@sjcrh/proteinpaint-server 2.116.1-0 → 2.116.1-1

package/dataset/termdb.test.js

@@ -20,6 +20,7 @@ var termdb_test_default = {
       file: "files/hg38/TermdbTest/db"
     },
     termdb: {
+      allowedTermTypes: ["geneVariant"],
       displaySampleIds: true,
       // allow to display sample-level data
       timeUnit: "years",
@@ -83,7 +84,12 @@ var termdb_test_default = {
           ignoreCnvValues: true
         }
       },
-      termid2totalsize2: {}
+      termid2totalsize2: {},
+      regression: {
+        settings: {
+          coxDisclaimer: "This is a test disclaimer for the cox regression analysis."
+        }
+      }
     },
     scatterplots: {
       plots: [
@@ -127,8 +133,6 @@ var termdb_test_default = {
     sunburst_twLst: [{ id: "sex", q: {} }]
   },
   queries: {
-    // temporary fix for genomeBrowser app to show gene model
-    defaultBlock2GeneMode: true,
     snvindel: {
       forTrack: true,
       byrange: {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.116.1-0",
+  "version": "2.116.1-1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -67,8 +67,8 @@
   "dependencies": {
     "@sjcrh/augen": "2.116.0",
     "@sjcrh/proteinpaint-rust": "2.116.0",
-    "@sjcrh/proteinpaint-shared": "2.116.0",
-    "@sjcrh/proteinpaint-types": "2.116.1-0",
+    "@sjcrh/proteinpaint-shared": "2.116.1-1",
+    "@sjcrh/proteinpaint-types": "2.116.1-1",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/termdb.config.js

@@ -2,7 +2,6 @@ import serverconfig from "#src/serverconfig.js";
 import { authApi } from "#src/auth.js";
 import { get_ds_tdb } from "#src/termdb.js";
 import { mayCopyFromCookie } from "#src/utils.js";
-import { mayComputeTermtypeByCohort } from "#src/termdb.server.init.ts";
 import { TermTypes } from "#shared/terms.js";
 const api = {
   endpoint: "termdb/config",
@@ -142,11 +141,10 @@ function addNonDictionaryQueries(c, ds, genome) {
   if (!q)
     return;
   c.queries = {
-    defaultCoord: q.defaultCoord || genome.defaultcoord
+    defaultCoord: q.defaultCoord || genome.defaultcoord,
+    gbRestrictMode: q.gbRestrictMode
   };
   const q2 = c.queries;
-  if (q.defaultBlock2GeneMode)
-    q2.defaultBlock2GeneMode = q.defaultBlock2GeneMode;
   if (q.snvindel) {
     q2.snvindel = {
       allowSNPs: q.snvindel.allowSNPs,
@@ -256,7 +254,6 @@ function addNonDictionaryQueries(c, ds, genome) {
   }
 }
 function getAllowedTermTypes(ds) {
-  mayComputeTermtypeByCohort(ds);
   const typeSet = /* @__PURE__ */ new Set();
   for (const r of ds.cohort.termdb.termtypeByCohort) {
     if (r.termType)
@@ -266,9 +263,6 @@ function getAllowedTermTypes(ds) {
     for (const t of ds.cohort.termdb.allowedTermTypes)
       typeSet.add(t);
   }
-  if (ds?.queries?.defaultBlock2GeneMode) {
-    typeSet.add("geneVariant");
-  }
   if (ds?.queries?.geneExpression)
     typeSet.add(TermTypes.GENE_EXPRESSION);
   if (ds?.queries?.metaboliteIntensity)

package/routes/termdb.topMutatedGenes.js

@@ -1,4 +1,6 @@
 import { topMutatedGenePayload } from "#types/checkers";
+import { get_samples } from "#src/termdb.sql.js";
+import { mayLog } from "#src/helpers.ts";
 const api = {
   endpoint: "termdb/topMutatedGenes",
   methods: {
@@ -42,7 +44,96 @@ function validate_query_getTopMutatedGenes(ds, genome) {
     return;
   if (typeof q.get == "function")
     return;
+  if (!q.arguments) {
+    q.arguments = [];
+    q.arguments.push({ id: "maxGenes", label: "Gene Count", type: "number", value: 50 });
+    if (ds.queries.snvindel) {
+      q.arguments.push({ id: "snv_mfndi", label: "Protein-changing mutation", type: "boolean", value: true });
+      q.arguments.push({ id: "snv_splice", label: "Splice mutation", type: "boolean", value: true });
+      q.arguments.push({ id: "snv_utr", label: "UTR mutation", type: "boolean", value: true });
+      q.arguments.push({ id: "snv_s", label: "Silent mutation", type: "boolean", value: true });
+    }
+    if (ds.queries.svfusion) {
+      q.arguments.push({ id: "sv", label: "Structural variation", type: "boolean", value: true });
+      q.arguments.push({ id: "fusion", label: "RNA fusion", type: "boolean", value: true });
+    }
+    if (ds.queries.cnv) {
+      q.arguments.push({
+        id: "cnv",
+        type: "boolean",
+        label: "CNV",
+        checked: false,
+        noStyle: true,
+        //This is a hack
+        options: [
+          {
+            id: "cnv_ms",
+            label: "Max size",
+            type: "radio",
+            options: [
+              { id: "cnv_1mb", label: "<1Mb", value: "cnv_1mb" },
+              { id: "cnv_2mb", label: "<2Mb", value: "cnv_2mb" },
+              { id: "cnv_4mb", label: "<4Mb", value: "cnv_4mb" }
+            ]
+          },
+          {
+            id: "cnv_logratio",
+            label: "Min absolute log(ratio)",
+            type: "radio",
+            options: [
+              { id: "_01", label: ">0.1", value: "_01" },
+              { id: "_02", label: ">0.2", value: "_02" },
+              { id: "_03", label: ">0.3", value: "_03" }
+            ]
+          }
+        ]
+      });
+    }
+  }
   q.get = async (param) => {
+    let sampleStatement = "";
+    if (param.filter) {
+      const lst = await get_samples(param.filter, ds);
+      if (lst.length == 0)
+        throw "empty sample filter";
+      sampleStatement = `WHERE sample IN (${lst.map((i) => i.id).join(",")})`;
+    }
+    const fields = [];
+    if (param.snv_mfndi)
+      fields.push("snv_mfndi");
+    if (param.snv_splice)
+      fields.push("snv_splice");
+    if (param.snv_utr)
+      fields.push("snv_utr");
+    if (param.snv_s)
+      fields.push("snv_s");
+    if (param.sv)
+      fields.push("sv");
+    if (param.fusion)
+      fields.push("fusion");
+    if (param.cnv == 1 && param.cnv_ms?.type && param.cnv_logratio?.type) {
+      fields.push(param.cnv_ms.type + param.cnv_logratio.type);
+    }
+    if (!fields.length)
+      throw "no fields";
+    const query = `WITH
+		filtered AS (
+			SELECT genesymbol, ${fields.join("+")} AS total FROM genesamplemutationcount
+			${sampleStatement}
+		)
+		SELECT genesymbol, SUM(total) AS count
+		FROM filtered
+		GROUP BY genesymbol
+		ORDER BY count DESC
+		LIMIT ${param.maxGenes || 20}`;
+    const t = Date.now();
+    const genes = ds.cohort.db.connection.prepare(query).all();
+    mayLog("Top mutated gene sql", Date.now() - t, "ms");
+    const results = [];
+    for (const g of genes) {
+      results.push({ gene: g.genesymbol });
+    }
+    return results;
   };
 }
 export {