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workflow_processor.py

Source:workflow_processor.py

1import sys2import json3import os.path4import traceback5import tempfile6import requests7from ruamel import yaml8# import PandaLogger before idds modules not to change message levels of other modules9from pandacommon.pandalogger.PandaLogger import PandaLogger10from pandacommon.pandalogger.LogWrapper import LogWrapper11from pandaserver.workflow import pcwl_utils12from pandaserver.workflow import workflow_utils13from pandaserver.srvcore.CoreUtils import commands_get_status_output, clean_user_id14from pandaserver.srvcore.MailUtils import MailUtils15from idds.client.clientmanager import ClientManager16from idds.common.utils import get_rest_host17_logger = PandaLogger().getLogger('workflow_processor')18# process workflow19class WorkflowProcessor(object):20    # constructor21    def __init__(self, task_buffer=None, log_stream=None):22        self.taskBuffer = task_buffer23        self.log = _logger24    # process a file25    def process(self, file_name, to_delete=False, test_mode=False, get_log=False, dump_workflow=False):26        try:27            is_fatal = False28            is_OK = True29            request_id = None30            dump_str = None31            with open(file_name) as f:32                ops = json.load(f)33                user_name = clean_user_id(ops["userName"])34                base_platform = ops['data'].get('base_platform')35                for task_type in ops['data']['taskParams']:36                    ops['data']['taskParams'][task_type]['userName'] = user_name37                    if base_platform:38                        ops['data']['taskParams'][task_type]['basePlatform'] = base_platform39                log_token = '< id="{}" test={} outDS={} >'.format(user_name, test_mode, ops['data']['outDS'])40                tmpLog = LogWrapper(self.log, log_token)41                tmpLog.info('start {}'.format(file_name))42                sandbox_url = os.path.join(ops['data']['sourceURL'], 'cache', ops['data']['sandbox'])43                # IO through json files44                ops_file = tempfile.NamedTemporaryFile(delete=False, mode='w')45                json.dump(ops, ops_file)46                ops_file.close()47                # execute main in another process to avoid chdir mess48                tmp_stat, tmp_out = commands_get_status_output("python {} {} '{}' {} {} '{}' {}".format(49                    __file__, sandbox_url, log_token, dump_workflow, ops_file.name,50                    user_name, test_mode))51                if tmp_stat:52                    is_OK = False53                    tmpLog.error('main execution failed with {}:{}'.format(tmp_stat, tmp_out))54                else:55                    with open(tmp_out.split('\n')[-1]) as tmp_out_file:56                        is_OK, is_fatal, request_id, dump_str = json.load(tmp_out_file)57                    try:58                        os.remove(tmp_out)59                    except Exception:60                        pass61                if not get_log:62                    if is_OK:63                        tmpLog.info('is_OK={} request_id={}'.format(is_OK, request_id))64                    else:65                        tmpLog.info('is_OK={} is_fatal={} request_id={}'.format(is_OK, is_fatal, request_id))66                if to_delete or (not test_mode and (is_OK or is_fatal)):67                    dump_str = tmpLog.dumpToString() + dump_str68                    tmpLog.debug('delete {}'.format(file_name))69                    try:70                        os.remove(file_name)71                    except Exception:72                        pass73                    # send notification74                    if not test_mode and self.taskBuffer is not None:75                        toAdder = self.taskBuffer.getEmailAddr(user_name)76                        if toAdder is None or toAdder.startswith('notsend'):77                            tmpLog.debug('skip to send notification since suppressed')78                        else:79                            # message80                            if is_OK:81                                mailSubject = "PANDA Notification for Workflow {}".format(ops['data']['outDS'])82                                mailBody = "Hello,\n\nWorkflow:{} has been accepted with RequestID:{}\n\n".\83                                    format(ops['data']['outDS'], request_id)84                            else:85                                mailSubject = "PANDA WARNING for Workflow={}".format(ops['data']['outDS'])86                                mailBody = "Hello,\n\nWorkflow {} was not accepted\n\n".\87                                    format(ops['data']['outDS'], request_id)88                                mailBody += "Reason : %s\n" % dump_str89                            # send90                            tmpSM = MailUtils().send(toAdder, mailSubject, mailBody)91                            tmpLog.debug('sent message with {}'.format(tmpSM))92        except Exception as e:93            is_OK = False94            tmpLog.error("failed to run with {} {}".format(str(e), traceback.format_exc()))95        if get_log:96            ret_val = {'status': is_OK}97            if is_OK:98                ret_val['log'] = dump_str99            else:100                if dump_str is None:101                    ret_val['log'] = tmpLog.dumpToString()102                else:103                    ret_val['log'] = dump_str104            return ret_val105# execute chdir in another process106def