@sjcrh/proteinpaint-server 2.88.0 → 2.88.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.88.0",
+  "version": "2.88.2",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -60,8 +60,8 @@
   "dependencies": {
     "@sjcrh/augen": "2.87.0",
     "@sjcrh/proteinpaint-rust": "2.84.0",
-    "@sjcrh/proteinpaint-shared": "2.87.1",
-    "@sjcrh/proteinpaint-types": "2.88.0",
+    "@sjcrh/proteinpaint-shared": "2.88.2",
+    "@sjcrh/proteinpaint-types": "2.88.2",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/termdb.boxplot.js

@@ -159,15 +159,15 @@ function setDescrStats(boxplot, sortedValues) {
   const variance = squareDiffs / (sortedValues.length - 1);
   return [
     { id: "total", label: "Total", value: sortedValues.length },
-    { id: "min", label: "Minimum", value: roundValueAuto(sortedValues[0]) },
-    { id: "p25", label: "1st quartile", value: roundValueAuto(boxplot.p25) },
-    { id: "median", label: "Median", value: roundValueAuto(boxplot.p50) },
-    { id: "mean", label: "Mean", value: roundValueAuto(mean) },
-    { id: "p75", label: "3rd quartile", value: roundValueAuto(boxplot.p75) },
-    { id: "max", label: "Maximum", value: roundValueAuto(sortedValues[sortedValues.length - 1]) },
-    { id: "sd", label: "Standard deviation", value: isNaN(sd) ? null : roundValueAuto(sd) },
-    { id: "variance", label: "Variance", value: roundValueAuto(variance) },
-    { id: "iqr", label: "Inter-quartile range", value: roundValueAuto(boxplot.iqr) }
+    { id: "min", label: "Minimum", value: roundValueAuto(sortedValues[0], true) },
+    { id: "p25", label: "1st quartile", value: roundValueAuto(boxplot.p25, true) },
+    { id: "median", label: "Median", value: roundValueAuto(boxplot.p50, true) },
+    { id: "mean", label: "Mean", value: roundValueAuto(mean, true) },
+    { id: "p75", label: "3rd quartile", value: roundValueAuto(boxplot.p75, true) },
+    { id: "max", label: "Maximum", value: roundValueAuto(sortedValues[sortedValues.length - 1], true) },
+    { id: "sd", label: "Standard deviation", value: isNaN(sd) ? null : roundValueAuto(sd, true) },
+    { id: "variance", label: "Variance", value: roundValueAuto(variance, true) },
+    { id: "iqr", label: "Inter-quartile range", value: roundValueAuto(boxplot.iqr, true) }
   ];
 }
 function setUncomputableValues(values) {

package/routes/termdb.singlecellSamples.js

@@ -2,7 +2,7 @@ import fs from "fs";
 import path from "path";
 import { read_file } from "#src/utils.js";
 import run_R from "#src/run_R.js";
-import { joinUrl } from "#src/helpers.ts";
+import { joinUrl, mayLog } from "#src/helpers.ts";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
 import { termdbSingleCellSamplesPayload } from "#types/checkers";
@@ -227,7 +227,6 @@ function gdc_validateGeneExpression(G, ds, genome) {
   G.sample2gene2expressionBins = {};
   G.get = async (q) => {
     try {
-      const uuid = ds.__gdc.map2caseid.get(q.sample.sID);
       const fileid = q.sample.eID;
       const hdf5id = ds.__gdc.scrnaAnalysis2hdf5.get(fileid);
       if (!hdf5id)
@@ -241,7 +240,12 @@ function gdc_validateGeneExpression(G, ds, genome) {
         file_id: hdf5id
       };
       const { host } = ds.getHostHeaders(q);
-      const out = await ky.post(joinUrl(host.rest, "scrna_seq/gene_expression"), { timeout: false, json: body }).json();
+      const t = Date.now();
+      const response = await ky.post(joinUrl(host.rest, "scrna_seq/gene_expression"), { timeout: false, json: body });
+      if (!response.ok)
+        throw `HTTP Error: ${response.status} ${response.statusText}`;
+      const out = await response.json();
+      mayLog("gdc scrna gene exp", q.gene, Date.now() - t);
       const result = out.data[0].cells;
       const data = {};
       for (const r of result) {