@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/chunk-MFQACKYU.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/summary.ts"],
-  "sourcesContent": ["import { getCompInit, copyMerge, type ComponentApi, type RxComponent } from '#rx'\nimport { PlotBase, defaultUiLabels } from './PlotBase.ts'\nimport { Menu, Tabs } from '#dom'\nimport { fillTermWrapper } from '#termsetting'\n// import { recoverInit } from '../rx/src/recover'\nimport { getDefaultViolinSettings } from './violin.js'\nimport { getDefaultBarSettings } from './barchart.js'\nimport { getDefaultBoxplotSettings } from './boxplot/defaults'\nimport { getDefaultScatterSettings } from './scatter/settings/defaults'\nimport { isNumericTerm } from '#shared/terms.js'\nimport { term0_term2_defaultQ } from './controls'\nimport { importPlot } from './importPlot.js'\nimport { filterRxCompInit } from '#filter'\n\nclass SummaryPlot extends PlotBase implements RxComponent {\n\tstatic type = 'summary'\n\n\t// expected RxComponent props, some are already declared/set in PlotBase\n\ttype: string\n\tparentId?: string\n\tdom!: {\n\t\t[index: string]: any\n\t}\n\tcomponents: {\n\t\t[name: string]: ComponentApi | { [name: string]: ComponentApi }\n\t} = {}\n\n\terror: any\n\n\t// expected class-specific props\n\tchartsByType: { [chartType: string]: ComponentApi } = {}\n\tconfigTermKeys = ['term', 'term0', 'term2']\n\tconfig: any\n\ttabsData: any[]\n\tchartToggles: Tabs\n\n\tviolinContTerm?: 'term' | 'term2'\n\tboxContTerm?: 'term' | 'term2'\n\n\tconstructor(opts, api) {\n\t\tsuper(opts, api)\n\t\tthis.type = SummaryPlot.type\n\t\tthis.dom = this.getDom(opts)\n\t\tthis.tabsData = this.getTabsData()\n\t\tthis.chartToggles = new Tabs({ holder: this.dom.chartToggles, tabs: this.tabsData, noContent: true })\n\t\tthis.components = {\n\t\t\tplots: {}\n\t\t}\n\t}\n\n\tpreApiFreeze(api) {\n\t\tapi.getError = () => {\n\t\t\treturn this.error\n\t\t}\n\t}\n\n\tgetDom(opts) {\n\t\tconst holder = opts.holder\n\t\tholder.header.style('padding', 0)\n\n\t\tconst paneTitleDiv = holder.header\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('color', '#555') // changed from #999 to address Section 508 contrast issue\n\t\t\t.style('padding-left', '7px')\n\n\t\treturn {\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tholder,\n\t\t\tbody: holder.body\n\t\t\t\t// .style('margin-top', '-1px')\n\t\t\t\t.style('white-space', 'nowrap')\n\t\t\t\t.style('overflow-x', 'auto'),\n\n\t\t\t// will hold no data notice or the page title in multichart views\n\t\t\terrdiv: holder.body.append('div').attr('class', 'sja_errorbar').style('display', 'none').style('padding', '5px'),\n\n\t\t\tloading: holder.body.append('div').style('display', 'none').style('padding', '5px').html('Loading ...'),\n\n\t\t\t// dom.viz will hold the rendered view\n\t\t\tviz: holder.body.append('div'),\n\t\t\tplotDivs: {},\n\t\t\tpaneTitleDiv,\n\t\t\tpaneTitleText: paneTitleDiv\n\t\t\t\t.append('div')\n\t\t\t\t.classed('sjpp-term-header', true)\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('vertical-align', 'sub'),\n\t\t\tchartToggles: paneTitleDiv.append('div').style('display', 'inline-block').style('margin-left', '10px'),\n\t\t\tlocalRecoverDiv: paneTitleDiv.append('div').style('display', 'inline-block'),\n\t\t\tfilterDiv: holder.header.append('div').style('display', 'inline-block').style('zoom', 0.9)\n\t\t}\n\t}\n\n\tgetTabsData() {\n\t\tconst callback = (event, tab) => this.tabClickCallback(event, tab)\n\t\treturn [\n\t\t\t{\n\t\t\t\tchildType: 'barchart',\n\t\t\t\tlabel: 'Barchart',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tdisabled: () => false,\n\t\t\t\tgetConfig: async () => {\n\t\t\t\t\tif (!this.config) return\n\t\t\t\t\tconst config: any = { id: this.id, childType: 'barchart' }\n\t\t\t\t\tconst { term, term2 } = this.config || {}\n\t\t\t\t\tif (term) {\n\t\t\t\t\t\tconst mode = isNumericTerm(term?.term) ? 'discrete' : term?.q.mode || 'discrete'\n\t\t\t\t\t\tconfig.term = await this.getWrappedTermCopy(term, mode)\n\t\t\t\t\t}\n\t\t\t\t\tif (term2) {\n\t\t\t\t\t\tconst mode = isNumericTerm(term2.term) ? 'discrete' : term2.q.mode || 'discrete'\n\t\t\t\t\t\tconfig.term2 = await this.getWrappedTermCopy(term2, mode)\n\t\t\t\t\t}\n\t\t\t\t\treturn config\n\t\t\t\t},\n\t\t\t\tactive: true,\n\t\t\t\tcallback\n\t\t\t},\n\t\t\t{\n\t\t\t\tchildType: 'violin',\n\t\t\t\tlabel: 'Violin',\n\t\t\t\tdisabled: () => false,\n\t\t\t\tisVisible: () => isNumericTerm(this.config?.term?.term) || isNumericTerm(this.config?.term2?.term),\n\t\t\t\tgetConfig: async () => {\n\t\t\t\t\tconst term = this.config?.term\n\t\t\t\t\tconst term2 = this.config.term2\n\n\t\t\t\t\tlet _term, _term2\n\t\t\t\t\tthis.violinContTerm = isNumericTerm(term?.term) ? 'term' : 'term2'\n\n\t\t\t\t\t//If the first term was continuous or is coming as continuous\n\t\t\t\t\tif ((this.violinContTerm && this.violinContTerm === 'term') || term.q?.mode == 'continuous') {\n\t\t\t\t\t\t// must mean coming from scatter plot\n\t\t\t\t\t\t_term = await this.getWrappedTermCopy(term, 'continuous')\n\t\t\t\t\t\t_term2 = await this.getWrappedTermCopy(term2, 'discrete')\n\t\t\t\t\t\tthis.violinContTerm = 'term'\n\t\t\t\t\t}\n\t\t\t\t\t//If the second term was continuous or is coming as continuous\n\t\t\t\t\telse if ((this.violinContTerm && this.violinContTerm === 'term2') || term2?.q?.mode == 'continuous') {\n\t\t\t\t\t\t// must mean coming from barchart\n\t\t\t\t\t\t_term = await this.getWrappedTermCopy(term, 'discrete')\n\t\t\t\t\t\t_term2 = await this.getWrappedTermCopy(term2, 'continuous')\n\t\t\t\t\t\tthis.violinContTerm = 'term2'\n\t\t\t\t\t}\n\t\t\t\t\t//If the second term is coming as discrete from the scatter\n\t\t\t\t\telse if (term2?.q?.mode == 'discrete') {\n\t\t\t\t\t\t// must mean coming from barchart\n\t\t\t\t\t\t_term = await this.getWrappedTermCopy(term, 'discrete')\n\t\t\t\t\t\t_term2 = await this.getWrappedTermCopy(term2, 'continuous')\n\t\t\t\t\t\tthis.violinContTerm = 'term2'\n\t\t\t\t\t}\n\t\t\t\t\t//by default\n\t\t\t\t\telse {\n\t\t\t\t\t\t_term = await this.getWrappedTermCopy(term, 'continuous')\n\t\t\t\t\t\t_term2 = await this.getWrappedTermCopy(term2, 'discrete')\n\t\t\t\t\t\tthis.violinContTerm = 'term'\n\t\t\t\t\t}\n\t\t\t\t\tconst config = { childType: 'violin', term: _term, term2: _term2 }\n\t\t\t\t\treturn config\n\t\t\t\t},\n\t\t\t\tactive: false,\n\t\t\t\tcallback\n\t\t\t},\n\t\t\t{\n\t\t\t\tchildType: 'boxplot',\n\t\t\t\tlabel: 'Boxplot',\n\t\t\t\tdisabled: () => false,\n\t\t\t\tisVisible: () => isNumericTerm(this.config?.term?.term) || isNumericTerm(this.config?.term2?.term),\n\t\t\t\tgetConfig: async () => {\n\t\t\t\t\tconst _term = this.config?.term\n\t\t\t\t\tconst _term2 = this.config.term2\n\n\t\t\t\t\tlet termMode = 'continuous',\n\t\t\t\t\t\tterm2Mode = 'discrete'\n\t\t\t\t\tthis.boxContTerm = isNumericTerm(_term?.term) ? 