diff options
Diffstat (limited to 'uploader/genotypes')
| -rw-r--r-- | uploader/genotypes/views.py | 59 |
1 files changed, 31 insertions, 28 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index e6b1ba7..54c2444 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -12,12 +12,12 @@ from flask import (flash, from uploader.ui import make_template_renderer from uploader.oauth2.client import oauth2_post from uploader.authorisation import require_login +from uploader.route_utils import generic_select_population +from uploader.datautils import safe_int, enumerate_sequence from uploader.species.models import all_species, species_by_id from uploader.monadic_requests import make_either_error_handler from uploader.request_checks import with_species, with_population -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 uploader.population.models import population_by_species_and_id from .models import (genotype_markers, genotype_dataset, @@ -35,8 +35,15 @@ def index(): 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)), + species=all_species(conn), activelink="genotypes") + + species_id = request.args.get("species_id") + if species_id == "CREATE-SPECIES": + return redirect(url_for( + "species.create_species", + return_to="species.populations.genotypes.select_population")) + 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')}'!", @@ -50,28 +57,16 @@ def index(): methods=["GET"]) @require_login @with_species(redirect_uri="species.populations.genotypes.index") -def select_population(species: dict, species_id: int): +def select_population(species: dict, species_id: int):# pylint: disable=[unused-argument] """Select the population under which the genotypes go.""" - with database_connection(app.config["SQL_URI"]) as conn: - 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"])) + return generic_select_population( + species, + "genotypes/select-population.html", + request.args.get("population_id") or "", + "species.populations.genotypes.select_population", + "species.populations.genotypes.list_genotypes", + "genotypes", + "Invalid population selected!") @genotypesbp.route( @@ -96,16 +91,24 @@ def list_genotypes(species: dict, population: dict, **kwargs):# pylint: disable= activelink="list-genotypes") -@genotypesbp.route("/<int:species_id>/genotypes/list-markers", methods=["GET"]) +@genotypesbp.route( + "/<int:species_id>/populations/<int:population_id>/genotypes/list-markers", + methods=["GET"]) @require_login -@with_species(redirect_uri="species.populations.genotypes.index") -def list_markers(species: dict, **kwargs):# pylint: disable=[unused-argument] +@with_population(species_redirect_uri="species.populations.genotypes.index", + redirect_uri="species.populations.genotypes.select_population") +def list_markers( + species: dict, + population: dict, + **kwargs +):# pylint: disable=[unused-argument] """List a species' genetic markers.""" with database_connection(app.config["SQL_URI"]) as conn: 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("genotypes/list-markers.html", species=species, + population=population, total_markers=genotype_markers_count( conn, species["SpeciesId"]), start_from=start_from, |