def check_upgrade():
server_file = curl(PIFM_HOST + '/client_agent/pifm_agent.py')
server_sum = awk(
md5sum(
grep(server_file, '-v', '^PIFM_HOST')
), '{print $1}'
)
local_sum = awk(
md5sum(
grep('-v', '^PIFM_HOST', OUR_SCRIPT)
), '{print $1}'
)
if str(server_sum) != str(local_sum):
logging.info(
"server: {server}, local: {local}, should update.".format(
server=server_sum,
local=local_sum
)
)
with open(TMP_SCRIPT, 'w') as f:
f.write(str(server_file))
sed('-i',
"0,/def/ s#http://pi_director#{myhost}#".format(myhost=PIFM_HOST),
OUR_SCRIPT
)
status = python('-m', 'py_compile', TMP_SCRIPT)
if (status.exit_code == 0):
shutil.copy(TMP_SCRIPT, OUR_SCRIPT)
os.chmod(OUR_SCRIPT, 0755)
sys.exit(0)
def make_stats(self, rerun = False):
self.stats = {}
if os.path.exists(self.out_dir + "mapper/"):
if os.path.exists(self.out_dir + self.name + "_stats.json") and not rerun:
print "Loading stats for", self.name
with open(self.out_dir + self.name + "_stats.json") as handle:
self.stats = json.load(handle)
else:
print "Computing stats for", self.name
self.stats['raw_reads'] = self.pairs
self.stats['output'] = self.out_dir
print "Computing raw number of paired-reads"
self.stats['read_count'] = int(sh.zgrep("-Ec", "$", self.reads))/4
print "Computing clean number of paired-reads"
self.stats['clean_read_count'] = int(sh.grep("-Ec", "$", self.reads.replace("fastq.gz","clean.fastq")))/4
self.stats['ratios'] = float(self.stats['clean_read_count'])/float(self.stats['read_count'])
for k in tqdm(self.success_ks):
self.stats[k] = {}
self.stats[k]['Success'] = os.path.exists(self.out_dir + "ray_" + str(k) + "/Contigs.fasta")
if self.stats[k]['Success']:
t=sh.assemstats(0,self.out_dir + "ray_" + str(k) + "/Contigs.fasta" )
self.stats[k]['Assembly'] = {a:b for a,b in zip(*[[w.strip() for w in l.split("\t")][1:] for l in str(t).split("\n")[0:2]])}
self.stats[k]['mapped_frac'] = float(sh.grep("overall", self.out_dir + "map_" + str(k) + ".err").split(" ")[0][0:-1])/100
self.stats[k]['dupli_frac'] = float(sh.grep("Unknown", self.out_dir + "mapper/ray_" +str(k)+ "_" + self.name+ "-smd.metrics").split("\t")[7])
with open(self.out_dir + self.name + "_stats.json", 'w') as handle:
json.dump(self.stats, handle)
def assert_hg_count(count, rev=None):
'''Assuming you are in an hg repository, assert that ``count`` commits
have been made to that repo.'''
if rev:
assert sh.grep(sh.hg.log(rev=rev), 'changeset:').stdout.count(b'\n') == count
else:
assert sh.grep(sh.hg.log(), 'changeset:').stdout.count(b'\n') == count
def assert_hg_count(count, rev=None):
"""Assuming you are in an hg repository, assert that ``count`` commits
have been made to that repo."""
if rev:
assert sh.grep(sh.hg.log(rev=rev), "changeset:").stdout.count(b"\n") == count
else:
assert sh.grep(sh.hg.log(), "changeset:").stdout.count(b"\n") == count
def check_if_running_polkit_auth():
"""
check if polkit authentication agent is running
and launch it if it is not
"""
try:
grep(ps('aux'), '[p]olkit-gnome-authentication-agent-1')
except sh.ErrorReturnCode_1:
logger.debug('polkit auth agent not found, trying to launch it...')
run_polkit_auth_agent()
def parse_rdf(self):
""" cat|grep's the rdf file for minimum metadata
"""
# FIXME: make this an rdf parser if I can
_title = sh.grep(sh.cat(self.rdf_path), 'dcterms:title', _tty_out=False)
try:
_author = sh.grep(sh.cat(self.rdf_path), 'name', _tty_out=False)
self.author = self._clean_properties(_author)
except sh.ErrorReturnCode_1:
self.author = "Various"
self.title = self._clean_properties(_title)
def _info_celery(self):
d = {}
try:
lines = sh.grep(
sh.grep(self._ps(), "celery"), "worker").split("\n")[:-1]
for line in lines:
(pid, command) = line.lstrip().split(" ", 1)
d[pid] = line
except:
pass
return d
def find_process_pid(process_line, child_process=False):
ps_opts = 'auxww' if not child_process else 'auxfww'
try:
pid = sh.awk(
sh.grep(
sh.grep(sh.ps(ps_opts, _piped=True, _tty_out=False), "-ie", process_line),
'-v', 'grep'),
"{print $2}",
)
except sh.ErrorReturnCode:
raise AssertionError("Cannot find process pid")
return pid.strip()
def cache_ssh_key(hostname):
"""
Request the host's key and cache it in .ssh/known_hosts
http://serverfault.com/questions/321167/add-correct-host-key-in-known-hosts-multiple-ssh-host-keys-per-hostname
"""
try:
sh.grep('-q', hostname, SSH_KNOWN_HOSTS)
except sh.ErrorReturnCode:
with open(SSH_KNOWN_HOSTS, 'ab') as known_hosts_file:
known_hosts_file.write('\n')
keyscan = sh.Command('ssh-keyscan')
keyscan('-t', 'rsa', hostname, _out=known_hosts_file)
def findContainer(name):
container=""
try:
container = sh.awk("{print $1}", _in=sh.head("-n 1", _in=sh.grep(name, _in=sh.docker.ps())))
except:
print "container not available"
return container.rstrip()
def get(self):
query = unquote(self.get_argument('q'))
try:
results = str(grep('-R', '--exclude-dir', '.git', query,
self.settings.repo))
except ErrorReturnCode_1 as e:
results = ''
try:
results += str(find(self.settings.repo, '-type', 'f', '-name',
'*' + query + '*', '-not', '(', '-path',
'%s/%s/*' % (self.settings.repo, '.git') ))
except ErrorReturnCode_1 as e:
pass
results = results.replace(self.settings.repo, '').split('\n')[:-1]
formatted_results = []
for result in results:
if 'Binary file' in result or result == '':
continue
# TODO this doesn't play well with colons in filenames
stuff = result.split(':')
filename = stuff[0]
if path.basename(filename).startswith('.'):
filename = path.join(path.dirname(filename),
path.basename(filename)[1:])
