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"""Endpoints handling species."""
from flask import (flash,
request,
url_for,
redirect,
Blueprint,
current_app as app,
render_template as flask_render_template)
from uploader.authorisation import require_login
from uploader.db_utils import database_connection
from .models import all_species, save_species, species_by_id
speciesbp = Blueprint("species", __name__)
def render_template(template, **kwargs):
"""Render template for species."""
return flask_render_template(
template,
**{
**kwargs,
"activelink": kwargs.get("activelink", "species")
})
@speciesbp.route("/", methods=["GET"])
def list_species():
"""List and display all the species in the database."""
with database_connection(app.config["SQL_URI"]) as conn:
return render_template("species/list-species.html",
allspecies=all_species(conn))
@speciesbp.route("/<int:species_id>", methods=["GET"])
@require_login
def view_species(species_id: int):
"""View details of a particular species and menus to act upon it."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if bool(species):
return render_template("species/view-species.html",
species=species,
activelink="view-species")
flash("Could not find a species with the given identifier.",
"alert-danger")
return redirect(url_for("species.view_species"))
@speciesbp.route("/create", methods=["GET", "POST"])
@require_login
def create_species():
"""Create a new species."""
# We can use uniprot's API to fetch the details with something like
# https://rest.uniprot.org/taxonomy/<taxonID> e.g.
# https://rest.uniprot.org/taxonomy/6239
if request.method == "GET":
return render_template("species/create-species.html",
activelink="create-species")
with (database_connection(app.config["SQL_URI"]) as conn,
conn.cursor() as cursor):
error = False
taxon_id = request.form.get("species_taxonomy_id", "").strip() or None
common_name = request.form.get("common_name", "").strip()
if not bool(common_name):
flash("The common species name MUST be provided.", "alert-danger")
error = True
scientific_name = request.form.get("scientific_name", "").strip()
if not bool(scientific_name):
flash("The species' scientific name MUST be provided.",
"alert-danger")
error = True
parts = tuple(name.strip() for name in scientific_name.split(" "))
if len(parts) != 2 or not all(bool(name) for name in parts):
flash("The scientific name you provided is invalid.", "alert-danger")
error = True
cursor.execute(
"SELECT * FROM Species WHERE FullName=%s", (scientific_name,))
res = cursor.fetchone()
if bool(res):
flash("A species already exists with the provided scientific name.",
"alert-danger")
error = True
if bool(taxon_id):
cursor.execute(
"SELECT * FROM Species WHERE TaxonomyId=%s", (taxon_id,))
res = cursor.fetchone()
if bool(res):
flash("A species already exists with the provided scientific name.",
"alert-danger")
error = True
if error:
return redirect(url_for("species.create_species",
common_name=common_name,
scientific_name=scientific_name,
taxon_id=taxon_id))
species = save_species(conn, common_name, scientific_name, taxon_id)
flash("Species saved successfully!", "alert-success")
return redirect(url_for("species.view_species", species_id=species["species_id"]))
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