@sjcrh/proteinpaint-server 2.33.0 → 2.34.1-0

package/dataset/clinvar.hg19.js

@@ -24,9 +24,9 @@ exports.default = {
                     }
                 ]
             },
-            variantUrl: {
+            ssmUrl: {
                 base: 'https://www.ncbi.nlm.nih.gov/clinvar/variation/',
-                key: 'vcf_id',
+                namekey: 'vcf_id',
                 linkText: 'ClinVar',
                 shownSeparately: true
             },

package/dataset/clinvar.hg38.js

@@ -42,9 +42,9 @@ exports.default = {
                     }
                 ]
             },
-            variantUrl: {
+            ssmUrl: {
                 base: 'https://www.ncbi.nlm.nih.gov/clinvar/variation/',
-                key: 'vcf_id',
+                namekey: 'vcf_id',
                 linkText: 'ClinVar',
                 shownSeparately: true
             },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.33.0",
+  "version": "2.34.1-0",
   "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": "2.32.2-0",
-    "@sjcrh/proteinpaint-rust": "2.33.0",
+    "@sjcrh/proteinpaint-rust": "2.34.0",
     "better-sqlite3": "^7.5.3",
     "body-parser": "^1.15.2",
     "canvas": "~2.9.3",

package/routes/gdc.topVariablyExpressedGenes.ts

@@ -8,14 +8,8 @@ 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'
 
 const gdcGenome = 'hg38'
 const gdcDslabel = 'GDC'
@@ -71,7 +65,7 @@ async function getGenes(q: GdcTopVariablyExpressedGenesRequest, ds: any, genome:
 	}
 
 	// change to this when api is available on prod
-	const url = path.join(geneExpHost, '/gene_expression/gene_selection')
+	const url = path.join(apihost, '/gene_expression/gene_selection')
 
 	try {
 		const response = await got.post(url, {

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
 }