster.replace(regex, '').trim()).text(cluster)\n\t\t}\n\t}\n\n\t//********** Plot Config Helpers **********/\n\tasync getSingleCellConfig(plotName: string): Promise<object> {\n\t\tif (!this.item) throw new Error('No item selected')\n\t\tconst plot = this.scTermdbConfig.data.plots.find(p => p.name == plotName)\n\t\tif (!plot) throw new Error(`No plot by name ${plotName} in data.plots.`)\n\t\tconst sample = this.item\n\t\tconst isMeta = sample?.isMetaResult || false\n\t\tconst config: any = {\n\t\t\tchartType: 'sampleScatter',\n\t\t\tname: `${isMeta ? '' : 'Sample: '}${this.item.sID}`,\n\t\t\tsample,\n\t\t\tsingleCellPlot: {\n\t\t\t\tname: plotName,\n\t\t\t\tsample\n\t\t\t}\n\t\t}\n\t\tif (plot.colorColumns?.[0]) {\n\t\t\t// apply optional color term. hardcodes to 1st of the array\n\t\t\tconfig.colorTW = await this.makeScctTW(sample, plot)\n\t\t}\n\t\treturn config\n\t}\n\n\t// Quick fix. Eventually use the handler to get the proper term from the termdbConfig\n\tasync makeScctTW(item: { sID: string; eID: string }, plot: any) {\n\t\tconst colorColName = plot.colorColumns[0].name\n\t\tconst savedTerm = this.scctTerms?.find(t => t.name == colorColName && t.plot == plot.name)\n\t\tif (!savedTerm)\n\t\t\tthrow new Error(\n\t\t\t\t`No term found for colorColumn=${colorColName} in .termType2terms.[TermTypeGroups.SINGLECELL_CELLTYPE] for plot ${plot.name}`\n\t\t\t)\n\t\tconst term = Object.assign(structuredClone(savedTerm), {\n\t\t\tsample: item\n\t\t})\n\t\tconst id = await digestMessage(`${plot.name}-${item.sID}-${item.eID}`)\n\t\treturn Object.assign({ $id: id }, { term })\n\t}\n}\n", "import type { Sections } from './Sections'\nimport type { Div, Elem } from '../../../types/d3'\nimport type { SCViewer } from '../SC'\nimport type { SingleCellSample } from '#types'\nimport type { GroupByOptions } from '../settings/Settings'\n\n/** Manages the mapping and rendering of the sections based on the groupBy option.\n * sections{} maps the section key (i.e. sampleId, plotName, or none) to the section\n * wrapper, title, subplots div, and the sandboxes in that section.\n *\n * Initializing and destroying the plot components is within SC.ts\n * (i.e. sc.components.plots[plotId]). This ensures plots are responsive to state changes.\n */\nexport class SectionRenderer {\n\tsections: Sections\n\tholder: Div\n\t/** Maps the plotId to either the sampleId, plotName, or none (i.e. key in sections map)\n\t * as a reverse lookup. Used in tandem with sections{} to manage the sandboxes\n\t * within each section. */\n\tplotId2Key: Map<string, string>\n\tgroupBy: (typeof GroupByOptions)[number]\n\n\tconstructor(sectionsDiv: Div, groupBy: (typeof GroupByOptions)[number]) {\n\t\tthis.sections = {}\n\t\tthis.holder = sectionsDiv\n\t\t//Key may be either sampleId, plotName, or none\n\t\tthis.plotId2Key = new Map()\n\t\tthis.groupBy = groupBy\n\t}\n\n\t/** Send the sc with the updated state. May not be necessary long term. If not,\n\t * remove and put in the constructor. */\n\tasync update(sc: SCViewer, subplots: any, groupBy: (typeof GroupByOptions)[number]) {\n\t\tif (groupBy !== this.groupBy) {\n\t\t\tthis.groupBy = groupBy\n\t\t\tthis.regroupSections(sc, subplots)\n\t\t\treturn\n\t\t}\n\t\tconst activeSubplots = new Set(subplots.map(s => s.id))\n\n\t\t/** Reconcile stale sandbox wrappers using section state.