def get_task_and_workflow_options(testkit_cfg):
parsed_cfg = config_parser_to_butler(testkit_cfg)
workflow_options, task_options = [], []
def __get_option_type(val):
option_type = "pbsmrtpipe.option_types.string"
if isinstance(val, bool):
option_type = "pbsmrtpipe.option_types.boolean"
elif isinstance(val, int):
option_type = "pbsmrtpipe.option_types.integer"
elif isinstance(val, float):
option_type = "pbsmrtpipe.option_types.float"
return option_type
if not parsed_cfg.preset_xml in [None, '']:
presets = parse_pipeline_preset_xml(parsed_cfg.preset_xml)
for option_id, option_value in presets.task_options:
log.info("task_option: {i} = {v}".format(i=option_id,
v=option_value))
task_options.append(dict(
optionId=option_id,
value=option_value,
optionTypeId=__get_option_type(option_value)))
for option_id, option_value in presets.workflow_options:
log.info("workflow_option: {i} = {v}".format(i=option_id,
v=option_value))
workflow_options.append(dict(
optionId=option_id,
value=option_value,
optionTypeId=__get_option_type(option_value)))
return task_options, workflow_options
def pipeline_id_from_testkit_cfg(testkit_cfg):
parsed_cfg = config_parser_to_butler(testkit_cfg)
parsed_dict = parsed_cfg.__dict__
tree = ET.parse(parsed_dict['workflow_xml'])
root = tree.getroot()
pipeline_id = root[0].attrib['id']
return pipeline_id
def get_task_and_workflow_options(testkit_cfg):
parsed_cfg = config_parser_to_butler(testkit_cfg)
workflow_options, task_options = [], []
def __get_option_type(val):
option_type = "pbsmrtpipe.option_types.string"
if isinstance(val, bool):
option_type = "pbsmrtpipe.option_types.boolean"
elif isinstance(val, int):
option_type = "pbsmrtpipe.option_types.integer"
elif isinstance(val, float):
option_type = "pbsmrtpipe.option_types.float"
return option_type
if not parsed_cfg.preset_xml in [None, '']:
presets = parse_pipeline_preset_xml(parsed_cfg.preset_xml)
for option_id, option_value in presets.task_options:
log.info("task_option: {i} = {v}".format(i=option_id,
v=option_value))
task_options.append(dict(
optionId=option_id,
value=option_value,
optionTypeId=__get_option_type(option_value)))
for option_id, option_value in presets.workflow_options:
log.info("workflow_option: {i} = {v}".format(i=option_id,
v=option_value))
workflow_options.append(dict(
optionId=option_id,
value=option_value,
optionTypeId=__get_option_type(option_value)))
return task_options, workflow_options
def pipeline_id_from_testkit_cfg(testkit_cfg):
parsed_cfg = config_parser_to_butler(testkit_cfg)
parsed_dict = parsed_cfg.__dict__
tree = ET.parse(parsed_dict['workflow_xml'])
root = tree.getroot()
pipeline_id = root[0].attrib['id']
return pipeline_id
def run_butler_tests_from_cfg(testkit_cfg,
output_dir,
output_xml,
service_access_layer,
services_job_id=None,
nunit_out=None):
job_id = job_id_from_testkit_cfg(testkit_cfg)
butler = config_parser_to_butler(testkit_cfg)
test_cases = parse_cfg_file(testkit_cfg)
_patch_test_cases_with_service_access_layer(test_cases,
service_access_layer,
job_id=services_job_id)
log.info("running tests...")
