From f04e340323d0e289aaa379ab1a8d82033da73e62 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 27 Sep 2024 11:43:48 -0500
Subject: Show some details for a phenotype dataset.

---
 uploader/phenotypes/views.py | 47 ++++++++++++++++++++++++++++++++++----------
 1 file changed, 37 insertions(+), 10 deletions(-)

(limited to 'uploader/phenotypes/views.py')

diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 88cb89c..4565844 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -1,20 +1,24 @@
 """Views handling ('classical') phenotypes."""
-from flask import (request,
+from flask import (flash,
+                   request,
                    url_for,
                    redirect,
                    Blueprint,
                    render_template,
                    current_app as app)
 
-from uploader.datautils import order_by_family
 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)
 
-from .models import datasets_by_population, phenotypes_data
+from .models import (dataset_by_id,
+                     phenotypes_count,
+                     dataset_phenotypes,
+                     datasets_by_population)
 
 phenotypesbp = Blueprint("phenotypes", __name__)
 
@@ -40,7 +44,7 @@ def index():
                     methods=["GET"])
 @require_login
 @with_species(redirect_uri="species.populations.phenotypes.index")
-def select_population(species: dict, **kwargs):
+def select_population(species: dict, **kwargs):# pylint: disable=[unused-argument]
     """Select the population for your phenotypes."""
     with database_connection(app.config["SQL_URI"]) as conn:
         if not bool(request.args.get("population_id")):
@@ -58,7 +62,7 @@ def select_population(species: dict, **kwargs):
             flash("No such population found!", "alert-danger")
             return redirect(url_for(
                 "species.populations.phenotypes.select_population",
-                species_id=species_id))
+                species_id=species["SpeciesId"]))
 
         return redirect(url_for("species.populations.phenotypes.list_datasets",
                                 species_id=species["SpeciesId"],
@@ -72,7 +76,7 @@ def select_population(species: dict, **kwargs):
 @require_login
 @with_population(species_redirect_uri="species.populations.phenotypes.index",
                  redirect_uri="species.populations.phenotypes.select_population")
-def list_datasets(species: int, population: int, **kwargs):
+def list_datasets(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
     """List available phenotype datasets."""
     with database_connection(app.config["SQL_URI"]) as conn:
         return render_template("phenotypes/list-datasets.html",
@@ -92,9 +96,32 @@ def list_datasets(species: int, population: int, **kwargs):
 @require_login
 @with_population(species_redirect_uri="species.populations.phenotypes.index",
                  redirect_uri="species.populations.phenotypes.select_population")
-def view_dataset(species: int, population: int, dataset_id: int, **kwargs):
+def view_dataset(# pylint: disable=[unused-argument]
+        species: dict, population: dict, dataset_id: int, **kwargs):
     """View a specific dataset"""
     with database_connection(app.config["SQL_URI"]) as conn:
-        from flask import jsonify
-        return jsonify(phenotypes_data(
-            conn, population["Id"], dataset_id, offset=0, limit=20))
+        dataset = dataset_by_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(
+                "species.populations.phenotypes.list_datasets",
+                species_id=species["SpeciesId"],
+                population_id=population["Id"]))
+
+        start_at = max(safe_int(request.args.get("start_at") or 0), 0)
+        count = int(request.args.get("count") or 20)
+        return render_template("phenotypes/view-dataset.html",
+                               species=species,
+                               population=population,
+                               dataset={"Id": dataset_id},
+                               phenotype_count=phenotypes_count(
+                                   conn, population["Id"], dataset_id),
+                               phenotypes=enumerate_sequence(
+                                   dataset_phenotypes(conn,
+                                                      population["Id"],
+                                                      dataset_id,
+                                                      offset=start_at,
+                                                      limit=count),
+                                   start=start_at+1),
+                               activelink="view-dataset")
-- 
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