@sjcrh/proteinpaint-client 2.204.0 → 2.205.0

package/dist/chunk-L743GRJE.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/sampleView.ts"],
+  "sourcesContent": ["import { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase } from '#plots/PlotBase.js'\nimport { select } from 'd3-selection'\nimport { getBrainImagingSampleSet } from './getBrainImagingSampleSet.ts'\nimport { DEFAULT_SAMPLE_TYPE, isNumericTerm, ROOT_SAMPLE_TYPE, getDateStrFromNumber } from '#shared/terms.js'\nimport { sayerror } from '#dom'\n\nconst root_ID = 'root'\nconst samplesLimit = 15\n\nclass SampleView extends PlotBase implements RxComponent {\n\tstatic type = 'sampleView'\n\n\ttype: string\n\ttermsByCohort: any\n\tdom!: {\n\t\theader: any\n\t\tholder: any\n\t\tcontrolsDiv: any\n\t\tsampleDiv: any\n\t\tshowPlotsDiv: any\n\t\tloadingDiv: any\n\t\tplotsDiv: any\n\t\tnoteDiv?: any\n\t\tdownloadbt?: any\n\t\ttableDiv?: any\n\t\tmessageDiv?: any\n\t}\n\tvocabApi: any\n\tsamplesData!: any\n\tsample!: { sampleId: any; sampleName: string }\n\tconfig!: any\n\tsettings!: any\n\ttermsById!: Record<string, any>\n\tsampleDataByTermId!: Record<string, any>\n\torderedVisibleTerms!: any[]\n\tdiscoPlots!: any[]\n\tsingleSamplePlots!: Record<string, any[]>\n\tbrainPlots!: any[]\n\timagePlots!: any[]\n\tvisiblePlots!: boolean\n\trenderSampleDictionary!: () => void\n\n\tconstructor(opts, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = SampleView.type\n\t\tthis.setDom(opts)\n\t\tsetInteractivity(this)\n\t\tsetRenderers(this)\n\t}\n\n\tsetDom(opts) {\n\t\topts.holder.style('position', 'relative')\n\t\tconst div = opts.holder.append('div')\n\n\t\tconst controlsDiv = div.append('div').style('display', 'inline-block')\n\t\tconst headerDiv = div.append('div').style('display', 'inline-block').style('padding', '20px')\n\t\tconst contentDiv = div\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('flex-direction', 'row')\n\t\t\t.style('flex-wrap', 'wrap')\n\t\t\t.style('justify-content', 'flex-start')\n\t\t\t.style('width', '100vw')\n\n\t\tconst plotsDiv = contentDiv //div.append('div').style('display', 'inline-block').style('margin-top', '10px') //div with plots\n\t\tconst sampleDiv = headerDiv.insert('div').style('display', 'inline-block')\n\t\tconst showPlotsDiv = headerDiv.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\n\t\t// loading overlay shown over the sandbox while sample data is fetched/rendered;\n\t\t// reuses the shared .sjpp-loading-overlay box + .sjpp-spinner glyph\n\t\tconst loadingDiv = opts.holder.append('div').attr('class', 'sjpp-loading-overlay').style('display', 'none')\n\t\tloadingDiv.append('div').attr('class', 'sjpp-spinner')\n\n\t\tthis.dom = {\n\t\t\theader: opts.header,\n\t\t\tholder: opts.holder,\n\t\t\tcontrolsDiv,\n\t\t\tsampleDiv,\n\t\t\tshowPlotsDiv,\n\t\t\tloadingDiv,\n\t\t\tplotsDiv\n\t\t}\n\t}\n\n\tasync init(appState) {\n\t\tthis.termsByCohort = {}\n\n\t\tawait this.setSampleSelect(appState)\n\t\tconst state = this.getState(appState)\n\n\t\tawait this.setControls(state)\n\t}\n\n\tasync setSampleSelect(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\n\t\tconst sampleDiv = this.dom.sampleDiv\n\t\tif (this.dom.header) this.dom.header.html(`Sample View`)\n\n\t\tif (config.samples && config.samples.length > 1) {\n\t\t\t// const sampleLabel = sampleDiv.insert('label').style('vertical-align', 'top').html('Samples:')\n\n\t\t\tconst select = sampleDiv\n\t\t\t\t.insert('select')\n\t\t\t\t.style('margin', '0px 5px')\n\t\t\t\t.property('multiple', true)\n\t\t\t\t.attr('id', 'select')\n\t\t\tselect\n\t\t\t\t.selectAll('option')\n\t\t\t\t.data(config.samples)\n\t\t\t\t.enter()\n\t\t\t\t.append('option')\n\t\t\t\t.attr('value', d => d.sampleId)\n\t\t\t\t.property('selected', (d, _i) => _i < samplesLimit)\n\t\t\t\t.html((d, _) => d.sampleName)\n\n\t\t\tthis.dom.noteDiv = sampleDiv\n\t\t\t\t.insert('div')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.style('vertical-align', 'top')\n\t\t\t\t.style('font-size', '0.8em')\n\t\t\t\t.style('color', '#aaa')\n\t\t\t\t.html(\n\t\t\t\t\t`*Note that only ${samplesLimit} samples can be selected.<br/>&nbsp;Navigate through the list to view all the samples.`\n\t\t\t\t)\n\t\t\tif (config.samples.length > samplesLimit) this.dom.noteDiv.style('display', 'inline-block')\n\n\t\t\tselect.on('change', () => {\n\t\t\t\tconst options = select.node().options\n\t\t\t\tconst samples: unknown[] = []\n\t\t\t\tlet count = 0\n\t\t\t\tfor (const option of options) {\n\t\t\t\t\tif (option.selected) {\n\t\t\t\t\t\tif (count < samplesLimit) {\n\t\t\t\t\t\t\tconst sampleId = Number(option.value)\n\t\t\t\t\t\t\tconst sampleName = config.samples.find(s => s.sampleId == sampleId).sampleName\n\t\t\t\t\t\t\tconst sample = { sampleId, sampleName }\n\t\t\t\t\t\t\tsamples.push(sample)\n\t\t\t\t\t\t\tcount++\n\t\t\t\t\t\t} else option.selected = false\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config: { samples } })\n\t\t\t})\n\t\t} else {\n\t\t\tthis.samplesData = await this.vocabApi.getSamplesByName({\n\t\t\t\tfilter: appState.termfilter?.filter\n\t\t\t})\n\t\t\tif (Object.keys(this.samplesData).length == 0) throw 'No accessible samples found'\n\t\t\tconst callback = sampleName => {\n\t\t\t\tif (this.samplesData[sampleName]) {\n\t\t\t\t\tconst samples = getSamplesRelated(this.samplesData, sampleName, null, undefined)\n\n\t\t\t\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config: { samples } })\n\t\t\t\t\tthis.dom.downloadbt.property('disabled', false)\n\t\t\t\t} else {\n\t\t\t\t\tthis.dom.tableDiv.style('display', 'none')\n\t\t\t\t\tfor (const div of this.discoPlots) div.cellDiv.style('display', 'none')\n\t\t\t\t\tfor (const div of Object.values(this.singleSamplePlots)) {\n\t\t\t\t\t\tdiv.forEach(p => p.cellDiv.style('display', 'none'))\n\t\t\t\t\t}\n\t\t\t\t\tfor (const div of this.brainPlots) div.cellDiv.style('display', 'none')\n\n\t\t\t\t\tif (sampleName != '') {\n\t\t\t\t\t\tthis.dom.downloadbt.property('disabled', true)\n\t\t\t\t\t\tconst errorDiv = sampleDiv.append('div')\n\t\t\t\t\t\tsayerror(errorDiv, `Invalid sample ID: ${sampleName}. Please check the sample ID.