@sjcrh/proteinpaint-server 2.210.1 → 2.211.0

package/dataset/termdb.test.js

@@ -74,6 +74,13 @@ function termdb_test_default() {
         allowedTermTypes: ["geneVariant"],
         displaySampleIds: () => true,
         // allow to display sample-level data
+        /* the hg38-test gene db is a stub of ~11 genes, while the expression matrix of this
+        ds carries the real gene universe (topVariablyExpressedGenes answers ISG15, MXRA8, ...).
+        Without this, every one of those genes would be rejected as unknown to the genome before
+        its data is read -- see geneRefValidation.ts, which validates against the gene db.
+        geneVariant and isoformExpression stay validated: their fixtures are genes/isoforms that
+        the stub gene db does have */
+        skipGeneNameValidation: ["geneExpression"],
         timeUnit: "years",
         ageEndOffset: 274e-5,
         // number of years to offset ending age of patients

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.210.1",
+  "version": "2.211.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,7 +61,7 @@
     "@sjcrh/proteinpaint-r": "2.207.1",
     "@sjcrh/proteinpaint-rust": "2.209.0",
     "@sjcrh/proteinpaint-shared": "2.210.1",
-    "@sjcrh/proteinpaint-types": "2.210.1",
+    "@sjcrh/proteinpaint-types": "2.211.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",
@@ -121,5 +121,5 @@
       ]
     ]
   },
-  "_buildTime": "2026-09-21T21:01:24Z"
+  "_buildTime": "2026-09-24T02:12:34Z"
 }

package/routes/termdb.proteome.js

@@ -180,7 +180,7 @@ async function validate_query_proteome(ds) {
       }
     }
   }
-  const geneIndexHint = q.db.prepare(`SELECT 1 FROM sqlite_master WHERE type = 'index' AND name = 'proteome_abundance_gene'`).get() ? " INDEXED BY proteome_abundance_gene" : "";
+  const geneIndexHint = q.db.prepare("SELECT 1 FROM sqlite_master WHERE type = ? AND name = ?").get("index", "proteome_abundance_gene") ? " INDEXED BY proteome_abundance_gene" : "";
   q.find = async (arg) => {
     const proteins = arg?.proteins;
     if (!Array.isArray(proteins) || proteins.length == 0) throw "queries.proteome.find arg.proteins[] missing";