string = ''.join(stuff[1:])
string = self._highlight(string, query)
formatted_results.append({'filename': filename, 'string': string})
self.render('search.html', query=query, results=formatted_results)
def ip_adresses():
"""
IP Host und Device auslesen bzw setzen
"""
check = sh.ifconfig
check = sh.grep("inet")
print check
def get_free_mb(folder):
df_result = grep(df("-k", folder), "/")
kb_sizes = map(int, filter(is_int, df_result.split(" ")))
available_mb = kb_sizes[2] / 1024
return available_mb
def findImage(repository, tag):
container=""
try:
container = sh.awk("{print $3}", _in=sh.head("-n 1", _in=sh.grep(tag, _in=sh.docker("images", repository))))
except:
print "container not available"
return container.rstrip()
def check_if_needed(path):
if path[-6:] == '_r.MOV':
return False
file_name, ext = os.path.splitext(path)
conv_name = os.path.join(WORKDIR, file_name + '_r' + ext)
if os.path.isfile(conv_name):
return False
try:
result = grep(grep(mediainfo(path), i='Rotation'), '180')
except sh.ErrorReturnCode_1 as e:
return False
return True
def _get_last_two_deploys(environment):
import sh
git = sh.git.bake(_tty_out=False)
pipe = git('tag')
pipe = sh.grep(pipe, environment)
pipe = sh.sort(pipe, '-rn')
pipe = sh.head(pipe, '-n2')
return pipe.strip().split('\n')
def force_push(git, branch):
try:
git.push('origin', branch, '--force')
except sh.ErrorReturnCode_128 as e:
# oops we're using a read-only URL, so change to the suggested url
line = sh.grep(' Use ', _in=e.stderr)
edit_url = line.strip().split()[1]
git.remote('set-url', 'origin', edit_url)
git.push('origin', branch, '--force')
def get_vendor(mac):
if not mac:
return None
grepped = grep(
mac.upper().replace(':','')[:6],
OUI_FILE,
_ok_code=[0,1]
)
return str(grepped)[7:] or '<unknown vendor>'
def get_node_ip():
"""Returns the node's IP, for the interface
that is being used as the default gateway.
This should work on both MacOS X and Linux."""
try:
default_interface = grep(netstat('-nr'), '-e', '^default', '-e' '^0.0.0.0').split()[-1]
my_ip = ifaddresses(default_interface)[2][0]['addr']
return my_ip
except:
raise Exception("Unable to resolve local IP address.")
def refresh(self):
self.vms = {}
lines = grep (nova("list"), "|").split("\n")[1:-1]
for line in lines:
line = line[2:-2]
(id, name, status, networks) = line.split("|")
self.vms[id] = {"id": id.strip(),
"name":name.strip(),
"status":status.strip(),
"networks": networks.strip()}
def get_remote_branches(origin, git=None):
git = git or get_git()
branches = [
line.strip().replace('origin/HEAD -> ', '')[len(origin) + 1:]
for line in
sh.grep(
git.branch('--remote'), r'^ {}'.format(origin)
).strip().split('\n')
]
return branches
def has_line(path, line):
"""
Check if a certain file has a given line.
"""
from sh import grep
# Check if we have the option already in /etc/sudoers
# http://man.cx/grep#heading14 -> 1 == no lines
grep_status = grep(line, path, _ok_code=[0, 1]).exit_code
return grep_status == 0
def get_unmerged_remote_branches(git=None):
git = git or get_git()
try:
lines = sh.grep(
git.branch('--remote', '--no-merged', 'origin/master'),
'^ origin',
).strip().split('\n')
except sh.ErrorReturnCode_1:
lines = []
branches = [line.strip()[len('origin/'):] for line in lines]
return branches
def dhclient(iface, enable, script=None):
# Disable the dhcp client and flush interface
try:
dhclients = sh.awk(
sh.grep(
sh.grep(sh.ps("ax"), iface, _timeout=5),
"dhclient", _timeout=5),
"{print $1}")
dhclients = dhclients.split()
for dhclient in dhclients:
sh.kill(dhclient)
except Exception as e:
_logger.info("Failed to stop dhclient: %s" % e)
pass
if enable:
if script:
sh.dhclient("-nw", "-sf", script, iface, _bg=True)
else:
sh.dhclient("-nw", iface, _bg=True)
def __get_host_count(self, host_type=""):
"""
Get the current number of VMs running that match
host_type string
"""
hosts = 0
if host_type:
hosts = sh.wc(sh.awk(sh.grep(sh.virsh('list', '--all'), '%s' % host_type), '{print $2}'), '-l')
else:
sys.exit("Can't count non-existant host_type")
return str(hosts).rstrip()
def device_list():
"""
Get udid from iPhone and iPad plugged into the computer
Returns a list
"""
# TODO: separate iPhone and iPad
raw = sh.sed(sh.system_profiler("SPUSBDataType"), "-n", "-e",
'/iPad/,/Serial/p', "-e", '/iPhone/,/Serial/p')
devices = sh.awk(
sh.grep(raw, "Serial Number:"), "-F", ": ", "{print $2}").split('\n')
return [device for device in devices if device]
def monitor_publisher_size():
#ps aux | grep publish | awk '{print $6}'
from sh import ps, grep, pkill
try:
psinfo = grep(ps('aux'), 'publish')
mem_used = int(psinfo.strip().split()[5])
print 'mem_publish:', mem_used
if mem_used >= 1 * 1024 * 1024: #(1G = 1*1024*1024K)
pkill('-f', 'publish.py')
except Exception:
import traceback
traceback.print_exc()
def get_cmd_from_ps(needle):
result = sh.grep(sh.cat(sh.ps('-wwaeopid,cmd')), needle)
if result.exit_code == 0:
for line in result.stdout.split('\n'):
line = line.strip()
if not line:
continue
match = re.search(r'^(\d*)\s*(.*)', line)
if match.group(2).startswith('grep'):
continue
return match.group(2)
raise KeyError('Failed to find: %s' % needle)
def get_commit_files(file_type):
system("git diff --cached --name-status > /tmp/git_hook")
files = awk(
grep(
cat("/tmp/git_hook"), "-P", "A|M.*.%s$" % file_type,
_ok_code = [0, 1]
), "{print $2}", _iter = True
)
exten = ".%s" % file_type
return [path[:path.rindex(exten) + len(exten)] for path in files]
def ir_get_dev(self):
"""
get real ir device.