`)\n\t\t\t\t\t\tsetTimeout(() => {\n\t\t\t\t\t\t\terrorDiv.remove()\n\t\t\t\t\t\t}, 6000)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tconst hasSampleAncestry = appState.termdbConfig.hasSampleAncestry\n\t\t\tconst sampleName = searchSampleInput(this.dom.sampleDiv, this.samplesData, hasSampleAncestry, callback, undefined)\n\t\t\tthis.sample = config.sample || { sampleId: this.samplesData[sampleName!].id, sampleName: sampleName! }\n\t\t\t// When the plot is opened for an already-chosen sample (config.sample, e.g. from the omnisearch\n\t\t\t// or a scatter point click), show that name in the search box. Its data is rendered either way,\n\t\t\t// but an empty box reads as \"type a sample name to see details\".\n\t\t\tif (config.sample?.sampleName) sampleDiv.select('input').property('value', config.sample.sampleName)\n\n\t\t\tthis.dom.downloadbt = sampleDiv\n\t\t\t\t.insert('button')\n\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t.style('vertical-align', 'top')\n\t\t\t\t.text('Download')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tthis.downloadData()\n\t\t\t\t})\n\t\t\tthis.dom.messageDiv = sampleDiv\n\t\t\t\t.insert('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.style('vertical-align', 'top')\n\t\t\t\t.html('&nbsp;&nbsp;Downloading data ...')\n\t\t}\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots?.find(p => p.id === this.id)\n\t\tlet samples = config.samples || getSamplesRelated(this.samplesData, this.sample.sampleName, null, undefined)\n\n\t\tif (config.samples?.length > 15) samples = config.samples.filter((s, i) => i < 15)\n\t\tconst q = appState.termdbConfig.queries\n\n\t\tconst state: {\n\t\t\tconfig: any\n\t\t\ttermfilter: any\n\t\t\tactiveCohort: any\n\t\t\tterms: any\n\t\t\texpandedTermIds: any\n\t\t\tsamples: any\n\t\t\tsingleSampleGenomeQuantification: any\n\t\t\tsingleSampleMutation: any\n\t\t\tNIdata: any\n\t\t\thasVerifiedToken: any\n\t\t\ttokenVerificationPayload: any\n\t\t\ttermdbConfig: any\n\t\t\tvocab: any\n\t\t\ttoSelectCohort?: boolean\n\t\t\tcohortValuelst?: any\n\t\t} = {\n\t\t\tconfig,\n\t\t\ttermfilter: appState.termfilter,\n\t\t\t// TODO: use state.config drectly, instead of having to extract\n\t\t\t// selected config.key-values into the component state\n\t\t\tactiveCohort: config.activeCohort,\n\t\t\tterms: config.terms,\n\t\t\texpandedTermIds: config.expandedTermIds,\n\t\t\tsamples,\n\t\t\tsingleSampleGenomeQuantification: q?.singleSampleGenomeQuantification,\n\t\t\tsingleSampleMutation: q?.singleSampleMutation,\n\t\t\tNIdata: q?.NIdata,\n\t\t\thasVerifiedToken: this.app.vocabApi.hasVerifiedToken(),\n\t\t\ttokenVerificationPayload: this.app.vocabApi.tokenVerificationPayload,\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\tvocab: appState.vocab\n\t\t}\n\t\tif (appState.termdbConfig.selectCohort) {\n\t\t\tstate.toSelectCohort = true\n\t\t\tconst choice = appState.termdbConfig.selectCohort.values[state.activeCohort]\n\t\t\tif (choice) {\n\t\t\t\t// a selection has been made\n\t\t\t\tstate.cohortValuelst = choice.keys\n\t\t\t}\n\t\t}\n\n\t\treturn state\n\t}\n\n\tasync main() {\n\t\tif (this.mayRequireToken()) return\n\t\tthis.dom.loadingDiv.style('display', '')\n\t\ttry {\n\t\t\tthis.config = structuredClone(this.state.config)\n\t\t\tthis.settings = this.state.config.settings.sampleView\n\t\t\tthis.dom.plotsDiv.selectAll('*').remove()\n\n\t\t\tthis.termsById = this.getTermsById(this.state)\n\t\t\tthis.sampleDataByTermId = {}\n\t\t\tconst root = this.termsById[root_ID]\n\t\t\troot.terms = await this.requestTermRecursive(root)\n\t\t\tthis.orderedVisibleTerms = this.getOrderedVisibleTerms(root)\n\t\t\tif (this.dom.downloadbt)\n\t\t\t\tthis.dom.downloadbt.style('display', this.settings.showDictionary ? 'inline-block' : 'none')\n\n\t\t\tif (this.settings.showDictionary) this.renderSampleDictionary()\n\t\t\tthis.dom.tableDiv.style('display', this.settings.showDictionary ? 'block' : 'none')\n\n\t\t\tawait this.renderPlots(this.state, this.state.samples)\n\t\t\tthis.showVisiblePlots()\n\t\t} finally {\n\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t}\n\t}\n\n\tasync setControls(state) {\n\t\tconst q = state.termdbConfig.queries\n\t\tconst hasPlots = q?.singleSampleMutation || q?.singleSampleGenomeQuantification || q?.NIdata || q?.images\n\t\tif (hasPlots) {\n\t\t\tthis.dom.showPlotsDiv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('id', 'showDictionary')\n\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t.property('checked', true)\n\t\t\t\t.on('change', e => {\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\tconfig: { settings: { sampleView: { showDictionary: e.target.checked } } }\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t\tthis.dom.showPlotsDiv.append('label').text('Show Dictionary').attr('for', 'showDictionary')\n\t\t}\n\n\t\tif (q?.singleSampleMutation) {\n\t\t\tthis.dom.showPlotsDiv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t.property('checked', true)\n\t\t\t\t.attr('id', 'showDisco')\n\t\t\t\t.on('change', e => {\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\tconfig: { settings: { sampleView: { showDisco: e.target.checked } } }\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t\tthis.dom.showPlotsDiv.append('label').text('Show Disco').attr('for', 'showDisco')\n\t\t}\n\n\t\tif (q?.singleSampleGenomeQuantification) {\n\t\t\tfor (const ssgqKey in q.singleSampleGenomeQuantification) {\n\t\t\t\tconst label = ssgqKey.replace(/([a-z](?=[A-Z]))/g, '$1 ')\n\n\t\t\t\tthis.dom.showPlotsDiv\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t\t.property('checked', true)\n\t\t\t\t\t.attr('id', ssgqKey)\n\t\t\t\t\t.on('change', (e: Event) => {\n\t\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\t\tconfig: { settings: { sampleView: { [ssgqKey]: (e.target as HTMLInputElement).checked } } }\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\tthis.dom.showPlotsDiv\n\t\t\t\t\t.append('label')\n\t\t\t\t\t.text('Show ' + label)\n\t\t\t\t\t.attr('for', ssgqKey)\n\t\t\t}\n\t\t}\n\t\tif (q?.images) {\n\t\t\tthis.dom.showPlotsDiv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t.property('checked', true)\n\t\t\t\t.attr('id', 'showImages')\n\t\t\t\t.on('change', e => {\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\tconfig: { settings: { sampleView: { showImages: e.target.checked } } }\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t\tthis.dom.showPlotsDiv.append('label').text('Show Images').attr('for', 'showImages')\n\t\t}\n\n\t\tif (q?.NIdata) {\n\t\t\tthis.dom.showPlotsDiv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t.property('checked', true)\n\t\t\t\t.attr('id', 'showBrainImaging')\n\t\t\t\t.on('change', e => {\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\tconfig: { settings: { sampleView: { showBrainImaging: e.target.checked } } }\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t\tthis.dom.showPlotsDiv.append('label').text('Show brain imaging').attr('for', 'showBrainImaging')\n\t\t}\n\t}\n\n\tgetTermsById(state) {\n\t\tif (!