@sjcrh/proteinpaint-server 2.112.0 → 2.113.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.112.0",
+  "version": "2.113.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -18,6 +18,9 @@
     "prestart": "tsx emitImports.js dev > server.js",
     "start": "tsx watch . /start.js",
     "test:unit": "tsx emitImports.js unit > serverTests.js && c8 tsx serverTests.js && rm -rf ./cache",
+    "precombined:coverage": "tsx emitImports.js unit > serverTests.js",
+    "combined:coverage": "closeCoverageKey=test c8 --all --src=proteinpaint/server --experimental-monocart -r=v8 -r=html -r=json -r=markdown-summary -r=markdown-details -o=./.coverage tsx ./coverage.js & ",
+    "postcombined:coverage": "rm -rf ./cache",
     "getconf": "../build/getConfigProp.js",
     "doc": "../augen/build.sh routes shared/types/routes shared/checkers ../public/docs/server",
     "mjs": "esbuild \"$DIR/*.ts\" --platform=node --outdir=\"$DIR\" --format=esm",
@@ -49,6 +52,8 @@
     "c8": "^10.1.3",
     "esbuild": "^0.19.12",
     "glob": "^10.4.5",
+    "monocart-coverage-reports": "^2.12.1",
+    "node-notifier": "^9.0.1",
     "node-watch": "^0.7.1",
     "nodemon": "^2.0.19",
     "prettier": "^2.8.8",
@@ -59,10 +64,10 @@
     "typescript": "^5.6.3"
   },
   "dependencies": {
-    "@sjcrh/augen": "2.109.1-0",
+    "@sjcrh/augen": "2.113.0",
     "@sjcrh/proteinpaint-rust": "2.112.0",
-    "@sjcrh/proteinpaint-shared": "2.112.0",
-    "@sjcrh/proteinpaint-types": "2.112.0",
+    "@sjcrh/proteinpaint-shared": "2.113.0",
+    "@sjcrh/proteinpaint-types": "2.113.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/termdb.DE.js

@@ -196,7 +196,10 @@ async function run_DE(param, ds, term_results, term_results2) {
     cachedir: serverconfig.cachedir,
     min_count: param.min_count,
     min_total_count: param.min_total_count,
-    storage_type: param.storage_type
+    storage_type: param.storage_type,
+    DE_method: param.method,
+    mds_cutoff: 1e4
+    // If the dimensions of the read counts matrix is below this threshold, only then the mds image will be generated as its very compute intensive. Number of genes * Number of samples < mds_cutoff for mds generation
   };
   if (param.tw) {
     expression_input.conf1 = [...conf1_group2, ...conf1_group1];
@@ -213,7 +216,7 @@ async function run_DE(param, ds, term_results, term_results2) {
     }
   }
   const sample_size_limit = 8;
-  if (group1names.length <= sample_size_limit && group2names.length <= sample_size_limit || param.method == "edgeR") {
+  if (group1names.length <= sample_size_limit && group2names.length <= sample_size_limit || param.method == "edgeR" || param.method == "limma") {
     const time12 = (/* @__PURE__ */ new Date()).valueOf();
     const result2 = JSON.parse(
       await run_R(path.join(serverconfig.binpath, "utils", "edge.R"), JSON.stringify(expression_input))
@@ -222,21 +225,21 @@ async function run_DE(param, ds, term_results, term_results2) {
     param.method = "edgeR";
     const ql_imagePath = path.join(serverconfig.cachedir, result2.edgeR_ql_image_name[0]);
     mayLog("ql_imagePath:", ql_imagePath);
-    const mds_imagePath = path.join(serverconfig.cachedir, result2.edgeR_mds_image_name[0]);
-    mayLog("mds_imagePath:", mds_imagePath);
-    await readFileAndDelete(mds_imagePath, "mds_image", result2);
     await readFileAndDelete(ql_imagePath, "ql_image", result2);
+    if (result2.edgeR_mds_image_name) {
+      const mds_imagePath = path.join(serverconfig.cachedir, result2.edgeR_mds_image_name[0]);
+      mayLog("mds_imagePath:", mds_imagePath);
+      await readFileAndDelete(mds_imagePath, "mds_image", result2);
+    }
+    const images = [result2.ql_image];
+    if (result2.mds_image)
+      images.push(result2.mds_image);
     return {
       data: result2.gene_data,
       sample_size1,
       sample_size2,
       method: param.method,
-      images: [
-        result2.mds_image,
-        // MDS image
-        result2.ql_image
-        // QL fit image
-      ]
+      images
     };
   }
   const time1 = (/* @__PURE__ */ new Date()).valueOf();
@@ -259,7 +262,7 @@ async function readFileAndDelete(file, key, response) {
       throw err;
   });
 }
-async function validate_query_rnaseqGeneCount(ds, genome) {
+async function validate_query_rnaseqGeneCount(ds) {
   const q = ds.queries.rnaseqGeneCount;
   if (!q)
     return;
@@ -278,6 +281,7 @@ async function validate_query_rnaseqGeneCount(ds, genome) {
       const time1 = (/* @__PURE__ */ new Date()).valueOf();
       const result = await run_rust("DEanalysis", JSON.stringify(get_samples_from_hdf5));
       const time2 = (/* @__PURE__ */ new Date()).valueOf();
+      mayLog("Time taken to query gene expression:", time2 - time1, "ms");
       samples = result.split(",");
     } else
       throw "unknown storage type:" + ds.queries.rnaseqGeneCount.storage_type;

package/routes/termdb.cluster.js

@@ -67,22 +67,32 @@ async function getResult(q, ds, genome) {
     _q = JSON.parse(JSON.stringify(q));
     _q.forClusteringAnalysis = true;
   }
-  let term2sample2value, byTermId, bySampleId;
+  let term2sample2value, byTermId, bySampleId, skippedSexChrGenes;
   if (q.dataType == NUMERIC_DICTIONARY_TERM) {
     ;
     ({ term2sample2value, byTermId, bySampleId } = await getNumericDictTermAnnotation(q, ds, genome));
   } else {
     ;
-    ({ term2sample2value, byTermId, bySampleId } = await ds.queries[q.dataType].get(_q));
+    ({ term2sample2value, byTermId, bySampleId, skippedSexChrGenes } = await ds.queries[q.dataType].get(_q));
   }
-  const removedHierClusterTerms = [];
+  const noValueTerms = [];
   for (const [term, obj] of term2sample2value) {
     if (Object.keys(obj).length === 0) {
-      removedHierClusterTerms.push(term);
+      noValueTerms.push(term);
       term2sample2value.delete(term);
       delete byTermId[term];
     }
   }
+  const removedHierClusterTerms = [];
+  if (noValueTerms.length) {
+    removedHierClusterTerms.push({
+      text: `Skipped ${q.dataType == TermTypes.GENE_EXPRESSION ? "genes" : "items"} with no data`,
+      lst: noValueTerms
+    });
+  }
+  if (skippedSexChrGenes?.length) {
+    removedHierClusterTerms.push({ text: "Skipped sex chromosome genes", lst: skippedSexChrGenes });
+  }
   if (term2sample2value.size == 0)
     throw "no data";
   if (term2sample2value.size == 1) {

package/routes/termdb.config.js

@@ -164,9 +164,6 @@ function addNonDictionaryQueries(c, ds, genome) {
   }
   if (q.ld) {
     q2.ld = JSON.parse(JSON.stringify(q.ld));
-    for (const i of q2.ld.tracks) {
-      delete i.file;
-    }
   }
   if (q.cnv) {
     q2.cnv = {};