def __init__(self):
self.parser = SeqalConfig()
# set default properties
self.properties = {
self.ConfLogLevel: self.DefaultLogLevel,
'mapred.create.symlink': 'yes',
'mapred.compress.map.output': 'true',
}
self.hdfs = None
self.options = None
self.left_over_args = None
self.logger = None
def __init__(self):
self.parser = SeqalConfig()
# set default properties
self.properties = {
self.ConfLogLevel: self.DefaultLogLevel,
'hadoop.pipes.java.recordreader': 'true',
'hadoop.pipes.java.recordwriter': 'true',
'mapred.create.symlink': 'yes',
'mapred.compress.map.output': 'true',
'bl.libhdfs.opts': '-Xmx48m'
}
self.hdfs = None
self.options = None
def __init__(self):
self.parser = SeqalConfig()
# set default properties
self.properties = {
self.ConfLogLevel: self.DefaultLogLevel,
'mapred.create.symlink': 'yes',
'mapred.compress.map.output': 'true',
}
self.hdfs = None
self.options = None
self.left_over_args = None
self.logger = None
def __init__(self):
self.parser = SeqalConfig()
# set default properties
self.properties = {
self.ConfLogLevel: self.DefaultLogLevel,
'hadoop.pipes.java.recordreader': 'true',
'hadoop.pipes.java.recordwriter': 'true',
'mapred.create.symlink': 'yes',
'mapred.compress.map.output': 'true',
'bl.libhdfs.opts': '-Xmx48m'
}
self.hdfs = None
self.options = None
class SeqalRun(object):
DefaultReduceTasksPerNode = 6
LogName = "seqal"
DefaultLogLevel = 'INFO'
ConfLogLevel = 'seal.seqal.log.level'
ConfLogLevel_deprecated = 'bl.seqal.log.level'
def __init__(self):
self.parser = SeqalConfig()
# set default properties
self.properties = {
self.ConfLogLevel: self.DefaultLogLevel,
'hadoop.pipes.java.recordreader': 'true',
'hadoop.pipes.java.recordwriter': 'true',
'mapred.create.symlink': 'yes',
'mapred.compress.map.output': 'true',
'bl.libhdfs.opts': '-Xmx48m'
}
self.hdfs = None
self.options = None
def parse_cmd_line(self):
self.options, self.left_over_args = self.parser.load_config_and_cmd_line(
)
# set the job name. Do it here so the user can override it
self.properties[
'mapred.job.name'] = 'seqal_aln_%s' % self.options.output
# now collect the property values specified in the options and
# copy them to properties
for k, v in self.options.properties.iteritems():
self.properties[k] = v
# create a logger
logging.basicConfig()
self.logger = logging.getLogger(self.__class__.LogName)
# temporarily set to a high logging level in case we have to print warnings
# regarding deprecated properties
self.logger.setLevel(logging.DEBUG)
# warn for deprecated bl.seqal.log.level property
if self.properties.has_key(self.ConfLogLevel_deprecated):
deprecation.deprecation_warning(self.logger,
self.ConfLogLevel_deprecated,
self.ConfLogLevel)
if self.properties[self.ConfLogLevel] == self.DefaultLogLevel and \
self.properties[self.ConfLogLevel_deprecated] != self.DefaultLogLevel:
# the deprecated property is different from default, while the new property is not. Therefore,
# the user has set the deprecated property to a new value. We'll use that one.
self.properties[self.ConfLogLevel] = self.properties[
self.ConfLogLevel_deprecated]
self.logger.warning(
"Using value %s for property %s (value taken from its deprecated equivalent property %s).",
self.properties[self.ConfLogLevel], self.ConfLogLevel,
self.ConfLogLevel_deprecated)
# Set proper logging level
log_level = getattr(logging, self.properties['seal.seqal.log.level'],
None)
if log_level is None:
self.logger.setLevel(logging.DEBUG)
self.logger.warning(
"Invalid configuration value '%s' for %s. Check your configuration.",
self.ConfLogLevel, self.properties['seal.seqal.log.level'])
self.logger.warning("Falling back to DEBUG")
self.logger.warning(
"Valid values for seal.seqal.log.level are: DEBUG, INFO, WARNING, ERROR, CRITICAL; default: %s",
SeqalRun.DefaultLogLevel)
else:
self.logger.setLevel(log_level)
# reference
self.properties[
'mapred.cache.archives'] = '%s#reference' % self.options.reference
# set the number of reduce tasks
if self.options.align_only:
n_red_tasks = 0
if self.options.num_reducers and self.options.num_reducers > 0:
self.logger.warning(
"Number of reduce tasks must be 0 when doing --align-only."
)
self.logger.warning("Ignoring request for %d reduce tasks",
self.options.num_reducers)
elif self.options.num_reducers:
n_red_tasks = self.options.num_reducers
else:
n_red_tasks = SeqalRun.DefaultReduceTasksPerNode * hadut.num_nodes(
)
self.properties['mapred.reduce.tasks'] = n_red_tasks
def __write_pipes_script(self, fd):
ld_path = ":".join(
filter(lambda x: x, [os.environ.get('LD_LIBRARY_PATH', None)]))
pypath = os.environ.get('PYTHONPATH', '')
self.logger.debug("LD_LIBRARY_PATH for tasks: %s", ld_path)
self.logger.debug("PYTHONPATH for tasks: %s", pypath)
fd.write("#!/bin/bash\n")
fd.write('""":"\n')
# should we set HOME to ~? Hadoop by default sets $HOME to /homes, unless the
# cluster administrator sets mapreduce.admin.user.home.dir. This kills local installations
#fd.write('[ -d "${HOME}" ] || export HOME="$(echo ~)"\n')
# which causes python not to add installations under ~/.local/ to the PYTHONPATH
fd.write(
'export LD_LIBRARY_PATH="%s" # Seal dir + LD_LIBRARY_PATH copied from the env where you ran %s\n'
% (ld_path, sys.argv[0]))
fd.write('export PYTHONPATH="%s"\n' % pypath)
if self.logger.isEnabledFor(logging.DEBUG):
fd.write('env >&2\n') # write the environment to the stderr log
fd.write(
'echo >&2; cat $0 >&2\n') # write the script to the stderr log
fd.write('exec "%s" -u "$0" "$@"\n' % sys.executable)
fd.write('":"""\n')
script = """
import sys
try:
from seal.seqal import run_task
run_task()
except ImportError as e:
sys.stderr.write(str(e) + "\\n")
sys.stderr.write("Can't import seal module\\n")
sys.stderr.write("Did you install Seal to a system path on all the nodes?\\n")
sys.stderr.write("If you installed to a non-system path (e.g. your home directory)\\n")
sys.stderr.write("you'll have to set PYTHONPATH to point to it.\\n")
sys.stderr.write("Current Python library paths:\\n")
sys.stderr.write(" sys.path: %s:\\n" % ':'.join(map(str, sys.path)))
"""
fd.write(script)
def run(self):
if self.options is None:
raise RuntimeError("You must call parse_cmd_line before run")
if self.logger.isEnabledFor(logging.DEBUG):
self.logger.debug("Running Seqal")
self.logger.debug(
"Properties:\n%s", "\n".join(
sorted([
"%s = %s" % (str(k), str(v))
for k, v in self.properties.iteritems()
])))
self.logger.info("Input: %s; Output: %s; reference: %s",
self.options.input, self.options.output,
self.options.reference)
try:
self.hdfs = phdfs.hdfs('default', 0)
self.__validate()
self.remote_bin_name = tempfile.mktemp(prefix='seqal_bin.',
suffix=str(random.random()),
dir='')
try:
with self.hdfs.open_file(self.remote_bin_name, 'w') as script:
self.__write_pipes_script(script)
full_name = self.hdfs.get_path_info(
self.remote_bin_name)['name']
return hadut.run_pipes(full_name,
self.options.input,
self.options.output,
properties=self.properties,
args_list=self.left_over_args)
finally:
try:
self.hdfs.delete(
self.remote_bin_name
) # delete the temporary pipes script from HDFS
self.logger.debug("pipes script %s deleted",
self.remote_bin_name)
except:
self.logger.error(
"Error deleting the temporary pipes script %s from HDFS",
self.remote_bin_name)
## don't re-raise the exception. We're on our way out
finally:
if self.hdfs:
tmp = self.hdfs
self.hdfs = None
tmp.close()
self.logger.debug("HDFS closed")
def __validate(self):
if self.properties['mapred.reduce.tasks'] == 0:
self.logger.info("Running in alignment-only mode (no rmdup).")