(state.activeCohort in this.termsByCohort)) {\n\t\t\tthis.termsByCohort[state.activeCohort] = {\n\t\t\t\t[root_ID]: {\n\t\t\t\t\tid: root_ID,\n\t\t\t\t\t__tree_isroot: true // must not delete this flag\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn this.termsByCohort[state.activeCohort]\n\t}\n\n\tasync requestTermRecursive(term: any, _ancestry: string[] = [root_ID]) {\n\t\t/* will request child terms for this entire branch recursively\n\n\t\tmust synthesize request string (dataName) for every call\n\t\tand get cached result for the same dataName which has been requested before\n\t\tthis is to support future features\n\t\te.g. to show number of samples for each term that can change based on filters\n\t\twhere the same child terms already loaded must be re-requested with the updated filter parameters to update\n\n\t\tCAUTION\n\t\twill be great if tree_collapse will not trigger this function\n\t\tbut hard to do given that main() has no way of telling what action was dispatched\n\t\tto prevent previously loaded .terms[] for the collapsing term from been wiped out of termsById,\n\t\tneed to add it back TERMS_ADD_BACK\n \n\t\tNOTE: !!!! sortVisibleTerms() assumes that the child terms in the response.lst[]\n\t\t\t\t\tare returned in order. If not, a term.order can be used to sort the child terms array\n\t\t*/\n\t\tconst data = await this.vocabApi.getTermChildren(\n\t\t\tterm,\n\t\t\tthis.state.toSelectCohort ? this.state.cohortValuelst : null,\n\t\t\tthis.state.termfilter.filter\n\t\t)\n\t\tif (data.error) throw data.error\n\t\tif (!data.lst || data.lst.length == 0) {\n\t\t\t// do not throw exception; its children terms may have been filtered out\n\t\t\treturn []\n\t\t}\n\t\tconst terms: any[] = []\n\t\tconst parent_id = _ancestry.slice(-1)[0]\n\t\tfor (const t of data.lst) {\n\t\t\tt.parent_id = parent_id\n\t\t\tconst ancestry = [..._ancestry]\n\t\t\tconst copy = structuredClone(t)\n\t\t\tcopy.ancestry = ancestry\n\t\t\tterms.push(copy)\n\t\t\t// rehydrate expanded terms as needed\n\t\t\t// fills in termsById, for recovering tree\n\n\t\t\tif (!copy.isleaf && this.config.expandedTermIds.includes(copy.id)) {\n\t\t\t\tcopy.terms = await this.requestTermRecursive(copy, [...ancestry, t.id])\n\t\t\t\tif (this.state.samples) await this.fillSampleData(copy.terms)\n\t\t\t} else {\n\t\t\t\tconst t0 = this.termsById[copy.id]\n\t\t\t\tif (this.state.samples) await this.fillSampleData([copy])\n\n\t\t\t\tif (t0 && t0.terms) {\n\t\t\t\t\tcopy.terms = t0.terms\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tthis.termsById[copy.id] = copy\n\t\t}\n\t\treturn terms\n\t}\n\n\tgetOrderedVisibleTerms(_root) {\n\t\tconst visibleTerms = Object.values(this.termsById).filter(this.isVisibleTermId.bind(this))\n\t\tconst orderedVisibleTerms = []\n\t\tthis.sortVisibleTerms(this.termsById[root_ID], visibleTerms, orderedVisibleTerms)\n\t\treturn orderedVisibleTerms\n\t}\n\n\tisVisibleTermId(term) {\n\t\tif (term.parent_id == root_ID) return true\n\t\tif (!term.ancestry) return false\n\t\tfor (const pid of term.ancestry) {\n\t\t\tif (pid === root_ID) continue\n\t\t\tif (!this.config.expandedTermIds.includes(pid)) return false\n\t\t}\n\t\treturn true\n\t}\n\n\tsortVisibleTerms(currParent: any, remainingTerms: any[], currOrder: any[] = []) {\n\t\tconst unorderedTerms: any[] = []\n\t\tconst orderedTerms: any[] = []\n\t\tfor (const term of remainingTerms) {\n\t\t\tif (term.parent_id == currParent.id) {\n\t\t\t\torderedTerms.push(term)\n\t\t\t} else unorderedTerms.push(term)\n\t\t}\n\t\t// remove ordered terms from the remainingTerms array\n\t\tremainingTerms.splice(0, remainingTerms.length, ...unorderedTerms)\n\t\tif (remainingTerms.length) {\n\t\t\tfor (const term of orderedTerms) {\n\t\t\t\tcurrOrder.push(term)\n\t\t\t\tif (!term.isleaf && remainingTerms.length) {\n\t\t\t\t\tthis.sortVisibleTerms(term, remainingTerms, currOrder)\n\t\t\t\t}\n\t\t\t}\n\t\t} else {\n\t\t\tcurrOrder.push(...orderedTerms)\n\t\t}\n\t}\n\n\tasync fillSampleData(terms: any[]) {\n\t\tconst term_ids: string[] = []\n\t\tfor (const term of terms) term_ids.push(term.id)\n\t\tfor (const sample of this.state.samples) {\n\t\t\tconst data = await this.vocabApi.getSingleSampleData({\n\t\t\t\tsampleId: sample.sampleId,\n\t\t\t\tterm_ids,\n\t\t\t\tfilter: this.state.termfilter.filter\n\t\t\t})\n\t\t\tif ('error' in data) throw data.error\n\t\t\tif (!this.sampleDataByTermId[sample.sampleId]) this.sampleDataByTermId[sample.sampleId] = {}\n\t\t\tfor (const id in data) this.sampleDataByTermId[sample.sampleId][id] = data[id]\n\t\t}\n\t}\n\n\tasync downloadData() {\n\t\tthis.dom.messageDiv.style('display', 'block')\n\t\tthis.dom.downloadbt.style('display', 'none')\n\t\tconst filename = `samples.tsv`\n\t\tconst sampleData = {}\n\t\tlet lines = 'Sample'\n\t\tfor (const sample of this.state.samples) {\n\t\t\tsampleData[sample.sampleId] = await this.vocabApi.getSingleSampleData({\n\t\t\t\tsampleId: sample.sampleId,\n\t\t\t\t/** term_ids is required for getSingleSampleData but not\n\t\t\t\t * available in this instance. Pass empty array.