Python subprocess.getoutput函数代码示例

def run_antechamber(molecule_name, input_filename, charge_method="bcc", net_charge=None, gaff_mol2_filename=None, frcmod_filename=None):
    """Run AmberTools antechamber and parmchk2 to create GAFF mol2 and frcmod files.

    Parameters
    ----------
    molecule_name : str
        Name of the molecule to be parameterized, will be used in output filenames.
    ligand_filename : str
        The molecule to be parameterized.  Must be tripos mol2 format.
    charge_method : str, optional
        If not None, the charge method string will be passed to Antechamber.
    net_charge : int, optional
        If not None, net charge of the molecule to be parameterized.
        If None, Antechamber sums up partial charges from the input file.
    gaff_mol2_filename : str, optional, default=None
        Name of GAFF mol2 filename to output.  If None, uses local directory
        and molecule_name
    frcmod_filename : str, optional, default=None
        Name of GAFF frcmod filename to output.  If None, uses local directory
        and molecule_name

    Returns
    -------
    gaff_mol2_filename : str
        GAFF format mol2 filename produced by antechamber
    frcmod_filename : str
        Amber frcmod file produced by prmchk
    """

    ext = parse_ligand_filename(input_filename)[1]

    filetype = ext[1:]
    if filetype != "mol2":
        raise(ValueError("Must input mol2 filename"))


    if gaff_mol2_filename is None:
        gaff_mol2_filename = molecule_name + '.gaff.mol2'
    if frcmod_filename is None:
        frcmod_filename = molecule_name + '.frcmod'

    cmd = "antechamber -i %s -fi mol2 -o %s -fo mol2 -s 2" % (input_filename, gaff_mol2_filename)
    if charge_method is not None:
        cmd += ' -c %s' % charge_method

    if net_charge is not None:
        cmd += ' -nc %d' % net_charge

    logger.debug(cmd)

    output = getoutput(cmd)
    logger.debug(output)

    cmd = "parmchk2 -i %s -f mol2 -o %s" % (gaff_mol2_filename, frcmod_filename)
    logger.debug(cmd)

    output = getoutput(cmd)
    logger.debug(output)

    return gaff_mol2_filename, frcmod_filename

def cpu_check():
    """
    TODO: split processor num / ssse3
    """
    ret = {
            "key": "cpu",
            "cn_desc": "cpu",
            }
    output = getoutput('cat /proc/cpuinfo').splitlines()
    # 某行类似processor : 3
    lines = [l for l in output if l.strip() and l.split()[0] == 'processor']
    cpu_num = len(lines)
    fail_standalone = False
    fail_cluster = False
    fail_reason = ""
    if cpu_num < CLUSTER_SYS_REQ['MIN_CPU_CORE_NUM']:
        fail_cluster |= True
        fail_reason = "集群版最低CPU核数：%d" % CLUSTER_SYS_REQ['MIN_CPU_CORE_NUM']
    if cpu_num < STANDALONE_SYS_REQ['MIN_CPU_CORE_NUM']:
        fail_standalone = True
        fail_reason = fail_reason + ", 单机版最低CPU核数：%d" % STANDALONE_SYS_REQ['MIN_CPU_CORE_NUM']
    support_ssse3 = len([l for l in output if 'flags' in l and 'ssse3' in l]) > 0
    fail_cluster |= not support_ssse3
    if not support_ssse3:
        fail_reason = fail_reason + ", 集群版要求CPU支持ssse3指令集"
    ret.update({
        "value": "processor num: %d, support ssse3: %r" % (cpu_num, support_ssse3),
        "pass_standalone": not fail_standalone,
        "pass_cluster": not fail_cluster,
        "fail_reason": fail_reason,
        "lscpu": getoutput("lscpu"),
        "proc_cpuinfo": getoutput("cat /proc/cpuinfo"),
        })
    return ret

def create_db_image(drucker):
    """Create database image from database container"""
    print(
        colorful.white_on_blue(
            "Committing %s image from %s container..."
            % (drucker.vars.DB_IMAGE, drucker.vars.DB_CONTAINER)
        )
    )

    subprocess.run(
        'docker commit -m "%s on %s" %s %s'
        % (
            drucker.vars.DB_CONTAINER,
            str(date.today()),
            drucker.vars.DB_CONTAINER,
            drucker.vars.DB_IMAGE,
        ),
        shell=True,
    )