"""
try:
out = sh.grep(sh.dmesg(), IR_MODULE, _iter = True)
count = len(out)
if count > 0 and out.exit_code == 0:
lines = filter(lambda x : x, out.stdout.split("\n"))
last_line = lines[-1].split(IR_MODULE + " as")
if len(last_line) > 1:
path = "/sys" + last_line[-1].strip() + "/event1/uevent"
out = sh.grep("DEVNAME", path, _iter = True)
if out > 0 and out.exit_code == 0:
lines = filter(lambda x : x, out.stdout.split("\n"))
last_line = lines[-1].split("=")
if len(last_line) > 1:
dev = "/dev/" + last_line[-1].strip()
return dev
return None
except Exception, e:
return None
def remote_url(git, remote, original="origin"):
origin_url = sh.grep(git.remote("-v"), original).split()[1]
repo_name = origin_url.rsplit("/", 1)[1]
return "https://github.com/{}/{}".format(remote, repo_name)
out = 'csv/time.csv'
t0 = 0
with open(out, 'w+') as f:
f.write("P\tmean\trel-err\tspeedup\tefficiency\n")
for P in P_list:
name = 'P{}'.format(P)
out = 'out/' + name
try:
#sh.tail('-1', sh.grep('^stats', out), _out=buf)
buf = StringIO()
sh.tail(sh.grep('^stats', out), '-1', _out=buf)
line = buf.getvalue()
except:
line = ""
if line == "": continue
mean = float(get_field(line, "mean"))
sem = float(get_field(line, "sem"))
rel_error = sem * 1.96 / mean
if P == 1:
speedup = 1
t0 = mean
else:
speedup = t0 / mean
def get_subclasses(name):
try:
res = sh.grep("-r", str("@interface \w* : " + name), ".")
return len(res.splitlines())
except:
return 0
def __init__(self):
"""Loads dynamic libraries"""
try:
if 'LIBCASM' in os.environ:
libcasm_path = os.environ['LIBCASM']
else:
casm_path = find_executable('ccasm')
if platform == 'darwin':
libcasm_path = sh.grep(sh.otool('-L', casm_path),
'libcasm').split()[0]
libcasm_path = libcasm_path.replace(
'@loader_path', dirname(casm_path))
else:
libcasm_path = sh.grep(sh.ldd(casm_path),
'libcasm').split()[2]
libccasm_path = libcasm_path.replace('libcasm', 'libccasm')
self.lib_casm = ctypes.CDLL(libcasm_path,
mode=ctypes.RTLD_GLOBAL)
self.lib_ccasm = ctypes.CDLL(libccasm_path,
mode=ctypes.RTLD_GLOBAL)
except Exception as e:
print("\n~~~ Error loading casm libraries ~~~")
if 'LIBCASM' in os.environ:
libcasm_path = os.environ['LIBCASM']
print("Looking for libcasm at LIBCASM:", libcasm_path)
if not os.path.exists(libcasm_path):
print("File does not exist")
print(
"Install CASM if it is not installed, or update your PATH, or set LIBCASM to the location of libcasm."
)
else:
print(
"File exists, but for unknown reason could not be loaded."
)
else:
casm_path = find_executable('ccasm')
print("find_executable('ccasm'):", casm_path)
if casm_path is None:
print(
"Could not find 'ccasm' executable. CASM is not installed on your PATH."
)
print(
"Install CASM if it is not installed, or update your PATH, or set LIBCASM to the location of libcasm."
)
elif basename(dirname(casm_path)) == ".libs":
print(
"Found 'ccasm' executable in a '.libs' directory. Are you running tests?"
)
if platform == 'darwin':
check = join(dirname(casm_path), "libcasm.dylib")
else:
check = join(dirname(casm_path), "libcasm.so")
if os.path.exists(check):
print("You probably need to set LIBCASM=" + check)
else:
print(
"You probably need to re-make or update your PATH"
)
else:
print(
"Found 'ccasm', but for unknown reason could not determine libcasm location."
)
if platform == 'darwin':
print("otool -L:")
res = sh.otool('-L', casm_path)
for val in res:
print(val.strip())
else:
print("ldd:")
res = sh.ldd(casm_path)
for val in res:
print(val.strip())
print("")
raise e
#### Argument types
self.lib_ccasm.casm_STDOUT.restype = ctypes.c_void_p
self.lib_ccasm.casm_STDERR.restype = ctypes.c_void_p
self.lib_ccasm.casm_nullstream.restype = ctypes.c_void_p
self.lib_ccasm.casm_ostringstream_new.restype = ctypes.c_void_p
self.lib_ccasm.casm_ostringstream_delete.argtypes = [
ctypes.c_void_p
]
self.lib_ccasm.casm_ostringstream_delete.restype = None
self.lib_ccasm.casm_ostringstream_size.argtypes = [ctypes.c_void_p]
self.lib_ccasm.casm_ostringstream_size.restype = ctypes.c_ulong
self.lib_ccasm.casm_ostringstream_strcpy.argtypes = [
ctypes.c_void_p,
ctypes.POINTER(ctypes.c_char)
]
self.lib_ccasm.casm_ostringstream_strcpy.restype = ctypes.POINTER(
ctypes.c_char)
self.lib_ccasm.casm_primclex_null.argtypes = None
self.lib_ccasm.casm_primclex_null.restype = ctypes.c_void_p
self.lib_ccasm.casm_primclex_new.argtypes = [
ctypes.c_char_p, ctypes.c_void_p, ctypes.c_void_p
]
self.lib_ccasm.casm_primclex_new.restype = ctypes.c_void_p
self.lib_ccasm.casm_primclex_delete.argtypes = [ctypes.c_void_p]
self.lib_ccasm.casm_primclex_delete.restype = None
self.lib_ccasm.casm_primclex_refresh.argtypes = [
ctypes.c_void_p, ctypes.c_void_p, ctypes.c_void_p,
ctypes.c_bool, ctypes.c_bool, ctypes.c_bool, ctypes.c_bool,
ctypes.c_bool
]
self.lib_ccasm.casm_primclex_refresh.restype = None
self.lib_ccasm.casm_command_list.argtypes = [ctypes.c_void_p]
self.lib_ccasm.casm_command_list.restype = None
self.lib_ccasm.casm_capi.argtypes = [
ctypes.c_char_p, ctypes.c_void_p, ctypes.c_char_p,
ctypes.c_void_p, ctypes.c_void_p
]
self.lib_ccasm.casm_capi.restype = ctypes.c_int
def count(self):
if self.gziped: return int(sh.zgrep('-c', "^+$", self.fwd_path, _ok_code=[0,1]))
else: return int(sh.grep('-c', "^+$", self.fwd_path, _ok_code=[0,1]))
sep=" ",
file=sys.stderr)
elif args.Extract == True:
print("Detected",
len(Samples),
"individuals for EXTRACTION.",
sep=" ",
file=sys.stderr)
#Get sample index in geno and ind files.
