From d13071900de2ba73b829f52b96a1593da600118a Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 26 Sep 2024 14:18:45 -0500
Subject: Initialise the phenotypes section.

---
 uploader/phenotypes/__init__.py          |  2 ++
 uploader/phenotypes/views.py             | 25 +++++++++++++++++++++++++
 uploader/population/views.py             |  2 ++
 uploader/templates/base.html             |  3 +--
 uploader/templates/phenotypes/base.html  | 12 ++++++++++++
 uploader/templates/phenotypes/index.html | 26 ++++++++++++++++++++++++++
 6 files changed, 68 insertions(+), 2 deletions(-)
 create mode 100644 uploader/phenotypes/__init__.py
 create mode 100644 uploader/phenotypes/views.py
 create mode 100644 uploader/templates/phenotypes/base.html
 create mode 100644 uploader/templates/phenotypes/index.html

diff --git a/uploader/phenotypes/__init__.py b/uploader/phenotypes/__init__.py
new file mode 100644
index 0000000..c17d32c
--- /dev/null
+++ b/uploader/phenotypes/__init__.py
@@ -0,0 +1,2 @@
+"""Package for handling ('classical') phenotype data"""
+from .views import phenotypesbp
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
new file mode 100644
index 0000000..862a224
--- /dev/null
+++ b/uploader/phenotypes/views.py
@@ -0,0 +1,25 @@
+"""Views handling ('classical') phenotypes."""
+from flask import request, 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
+
+phenotypesbp = Blueprint("phenotypes", __name__)
+
+@phenotypesbp.route("/phenotypes", methods=["GET"])
+@require_login
+def index():
+    """Direct entry-point for phenotypes data handling."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        if not bool(request.args.get("species_id")):
+            return render_template("phenotypes/index.html",
+                                   species=order_by_family(all_species(conn)),
+                                   activelink="phenotypes")
+
+        species = species_by_id(conn, request.args.get("species_id"))
+        if not bool(species):
+            flash("No such species!", "alert-danger")
+            return redirect(url_for("species.populations.phenotypes.index"))
+        return "Would lead you to go select population…"
diff --git a/uploader/population/views.py b/uploader/population/views.py
index 631f0be..23bf242 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -18,6 +18,7 @@ from uploader.oauth2.client import oauth2_post
 from uploader.ui import make_template_renderer
 from uploader.authorisation import require_login
 from uploader.genotypes.views import genotypesbp
+from uploader.phenotypes.views import phenotypesbp
 from uploader.expression_data.views import exprdatabp
 from uploader.db_utils import database_connection
 from uploader.datautils import enumerate_sequence
@@ -35,6 +36,7 @@ __active_link__ = "populations"
 popbp = Blueprint("populations", __name__)
 popbp.register_blueprint(samplesbp, url_prefix="/")
 popbp.register_blueprint(genotypesbp, url_prefix="/")
+popbp.register_blueprint(phenotypesbp, url_prefix="/")
 popbp.register_blueprint(exprdatabp, url_prefix="/")
 render_template = make_template_renderer("populations")
 
diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index b297669..019aa39 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -68,8 +68,7 @@
             sections, etc.
           -->
         <li {%if activemenu=="phenotypes"%}class="activemenu"{%endif%}>
-          <a href="#"
-             class="not-implemented"
+          <a href="{{url_for('species.populations.phenotypes.index')}}"
              title="Upload phenotype data.">Phenotype Data</a></li>
         <li {%if activemenu=="expression-data"%}class="activemenu"{%endif%}>
           <a href="{{url_for('species.populations.expression-data.index')}}"
diff --git a/uploader/templates/phenotypes/base.html b/uploader/templates/phenotypes/base.html
new file mode 100644
index 0000000..3bc5dea
--- /dev/null
+++ b/uploader/templates/phenotypes/base.html
@@ -0,0 +1,12 @@
+{%extends "populations/base.html"%}
+
+{%block lvl3_breadcrumbs%}
+<li {%if activelink=="phenotypes"%}
+    class="breadcrumb-item active"
+    {%else%}
+    class="breadcrumb-item"
+    {%endif%}>
+  <a href="{{url_for('species.populations.phenotypes.index')}}">Phenotypes</a>
+</li>
+{%block lvl4_breadcrumbs%}{%endblock%}
+{%endblock%}
diff --git a/uploader/templates/phenotypes/index.html b/uploader/templates/phenotypes/index.html
new file mode 100644
index 0000000..0c691e6
--- /dev/null
+++ b/uploader/templates/phenotypes/index.html
@@ -0,0 +1,26 @@
+{%extends "phenotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "species/macro-select-species.html" import select_species_form%}
+
+{%block title%}Phenotypes{%endblock%}
+
+{%block pagetitle%}Phenotypes{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+  <p>This section deals with phenotypes that
+    <span class="text-warning">
+      <span class="glyphicon glyphicon-exclamation-sign"></span>
+      … what are the characteristics of these phenotypes? …</span></p>
+  <p>Select the species to begin the process of viewing/uploading data about
+    your phenotypes</p>
+</div>
+
+<div class="row">
+  {{select_species_form(url_for("species.populations.phenotypes.index"),
+  species)}}
+</div>
+{%endblock%}
-- 
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