@sjcrh/proteinpaint-server 2.40.6 → 2.40.8

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.40.6",
+  "version": "2.40.8",
   "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

@@ -157,7 +157,7 @@ export async function validate_query_geneExpression(ds: any, genome: any) {
 		return
 	}
 	if (q.src == 'native') {
-		validateNative(q, ds, genome)
+		await validateNative(q, ds, genome)
 		return
 	}
 	throw 'unknown queries.geneExpression.src'
@@ -165,6 +165,7 @@ 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[]
@@ -177,7 +178,7 @@ async function validateNative(q: GeneExpressionQueryNative, ds: any, genome: any
 		if (l.slice(0, 4).join('\t') != '#chr\tstart\tstop\tgene') throw 'header line has wrong content for columns 1-4'
 		for (let i = 4; i < l.length; i++) {
 			const id = ds.cohort.termdb.q.sampleName2id(l[i])
-			if (id == undefined) throw 'unknown sample from header'
+			if (id == undefined) throw 'queries.geneExpression: unknown sample from header: ' + l[i]
 			q.samples.push(id)
 		}
 		console.log(q.samples.length, 'samples from geneExpression of', ds.label)
@@ -203,13 +204,14 @@ 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) }
 			}
 		}
@@ -238,7 +240,7 @@ 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?
 						const v = Number(l[i])

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
 		}