Index = {}
Sex = {}
Pop = {}
for i in Samples:
for line in sh.grep(sh.cat("-n", args.indFn),
"{}".format(i),
_ok_code=[0, 1]):
fields = line.strip().split()
if fields[1] == i:
Index[fields[1]] = (int(fields[0]) - 1)
Sex[fields[1]] = fields[2]
Pop[fields[1]] = fields[3]
print("Indexed", len(Index), "individuals.", sep=" ", file=sys.stderr)
IndOutFile = open(args.Output + ".ind", "w")
GenoOutFile = open(args.Output + ".geno", "w")
SnpOutFile = open(args.Output + ".snp", "w")
#Extract function
if args.Extract == True:
print('-' * 50)
from sh import ls, glob
print(ls('-ld', glob('/etc/pr*')))
print('-' * 50)
w = sh.who()
print(w)
print('-' * 50)
disk_usage = sh.df('-h')
print(disk_usage)
print('-' * 50)
from sh import uname
print(uname())
print(uname('-a'))
print(uname(a=True))
print('-' * 50)
from sh import grep, wc
# grep 'sh' /etc/passwd | wc -l
print(grep('sh', '/etc/passwd'))
print(wc(grep('sh', '/etc/passwd'), l=True))
print('-' * 50)
from sh import tr
fruits = 'apple banana mango orange'.split()
print(tr("[:lower:]", "[:upper:]", _in=fruits))
def searchUser(self):
#由于可能会遇到新入职的老师还没有开通邮箱，此时传入的字段为空，则应该跳过
if self.username != 'None' and self.username != '' and self.username is not None:
#添加部门属性ldif文件
add_DEPART_LDAP_TPL = DEPART_LDAP_TPL.format_map(
{'depart_name': self.departName})
with open('/tmp/temp_depart.ldif', 'w',
encoding='utf-8') as file_handler:
file_handler.write(add_DEPART_LDAP_TPL)
try:
departadd_res = sh.ldapadd('-x', '-D',
'cn=root,dc=limikeji,dc=com', '-w',
'limikeji', '-f',
'/tmp/temp_depart.ldif')
print(departadd_res)
except sh.ErrorReturnCode_68:
# 当部门已近存在的时候会触发一个错误的退出，退出的code为68，不过即使重复添加也没有什么问题，因此这里直接pass掉不做任何处理
pass
#查询过滤LDAP
try:
ldap_res = sh.grep(
sh.ldapsearch('-x', '-D', 'cn=root,dc=limikeji,dc=com',
'-w', 'limikeji', 'uid=%s' % self.username),
'mail').stdout.decode('utf-8')
except sh.ErrorReturnCode_1:
new_USER_LDAP_TPL = USER_LDAP_TPL.format_map({
'username':
self.username,
'userid':
str(self.userid).lstrip('0').replace(
'-', '9'
), #因为取钉钉上的userid，但是ldap添加人员信息uid不能0开始，部分userid还有'-'这个符号
'useralias':
self.useralias,
'SSHA':
'{SSHA}'
})
with open(
'/alidata/scripts/ldap/log/users/new_user/new_user_%s'
% time.strftime('%Y-%m-%d', time.localtime()),
'a',
encoding='utf-8') as file_handler:
file_handler.write(
'新增人员姓名:{},userid:{},useralias:{},departname:{}'.
