From d48cfff120562592d6535d493412ee1881487c38 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 17 Sep 2024 12:58:13 -0500
Subject: Provide entry-point of genotypes.

---
 uploader/genotypes/views.py             | 34 ++++++++++++++++++++++++++++++---
 uploader/templates/genotypes/index.html | 14 +++++++++++++-
 2 files changed, 44 insertions(+), 4 deletions(-)

(limited to 'uploader')

diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 2b4ed10..65cdf4b 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -1,12 +1,40 @@
 """Views for the genotypes."""
-from flask import Blueprint, render_template
+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
 
 genotypesbp = Blueprint("genotypes", __name__)
 
-@genotypesbp.route("/genotypes")
+@genotypesbp.route("populations/genotypes", methods=["GET"])
 @require_login
 def index():
     """Direct entry-point for genotypes."""
-    return render_template("genotypes/index.html")
+    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)),
+                                   activelink="genotypes")
+        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')}'!",
+                  "alert-danger")
+            return redirect(url_for("species.populations.genotypes.index"))
+        return redirect(url_for("species.populations.genotypes.select_population",
+                                species_id=species["SpeciesId"]))
+
+
+@genotypesbp.route("/<int:species_id>/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}…"
diff --git a/uploader/templates/genotypes/index.html b/uploader/templates/genotypes/index.html
index 4f5c3a8..9ffea73 100644
--- a/uploader/templates/genotypes/index.html
+++ b/uploader/templates/genotypes/index.html
@@ -11,7 +11,19 @@
 {{flash_all_messages()}}
 
 <div class="row">
-  <p><strong>We have not implemented this part yet!</strong></p>
+  <p>
+    This section allows you to upload genotype information for your experiments,
+    in the case that you have not previously done so.
+  </p>
+  <p>
+    We'll need to link the genotypes to the species and population, so do please
+    go ahead and select those in the next two steps.
+  </p>
+</div>
+
+<div class="row">
+  {{select_species_form(url_for("species.populations.genotypes.index"),
+  species)}}
 </div>
 
 <div class="row">
-- 
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