'term' : 'term2'\n\n\t\t\t\t\t//If the first term was continuous or is coming as continuous\n\t\t\t\t\tif ((this.boxContTerm && this.boxContTerm === 'term') || _term.q?.mode == 'continuous') {\n\t\t\t\t\t\t// must mean coming from scatter plot\n\t\t\t\t\t\ttermMode = 'continuous'\n\t\t\t\t\t\tterm2Mode = 'discrete'\n\t\t\t\t\t\tthis.boxContTerm = 'term'\n\t\t\t\t\t}\n\t\t\t\t\t//If the second term was continuous or is coming as continuous\n\t\t\t\t\telse if ((this.boxContTerm && this.boxContTerm === 'term2') || _term2?.q?.mode == 'continuous') {\n\t\t\t\t\t\t// must mean coming from barchart\n\t\t\t\t\t\ttermMode = 'discrete'\n\t\t\t\t\t\tterm2Mode = 'continuous'\n\t\t\t\t\t\tthis.boxContTerm = 'term2'\n\t\t\t\t\t}\n\t\t\t\t\t//If the second term is coming as discrete from the scatter\n\t\t\t\t\telse if (_term2?.q?.mode == 'discrete') {\n\t\t\t\t\t\t// must mean coming from barchart\n\t\t\t\t\t\ttermMode = 'discrete'\n\t\t\t\t\t\tterm2Mode = 'continuous'\n\t\t\t\t\t\tthis.boxContTerm = 'term2'\n\t\t\t\t\t}\n\n\t\t\t\t\tconst term = await this.getWrappedTermCopy(_term, termMode)\n\t\t\t\t\tconst term2 = await this.getWrappedTermCopy(_term2, term2Mode)\n\t\t\t\t\tconst config = {\n\t\t\t\t\t\tchildType: 'boxplot',\n\t\t\t\t\t\tterm,\n\t\t\t\t\t\tterm2\n\t\t\t\t\t}\n\t\t\t\t\treturn config\n\t\t\t\t},\n\t\t\t\tactive: false,\n\t\t\t\tcallback\n\t\t\t},\n\t\t\t{\n\t\t\t\tchildType: 'sampleScatter',\n\t\t\t\tlabel: 'Scatter',\n\t\t\t\tdisabled: () => false,\n\t\t\t\tisVisible: () => {\n\t\t\t\t\treturn isNumericTerm(this.config?.term.term) && isNumericTerm(this.config?.term2?.term)\n\t\t\t\t},\n\t\t\t\tgetConfig: async () => {\n\t\t\t\t\tconst _term = await this.getWrappedTermCopy(this.config?.term, 'continuous')\n\t\t\t\t\tconst _term2 = await this.getWrappedTermCopy(this.config?.term2, 'continuous')\n\t\t\t\t\tconst config = {\n\t\t\t\t\t\tchildType: 'sampleScatter',\n\t\t\t\t\t\tterm: _term,\n\t\t\t\t\t\tterm2: _term2,\n\t\t\t\t\t\tgroups: [],\n\t\t\t\t\t\tterm0: this.config.term0\n\t\t\t\t\t}\n\t\t\t\t\treturn config\n\t\t\t\t},\n\t\t\t\tactive: false,\n\t\t\t\tcallback\n\t\t\t}\n\t\t]\n\t}\n\n\tasync init(appState) {\n\t\tconst state = this.getState(appState)\n\t\tconst config = structuredClone(state.config)\n\t\tthis.initUi(this.opts, config)\n\n\t\t// this.components.recover = await recoverInit({\n\t\t// \tapp: this.app,\n\t\t// \tholder: this.dom.localRecoverDiv,\n\t\t// \tgetState: appState => this.getState(appState),\n\t\t// \treactsTo: action => action.id == this.id && action.type == 'plot_edit' && action._scope_ != 'none',\n\t\t// \tplot_id: this.id,\n\t\t// \tmaxHistoryLen: 10,\n\t\t// \tmargin: '5px 10px' //Prevents a gap appearing between the tabs and sandbox content\n\t\t// })\n\t\tif (config?.hidePlotFilter) return\n\t\tthis.components.filter = await filterRxCompInit({\n\t\t\tapp: this.app,\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tparentId: this.id,\n\t\t\tholder: this.dom.filterDiv,\n\t\t\thideLabel: true,\n\n\t\t\temptyLabel: '+Add new filter',\n\t\t\tcallback: filter => {\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\tid: this.id,\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tconfig: { filter }\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.includes('cache_termq')) return true\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\tif (action.type.startsWith('plot_')) {\n\t\t\t\treturn action.id === this.id || action.id == this.parentId\n\t\t\t}\n\t\t}\n\t\tif (action.type.startsWith('filter')) return true\n\t\tif (action.type.startsWith('cohort')) return true\n\t\tif (action.type == 'app_refresh') return true\n\t\treturn false\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='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\treturn {\n\t\t\ttermfilter: appState.termfilter,\n\t\t\tconfig,\n\t\t\t// quick fix to skip history tracking as needed\n\t\t\t_scope_: appState._scope_\n\t\t}\n\t}\n\n\tasync main() {\n\t\tdelete this.error\n\t\tthis.dom.errdiv.style('display', 'none').html('')\n\t\tthis.dom.loading.style('display', '')\n\n\t\tthis.config = await this.getMutableConfig()\n\t\tthis.maySetSandboxHeader()\n\n\t\tif (!this.components.plots[this.config.childType]) {\n\t\t\tawait this.setComponent(this.config)\n\t\t}\n\n\t\tthis.dom.loading.style('display', 'none')\n\t\tthis.render()\n\n\t\tconst activeTabIndex = this.tabsData.findIndex(tab => tab.childType == this.config.childType)\n\t\tthis.chartToggles.update(activeTabIndex)\n\n\t\t//Only show tabs when more than one are present\n\t\tconst numVisTabs = this.tabsData.filter(d => d.isVisible()).length\n\t\tif (numVisTabs > 1) this.dom.chartToggles.style('display', 'inline-block')\n\t\telse this.dom.chartToggles.style('display', 'none')\n\t}\n\n\tmaySetSandboxHeader() {\n\t\tconst { term, term2, headerText, assayCohortTitle } = this.config\n\t\tconst mainTerm = term.getTitleText?.() || term.term.name\n\t\tconst _headerPretext = headerText ? `${headerText} ` : ''\n\t\t//TODO: Should change .assayCohortTitle to headerSuffix, something more generic\n\t\tconst _headerSuffix = assayCohortTitle ? ` (${assayCohortTitle})` : ''\n\t\tconst titleBase = mainTerm + _headerSuffix\n\t\tif (term2?.type) {\n\t\t\tthis.dom.paneTitleText.html(`${_headerPretext}${term2.getTitleText?.() || term2.term.name} vs ${titleBase}`)\n\t\t} else {\n\t\t\tthis.dom.paneTitleText.html(`${_headerPretext}${titleBase}`)\n\t\t}\n\t}\n\n\tasync setComponent(config) {\n\t\t// !!! quick fix for rollup to bundle,\n\t\t// will eventually need to move to a subnested folder structure\n\t\tconst _ = await importPlot(config.childType, `unsupported childType='${config.childType}'`)\n\t\tthis.dom.plotDivs[config.childType] = this.dom.viz.append('div')\n\n\t\t// assumes only 1 chart per chartType would be rendered in the summary sandbox\n\t\tconst componentOpts: { [index: string]: any } = {\n\t\t\tapp: this.app,\n\t\t\tholder: this.dom.plotDivs[config.childType],\n\t\t\tid: this.id,\n\t\t\tparent: this.api\n\t\t}\n\t\t/** Summary child plots may have two parents (e.g. SC -> summary -> child plot).\n\t\t * Pass the root parentId to the child plot.*/\n\t\tif (config.parentId) componentOpts.parentId = config.parentId\n\t\tthis.components.plots[config.childType] = await _.componentInit(componentOpts)\n\t}\n\n\tdestroy() {\n\t\t// the dom.holder itself is not a d3-selection,\n\t\t// so need to specify a destroy function here\n\t\t// since the default rx.componentApi.destroy()\n\t\t// does not work when dom.holder is not a d3-selection\n\t\tthis.dom.holder.app_div.selectAll('*').remove()\n\t\tthis.dom.holder.app_div.remove()\n\t\tfor (const key in this.dom) {\n\t\t\tdelete this.dom[key]\n\t\t}\n\t}\n\n\tinitUi(opts, config) {\n\t\tthis.dom.paneTitleText.html(config.term.term.name)\n\t\tthis.chartToggles.main()\n\t}\n\n\tasync tabClickCallback(event, tab) {\n\t\tif (!tab || !tab.getConfig) return\n\t\tlet config\n\t\ttry {\n\t\t\tthis.dom.viz.style('display', 'none')\n\t\t\tthis.dom.loading.style('display', '')\n\t\t\tconfig = await tab.getConfig()\n\t\t\tthis.dom.loading.style('display', 'none')\n\t\t\tthis.dom.viz.style('display', '')\n\t\t\tif (config)\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tconfig: config\n\t\t\t\t})\n\t\t} catch (e: any) {\n\t\t\tthis.dom.loading.style('display', 'none')\n\t\t\tthis.error = e\n\t\t\tthis.dom.errdiv.style('display', '').html(`Error: ${e.message || e.error || e}`)\n\t\t}\n\t}\n\n\tasync getWrappedTermCopy(term, mode) {\n\t\tif (!term) return\n\t\tconst tw = structuredClone(term)\n\t\t// TODO: this is not type safe, assumes any q{} can be set to any mode\n\t\ttw.q.mode = mode // {mode, isAtomic: true}\n\t\t// If tw.q is empty/undefined, the default q\n\t\t// will be assigned by fillTw by term type\n\t\tawait fillTermWrapper(tw, this.app.vocabApi)\n\t\treturn tw\n\t}\n\n\trender() {\n\t\tfor (const childType of Object.keys(this.components.plots)) {\n\t\t\tconst chart = this.components.plots[childType]\n\t\t\t// hide non-active charts first, so not to momentarily have two visible charts\n\t\t\tif (chart.type != this.config.childType) {\n\t\t\t\tthis.dom.plotDivs[chart.type].style('display', 'none')\n\t\t\t}\n\t\t}\n\n\t\tthis.dom.plotDivs[this.config.childType].style('display', '')\n\t}\n\n\tgetChartImages() {\n\t\tconst chart = this.components.plots[this.config.childType]\n\t\tif (chart?.getChartImages) {\n\t\t\treturn chart.getChartImages()\n\t\t}\n\t\treturn null\n\t}\n}\n\nexport const