def testrr_helper (filee, jalangi, norm_fn, record_fn, instrument_fn=instrument):
try:
shutil.rmtree("jalangi_tmp")
except: pass
os.mkdir("jalangi_tmp")
os.mkdir("jalangi_tmp/out")
os.putenv("JALANGI_HOME", jalangi.get_home())
os.chdir("jalangi_tmp")
(instrumented_f, out) = instrument_fn(os.path.join(os.pardir,filee), jalangi=jalangi)
try: # Ignore failures on first iteration
os.remove("inputs.js")
shutil.copy("jalangi_inputs{}.js".format(i), "inputs.js")
except:
pass
if not os.path.isfile("inputs.js"):
util.mkempty("inputs.js")
print "---- Running without instrumentation ----"
try:
os.remove("jalangi_trace")
except:
pass
norm = norm_fn(os.path.join(os.pardir,filee + ".js"), jalangi=jalangi)
with open("jalangi_normal", "w") as normfile:
normfile.write(norm)
print norm
print "---- Recording execution of {} ----".format(filee)
rec = record_fn(os.path.join(os.pardir,filee), instrumented_f)
with open("jalangi_record", "w") as recfile:
recfile.write(rec)
print rec
print "---- Replaying {} ----".format(filee)
os.putenv("JALANGI_MODE", "replay")
os.putenv("JALANGI_ANALYSIS", "none")
rep = replay()
with open("jalangi_replay", "w") as repfile:
repfile.write(rep)
print rep
try:
wcl = util.count_lines("jalangi_trace")
with open("../jalangi_test_results", 'a') as f:
f.write("# of lines in jalangi_trace for {}: {}".format(filee,str(wcl)))
f.write("\n")
except: pass
if norm != rep: #TODO: Factor out this.
print "{}.js failed".format(filee)
import difflib
with open("../jalangi_test_results", 'a') as f:
f.write("\n")
for line in difflib.unified_diff(norm.splitlines(1), rec.splitlines(1), fromfile='normal.{}'.format(filee), tofile='replay.{}'.format(filee)):
f.write(line)
if rec != rep:
print "{}.js failed".format(filee)
import difflib
with open("../jalangi_test_results", 'a') as f:
f.write("\n")
for line in difflib.unified_diff(rec.splitlines(1), rep.splitlines(1), fromfile='record.{}'.format(filee), tofile='replay.{}'.format(filee)):
f.write(line)
util.move_coverage(jalangi)
def _create_local_mapping(location, outer_loop=True):
f = open(location, 'r')
if outer_loop:
nlines = util.count_lines(location)
progress = tqdm(total=nlines)
progress.set_description('Reading ' + location.split('/')[-1])
ids = set()
for line in f:
line = line.split(' ')
pid1 = line[0]
pid2 = line[1]
ids.add(pid1)
ids.add(pid2)
if outer_loop:
progress.update(1)
if outer_loop:
progress.close()
nids = len(ids)
ids_list = list(ids)
f.close()
return ids_list
def read_cog_links(location=settings.COG_LINKS):
f = open(location, 'r')
association_mapping = {}
progress = tqdm(total=util.count_lines(location))
first = True
for line in f:
if first:
first = False
progress.update(1)
continue
else:
line = line.strip('\n').split(' ')
cog_1 = line[0]
cog_2 = line[1]
ascore = int(line[2])
if line[0] in association_mapping:
association_mapping[cog_1].append([cog_2, ascore])
else:
association_mapping[cog_1] = [[cog_2, ascore]]
if line[1] in association_mapping:
association_mapping[cog_2].append([cog_1, ascore])
else:
association_mapping[cog_2] = [[cog_1, ascore]]
progress.set_description('Reading COG ' + cog_1)
progress.update(1)
progress.close()
return association_mapping
def create_graph(name, weighted=False):
i = open(settings.INDIVIDUAL_PPI_DIR + '/' + name + '.txt', 'r')
if weighted:
o = open(settings.INDIVIDUAL_W_GRAPH_DIR + '/' + name + '.txt', 'wb')
else:
o = open(settings.INDIVIDUAL_UW_GRAPH_DIR + '/' + name + '.txt', 'wb')
nd = re.compile(r'[^\d.]+')
for line in tqdm(i,
total=util.count_lines(settings.INDIVIDUAL_PPI_DIR + '/' +
name + '.txt')):
try:
v = line.split(' ')
w = int(v[2]) + int(v[3]) + int(v[4]) + int(v[5]) + int(
v[6]) + int(v[7])
n1 = int(nd.sub('', v[0].split('.')[1]).lstrip('0'))
n2 = int(nd.sub('', v[1].split('.')[1]).lstrip('0'))
