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"""The endpoints for the platforms"""
from flask import (
flash,
request,
url_for,
redirect,
Blueprint,
current_app as app)
from uploader.ui import make_template_renderer
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 .models import platforms_by_species, species_platforms_count
platformsbp = Blueprint("platforms", __name__)
render_template = make_template_renderer("platforms")
@platformsbp.route("platforms", methods=["GET"])
@require_login
def index():
"""Entry-point to the platforms feature."""
with database_connection(app.config["SQL_URI"]) as conn:
if not bool(request.args.get("species_id")):
return render_template(
"platforms/index.html",
species=order_by_family(all_species(conn)),
activelink="platforms")
species = species_by_id(conn, request.args["species_id"])
if not bool(species):
flash("No species selected.", "alert-danger")
return redirect(url_for("species.platforms.index"))
return redirect(url_for("species.platforms.list_platforms",
species_id=species["SpeciesId"]))
@platformsbp.route("<int:species_id>/platforms", methods=["GET"])
@require_login
def list_platforms(species_id: int):
"""List all the available genetic sequencing platforms."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if not bool(species):
flash("No species provided.", "alert-danger")
return redirect(url_for("species.platforms.index"))
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(
"platforms/list-platforms.html",
species=species,
platforms=enumerate_sequence(
platforms_by_species(conn,
species_id,
offset=start_from,
limit=count),
start=start_from+1),
start_from=start_from,
count=count,
total_platforms=species_platforms_count(conn, species_id),
activelink="list-platforms")
@platformsbp.route("<int:species_id>/platforms/create", methods=["GET", "POST"])
@require_login
def create_platform(species_id: int):
"""Create a new genetic sequencing platform."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if not bool(species):
flash("No species provided.", "alert-danger")
return redirect(url_for("species.platforms.index"))
if request.method == "GET":
return render_template(
"platforms/create-platform.html",
species=species,
activelink="create-platform")
raise NotImplementedError("This still needs to be implemented.")
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