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"""Views dealing with populations/inbredsets"""
from flask import (flash,
request,
url_for,
redirect,
Blueprint,
current_app as app)
from uploader.ui import make_template_renderer
from uploader.authorisation import require_login
from uploader.db_utils import database_connection
from uploader.species.models import (all_species,
species_by_id,
order_species_by_family)
from .models import (save_population,
populations_by_species,
population_by_species_and_id)
__active_link__ = "populations"
popbp = Blueprint("populations", __name__)
render_template = make_template_renderer("populations")
@popbp.route("/populations", methods=["GET", "POST"])
@require_login
def index():
"""Entry point for populations."""
with database_connection(app.config["SQL_URI"]) as conn:
if not bool(request.args.get("species_id")):
return render_template(
"populations/index.html",
species=order_species_by_family(all_species(conn)))
species = species_by_id(conn, request.args.get("species_id"))
if not bool(species):
flash("Invalid species identifier provided!", "alert-danger")
return redirect(url_for("species.populations.index"))
return redirect(url_for("species.populations.list_species_populations",
species_id=species["SpeciesId"]))
@popbp.route("/<int:species_id>/populations", methods=["GET"])
@require_login
def list_species_populations(species_id: int):
"""List a particular species' populations."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if not bool(species):
flash("No species was found for given ID.", "alert-danger")
return redirect(url_for("species.populations.index"))
return render_template(
"populations/list-populations.html",
species=species,
populations=populations_by_species(conn, species_id),
activelink="list-populations")
def valid_population_name(population_name) -> bool:
"""Check whether the given name is a valid population name."""
raise NotImplementedError("Please implement this…")
@popbp.route("/<int:species_id>/create-population/", methods=["GET", "POST"])
@require_login
def create_population(species_id: int):
"""Create a new population."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if request.method == "GET":
return render_template(
"populations/create-population.html",
species=species,
continue_to=request.args.get("continue_uri"))
error = False
if not bool(species):
flash("You must select a species.", "alert-danger")
error = True
population_name = request.form.get("population_name", "").strip()
if not bool(population_name):
flash("You must provide a name for the population!", "alert-danger")
error = True
if not valid_population_name(population_name):
flash("The population name can only contain letters, numbers, "
"hyphens and underscores.",
"alert-danger")
error = True
population_fullname = request.form.get("inbredset_fullname", "").strip()
if not bool(population_fullname):
flash("You MUST provide a Full Name for the population."
"alert-danger")
error = True
if error:
return redirect(url_for("species.populations.create_population",
**dict(request.args)))
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
})
return redirect(url_for("species.populations.view_population",
species_id=species["SpeciesId"],
population_id=new_population["InbredSetId"]))
@popbp.route("/<int:species_id>/populations/<int:population_id>",
methods=["GET"])
@require_login
def view_population(species_id: int, population_id: int):
"""View the details of a population."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
population = population_by_species_and_id(conn, species_id, population_id)
error = False
if not bool(species):
flash("You must select a species.", "alert-danger")
error = True
if not bool(population):
flash("You must select a population.", "alert-danger")
error = True
if error:
return redirect(url_for("species.populations.index"))
return render_template("populations/view-population.html",
species=species,
population=population,
activelink="view-population")
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