if weighted and w > 0:
o.write(str(n1) + ' ' + str(n2) + ' ' + str(w) + '\n')
if not weighted and w > 0:
o.write(str(n1) + ' ' + str(n2) + '\n')
except:
print "ERROR - ", line
pass
o.close()
def visualize_graph(graph_path, output=''):
weighted = False
if settings.INDIVIDUAL_W_GRAPH_DIR in graph_path:
weighted = True
G = pgv.AGraph()
for line in tqdm(open(graph_path, 'r'),
total=util.count_lines(graph_path)):
v = line.split(' ')
n1 = v[0]
n2 = v[1]
G.add_edge(n1, n2)
if weighted:
edge = G.get_edge(n1, n2)
edge.attr['weight'] = int(v[2])
if output == '':
output = graph_path.split('/')[-1].strip('.txt') + '.dot'
G.write(output)
def save_graph(data, fname, tag):
# `data` are the groups (by ID)
# `fname` is the raw data file
# `tag` helps create a uniquely-named output file
new_name = util.gen_name(fname, tag, "png")
plt.xlabel("Avg. Runtime (ms)", )
plt.ylabel("Num. Configs")
plt.title(new_name.rsplit(".", 1)[0].rsplit("/", 1)[-1])
num_configs = util.count_lines(fname) - 1
bin_width = data[0]["max"] - data[0]["min"]
# Plot bins
for bkt in data:
# x-position is average runtime, height is count
plt.bar(bkt["min"],
bkt["count"],# / num_configs,
alpha=0.6,
bottom=0,
# label="%s - %s" % (bkt["min"], bkt["max"]),
width=bin_width)
# Add median line (take median of alread-computed rows' medians)
md = statistics.median([bkt["median"] for bkt in data if bkt["median"] is not None])
plt.axvline(md, color='k', linestyle="solid", linewidth=5, label="median = %s" % int(md))
# Add UNTYPED & TYPED configuration line
arbitrary_key = next((bkt["data"][0]["key"] for bkt in data if bkt["data"]))
untyped = statistics.mean(get_row(fname, "".join(("0" for _ in arbitrary_key))))
typed = statistics.mean(get_row(fname, "".join(("1" for _ in arbitrary_key))))
plt.axvline(untyped, color='g', linestyle='dashed', linewidth=5, label="untyped = %s" % int(untyped))
plt.axvline(typed, color='r', linestyle='dotted', linewidth=5, label="typed = %s" % int(typed))
plt.xticks(sorted([bkt["min"] for bkt in data] + [data[-1]["max"]]))#, rotation="vertical")
plt.xlim(xmax=data[-1]["max"])
#plt.ylim(ymax=0.5) #50%
lgd = plt.legend(bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0.)
plt.savefig(new_name,bbox_extra_artists=(lgd,), bbox_inches='tight')
print("Saved plot to '%s'" % new_name)
plt.clf()
return new_name
def concolic (filee, inputs, jalangi=util.DEFAULT_INSTALL):
try:
shutil.rmtree("jalangi_tmp")
except: pass
os.mkdir("jalangi_tmp")
os.mkdir("jalangi_tmp/out")
os.putenv("JALANGI_HOME", jalangi.get_home())
os.chdir("jalangi_tmp")
(instrumented_f, out) = instrument(os.path.join(os.pardir,filee), jalangi=jalangi)
i = 0
iters = 0
mismatch = False
while i <= iters and i <= inputs:
try: # Ignore failures on first iteration
os.remove("inputs.js")
shutil.copy("jalangi_inputs{}.js".format(i), "inputs.js")
except:
pass
if not os.path.isfile("inputs.js"):
util.mkempty("inputs.js")
print "==== Input {} ====".format(i)
print "---- Runing without instrumentation ----"
try:
os.remove("jalangi_trace")
except:
pass
norm = util.run_node_script(os.path.join(os.pardir,filee + ".js"), jalangi=jalangi, savestderr=True)
#(open("jalangi_normal", "w")).write(norm)
print "---- Recording execution of {} ----".format(filee)
rec = record(os.path.join(os.pardir,filee), instrumented_f)
print "---- Replaying {} ----".format(filee)
os.putenv("JALANGI_MODE", "replay")
os.putenv("JALANGI_ANALYSIS", "analyses/concolic/SymbolicEngine")
rep = replay()
(open("jalangi_replay", "w")).write(rep)
print rep
try:
wcl = util.count_lines("jalangi_trace")
with open("../jalangi_test_results", 'a') as f:
f.write("# of lines in jalangi_trace for {}: {}".format(filee,str(wcl)))
f.write("\n")
except: pass
if norm != rep: #TODO: Factor out this.