# validate conditions
if phdfs.path.exists(self.options.output):
raise SeqalConfigError(
"Output directory %s already exists. Please delete it or specify a different output directory."
% self.options.output)
if not phdfs.path.exists(self.options.reference):
raise SeqalConfigError("Can't read reference archive %s" %
self.options.reference)
class SeqalRun(object):
DefaultReduceTasksPerNode = 6
LogName = "seqal"
DefaultLogLevel = 'INFO'
ConfLogLevel = 'seal.seqal.log.level'
ConfLogLevel_deprecated = 'bl.seqal.log.level'
def __init__(self):
self.parser = SeqalConfig()
# set default properties
self.properties = {
self.ConfLogLevel: self.DefaultLogLevel,
'hadoop.pipes.java.recordreader': 'true',
'hadoop.pipes.java.recordwriter': 'true',
'mapred.create.symlink': 'yes',
'mapred.compress.map.output': 'true',
'bl.libhdfs.opts': '-Xmx48m'
}
self.hdfs = None
self.options = None
def parse_cmd_line(self, args):
self.options, self.left_over_args = self.parser.load_config_and_cmd_line(args)
# set the job name. Do it here so the user can override it
self.properties['mapred.job.name'] = 'seqal_aln_%s' % self.options.output
# now collect the property values specified in the options and
# copy them to properties
for k,v in self.options.properties.iteritems():
self.properties[k] = v
# create a logger
logging.basicConfig()
self.logger = logging.getLogger(self.__class__.LogName)
# temporarily set to a high logging level in case we have to print warnings
# regarding deprecated properties
self.logger.setLevel(logging.DEBUG)
# warn for deprecated bl.seqal.log.level property
if self.properties.has_key(self.ConfLogLevel_deprecated):
deprecation.deprecation_warning(self.logger, self.ConfLogLevel_deprecated, self.ConfLogLevel)
if self.properties[self.ConfLogLevel] == self.DefaultLogLevel and \
self.properties[self.ConfLogLevel_deprecated] != self.DefaultLogLevel:
# the deprecated property is different from default, while the new property is not. Therefore,
# the user has set the deprecated property to a new value. We'll use that one.
self.properties[self.ConfLogLevel] = self.properties[self.ConfLogLevel_deprecated]
self.logger.warning("Using value %s for property %s (value taken from its deprecated equivalent property %s).",
self.properties[self.ConfLogLevel], self.ConfLogLevel, self.ConfLogLevel_deprecated)
# Set proper logging level
log_level = getattr(logging, self.properties['seal.seqal.log.level'], None)
if log_level is None:
self.logger.setLevel(logging.DEBUG)
self.logger.warning("Invalid configuration value '%s' for %s. Check your configuration.", self.ConfLogLevel, self.properties['seal.seqal.log.level'])
self.logger.warning("Falling back to DEBUG")
self.logger.warning("Valid values for seal.seqal.log.level are: DEBUG, INFO, WARNING, ERROR, CRITICAL; default: %s", SeqalRun.DefaultLogLevel)
else:
self.logger.setLevel(log_level)
# reference
self.properties['mapred.cache.archives'] = '%s#reference' % self.options.reference
# set the number of reduce tasks
if self.options.align_only:
n_red_tasks = 0
if self.options.num_reducers and self.options.num_reducers > 0:
self.logger.warning("Number of reduce tasks must be 0 when doing --align-only.")
