def configure_analyst_opsvm():
'''
Configures Anaylyst for OPSVM
'''
if not service_running('plumgrid'):
restart_pg()
opsvm_ip = pg_gw_context._pg_dir_context()['opsvm_ip']
NS_ENTER = ('/opt/local/bin/nsenter -t $(ps ho pid --ppid $(cat '
'/var/run/libvirt/lxc/plumgrid.pid)) -m -n -u -i -p ')
sigmund_stop = NS_ENTER + '/usr/bin/service plumgrid-sigmund stop'
sigmund_status = NS_ENTER \
+ '/usr/bin/service plumgrid-sigmund status'
sigmund_autoboot = NS_ENTER \
+ '/usr/bin/sigmund-configure --ip {0} --start --autoboot' \
.format(opsvm_ip)
try:
status = subprocess.check_output(sigmund_status, shell=True)
if 'start/running' in status:
if subprocess.call(sigmund_stop, shell=True):
log('plumgrid-sigmund couldn\'t be stopped!')
return
subprocess.check_call(sigmund_autoboot, shell=True)
status = subprocess.check_output(sigmund_status, shell=True)
except:
log('plumgrid-sigmund couldn\'t be started!')
python类check_output()的实例源码
def service_running(service_name):
"""Determine whether a system service is running"""
if init_is_systemd():
return service('is-active', service_name)
else:
try:
output = subprocess.check_output(
['service', service_name, 'status'],
stderr=subprocess.STDOUT).decode('UTF-8')
except subprocess.CalledProcessError:
return False
else:
# This works for upstart scripts where the 'service' command
# returns a consistent string to represent running 'start/running'
if ("start/running" in output or "is running" in output or
"up and running" in output):
return True
# Check System V scripts init script return codes
if service_name in systemv_services_running():
return True
return False
def hugepage_support(user, group='hugetlb', nr_hugepages=256,
max_map_count=65536, mnt_point='/run/hugepages/kvm',
pagesize='2MB', mount=True, set_shmmax=False):
"""Enable hugepages on system.
Args:
user (str) -- Username to allow access to hugepages to
group (str) -- Group name to own hugepages
nr_hugepages (int) -- Number of pages to reserve
max_map_count (int) -- Number of Virtual Memory Areas a process can own
mnt_point (str) -- Directory to mount hugepages on
pagesize (str) -- Size of hugepages
mount (bool) -- Whether to Mount hugepages
"""
group_info = add_group(group)
gid = group_info.gr_gid
add_user_to_group(user, group)
if max_map_count < 2 * nr_hugepages:
max_map_count = 2 * nr_hugepages
sysctl_settings = {
'vm.nr_hugepages': nr_hugepages,
'vm.max_map_count': max_map_count,
'vm.hugetlb_shm_group': gid,
}
if set_shmmax:
shmmax_current = int(check_output(['sysctl', '-n', 'kernel.shmmax']))
shmmax_minsize = bytes_from_string(pagesize) * nr_hugepages
if shmmax_minsize > shmmax_current:
sysctl_settings['kernel.shmmax'] = shmmax_minsize
sysctl.create(yaml.dump(sysctl_settings), '/etc/sysctl.d/10-hugepage.conf')
mkdir(mnt_point, owner='root', group='root', perms=0o755, force=False)
lfstab = fstab.Fstab()
fstab_entry = lfstab.get_entry_by_attr('mountpoint', mnt_point)
if fstab_entry:
lfstab.remove_entry(fstab_entry)
entry = lfstab.Entry('nodev', mnt_point, 'hugetlbfs',
'mode=1770,gid={},pagesize={}'.format(gid, pagesize), 0, 0)
lfstab.add_entry(entry)
if mount:
fstab_mount(mnt_point)
def is_crm_leader(resource, retry=False):
"""
Returns True if the charm calling this is the elected corosync leader,
as returned by calling the external "crm" command.
We allow this operation to be retried to avoid the possibility of getting a
false negative. See LP #1396246 for more info.
"""
if resource == DC_RESOURCE_NAME:
return is_crm_dc()
cmd = ['crm', 'resource', 'show', resource]
try:
status = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
if not isinstance(status, six.text_type):
status = six.text_type(status, "utf-8")
except subprocess.CalledProcessError:
status = None
if status and get_unit_hostname() in status:
return True
if status and "resource %s is NOT running" % (resource) in status:
raise CRMResourceNotFound("CRM resource %s not found" % (resource))
return False
def config(scope=None):
"""Juju charm configuration"""
config_cmd_line = ['config-get']
if scope is not None:
config_cmd_line.append(scope)
else:
config_cmd_line.append('--all')
config_cmd_line.append('--format=json')
try:
config_data = json.loads(
subprocess.check_output(config_cmd_line).decode('UTF-8'))
if scope is not None:
return config_data
return Config(config_data)
except ValueError:
return None
def test_get_container_ip(containers):
"""
Asserts that when an existing container is queried for its IP it returns
the specified projects and services IP address.
