From 8595c75345fb5849a4d8894f3ee7a926dd8cdf8f Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 8 Jan 2024 07:25:35 +0300
Subject: Upload R/qtl2 zip bundle and check for errors.

---
 qc_app/upload/rqtl2.py | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

(limited to 'qc_app/upload')

diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 681e54c..53e7f3f 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -1,4 +1,6 @@
 """Module to handle uploading of R/qtl2 bundles."""
+from pathlib import Path
+from zipfile import ZipFile, is_zipfile
 
 from flask import (
     flash,
@@ -9,6 +11,10 @@ from flask import (
     render_template,
     current_app as app)
 
+from r_qtl import r_qtl2
+from r_qtl.errors import InvalidFormat
+
+from qc_app.files import save_file
 from qc_app.dbinsert import species as all_species
 from qc_app.db_utils import with_db_connection, database_connection
 from qc_app.db import (
@@ -96,3 +102,53 @@ def create_population(species_id: int):
                 population_id=new_population["population_id"],
                 pgsrc="create-population"),
         code=307)
+
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+              "/rqtl2-bundle"),
+    methods=["GET", "POST"])
+def upload_rqtl2_bundle(species_id: int, population_id: int):
+    """Allow upload of R/qtl2 bundle."""
+    this_page_with_errors = redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
+                                             species_id=species_id,
+                                             population_id=population_id,
+                                             pgsrc="error"),
+                                     code=307)
+
+    with database_connection(app.config["SQL_URI"]) as conn:
+        species = species_by_id(conn, species_id)
+        population = population_by_species_and_id(
+            conn, species["SpeciesId"], population_id)
+        if not bool(species):
+            flash("Invalid species!", "alert-error error-rqtl2")
+            return redirect(url_for("upload.rqtl2.select_species"))
+        if not bool(population):
+            flash("Invalid Population!", "alert-error error-rqtl2")
+            return redirect(
+                url_for("upload.rqtl2.select_population", pgsrc="error"),
+                code=307)
+        if request.method == "GET" or (
+                request.method == "POST"
+                and bool(request.args.get("pgsrc"))):
+            return render_template("rqtl2/upload-rqtl2-bundle.html",
+                                   species=species,
+                                   population=population)
+
+        the_file = save_file(
+            request.files.get("rqtl2_bundle"), Path(app.config["UPLOAD_FOLDER"]))
+        if not bool(the_file):
+            flash("Please provide a valid R/qtl2 zip bundle.",
+                  "alert-error alert-danger error-rqtl2")
+            return this_page_with_errors
+
+        if not is_zipfile(the_file):
+            flash("Invalid file! Expected a zip file.",
+                  "alert-error alert-danger error-rqtl2")
+            return this_page_with_errors
+
+        try:
+            with ZipFile(the_file, "r") as zfile:
+                r_qtl2.validate_bundle(zfile)
+                return "WOULD PROCESS THE BUNDLE..."
+        except InvalidFormat as invf:
+            flash("".join(invf.args), "alert-error alert-danger error-rqtl2")
+            return this_page_with_errors
-- 
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