How to use run_safe method in localstack

Best Python code snippet using localstack_python

adb.py

Source:adb.py

...19ADB_BRIDGE_DIR = realpath(INPUTS_DIR + '/adb_bridge')20ADB_BIN_DIR = realpath(INPUTS_DIR + '/external/adb')21ANDROID_TMP_DIR = '/data/local/tmp'22# Print adb output to stdout when "-v" is passed to QCSuper23def run_safe(args, **kwargs):24    debug('[>] Running adb command: ' + list2cmdline(args))25    result = run(args, **kwargs)26    result_string = ((result.stdout or b'') + (result.stderr or b''))27    if result and result_string:28        debug('[<] Obtained result for running "%s": %s' % (list2cmdline(args), result_string))29    return result30"""31    This class implements reading Qualcomm DIAG data from a the /dev/diag32    character device, on a remote Android device connected through ADB.33    34    For this, it uploads the C program located in "./adb_bridge/" which35    creates a TCP socket acting as a proxy to /dev/diag.36"""37QCSUPER_TCP_PORT = 4355538if platform in ('cygwin', 'win32'):39    adb_exe = ADB_BIN_DIR + '/adb_windows.exe'40elif platform == 'darwin':41    adb_exe = which('adb') or ADB_BIN_DIR + '/adb_macos'42else:43    adb_exe = which('adb') or ADB_BIN_DIR + '/adb_linux'44class AdbConnector(HdlcMixin, BaseInput):45    46    def __init__(self):47        48        self.su_command = '%s'49        50        # Whether we can use "adb exec-out" instead51        # of "adb shell" (we should do it if the52        # remote phone supports it)53        self.can_use_exec_out = None # (boolean, None = unknown)54        55        self.ADB_TIMEOUT = 1056        57        # Send batch commands to check for the writability of /dev/diag through58        # adb, and for the availability of the "su" command59        60        bash_output = self.adb_shell(61            'test -w /dev/diag; echo DIAG_NOT_WRITEABLE=$?; ' +62            'test -e /dev/diag; echo DIAG_NOT_EXISTS=$?; ' +63            'test -r /dev; echo DEV_NOT_READABLE=$?; ' +64            'su -c id'65        )66        67        # Check for the presence of /dev/diag68        69        if not search('DIAG_NOT_WRITEABLE=[01]', bash_output):70            71            print('Could not run a bash command your phone, is adb functional?')72            73            exit(bash_output)74        75        # If writable, continue76        77        elif 'DIAG_NOT_WRITEABLE=0' in bash_output:78            79            pass80        # If not present, raise an error81        82        elif 'DEV_NOT_READABLE=0' in bash_output and 'DIAG_NOT_EXISTS=1' in bash_output:83            84            exit('Could not find /dev/diag, does your phone have a Qualcomm chip?')85        # If maybe present but not writable, check for root86        87        elif 'uid=0' in bash_output:88            89            self.su_command = 'su -c "%s"'90        91        elif 'uid=0' in self.adb_shell('su 0,0 sh -c "id"'):92            93            self.su_command = 'su 0,0 sh -c "%s"'94    95        else:96            97            # "adb shell su" didn't work, try "adb root"98            99            adb = run_safe([adb_exe, 'root'], stdout = PIPE, stderr = STDOUT, stdin = DEVNULL)100            101            if b'cannot run as root' in adb.stdout:102                103                exit('Could not get root to adb, is your phone rooted?')104        105            run_safe([adb_exe, 'wait-for-device'], stdin = DEVNULL, check = True)106        107        # Once root has been obtained, send batch commands to check108        # for the presence of /dev/diag through adb109        110        bash_output = self.adb_shell(111            'test -e /dev/diag; echo DIAG_NOT_EXISTS=$?'112        )113        114        # If not present, raise an error115        116        if 'DIAG_NOT_EXISTS=1' in bash_output:117            118            exit('Could not find /dev/diag, does your phone have a Qualcomm chip?')119        120        # Upload the adb_bridge121        122        adb = run_safe([adb_exe, 'push', ADB_BRIDGE_DIR + '/adb_bridge', ANDROID_TMP_DIR],123            124            stdin = DEVNULL, stdout = PIPE, stderr = STDOUT125        )126    127        if b'error' in adb.stdout or adb.returncode != 0:128            129            exit(adb.stdout.decode('utf8'))130        131        # Launch the adb_bridge132        133        self._relaunch_adb_bridge()134        self.packet_buffer = b''135        136        super().