Switching to streaming response to avoid writing geneset file to disk

src/geneweaver/api/controller/genesets.py

@@ -1,13 +1,12 @@
 """Endpoints related to genesets."""
 
 import json
-import os
 import time
 from tempfile import TemporaryDirectory
 from typing import Optional, Set
 
 from fastapi import APIRouter, Depends, HTTPException, Path, Query, Security
-from fastapi.responses import FileResponse
+from fastapi.responses import FileResponse, StreamingResponse
 from geneweaver.api import dependencies as deps
 from geneweaver.api.schemas.apimodels import GeneValueReturn
 from geneweaver.api.schemas.auth import UserInternal
@@ -189,7 +188,7 @@ def get_export_geneset_by_id_type(
     cursor: Optional[deps.Cursor] = Depends(deps.cursor),
     temp_dir: TemporaryDirectory = Depends(deps.get_temp_dir),
     gene_id_type: Optional[GeneIdentifier] = None,
-) -> FileResponse:
+) -> StreamingResponse:
     """Export geneset into JSON file. Search by ID and optional gene identifier type."""
     timestr = time.strftime("%Y%m%d-%H%M%S")
 
@@ -214,15 +213,19 @@ def get_export_geneset_by_id_type(
         geneset_filename = f"geneset_{geneset_id}_{timestr}.json"
 
     # Write the data to temp file
-    temp_file_path = os.path.join(temp_dir, geneset_filename)
-    with open(temp_file_path, "w") as f:
-        json.dump(response, f, default=str)
+    from io import StringIO
+
+    buffer = StringIO()
+
+    json.dump(response, buffer, default=str)
+
+    buffer.seek(0)
 
     # Return as a download
-    return FileResponse(
-        path=temp_file_path,
+    return StreamingResponse(
+        buffer,
         media_type="application/octet-stream",
-        filename=geneset_filename,
+        headers={"Content-Disposition": f"attachment; filename={geneset_filename}"},
     )
 
 

tests/controllers/test_genesets.py

@@ -66,7 +66,6 @@ def test_export_geneset_w_gene_id_type(mock_service_get_geneset_w_gene_id_type,
     response = client.get("/api/genesets/1234/file?gene_id_type=2")
 
     assert response.headers.get("content-type") == "application/octet-stream"
-    assert int(response.headers.get("content-length")) > 0
     assert response.status_code == 200