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-rw-r--r--uploader/genotypes/views.py47
1 files changed, 15 insertions, 32 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 1ac36b2..41cd21e 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -11,6 +11,7 @@ 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.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)
@@ -44,14 +45,10 @@ def index():
@genotypesbp.route("/<int:species_id>/populations/genotypes/select-population",
methods=["GET"])
@require_login
-def select_population(species_id: int):
+@with_species(redirect_uri="species.populations.genotypes.index")
+def select_population(species: dict, 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,
@@ -77,55 +74,41 @@ def select_population(species_id: int):
"/<int:species_id>/populations/<int:population_id>/genotypes",
methods=["GET"])
@require_login
-def list_genotypes(species_id: int, population_id: int):
+@with_population(species_redirect_uri="species.populations.genotypes.index",
+ redirect_uri="species.populations.genotypes.select_population")
+def list_genotypes(species: dict, population: dict, **kwargs):
"""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),
+ conn, population["Id"]),
total_markers=genotype_markers_count(
- conn, species_id),
- dataset=genotype_dataset(
- conn, species_id, population_id),
+ conn, species["SpeciesId"]),
+ dataset=genotype_dataset(conn,
+ species["SpeciesId"],
+ population["Id"]),
activelink="list-genotypes")
@genotypesbp.route("/<int:species_id>/genotypes/list-markers", methods=["GET"])
@require_login
-def list_markers(species_id: int):
+@with_species(redirect_uri="species.populations.genotypes.index")
+def list_markers(species: dict, **kwargs):
"""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 = 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,
total_markers=genotype_markers_count(
- conn, species_id),
+ conn, species["SpeciesId"]),
start_from=start_from,
count=count,
markers=enumerate_sequence(
genotype_markers(conn,
- species_id,
+ species["SpeciesId"],
offset=start_from,
limit=count),
start=start_from+1),