@sjcrh/proteinpaint-server 2.43.0 → 2.43.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.43.0",
+  "version": "2.43.2",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "server.js",
   "bin": "start.js",
@@ -71,6 +71,7 @@
     "image-size": "^0.5.5",
     "jsonwebtoken": "^9.0.0",
     "jstat": "^1.9.3",
+    "ky": "^1.2.1",
     "lazy": "^1.0.11",
     "micromatch": "^4.0.5",
     "minimatch": "^3.1.2",

package/routes/termdb.singlecellSamples.ts

@@ -2,13 +2,7 @@ import fs from 'fs'
 import path from 'path'
 import { read_file } from '#src/utils.js'
 import serverconfig from '#src/serverconfig.js'
-import {
-	SingleCellQuery,
-	SingleCellSamplesNative,
-	SingleCellSamplesGdc,
-	SingleCellDataNative,
-	SingleCellDataGdc
-} from '#shared/types/dataset.ts'
+import { SingleCellQuery, SingleCellSamplesNative, SingleCellDataNative } from '#shared/types/dataset.ts'
 import {
 	Sample,
 	TermdbSinglecellsamplesRequest,
@@ -70,7 +64,7 @@ export async function validate_query_singleCell(ds: any, genome: any) {
 	if (q.samples.src == 'gdcapi') {
 		gdc_validate_query_singleCell_samples(ds, genome)
 	} else if (q.samples.src == 'native') {
-		validateSamplesNative(q.samples as SingleCellSamplesNative, ds)
+		getSamplesNative(q.samples as SingleCellSamplesNative, ds)
 	} else {
 		throw 'unknown singleCell.samples.src'
 	}
@@ -79,29 +73,43 @@ export async function validate_query_singleCell(ds: any, genome: any) {
 	if (q.data.src == 'gdcapi') {
 		gdc_validate_query_singleCell_data(ds, genome)
 	} else if (q.data.src == 'native') {
-		validateDataNative(q.data as SingleCellDataNative, ds)
+		getDataNative(q.data as SingleCellDataNative, ds)
 	} else {
 		throw 'unknown singleCell.data.src'
 	}
 	// q.data.get() added
 }
 
-function validateSamplesNative(S: SingleCellSamplesNative, ds: any) {
+async function getSamplesNative(S: SingleCellSamplesNative, ds: any) {
 	// for now use this quick fix method to pull sample ids annotated by this term
 	// to support situation where not all samples from a dataset has sc data
-	const samples = [] as Sample[] // list of sample ids with sc data
-	const s = ds.cohort.termdb.q.getAllValues4term(S.isSampleTerm)
-	for (const id of s.keys()) {
-		samples.push({ sample: ds.cohort.termdb.q.id2sampleName(id) })
+	const isSamples = ds.cohort.termdb.q.getAllValues4term(S.isSampleTerm)
+	if (isSamples.size == 0) throw 'no samples found that are identified by isSampleTerm'
+	const samples = [] as any // array of samples with sc data to be sent to client and list in table; cannot use Sample type for the use of "sampleid" temp property
+	for (const sampleid of isSamples.keys()) {
+		if (isSamples.get(sampleid) == '1')
+			samples.push({
+				sample: ds.cohort.termdb.q.id2sampleName(sampleid), // string name for display
+				sampleid // temporarily kept to assign term value to each sample
+			})
 	}
-	if (samples.length == 0) throw 'no sample with sc data'
-	// getter returns array of {sample:<samplename>, files:[]} where files is gdc specific. each sample is an obj and allows to add ds-specific stuff
+	if (S.sampleColumns) {
+		// has optional terms to show as table columns and annotate samples
+		for (const term of S.sampleColumns) {
+			const s2v = ds.cohort.termdb.q.getAllValues4term(term.termid) // map. k: sampleid, v: term value
+			for (const s of samples) {
+				if (s2v.has(s.sampleid)) s[term.termid] = s2v.get(s.sampleid)
+			}
+		}
+	}
+	for (const s of samples) delete s.sampleid
+
 	S.get = () => {
-		return { samples, fields: ['sample'], columnNames: ['Sample'] }
+		return { samples: samples as Sample[] }
 	}
 }
 
-function validateDataNative(D: SingleCellDataNative, ds: any) {
+function getDataNative(D: SingleCellDataNative, ds: any) {
 	const nameSet = new Set() // guard against duplicating plot names
 	for (const plot of D.plots) {
 		if (nameSet.has(plot.name)) throw 'duplicate plot.name'
@@ -110,19 +118,11 @@ function validateDataNative(D: SingleCellDataNative, ds: any) {
 
 	// scoped and cached for runtime
 	const _terms = [] as any
-	const _tid2cellvalue = {} as any
 
 	for (const tid of D.termIds) {
 		const t = ds.cohort.termdb.q.termjsonByOneid(tid)
 		if (!t) throw 'invalid term id from queries.singleCell.data.termIds[]'
 		_terms.push(t)
-		// _tid2cellvalue[tid] = {}
-		// const clusterMap = ds.cohort.termdb.q.getAllValues4term(tid)
-		// for(const [id, cluster] of clusterMap)
-		// {
-		// 	const name = ds.cohort.termdb.q.id2sampleName(id)
-		// 	_tid2cellvalue[tid][name] = cluster
-		// }
 	}
 	D.get = async q => {
 		// if sample is int, may convert to string