@sjcrh/proteinpaint-server 2.96.1 → 2.96.2-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.96.1",
+  "version": "2.96.2-0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -42,6 +42,7 @@
     "@babel/preset-env": "^7.9.6",
     "@babel/preset-typescript": "^7.21.4",
     "@babel/register": "^7.14.5",
+    "@sjcrh/proteinpaint-types": "2.96.2-0",
     "@types/node": "^20.11.24",
     "@types/tough-cookie": "^4.0.5",
     "@typescript-eslint/eslint-plugin": "^8.13.0",
@@ -61,7 +62,6 @@
     "@sjcrh/augen": "2.87.0",
     "@sjcrh/proteinpaint-rust": "2.84.0",
     "@sjcrh/proteinpaint-shared": "2.96.0",
-    "@sjcrh/proteinpaint-types": "2.96.1",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/termdb.DE.js

@@ -1,6 +1,7 @@
 import path from "path";
 import { diffExpPayload } from "#types/checkers";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
+import { getData } from "../src/termdb.matrix.js";
 import { get_ds_tdb } from "../src/termdb.js";
 import run_R from "../src/run_R.js";
 import serverconfig from "../src/serverconfig.js";
@@ -25,7 +26,22 @@ function init({ genomes }) {
       if (!genome)
         throw "invalid genome";
       const [ds] = get_ds_tdb(genome, q);
-      const results = await run_DE(req.query, ds);
+      let term_results = [];
+      if (q.tw) {
+        const terms = [q.tw];
+        term_results = await getData(
+          {
+            filter: q.filter,
+            filter0: q.filter0,
+            terms
+          },
+          ds,
+          genome
+        );
+        if (term_results.error)
+          throw term_results.error;
+      }
+      const results = await run_DE(req.query, ds, term_results);
       res.send(results);
     } catch (e) {
       res.send({ status: "error", error: e.message || e });
@@ -34,7 +50,7 @@ function init({ genomes }) {
     }
   };
 }
-async function run_DE(param, ds) {
+async function run_DE(param, ds, term_results) {
   if (param.samplelst?.groups?.length != 2)
     throw ".samplelst.groups.length!=2";
   if (param.samplelst.groups[0].values?.length < 1)
@@ -48,6 +64,7 @@ async function run_DE(param, ds) {
   if (!q.file)
     throw "unknown data type for rnaseqGeneCount";
   const group1names = [];
+  const conf1_group1 = [];
   for (const s of param.samplelst.groups[0].values) {
     if (!Number.isInteger(s.sampleId))
       continue;
@@ -56,10 +73,14 @@ async function run_DE(param, ds) {
       continue;
     if (q.allSampleSet.has(n)) {
       group1names.push(n);
+      if (param.tw) {
+        conf1_group1.push(term_results.samples[s.sampleId][param.tw.$id]["value"]);
+      }
     } else {
     }
   }
   const group2names = [];
+  const conf1_group2 = [];
   for (const s of param.samplelst.groups[1].values) {
     if (!Number.isInteger(s.sampleId))
       continue;
@@ -68,6 +89,9 @@ async function run_DE(param, ds) {
       continue;
     if (q.allSampleSet.has(n)) {
       group2names.push(n);
+      if (param.tw) {
+        conf1_group2.push(term_results.samples[s.sampleId][param.tw.$id]["value"]);
+      }
     } else {
     }
   }
@@ -88,6 +112,10 @@ async function run_DE(param, ds) {
     min_total_count: param.min_total_count,
     storage_type: param.storage_type
   };
+  if (param.tw) {
+    expression_input.conf1 = [...conf1_group2, ...conf1_group1];
+    expression_input.conf1_type = param.tw.term.type;
+  }
   const sample_size_limit = 8;
   let result;
   if (group1names.length <= sample_size_limit && group2names.length <= sample_size_limit || param.method == "edgeR") {
@@ -102,18 +130,6 @@ async function run_DE(param, ds) {
       }
     }
     param.method = "edgeR";
-  } else if (param.method == "wilcoxon") {
-    const time1 = (/* @__PURE__ */ new Date()).valueOf();
-    const rust_output = await run_rust("DEanalysis", JSON.stringify(expression_input));
-    const time2 = (/* @__PURE__ */ new Date()).valueOf();
-    for (const line of rust_output.split("\n")) {
-      if (line.startsWith("adjusted_p_values:")) {
-        result = JSON.parse(line.replace("adjusted_p_values:", ""));
-      } else {
-      }
-    }
-    console.log("Time taken to run rust DE pipeline:", time2 - time1, "ms");
-    param.method = "wilcoxon";
   } else {
     const time1 = (/* @__PURE__ */ new Date()).valueOf();
     const rust_output = await run_rust("DEanalysis", JSON.stringify(expression_input));