Changed graph to accomodate networkx

Given object, each node is structured n:{obj=object}, where n=id(object)

tests/test_wc_rules.py

@@ -189,15 +189,20 @@ class z(bio.Site):pass
 		x1.add_bond_to(z1)
 		y1.init_binding_state()
 		c1.add([A1,B1])
-
+			
 		g = c1.graph
-		nodes = sorted(list(x.label for x in g.nodes()))
-		edges = sorted(list(tuple(x.label for x in edge) for edge in g.edges() ) )
+
+		def get_node_label(graph,node): return graph.node[node]['obj'].label
+
+		nodes1 = sorted([get_node_label(g,x) for x in g.nodes()])
 		nodes2 = ['A', 'B', 'BindingState', 'BindingState', 'BindingState', 'Complex', 'PhosphorylationState', 'x', 'y', 'z']
-		edges2 = [('A', 'x'), ('A', 'y'), ('B', 'z'), ('Complex', 'A'), ('Complex', 'B'), ('x', 'BindingState'), ('y', 'BindingState'), ('z', 'BindingState'), ('z', 'PhosphorylationState')]
-		self.assertEqual(nodes,nodes2)
-		self.assertEqual(edges,edges2)
 
+		edges1 = sorted([tuple([get_node_label(g,x) for x in edge]) for edge in g.edges()])
+		edges2 = [('A', 'x'), ('A', 'y'), ('B', 'z'), ('BindingState', 'x'), ('BindingState', 'z'), ('Complex', 'A'), ('Complex', 'B'), ('x', 'BindingState'), ('y', 'BindingState'), ('z', 'BindingState'), ('z', 'PhosphorylationState')]
+
+		self.assertEqual(nodes1,nodes2)
+		self.assertEqual(edges2,edges2)
+
 
 	def test_current(self):pass
 

wc_rules/bioschema.py

@@ -10,6 +10,7 @@
 import wc_rules.utils as utils
 import wc_rules.ratelaw as rl
 import wc_rules.graph_utils as g
+import networkx as nx
 
 ###### Structures ######
 class BaseClass(core.Model):
@@ -39,15 +40,12 @@ def label(self):
 		return self.__class__.__name__
 
 	##### Graph Methods #####
-	def node_match(self,other):
-		return g.node_compare(self,other)
+	def get_graph(self,recurse=True,memo=None):
+		return g.get_graph(self,recurse=recurse,memo=memo)
 
-	def get_edges(self):
-		return g.get_edges(self)
-
 	@property
 	def graph(self):
-		return g.get_graph(self)
+		return self.get_graph(recurse=True)
 
 class Complex(BaseClass):
 	class GraphMeta(BaseClass.GraphMeta):
@@ -240,6 +238,7 @@ def set_target(self,value):
 		self.target = value
 		return self
 
+
 class BondOperation(Operation):
 	sites = core.OneToManyAttribute(Site,related_name='bond_op')
 	@property
@@ -302,7 +301,7 @@ class Dephosphorylate(SetFalse): pass
 
 def main():
 	pass
-
+		
 if __name__ == '__main__': 
 	main()
 

wc_rules/graph_utils.py

@@ -39,18 +39,37 @@ def node_compare(current,other):
 		if current_attr != other_attr: return False
 	return True
 
-def get_edges(node):
-	edges = []
-	for attrname in node.__class__.GraphMeta.outward_edges:
-		if getattr(node,attrname) is not None:
-			attr_obj = getattr(node,attrname)
-			if isinstance(attr_obj,core.RelatedManager):
-				for x in attr_obj:
-					edges.append(tuple([node,x]))
-					edges.extend(x.get_edges())
-			else:
-				edges.append(tuple([node,attr_obj]))
-	return edges
+def get_graph(current_obj,recurse=True,memo=None):
+	def update_graph(graph,obj1):
+		if id(obj1) not in graph:
+			graph.add_node(id(obj1),obj=obj1)
+		else:
+			graph.node[id(obj1)]['obj'] = obj1
 
-def get_graph(node):
-	return nx.DiGraph(node.get_edges())
+	# Initializing if a memo is not provided
+	if memo is None:
+		memo = nx.DiGraph()
+	# Adding node if not already in memo, else updating it
+	update_graph(memo,current_obj)
+
+	# getting list of next nodes to check
+	next_nodes = []
+	for attrname in current_obj.__class__.GraphMeta.outward_edges:
+		if getattr(current_obj,attrname) is not None:
+			attr = getattr(current_obj,attrname)
+			if isinstance(attr,list):
+				next_nodes.extend(attr)
+			else:
+				next_nodes.append(attr)
+	# for each node in next_nodes,
+	# if an edge already exists, ignore
+	# if adding a new edge, recurse onto that node using current memo
+	for x in next_nodes:
+		update_graph(memo,x)
+		e = tuple([id(current_obj),id(x)])
+		if e not in memo.edges():
+			memo.add_edge(*e)
+			if recurse is True:
+				memo2 = x.get_graph(recurse=True,memo=memo)
+				memo = memo2
+	return memo