samples: Fix bugs in code saving samples to db

* Check whether first row in file is for headings
* Break infinite loop: check batch has content
* Update saving of uploaded files

1 files changed, 5 insertions, 7 deletions

diff --git a/qc_app/files.py b/qc_app/files.py
index 6485b27..0304296 100644
--- a/qc_app/files.py
+++ b/qc_app/files.py
@@ -3,18 +3,16 @@ from pathlib import Path
 from typing import Union
 
 from werkzeug.utils import secure_filename
-from flask import (
-    request,
-    current_app as app)
+from werkzeug.datastructures import FileStorage
 
-def save_file(key: str, upload_dir: Path) -> Union[Path, bool]:
+def save_file(fileobj: FileStorage, upload_dir: Path) -> Union[Path, bool]:
     """Save the uploaded file and return the path."""
-    if not bool(request.files.get(key)):
+    if not bool(fileobj):
         return False
-    filename = Path(secure_filename(request.files[key].filename))
+    filename = Path(secure_filename(fileobj.filename)) # type: ignore[arg-type]
     if not upload_dir.exists():
         upload_dir.mkdir()
 
     filepath = Path(upload_dir, filename)
-    request.files["samples_file"].save(filepath)
+    fileobj.save(filepath)
     return filepath