@sjcrh/proteinpaint-server 2.155.0 → 2.157.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.155.0",
+  "version": "2.157.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,11 +61,11 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.143.0",
-    "@sjcrh/proteinpaint-python": "2.153.1-3",
+    "@sjcrh/proteinpaint-python": "2.157.0",
     "@sjcrh/proteinpaint-r": "2.152.1-0",
-    "@sjcrh/proteinpaint-rust": "2.152.1-0",
-    "@sjcrh/proteinpaint-shared": "2.153.1-2",
-    "@sjcrh/proteinpaint-types": "2.153.1-2",
+    "@sjcrh/proteinpaint-rust": "2.157.0",
+    "@sjcrh/proteinpaint-shared": "2.157.0",
+    "@sjcrh/proteinpaint-types": "2.157.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/grin2.js

@@ -2,6 +2,7 @@ import { GRIN2Payload } from "#types/checkers";
 import serverconfig from "#src/serverconfig.js";
 import path from "path";
 import { run_python } from "@sjcrh/proteinpaint-python";
+import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { mayLog } from "#src/helpers.ts";
 import { get_samples } from "#src/termdb.sql.js";
 import { read_file, file_is_readable } from "#src/utils.js";
@@ -88,10 +89,6 @@ async function runGrin2(g, ds, request) {
     genedb: path.join(serverconfig.tpmasterdir, g.genedb.dbfile),
     chromosomelist: {},
     lesion: JSON.stringify(lesions),
-    devicePixelRatio: request.devicePixelRatio,
-    pngDotRadius: request.pngDotRadius,
-    width: request.width,
-    height: request.height,
     cacheFileName: generateCacheFileName(),
     availableDataTypes: getAvailableDataTypes(request),
     maxGenesToShow: request.maxGenesToShow
@@ -114,14 +111,29 @@ async function runGrin2(g, ds, request) {
   const grin2AnalysisTimeToPrint = Math.round(grin2AnalysisTime / 1e3);
   mayLog(`[GRIN2] Python processing took ${grin2AnalysisTimeToPrint} seconds`);
   const resultData = JSON.parse(pyResult);
-  if (!resultData?.png?.[0]) {
-    throw new Error("Invalid Python output: missing PNG data");
+  const rustInput = {
+    file: resultData.cacheFileName,
+    type: "grin2",
+    chrSizes: pyInput.chromosomelist,
+    plot_width: request.width,
+    plot_height: request.height,
+    device_pixel_ratio: request.devicePixelRatio,
+    png_dot_radius: request.pngDotRadius
+  };
+  const manhattanPlotStart = Date.now();
+  const rsResult = await run_rust("manhattan_plot", JSON.stringify(rustInput));
+  const manhattanPlotTime = Date.now() - manhattanPlotStart;
+  const manhattanPlotTimeToPrint = Math.round(manhattanPlotTime / 1e3);
+  mayLog(`[GRIN2] Manhattan plot generation took ${manhattanPlotTimeToPrint} seconds`);
+  const manhattanPlotData = JSON.parse(rsResult);
+  if (!manhattanPlotData?.png) {
+    throw new Error("Invalid Rust output: missing PNG data");
   }
   const totalTime = Math.round((Date.now() - startTime) / 1e3);
   const response = {
     status: "success",
-    pngImg: resultData.png[0],
-    plotData: resultData.plotData,
+    pngImg: manhattanPlotData.png,
+    plotData: manhattanPlotData.plot_data,
     topGeneTable: resultData.topGeneTable,
     totalGenes: resultData.totalGenes,
     showingTop: resultData.showingTop,