    print(colorful.white_on_blue("Deleting initial container..."))
    subprocess.getoutput(
        "docker rm -f %s > /dev/null 2>&1" % (drucker.vars.DB_CONTAINER)
    )
    create_db_container(drucker)

def run_pbs_jobs(c, config_file, strategies_file, subject_list_file, p_name):



    import subprocess
    from time import strftime


    try:
        sublist = yaml.load(open(os.path.realpath(subject_list_file), 'r'))
    except:
        raise Exception ("Subject list is not in proper YAML format. Please check your file")
    
    temp_files_dir = os.path.join(os.getcwd(), 'cluster_temp_files')
    shell = subprocess.getoutput('echo $SHELL')
    subject_bash_file = os.path.join(temp_files_dir, 'submit_%s.pbs' % str(strftime("%Y_%m_%d_%H_%M_%S")))
    f = open(subject_bash_file, 'w')
    print('#! %s' % shell, file=f)
    print('#PBS -S %s' % shell, file=f)
    print('#PBS -V', file=f)
    print('#PBS -t 1-%d' % len(sublist), file=f)
    print('#PBS -q %s' % c.queue, file=f)
    print('#PBS -l nodes=1:ppn=%d' % c.numCoresPerSubject, file=f)
    print('#PBS -e %s' % os.path.join(temp_files_dir, 'c-pac_%s.err' % str(strftime("%Y_%m_%d_%H_%M_%S"))), file=f)
    print('#PBS -o %s' % os.path.join(temp_files_dir, 'c-pac_%s.out' % str(strftime("%Y_%m_%d_%H_%M_%S"))), file=f)
    print('source ~/.bashrc', file=f)

    print("python -c \"import CPAC; CPAC.pipeline.cpac_pipeline.run(\\\"%s\\\",\\\"%s\\\",\\\"${PBS_ARRAYID}\\\",\\\"%s\\\", \\\"%s\\\" , \\\"%s\\\", \\\"%s\\\", \\\"%s\\\") \" " % (str(config_file), \
        subject_list_file, strategies_file, c.maskSpecificationFile, c.roiSpecificationFile, c.templateSpecificationFile, p_name), file=f)
#    print >>f, "python -c \"import CPAC; CPAC.pipeline.cpac_pipeline.py -c %s -s %s -indx ${PBS_ARRAYID} -strategies %s \" " %(str(config_file), subject_list_file, strategies_file)
    #print >>f, "python CPAC.pipeline.cpac_pipeline.py -c ", str(config_file), "-s ", subject_list_file, " -indx ${PBS_ARRAYID} -strategies ", strategies_file
    f.close()

    subprocess.getoutput('chmod +x %s' % subject_bash_file )

def menu():
	requestMenu = subprocess.getoutput("echo `zenity --list --title='PTTP' --text='What type of request do you want to make?' --column='Request type' 'GET' 'POST'`")
	requestMenu = requestMenu.split("\n")
	requestMenu = requestMenu[len(requestMenu) - 1]

	if requestMenu == "GET":
		#Do a GET request
		getMenu = subprocess.getoutput("echo `zenity --list --title='PTTP' --text='Authentication/response:' --column='Option' 'No authentication' 'Basic authentication' 'No authentication (plain text)' 'Basic authentication (plain text)'`")
		getMenu = getMenu.split("\n")
		getMenu = getMenu[len(getMenu) - 1]
		try:
			get(getMenu)
		except(urllib.error.HTTPError, urllib.error.URLError) as error:
			os.system("zenity --error --title='PTTP' --text='"+format(error)+"'")
		except:
			os.system("zenity --error --title='PTTP' --text='Oops! There was an error in your request.'")
	elif requestMenu == "POST":
		#Do a POST request
		postMenu = subprocess.getoutput("echo `zenity --list --title='PTTP' --text='Authentication/response:' --column='Option' 'No authentication' 'Basic authentication' 'No authentication (plain text)' 'Basic authentication (plain text)'`")
		postMenu = postMenu.split("\n")
		postMenu = postMenu[len(postMenu) - 1]
		try:
			post(postMenu)
		except(urllib.error.HTTPError, urllib.error.URLError) as error:
			os.system("zenity --error --title='PTTP' --text='"+format(error)+"'")
		except:
			os.system("zenity --error --title='PTTP' --text='Oops! There was an error in your request.'")
	else:
		sys.exit()

 def _learn(self, irc, msg, channel, text, probability):
     """Internal method for learning phrases."""
     
     if os.path.exists(self._getBrainDirectoryForChannel(channel)):
         # Does this channel have a directory for the brain file stored and does this file exist?
         
