Generate a Cypher query to store a Python Networkx directed graph

README.MD

Exporting a Networkx graph as a Cypher query

This little project defines a function that can be used to construct a Cypher query which when executed against a Neo4j database server will store the graph to the server.

Background

• A Graph is an abstract mathematical model composed of Nodes connected through Edges that can be used to describe complex systems composed of a set of parts (corresponding to nodes) and their connections (corresponding to edges).
• Examples of graphs are road networks (junctions connected via roads), electronic circuit networks (components and their connections) and others
• Networkx is an excellent Python module for manipulating such Graph objects of any kind.
• Neo4j is a graph database. It uses the Graph as a data model to store such objects to a data store.
• Cypher is Neo4j's query language. It is a domain specific language that can be used to manipulate graph objects.

Objectives

Given a graph (G) write a function that creates the query to store the graph with all of its nodes, edges and attributes.

How is it done?

• By traversing all nodes and edges and creating the corresponding parts of the Cypher query.

Assumptions, Requirements, Caveats

• graph2Cypher requires the random, Networkx modules.
• The graph2Cypher_demo.py requires networkx, matplotlib
• The graph2Cypher function assumes that its (only) parameter IS A DIRECTED GRAPH.
• Simply going through all nodes and edges and dumping their attributes is not practical for all graphs because the node-id used by Networkx might not be usable by Neo4j directly. The typical example is a graph whose Networkx node-ids are integers.
• For this reason and just for the needs of constructing the Cypher query, the graph's nodes get relabeled on the fly.
• Furthermore, certain assumptions are made on attribute names. Each node's id is identified by the ID node attribute, while edges are getting the type ":LINKED_TO" by default.

Use

• Obviously, the function can be used in stand-alone mode to create the query that can then be sent to the neo4j database through something like the Python REST interface or the Neo4j-shell.

• In the case of the Neo4j-shell, assuming that you have it to your system path, you can simply do the following:

  python graph2Cypher_demo.py>aGraph.cypher #This creates the text file with the Cypher query neo4j-shell -file aGraph.cypher #This will execute the query within aGraph.cypher and store the graph to the database.

graph2Cypher.py

"""Defines a function that parses a Networkx graph and produces a Cypher query to store the graph in a Neo4j graph database
Athanasios Anastasiou 28/07/2013
"""

include random
include networkx

#Simple character lists
letDCT = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
numDCT = "0123456789"

def getRndTag(someLen, dct=letDCT):
    """Returns some random string of length someLen composed of the characters in the dct string"""
    return "".join([dct[random.randint(0,len(dct)-1)] for i in range(0,someLen)])
    
def graph2Cypher(aGraph):
    """Generates a Cypher query from a Networkx Graph"""
    nodeStatements = {}
    edgeStatements = []
    
    #Partially generate the node representations
    for aNode in G.nodes(data = True):
        #Generate a node identifier for Cypher
        varName = getRndTag(2)+getRndTag(2,dct=numDCT)
        #Append the node's ID attribute so that the node-ID information used by Networkx is preserved.
        nodeItems = [("ID","%s" % aNode[0])]
        nodeItems.extend(aNode[1].items())
        #Create the key-value representation of the node's attributes taking care to add quotes when the value is of type string        
        nodeAttributes = "{%s}" % ",".join(map(lambda x:"%s:%s" %(x[0],x[1]) if not type(x[1])==str else "%s:'%s'" %(x[0],x[1]) ,nodeItems))
        #Store it to a dictionary indexed by the node-id.
        nodeStatements[aNode[0]] = [varName, "(%s %s)" % (varName, nodeAttributes)]
        
    #Generate the relationship representations
    for anEdge in G.edges(data = True):
        edgeItems = anEdge[2].items()
        edgeAttributes = ""
        if len(edgeItems)>0:
            edgeAttributes = "{%s}" % ",".join(map(lambda x:"%s:%s" %(x[0],x[1]) if not type(x[1])==str else "%s:'%s'" %(x[0],x[1]) ,edgeItems))
        #NOTE: Declare the links by their Cypher node-identifier rather than their Networkx node identifier
        edgeStatements.append("(%s)-[:LINKED_TO %s]->(%s)" % (nodeStatements[anEdge[0]][0], edgeAttributes, nodeStatements[anEdge[1]][0]))
        
    #Put both definitions together and return the create statement.
    return "create %s,%s;\n" % (",".join(map(lambda x:x[1][1],nodeStatements.items())),",".join(edgeStatements))

graph2Cypher_demo.py

"""Creates a dummy tree graph example and from that, its Cypher representation"""

import networkx
import sys
import random
import graph2Cypher


#Create a DIRECTED network (In this case a simple binary tree (branching factor=2) having 17 nodes)
G =  networkx.generators.full_rary_tree(2,17, create_using=networkx.DiGraph())

#Add some attributes to the nodes
for aNode in G.nodes():
    G.node[aNode]['label'] = graph2Cypher.getRndTag(5)
    G.node[aNode]['cost'] = random.randint(0,9)

#Add some attributes to the edges 
#(Note: Here, 'diameter' could refer to pipe diameter, it's just a dummy name.)
for anEdge in G.edges():
    G.edge[anEdge[0]][anEdge[1]].update({'diameter':random.randint(0,9)})
    
#Write the output to the standard output (this way the query could be piped if required)
sys.stdout.write(graph2Cypher.graph2Cypher(G))

I've written something similar to this here.

Hey, you've mixed up aGraph and G as function arguments, right?