From 7531b17018a0a81edce95802cc370661106cc481 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 18 Sep 2024 01:27:22 -0500
Subject: Document the menu on the home page.

---
 uploader/base_routes.py       |  5 ++-
 uploader/templates/base.html  |  4 +--
 uploader/templates/index.html | 80 ++++++++++++++++++++++++++++++++++++++++++-
 uploader/templates/login.html |  2 +-
 4 files changed, 86 insertions(+), 5 deletions(-)

diff --git a/uploader/base_routes.py b/uploader/base_routes.py
index 88247b2..a20b7ff 100644
--- a/uploader/base_routes.py
+++ b/uploader/base_routes.py
@@ -1,5 +1,6 @@
 """Basic routes required for all pages"""
 import os
+from urllib.parse import urljoin
 
 from flask import (
     Blueprint,
@@ -23,7 +24,9 @@ def favicon():
 @base.route("/", methods=["GET"])
 def index():
     """Load the landing page"""
-    return render_template("index.html" if user_logged_in() else "login.html")
+    return render_template("index.html" if user_logged_in() else "login.html",
+                           gn2server_intro=urljoin(app.config["GN2_SERVER_URL"],
+                                                   "/intro"))
 
 def appenv():
     """Get app's guix environment path."""
diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index 3af14ef..886f503 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -48,10 +48,10 @@
                title="View and manage species information.">Species</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('species.populations.genotypes.index')}}"
+               title="Upload Genotype data.">Genotype Data</a></li>
         <li><a href="{{url_for('expression-data.index.index')}}"
                title="Upload expression data.">Expression Data</a></li>
         <li><a href="#"
diff --git a/uploader/templates/index.html b/uploader/templates/index.html
index e3f5af4..0fa4a1b 100644
--- a/uploader/templates/index.html
+++ b/uploader/templates/index.html
@@ -18,9 +18,87 @@
   <div class="explainer">
     <p>Welcome to the <strong>GeneNetwork Data Quality Control and Upload System</strong>. This system is provided to help in uploading your data onto GeneNetwork where you can do analysis on it.</p>
 
-    <p>Click on the menu items on the left to select the kind of data you want to upload.</p>
+    <p>The sections below provide an overview of what features the menu items on
+      the left provide to you. Please peruse the information to get a good
+      big-picture understanding of what the system provides you and how to get
+      the most out of it.</p>
 
     {%block extrapageinfo%}{%endblock%}
+
+    <h2>Species</h2>
+
+    <p>The GeneNetwork service provides datasets and tools for doing genetic
+      studies &mdash; from
+      <a href="{{gn2server_intro}}"
+         target="_blank"
+         title="GeneNetwork introduction — opens in a new tab.">
+        its introduction</a>:
+
+      <blockquote class="blockquote">
+        <p>GeneNetwork is a group of linked data sets and tools used to study
+          complex networks of genes, molecules, and higher order gene function
+          and phenotypes. &hellip;</p>
+      </blockquote>
+    </p>
+
+    <p>With this in mind, it follows that the data in the system is centered
+      aroud a variety of species. The <strong>species section</strong> will
+      list the currently available species in the system, and give you the
+      ability to add new ones, if the one you want to work on does not currently
+      exist on GeneNetwork</p>
+
+    <h2>Populations</h2>
+
+    <p>Your studies will probably focus on a particular subset of the entire
+      species you are interested in &ndash your population.</p>
+    <p>Populations are a way to organise the species data so as to link data to
+      specific know populations for a particular species, e.g. The BXD
+      population of mice (Mus musculus)</p>
+    <p>In older GeneNetwork documentation, you might run into the term
+      <em>InbredSet</em>. Should you run into it, it is a term that we've
+      deprecated that essentially just means the population.</p>
+
+    <h2>Samples</h2>
+
+    <p>These are the samples or individuals (sometimes cases) that were involved
+      in the experiment, and from whom the data was derived.</p>
+
+    <h2>Genotype Data</h2>
+
+    <p>This section will allow you to view and upload the genetic markers for
+      your species, and the genotype encodings used for your particular
+      population.</p>
+    <p>While, technically, genetic markers relate to the species in general, and
+      not to a particular population, the data (allele information) itself
+      relates to the particular population it was generated from &ndash;
+      specifically, to the actual individuals used in the experiment.</p>
+    <p>This is the reason why the genotype data information comes under the
+      population, and will check for the prior existence of the related
+      samples/individuals before attempting an upload of your data.</p>
+
+    <h2>Expression Data</h2>
+
+    <p class="text-danger">
+      <span class="glyphicon glyphicon-exclamation-sign"></span>
+      <strong>TODO</strong>: Document this &hellip;</p>
+
+    <h2>Phenotype Data</h2>
+
+    <p class="text-danger">
+      <span class="glyphicon glyphicon-exclamation-sign"></span>
+      <strong>TODO</strong>: Document this &hellip;</p>
+
+    <h2>Individual Data</h2>
+
+    <p class="text-danger">
+      <span class="glyphicon glyphicon-exclamation-sign"></span>
+      <strong>TODO</strong>: Document this &hellip;</p>
+
+    <h2>RNA-Seq Data</h2>
+
+    <p class="text-danger">
+      <span class="glyphicon glyphicon-exclamation-sign"></span>
+      <strong>TODO</strong>: Document this &hellip;</p>
   </div>
 </div>
 
diff --git a/uploader/templates/login.html b/uploader/templates/login.html
index bbca42f..1f71416 100644
--- a/uploader/templates/login.html
+++ b/uploader/templates/login.html
@@ -5,7 +5,7 @@
 {%block pagetitle%}log in{%endblock%}
 
 {%block extrapageinfo%}
-<p>
+<p class="text-dark text-primary">
   You <strong>do need to be logged in</strong> to upload data onto this system.
   Please do that by clicking the "Log In" button at the top of the page.</p>
 {%endblock%}
-- 
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