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authorFrederick Muriuki Muriithi2024-01-08 07:25:35 +0300
committerFrederick Muriuki Muriithi2024-01-08 07:25:35 +0300
commit8595c75345fb5849a4d8894f3ee7a926dd8cdf8f (patch)
treeee4a18e3aed146028b5a9463ecc2d5c12252d81c /qc_app/upload
parentea89a07e6d04c2fe58f94839eb9916b365b2f3f2 (diff)
downloadgn-uploader-8595c75345fb5849a4d8894f3ee7a926dd8cdf8f.tar.gz
Upload R/qtl2 zip bundle and check for errors.
Diffstat (limited to 'qc_app/upload')
-rw-r--r--qc_app/upload/rqtl2.py56
1 files changed, 56 insertions, 0 deletions
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