         text = self._cleanText(text)
         
         if text and len(text) > 1 and not text.isspace():
     
             self.log.debug("Learning: {0}".format(text))
             cobeBrain = Brain(self._getBrainDirectoryForChannel(channel))
             cobeBrain.learn(text)
             
             if random.randint(0, 10000) <= probability:
                 self._reply(irc, msg, channel, text)
             
     else: # Nope, let's make it!
                     
         subprocess.getoutput('{0} {1}'.format(self._doCommand(channel), 'init'))
         
         text = self._cleanText(text)
         
         if text and len(text) > 1 and not text.isspace():
     
             self.log.debug("Learning: {0}".format(text))
             cobeBrain = Brain(self._getBrainDirectoryForChannel(channel))
             cobeBrain.learn(text)
             
             if random.randint(0, 10000) <= probability:
                 self._reply(irc, msg, channel, text)

 def _update_repos(self):
     '''
     Prepare the reposiroties, return dict with repo information:
     {'<repo dir>': {'last_rev': '<last revision number>',
                      'files': '<list of files changed since last revision>'}
     '''
     repo_info = {}
     for base in self.roots:
         repo_info[base] = {}
         if not os.path.isdir(base):
             # checkout the repo
             co_cmd = 'svn co ' + self.roots[base] + ' ' + base
             lines = bytes.decode(subprocess.getoutput(co_cmd)).splitlines()
             repo_info[base]['last_rev'] = None
             repo_info[base]['files'] = self._find_pkgbuilds(base, lines)
         else:
             # Check the release numbers and run an update
             l_cmd = 'svn info ' + base + " | grep Revision: | awk '{print $2}'"
             l_rev = int(subprocess.getoutput(i_cmd).strip())
             repo_info['last_rev'] = str(l_rev)
             r_cmd = 'svn info ' + self.roots[base] + " | grep Revision: | awk '{print $2}'"
             r_rev = int(subprocess.getoutput(r_cmd).strip())
             if r_rev > l_rev:
                 # The local repo is out of date, update!
                 u_cmd = 'svn up ' + base
                 lines = bytes.decode(subprocess.getoutput(u_cmd)).splitlines()
                 repo_info[base]['files'] = self._find_pkgbuilds(base, lines)
     return repo_info

 def _resolution(self):
     width=0
     heigth=0
     if(SystemInformations._platform(self) != "Windows"):            
         resolution = str(subprocess.getoutput("xrandr | grep connected"))
         resolution = re.sub("[a-z]*-[0-9]*", "", resolution)
         resolution = re.sub("\).*", "", resolution)
         resolution = re.sub("\+.* ", "", resolution)
         resolution = re.sub("[^0-9^\n]*", "", resolution)
         parseResolution = resolution.split("\n")
         for x in range(0, len(parseResolution)):
             if(width != 0):
                 if(parseResolution[x][0:4] != ""):
                     width=width+int(parseResolution[x][0:4])
             else:
                 if(parseResolution[x][0:4] != ""):
                     width=int(parseResolution[x][0:4])
                 
             if(heigth != 0):
                 if(parseResolution[x][4:9] != ""):
                     if(heigth < int(parseResolution[x][4:9])):
                         heigth = int(parseResolution[x][4:9])
             else:
                 if(parseResolution[x][4:9] != ""):
                     heigth=int(parseResolution[x][4:9])            
         
     else:
         resolution=re.sub("\n","",subprocess.getoutput("wmic path Win32_VideoController  get CurrentHorizontalResolution,CurrentVerticalResolution"))
         resolution=re.sub(" *","",resolution)
         resolution=re.sub("CurrentHorizontalResolution","",resolution)
         resolution=re.sub("CurrentVerticalResolution","",resolution)
         width=int(resolution[0:4])
         heigth=int(resolution[4:8])            
     totalResolution = str(width)+"x"+str(heigth)
     return totalResolution

def test_nfs_getfacl():
	# mesures sur le getfacl
	test = RandomGen()

	path = '/mnt/nfs/test-acl' # NFS mounted directory
	u = subprocess.getoutput('rm ' + path + "/*")	# clean directory
	print("test acl getfacl\n")
	f = open('/tmp/acl-result-getfacl','w')
	for i in range(37):

		test.getUserList()
		testfile = 'testfile' + str(i)

