@sjcrh/proteinpaint-server 2.170.26 → 2.170.27

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.170.26",
+  "version": "2.170.27",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -64,9 +64,9 @@
     "@sjcrh/augen": "2.143.0",
     "@sjcrh/proteinpaint-python": "2.169.0",
     "@sjcrh/proteinpaint-r": "2.152.1-0",
-    "@sjcrh/proteinpaint-rust": "2.170.0",
+    "@sjcrh/proteinpaint-rust": "2.170.27-1ac4377f6.0",
     "@sjcrh/proteinpaint-shared": "2.170.21",
-    "@sjcrh/proteinpaint-types": "2.170.26",
+    "@sjcrh/proteinpaint-types": "2.170.27",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/gdc.maf.js

@@ -26,7 +26,8 @@ function init({ genomes }) {
       if (!g) throw "hg38 missing";
       const ds = g.datasets.GDC;
       if (!ds) throw "hg38 GDC missing";
-      const payload = await listMafFiles(req.query, ds);
+      const q = req.query;
+      const payload = await listMafFiles(q, ds);
       res.send(payload);
     } catch (e) {
       res.send({ status: "error", error: e.message || e });
@@ -48,7 +49,7 @@ async function listMafFiles(q, ds) {
   if (q.filter0) {
     case_filters.content.push(q.filter0);
   }
-  const { host } = ds.getHostHeaders(q);
+  const { host, headers } = ds.getHostHeaders(q);
   const body = {
     filters,
     size: maxFileNumber,
@@ -66,7 +67,7 @@ async function listMafFiles(q, ds) {
     ].join(",")
   };
   if (case_filters.content.length) body.case_filters = case_filters;
-  const response = await ky.post(joinUrl(host.rest, "files"), { timeout: false, json: body });
+  const response = await ky.post(joinUrl(host.rest, "files"), { headers, 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";

package/routes/gdc.mafBuild.js

@@ -20,11 +20,11 @@ const api = {
 function init({ genomes }) {
   return async (req, res) => {
     try {
-      const q = req.query;
       const g = genomes.hg38;
       if (!g) throw "hg38 missing";
       const ds = g.datasets.GDC;
       if (!ds) throw "hg38 GDC missing";
+      const q = req.query;
       await buildMaf(q, res, ds);
     } catch (e) {
       if (e.stack) console.log(e.stack);
@@ -34,14 +34,15 @@ function init({ genomes }) {
 }
 async function buildMaf(q, res, ds) {
   const t0 = Date.now();
-  const { host } = ds.getHostHeaders(q);
-  const fileLst2 = await getFileLstUnderSizeLimit(q.fileIdLst, host);
+  const { host, headers } = ds.getHostHeaders(q);
+  const fileLst2 = await getFileLstUnderSizeLimit(q.fileIdLst, host, headers);
   mayLog(`${fileLst2.length} out of ${q.fileIdLst.length} input MAF files accepted by size limit`, Date.now() - t0);
   const arg = {
     fileIdLst: fileLst2,
     columns: q.columns,
-    host: joinUrl(host.rest, "data")
+    host: joinUrl(host.rest, "data"),
     // must use the /data/ endpoint from current host
+    headers
   };
   const boundary = "------------------------GDC-MAF-BUILD";
   res.setHeader("Content-Type", `multipart/form-data; boundary=${boundary}`);
@@ -97,7 +98,7 @@ async function buildMaf(q, res, ds) {
     if (end) res.end();
   }
 }
-async function getFileLstUnderSizeLimit(lst, host) {
+async function getFileLstUnderSizeLimit(lst, host, headers) {
   if (lst.length == 0) throw "fileIdLst[] not array or blank";
   const body = {
     filters: {
@@ -107,7 +108,7 @@ async function getFileLstUnderSizeLimit(lst, host) {
     size: 1e4,
     fields: "file_size"
   };
-  const response = await ky.post(joinUrl(host.rest, "files"), { timeout: false, json: body });
+  const response = await ky.post(joinUrl(host.rest, "files"), { headers, 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";

package/routes/termdb.singlecellSamples.js

@@ -215,9 +215,13 @@ function gdc_validateGeneExpression(G, ds, genome) {
         gene_ids: [gencodeId],
         file_id: hdf5id
       };
-      const { host } = ds.getHostHeaders(q);
+      const { host, headers } = ds.getHostHeaders(q);
       const t = Date.now();
-      const response = await ky.post(joinUrl(host.rest, "scrna_seq/gene_expression"), { timeout: false, json: body });
+      const response = await ky.post(joinUrl(host.rest, "scrna_seq/gene_expression"), {
+        timeout: false,
+        headers,
+        json: body
+      });
       if (!response.ok) throw new Error(`HTTP Error: ${response.status} ${response.statusText}`);
       const out = await response.json();
       mayLog("gdc scrna gene exp", q.gene, Date.now() - t);