def test_jit_2(self):
G = nx.Graph()
G.add_node(1, node_data=3)
G.add_node(3, node_data=0)
G.add_edge(1, 2, weight=9, something=0)
G.add_edge(2, 3, weight=4, something=3)
G.add_edge(1, 2)
d = jit_data(G)
K = jit_graph(json.loads(d))
assert_true(nx.is_isomorphic(G, K))
def test_jit_directed(self):
G = nx.DiGraph()
G.add_node(1, node_data=3)
G.add_node(3, node_data=0)
G.add_edge(1, 2, weight=9, something=0)
G.add_edge(2, 3, weight=4, something=3)
G.add_edge(1, 2)
d = jit_data(G)
K = jit_graph(json.loads(d), create_using=nx.DiGraph())
assert nx.is_isomorphic(G, K)
def test_jit_2(self):
G = nx.Graph()
G.add_node(1, node_data=3)
G.add_node(3, node_data=0)
G.add_edge(1, 2, weight=9, something=0)
G.add_edge(2, 3, weight=4, something=3)
G.add_edge(1, 2)
d = jit_data(G)
K = jit_graph(json.loads(d))
assert_true(nx.is_isomorphic(G, K))
def test_jit(self):
G = nx.Graph()
G.add_node('Node1', node_data='foobar')
G.add_node('Node3', node_data='bar')
G.add_node('Node4')
G.add_edge('Node1', 'Node2', weight=9, something='isSomething')
G.add_edge('Node2', 'Node3', weight=4, something='isNotSomething')
G.add_edge('Node1', 'Node2')
d = jit_data(G)
K = jit_graph(json.loads(d))
assert nx.is_isomorphic(G, K)
def test_jit(self):
G = nx.Graph()
G.add_node('Node1', node_data='foobar')
G.add_node('Node3', node_data='bar')
G.add_node('Node4')
G.add_edge('Node1', 'Node2', weight=9, something='isSomething')
G.add_edge('Node2', 'Node3', weight=4, something='isNotSomething')
G.add_edge('Node1', 'Node2')
d = jit_data(G)
K = jit_graph(json.loads(d))
assert_true(nx.is_isomorphic(G, K))
def test_jit(self):
G = nx.Graph()
G.add_node("Node1", node_data="foobar")
G.add_node("Node3", node_data="bar")
G.add_node("Node4")
G.add_edge("Node1", "Node2", weight=9, something="isSomething")
G.add_edge("Node2", "Node3", weight=4, something="isNotSomething")
G.add_edge("Node1", "Node2")
d = jit_data(G)
K = jit_graph(json.loads(d))
assert nx.is_isomorphic(G, K)
def test_jit_multi_directed(self):
G = nx.MultiDiGraph()
G.add_node(1, node_data=3)
G.add_node(3, node_data=0)
G.add_edge(1, 2, weight=9, something=0)
G.add_edge(2, 3, weight=4, something=3)
G.add_edge(1, 2)
pytest.raises(nx.NetworkXNotImplemented, jit_data, G)
H = nx.DiGraph(G)
d = jit_data(H)
K = jit_graph(json.loads(d), create_using=nx.MultiDiGraph())
assert nx.is_isomorphic(H, K)
K.add_edge(1, 2)
assert not nx.is_isomorphic(H, K)
assert nx.is_isomorphic(G, K)
def test_jit_multi_directed(self):
G = nx.MultiDiGraph()
G.add_node(1, node_data=3)
G.add_node(3, node_data=0)
G.add_edge(1, 2, weight=9, something=0)
G.add_edge(2, 3, weight=4, something=3)
G.add_edge(1, 2)
assert_raises(nx.NetworkXNotImplemented, jit_data, G)
H = nx.DiGraph(G)
d = jit_data(H)
K = jit_graph(json.loads(d), create_using=nx.MultiDiGraph())
assert_true(nx.is_isomorphic(H, K))
K.add_edge(1, 2)
assert_false(nx.is_isomorphic(H, K))
assert_true(nx.is_isomorphic(G, K))
__author__ = """Ollie Glass ([email protected])""" import json import matplotlib.pyplot as plt import networkx as nx from networkx.readwrite.json_graph import jit_data, jit_graph # add some nodes to a graph G = nx.Graph() G.add_node("one", type="normal") G.add_node("two", type="special") G.add_node("solo") # add edges G.add_edge("one", "two") G.add_edge("two", 3, type="extra special") # convert to JIT JSON jit_json = jit_data(G, indent=4) print(jit_json) X = jit_graph(json.loads(jit_json)) print("Nodes: %s" % list(X.nodes(data=True))) print("Edges: %s" % list(X.edges(data=True))) nx.draw(G, with_labels=True) plt.show()
def main():
start = time.time()
print "\nstart " + sys.argv[2]
callGraphDir = sys.argv[1] + "/graphs/callGraph"
interGraphDir = sys.argv[1] + "/interGraphs"
targetGraphDir = sys.argv[1] + "/graphs/" + sys.argv[2]
pathToFileA = sys.argv[3]
pathToFileB = sys.argv[4]
fileId = sys.argv[2]
fileId = "_" + hashlib.md5(fileId.encode()).hexdigest()