format(self.username, self.userid, self.useralias,
self.departName) + '\n')
with open('/tmp/temp_user.ldif', 'w',
encoding='utf-8') as file_handler:
file_handler.write(new_USER_LDAP_TPL)
try:
adduser_res = sh.ldapadd('-x', '-D',
'cn=root,dc=limikeji,dc=com',
'-w', 'limikeji', '-f',
'/tmp/temp_user.ldif')
# print(adduser_res)
# 添加以及更新人员部门属性信息
new_ATTR_MODIFY = ATTR_MODIFY.format_map({
'depart_name':
self.departName,
'username':
self.username
})
add_ATTR_MODIFY_ALL = ATTR_MODIFY_ALL.format_map(
{'username': self.username})
with open('/tmp/temp_user_attr_modify.ldif',
'w',
encoding='utf-8') as file_handler:
file_handler.write(new_ATTR_MODIFY)
with open('/tmp/temp_user_Azu.ldif', 'w',
encoding='utf-8') as file: # 添加新增人员到一个大组
file.write(add_ATTR_MODIFY_ALL)
try:
addzu_res = sh.ldapadd(
'-x', '-D', 'cn=root,dc=limikeji,dc=com', '-w',
'limikeji', '-f',
'/tmp/temp_user_attr_modify.ldif')
# print(addzu_res)
except sh.ErrorReturnCode_20 or sh.ErrorReturnCode_20 as error:
# ldap_modify: Type or value exists (20)
print(
'\033[0;36;40ml add %s faild Invalid syntax (21)\033[0m'
% self.username)
print(
'\033[0;36;40mldap_modify: Type or value exists (20)\033[0m'
)
try:
azu_res = sh.ldapadd('-x', '-D',
'cn=root,dc=limikeji,dc=com',
'-w', 'limikeji', '-f',
'/tmp/temp_user_Azu.ldif')
# print(azu_res)
except sh.ErrorReturnCode_20 as error:
# ldap_modify: Type or value exists (20)
print(
'\033[0;36;40mldap_modify: Type or value exists (20),添加到A组失败 \033[0m'
)
except sh.ErrorReturnCode_21 as error:
# ldap_add: Invalid syntax (21)
print(str(error))
else:
pass
with open('/alidata/scripts/ldap/log/users/new_user/new_user_%s' %
time.strftime('%Y-%m-%d', time.localtime()),
'a',
encoding='utf-8') as file_handler:
file_handler.write(
'新增失败人员姓名:{},userid:{},useralias:{},departname:{}'.format(
self.username, self.userid, self.useralias,
self.departName) + '\n')
def delete_Depart_User(self):
try:
ldap_res = sh.cut(
sh.cut(
sh.cut(
sh.grep(
sh.ldapsearch('-x', '-D',
'cn=root,dc=limikeji,dc=com', '-w',
'limikeji',
'cn=%s' % self.departName), 'uid'),
'-d', ' ', '-f2'), '-d', ',', '-f1'), '-d', '=',
'-f2').stdout.decode('utf-8')
ldap_resList = str(ldap_res).split('\n')[:-1] #部门所有的人员姓名
if 'test' in ldap_resList:
ldap_resList.remove('test')
# print('删除组%s'%self.departName)
# 再删除部门中的用户，如果只是删除用户的话，那么部门中仍然可以看到用户，只是用户的dn是不可用的
for user in ldap_resList:
try:
ldap_res = sh.grep(
sh.ldapsearch('-x', '-D',
'cn=root,dc=limikeji,dc=com', '-w',
'limikeji', 'uid=%s' % user),
'mail').stdout.decode('utf-8')
# print(ldap_res)
except sh.ErrorReturnCode_1:
with open('/tmp/temp_user_delete_attr.ldif',
'w',
encoding='utf-8') as file_handler:
file_handler.write(
ATTR_DELETE_MODIFY.format_map({
'depart_name':
self.departName,
'username':
user
}))
sh.ldapadd('-x', '-D', 'cn=root,dc=limikeji,dc=com',
'-w', 'limikeji', '-f',
'/tmp/temp_user_delete_attr.ldif')
else:
# print('删除组%s' % self.departName)
# 再删除部门中的用户，如果只是删除用户的话，那么部门中仍然可以看到用户，只是用户的dn是不可用的，显示结果为一个红叉
for user in ldap_resList:
try:
ldap_res = sh.grep(
sh.ldapsearch('-x', '-D',
'cn=root,dc=limikeji,dc=com', '-w',
'limikeji', 'uid=%s' % user),
'mail').stdout.decode('utf-8')
# print(ldap_res)
except sh.ErrorReturnCode_1:
with open('/tmp/temp_user_delete_attr.ldif',
'w',
encoding='utf-8') as file_handler:
file_handler.write(
ATTR_DELETE_MODIFY.format_map({
'depart_name':
self.departName,
'username':
user
}))
sh.ldapadd('-x', '-D', 'cn=root,dc=limikeji,dc=com',
'-w', 'limikeji', '-f',
'/tmp/temp_user_delete_attr.ldif')
except sh.ErrorReturnCode_1:
pass
time.sleep(1)
## Step 4
## Configure radvd to use that prefix
print('Creating radvd.conf')
with open(HOMEDIR + '/radvd.conf.in') as fin:
conf = fin.read()
confout = conf.replace('%PREFIX%', prefix)
confout = confout.replace('%INTERFACE%', BORDERROUTER_INTERFACE)
with open(HOMEDIR + '/radvd.conf', 'w') as fout:
fout.write(confout)
## Step 5
## Run the BorderRouter
try:
out = grep(ps('-A'), 'BorderRouterC')
print('BorderRouter already running.')
print('Killing BorderRouter...')
sudo.pkill('-9', 'BorderRouterC')
except Exception:
pass
print('Starting Border Router.')
subprocess.call([
"screen", "-d", "-m", "-S", "border-router", "sudo",
HOMEDIR + "/BorderRouterC", '-i', BORDERROUTER_INTERFACE
])
time.sleep(5)
## Step 6
## Run radvd
import sh
print(sh.wpa_cli("-i", "wlan0", "list_networks"))
search1 = "SmashCam01"
networkNum = sh.cut(sh.grep(sh.wpa_cli("-i", "wlan0", "list_networks"), search1), "-f", "1")
sh.wpa_cli("-i", "wlan0", "select_network", networkNum)
print(sh.wpa_cli("-i", "wlan0", "list_networks"))
def getErrorLogs(project):
"""
Récupération des logs d"erreurs
===============================
Author: Fabien Bellanger
:param project: Nom du projet
:type project: string
:return: Une chaîne de caractères contenant les erreurs
:rtype: string
"""
filePath = getFileName(project)
oldFilePath = filePath + ".1"
error = {}
filesToRead = []
# Les fichiers de log doivent exister et ne doivent pas être vide
# ---------------------------------------------------------------
if path.isfile(filePath) and path.getsize(filePath) != 0:
filesToRead.append(filePath)
if path.isfile(oldFilePath) and path.getsize(oldFilePath) != 0:
filesToRead.append(oldFilePath)
if len(filesToRead) > 0:
buffer = StringIO()
linesArray = []
lineArray = {}
linesNumber = 0
for fileToRead in filesToRead:
try:
for line in sh.grep(config.GREP_PATTERN, fileToRead):
# On parse la chaîne pour extraire la date, l'heure et le message
# ---------------------------------------------------------------
matchObject = re.match(config.GREP_REGEX, line, re.M|re.I)
if matchObject:
date = matchObject.group(1)
time = matchObject.group(2)
client = matchObject.group(4) if (matchObject.group(4)) else ""
server = matchObject.group(5) if (matchObject.group(5)) else ""
request = matchObject.group(6) if (matchObject.group(6)) else ""
upstream = matchObject.group(7) if (matchObject.group(7)) else ""
host = matchObject.group(8) if (matchObject.group(8)) else ""
if matchObject.group(3):
message = matchObject.group(3)
elif matchObject.group(9):
message = matchObject.group(9)
