@sjcrh/proteinpaint-server 2.40.0 → 2.40.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.40.0",
+  "version": "2.40.1",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "server.js",
   "bin": "start.js",

package/routes/gdc.maf.ts

@@ -8,8 +8,6 @@ this route lists available gdc MAF files based on user's cohort filter
 and return them to client to be shown in a table for selection
 */
 
-const apihost = process.env.PP_GDC_HOST || 'https://api.gdc.cancer.gov' // to switch to serverconfig export
-
 const maxFileNumber = 1000 // determines max number of files to return to client
 // preliminary testing:
 // 36s for 1000 (87Mb)
@@ -60,7 +58,7 @@ function init({ genomes }) {
 			const ds = g.datasets.GDC
 			if (!ds) throw 'hg38 GDC missing'
 
-			const payload = await listMafFiles(req.query as GdcMafRequest)
+			const payload = await listMafFiles(req.query as GdcMafRequest, ds)
 			res.send(payload)
 		} catch (e: any) {
 			res.send({ status: 'error', error: e.message || e })
@@ -80,7 +78,7 @@ ds {
 	}
 }
 */
-async function listMafFiles(q: GdcMafRequest) {
+async function listMafFiles(q: GdcMafRequest, ds) {
 	const filters = {
 		op: 'and',
 		content: [
@@ -95,7 +93,7 @@ async function listMafFiles(q: GdcMafRequest) {
 		case_filters.content.push(q.filter0)
 	}
 
-	const headers = { 'Content-Type': 'application/json', Accept: 'application/json' }
+	const { host, headers } = ds.getHostHeaders(q)
 
 	const data = {
 		filters,
@@ -111,7 +109,7 @@ async function listMafFiles(q: GdcMafRequest) {
 		].join(',')
 	}
 
-	const response = await got.post(path.join(apihost, 'files'), { headers, body: JSON.stringify(data) })
+	const response = await got.post(path.join(host.rest, 'files'), { headers, body: JSON.stringify(data) })
 
 	let re
 	try {

package/routes/gdc.mafBuild.ts

@@ -7,8 +7,6 @@ import Readable from 'stream'
 import { GdcMafBuildRequest } from '#shared/types/routes/gdc.mafBuild.ts'
 import { maxTotalSizeCompressed } from './gdc.maf.ts'
 
-const apihost = process.env.PP_GDC_HOST || 'https://api.gdc.cancer.gov'
-
 export const api = {
 	endpoint: 'gdc/mafBuild',
 	methods: {
@@ -27,7 +25,11 @@ export const api = {
 function init({ genomes }) {
 	return async (req: any, res: any): Promise<void> => {
 		try {
-			await buildMaf(req.query as GdcMafBuildRequest, res)
+			const g = genomes.hg38
+			if (!g) throw 'hg38 missing'
+			const ds = g.datasets.GDC
+			if (!ds) throw 'hg38 GDC missing'
+			await buildMaf(req.query as GdcMafBuildRequest, res, ds)
 		} catch (e: any) {
 			if (e.stack) console.log(e.stack)
 			res.send({ status: 'error', error: e.message || e })
@@ -39,10 +41,10 @@ function init({ genomes }) {
 q{}
 res{}
 */
-async function buildMaf(q: GdcMafBuildRequest, res: any) {
+async function buildMaf(q: GdcMafBuildRequest, res: any, ds) {
 	const t0 = Date.now()
-
-	const fileLst2 = (await getFileLstUnderSizeLimit(q.fileIdLst)) as string[]
+	const { host, headers } = ds.getHostHeaders(q)
+	const fileLst2 = (await getFileLstUnderSizeLimit(q.fileIdLst, host, headers)) as string[]
 
 	if (serverconfig.debugmode)
 		console.log(
@@ -53,7 +55,7 @@ async function buildMaf(q: GdcMafBuildRequest, res: any) {
 	const arg = {
 		fileIdLst: fileLst2,
 		columns: q.columns,
-		host: path.join(apihost, 'data') // must use the /data/ endpoint from current host
+		host: path.join(host.rest, 'data') // must use the /data/ endpoint from current host
 	}
 
 	const rustStream = run_rust_stream('gdcmaf', JSON.stringify(arg))
@@ -80,7 +82,7 @@ excess files are not processed in order not to crash server
 must not rely on file size sent by client, as that can be spoofed and never to be trusted
 it's inexpensive to query api for this
 */
-async function getFileLstUnderSizeLimit(lst: string[]) {
+async function getFileLstUnderSizeLimit(lst: string[], host, headers) {
 	if (lst.length == 0) throw 'fileIdLst[] not array or blank'
 	const data = {
 		filters: {
@@ -90,8 +92,7 @@ async function getFileLstUnderSizeLimit(lst: string[]) {
 		size: 10000,
 		fields: 'file_size'
 	}
-	const headers = { 'Content-Type': 'application/json', Accept: 'application/json' }
-	const response = await got.post(path.join(apihost, 'files'), { headers, body: JSON.stringify(data) })
+	const response = await got.post(path.join(host.rest, 'files'), { headers, body: JSON.stringify(data) })
 	let re
 	try {
 		re = JSON.parse(response.body)

