def buildCallGraph(self):
g = CGraph()
ep = self.pyew.ep
try:
l = set(self.pyew.exports.keys())
l.add(self.pyew.ep)
except:
print "Error:", sys.exc_info()[1]
l = set([self.pyew.ep])
raise
functions = []
nodes = {}
""" Compute the entry points initial graph """
for ep in l:
if self.pyew.functions.has_key(ep):
fep = self.pyew.functions[ep]
for c in fep.connections:
if c in self.pyew.functions:
if c not in functions:
functions.append(c)
if self.pyew.names[ep] not in nodes:
n1 = CNode(self.pyew.names[ep])
nodes[self.pyew.names[ep]] = n1
else:
n1 = nodes[self.pyew.names[ep]]
if self.pyew.names[c] not in nodes:
n2 = CNode(self.pyew.names[c])
nodes[self.pyew.names[c]] = n2
else:
n2 = nodes[self.pyew.names[c]]
g.addEdge(n1, n2)
""" Add all the remaining functions """
dones = set()
while len(functions) > 0:
addr = functions.pop()
f = self.pyew.functions[addr]
for c in f.connections:
if c in self.pyew.functions and c not in dones:
functions.append(c)
dones.add(c)
if self.pyew.names[addr] not in nodes:
n1 = CNode(self.pyew.names[addr])
nodes[self.pyew.names[addr]] = n1
else:
n1 = nodes[self.pyew.names[addr]]
if self.pyew.names[c] not in nodes:
n2 = CNode(self.pyew.names[c])
nodes[self.pyew.names[c]] = n2
else:
n2 = nodes[self.pyew.names[c]]
g.addEdge(n1, n2)
return g
def buildCallGraph(self):
g = CGraph()
ep = self.pyew.ep
try:
l = set(self.pyew.exports.keys())
l.add(self.pyew.ep)
except:
print "Error:", sys.exc_info()[1]
l = set([self.pyew.ep])
raise
functions = []
nodes = {}
""" Compute the entry points initial graph """
for ep in l:
if self.pyew.functions.has_key(ep):
fep = self.pyew.functions[ep]
for c in fep.connections:
if c in self.pyew.functions:
if c not in functions:
functions.append(c)
if self.pyew.names[ep] not in nodes:
n1 = CNode(self.pyew.names[ep])
nodes[self.pyew.names[ep]] = n1
else:
n1 = nodes[self.pyew.names[ep]]
if self.pyew.names[c] not in nodes:
n2 = CNode(self.pyew.names[c])
nodes[self.pyew.names[c]] = n2
else:
n2 = nodes[self.pyew.names[c]]
g.addEdge(n1, n2)
""" Add all the remaining functions """
dones = set()
while len(functions) > 0:
addr = functions.pop()
f = self.pyew.functions[addr]
for c in f.connections:
if c in self.pyew.functions and c not in dones:
functions.append(c)
dones.add(c)
if self.pyew.names[addr] not in nodes:
n1 = CNode(self.pyew.names[addr])
nodes[self.pyew.names[addr]] = n1
else:
n1 = nodes[self.pyew.names[addr]]
if self.pyew.names[c] not in nodes:
n2 = CNode(self.pyew.names[c])
nodes[self.pyew.names[c]] = n2
else:
n2 = nodes[self.pyew.names[c]]
g.addEdge(n1, n2)
return g
def buildFlowGraph(self, f):
fg = CGraph()
func = self.pyew.functions[f]
bbs = {}
nodes = {}
for bb in func.basic_blocks:
instructions = set()
bb_start = bb.instructions[0].offset
end_offset = bb.instructions[-1].offset
bb_end = end_offset + bb.instructions[-1].size
buf = self.pyew.getBytes(bb_start, bb_end-bb_start)
instructions = self.pyew.disassemble(buf=buf, baseoffset=bb_start, marker=False)
instructions = instructions.split("\n")
if instructions[-1] == "":
del instructions[len(instructions)-1]
bbs[bb_start] = instructions
bbs[end_offset] = instructions
n = CNode(str(bb.offset), data=instructions)
fg.addNode(n)
nodes[bb.offset] = n
for bb in func.basic_blocks:
next_head = self.pyew.NextHead(bb.instructions[-1].offset)
for conn in bb.connections:
a, b = conn
if nodes.has_key(b) and nodes.has_key(bb.offset):
if len(bb.connections) == 1:
color = 0 # edge always
elif next_head == b:
color = 2 # edge false or unknown
else:
color = 1 # edge true
fg.addEdge(nodes[bb.offset], nodes[b], value=color)
return fg
def GET(self):
if not 'user' in session or session.user is None:
f = register_form()
return render.login(f)
i = web.input(id=None)
if i.id is None or not i.id.isdigit():
return render.error("No cluster id specified or invalid one.")
