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"""Code regarding samples"""
import MySQLdb as mdb
from MySQLdb.cursors import DictCursor
from flask import (
flash, request, url_for, redirect, Blueprint, render_template, current_app as app)
from .db_utils import with_db_connection
from .dbinsert import species_by_id, groups_by_species
samples = Blueprint("samples", __name__)
@samples.route("/upload/species", methods=["POST"])
def select_species():
"""Select the species."""
index_page = redirect(url_for("entry.upload_file"))
species_id = request.form.get("species_id")
if bool(species_id):
species_id = int(species_id)
species = species_by_id(species_id)
if bool(species):
return render_template(
"samples/select-population.html",
species=species,
populations=groups_by_species(species_id))
flash("Invalid species selected!", "alert-error")
flash("You need to select a species", "alert-error")
return index_page
def save_population(conn: mdb.Connection, population_details: dict) -> int:
"""Save the population details to the db."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT MAX(Id) AS last_id FROM InbredSet")
new_id = cursor.fetchone()["last_id"] + 1
cursor.execute(
"INSERT INTO InbredSet("
"Id, InbredSetId, InbredSetName, Name, SpeciesId, FullName, "
"MenuOrderId, Description"
") "
"VALUES ("
"%(Id)s, %(InbredSetId)s, %(InbredSetName)s, %(Name)s, "
"%(SpeciesId)s, %(FullName)s, %(MenuOrderId)s, %(Description)s"
")",
{
"Id": new_id,
"InbredSetId": new_id,
"MenuOrderId": 0,
**population_details
})
return new_id
def population_by_id(conn: mdb.Connection, population_id: int) -> dict:
"""Get the grouping/population by id."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT * FROM InbredSet WHERE InbredSetId=%s",
(population_id,))
return cursor.fetchone()
@samples.route("/upload/create-population", methods=["POST"])
def create_population():
"""Create new grouping/population."""
species_page = redirect(url_for("samples.select_species"), code=307)
species = species_by_id(request.form.get("species_id"))
pop_name = request.form.get("inbredset_name").strip()
pop_fullname = request.form.get("inbredset_fullname").strip()
if not bool(species):
flash("Invalid species!", "alert-error error-create-population")
return species_page
if (not bool(pop_name)) or (not bool(pop_fullname)):
flash("You *MUST* provide a grouping/population name",
"alert-error error-create-population")
return species_page
pop_id = with_db_connection(lambda conn: save_population(conn, {
"SpeciesId": species["SpeciesId"],
"Name": pop_name,
"InbredSetName": pop_fullname,
"FullName": pop_fullname,
"Family": request.form.get("inbredset_family") or None,
"Description": request.form.get("description") or None
}))
flash("Grouping/Population created successfully.", "alert-success")
return render_template(
"samples/upload-samples.html",
species=species,
population=with_db_connection(
lambda conn: population_by_id(conn, pop_id)))
@samples.route("/upload/select-population", methods=["POST"])
def select_population():
"""Select from existing groupings/populations."""
species_page = redirect(url_for("samples.select_species"), code=307)
species = species_by_id(request.form.get("species_id"))
pop_id = int(request.form.get("inbredset_id"))
population = with_db_connection(lambda conn: population_by_id(conn, pop_id))
if not bool(species):
flash("Invalid species!", "alert-error error-select-population")
return species_page
if not bool(population):
flash("Invalid grouping/population!",
"alert-error error-select-population")
return species_page
return render_template("samples/upload-samples.html",
species=species,
population=population)
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