From 542a808ab82465e8ce25e6c5b13dbbcabb0e7c86 Mon Sep 17 00:00:00 2001
From: sepro <sebastian.proost@gmail.com>
Date: Fri, 31 Mar 2017 14:24:46 +0200
Subject: [PATCH] qtip possible everywhere

---
 planet/controllers/sequence.py                | 13 +++++++
 planet/models/expression/profiles.py          |  2 +-
 planet/models/trees.py                        |  3 +-
 .../admin/add/sequence_descriptions.html      |  2 +-
 planet/templates/base.html                    | 38 +++++++++++++++++++
 planet/templates/expression_graph.html        |  2 -
 planet/templates/expression_heatmap.html      |  8 +++-
 planet/templates/tooltips/sequence.html       | 11 ++++++
 tests/website.py                              |  6 ++-
 9 files changed, 78 insertions(+), 7 deletions(-)
 create mode 100644 planet/templates/tooltips/sequence.html

diff --git a/planet/controllers/sequence.py b/planet/controllers/sequence.py
index 69b10a6..163123a 100644
--- a/planet/controllers/sequence.py
+++ b/planet/controllers/sequence.py
@@ -52,6 +52,19 @@ def sequence_view(sequence_id):
                            )
 
 
+@sequence.route('/tooltip/<sequence_id>')
+@cache.cached()
+def sequence_tooltip(sequence_id):
+    """
+    Get a sequence based on the ID and show the details for this sequence
+
+    :param sequence_id: ID of the sequence
+    """
+    current_sequence = Sequence.query.get_or_404(sequence_id)
+
+    return render_template('tooltips/sequence.html', sequence=current_sequence)
+
+
 @sequence.route('/modal/coding/<sequence_id>')
 def sequence_modal_coding(sequence_id):
     """
diff --git a/planet/models/expression/profiles.py b/planet/models/expression/profiles.py
index 89d0423..21e2408 100644
--- a/planet/models/expression/profiles.py
+++ b/planet/models/expression/profiles.py
@@ -100,7 +100,7 @@ def get_heatmap(species_id, probes):
                 else:
                     values[o] = log(values[o]/row_mean, 2)
 
-            output.append({"name": name, "values": values})
+            output.append({"name": name, "values": values, "sequence_id": profile.sequence_id})
 
         return {'order': order, 'heatmap_data': output}
 
diff --git a/planet/models/trees.py b/planet/models/trees.py
index d094166..ab88a57 100644
--- a/planet/models/trees.py
+++ b/planet/models/trees.py
@@ -24,7 +24,8 @@ class Tree(db.Model):
     id = db.Column(db.Integer, primary_key=True)
 
     label = db.Column(db.String(50, collation=SQL_COLLATION), index=True)
-    data = db.Column(db.Text)
+    data_newick = db.Column(db.Text)
+    data_phyloxml = db.Column(db.Text)
 
     method_id = db.Column(db.Integer, db.ForeignKey('tree_methods.id'), index=True)
     cluster_id = db.Column(db.Integer, db.ForeignKey('coexpression_clusters.id'), index=True)
diff --git a/planet/templates/admin/add/sequence_descriptions.html b/planet/templates/admin/add/sequence_descriptions.html
index f4ffc4b..46a00b6 100644
--- a/planet/templates/admin/add/sequence_descriptions.html
+++ b/planet/templates/admin/add/sequence_descriptions.html
@@ -2,7 +2,7 @@
 
 {% block body %}
 {% if form %}
-<h1>Add XRefs <small>(to sequences)</small></h1>
+<h1>Add Descriptions <small>(to sequences)</small></h1>
 <div class="row">
     <div class="col-lg-8 col-md-8 col-sm-6 col-xs-12">
         <form method="POST"  action="{{ url_for('admin_controls.add_descriptions') }}"  role="form" enctype="multipart/form-data">
diff --git a/planet/templates/base.html b/planet/templates/base.html
index 1b6d268..fae7993 100644
--- a/planet/templates/base.html
+++ b/planet/templates/base.html
@@ -161,8 +161,46 @@
         <script src="{{ url_for('static', filename='js/planet_loader.js') }}"></script>
         <script src="{{ url_for('static', filename='js/planet_pagination.js') }}"></script>
         <script src="{{ url_for('static', filename='js/planet_ajax_table.js') }}"></script>
+        <script src="{{ url_for('static', filename='js/jquery.qtip.min.js') }}"></script>
         <!-- code to reload modal on each click -->
         <script>
+          $(function () {
+                 $('.qtip_tooltip').each(function() {
+                     $(this).qtip({
+                        content: {
+                            text: function(event, api) {
+                                $.ajax({
+                                    url: api.elements.target.attr('qtip_href')
+                                })
+                                .then(function(content) {
+                                    // Set the tooltip content upon successful retrieval
+                                    api.set('content.text', content);
+                                }, function(xhr, status, error) {
+                                    // Upon failure... set the tooltip content to error
+                                    api.set('content.text', status + ': ' + error);
+                                });
+
+                                return 'Loading...'; // Set some initial text
+                            }
+                        },
+                        show: {
+                            effect: function() {
+                                $(this).fadeTo(500, 1);
+                            }
+                        },
+                        hide: {
+                            effect: function() {
+                                $(this).fadeTo(500, 0);
+                            }
+                        },
+                        position: {
+                            viewport: $(window)
+                        },
+                        style: 'qtip-bootstrap'
+                     });
+                 });
+             });
+
             $(function () {
 
