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 add_get_job_list_options(p):
fs = [
add_base_and_sal_options,
add_max_items_option(25, "Max Number of jobs")
]
f = compose(*fs)
return f(p)
def test_simple(self):
def f(x): return x * 2
def g(y): return y + 2
h = compose(f, g)
value = h(7)
assert value == 18
def get_parser():
desc = "Run multiple testkit.cfg files in parallel"
p = get_default_argparser(__version__, desc)
fs = [
add_log_debug_option, TU.add_override_chunked_mode,
TU.add_override_distribute_option, add_ignore_test_failures_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.add_argument("-j",
"--junit-xml",
dest="junit_out",
action="store",
default="junit_combined_results.xml",
help="JUnit output file for all tests")
p.set_defaults(func=_args_run_multi_testkit_cfg)
return p
def add_base_options_with_emit_tool_contract(p):
funcs = [
add_base_options, add_resolved_tool_contract_option,
add_emit_tool_contract_option
]
fs = compose(*funcs)
return fs(p)
def test_simple(self):
f = lambda x: x * 2
g = lambda y: y + 2
h = compose(f, g)
value = h(7)
self.assertEquals(value, 18)
def test_simple(self):
f = lambda x: x * 2
g = lambda y: y + 2
h = compose(f, g)
value = h(7)
self.assertEquals(value, 18)
def test_partial(self):
def add(a, b):
return a + b
add_five = functools.partial(add, 5)
add_two = functools.partial(add, 2)
f = compose(add_five, add_two)
value = f(5)
self.assertEquals(value, 12)
def test_partial(self):
def add(a, b):
return a + b
add_five = functools.partial(add, 5)
add_two = functools.partial(add, 2)
f = compose(add_five, add_two)
value = f(5)
self.assertEquals(value, 12)
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_json_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_preset_json_option,
_add_output_dir_option, _add_entry_point_single_task_option,
_add_task_id_run_option, add_log_debug_option
]
f = compose(*funcs)
return f(p)
def get_parser():
desc = "Testkit Tool to run pbsmrtpipe jobs."
p = get_default_argparser_with_base_opts(__version__, desc)
funcs = [
TU.add_override_chunked_mode, TU.add_override_distribute_option,
_add_config_file_option, add_tests_only_option,
add_ignore_test_failures_option, add_output_xml_option
]
f = compose(*funcs)
p = f(p)
return p
def get_parser():
desc = "Testkit Tool to run pbsmrtpipe jobs."
p = get_default_argparser_with_base_opts(__version__, desc)
funcs = [TU.add_override_chunked_mode,
TU.add_override_distribute_option,
_add_config_file_option,
add_tests_only_option,
add_ignore_test_failures_option,
add_output_xml_option]
f = compose(*funcs)
p = f(p)
return p
def _f():
return compose([])
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 _merge_xml_results(xml_type, merge_function, testkit_cfgs, output_file,
file_base):
log.info("Combining individual %s XML files", xml_type)
xml_files = []
for testkit_cfg in testkit_cfgs:
xml_file = os.path.join(os.path.dirname(testkit_cfg), file_base)
if os.path.exists(xml_file):
xml_files.append(xml_file)
if len(xml_files) == 0:
log.error("No %s XML outputs found", xml_type)
else:
merge_function(output_file, xml_files)
def add_base_options(p):
funcs = [add_debug_option, add_log_level_option]
fs = compose(*funcs)
return fs(p)
def add_sal_and_xml_dir_options(p):
fx = [add_common_options,
add_sal_options,
add_xml_or_dir_option]
f = compose(*fx)
return f(p)
def add_base_and_sal_options(p):
fx = [add_common_options, add_sal_options]
f = compose(*fx)
return f(p)
def add_sal_and_xml_dir_options(p):
fx = [add_common_options,
add_sal_options,
add_xml_or_dir_option]
f = compose(*fx)
return f(p)
def _f():
return compose([])
"Invalid DataSet(s) {p} {e}".format(p=path, e=e))
return wrapper
def _validate_xml(path):
try:
p = ET.parse(path)
_ = p.getroot()
return path
except ET.ParseError as e:
raise argparse.ArgumentTypeError("Invalid XML file {p} {e}".format(
p=path, e=e))
validate_xml_file = compose(_validate_xml, validate_file)
validate_subreadset = compose(_validate_dataset(SubreadSet), validate_xml_file)
valdiate_hdfsubreadset = compose(_validate_dataset(HdfSubreadSet),
validate_xml_file)
validate_alignmentset = compose(_validate_dataset(AlignmentSet),
validate_xml_file)
# These are really 'options', but keeping the naming convention consistent
add_input_fofn_option = _add_input_file_option(
'input_fofn', validate_fofn, "Path to input.fofn (File of File names)")
add_input_fasta_option = _add_input_file_option('fasta', validate_file,
"Path to Fasta file.")
add_input_fasta_reference_option = _add_input_file_option(
'fasta', validate_file, "Path to PacBio Reference Entry Fasta file.")
add_input_fastq_option = _add_input_file_option('fastq', validate_file,
def add_base_options(p):
funcs = [add_debug_option,
add_log_level_option]
fs = compose(*funcs)
return fs(p)
def add_base_and_sal_options(p):
fx = [add_common_options, add_sal_options]
f = compose(*fx)
return f(p)
def add_base_options_with_emit_tool_contract(p):
funcs = [add_base_options,
add_resolved_tool_contract_option,
add_emit_tool_contract_option]
fs = compose(*funcs)
return fs(p)
def add_get_job_list_options(p):
fs = [add_base_and_sal_options,
add_max_items_option(25, "Max Number of jobs")]
f = compose(*fs)
return f(p)
# If this raises, the error is a mangled from argparse and yields
# a cryptic error message
raise argparse.ArgumentTypeError("Invalid DataSet(s) {p} {e}".format(p=path, e=e))
return wrapper
def _validate_xml(path):
try:
p = ET.parse(path)
_ = p.getroot()
return path
except ET.ParseError as e:
raise argparse.ArgumentTypeError("Invalid XML file {p} {e}".format(p=path, e=e))
validate_xml_file = compose(_validate_xml, validate_file)
validate_subreadset = compose(_validate_dataset(SubreadSet), validate_xml_file)
valdiate_hdfsubreadset = compose(_validate_dataset(HdfSubreadSet), validate_xml_file)
validate_alignmentset = compose(_validate_dataset(AlignmentSet), validate_xml_file)
# These are really 'options', but keeping the naming convention consistent
add_input_fofn_option = _add_input_file_option('input_fofn', validate_fofn, "Path to input.fofn (File of File names)")
add_input_fasta_option = _add_input_file_option('fasta', validate_file, "Path to Fasta file.")
add_input_fasta_reference_option = _add_input_file_option('fasta', validate_file, "Path to PacBio Reference Entry Fasta file.")
add_input_fastq_option = _add_input_file_option('fastq', validate_file, "Path to Fastq file")
add_input_alignmentset_option = _add_input_file_option('alignmentset', validate_alignmentset, "Path to AlignmentSet XML file")
add_input_hdfsubreadset_option = _add_input_file_option('hdfsubreadset', valdiate_hdfsubreadset, "Path to HdfSubreadSet XML file")
add_input_subreadset_option = _add_input_file_option('subreadset', validate_subreadset, "Path to SubreadSet XML file")
add_input_csv_option = _add_input_file_option('csv', validate_file, "Path to CSV")