@sjcrh/proteinpaint-server 2.91.1-1 → 2.92.1-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.91.1-1",
+  "version": "2.92.1-0",
   "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/augen": "2.87.0",
     "@sjcrh/proteinpaint-rust": "2.84.0",
     "@sjcrh/proteinpaint-shared": "2.88.2",
-    "@sjcrh/proteinpaint-types": "2.89.1",
+    "@sjcrh/proteinpaint-types": "2.92.1-0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/termdb.DE.js

@@ -80,8 +80,8 @@ async function run_DE(param, ds) {
   const cases_string = group1names.map((i) => i).join(",");
   const controls_string = group2names.map((i) => i).join(",");
   const expression_input = {
-    case: cases_string,
-    control: controls_string,
+    case: controls_string,
+    control: cases_string,
     data_type: "do_DE",
     input_file: q.file,
     min_count: param.min_count,
@@ -92,11 +92,15 @@ async function run_DE(param, ds) {
   let result;
   if (group1names.length <= sample_size_limit && group2names.length <= sample_size_limit || param.method == "edgeR") {
     const time1 = (/* @__PURE__ */ new Date()).valueOf();
-    result = JSON.parse(
-      await run_R(path.join(serverconfig.binpath, "utils", "edge.R"), JSON.stringify(expression_input))
-    );
+    const r_output = await run_R(path.join(serverconfig.binpath, "utils", "edge.R"), JSON.stringify(expression_input));
     const time2 = (/* @__PURE__ */ new Date()).valueOf();
     console.log("Time taken to run edgeR:", time2 - time1, "ms");
+    for (const line of r_output.split("\n")) {
+      if (line.startsWith("adjusted_p_values:")) {
+        result = JSON.parse(line.replace("adjusted_p_values:", ""));
+      } else {
+      }
+    }
     param.method = "edgeR";
   } else if (param.method == "wilcoxon") {
     const time1 = (/* @__PURE__ */ new Date()).valueOf();

package/routes/termdb.config.js

@@ -219,8 +219,7 @@ function addNonDictionaryQueries(c, ds, genome) {
       data: {
         sameLegend: q.singleCell.data.sameLegend,
         refName: q.singleCell.data.refName,
-        width: q.singleCell.data.width,
-        height: q.singleCell.data.height,
+        settings: q.singleCell.data.settings,
         plots: q.singleCell.data.plots.map((p) => {
           return { name: p.name, colorColumns: p.colorColumns.map((c2) => c2.name), selected: p.selected };
         })

package/routes/termdb.singlecellSamples.js

@@ -254,7 +254,7 @@ function gdc_validateGeneExpression(G, ds, genome) {
     } catch (e) {
       if (e.stack)
         console.log(e.stack);
-      return { error: e.message || e };
+      return { error: "GDC scRNAseq gene expression request failed with error: " + (e.message || e) };
     }
   };
 }