From a7f158de3cafddcca9c788829a263eb444fa7b59 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 17 Sep 2024 15:01:27 -0500
Subject: Select genotype's population.

---
 uploader/genotypes/views.py                        | 39 ++++++++++++++++++++--
 .../templates/genotypes/select-population.html     | 31 +++++++++++++++++
 2 files changed, 68 insertions(+), 2 deletions(-)
 create mode 100644 uploader/templates/genotypes/select-population.html

(limited to 'uploader')

diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 65cdf4b..885e008 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -11,6 +11,8 @@ 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.population.models import (populations_by_species,
+                                        population_by_species_and_id)
 
 genotypesbp = Blueprint("genotypes", __name__)
 
@@ -32,9 +34,42 @@ def index():
                                 species_id=species["SpeciesId"]))
 
 
-@genotypesbp.route("/<int:species_id>/genotypes/select-population",
+@genotypesbp.route("/<int:species_id>/populations/genotypes/select-population",
                    methods=["GET"])
 @require_login
 def select_population(species_id: int):
     """Select the population under which the genotypes go."""
-    return f"Would select population with species {species_id}…"
+    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,
+                                   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"]))
+
+
+@genotypesbp.route(
+    "/<int:species_id>/populations/<int:population_id>/genotypes",
+    methods=["GET"])
+@require_login
+def list_genotypes(species_id: int, population_id: int):
+    """List genotype details for species and population."""
+    return f"Would list geno info for population {population_id} from species {species_id}"
diff --git a/uploader/templates/genotypes/select-population.html b/uploader/templates/genotypes/select-population.html
new file mode 100644
index 0000000..7c81943
--- /dev/null
+++ b/uploader/templates/genotypes/select-population.html
@@ -0,0 +1,31 @@
+{%extends "genotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "species/macro-display-species-card.html" import display_species_card%}
+{%from "populations/macro-select-population.html" import select_population_form%}
+
+{%block title%}Genotypes{%endblock%}
+
+{%block pagetitle%}Genotypes{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+  <p>
+    You have indicated that you intend to upload the genotypes for species
+    '{{species.FullName}}'. We now just require the population for your
+    experiment/study, and you should be good to go.
+  </p>
+</div>
+
+<div class="row">
+  {{select_population_form(url_for("species.populations.genotypes.select_population",
+  species_id=species.SpeciesId),
+  populations)}}
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_species_card(species)}}
+{%endblock%}
-- 
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