"""
actual_ip = Containers.get_container_ip_address(
project=containers.project,
service=ZOOKEEPER,
timeout_seconds=5
)
container_id = Containers.get_container_info(
project=containers.project,
service=ZOOKEEPER
)['Id']
command = "docker inspect --format '{{{{ .NetworkSettings.IPAddress }}}}' {container_id}" \
.format(container_id=container_id)
expected_ip = subprocess.check_output([command], shell=True)
assert expected_ip.rstrip() == actual_ip
def fstab_mount(mountpoint):
"""Mount filesystem using fstab"""
cmd_args = ['mount', mountpoint]
try:
subprocess.check_output(cmd_args)
except subprocess.CalledProcessError as e:
log('Error unmounting {}\n{}'.format(mountpoint, e.output))
return False
return True
def relation_get(attribute=None, unit=None, rid=None):
"""Get relation information"""
_args = ['relation-get', '--format=json']
if rid:
_args.append('-r')
_args.append(rid)
_args.append(attribute or '-')
if unit:
_args.append(unit)
try:
return json.loads(subprocess.check_output(_args).decode('UTF-8'))
except ValueError:
return None
except CalledProcessError as e:
if e.returncode == 2:
return None
raise
def service(name, action):
"""
Open/close access to a service
:param name: could be a service name defined in `/etc/services` or a port
number.
:param action: `open` or `close`
"""
if action == 'open':
subprocess.check_output(['ufw', 'allow', str(name)],
universal_newlines=True)
elif action == 'close':
subprocess.check_output(['ufw', 'delete', 'allow', str(name)],
universal_newlines=True)
else:
raise UFWError(("'{}' not supported, use 'allow' "
"or 'delete'").format(action))
def run_action(self, unit_sentry, action,
_check_output=subprocess.check_output,
params=None):
"""Run the named action on a given unit sentry.
params a dict of parameters to use
_check_output parameter is used for dependency injection.
@return action_id.
"""
unit_id = unit_sentry.info["unit_name"]
command = ["juju", "action", "do", "--format=json", unit_id, action]
if params is not None:
for key, value in params.iteritems():
command.append("{}={}".format(key, value))
self.log.info("Running command: %s\n" % " ".join(command))
output = _check_output(command, universal_newlines=True)
data = json.loads(output)
action_id = data[u'Action queued with id']
return action_id
def generate2():
"""
Call an external Python 2 program to retrieve the AST symbols of that
language version
:return:
"""
import subprocess as sp
import tempfile, shutil, sys, traceback
tempdir = tempfile.mkdtemp()
tempfile = os.path.join(tempdir, "py2_ast_code.py")
py2_proc_out = ""
try:
with open(tempfile, 'w') as py2code:
py2code.write(generate_str + WRITESYMS_CODE)
py2_proc_out = sp.check_output(["python2", tempfile]).decode()
finally:
try:
shutil.rmtree(tempdir)
except:
print("Warning: error trying to delete the temporal directory:", file=sys.stderr)
print(traceback.format_exc(), file=sys.stderr)
return set(py2_proc_out.splitlines())
def bruteforce(self, ip_address, port, userList, passList):
print "INFO: Performing hydra msSql scan against " + ip_address
hydraCmd = "hydra -L %s -P %s -f -e n -o pillageResults/%s_msSqlhydra.txt -u %s -s %s mssql" % (userList, passList, ip_address, ip_address, port)
creds={}
try:
results = subprocess.check_output(hydraCmd, shell=True)
resultarr = results.split("\n")
for result in resultarr:
if "login:" in result:
print "[*] Valid msSql credentials found: " + result
resultList=result.split()
self.username=resultList[4]
if resultList[6]:
self.password=resultList[6]
else:
self.password=''
except:
print "INFO: No valid msSql credentials found"
def webEnum(self, args):
print "INFO: Performing nmap http script scan for {}:{}".format(args[0],args[1])
nmapSCAN = "nmap -sV -Pn -vv -p {} --script='(http* or ssl*) and not (dos or fuzzer or brute)' -oN {}_http.nmap {}".format(args[1],args[0],args[0])
subprocess.check_output(nmapSCAN, shell=True)
print "INFO: Performing nikto scan on {}:{}".format(args[0],args[1])
script="nikto -host {} -port {} -C all >> {}_nikto_{}.txt".format(args[0],args[1],args[0],args[1])
subprocess.check_output(script, shell=True)
'''
print "INFO: Performing dirb scan on {}:{}".format(args[0],args[1])
dirbList="/usr/share/wordlists/dirbuster/directory-list-2.3-small.txt"
