From 36fc8996fa830078866e17aab7d9c177c74c835b Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 13 Sep 2024 09:18:18 -0500
Subject: Initialise genotypes' UI

---
 uploader/genotypes/__init__.py          |  1 +
 uploader/genotypes/views.py             | 12 ++++++++++++
 uploader/population/views.py            |  4 +++-
 uploader/templates/base.html            |  4 ++--
 uploader/templates/genotypes/base.html  | 12 ++++++++++++
 uploader/templates/genotypes/index.html | 24 ++++++++++++++++++++++++
 6 files changed, 54 insertions(+), 3 deletions(-)
 create mode 100644 uploader/genotypes/__init__.py
 create mode 100644 uploader/genotypes/views.py
 create mode 100644 uploader/templates/genotypes/base.html
 create mode 100644 uploader/templates/genotypes/index.html

diff --git a/uploader/genotypes/__init__.py b/uploader/genotypes/__init__.py
new file mode 100644
index 0000000..d0025d6
--- /dev/null
+++ b/uploader/genotypes/__init__.py
@@ -0,0 +1 @@
+"""The Genotypes module."""
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
new file mode 100644
index 0000000..2b4ed10
--- /dev/null
+++ b/uploader/genotypes/views.py
@@ -0,0 +1,12 @@
+"""Views for the genotypes."""
+from flask import Blueprint, render_template
+
+from uploader.authorisation import require_login
+
+genotypesbp = Blueprint("genotypes", __name__)
+
+@genotypesbp.route("/genotypes")
+@require_login
+def index():
+    """Direct entry-point for genotypes."""
+    return render_template("genotypes/index.html")
diff --git a/uploader/population/views.py b/uploader/population/views.py
index 003787a..e870c85 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -10,10 +10,11 @@ from flask import (flash,
                    Blueprint,
                    current_app as app)
 
+from uploader.samples.views import samplesbp
 from uploader.ui import make_template_renderer
 from uploader.authorisation import require_login
 from uploader.db_utils import database_connection
-from uploader.samples.views import samplesbp
+from uploader.genotypes.views import genotypesbp
 from uploader.species.models import (all_species,
                                      species_by_id,
                                      order_species_by_family)
@@ -27,6 +28,7 @@ from .models import (save_population,
 __active_link__ = "populations"
 popbp = Blueprint("populations", __name__)
 popbp.register_blueprint(samplesbp, url_prefix="/")
+popbp.register_blueprint(genotypesbp, url_prefix="/")
 render_template = make_template_renderer("populations")
 
 
diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index d68c6c0..cc37c3e 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -46,10 +46,10 @@
         <li><a href="/" >Home</a></li>
         <li><a href="{{url_for('species.list_species')}}"
                title="View and manage species information.">Species</a></li>
-        <li><a href="#"
-               title="Upload Genotype data.">Genotype Data</a></li>
         <li><a href="{{url_for('species.populations.index')}}"
                title="View and manage species populations.">Populations</a></li>
+        <li><a href="{{url_for('species.populations.genotypes.index')}}"
+               title="Upload Genotype data.">Genotype Data</a></li>
         <li><a href="{{url_for('species.populations.samples.index')}}"
                title="Upload population samples.">Samples</a></li>
         <li><a href="{{url_for('expression-data.index.index')}}"
diff --git a/uploader/templates/genotypes/base.html b/uploader/templates/genotypes/base.html
new file mode 100644
index 0000000..1b274bf
--- /dev/null
+++ b/uploader/templates/genotypes/base.html
@@ -0,0 +1,12 @@
+{%extends "populations/base.html"%}
+
+{%block lvl3_breadcrumbs%}
+<li {%if activelink=="genotypes"%}
+    class="breadcrumb-item active"
+    {%else%}
+    class="breadcrumb-item"
+    {%endif%}>
+  <a href="{{url_for('species.populations.genotypes.index')}}">Genotypes</a>
+</li>
+{%block lvl4_breadcrumbs%}{%endblock%}
+{%endblock%}
diff --git a/uploader/templates/genotypes/index.html b/uploader/templates/genotypes/index.html
new file mode 100644
index 0000000..4f5c3a8
--- /dev/null
+++ b/uploader/templates/genotypes/index.html
@@ -0,0 +1,24 @@
+{%extends "genotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "species/macro-select-species.html" import select_species_form%}
+
+{%block title%}Genotypes{%endblock%}
+
+{%block pagetitle%}Genotypes{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+  <p><strong>We have not implemented this part yet!</strong></p>
+</div>
+
+<div class="row">
+  <h3>Some Important Concepts to Consider/Remember</h3>
+  <ul>
+    <li>Reference vs. Non-reference alleles</li>
+    <li>In <em>GenoCode</em> table, items are ordered by <strong>InbredSet</strong></li>
+  </ul>
+</div>
+{%endblock%}
-- 
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