From b9d5ccec72c08d1530b33d984b50a101f1a2df86 Mon Sep 17 00:00:00 2001
From: sepro <sebastian.proost@gmail.com>
Date: Tue, 12 Sep 2017 16:40:13 +0200
Subject: [PATCH] graphs now use the networks hrr limit for the control panel's
 slider + fixed unit tests

---
 planet/controllers/custom_network.py     | 4 +++-
 planet/controllers/expression_cluster.py | 4 +++-
 planet/controllers/expression_network.py | 3 ++-
 planet/controllers/graph_comparison.py   | 4 +++-
 planet/templates/expression_graph.html   | 4 ++--
 tests/website.py                         | 3 +++
 6 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/planet/controllers/custom_network.py b/planet/controllers/custom_network.py
index 34390f3..e46d32d 100644
--- a/planet/controllers/custom_network.py
+++ b/planet/controllers/custom_network.py
@@ -38,6 +38,7 @@ def custom_network_main():
         # make probe list unique
         probes = list(set(probes))
 
+        network_method = ExpressionNetworkMethod.query.get_or_404(method_id)
         network = ExpressionNetwork.get_custom_network(method_id, probes)
 
         network_cytoscape = CytoscapeHelper.parse_network(network)
@@ -47,7 +48,8 @@ def custom_network_main():
         network_cytoscape = CytoscapeHelper.add_cluster_data_nodes(network_cytoscape, cluster_method_id)
         network_cytoscape = CytoscapeHelper.add_specificity_data_nodes(network_cytoscape, specificity_method_id)
 
-        return render_template("expression_graph.html", graph_data=Markup(json.dumps(network_cytoscape)))
+        return render_template("expression_graph.html", graph_data=Markup(json.dumps(network_cytoscape)),
+                               cutoff=network_method.hrr_cutoff)
     else:
 
         example = {
diff --git a/planet/controllers/expression_cluster.py b/planet/controllers/expression_cluster.py
index dab3925..2bef993 100644
--- a/planet/controllers/expression_cluster.py
+++ b/planet/controllers/expression_cluster.py
@@ -116,7 +116,9 @@ def expression_cluster_graph(cluster_id, family_method_id=None):
         else:
             family_method_id = None
 
-    return render_template("expression_graph.html", cluster=cluster, family_method_id=family_method_id)
+    return render_template("expression_graph.html", cluster=cluster,
+                           family_method_id=family_method_id,
+                           cutoff=cluster.method.network_method.hrr_cutoff)
 
 
 @expression_cluster.route('/json/<cluster_id>')
diff --git a/planet/controllers/expression_network.py b/planet/controllers/expression_network.py
index fafd830..8774345 100644
--- a/planet/controllers/expression_network.py
+++ b/planet/controllers/expression_network.py
@@ -60,7 +60,8 @@ def expression_network_graph(node_id, family_method_id=None):
 
     depth = 1 if enable_second_level else 0
 
-    return render_template("expression_graph.html", node=node, depth=depth, family_method_id=family_method_id)
+    return render_template("expression_graph.html", node=node, depth=depth, family_method_id=family_method_id,
+                           cutoff=node.method.hrr_cutoff)
 
 
 @expression_network.route('/download/neighbors/<node_id>')
diff --git a/planet/controllers/graph_comparison.py b/planet/controllers/graph_comparison.py
index 906d32c..f10d6b9 100644
--- a/planet/controllers/graph_comparison.py
+++ b/planet/controllers/graph_comparison.py
@@ -33,8 +33,10 @@ def graph_comparison_cluster(one, two, family_method_id=1):
     cluster_one = CoexpressionCluster.query.get_or_404(one)
     cluster_two = CoexpressionCluster.query.get_or_404(two)
 
+    cutoff = max([cluster_one.method.network_method.hrr_cutoff, cluster_two.method.network_method.hrr_cutoff])
+
     return render_template('expression_graph.html', cluster_one=cluster_one, cluster_two=cluster_two,
-                           family_method_id=family_method_id)
+                           family_method_id=family_method_id, cutoff=cutoff)
 
 
 @graph_comparison.route('/cluster/json/<int:one>/<int:two>')
diff --git a/planet/templates/expression_graph.html b/planet/templates/expression_graph.html
index 833ab2a..c6d7a89 100644
--- a/planet/templates/expression_graph.html
+++ b/planet/templates/expression_graph.html
@@ -149,8 +149,8 @@
             {% if not sequence %}
             <li>
                 <div>
-                <br /><p><strong><abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='hrr') }}" data-target="#helpModal">HRR</abbr> Score</strong> <span id="cy-edge-score-value" class="text-muted">30</span></p>
-                <input id="cy-edge-score" data-slider-id='cy-edge-score-slider' type="text" data-slider-min="0" data-slider-max="100" data-slider-step="1" data-slider-value="100" data-slider-tooltip="hide"/>
+                <br /><p><strong><abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='hrr') }}" data-target="#helpModal">HRR</abbr> Score</strong> <span id="cy-edge-score-value" class="text-muted">{{cutoff}}</span></p>
+                <input id="cy-edge-score" data-slider-id='cy-edge-score-slider' type="text" data-slider-min="0" data-slider-max="{{cutoff}}" data-slider-step="1" data-slider-value="{{cutoff}}" data-slider-tooltip="hide"/>
                 </div>
             </li>
             {% endif %}
diff --git a/tests/website.py b/tests/website.py
index e7c30a5..53fa1e5 100644
--- a/tests/website.py
+++ b/tests/website.py
@@ -91,6 +91,9 @@ def setUp(self):
         db.session.commit()
 
         test_expression_network_method = ExpressionNetworkMethod(test_species.id, "Test network method")
+        test_expression_network_method.pcc_cutoff = 0.0
+        test_expression_network_method.hrr_cutoff = 100
+        test_expression_network_method.enable_second_level = 0
         db.session.add(test_expression_network_method)
         db.session.commit()