summaryInit = getCompInit(SummaryPlot)\nexport const componentInit = summaryInit\n\nexport async function getPlotConfig(opts, app) {\n\tif (!opts.term) throw 'summary getPlotConfig: opts.term{} missing'\n\ttry {\n\t\topts.term = await fillTermWrapper(\n\t\t\topts.term,\n\t\t\tapp.vocabApi,\n\t\t\topts.term.q || { geneVariant: { type: 'predefined-groupset' } }\n\t\t)\n\t\t// supply term0_term2_defaultQ if opts.term0/2.bins/q is undefined\n\t\t// e.g. for scatterplot, opts.term2.q.mode='continuous' so will not\n\t\t// want to override with q.mode from term0_term2_defaultQ\n\t\tif (opts.term2)\n\t\t\topts.term2 = await fillTermWrapper(\n\t\t\t\topts.term2,\n\t\t\t\tapp.vocabApi,\n\t\t\t\topts.term2.bins || opts.term2.q ? undefined : term0_term2_defaultQ\n\t\t\t)\n\t\tif (opts.term0)\n\t\t\topts.term0 = await fillTermWrapper(\n\t\t\t\topts.term0,\n\t\t\t\tapp.vocabApi,\n\t\t\t\topts.term0.bins || opts.term0.q ? undefined : term0_term2_defaultQ\n\t\t\t)\n\t\t// dynamic scatterplot is a child type of summary and following args are possible; if present, initialize them\n\t\tif (opts.colorTW) opts.colorTW = await fillTermWrapper(opts.colorTW, app.vocabApi)\n\t\tif (opts.shapeTW) opts.shapeTW = await fillTermWrapper(opts.shapeTW, app.vocabApi)\n\t\tif (opts.scaleDotTW) opts.scaleDotTW = await fillTermWrapper(opts.scaleDotTW, app.vocabApi)\n\t} catch (e: any) {\n\t\tif (e.stack) console.log(e.stack)\n\t\tthrow `${e} [summary getPlotConfig()]`\n\t}\n\n\tconst config = {\n\t\tchartType: 'summary',\n\t\tchildType: 'barchart',\n\t\tterm: opts.term,\n\t\tgroups: [],\n\t\tcontrolLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),\n\t\t//Allow hiding the plot filter when appropriate (e.g. single cell summary plots)\n\t\thidePlotFilter: opts.hidePlotFilter || false,\n\t\tsettings: {\n\t\t\tcontrols: {\n\t\t\t\tisOpen: false\n\t\t\t},\n\t\t\tcommon: {\n\t\t\t\tuse_logscale: false, // flag for y-axis scale type, 0=linear, 1=log\n\t\t\t\tuse_percentage: false\n\t\t\t\t// Move to barchart settings\n\t\t\t\t// barheight: 300, // maximum bar length\n\t\t\t\t// barwidth: 20, // bar thickness\n\t\t\t\t// barspace: 2 // space between two bars\n\t\t\t},\n\n\t\t\tbarchart: getDefaultBarSettings(app),\n\n\t\t\tviolin: getDefaultViolinSettings(app),\n\n\t\t\tboxplot: getDefaultBoxplotSettings(app),\n\n\t\t\tsampleScatter: getDefaultScatterSettings(opts)\n\t\t},\n\t\tmayAdjustConfig(config, edits: { childType?: string } = {}) {\n\t\t\treturn mayAdjustConfig(config, opts, edits)\n\t\t}\n\t}\n\t//config.mayAdjustConfig(config)\n\n\t// TODO: may do similar thing for custom term\n\tif (config.term.term.type == 'geneVariant') config.settings.barchart.colorBars = true\n\n\t// may apply term-specific changes to the default object\n\tcopyMerge(config, opts)\n\t// always use the dataset-configured control/ui labels\n\t// to override ui labels from recovered session state\n\tObject.assign(config.controlLabels, app.vocabApi.termdbConfig.uiLabels || {})\n\treturn config\n}\n\nconst discreteByContinuousPlots = new Set(['violin', 'boxplot'])\n\n/**\n * Adjusts the childType of a summary plot config based on the term types and modes.\n * This is exported so it can be tested directly.\n */\nexport function mayAdjustConfig(config, opts, edits: { childType?: string } = {}) {\n\t/*\n\t\twhen recovering from state rehydration:\n\t\t- Mass store must call mayAdjustConfig(), if available, since the recovered state\n\t\tmay be partial such as from an example url. Even a previously saved \"full\" state\n\t\tmay still need to be filled or reshaped with new state config/settings.\n\t*/\n\n\tif (edits.childType) {\n\t\t// no need to set config.childType if a value is already specified\n\t\t// in an edits object (optional second argument), as processed by mass store\n\t\tif (config.childType != edits.childType) throw `action.config.childType was not applied in mass store.plot_edit()`\n\t\treturn\n\t}\n\t// config.childType may be stale, OR edits.childType may not be available,\n\t// when the summary plot_edit is triggered by replacing a term, such as replacing\n\t// categorical overlay with numeric, in which case the dispatched action might not\n\t// know in advance what the chiltType should be. It is much more reliable and consistent\n\t// to determine the default plots here, depending on the processed config.\n\tif (config.term?.q?.mode == 'continuous' && config.term2?.q?.mode == 'continuous') {\n\t\t// TODO: may need more logic later if more than one summary childType,\n\t\t// besides scatter, can support 2 continuous terms\n\t\tconfig.childType = 'sampleScatter'\n\t} else if (config.term?.term?.type == 'termCollection') {\n\t\tif (config.term.term.memberType == 'categorical') {\n\t\t\tconfig.childType = 'barchart' // ok to overwrite as it can only be barchart\n\t\t} else if (config.term.term.memberType == 'numeric') {\n\t\t\tif (config.childType) {\n\t\t\t\t// already given.\n\t\t\t\tif (config.childType == 'barchart') {\n\t\t\t\t\t// wrong type, overwrite with default\n\t\t\t\t\tconfig.childType = 'violin'\n\t\t\t\t} else {\n\t\t\t\t\t// do not overwrite e.g. if value is boxplot. though this is not further validated\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tconfig.childType = 'violin'\n\t\t\t}\n\t\t} else {\n\t\t\tthrow new Error('config.term.term.memberType not categorical or numeric')\n\t\t}\n\t} else if (config.term?.q?.mode == 'continuous' || config.term2?.q?.mode == 'continuous') {\n\t\tif (!discreteByContinuousPlots.has(config.childType)) {\n\t\t\t// only change config.childType if the current value is not supported by discrete + continuous tw\n\t\t\tif (opts.childType && !discreteByContinuousPlots.has(opts.childType)) {\n\t\t\t\tconsole.warn(\n\t\t\t\t\t`ignoring summary opts.childType='${opts.childType}' since it does not support plotting discrete by continuous tw's`\n\t\t\t\t)\n\t\t\t\tconfig.childType = 'violin'\n\t\t\t} else {\n\t\t\t\tconfig.childType = opts.childType || 'violin'\n\t\t\t}\n\t\t}\n\t} else {\n\t\t// TODO: may need more logic later if more than one summary childType,\n\t\t// besides barchart, can support discrete tw only\n\t\tconfig.childType = 'barchart'\n\t}\n}\n"],
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-  "names": ["config"]
-}

package/dist/chunk-MVGAGTM3.js

@@ -1,343 +0,0 @@
-import {
-  storeInit
-} from "./chunk-USFSHSCJ.js";
-import {
-  summaryInit
-} from "./chunk-MFQACKYU.js";
-import {
-  navInit
-} from "./chunk-DBKNWR4J.js";
-import {
-  AppBase,
-  downloadSVGsAsPdf,
-  filterRxCompInit,
-  newSandboxDiv,
-  sayerror,
-  vocabInit
-} from "./chunk-5VOPABBA.js";
-import {
-  importPlot
-} from "./chunk-Z5U6HOE4.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  AppApi,
-  getCompInit,
-  multiInit
-} from "./chunk-M3J4MINX.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// mass/plot.js
-var MassPlot = class _MassPlot {
-  static type = "plot";
-  constructor(opts) {
-    this.type = _MassPlot.type;
-    setRenderers(this);
-    this.initUi(opts);
-  }
-  reactsTo(action) {
-    if (action.type.includes("cache_termq")) return true;
-    if (action.type.endsWith("_group")) return true;
-    if (action.type.startsWith("plot_")) {
-      return action.id === this.id || action.id == this.parentId || action.config?.parentId === this.id || action.parentId === this.id;
-    }
-    if (action.type.startsWith("filter")) return true;
-    if (action.type.startsWith("cohort")) return true;
-    if (action.type == "app_refresh") return true;
-    if (action.type.endsWith("customTerm")) return true;
-  }
-  // !!! NOTE: This getState() method is reused by the plot-specific recover component.
