@sjcrh/proteinpaint-server 2.108.0 → 2.108.3-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.108.0",
+  "version": "2.108.3-0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -59,7 +59,7 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.87.0",
-    "@sjcrh/proteinpaint-rust": "2.99.0",
+    "@sjcrh/proteinpaint-rust": "2.108.3-0",
     "@sjcrh/proteinpaint-shared": "2.108.0",
     "@sjcrh/proteinpaint-types": "2.108.0",
     "@types/express": "^5.0.0",

package/routes/gdc.maf.js

@@ -101,8 +101,10 @@ async function listMafFiles(q, ds) {
       if (normalTypeName)
         file.sample_types.push(normalTypeName);
     }
+    file.sample_types = [...new Set(file.sample_types)];
     files.push(file);
   }
+  files.sort((a, b) => b.file_size - a.file_size);
   const result = {
     files,
     filesTotal: re.data.pagination.total,

package/routes/gdc.mafBuild.js

@@ -1,6 +1,6 @@
 import ky from "ky";
 import { joinUrl } from "#shared/joinUrl.js";
-import { run_rust_stream } from "@sjcrh/proteinpaint-rust";
+import { stream_rust } from "@sjcrh/proteinpaint-rust";
 import { gdcMafPayload } from "#types/checkers";
 import { maxTotalSizeCompressed } from "./gdc.maf.ts";
 import { mayLog } from "#src/helpers.ts";
@@ -46,19 +46,26 @@ async function buildMaf(q, res, ds) {
     host: joinUrl(host.rest, "data")
     // must use the /data/ endpoint from current host
   };
-  const rustStream = run_rust_stream("gdcmaf", JSON.stringify(arg));
-  res.setHeader("Content-Type", "application/octet-stream");
-  res.setHeader("Content-Disposition", "attachment; filename=cohort.maf.gz");
-  rustStream.pipe(res);
-  rustStream.on("end", () => {
+  const boundary = "GDC_MAF_MULTIPART_BOUNDARY";
+  res.setHeader("content-type", `multipart/mixed; boundary=${boundary}`);
+  res.write(`--${boundary}`);
+  res.write("\ncontent-disposition: attachment; filename=cohort.maf.gz");
+  res.write("\ncontent-type: application/octet-stream\n\n");
+  res.flush();
+  const rustStream = stream_rust("gdcmaf", JSON.stringify(arg), emitJson);
+  rustStream.pipe(res, { end: false });
+  function emitJson(data, end = true) {
+    res.write(`
+--${boundary}`);
+    res.write("\ncontent-type: application/json");
+    const json = typeof data === "string" ? data : JSON.stringify(data || { ok: true, status: "ok" });
+    res.write("\n\n" + json);
+    res.write(`
+--${boundary}--`);
     mayLog("rust gdcmaf", Date.now() - t0);
-    res.end();
-  });
-  rustStream.on("error", (err) => {
-    console.error(err);
-    res.statusCode = 500;
-    res.end("Internal Server Error");
-  });
+    if (end)
+      res.end();
+  }
 }
 async function getFileLstUnderSizeLimit(lst, host) {
   if (lst.length == 0)

package/routes/termdb.cluster.js

@@ -74,6 +74,12 @@ async function getResult(q, ds, genome) {
     ;
     ({ term2sample2value, byTermId, bySampleId } = await ds.queries[q.dataType].get(_q));
   }
+  for (const [term, obj] of term2sample2value) {
+    if (Object.keys(obj).length === 0) {
+      term2sample2value.delete(term);
+      delete byTermId[term];
+    }
+  }
   if (term2sample2value.size == 0)
     throw "no data";
   if (term2sample2value.size == 1) {