*/\n\t\t\t\tterm_ids: [],\n\t\t\t\tfilter: this.state.termfilter.filter || []\n\t\t\t})\n\t\t\tlines += `\\t${sample.sampleName}`\n\t\t}\n\t\tlines += '\\n'\n\n\t\tconst sampleId = this.state.samples[0].sampleId\n\t\tfor (const termId in sampleData[sampleId]) {\n\t\t\tconst term = sampleData[sampleId][termId].term\n\t\t\tlines += `${term.name}`\n\t\t\tfor (const sampleId in sampleData) {\n\t\t\t\tconst data = sampleData[sampleId]\n\t\t\t\tlet value = getTermValue(term, data)\n\t\t\t\tif (value == null) value = 'Missing'\n\t\t\t\tlines += `\\t${value}`\n\t\t\t}\n\t\t\tlines += '\\n'\n\t\t}\n\t\tconst dataStr = 'data:text/tsv;charset=utf-8,' + encodeURIComponent(lines)\n\n\t\tconst link = document.createElement('a')\n\t\tlink.setAttribute('href', dataStr)\n\t\t// If you don't know the name or want to use\n\t\t// the webserver default set name = ''\n\t\tlink.setAttribute('download', filename)\n\t\tdocument.body.appendChild(link)\n\t\tlink.click()\n\t\tlink.remove()\n\t\tthis.dom.messageDiv.style('display', 'none')\n\t\tthis.dom.downloadbt.style('display', 'inline-block')\n\t}\n\n\tmayRequireToken() {\n\t\tif (this.state.hasVerifiedToken) {\n\t\t\tthis.dom.holder.style('display', 'block')\n\t\t\treturn false\n\t\t} else {\n\t\t\tconst e = this.state.tokenVerificationPayload\n\t\t\tconst missingAccess = e?.error == 'Missing access' && this.state.termdbConfig.dataDownloadCatch?.missingAccess\n\t\t\tconst message = missingAccess?.message?.replace('MISSING-ACCESS-LINK', missingAccess?.links[e?.linkKey])\n\t\t\tconst helpLink = this.state.termdbConfig.dataDownloadCatch?.helpLink\n\t\t\tthis.dom.holder\n\t\t\t\t.style('color', '#e44')\n\t\t\t\t.style('padding', '10px')\n\t\t\t\t.html(\n\t\t\t\t\tmessage ||\n\t\t\t\t\t\t(this.state.tokenVerificationMessage || 'Requires sign-in') +\n\t\t\t\t\t\t\t(helpLink ? ` <a href='${helpLink}' target=_blank>Tutorial</a>` : '')\n\t\t\t\t)\n\n\t\t\treturn true\n\t\t}\n\t}\n\n\tshowVisiblePlots() {\n\t\tthis.visiblePlots = false\n\t\tthis.showPlotsFromCategory(this.discoPlots, 'showDisco')\n\t\tfor (const ssgqKey in this.state.singleSampleGenomeQuantification)\n\t\t\tthis.showPlotsFromCategory(this.singleSamplePlots[ssgqKey], ssgqKey)\n\t\tthis.showPlotsFromCategory(this.brainPlots, 'showBrain')\n\t\tthis.showPlotsFromCategory(this.imagePlots, 'showImages')\n\t\tif (this.state.samples.length == 1 && this.visiblePlots)\n\t\t\tthis.dom.tableDiv.style('max-width', '48vw').style('max-height', '40vw').attr('class', 'sjpp_show_scrollbar')\n\t\telse this.dom.tableDiv.style('max-width', '').style('max-height', '').attr('class', '')\n\t}\n\n\tshowPlotsFromCategory(plots, key) {\n\t\tfor (const div of plots) {\n\t\t\tconst visibleSample = this.state.samples.find(s => s.sampleName == div.sample.sampleName)\n\t\t\tconst visiblePlot = this.settings[key] && visibleSample\n\t\t\tif (visiblePlot) this.visiblePlots = true\n\t\t\tdiv.cellDiv.style('display', visiblePlot ? 'table-cell' : 'none')\n\t\t}\n\t}\n\n\tasync renderPlots(state, samples) {\n\t\tconst plotsDiv = this.dom.plotsDiv\n\t\tthis.discoPlots = []\n\t\tthis.singleSamplePlots = {}\n\t\tthis.brainPlots = []\n\t\tthis.imagePlots = []\n\t\t// const q = state.termdbConfig.queries\n\t\tif (state.termdbConfig?.queries?.singleSampleMutation) {\n\t\t\tconst div = plotsDiv.append('div')\n\t\t\tif (state.samples.length == 1) div.style('display', 'inline-block').style('width', '50vw')\n\t\t\tlet someFound = false\n\t\t\tfor (const sample of samples) {\n\t\t\t\tconst cellDiv = div.append('div').style('display', 'inline-block')\n\t\t\t\tthis.discoPlots.push({ sample, cellDiv })\n\t\t\t\tconst header = cellDiv.insert('div')\n\t\t\t\tconst discoPlotImport = await import('./plot.disco.js')\n\t\t\t\tconst found = await discoPlotImport.default(\n\t\t\t\t\tstate.termdbConfig,\n\t\t\t\t\tstate.vocab.dslabel,\n\t\t\t\t\t{ sample_id: sample.sampleName },\n\t\t\t\t\tcellDiv,\n\t\t\t\t\tthis.app.opts.genome,\n\t\t\t\t\t{}, //overrides\n\t\t\t\t\tfalse //showError\n\t\t\t\t)\n\t\t\t\tif (found) {\n\t\t\t\t\tif (state.samples.length > 1)\n\t\t\t\t\t\theader.style('font-weight', 'bold').style('padding-left', '20px').text(sample.sampleName)\n\t\t\t\t\tsomeFound = true\n\t\t\t\t}\n\t\t\t}\n\t\t\tthis.dom.showPlotsDiv.select('input[id=showDisco').style('display', someFound ? 'inline-block' : 'none')\n\t\t\tthis.dom.showPlotsDiv.select('label[for=showDisco').style('display', someFound ? 'inline-block' : 'none')\n\t\t}\n\t\tif (state.termdbConfig.queries?.singleSampleGenomeQuantification) {\n\t\t\tfor (const k in state.termdbConfig.queries.singleSampleGenomeQuantification) {\n\t\t\t\tlet someFound = false\n\t\t\t\tthis.singleSamplePlots[k] = []\n\t\t\t\tconst div = plotsDiv.append('div')\n\t\t\t\tif (state.samples.length == 1) div.style('display', 'inline-block').style('width', '50vw')\n\t\t\t\tfor (const sample of samples) {\n\t\t\t\t\tconst label = (k.match(/[A-Z][a-z]+|[0-9]+/g) || []).join(' ')\n\t\t\t\t\tconst plotDiv = div.insert('div').style('display', 'table-cell').style('padding', '20px')\n\t\t\t\t\tthis.singleSamplePlots[k].push({ sample, cellDiv: plotDiv })\n\t\t\t\t\tif (state.samples.length > 1)\n\t\t\t\t\t\tplotDiv.insert('div').style('font-weight', 'bold').text(`${sample.sampleName} ${label}`)\n\t\t\t\t\tconst ssgqImport = await import('./plot.ssgq.js')\n\t\t\t\t\tconst found = await ssgqImport.plotSingleSampleGenomeQuantification(\n\t\t\t\t\t\tstate.termdbConfig,\n\t\t\t\t\t\tstate.vocab.dslabel,\n\t\t\t\t\t\tk,\n\t\t\t\t\t\t{ sample_id: sample.sampleName },\n\t\t\t\t\t\tplotDiv.insert('div'),\n\t\t\t\t\t\tthis.app.opts.genome,\n\t\t\t\t\t\tnull, //geneName\n\t\t\t\t\t\tfalse //showError\n\t\t\t\t\t)\n\t\t\t\t\tif (found) someFound = true\n\t\t\t\t}\n\t\t\t\tthis.dom.showPlotsDiv.select(`input[id=${k}`).style('display', someFound ? 'inline-block' : 'none')\n\t\t\t\tthis.dom.showPlotsDiv.select(`label[for=${k}`).style('display', someFound ? 'inline-block' : 'none')\n\t\t\t}\n\t\t}\n\t\tif (state.termdbConfig.queries?.NIdata) {\n\t\t\t// show a single brain imaging plot per sample, using the first template as the default\n\t\t\tconst k = Object.keys(state.termdbConfig.queries.NIdata)[0]\n\t\t\t// find which of the samples actually have imaging files, to skip the ones without\n\t\t\tlet available = new Set()\n\t\t\ttry {\n\t\t\t\tavailable = k ? await getBrainImagingSampleSet(state.vocab.genome, state.vocab.dslabel, k) : new Set<string>()\n\t\t\t} catch (e) {\n\t\t\t\t// on error keep the empty set: no brain imaging plots are shown\n\t\t\t\tconsole.error('brainImagingSamples request failed:', e)\n\t\t\t}\n\t\t\tconst samplesWithImaging = samples.filter(s => available.has(s.sampleName))\n\t\t\tif (samplesWithImaging.length) {\n\t\t\t\tconst div = plotsDiv.append('div')\n\t\t\t\tif (state.samples.length == 1) div.style('display', 'inline-block').style('width', '50vw')\n\t\t\t\tfor (const sample of samplesWithImaging) {\n\t\t\t\t\tconst plotDiv = div.insert('div').style('display', 'inline-block')\n\t\t\t\t\tthis.brainPlots.push({ sample, cellDiv: plotDiv })\n\t\t\t\t\tif (state.samples.length > 1)\n\t\t\t\t\t\tplotDiv.insert('div').style('font-weight', 'bold').style('padding-left', '20px').text(sample.sampleName)\n\n\t\t\t\t\tconst brainImagingImport = await