def main(argv=sys.argv, out=sys.stdout):
setup_log_ = functools.partial(
setup_log, str_formatter='%(asctime)s [%(levelname)s] %(message)s')
try:
return pbparser_runner(
argv=argv[1:],
parser=get_parser(),
args_runner_func=args_runner,
contract_runner_func=resolved_tool_contract_runner,
alog=logging.getLogger(__name__),
setup_log_func=setup_log_)
# FIXME is there a more central place to deal with this?
except Exception as e:
type, value, tb = sys.exc_info()
traceback.print_exc(file=sys.stderr)
# Note: if kt.args.usePdb
# This won't work. If an exception is raised in parseArgs,
# then kt.args is not defined yet.
if '--pdb' in argv:
try:
# this has better integration with ipython and is nicer
# pip install ipdb
import ipdb
ipdb.post_mortem(tb)
except ImportError:
import pdb
pdb.post_mortem(tb)
else:
# exit non-zero
raise
def main(argv=sys.argv, out=sys.stdout):
setup_log_ = functools.partial(setup_log,
str_formatter='%(asctime)s [%(levelname)s] %(message)s')
try:
return pbparser_runner(
argv=argv[1:],
parser=get_parser(),
args_runner_func=args_runner,
contract_runner_func=resolved_tool_contract_runner,
alog=logging.getLogger(__name__),
setup_log_func=setup_log_)
# FIXME is there a more central place to deal with this?
except Exception as e:
type, value, tb = sys.exc_info()
traceback.print_exc(file=sys.stderr)
# Note: if kt.args.usePdb
# This won't work. If an exception is raised in parseArgs,
# then kt.args is not defined yet.
if '--pdb' in argv:
try:
# this has better integration with ipython and is nicer
# pip install ipdb
import ipdb
ipdb.post_mortem(tb)
except ImportError:
import pdb
pdb.post_mortem(tb)
else:
# exit non-zero
raise
def main(argv=sys.argv):
mp = get_contract_parser()
return pbparser_runner(argv[1:],
mp, args_runner,
rtc_runner,
log,
setup_log)
def main(argv=sys.argv):
return pbparser_runner(argv[1:],
get_parser(),
run_args,
run_rtc,
log,
setup_log)
def main(argv=sys.argv):
mp = get_contract_parser()
return pbparser_runner(argv[1:],
mp, args_runner,
rtc_runner,
log,
setup_log)
def main(argv=sys.argv):
return pbparser_runner(argv[1:],
_get_parser(),
_args_runner,
_resolved_tool_contract_runner,
log,
setup_log)
def main(argv=sys.argv):
return pbparser_runner(argv[1:],
get_parser(),
args_runner,
rtc_runner,
log,
setup_log)
def main(argv=sys.argv):
return pbparser_runner(argv=argv[1:],
parser=get_parser(),
args_runner_func=args_runner,
contract_runner_func=resolved_tool_contract_runner,
alog=log,
setup_log_func=setup_log)
def main(argv=sys.argv):
return pbparser_runner(argv[1:],
gather_report.get_parser(constants=Constants),
gather_report.args_runner,
gather_report.rtc_runner,
log,
setup_log)
def main(argv=sys.argv):
return pbparser_runner(argv[1:],
get_parser(),
args_runner,
rtc_runner,
log,
setup_log)
def main(argv=sys.argv):
mp = scatter_alignments_reference.get_contract_parser(
tool_id=TOOL_ID, module_name=MODULE_NAME)
return pbparser_runner(argv[1:], mp,
scatter_alignments_reference.args_runner,
scatter_alignments_reference.rtc_runner, log,
setup_log)
def main(argv=sys.argv):
mp = get_parser()
summarize_coverage.add_options_to_parser(mp,
ds_type=FileTypes.DS_ALIGN_CCS)
return pbparser_runner(argv[1:], mp, summarize_coverage.args_runner,
summarize_coverage.resolved_tool_contract_runner,
log, setup_log)
def main(argv=sys.argv[1:]):
"""Main point of Entry"""
return pbparser_runner(argv,
get_parser(),
args_runner,
resolved_tool_contract_runner,
log,
setup_log)
def main(argv=sys.argv):
"""Main point of Entry"""
return pbparser_runner(argv=argv[1:],
parser=_get_parser(),
args_runner_func=_args_runner,
contract_runner_func=_resolved_tool_contract_runner,
alog=log,
setup_log_func=setup_log)
def main():
"""main"""
mp = get_contract_parser()
return pbparser_runner(sys.argv[1:],
mp, args_runner,
rtc_runner,
log,
setup_log)
def main(argv=sys.argv):
return pbparser_runner(
argv=argv[1:],
parser=get_parser(),