### read files ###
# replace id of node
# BB_entry11[...];
# BB139 [...]
# BB_entry11 -> BB139 [...]
with open(targetGraphDir + "/locMap_A.json") as f:
locMapA = json.load(f)
with open(targetGraphDir + "/locMap_B.json") as f:
locMapB = json.load(f)
for obj in locMapA + locMapB:
obj['blockId'] = obj['blockId'] + fileId
with open(targetGraphDir + "/flowgraphs_A", 'r') as f:
dotA = f.readlines()
newLines = []
for l in dotA:
s = re.split('(BB\d+|BB_entry\d+)', l)
l = ""
for i in range(0, len(s)):
l += s[i]
if i % 2 == 1:
l += fileId
newLines.append(l)
dotA = newLines
with open(targetGraphDir + "/flowgraphs_replaced_A", 'w') as f:
f.writelines(dotA)
CFGA = nx.drawing.nx_agraph.read_dot(targetGraphDir +
"/flowgraphs_replaced_A")
with open(targetGraphDir + "/flowgraphs_B", 'r') as f:
dotB = f.readlines()
newLines = []
for l in dotB:
s = re.split('(BB\d+|BB_entry\d+)', l)
l = ""
for i in range(0, len(s)):
l += s[i]
if i % 2 == 1:
l += fileId
newLines.append(l)
dotB = newLines
with open(targetGraphDir + "/flowgraphs_replaced_B", 'w') as f:
f.writelines(dotB)
CFGB = nx.drawing.nx_agraph.read_dot(targetGraphDir +
"/flowgraphs_replaced_B")
print "create graphs " + str(time.time() - start)
with open(callGraphDir + "/callgraph_A.json") as f:
CGEdgesA = json.load(f)
with open(callGraphDir + "/callgraph_B.json") as f:
CGEdgesB = json.load(f)
# mark file of node
for data in CFGA.nodes.values():
data['file'] = pathToFileA
for data in CFGB.nodes.values():
data['file'] = pathToFileB
### compute difference ###
diffMapA = {'added': [], 'changed': []}
diffMapB = {'added': [], 'changed': []}
summerizeDiff(dotA, dotB, diffMapA, diffMapB, fileId)
# print diffMapA
# mark diffent node
markDiffNode(CFGA, CFGB, diffMapA, diffMapB)
### calcurate affected node ###
# map location to node
for id, data in CFGA.nodes.items():
data['locList'] = []
for obj in locMapA:
if obj['blockId'] == id:
data['locList'].append(obj['loc'])
for id, data in CFGB.nodes.items():
data['locList'] = []
for obj in locMapB:
if obj['blockId'] == id:
data['locList'].append(obj['loc'])
# mark read and write variable and call block
for data in CFGA.nodes.values() + CFGB.nodes.values():
data['read'] = readVars(data) #{name: x, loc: [0,0,0,0]}
data['write'] = writeVar(data) #{name: x, loc: [0,0,0,0]}
data['cond'] = condLoc(data) #[0,0,0,0] or null
if 'label' in data.keys():
if re.match('{\d+: call', data['label']):
data['call'] = True
# delete gray edge
for id, data in CFGA.edges.items():
if 'color' in data and data['color'] == 'gray':
CFGA.remove_edge(id[0], id[1])
for id, data in CFGB.edges.items():
if 'color' in data and data['color'] == 'gray':
CFGB.remove_edge(id[0], id[1])
### get subGraph of each function
funcListA = {}
entriesA = filter(lambda n: 'BB_entry' in n, CFGA.nodes)
for en in entriesA:
clusterId = en[8:]
name = getFuncName(clusterId, fileId, dotA)
CFGA.nodes[en]['funcName'] = name
subGraph = nx.Graph.subgraph(
CFGA, filter(lambda n: nx.has_path(CFGA, en, n), CFGA.nodes))
for data in subGraph.nodes.values():
data["entry"] = en
markAffected(subGraph, diffMapA, en, fileId)
cdg = createCDG(subGraph, clusterId, name, pathToFileA)
funcListA[clusterId] = {
"funcName": name,
"subGraph": subGraph,
"CDG": cdg
}
funcListB = {}
entriesB = filter(lambda n: 'BB_entry' in n, CFGB.nodes)
for en in entriesB:
clusterId = en[8:]
name = getFuncName(clusterId, fileId, dotB)
CFGB.nodes[en]['funcName'] = name
subGraph = nx.Graph.subgraph(
CFGB, filter(lambda n: nx.has_path(CFGB, en, n), CFGB.nodes))