\n\t\t * Subplot lifecycle is managed by SubplotManager. */\n\t\tfor (const plotId of Array.from(this.plotId2Key.keys())) {\n\t\t\tif (!activeSubplots.has(plotId)) this.removeSandbox(plotId)\n\t\t}\n\n\t\tfor (const subplot of subplots) {\n\t\t\tconst key = this.getKey(subplot, sc)\n\t\t\tif (!key) continue\n\t\t\tif (!this.sections[key]) this.initSection(key, sc)\n\t\t\tif (!this.sections[key].sandboxes[subplot.id]) {\n\t\t\t\tthis.plotId2Key.set(subplot.id, key)\n\t\t\t\tsc.subplotManager.setSectionKey(subplot.id, key)\n\t\t\t\tawait this.initSandbox(sc, subplot, key)\n\t\t\t}\n\t\t}\n\n\t\t/** Remove sections after iterating through subplots to avoid\n\t\t * deleting sections before they can be re-rendered with the correct plots */\n\t\tfor (const key of Object.keys(this.sections)) {\n\t\t\tif (Object.keys(this.sections[key].sandboxes).length === 0) {\n\t\t\t\tthis.removeSection(key, sc)\n\t\t\t}\n\t\t}\n\t}\n\n\t/** Reparent existing sandboxes into new section containers\n\t * without destroying/recreating plot components. */\n\tprivate regroupSections(sc: SCViewer, subplots: any[]) {\n\t\t// Detach existing sandbox from their parents before clearing\n\t\tconst detached: Map<string, any> = new Map()\n\t\tfor (const [plotId, key] of this.plotId2Key) {\n\t\t\tconst sandboxNode = this.sections[key]?.sandboxes[plotId]\n\t\t\tif (sandboxNode) {\n\t\t\t\t// Remove from current parent without destroying\n\t\t\t\tsandboxNode.remove()\n\t\t\t\tdetached.set(plotId, sandboxNode)\n\t\t\t}\n\t\t}\n\n\t\t// Clear the section wrappers since sandboxes are already detached\n\t\tthis.holder.selectAll('*').remove()\n\t\tthis.sections = {}\n\t\tthis.plotId2Key = new Map()\n\n\t\t// Regroup into new sections, reparenting existing sandbox\n\t\tfor (const subplot of subplots) {\n\t\t\tconst key = this.getKey(subplot, sc)\n\t\t\tif (!key) continue\n\t\t\tif (!this.sections[key]) this.initSection(key, sc)\n\n\t\t\tthis.plotId2Key.set(subplot.id, key)\n\t\t\tsc.subplotManager.setSectionKey(subplot.id, key)\n\t\t\tconst existing = detached.get(subplot.id)\n\t\t\tif (existing) {\n\t\t\t\t// Reparent the existing sandbox into the new section\n\t\t\t\tthis.sections[key].subplots.node()!.prepend(existing.node())\n\t\t\t\tthis.sections[key].sandboxes[subplot.id] = existing\n\t\t\t}\n\t\t}\n\t}\n\n\tgetKey(subplot: any, sc): string | undefined {\n\t\tif (this.groupBy === 'none') return 'none'\n\t\tif (this.groupBy === 'sample') return this.getSampleId(subplot)\n\t\treturn sc.subplotManager.getPlotName(subplot)\n\t}\n\n\t/** Extract sID from a subplot's config.\n\t * Actual subplots store sample as {sID, eID} at top level or on term.term.sample. */\n\tgetSampleId(subplot: any): string | undefined {\n\t\treturn subplot.sample?.sID || subplot.singleCellPlot?.sample?.sID || subplot.term?.term?.sample?.sID\n\t}\n\n\tinitSection(key: string, sc: SCViewer) {\n\t\tconst item = this.findSampleMetadata(key, sc)\n\n\t\tconst titleAttrText =\n\t\t\tthis.groupBy == 'sample' ? 'this sample section' : this.groupBy == 'plot' ? 'this plot section' : 'all plots'\n\t\tconst sectionWrapper = this.holder\n\t\t\t.insert('div', ':first-child')\n\t\t\t.style('padding', '10px')\n\t\t\t.attr('data-testid', `sjpp-sc-section-wrapper-${key}`)\n\n\t\t//delete section btn\n\t\tsectionWrapper\n\t\t\t.append('span')\n\t\t\t.attr('data-testid', `sjpp-sc-section-remove-btn-${key}`)\n\t\t\t.style('margin', '0px 5px')\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.attr('title', `Remove ${titleAttrText}`)\n\t\t\t.html(\n\t\t\t\t`<svg xmlns=\"http://www.w3.org/2000/svg\" width=\"12\" height=\"12\" fill=\"#000\" class=\"bi bi-x-lg\" viewBox=\"0 0 12 12\">\n                <path\n                    stroke=\"#000\"\n                    transform=\"scale(0.75)\"\n                    d=\"M2.146 2.854a.5.5 0 1 1 .708-.708L8 7.293l5.146-5.147a.5.5 0 0 1 .708.708L8.707 8l5.147 5.146a.5.5 0 0 1-.708.708L8 8.707l-5.146 5.147a.5.5 0 0 1-.708-.708L7.293 8 2.146 2.854Z\"/>\n                </svg>`\n\t\t\t)\n\t\t\t.on('click', () => {\n\t\t\t\tthis.removeSection(key, sc)\n\t\t\t})\n\n\t\tconst titleText = this.makeSectionTitleText(key, item)\n\t\tconst titleWrapper = sectionWrapper.append('span').style('font-weight', 600).style('opacity', 0.7).text(titleText)\n\t\tif (titleText.length) {\n\t\t\tconst arrow = titleWrapper\n\t\t\t\t.append('span')\n\t\t\t\t.style('font-size', '0.8em')\n\t\t\t\t.style('padding-left', '3px')\n\t\t\t\t.attr('title', `Show/hide plots in ${titleAttrText}`)\n\t\t\t\t.text('\u25BC')\n\n\t\t\ttitleWrapper.on('click', () => {\n\t\t\t\tconst isHidden = this.sections[key].subplots.style('display') === 'none'\n\t\t\t\tthis.sections[key].subplots.style('display', isHidden ? 