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"""Views for the genotypes."""
from requests.models import Response
from MySQLdb.cursors import DictCursor
from flask import (flash,
request,
url_for,
redirect,
Blueprint,
render_template,
current_app as app)
from uploader.ui import make_template_renderer
from uploader.oauth2.client import oauth2_post
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.request_checks import with_species, with_population
from uploader.datautils import safe_int, order_by_family, enumerate_sequence
from uploader.population.models import (populations_by_species,
population_by_species_and_id)
from .models import (genotype_markers,
genotype_dataset,
save_new_dataset,
genotype_markers_count,
genocode_by_population)
genotypesbp = Blueprint("genotypes", __name__)
render_template = make_template_renderer("genotypes")
@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
@with_species(redirect_uri="species.populations.genotypes.index")
def select_population(species: dict, species_id: int):
"""Select the population under which the genotypes go."""
with database_connection(app.config["SQL_URI"]) as conn:
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
@with_population(species_redirect_uri="species.populations.genotypes.index",
redirect_uri="species.populations.genotypes.select_population")
def list_genotypes(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
"""List genotype details for species and population."""
with database_connection(app.config["SQL_URI"]) as conn:
return render_template("genotypes/list-genotypes.html",
species=species,
population=population,
genocode=genocode_by_population(
conn, population["Id"]),
total_markers=genotype_markers_count(
conn, species["SpeciesId"]),
dataset=genotype_dataset(conn,
species["SpeciesId"],
population["Id"]),
activelink="list-genotypes")
@genotypesbp.route("/<int:species_id>/genotypes/list-markers", methods=["GET"])
@require_login
@with_species(redirect_uri="species.populations.genotypes.index")
def list_markers(species: dict, **kwargs):# pylint: disable=[unused-argument]
"""List a species' genetic markers."""
with database_connection(app.config["SQL_URI"]) as conn:
start_from = max(safe_int(request.args.get("start_from") or 0), 0)
count = safe_int(request.args.get("count") or 20)
return render_template("genotypes/list-markers.html",
species=species,
total_markers=genotype_markers_count(
conn, species["SpeciesId"]),
start_from=start_from,
count=count,
markers=enumerate_sequence(
genotype_markers(conn,
species["SpeciesId"],
offset=start_from,
limit=count),
start=start_from+1),
activelink="list-markers")
@genotypesbp.route(
"/<int:species_id>/populations/<int:population_id>/genotypes/datasets/"
"<int:dataset_id>/view",
methods=["GET"])
@require_login
def view_dataset(species_id: int, population_id: int, dataset_id: int):
"""View details regarding a specific dataset."""
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"))
population = population_by_species_and_id(
conn, species_id, 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))
dataset = genotype_dataset(conn, species_id, population_id, dataset_id)
if not bool(dataset):
flash("Could not find such a dataset!", "alert-danger")
return redirect(url_for(
"species.populations.genotypes.list_genotypes",
species_id=species_id,
population_id=population_id))
return render_template("genotypes/view-dataset.html",
species=species,
population=population,
dataset=dataset,
activelink="view-dataset")
@genotypesbp.route(
"/<int:species_id>/populations/<int:population_id>/genotypes/datasets/"
"create",
methods=["GET", "POST"])
@require_login
@with_population(species_redirect_uri="species.populations.genotypes.index",
redirect_uri="species.populations.genotypes.select_population")
def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
"""Create a genotype dataset."""
with (database_connection(app.config["SQL_URI"]) as conn,
conn.cursor(cursorclass=DictCursor) as cursor):
if request.method == "GET":
return render_template("genotypes/create-dataset.html",
species=species,
population=population,
activelink="create-dataset")
form = request.form
new_dataset = save_new_dataset(
cursor,
population["Id"],
form["geno-dataset-name"],
form["geno-dataset-fullname"],
form["geno-dataset-shortname"])
def __success__(_success):
flash("Successfully created genotype dataset.", "alert-success")
return redirect(url_for(
"species.populations.genotypes.list_genotypes",
species_id=species["SpeciesId"],
population_id=population["Id"]))
def __fail__(error):
msg = "There was an error creating the genotype dataset."
if issubclass(type(error), Exception):
app.logger.debug("\n\n%s (Exception)\n\n", msg, exc_info=True)
raise error
if issubclass(type(error), Response):
try:
_data = error.json()
except Exception as _exc:
raise Exception(error.content) from _exc
raise Exception(_data)
app.logger.debug("\n\n%s\n\n", msg)
raise Exception(error)
return oauth2_post(
"auth/resource/genotypes/create",
json={
**dict(request.form),
"species_id": species["SpeciesId"],
"population_id": population["Id"],
"dataset_id": new_dataset["Id"],
"dataset_name": form["geno-dataset-name"],
"dataset_fullname": form["geno-dataset-fullname"],
"dataset_shortname": form["geno-dataset-shortname"],
"public": "on"
}
).either(__fail__, __success__)
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