aboutsummaryrefslogtreecommitdiff
path: root/uploader/phenotypes
diff options
context:
space:
mode:
Diffstat (limited to 'uploader/phenotypes')
-rw-r--r--uploader/phenotypes/views.py57
1 files changed, 50 insertions, 7 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 4565844..a79e863 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -1,4 +1,6 @@
"""Views handling ('classical') phenotypes."""
+from functools import wraps
+
from flask import (flash,
request,
url_for,
@@ -89,19 +91,60 @@ def list_datasets(species: dict, population: dict, **kwargs):# pylint: disable=[
activelink="list-datasets")
+def with_dataset(
+ species_redirect_uri: str,
+ population_redirect_uri: str,
+ redirect_uri: str
+):
+ """Ensure the dataset actually exists."""
+ def __decorator__(func):
+ @wraps(func)
+ @with_population(species_redirect_uri, population_redirect_uri)
+ def __with_dataset__(**kwargs):
+ try:
+ _spcid = int(kwargs["species_id"])
+ _popid = int(kwargs["population_id"])
+ _dsetid = int(kwargs.get("dataset_id"))
+ select_dataset_uri = redirect(url_for(
+ redirect_uri, species_id=_spcid, population_id=_popid))
+ if not bool(_dsetid):
+ flash("You need to select a valid 'dataset_id' value.",
+ "alert-danger")
+ return select_dataset_uri
+ with database_connection(app.config["SQL_URI"]) as conn:
+ dataset = dataset_by_id(conn, _spcid, _popid, _dsetid)
+ if not bool(dataset):
+ flash("You must select a valid dataset.",
+ "alert-danger")
+ return select_dataset_uri
+ except ValueError as _verr:
+ app.logger.debug(
+ "Exception converting 'dataset_id' to integer: %s",
+ kwargs.get("dataset_id"),
+ exc_info=True)
+ flash("Expected 'dataset_id' value to be an integer."
+ "alert-danger")
+ return select_dataset_uri
+ return func(dataset=dataset, **kwargs)
+ return __with_dataset__
+ return __decorator__
+
+
@phenotypesbp.route(
"<int:species_id>/populations/<int:population_id>/phenotypes/datasets"
"/<int:dataset_id>/view",
methods=["GET"])
@require_login
-@with_population(species_redirect_uri="species.populations.phenotypes.index",
- redirect_uri="species.populations.phenotypes.select_population")
+@with_dataset(
+ species_redirect_uri="species.populations.phenotypes.index",
+ population_redirect_uri="species.populations.phenotypes.select_population",
+ redirect_uri="species.populations.phenotypes.list_datasets")
def view_dataset(# pylint: disable=[unused-argument]
- species: dict, population: dict, dataset_id: int, **kwargs):
+ species: dict, population: dict, dataset: dict, **kwargs):
"""View a specific dataset"""
with database_connection(app.config["SQL_URI"]) as conn:
dataset = dataset_by_id(
- conn, species["SpeciesId"], population["Id"], dataset_id)
+ conn, species["SpeciesId"], population["Id"], dataset["Id"])
if not bool(dataset):
flash("Could not find such a phenotype dataset!", "alert-danger")
return redirect(url_for(
@@ -114,13 +157,13 @@ def view_dataset(# pylint: disable=[unused-argument]
return render_template("phenotypes/view-dataset.html",
species=species,
population=population,
- dataset={"Id": dataset_id},
+ dataset=dataset,
phenotype_count=phenotypes_count(
- conn, population["Id"], dataset_id),
+ conn, population["Id"], dataset["Id"]),
phenotypes=enumerate_sequence(
dataset_phenotypes(conn,
population["Id"],
- dataset_id,
+ dataset["Id"],
offset=start_at,
limit=count),
start=start_at+1),