core_exec(sandbox_url, log_token, dump_workflow, ops_file, user_name, test_mode):107    tmpLog = LogWrapper(_logger, log_token)108    is_OK = True109    is_fatal = False110    request_id = None111    if dump_workflow == 'True':112        dump_workflow = True113    else:114        dump_workflow = False115    if test_mode == 'True':116        test_mode = True117    else:118        test_mode = False119    try:120        with open(ops_file) as f:121            ops = json.load(f)122        try:123            os.remove(ops_file)124        except Exception:125            pass126        # go to temp dir127        cur_dir = os.getcwd()128        with tempfile.TemporaryDirectory() as tmp_dirname:129            os.chdir(tmp_dirname)130            # download sandbox131            tmpLog.info('downloading sandbox from {}'.format(sandbox_url))132            with requests.get(sandbox_url, allow_redirects=True, verify=False, stream=True) as r:133                if r.status_code == 400:134                    tmpLog.error("not found")135                    is_fatal = True136                    is_OK = False137                elif r.status_code != 200:138                    tmpLog.error("bad HTTP response {}".format(r.status_code))139                    is_OK = False140                # extract sandbox141                if is_OK:142                    with open(ops['data']['sandbox'], 'wb') as fs:143                        for chunk in r.raw.stream(1024, decode_content=False):144                            if chunk:145                                fs.write(chunk)146                        fs.close()147                        tmp_stat, tmp_out = commands_get_status_output(148                            'tar xvfz {}'.format(ops['data']['sandbox']))149                        if tmp_stat != 0:150                            tmpLog.error(tmp_out)151                            dump_str = 'failed to extract {}'.format(ops['data']['sandbox'])152                            tmpLog.error(dump_str)153                            is_fatal = True154                            is_OK = False155                # parse workflow files156                if is_OK:157                    tmpLog.info('parse workflow')158                    if ops['data']['language'] == 'cwl':159                        nodes, root_in = pcwl_utils.parse_workflow_file(ops['data']['workflowSpecFile'],160                                                                        tmpLog)161                        with open(ops['data']['workflowInputFile']) as workflow_input:162                            data = yaml.safe_load(workflow_input)163                        s_id, t_nodes, nodes = pcwl_utils.resolve_nodes(nodes, root_in, data, 0, set(),164                                                                        ops['data']['outDS'], tmpLog)165                        workflow_utils.set_workflow_outputs(nodes)166                        id_node_map = workflow_utils.get_node_id_map(nodes)167                        [node.resolve_params(ops['data']['taskParams'], id_node_map) for node in nodes]168                        dump_str = "the description was internally converted as follows\n" \169                                   + workflow_utils.dump_nodes(nodes)170                        tmpLog.info(dump_str)171                        for node in nodes:172                            s_check, o_check = node.verify()173                            tmp_str = 'Verification failure in ID:{} {}'.format(node.id, o_check)174                            if not s_check:175                                tmpLog.error(tmp_str)176                                dump_str += tmp_str177                                dump_str += '\n'178                                is_fatal = True179                                is_OK = False180                    else:181                        dump_str = "{} is not supported to describe the workflow"182                        tmpLog.error(dump_str)183                        is_fatal = True184                        is_OK = False185                    # convert to workflow186                    if is_OK:187                        workflow_to_submit, dump_str_list = workflow_utils.convert_nodes_to_workflow(nodes)188                        try:189                            if workflow_to_submit:190                                if not test_mode:191                                    tmpLog.info('submit workflow')192                                    wm = ClientManager(host=get_rest_host())193                                    request_id = wm.submit(workflow_to_submit, username=user_name)194                            else:195                                dump_str = 'workflow is empty'196                                tmpLog.error(dump_str)197                                is_fatal = True198                                is_OK = False199                        except Exception as e:200                            dump_str = 'failed to submit the workflow with {}'.format(str(e))201                            tmpLog.error('{} {}'.format(dump_str, traceback.format_exc()))202                        if dump_workflow:203                            tmpLog.debug('\n' + ''.join(dump_str_list))204        os.chdir(cur_dir)205    except Exception as e:206        is_OK = False207        is_fatal = True208        tmpLog.error("failed to run with {} {}".format(str(e), traceback.format_exc()))209    with tempfile.NamedTemporaryFile(delete=False, mode='w') as tmp_json:210        json.dump([is_OK, is_fatal, request_id, tmpLog.dumpToString()], tmp_json)211        print(tmp_json.name)212    sys.exit(0)213if __name__ == "__main__":...