self.logger.warning("Ignoring request for %d reduce tasks", self.options.num_reducers)
elif self.options.num_reducers:
n_red_tasks = self.options.num_reducers
else:
n_red_tasks = SeqalRun.DefaultReduceTasksPerNode * hadut.get_num_nodes()
self.properties['mapred.reduce.tasks'] = n_red_tasks
def __write_pipes_script(self, fd):
ld_path = ":".join( filter(lambda x:x, [os.environ.get('LD_LIBRARY_PATH', None)]) )
pypath = os.environ.get('PYTHONPATH', '')
self.logger.debug("LD_LIBRARY_PATH for tasks: %s", ld_path)
self.logger.debug("PYTHONPATH for tasks: %s", pypath)
fd.write("#!/bin/bash\n")
fd.write('""":"\n')
# should we set HOME to ~? Hadoop by default sets $HOME to /homes, unless the
# cluster administrator sets mapreduce.admin.user.home.dir. This kills local installations
#fd.write('[ -d "${HOME}" ] || export HOME="$(echo ~)"\n')
# which causes python not to add installations under ~/.local/ to the PYTHONPATH
fd.write('export LD_LIBRARY_PATH="%s" # Seal dir + LD_LIBRARY_PATH copied from the env where you ran %s\n' % (ld_path, sys.argv[0]))
fd.write('export PYTHONPATH="%s"\n' % pypath)
if self.logger.isEnabledFor(logging.DEBUG):
fd.write('env >&2\n') # write the environment to the stderr log
fd.write('echo >&2; cat $0 >&2\n') # write the script to the stderr log
fd.write('exec "%s" -u "$0" "$@"\n' % sys.executable)
fd.write('":"""\n')
script = """
import sys
try:
from seal.seqal import run_task
run_task()
except ImportError as e:
sys.stderr.write(str(e) + "\\n")
sys.stderr.write("Can't import seal module\\n")
sys.stderr.write("Did you install Seal to a system path on all the nodes?\\n")
sys.stderr.write("If you installed to a non-system path (e.g. your home directory)\\n")
sys.stderr.write("you'll have to set PYTHONPATH to point to it.\\n")
sys.stderr.write("Current Python library paths:\\n")
sys.stderr.write(" sys.path: %s:\\n" % ':'.join(map(str, sys.path)))
"""
fd.write(script)
def run(self):
if self.options is None:
raise RuntimeError("You must call parse_cmd_line before run")
if self.logger.isEnabledFor(logging.DEBUG):
self.logger.debug("Running Seqal")
self.logger.debug("Properties:\n%s", "\n".join( sorted([ "%s = %s" % (str(k), str(v)) for k,v in self.properties.iteritems() ]) ))
self.logger.info("Input: %s; Output: %s; reference: %s", self.options.input, self.options.output, self.options.reference)
try:
self.hdfs = phdfs.hdfs('default', 0)
self.__validate()
self.remote_bin_name = tempfile.mktemp(prefix='seqal_bin.', suffix=str(random.random()), dir='')
try:
with self.hdfs.open_file(self.remote_bin_name, 'w') as script:
self.__write_pipes_script(script)
full_name = self.hdfs.get_path_info(self.remote_bin_name)['name']
return seal_utilities.run_pipes(full_name, self.options.input, self.options.output,
properties=self.properties, args_list=self.left_over_args)
finally:
try:
self.hdfs.delete(self.remote_bin_name) # delete the temporary pipes script from HDFS
self.logger.debug("pipes script %s deleted", self.remote_bin_name)
except:
self.logger.error("Error deleting the temporary pipes script %s from HDFS", self.remote_bin_name)
## don't re-raise the exception. We're on our way out
finally:
if self.hdfs:
tmp = self.hdfs
self.hdfs = None
tmp.close()
self.logger.debug("HDFS closed")
def __validate(self):
if self.properties['mapred.reduce.tasks'] == 0:
self.logger.info("Running in alignment-only mode (no rmdup).")
