From de84b015bdb76af23b333beb3469b3a7f9a8f352 Mon Sep 17 00:00:00 2001
From: sepro <sebastian.proost@gmail.com>
Date: Thu, 30 Nov 2017 14:18:22 +0100
Subject: [PATCH] test version of multi ecc network

---
 conekt/controllers/ecc.py                     | 14 +++++
 .../relationships/sequence_sequence_ecc.py    | 58 +++++++++++++++++--
 conekt/templates/expression_graph.html        | 18 ++++--
 3 files changed, 80 insertions(+), 10 deletions(-)

diff --git a/conekt/controllers/ecc.py b/conekt/controllers/ecc.py
index e248820..798eebc 100644
--- a/conekt/controllers/ecc.py
+++ b/conekt/controllers/ecc.py
@@ -36,6 +36,19 @@ def ecc_graph(sequence, network, family):
                            family_method_id=family)
 
 
+@ecc.route('/graph_multi/')
+def ecc_graph_multi():
+    """
+    Returns a page rendering the ECC graph for a specific pair of sequences
+
+    :param ecc_id: internal ID of the sequence to sequence ECC relationship
+    :return: Response with html page that shows the pairwise ECC network
+    """
+
+    return render_template("expression_graph.html",
+                           ecc_multi=True)
+
+
 @ecc.route('/graph_pair/<int:ecc_id>')
 def ecc_graph_pair(ecc_id):
     """
@@ -107,5 +120,6 @@ def ecc_graph_multi_json():
     network_cytoscape = CytoscapeHelper.add_family_data_nodes(network_cytoscape, family)
     network_cytoscape = CytoscapeHelper.add_lc_data_nodes(network_cytoscape)
     network_cytoscape = CytoscapeHelper.add_species_data_nodes(network_cytoscape)
+    network_cytoscape = CytoscapeHelper.connect_homologs(network_cytoscape)
 
     return json.dumps(network_cytoscape)
diff --git a/conekt/models/relationships/sequence_sequence_ecc.py b/conekt/models/relationships/sequence_sequence_ecc.py
index c1bf778..cb89793 100644
--- a/conekt/models/relationships/sequence_sequence_ecc.py
+++ b/conekt/models/relationships/sequence_sequence_ecc.py
@@ -151,8 +151,6 @@ def get_ecc_pair_network(ecc_id):
         query_network_data = json.loads(query_network)
         target_network_data = json.loads(target_network)
 
-        # print(query_network_data)
-
         sequences = [association.query_sequence.id, association.target_sequence.id]
 
         for n in query_network_data:
@@ -211,11 +209,32 @@ def get_ecc_multi_network(gf_method_id, sequence_ids):
                         SequenceSequenceECCAssociation.target_id.in_(sequence_ids))).\
             all()
 
-        nodes = []
-        edges = []
+        nodes, edges = [], []
         node_sequence_ids = []
 
+        networks = []
+
         for a in associations:
+            query_network = a.query_sequence.network_nodes.filter_by(
+                method_id=a.query_network_method_id).first_or_404().network
+            target_network = a.target_sequence.network_nodes.filter_by(
+                method_id=a.target_network_method_id).first_or_404().network
+
+            if query_network not in networks:
+                networks.append((a.query_id,
+                                 a.query_sequence.name,
+                                 a.query_sequence.species_id,
+                                 a.query_sequence.species.name,
+                                 a.query_network_method_id,
+                                 query_network))
+            if target_network not in networks:
+                networks.append((a.target_id,
+                                 a.target_sequence.name,
+                                 a.target_sequence.species_id,
+                                 a.target_sequence.species.name,
+                                 a.target_network_method_id,
+                                 target_network))
+
             if a.query_id not in node_sequence_ids:
                 node_sequence_ids.append(a.query_id)
                 nodes.append({"id": a.query_sequence.name,
@@ -244,4 +263,35 @@ def get_ecc_multi_network(gf_method_id, sequence_ids):
                           'ecc_pair_color': "#D33",
                           "edge_type": "ecc"})
 
