@sjcrh/proteinpaint-server 2.40.7 → 2.41.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.40.7",
+  "version": "2.41.0",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "server.js",
   "bin": "start.js",

package/routes/termdb.cluster.ts

@@ -104,9 +104,7 @@ async function doClustering(data: any, q: TermdbClusterRequest) {
 	const Rinputfile = path.join(serverconfig.cachedir, Math.random().toString() + '.json')
 	await utils.write_file(Rinputfile, JSON.stringify(inputData))
 	const Routput = JSON.parse(await lines2R(path.join(serverconfig.binpath, 'utils/hclust.R'), [], [Rinputfile]))
-	fs.unlink(Rinputfile, (arg: any) => {
-		return
-	})
+	await fs.promises.unlink(Rinputfile)
 
 	const row_names_index: number[] = Routput.RowOrder.map(row => inputData.row_names.indexOf(row.name)) // sorted rows. value is array index in input data
 	const col_names_index: number[] = Routput.ColOrder.map(col => inputData.col_names.indexOf(col.name)) // sorted columns, value is array index from input array
@@ -165,6 +163,7 @@ export async function validate_query_geneExpression(ds: any, genome: any) {
 
 async function validateNative(q: GeneExpressionQueryNative, ds: any, genome: any) {
 	q.file = path.join(serverconfig.tpmasterdir, q.file)
+	if (!q.samples) q.samples = []
 	await utils.validate_tabixfile(q.file)
 	q.nochr = await utils.tabix_is_nochr(q.file, null, genome)
 	q.samples = [] as number[]
@@ -183,16 +182,6 @@ async function validateNative(q: GeneExpressionQueryNative, ds: any, genome: any
 		console.log(q.samples.length, 'samples from geneExpression of', ds.label)
 	}
 
-	/*
-	query exp data one gene at a time
-	param{}
-	.genes[{}]
-		.gene=str
-		.chr=str
-		.start=int
-		.stop=int
-	.filterObj{}
-	*/
 	q.get = async (param: TermdbClusterRequest) => {
 		const limitSamples = await mayLimitSamples(param, q.samples, ds)
 		if (limitSamples?.size == 0) {
@@ -203,17 +192,19 @@ async function validateNative(q: GeneExpressionQueryNative, ds: any, genome: any
 		// has at least 1 sample passing filter and with exp data
 		// TODO what if there's just 1 sample not enough for clustering?
 		const bySampleId = {}
+		const samples = q.samples || []
 		if (limitSamples) {
 			for (const sid of limitSamples) {
 				bySampleId[sid] = { label: ds.cohort.termdb.q.id2sampleName(sid) }
 			}
 		} else {
 			// use all samples with exp data
-			for (const sid of q.samples) {
+			for (const sid of samples) {
 				bySampleId[sid] = { label: ds.cohort.termdb.q.id2sampleName(sid) }
 			}
 		}
 
+		// only valid genes with data are added. invalid genes or genes missing from data file is not added. backend returned genes is allowed to be fewer than supplied by client
 		const gene2sample2value = new Map() // k: gene symbol, v: { sampleId : value }
 
 		for (const g of param.genes) {
@@ -230,7 +221,7 @@ async function validateNative(q: GeneExpressionQueryNative, ds: any, genome: any
 				g.chr = j.chr
 			}
 
