@sjcrh/proteinpaint-server 2.57.0 → 2.57.1-1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.57.0",
+  "version": "2.57.1-1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,7 +61,7 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.46.0",
-    "@sjcrh/proteinpaint-rust": "2.55.0",
+    "@sjcrh/proteinpaint-rust": "2.57.1-1",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/genesetOverrepresentation.js

@@ -0,0 +1,56 @@
+import { run_rust } from "@sjcrh/proteinpaint-rust";
+const api = {
+  endpoint: "genesetOverrepresentation",
+  methods: {
+    all: {
+      init,
+      request: {
+        typeId: "genesetOverrepresentationRequest"
+      },
+      response: {
+        typeId: "genesetOverrepresentationResponse"
+        // will combine this with type checker
+        //valid: (t) => {}
+      }
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const results = await run_genesetOverrepresentation_analysis(
+        req.query,
+        genomes
+      );
+      res.send(results);
+    } catch (e) {
+      res.send({ status: "error", error: e.message || e });
+    }
+  };
+}
+async function run_genesetOverrepresentation_analysis(q, genomes) {
+  if (!genomes[q.genome].termdbs)
+    throw "termdb database is not available for " + q.genome;
+  const gene_overrepresentation_input = {
+    sample_genes: q.sample_genes,
+    background_genes: q.background_genes,
+    db: genomes[q.genome].termdbs.msigdb.cohort.db.connection.name,
+    gene_set_group: q.geneSetGroup
+  };
+  const time1 = (/* @__PURE__ */ new Date()).valueOf();
+  const rust_output = await run_rust("genesetORA", JSON.stringify(gene_overrepresentation_input));
+  const time2 = (/* @__PURE__ */ new Date()).valueOf();
+  console.log("Time taken to run rust gene over representation pipeline:", time2 - time1, "ms");
+  let result;
+  for (const line of rust_output.split("\n")) {
+    if (line.startsWith("pathway_p_values:")) {
+      result = JSON.parse(line.replace("pathway_p_values:", ""));
+    } else {
+      console.log(line);
+    }
+  }
+  return result;
+}
+export {
+  api
+};

package/routes/termdb.categories.js

@@ -87,10 +87,23 @@ function init({ genomes }) {
 async function trigger_getcategories(q, res, tdb, ds, genome) {
   if (!q.tid)
     throw ".tid missing";
-  const term = q.type == "geneVariant" ? { name: q.tid, type: "geneVariant", isleaf: true } : tdb.q.termjsonByOneid(q.tid);
+  let term;
+  if (q.type == "geneVariant") {
+    term = { id: q.name, name: q.name, type: "geneVariant", isleaf: true };
+    if (q.gene) {
+      term.gene = q.gene;
+    } else {
+      term.chr = q.chr;
+      term.start = q.start;
+      term.stop = q.stop;
+    }
+  } else {
+    term = tdb.q.termjsonByOneid(q.tid);
+  }
+  const tw = q.type == "geneVariant" ? { $id: q.gene || q.name || q.tid, term, q: { isAtomic: true } } : { $id: q.tid, id: q.tid, term, q: q.term1_q || getDefaultQ(term, q) };
   const arg = {
     filter: q.filter,
-    terms: q.type == "geneVariant" ? [{ term, q: { isAtomic: true } }] : [{ id: q.tid, term, q: q.term1_q || getDefaultQ(term, q) }],
+    terms: [tw],
     currentGeneNames: q.currentGeneNames,
     // optional, from mds3 mayAddGetCategoryArgs()
     rglst: q.rglst
@@ -112,7 +125,8 @@ async function trigger_getcategories(q, res, tdb, ds, genome) {
     }
     const sampleCountedFor = /* @__PURE__ */ new Set();
     for (const [sampleId, sampleData] of Object.entries(samples)) {
-      const values = sampleData[q.tid].values;
+      const key = tw.$id;
+      const values = sampleData[key].values;
       sampleCountedFor.clear();
       for (const value of values) {
         if (!dtClassMap.has(value.dt)) {

package/routes/termdb.cluster.js

@@ -136,6 +136,7 @@ async function validate_query_geneExpression(ds, genome) {
   const q = ds.queries.geneExpression;
   if (!q)
     return;
+  q.gene2density = {};
   if (q.src == "gdcapi") {
     gdc_validate_query_geneExpression(ds, genome);
     return;

package/routes/termdb.config.js

@@ -206,6 +206,8 @@ function getAllowedTermTypes(ds) {
   if (ds?.queries?.defaultBlock2GeneMode) {
     typeSet.add("geneVariant");
   }
+  if (ds?.queries?.geneExpression)
+    typeSet.add("geneExpression");
   return [...typeSet];
 }
 export {