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-rw-r--r--qc_app/files.py6
-rw-r--r--qc_app/samples.py9
-rw-r--r--qc_app/upload/rqtl2.py16
3 files changed, 17 insertions, 14 deletions
diff --git a/qc_app/files.py b/qc_app/files.py
index baac5ec..b163612 100644
--- a/qc_app/files.py
+++ b/qc_app/files.py
@@ -1,17 +1,15 @@
"""Utilities to deal with uploaded files."""
import hashlib
from pathlib import Path
-from typing import Union
from datetime import datetime
from flask import current_app
from werkzeug.utils import secure_filename
from werkzeug.datastructures import FileStorage
-def save_file(fileobj: FileStorage, upload_dir: Path) -> Union[Path, bool]:
+def save_file(fileobj: FileStorage, upload_dir: Path) -> Path:
"""Save the uploaded file and return the path."""
- if not bool(fileobj):
- return False
+ assert bool(fileobj), "Invalid file object!"
hashed_name = hashlib.sha512(
f"{fileobj.filename}::{datetime.now().isoformat()}".encode("utf8")
).hexdigest()
diff --git a/qc_app/samples.py b/qc_app/samples.py
index 55e94ab..1845818 100644
--- a/qc_app/samples.py
+++ b/qc_app/samples.py
@@ -219,9 +219,12 @@ def upload_samples():
flash("Invalid grouping/population!", "alert-error")
return samples_uploads_page
- samples_file = save_file(request.files["samples_file"], Path(app.config["UPLOAD_FOLDER"]))
- if not bool(samples_file):
- flash("You need to provide a file with the samples data.")
+ try:
+ samples_file = save_file(request.files["samples_file"],
+ Path(app.config["UPLOAD_FOLDER"]))
+ except AssertionError:
+ flash("You need to provide a file with the samples data.",
+ "alert-error")
return samples_uploads_page
firstlineheading = (request.form.get("first_line_heading") == "on")
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index afe0c2e..b96d9f0 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -152,13 +152,15 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
species=species,
population=population)
- if not bool(request.files.get("rqtl2_bundle_file")):
- raise __RequestError__("No R/qtl2 zip bundle provided.")
-
- the_file = save_file(request.files["rqtl2_bundle_file"],
- Path(app.config["UPLOAD_FOLDER"]))
- if not bool(the_file):
- raise __RequestError__("Please provide a valid R/qtl2 zip bundle.")
+ try:
+ the_file = save_file(request.files["rqtl2_bundle_file"],
+ Path(app.config["UPLOAD_FOLDER"]))
+ except AssertionError:
+ flash("Please provide a valid R/qtl2 zip bundle.",
+ "alert-error error-rqtl2")
+ return redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
+ species_id=species_id,
+ population_id=population_id))
if not is_zipfile(str(the_file)):
raise __RequestError__("Invalid file! Expected a zip file.")