@sjcrh/proteinpaint-server 2.104.0 → 2.106.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.104.0",
+  "version": "2.106.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -60,8 +60,8 @@
   "dependencies": {
     "@sjcrh/augen": "2.87.0",
     "@sjcrh/proteinpaint-rust": "2.99.0",
-    "@sjcrh/proteinpaint-shared": "2.99.1",
-    "@sjcrh/proteinpaint-types": "2.104.0",
+    "@sjcrh/proteinpaint-shared": "2.106.0",
+    "@sjcrh/proteinpaint-types": "2.106.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/gdc.maf.js

@@ -1,6 +1,6 @@
 import { gdcMafPayload } from "#types/checkers";
-import path from "path";
-import got from "got";
+import ky from "ky";
+import { joinUrl } from "#shared/joinUrl.js";
 import serverconfig from "#src/serverconfig.js";
 const maxFileNumber = 1e3;
 const allowedWorkflowType = "Aliquot Ensemble Somatic Variant Merging and Masking";
@@ -49,8 +49,8 @@ async function listMafFiles(q, ds) {
   if (q.filter0) {
     case_filters.content.push(q.filter0);
   }
-  const { host, headers } = ds.getHostHeaders(q);
-  const data = {
+  const { host } = ds.getHostHeaders(q);
+  const body = {
     filters,
     size: maxFileNumber,
     fields: [
@@ -62,19 +62,16 @@ async function listMafFiles(q, ds) {
       // case uuid for making case url link to portal
       "cases.submitter_id",
       // used when listing all cases & files
-      "cases.samples.sample_type"
-      // may add diagnosis and primary site
+      "cases.samples.tissue_type",
+      "cases.samples.tumor_descriptor"
     ].join(",")
   };
   if (case_filters.content.length)
-    data.case_filters = case_filters;
-  const response = await got.post(path.join(host.rest, "files"), { headers, body: JSON.stringify(data) });
-  let re;
-  try {
-    re = JSON.parse(response.body);
-  } catch (_) {
-    throw "invalid JSON from " + api.endpoint;
-  }
+    body.case_filters = case_filters;
+  const response = await ky.post(joinUrl(host.rest, "files"), { timeout: false, json: body });
+  if (!response.ok)
+    throw `HTTP Error: ${response.status} ${response.statusText}`;
+  const re = await response.json();
   if (!Number.isInteger(re.data?.pagination?.total))
     throw "re.data.pagination.total is not int";
   if (!Array.isArray(re.data?.hits))
@@ -89,10 +86,20 @@ async function listMafFiles(q, ds) {
       project_id: c.project.project_id,
       file_size: h.file_size,
       case_submitter_id: c.submitter_id,
-      case_uuid: c.case_id
+      case_uuid: c.case_id,
+      sample_types: []
     };
     if (c.samples) {
-      file.sample_types = c.samples.map((i) => i.sample_type).sort();
+      let normalTypeName;
+      for (const { tumor_descriptor, tissue_type } of c.samples) {
+        if (tissue_type == "Normal") {
+          normalTypeName = (tumor_descriptor == "Not Applicable" ? "" : tumor_descriptor + " ") + tissue_type;
+          continue;
+        }
+        file.sample_types.push(tumor_descriptor + " " + tissue_type);
+      }
+      if (normalTypeName)
+        file.sample_types.push(normalTypeName);
     }
     files.push(file);
   }

