@sjcrh/proteinpaint-server 2.98.2-1 → 2.99.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.98.2-1",
+  "version": "2.99.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -59,9 +59,9 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.87.0",
-    "@sjcrh/proteinpaint-rust": "2.84.0",
-    "@sjcrh/proteinpaint-shared": "2.98.0",
-    "@sjcrh/proteinpaint-types": "2.98.2-1",
+    "@sjcrh/proteinpaint-rust": "2.99.0",
+    "@sjcrh/proteinpaint-shared": "2.99.0",
+    "@sjcrh/proteinpaint-types": "2.99.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/correlationVolcano.js

@@ -70,16 +70,10 @@ async function compute(q, ds, genome) {
     terms: [...vtid2array.values()]
   };
   const time1 = Date.now();
-  const r_output = await run_R(path.join(serverconfig.binpath, "utils", "corr.R"), JSON.stringify(input));
+  const output = {
+    terms: JSON.parse(await run_R(path.join(serverconfig.binpath, "utils", "corr.R"), JSON.stringify(input)))
+  };
   mayLog("Time taken to run correlation analysis:", Date.now() - time1);
-  let json_result;
-  for (const line of r_output.split("\n")) {
-    if (line.startsWith("adjusted_p_values:")) {
-      json_result = JSON.parse(line.replace("adjusted_p_values:", ""));
-    } else {
-    }
-  }
-  const output = { terms: json_result };
   const result = { variableItems: [] };
   for (const t of output.terms) {
     const t2 = {

package/routes/termdb.DE.js

@@ -4,6 +4,7 @@ import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { getData } from "../src/termdb.matrix.js";
 import { get_ds_tdb } from "../src/termdb.js";
 import run_R from "../src/run_R.js";
+import { mayLog } from "#src/helpers.ts";
 import serverconfig from "../src/serverconfig.js";
 const api = {
   endpoint: "DEanalysis",
@@ -120,27 +121,15 @@ async function run_DE(param, ds, term_results) {
   let result;
   if (group1names.length <= sample_size_limit && group2names.length <= sample_size_limit || param.method == "edgeR") {
     const time1 = (/* @__PURE__ */ new Date()).valueOf();
-    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 {
-      }
-    }
+    result = JSON.parse(
+      await run_R(path.join(serverconfig.binpath, "utils", "edge.R"), JSON.stringify(expression_input))
+    );
+    mayLog("Time taken to run edgeR:", Date.now() - time1, "ms");
     param.method = "edgeR";
   } else {
     const time1 = (/* @__PURE__ */ new Date()).valueOf();
-    const rust_output = await run_rust("DEanalysis", JSON.stringify(expression_input));
-    const time2 = (/* @__PURE__ */ new Date()).valueOf();
-    for (const line of rust_output.split("\n")) {
-      if (line.startsWith("adjusted_p_values:")) {
-        result = JSON.parse(line.replace("adjusted_p_values:", ""));
-      } else {
-      }
-    }
-    console.log("Time taken to run rust DE pipeline:", time2 - time1, "ms");
+    result = JSON.parse(await run_rust("DEanalysis", JSON.stringify(expression_input)));
+    mayLog("Time taken to run rust DE pipeline:", Date.now() - time1, "ms");
     param.method = "wilcoxon";
   }
   return { data: result, sample_size1, sample_size2, method: param.method };

package/routes/termdb.singlecellSamples.js

@@ -1,7 +1,6 @@
 import fs from "fs";
 import path from "path";
-import { read_file } from "#src/utils.js";
-import run_R from "#src/run_R.js";
+import { read_file, file_is_readable } from "#src/utils.js";
 import { joinUrl, mayLog } from "#src/helpers.ts";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
@@ -138,16 +137,7 @@ function validateDataNative(D, ds) {
           (q.sample.eID || q.sample.sID) + plot.fileSuffix
         );
         if (!file2Lines[tsvfile]) {
-          try {
-            await fs.promises.stat(tsvfile);
-          } catch (e) {
-            if (e.code == "ENOENT") {
-              continue;
-            }
-            if (e.code == "EACCES")
-              throw "cannot read file, permission denied";
-            throw "failed to load sc data file";
-          }
+          await file_is_readable(tsvfile);
           file2Lines[tsvfile] = (await read_file(tsvfile)).trim().split("\n");
         }
         const colorColumn = plot.colorColumns.find((c) => c.name == q.colorBy?.[plot.name]) || plot.colorColumns[0];
@@ -195,52 +185,28 @@ function validateDataNative(D, ds) {
 }
 function validateGeneExpressionNative(G) {
   G.sample2gene2expressionBins = {};
-  if (G.storage_type == "RDS" || !G.storage_type) {
-    G.get = async (q) => {
-      const rdsfile = path.join(serverconfig.tpmasterdir, G.folder, (q.sample.eID || q.sample.sID) + ".rds");
-      try {
-        await fs.promises.stat(rdsfile);
-      } catch (_) {
-        return {};
-      }
-      let out;
-      try {
-        out = JSON.parse(
-          await run_R(path.join(serverconfig.binpath, "utils", "getGeneFromMatrix.R"), null, [rdsfile, q.gene])
-        );
-      } catch (_) {
-        return {};
-      }
-      return out;
-    };
-  } else if (G.storage_type == "HDF5") {
-    G.get = async (q) => {
-      const rdsfile = path.join(serverconfig.tpmasterdir, G.folder, (q.sample.eID || q.sample.sID) + ".h5");
-      try {
-        await fs.promises.stat(rdsfile);
-      } catch (_) {
-        return {};
-      }
-      const read_hdf5_input_type = { gene: q.gene, hdf5_file: rdsfile };
-      let out;
-      try {
-        const time1 = (/* @__PURE__ */ new Date()).valueOf();
-        const rust_output = await run_rust("readHDF5", JSON.stringify(read_hdf5_input_type));
-        const time2 = (/* @__PURE__ */ new Date()).valueOf();
-        console.log("Time taken to query HDF5 file:", time2 - time1, "ms");
-        for (const line of rust_output.split("\n")) {
-          if (line.startsWith("output_string:")) {
-            out = JSON.parse(line.replace("output_string:", ""));
-          } else {
-            console.log(line);
-          }
+  G.get = async (q) => {
+    const h5file = path.join(serverconfig.tpmasterdir, G.folder, (q.sample.eID || q.sample.sID) + ".h5");
+    await file_is_readable(h5file);
+    const read_hdf5_input_type = { gene: q.gene, hdf5_file: h5file };
+    let out;
+    try {
+      const time1 = Date.now();
+      const rust_output = await run_rust("readHDF5", JSON.stringify(read_hdf5_input_type));
+      mayLog("Time taken to query HDF5 file:", Date.now() - time1, "ms");
+      for (const line of rust_output.split("\n")) {
+        if (line.startsWith("output_string:")) {
+          out = JSON.parse(line.replace("output_string:", ""));
+        } else {
+          console.log(line);
         }
-      } catch (_) {
-        return {};
       }
-      return out;
-    };
-  }
+    } catch (e) {
+      console.log(e);
+      throw "error reading h5 file: " + e;
+    }
+    return out;
+  };
 }
 function gdc_validateGeneExpression(G, ds, genome) {
   G.sample2gene2expressionBins = {};