'block' : 'none')\n\t\t\t\tarrow.text(isHidden ? '\u25BC' : '\u25B2')\n\t\t\t})\n\t\t}\n\n\t\tthis.sections[key] = {\n\t\t\tsectionWrapper,\n\t\t\ttitle: titleWrapper,\n\t\t\tsubplots: sectionWrapper.append('div').attr('data-testid', `sjpp-sc-subplots-${key}`),\n\t\t\tsandboxes: {}\n\t\t}\n\t}\n\n\t/** Look up sample metadata from the fetched items list.\n\t * For experiment datasets, matches sID against experiments[].sampleName.\n\t * For non-experiment datasets, matches sID against item.sample. */\n\tfindSampleMetadata(sampleId: string, sc: SCViewer): SingleCellSample | undefined {\n\t\tif (!sc.items) return undefined\n\t\treturn sc.items.find(item => item.sample === sampleId || item.experiments?.some(e => e.sampleName === sampleId))\n\t}\n\n\tmakeSectionTitleText(key: string, item?: SingleCellSample) {\n\t\tif (this.groupBy === 'none') return 'All plots'\n\t\tif (this.groupBy === 'plot') return key\n\t\tconst caseText = item?.sample && item.sample !== key ? `Case: ${item.sample}` : ''\n\t\tconst isMeta = item?.isMetaResult || false\n\t\tconst itemText = `${isMeta ? '' : 'Sample: '}${key}`\n\t\tconst projectText = item?.['project id'] ? `Project: ${item['project id']}` : ''\n\t\treturn [itemText, caseText, projectText].filter(Boolean).join(' ')\n\t}\n\n\tasync initSandbox(sc: any, subplot: any, key: string) {\n\t\tconst sandboxHolder = this.sections[key].subplots\n\t\t\t.insert('div', ':first-child')\n\t\t\t.attr('data-testid', `sjpp-sc-sandbox-${subplot.id}`) as any as Elem\n\n\t\tconst sandboxDiv = await sc.subplotManager.initSubplotSandbox(sandboxHolder, subplot, {\n\t\t\tsectionKey: key\n\t\t})\n\t\tthis.sections[key].sandboxes[subplot.id] = sandboxDiv\n\t}\n\n\tremoveSection(key: string, sc: SCViewer) {\n\t\tconst subactions: { type: string; id: string; parentId: string }[] = []\n\t\tfor (const plotId of Object.keys(this.sections[key].sandboxes || {})) {\n\t\t\tthis.removeSandbox(plotId, key)\n\t\t\t/** Need to remove plots from the state to prevent main from re-rendering\n\t\t\t * and memory leak from orphaned components after the section is deleted. */\n\t\t\tsubactions.push({\n\t\t\t\ttype: 'plot_delete',\n\t\t\t\tid: plotId,\n\t\t\t\tparentId: sc.id\n\t\t\t})\n\t\t}\n\t\tif (subactions.length > 0) {\n\t\t\tsc.app.dispatch({\n\t\t\t\ttype: 'app_refresh',\n\t\t\t\tsubactions\n\t\t\t})\n\t\t}\n\t\tthis.sections[key].sectionWrapper.remove()\n\t\tdelete this.sections[key]\n\t}\n\n\tremoveSandbox(plotId: string, _key?: string) {\n\t\tconst key = _key || this.plotId2Key.get(plotId)\n\t\tif (!key) return\n\t\tconst section = this.sections[key]\n\t\tconst sandbox = section?.sandboxes?.[plotId]\n\t\tif (sandbox) sandbox.remove()\n\t\tif (section?.sandboxes?.[plotId]) delete section.sandboxes[plotId]\n\t\t//Remove the reference to the plotId in plot2Sample map to avoid memory leak\n\t\tthis.plotId2Key.delete(plotId)\n\t}\n}\n", "import type { SCSample } from '../SCTypes'\n\nexport const GroupByOptions = ['none', 'sample', 'plot'] as const\n\nexport type Settings = {\n\tsc: SCSettings\n\thierCluster: {\n\t\tunit: string\n\t\tyDendrogramHeight: number\n\t\tclusterSamples: boolean\n\t}\n}\n\nexport type SCSettings = {\n\tcolumns: {\n\t\t/** Defined column name for 'sample' column*/\n\t\tsample: string\n\t}\n\t/** Active item chosen by the user */\n\titem: SCSample | undefined\n\tgroupBy: (typeof GroupByOptions)[number]\n}\n", "import