From bfe8e243002ab6ba8a4658f2a5eaef73de16c8a8 Mon Sep 17 00:00:00 2001
From: sepro <sebastian.proost@gmail.com>
Date: Thu, 9 Nov 2017 16:22:22 +0100
Subject: [PATCH] hiding trees when they haven not been reconciled yet. updated
 names in plot

---
 conekt/helpers/cytoscape.py            |  9 ++++++++-
 conekt/models/xrefs.py                 | 11 ++++++++++-
 conekt/static/js/cytoscape.cycss       |  2 +-
 conekt/templates/expression_graph.html |  8 ++++----
 conekt/templates/tree.html             | 11 ++++++++++-
 5 files changed, 33 insertions(+), 8 deletions(-)

diff --git a/conekt/helpers/cytoscape.py b/conekt/helpers/cytoscape.py
index 85556a8..eeff254 100644
--- a/conekt/helpers/cytoscape.py
+++ b/conekt/helpers/cytoscape.py
@@ -188,7 +188,8 @@ def add_lc_data_nodes(network):
     @staticmethod
     def add_descriptions_nodes(network):
         """
-        Adds the description to nodes (if available) and alternative names (aka gene tokens) to a cytoscape.js network
+        Adds the description to nodes (if available), the best name to display and alternative names (aka gene tokens)
+        to a cytoscape.js network
 
         :param network: Cytoscape.js compatible network object
         :return: Network with descriptions and tokens added
@@ -203,6 +204,7 @@ def add_descriptions_nodes(network):
         sequences = Sequence.query.filter(Sequence.id.in_(sequence_ids)).all()
 
         descriptions = {s.id: s.description for s in sequences}
+        best_names = {s.id: s.best_name for s in sequences}
         tokens = {s.id: ", ".join([x.name for x in s.xrefs if x.platform == 'token']) for s in sequences}
 
         # Set empty tokens to None
@@ -217,6 +219,11 @@ def add_descriptions_nodes(network):
                 else:
                     node["data"]["description"] = None
 
+                if node["data"]["gene_id"] in best_names.keys():
+                    node["data"]["best_name"] = best_names[node["data"]["gene_id"]]
+                else:
+                    node["data"]["best_name"] = node["data"]["gene_name"]
+
                 if node["data"]["gene_id"] in tokens.keys():
                     node["data"]["tokens"] = tokens[node["data"]["gene_id"]]
                 else:
diff --git a/conekt/models/xrefs.py b/conekt/models/xrefs.py
index bda6ed4..8290731 100644
--- a/conekt/models/xrefs.py
+++ b/conekt/models/xrefs.py
@@ -62,7 +62,7 @@ def add_xref_genes_from_file(species_id, filename):
         seq_dict = {s.name.upper(): s for s in sequences}
 
         with open(filename, "r") as f:
-            for line in f:
+            for i, line in enumerate(f):
                 sequence, name, platform, url = line.split('\t')
 
                 xref = XRef()
@@ -73,11 +73,20 @@ def add_xref_genes_from_file(species_id, filename):
                 if sequence.upper() in seq_dict.keys():
                     s = seq_dict[sequence.upper()]
                     s.xrefs.append(xref)
+
+                if i % 400 == 0:
+                    # Update every 400 lines
                     try:
                         db.session.commit()
                     except Exception as e:
                         db.session.rollback()
 
+            # Commit final changes
+            try:
+                db.session.commit()
+            except Exception as e:
+                db.session.rollback()
+
     @staticmethod
     def add_xref_families_from_file(gene_family_method_id, filename):
         gf_method = GeneFamilyMethod.query.get(gene_family_method_id)
diff --git a/conekt/static/js/cytoscape.cycss b/conekt/static/js/cytoscape.cycss
index 2e2674f..18b927b 100644
--- a/conekt/static/js/cytoscape.cycss
+++ b/conekt/static/js/cytoscape.cycss
@@ -1,5 +1,5 @@
 node {
-        content: data(gene_name);
+        content: data(best_name);
         text-valign: center;
         color: black;
         background-color: data(color);
diff --git a/conekt/templates/expression_graph.html b/conekt/templates/expression_graph.html
index 9a7b6d4..e8f930c 100644
--- a/conekt/templates/expression_graph.html
+++ b/conekt/templates/expression_graph.html
@@ -227,10 +227,10 @@ <h1>ECC pair</h1>
             <div class="modal-header">
             <h4 class="modal-title" id="dataModalLabel"><strong>Export Data</strong></h4>
             </div>
-            <div class="modal-body" syle="width:700px;height:200px">
-                <button class="btn btn-primary" id="cy-download-xgmml">XGMML</button> <span class="text-muted">(compatible with Cytoscape)</span>
+            <div class="modal-body" syle="width:700px;min-height:200px">
+                <button class="btn btn-primary" id="cy-download-xgmml">XGMML</button> <span class="text-muted">(compatible with <a href="http://www.cytoscape.org/">Cytoscape</a>)</span>
                 <hr />
-                <h3>Other formats</h3>
+                <h3>Other formats, compatible with <a href="http://js.cytoscape.org/">Cytoscape.js</a></h3>
                 <button class="btn btn-default" id="cy-download-json">JSON</button> <span class="text-muted">(network only)</span> <br/><br/>
                 <button class="btn btn-default" id="cy-download-jsoncy">JSON</button> <span class="text-muted">(network + colors/shapes)</span> <br/><br/>
             </div>
@@ -247,7 +247,7 @@ <h3>Other formats</h3>
             <div class="modal-header">
             <h4 class="modal-title" id="imageModalLabel"><strong>Export Image</strong></h4>
             </div>
-            <div class="modal-body" syle="width:700px;height:200px">
+            <div class="modal-body" style="width:700px;min-height:200px">
                 <table>
                     <tbody>
                     <tr>
diff --git a/conekt/templates/tree.html b/conekt/templates/tree.html
index 0442bdc..f9a13ad 100644
--- a/conekt/templates/tree.html
+++ b/conekt/templates/tree.html
@@ -51,6 +51,7 @@ <h1><strong><em>Tree Methods</em></strong></h1>
         </ol>
      <h1>{{ tree.label }}: <strong>{{ tree.method.description }}</strong></h1>
      <p>Tree for gene family <a href="{{ url_for('family.family_view', family_id=tree.family.id) }}">{{ tree.family.name }}</a></p>
+    {% if tree.phyloxml %}
     <div class="row">
         <div class="col-lg-12">
             <div id="phyd3" style="height:600px">
@@ -96,6 +97,14 @@ <h1>{{ tree.label }}: <strong>{{ tree.method.description }}</strong></h1>
             </div>
         </div>
     </div>
+    {% else %}
+
+    <div class="alert alert-warning">
+      <strong>PhyloXML data empty. Cannot draw tree!</strong> This indicates trees included in the database haven't been
+        reconciled yet.
+    </div>
+
+    {% endif %}
     <br /><br />
     {{ macro.pagination('Sequences',
         url_for('tree.tree_sequences', tree_id=tree.id),
@@ -119,7 +128,7 @@ <h1>{{ tree.label }}: <strong>{{ tree.method.description }}</strong></h1>
                 $("#methods_table").stupidtable();
             });
         </script>
-    {% else %}
+    {% elif tree and tree.phyloxml %}
         <script src="{{ url_for('static', filename='js/d3.v3.min.js') }}"></script>
         <script src="{{ url_for('static', filename='js/phyd3.min.js') }}"></script>
         <script>