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"""Entry-point module"""
import os
import mimetypes
from typing import Tuple
from zipfile import ZipFile, is_zipfile
from werkzeug.utils import secure_filename
from flask import (
flash,
request,
url_for,
redirect,
Blueprint,
render_template,
current_app as app)
from qc_app.db import species
from qc_app.db_utils import with_db_connection
entrybp = Blueprint("entry", __name__)
def errors(rqst) -> Tuple[str, ...]:
"""Return a tuple of the errors found in the request `rqst`. If no error is
found, then an empty tuple is returned."""
def __filetype_error__():
return (
("Invalid file type provided.",)
if rqst.form.get("filetype") not in ("average", "standard-error")
else tuple())
def __file_missing_error__():
return (
("No file was uploaded.",)
if ("qc_text_file" not in rqst.files or
rqst.files["qc_text_file"].filename == "")
else tuple())
def __file_mimetype_error__():
text_file = rqst.files["qc_text_file"]
return (
(
("Invalid file! Expected a tab-separated-values file, or a zip "
"file of the a tab-separated-values file."),)
if text_file.mimetype not in (
"text/plain", "text/tab-separated-values",
"application/zip")
else tuple())
return (
__filetype_error__() +
(__file_missing_error__() or __file_mimetype_error__()))
def zip_file_errors(filepath, upload_dir) -> Tuple[str, ...]:
"""Check the uploaded zip file for errors."""
zfile_errors: Tuple[str, ...] = tuple()
if is_zipfile(filepath):
with ZipFile(filepath, "r") as zfile:
infolist = zfile.infolist()
if len(infolist) != 1:
zfile_errors = zfile_errors + (
("Expected exactly one (1) member file within the uploaded zip "
f"file. Got {len(infolist)} member files."),)
if len(infolist) == 1 and infolist[0].is_dir():
zfile_errors = zfile_errors + (
("Expected a member text file in the uploaded zip file. Got a "
"directory/folder."),)
if len(infolist) == 1 and not infolist[0].is_dir():
zfile.extract(infolist[0], path=upload_dir)
mime = mimetypes.guess_type(f"{upload_dir}/{infolist[0].filename}")
if mime[0] != "text/tab-separated-values":
zfile_errors = zfile_errors + (
("Expected the member text file in the uploaded zip file to"
" be a tab-separated file."),)
return zfile_errors
@entrybp.route("/", methods=["GET", "POST"])
def upload_file():
"""Enables uploading the files"""
if request.method == "GET":
return render_template(
"index.html", species=with_db_connection(species))
upload_dir = app.config["UPLOAD_FOLDER"]
request_errors = errors(request)
if request_errors:
for error in request_errors:
flash(error, "alert-error error-expr-data")
return render_template(
"index.html", species=with_db_connection(species)), 400
filename = secure_filename(request.files["qc_text_file"].filename)
if not os.path.exists(upload_dir):
os.mkdir(upload_dir)
filepath = os.path.join(upload_dir, filename)
request.files["qc_text_file"].save(os.path.join(upload_dir, filename))
zip_errors = zip_file_errors(filepath, upload_dir)
if zip_errors:
for error in zip_errors:
flash(error, "alert-error error-expr-data")
return render_template(
"index.html", species=with_db_connection(species)), 400
return redirect(url_for("parse.parse",
speciesid=request.form["speciesid"],
filename=filename,
filetype=request.form["filetype"]))
@entrybp.route("/data-review", methods=["GET"])
def data_review():
"""Provide some help on data expectations to the user."""
return render_template("data_review.html")
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