+        new_edges = []
+
+        for sequence_id, sequence_name, species_id, species_name, network_method_id, n in networks:
+            network_data = json.loads(n)
+            for node in network_data:
+                gene_id = node['gene_id'] if 'gene_id' in node.keys() else None
+                gene_name = node['gene_name'] if 'gene_name' in node.keys() else None
+
+                if gene_id not in node_sequence_ids:
+                    node_sequence_ids.append(gene_id)
+                    nodes.append({
+                        "id": gene_name,
+                        "name": gene_name,
+                        "species_id": species_id,
+                        "species_name": species_name,
+                        "gene_id": gene_id,
+                        "gene_name": gene_name,
+                        "network_method_id": network_method_id,
+                        "node_type": "target"
+                    })
+
+                if (sequence_name, gene_name) not in new_edges:
+                    new_edges.append((sequence_name, gene_name))
+                    new_edges.append((gene_name, sequence_name))
+
+                    edges.append({"source": sequence_name,
+                                  "target": gene_name,
+                                  "link_score": node['link_score'] if 'link_score' in node else 0,
+                                  "edge_type": "expression",
+                                  'ecc_pair_color': "#3D3"})
+
         return {"nodes": nodes, "edges": edges}, gf_method_id
diff --git a/conekt/templates/expression_graph.html b/conekt/templates/expression_graph.html
index ea5d569..b65f7bf 100644
--- a/conekt/templates/expression_graph.html
+++ b/conekt/templates/expression_graph.html
@@ -13,6 +13,8 @@
         Custom network graph
     {% elif ecc_pair %}
         ECC Pair graph
+    {% elif ecc_multi %}
+        ECC Network
     {% endif %}
 {% endblock %}
 
@@ -34,6 +36,8 @@ <h1><abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='
             <h1>Custom network</h1>
             {% elif ecc_pair %}
             <h1>ECC pair</h1>
+            {% elif ecc_multi %}
+            <h1>ECC multi</h1>
             {% endif %}
              </div>
             <div class="clearfix">
@@ -63,7 +67,7 @@ <h1>ECC pair</h1>
                                     {% if cluster or cluster_one %}
                                     <li><a href="#" class="cy-node-color" attr="neighbors">Neighbors</a></li>
                                     {% endif %}
-                                    {% if sequence or ecc_pair %}
+                                    {% if sequence or ecc_pair or ecc_multi %}
                                     <li><a href="#" class="cy-node-color" attr="species_color">Species</a></li>
                                     {% endif %}
                                     {% if graph_data %}
@@ -92,7 +96,7 @@ <h1>ECC pair</h1>
                                     <li><a href="#" class="cy-edge-color" attr="depth_color">Depth</a></li>
                                     <li><a href="#" class="cy-edge-color" attr="link_pcc">PCC</a></li>
                                     <li><a href="#" class="cy-edge-color" attr="hrr">HRR</a></li>
-                                    {% elif ecc_pair %}
+                                    {% elif ecc_pair or ecc_multi %}
                                     <li><a href="#" class="cy-edge-color" attr="ecc_pair_color">Type</a></li>
                                     {% elif not sequence %}
                                     <li><a href="#" class="cy-edge-color" attr="link_score">Score</a></li>
@@ -111,7 +115,7 @@ <h1>ECC pair</h1>
                                     {% if sequence %}
                                     <li><a href="#" class="cy-edge-width" attr="ecc_width">ECC</a></li>
                                     {% endif %}
-                                    {% if not sequence and not ecc_pair %}
+                                    {% if not sequence and not ecc_pair and not ecc_multi %}
                                     <li><hr /></li>
                                     <li class="dropdown-header"><abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='hrr') }}" data-target="#helpModal">HRR</abbr> Filter</li>
                                     <li><p><strong>Cutoff:</strong> <span id="cy-edge-score-value" class="text-muted">{{cutoff}}</span></p></li>
@@ -206,12 +210,14 @@ <h1>ECC pair</h1>
             <div id="cy" json="{{ url_for('expression_cluster.expression_cluster_json', cluster_id=cluster.id, family_method_id=family_method_id) }}" cycss="{{ url_for('static', filename='js/cytoscape.cycss') }}"></div>
             {% elif cluster_one %}
             <div id="cy" json="{{ url_for('graph_comparison.graph_comparison_cluster_json', one=cluster_one.id, two=cluster_two.id, family_method_id=family_method_id) }}" cycss="{{ url_for('static', filename='js/cytoscape.cycss') }}"></div>
-           {% elif sequence %}
+            {% elif sequence %}
             <div id="cy" json="{{ url_for('ecc.ecc_graph_json', sequence=sequence.id, network=network_method_id, family=family_method_id) }}" cycss="{{ url_for('static', filename='js/cytoscape.cycss') }}"></div>
-           {% elif graph_data %}
+            {% elif graph_data %}
             <div id="cy" cycss="{{ url_for('static', filename='js/cytoscape.cycss') }}"></div>
-           {% elif ecc_pair %}
+            {% elif ecc_pair %}
             <div id="cy" json="{{ url_for('ecc.ecc_graph_pair_json', ecc_id = ecc_pair.id) }}" cycss="{{ url_for('static', filename='js/cytoscape.cycss') }}"></div>
+            {% elif ecc_multi %}
+            <div id="cy" json="{{ url_for('ecc.ecc_graph_multi_json') }}" cycss="{{ url_for('static', filename='js/cytoscape.cycss') }}"></div>
             {% endif %}