setup.py

Source:setup.py

1from distutils.core import setup, Extension2from os import path3from codecs import open4import os5import sys6is_fatal = False7'/usr/lib/jvm/jre-1.7.0/lib/amd64/server/'8# Both MapR and non-MapR environments require the libjvm.so file9libjvm_dir = os.environ.get('PYCHBASE_LIBJVM_DIR', None)10if libjvm_dir is None:11    sys.stderr.write('WARNING: $PYCHBASE_LIBJVM_DIR not set, trying $JAVA_HOME...\n')12    java_home = os.environ.get('JAVA_HOME', None)13    if java_home is None:14        sys.stderr.write("WARNING: $JAVA_HOME not set, trying '/usr/lib/jvm/jre-1.7.0/'\n")15        java_home = '/usr/lib/jvm/jre-1.7.0/'16    if os.path.isdir(java_home):17        if os.path.isdir(os.path.join(java_home, 'lib', 'amd64', 'server')):18            sys.stderr.write('WARNING: Located %s\n' % os.path.join(java_home, 'lib', 'amd64', 'server'))19            libjvm_dir = os.path.join(java_home, 'lib', 'amd64', 'server')20        elif os.path.isdir(os.path.join(java_home, 'jre', 'lib', 'amd64', 'server')):21            sys.stderr.write('WARNING: Located %s\n' % os.path.join(java_home, 'jre', 'lib', 'amd64', 'server'))22            libjvm_dir = os.path.join(java_home, 'jre', 'lib', 'amd64', 'server')23        else:24            sys.stderr.write("ERROR: Could not detect the directory of libjvm.so from $JAVA_HOME\n")25            is_fatal = True26    else:27        is_fatal = True28else:29    if not os.path.isdir(libjvm_dir):30        sys.stderr.write("ERROR: libjvm directory does not exist '%s' \n" % libjvm_dir)31        is_fatal = True32is_mapr = os.environ.get('PYCHBASE_IS_MAPR', None)33if is_mapr is None:34    sys.stderr.write('WARNING: $PYCHBASE_IS_MAPR not set, defaulting to True. This will not work on Non-MapR environments. \n\tPlease export $PYCHBASE_IS_MAPR=FALSE if this is on Cloudera/etc\n')35    is_mapr = 'TRUE'36else:37    if is_mapr.upper() == 'TRUE':38        is_mapr = True39    elif is_mapr.upper() == 'FALSE':40        is_mapr = False41    else:42        sys.stderr.write("WARNING: $PYCHBASE_IS_MAPR should be 'TRUE' or 'FALSE', not '%s', I am defaulting to TRUE\n" % is_mapr)43define_macros = []44if is_mapr:45    define_macros.append(('PYCHBASE_MAPR', '1'))46libraries = ['jvm']47library_dirs = [libjvm_dir]48if is_mapr:49    libraries.append('MapRClient')50    include_dir = os.environ.get('PYCHBASE_INCLUDE_DIR', None)51    if include_dir is None:52        sys.stderr.write("WARNING: $PYCHBASE_INCLUDE_DIR not set. I am defaulting to '/opt/mapr/include'\n")53        include_dir = '/opt/mapr/include'54    library_dir = os.environ.get('PYCHBASE_LIBRARY_DIR', None)55    if library_dir is None:56        sys.stderr.write("WARNING: $PYCHBASE_LIBRARY_DIR not set. I am defaulting to '/opt/mapr/lib'\n")57        library_dir = '/opt/mapr/lib'58    if not os.path.isdir(include_dir):59        sys.stderr.write("ERROR: $PYCHASE_INCLUDE_DIR '%s' does not exist.\n" % include_dir)60        is_fatal = True61    if not os.path.isdir(library_dir):62        sys.stderr.write("ERROR: $PYCHBASE_LIBRARY_DIR '%s' does not exist.\n" % library_dir)63        is_fatal = True64else:65    libraries.append('hbase')66    include_dir = os.environ.get('PYCHBASE_INCLUDE_DIR', None)67    if include_dir is None:68        sys.stderr.write("ERROR: Non-MapR environments must set the $PYCHBASE_INCLUDE_DIR environment variable.\n")69        is_fatal = True70    else:71        if not os.path.isdir(include_dir):72            sys.stderr.write("ERROR: $PYCHBASE_INCLUDE_DIR '%s' does not exist.\n" % include_dir)73            is_fatal = True74    library_dir = os.environ.get('PYCHBASE_LIBRARY_DIR', None)75    if library_dir is None:76        sys.stderr.write("ERROR: Non-MapR environments must set the $PYCHBASE_LIBRARY_DIR environment variable.\n")77        is_fatal = True78    else:79        if not os.path.isdir(library_dir):80            sys.stderr.write("ERROR: $PYCHBASE_LIBRARY_DIR does '%s' does not exist.\n" % library_dir)81            is_fatal = True82if is_fatal:83    sys.stderr.write('ERROR: Failed to install pychbase due to environment variables being set incorrectly. \n\tPlease read the warning/error messages above and consult the readme\n')84    raise ValueError("Failed to install. Please check the readme")85include_dirs = [include_dir]86library_dirs.append(library_dir)87print("include_dirs is %s" % include_dirs)88print("library_dirs is %s" % library_dirs)89print("libraries is %s" % libraries)90here = path.abspath(path.dirname(__file__))91long_description = 'A Python wrapper for the libhbase C API to HBase'92try:93    import requests94    def read_md(file_name):95        try:96            with open(file_name, 'r') as f:97                contents = f.read()98        except IOError as ex:99            return long_description100        try:101            r = requests.post(url='http://c.docverter.com/convert',102                              data={'to': 'rst', 'from': 'markdown'},103                              files={'input_files[]': contents})104            if not r.ok:105                raise Exception(r.text)106            return r.text107        except Exception as ex:108            print ex109            return open(file_name, 'r').read()110except ImportError:111    def read_md(file_name):112        try:113            with open(file_name, 'r') as f:114                print("requests module not available-- cannot convert MD to RST")115                return f.read()116        except IOError:117            return long_description118module1 = Extension('pychbase._pychbase',119                    sources=['pychbase.cc'],120                    include_dirs=include_dirs,121                    libraries=libraries,122                    library_dirs=library_dirs,123                    define_macros=define_macros)124setup(name='pychbase',125      version='0.1.8',126      description=long_description,127      long_description=read_md('README.md'),128      url='https://github.com/mkmoisen/pychbase',129      download_url='https://github.com/mkmoisen/pychbase/tarball/0.1',130      author='Matthew Moisen',131      author_email='mmoisen@cisco.com',132      license='MIT',133      classifiers=[134          'Development Status :: 3 - Alpha',135          'Intended Audience :: Developers',136          'License :: OSI Approved :: MIT License',137          'Programming Language :: Python :: 2.7',138          'Programming Language :: Python :: Implementation :: CPython',139          'Natural Language :: English',140          'Operating System :: POSIX :: Linux',141          'Topic :: Database',142      ],143      keywords='hbase libhbase',144      ext_modules=[module1],...

