invalid sample names from big files found on mds3 init is reported to…

client/mass/about.ts

@@ -181,6 +181,20 @@ export class MassAbout {
 										lst: []
 									}
 								})
+							if (clearOnChange.groups) {
+								for (const group of state.groups) {
+									subactions.push({
+										type: 'delete_group',
+										name: group.name
+									})
+								}
+								for (const term of state.customTerms) {
+									subactions.push({
+										type: 'delete_customTerm',
+										name: term.name
+									})
+								}
+							}
 							subactions.push({ type: 'cohort_set', activeCohort: i })
 							app.dispatch({
 								type: 'app_refresh',
@@ -227,6 +241,7 @@ export class MassAbout {
 		if (!result.cfeatures.length) return
 		for (const feature of result.features) rows.push([{ value: feature.name }])
 		for (const cohort of result.cohorts) {
+			if (cohort.subcohorts?.length) continue
 			columns.push({ label: cohort.name })
 			for (const [i, feature] of result.features.entries()) {
 				const cf = result.cfeatures.find(cf => cf.idfeature === feature.idfeature && cf.cohort === cohort.cohort)

client/mass/store.js

@@ -97,6 +97,7 @@ class TdbStore {
 				let plot
 				try {
 					const _ = await import(`../plots/${savedPlot.chartType}.js`)
+					// this.state{} is already fully set with initial state, thus okay to pass to getPlotConfig()
 					plot = await _.getPlotConfig(savedPlot, this.app, this.state.activeCohort)
 				} catch (e) {
 					this.app.printError(e)

client/plots/genomeBrowser.controls.js

@@ -1,8 +1,6 @@
 import { getCompInit } from '#rx'
-import { Menu } from '#dom/menu'
-import { make_one_checkbox } from '#dom/checkbox'
+import { Menu, Tabs, make_one_checkbox } from '#dom'
 import { filterInit, getNormalRoot, getFilterItemByTag } from '#filter/filter'
-import { Tabs } from '../dom/toggleButtons'
 import { appInit } from '#termdb/app'
 
 /*
@@ -13,7 +11,6 @@ main
 		render1group
 			makePrompt2addNewGroup
 				launchMenu_createGroup
-					mayGetActiveCohortIdx
 			render1group_info
 			render1group_population
 			render1group_filter
@@ -51,6 +48,7 @@ class GbControls {
 		//delete this._partialData
 
 		return {
+			activeCohort: appState.activeCohort,
 			config,
 			termdbConfig: appState.termdbConfig,
 			filter: getNormalRoot(appState.termfilter.filter)
@@ -395,7 +393,6 @@ async function render1group_filter(self, groupIdx, group, div) {
 	when initiating the filter ui, must join group's filter with mass global filter and submit the joined filter to main()
 	this allows tvs edit to show correct number of samples
 	*/
-
 	let span
 	if (!self.filterUI[groupIdx]) {
 		self.filterUI[groupIdx] = await filterInit({
@@ -580,7 +577,10 @@ function launchMenu_createGroup(self, groupIdx, div) {
 			const arg = {
 				holder: tab.contentHolder,
 				vocabApi: self.app.vocabApi,
-				state: { termfilter: { filter: self.state.filter } },
+				state: {
+					activeCohort: self.state.activeCohort,
+					termfilter: { filter: self.state.filter }
+				},
 				tree: {
 					click_term2select_tvs: tvs => {
 						/////////////////////////////////
@@ -605,8 +605,6 @@ function launchMenu_createGroup(self, groupIdx, div) {
 					}
 				}
 			}
-			const activeCohortIdx = mayGetActiveCohortIdx(self)
-			if (Number.isInteger(activeCohortIdx)) arg.state.activeCohort = activeCohortIdx
 			appInit(arg)
 			continue
 		}
@@ -637,20 +635,3 @@ export function mayUpdateGroupTestMethodsIdx(self, d) {
 		// otherwise, do not change existing method idx
 	}
 }
-
-// from mass filter, find a tvs as cohortFilter, to know its array index in selectCohort.values[]
-// return undefined for anything that's not valid
-function mayGetActiveCohortIdx(self) {
-	if (!self.state.config.filter) return // no mass filter
-	const cohortFilter = getFilterItemByTag(self.config.filter, 'cohortFilter') // the tvs object
-	if (cohortFilter && self.state.termdbConfig.selectCohort) {
-		// the tvs is found
-		const cohortName = cohortFilter.tvs.values
-			.map(d => d.key)
-			.sort()
-			.join(',')
-		const idx = self.state.termdbConfig.selectCohort.values.findIndex(v => v.keys.sort().join(',') == cohortName)
-		if (idx == -1) throw 'subcohort key is not in selectCohort.values[]'
-		return idx
-	}
-}

