@sjcrh/proteinpaint-server 2.128.0 → 2.128.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.128.0",
+  "version": "2.128.1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -63,9 +63,9 @@
     "@sjcrh/augen": "2.121.0",
     "@sjcrh/proteinpaint-python": "2.118.0",
     "@sjcrh/proteinpaint-r": "2.126.2",
-    "@sjcrh/proteinpaint-rust": "2.126.2",
+    "@sjcrh/proteinpaint-rust": "2.128.1",
     "@sjcrh/proteinpaint-shared": "2.126.0",
-    "@sjcrh/proteinpaint-types": "2.128.0",
+    "@sjcrh/proteinpaint-types": "2.128.1",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/gdcGRIN2list.js

@@ -36,19 +36,29 @@ function init({ genomes }) {
   };
 }
 async function listMafFiles(q, ds) {
+  const shouldRetrieveMaf = !!q.mafOptions;
+  const experimentalStrategy = q.mafOptions?.experimentalStrategy;
+  if (shouldRetrieveMaf && !experimentalStrategy) {
+    throw "Missing experimentalStrategy parameter for MAF file retrieval";
+  }
   const dataFormatFilter = {
     op: "and",
     content: [{ op: "=", content: { field: "data_format", value: "MAF" } }]
   };
-  const filters = {
-    op: "and",
-    content: [
-      dataFormatFilter,
-      { op: "=", content: { field: "experimental_strategy", value: q.experimentalStrategy } },
-      { op: "=", content: { field: "analysis.workflow_type", value: allowedWorkflowType } },
-      { op: "=", content: { field: "access", value: "open" } }
-    ]
-  };
+  let filters;
+  if (shouldRetrieveMaf) {
+    filters = {
+      op: "and",
+      content: [
+        dataFormatFilter,
+        { op: "=", content: { field: "experimental_strategy", value: experimentalStrategy } },
+        { op: "=", content: { field: "analysis.workflow_type", value: allowedWorkflowType } },
+        { op: "=", content: { field: "access", value: "open" } }
+      ]
+    };
+  } else {
+    throw "At least one file type option must be specified (mafOptions, cnvOptions, or fusionOptions)";
+  }
   const case_filters = { op: "and", content: [] };
   if (q.filter0) {
     case_filters.content.push(q.filter0);
@@ -61,11 +71,8 @@ async function listMafFiles(q, ds) {
       "id",
       "file_size",
       "cases.project.project_id",
-      // for display only
       "cases.case_id",
-      // case uuid for making case url link to portal
       "cases.submitter_id",
-      // used when listing all cases & files
       "cases.samples.tissue_type",
       "cases.samples.tumor_descriptor"
     ].join(",")
@@ -114,7 +121,14 @@ async function listMafFiles(q, ds) {
   const result = {
     files,
     filesTotal: re.data.pagination.total,
-    maxTotalSizeCompressed
+    maxTotalSizeCompressed,
+    fileCounts: {
+      maf: files.length
+    },
+    appliedFilters: {
+      fileTypes: shouldRetrieveMaf ? ["MAF"] : [],
+      experimentalStrategy
+    }
   };
   return result;
 }

package/routes/genesetEnrichment.js

@@ -3,7 +3,9 @@ import fs from "fs";
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
 import { run_python } from "@sjcrh/proteinpaint-python";
+import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { mayLog } from "#src/helpers.ts";
+import { formatElapsedTime } from "@sjcrh/proteinpaint-shared/time.js";
 const api = {
   endpoint: "genesetEnrichment",
   methods: {
@@ -54,33 +56,46 @@ async function run_genesetEnrichment_analysis(q, genomes) {
     db: genomes[q.genome].termdbs.msigdb.cohort.db.connection.name,
     // For now msigdb has been added, but later databases other than msigdb may be used
     geneset_group: q.geneSetGroup,
-    cachedir: cachedir_gsea,
-    geneset_name: q.geneset_name,
-    pickle_file: q.pickle_file,
-    num_permutations: q.num_permutations,
     genedb: path.join(serverconfig.tpmasterdir, genomes[q.genome].genedb.dbfile),
     filter_non_coding_genes: q.filter_non_coding_genes
   };
-  const gsea_output = await run_python("gsea.py", "/" + JSON.stringify(genesetenrichment_input));
-  let result;
-  let data_found = false;
-  let image_found = false;
-  for (const line of gsea_output.split("\n")) {
-    if (line.startsWith("result: ")) {
-      result = JSON.parse(line.replace("result: ", ""));
-      data_found = true;
-    } else if (line.startsWith("image: ")) {
-      result = JSON.parse(line.replace("image: ", ""));
-      image_found = true;
-    } else {
-      mayLog(line);
+  let gsea_output;
+  if (q.method == "blitzgsea") {
+    genesetenrichment_input.cachedir = cachedir_gsea;
+    genesetenrichment_input.pickle_file = q.pickle_file;
+    genesetenrichment_input.geneset_name = q.geneset_name;
+    genesetenrichment_input.num_permutations = q.num_permutations;
+    const time1 = (/* @__PURE__ */ new Date()).valueOf();
+    gsea_output = await run_python("gsea.py", "/" + JSON.stringify(genesetenrichment_input));
+    mayLog("Time taken to run blitzgsea:", formatElapsedTime(Date.now() - time1));
+    let result;
+    let data_found = false;
+    let image_found = false;
+    for (const line of gsea_output.split("\n")) {
+      if (line.startsWith("result: ")) {
+        result = JSON.parse(line.replace("result: ", ""));
+        data_found = true;
+      } else if (line.startsWith("image: ")) {
+        result = JSON.parse(line.replace("image: ", ""));
+        image_found = true;
+      } else {
+        mayLog(line);
+      }
     }
+    if (data_found)
+      return result;
+    const image_file_name = path.join(cachedir_gsea, result.image_file);
+    if (image_found)
+      return image_file_name;
+    throw "data or image not found in gsea output; this should not happen";
+  } else if (q.method == "cerno") {
+    const time1 = (/* @__PURE__ */ new Date()).valueOf();
+    gsea_output = JSON.parse(await run_rust("cerno", JSON.stringify(genesetenrichment_input)));
+    mayLog("Time taken to run CERNO:", formatElapsedTime(Date.now() - time1));
+    return gsea_output;
+  } else {
+    throw "Unknown method:" + q.method;
   }
-  if (data_found)
-    return result;
-  if (image_found)
-    return path.join(cachedir_gsea, result.image_file);
-  throw "data or image not found in gsea output; this should not happen";
 }
 export {
   api