From c1a7d45f2c4d1b9fd7750350745c9cf7a8555777 Mon Sep 17 00:00:00 2001
From: sepro <sebastian.proost@gmail.com>
Date: Wed, 26 Oct 2016 11:26:10 +0200
Subject: [PATCH] redesign sequence page

---
 planet/models/sequences.py     | 11 ++++++++
 planet/templates/sequence.html | 46 +++++++++++++++++++++++++++++++---
 2 files changed, 53 insertions(+), 4 deletions(-)

diff --git a/planet/models/sequences.py b/planet/models/sequences.py
index 4294df8..62315e2 100644
--- a/planet/models/sequences.py
+++ b/planet/models/sequences.py
@@ -75,4 +75,15 @@ def aliases(self):
 
         return ", ".join(t) if len(t) > 0 else None
 
+    @property
+    def readable_type(self):
+        conversion = {'protein_coding': 'protein coding',
+                      'TE': 'transposable element',
+                      'RNA': 'RNA'}
+
+        if self.type in conversion.keys():
+            return conversion[self.type]
+        else:
+            return 'other'
+
 
diff --git a/planet/templates/sequence.html b/planet/templates/sequence.html
index 791c224..ab5d536 100644
--- a/planet/templates/sequence.html
+++ b/planet/templates/sequence.html
@@ -10,21 +10,44 @@
         <li><a href="{{ url_for('species.species_view', species_id=sequence.species.id) }}"><em>{{ sequence.species.name }}</em></a></li>
         <li class="active">Sequence: <strong>{{ sequence.name }}</strong></li>
     </ol>
-    <h1><strong>{{ sequence.name }}</strong> <small>({{ sequence.type }})</small></h1>
+    <h1><strong>{{ sequence.name }}</strong> <small>({{ sequence.readable_type }})</small></h1>
     <br />
 
     {% if sequence.description %}
 
-    <strong>Description: </strong> {{sequence.description}}
+    <p><strong>Description: </strong> {{sequence.description}}</p>
 
     {% else %}
 
-    <span class="text-muted"><em>No description available</em></span>
+    <p><span class="text-muted"><em>No description available</em></span></p>
 
     {% endif %}
+
     <br />
     <p>Sequence: <a href="{{ url_for('sequence.sequence_modal_coding', sequence_id=sequence.id) }}" data-target="#profileModal">coding</a> (<a href="{{ url_for('sequence.sequence_fasta_coding', sequence_id=sequence.id) }}">download</a>) {%- if sequence.type == 'protein_coding' -%}, <a href="{{ url_for('sequence.sequence_modal_protein', sequence_id=sequence.id) }}" data-target="#profileModal">protein</a> (<a href="{{ url_for('sequence.sequence_fasta_protein', sequence_id=sequence.id) }}">download</a>) {% endif %}</p>
 
+    {% if expression_profiles|count > 0 %}
+        {% for profile in expression_profiles %}
+            {% if loop.first %}
+                <h3>Expression profile <small>(<a href="{{ url_for('expression_profile.expression_profile_view', profile_id=profile.id) }}">view details</a>)</small></h3>
+                <div style="height:350px; max-height:350px; margin-top:30px">
+                    <canvas id="expression-profile" class="center-block" height="350"/>
+                </div>
+            {% endif %}
+        {% endfor %}
+        {% if expression_profiles|count > 1 %}
+            <p>All profiles  </p>
+            <ul>
+            {% for profile in expression_profiles %}
+                <li><a href="{{ url_for('expression_profile.expression_profile_view', profile_id=profile.id) }}">{{ profile.probe }}</a> | <a href="{{ url_for('expression_profile.expression_profile_modal', profile_id=profile.id) }}" data-target="#profileModal">Show profile</a></li>
+            {% endfor %}
+            </ul>
+        {% endif %}
+    {% else %}
+        <h3>Expression profile</h3>
+        <p><span class="text-muted"><em>No expression profile available</em></span></p>
+    {% endif %}
+    <br />
     <h3>Sequence details</h3>
     <div class="row">
         <div class="col-lg-4 col-md-6 col-sm-12">
@@ -308,6 +331,7 @@ <h3>Sequence details</h3>
     {% endblock %}
 </div>
 {% block extrajs %}
+<script src="{{ url_for('static', filename='js/Chart.min.js') }}"></script>
 <script>
 
 $(function () {
@@ -331,7 +355,21 @@ <h3>Sequence details</h3>
     $(".parent_term").toggle();
 });
 })
+{% if expression_profiles|count > 0 %}
+        {% for profile in expression_profiles %}
+            {% if loop.first %}
+                Chart.defaults.global.responsive = true;
+                Chart.defaults.global.maintainAspectRatio = false;
+                $( document ).ready(function() {
+                    $.getJSON( "{{ url_for('expression_profile.expression_profile_plot_json', profile_id=profile.id) }}", function( data ) {
+                        var ctx = document.getElementById("expression-profile").getContext("2d");
+                        var myChart = new Chart(ctx, data);
+                    });
+                });
+            {% endif %}
+        {% endfor %}
+{% endif %}
 
 </script>
-<script src="{{ url_for('static', filename='js/Chart.min.js') }}"></script>
+
 {% endblock %}