args_runner_func=args_runner,
contract_runner_func=resolved_tool_contract_runner,
alog=log,
setup_log_func=setup_log)
def main():
"""Main"""
return pbparser_runner(sys.argv[1:],
get_contract_parser(),
_args_run,
_rtc_runner,
log,
setup_log)
def main(argv=sys.argv):
mp = get_contract_parser_impl(Constants)
return pbparser_runner(argv[1:],
mp,
_args_runner,
_rtc_runner,
log,
setup_log)
def main(argv=sys.argv):
mp = get_contract_parser()
return pbparser_runner(argv[1:],
mp,
_args_run_to_random_fasta_file,
_rtc_runner,
log,
setup_log)
def main():
"""main"""
mp = get_contract_parser()
return pbparser_runner(sys.argv[1:],
mp, args_runner,
rtc_runner,
log,
setup_log)
def main(argv=sys.argv):
# New interface that supports running resolved tool contracts
log.info("Starting {f} version {v} pbcommand example dev app".format(
f=__file__, v=__version__))
p = get_contract_parser()
return pbparser_runner(argv[1:], p, args_runner,
resolved_tool_contract_runner, log, setup_log)
def main(argv=sys.argv):
mp = get_parser()
summarize_coverage.add_options_to_parser(mp, ds_type=FileTypes.DS_ALIGN_CCS)
return pbparser_runner(argv[1:],
mp,
summarize_coverage.args_runner,
summarize_coverage.resolved_tool_contract_runner,
log,
setup_log)
def main(argv=sys.argv[1:], driver_class=CoverageReport):
"""Main point of Entry"""
driver = driver_class()
return pbparser_runner(argv,
driver.get_parser(),
driver.args_runner,
driver.resolved_tool_contract_runner,
log,
setup_log)
def main(argv=sys.argv):
logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger()
return pbparser_runner(argv[1:],
get_parser(),
args_runner,
rtc_runner,
log,
setup_log)
def main(argv=sys.argv,
get_parser_func=get_contract_parser,
contract_runner_func=resolved_tool_contract_runner):
return pbparser_runner(argv=argv[1:],
parser=get_parser_func(),
args_runner_func=args_runner,
contract_runner_func=contract_runner_func,
alog=logging.getLogger(__name__),
setup_log_func=setup_log)
def main(argv=sys.argv):
mp = get_subreads_report_parser(Constants.TOOL_ID, __version__, spec.title,
__doc__, Constants.DRIVER_EXE)
return pbparser_runner(argv[1:],
mp,
args_runner,
resolved_tool_contract_runner,
log,
setup_log)
def main(argv=sys.argv, get_parser_func=get_contract_parser,
contract_runner_func=resolved_tool_contract_runner):
return pbparser_runner(
argv=argv[1:],
parser=get_parser_func(),
args_runner_func=args_runner,
contract_runner_func=contract_runner_func,
alog=logging.getLogger(__name__),
setup_log_func=setup_log)
def main():
"""main"""
mp = get_contract_parser()
return pbparser_runner(argv=sys.argv[1:],
parser=mp,
args_runner_func=args_runner,
contract_runner_func=resolved_tool_contract_runner,
alog=log,
setup_log_func=setup_log)
def main(argv=sys.argv):
setup_log_ = functools.partial(setup_log,
str_formatter=LogFormats.LOG_FMT_LVL)
return pbparser_runner(argv=argv[1:],
parser=get_parser(),
args_runner_func=args_runner,
contract_runner_func=resolved_tool_contract_runner,
alog=logging.getLogger(),
setup_log_func=setup_log_)
def main(argv=sys.argv[1:], driver_class=CoverageReport):
"""Main point of Entry"""
driver = driver_class()
return pbparser_runner(argv,
driver.get_parser(),
driver.args_runner,
driver.resolved_tool_contract_runner,
log,
setup_log)
def main(argv=sys.argv, get_parser_func=_get_parser,
args_runner_func=_args_runner,
rtc_runner_func=_resolved_tool_contract_runner):
mp = get_parser_func()
return pbparser_runner(argv[1:],
mp,
args_runner_func,
rtc_runner_func,
log,
setup_log)
def main(argv=sys.argv):
setup_log_ = functools.partial(setup_log,
str_formatter=LogFormats.LOG_FMT_LVL)
return pbparser_runner(
argv=argv[1:],
parser=get_parser(),
args_runner_func=args_runner,
contract_runner_func=resolved_tool_contract_runner,
alog=logging.getLogger(),
setup_log_func=setup_log_)
def main(argv=sys.argv):
log.info("Starting {f} version {v} pbcommand example dev app".format(f=__file__, v=__version__))
