X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/65a84ec3801f6b76ccc2e6af07511851b4dc3aba..HEAD:/sdk/python/arvados/__init__.py diff --git a/sdk/python/arvados/__init__.py b/sdk/python/arvados/__init__.py index e90f381298..8d9a5690b4 100644 --- a/sdk/python/arvados/__init__.py +++ b/sdk/python/arvados/__init__.py @@ -6,8 +6,8 @@ This module provides the entire Python SDK for Arvados. The most useful modules include: -* arvados.api - After you `import arvados`, you can call `arvados.api.api` as - `arvados.api` to construct a client object. +* arvados.api - After you `import arvados`, you can call `arvados.api` as a + shortcut to the client constructor function `arvados.api.api`. * arvados.collection - The `arvados.collection.Collection` class provides a high-level interface to read and write collections. It coordinates sending @@ -26,15 +26,23 @@ import types from collections import UserDict -from .api import api, api_from_config, http_cache -from .collection import CollectionReader, CollectionWriter, ResumableCollectionWriter +from . import api, errors, util +from .api import api_from_config, http_cache +from .collection import CollectionReader from arvados.keep import * -from arvados.stream import * from .arvfile import StreamFileReader from .logging import log_format, log_date_format, log_handler from .retry import RetryLoop -import arvados.errors as errors -import arvados.util as util + +# Previous versions of the PySDK used to say `from .api import api`. This +# made it convenient to call the API client constructor, but difficult to +# access the rest of the `arvados.api` module. The magic below fixes that +# bug while retaining backwards compatibility: `arvados.api` is now the +# module and you can import it normally, but we make that module callable so +# all the existing code that says `arvados.api('v1', ...)` still works. +class _CallableAPIModule(api.__class__): + __call__ = staticmethod(api.api) +api.__class__ = _CallableAPIModule # Override logging module pulled in via `from ... import *` # so users can `import arvados.logging`. @@ -46,136 +54,3 @@ logger = stdliblog.getLogger('arvados') logger.addHandler(log_handler) logger.setLevel(stdliblog.DEBUG if config.get('ARVADOS_DEBUG') else stdliblog.WARNING) - -@util._deprecated('3.0', 'arvados-cwl-runner or the containers API') -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 - -_current_task = None -@util._deprecated('3.0', 'arvados-cwl-runner or the containers API') -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 - -_current_job = None -@util._deprecated('3.0', 'arvados-cwl-runner or the containers API') -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 - -@util._deprecated('3.0', 'arvados-cwl-runner or the containers API') -def getjobparam(*args): - return current_job()['script_parameters'].get(*args) - -@util._deprecated('3.0', 'arvados-cwl-runner or the containers API') -def get_job_param_mount(*args): - return os.path.join(os.environ['TASK_KEEPMOUNT'], current_job()['script_parameters'].get(*args)) - -@util._deprecated('3.0', 'arvados-cwl-runner or the containers API') -def get_task_param_mount(*args): - return os.path.join(os.environ['TASK_KEEPMOUNT'], current_task()['parameters'].get(*args)) - -class JobTask(object): - @util._deprecated('3.0', 'arvados-cwl-runner or the containers API') - def __init__(self, parameters=dict(), runtime_constraints=dict()): - print("init jobtask %s %s" % (parameters, runtime_constraints)) - -class job_setup(object): - @staticmethod - @util._deprecated('3.0', 'arvados-cwl-runner or the containers API') - 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 - @util._deprecated('3.0', 'arvados-cwl-runner or the containers API') - 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)