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thisisanshgupta
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Pycode

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default=None)
parser.add_argument('--report-type',
help='The output report type. By default metapipe will '
'print updates to the console. \nOptions: {}. '
'(Default: ""%(default)s)""'.format(QUEUE_TYPES.keys()),
default='text')
parser.add_argument('-v','--version',
help='Displays the current version of the application.',
action='store_true')
args = parser.parse_args()
if args.version:
print('Version: {}'.format(__version__))
sys.exit(0)
try:
with open(args.input) as f:
config = f.read()
except IOError:
print('No valid config file found.')
return -1
run(config, args.max_jobs, args.output, args.job_type, args.report_type,
args.shell, args.temp, args.run)"
144,"def run(config, max_jobs, output=sys.stdout, job_type='local',
report_type='text', shell='/bin/bash', temp='.metapipe', run_now=False):
"""""" Create the metapipe based on the provided input. """"""
if max_jobs == None:
max_jobs = cpu_count()
parser = Parser(config)
try:
command_templates = parser.consume()
except ValueError as e:
raise SyntaxError('Invalid config file. \n%s' % e)
options = '\n'.join(parser.global_options)
queue_type = QUEUE_TYPES[report_type]
pipeline = Runtime(command_templates,queue_type,JOB_TYPES,job_type,max_jobs)
template = env.get_template('output_script.tmpl.sh')
with open(temp, 'wb') as f:
pickle.dump(pipeline, f, 2)
script = template.render(shell=shell,
temp=os.path.abspath(temp), options=options)
if run_now:
output = output if output != sys.stdout else PIPELINE_ALIAS
submit_job = make_submit_job(shell, output, job_type)
submit_job.submit()
try:
f = open(output, 'w')
output = f
except TypeError:
pass
output.write(script)
f.close()"
145,"def make_submit_job(shell, output, job_type):
"""""" Preps the metapipe main job to be submitted. """"""
run_cmd = [shell, output]
submit_command = Command(alias=PIPELINE_ALIAS, cmds=run_cmd)
submit_job = get_job(submit_command, job_type)
submit_job.make()
return submit_job"
146,"def yaml(modules_to_register: Iterable[Any] = None, classes_to_register: Iterable[Any] = None) -> ruamel.yaml.YAML:
"""""" Create a YAML object for loading a YAML configuration.
Args:
modules_to_register: Modules containing classes to be registered with the YAML object. Default: None.
classes_to_register: Classes to be registered with the YAML object. Default: None.
Returns:
A newly creating YAML object, configured as apporpirate.
""""""
# Defein a round-trip yaml object for us to work with. This object should be imported by other modules
# NOTE: ""typ"" is a not a typo. It stands for ""type""
yaml = ruamel.yaml.YAML(typ = ""rt"")
# Register representers and constructors
# Numpy
yaml.representer.add_representer(np.ndarray, numpy_to_yaml)
yaml.constructor.add_constructor(""!numpy_array"", numpy_from_yaml)
# Register external classes
yaml = register_module_classes(yaml = yaml, modules = modules_to_register)
yaml = register_classes(yaml = yaml, classes = classes_to_register)
return yaml"
147,"def register_classes(yaml: ruamel.yaml.YAML, classes: Optional[Iterable[Any]] = None) -> ruamel.yaml.YAML:
"""""" Register externally defined classes. """"""
# Validation
if classes is None:
classes = []
# Register the classes
for cls in classes:
logger.debug(f""Registering class {cls} with YAML"")
yaml.register_class(cls)
return yaml"