"""Views for the genotypes."""
from flask import (flash,
                   request,
                   url_for,
                   redirect,
                   Blueprint,
                   render_template,
                   current_app as app)

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.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_markers_count,
                     genocode_by_population)

genotypesbp = Blueprint("genotypes", __name__)

@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
def select_population(species_id: int):
    """Select the population under which the genotypes go."""
    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"))

        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
def list_genotypes(species_id: int, population_id: int):
    """List genotype details for species and population."""
    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))

        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_id),
                               activelink="list-genotypes")


@genotypesbp.route("/<int:species_id>/genotypes/list-markers", methods=["GET"])
@require_login
def list_markers(species_id: int):
    """List a species' genetic markers."""
    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"))

        start_from = safe_int(request.args.get("start_from") or 0)
        if start_from < 0:
            start_from = 0
        count = safe_int(request.args.get("count") or 20)
        markers = enumerate_sequence(
            genotype_markers(conn, species_id, offset=start_from, limit=count),
            start=start_from+1)
        return render_template("genotypes/list-markers.html",
                               species=species,
                               total_markers=genotype_markers_count(
                                   conn, species_id),
                               start_from=start_from,
                               count=count,
                               markers=markers,
                               activelink="list-markers")