import('./plot.brainImaging.js')\n\t\t\t\t\tbrainImagingImport.default(\n\t\t\t\t\t\tstate.termdbConfig,\n\t\t\t\t\t\tstate.vocab.dslabel,\n\t\t\t\t\t\tk,\n\t\t\t\t\t\t{ sample_id: sample.sampleName },\n\t\t\t\t\t\tplotDiv,\n\t\t\t\t\t\tthis.app.opts.genome\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (state.termdbConfig?.queries?.images) {\n\t\t\tconst div = plotsDiv.append('div')\n\t\t\tif (state.samples.length == 1) div.style('display', 'inline-block').style('width', '50vw')\n\t\t\tfor (const sample of samples) {\n\t\t\t\tconst cellDiv = div.append('div').style('display', 'inline-block')\n\t\t\t\tthis.imagePlots.push({ sample, cellDiv })\n\t\t\t\tif (state.samples.length > 1)\n\t\t\t\t\tcellDiv.insert('div').style('font-weight', 'bold').style('padding-left', '20px').text(sample.sampleName)\n\t\t\t\tconst imagePlotImport = await import('./imagePlot.js')\n\t\t\t\timagePlotImport.renderImagePlot(state, cellDiv, sample)\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function getTermValue(term, data) {\n\tlet value = data[term.id]?.value\n\tif (value == null || value == undefined || value == 'undefined') return null\n\tif (term.type == 'date') return getDateStrFromNumber(value)\n\tif (isNumericTerm(term)) {\n\t\tvalue = term.values?.[value]?.label || term.values?.[value]?.key || value\n\t\tif (isNaN(value)) return value\n\t\treturn value % 1 == 0 ? value.toString() : value.toFixed(2).toString()\n\t}\n\n\tif (term.type == 'categorical') return term.values[value]?.label || term.values[value]?.key\n\n\tif (term.type == 'condition') {\n\t\tconst values = value.toString().split(' ')\n\t\tconst [years, statusKey] = values\n\t\tconst status = term.values[statusKey].label || term.values[statusKey].key\n\t\treturn `Max grade: ${status}, Time to event: ${Number(years).toFixed(1)} years`\n\t}\n\tif (term.type == 'survival') {\n\t\tconst values = value.split(' ')\n\t\tconst [years, statusKey] = values\n\t\tconst status = term.values?.[statusKey]?.label || term.values?.[statusKey]?.key || statusKey\n\t\treturn `${status} after ${Number(years).toFixed(1)} years`\n\t}\n\treturn null\n}\n\nexport const sampleViewInit = getCompInit(SampleView)\nexport const componentInit = sampleViewInit\n\nfunction setRenderers(self) {\n\tself.renderSampleDictionary = function () {\n\t\tthis.dom.tableDiv = this.dom.plotsDiv.append('div').style('display', 'inline-block').style('padding', '20px')\n\t\tconst table = this.dom.tableDiv.append('table').style('border-collapse', 'collapse')\n\t\tconst thead = table.append('thead')\n\t\tconst theadrow = thead.append('tr')\n\t\tconst tbody = table.append('tbody')\n\t\t// use an array to support multiple visible samples,\n\t\t// but prototyping with just one sample for now\n\t\tconst visibleSamples: any[] = []\n\t\tfor (const sample of self.state.samples) visibleSamples.push(self.sampleDataByTermId[sample.sampleId])\n\t\t// for the column names, just need the first column name + sample data\n\t\tself.renderTHead(['', ...self.state.samples.map(s => s.sampleName)], theadrow)\n\t\tconst tBodyData = self.orderedVisibleTerms.map((term, _trIndex) => [\n\t\t\t{ term }, // first column, no sample data\n\t\t\t// create data to bind for each sample column\n\t\t\t...visibleSamples.map(sample => ({ term, sample }))\n\t\t])\n\t\tself.renderTBody(tBodyData, tbody)\n\t}\n\n\tself.renderTHead = function (data, theadrow) {\n\t\tconst trs = theadrow.selectAll('th').data(data)\n\t\ttrs.exit().remove()\n\t\ttrs.html(self.getThHtml)\n\t\ttrs.enter().append('th').style('padding', '5px 10px').style('text-align', 'end').html(self.getThHtml)\n\t}\n\n\tself.getThHtml = d => d\n\n\tself.renderTBody = function (data, tbody) {\n\t\tconst trs = tbody.selectAll('tr').data(data)\n\t\ttrs.exit().remove()\n\t\ttrs.each(self.renderTr)\n\t\ttrs.enter().append('tr').each(self.renderTr)\n\t}\n\n\tself.renderTr = function (trData, _trIndex) {\n\t\tconst tds = select(this)\n\t\t\t.selectAll('td')\n\t\t\t.data(trData, (d: any) => d)\n\t\ttds.exit().remove()\n\t\ttds.each(self.renderTd)\n\t\ttds\n\t\t\t.enter()\n\t\t\t.append('td')\n\t\t\t.style('border-bottom', 'solid 1px rgb(245,245,245)')\n\t\t\t.style('text-align', (d, _i) => (_i === 0 ? 'left' : 'center'))\n\t\t\t.style('padding', '2px 10px')\n\t\t\t.each(self.renderTd)\n\t}\n\n\tself.renderTd = function (d, _i) {\n\t\tif (!d.sample) {\n\t\t\t// first column for tree dict variables\n\t\t\tself.renderTerm(select(this))\n\t\t\treturn\n\t\t}\n\t\t//const sampleId = Number(d.sample.sampleId)\n\t\t// const data = d.sample\n\t\tconst term = d.term\n\t\tconst isNumeric = isNumericTerm(term)\n\t\tconst value = getTermValue(d.term, d.sample)\n\t\tconst td = select(this)\n\t\t\t.datum(d)\n\t\t\t.style('text-align', 'end')\n\t\t\t.style('padding', '5px 10px')\n\n\t\t\t// !!! TODO: use getTermValue only for actual data !!!\n\t\t\t.html(d.sample[d.term.id]?.label || value)\n\t\tif (isNumeric)\n\t\t\ttd.append('button')\n\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t.text('Plot')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tconst tw = { id: term.id, q: { mode: 'continuous' } }\n\t\t\t\t\tself.app.dispatch({ type: 'plot_create', config: { chartType: 'violin', term: tw, value } })\n\t\t\t\t})\n\t}\n\n\tself.renderTerm = function (td) {\n\t\t// must get the current data, since each row's data gets replaced\n\t\t// as child terms get inserted between each row\n\t\tconst d = td.datum() // current data\n\t\tif (!td.select('span').size()) {\n\t\t\tconst span = td.append('span')\n\n\t\t\tspan\n\t\t\t\t.append('button')\n\t\t\t\t.style('border-width', 0)\n\t\t\t\t.style('border-radius', '5px')\n\t\t\t\t.style('width', '28px')\n\t\t\t\t.style('height', '28px')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\tspan.append('span').style('margin-left', `3px`).style('cursor', 'pointer')\n\t\t\ttd.on('click', self.toggleTerm)\n\t\t}\n\t\tconst leftIndent = (d.term.ancestry.length - 1) * 24\n\t\tconst span = td.select(':scope>span').style('margin-left', `${leftIndent}px`)\n\t\tspan\n\t\t\t.select('button')\n\t\t\t.style('display', d.term.isleaf ? 