-			gene2sample2value.set(g.gene, {})
+			const s2v = {}
 			await utils.get_lines_bigfile({
 				args: [q.file, (q.nochr ? g.chr?.replace('chr', '') : g.chr) + ':' + g.start + '-' + g.stop], // must do g.chr?.replace to avoid tsc error
 				callback: line => {
@@ -238,16 +229,17 @@ async function validateNative(q: GeneExpressionQueryNative, ds: any, genome: any
 					// case-insensitive match! FIXME if g.gene is alias won't work
 					if (l[3].toLowerCase() != g.gene.toLowerCase()) return
 					for (let i = 4; i < l.length; i++) {
-						const sampleId = q.samples[i - 4]
+						const sampleId = samples[i - 4]
 						if (limitSamples && !limitSamples.has(sampleId)) continue // doing filtering and sample of current column is not used
-						// if l[i] is blank string?
+						if (!l[i]) continue // blank string
 						const v = Number(l[i])
 						if (Number.isNaN(v)) throw 'exp value not number'
-						gene2sample2value.get(g.gene)[sampleId] = v
+						s2v[sampleId] = v
 					}
 				}
 			} as any)
 			// Above!! add "as any" to suppress a npx tsc alert
+			if (Object.keys(s2v).length) gene2sample2value.set(g.gene, s2v) // only add gene if has data
 		}
 		// pass blank byTermId to match with expected output structure
 		const byTermId = {}

package/routes/termdb.getdescrstats.ts

@@ -1,11 +1,11 @@
 import { getdescrstatsRequest, getdescrstatsResponse } from '#shared/types/routes/termdb.getdescrstats.ts'
-import * as termdbsql from '../src/termdb.sql.js'
+import { get_rows_by_one_key } from '../src/termdb.sql.js'
 import Summarystats from '../shared/descriptive.stats.js'
 
 export const api: any = {
 	endpoint: 'termdb/descrstats',
 	methods: {
-		get: {
+		all: {
 			init,
 			request: {
 				typeId: 'getdescrstatsRequest'
@@ -20,7 +20,6 @@ export const api: any = {
 							genome: 'hg38-test',
 							dslabel: 'TermdbTest',
 							embedder: 'localhost',
-							getdescrstats: 1,
 							tid: 'hrtavg',
 							filter: {
 								type: 'tvslst',
@@ -51,10 +50,6 @@ export const api: any = {
 					}
 				}
 			]
-		},
-		post: {
-			alternativeFor: 'get',
-			init
 		}
 	}
 }
@@ -84,14 +79,14 @@ async function trigger_getdescrstats(q: any, res: any, ds: any) {
 	const term = ds.cohort.termdb.q.termjsonByOneid(q.tid)
 	if (!term) throw 'invalid termid'
 	if (term.type != 'float' && term.type != 'integer') throw 'not numerical term'
-	const rows = await termdbsql.get_rows_by_one_key({
+	const rows = await get_rows_by_one_key({
 		ds,
 		key: q.tid,
-		filter: q.filter ? (typeof q.filter == 'string' ? JSON.parse(q.filter) : q.filter) : null
+		filter: q.filter
 	})
 	const values: number[] = []
 	for (const { value } of rows) {
-		if (term.values && term.values[value] && term.values[value].uncomputable) {
+		if (term.values?.[value]?.uncomputable) {
 			// skip uncomputable values
 			continue
 		}

package/routes/termdb.singlecellSamples.ts

@@ -152,15 +152,16 @@ function validateDataNative(D: SingleCellDataNative, ds: any) {
 					const cellId = l[0],
 						x = Number(l[4]), // FIXME standardize, or define idx in plot
 						y = Number(l[5])
+					const category = l[plot.colorColumn?.index] || ''
 					if (!cellId) throw 'cell id missing'
 					if (!Number.isFinite(x) || !Number.isFinite(y)) throw 'x/y not number'
-					cells.push({ cellId, x, y })
+					cells.push({ cellId, x, y, category })
 
 					for (const tid of D.termIds) {
 						tid2cellvalue[tid][cellId] = l[1]
 					}
 				}
-				plots.push({ name: plot.name, cells })
+				plots.push({ name: plot.name, cells, colorBy: plot.colorColumn?.name })
 			}
 			if (plots.length == 0) {
 				// no data available for this sample

package/routes/termdb.topVariablyExpressedGenes.ts

@@ -12,7 +12,7 @@ import { get_samples } from '#src/termdb.sql.js'
 export const api = {
 	endpoint: 'termdb/topVariablyExpressedGenes',
 	methods: {
-		get: {
+		all: {
 			init,
 			request: {
 				typeId: 'TermdbTopVariablyExpressedGenesRequest'