exit_code = run_butler_tests(test_cases=test_cases,
output_dir=output_dir,
output_xml=output_xml,
job_id=job_id,
requirements=butler.requirements)
if nunit_out is not None and len(butler.xray_tests) > 0:
write_nunit_output(name=job_id,
xunit_out=output_xml,
nunit_out=nunit_out,
requirements=butler.requirements,
tests=butler.xray_tests)
return exit_code
def _args_run_butler(args):
butler = B.config_parser_to_butler(args.testkit_cfg)
test_cases = L.parse_cfg_file(args.testkit_cfg)
if not os.path.exists(butler.output_dir):
os.mkdir(butler.output_dir)
output_xml = os.path.join(butler.output_dir, "testkit_xunit.xml")
force_distribute, force_chunk = resolve_dist_chunk_overrides(args)
if args.only_tests:
return run_butler_tests(test_cases, butler.output_dir, output_xml, butler.job_id)
else:
rcode = run_butler(
butler,
test_cases,
output_xml,
log_file=args.log_file,
log_level=args.log_level,
force_distribute=force_distribute,
force_chunk=force_chunk,
)
return rcode
def pipeline_id_from_testkit_cfg(testkit_cfg):
parsed_cfg = config_parser_to_butler(testkit_cfg)
if parsed_cfg.workflow_xml is not None:
tree = ET.parse(parsed_cfg.workflow_xml)
root = tree.getroot()
return root[0].attrib['id']
else:
return parsed_cfg.pipeline_id
def pipeline_id_from_testkit_cfg(testkit_cfg):
parsed_cfg = config_parser_to_butler(testkit_cfg)
if parsed_cfg.workflow_xml is not None:
tree = ET.parse(parsed_cfg.workflow_xml)
root = tree.getroot()
return root[0].attrib['id']
else:
return parsed_cfg.pipeline_id
def get_task_and_workflow_options(testkit_cfg):
parsed_cfg = config_parser_to_butler(testkit_cfg)
workflow_options, task_options = [], []
def __get_option_type(val):
option_type = TaskOptionTypes.STR
if isinstance(val, bool):
option_type = TaskOptionTypes.BOOL
elif isinstance(val, int):
option_type = TaskOptionTypes.INT
elif isinstance(val, float):
option_type = TaskOptionTypes.FLOAT
elif val is None:
val = ""
return option_type, val
rtasks_d, _, _, _ = L.load_all()
if not parsed_cfg.preset_xml in [None, '']:
if not parsed_cfg.preset_json in [None, '']:
raise ValueError(
"Please use either preset_json or preset_xml, not both")
presets = parse_pipeline_preset_xml(parsed_cfg.preset_xml)
task_opts_d = validate_raw_task_options(rtasks_d,
dict(presets.task_options))
for option_id, option_value in task_opts_d.iteritems():
log.info("task_option: {i} = {v}".format(i=option_id,
v=option_value))
option_type, option_value = __get_option_type(option_value)
task_options.append(
dict(optionId=option_id,
value=option_value,
optionTypeId=option_type))
for option_id, option_value in presets.workflow_options:
log.info("workflow_option: {i} = {v}".format(i=option_id,
v=option_value))
workflow_options.append(
dict(optionId=option_id,
value=option_value,
optionTypeId=__get_option_type(option_value)[0]))
elif not parsed_cfg.preset_json in [None, '']:
presets = parse_pipeline_preset_json(parsed_cfg.preset_json)
for option_id, option_value in presets.task_options:
log.info("task_option: {i} = {v}".format(i=option_id,
v=option_value))
option_type, option_value = __get_option_type(option_value)
task_options.append(
dict(optionId=option_id,
value=option_value,
optionTypeId=option_type))
for option_id, option_value in presets.workflow_options:
log.info("workflow_option: {i} = {v}".format(i=option_id,
v=option_value))
workflow_options.append(
dict(optionId=option_id,
value=option_value,
optionTypeId=__get_option_type(option_value)[0]))
return task_options, workflow_options
def get_task_and_workflow_options(testkit_cfg):
parsed_cfg = config_parser_to_butler(testkit_cfg)
workflow_options, task_options = [], []
def __get_option_type(val):
option_type = to_opt_type_ns("string")
if isinstance(val, bool):
option_type = to_opt_type_ns("boolean")
elif isinstance(val, int):
option_type = to_opt_type_ns("integer")
elif isinstance(val, float):
option_type = to_opt_type_ns("float")
elif val is None:
val = ""
return option_type, val
if not parsed_cfg.preset_xml in [None, '']:
if not parsed_cfg.preset_json in [None, '']:
raise ValueError(
"Please use either preset_json or preset_xml, not both")
presets = parse_pipeline_preset_xml(parsed_cfg.preset_xml)
for option_id, option_value in presets.task_options:
log.info("task_option: {i} = {v}".format(i=option_id,
v=option_value))
option_type, option_value = __get_option_type(option_value)
task_options.append(
dict(optionId=option_id,
value=option_value,
optionTypeId=option_type))