# validate conditions
if phdfs.path.exists(self.options.output):
raise SeqalConfigError("Output directory %s already exists. Please delete it or specify a different output directory." % self.options.output)
if not phdfs.path.exists(self.options.reference):
raise SeqalConfigError("Can't read reference archive %s" % self.options.reference)
class SeqalSubmit(object):
DefaultReduceTasksPerNode = 6
LogName = "seqal"
DefaultLogLevel = 'INFO'
ConfLogLevel = 'seal.seqal.log.level'
ConfLogLevel_deprecated = 'bl.seqal.log.level'
def __init__(self):
self.parser = SeqalConfig()
# set default properties
self.properties = {
self.ConfLogLevel: self.DefaultLogLevel,
'mapred.create.symlink': 'yes',
'mapred.compress.map.output': 'true',
}
self.hdfs = None
self.options = None
self.left_over_args = None
self.logger = None
def parse_cmd_line(self, args):
self.options, self.left_over_args = self.parser.load_config_and_cmd_line(
args)
# set the job name. Do it here so the user can override it
self.properties[
'mapred.job.name'] = 'seqal_aln_%s' % self.options.output
# now collect the property values specified in the options and
# copy them to properties
for k, v in self.options.properties.iteritems():
self.properties[k] = v
# create a logger
logging.basicConfig()
self.logger = logging.getLogger(self.__class__.LogName)
# temporarily set to a high logging level in case we have to print warnings
# regarding deprecated properties
self.logger.setLevel(logging.DEBUG)
# warn for deprecated bl.seqal.log.level property
if self.properties.has_key(self.ConfLogLevel_deprecated):
deprecation.deprecation_warning(self.logger,
self.ConfLogLevel_deprecated,
self.ConfLogLevel)
if self.properties[self.ConfLogLevel] == self.DefaultLogLevel and \
self.properties[self.ConfLogLevel_deprecated] != self.DefaultLogLevel:
# the deprecated property is different from default, while the new property is not. Therefore,
# the user has set the deprecated property to a new value. We'll use that one.
self.properties[self.ConfLogLevel] = self.properties[
self.ConfLogLevel_deprecated]
self.logger.warning(
"Using value %s for property %s (value taken from its deprecated equivalent property %s).",
self.properties[self.ConfLogLevel], self.ConfLogLevel,
self.ConfLogLevel_deprecated)
# Set proper logging level
log_level = getattr(logging, self.properties['seal.seqal.log.level'],
None)
if log_level is None:
self.logger.setLevel(logging.DEBUG)
self.logger.warning(
"Invalid configuration value '%s' for %s. Check your configuration.",
self.ConfLogLevel, self.properties['seal.seqal.log.level'])
self.logger.warning("Falling back to DEBUG")
self.logger.warning(
"Valid values for seal.seqal.log.level are: DEBUG, INFO, WARNING, ERROR, CRITICAL; default: %s",
SeqalSubmit.DefaultLogLevel)
else:
self.logger.setLevel(log_level)
# reference
self.properties[
'mapred.cache.archives'] = '%s#reference' % self.options.reference
# set the number of reduce tasks
if self.options.align_only:
n_red_tasks = 0
if self.options.num_reducers and self.options.num_reducers > 0:
self.logger.warning(
"Number of reduce tasks must be 0 when doing --align-only."