# Un message est-il déjà dans le tableau ?
currentIndex = 0
linesArrayNumber = len(linesArray)
while not (currentIndex == linesArrayNumber or linesArray[currentIndex]["message"] == message):
currentIndex += 1
if currentIndex == linesArrayNumber:
# Pas de message trouvé, on ajoute au tableau
lineArray = {
"date": date,
"timeStart": time,
"message": message,
"timeEnd": time,
"number": 1,
}
linesArray.append(lineArray)
else:
# On modifie l'heure de fin et le compteur
linesArray[currentIndex]["timeEnd"] = time
linesArray[currentIndex]["number"] += 1
# Nombre de lignes total
linesNumber += 1
except sh.ErrorReturnCode_1:
print(Fore.RED + "[Erreur]",
Fore.GREEN + "{:<30s}" . format("[" + project + "]"),
Style.RESET_ALL + " : Fichier non trouvé ou vide ou bien pas de résultat")
except sh.ErrorReturnCode_2:
print(Fore.RED + "[Erreur]",
Fore.GREEN + "{:<30s}" . format("[" + project + "]"),
Style.RESET_ALL + " : Fichier non trouvé ou vide ou bien pas de résultat")
# Ajout à la chaîne de caractères d'erreurs globale
# -------------------------------------------------
error = displayProject(project, linesNumber, linesArray)
else:
print(Fore.RED + "[Erreur]",
Fore.GREEN + "{:<30s}" . format("[" + project + "]"),
Style.RESET_ALL + " : Fichiers non trouvés ou vides")
return error
def register_error_in_database(self, session: Session):
"""
This methode create database object associated to the statification with the result of the log
that scrapy has generated.
:param session
:raise NoResultFound if there is no statification with empty commit sha
"""
# finalization of the statification by removing unwanted files and directories and empty directories
self.delete_files()
self.delete_directories()
self.delete_empty_directories()
# get the statification with empty commit
statification = Statification.get_statification(session, '')
# open the log file that contain scrapy errors
f_file = open(self.s_log_file)
expecting_other_line_for_error_message = False
s_error_message = ''
# for each line will look for information that will be used to fill object of the database
for line in f_file:
# check if the line contain a warning or a info
if re.match('(.*)WARNING(.*)', line) or re.match(
'(.*)INFO(.*)', line) or re.match('(.*) ERROR:(.*)', line):
expecting_other_line_for_error_message = False
if expecting_other_line_for_error_message:
s_error_message += line
if (not expecting_other_line_for_error_message
) and s_error_message != '':
statification.add_object_to_statification(
ScrapyError, session, s_error_message)
s_error_message = ''
# in the case the line match an External link
if re.match('(.*) INFO: External link detected(.*)', line):
# we get the second part of the line there are also [] in the first part
s_trunked_line = line[line.index('INFO: External link detected'
):len(line)]
# we get the position of begining of the URL
i_start_url = s_trunked_line.index('[')
# we ge the position of the end of the URL
i_end_url = s_trunked_line.index(']')
# we get the position of the begining of the source url
i_start_source = s_trunked_line.index(' in ') + 4
try:
# we create and add a new ExtenalLink to our statification
statification.add_object_to_statification(
ExternalLink, session,
s_trunked_line[i_start_source:len(s_trunked_line)],
s_trunked_line[i_start_url + 1:i_end_url])
except ValueError as e:
self.logger.info(e)
# in the case the line match a Scrapy Error
elif re.match('(.*) ERROR:(.*)', line):
expecting_other_line_for_error_message = True
# retrieve the Scrapy Error
s_trunked_line = line[line.index('ERROR: ') + 7:len(line)]
s_error_message += s_trunked_line
# in the case the line match an error for type MIME
elif re.match('(.*) WARNING: Forbidden content (.*)', line):
# we get the second part of the line where begin the information that interest us
s_trunked_line = line[line.index('WARNING: Forbidden content '
):len(line)]
# get the starting position of the Error type MIME
i_start_error_mime = s_trunked_line.index('[')
# get the end position of the error type MIME
i_end_error_mime = s_trunked_line.index(']')
# get the error type MIME
s_error_mime = s_trunked_line[i_start_error_mime +
1:i_end_error_mime]
# get the source of the error
s_source_link = s_trunked_line[s_trunked_line.
index('detected in') +
12:len(s_trunked_line)]
try:
# create an ErrorTypeMIME associated to the statification
statification.add_object_to_statification(
ErrorTypeMIME, session, s_error_mime, s_source_link)
except ValueError as e:
self.logger.info(e)
# in the case the line match an HTTP error
elif re.match('(.*) WARNING: HTTP error (.*)', line):
# we get the second part of the line where begin the information that interest us
s_trunked_line = line[line.index('WARNING: HTTP error '
):len(line)]
# we get the starting position of the Error Code
i_start_error_code = s_trunked_line.index('[')
# we get the end position of the Error Code
i_end_error_code = s_trunked_line.index(']')
# we get the start position of the url source of the error
i_start_url = s_trunked_line.index(' for ')
# we get the end position of the url source of the error
i_end_url = s_trunked_line.index(' from ')
# we retrieve the error code
s_error_code = s_trunked_line[i_start_error_code +
1:i_end_error_code]
# we retrieve the url that cause the error
s_url = s_trunked_line[i_start_url + 5:i_end_url]
# we retrieve the url of the source where was found the url that caused the error
s_url_source = s_trunked_line[i_end_url +
6:len(s_trunked_line) - 1]
try:
# we create a new HtmlError associated to the statification
statification.add_object_to_statification(
HtmlError, session, s_error_code, s_url, s_url_source)
except ValueError as e:
self.logger.info(e)
elif re.match('(.*)response_received_count(.*)', line):
# we get the second part of the line where begin the information that interest us
s_value_item_scraped_count = line[line.index(': ') +
2:line.index(',')]
try:
# set the number of crawled item into the statification object
statification.upd_nb_item(session, statification.commit,
int(s_value_item_scraped_count))
except ValueError as e:
self.logger.info(e)
try:
# retrieve the list of type file with number of file for each type
s_result_type_files = sh.uniq(
sh.sort(
sh.grep(
sh.find(sh.glob(self.s_repository_path + '/*'),
'-type', 'f'), '-o', '-E', '\.[a-zA-Z0-9]+$')),
'-c')
# the result is a string so we need to get a table,
# here we get a table made of each line returned, we remove all space
a_table_result_type_files = s_result_type_files.replace(
' ', '').split('\n')
# browse the line of result
for row in a_table_result_type_files:
if row:
# a line is composed of a number followed by a type like "42.png",
# we separate the number and the type
s_type_file = row.split('.')
