"""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, send_from_directory) from qc_app.db import species from qc_app.db_utils import with_db_connection entrybp = Blueprint("entry", __name__) @entrybp.route("/favicon.ico", methods=["GET"]) def favicon(): """Return the favicon.""" return send_from_directory(os.path.join(app.root_path, "static"), "images/CITGLogo.png", mimetype="image/png") 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"]) def index(): """Load the landing page""" return render_template("index.html") @entrybp.route("/upload", methods=["GET", "POST"]) def upload_file(): """Enables uploading the files""" if request.method == "GET": return render_template( "select_species.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 redirect(url_for("entry.upload_file")) 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")