def _add_run_reference_dataset_report(p):
opts = [add_log_debug_option,
U.add_report_output,
U.add_ds_reference_input]
f = compose(*opts)
return f(p)
def get_parser():
desc = "Run multiple testkit.cfg files in parallel"
p = get_default_argparser(__version__, desc)
fs = [
TU.add_debug_option, TU.add_override_chunked_mode,
TU.add_override_distribute_option
]
f = compose(*fs)
p = f(p)
p.add_argument(
'testkit_cfg_fofn',
type=validate_testkit_cfg_fofn,
help=
"File of butler.cfg file name relative to the current dir (e.g., RS_Resquencing/testkit.cfg"
)
p.add_argument('-n',
'--nworkers',
type=int,
default=1,
help="Number of jobs to concurrently run.")
p.set_defaults(func=_args_run_multi_testkit_cfg)
return p
def add_task_parser_options(p):
funcs = [
TU.add_override_chunked_mode, TU.add_override_distribute_option,
_add_webservice_config, _add_rc_preset_xml_option,
_add_preset_xml_option, _add_output_dir_option,
_add_entry_point_option, _add_task_id_option, TU.add_debug_option
]
f = compose(*funcs)
return f(p)
def __add_pipeline_parser_options(p):
"""Common options for all running pipelines or tasks"""
funcs = [
TU.add_override_chunked_mode, TU.add_override_distribute_option,
_add_webservice_config, _add_rc_preset_xml_option,
_add_preset_xml_option, _add_output_dir_option,
_add_entry_point_option, TU.add_debug_option
]
f = compose(*funcs)
return f(p)
def __add_pipeline_parser_options(p):
"""Common options for all running pipelines or tasks"""
funcs = [TU.add_override_chunked_mode,
TU.add_override_distribute_option,
_add_webservice_config,
_add_rc_preset_xml_option,
_add_preset_xml_option,
_add_output_dir_option,
_add_entry_point_option,
add_log_debug_option]
f = compose(*funcs)
return f(p)
def add_task_parser_options(p):
funcs = [
TU.add_override_chunked_mode,
TU.add_override_distribute_option,
_add_webservice_config,
_add_rc_preset_xml_option,
_add_preset_xml_option,
_add_output_dir_option,
_add_entry_point_option,
_add_task_id_option,
add_log_debug_option]
f = compose(*funcs)
return f(p)
def get_parser():
desc = "Run multiple testkit.cfg files in parallel"
p = get_default_argparser(__version__, desc)
fs = [TU.add_debug_option,
TU.add_override_chunked_mode,
TU.add_override_distribute_option]
f = compose(*fs)
p = f(p)
p.add_argument('testkit_cfg_fofn', type=validate_testkit_cfg_fofn,
help="File of butler.cfg file name relative to the current dir (e.g., RS_Resquencing/testkit.cfg")
p.add_argument('-n', '--nworkers', type=int, default=1, help="Number of jobs to concurrently run.")
p.set_defaults(func=_args_run_multi_testkit_cfg)
return p
def get_parser():
desc = "Testkit Tool to run pbsmrtpipe jobs."
p = get_default_argparser(__version__, desc)
funcs = [TU.add_override_chunked_mode,
TU.add_override_distribute_option,
_add_config_file_option,
add_tests_only_option,
add_log_level_option,
add_log_file_options,
TU.add_debug_option]
f = compose(*funcs)
p = f(p)
return p
return testkit_cfgs
def testkit_cfg_fofn_to_files(fofn):
return _testkit_cfg_fofn_to_files(fofn, os.path.dirname(fofn))
def _validate_testkit_cfg_fofn(path):
p = os.path.abspath(path)
# files will be relative the supplied fofn
dir_name = os.path.dirname(p)
_testkit_cfg_fofn_to_files(p, dir_name)
return p
validate_testkit_cfg_fofn = compose(_validate_testkit_cfg_fofn, validate_file)
def _run_testkit_cfg(testkit_cfg, debug=False, misc_opts=""):
os.chdir(os.path.dirname(testkit_cfg))
cmd = "{e} --debug {m} {c}".format(c=testkit_cfg, e=_EXE, m=misc_opts)
rcode, stdout, stderr, run_time = backticks(cmd)
if debug:
log.debug(" ".join([str(i) for i in [cmd, rcode, stdout, stderr]]))
# Returning the butler cfg is a bit odd, but this is necessary for the
# parallelism to work consistently with the serial version
return testkit_cfg, rcode, stdout, stderr, run_time
return testkit_cfgs
def testkit_cfg_fofn_to_files(fofn):
return _testkit_cfg_fofn_to_files(fofn, os.path.dirname(fofn))
def _validate_testkit_cfg_fofn(path):
p = os.path.abspath(path)
# files will be relative the supplied fofn
dir_name = os.path.dirname(p)
_testkit_cfg_fofn_to_files(p, dir_name)
return p
validate_testkit_cfg_fofn = compose(_validate_testkit_cfg_fofn, validate_file)
def _run_testkit_cfg(testkit_cfg, debug=False, misc_opts=""):
os.chdir(os.path.dirname(testkit_cfg))
cmd = "{e} --debug {m} {c}".format(c=testkit_cfg, e=_EXE, m=misc_opts)
rcode, stdout, stderr, run_time = backticks(cmd)
if debug:
log.debug(" ".join([str(i) for i in [cmd, rcode, stdout, stderr]]))
# Returning the butler cfg is a bit odd, but this is necessary for the
# parallelism to work consistently with the serial version
return testkit_cfg, rcode, stdout, stderr, run_time