script="dirb {}://{}:{} {} -S -w >> {}_dirb_{}.txt".format(args[2],args[0],args[1],dirbList,args[0],args[1])
subprocess.call(script, shell=True)
'''
print "INFO: Finished http module for {}:{}".format(args[0],args[1])
def smbEnum(self, args):
print "INFO: Performing nmap smb script scan for {}:{}".format(args[0],args[1])
nmapSCAN = "nmap -sV -Pn -vv -p {} --script='(smb*) and not (brute or broadcast or dos or external or fuzzer)' --script-args=unsafe=1 -oN {}_smb.nmap {}".format(args[1],args[0],args[0])
subprocess.check_output(nmapSCAN, shell=True)
print "INFO: Performing ntbscan for {}:{}".format(args[0],args[1])
nbtSCAN = "nbtscan -r -v -h {} >> {}_smbNbt.txt".format(args[0],args[0])
subprocess.check_output(nbtSCAN, shell=True)
print "INFO: Performing enum4Linux scan for {}:{}".format(args[0],args[1])
try:
enumSCAN = "enum4linux -a -M -v {} >> {}_smbEnum.txt".format(args[0],args[0])
subprocess.check_output(enumSCAN, shell=True)
except:
print "ERROR: enum4Linux scan FAILED for {}:{}".format(args[0],args[1])
print "INFO: Finished smb module for {}:{}".format(args[0],args[1])
def compiler_is_clang(comp) :
print("check for clang compiler ...", end=' ')
try:
cc_output = subprocess.check_output(comp+['--version'],
stderr = subprocess.STDOUT, shell=False)
except OSError as ex:
print("compiler test call failed with error {0:d} msg: {1}".format(ex.errno, ex.strerror))
print("no")
return False
ret = re.search(b'clang', cc_output) is not None
if ret :
print("yes")
else:
print("no")
return ret
def check_integrity(self):
from subprocess import check_output
reads = 0
try:
p = check_output("samtools view -c %s" % self.path, shell=True)
reads = int(p.split("\n")[0].strip())
except Exception as e:
print e
pass
has_index = False
has_indate_index = None
if os.path.exists(self.path + ".bai"):
has_index = True
if os.path.getmtime(self.path) <= os.path.getmtime(self.path + ".bai"):
has_indate_index = True
else:
has_indate_index = False
return {
("has_reads", "has 0 reads"): reads > 0,
("has_index", "has no BAI"): has_index,
("has_indate_index", "has a BAI older than itself"): has_indate_index,
}
def status_get():
"""Retrieve the previously set juju workload state and message
If the status-get command is not found then assume this is juju < 1.23 and
return 'unknown', ""
"""
cmd = ['status-get', "--format=json", "--include-data"]
try:
raw_status = subprocess.check_output(cmd)
except OSError as e:
if e.errno == errno.ENOENT:
return ('unknown', "")
else:
raise
else:
status = json.loads(raw_status.decode("UTF-8"))
return (status["status"], status["message"])
def config(scope=None):
"""Juju charm configuration"""
config_cmd_line = ['config-get']
if scope is not None:
config_cmd_line.append(scope)
else:
config_cmd_line.append('--all')
config_cmd_line.append('--format=json')
try:
config_data = json.loads(
subprocess.check_output(config_cmd_line).decode('UTF-8'))
if scope is not None:
return config_data
return Config(config_data)
except ValueError:
return None
def relation_get(attribute=None, unit=None, rid=None):
"""Get relation information"""
_args = ['relation-get', '--format=json']
if rid:
_args.append('-r')
_args.append(rid)
_args.append(attribute or '-')
if unit:
_args.append(unit)
try:
return json.loads(subprocess.check_output(_args).decode('UTF-8'))
except ValueError:
return None
except CalledProcessError as e:
if e.returncode == 2:
return None
raise
def is_crm_dc():
"""
Determine leadership by querying the pacemaker Designated Controller
"""
cmd = ['crm', 'status']
try:
status = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
if not isinstance(status, six.text_type):
status = six.text_type(status, "utf-8")
except subprocess.CalledProcessError as ex:
raise CRMDCNotFound(str(ex))
current_dc = ''
for line in status.split('\n'):
if line.startswith('Current DC'):
# Current DC: juju-lytrusty-machine-2 (168108163) - partition with quorum
current_dc = line.split(':')[1].split()[0]
if current_dc == get_unit_hostname():
return True
elif current_dc == 'NONE':
raise CRMDCNotFound('Current DC: NONE')
return False
def get_unmapped_read_count_from_indexed_bam(bam_file_name):
"""
Get number of unmapped reads from an indexed BAM file.