# PbParser instance, this has both the argparse instance and the tool contract
# instance.
mp = get_contract_parser()
# To Access the argparse instance
# mp.arg_parser.parser
# The Tool Contract parser
# mp.tool_contract_parser.parser
return pbparser_runner(argv[1:], mp, args_runner, resolved_tool_contract_runner, log, setup_log)
def main(argv=sys.argv, get_parser_func=get_contract_parser,
contract_runner_func=resolved_tool_contract_runner):
"""Main, supporting both args runner and tool contract runner."""
return pbparser_runner(
argv=argv[1:],
parser=get_parser_func(),
args_runner_func=args_runner,
contract_runner_func=contract_runner_func,
alog=logging.getLogger(__name__),
setup_log_func=setup_log)
def main(argv=sys.argv):
# New interface that supports running resolved tool contracts
log.info("Starting {f} version {v} pbcommand example dev app".format(f=__file__, v=__version__))
p = get_contract_parser()
return pbparser_runner(argv[1:], p,
args_runner,
resolved_tool_contract_runner,
log,
setup_log)
def main(argv=sys.argv):
mp = scatter_alignments_reference.get_contract_parser(
tool_id=TOOL_ID,
module_name=MODULE_NAME)
return pbparser_runner(argv[1:],
mp,
scatter_alignments_reference.args_runner,
scatter_alignments_reference.rtc_runner,
log,
setup_log)
def main(argv=sys.argv, get_parser_func=_get_parser,
args_runner_func=_args_runner,
rtc_runner_func=_resolved_tool_contract_runner):
mp = get_parser_func()
return pbparser_runner(argv[1:],
mp,
args_runner_func,
rtc_runner_func,
log,
setup_log)
def main(argv=sys.argv):
log.info("Starting {f} version {v} pbcommand example dev app".format(f=__file__, v=__version__))
p = get_contract_parser()
return pbparser_runner(argv[1:],
p,
_args_runner, # argparse runner func
_resolved_tool_contract_runner, # tool contract runner func
log, # log instance
setup_log # setup log func
)
def main(argv=sys.argv,
get_parser_func=get_contract_parser,
contract_runner_func=resolved_tool_contract_runner):
"""Main, supporting both args runner and tool contract runner."""