__init__()137    138    def _relaunch_adb_bridge(self):139        140        if hasattr(self, 'adb_proc'):141            self.adb_proc.terminate()142        143        self.adb_shell(144            'killall -q adb_bridge; ' +145            'chmod 755 ' + ANDROID_TMP_DIR + '/adb_bridge'146        )147        148        run_safe([adb_exe, 'forward', 'tcp:' + str(QCSUPER_TCP_PORT), 'tcp:' + str(QCSUPER_TCP_PORT)], check = True, stdin = DEVNULL)149        150        self.adb_proc = Popen([adb_exe, 'exec-out' if self.can_use_exec_out else 'shell', self.su_command % (ANDROID_TMP_DIR + '/adb_bridge')],151            152            stdin = DEVNULL, stdout = PIPE, stderr = STDOUT,153            preexec_fn = setpgrp,154            bufsize = 0, universal_newlines = True155        )156    157        for line in self.adb_proc.stdout:158            159            if 'Connection to Diag established' in line:160                161                break162            163            else:164                165                stderr.write(line)166                stderr.flush()167        self.socket = socket(AF_INET, SOCK_STREAM)168        169        try:170            171            self.socket.connect(('localhost', QCSUPER_TCP_PORT))172        173        except Exception:174            175            self.adb_proc.terminate()176            177            exit('Could not communicate with the adb_bridge through TCP')178        179        self.received_first_packet = False180    181    """182        This utility function tries to run a command to adb,183        raising an exception when it is unreachable.184        185        :param command: A shell command (string)186        187        :returns The combined stderr and stdout from "adb shell" (string)188    """189    190    def adb_shell(self, command):191        192        try:193            194            # Can we use "adb exec-out"?195            196            if self.can_use_exec_out is None:197                        198                adb = run_safe([adb_exe, 'exec-out', 'id'],199                    200                    stdin = DEVNULL, stdout = PIPE, stderr = STDOUT, timeout = self.ADB_TIMEOUT201                )202            203                self.can_use_exec_out = (adb.returncode == 0)204            205            # Can we execute commands?206            207            adb = run_safe([adb_exe, 'exec-out' if self.can_use_exec_out else 'shell', self.su_command % command],208                209                stdin = DEVNULL, stdout = PIPE, stderr = STDOUT, timeout = self.ADB_TIMEOUT210            )211        212        except TimeoutExpired:213            214            exit('Communication with adb timed out, is your phone displaying ' +215                'a confirmation dialog?')216        if b'error' in adb.stdout or adb.returncode != 0:217    218            if b'device not found' in adb.stdout or b'no devices' in adb.stdout:219            220                exit('Could not connect to the adb, is your phone plugged with USB '221                    + 'debugging enabled?')222            223            elif b'confirmation dialog on your device' in adb.stdout:224            225                exit('Could not connect to the adb, is your phone displaying ' +226                    'a confirmation dialog?')227            228            else:229                230                print('Could not connect to your device through adb')231            232            exit(adb.stdout.decode('utf8'))233        234        return adb.stdout.decode('utf8').strip()235    236    def __del__(self):237        238        try:239            240            if hasattr(self, 'adb_proc'):241                self.adb_proc.terminate()242        243        except Exception:244            245            pass246    247    def send_request(self, packet_type, packet_payload):248        249        raw_payload = self.hdlc_encapsulate(bytes([packet_type]) + packet_payload)250        251        self.socket.send(raw_payload)252    253    def get_gps_location(self):254        255        lat = None256        lng = None257        258        gps_info = run_safe([adb_exe, 'exec-out' if self.can_use_exec_out else 'shell', 'dumpsys', 'location'], stdout = PIPE)259        gps_info = gps_info.stdout.decode('utf8')260        261        gps_info = search('(\d+\.\d+),(\d+\.\d+)', gps_info)262        if gps_info:263            lat, lng = map(float, gps_info.groups())264        265        return lat, lng266    267    def read_loop(self):268        269        while True:270            271            while self.TRAILER_CHAR not in self.packet_buffer:272                ...

