@sjcrh/proteinpaint-server 2.70.4-2 → 2.71.0

package/dataset/termdb.test.js

@@ -194,39 +194,38 @@ var termdb_test_default = {
     topVariablyExpressedGenes: { src: "native" }
   },
   assayAvailability: {
-    // use "genetic_race" as fake sources of assay availability
+    // term used below must be annotated on samples rather than patients(root). otherwise matrix will pull wrong samples for geneVariant term
     byDt: {
       // snvindel, differentiating sample origin
       1: {
         byOrigin: {
           germline: {
-            term_id: "genetic_race",
+            term_id: "assayavailability_germline",
             label: "Germline",
             // human readable label of this origin
-            yes: { value: ["European Ancestry", "Asian Ancestry"] },
-            no: { value: ["Multi-Ancestry-Admixed", "African Ancestry"] }
+            yes: { value: ["1"] },
+            no: { value: ["2"] }
           },
           somatic: {
-            term_id: "genetic_race",
+            term_id: "wgs_curated",
             label: "Somatic",
-            yes: { value: ["European Ancestry", "African Ancestry"] },
-            no: { value: ["Multi-Ancestry-Admixed", "Asian Ancestry"] }
+            yes: { value: ["1"] },
+            no: { value: ["0"] }
+            // the category doesn't exist in termdb but is still supplied since somatic.no{} is required
           }
         }
       },
       // fusion
       2: {
-        //mutations are detected from RNAseq
-        term_id: "genetic_race",
-        yes: { value: ["European Ancestry", "African Ancestry"] },
-        no: { value: ["Asian Ancestry", "Multi-Ancestry-Admixed"] }
+        term_id: "assayavailability_fusion",
+        yes: { value: ["1"] },
+        no: { value: ["2"] }
       },
       // cnv
       4: {
-        // mutations are detected from Methylation
-        term_id: "genetic_race",
-        yes: { value: ["European Ancestry", "African Ancestry"] },
-        no: { value: ["Asian Ancestry", "Multi-Ancestry-Admixed"] }
+        term_id: "assayavailability_cnv",
+        yes: { value: ["1"] },
+        no: { value: ["2"] }
       }
     }
   }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.70.4-2",
+  "version": "2.71.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -44,7 +44,6 @@
     "@babel/preset-typescript": "^7.21.4",
     "@babel/register": "^7.14.5",
     "@types/node": "^20.11.24",
-    "@types/qs": "^6.9.15",
     "@typescript-eslint/eslint-plugin": "^5.60.0",
     "babel-loader": "^8.2.2",
     "esbuild": "^0.19.12",
@@ -63,7 +62,6 @@
   "dependencies": {
     "@sjcrh/augen": "2.46.0",
     "@sjcrh/proteinpaint-rust": "2.61.1",
-    "axios": "^1.7.2",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",
@@ -83,7 +81,6 @@
     "minimatch": "^3.1.2",
     "node-fetch": "^2.6.1",
     "partjson": "^0.58.2",
-    "qs": "^6.12.3",
     "tiny-async-pool": "^1.2.0",
     "typedoc-plugin-missing-exports": "^2.0.1"
   },

package/routes/gdc.topMutatedGenes.js

@@ -218,6 +218,7 @@ const queryV2 = {
       }
     };
     if (q.filter0) {
+      variables.ssmCase.content.push(JSON.parse(JSON.stringify(q.filter0)));
       variables.caseFilters.content.push(JSON.parse(JSON.stringify(q.filter0)));
       variables.geneCaseFilter.content.push(JSON.parse(JSON.stringify(q.filter0)));
       variables.cnvLossFilters.content.push(JSON.parse(JSON.stringify(q.filter0)));

package/routes/termdb.config.js

@@ -182,11 +182,6 @@ function addNonDictionaryQueries(c, ds, genome) {
       type: q.DZImages.type
     };
   }
-  if (q.TiaImages) {
-    q2.TiaImages = {
-      type: q.TiaImages.type
-    };
-  }
   if (q.singleSampleGbtk) {
     q2.singleSampleGbtk = {};
     for (const k in q.singleSampleGbtk) {