added help and popup

planet/controllers/help.py

@@ -14,7 +14,10 @@
             "neighborhood": "modals/help/neighborhood.html",
             "hrr": "modals/help/hrr.html",
             "blast": "modals/help/blast.html",
-            "pcc": "modals/help/pcc.html"}
+            "pcc": "modals/help/pcc.html",
+            "lowabundance": "modals/help/low_abundance.html"}
+
+__POPUPS = {"lowabundance": "tooltips/low_abundance.html"}
 
 help = Blueprint('help', __name__)
 
@@ -32,3 +35,17 @@ def help_topic(topic):
     else:
         abort(404)
 
+
+@help.route('/popup/<topic>')
+def help_popup(topic):
+    """
+    Generic function to get help popups
+
+    :param topic: name of the topic
+    :return: renders template for the topic if found, 404 if not.
+    """
+    if topic in __POPUPS.keys():
+        return render_template(__POPUPS[topic])
+    else:
+        abort(404)
+

planet/templates/expression_profile.html

@@ -34,7 +34,7 @@ <h1>Expression profile for: <strong>{{ profile.probe }}</strong></h1>
 
     {% if profile.low_abundance %}
     <br />
-    <span class="warning-message"><i class="fa fa-exclamation-triangle" aria-hidden="true"></i> <strong>Attention:</strong> This gene has <strong>low abundance</strong>.</span>
+    <span class="warning-message"><i class="fa fa-exclamation-triangle" aria-hidden="true"></i> <strong>Attention:</strong> This gene has <strong><abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='lowabundance') }}" data-target="#helpModal">low abundance</abbr></strong>.</span>
     <br /><br />
     {% endif %}
 

planet/templates/modals/help/low_abundance.html

@@ -0,0 +1,12 @@
+<div class="modal-header">
+<h4 class="modal-title" id="myModalLabel"><strong>Low (Transcript) Abundance</strong></h4>
+</div>
+<div class="modal-body" syle="width:700px;height:200px">
+    <p>Some transcripts have low abundance in all conditions in the expression profiles. For these genes, random
+       stochastic effects can cause sharp peaks in their profile. These are likely <strong>not</strong> biologically
+       relevant and should be interpreted with <strong>caution</strong>.</p>
+
+</div>
+<div class="modal-footer">
+    <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+</div>

planet/templates/search_specific_profiles.html

@@ -92,7 +92,8 @@ <h1><em>{{species.name}}</em> profiles specific for <strong>{{condition}}</stron
                         <td>{{ r.entropy|round(2) }}</td>
                         <td>{% if r.tau %}{{ r.tau|round(2) }}{% else %}<span class="text-muted">None</span>{% endif %}</td>
                         <td><a href="{{url_for('expression_profile.expression_profile_view', profile_id=r.profile_id)}}">view profile</a></td>
-                        <td>{% if r.profile.low_abundance %}<span class="warning-message"><i class="fa fa-exclamation-triangle" aria-hidden="true"></i></span>{% endif %}</td>
+                        <td>{% if r.profile.low_abundance %}<span class="warning-message qtip_tooltip"
+                               qtip_href="{{ url_for('help.help_popup', topic='lowabundance') }}"><i class="fa fa-exclamation-triangle" aria-hidden="true"></i></span>{% endif %}</td>
                     </tr>
                 {% endif %}
             {% endfor %}

planet/templates/tooltips/low_abundance.html

@@ -0,0 +1,7 @@
+<div>
+    <div><strong>Low (Transcript) Abundance</strong></div>
+    <hr />
+    <p>Some transcripts have low abundance in all conditions in the expression profiles. For these genes, random
+       stochastic effects can cause sharp peaks in their profile. These are likely <strong>not</strong> biologically
+       relevant and should be interpreted with <strong>caution</strong>.</p>
+</div>