-  // When logging something within getState, it may have been called by either the plot or recover instance
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      termfilter: appState.termfilter,
-      config,
-      groups: appState.groups,
-      // quick fix to skip history tracking as needed
-      _scope_: appState._scope_
-    };
-  }
-  async main() {
-    this.dom.errdiv.style("display", "none").style("background-color", "rgba(255,100,100,0.2)").html("");
-    if (!this.components) await this.setComponents(this.opts);
-  }
-  async setComponents(opts) {
-    const _ = await importPlot(opts.chartType);
-    const promises = {
-      // recover: recoverInit({
-      // 	app: this.app,
-      // 	holder: this.dom.localRecoverDiv,
-      // 	getState: appState => this.getState(appState),
-      // 	reactsTo: action =>
-      // 		action.id == this.id &&
-      // 		(action.type == 'plot_edit' || action.type == 'plot_nestedEdits') &&
-      // 		action._track_ != 'none',
-      // 	plot_id: this.id,
-      // 	maxHistoryLen: 10,
-      // 	hideLabel: true
-      // }),
-      chart: _.componentInit({
-        app: this.app,
-        holder: this.dom.viz,
-        header: this.dom.paneTitleDiv,
-        id: this.id,
-        plotDiv: select_default(this.dom.holder.app_div.node().parentNode),
-        /******* reason for passing plotDiv to chart ********
-        				- this plot instance may allow to launch a new plot as a persistent sandbox
-        				  inside mass plotDiv, maintaining the uniform plot appearance despite it's ad-hoc
-        				  the new plot is not a formal mass plot type, and cannot be done via app.dispatch()
-        				  thus the need to directly access plotDiv
-        				- example: mds3 tk from genome browser can launch disco etc
-        				- having access to plotDiv may offer flexibility for the plot to do stuff
-        
-        				since plot.js has no access to mass app .dom.plotDiv in which all apps are shown,
-        				this workarounds gets the parent node of sandbox.app_div which is app.dom.plotDiv
-        				*/
-        getFilterImage: async () => this.components.filter.getFilterImage()
-      })
-    };
-    if (!this.state.config.hidePlotFilter) {
-      const filterDisabledMsg = this.app.vocabApi.termdbConfig?.plotFilter?.disabledMessage;
-      const filterHolder = filterDisabledMsg ? this.dom.filterDiv.append("div").style("pointer-events", "none").style("opacity", 0.5) : this.dom.filterDiv;
-      if (filterDisabledMsg) this.dom.filterDiv.attr("title", filterDisabledMsg).style("cursor", "not-allowed");
-      promises.filter = filterRxCompInit({
-        app: this.app,
-        vocabApi: this.app.vocabApi,
-        parentId: this.id,
-        holder: filterHolder,
-        hideLabel: true,
-        emptyLabel: "+Add new filter",
-        callback: (filter) => {
-          this.app.dispatch({
-            id: this.id,
-            type: "plot_edit",
-            config: { filter }
-          });
-        }
-      });
-    }
-    this.components = await multiInit(promises);
-  }
-  destroy() {
-    this.dom.holder.app_div.selectAll("*").remove();
-    this.dom.holder.app_div.remove();
-    for (const key in this.dom) {
-      delete this.dom[key];
-    }
-  }
-};
-var plotInit = getCompInit(MassPlot);
-function setRenderers(self) {
-  self.initUi = function(opts) {
-    const holder = opts.holder;
-    opts.holder.app_div.attr("data-testid", "sjpp-massplot-sandbox-" + opts.chartType);
-    holder.header.style("padding", 0);
-    try {
-      self.dom = {
-        tip: new Menu({ padding: "0px" }),
-        holder,
-        paneTitleDiv: holder.header.append("div").style("display", "inline-block").style("color", "#555").style("padding-left", "7px").style("vertical-align", "sub"),
-        localRecoverDiv: holder.header.append("div").style("display", "inline-block"),
-        filterDiv: holder.header.append("div").style("display", "inline-block").style("zoom", 0.9),
-        body: holder.body.style("white-space", "nowrap").style("overflow-x", "auto"),
-        // will hold no data notice or the page title in multichart views
-        errdiv: holder.body.append("div").style("display", "none").style("padding", "5px").style("background-color", "rgba(255,100,100,0.2)"),
-        // dom.viz will hold the rendered view
-        viz: holder.body.append("div")
-      };
-    } catch (e) {
-      self.dom.errdiv.style("display", "none").text(e);
-    }
-  };
-}
-
-// mass/app.ts
-var MassApp = class extends AppBase {
-  // expected class-specific props
-  constructor(opts, api) {
-    super(opts);
-    this.components = {};
-    this.wasDestroyed = false;
-    this.api = api;
-    if (opts.addLoginCallback) {
-      opts.addLoginCallback(() => this.api.dispatch({ type: "app_refresh" }));
-    }
-    this.type = "app";
-    this.dom = {
-      holder: opts.holder,
-      // do not modify holder style
-      topbar: opts.holder.append("div"),
-      errdiv: opts.holder.append("div"),
-      plotDiv: opts.holder.append("div")
-    };
-    this.plotIdToSandboxId = {};
-  }
-  static {
-    this.type = "app";
-  }
-  async preApiFreeze(api) {
-    try {
-      api.tip = new Menu({ padding: "5px" });
-      api.tip.d.on("keyup", (event) => {
-        if (event.key == "Escape") api.tip.hide();
-      });
-      api.printError = (e) => this.printError(e);
-      api.vocabApi = await vocabInit({
-        app: api,
-        state: { vocab: this.opts.state.vocab },
-        fetchOpts: this.opts.fetchOpts,
-        getDatasetAccessToken: this.opts.getDatasetAccessToken
-      });
-      api.hasWebGL = function() {
-        try {
-          const canvas = document.createElement("canvas");
-          return !!(window.WebGLRenderingContext && (canvas.getContext("webgl") || canvas.getContext("experimental-webgl")));
-        } catch (_) {
-          return false;
-        }
-      };
-      this.opts.state.vocab = api.vocabApi.vocab;
-    } catch (e) {
-      console.log(`preApiFreeze error`, e);
-      throw e;
-    }
-  }
-  async init() {
-    try {
-      const debounceInterval = "debounceInterval" in this.opts ? this.opts.debounceInterval : 0;
-      const embeddedSessionState = this.opts.embeddedSessionState;
-      if (embeddedSessionState) {
-        Object.assign(this.opts.state, embeddedSessionState);
-      }
-      this.store = await storeInit({ app: this.api, state: this.opts.state, debounceInterval });
-      this.state = await this.store.copyState();
-      this.components = {};
-      if (this.state.nav.header_mode != "hidden") {
-        this.components.nav = await navInit({
-          app: this.api,
-          holder: this.dom.topbar,
-          header_mode: this.state && this.state.nav && this.state.nav.header_mode,
-          vocab: this.state.vocab,
-          massSessionDuration: this.state.termdbConfig.massSessionDuration,
-          // this.opts.massSessionDuration
-          pkgver: this.opts.pkgver,
-          downloadPlots: () => {
-            this.downloadPlots();
-          }
-        });
-      }
-      this.components.plots = {};
-      if (this.opts.app?.doNotAwaitInitRender) {
-        this.api.dispatch();
-      } else {
-        await this.api.dispatch();
-      }
-    } catch (e) {
-      this.printError(e);
-      throw e;
-    }
-  }
-  async main() {
-    await this.api.vocabApi.main();
-    this.dom.plotDiv?.style(
-      "display",
-      this.state.nav?.header_mode != "hidden" && this.state.nav?.activeTab == 0 ? "none" : "block"
-    );
-    const newPlots = {};
-    let sandbox;
-    for (const plot of this.state.plots) {