for data in subGraph.nodes.values():
data["entry"] = en
markAffected(subGraph, diffMapB, en, fileId)
cdg = createCDG(subGraph, clusterId, name, pathToFileB)
funcListB[clusterId] = {
"funcName": name,
"subGraph": subGraph,
"CDG": cdg
}
print "mark node information " + str(time.time() - start)
### compute distance from each node to each node in ICDG ###
# create ICFG and ICDG with callgraph
# not correspond to function passed as arguments
ICFGA = nx.DiGraph()
if os.path.exists(interGraphDir + '/ICFG_A.json'):
with open(interGraphDir + '/ICFG_A.json') as f:
ICFGA = json_graph.jit_graph(json.load(f),
create_using=nx.DiGraph())
ICFGB = nx.DiGraph()
if os.path.exists(interGraphDir + '/ICFG_B.json'):
with open(interGraphDir + '/ICFG_B.json') as f:
ICFGB = json_graph.jit_graph(json.load(f),
create_using=nx.DiGraph())
ICDGA = nx.DiGraph()
if os.path.exists(interGraphDir + '/ICDG_A.json'):
with open(interGraphDir + '/ICDG_A.json') as f:
ICDGA = json_graph.jit_graph(json.load(f),
create_using=nx.DiGraph())
ICDGB = nx.DiGraph()
if os.path.exists(interGraphDir + '/ICDG_B.json'):
with open(interGraphDir + '/ICDG_B.json') as f:
ICDGB = json_graph.jit_graph(json.load(f),
create_using=nx.DiGraph())
updateICFGandICDG(ICFGA, ICDGA, funcListA, CGEdgesA, pathToFileA)
updateICFGandICDG(ICFGB, ICDGB, funcListB, CGEdgesB, pathToFileB)
# map next node in icfg to node
for id, data in ICDGA.nodes.items():
data['next'] = list(ICFGA.succ[id])
for id, data in ICDGB.nodes.items():
data['next'] = list(ICFGB.succ[id])
with open(interGraphDir + '/ICFG_A.json', 'w') as f:
f.write(json_graph.jit_data(ICFGA, 2))
with open(interGraphDir + '/ICFG_B.json', 'w') as f:
f.write(json_graph.jit_data(ICFGB, 2))
with open(interGraphDir + '/ICDG_A.json', 'w') as f:
f.write(json_graph.jit_data(ICDGA, 2))
with open(interGraphDir + '/ICDG_B.json', 'w') as f:
f.write(json_graph.jit_data(ICDGB, 2))
with open(interGraphDir + '/nodeMap_A.json', 'w') as f:
json.dump(dict(ICDGA.nodes(data=True)), f, indent=2)
with open(interGraphDir + '/nodeMap_B.json', 'w') as f:
json.dump(dict(ICDGB.nodes(data=True)), f, indent=2)
edgeListA = map(lambda x: {
"from": x[0],
"to": x[1],
"data": x[2]
}, ICDGA.edges(data=True))
edgeListB = map(lambda x: {
"from": x[0],
"to": x[1],
"data": x[2]
}, ICDGB.edges(data=True))
with open(interGraphDir + '/edgeList_A.json', 'w') as f:
json.dump(edgeListA, f, indent=2)
with open(interGraphDir + '/edgeList_B.json', 'w') as f:
json.dump(edgeListB, f, indent=2)
print "create icfg and icdg " + str(time.time() - start)
def save_test_ontology_to_json(G):
with open('Climate_Mind_Digraph_Test_Ont.json', 'w') as outfile:
outfile.write(json_graph.jit_data(G, indent=4))
def save_graph_to_json(G):
with open('Climate_Mind_DiGraph.json', 'w') as outfile:
outfile.write(json_graph.jit_data(G, indent=4))
An example showing how to use the JavaScript InfoVis Toolkit (JIT) JSON export See the JIT documentation and examples at http://thejit.org """ __author__ = """Ollie Glass ([email protected])""" import json import networkx as nx from networkx.readwrite.json_graph import jit_data, jit_graph # add some nodes to a graph G = nx.Graph() G.add_node("one", type="normal") G.add_node("two", type="special") G.add_node("solo") # add edges G.add_edge("one", "two") G.add_edge("two", 3, type="extra special") # convert to JIT JSON jit_json = jit_data(G, indent=4) print(jit_json) X = jit_graph(json.loads(jit_json)) print("Nodes: %s" % list(X.nodes(data=True))) print("Edges: %s" % list(X.edges(data=True)))