Code to fetch network from the db is optimized and multiple bugs have…

… been fixed !!

planet/controllers/expression_network.py

@@ -1,39 +1,51 @@
-from flask import Blueprint, redirect, url_for, render_template, Response
-from sqlalchemy.sql import or_, and_
+from flask import Blueprint, url_for, render_template, flash, redirect
+from sqlalchemy.sql import and_
 
 from planet.models.expression_networks import ExpressionNetworkMethod, ExpressionNetwork
 
 import json
 
+
 expression_network = Blueprint('expression_network', __name__)
 
+
 @expression_network.route('/')
 def expression_network_overview():
+    """
+    Overview of all networks in the current database with basic information
+    """
     networks = ExpressionNetworkMethod.query.all()
 
     return render_template("expression_network.html", networks=networks)
 
 
-def __process_link(link):
-    output = {}
-    if link["gene_id"] is not None:
-        output = {"data": {"id": link["probe_name"],
-                               "name": link["probe_name"],
-                               "gene_link": url_for('sequence.sequence_view', sequence_id=link["gene_id"]),
-                               "gene_name": link["gene_name"],
-                               "node_type": "linked"}}
-    else:
-        output = {"data": {"id": link["probe_name"],
-                               "name": link["probe_name"],
-                               "gene_link": url_for('sequence.sequence_view', sequence_id=""),
-                               "gene_name": link["gene_name"],
-                               "node_type": "linked"}}
+@expression_network.route('/view/<node_id>')
+@expression_network.route('/view/<node_id>/<int:depth>')
+def expression_network_view(node_id, depth=0):
+    """
+    Page that displays the network graph for a specific network's probe, the depth indicates how many steps away from
+    the query gene the network is retrieved. For performance reasons depths > 2 are not allowed
+
+    :param node_id: id of the network's probe (the query) to visualize
+    :param depth: How many steps to include, 0 only the query and the direct neighborhood, 1 a step further, ...
+    """
+    if depth > 2:
+        flash("Depth cannot be larger than 2. Showing the network with depth 2", "warning")
+        return redirect(url_for('expression_network.expression_network_view', node_id=node_id, depth=2))
+
+    node = ExpressionNetwork.query.get(node_id)
+    return render_template("expression_graph.html", node=node, depth=depth)
 
-    return output
 
 @expression_network.route('/json/<node_id>')
 @expression_network.route('/json/<node_id>/<int:depth>')
 def expression_network_json(node_id, depth=0):
+    """
+    Generates JSON output compatible with cytoscape.js (see planet/static/planet_graph.js for details how to render)
+
+    :param node_id: id of the network's probe (the query) to visualize
+    :param depth: How many steps to include, 0 only the query and the direct neighborhood, 1 a step further, ...
+    """
     node = ExpressionNetwork.query.get(node_id)
     links = json.loads(node.network)
 
@@ -44,7 +56,8 @@ def expression_network_json(node_id, depth=0):
                        "name": node.probe,
                        "gene_link": url_for('sequence.sequence_view', sequence_id=node.gene_id),
                        "gene_name": node.gene.name,
-                       "node_type": "query"}}]
+                       "node_type": "query",
+                       "color": "#888"}}]
     edges = []
 
     # lists necessary for doing deeper searches
@@ -53,9 +66,14 @@ def expression_network_json(node_id, depth=0):
     existing_nodes = [node.probe]
 
     # add direct neighbors of the gene of interest
+
     for link in links:
         nodes.append(__process_link(link))
-        edges.append({"data": {"source": node.probe, "target": link["probe_name"], "depth": 0}})
+        edges.append({"data": {"source": node.probe,
+                               "target": link["probe_name"],
+                               "depth": 0,
+                               "link_score": link["link_score"],
+                               "color": "#CCC"}})
         additional_nodes.append(link["probe_name"])
         existing_edges.append([node.probe, link["probe_name"]])
         existing_edges.append([link["probe_name"], node.probe])
@@ -78,7 +96,11 @@ def expression_network_json(node_id, depth=0):
                     next_nodes.append(link["probe_name"])
 
                 if [new_node.probe, link["probe_name"]] not in existing_edges:
-                    edges.append({"data": {"source": new_node.probe, "target": link["probe_name"], "depth": i}})
+                    edges.append({"data": {"source": new_node.probe,
+                                           "target": link["probe_name"],
+                                           "depth": i,
+                                           "link_score": link["link_score"],
+                                           "color": "#CCC"}})
                     existing_edges.append([new_node.probe, link["probe_name"]])
                     existing_edges.append([link["probe_name"], new_node.probe])
 