return pbparser_runner(argv=argv[1:],
parser=get_parser_func(),
args_runner_func=args_runner,
contract_runner_func=contract_runner_func,
alog=logging.getLogger(__name__),
setup_log_func=setup_log)
def main():
"""main"""
mp = get_contract_parser()
return pbparser_runner(
argv=sys.argv[1:],
parser=mp,
args_runner_func=args_runner,
contract_runner_func=resolved_tool_contract_runner,
alog=log,
setup_log_func=setup_log)
def main(argv=sys.argv):
log.info("Starting {f} version {v} pbcommand example dev app".format(f=__file__, v=__version__))
p = get_contract_parser()
return pbparser_runner(argv[1:],
p,
_args_runner, # argparse runner func
_resolved_tool_contract_runner, # tool contract runner func
log, # log instance
setup_log # setup log func
)
def main(argv=sys.argv):
mp = get_parser()
setup_log_ = functools.partial(
setup_log, str_formatter='%(asctime)s [%(levelname)s] %(message)s')
return pbparser_runner(argv=argv[1:],
parser=mp,
args_runner_func=args_runner,
contract_runner_func=resolved_tool_contract_runner,
alog=logging.getLogger(__name__),
setup_log_func=setup_log_)
def main():
"""Main"""
argv = sys.argv
mp = get_contract_parser()
return pbparser_runner(argv[1:],
mp,
_args_run,
_rtc_runner,
log,
setup_log)
def main(argv=sys.argv):
mp = get_parser()
setup_log_ = functools.partial(setup_log,
str_formatter='%(asctime)s [%(levelname)s] %(message)s')
return pbparser_runner(
argv=argv[1:],
parser=mp,
args_runner_func=args_runner,
contract_runner_func=resolved_tool_contract_runner,
alog=logging.getLogger(__name__),
setup_log_func=setup_log_)
def main(argv=sys.argv):
logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger()
p = get_parser(tool_id=Constants.TOOL_ID,
file_type=FileTypes.DS_ALIGN_CCS,
driver_exe=Constants.DRIVER,
version=Constants.VERSION,
description=__doc__)
return pbparser_runner(argv[1:], p,
lambda rtc: args_runner(rtc, Constants.TOOL_ID),
lambda rtc: rtc_runner(rtc, Constants.TOOL_ID), log,
setup_log)
def main(argv=sys.argv):
log.info("Starting {f} version {v} pbcommand example dev app".format(
f=__file__, v=__version__))
# PbParser instance, this has both the argparse instance and the tool contract
# instance.
mp = get_contract_parser()
# To Access the argparse instance
# mp.arg_parser.parser
# The Tool Contract parser
# mp.tool_contract_parser.parser
return pbparser_runner(argv[1:], mp, args_runner,
resolved_tool_contract_runner, log, setup_log)
def main(argv=sys.argv):
logFormat = '[%(levelname)s] %(message)s'
logging.basicConfig(level=logging.WARN, format=logFormat)
log = logging.getLogger()
def dummy_setup(*args, **kwargs):
pass
return pbparser_runner(
argv=argv[1:],
parser=get_parser(),
args_runner_func=args_runner,
contract_runner_func=resolved_tool_contract_runner,
alog=log,
setup_log_func=dummy_setup)
def main(argv=sys.argv):
logFormat = '[%(levelname)s] %(message)s'
logging.basicConfig(level=logging.WARN, format=logFormat)
log = logging.getLogger()
def dummy_setup(*args, **kwargs):
pass
return pbparser_runner(argv=argv[1:],
parser=get_parser(),
args_runner_func=args_runner,
contract_runner_func=resolved_tool_contract_runner,
alog=log,
setup_log_func=dummy_setup)
def main(argv=sys.argv):
mp = get_parser()
logging.basicConfig(level=logging.INFO)
log.setLevel(logging.INFO)
return pbparser_runner(argv[1:],
mp,
args_runner,
resolved_tool_contract_runner,
log,
# FIXME for some bizarre reason, calling setup_log
# here results in the input log file being written
# to when run in 'args' mode. this has to be a bug
# somewhere but it might be in the core library...
lambda alog, **kw: alog)
def main(argv=sys.argv):
logging.basicConfig(level=logging.INFO)
log.setLevel(logging.INFO)
return pbparser_runner(
argv[1:],
_get_parser(),
_args_runner,
_resolved_tool_contract_runner,
log,
# FIXME for some bizarre reason, calling setup_log
# here results in the input log file being written
# to when run in 'args' mode. this has to be a bug
# somewhere but it might be in the core library...
lambda alog, **kw: alog)
def main(argv=sys.argv[1:]):
"""Main point of Entry"""
return pbparser_runner(argv, get_parser(), args_runner,
resolved_tool_contract_runner, log, setup_log)
def main(argv=sys.argv):
mp = get_contract_parser_impl(Constants)
return pbparser_runner(argv[1:], mp, _args_runner, _rtc_runner, log,
setup_log)
def main(argv=sys.argv):
return pbparser_runner(argv[1:], get_parser(), run_args, run_rtc, log,
setup_log)
def main():
"""Main"""
return pbparser_runner(sys.argv[1:], get_contract_parser(), _args_run,
_rtc_runner, log, setup_log)
