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"""Views dealing with populations/inbredsets"""
import re
import json
import base64
import traceback
from requests.models import Response
from MySQLdb.cursors import DictCursor
from flask import (flash,
request,
url_for,
redirect,
Blueprint,
current_app as app)
from uploader.samples.views import samplesbp
from uploader.oauth2.client import oauth2_post
from uploader.ui import make_template_renderer
from uploader.authorisation import require_login
from uploader.genotypes.views import genotypesbp
from uploader.expression_data.views import exprdatabp
from uploader.db_utils import database_connection
from uploader.datautils import enumerate_sequence
from uploader.species.models import (all_species,
species_by_id,
order_species_by_family)
from .models import (save_population,
population_families,
populations_by_species,
population_genetic_types,
population_by_species_and_id)
__active_link__ = "populations"
popbp = Blueprint("populations", __name__)
popbp.register_blueprint(samplesbp, url_prefix="/")
popbp.register_blueprint(genotypesbp, url_prefix="/")
popbp.register_blueprint(exprdatabp, url_prefix="/")
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=enumerate_sequence(populations_by_species(
conn, species_id)),
activelink="list-populations")
def valid_population_name(population_name: str) -> bool:
"""
Check whether the given name is a valid population name.
Parameters
----------
population_name: a string of characters.
Checks For
----------
* The name MUST start with an alphabet [a-zA-Z]
* The name MUST end with an alphabet [a-zA-Z] or number [0-9]
* The name MUST be composed of alphabets [a-zA-Z], numbers [0-9],
underscores (_) and/or hyphens (-).
Returns
-------
Boolean indicating whether or not the name is valid.
"""
pattern = re.compile(r"^[a-zA-Z]+[a-zA-Z0-9_-]*[a-zA-Z0-9]$")
return bool(pattern.match(population_name))
@popbp.route("/<int:species_id>/populations/create", methods=["GET", "POST"])
@require_login
def create_population(species_id: int):
"""Create a new population."""
with (database_connection(app.config["SQL_URI"]) as conn,
conn.cursor(cursorclass=DictCursor) as cursor):
species = species_by_id(conn, species_id)
if request.method == "GET":
error_values = request.args.get("error_values")
if not bool(error_values):
error_values = base64.b64encode(
'{"errors":{}, "error_values": {}}'.encode("utf8")
).decode("utf8")
error_values = json.loads(base64.b64decode(
error_values.encode("utf8")).decode("utf8"))# type: ignore[union-attr]
return render_template(
"populations/create-population.html",
species=species,
families = population_families(conn),
genetic_types = population_genetic_types(conn),
mapping_methods=(
{"id": "0", "value": "No mapping support"},
{"id": "1", "value": "GEMMA, QTLReaper, R/qtl"},
{"id": "2", "value": "GEMMA"},
{"id": "3", "value": "R/qtl"},
{"id": "4", "value": "GEMMA, PLINK"}),
activelink="create-population",
**error_values)
if not bool(species):
flash("You must select a species.", "alert-danger")
return redirect(url_for("species.populations.index"))
errors: tuple[tuple[str, str], ...] = tuple()
population_name = (request.form.get(
"population_name") or "").strip()
if not bool(population_name):
errors = errors + (("population_name",
"You must provide a name for the population!"),)
if not valid_population_name(population_name):
errors = errors + ((
"population_name",
"The population name can only contain letters, numbers, "
"hyphens and underscores."),)
population_fullname = (request.form.get(
"population_fullname") or "").strip()
if not bool(population_fullname):
errors = errors + (
("population_fullname", "Full Name MUST be provided."),)
if bool(errors):
values = base64.b64encode(
json.dumps({
"errors": dict(errors),
"error_values": dict(request.form)
}).encode("utf8"))
return redirect(url_for("species.populations.create_population",
species_id=species["SpeciesId"],
error_values=values))
new_population = save_population(cursor, {
"SpeciesId": species["SpeciesId"],
"Name": population_name,
"InbredSetName": population_fullname,
"FullName": population_fullname,
"InbredSetCode": request.form.get("population_code") or None,
"Description": request.form.get("population_description") or None,
"Family": request.form.get("population_family") or None,
"MappingMethodId": request.form.get("population_mapping_method_id"),
"GeneticType": request.form.get("population_genetic_type") or None
})
def __handle_error__(error):
error_format = (
"\n\nThere was an error creating the population:\n\t%s\n\n")
if issubclass(type(error), Exception):
app.logger.debug(error_format, traceback.format_exc())
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(error_format, error)
raise Exception(error)
def __flash_success__(_success):
flash("Successfully created resource.", "alert-success")
return redirect(url_for(
"species.populations.view_population",
species_id=species["SpeciesId"],
population_id=new_population["InbredSetId"]))
app.logger.debug("We begin setting up the privileges here…")
return oauth2_post(
"auth/resource/populations/create",
json={
**dict(request.form),
"species_id": species_id,
"population_id": new_population["Id"],
"public": "on"
}
).either(__handle_error__, __flash_success__)
@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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