@sjcrh/proteinpaint-server 2.81.6 → 2.82.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.81.6",
+  "version": "2.82.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -43,7 +43,7 @@
     "@babel/preset-env": "^7.9.6",
     "@babel/preset-typescript": "^7.21.4",
     "@babel/register": "^7.14.5",
-    "@sjcrh/proteinpaint-types": "2.81.5",
+    "@sjcrh/proteinpaint-types": "2.82.0",
     "@types/node": "^20.11.24",
     "@types/tough-cookie": "^4.0.5",
     "@typescript-eslint/eslint-plugin": "^5.60.0",

package/routes/brainImaging.js

@@ -63,14 +63,15 @@ async function getBrainImage(query, genomes) {
     }
     return new Promise((resolve, reject) => {
       const filePaths = query.selectedSampleFileNames.map((file) => path.join(dirPath, file));
-      const ps = spawn("python3", [
+      const cmd = [
         `${serverconfig.binpath}/../python/src/plotBrainImaging.py`,
         refFile,
         query.l,
         query.f,
         query.t,
         ...filePaths
-      ]);
+      ];
+      const ps = spawn(serverconfig.python, cmd);
       const imgData = [];
       ps.stdout.on("data", (data) => {
         imgData.push(data);

package/routes/termdb.singlecellSamples.js

@@ -131,7 +131,8 @@ function validateDataNative(D, ds) {
         }
         const colorColumn = plot.colorColumns.find((c) => c.name == q.colorBy?.[plot.name]) || plot.colorColumns[0];
         const lines = file2Lines[tsvfile];
-        const cells = [];
+        const expCells = [];
+        const noExpCells = [];
         for (let i = 1; i < lines.length; i++) {
           const l = lines[i].split("	");
           const cellId = lines.length > 3 ? l[0] : void 0, x = Number(l[plot.coordsColumns.x]), y = Number(l[plot.coordsColumns.y]);
@@ -144,13 +145,17 @@ function validateDataNative(D, ds) {
           if (geneExpMap) {
             if (geneExpMap[cellId] !== void 0) {
               cell.geneExp = geneExpMap[cellId];
+              expCells.push(cell);
+            } else {
+              noExpCells.push(cell);
             }
-          }
-          cells.push(cell);
+          } else
+            noExpCells.push(cell);
         }
         plots.push({
           name: plot.name,
-          cells,
+          expCells,
+          noExpCells,
           colorColumns: plot.colorColumns.map((c) => c.name),
           colorBy: colorColumn?.name,
           colorMap: colorColumn?.colorMap