package/routes/gdc.topMutatedGenes.ts

@@ -2,13 +2,9 @@ import { GdcTopMutatedGeneRequest, GdcTopMutatedGeneResponse, Gene } from '#shar
 import { mclasscnvgain, mclasscnvloss, dtsnvindel } from '#shared/common.js'
 import got from 'got'
 import serverconfig from '#src/serverconfig.js'
-import { getheaders } from '#src/mds3.gdc.js'
 
 // TODO change to /termdb/topMutatedGenes
 
-const apihost = process.env.PP_GDC_HOST || 'https://api.gdc.cancer.gov'
-const apihostGraphql = apihost + (apihost.includes('/v0') ? '' : '/v0') + '/graphql'
-
 export const api = {
 	endpoint: 'gdc/topMutatedGenes',
 	methods: {
@@ -24,7 +20,7 @@ export const api = {
 	}
 }
 
-function init() {
+function init({ genomes }) {
 	/*
 	genomes parameter is currently not used
 	could be used later to:
@@ -33,8 +29,12 @@ function init() {
 	*/
 	return async (req: any, res: any): Promise<void> => {
 		const q: GdcTopMutatedGeneRequest = req.query
+		const g = genomes.hg38
+		if (!g) throw 'hg38 missing'
+		const ds = g.datasets.GDC
+		if (!ds) throw 'hg38 GDC missing'
 		try {
-			const genes = await getGenesGraphql(q)
+			const genes = await getGenesGraphql(q, ds)
 			const payload: GdcTopMutatedGeneResponse = { genes }
 			res.send(payload)
 		} catch (e: any) {
@@ -437,9 +437,11 @@ const queryV2: any = {
 	}
 }
 
-async function getGenesGraphql(q: GdcTopMutatedGeneRequest) {
+async function getGenesGraphql(q: GdcTopMutatedGeneRequest, ds) {
 	let query: string, variables: object
+	const { host, headers } = ds.getHostHeaders(q)
 
+	// TODO: change this condition to use host.geneExp != host.rest ???
 	if (serverconfig.features?.geneExpHost) {
 		// quick fix! this is only set on local dev machines, meaning it's using v1 api; delete this after soft launch!!
 		query = queryV1.query
@@ -450,8 +452,8 @@ async function getGenesGraphql(q: GdcTopMutatedGeneRequest) {
 		variables = queryV2.getVariables(q)
 	}
 
-	const response = await got.post(apihostGraphql, {
-		headers: getheaders(q),
+	const response = await got.post(host.graphql, {
+		headers,
 		body: JSON.stringify({ query, variables })
 	})
 
@@ -510,7 +512,7 @@ this api only gets ssm-cases and does not account for cnv cases, will not return
 thus is replaced by getGenesGraphql
 async function getGenes(q: GdcTopMutatedGeneRequest) {
 	const _f = q.filter0 || { op: 'and', content: [] } // allow blank filter to test geneset edit ui (without filter)
-	const response = await got.post(path.join(apihost, '/analysis/top_mutated_genes_by_project'), {
+	const response = await got.post(path.join(host.rest, '/analysis/top_mutated_genes_by_project'), {
 		headers: { 'Content-Type': 'application/json', Accept: 'application/json' },
 		body: JSON.stringify({
 			size: q.maxGenes || 50,

package/routes/termdb.topVariablyExpressedGenes.ts

@@ -2,7 +2,7 @@ import {
 	TermdbTopVariablyExpressedGenesRequest,
 	TermdbTopVariablyExpressedGenesResponse
 } from '#shared/types/routes/termdb.topVariablyExpressedGenes.ts'
-import { gdcGetCasesWithExressionDataFromCohort, apihost, geneExpHost } from '../src/mds3.gdc.js'
+import { gdcGetCasesWithExressionDataFromCohort } from '../src/mds3.gdc.js'
 import path from 'path'
 import { run_rust } from '@sjcrh/proteinpaint-rust'
 import got from 'got'
@@ -142,11 +142,11 @@ function gdcValidateQuery(ds: any, genome: any) {
 		}
 
 		// change to this when api is available on prod
-		const url = path.join(geneExpHost, '/gene_expression/gene_selection')
-
+		const { host, headers } = ds.getHostHeaders(q)
+		const url = path.join(host.geneExp, '/gene_expression/gene_selection')
 		try {
 			const response = await got.post(url, {
-				headers: { 'Content-Type': 'application/json', Accept: 'application/json' },
+				headers,
 				body: JSON.stringify(getGeneSelectionArg(q, caseLst))
 			})