type { SCActiveSubplot, SCDom, SCFormattedState, SCTableData } from '../SCTypes'\nimport type { SCInteractions } from '../interactions/SCInteractions'\nimport { SampleTableRenderer } from './SampleTableRenderer'\nimport { PlotButtons } from './PlotButtons'\nimport { SectionRenderer } from './SectionRenderer'\nimport type { SCViewer } from '../SC.ts'\nimport type { SubplotManager } from '../subplots/SubplotManager.ts'\nimport { GroupByOptions, type SCSettings, type Settings } from '../settings/Settings'\nimport { make_radios } from '#dom'\n\n/** Manages the initial rendering of the sample table and the dynamic\n * rendering of the plot buttons and sections based on the selected sample and plots.\n * .update() from sc.main() updates the plot buttons and sections. */\nexport class SCViewRenderer {\n\t//On load, show table\n\t//Eventually maybe an app dispatch and not a flag\n\tstatic inUse: boolean = true\n\n\tsc: SCViewer\n\tdom: SCDom\n\tinteractions: SCInteractions\n\tplotBtns!: PlotButtons\n\tsectionRenderer!: SectionRenderer\n\tsampleTableRenderer!: SampleTableRenderer\n\n\tconstructor(sc: SCViewer) {\n\t\tthis.sc = sc\n\t\tthis.dom = sc.dom\n\t\tthis.interactions = sc.interactions\n\t}\n\n\trender(settings: SCSettings, state: SCFormattedState) {\n\t\tthis.renderSelectBtn()\n\t\tthis.renderGroupByOptions(settings)\n\t\tthis.plotBtns = new PlotButtons(this.interactions, this.dom.plotsBtnsDiv, state.termdbConfig)\n\t\tthis.sectionRenderer = new SectionRenderer(this.dom.sectionsDiv, settings.groupBy)\n\t\t// this.dom.plotsBtnsDiv.style('display', 'none')\n\t}\n\n\t/** Renders the select btn at the top of the page that\n\t * show/hides the item table and plot buttons */\n\trenderSelectBtn() {\n\t\tthis.dom.controlsDiv.style('padding', '10px')\n\n\t\tconst btn = this.dom.controlsDiv\n\t\t\t.append('button')\n\t\t\t.attr('data-testid', 'sjpp-sc-item-table-select-btn')\n\t\t\t.attr('title', 'Show/hide sample table and plot buttons')\n\t\t\t.style('border-radius', '20px')\n\t\t\t.style('padding', '5px 10px')\n\t\t\t.style('background-color', 'transparent')\n\t\t\t//Will need to use ds specific keys/logic here\n\t\t\t.text('Select sample and plots')\n\n\t\tconst arrowSpan = btn.append('span').style('font-size', '0.8em').style('padding-left', '3px').text('\u25BC')\n\n\t\tbtn.on('click', () => {\n\t\t\tSCViewRenderer.inUse = !SCViewRenderer.inUse\n\t\t\tarrowSpan.text(SCViewRenderer.inUse ? '\u25BC' : '\u25B2')\n\t\t\tthis.dom.tableDiv.style('display', SCViewRenderer.inUse ? 'block' : 'none')\n\t\t\tthis.dom.plotsBtnsDiv.style('display', SCViewRenderer.inUse ? 'block' : 'none')\n\t\t})\n\t}\n\n\trenderGroupByOptions(settings: SCSettings) {\n\t\tthis.dom.controlsDiv\n\t\t\t.append('span')\n\t\t\t.style('padding', '3px 0px 3px 20px')\n\t\t\t.style('opacity', 0.7)\n\t\t\t.text('Group plots by:')\n\t\tconst optionsDiv = this.dom.controlsDiv.append('span').style('display', 'inline-block')\n\t\tconst options = GroupByOptions.map(option => {\n\t\t\treturn {\n\t\t\t\tlabel: `${option.charAt(0).toUpperCase() + option.slice(1)}`,\n\t\t\t\tvalue: option,\n\t\t\t\tchecked: settings.groupBy === option\n\t\t\t}\n\t\t})\n\t\tmake_radios({\n\t\t\tholder: optionsDiv,\n\t\t\tstyles: { display: 'inline-block' },\n\t\t\toptions,\n\t\t\tcallback: async value => {\n\t\t\t\tawait this.sc.