From 0b37b9b3fa4fead86787a705713645fa14530a54 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 23 Sep 2024 14:28:49 -0500
Subject: Initialise the "Expression Data" section.

---
 uploader/expression_data/index.py | 125 --------------------------------------
 1 file changed, 125 deletions(-)
 delete mode 100644 uploader/expression_data/index.py

(limited to 'uploader/expression_data/index.py')

diff --git a/uploader/expression_data/index.py b/uploader/expression_data/index.py
deleted file mode 100644
index db23136..0000000
--- a/uploader/expression_data/index.py
+++ /dev/null
@@ -1,125 +0,0 @@
-"""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 uploader.species.models import all_species as species
-from uploader.authorisation import require_login
-from uploader.db_utils import with_db_connection
-
-indexbp = Blueprint("index", __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
-
-
-@indexbp.route("/", methods=["GET"])
-@require_login
-def index():
-    """Display the expression data index page."""
-    return render_template("expression-data/index.html")
-
-
-@indexbp.route("/upload", methods=["GET", "POST"])
-@require_login
-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("expression-data.index.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("expression-data.index.upload_file"))
-
-    return redirect(url_for("expression-data.parse.parse",
-                            speciesid=request.form["speciesid"],
-                            filename=filename,
-                            filetype=request.form["filetype"]))
-
-@indexbp.route("/data-review", methods=["GET"])
-@require_login
-def data_review():
-    """Provide some help on data expectations to the user."""
-    return render_template("data_review.html")
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