@@ -92,15 +114,38 @@ def expression_network_json(node_id, depth=0):
         for link in new_links:
             if link["probe_name"] in existing_nodes:
                 if [new_node.probe, link["probe_name"]] not in existing_edges:
-                    edges.append({"data": {"source": new_node.probe, "target": link["probe_name"], "depth": depth+1}})
+                    edges.append({"data": {"source": new_node.probe,
+                                           "target": link["probe_name"],
+                                           "depth": depth+1,
+                                           "link_score": link["link_score"],
+                                           "color": "#CCC"}})
                     existing_edges.append([new_node.probe, link["probe_name"]])
                     existing_edges.append([link["probe_name"], new_node.probe])
 
     return json.dumps({"nodes": nodes, "edges": edges})
 
 
-@expression_network.route('/view/<node_id>')
-@expression_network.route('/view/<node_id>/<int:depth>')
-def expression_network_view(node_id, depth=0):
-    node = ExpressionNetwork.query.get(node_id)
-    return render_template("expression_graph.html", node=node, depth=depth)
+def __process_link(linked_probe):
+    """
+    Internal function that processes a linked probe (from the ExpressionNetwork.network field) to a data entry
+    compatible with cytoscape.js
+
+    :param linked_probe: hash with information from ExpressionNetwork.network field
+    :return: a hash formatted for use as a node with cytoscape.js
+    """
+    if linked_probe["gene_id"] is not None:
+        return {"data": {"id": linked_probe["probe_name"],
+                         "name": linked_probe["probe_name"],
+                         "gene_link": url_for('sequence.sequence_view', sequence_id=linked_probe["gene_id"]),
+                         "gene_name": linked_probe["gene_name"],
+                         "node_type": "linked",
+                         "color": "#888"}}
+    else:
+        return {"data": {"id": linked_probe["probe_name"],
+                         "name": linked_probe["probe_name"],
+                         "gene_link": url_for('sequence.sequence_view', sequence_id=""),
+                         "gene_name": linked_probe["gene_name"],
+                         "node_type": "linked",
+                         "color": "#888"}}
+
+

planet/static/js/planet_graph.js

@@ -8,7 +8,8 @@ $('#cy').cytoscape({
       .css({
         'content': 'data(gene_name)',
         'text-valign': 'center',
-        'color': 'white',
+        'color': '#FFF',
+        'background-color': 'data(color)',
         'text-outline-width': 1,
         'text-outline-color': '#888'
       })
@@ -22,6 +23,8 @@ $('#cy').cytoscape({
       .css({
         'curve-style': 'haystack',
         'opacity': 0.75,
+        'width': 'mapData(depth, 4, 0, 1, 5)',
+        'line-color': 'data(color)'
       })
     .selector(':selected')
       .css({
@@ -38,16 +41,15 @@ $('#cy').cytoscape({
     padding: 20
   },
 
-  // on graph initial layout done (could be async depending on layout...)
+
   ready: function(){
     window.cy = this;
-
-    // giddy up...
 
 
     cy.nodes().forEach(function(n){
     var g = n.data('gene_link');
 
+    // code to add tooltips to the selected node
     n.qtip({
       content: [
         {

utils/color.py

@@ -0,0 +1,11 @@
+"""
+A set of functions designed to work with colors for websites
+"""
+import hashlib
+
+
+def string_to_hex_color(input_string):
+    hashed_string = hashlib.sha1(str(input_string).encode('utf-8')).hexdigest()
+    color = "#" + hashed_string[0:3].upper()
+
+    return color