		u = subprocess.getoutput('touch ' + path + "/" + testfile)
		print("setfacl " + str(i) + " " + u)
		for j in range(i):
			user = test.uList.pop()
			mode = test.createRandomMode()
			u = subprocess.getoutput('setfacl -m u:' + user + ':' + mode + " " + path + "/" + testfile)

		t1=time.time()
		u = subprocess.getoutput('getfacl ' + path + "/" + testfile)
		print("getfacl - " + str(i) + u + "\n")
		t2=time.time()
		f.write(str(i) + "\t" + str(t2-t1)+"\n")
		f.close()

def library_install_objdump(path, level):
    if path in skip_libs or path in done:
        return

    if level > 0:
        lib = find_dll(path)
        if lib == "":  # not found
            skip_libs.append(path)
            print("Not found: " + path)
            return
        print(lib)
        subprocess.getoutput("cp " + lib + " " + build_path)

    else:
        print("Processing target " + path)
        lib = path

    done.append(path)

    command = objdump_path + " -p " + lib + " | grep -o ': .*\.dll$'"
    res = subprocess.getstatusoutput(command)
    if (res[0] > 0):
        print("Error: objdump failed with " + lib)
    else:
        dlls = subprocess.getoutput(command).split("\n")
        for line in dlls:
            dll = (line.split(": "))[1]
            if dll not in done and dll not in skip_libs:
                level += 1
                library_install_objdump(dll, level)

def test_acl_default(path):

# set default acl on the test directory
	u = subprocess.getoutput('mkdir ' + path + "/" + testdir)
	u = subprocess.getoutput('getfacl ' + path + "/" + testdir)
	acl=[]
	for i in range (len(splitedresult)-1):
		splitedline = splitedresult[i].split('::')
		name = splitedline[0]
		entry = splitedline[1]
		acl.append(name,entry)
# create a file in this directory
	u = subprocess.getoutput('touch ' + path + "/" + testdir + testfile)
# get the file's ACL and verify
	u = subprocess.getoutput('getfacl ' + path + "/" + testdir + testfile)
	splitedresult = u.split('\n')
	acl2=[]
	for i in range (len(splitedresult)-1):
		splitedline = splitedresult[i].split('::')
		name = splitedline[0]
		entry = splitedline[1]
		acl2.append(name,entry)

	result_final = True
	while i < len(acl2):
		result = False
		while j < len(acl2) and result == False:
			if acl2[i] == acl[j]:
				result = True
		if result == False:
			result_final = False

def restruct_linux():
    qmake = sys.argv[3]
    # Copy the entire directory
    for d in ['bin', 'lib', 'libexec', 'share']:
        shutil.copytree(os.path.join(app_bundle, d), os.path.join(target_path, d), symlinks=True)

    # Copy Qt libs
    qtlibs_dir = subprocess.getoutput('%s -query QT_INSTALL_LIBS' % qmake).strip()
    for lib in ['Core', 'Gui', 'Widgets', 'Concurrent', 'Network', 'PrintSupport',
                'Qml', 'Quick', 'QuickWidgets', 'Xml', 'Svg', 'XcbQpa', 'Sql']:
        shutil.copy(os.path.join(qtlibs_dir, 'libQt5%s.so.5'%lib), lib_dir)

    # Copy Qt plugins
    qtplugins_dir = subprocess.getoutput('%s -query QT_INSTALL_PLUGINS' % qmake).strip()
    os.makedirs(plugins_dir)
    for plugin in ['bearer', 'designer', 'iconengines', 'imageformats',
                   'platforms', 'sqldrivers', 'xcbglintegrations']:
        shutil.copytree(os.path.join(qtplugins_dir, plugin), os.path.join(plugins_dir, plugin))
    # Copy QtQuick modules
    qtqml_dir = subprocess.getoutput('%s -query QT_INSTALL_QML' % qmake).strip()
    shutil.copytree(qtqml_dir, qml_dir)
    # Fix qt.conf
    open(os.path.join(bin_dir, 'qt.conf'), 'w').write('[Paths]\nPrefix = ..\n')
    open(os.path.join(libexec_dir, 'qtcreator', 'qt.conf'), 'w').write('[Paths]\nPrefix = ../..\n')
    # Fix rpath of qtcreator and executibles under libexec
    cmd = "chrpath -r '$ORIGIN/../lib/qtcreator:$ORIGIN/../lib:' " + os.path.join(bin_dir, 'qtcreator')
    os.system(cmd)
    for f in os.listdir(os.path.join(libexec_dir, 'qtcreator')):
        cmd = "chrpath -r '$ORIGIN/../../lib/qtcreator:$ORIGIN/../../lib:' " + os.path.join(libexec_dir, 'qtcreator', f)
        os.system(cmd)

def main():
    print('Strated ---------------------')