1step_match.py

Source:1step_match.py

...34    if log_file is not None:35        log_file.write(log_line)36        log_file.write("\n")37        log_file.flush()38def run_safe(command, output_fn=None, output_fo=None, err_msg=None, thr_exc=True, silent=False):39    """Run a shell command safely.40    Args:41        command (list of str): Command to execute.42        output_fn (str): Name of a file for storing the output.43        output_fo (fileobject): Output file object. If both params are None, the standard output is used.44        err_msg (str): Error message if the command fails.45        thr_exc (bool): Through exception if the command fails. error_msg or thr_exc must be set.46        silent (bool): Silent mode (print messages only if the command fails).47    Raises:48        RuntimeError: Command exited with a non-zero code.49    """50    assert output_fn is None or output_fo is None51    assert err_msg is not None or thr_exc52    assert len(command) > 053    command_safe = []54    for part in command:55        part = str(part)56        if " " in part:57            part = '"{}"'.format(part)58        command_safe.append(part)59    command_str = " ".join(command_safe)60    if not silent:61        message("Shell command:", command_str)62    if output_fn is None:63        if output_fo is None:64            out_fo = sys.stdout65        else:66            out_fo = output_fo67    else:68        out_fo = open(output_fn, "w+")69    if out_fo == sys.stdout:70        p = subprocess.Popen("/bin/bash -e -o pipefail -c '{}'".format(command_str), shell=True)71    else:72        p = subprocess.Popen("/bin/bash -e -o pipefail -c '{}'".format(command_str), shell=True, stdout=out_fo)73    stdout, stderr = p.communicate()74    error_code = p.returncode75    if output_fn is not None:76        out_fo.close()77    if error_code == 0 or error_code == 141:78        if not silent:79            message("Finished")80    else:81        message("Unfinished, an error occurred (error code {}): {}".format(error_code, command_str))82        if err_msg is not None:83            print('Error: {}'.format(err_msg), file=sys.stderr)84        if thr_exc:85            raise RuntimeError("A command failed, see messages above.")86        sys.exit(1)87def create_bwa_index(fa):88    # cmd('"{bwa}" index "{fa}"'.format(bwa=bwa,fa=fa))89    run_safe([bwa, 'fa2pac', fa, fa])90    run_safe([bwa, 'pac2bwtgen', fa + ".pac", fa + ".bwt", ">", "/dev/null"])91    run_safe([bwa, 'bwtupdate', fa + ".bwt"])92    run_safe([bwa, 'bwt2sa', fa + ".bwt", fa + ".sa"])93def create_klcp(fa, k):94    run_safe([prophyle_index, 'klcp', '-k', k, fa, ">", "/dev/null"])95def query(fa, fq, k, u=False, v=False, t=1):96    params = ""97    cmd = [prophyle_index, 'query', "-v" if v else "", "-u" if u else "", '-k', k, '-t', t, fa, fq]98    run_safe(cmd)99def main():100    parser = argparse.ArgumentParser(description='Single-command ProPhex matching.')101    parser.add_argument(102        '-k',103        type=int,104        metavar='int',105        dest='k',106        required=True,107        help='k-mer length',108    )109    parser.add_argument(110        '-t',111        type=int,112        default=1,...

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