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.sc.id,\n\t\t\t\t\tconfig: { settings: { sc: { ...settings, groupBy: value } } }\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\tasync update(\n\t\tsettings: Settings,\n\t\tdata: any,\n\t\tactiveSubplots: SCActiveSubplot[],\n\t\ttableData: SCTableData,\n\t\tsubplotManager: SubplotManager\n\t) {\n\t\tthis.sampleTableRenderer = new SampleTableRenderer(this.dom, this.interactions, tableData)\n\t\tthis.plotBtns.update(settings, data)\n\t\t//Also handles when settings.sc.groupBy == 'none' to show all plots in one section\n\t\tawait this.sectionRenderer.update(\n\t\t\tthis.sc,\n\t\t\tactiveSubplots.map(s => s.subplot),\n\t\t\tsettings.sc.groupBy\n\t\t)\n\t\tconst activeSandboxes = subplotManager.getSampleSandboxes()\n\t\tthis.sampleTableRenderer.updatePlotBtns(activeSandboxes)\n\t}\n}\n", "import { getGEunit } from '#tw/geneExpression'\nimport type { Settings } from './Settings'\n\n/** Define all subplot settings here */\nexport function getDefaultSCAppSettings(overrides = {}, app): Settings {\n\tconst defaults: Settings = {\n\t\tsc: {\n\t\t\tcolumns: {\n\t\t\t\tsample: 'Sample'\n\t\t\t},\n\t\t\titem: undefined,\n\t\t\tgroupBy: 'sample'\n\t\t},\n\t\thierCluster: {\n\t\t\tunit: getGEunit(app.vocabApi),\n\t\t\tyDendrogramHeight: 0,\n\t\t\tclusterSamples: false\n\t\t}\n\t}\n\treturn Object.assign(defaults, overrides)\n}\n", "import { importPlot } from '#plots/importPlot.js'\nimport { getCompInit, multiInit, type RxComponent, type ComponentApi } from '#rx'\nimport { filterRxCompInit } from '#filter'\nimport type { MassAppApi } from '#mass/types/mass'\n\n/** Wrapper for subplot sanbdoxes created dynamically.\n * Builds out the expected dom structure and extra functionality (e.g. plot filter)\n *\n * Note: #mass/app.ts expects parent plots to manage plot init for all subplots,\n * which means plotInit() and summaryInit() are never called for subplots.\n * The functionality here is sligthly different from MassPlot && plotInit()\n * in #mass/plot.js to support dynamic creation and destory within the parent */\n\nclass DynamicSubplot implements RxComponent {\n\tstatic type = 'dynamicSubplot'\n\n\ttype: string\n\topts!: { [index: string]: any }\n\tapp: MassAppApi\n\tid!: string\n\tstate: any\n\tcomponents!: { [name: string]: ComponentApi }\n\tdom: { [index: string]: any } = {}\n\tparentId?: string\n\n\tconstructor(opts) {\n\t\tthis.type = DynamicSubplot.type\n\t\tthis.opts = opts\n\t\tthis.app = opts.app\n\t\tthis.parentId = opts?.parentId\n\t}\n\n\tasync init() {\n\t\tthis.opts.holder.app_div.attr('data-testid', 'sjpp-sc-subplot-sandbox-' + this.opts.chartType)\n\n\t\t/** Summary expects the entire sandbox. No need to create dom. */\n\t\tif (this.opts.chartType == 'summary') return\n\n\t\tthis.dom = {\n\t\t\tholder: this.opts.holder,\n\t\t\tviz: this.opts.holder.body.append('div').style('position', 'relative'),\n\t\t\tpaneTitleDiv: this.opts.holder.header.append('div').style('position', 'relative'),\n\t\t\tfilterDiv: this.opts.holder.header.append('div').style('position', 'relative'),\n\t\t\terrorDiv: this.opts.holder.body.append('div').style('position', 'relative')\n\t\t}\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\treturn {\n\t\t\tconfig\n\t\t}\n\t}\n\n\tasync main() {\n\t\tif (!this.components) await this.setComponents()\n\t}\n\n\tasync setComponents() {\n\t\tconst _ = await importPlot(this.opts.chartType)\n\t\tconst chartOpts: { [index: string]: any } = {\n\t\t\tapp: this.app,\n\t\t\tid: this.id,\n\t\t\tparentId: this.parentId\n\t\t}\n\t\tif (this.opts.chartType == 'summary') {\n\t\t\tchartOpts.holder = this.opts.holder\n\t\t\tchartOpts.hidePlotFilter = this.opts.isMetaResult\n\t\t} else {\n\t\t\tchartOpts.holder = this.dom.viz\n\t\t\tchartOpts.header = this.dom.paneTitleDiv\n\t\t}\n\t\tconst promises: { [index: string]: any } = {\n\t\t\tchart: _.componentInit(chartOpts)\n\t\t}\n\n\t\t/** Summary inits its own plot filter */\n\t\tif (!this.state.config?.hidePlotFilter && this.opts.isMetaResult && this.opts.chartType != 'summary') {\n\t\t\tpromises.filter = filterRxCompInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tparentId: this.id,\n\t\t\t\tholder: this.dom.filterDiv,\n\t\t\t\thideLabel: true,\n\t\t\t\temptyLabel: '+Add new filter',\n\t\t\t\tcallback: filter => {\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tconfig: { filter }\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\tthis.components = await multiInit(promises)\n\t}\n\n\tdestroy() {\n\t\tconst appDiv = this.dom?.holder?.app_div\n\t\tif (appDiv) {\n\t\t\tappDiv.selectAll('*').remove()\n\t\t\tappDiv.remove()\n\t\t}\n\t\tfor (const key in this.dom) {\n\t\t\tdelete this.dom[key]\n\t\t}\n\t}\n}\n\nexport const dynamicSubplotInit = getCompInit(DynamicSubplot)\n", "import type { SCViewer } from '../SC'\nimport { newSandboxDiv } from '#dom'\nimport { dynamicSubplotInit } from './DynamicSubplot'\nimport type { SCActiveSubplot, SCSampleSandbox } from '../SCTypes'\n\n/** Instead of managing multiple maps of the subplots (e.g within the \n * SampleTableRenderer, SectionRenderer, etc.), use this manager to keep track\n * of all the subplots, their dom, sections, etc. \n) */\n\nexport class SubplotManager {\n\tsc: SCViewer\n\tscCompPlots: { [key: string]: any }\n\t/** Maps plotId to active subplot information */\n\trecords: Map<string, SCActiveSubplot>\n\n\tconstructor(sc: SCViewer) {\n\t\tthis.sc = sc\n\t\tthis.scCompPlots = this.sc.components.plots\n\t\tthis.records = new Map()\n\t}\n\n\tmap(subplots: any[]): SCActiveSubplot[] {\n\t\tconst subplotIds = new Set(subplots.map(s => s.id))\n\t\tfor (const compPlotId of Object.keys(this.scCompPlots)) {\n\t\t\tif (!subplotIds.has(compPlotId)) {\n\t\t\t\tthis.removeSubplot(compPlotId)\n\t\t\t}\n\t\t}\n\n\t\tfor (const recordId of Array.from(this.records.keys())) {\n\t\t\tif (!subplotIds.has(recordId)) this.records.delete(recordId)\n\t\t}\n\n\t\tfor (const subplot of subplots) {\n\t\t\tthis.updateSubplotRecord(subplot)\n\t\t}\n\n\t\treturn this.getActiveSubplotsFlat()\n\t}\n\n\tupdateSubplotRecord(subplot) {\n\t\tconst existing = this.records.get(subplot.id)\n\t\tconst sampleId = this.getSampleId(subplot)\n\t\tconst isMeta = (sampleId && this.sc.viewModel.metaResultIds.has(sampleId)) || false\n\t\tthis.records.set(subplot.id, {\n\t\t\tplotId: subplot.id,\n\t\t\tsampleId,\n\t\t\tplotName: this.getPlotName(subplot),\n\t\t\tsectionKey: existing?.sectionKey,\n\t\t\tsubplot,\n\t\t\tsandboxDiv: existing?.sandboxDiv,\n\t\t\tisMetaResult: isMeta\n\t\t})\n\t}\n\n\tremoveSubplot(subplotId) {\n\t\tif (this.scCompPlots[subplotId]) this.scCompPlots[subplotId].destroy()\n\t\tdelete this.scCompPlots[subplotId]\n\t\tthis.records.delete(subplotId)\n\t}\n\n\tasync initSubplotSandbox(sandboxHolder, subplot, initOpts: { sectionKey?: string; onClose?: () => void } = {}) {\n\t\tconst sandbox = newSandboxDiv(sandboxHolder, {\n\t\t\tclose: () => {\n\t\t\t\t/** destroy this dom and component before app.dispatch.\n\t\t\t\t * Avoids the component attempting to update after\n\t\t\t\t * the plot is deleted from the state. */\n\t\t\t\tthis.removeSubplot(subplot.id)\n\t\t\t\tthis.sc.app.dispatch({\n\t\t\t\t\ttype: 'plot_delete',\n\t\t\t\t\tid: subplot.id,\n\t\t\t\t\tparentId: this.sc.id\n\t\t\t\t})\n\t\t\t\tif (initOpts.onClose) initOpts.onClose()\n\t\t\t},\n\t\t\tplotId: subplot.id\n\t\t})\n\n\t\tconst subplotOpts = Object.assign({}, subplot, {\n\t\t\tapp: this.sc.app,\n\t\t\tparentId: this.sc.id,\n\t\t\tid: subplot.id,\n\t\t\tholder: sandbox,\n\t\t\tisMetaResult: this.records.get(subplot.id)?.isMetaResult || false\n\t\t})\n\n\t\tthis.scCompPlots[subplot.id] = await dynamicSubplotInit(subplotOpts)\n\t\tthis.setSandbox(subplot.id, sandbox.app_div)\n\t\tif (initOpts.sectionKey) this.setSectionKey(subplot.id, initOpts.sectionKey)\n\t\treturn sandbox.app_div\n\t}\n\n\tsetSandbox(plotId: string, sandboxDiv: any) {\n\t\tconst record = this.records.get(plotId)\n\t\tif (!record) return\n\t\trecord.sandboxDiv = sandboxDiv\n\t\tthis.records.set(plotId, record)\n\t}\n\n\tsetSectionKey(plotId: string, sectionKey?: string) {\n\t\tconst record = this.records.get(plotId)\n\t\tif (!record) return\n\t\trecord.sectionKey = sectionKey\n\t\tthis.records.set(plotId, record)\n\t}\n\n\tgetActiveSubplotsFlat(): SCActiveSubplot[] {\n\t\treturn Array.from(this.records.values())\n\t}\n\n\tgetSampleId(subplot: any): string | undefined {\n\t\treturn subplot.sample?.sID || subplot.singleCellPlot?.sample?.sID || subplot.term?.term?.sample?.sID\n\t}\n\n\tgetPlotName(subplot: any): string {\n\t\t/** Hardcoding logic for some transient and parent plots for now. May consider\n\t\t * adding to the config if this becomes more complex. Must weight against\n\t\t * adding unnecessary complexity to the config for edge cases though.*/\n\t\tconst nameOverrides = new Map([\n\t\t\t['GeneExpInput', 'Gene expression'],\n\t\t\t['imagePlot', subplot?.imgDir?.label || 'Image'],\n\t\t\t['dictionary', 'Summary'],\n\t\t\t['summary', 'Summary']\n\t\t])\n\t\tlet plotName = subplot?.plotName || nameOverrides.get(subplot?.chartType) || subplot?.singleCellPlot?.name\n\t\tif (!plotName) {\n\t\t\tif (subplot?.term?.term?.plot) plotName = subplot.term.term.plot\n\t\t\telse plotName = subplot.chartType || 'Plot'\n\t\t}\n\t\treturn plotName\n\t}\n\n\tgetSampleSandboxes(activeSubplots: SCActiveSubplot[] = this.getActiveSubplotsFlat()): Map<string, SCSampleSandbox[]> {\n\t\tconst sandboxes = new Map<string, SCSampleSandbox[]>()\n\t\tfor (const active of activeSubplots) {\n\t\t\tif (!active.sampleId || !active.sandboxDiv) continue\n\t\t\tif (!sandboxes.has(active.sampleId)) sandboxes.set(active.sampleId, [])\n\t\t\tsandboxes.get(active.sampleId)!.push({ plotId: active.plotId, div: active.sandboxDiv, plotName: active.plotName })\n\t\t}\n\t\treturn sandboxes\n\t}\n}\n", "import type { BasePlotConfig, MassAppApi, MassState } from '#mass/types/mass'\nimport type { SCConfigOpts, SCDom, SCFormattedState, SCViewerOpts, SampleColumn } from './SCTypes'\nimport type { SingleCellSample } from '#types'\nimport { PlotBase } from '../PlotBase.ts'\nimport { getCompInit, copyMerge, type RxComponent } from '#rx'\nimport { SCModel } from './model/SCModel'\nimport { SCViewModel } from './viewModel/SCViewModel'\nimport { SCInteractions } from './interactions/SCInteractions'\nimport { SCViewRenderer } from './view/SCViewRenderer'\nimport { getDefaultSCAppSettings } from './settings/defaults.ts'\nimport { getCombinedTermFilter } from '#filter'\nimport { SubplotManager } from './subplots/SubplotManager.ts'\n\n/** Viewer for single cell data. Renders a sample table and associated subplots for each sample.*/\nexport class SCViewer extends PlotBase implements RxComponent {\n\tstatic type = 'sc'\n\n\ttype: string\n\tcomponents: { plots: { [key: string]: any } }\n\tdom: SCDom\n\tinteractions!: SCInteractions\n\titems!: SingleCellSample[]\n\titemColumns!: SampleColumn[]\n\tmodel!: SCModel\n\tsubplotManager!: SubplotManager\n\tview!: SCViewRenderer\n\tviewModel!: SCViewModel\n\n\tconstructor(opts: SCViewerOpts, api: any) {\n\t\tsuper(opts, api)\n\t\tthis.type = SCViewer.type\n\t\tthis.components = {\n\t\t\tplots: {}\n\t\t}\n\t\tconst div = opts.holder\n\t\t\t.classed('sjpp-sc-main', true)\n\t\t\t.append('div')\n\t\t\t.style('padding', '5px')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\n\t\tthis.dom = {\n\t\t\tdiv,\n\t\t\tloading: opts.holder\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-sc-main-loading')\n\t\t\t\t.attr('data-testid', 'sjpp-sc-main-loading')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('top', '0')\n\t\t\t\t.style('left', '0')\n\t\t\t\t.style('width', '100%')\n\t\t\t\t.style('height', '100%')\n\t\t\t\t.style('background-color', 'rgba(255, 255, 255, 0.95)')\n\t\t\t\t.style('text-align', 'center'),\n\t\t\tcontrolsDiv: div.append('div').attr('id', 'sjpp-sc-controls-btn'),\n\t\t\ttableDiv: div.append('div').attr('id', 'sjpp-sc-item-table'),\n\t\t\tplotsBtnsDiv: div.append('div').attr('id', 'sjpp-sc-plot-buttons').style('display', 'none'),\n\t\t\tsectionsDiv: div.append('div').attr('id', 'sjpp-sc-sections')\n\t\t}\n\n\t\t//opts.header is the sandbox header\n\t\tif (opts.header) opts.header.html(`SINGLE CELL`).style('font-size', '0.9em')\n\t}\n\n\tgetState(appState: any): SCFormattedState {\n\t\tconst config = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow new Error(\n\t\t\t\t`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t\t)\n\t\t}\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter)\n\n\t\treturn {\n\t\t\tconfig,\n\t\t\tsubplots: appState.plots.filter(p => p.parentId === this.id),\n\t\t\ttermfilter,\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\tvocab: appState.vocab\n\t\t}\n\t}\n\n\tasync init(appState: MassState) {\n\t\tconst state = this.getState(appState) as SCFormattedState\n\t\t/** ds defines defaults in termdbConfig.queries.singleCell\n\t\t * see Dataset type when resuming development */\n\t\tconst dsScSamples = state.termdbConfig.queries?.singleCell?.samples\n\t\tthis.model = new SCModel(this)\n\t\ttry {\n\t\t\tthis.itemColumns = await this.model.getColumnLabels(dsScSamples)\n\t\t} catch (e: any) {\n\t\t\tif (e instanceof Error) console.error(`${e.message || e} [SC init()]`)\n\t\t\telse if (e.stack) console.log(e.stack)\n\t\t\tthrow new Error(e.message || e)\n\t\t}\n\t\tthis.viewModel = new SCViewModel(this.app, this.itemColumns)\n\t\tthis.interactions = new SCInteractions(this)\n\t\tthis.subplotManager = new SubplotManager(this)\n\t\tthis.view = new SCViewRenderer(this)\n\t\t/** Only renders the controls above the table */\n\t\tthis.view.render(state.config.settings.sc, state)\n\t}\n\n\tasync main() {\n\t\tif (!this.model) throw new Error(`Model not initialized`)\n\t\tif (!this.viewModel) throw new Error(`ViewModel not initialized`)\n\t\tif (!this.view) throw new Error(`View not initialized`)\n\t\tif (!this.interactions) throw new Error(`Interactions not initialized`)\n\n\t\tconst state = structuredClone(this.state) as SCFormattedState\n\t\tconst config = state.config\n\n\t\tsuper.toggleLoadingDiv()\n\n\t\tlet data: any\n\t\ttry {\n\t\t\tconst allSampleData = await this.model.getAllSampleData(state)\n\t\t\tif (!allSampleData || allSampleData.error) {\n\t\t\t\tsuper.toggleLoadingDiv('none')\n\t\t\t\tsuper.printError(allSampleData?.error || 'No samples found for this dataset')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tthis.items = allSampleData.samples\n\n\t\t\tthis.viewModel.processData(config, allSampleData.samples)\n\n\t\t\tif (config.settings?.sc?.item) {\n\t\t\t\tconst sampleData = await this.model.getSampleData()\n\t\t\t\tif (!sampleData || sampleData.error) {\n\t\t\t\t\tsuper.toggleLoadingDiv('none')\n\t\t\t\t\tsuper.printError(sampleData?.error || 'No data found for this sample')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tdata = sampleData\n\t\t\t}\n\t\t} catch (e: any) {\n\t\t\tif (e instanceof Error) console.error(`${e.message || e} [SC main()]`)\n\t\t\telse if (e.stack) console.log(e.stack)\n\t\t\tsuper.toggleLoadingDiv('none')\n\t\t\tsuper.printError(e.message || e)\n\t\t\treturn\n\t\t}\n\t\tconst activeSubplots = this.subplotManager.map(state.subplots)\n\t\tawait this.view.update(config.settings, data, activeSubplots, this.viewModel.tableData, this.subplotManager)\n\t\tsuper.toggleLoadingDiv('none')\n\t}\n}\n\nexport const SCInit = getCompInit(SCViewer)\nexport const componentInit = SCInit\n\nexport function getPlotConfig(opts: SCConfigOpts, app: MassAppApi) {\n\tconst config = {\n\t\tchartType: 'sc',\n\t\tsettings: getDefaultSCAppSettings(opts.overrides, app)\n\t} as any\n\n\treturn copyMerge(config, opts)\n}\n"],
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+}