@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/chunk-DMOTISFN.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/sampleView.js"],
+  "sourcesContent": ["import { getCompInit, copyMerge } from '#rx'\nimport { PlotBase } from '#plots/PlotBase.js'\nimport { select } from 'd3-selection'\nimport { controlsInit } from './controls'\nimport { getNormalRoot } from '#filter'\nimport { dofetch3 } from '#common/dofetch'\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 {\n\tstatic type = 'sampleView'\n\n\tconstructor(opts, api) {\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\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\tconst 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, i) => 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', e => {\n\t\t\t\tconst options = select.node().options\n\t\t\t\tconst samples = []\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)\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)\n\t\t\tthis.sample = config.sample || { sampleId: this.samplesData[sampleName].id, 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', e => {\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)\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,\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 =\n\t\t\tq?.singleSampleMutation ||\n\t\t\tq?.singleSampleGenomeQuantification ||\n\t\t\tq?.NIdata ||\n\t\t\tq?.images ||\n\t\t\tq?.DZImages ||\n\t\t\tq?.WSImages\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?.DZImages) {\n\t\t\tthis.dom.showPlotsDiv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('id', 'showDzi')\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: { showDzi: e.target.checked } } }\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t\tthis.dom.showPlotsDiv.append('label').attr('for', 'showDzi').text('Show DZI images')\n\t\t}\n\n\t\tif (q?.WSImages) {\n\t\t\tthis.dom.showPlotsDiv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('id', 'showWsi')\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: { showWsi: e.target.checked } } }\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t\tthis.dom.showPlotsDiv.append('label').attr('for', 'showWsi').text('Show WSI images')\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 => {\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.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, _ancestry = [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 = []\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, remainingTerms, currOrder = []) {\n\t\tconst unorderedTerms = []\n\t\tconst orderedTerms = []\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) {\n\t\tconst term_ids = []\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\tthis.showPlotsFromCategory(this.dziPlots, 'showDzi')\n\t\tthis.showPlotsFromCategory(this.wsiPlots, 'showWsi')\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\tthis.dziPlots = []\n\t\tthis.wsiPlots = []\n\t\tconst q = state.termdbConfig.queries\n\t\tif (state.termdbConfig.queries?.DZImages) {\n\t\t\tlet 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 data = await dofetch3('sampledzimages', {\n\t\t\t\t\tbody: {\n\t\t\t\t\t\tgenome: this.app.opts.genome.name,\n\t\t\t\t\t\tdslabel: state.vocab.dslabel,\n\t\t\t\t\t\tsample_id: sample.sampleName\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\tif (data.sampleDZImages?.length > 0) {\n\t\t\t\t\tconst cellDiv = div.append('div').style('display', 'inline-block')\n\t\t\t\t\tthis.dziPlots.push({ sample, cellDiv })\n\t\t\t\t\tconst dziviewer = await import('./dziviewer/plot.dzi.js')\n\t\t\t\t\tdziviewer.default(state.vocab.dslabel, cellDiv, this.app.opts.genome, sample.sampleName, data.sampleDZImages)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (state.termdbConfig.queries?.WSImages) {\n\t\t\tlet 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.wsiPlots.push({ sample, cellDiv })\n\t\t\t\tconst wsiViewer = await import('./wsiviewer/plot.wsi.js')\n\t\t\t\twsiViewer.default(state.vocab.dslabel, cellDiv, this.app.opts.genome, sample.sampleName)\n\t\t\t}\n\t\t}\n\n\t\tif (state.termdbConfig?.queries?.singleSampleMutation) {\n\t\t\tlet 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\tlet 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\tlet div = plotsDiv.append('div')\n\t\t\tif (state.samples.length == 1) div.style('display', 'inline-block')\n\n\t\t\tfor (const k in state.termdbConfig.queries?.NIdata) {\n\t\t\t\tlet 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 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\tlet 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\tlet [years, status] = values\n\t\tstatus = term.values[status].label || term.values[status].key\n\t\treturn `Max grade: ${status}, Time to event: ${Number(years).toFixed(1)} years`\n\t}\n\tif (term.type == 'survival') {\n\t\tconst values = value.split(' ')\n\t\tlet [years, status] = values\n\t\tstatus = term.values?.[status]?.label || term.values?.[status]?.key || status\n\t\treturn `${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 = []\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 => 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\tconst 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', e => {\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\tconst btn = span\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) ? 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+  "names": ["sampleName", "sampleId", "div", "span", "childrenByParent", "rootFor"]
+}

package/dist/chunk-E2GHT7RH.js

@@ -0,0 +1,39 @@
+import {
+  isNumeric
+} from "./chunk-75T7ESEO.js";
+
+// common/urlmap.js
+function urlmap_default(search = "", log = console.warn) {
+  const location = search ? { search } : window.location;
+  const urlp = /* @__PURE__ */ new Map();
+  for (const s of location.search.substr(1).split("&")) {
+    if (!s) continue;
+    const l = s.split("=");
+    if (l.length == 2 && l[0] != "" && l[1] != "") {
+      let value = decodeURIComponent(l[1]);
+      if (
+        // assume JSON encoding when the string is enclosed by matching characters below
+        value.startsWith('"') && value.endsWith('"') || value.startsWith("{") && value.endsWith("}") || value.startsWith("[") && value.endsWith("]")
+      ) {
+        try {
+          value = JSON.parse(value);
+        } catch (e) {
+          log(e);
+        }
+      } else if (isNumeric(value)) {
+        value = Number(value);
+      }
+      urlp.set(l[0].toLowerCase(), value);
+    } else if (l.length > 2) {
+      log(`unexpected '=' character in the URL parameter value for '${l[0]}'`);
+    } else {
+      log(`Invalid url parameter: '${s}'`);
+    }
+  }
+  return urlp;
+}
+
+export {
+  urlmap_default
+};
+//# sourceMappingURL=chunk-E2GHT7RH.js.map

package/dist/chunk-E2JRANYL.js

@@ -0,0 +1,299 @@
+import {
+  first_genetrack_tolist,
+  gmmode,
+  sayerror
+} from "./chunk-73PFJ2VF.js";
+import {
+  dofetch3
+} from "./chunk-X4QQRHFB.js";
+import {
+  codon_stop,
+  nt2aa,
+  proteinDomainColorScale
+} from "./chunk-GEQUQ3GG.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// common/snp.js
+async function string2snp(genome, str) {
+  const data = await dofetch3("snp", {
+    method: "POST",
+    body: JSON.stringify({ byName: true, genome: genome.name, lst: [str] })
+  });
+  if (data.error) throw data.error;
+  if (!data.results || data.results.length == 0) throw str + ": not a SNP";
+  for (const i of data.results) {
+    const chr = genome.chrlookup[i.chrom.toUpperCase()];
+    if (chr && chr.major) {
+      return {
+        chr: i.chrom,
+        start: i.chromStart,
+        stop: i.chromEnd
+      };
+    }
+  }
+  const r = data.results[0];
+  return {
+    chr: r.chrom,
+    start: r.chromStart,
+    stop: r.chromEnd
+  };
+}
+
+// src/block.init.js
+async function block_init_default(arg) {
+  if (!arg.holder) throw "No holder for block.init";
+  if (!arg.genome) throw "no genome";
+  if (arg.holder instanceof Element) arg.holder = select_default(arg.holder);
+  if (!arg.tklst) arg.tklst = [];
+  if (arg.query) {
+    await step1_findgm(arg);
+    return;
+  }
+  if (arg.model && arg.allmodels) {