)
self.logger.warning("Ignoring request for %d reduce tasks",
self.options.num_reducers)
elif self.options.num_reducers:
n_red_tasks = self.options.num_reducers
else:
n_red_tasks = SeqalSubmit.DefaultReduceTasksPerNode * hadut.get_num_nodes(
)
self.properties['mapred.reduce.tasks'] = n_red_tasks
def run(self):
self.logger.setLevel(logging.DEBUG)
if self.options is None:
raise RuntimeError("You must call parse_cmd_line before run")
if self.logger.isEnabledFor(logging.DEBUG):
self.logger.debug("Running Seqal")
self.logger.debug(
"Properties:\n%s", "\n".join(
sorted([
"%s = %s" % (str(k), str(v))
for k, v in self.properties.iteritems()
])))
self.logger.info("Input: %s; Output: %s; reference: %s",
self.options.input, self.options.output,
self.options.reference)
pydoop_argv = ['submit']
# some properties have "pydoop submit" command line arguments which should be preferred
if self.properties.has_key('mapred.job.name'):
pydoop_argv.extend(
('--job-name', self.properties.pop('mapred.job.name')))
if self.properties.has_key('mapred.reduce.tasks'):
pydoop_argv.extend(
('--num-reducers',
str(self.properties.pop('mapred.reduce.tasks'))))
if self.properties.has_key('mapred.cache.archives'):
pydoop_argv.extend(('--cache-archive',
self.properties.pop('mapred.cache.archives')))
pydoop_argv.extend("-D{}={}".format(k, v)
for k, v in self.properties.iteritems())
pydoop_argv.append('seal.seqal.seqal_run')
pydoop_argv.extend(('--entry-point', 'run_job'))
pydoop_argv.extend(self.left_over_args)
pydoop_argv.append(self.options.input)
pydoop_argv.append(self.options.output)
self.logger.debug("Calling pydoop.app.main with these args:")
self.logger.debug(pydoop_argv)
self.logger.info("Lauching job")
pydoop_main(pydoop_argv)
self.logger.info("finished")
def __validate(self):
if self.properties['mapred.reduce.tasks'] == 0:
self.logger.info("Running in alignment-only mode (no rmdup).")
# validate conditions
if phdfs.path.exists(self.options.output):
raise SeqalConfigError(
"Output directory %s already exists. "
"Please delete it or specify a different output directory." %
self.options.output)
if not phdfs.path.exists(self.options.reference):
raise SeqalConfigError("Can't read reference archive %s" %
self.options.reference)
class SeqalSubmit(object):
DefaultReduceTasksPerNode = 6
LogName = "seqal"
DefaultLogLevel = 'INFO'
ConfLogLevel = 'seal.seqal.log.level'
ConfLogLevel_deprecated = 'bl.seqal.log.level'
def __init__(self):
self.parser = SeqalConfig()
# set default properties
self.properties = {
self.ConfLogLevel: self.DefaultLogLevel,
'mapred.create.symlink': 'yes',
'mapred.compress.map.output': 'true',
}
self.hdfs = None
self.options = None
self.left_over_args = None
self.logger = None
def parse_cmd_line(self, args):
self.options, self.left_over_args = self.parser.load_config_and_cmd_line(args)
# set the job name. Do it here so the user can override it
self.properties['mapred.job.name'] = 'seqal_aln_%s' % self.options.output
# now collect the property values specified in the options and
# copy them to properties
for k,v in self.options.properties.iteritems():
self.properties[k] = v
# create a logger
logging.basicConfig()
self.logger = logging.getLogger(self.__class__.LogName)
# temporarily set to a high logging level in case we have to print warnings
# regarding deprecated properties
self.logger.setLevel(logging.DEBUG)
# warn for deprecated bl.seqal.log.level property
if self.properties.has_key(self.ConfLogLevel_deprecated):
deprecation.deprecation_warning(self.logger, self.ConfLogLevel_deprecated, self.ConfLogLevel)
if self.properties[self.ConfLogLevel] == self.DefaultLogLevel and \
self.properties[self.ConfLogLevel_deprecated] != self.DefaultLogLevel:
# the deprecated property is different from default, while the new property is not. Therefore,
# the user has set the deprecated property to a new value. We'll use that one.
self.properties[self.ConfLogLevel] = self.properties[self.ConfLogLevel_deprecated]
self.logger.warning("Using value %s for property %s (value taken from its deprecated equivalent property %s).",
self.properties[self.ConfLogLevel], self.ConfLogLevel, self.ConfLogLevel_deprecated)
# Set proper logging level
log_level = getattr(logging, self.properties['seal.seqal.log.level'], None)
if log_level is None:
self.logger.setLevel(logging.DEBUG)
self.logger.warning("Invalid configuration value '%s' for %s. Check your configuration.",
self.ConfLogLevel, self.properties['seal.seqal.log.level'])
self.logger.warning("Falling back to DEBUG")
self.logger.warning("Valid values for seal.seqal.log.level are: DEBUG, INFO, WARNING, ERROR, CRITICAL; default: %s",
SeqalSubmit.DefaultLogLevel)
else:
self.logger.setLevel(log_level)
# reference
self.properties['mapred.cache.archives'] = '%s#reference' % self.options.reference
# set the number of reduce tasks
if self.options.align_only:
n_red_tasks = 0
if self.options.num_reducers and self.options.num_reducers > 0:
self.logger.warning("Number of reduce tasks must be 0 when doing --align-only.")
self.logger.warning("Ignoring request for %d reduce tasks", self.options.num_reducers)
elif self.options.num_reducers:
n_red_tasks = self.options.num_reducers
else:
n_red_tasks = SeqalSubmit.DefaultReduceTasksPerNode * hadut.get_num_nodes()
self.properties['mapred.reduce.tasks'] = n_red_tasks
def run(self):
self.logger.setLevel(logging.DEBUG)
if self.options is None:
raise RuntimeError("You must call parse_cmd_line before run")
if self.logger.isEnabledFor(logging.DEBUG):
self.logger.debug("Running Seqal")
self.logger.debug("Properties:\n%s",
"\n".join( sorted([ "%s = %s" % (str(k), str(v)) for k,v in self.properties.iteritems() ]) ))
self.logger.info("Input: %s; Output: %s; reference: %s",
self.options.input, self.options.output, self.options.reference)
pydoop_argv = [ 'submit' ]
# some properties have "pydoop submit" command line arguments which should be preferred
if self.properties.has_key('mapred.job.name'):
pydoop_argv.extend( ('--job-name', self.properties.pop('mapred.job.name')) )
if self.properties.has_key('mapred.reduce.tasks'):
pydoop_argv.extend( ('--num-reducers', str(self.properties.pop('mapred.reduce.tasks'))) )
if self.properties.has_key('mapred.cache.archives'):
pydoop_argv.extend( ('--cache-archive', self.properties.pop('mapred.cache.archives')) )
pydoop_argv.extend( "-D{}={}".format(k, v) for k, v in self.properties.iteritems() )
pydoop_argv.append('seal.seqal.seqal_run')
pydoop_argv.extend( ('--entry-point', 'run_job' ))
pydoop_argv.extend(self.left_over_args)
pydoop_argv.append(self.options.input)
pydoop_argv.append(self.options.output)
self.logger.debug("Calling pydoop.app.main with these args:")
self.logger.debug(pydoop_argv)
self.logger.info("Lauching job")
pydoop_main(pydoop_argv)
self.logger.info("finished")
def __validate(self):
if self.properties['mapred.reduce.tasks'] == 0:
self.logger.info("Running in alignment-only mode (no rmdup).")
# validate conditions
if phdfs.path.exists(self.options.output):
raise SeqalConfigError(
"Output directory %s already exists. "
"Please delete it or specify a different output directory." % self.options.output)
if not phdfs.path.exists(self.options.reference):
raise SeqalConfigError("Can't read reference archive %s" % self.options.reference)
