@sjcrh/proteinpaint-server 2.35.2-0 → 2.37.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.35.2-0",
+  "version": "2.37.0",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "server.js",
   "bin": "start.js",
@@ -57,7 +57,7 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.35.0",
-    "@sjcrh/proteinpaint-rust": "2.34.0",
+    "@sjcrh/proteinpaint-rust": "2.37.0",
     "better-sqlite3": "^7.5.3",
     "body-parser": "^1.15.2",
     "canvas": "~2.9.3",

package/routes/{termdb.termbyid.ts → termdb.termsbyids.ts}

@@ -1,32 +1,17 @@
-// import { gettermbyidRequest, gettermbyidResponse } from '#shared/types/routes/termdb.termbyid'
+import { gettermsbyidsRequest, gettermsbyidsResponse } from '#shared/types/routes/termdb.termsbyids.js'
 import { copy_term } from '#src/termdb.js'
 
 export const api: any = {
-	endpoint: 'termdb/termbyid',
+	endpoint: 'termdb/termsbyids',
 	methods: {
 		get: {
 			init,
 			request: {
-				typeId: 'gettermbyidRequest'
+				typeId: 'gettermsbyidsRequest'
 			},
 			response: {
-				typeId: 'gettermbyidResponse'
-			},
-			examples: [
-				{
-					request: {
-						body: {
-							genome: 'hg38-test',
-							dslabel: 'TermdbTest',
-							embedder: 'localhost',
-							gettermbyid: 'subcohort'
-						}
-					},
-					response: {
-						header: { status: 200 }
-					}
-				}
-			]
+				typeId: 'gettermsbyidsResponse'
+			}
 		},
 		post: {
 			alternativeFor: 'get',
@@ -46,7 +31,7 @@ function init({ genomes }) {
 			const tdb = ds.cohort.termdb
 			if (!tdb) throw 'invalid termdb object'
 
-			await trigger_gettermbyid(q, res, tdb) // as getcategoriesResponse
+			await trigger_gettermsbyid(q, res, tdb) // as getcategoriesResponse
 		} catch (e) {
 			// eslint-disable-next-line @typescript-eslint/ban-ts-comment
 			// @ts-ignore
@@ -56,13 +41,23 @@ function init({ genomes }) {
 	}
 }
 
-async function trigger_gettermbyid(
-	q: { gettermbyid: any },
-	res: { send: (arg0: { term: any }) => void },
+async function trigger_gettermsbyid(
+	q: { ids: any },
+	res: { send: (arg0: { terms: any }) => void },
 	tdb: { q: { termjsonByOneid: (arg0: any) => any } }
 ) {
-	const t = tdb.q.termjsonByOneid(q.gettermbyid)
+	const terms = {}
+	for (const id of q.ids) {
+		const term = tdb.q.termjsonByOneid(id)
+		if (term) {
+			if (term.type == 'categorical' && !term.values && !term.groupsetting?.inuse) {
+				term.values = {}
+				term.samplecount = {}
+			}
+		}
+		terms[id] = term ? copy_term(term) : undefined
+	}
 	res.send({
-		term: t ? copy_term(t) : undefined
+		terms
 	})
 }

package/routes/termdb.topVariablyExpressedGenes.ts

@@ -31,7 +31,11 @@ function init({ genomes }) {
 			const ds = genome.datasets?.[q.dslabel]
 			if (!ds) throw 'invalid dslabel'
 			if (!ds.queries?.topVariablyExpressedGenes) throw 'not supported on dataset'
+
+			const t: number = new Date().getTime()
 			const genes = await ds.queries.topVariablyExpressedGenes.getGenes(q)
+			if (serverconfig.debugmode) console.log('topVariablyExpressedGenes', new Date().getTime() - t, 'ms')
+
 			res.send({ genes } as TermdbTopVariablyExpressedGenesResponse)
 		} catch (e: any) {
 			res.send({ status: 'error', error: e.message || e })
@@ -139,7 +143,7 @@ function gdcValidateQuery(ds: any, genome: any) {
 		// limit the case_ids length, and restrict pool to CGC genes, otherwise the request times out !!!
 		// must revert asap
 		return {
-			case_ids: caseLst.slice(0, 20),
+			case_ids: caseLst, //.slice(0, 20),
 			gene_ids: tempGetCGCgenes(genome),
 			selection_size: Number(q.maxGenes)
 		}