package/routes/gdc.mafBuild.js

@@ -1,9 +1,9 @@
-import got from "got";
-import path from "path";
+import ky from "ky";
+import { joinUrl } from "#shared/joinUrl.js";
 import { run_rust_stream } from "@sjcrh/proteinpaint-rust";
-import serverconfig from "#src/serverconfig.js";
 import { gdcMafPayload } from "#types/checkers";
 import { maxTotalSizeCompressed } from "./gdc.maf.ts";
+import { mayLog } from "#src/helpers.ts";
 const api = {
   endpoint: "gdc/mafBuild",
   methods: {
@@ -37,17 +37,13 @@ function init({ genomes }) {
 }
 async function buildMaf(q, res, ds) {
   const t0 = Date.now();
-  const { host, headers } = ds.getHostHeaders(q);
-  const fileLst2 = await getFileLstUnderSizeLimit(q.fileIdLst, host, headers);
-  if (serverconfig.debugmode)
-    console.log(
-      `${fileLst2.length} out of ${q.fileIdLst.length} input MAF files accepted by size limit`,
-      Date.now() - t0
-    );
+  const { host } = ds.getHostHeaders(q);
+  const fileLst2 = await getFileLstUnderSizeLimit(q.fileIdLst, host);
+  mayLog(`${fileLst2.length} out of ${q.fileIdLst.length} input MAF files accepted by size limit`, Date.now() - t0);
   const arg = {
     fileIdLst: fileLst2,
     columns: q.columns,
-    host: path.join(host.rest, "data")
+    host: joinUrl(host.rest, "data")
     // must use the /data/ endpoint from current host
   };
   const rustStream = run_rust_stream("gdcmaf", JSON.stringify(arg));
@@ -55,8 +51,7 @@ async function buildMaf(q, res, ds) {
   res.setHeader("Content-Disposition", "attachment; filename=cohort.maf.gz");
   rustStream.pipe(res);
   rustStream.on("end", () => {
-    if (serverconfig.debugmode)
-      console.log("rust gdcmaf", Date.now() - t0);
+    mayLog("rust gdcmaf", Date.now() - t0);
     res.end();
   });
   rustStream.on("error", (err) => {
@@ -65,10 +60,10 @@ async function buildMaf(q, res, ds) {
     res.end("Internal Server Error");
   });
 }
-async function getFileLstUnderSizeLimit(lst, host, headers) {
+async function getFileLstUnderSizeLimit(lst, host) {
   if (lst.length == 0)
     throw "fileIdLst[] not array or blank";
-  const data = {
+  const body = {
     filters: {
       op: "in",
       content: { field: "file_id", value: lst }
@@ -76,13 +71,10 @@ async function getFileLstUnderSizeLimit(lst, host, headers) {
     size: 1e4,
     fields: "file_size"
   };
-  const response = await got.post(path.join(host.rest, "files"), { headers, body: JSON.stringify(data) });
-  let re;
-  try {
-    re = JSON.parse(response.body);
-  } catch (_) {
-    throw "invalid json from getFileLstUnderSizeLimit";
-  }
+  const response = await ky.post(joinUrl(host.rest, "files"), { timeout: false, json: body });
+  if (!response.ok)
+    throw `HTTP Error: ${response.status} ${response.statusText}`;
+  const re = await response.json();
   if (!Array.isArray(re.data?.hits))
     throw "re.data.hits[] not array";
   const out = [];

package/routes/genesetEnrichment.js

@@ -56,6 +56,7 @@ async function run_genesetEnrichment_analysis(q, genomes) {
     cachedir: serverconfig.cachedir,
     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
   };

package/routes/termdb.DE.js

@@ -120,6 +120,9 @@ async function run_DE(param, ds, term_results) {
   const sample_size_limit = 8;
   let result;
   if (group1names.length <= sample_size_limit && group2names.length <= sample_size_limit || param.method == "edgeR") {
+    if (param.method == "edgeR") {
+      expression_input.VarGenes = param.VarGenes;
+    }
     const time1 = (/* @__PURE__ */ new Date()).valueOf();
     result = JSON.parse(
       await run_R(path.join(serverconfig.binpath, "utils", "edge.R"), JSON.stringify(expression_input))

package/routes/termdb.config.js

@@ -215,7 +215,6 @@ function addNonDictionaryQueries(c, ds, genome) {
   if (q.singleCell) {
     q2.singleCell = {
       samples: {
-        firstColumnName: q.singleCell.samples.firstColumnName,
         sampleColumns: q.singleCell.samples.sampleColumns,
         experimentColumns: q.singleCell.samples.experimentColumns,
         extraSampleTabLabel: q.singleCell.samples.extraSampleTabLabel