Store sample ancestry in sample refs. Group samples by sample type in matrix

client/plots/matrix/matrix.groups.js

@@ -1,6 +1,7 @@
 import { sample_match_termvaluesetting } from '#shared/filter.js'
 import { getSampleSorter, getTermSorter, getSampleGroupSorter, getMclassSorter } from './matrix.sort'
 import { dtsnvindel, dtcnv, dtfusionrna, dtgeneexpression, dtsv } from '#shared/common.js'
+import { ROOT_SAMPLE_TYPE } from '#shared/terms.js'
 
 export function getTermOrder(data) {
 	const s = this.settings.matrix
@@ -136,6 +137,37 @@ export function getSampleGroups(data) {
 				sampleGroups.set(key, grp)
 			}
 			sampleGroups.get(key).lst.push(row)
+		} else if (this.state.termdbConfig.hasSampleAncestry) {
+			// has sample ancestry
+			// group samples by sample type (hardcoded to be root sample type)
+			let key, name
+			if (!row._ref_) continue
+			if (row._ref_.sampleType === ROOT_SAMPLE_TYPE) {
+				// sample is root sample
+				key = row.sample
+				name = row.label
+			} else {
+				// sample is not root sample
+				// check its ancestors
+				if (!row._ref_.ancestors?.length) continue
+				const ancestors = row._ref_.ancestors.filter(a => a.sample_type === ROOT_SAMPLE_TYPE)
+				if (!ancestors.length) continue
+				if (ancestors.length > 1) throw new Error('multiple root samples present')
+				const ancestor = ancestors[0]
+				key = ancestor.ancestor_id
+				name = ancestor.ancestor_name
+			}
+			if (!key) continue
+			if (!sampleGroups.has(key)) {
+				const grp = {
+					name,
+					id: key,
+					lst: [],
+					legendGroups: {}
+				}
+				sampleGroups.set(key, grp)
+			}
+			sampleGroups.get(key).lst.push(row)
 		} else {
 			defaultSampleGrp.lst.push(row)
 		}

server/src/termdb.server.init.ts

@@ -126,16 +126,19 @@ export function server_init_db_queries(ds) {
 	}
 	if (tables.has('sampleidmap')) {
 		const i2s = new Map(),
-			s2i = new Map()
+			s2i = new Map(),
+			i2type = new Map()
 		const rows = cn.prepare('SELECT * FROM sampleidmap').all()
 		let totalCount = 0
-		for (const { id, name } of rows) {
+		for (const { id, name, sample_type } of rows) {
 			i2s.set(id, name)
 			s2i.set(name, id)
+			i2type.set(id, sample_type)
 			totalCount++ //for dbs without cohorts or types
 		}
 		q.id2sampleName = id => i2s.get(id)
 		q.sampleName2id = s => s2i.get(s)
+		q.id2sampleType = id => i2type.get(id)
 		if (tables.has('cohort_sample_types')) {
 			const rows = cn.prepare('SELECT * from cohort_sample_types').all()
 			q.getCohortSampleCount = cohortKey => {
@@ -569,6 +572,43 @@ export function server_init_db_queries(ds) {
 		const rows = sql.all()
 		return rows
 	}
+
+	if (ds.cohort.termdb.hasSampleAncestry) {
+		// ds has sample ancestry
+		// store sample ancestry in sample refs
+		const i2ancestors = new Map()
+		{
+			const rows = cn.prepare('SELECT * FROM sample_ancestry').all()
+			for (const row of rows) {
+				const id = row.sample_id
+				if (!i2ancestors.has(id)) i2ancestors.set(id, [])
+				const ancestors = i2ancestors.get(id)
+				const ancestor = {
+					ancestor_id: row.ancestor_id,
+					ancestor_name: q.id2sampleName(row.ancestor_id),
+					sample_type: q.id2sampleType(row.ancestor_id),
+					distance: row.distance
+				}
+				ancestors.push(ancestor)
+			}
+		}
+
+		const i2refs = new Map()
+		{
+			const rows = cn.prepare('SELECT * FROM sampleidmap').all()
+			for (const row of rows) {
+				const id = row.id
+				const name = row.name
+				const refs: any = { label: name, sample: id, sampleType: q.id2sampleType(id) }
+				const ancestors = i2ancestors.get(row.id)
+				if (ancestors) refs.ancestors = ancestors
+				Object.freeze(refs)
+				i2refs.set(id, refs)
+			}
+		}
+
+		q.id2sampleRefs = id => structuredClone(i2refs.get(id)) // returns sample refs to be used in bySampleId{} object, returning clone as some code (e.g. server/src/termdb.get_matrix.js) needs to modify the sample refs object
+	}
 }
 
 // ds computes term visibility in dictionary based on client auth; returns list of visible terms