@sjcrh/proteinpaint-server 2.30.2 → 2.30.4

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.30.2",
+  "version": "2.30.4",
   "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

@@ -1,12 +1,13 @@
 import { GdcMafResponse, File } from '#shared/types/routes/gdc.maf.ts'
-import { fileSize } from '#shared/fileSize.js'
 import path from 'path'
 import got from 'got'
+import serverconfig from '#src/serverconfig.js'
 
 const apihost = process.env.PP_GDC_HOST || 'https://api.gdc.cancer.gov'
 const maxFileNumber = 1000
 const allowedWorkflowType = 'Aliquot Ensemble Somatic Variant Merging and Masking'
 const allowedExpStrategy = new Set(['WXS', 'Targeted Sequencing'])
+const maxTotalSizeCompressed = serverconfig.features.gdcMafMaxFileSize || 50000000 // 50Mb
 
 export const api = {
 	endpoint: 'gdc/maf',
@@ -146,7 +147,7 @@ async function listMafFiles(req: any) {
 		const file = {
 			id: h.id,
 			project_id: c.project.project_id,
-			file_size: fileSize(h.file_size)
+			file_size: h.file_size
 		} as File
 
 		file.case_submitter_id = c.submitter_id
@@ -161,7 +162,8 @@ async function listMafFiles(req: any) {
 
 	const result = {
 		files,
-		filesTotal: re.data.pagination.total
+		filesTotal: re.data.pagination.total,
+		maxTotalSizeCompressed
 	} as GdcMafResponse
 
 	return result

package/routes/gdc.mafBuild.ts

@@ -42,7 +42,10 @@ req.query {
 res{}
 */
 async function buildMaf(req: any, res: any) {
+	const t0 = new Date()
+
 	const fileLst2 = (await getFileLstUnderSizeLimit(req.query.fileIdLst)) as string[]
+	console.log('test gdc maf sizes', new Date() - t0)
 
 	const outFile = path.join(serverconfig.cachedir, 'gdcMaf.' + Math.random().toString()) // should be a gzipped file. does it need to end with '.gz' or it's auto-added?
 
@@ -54,6 +57,8 @@ async function buildMaf(req: any, res: any) {
 
 	await run_rust('gdcmaf', JSON.stringify(arg))
 
+	console.log('rust gdcmaf', new Date() - t0)
+
 	const data = await fs.promises.readFile(outFile)
 
 	// by directly returning a blob, it won't tell client how many files are used