try:
# create a new ScannedFile associated to the statificaiton
statification.add_object_to_statification(
ScannedFile, session, s_type_file[1],
int(s_type_file[0]))
except ValueError as e:
self.logger.info(e)
except sh.ErrorReturnCode_1:
self.logger.info('There is no folder in the static repository')
finally:
# in all case we need to close the file
f_file.close()
# change the status of the statification (NEED TO BE DONE AT THE END !!)
statification.upd_status(session, '', Status.STATIFIED)
from sh import uname, sed, dpkg, awk, grep
# Get our current kernel version
# $(uname -r | sed -r 's/-[a-z]+//')
kernel_version = sed(uname('-r'), '-r', 's/-[a-z]+//').strip()
print('kernel version:', kernel_version)
# get & filter package list
packages = \
grep(
awk(
dpkg('-l', 'linux-image-[0-9]*', 'linux-headers-[0-9]*', _env={'COLUMNS': '200'}),
'/ii/{print $2}'
),
'-ve',
kernel_version
)
print(packages.strip())
def _on_poll(self, param):
action_result = self.add_action_result(phantom.ActionResult(dict(param)))
ret_val, resp_json = self._make_slack_rest_call(action_result, consts.SLACK_AUTH_TEST, {})
if not ret_val:
return ret_val
bot_id = resp_json.get('user_id')
if not bot_id:
return action_result.set_status(phantom.APP_ERROR, "Could not get bot ID from Slack")
pid = self._state.get('pid', '')
if pid:
try:
if 'slack_bot.pyc' in sh.ps('ww', pid): # pylint: disable=E1101
self.save_progress("Detected SlackBot running with pid {0}".format(pid))
return action_result.set_status(phantom.APP_SUCCESS, "SlackBot already running")
except:
pass
config = self.get_config()
bot_token = config.get('bot_token', '')
ph_auth_token = config.get('ph_auth_token', None)
if not ph_auth_token:
return action_result.set_status(phantom.APP_ERROR, "The ph_auth_token asset configuration parameter is required to run the on_poll action.")
app_version = self.get_app_json().get('app_version', '')
try:
ps_out = sh.grep(sh.ps('ww', 'aux'), 'slack_bot.pyc') # pylint: disable=E1101
if app_version not in ps_out:
old_pid = shlex.split(str(ps_out))[1]
self.save_progress("Found an old version of slackbot running with pid {}, going to kill it".format(old_pid))
sh.kill(old_pid) # pylint: disable=E1101
except:
pass
try:
if bot_token in sh.grep(sh.ps('ww', 'aux'), 'slack_bot.pyc'): # pylint: disable=E1101
return action_result.set_status(phantom.APP_ERROR, "Detected an instance of SlackBot running with the same bot token. Not going to start new instance.")
except:
pass
self.save_progress("Starting SlackBot")
ret_val, base_url = self._get_phantom_base_url_slack(action_result)
if phantom.is_fail(ret_val):
return ret_val
slack_bot_filename = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'slack_bot.pyc')
base_url += '/' if not base_url.endswith('/') else ''
proc = subprocess.Popen(['phenv', 'python2.7', slack_bot_filename, bot_token, bot_id, base_url, app_version, ph_auth_token])
self._state['pid'] = proc.pid
self.save_progress("Started SlackBot with pid: {0}".format(proc.pid))
return action_result.set_status(phantom.APP_SUCCESS, "SlackBot started")
def svnurl_for_path(path):
cd(path)
url = grep(svn.info(), "URL: ")
url = url.replace("URL: ", "").replace("\n", "")
return url
#!/usr/bin/python
# -*- coding: utf-8 -*-
import csv
import sys
from sh import grep,cat,awk
log_file = sys.argv[1]
file_name = sys.argv[2]
total_topology = ['3_clique','4_circle','4_clique','7_circle','7_clique','7_bridge','7_star']
txn_num = [5000,10000,15000,20000]
total_num = []
oret = awk(grep(grep(grep(cat('%s'%log_file),5000),'-v','configure'),'-v',15000),'{print $7}').split()
i = 0
for tps in oret:
tps_num = tps.replace('/s','')
total_num.append([5000,tps_num,total_topology[i]])
i+=1
for tx_nm in txn_num[1:]:
oret = awk(grep(grep(cat('%s'%log_file),tx_nm),'-v','configure'),'{print $7}').split()
i = 0
for tps in oret:
tps_num = tps.replace('/s', '')
total_num.append([tx_nm, tps_num, total_topology[i]])
i += 1
with open(file_name,"w") as csvfile:
writer = csv.writer(csvfile)
writer.writerow(['num_txn','TPS','cluster_size'])
writer.writerows(sorted(total_num,key=lambda stu:stu[2]))
def parse(filename, **kwargs):
# cat outfile | grep ip | cut -d '|' -f 2 | cut -d ' ' -f 3 | cut -d '.' -f 4 | sort -n | wc -l
return sh.sort(cut(cut(cut(grep(cat(filename), "ip"), d="|", f=2), d=" ", f=3), d=".", f=4), "-n", _out=kwargs.get("_out"))
from sh import grep, pwd, kate
import sys
print(pwd())
found = grep("-Frne", sys.argv[-1])
files = {occurence.split(":")[0] for occurence in found}
for file in files:
print("\t", file)
askopenall = input("Open all files ? (y/n)")
if askopenall == "y":
for file in files:
p = kate(file, _bg=True)
p.wait()
for file in files:
askopen = input("Open file %s ? (y/n)" % file) or "y"
if askopen == "y":
print("open")
try:
import sh
except ImportError:
import pip
pip.main(["install", "sh>=1.12"])
import sh
GRAPHENE_DIR = os.path.abspath("./graphene/")
# Copy config file
sh.cp("config/config.py", "sgx/config.py")
# Check if swig >= 3.0.10 is installed
try:
out = sh.grep(sh.dpkg("-s", "swig", "swig3.0"), '^Version:')
version = out.split(" ")[-1].split("-")[0]
except sh.ErrorReturnCode_1:
version = None
if not version:
exit("Error: Couldn't find swig")
if LooseVersion(version) < LooseVersion("3.0.10"):
exit(
"Error: swig version is lower than 3.0.10. Install swig 3.0.10 or higher."