Args:
bam_file_name (str): Name of indexed BAM file.
Returns:
int: number of unmapped reads in the BAM
Note:
BAM must be indexed for lookup using samtools.
"""
index_output = subprocess.check_output('samtools idxstats %s' % bam_file_name, shell=True)
return int(index_output.strip().split('\n')[-1].split()[-1])
def get_bcl2fastq_v2(hostname):
try:
subprocess.check_call(["which", "bcl2fastq"])
# Restore the LD_LIBRARY_PATH set aside by sourceme.bash/shell10x.
# Required for some installations of bcl2fastq.
new_environ = dict(os.environ)
new_environ['LD_LIBRARY_PATH'] = os.environ.get('_TENX_LD_LIBRARY_PATH', '')
output = subprocess.check_output(["bcl2fastq", "--version"], env=new_environ, stderr=subprocess.STDOUT)
match = None
for l in output.split("\n"):
match = re.match("bcl2fastq v([0-9.]+)", l)
if match is not None:
return (match.groups()[0], None)
return (None, "bcl2fastq version not recognized -- please check the output of bcl2fastq --version")
except subprocess.CalledProcessError:
msg = "On machine: %s, bcl2fastq not found on PATH." % hostname
return (None, msg)
def parse_ab3_defines(defines_file): # , pkg_name):
try:
fp = open(defines_file, 'rt')
abd_cont = fp.read()
fp.close()
except:
print('[E] Failed to load autobuild defines file! Do you have read permission?')
return False
script = "ARCH={}\n".format(
get_arch_name()) + abd_cont + gen_laundry_list(['PKGNAME', 'PKGDEP', 'BUILDDEP'])
try:
# Better to be replaced by subprocess.Popen
abd_out = subprocess.check_output(script, shell=True)
except:
print('[E] Malformed Autobuild defines file found! Couldn\'t continue!')
return False
abd_fp = io.StringIO('[wrap]\n' + abd_out.decode('utf-8'))
abd_config = RawConfigParser()
abd_config.read_file(abd_fp)
abd_config_dict = {}
for i in abd_config['wrap']:
abd_config_dict[i.upper()] = abd_config['wrap'][i]
return abd_config_dict
def test_RTagsDaemonStartClean(self):
try:
os.chdir("clean")
except OSError:
print("Test Error: Couldn't cd into 'dirty' test directory.")
raise
self.assertFalse(self.cmake_build_info["build_dir"].is_dir())
self.plugin.setup_rtags_daemon()
try:
rtags_daemon_status = subprocess.check_output(
self.cmake_cmd_info["rtags_status"])
except subprocess.CalledProcessError as e:
print(e.output)
self.assertTrue(
len("*********************************\nfileids\n*********************************\n*********************************\nheadererrors\n*********************************\n*********************************\ninfo\n*********************************\nRunning a release build\nsocketFile: /Users/phillipbonhomme/.rdm\ndataDir: /Users/phillipbonhomme/.cache/rtags/\noptions: 0x14jobCount: 4\nrpVisitFileTimeout: 60000\nrpIndexDataMessageTimeout: 60000\nrpConnectTimeout: 0\nrpConnectTimeout: 0\ndefaultArguments: List<String>(-ferror-limit=50, -Wall, -fspell-checking, -Wno-unknown-warning-option\")\nincludePaths: List<Source::Include>(\")\ndefines: List<Source::Define>(-DRTAGS=\")\nignoredCompilers: Set<Path>(\")\n*********************************\njobs\n*********************************\n"
) <= len(str(rtags_daemon_status)))
def test_RTagsDaemonStartDirty(self):
try:
os.chdir("dirty")
except OSError:
print("Test Error: Couldn't cd into 'dirty' test directory.")