package/routes/termdb.DE.js

@@ -11,7 +11,7 @@ import imagesize from "image-size";
 import { get_header_txt } from "#src/utils.js";
 import { formatElapsedTime } from "@sjcrh/proteinpaint-shared/time.js";
 const api = {
-  endpoint: "DEanalysis",
+  endpoint: "termdb/DE",
   methods: {
     get: {
       ...diffExpPayload,
@@ -28,7 +28,7 @@ function init({ genomes }) {
     try {
       const q = req.query;
       const genome = genomes[q.genome];
-      if (!genome) throw "invalid genome";
+      if (!genome) throw new Error("invalid genome");
       const [ds] = get_ds_tdb(genome, q);
       let term_results = [];
       if (q.tw) {
@@ -41,7 +41,7 @@ function init({ genomes }) {
           },
           ds
         );
-        if (term_results.error) throw term_results.error;
+        if (term_results.error) throw new Error(term_results.error);
       }
       let term_results2 = [];
       if (q.tw2) {
@@ -54,10 +54,10 @@ function init({ genomes }) {
           },
           ds
         );
-        if (term_results2.error) throw term_results2.error;
+        if (term_results2.error) throw new Error(term_results2.error);
       }
       const results = await run_DE(req.query, ds, term_results, term_results2);
-      if (!results || !results.data) throw "No data [termdb.DE.ts init()]";
+      if (!results || !results.data) throw new Error("No data available");
       res.send(results);
     } catch (e) {
       res.send({ status: "error", error: e.message || e });
@@ -66,13 +66,13 @@ function init({ genomes }) {
   };
 }
 async function run_DE(param, ds, term_results, term_results2) {
-  if (param.samplelst?.groups?.length != 2) throw ".samplelst.groups.length!=2";
-  if (param.samplelst.groups[0].values?.length < 1) throw "samplelst.groups[0].values.length<1";
-  if (param.samplelst.groups[1].values?.length < 1) throw "samplelst.groups[1].values.length<1";
+  if (param.samplelst?.groups?.length != 2) throw new Error(".samplelst.groups.length!=2");
+  if (param.samplelst.groups[0].values?.length < 1) throw new Error("samplelst.groups[0].values.length<1");
+  if (param.samplelst.groups[1].values?.length < 1) throw new Error("samplelst.groups[1].values.length<1");
   const q = ds.queries.rnaseqGeneCount;
   if (!q) return;
-  if (!q.file) throw "unknown data type for rnaseqGeneCount";
-  if (!q.storage_type) throw "storage_type is not defined";
+  if (!q.file) throw new Error("unknown data type for rnaseqGeneCount");
+  if (!q.storage_type) throw new Error("storage_type is not defined");
   param.storage_type = q.storage_type;
   const group1names = [];
   const conf1_group1 = [];
@@ -178,7 +178,7 @@ async function run_DE(param, ds, term_results, term_results2) {
       }
     };
   }
-  if (alerts.length) throw alerts.join(" | ");
+  if (alerts.length) throw new Error(alerts.join(" | "));
   const cases_string = group2names.map((i) => i).join(",");
   const controls_string = group1names.map((i) => i).join(",");
   const expression_input = {
@@ -199,14 +199,14 @@ async function run_DE(param, ds, term_results, term_results2) {
     expression_input.conf1 = [...conf1_group2, ...conf1_group1];
     expression_input.conf1_mode = param.tw.q.mode;
     if (new Set(expression_input.conf1).size === 1) {
-      throw "Confounding variable 1 has only one value";
+      throw new Error("Confounding variable 1 has only one value");
     }
   }
   if (param.tw2) {
     expression_input.conf2 = [...conf2_group2, ...conf2_group1];
     expression_input.conf2_mode = param.tw2.q.mode;
     if (new Set(expression_input.conf2).size === 1) {
-      throw "Confounding variable 2 has only one value";
+      throw new Error("Confounding variable 2 has only one value");
     }
   }
   const sample_size_limit = 8;
@@ -261,13 +261,13 @@ async function readFileAndDelete(file, key, response) {
   };
   response[key] = obj;
   fs.unlink(file, (err) => {
-    if (err) throw err;
+    if (err) throw new Error(err.message || String(err));
   });
 }
 async function validate_query_rnaseqGeneCount(ds) {
   const q = ds.queries.rnaseqGeneCount;
   if (!q) return;
-  if (!q.file) throw "unknown data type for rnaseqGeneCount";
+  if (!q.file) throw new Error("unknown data type for rnaseqGeneCount");
   q.file = path.join(serverconfig.tpmasterdir, q.file);
   {
     let samples = [];
@@ -283,10 +283,10 @@ async function validate_query_rnaseqGeneCount(ds) {
       const time2 = (/* @__PURE__ */ new Date()).valueOf();
       mayLog("Time taken to query gene expression:", time2 - time1, "ms");
       const vr = JSON.parse(result);
-      if (vr.status !== "success") throw vr.message;
-      if (!Array.isArray(vr.samples)) throw "HDF5 file has no samples, please check file.";
+      if (vr.status !== "success") throw new Error(vr.message);
+      if (!Array.isArray(vr.samples)) throw new Error("HDF5 file has no samples, please check file.");
       samples = vr.samples;
-    } else throw "unknown storage type:" + ds.queries.rnaseqGeneCount.storage_type;
+    } else throw new Error("unknown storage type:" + ds.queries.rnaseqGeneCount.storage_type);
     q.allSampleSet = new Set(samples);
     const unknownSamples = [];
     for (const n of q.allSampleSet) {

package/routes/termdb.singlecellDEgenes.js

@@ -19,12 +19,13 @@ function init({ genomes }) {
     let result;
     try {
       const g = genomes[q.genome];
-      if (!g) throw "invalid genome name";
+      if (!g) throw new Error("invalid genome name");
       const ds = g.datasets[q.dslabel];
-      if (!ds) throw "invalid dataset name";
-      if (!ds.queries?.singleCell?.DEgenes) throw "not supported on this dataset";
+      if (!ds) throw new Error("invalid dataset name");
+      if (!ds.queries?.singleCell?.DEgenes || !ds.queries.singleCell.DEgenes.get)
+        throw new Error("DE genes not supported on this dataset.");
       result = await ds.queries.singleCell.DEgenes.get(q);
-      if (!result || !result.genes || !result?.genes?.length) {
+      if (!result || !result.data || !result?.data?.length) {
         result = {
           status: 404,
           error: !result ? "No data found." : "No differentially expressed genes found."
@@ -44,7 +45,7 @@ async function validate_query_singleCell_DEgenes(ds) {
   if (ds.queries.singleCell.DEgenes.src == "gdcapi") {
     gdc_validate_query_singleCell_DEgenes(ds);
   } else {
-    throw "unknown singleCell.DEgenes.src";
+    throw new Error("unknown singleCell.DEgenes.src");
   }
 }
 export {