+    await step2_getseq(arg);
+    return;
+  }
+}
+async function step1_findgm(arg) {
+  const wait = arg.holder.append("p").style("font-size", "2em").style("color", "#858585").text("Searching for " + arg.query + " ...");
+  const data = await dofetch3("genelookup", {
+    body: { deep: 1, input: arg.query, genome: arg.genome.name }
+  });
+  if (!data) throw "querying genes: server error";
+  if (data.error) throw "error querying genes: " + data.error;
+  if (!data.gmlst || data.gmlst.length == 0) {
+    if (arg.genome.hasSNP) {
+      try {
+        const r = await string2snp(arg.genome, arg.query);
+        wait.remove();
+        const par = {
+          genome: arg.genome,
+          holder: arg.holder,
+          chr: r.chr,
+          start: Math.max(0, r.start - 300),
+          stop: r.start + 300,
+          nobox: true,
+          tklst: arg.tklst,
+          debugmode: arg.debugmode
+        };
+        first_genetrack_tolist(arg.genome, par.tklst);
+        const b = await import("./block-J3A3RIGS.js");
+        const block = new b.Block(par);
+        block.addhlregion(r.chr, r.start, r.stop - 1);
+      } catch (e) {
+        wait.text("Not a gene or SNP: " + arg.query);
+      }
+    } else {
+      wait.text("No match to gene: " + arg.query);
+    }
+    return;
+  }
+  wait.remove();
+  arg.allmodels = data.gmlst;
+  for (const m of arg.allmodels) {
+    if (m.isoform.toUpperCase() == (data.found_isoform ? data.found_isoform.toUpperCase() : arg.query.toUpperCase())) {
+      arg.model = m;
+      await step2_getseq(arg);
+      return;
+    }
+  }
+  const defaultisoforms = [];
+  for (const m of arg.allmodels) {
+    if (!m.isoform) throw "isoform missing from one gene model: " + JSON.stringify(m);
+    const n = m.isoform.toUpperCase();
+    if (arg.genome.isoformcache.has(n)) {
+      let nothas = true;
+      for (const m2 of arg.genome.isoformcache.get(n)) {
+        if (m2.chr == m.chr && m2.start == m.start && m2.stop == m.stop && m2.strand == m.strand) {
+          nothas = false;
+          break;
+        }
+      }
+      if (nothas) {
+        arg.genome.isoformcache.get(n).push(m);
+      }
+    } else {
+      arg.genome.isoformcache.set(n, [m]);
+    }
+    if (m.isoform.toUpperCase() == arg.query.toUpperCase()) {
+      defaultisoforms.push(m);
+      break;
+    }
+    if (m.isdefault) {
+      defaultisoforms.push(m);
+    }
+  }
+  if (defaultisoforms.length == 1) {
+    arg.model = defaultisoforms[0];
+  } else if (defaultisoforms.length > 1) {
+    for (const m of defaultisoforms) {
+      if (m.chr == "chrY") {
+        continue;
+      }
+      const chr = arg.genome.chrlookup[m.chr.toUpperCase()];
+      if (!chr) {
+        continue;
+      }
+      if (!chr.major) {
+        continue;
+      }
+      arg.model = m;
+      break;
+    }
+    if (!arg.model) {
+      arg.model = defaultisoforms[0];
+    }
+  }
+  if (!arg.model) {
+    arg.model = arg.allmodels[0];
+  }
+  await step2_getseq(arg);
+}
+async function step2_getseq(arg) {
+  if (arg.model.genomicseq) {
+    checker();
+    step2_getpdomain(arg);
+    return;
+  }
+  const par = {
+    genome: arg.genome.name,
+    coord: arg.model.chr + ":" + (arg.model.start + 1) + "-" + arg.model.stop
+  };
+  const data = await dofetch3("ntseq", { method: "POST", body: JSON.stringify(par) });
+  if (!data) throw "getting sequence: server error";
+  if (data.error) throw "getting sequence: " + data.error;
+  if (!data.seq) throw "no nt seq???";
+  arg.model.genomicseq = data.seq.toUpperCase();
+  arg.model.aaseq = nt2aa(arg.model);
+  checker();
+  await step2_getpdomain(arg);
+  function checker() {
+    if (arg.model.aaseq) {
+      const stop = arg.model.aaseq.indexOf(codon_stop);
+      const cdslen = arg.model.cdslen - (arg.model.startCodonFrame ? 3 - arg.model.startCodonFrame : 0);
+      if (stop != -1 && stop < cdslen / 3 - 1) {
+        sayerror(arg.holder, "Translating " + arg.model.isoform + " ends at " + stop + " AA, expecting " + cdslen / 3);
+      }
+    }
+  }
+}
+async function step2_getpdomain(arg) {