db = open_db()
where = "id = $id"
sql_vars = {"id": int(i.id)}
ret = db.select("clusters", what="graph", vars=sql_vars, where=where)
rows = list(ret)
if len(rows) == 0:
return render.error("Invalid cluster id.")
g_text = rows[0]["graph"]
g = CGraph()
g.fromDict(json.loads(g_text))
json_graph = graph2json(g)
return json_graph
def GET(self):
if not 'user' in session or session.user is None:
f = register_form()
return render.login(f)
i = web.input(id=None)
if i.id is None or not i.id.isdigit():
return render.error("No cluster id specified or invalid one.")
db = open_db()
where = "id = $id"
sql_vars = {"id": int(i.id)}
ret = db.select("clusters", what="graph", vars=sql_vars, where=where)
rows = list(ret)
if len(rows) == 0:
return render.error("Invalid cluster id.")
g_text = rows[0]["graph"]
g = CGraph()
g.fromDict(json.loads(g_text))
for node in list(g.nodes()):
if node.name.startswith("New node "):
g.renameNode(node.name,
node.name.replace("New node ", "Cluster "))
else:
data = get_sample_data(node.name)
tmp = "%s%s"
if data["description"] is not None:
tmp %= (data["description"], " - " + data["hash"])
else:
tmp %= (data["hash"], "")
g.renameNode(node.name, tmp)
dot = g.toGml()
return dot
def buildFlowGraph(self, f):
fg = CGraph()
func = self.pyew.functions[f]
bbs = {}
nodes = {}
for bb in func.basic_blocks:
instructions = set()
bb_start = bb.instructions[0].offset
end_offset = bb.instructions[-1].offset
bb_end = end_offset + bb.instructions[-1].size
buf = self.pyew.getBytes(bb_start, bb_end-bb_start)
instructions = self.pyew.disassemble(buf=buf, baseoffset=bb_start, marker=False)
instructions = instructions.split("\n")
if instructions[-1] == "":
del instructions[len(instructions)-1]
bbs[bb_start] = instructions
bbs[end_offset] = instructions
n = CNode(str(bb.offset), data=instructions)
fg.addNode(n)
nodes[bb.offset] = n
for bb in func.basic_blocks:
next_head = self.pyew.NextHead(bb.instructions[-1].offset)
for conn in bb.connections:
a, b = conn
if nodes.has_key(b) and nodes.has_key(bb.offset):
if len(bb.connections) == 1:
color = 0 # edge always
elif next_head == b:
color = 2 # edge false or unknown
else:
color = 1 # edge true
fg.addEdge(nodes[bb.offset], nodes[b], value=color)
return fg
def make_tree_for(self, group):
""" Make a phylogenetic tree for the given group. """
l = list(group)
l.sort()
s = str(l)
if s in self.groups_done:
if self.debug:
print "Already clustered group found, skipping..."
return None
g = CGraph()
g.letter = self.ascii_letters[self.last_letter]
self.last_letter += 1
group = list(group)
dm = self.diff_matrix
parent = None
name = "New node %d"
node_num = 0
nodes = {}
previous_node_name = node_name = None
total_groups = len(group) - 1
groups = 0
for it in xrange(len(group) - 1):
groups += 1
node_num += 1
# start by building a smaller difference matrix only for the samples
# in this specific group
dm = self.get_diff_matrix_for(group, dm)
qm, lowest = self.get_q_matrix(dm)
group = dm.keys()
new_group = list(group)
# Build a new node with the highest value found so far
if node_name is not None:
previous_node_name = node_name
node_name = name % node_num
n = CNode(node_name, shape="point")
g.addNode(n)
nodes[node_name] = n
if parent is None:
parent = n
# Create the edges between the new node 'n' and the samples wih the
# lowest Q matrix value
if it != 0:
lowest = None
n1, n2 = self.get_neighbors(qm, group, lowest, previous_node_name)
if not nodes.has_key(n1):
nodes[n1] = CNode(n1)
if not nodes.has_key(n2):
nodes[n2] = CNode(n2)
dfu = dgu = 0 #self.get_dfg_distances(n1, n2, dm)
if not g.edgeExists(nodes[n1], n):
g.addEdge(n, nodes[n1], check_dups=True, label=str(dfu))
if not g.edgeExists(nodes[n2], n):
g.addEdge(n, nodes[n2], check_dups=True, label=str(dgu))
if n1 in new_group:
new_group.remove(n1)
if n2 in new_group:
new_group.remove(n2)
new_group.append(node_name)
dm = self.update_diff_matrix(node_name, n1, n2, new_group, dm)
group = new_group
self.groups_done.add(s)
return g
