Package arvados
Sub-modules
arvados.apiarvados.arvfilearvados.cachearvados.collectionarvados.commandsarvados.configarvados.cruncharvados.errorsarvados.eventsarvados.keeparvados.retryarvados.safeapiarvados.streamarvados.timerarvados.util
Functions
def current_job(num_retries=5)-
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def current_job(num_retries=5): global _current_job if _current_job: return _current_job for tries_left in RetryLoop(num_retries=num_retries, backoff_start=2): try: job = api('v1').jobs().get(uuid=os.environ['JOB_UUID']).execute() job = UserDict(job) job.tmpdir = os.environ['JOB_WORK'] _current_job = job return job except errors.ApiError as error: if retry.check_http_response_success(error.resp.status) is None and tries_left > 0: logger.debug("current_job: jobs().get() raised {}, retrying with {} tries left".format(repr(error),tries_left)) else: raise def current_task(num_retries=5)-
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def current_task(num_retries=5): global _current_task if _current_task: return _current_task for tries_left in RetryLoop(num_retries=num_retries, backoff_start=2): try: task = api('v1').job_tasks().get(uuid=os.environ['TASK_UUID']).execute() task = UserDict(task) task.set_output = types.MethodType(task_set_output, task) task.tmpdir = os.environ['TASK_WORK'] _current_task = task return task except errors.ApiError as error: if retry.check_http_response_success(error.resp.status) is None and tries_left > 0: logger.debug("current_task: job_tasks().get() raised {}, retrying with {} tries left".format(repr(error),tries_left)) else: raise def get_job_param_mount(*args)-
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def get_job_param_mount(*args): return os.path.join(os.environ['TASK_KEEPMOUNT'], current_job()['script_parameters'].get(*args)) def get_task_param_mount(*args)-
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def get_task_param_mount(*args): return os.path.join(os.environ['TASK_KEEPMOUNT'], current_task()['parameters'].get(*args)) def getjobparam(*args)-
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def getjobparam(*args): return current_job()['script_parameters'].get(*args) def task_set_output(self, s, num_retries=5)-
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def task_set_output(self, s, num_retries=5): for tries_left in RetryLoop(num_retries=num_retries, backoff_start=0): try: return api('v1').job_tasks().update( uuid=self['uuid'], body={ 'output':s, 'success':True, 'progress':1.0 }).execute() except errors.ApiError as error: if retry.check_http_response_success(error.resp.status) is None and tries_left > 0: logger.debug("task_set_output: job_tasks().update() raised {}, retrying with {} tries left".format(repr(error),tries_left)) else: raise
Classes
class JobTask (parameters={}, runtime_constraints={})-
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class JobTask(object): def __init__(self, parameters=dict(), runtime_constraints=dict()): print("init jobtask %s %s" % (parameters, runtime_constraints)) class job_setup-
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class job_setup(object): @staticmethod def one_task_per_input_file(if_sequence=0, and_end_task=True, input_as_path=False, api_client=None): if if_sequence != current_task()['sequence']: return if not api_client: api_client = api('v1') job_input = current_job()['script_parameters']['input'] cr = CollectionReader(job_input, api_client=api_client) cr.normalize() for s in cr.all_streams(): for f in s.all_files(): if input_as_path: task_input = os.path.join(job_input, s.name(), f.name()) else: task_input = f.as_manifest() new_task_attrs = { 'job_uuid': current_job()['uuid'], 'created_by_job_task_uuid': current_task()['uuid'], 'sequence': if_sequence + 1, 'parameters': { 'input':task_input } } api_client.job_tasks().create(body=new_task_attrs).execute() if and_end_task: api_client.job_tasks().update(uuid=current_task()['uuid'], body={'success':True} ).execute() exit(0) @staticmethod def one_task_per_input_stream(if_sequence=0, and_end_task=True): if if_sequence != current_task()['sequence']: return job_input = current_job()['script_parameters']['input'] cr = CollectionReader(job_input) for s in cr.all_streams(): task_input = s.tokens() new_task_attrs = { 'job_uuid': current_job()['uuid'], 'created_by_job_task_uuid': current_task()['uuid'], 'sequence': if_sequence + 1, 'parameters': { 'input':task_input } } api('v1').job_tasks().create(body=new_task_attrs).execute() if and_end_task: api('v1').job_tasks().update(uuid=current_task()['uuid'], body={'success':True} ).execute() exit(0)Static methods
def one_task_per_input_file(if_sequence=0, and_end_task=True, input_as_path=False, api_client=None)-
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@staticmethod def one_task_per_input_file(if_sequence=0, and_end_task=True, input_as_path=False, api_client=None): if if_sequence != current_task()['sequence']: return if not api_client: api_client = api('v1') job_input = current_job()['script_parameters']['input'] cr = CollectionReader(job_input, api_client=api_client) cr.normalize() for s in cr.all_streams(): for f in s.all_files(): if input_as_path: task_input = os.path.join(job_input, s.name(), f.name()) else: task_input = f.as_manifest() new_task_attrs = { 'job_uuid': current_job()['uuid'], 'created_by_job_task_uuid': current_task()['uuid'], 'sequence': if_sequence + 1, 'parameters': { 'input':task_input } } api_client.job_tasks().create(body=new_task_attrs).execute() if and_end_task: api_client.job_tasks().update(uuid=current_task()['uuid'], body={'success':True} ).execute() exit(0) def one_task_per_input_stream(if_sequence=0, and_end_task=True)-
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@staticmethod def one_task_per_input_stream(if_sequence=0, and_end_task=True): if if_sequence != current_task()['sequence']: return job_input = current_job()['script_parameters']['input'] cr = CollectionReader(job_input) for s in cr.all_streams(): task_input = s.tokens() new_task_attrs = { 'job_uuid': current_job()['uuid'], 'created_by_job_task_uuid': current_task()['uuid'], 'sequence': if_sequence + 1, 'parameters': { 'input':task_input } } api('v1').job_tasks().create(body=new_task_attrs).execute() if and_end_task: api('v1').job_tasks().update(uuid=current_task()['uuid'], body={'success':True} ).execute() exit(0)