-      if (plot.parentId) continue;
-      if (this.components.plots && !(plot.id in this.components.plots)) {
-        sandbox = newSandboxDiv(this.dom.plotDiv, {
-          close: () => {
-            this.api.dispatch({
-              type: "plot_delete",
-              id: plot.id
-            });
-          },
-          plotId: plot.id,
-          beforePlotId: plot.insertBefore || null,
-          style: {
-            width: "98.5%"
-          }
-        });
-        if (plot.chartType == "summary")
-          newPlots[plot.id] = summaryInit(Object.assign({ app: this.api, holder: sandbox }, plot));
-        else newPlots[plot.id] = plotInit(Object.assign({ app: this.api, holder: sandbox }, plot));
-      }
-    }
-    const numNewPlots = Object.keys(newPlots).length;
-    if (numNewPlots) {
-      await Promise.all(Object.values(newPlots));
-      for (const plotId in newPlots) {
-        this.components.plots[plotId] = await newPlots[plotId];
-      }
-    }
-    for (const plotId in this.components.plots) {
-      if (!this.state.plots.find((p) => p.id === plotId)) {
-        this.components.plots[plotId].destroy();
-        delete this.components.plots[plotId];
-      }
-    }
-  }
-  printError(e) {
-    const errdiv = e.errdiv || this.dom.errdiv;
-    if (errdiv) errdiv.style("display", "").html("").style("background-color", "");
-    sayerror(errdiv || this.opts.holder, "Error: " + (e.message || e.error || e));
-    if (e.stack) console.log(e.stack);
-    this.bus.emit("error");
-    if (this.opts?.debug) {
-      console.groupCollapsed("Stack trace from MassApp.printError() call.");
-      console.trace();
-      console.groupEnd();
-    }
-  }
-  skipPrevActionAbort(action) {
-    if (!action) return false;
-    if (action.type.startsWith("filter")) return false;
-    if (action.type.startsWith("cohort")) return false;
-    if (action.type == "app_refresh") {
-      if (action.subactions) {
-        return action.subactions.find((a) => a.type.startsWith("filter") || a.type.startsWith("cohort")) ? false : true;
-      }
-    }
-    return true;
-  }
-  async downloadPlots() {
-    const chartImagesAll = [];
-    let i = 1;
-    const values = Object.values(this.components.plots);
-    for (const plot of values) {
-      const chart = plot.type == "plot" ? plot.getComponents("chart") : plot;
-      const chartImages = chart.getChartImages ? chart.getChartImages() : null;
-      if (!chartImages) {
-        console.log(`The ${chart.type} does not support downloading images yet`);
-        continue;
-      }
-      for (const chartImage of chartImages) {
-        if (values.length > 1) chartImage.name = `${i}. ${chartImage.name}`;
-        chartImagesAll.push(chartImage);
-      }
-      i++;
-    }
-    if (chartImagesAll.length > 0) {
-      const filters = [];
-      const globalFilterImg = await this.components.nav.getComponents("filter").getFilterImage();
-      if (globalFilterImg) filters.push(globalFilterImg);
-      downloadSVGsAsPdf(chartImagesAll, "plots", "landscape", filters);
-    } else alert("No chart images available for download");
-  }
-};
-var appInit = AppApi.getInitFxn(MassApp);
-
-export {
-  appInit
-};
-//# sourceMappingURL=chunk-MVGAGTM3.js.map

package/dist/chunk-MVGAGTM3.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../mass/plot.js", "../mass/app.ts"],
-  "sourcesContent": ["import { getCompInit, copyMerge, multiInit } from '#rx'\nimport { Menu } from '#dom/menu'\n// import { recoverInit } from '../rx/src/recover'\nimport { select as d3select } from 'd3-selection'\nimport { importPlot } from '#plots/importPlot.js'\nimport { filterRxCompInit } from '#filter'\n\n/*\n\tMassPlot is a \"wrapper\" for chart component(s).\n\tIt creates expected plot-specific elements like an error div, undo-redo buttons, and local filter.\n*/\nclass MassPlot {\n\tstatic type = 'plot'\n\n\tconstructor(opts) {\n\t\tthis.type = MassPlot.type\n\t\tsetRenderers(this)\n\t\tthis.initUi(opts)\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.includes('cache_termq')) return true\n\t\tif (action.type.endsWith('_group')) return true\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\t// action.parentId == this.id is a special case to react when deleting a child plot of this plot,\n\t\t\t// for example in the profile comparison, when closing one of the comparison plots\n\t\t\treturn (\n\t\t\t\taction.id === this.id ||\n\t\t\t\taction.id == this.parentId ||\n\t\t\t\taction.config?.parentId === this.id ||\n\t\t\t\taction.parentId === this.id\n\t\t\t)\n\t\t}\n\t\tif (action.type.startsWith('filter')) return true\n\t\tif (action.type.startsWith('cohort')) return true\n\t\tif (action.type == 'app_refresh') return true\n\t\tif (action.type.endsWith('customTerm')) return true\n\t}\n\n\t// !!! NOTE: This getState() method is reused by the plot-specific recover component.\n\t// When logging something within getState, it may have been called by either the plot or recover instance\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\ttermfilter: appState.termfilter,\n\t\t\tconfig,\n\t\t\tgroups: appState.groups,\n\t\t\t// quick fix to skip history tracking as needed\n\t\t\t_scope_: appState._scope_\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.dom.errdiv.style('display', 'none').style('background-color', 'rgba(255,100,100,0.2)').html('')\n\t\tif (!this.components) await this.setComponents(this.opts)\n\t}\n\n\tasync setComponents(opts) {\n\t\tconst _ = await importPlot(opts.chartType)\n\t\tconst promises = {\n\t\t\t// recover: recoverInit({\n\t\t\t// \tapp: this.app,\n\t\t\t// \tholder: this.dom.localRecoverDiv,\n\t\t\t// \tgetState: appState => this.getState(appState),\n\t\t\t// \treactsTo: action =>\n\t\t\t// \t\taction.id == this.id &&\n\t\t\t// \t\t(action.type == 'plot_edit' || action.type == 'plot_nestedEdits') &&\n\t\t\t// \t\taction._track_ != 'none',\n\t\t\t// \tplot_id: this.id,\n\t\t\t// \tmaxHistoryLen: 10,\n\t\t\t// \thideLabel: true\n\t\t\t// }),\n\t\t\tchart: _.componentInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tholder: this.dom.viz,\n\t\t\t\theader: this.dom.paneTitleDiv,\n\t\t\t\tid: this.id,\n\t\t\t\tplotDiv: d3select(this.dom.holder.app_div.node().parentNode),\n\t\t\t\t/******* reason for passing plotDiv to chart ********\n\t\t\t\t- this plot instance may allow to launch a new plot as a persistent sandbox\n\t\t\t\t  inside mass plotDiv, maintaining the uniform plot appearance despite it's ad-hoc\n\t\t\t\t  the new plot is not a formal mass plot type, and cannot be done via app.dispatch()\n\t\t\t\t  thus the need to directly access plotDiv\n\t\t\t\t- example: mds3 tk from genome browser can launch disco etc\n\t\t\t\t- having access to plotDiv may offer flexibility for the plot to do stuff\n\n\t\t\t\tsince plot.js has no access to mass app .dom.plotDiv in which all apps are shown,\n\t\t\t\tthis workarounds gets the parent node of sandbox.app_div which is app.dom.plotDiv\n\t\t\t\t*/\n\t\t\t\tgetFilterImage: async () => this.components.filter.getFilterImage()\n\t\t\t})\n\t\t}\n\n\t\tif (!this.state.config.hidePlotFilter) {\n\t\t\tconst filterDisabledMsg = this.app.vocabApi.termdbConfig?.plotFilter?.disabledMessage\n\t\t\t/*\n\t\t\tWhen the local filter is disabled (e.g. for the public/unauthenticated view), render it\n\t\t\tinto an inner greyed, non-interactive div while the outer filterDiv keeps pointer events\n\t\t\tso its tooltip explaining why still appears on hover.