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-rw-r--r--uploader/genotypes/views.py45
1 files changed, 20 insertions, 25 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 0433420..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(