@sjcrh/proteinpaint-server 2.48.1 → 2.49.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.48.1",
+  "version": "2.49.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,7 +61,7 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.46.0",
-    "@sjcrh/proteinpaint-rust": "2.44.0",
+    "@sjcrh/proteinpaint-rust": "2.49.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",
@@ -97,7 +97,7 @@
     "start.js",
     "src/app.js",
     "src/serverconfig.js",
-    "src/lines2R.js",
+    "src/run_R.js",
     "src/mds3.gdc.filter.js",
     "src/checkReadingFrame.js",
     "src/bedj.parseBed.js",

package/routes/burden.js

@@ -1,7 +1,6 @@
-import lines2R from "#src/lines2R.js";
+import run_R from "#src/run_R.js";
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
-import { write_file } from "#src/utils.js";
 const api = {
   endpoint: "burden",
   methods: {
@@ -69,23 +68,21 @@ const api = {
   }
 };
 async function getBurdenEstimates(q, ds) {
-  const infile = path.join(serverconfig.cachedir, Math.random().toString() + ".json");
   for (const k in q.query) {
     q.query[k] = Number(q.query[k]);
   }
   const data = Object.assign({}, defaults, q.query);
-  await write_file(infile, JSON.stringify(data));
   const { fit, surv, sample } = ds.cohort.cumburden.files;
   if (!fit || !surv || !sample)
     throw `missing one or more of ds.cohort.burden.files.{fit, surv, sample}`;
   const args = [
-    infile,
     `${serverconfig.tpmasterdir}/${fit}`,
     `${serverconfig.tpmasterdir}/${surv}`,
     `${serverconfig.tpmasterdir}/${sample}`
   ];
-  const Routput = await lines2R(path.join(serverconfig.binpath, "utils/burden.R"), [], args);
-  const estimates = JSON.parse(Routput[0]);
+  const estimates = JSON.parse(
+    await run_R(path.join(serverconfig.binpath, "utils", "burden.R"), JSON.stringify(data), args)
+  );
   return estimates;
 }
 function formatPayload(estimates) {

package/routes/termdb.cluster.js

@@ -1,6 +1,5 @@
 import path from "path";
-import fs from "fs";
-import lines2R from "#src/lines2R.js";
+import run_R from "#src/run_R.js";
 import * as utils from "#src/utils.js";
 import serverconfig from "#src/serverconfig.js";
 import { gdc_validate_query_geneExpression } from "#src/mds3.gdc.js";
@@ -90,10 +89,9 @@ async function doClustering(data, q) {
     }
     inputData.matrix.push(getZscore(row));
   }
-  const Rinputfile = path.join(serverconfig.cachedir, Math.random().toString() + ".json");
-  await utils.write_file(Rinputfile, JSON.stringify(inputData));
-  const Routput = JSON.parse(await lines2R(path.join(serverconfig.binpath, "utils/hclust.R"), [], [Rinputfile]));
-  await fs.promises.unlink(Rinputfile);
+  const Routput = JSON.parse(
+    await run_R(path.join(serverconfig.binpath, "utils", "hclust.R"), JSON.stringify(inputData))
+  );
   const row_names_index = Routput.RowOrder.map((row) => inputData.row_names.indexOf(row.name));
   const col_names_index = Routput.ColOrder.map((col) => inputData.col_names.indexOf(col.name));
   const output_matrix = [];