Merge pull request #100 from bento-platform/fix/temp-file-writing

fix: write temp file uploads (during upload) to ingest tmp dir

chord_drs/app.py

@@ -13,13 +13,15 @@
 from .constants import SERVICE_NAME
 from .db import db
 from .metrics import metrics
+from .request import DrsRequest
 from .routes import drs_service
 
 
 MIGRATION_DIR = os.path.join(APP_DIR, "migrations")
 
 application = Flask(__name__)
 application.config.from_object(Config)
+application.request_class = DrsRequest
 
 # Set up CORS
 CORS(

chord_drs/request.py

@@ -0,0 +1,18 @@
+from flask import Request, current_app
+from tempfile import SpooledTemporaryFile
+from typing import IO, Optional
+
+__all__ = ["DrsRequest"]
+
+MAX_IN_MEMORY_SIZE = 1024 * 1024  # 1 MB
+
+
+class DrsRequest(Request):
+    def _get_file_stream(
+        self,
+        total_content_length: Optional[int],
+        content_type: Optional[str],
+        filename: Optional[str] = None,
+        content_length: Optional[int] = None,
+    ) -> IO[bytes]:
+        return SpooledTemporaryFile(max_size=MAX_IN_MEMORY_SIZE, dir=current_app.config["DRS_INGEST_TMP_DIR"])

chord_drs/routes.py

@@ -449,6 +449,7 @@ def object_ingest():
         filename: str | None = None  # no override, use path filename if path is specified instead of a file upload
         if file is not None:
             logger.debug(f"ingest - received file object: {file}")
+            logger.debug(f"ingest - writing to temporary path: {t_obj_path}")
             file.save(t_obj_path)
             obj_path = t_obj_path
             filename = file.filename  # still may be none, in which case the temporary filename will be used

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "chord-drs"
-version = "0.16.0"
+version = "0.16.1"
 description = "An implementation of a data repository system (as per GA4GH's specs) for the Bento platform."
 authors = ["David Lougheed <[email protected]>"]
 license = "LGPL-3.0"