)
# Check if apport is installed (it produces error messages when executing Python with Graphene)
try:
sh.dpkg("-s", "python3-apport")
exit("Error: python3-apport is installed. Please uninstall it.")
except sh.ErrorReturnCode_1:
inheritable_methods = get_inheritable_methods(superclass_headers)
superclass_methods = get_superclass_methods(superclass_headers)
nrOvMethods = 0
for method in methods:
if (method in inheritable_methods) or (method in superclass_methods):
nrOvMethods = nrOvMethods + 1
effCoupling = 0
with open(file_path, 'r') as f:
s = f.read()
matches = re.findall('#import \".*\.h\"', s)
effCoupling = len(matches) - 1
import_regexp = str("#import " + '"' + header_file_name + '"')
affCoupling = len(sh.grep("-r", import_regexp, ".").splitlines()) - 1
rfc = 0
with open(file_path, 'r') as f:
s = f.read()
matches = re.findall('\[', s)
rfc = len(matches) - 1
nsb = get_nesting_level(file_path)
lcom = get_lcom(file_path, header_file_path)
sub = get_subclasses(file_name[:-2])
print(
str(loc - nrComments) + "\t" + str(nrMethods) + "\t" + str(nrOvMethods) +
# Remove the duplicate case
if i > 1 and char == input_string[i - 1]:
continue
res.append(char)
get_jumble(input_string[:i] + input_string[i + 1:], dict_set, ret, res)
res.pop()
if __name__ == '__main__':
file_list = glob.glob('./dict/*')
dict_set = get_dict(file_list)
ret = []
input_string = raw_input("Enter a jumble:").lower()
# Sort the string to avoid duplicate
input_string = sorted(input_string)
get_jumble(input_string, dict_set, ret, [])
print ret
# The work below is irrelevant to the answer.
print '-' * 20
print 'This dictionary has so many single character that making me doubt my solution'
print "So here's the proof:"
import sh # You may need to sudo pip install sh
import os
cur_path = os.getcwd()
for result in ret:
print sh.grep('^%s$' % result, os.getcwd(), '-r')
#_*_ coding: utf-8 _*_
__version__ = '0.1'
import sh
check = sh.ifconfig
check = sh.grep("inet")
print check
def get_list_of_running_process():
process_name = sys.argv[1]
list_of_process = sh.grep(sh.ps('-aux', _piped=True), '-v', 'python')
return list_of_process
import sh as bada
x = bada.curl("http://ndtv.com", "-v")
print x
print("the number of files in my currenyt directory is : \n")
#print ( bada.wc(bada.find("/home/amardeep/"), "-l"))
print(bada.grep(bada.dmidecode(), "AMD"))
print("printing my current processor and memory information: \n")
print(bada.tail(bada.head("-n", 130, "dmi.txt"), "-n", 20))
print "getting current directory \n", bada.pwd()
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sh,os,sys
try:
sh.grep(sh.grep(sh.ps('ux'),'sslocal'),v='grep')
except Exception, e:
os.system("sslocal -c $HOME/.outwall/sslocal_config.json &")
finally:
command_string=' '.join(sys.argv[1:])
print command_string
os.system("$HOME/.outwall/proxychains-4.8.1/proxychains4 -f $HOME/.outwall/proxychains.conf "+command_string )
usage()
i = None
k = None
o = None
for opt, arg in opts:
if opt in ("-h", "--help"):
usage()
elif opt in ("-i", "--input"):
i = str(arg)
elif opt in ("-k", "--keyword"):
k = str(arg)
elif opt in ("-o", "--output"):
o = str(arg)
if not any(var is None for var in [i, k, o]):
return i, k, o
print("The parameters are not yet specified!")
usage()
def var_to_file(var_to_write, file_to_write):
file = open(file_to_write, 'w')
file.write(var_to_write)
file.close()
###################################################
inputFile, inputKeyWord, outputFile = main()
output = str(sh.head("-n 1", inputFile)) + str(sh.grep(inputKeyWord,
inputFile))
var_to_file(output, outputFile)
from sh import nova
from sh import grep
from pprint import pprint
print 70 * "-"
a = nova("list")
print a
print 70 * "-"
b = grep(a, "|")
print b
print 70 * "-"
c = b.split("\n")
print c
print 70 * "-"
lines = grep(nova("list"), "|").split("\n")
pprint(lines)
print " I am there"
lines = lines[1:-1]
pprint(lines)
print " I am here"
vms = {}
print 70 * "="
pprint(lines)
print 70 * "="
#!/usr/bin/env python
from sh import grep, netstat
print(grep(netstat('-an'), 'LISTEN')) # <1>
# boucle sur les fichiers récupérés
for filename in os.listdir(temp_dir):
if filename.endswith(".mp3"):
cnt_f = cnt_f + 1
# reencode pour prendre moins de place
subprocess.call([
'lame', '--mp3input', '-b', '32', temp_dir + "/" + filename,
temp_dir + "/B_" + filename
],
shell=False)
os.rename(temp_dir + "/B_" + filename, temp_dir + "/" + filename)
# construction des items à ajouter dans le feed.xml
titre = sh.cut(
sh.grep(
sh.ffprobe("-v", "error", "-show_format",
temp_dir + "/" + filename), "title"), "-d", "=",
"-f2")
titre = str(titre)
titre = titre.replace('\n', '')
fichier = open(temp_dir + "/" + "items.xml", "a")
fichier.write("<item>\n")
fichier.write("<title><![CDATA[" + titre + "]]></title>\n")
fichier.write(
"<link>https://raw.githubusercontent.com/tcaenen/tt_pod/master/media/"
+ filename + "</link>\n")
fichier.write(
'<enclosure url="https://raw.githubusercontent.com/tcaenen/tt_pod/master/media/'
+ filename +
'" length="30066338" type="audio/mpeg"></enclosure>\n')
fichier.write(
