def startup(self):
self.graph_db = py2neo.Graph()
self.selectors = {}
# setup selectors
for node_type in NodeTypes:
self.selectors[node_type] = py2neo.NodeSelector(
self.graph_db).select(node_type.name)
self._has_started_up = True
def drop_db_link_props(tx):
selector = py2neo.NodeSelector(tx)
for node in selector.select('link_props'):
match = [
is_test_dpid(node[rel]) for rel in ('src_switch', 'dst_switch')
]
if not all(match):
continue
tx.delete(node)
def fromNeo():
py2neo.authenticate("localhost:7474", "neo4j", "neo4j")
neoGraph = py2neo.Graph("http://localhost:7474/")
neoSelector = py2neo.NodeSelector(neoGraph)
query = neoGraph.run("MATCH (f:FUNCTION)-->(s:STRING) WHERE s.string CONTAINS 'OpenSSL' RETURN DISTINCT f.sample")
print (query.dump())
query = neoGraph.run("MATCH (s:SAMPLE {sha1: '04301b59c6eb71db2f701086b617a98c6e026872'})-[rels*]->(c) RETURN *")
print (query.dump())
def drop_db_switches(tx):
selector = py2neo.NodeSelector(tx)
for node in selector.select('switch'):
if not is_test_dpid(node['name']):
continue
tx.delete(node)
def toNeo(graphity, allAtts):
# GRAPH DB STUFF - NEO4J
# receives the NetworkX graph and accompanying sample data
# pushes the graph to Neo4J
### NetworkX Graph Structure ###
# FUNCTION as node, attributes: function address, size, calltype, list of calls, list of strings, count of calls; functiontype[Standard, Callback, Export], alias (e.g. export name)
# FUNCTIoN REFERENCE as edge (function address -> target address), attributes: ref offset (at)
# CALLBACK REFERENCE as edge (currently for threads and Windows hooks)
# API CALLS (list attribute of function node): address, API name
# STRINGS (list attribute of function node): address, string
####
py2neo.authenticate("localhost:7474", "neo4j", "neo4j")
neoGraph = py2neo.Graph("http://localhost:7474/")
neoSelector = py2neo.NodeSelector(neoGraph)
# flush of the DB, for test purposes
neoGraph.delete_all()
mySha1 = allAtts['sha1']
if neoSelector.select("SAMPLE", sha1=mySha1).first():
print("Graph for sample %s already exists in Neo4j instance!" % mySha1)
else:
# create master node for binary information
sampleNode = py2neo.Node("SAMPLE", sha1=mySha1, fileSize=allAtts['filesize'], binType=allAtts['filetype'], imphash=allAtts['imphash'], compilation=allAtts['compilationts'], addressEp=allAtts['addressep'], sectionEp=allAtts['sectionep'], sectionCount=allAtts['sectioncount'], originalFilename=allAtts['originalfilename'])
neoGraph.create(sampleNode)
# get nodes with 0 indegree, prepare relations from master node
indegrees = graphity.in_degree()
rootlist = []
for val in indegrees:
if indegrees[val] == 0:
rootlist.append(val)
# parsing of the NetworkX graph - functions, APIs and strings are all Neo4j nodes
for nxNode in graphity.nodes(data=True):
funcAddress = nxNode[0]
funcCalltype = nxNode[1]['calltype']
funcSize = nxNode[1]['size']
funcAlias = ''
funcType = ''
if nxNode[1].get('functiontype') : funcType = nxNode[1]['functiontype']
if nxNode[1].get('alias') : funcAlias = nxNode[1]['alias']
# sha1 serves as link to master node, but also as node identifier in combination with the function address
# TODO for saving memory, explore possibility of replacing sha1 with an index, as sha info is held in master node anyway
functionNode = py2neo.Node("FUNCTION", sample=mySha1, address=funcAddress, callType=funcCalltype, funcSize=funcSize, funcType=funcType, alias=funcAlias)
neoGraph.create(functionNode)
if funcAddress in rootlist:
rootrel = py2neo.Relationship(sampleNode, "virtual_relationship", functionNode)
neoGraph.create(rootrel)
stringList = nxNode[1]['strings']
for stringData in stringList:
strRefAddress = stringData[0]
theString = stringData[1]
# TODO think about string attributes to store, e.g. entropy, len
try:
# create string node or merge if string already exists, add relationship
stringNode = py2neo.Node("STRING", string=theString)
# TODO try this using Subgraph class, less interaction with DB server
neoGraph.merge(stringNode)
stringRel = py2neo.Relationship(functionNode, "references_string", stringNode, address=strRefAddress)
neoGraph.create(stringRel)
except:
print("ERROR with this string %s" % theString)
callsList = nxNode[1]['calls']
for callData in callsList:
callRefAddress = callData[0]
callApiName = callData[1]
# create API node or merge if API already exists, add relationship
apiNode = py2neo.Node("API", apiname=callApiName)
neoGraph.merge(apiNode)
apiRel = py2neo.Relationship(functionNode, "calls_api", apiNode, address=callRefAddress)
neoGraph.create(apiRel)
for from_node, to_node, properties in graphity.edges(data=True):
realFromNode = neoSelector.select("FUNCTION", sample=mySha1, address=from_node).first()
realToNode = neoSelector.select("FUNCTION", sample=mySha1, address=to_node).first()
funcCallsFunc = py2neo.Relationship(realFromNode, "calls_sub", realToNode)
neoGraph.create(funcCallsFunc)
# -*- coding: utf-8 -*-
import py2neo as gp
from py2neo.ogm import *
from pandas import DataFrame
import sys
import os
ID = sys.argv[1]
password = sys.argv[2]
gp.authenticate("localhost:7474",ID,password)
graph = gp.Graph()
selector = gp.NodeSelector(graph)
def readPpiNetwork(filename):
dico = {}
fic = open(filename)
dis = fic.readline().rstrip()
for line in fic.readlines():
rel = line.rstrip().rsplit('\t')
if rel[0] in dico:
dico[rel[0]][rel[1]]=float(rel[2])
else:
dico[rel[0]]={}
dico[rel[0]][rel[1]]=float(rel[2])
return dis,dico
for fichier in os.listdir("./prototype/datasets/interaction_networks/"):
dis,relationdict = readPpiNetwork("./prototype/datasets/interaction_networks/"+fichier)
if (i + 1) % self.iter == 0:
self.commit()
logger.debug("%s nodes added" % (i + 1))
# a new transaction
self.begin()
# outside cicle
if (i + 1) % self.iter != 0:
self.commit()
logger.debug("%s nodes added" % (i + 1))
# closing file
handle.close()
# get a selector
selector = py2neo.NodeSelector(self.graph)
# now add relations. Count them
count = 0
# debug
logger.info("Adding iterations...")
# get a new transaction object
self.begin()
for tax_id, parent_tax_id in self.all_relations.iteritems():
neo_nodes = selector.select(TaxNode.label, tax_id=tax_id)
# Reading from a list (tax_id are unique, so there are 1 results)
for neo_node in list(neo_nodes):