               $("#leafy_loader").html(get_loader_svg('loader_leafy'));
diff --git a/planet/templates/expression_graph.html b/planet/templates/expression_graph.html
index 66526ca..f31201d 100644
--- a/planet/templates/expression_graph.html
+++ b/planet/templates/expression_graph.html
@@ -372,8 +372,6 @@ <h4 class="modal-title" id="imageModalLabel"><strong>Export Image</strong></h4>
 <script src="{{ url_for('static', filename='js/cytoscape.min.js') }}"></script>
 
 <!--<script src="{{ url_for('static', filename='js/cytoscape-cose-bilkent.js') }}"></script>-->
-
-<script src="{{ url_for('static', filename='js/jquery.qtip.min.js') }}"></script>
 <script src="{{ url_for('static', filename='js/cytoscape-qtip.js') }}"></script>
 <script src="{{ url_for('static', filename='js/planet_graph.js') }}"></script>
 <script>
diff --git a/planet/templates/expression_heatmap.html b/planet/templates/expression_heatmap.html
index 8c6db3f..546fc47 100644
--- a/planet/templates/expression_heatmap.html
+++ b/planet/templates/expression_heatmap.html
@@ -50,7 +50,13 @@ <h1>Heatmap</h1>
             <tbody>
             {% for p in profiles  %}
                 <tr class="heatmap">
-                    <td>{{ p.name }}</td>
+                    {% if p.sequence_id %}
+                        <td><a href="{{ url_for('sequence.sequence_view', sequence_id=p.sequence_id) }}"
+                               class="qtip_tooltip"
+                               qtip_href="{{ url_for('sequence.sequence_tooltip', sequence_id=p.sequence_id) }}">{{ p.name }}</a></td>
+                    {% else %}
+                        <td>{{ p.name }}</td>
+                    {% endif %}
                     {% for o in order %}
                     <td class="value">{{ p['values'][o]|round(2) }}</td>
                     {% endfor %}
diff --git a/planet/templates/tooltips/sequence.html b/planet/templates/tooltips/sequence.html
new file mode 100644
index 0000000..27f1bba
--- /dev/null
+++ b/planet/templates/tooltips/sequence.html
@@ -0,0 +1,11 @@
+<div>
+    {% if sequence.aliases %}
+    <div><strong>Aliases: </strong>{{ sequence.aliases }}</div>
+    <hr />
+    {% endif %}
+    {% if sequence.description %}
+        <div><strong>Description: </strong>{{ sequence.description }}</div>
+    {% else %}
+        <div><em class="text-muted">No description available</em></div>
+    {% endif %}
+</div>
\ No newline at end of file
diff --git a/tests/website.py b/tests/website.py
index 52bfe43..06bff7b 100644
--- a/tests/website.py
+++ b/tests/website.py
@@ -252,6 +252,10 @@ def test_sequence(self):
         self.assert_template_used('sequence.html')
         self.assert200(response)
 
+        response = self.client.get("/sequence/tooltip/%d" % sequence.id)
+        self.assert_template_used('tooltips/sequence.html')
+        self.assert200(response)
+
         response = self.client.get("/sequence/fasta/coding/%d" % sequence.id)
         self.assert200(response)
         data = response.data.decode("utf-8").strip()
@@ -678,7 +682,7 @@ def test_heatmap(self):
         response = self.client.post('/heatmap/', data=dict(probes=profile.probe, species_id=profile.species_id))
         self.assert_template_used('expression_heatmap.html')
         self.assert200(response)
-        self.assertTrue('<td>' + profile.probe + '</td>' in response.data.decode('utf-8'))
+        self.assertTrue(profile.probe in response.data.decode('utf-8'))
 
         response = self.client.get('/heatmap/cluster/%d' % cluster.id)
         self.assert_template_used('expression_heatmap.html')