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authorFrederick Muriuki Muriithi2024-07-25 11:07:33 -0500
committerFrederick Muriuki Muriithi2024-07-25 14:34:09 -0500
commit754e8f214b940e05298cb360ed829f5c685d55a5 (patch)
tree62c2c5b601746621f0949b38937ad232f006dee2 /uploader/entry.py
parentde9e1b9fe37928b864bea28b408de6c14d04526b (diff)
downloadgn-uploader-754e8f214b940e05298cb360ed829f5c685d55a5.tar.gz
Rename module: qc_app --> uploader
Diffstat (limited to 'uploader/entry.py')
-rw-r--r--uploader/entry.py127
1 files changed, 127 insertions, 0 deletions
diff --git a/uploader/entry.py b/uploader/entry.py
new file mode 100644
index 0000000..4a02f1e
--- /dev/null
+++ b/uploader/entry.py
@@ -0,0 +1,127 @@
+"""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 uploader.db import species
+from uploader.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-danger 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-danger error-expr-data")
+ return redirect(url_for("entry.upload_file"))
+
+ 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")