'none' : '')\n\t\t\t.html(self.config.expandedTermIds.includes(d.term.id) ? '-' : '+')\n\t\tspan.select('span').html(d.term.name)\n\t\treturn\n\t}\n}\n\nfunction setInteractivity(self) {\n\tself.toggleTerm = function () {\n\t\tconst d = select(this).datum() as any\n\t\tif (d.term.isleaf) return\n\t\tconst expandedTermIds = self.config.expandedTermIds.slice() // create a copy\n\t\tconst i = expandedTermIds.indexOf(d.term.id)\n\t\tif (i == -1) expandedTermIds.push(d.term.id)\n\t\telse expandedTermIds.splice(i, 1)\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.id,\n\t\t\tconfig: { expandedTermIds }\n\t\t})\n\t}\n}\n\nexport async function getPlotConfig(opts: any, app: any) {\n\tconst q = app.getState()?.termdbConfig?.queries\n\tconst settings = {\n\t\tsampleView: {\n\t\t\tshowDictionary: true,\n\t\t\tshowDisco: true,\n\t\t\tshowBrain: true,\n\t\t\tshowImages: true\n\t\t}\n\t}\n\tif (q)\n\t\t//Init show property for each genome quantification plot to true\n\t\tfor (const ssgqKey in q.singleSampleGenomeQuantification) settings.sampleView[ssgqKey] = true\n\tconst config = { activeCohort: 0, sample: null, expandedTermIds: [root_ID], settings, hidePlotFilter: true }\n\treturn copyMerge(config, opts)\n}\n\nexport function searchSampleInput(\n\tholder: any,\n\tsamplesData: any,\n\thasSampleAncestry: any,\n\tcallback: (name: string) => void,\n\tkeyUpCallback?: (str: string) => void\n) {\n\tconst limit = 100\n\tconst allSamples: string[] = []\n\tfor (const sample in samplesData) {\n\t\tconst sample_type = samplesData[sample].sample_type\n\t\tif (\n\t\t\tsample_type == ROOT_SAMPLE_TYPE ||\n\t\t\tsample_type == null ||\n\t\t\t(!hasSampleAncestry && sample_type == DEFAULT_SAMPLE_TYPE)\n\t\t)\n\t\t\t//If the dataset has no ancestors, all the samples should be root'\n\t\t\tallSamples.push(sample)\n\t}\n\tconst isBigDataset = allSamples.length > 10000\n\n\tif (allSamples.length == 0)\n\t\t//Happens if it requires sign in first\n\t\treturn\n\n\t// === Precompute Hierarchy labels once ===\n\tconst { childrenByParent, rootFor } = buildHierarchy(samplesData)\n\tconst sampleName = allSamples[0]\n\tconst input = holder\n\t\t.append('input')\n\t\t.attr('list', 'sampleDatalist')\n\t\t.property('autocomplete', 'off')\n\t\t.attr('placeholder', sampleName)\n\t\t.style('width', '250px')\n\n\tholder.style('opacity', '0.8')\n\tconst datalist = holder.append('datalist').attr('id', 'sampleDatalist')\n\taddOptions(allSamples)\n\tinput.on('keyup', () => {\n\t\tdatalist.selectAll('*').remove()\n\t\tconst str = input.node().value.toLowerCase()\n\t\tif (keyUpCallback) keyUpCallback(str)\n\t\tconst options: string[] = []\n\t\tfor (const sample of allSamples) {\n\t\t\tif (sample.toLowerCase().startsWith(str)) options.push(sample)\n\t\t\tif (options.length == limit && allSamples.length > 10000) break\n\t\t}\n\t\tfor (const sample of allSamples) {\n\t\t\tif (sample.toLowerCase().includes(str) && !options.includes(sample)) options.push(sample)\n\t\t\tif (options.length == limit && allSamples.length > 10000) break\n\t\t}\n\t\tif (options.length > 1 || (options.length == 1 && input.node().value != options[0])) addOptions(options)\n\t})\n\tinput.on('change', () => {\n\t\tconst sampleName = input.node().value\n\t\tcallback(sampleName)\n\t})\n\tfunction addOptions(options) {\n\t\tdatalist\n\t\t\t.selectAll('option')\n\t\t\t.data(options.filter((s, i) => i < limit))\n\t\t\t.enter()\n\t\t\t.append('option')\n\t\t\t.attr('value', d => d)\n\t\t\t.attr(\n\t\t\t\t'label',\n\t\t\t\t(d, i) =>\n\t\t\t\t\tgetLabel(d, childrenByParent, rootFor) +\n\t\t\t\t\t(i + 1 == limit\n\t\t\t\t\t\t? isBigDataset\n\t\t\t\t\t\t\t? ` Showing first ${i + 1} hits`\n\t\t\t\t\t\t\t: ` Showing ${i + 1} of ${options.length} hits`\n\t\t\t\t\t\t: i + 1 === options.length && i > 0\n\t\t\t\t\t\t? `  (Found ${options.length} hits)`\n\t\t\t\t\t\t: '')\n\t\t\t)\n\t}\n\n\tfunction getLabel(sampleName, childrenByParent, rootFor) {\n\t\tconst rootName = rootFor.get(sampleName) || sampleName\n\t\tif (!childrenByParent.has(rootName)) return sampleName\n\n\t\tconst rootChildren = childrenByParent.get(rootName) || []\n\t\tif (rootChildren.length === 0) return sampleName\n\n\t\tconst parts: string[] = []\n\t\tfor (const child of rootChildren) {\n\t\t\tconst chain: string[] = [child]\n\t\t\tlet cur = child\n\t\t\tlet kids = childrenByParent.get(cur) || []\n\t\t\twhile (kids.length > 0) {\n\t\t\t\tchain.push(kids[0])\n\t\t\t\tcur = kids[0]\n\t\t\t\tkids = childrenByParent.get(cur) || []\n\t\t\t}\n\t\t\tparts.push(chain.length > 1 ? chain.join(' > ') : child)\n\t\t}\n\t\treturn parts.join(', ')\n\t}\n\treturn sampleName\n}\n\nfunction buildHierarchy(samplesData: any) {\n\tconst childrenByParent = new Map<string, string[]>()\n\tconst rootFor = new Map<string, string>()\n\n\t// Build children map + find roots\n\tfor (const s of Object.values(samplesData) as any[]) {\n\t\tconst childName: string = s.name\n\t\tconst parentName: string = s.ancestor_name\n\t\tif (parentName) {\n\t\t\tif (!childrenByParent.has(parentName)) {\n\t\t\t\tchildrenByParent.set(parentName, [])\n\t\t\t}\n\t\t\tchildrenByParent.get(parentName)!.push(childName)\n\t\t}\n\n\t\t// find root for this sample\n\t\tlet root: string = childName\n\t\tlet curr: any = s\n\t\twhile (curr?.ancestor_name) {\n\t\t\troot = curr.ancestor_name\n\t\t\tcurr = samplesData[root]\n\t\t}\n\t\trootFor.set(childName, root)\n\t}\n\n\t// Sort every children list once\n\tfor (const list of childrenByParent.values()) {\n\t\tlist.sort((a, b) => {\n\t\t\tconst na = Number(a)\n\t\t\tconst nb = Number(b)\n\t\t\treturn !isNaN(na) && !isNaN(nb) ? na - nb : a.localeCompare(b)\n\t\t})\n\t}\n\treturn { childrenByParent, rootFor }\n}\n\n//Get samples related through parent\nexport function getSamplesRelated(\n\tsamplesData: any,\n\tsampleName: string,\n\tchildrenByParent: Map<string, any> | null = null,\n\trootFor?: Map<string, string>\n) {\n\tif (!samplesData[sampleName]) return []\n\n\t// Fast path: use precomputed data when available\n\tlet rootName\n\tif (rootFor && childrenByParent) {\n\t\trootName = rootFor.get(sampleName)\n\t} else {\n\t\t// Fallback: compute root on the fly if precomputed data is not available (only when called from getState() or elsewhere)\n\t\trootName = sampleName\n\t\tlet current = samplesData[sampleName]\n\t\twhile (current?.ancestor_name) {\n\t\t\trootName = current.ancestor_name\n\t\t\tcurrent = samplesData[rootName]\n\t\t}\n\t}\n\n\tconst root = samplesData[rootName]\n\tif (!root) return []\n\n\t// Use precomputed children map if available, otherwise build it (slow path)\n\tlet kidsMap = childrenByParent\n\tif (!kidsMap) {\n\t\tkidsMap = new Map()\n\t\tfor (const s of Object.values(samplesData) as any[]) {\n\t\t\tif (s.ancestor_name) {\n\t\t\t\tif (!kidsMap.has(s.ancestor_name)) kidsMap.set(s.ancestor_name, [])\n\t\t\t\tkidsMap.get(s.ancestor_name)!.push(s)\n\t\t\t}\n\t\t}\n\n\t\t// Sort children\n\t\tfor (const list of kidsMap.values()) {\n\t\t\tlist.sort((a, b) => {\n\t\t\t\tconst na = Number(a.name)\n\t\t\t\tconst nb = Number(b.name)\n\t\t\t\tif (!isNaN(na) && !isNaN(nb)) return na - nb\n\t\t\t\treturn a.name.localeCompare(b.name)\n\t\t\t})\n\t\t}\n\t}\n\n\t// Collect in pre-order\n\tconst samples: { sampleId: any; sampleName: string }[] = []\n\tconst hasChildren = (kidsMap!.get(rootName!) || []).length > 0\n\n\t// Include root only if it has no descendants or isn't just a grouping node\n\tif (root.sample_type !