\n\t\t\t*/\n\t\t\tconst filterHolder = filterDisabledMsg\n\t\t\t\t? this.dom.filterDiv.append('div').style('pointer-events', 'none').style('opacity', 0.5)\n\t\t\t\t: this.dom.filterDiv\n\t\t\tif (filterDisabledMsg) this.dom.filterDiv.attr('title', filterDisabledMsg).style('cursor', 'not-allowed')\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: filterHolder,\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\t// the dom.holder itself is not a d3-selection,\n\t\t// so need to specify a destroy function here\n\t\t// since the default rx.componentApi.destroy()\n\t\t// does not work when dom.holder is not a d3-selection\n\t\tthis.dom.holder.app_div.selectAll('*').remove()\n\t\tthis.dom.holder.app_div.remove()\n\t\tfor (const key in this.dom) {\n\t\t\tdelete this.dom[key]\n\t\t}\n\t}\n}\n\nexport const plotInit = getCompInit(MassPlot)\n\nfunction setRenderers(self) {\n\tself.initUi = function (opts) {\n\t\t// opts={app, chartType:str, holder, id, debug}\n\n\t\tconst holder = opts.holder // \"sandbox\" obj: {app_div, body, header, header_row, id}\n\n\t\t// since chartType is already given in constructor opts, create test id with chart type as a simple way to identify the box\n\t\topts.holder.app_div.attr('data-testid', 'sjpp-massplot-sandbox-' + opts.chartType)\n\n\t\tholder.header.style('padding', 0)\n\n\t\ttry {\n\t\t\tself.dom = {\n\t\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\t\tholder,\n\t\t\t\tpaneTitleDiv: holder.header\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('color', '#555')\n\t\t\t\t\t.style('padding-left', '7px')\n\t\t\t\t\t.style('vertical-align', 'sub'),\n\t\t\t\tlocalRecoverDiv: holder.header.append('div').style('display', 'inline-block'),\n\t\t\t\tfilterDiv: holder.header.append('div').style('display', 'inline-block').style('zoom', 0.9),\n\t\t\t\tbody: holder.body.style('white-space', 'nowrap').style('overflow-x', 'auto'),\n\n\t\t\t\t// will hold no data notice or the page title in multichart views\n\t\t\t\terrdiv: holder.body\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'none')\n\t\t\t\t\t.style('padding', '5px')\n\t\t\t\t\t.style('background-color', 'rgba(255,100,100,0.2)'),\n\n\t\t\t\t// dom.viz will hold the rendered view\n\t\t\t\tviz: holder.body.append('div')\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tself.dom.errdiv.style('display', 'none').text(e)\n\t\t}\n\t}\n}\n", "import { AppApi, type StoreApi, type ComponentApi, type RxApp } from '#rx'\nimport { AppBase } from '#plots/AppBase.ts'\nimport { storeInit } from './store'\nimport { vocabInit } from '#termdb/vocabulary'\nimport { navInit } from './nav'\nimport { plotInit } from './plot'\nimport { summaryInit } from '#plots/summary.js'\nimport { sayerror, Menu, newSandboxDiv, downloadSVGsAsPdf } from '#dom'\n\n/*\nopts{}\n.genome{}\n\tclient-side genome object\n\tshould be required\n.state{}\n\trequired, will fill-in or override store.defaultState\n \t.genome\n \t.dslabel\n \t.tree{} etc\n\n.app\n\t.onFilterChange\n\tIf it is provided when the global filter is edited\n\tthis function is called (from mass/store). Used by the profile dataset so far,\n\tto clear the profile local filters\n*/\n\nclass MassApp extends AppBase implements RxApp {\n\tstatic type = 'app'\n\n\t// expected RxApp, some are already declared/set in AppBase\n\tapi: AppApi\n\ttype: string\n\tparentId?: string\n\tdom!: {\n\t\t[index: string]: any\n\t}\n\tcomponents: {\n\t\t[name: string]: ComponentApi | { [name: string]: ComponentApi }\n\t} = {}\n\n\twasDestroyed = false\n\tstore!: StoreApi\n\tplotIdToSandboxId: { [plotId: string]: string }\n\tbus!: any\n\n\t// expected class-specific props\n\n\tconstructor(opts, api) {\n\t\tsuper(opts)\n\t\tthis.api = api\n\n\t\tif (opts.addLoginCallback) {\n\t\t\topts.addLoginCallback(() => this.api.dispatch({ type: 'app_refresh' }))\n\t\t}\n\n\t\tthis.type = 'app'\n\t\t// this will create divs in the correct order\n\t\tthis.dom = {\n\t\t\tholder: opts.holder, // do not modify holder style\n\t\t\ttopbar: opts.holder.append('div'),\n\t\t\terrdiv: opts.holder.append('div'),\n\t\t\tplotDiv: opts.holder.append('div')\n\t\t}\n\n\t\t// track plots by ID, and assign\n\t\tthis.plotIdToSandboxId = {}\n\t}\n\n\tasync preApiFreeze(api) {\n\t\ttry {\n\t\t\tapi.tip = new Menu({ padding: '5px' })\n\t\t\tapi.tip.d.on('keyup', event => {\n\t\t\t\tif (event.key == 'Escape') api.tip.hide()\n\t\t\t})\n\t\t\tapi.printError = e => this.printError(e)\n\n\t\t\t// TODO: only pass state.genome, dslabel to vocabInit\n\t\t\tapi.vocabApi = await vocabInit({\n\t\t\t\tapp: api,\n\t\t\t\tstate: { vocab: this.opts.state.vocab },\n\t\t\t\tfetchOpts: this.opts.fetchOpts,\n\t\t\t\tgetDatasetAccessToken: this.opts.getDatasetAccessToken\n\t\t\t})\n\n\t\t\tapi.hasWebGL = function () {\n\t\t\t\t//Copied from static/js/WEBGL.js\n\t\t\t\ttry {\n\t\t\t\t\tconst canvas = document.createElement('canvas')\n\t\t\t\t\treturn !!(\n\t\t\t\t\t\twindow.WebGLRenderingContext &&\n\t\t\t\t\t\t(canvas.getContext('webgl') || canvas.getContext('experimental-webgl'))\n\t\t\t\t\t)\n\t\t\t\t} catch (_) {\n\t\t\t\t\treturn false\n\t\t\t\t}\n\t\t\t}\n\t\t\t// the vocabApi's vocab may be reprocessed from the original input\n\t\t\tthis.opts.state.vocab = api.vocabApi.vocab\n\t\t} catch (e) {\n\t\t\tconsole.log(`preApiFreeze error`, e)\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tasync init() {\n\t\t// catch initialization error\n\t\ttry {\n\t\t\t// TODO: may default later to having a debouncer ???\n\t\t\tconst debounceInterval = 'debounceInterval' in this.opts ? this.opts.debounceInterval : 0\n\t\t\t// NOTE: Within the same browser tab, a refresh should load the embedder's intended page\n\t\t\t// and not the recovered session, to avoid confusing default page load behavior. If a user\n\t\t\t// wants to see the initial recovered state view in the embedder portal, they would have\n\t\t\t// to click on a link again. May revisit this approach and reactivate the commented out code below.\n\t\t\tconst embeddedSessionState = this.opts.embeddedSessionState // || JSON.parse(sessionStorage.getItem('embeddedSessionState') || `null`)\n\t\t\tif (embeddedSessionState) {\n\t\t\t\t// may assume session state recovery for an embedder portal\n\t\t\t\t// see the comment about potential race-condition in childCorsMessage embedder-helpers.js\n\t\t\t\tObject.assign(this.opts.state, embeddedSessionState)\n\t\t\t}\n\t\t\tthis.store = await storeInit({ app: this.api, state: this.opts.state, debounceInterval })\n\t\t\tthis.state = await this.store.copyState()\n\t\t\tthis.components = {}\n\t\t\tif (this.state.nav.header_mode != 'hidden') {\n\t\t\t\tthis.components.nav = await navInit({\n\t\t\t\t\tapp: this.api,\n\t\t\t\t\tholder: this.dom.topbar,\n\t\t\t\t\theader_mode: this.state && this.state.nav && this.state.nav.header_mode,\n\t\t\t\t\tvocab: this.state.vocab,\n\t\t\t\t\tmassSessionDuration: this.state.termdbConfig.massSessionDuration, // this.opts.massSessionDuration\n\t\t\t\t\tpkgver: this.opts.pkgver,\n\t\t\t\t\tdownloadPlots: () => {\n\t\t\t\t\t\tthis.downloadPlots()\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t\tthis.components.plots = {}\n\t\t\tif (this.opts.app?.doNotAwaitInitRender) {\n\t\t\t\t// do not await to return the instance sooner and allow calling appApi.triggerAbort() before initial render,\n\t\t\t\t// instead of waiting for initial data loading and rendering\n\t\t\t\tthis.api.dispatch()\n\t\t\t} else {\n\t\t\t\tawait this.api.dispatch()\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tthis.printError(e)\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tasync main() {\n\t\tawait this.api.vocabApi.main()\n\t\t//Do not show the plots below the about tab\n\t\tthis.dom.plotDiv?.style(\n\t\t\t'display',\n\t\t\tthis.state.nav?.header_mode != 'hidden' && this.state.nav?.activeTab == 0 ? 