    # execute(['ls', '-ls'])

    # proc = subprocess.Popen(['ls -lsa'], stdout = subprocess.PIPE, shell = True)
    # (out, err) = proc.communicate()
    # proc_status = proc.wait()
    # print("Command exit status: " + str(proc_status))
    # print("Command output: " + str(out))

    # output = subprocess.check_output('ls -ls', shell = True)
    # print(output)

    ip = '178.62.18.112'
    cmd = 'ssh-keygen -f ~/.ssh/known_hosts -R ' + ip
    print('CMD [' + cmd + ']')
    stdoutdata = subprocess.getoutput(cmd)
    print('------- OUTPUT START --------')
    print(stdoutdata)
    print('======= OUTPUT END   ========')

    cmd = 'echo -e \"Host ${myvmip}\n\tStrictHostKeyChecking no\n\" >> ~/.ssh/config'
    print('CMD [' + cmd + ']')
    stdoutdata = subprocess.getoutput(cmd)
    print('------- OUTPUT START --------')
    print(stdoutdata)
    print('======= OUTPUT END   ========')

    # s = pxssh.pxssh()
    # s.login()
    print('Finished --------------------')

  def GetProtoRuleFormattedData(cls, rule_data, out_type):
    """Get the formatted proto dependency info for the output type.

    Args:
      rule_data: dict: The rule data for the proto rule.
      out_type: string: The type for which the proto data is to be generated.

    Return:
      dict: Corresponding rules generated for the out_type.
    """
    srcs = rule_data.get('src', set())

    protobuf_base_dir = cls.GetProtoBufBaseDir();
    out = {}
    if out_type.find('cc_') == 0 :  # Generated cc rule.
      pkg_config_cmd = ('export PKG_CONFIG_PATH=%s; '
          'pkg-config --define-variable=prefix=%s protobuf' %
          (os.path.join(protobuf_base_dir, 'lib/pkgconfig'), protobuf_base_dir))

      out['src'] = set([ cls.__GetOutFileName(x, '.pb.cc') for x in srcs ])
      out['hdr'] = set([ cls.__GetOutFileName(x, '.pb.h') for x in srcs ])
      out['flag'] = set(subprocess.getoutput(pkg_config_cmd + ' --cflags').split())
      out['link'] = set(subprocess.getoutput(pkg_config_cmd + ' --libs').split())
    else:
      TermColor.Error('Unsupported referrer type %s' % out_type)

    return out

def tmux_layout():
    """Layout for gdb-dashboard using tmux panes"""
    # Bug? Cursor (in the terminal) is gone in any tmux pane after this function.
    panes_tty = subprocess.getoutput(["tmux lsp -F'#{pane_tty}'"]).split('\n')
    panes_id = subprocess.getoutput(["tmux lsp -F'#{pane_id}'"]).split('\n')
    print("panes_tty =", panes_tty)
    if len(panes_tty) == 2:
        # Put the outout in the right pane, and enable history and stacklocals
        gdb.execute("dashboard -layout !stacklocals stack history !threads source")
        # gdb.execute("dashboard -output " + panes_tty[1])
        # gdb.execute("dashboard stacklocals -output " + panes_tty[1])
        right_tty = panes_tty[1]
        gdb.execute("dashboard stack -output "   + right_tty)
        gdb.execute("dashboard history -output " + right_tty)
        gdb.execute("dashboard source -output "  + right_tty)
    if len(panes_tty) == 3:
        # NOTE: Execute tmux_split_gdb (from ~/.tmux_utils)
        gdb.execute("dashboard -layout stacklocals stack history !threads source")
        # gdb.execute("dashboard -output " + panes_tty[1])
        right_tty = panes_tty[2]
        up_index = 0
        up_tty = panes_tty[up_index]
        gdb.execute("dashboard stacklocals -output " + right_tty)
        gdb.execute("dashboard stack -output "       + right_tty)
        gdb.execute("dashboard history -output "     + right_tty)
        gdb.execute("dashboard source -output "      + up_tty)
        pane_source_height = subprocess.getoutput(["tmux lsp -F'#{pane_height}'"]).split('\n')[up_index]
        gdb.execute("dashboard source -style context " + str(int(int(pane_source_height)/2.1)))