== ROOT_SAMPLE_TYPE || !hasChildren) {\n\t\tsamples.push({ sampleId: root.id, sampleName: root.name })\n\t}\n\n\tfunction traverse(parentName: string) {\n\t\tconst kids = kidsMap!.get(parentName) || []\n\t\tfor (const kid of kids) {\n\t\t\tsamples.push({ sampleId: kid.id, sampleName: kid.name })\n\t\t\ttraverse(kid.name)\n\t\t}\n\t}\n\n\ttraverse(rootName!)\n\treturn samples\n}\n"],
+  "mappings": 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+  "names": ["sampleName", "sampleId", "span", "childrenByParent", "rootFor"]
+}

package/dist/chunk-LGOTIL62.js

@@ -0,0 +1,54 @@
+import {
+  addGeneSearchbox
+} from "./chunk-J7JDCNLU.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+
+// termdb/handlers/snp.ts
+var SearchHandler = class {
+  init(opts) {
+    this.callback = opts.callback;
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: opts.holder,
+      searchOnly: "snp",
+      allowVariant: true,
+      callback: () => this.selectSnp(geneSearch)
+    });
+  }
+  async selectSnp(geneSearch) {
+    const { chr, ref, alt, fromWhat } = geneSearch;
+    if (!chr || !ref || !alt || !fromWhat) throw "missing chr, ref, alt, or fromWhat of snp";
+    let start, stop;
+    if (!geneSearch.start && !geneSearch.stop) {
+      if (geneSearch.pos) {
+        start = geneSearch.pos - 1;
+        stop = geneSearch.pos;
+      } else {
+        throw "missing coordinate of snp";
+      }
+    } else {
+      start = geneSearch.start;
+      stop = geneSearch.stop;
+    }
+    const term = {
+      id: fromWhat,
+      chr,
+      start,
+      stop,
+      name: fromWhat,
+      ref,
+      alt: typeof alt == "string" ? [alt] : alt,
+      // is string if input to geneSearch was in variant or hgvs format // TODO: update genesearch.ts to parse alternative alleles from any input format into arrays
+      type: "snp"
+    };
+    this.callback(term);
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-LGOTIL62.js.map

package/dist/chunk-LHP7RXET.js

@@ -0,0 +1,243 @@
+import {
+  keyupEnter
+} from "./chunk-J7JDCNLU.js";
+import {
+  get_bin_label,
+  get_bin_range_equation
+} from "./chunk-JYOIO5UY.js";
+import {
+  toStoredUnit,
+  toUserUnit
+} from "./chunk-W5J3LTYS.js";
+
+// termsetting/handlers/NumCustomBinEditor.ts
+var NumCustomBinEditor = class {
+  constructor(editHandler) {
+    this.dom = {};
+    this.editHandler = editHandler;
+    this.opts = editHandler.opts;
+    this.tw = editHandler.tw;
+    this.termsetting = editHandler.termsetting;
+  }
+  /* bin boundaries are stored in the term's own unit but entered and shown in its user-facing one.
+  both are identity functions unless the term declares valueConversion{} */
+  toDisplay(v) {
+    return toUserUnit(v, this.tw.term);
+  }
+  toStored(v) {
+    return toStoredUnit(v, this.tw.term);
+  }
+  async render(div) {
+    this.tw = this.editHandler.tw;
+    const isRemounting = !!this.dom.inputsDiv && this.editHandler.dom.binsDiv?.node().contains(this.dom.inputsDiv.node());
+    if (!isRemounting) this.q = this.getDefaultQ();
+    await this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+    if (isRemounting) return;
+    if (this.dom.inputsDiv) {
+      this.dom.inputsDiv.remove();
+      delete this.dom.inputsDiv;
+    }
+    this.dom.inputsDiv = div.append("div").style("display", "flex").style("width", "100%");
+    this.renderCustomBinInputs();
+  }
+  getBoundaryOpts() {
+    return {
+      values: this.q.lst.slice(1).map((bin) => ({ x: this.toDisplay(bin.startunbounded ? bin.stop : bin.start), isDraggable: true })),
+      // the dragged value arrives in display units, matching what the textarea holds
+      callback: (d, value) => {
+        const boundaryValues = this.q.lst.slice(1).map((d2) => "start" in d2 ? this.toDisplay(d2.start) : "");
+        boundaryValues[d.index] = value;
+        this.dom.customBinBoundaryInput.property("value", boundaryValues.join("\n"));
+        this.handleInputChange("drag");
+        return 0;
+      }
+    };
+  }
+  getDefaultQ() {
+    if (this.tw.q.mode == "discrete" && this.tw.q.type == "custom-bin") {
+      const copy = JSON.parse(JSON.stringify(this.tw.q));
+      copy.lst.forEach((bin) => {
+        if (!bin.label) bin.label = get_bin_label(bin, this.tw.q, this.tw.term.valueConversion);
+        bin.range = get_bin_range_equation(bin, this.tw.q, this.tw.term.valueConversion);
+      });
+      return copy;
+    }
+    const { min, max } = this.editHandler.handler.density_data;
+    const defaultCustomBoundary = (
+      /* when no sample is annotated by this term,
+      minvalue and maxvalue are both null
+      setting defaultCustomBoundary to arbitrary "0" will allow existing UI to work
+      but remains to be evaluated if is really okay to use 0
+      */
+      !Number.isFinite(min) || !Number.isFinite(max) ? 0 : (
+        // minvalue and maxvalue is valid number
+        max != min ? min + (max - min) / 2 : max
+      )
+    );
+    const firstBin = {
+      startunbounded: true,
+      startinclusive: false,
+      stopinclusive: false,
+      stop: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
+    };
+    const lastBin = {
+      stopunbounded: true,
+      startinclusive: true,
+      stopinclusive: false,
+      start: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
+    };
+    return {
+      mode: "discrete",
+      type: "custom-bin",
+      lst: [
+        // Type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' is not assignable to type 'StartUnboundedBin | FullyBoundedBin'.
+        // Property 'start' is missing in type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' but required in type 'FullyBoundedBin'.