for option_id, option_value in presets.workflow_options:
log.info("workflow_option: {i} = {v}".format(i=option_id,
v=option_value))
workflow_options.append(
dict(optionId=option_id,
value=option_value,
optionTypeId=__get_option_type(option_value)[0]))
elif not parsed_cfg.preset_json in [None, '']:
presets = parse_pipeline_preset_json(parsed_cfg.preset_json)
for option_id, option_value in presets.task_options:
log.info("task_option: {i} = {v}".format(i=option_id,
v=option_value))
option_type, option_value = __get_option_type(option_value)
task_options.append(
dict(optionId=option_id,
value=option_value,
optionTypeId=option_type))
for option_id, option_value in presets.workflow_options:
log.info("workflow_option: {i} = {v}".format(i=option_id,
v=option_value))
workflow_options.append(
dict(optionId=option_id,
value=option_value,
optionTypeId=__get_option_type(option_value)[0]))
return task_options, workflow_options
def get_task_and_workflow_options(testkit_cfg):
parsed_cfg = config_parser_to_butler(testkit_cfg)
workflow_options, task_options = [], []
def __get_option_type(val):
option_type = to_opt_type_ns("string")
if isinstance(val, bool):
option_type = to_opt_type_ns("boolean")
elif isinstance(val, int):
option_type = to_opt_type_ns("integer")
elif isinstance(val, float):
option_type = to_opt_type_ns("float")
elif val is None:
val = ""
return option_type, val
if not parsed_cfg.preset_xml in [None, '']:
if not parsed_cfg.preset_json in [None, '']:
raise ValueError("Please use either preset_json or preset_xml, not both")
presets = parse_pipeline_preset_xml(parsed_cfg.preset_xml)
for option_id, option_value in presets.task_options:
log.info("task_option: {i} = {v}".format(i=option_id,
v=option_value))
option_type, option_value = __get_option_type(option_value)
task_options.append(dict(
optionId=option_id,
value=option_value,
optionTypeId=option_type))
for option_id, option_value in presets.workflow_options:
log.info("workflow_option: {i} = {v}".format(i=option_id,
v=option_value))
workflow_options.append(dict(
optionId=option_id,
value=option_value,
optionTypeId=__get_option_type(option_value)[0]))
elif not parsed_cfg.preset_json in [None, '']:
presets = parse_pipeline_preset_json(parsed_cfg.preset_json)
for option_id, option_value in presets.task_options:
log.info("task_option: {i} = {v}".format(i=option_id,
v=option_value))
option_type, option_value = __get_option_type(option_value)
task_options.append(dict(
optionId=option_id,
value=option_value,
optionTypeId=option_type))
for option_id, option_value in presets.workflow_options:
log.info("workflow_option: {i} = {v}".format(i=option_id,
v=option_value))
workflow_options.append(dict(
optionId=option_id,
value=option_value,
optionTypeId=__get_option_type(option_value)[0]))
return task_options, workflow_options
def run_butler_tests_from_cfg(testkit_cfg, output_dir, output_xml,
service_access_layer, services_job_id=None):
job_id = job_id_from_testkit_cfg(testkit_cfg)
butler = config_parser_to_butler(testkit_cfg)
test_cases = parse_cfg_file(testkit_cfg)
_patch_test_cases_with_service_access_layer(test_cases,
service_access_layer,
job_id=services_job_id)
log.info("running tests...")
exit_code = run_butler_tests(
test_cases=test_cases,
output_dir=output_dir,
output_xml=output_xml,
job_id=job_id)
return exit_code
def run_butler_tests_from_cfg(testkit_cfg, output_dir, output_xml,
service_access_layer, services_job_id=None):
job_id = job_id_from_testkit_cfg(testkit_cfg)
butler = config_parser_to_butler(testkit_cfg)
test_cases = parse_cfg_file(testkit_cfg)
_patch_test_cases_with_service_access_layer(test_cases,
service_access_layer,
job_id=services_job_id)
log.info("running tests...")
exit_code = run_butler_tests(
test_cases=test_cases,
output_dir=output_dir,
output_xml=output_xml,
job_id=job_id)
return exit_code
def _args_run_butler(args):
butler = B.config_parser_to_butler(args.testkit_cfg)
test_cases = L.parse_cfg_file(args.testkit_cfg)
if not os.path.exists(butler.output_dir):
os.mkdir(butler.output_dir)
output_xml = args.output_xml
if output_xml is None:
output_xml = os.path.join(butler.output_dir, 'testkit_xunit.xml')
if args.log_file is None:
log_file = os.path.join(butler.output_dir, 'testkit.log')
else:
log_file = args.log_file
force_distribute, force_chunk = resolve_dist_chunk_overrides(args)
log_level = args.log_level
# Short hand for --log-level=DEBUG
if args.debug:
log_level = logging.DEBUG
if log_level == logging.DEBUG:
# The logger isn't setup yet
print "Args", args
if args.only_tests:
# in test only mode, only emit to stdout (to avoid overwritten the
# log file
setup_logger(None, level=log_level)
return run_butler_tests(test_cases, butler.output_dir, output_xml,
butler.job_id, butler.requirements)
else:
rcode = run_butler(butler,
test_cases,
output_xml,
log_file,
log_level=log_level,
force_distribute=force_distribute,
force_chunk=force_chunk,
ignore_test_failures=args.ignore_test_failures)
return rcode
def _args_run_butler(args):
butler = B.config_parser_to_butler(args.testkit_cfg)
test_cases = L.parse_cfg_file(args.testkit_cfg)
if not os.path.exists(butler.output_dir):
os.mkdir(butler.output_dir)
output_xml = args.output_xml
if output_xml is None:
output_xml = os.path.join(butler.output_dir, 'testkit_xunit.xml')
if args.log_file is None:
log_file = os.path.join(butler.output_dir, 'testkit.log')
else:
log_file = args.log_file
force_distribute, force_chunk = resolve_dist_chunk_overrides(args)
log_level = args.log_level
# Short hand for --log-level=DEBUG
if args.debug:
log_level = logging.DEBUG
if log_level == logging.DEBUG:
# The logger isn't setup yet
print "Args", args
if args.only_tests:
# in test only mode, only emit to stdout (to avoid overwritten the
# log file
setup_logger(None, level=log_level)
return run_butler_tests(test_cases, butler.output_dir, output_xml, butler.job_id)
else:
rcode = run_butler(butler, test_cases, output_xml, log_file,
log_level=log_level,
force_distribute=force_distribute,
force_chunk=force_chunk,
ignore_test_failures=args.ignore_test_failures)
return rcode
def run_services_testkit_job(host, port, testkit_cfg,
xml_out="test-output.xml",
ignore_test_failures=False,
time_out=1800, sleep_time=2):
"""
Given a testkit.cfg and host/port parameters:
1. convert the .cfg to a JSON file
2. connect to the SMRTLink services and start the job, then block
until it finishes
3. run the standard test suite on the job output
"""
butler = config_parser_to_butler(testkit_cfg)
test_cases = parse_cfg_file(testkit_cfg)
entrypoints = get_entrypoints(testkit_cfg)
pipeline_id = pipeline_id_from_testkit_cfg(testkit_cfg)
job_id = job_id_from_testkit_cfg(testkit_cfg)
log.info("job_id = {j}".format(j=job_id))
log.info("pipeline_id = {p}".format(p=pipeline_id))
log.info("url = {h}:{p}".format(h=host, p=port))
task_options, workflow_options = get_task_and_workflow_options(testkit_cfg)
sal = ServiceAccessLayer(host, port, sleep_time=sleep_time)
service_entrypoints = [ServiceEntryPoint.from_d(x) for x in
entrypoints_dicts(entrypoints)]
for ep, dataset_xml in entrypoints.iteritems():
log.info("Importing {x}".format(x=dataset_xml))
sal.run_import_local_dataset(dataset_xml)
log.info("starting anaylsis job...")
# XXX note that workflow options are currently ignored
engine_job = run_analysis_job(sal, job_id, pipeline_id,
service_entrypoints, block=True,
time_out=time_out,
task_options=task_options)
job_output_path = engine_job.path
log.info("running tests...")
exit_code = run_butler_tests(
test_cases=test_cases,
output_dir=job_output_path,
output_xml=xml_out,
job_id=job_id)
if ignore_test_failures and engine_job.was_successful():
return 0
return exit_code
def _args_run_butler(args):
butler = B.config_parser_to_butler(args.testkit_cfg)
test_cases = L.parse_cfg_file(args.testkit_cfg)
if not os.path.exists(butler.output_dir):
os.mkdir(butler.output_dir)
output_xml = os.path.join(butler.output_dir, 'testkit_xunit.xml')
force_distribute, force_chunk = resolve_dist_chunk_overrides(args)
if args.only_tests:
return run_butler_tests(test_cases, butler.output_dir, output_xml, butler.job_id)
else:
rcode = run_butler(butler, test_cases, output_xml,
log_file=args.log_file,
log_level=args.log_level,
force_distribute=force_distribute, force_chunk=force_chunk)
return rcode
def job_id_from_testkit_cfg(testkit_cfg):
parsed_cfg = config_parser_to_butler(testkit_cfg)
return parsed_cfg.job_id
def get_entrypoints(testkit_cfg):
parsed_cfg = config_parser_to_butler(testkit_cfg)
entrypoints = parsed_cfg.entry_points
return entrypoints
def job_id_from_testkit_cfg(testkit_cfg):
parsed_cfg = config_parser_to_butler(testkit_cfg)
return parsed_cfg.job_id
def _to_butler(self):
return B.config_parser_to_butler(self.path)
def _to_butler(self):
return B.config_parser_to_butler(self.path)
def get_entrypoints(testkit_cfg):
parsed_cfg = config_parser_to_butler(testkit_cfg)
entrypoints = parsed_cfg.entry_points
return entrypoints