client/plots/genomeBrowser.js

@@ -38,15 +38,7 @@ this{}
 				terms[]
 			geneSearchResult{}
 			snvindel {}
-				details {}
-					groupTypes[]
-					groups:[]
-						// each element is a group object
-						{type='info', infoKey=str}
-						{type='filter', filter={}}
-						{type='population', key, label, ..}
-					groupTestMethod{}
-					groupTestMethodsIdx
+				details {} // see type def
 				populations [{key,label}] // might not be part of state
 			ld {}
 				tracks[]
@@ -76,7 +68,7 @@ class genomeBrowser {
 		this.type = 'genomeBrowser'
 	}
 
-	async init() {
+	async init(appState) {
 		const holder = this.opts.holder.append('div')
 		this.opts.header
 			.append('div')
@@ -430,10 +422,11 @@ export const genomeBrowserInit = getCompInit(genomeBrowser)
 // this alias will allow abstracted dynamic imports
 export const componentInit = genomeBrowserInit
 
-export async function getPlotConfig(opts, app) {
+export async function getPlotConfig(opts, app, activeCohort) {
+	// 3rd arg is initial active cohort
 	try {
 		// request default queries config from dataset, and allows opts to override
-		return await getDefaultConfig(app.vocabApi, opts)
+		return await getDefaultConfig(app.vocabApi, opts, activeCohort)
 	} catch (e) {
 		throw `${e} [genomeBrowser getPlotConfig()]`
 	}
@@ -471,7 +464,7 @@ export function makeChartBtnMenu(holder, chartsInstance) {
 				// must do this as 'plot_prep' does not call getPlotConfig()
 				// request default queries config from dataset, and allows opts to override
 				// this config{} will become this.state.config{}
-				const config = await getDefaultConfig(chartsInstance.app.vocabApi)
+				const config = await getDefaultConfig(chartsInstance.app.vocabApi, null, chartsInstance.state.activeCohort)
 
 				config.chartType = 'genomeBrowser'
 				config.geneSearchResult = result
@@ -494,7 +487,7 @@ export function makeChartBtnMenu(holder, chartsInstance) {
 }
 
 // get default config of the app from vocabApi
-async function getDefaultConfig(vocabApi, override) {
+async function getDefaultConfig(vocabApi, override, activeCohort) {
 	const config = await vocabApi.getMds3queryDetails()
 	// request default variant filter (against vcf INFO)
 	const vf = await vocabApi.get_variantFilter()
@@ -506,6 +499,14 @@ async function getDefaultConfig(vocabApi, override) {
 		// test method may be inconsistent with group configuration (e.g. no fisher for INFO fields), update test method here
 		// 1st arg is a fake "self"
 		mayUpdateGroupTestMethodsIdx({ state: { config: c2 } }, c2.snvindel.details)
+		// a type=filter group may use filterByCohort. in such case, modify default state to assign proper filter based on current cohort
+		const gf = c2.snvindel.details.groups.find(i => i.type == 'filter')
+		if (gf && gf.filterByCohort) {
+			// modify and assign
+			gf.filter = gf.filterByCohort[vocabApi.termdbConfig.selectCohort.values[activeCohort].keys.join(',')]
+			if (!gf.filter) throw 'unknown filter by current cohort name'
+			delete gf.filterByCohort
+		}
 	}
 	return c2
 }

