@sjcrh/proteinpaint-server 2.148.1 → 2.149.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.148.1",
+  "version": "2.149.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -62,10 +62,10 @@
   "dependencies": {
     "@sjcrh/augen": "2.143.0",
     "@sjcrh/proteinpaint-python": "2.146.0",
-    "@sjcrh/proteinpaint-r": "2.146.4-0",
-    "@sjcrh/proteinpaint-rust": "2.148.1",
-    "@sjcrh/proteinpaint-shared": "2.147.1",
-    "@sjcrh/proteinpaint-types": "2.148.1",
+    "@sjcrh/proteinpaint-r": "2.149.0",
+    "@sjcrh/proteinpaint-rust": "2.149.0",
+    "@sjcrh/proteinpaint-shared": "2.149.0",
+    "@sjcrh/proteinpaint-types": "2.149.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/termdb.DE.js

@@ -182,6 +182,7 @@ async function run_DE(param, ds, term_results, term_results2) {
     cachedir: serverconfig.cachedir,
     min_count: param.min_count,
     min_total_count: param.min_total_count,
+    cpm_cutoff: param.cpm_cutoff,
     storage_type: param.storage_type,
     DE_method: param.method,
     mds_cutoff: 1e4
@@ -217,13 +218,17 @@ async function run_DE(param, ds, term_results, term_results2) {
     }
     const images = [result2.ql_image];
     if (result2.mds_image) images.push(result2.mds_image);
-    return {
+    const output = {
       data: result2.gene_data,
       sample_size2: result2.num_cases[0],
       sample_size1: result2.num_controls[0],
       method: param.method,
       images
     };
+    if (result2.bcv && result2.bcv[0] !== null && result2.bcv[0] !== void 0) {
+      output.bcv = result2.bcv[0];
+    }
+    return output;
   }
   const time1 = (/* @__PURE__ */ new Date()).valueOf();
   const result = JSON.parse(await run_rust("DEanalysis", JSON.stringify(expression_input)));

package/routes/termdb.descrstats.js

@@ -66,7 +66,7 @@ function getDescrStats(values, showOutlierRange = false) {
   if (!values.length) {
     return {};
   }
-  if (values.some((v) => !Number.isFinite(v))) throw "non-numeric values found";
+  if (values.some((v) => !Number.isFinite(v))) throw new Error("non-numeric values found");
   const sorted_arr = values.sort((a, b) => a - b);
   const n = sorted_arr.length;
   const median = computePercentile(sorted_arr, 50, true);

package/routes/termdb.violin.js

@@ -56,6 +56,8 @@ async function getViolin(q, ds) {
     },
     ds
   );
+  if (!data) throw "getData() returns nothing";
+  if (data.error) throw data.error;
   const samples = Object.values(data.samples);
   let values = samples.map((s) => s?.[q.tw.$id]?.value).filter((v) => typeof v === "number" && !q.tw.term.values?.[v]?.uncomputable);
   if (q.unit == "log") values = values.filter((v) => v > 0);

package/routes/wsimages.js

@@ -50,7 +50,8 @@ function init({ genomes }) {
         status: "ok",
         wsiSessionId: session.imageSessionId,
         overlays: session.overlays,
-        slide_dimensions: getWsiImageResponse.slide_dimensions
+        slide_dimensions: getWsiImageResponse.slide_dimensions,
+        mpp: getWsiImageResponse.mpp
       };
       res.status(200).json(payload);
     } catch (e) {