"""Module to handle uploading of R/qtl2 bundles."""

from flask import (
    flash,
    request,
    url_for,
    redirect,
    Blueprint,
    render_template,
    current_app as app)

from qc_app.dbinsert import species as all_species
from qc_app.db_utils import with_db_connection, database_connection
from qc_app.db import (
    species_by_id,
    save_population,
    populations_by_species,
    population_by_species_and_id)

rqtl2 = Blueprint("rqtl2", __name__)

@rqtl2.route("/", methods=["GET", "POST"])
@rqtl2.route("/select-species", methods=["POST"])
def select_species():
    """Select the species."""
    if request.method == "GET":
        return render_template("rqtl2/index.html", species=with_db_connection(all_species))

    species_id = request.form.get("species_id")
    species = with_db_connection(
        lambda conn: species_by_id(conn, species_id))
    if bool(species):
        return redirect(url_for(
            "upload.rqtl2.select_population", species_id=species_id))
    flash("Invalid species or no species selected!", "alert-error error-rqtl2")
    return redirect(url_for("upload.rqtl2.select_species"))

@rqtl2.route("/upload/species/<int:species_id>/select-population",
             methods=["GET", "POST"])
def select_population(species_id: int):
    """Select/Create the population to organise data under."""
    with database_connection(app.config["SQL_URI"]) as conn:
        species = species_by_id(conn, species_id)
        if not bool(species):
            flash("Invalid species selected!", "alert-error error-rqtl2")
            return redirect(url_for("upload.rqtl2.select_species"))

        if request.method == "GET":
            return render_template(
                "rqtl2/select-population.html",
                species=species,
                populations=populations_by_species(conn, species_id))

        population = population_by_species_and_id(
            conn, species["SpeciesId"], request.form.get("inbredset_id"))
        if not bool(population):
            flash("Invalid Population!", "alert-error error-rqtl2")
            return redirect(
                url_for("upload.rqtl2.select_population", pgsrc="error"),
                code=307)

        return redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
                                species_id=species["SpeciesId"],
                                population_id=population["InbredSetId"]))

@rqtl2.route("/upload/species/<int:species_id>/create-population",
             methods=["POST"])
def create_population(species_id: int):
    """Create a new population for the given species."""
    population_page = redirect(url_for("upload.rqtl2.select_population"))
    with database_connection(app.config["SQL_URI"]) as conn:
        species = species_by_id(conn, species_id)
        population_name = request.form.get("inbredset_name", "").strip()
        population_fullname = request.form.get("inbredset_fullname", "").strip()
        if not bool(species):
            flash("Invalid species!", "alert-error error-rqtl2")
            return redirect(url_for("upload.rqtl2.select_species"))
        if not bool(population_name):
            flash("Invalid Population Name!", "alert-error error-rqtl2")
            return population_page
        if not bool(population_fullname):
            flash("Invalid Population Full Name!", "alert-error error-rqtl2")
            return population_page
        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
        })

    flash("Population created successfully.", "alert-success")
    return redirect(
        url_for("upload.rqtl2.upload_rqtl2_bundle",
                population_id=new_population["population_id"],
                pgsrc="create-population"),
        code=307)