server/src/mds3.init.js

@@ -57,6 +57,7 @@ validate_query_snvindel
 	gdc.validate_query_snvindel_byisoform
 	gdc.validate_query_snvindel_byrange
 	snvindelByRangeGetter_bcf
+		validateSampleHeader2
 		mayLimitSamples
 			param2filter
 				tid2value2filter
@@ -705,13 +706,24 @@ function mayValidateSampleHeader(ds, samples, where) {
 function validateSampleHeader2(ds, samples, where) {
 	const sampleIds = []
 	// ds?.cohort?.termdb.q.sampleName2id must be present
+	const unknownSamples = [] // samples present in big file header but missing from db
 	for (const s of samples) {
 		const id = ds.cohort.termdb.q.sampleName2id(s.name)
-		if (!Number.isInteger(id)) throw 'unknown sample name from ' + where
+		if (!Number.isInteger(id)) {
+			unknownSamples.push(s.name)
+			// TODO if file with unknown sample should still be usable, slot a mock element in sampleIds[]. downstream query should be able to ignore it
+			continue
+		}
 		s.name = id
 		sampleIds.push(s)
 	}
 	console.log(samples.length, 'samples from ' + where + ' of ' + ds.label)
+	if (unknownSamples.length) {
+		// unknown samples can be safely reported to server log
+		console.log('unknown samples: ' + unknownSamples.join(', '))
+		// later attach a sanitized err msg to ds to report to client
+		throw 'unknown samples in big file'
+	}
 	return sampleIds
 }
 

server/src/mds3.variant.js

@@ -78,7 +78,15 @@ function validateParam(q, ds) {
 	if (q.details.groups.length > 2) throw 'q.details.groups[] has more than 2'
 	for (const g of q.details.groups) {
 		if (g.type == 'filter') {
-			if (typeof g.filter != 'object') throw '.filter not an object for group type=filter'
+			if (g.filter) {
+				if (typeof g.filter != 'object') throw '.filter not an object for group type=filter'
+			} else if (g.filterByCohort) {
+				if (!ds.cohort.termdb.selectCohort) throw 'filterByCohort in use but ds not using subcohort'
+				if (typeof g.filterByCohort != 'object') throw '.filterByCohort not an object for group type=filter'
+				// xx
+			} else {
+				throw 'unknown structure of group.type=filter'
+			}
 		} else if (g.type == 'population') {
 			if (!g.key) throw '.key missing from group type=population'
 			if (!ds.queries.snvindel?.populations) throw 'group type=population but this ds does not have populations'

shared/types/src/dataset.ts

@@ -242,6 +242,38 @@ type Population = {
 	/** if AC/AN of the population is ancestry-stratified, will be multiple elements of this array; otherwise just one */
 	sets: PopulationINFOset[]
 }
+/**
+accessible to client via termdb.js?for=mds3queryDetails
+part of state of genomeBrowser plot
+allowing for user modification
+*/
+type SnvindelComputeDetails = {
+	/**  xx
+	 */
+	groupTypes: any
+	/**  xx
+	 */
+	groups: (SnvindelComputeGroup_filter | SnvindelComputeGroup_population)[]
+	/**  xx
+	 */
+	groupTestMethods: any
+	/** array index of groupTestMethods[] */
+	groupTestMethodsIdx: number
+}
+type SnvindelComputeGroup_filter = {
+	type: 'filter'
+	/** a given filter applied to all cohorts */
+	filter?: any
+	/** filter per cohort. use either filter or filterByCohort */
+	filterByCohort?: any
+}
+type SnvindelComputeGroup_population = {
+	type: 'population'
+	key: string
+	label: string
+	allowto_adjust_race: boolean
+	adjust_race: boolean
+}
 
 /** a data type under ds.queries{} */
 type SnvIndelQuery = {
@@ -269,7 +301,7 @@ so that it can work for a termdb-less ds, e.g. clinvar, where termdbConfig canno
 	}
 	allowSNPs?: boolean
 	vcfid4skewerName?: boolean
-	details?: any
+	details?: SnvindelComputeDetails
 }
 
 type SvFusion = {