+  const isoform2gm = /* @__PURE__ */ new Map();
+  for (const m of arg.allmodels) {
+    if (!m.pdomains) {
+      m.pdomains = [];
+      m.domain_hidden = {};
+      if (!isoform2gm.has(m.isoform)) isoform2gm.set(m.isoform, []);
+      isoform2gm.get(m.isoform).push(m);
+    }
+  }
+  if (isoform2gm.size == 0) {
+    await step3(arg);
+    return;
+  }
+  const data = await dofetch3("pdomain", {
+    method: "POST",
+    body: JSON.stringify({ genome: arg.genome.name, isoforms: [...isoform2gm.keys()] })
+  });
+  if (data.error) throw "error getting protein domain: " + data.error;
+  if (!Array.isArray(data.lst)) throw ".lst[] not array";
+  for (const a of data.lst) {
+    for (const m of isoform2gm.get(a.name)) {
+      m.pdomains = a.pdomains;
+      if (arg.hidePdomain) {
+        for (const i of a.pdomains) {
+          m.domain_hidden[i.name + i.description] = 1;
+        }
+      }
+    }
+  }
+  if (arg.geneDomains) {
+    if (typeof arg.geneDomains != "object") throw "geneDomains not object";
+    for (const isoform in arg.geneDomains) {
+      const lst = isoform2gm.get(isoform);
+      if (!lst) throw `unknown isoform ${isoform} from geneDomains{}`;
+      for (const g of lst) {
+        if (!g.pdomains) g.pdomains = [];
+        if (!Array.isArray(arg.geneDomains[isoform])) throw `geneDomains[${isoform}] not array`;
+        for (const b of arg.geneDomains[isoform]) {
+          if (typeof b != "object") throw "element from geneDomains[] not object";
+          if (!Number.isInteger(b.start)) throw "start not integer from geneDomains[]";
+          if (!Number.isInteger(b.stop)) throw "stop not integer from geneDomains[]";
+          if (b.start > b.stop) throw "start>stop from geneDomains[]";
+          if (!b.name) b.name = "Custom domain";
+          if (!g.pdomains.find((a) => a.start == b.start && a.stop == b.stop && a.name == b.name)) g.pdomains.push(b);
+        }
+      }
+    }
+  }
+  const s = proteinDomainColorScale();
+  for (const lst of isoform2gm.values()) {
+    for (const g of lst) {
+      for (const d of g.pdomains || []) {
+        if (!d.color) d.color = s(d.name + d.description);
+      }
+    }
+  }
+  await step3(arg);
+}
+async function step3(arg) {
+  let mode = arg.gmmode;
+  if (!mode) {
+    if (arg.model.cdslen) {
+      mode = gmmode.protein;
+    } else {
+      mode = gmmode.exononly;
+    }
+  }
+  if (arg.dataset) {
+    if (!Array.isArray(arg.dataset)) throw "dataset is not array";
+    for (const dsname of arg.dataset) {
+      if (arg.genome.datasets[dsname] && !arg.genome.datasets[dsname].legacyDsIsUninitiated) continue;
+      const d = await dofetch3(`getDataset?genome=${arg.genome.name}&dsname=${dsname}`);
+      if (d.error) throw `invalid name from dataset[]: ${d.error}`;
+      if (!d.ds) throw ".ds missing";
+      const ds = arg.genome.datasets[d.ds.label];
+      Object.assign(ds, d.ds);
+      const _ = await import("./legacyDataset-4BXYHQTS.js");
+      _.validate_oldds(ds);
+      delete ds.legacyDsIsUninitiated;
+    }
+  }
+  const b = await import("./block-J3A3RIGS.js");
+  arg.__blockInstance = new b.Block({
+    genome: arg.genome,
+    holder: arg.holder,
+    nobox: true,
+    usegm: arg.model,
+    gmstackheight: 37,
+    allgm: arg.allmodels,
+    datasetlst: arg.dataset,
+    legacyDsFilter: arg.legacyDsFilter,
+    mset: arg.mset,
+    hlaachange: arg.hlaachange,
+    hlvariants: arg.hlvariants,
+    hlregions: arg.hlregions,
+    aarange: arg.aarange,
+    gmmode: mode,
+    hidedatasetexpression: arg.hidedatasetexpression,
+    hidegenecontrol: arg.hidegenecontrol,
+    hidegenelegend: arg.hidegenelegend,
+    variantPageCall_snv: arg.variantPageCall_snv,
+    datasetqueries: arg.datasetqueries,
+    samplecart: arg.samplecart,
+    debugmode: arg.debugmode,
+    tklst: arg.tklst,
+    mclassOverride: arg.mclassOverride,
+    hide_dsHandles: arg.hide_dsHandles,
+    onloadalltk_always: arg.onloadalltk_always,
+    onAddRemoveTk: arg.onAddRemoveTk
+  });
+}
+
+export {
+  string2snp,
+  block_init_default
+};
+//# sourceMappingURL=chunk-E2JRANYL.js.map