'none' : 'block'\n\t\t)\n\n\t\tconst newPlots = {}\n\t\tlet sandbox\n\t\tfor (const plot of this.state.plots) {\n\t\t\t// plots with parentId means the parent plot will trigger the plot instead of being triggered here\n\t\t\tif (plot.parentId) continue\n\t\t\tif (this.components.plots && !(plot.id in this.components.plots)) {\n\t\t\t\tsandbox = newSandboxDiv(this.dom.plotDiv, {\n\t\t\t\t\tclose: () => {\n\t\t\t\t\t\tthis.api.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_delete',\n\t\t\t\t\t\t\tid: plot.id\n\t\t\t\t\t\t})\n\t\t\t\t\t},\n\t\t\t\t\tplotId: plot.id,\n\t\t\t\t\tbeforePlotId: plot.insertBefore || null,\n\t\t\t\t\tstyle: {\n\t\t\t\t\t\twidth: '98.5%'\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\tif (plot.chartType == 'summary')\n\t\t\t\t\tnewPlots[plot.id] = summaryInit(Object.assign({ app: this.api, holder: sandbox }, plot))\n\t\t\t\telse newPlots[plot.id] = plotInit(Object.assign({ app: this.api, holder: sandbox }, plot))\n\t\t\t}\n\t\t}\n\n\t\t// simultaneous initialization of multiple new plots;\n\t\t// if done inside the for-of loop above, the await kewyword\n\t\t// will delay subsequent plot initializations\n\t\tconst numNewPlots = Object.keys(newPlots).length\n\t\tif (numNewPlots) {\n\t\t\tawait Promise.all(Object.values(newPlots))\n\t\t\tfor (const plotId in newPlots) {\n\t\t\t\tthis.components.plots[plotId] = await newPlots[plotId]\n\t\t\t}\n\t\t}\n\n\t\tfor (const plotId in this.components.plots) {\n\t\t\tif (!this.state.plots.find(p => p.id === plotId)) {\n\t\t\t\tthis.components.plots[plotId].destroy()\n\t\t\t\tdelete this.components.plots[plotId]\n\t\t\t}\n\t\t}\n\t}\n\n\tprintError(e) {\n\t\tconst errdiv = e.errdiv || this.dom.errdiv\n\t\tif (errdiv) errdiv.style('display', '').html('').style('background-color', '')\n\t\tsayerror(errdiv || this.opts.holder, 'Error: ' + (e.message || e.error || e))\n\t\tif (e.stack) console.log(e.stack)\n\t\tthis.bus.emit('error')\n\t\t/** .printError() maybe called from any component without a helpful\n\t\t * message or error object. Include the trace when in debug mode to\n\t\t * help identify the source of the error.\n\t\t * Collapsed for convenience. */\n\t\tif (this.opts?.debug) {\n\t\t\tconsole.groupCollapsed('Stack trace from MassApp.printError() call.')\n\t\t\tconsole.trace()\n\t\t\tconsole.groupEnd()\n\t\t}\n\t}\n\n\tskipPrevActionAbort(action) {\n\t\t// may skip aborting previously dispatched actions in AppApi.dispatch()\n\t\t// if the new dispatched action doesn't affect all components; this will\n\t\t// allow plots and control menus to continue rendering while creating,\n\t\t// editing, or deleting another plot\n\t\tif (!action) return false\n\t\tif (action.type.startsWith('filter')) return false\n\t\tif (action.type.startsWith('cohort')) return false\n\t\tif (action.type == 'app_refresh') {\n\t\t\tif (action.subactions) {\n\t\t\t\treturn action.subactions.find(a => a.type.startsWith('filter') || a.type.startsWith('cohort')) ? false : true\n\t\t\t}\n\t\t}\n\t\treturn true\n\t}\n\n\tasync downloadPlots() {\n\t\tconst chartImagesAll: any[] = []\n\t\tlet i = 1\n\t\tconst values: any[] = Object.values(this.components.plots)\n\t\tfor (const plot of values) {\n\t\t\tconst chart = plot.type == 'plot' ? plot.getComponents('chart') : plot // implies summary plot\n\t\t\tconst chartImages = chart.getChartImages ? chart.getChartImages() : null\n\t\t\tif (!chartImages) {\n\t\t\t\tconsole.log(`The ${chart.type} does not support downloading images yet`)\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tfor (const chartImage of chartImages) {\n\t\t\t\tif (values.length > 1) chartImage.name = `${i}. ${chartImage.name}`\n\t\t\t\tchartImagesAll.push(chartImage)\n\t\t\t}\n\t\t\ti++\n\t\t}\n\t\tif (chartImagesAll.length > 0) {\n\t\t\tconst filters: any[] = []\n\t\t\tconst globalFilterImg = await (this.components.nav as ComponentApi).getComponents('filter').getFilterImage()\n\t\t\tif (globalFilterImg) filters.push(globalFilterImg)\n\t\t\tdownloadSVGsAsPdf(chartImagesAll, 'plots', 'landscape', filters)\n\t\t} else alert('No chart images available for download')\n\t}\n}\n\nexport const appInit = AppApi.getInitFxn(MassApp)\n"],
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-  "names": []
-}

package/dist/chunk-NELOT3NJ.js

@@ -1,119 +0,0 @@
-import {
-  GENE_EXPRESSION,
-  METABOLITE_INTENSITY,
-  PROTEOME_ABUNDANCE,
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-I6WR4CG7.js";
-
-// common/termutils.js
-function sample_match_termvaluesetting(row, filter, geneVariant$ids) {
-  const lst = !filter ? [] : filter.type == "tvslst" ? filter.lst : [filter];
-  let numberofmatchedterms = 0;
-  for (const item of lst) {
-    if (item.type == "tvslst") {
-      if (sample_match_termvaluesetting(row, item)) {
-        numberofmatchedterms++;
-      }
-    } else {
-      const t = item.tvs;
-      let samplevalue;
-      if (t.term.type == "geneVariant") {
-        samplevalue = geneVariant$ids.map((g) => row[g]).filter((s) => s);
-      } else if (t.term.type == "integer" || t.term.type == "float" || t.term.type == GENE_EXPRESSION || t.term.type == METABOLITE_INTENSITY || t.term.type == PROTEOME_ABUNDANCE) {
-        samplevalue = row[t.term.id] || row[t.term.$id]?.key;
-      } else if (t.term.type == "survival") {
-        samplevalue = row[t.term.$id]?.key;
-      } else {
-        samplevalue = row[t.term.id] || row[t.term.$id]?.value;
-      }
-      let thistermmatch;
-      if (t.term.type == "categorical") {
-        if (samplevalue === void 0) {
-          if (t.isnot) thistermmatch = !thistermmatch;
-          if (thistermmatch) numberofmatchedterms++;
-          continue;
-        }
-        const valueset = t.valueset ? t.valueset : new Set(t.values.map((i) => i.key));
-        thistermmatch = valueset.has(samplevalue);
-      } else if (t.term.type == "integer" || t.term.type == "float" || t.term.type == GENE_EXPRESSION || t.term.type == METABOLITE_INTENSITY || t.term.type == PROTEOME_ABUNDANCE) {
-        if (samplevalue === void 0) {
-          if (t.isnot) thistermmatch = !thistermmatch;
-          if (thistermmatch) numberofmatchedterms++;
-          continue;
-        }
-        for (const range of t.ranges) {
-          if ("value" in range) {
-            thistermmatch = samplevalue === range.value;
-            if (thistermmatch) break;
-          } else if (samplevalue == range.name) {
-            thistermmatch = true;
-            break;
-          } else {
-            if (t.term.values) {
-              const v = t.term.values[samplevalue.toString()];
-              if (v && v.uncomputable) {
-                continue;
-              }
-            }
-            let left, right;
-            if (range.startunbounded) {
-              left = true;
-            } else if ("start" in range) {
-              if (range.startinclusive) {
-                left = samplevalue >= range.start;
-              } else {
-                left = samplevalue > range.start;
-              }
-            }
-            if (range.stopunbounded) {
-              right = true;
-            } else if ("stop" in range) {
-              if (range.stopinclusive) {
-                right = samplevalue <= range.stop;
-              } else {
-                right = samplevalue < range.stop;
-              }
-            }
-            thistermmatch = left && right;
-          }
-          if (thistermmatch) break;
-        }
-      } else if (t.term.type == "condition") {
-        const key = getPrecomputedKey(t);
-        const anno = samplevalue && samplevalue[key];
-        if (anno) {
-          thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
