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"""Views for the genotypes."""
from flask import (flash,
request,
url_for,
redirect,
Blueprint,
render_template,
current_app as app)
from uploader.datautils import order_by_family
from uploader.authorisation import require_login
from uploader.db_utils import database_connection
from uploader.species.models import all_species, species_by_id
from uploader.population.models import (populations_by_species,
population_by_species_and_id)
genotypesbp = Blueprint("genotypes", __name__)
@genotypesbp.route("populations/genotypes", methods=["GET"])
@require_login
def index():
"""Direct entry-point for genotypes."""
with database_connection(app.config["SQL_URI"]) as conn:
if not bool(request.args.get("species_id")):
return render_template("genotypes/index.html",
species=order_by_family(all_species(conn)),
activelink="genotypes")
species = species_by_id(conn, request.args.get("species_id"))
if not bool(species):
flash(f"Could not find species with ID '{request.args.get('species_id')}'!",
"alert-danger")
return redirect(url_for("species.populations.genotypes.index"))
return redirect(url_for("species.populations.genotypes.select_population",
species_id=species["SpeciesId"]))
@genotypesbp.route("/<int:species_id>/populations/genotypes/select-population",
methods=["GET"])
@require_login
def select_population(species_id: int):
"""Select the population under which the genotypes go."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if not bool(species):
flash("Invalid species provided!", "alert-danger")
return redirect(url_for("species.populations.genotypes.index"))
if not bool(request.args.get("population_id")):
return render_template("genotypes/select-population.html",
species=species,
populations=order_by_family(
populations_by_species(conn, species_id),
order_key="FamilyOrder"),
activelink="genotypes")
population = population_by_species_and_id(
conn, species_id, request.args.get("population_id"))
if not bool(population):
flash("Invalid population selected!", "alert-danger")
return redirect(url_for(
"species.populations.genotypes.select_population",
species_id=species_id))
return redirect(url_for("species.populations.genotypes.list_genotypes",
species_id=species_id,
population_id=population["Id"]))
@genotypesbp.route(
"/<int:species_id>/populations/<int:population_id>/genotypes",
methods=["GET"])
@require_login
def list_genotypes(species_id: int, population_id: int):
"""List genotype details for species and population."""
return f"Would list geno info for population {population_id} from species {species_id}"
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