exceptions.py

Source:exceptions.py

2class SENinjaError(Exception):3    def __init__(self, msg):4        self.message = msg5        super().__init__(msg)6    def is_fatal(self):7        raise NotImplementedError  # override8class DivByZero(SENinjaError):9    def __init__(self, pc):10        self.pc = pc11        self.message = "division by zero occurred at 0x%x" % pc12        super().__init__(self.message)13    def is_fatal(self):14        return False15class UnmappedRead(SENinjaError):16    def __init__(self, pc):17        self.pc = pc18        self.message = "unmapped read at 0x%x" % pc19        super().__init__(self.message)20    def is_fatal(self):21        return False22class UnmappedWrite(SENinjaError):23    def __init__(self, pc):24        self.pc = pc25        self.message = "unmapped write at 0x%x" % pc26        super().__init__(self.message)27    def is_fatal(self):28        return False29class NoDestination(SENinjaError):30    def __init__(self):31        self.message = "no destination"32        super().__init__(self.message)33    def is_fatal(self):34        return False35class UnconstrainedIp(SENinjaError):36    def __init__(self):37        self.message = "unconstrained ip"38        super().__init__(self.message)39    def is_fatal(self):40        return False41class UnsatState(SENinjaError):42    def __init__(self, pc):43        self.pc = pc44        self.message = "UNSAT state at 0x%x"45        super().__init__(self.message)46    def is_fatal(self):47        return True48class ModelError(SENinjaError):49    def __init__(self, model_name, msg):50        self.model_name = model_name51        self.message = "%s: %s" % (model_name, msg)52        super().__init__(self.message)53    def is_fatal(self):54        return True55class UnimplementedInstruction(SENinjaError):56    def __init__(self, instr_name, ip):57        self.instr_name = instr_name58        self.message = "%s instruction is unimplemented @ %#x" % (instr_name, ip)59        super().__init__(self.message)60    def is_fatal(self):61        return True62class UnimplementedModel(SENinjaError):63    def __init__(self, f_name):64        self.f_name = f_name65        self.message = "unimplemented model for function %s" % f_name66        super().__init__(self.message)67    def is_fatal(self):68        return True69class UnimplementedSyscall(SENinjaError):70    def __init__(self, syscall_n):71        self.syscall_n = syscall_n72        self.message = "unimplemented syscall %d" % syscall_n73        super().__init__(self.message)74    def is_fatal(self):75        return True76class UnsupportedOs(SENinjaError):77    def __init__(self, platform_name):78        self.platform_name = platform_name79        self.message = "unsupported os %s" % platform_name80        super().__init__(self.message)81    def is_fatal(self):82        return True83class UnsupportedArch(SENinjaError):84    def __init__(self, arch_name):85        self.arch_name = arch_name86        self.message = "unsupported arch %s" % arch_name87        super().__init__(self.message)88    def is_fatal(self):89        return True90# *****91class SENinjaExeption(Exception):92    pass93class ExitException(SENinjaExeption):...

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