@sjcrh/proteinpaint-server 2.34.0 → 2.34.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.34.0",
+  "version": "2.34.1",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "server.js",
   "bin": "start.js",

package/routes/gdc.topVariablyExpressedGenes.ts

@@ -8,14 +8,10 @@ import got from 'got'
 import serverconfig from '#src/serverconfig.js'
 
 // TODO make it general purpose based on ds.queries.geneExpression.topVariablyExpressedGenes{}; wait till case/gene link changes are done
-
-// TODO change when api is released to prod
-//const apihost = process.env.PP_GDC_HOST || 'https://api.gdc.cancer.gov'
-const apihost = 'https://uat-portal.gdc.cancer.gov/auth/api/v0/gene_expression/gene_selection'
-// temporarily hardcode to use the direct API URL,
-// previously hardcoded to use 'https://uat-portal.gdc.cancer.gov/auth/api/v0/'
-const geneExpHost = 'https://uat-api.gdc.cancer.gov'
 // https://github.com/NCI-GDC/gdcapi/blob/develop/openapi/gene-expression.yaml
+const apihost = process.env.PP_GDC_HOST || 'https://api.gdc.cancer.gov'
+// may override the geneExpHost for developers without access to qa/portal environments
+const geneExpHost = serverconfig.features?.geneExpHost || apihost
 
 const gdcGenome = 'hg38'
 const gdcDslabel = 'GDC'

package/routes/termdb.singlecellSamples.ts

@@ -93,7 +93,7 @@ function validateSamplesNative(S: SingleCellSamplesNative, ds: any) {
 		samples.push({ sample: ds.cohort.termdb.q.id2sampleName(id) })
 	}
 	if (samples.length == 0) throw 'no sample with sc data'
-	// getter returns array of {name:<samplename>, files:[]} where files is gdc specific. each sample is an obj and allows to add ds-specific stuff
+	// getter returns array of {sample:<samplename>, files:[]} where files is gdc specific. each sample is an obj and allows to add ds-specific stuff
 	S.get = () => samples
 }