-        }
-      } else if (t.term.type == "survival") {
-        if (samplevalue === void 0) {
-          if (t.isnot) thistermmatch = !thistermmatch;
-          if (thistermmatch) numberofmatchedterms++;
-          continue;
-        }
-        const valueset = t.valueset ? t.valueset : new Set(t.values.map((i) => i.key));
-        thistermmatch = valueset.has(samplevalue);
-      } else if (t.term.type == "geneVariant" && t.legendFilterType == "geneVariant_hard") {
-        const f = t.values[0];
-        thistermmatch = samplevalue.find((s) => {
-          for (const v of s.values) {
-            if (v.dt == f.dt && (!v.origin || v.origin == f.origin) && f.mclasslst.includes(v.class)) return true;
-          }
-        }) && true;
-      } else if (t.term.type == SINGLECELL_GENE_EXPRESSION) {
-      } else {
-        throw "unknown term type";
-      }
-      if (t.isnot) {
-        thistermmatch = !thistermmatch;
-      }
-      if (thistermmatch) numberofmatchedterms++;
-    }
-    if (filter.join == "or" && numberofmatchedterms) return true;
-  }
-  if (numberofmatchedterms == lst.length) return true;
-}
-
-export {
-  sample_match_termvaluesetting
-};
-//# sourceMappingURL=chunk-NELOT3NJ.js.map

package/dist/chunk-NELOT3NJ.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../common/termutils.js"],
-  "sourcesContent": ["import { SINGLECELL_GENE_EXPRESSION, GENE_EXPRESSION, METABOLITE_INTENSITY, PROTEOME_ABUNDANCE } from '#shared/terms.js'\n// import { dofetch3 } from '../src/client'\n\n/*\nto retrieve the termjson object of one term, using its id\nonly works for a termdb-enabled dataset\n\nif the function is attached to an instance with .state{ dslabel, genome }, then simply call:\n\tawait instance.getterm( ? )\n\notherwise, do:\n\tawait getterm( id, dslabel, genome )\n\n*/\n\nconst cache = { serverData: {} }\n\n/*\n\tGiven data of a sample and a filter, return if the sample match the filter\n\t\trow:{} data of a sample\n\t\tfilter\n\t\tgeneVariant$ids: [] array of $id of the geneVariant terms (in the matrix)\n*/\nexport function sample_match_termvaluesetting(row, filter, geneVariant$ids) {\n\tconst lst = !filter ? [] : filter.type == 'tvslst' ? filter.lst : [filter]\n\tlet numberofmatchedterms = 0\n\n\t/* for AND, require all terms to match */\n\tfor (const item of lst) {\n\t\tif (item.type == 'tvslst') {\n\t\t\tif (sample_match_termvaluesetting(row, item)) {\n\t\t\t\tnumberofmatchedterms++\n\t\t\t}\n\t\t} else {\n\t\t\tconst t = item.tvs\n\t\t\tlet samplevalue\n\t\t\tif (t.term.type == 'geneVariant') {\n\t\t\t\tsamplevalue = geneVariant$ids.map(g => row[g]).filter(s => s) // filter out the genes that are not annotated for the sample\n\t\t\t} else if (\n\t\t\t\tt.term.type == 'integer' ||\n\t\t\t\tt.term.type == 'float' ||\n\t\t\t\tt.term.type == GENE_EXPRESSION ||\n\t\t\t\tt.term.type == METABOLITE_INTENSITY ||\n\t\t\t\tt.term.type == PROTEOME_ABUNDANCE\n\t\t\t) {\n\t\t\t\tsamplevalue = row[t.term.id] || row[t.term.$id]?.key\n\t\t\t} else if (t.term.type == 'survival') {\n\t\t\t\tsamplevalue = row[t.term.$id]?.key\n\t\t\t} else {\n\t\t\t\tsamplevalue = row[t.term.id] || row[t.term.$id]?.value\n\t\t\t}\n\t\t\tlet thistermmatch\n\n\t\t\tif (t.term.type == 'categorical') {\n\t\t\t\tif (samplevalue === undefined) {\n\t\t\t\t\t// this sample has no anno for this term, check isnot\n\t\t\t\t\tif (t.isnot) thistermmatch = !thistermmatch\n\t\t\t\t\tif (thistermmatch) numberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t\t// t may be frozen, should not modify to attach valueset if missing\n\t\t\t\t}\n\t\t\t\tconst valueset = t.valueset ? t.valueset : new Set(t.values.map(i => i.key))\n\t\t\t\tthistermmatch = valueset.has(samplevalue)\n\t\t\t} else if (\n\t\t\t\tt.term.type == 'integer' ||\n\t\t\t\tt.term.type == 'float' ||\n\t\t\t\tt.term.type == GENE_EXPRESSION ||\n\t\t\t\tt.term.type == METABOLITE_INTENSITY ||\n\t\t\t\tt.term.type == PROTEOME_ABUNDANCE\n\t\t\t) {\n\t\t\t\tif (samplevalue === undefined) {\n\t\t\t\t\t// this sample has no anno for this term, check isnot\n\t\t\t\t\tif (t.isnot) thistermmatch = !thistermmatch\n\t\t\t\t\tif (thistermmatch) numberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\tfor (const range of t.ranges) {\n\t\t\t\t\tif ('value' in range) {\n\t\t\t\t\t\tthistermmatch = samplevalue === range.value // || \"\"+samplevalue == range.value || samplevalue == \"\"+range.value //; if (thistermmatch) console.log(i++)\n\t\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t\t} else if (samplevalue == range.name) {\n\t\t\t\t\t\tthistermmatch = true\n\t\t\t\t\t\tbreak\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// actual range\n\t\t\t\t\t\tif (t.term.values) {\n\t\t\t\t\t\t\tconst v = t.term.values[samplevalue.toString()]\n\t\t\t\t\t\t\tif (v && v.uncomputable) {\n\t\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tlet left, right\n\t\t\t\t\t\tif (range.startunbounded) {\n\t\t\t\t\t\t\tleft = true\n\t\t\t\t\t\t} else if ('start' in range) {\n\t\t\t\t\t\t\tif (range.startinclusive) {\n\t\t\t\t\t\t\t\tleft = samplevalue >= range.start\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tleft = samplevalue > range.start\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (range.stopunbounded) {\n\t\t\t\t\t\t\tright = true\n\t\t\t\t\t\t} else if ('stop' in range) {\n\t\t\t\t\t\t\tif (range.stopinclusive) {\n\t\t\t\t\t\t\t\tright = samplevalue <= range.stop\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tright = samplevalue < range.stop\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthistermmatch = left && right\n\t\t\t\t\t}\n\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t}\n\t\t\t} else if (t.term.type == 'condition') {\n\t\t\t\tconst key = getPrecomputedKey(t)\n\t\t\t\tconst anno = samplevalue && samplevalue[key]\n\t\t\t\tif (anno) {\n\t\t\t\t\tthistermmatch = Array.isArray(anno)\n\t\t\t\t\t\t? t.values.find(d => anno.includes(d.key))\n\t\t\t\t\t\t: t.values.find(d => d.key == anno)\n\t\t\t\t}\n\t\t\t} else if (t.term.type == 'survival') {\n\t\t\t\tif (samplevalue === undefined) {\n\t\t\t\t\t// this sample has no anno for this term, check isnot\n\t\t\t\t\tif (t.isnot) thistermmatch = !thistermmatch\n\t\t\t\t\tif (thistermmatch) numberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t\t// t may be frozen, should not modify to attach valueset if missing\n\t\t\t\t}\n\t\t\t\tconst valueset = t.valueset ? t.valueset : new Set(t.values.map(i => i.key))\n\t\t\t\tthistermmatch = valueset.has(samplevalue)\n\t\t\t} else if (t.term.type == 'geneVariant' && t.legendFilterType == 'geneVariant_hard') {\n\t\t\t\t// handle a matrix legend hard filter\n\t\t\t\t// values: [{ dt, origin, mclasslst:[key] }]\n\t\t\t\tconst f = t.values[0] //matrix geneVariant legend filter only has one item in tvs.values\n\t\t\t\tthistermmatch =\n\t\t\t\t\tsamplevalue.find(s => {\n\t\t\t\t\t\tfor (const v of s.values) {\n\t\t\t\t\t\t\tif (v.dt == f.dt && (!v.origin || v.origin == f.origin) && f.mclasslst.includes(v.class)) return true\n\t\t\t\t\t\t}\n\t\t\t\t\t}) && true\n\t\t\t} else if (t.term.type == SINGLECELL_GENE_EXPRESSION) {\n\t\t\t} else {\n\t\t\t\tthrow 'unknown term type'\n\t\t\t}\n\n\t\t\tif (t.isnot) {\n\t\t\t\tthistermmatch = !thistermmatch\n\t\t\t}\n\t\t\tif (thistermmatch) numberofmatchedterms++\n\t\t}\n\n\t\t// if one tvslst is matched with an \"or\" (Set UNION), then sample is okay\n\t\tif (filter.join == 'or' && numberofmatchedterms) return true\n\t}\n\n\t// for join=\"and\" (Set intersection)\n\tif (numberofmatchedterms == lst.length) return true\n}\n"],
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