import difflib
with open("../jalangi_test_results", 'a') as f:
f.write("\n")
for line in difflib.unified_diff(norm.splitlines(1), rec.splitlines(1), fromfile='normal.{}'.format(filee), tofile='replay.{}'.format(filee)):
f.write(line)
if rec != rep:
import difflib
with open("../jalangi_test_results", 'a') as f:
f.write("\n")
for line in difflib.unified_diff(rec.splitlines(1), rep.splitlines(1), fromfile='replay.{}'.format(filee), tofile='record.{}'.format(filee)):
f.write(line)
try:
iters = int(util.head("jalangi_tail",1)[0])
except: pass
i = i + 1
for i in glob.glob("jalangi_inputs*"):
print "*** Generated ({}:1:1) for ({}.js:1:1)".format(os.path.abspath(i),filee)
iters = iters + 1
if iters == inputs:
print "{}.js passed".format(filee)
else:
print "{}.js failed".format(filee)
util.move_coverage(jalangi)
def testrr_helper(filee,
jalangi,
norm_fn,
record_fn,
instrument_fn=instrument):
try:
shutil.rmtree("jalangi_tmp")
except:
pass
os.mkdir("jalangi_tmp")
os.mkdir("jalangi_tmp/out")
os.putenv("JALANGI_HOME", jalangi.get_home())
os.chdir("jalangi_tmp")
(instrumented_f, out) = instrument_fn(os.path.join(os.pardir, filee),
jalangi=jalangi)
try: # Ignore failures on first iteration
os.remove("inputs.js")
shutil.copy("jalangi_inputs{}.js".format(i), "inputs.js")
except:
pass
if not os.path.isfile("inputs.js"):
util.mkempty("inputs.js")
print "---- Running without instrumentation ----"
try:
os.remove("jalangi_trace")
except:
pass
norm = norm_fn(os.path.join(os.pardir, filee + ".js"), jalangi=jalangi)
with open("jalangi_normal", "w") as normfile:
normfile.write(norm)
print norm
print "---- Recording execution of {} ----".format(filee)
rec = record_fn(os.path.join(os.pardir, filee), instrumented_f)
with open("jalangi_record", "w") as recfile:
recfile.write(rec)
print rec
print "---- Replaying {} ----".format(filee)
os.putenv("JALANGI_MODE", "replay")
os.putenv("JALANGI_ANALYSIS", "none")
rep = replay()
with open("jalangi_replay", "w") as repfile:
repfile.write(rep)
print rep
try:
wcl = util.count_lines("jalangi_trace")
with open("../jalangi_test_results", 'a') as f:
f.write("# of lines in jalangi_trace for {}: {}".format(
filee, str(wcl)))
f.write("\n")
except:
pass
if norm != rep: #TODO: Factor out this.
print "{}.js failed".format(filee)
import difflib
with open("../jalangi_test_results", 'a') as f:
f.write("\n")
for line in difflib.unified_diff(
norm.splitlines(1),
rec.splitlines(1),
fromfile='normal.{}'.format(filee),
tofile='replay.{}'.format(filee)):
f.write(line)
if rec != rep:
print "{}.js failed".format(filee)
import difflib
with open("../jalangi_test_results", 'a') as f:
f.write("\n")
for line in difflib.unified_diff(
rec.splitlines(1),
rep.splitlines(1),
fromfile='record.{}'.format(filee),
tofile='replay.{}'.format(filee)):
f.write(line)
util.move_coverage(jalangi)
