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"""Module to handle uploading of R/qtl2 bundles."""
from pathlib import Path
from typing import Optional
from zipfile import ZipFile, is_zipfile
from flask import (
flash,
request,
url_for,
redirect,
Response,
Blueprint,
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, fullpath
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 (
species_by_id,
save_population,
populations_by_species,
population_by_species_and_id,
geno_dataset_by_species_and_population)
rqtl2 = Blueprint("rqtl2", __name__)
@rqtl2.route("/", methods=["GET", "POST"])
@rqtl2.route("/select-species", methods=["POST"])
def select_species():
"""Select the species."""
if request.method == "GET":
return render_template("rqtl2/index.html", species=with_db_connection(all_species))
species_id = request.form.get("species_id")
species = with_db_connection(
lambda conn: species_by_id(conn, species_id))
if bool(species):
return redirect(url_for(
"upload.rqtl2.select_population", species_id=species_id))
flash("Invalid species or no species selected!", "alert-error error-rqtl2")
return redirect(url_for("upload.rqtl2.select_species"))
@rqtl2.route("/upload/species/<int:species_id>/select-population",
methods=["GET", "POST"])
def select_population(species_id: int):
"""Select/Create the population to organise data under."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if not bool(species):
flash("Invalid species selected!", "alert-error error-rqtl2")
return redirect(url_for("upload.rqtl2.select_species"))
if request.method == "GET":
return render_template(
"rqtl2/select-population.html",
species=species,
populations=populations_by_species(conn, species_id))
population = population_by_species_and_id(
conn, species["SpeciesId"], request.form.get("inbredset_id"))
if not bool(population):
flash("Invalid Population!", "alert-error error-rqtl2")
return redirect(
url_for("upload.rqtl2.select_population", pgsrc="error"),
code=307)
return redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
species_id=species["SpeciesId"],
population_id=population["InbredSetId"]))
@rqtl2.route("/upload/species/<int:species_id>/create-population",
methods=["POST"])
def create_population(species_id: int):
"""Create a new population for the given species."""
population_page = redirect(url_for("upload.rqtl2.select_population"))
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
population_name = request.form.get("inbredset_name", "").strip()
population_fullname = request.form.get("inbredset_fullname", "").strip()
if not bool(species):
flash("Invalid species!", "alert-error error-rqtl2")
return redirect(url_for("upload.rqtl2.select_species"))
if not bool(population_name):
flash("Invalid Population Name!", "alert-error error-rqtl2")
return population_page
if not bool(population_fullname):
flash("Invalid Population Full Name!", "alert-error error-rqtl2")
return population_page
new_population = save_population(conn, {
"SpeciesId": species["SpeciesId"],
"Name": population_name,
"InbredSetName": population_fullname,
"FullName": population_fullname,
"Family": request.form.get("inbredset_family") or None,
"Description": request.form.get("description") or None
})
flash("Population created successfully.", "alert-success")
return redirect(
url_for("upload.rqtl2.upload_rqtl2_bundle",
population_id=new_population["population_id"],
pgsrc="create-population"),
code=307)
class __RequestError__(Exception): #pylint: disable=[invalid-name]
"""Internal class to avoid pylint's `too-many-return-statements` error."""
@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-step-01.html",
species=species,
population=population)
if not bool(request.files.get("rqtl2_bundle")):
raise __RequestError__("No R/qtl2 zip bundle provided.")
the_file = save_file(
request.files["rqtl2_bundle"], Path(app.config["UPLOAD_FOLDER"]))
if not bool(the_file):
raise __RequestError__("Please provide a valid R/qtl2 zip bundle.")
if not is_zipfile(str(the_file)):
raise __RequestError__("Invalid file! Expected a zip file.")
try:
with ZipFile(str(the_file), "r") as zfile:
r_qtl2.validate_bundle(zfile)
return render_template(
"rqtl2/upload-rqtl2-bundle-step-02.html",
species=species,
population=population,
rqtl2_bundle_file=the_file.name)
except (InvalidFormat, __RequestError__) as exc:
flash("".join(exc.args), "alert-error alert-danger error-rqtl2")
return this_page_with_errors
def check_errors(conn, *args, **kwargs) -> Optional[Response]:
"""Check for select errors in the forms and return a page to redirect to."""
species_id = kwargs.get("species_id") or request.form.get("species_id")
population_id = (kwargs.get("population_id")
or request.form.get("population_id"))
species = species_by_id(conn, species_id)
population = population_by_species_and_id(conn, species_id, population_id)
if "species" in args and not bool(species):
flash("Invalid species!", "alert-error error-rqtl2")
return redirect(url_for("upload.rqtl2.select_species"))
if "population" in args and not bool(population):
flash("Invalid Population!", "alert-error error-rqtl2")
return redirect(
url_for("upload.rqtl2.select_population", pgsrc="error"),
code=307)
if ("rqtl2_bundle_file" in args
and not bool(request.form.get("rqtl2_bundle_file"))):
flash("There is no file to process.",
"alert-error alert-danger error-rqtl2")
return redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
species_id=species_id,
population_id=population_id,
pgsrc="error"),
code=307)
return False
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
"/rqtl2-bundle/dataset-info"),
methods=["POST"])
def select_dataset_info(species_id: int, population_id: int):
"""
If `geno` files exist in the R/qtl2 bundle, prompt user to provide the
dataset the genotypes belong to.
"""
form = request.form
with database_connection(app.config["SQL_URI"]) as conn:
error_page = check_errors(conn, "species", "population", "rqtl2_bundle_file")
if bool(error_page):
return error_page
thefile = fullpath(form["rqtl2_bundle_file"])
with ZipFile(str(thefile), "r") as zfile:
cdata = r_qtl2.control_data(zfile)
if "geno" in cdata and not bool(form.get("geno_datasetid")):
return render_template(
"rqtl2/select-geno-dataset.html",
species=species_by_id(conn, species_id),
population=population_by_species_and_id(
conn, species_id, population_id),
rqtl2_bundle_file=thefile.name,
datasets=geno_dataset_by_species_and_population(
conn, species_id, population_id))
return "All data points collected. Should proceed to launching the job."
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
"/rqtl2-bundle/select-geno-dataset"),
methods=["POST"])
def select_geno_dataset(species_id: int, population_id: int) -> Response:
"""Select from existing geno datasets."""
return "IMPLEMENT THIS!!!"
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
"/rqtl2-bundle/create-geno-dataset"),
methods=["POST"])
def create_geno_dataset(species_id: int, population_id: int) -> Response:
"""Create a new geno dataset."""
return "IMPLEMENT THIS!!!"
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