raise
self.assertTrue(self.cmake_build_info["build_dir"].is_dir())
self.plugin.setup_rtags_daemon()
try:
rtags_daemon_status = subprocess.check_output(
self.cmake_cmd_info["rtags_status"])
except subprocess.CalledProcessError as e:
print(e.output)
self.assertTrue(
len("*********************************\nfileids\n*********************************\n*********************************\nheadererrors\n*********************************\n*********************************\ninfo\n*********************************\nRunning a release build\nsocketFile: /Users/phillipbonhomme/.rdm\ndataDir: /Users/phillipbonhomme/.cache/rtags/\noptions: 0x14jobCount: 4\nrpVisitFileTimeout: 60000\nrpIndexDataMessageTimeout: 60000\nrpConnectTimeout: 0\nrpConnectTimeout: 0\ndefaultArguments: List<String>(-ferror-limit=50, -Wall, -fspell-checking, -Wno-unknown-warning-option\")\nincludePaths: List<Source::Include>(\")\ndefines: List<Source::Define>(-DRTAGS=\")\nignoredCompilers: Set<Path>(\")\n*********************************\njobs\n*********************************\n"
) <= len(str(rtags_daemon_status)))
def test_RTagsClientStartDirty(self):
try:
os.chdir("dirty")
except OSError:
print("Test Error: Couldn't cd into 'dirty' test directory.")
raise
self.assertTrue(self.cmake_build_info["build_dir"].is_dir())
self.assertTrue(self.cmake_build_info["comp_data_cmake"].is_file())
self.plugin.setup_rtags_daemon()
self.plugin.connect_rtags_client()
try:
rtags_client_status = subprocess.check_output(
self.cmake_cmd_info["rtags_file_status"] +
[str(src_info["cpp"])])
except subprocess.CalledProcessError as e:
print(e.output)
self.assertTrue(str(rtags_client_status).find("managed"))
try:
rtags_client_status = subprocess.check_output(
self.cmake_cmd_info["rtags_file_status"] +
[str(src_info["test_cpp"])])
except subprocess.CalledProcessError as e:
print(e.output)
self.assertTrue(str(rtags_client_status).find("managed"))
def test_RTagsClientSetFile(self):
try:
os.chdir("dirty")
except OSError:
print("Test Error: Couldn't cd into 'dirty' test directory.")
raise
self.assertTrue(self.cmake_build_info["build_dir"].is_dir())
self.assertTrue(self.cmake_build_info["comp_data_cmake"].is_file())
self.plugin.setup_rtags_daemon()
self.plugin.connect_rtags_client()
self.plugin.rtags_set_file([str(src_info["cpp"])])
try:
rtags_client_status = subprocess.check_output(
self.cmake_cmd_info["rtags_file_status"] +
[str(src_info["cpp"])])
except subprocess.CalledProcessError as e:
print(e.output)
self.assertTrue(str(rtags_client_status).find("managed"))
def test_RTagsClientUpdateBuffers(self):
try:
os.chdir("dirty")
except OSError:
print("Test Error: Couldn't cd into 'dirty' test directory.")
raise
self.assertTrue(self.cmake_build_info["build_dir"].is_dir())
self.assertTrue(self.cmake_build_info["comp_data_cmake"].is_file())
self.plugin.setup_rtags_daemon()
self.plugin.connect_rtags_client()
self.plugin.update_rtags_buffers(
[str(src_info["test_cpp"]),
str(src_info["cpp"])])
try:
rtags_client_status = subprocess.check_output(
self.cmake_cmd_info["rtags_buffers"])
except subprocess.CalledProcessError as e:
print(e.output)
filepath = os.getcwd() + str(src_info["test_cpp"])
self.assertTrue(str(rtags_client_status).find(filepath))
def run_cmake(self):
print("Running CMake")
build_dir_cmd_out = subprocess.call(
["mkdir", "build"],
stdout=subprocess.DEVNULL,
stderr=subprocess.DEVNULL)
if build_dir_cmd_out != 0:
print("Can\'t setup CMake build directory.")
return
if self.cmake_build_info["build_dir"].is_dir():
try:
subprocess.check_output(
self.cmake_cmd_info["cmake_cmd"],
cwd=str(self.cmake_build_info["build_dir"]))
except subprocess.CalledProcessError as e:
print(e.output)
if not self.cmake_build_info["comp_data_cmake"].is_file():
print("Couldn't setup CMake Project")
return
else:
print("Couldn't setup CMake Project")
return
def run_script(script_name,running_mode):
subp.check_output(['bash','-c','chmod 755 '+script_name])
if running_mode=='NA':
output=subp.check_output(['bash','-c',script_name])
if output!='':
print output
if running_mode=='write_script':
pass
if running_mode=='sge':
memo='3G'
output=subp.check_output(['bash','-c','qsub -l h_vmem='+memo+' -o '+script_name+'.o -e '+script_name+'.e '+script_name])
#TODO: if you choose slurm, then you need to change the settings and provide a file with settings
if running_mode=='slurm':
memo='50G'
partition='akundaje'
output=subp.check_output(['bash','-c','sbatch --mem '+memo+' -o '+script_name+'.o -e '+script_name+'.e'+' -p '+partition+' '+script_name])