+        {
+          ...firstBin,
+          label: get_bin_label(firstBin, this.tw.q, this.tw.term.valueConversion),
+          range: get_bin_range_equation(firstBin, this.tw.q, this.tw.term.valueConversion)
+        },
+        {
+          ...lastBin,
+          label: get_bin_label(lastBin, this.tw.q, this.tw.term.valueConversion),
+          range: get_bin_range_equation(lastBin, this.tw.q, this.tw.term.valueConversion)
+        }
+        //satisfies StopUnboundedBin
+      ]
+    };
+  }
+  /******************* Functions for Numerical Custom size bins *******************/
+  renderCustomBinInputs() {
+    const q = this.q;
+    const boundaryDiv = this.dom.inputsDiv.append("div").style("margin-right", "20px");
+    this.dom.rangeAndLabelDiv = this.dom.inputsDiv.append("div");
+    boundaryDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Bin boundaries");
+    this.dom.customBinBoundaryInput = boundaryDiv.append("textarea").style("width", "100px").style("height", "70px").text(
+      q.lst.slice(1).map((d) => "start" in d ? this.toDisplay(d.start) : "").join("\n")
+    ).on("change", () => this.handleInputChange()).on("keyup", async (event) => {
+      if (!keyupEnter(event) && event.key != 8 && event.key != "Enter") return;
+      if (!this.dom.inputsDiv.selectAll("input").node().value) return;
+      this.handleInputChange();
+    });
+    boundaryDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
+    this.renderBoundaryInputDivs();
+  }
+  renderBoundaryInputDivs() {
+    const data = this.q.lst;
+    const holder = this.dom.rangeAndLabelDiv;
+    holder.selectAll("*").remove();
+    const grid = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center");
+    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
+    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Bin label");
+    for (const d of data) {
+      grid.append("div").attr("name", "range").html(d.range);
+      grid.append("div").append("input").attr("type", "text").style("margin", "2px 0px").property("value", d.label).on("change", function() {
+        d.label = this.value;
+      });
+    }
+    this.dom.customBinRanges = this.dom.inputsDiv.selectAll('div[name="range"]').data(data);
+    this.dom.customBinLabelInput = this.dom.inputsDiv.selectAll("input").data(data);
+  }
+  handleInputChange(eventType = "") {
+    const self = this.tw;
+    const inputs = this.dom.inputsDiv.selectAll("input");
+    inputs.property("value", "");
+    const data = this.processCustomBinInputs();
+    if (data == void 0) {
+      return;
+    }
+    if (self.q.hiddenValues) this.tw.q.hiddenValues = self.q.hiddenValues;
+    if (this.binsChanged(data, this.q.lst)) {
+      this.q.lst = data;
+    }
+    this.renderBoundaryInputDivs();
+    if (eventType != "drag") this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+  binsChanged(data, qlst) {
+    if (data.length != qlst.length) return true;
+    if (Object.keys(data[0]).length !== Object.keys(qlst[0]).length) return true;
+    for (const [i, bin] of qlst.entries()) {
+      for (const k of Object.keys(bin)) {
+        if (bin[k] && bin[k] !== data[i][k]) {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+  processCustomBinInputs() {
+    const self = this.termsetting;
+    const startinclusive = this.editHandler.boundaryInclusion == "startinclusive";
+    const stopinclusive = this.editHandler.boundaryInclusion == "stopinclusive";
+    const inputs = this.dom.inputsDiv.node().querySelectorAll("input");
+    const inputData = this.dom.customBinBoundaryInput.property("value").split("\n").filter((d) => d != "" && !isNaN(d));
+    const trackBins = new Set(inputData);
+    if (!trackBins.size) return this.tw.q.lst;
+    const sortedBins = Array.from(trackBins).map((v) => this.toStored(Number(v))).sort((a, b) => a - b);
+    const data = [
+      // first bin: StartUnbounded type
+      {
+        startunbounded: true,
+        stop: sortedBins[0],
+        startinclusive: false,
+        stopinclusive,
+        label: inputs[0].value
+      }
+    ];
+    if (!data[0].label) data[0].label = get_bin_label(data[0], self.q, self.term.valueConversion);
+    if (!data[0].range) data[0].range = get_bin_range_equation(data[0], self.q, self.term.valueConversion);
+    for (const [i, d] of sortedBins.entries()) {
+      let bin;
+      const label = inputs[i + 1]?.value || "";
+      if (i !== trackBins.size - 1) {
+        bin = {
+          start: +d,
+          startinclusive,
+          stopinclusive,
+          stop: sortedBins[i + 1],
+          label
+          //range: ''
+        };
+      } else {
+        bin = {
+          start: +d,
+          startinclusive,
+          stopinclusive: false,
+          stopunbounded: true,
+          label
+          //range: ''
+        };
+      }
+      if (bin.label === "" || bin.label === void 0) bin.label = get_bin_label(bin, self.q, self.term.valueConversion);
+      if (bin.range === "" || bin.range === void 0)
+        bin.range = get_bin_range_equation(bin, self.q, self.term.valueConversion);
+      data.push(bin);
+    }
+    return data;
+  }
+  getEditedQ(destroyDom = true) {
+    const lst = this.processCustomBinInputs();
+    if (destroyDom) {
+      for (const name of Object.keys(this.dom)) {
+        this.dom[name].remove();
+        delete this.dom[name];
+      }
+    }
+    return {
+      mode: "discrete",
+      type: "custom-bin",
+      lst
+    };
+  }
+  undoEdits() {
+    this.q = this.getDefaultQ();
+    this.dom.inputsDiv.selectAll("*").remove();
+    this.renderCustomBinInputs();
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+};
+
+export {
+  NumCustomBinEditor
+};
+//# sourceMappingURL=chunk-LHP7RXET.js.map

package/dist/chunk-LK2GHBUH.js

@@ -0,0 +1,123 @@
+import {
+  pickCollectionFraction,
+  renderTable
+} from "./chunk-J7JDCNLU.js";
+
+// termdb/handlers/termCollection.ts
+var SearchHandler = class {
+  async init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    opts.holder.style("display", "");
+    const termlst = opts.details.termlst ?? [];
+    const memberType = opts.details.memberType || opts.details.type;
+    if (opts.termCollectionSelectionMode === "fraction" && memberType === "numeric") {
+      pickCollectionFraction({
+        holder: opts.holder,
+        term: makeTerm(opts.details, termlst, opts.usecase),
+        callback: (tw) => opts.callback(tw)
+      });
+      return;
+    }
+    const tableDiv = opts.holder.append("div");
+    renderTable({
+      columns: [{ label: "VARIABLES" }],
+      rows: termlst.map((t) => {
+        return [{ value: t.name }];
+      }),
+      div: tableDiv,
+      maxWidth: "30vw",
+      maxHeight: "40vh",
+      // the button is disabled while the selection cannot be submitted
+      noButtonCallback: () => updateSelectBtn(),
+      striped: false,
+      showHeader: true,
+      //false,
+      selectAll: true,
+      columnButtons: void 0,
+      //Leave until table.js is typed
+      buttons: void 0
+    });
+    let categoryTable;
+    let ckSource = [];
+    if (opts.details.categoryKeys) {
+      ckSource = opts.details.categoryKeys;
+      const categoryDiv = opts.holder.append("div").style("margin-top", "15px");
+      const values = opts.details.termlst[0].values || {};
+      categoryTable = categoryDiv.append("div");
+      renderTable({
+        columns: [{ label: "CATEGORIES" }],
+        rows: ckSource.map((ck) => {
+          return [{ value: values[ck.key]?.label ?? ck.key, checked: ck.shown }];
+        }),
+        div: categoryTable,
+        maxWidth: "30vw",
+        maxHeight: "40vh",
+        noButtonCallback: () => updateSelectBtn(),
+        striped: false,
+        showHeader: true,
+        //false,
+        selectAll: true,
+        columnButtons: void 0,
+        //Leave until table.js is typed
+        buttons: void 0
+      });
+    }
+    function getRowChecks(div) {
+      const trs = div.select("table").select("tbody").node().querySelectorAll("tr");
+      return [...trs].map((tr) => tr.querySelectorAll("td")[1]?.querySelector("input")?.checked === true);
+    }
+    function getSelectedTermlst() {
+      const checked = getRowChecks(tableDiv);
+      return termlst.filter((term, i) => checked[i]);
+    }
+    function getCategoryKeys() {
+      if (!categoryTable) return void 0;
+      const checked = getRowChecks(categoryTable);
+      return ckSource.map((ck, i) => ({ key: ck.key, shown: checked[i] }));
+    }
+    function getSelectionError() {
+      if (getSelectedTermlst().length < 2) return "Select at least two variables.";
+      if (getCategoryKeys()?.every((ck) => !ck.shown)) return "Select at least one category.";
+      return void 0;
+    }
+    function updateSelectBtn() {
+      if (!selectBtn) return;
+      const error = getSelectionError();
+      selectBtn.property("disabled", Boolean(error)).attr("title", error || null);
+    }
+    const selectBtn = opts.holder.append("div").style("float", "right").style("padding", "6px 20px").append("button").attr("data-testid", "sjpp-term-collection-select").text("Select").on("click", () => {
+      opts.callback({
+        // makeTerm() extracts propsByTermId (color, etc) for the selected terms
+        ...makeTerm(opts.details, getSelectedTermlst(), opts.usecase),
+        categoryKeys: getCategoryKeys()
+      });
+    });
+    updateSelectBtn();
+  }
+};
+function makeTerm(details, termlst, usecase) {
+  const propsByTermId = {};
+  if (details.propsByTermId) {
+    for (const term of termlst) {
+      if (details.propsByTermId[term.id]) propsByTermId[term.id] = details.propsByTermId[term.id];
+    }
+  }
+  return {
+    type: "termCollection",
+    termIds: termlst.map((term) => term.id),
+    termlst,
+    name: details.name,
+    valueTransform: details.valueTransformByPlots?.[usecase?.target],
+    // memberType = ds.cohort.termdb.termCollections[].type for client code
+    memberType: details.memberType || details.type,
+    categoryKeys: details.categoryKeys,
+    isleaf: true,
+    propsByTermId
+  };
+}
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-LK2GHBUH.js.map