X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b16f84a8c5562cd5c3939e8c445dc86df2be2d4b..7407f41105f8000bb3908d41a31daaf3a30d9440:/sdk/cwl/arvados_cwl/__init__.py diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index 834ca195fd..6f2255b3f8 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -4,7 +4,7 @@ # SPDX-License-Identifier: Apache-2.0 # Implement cwl-runner interface for submitting and running work on Arvados, using -# either the Crunch jobs API or Crunch containers API. +# the Crunch containers API. from future.utils import viewitems from builtins import str @@ -23,7 +23,7 @@ import cwltool.workflow import cwltool.process import cwltool.argparser from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema -from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing +from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing import arvados import arvados.config @@ -36,10 +36,9 @@ from .perf import Perf from ._version import __version__ from .executor import ArvCwlExecutor -# These arn't used directly in this file but +# These aren't used directly in this file but # other code expects to import them from here from .arvcontainer import ArvadosContainer -from .arvjob import ArvadosJob from .arvtool import ArvadosCommandTool from .fsaccess import CollectionFsAccess, CollectionCache, CollectionFetcher from .util import get_current_container @@ -97,32 +96,32 @@ def arg_parser(): # type: () -> argparse.ArgumentParser exgroup = parser.add_mutually_exclusive_group() exgroup.add_argument("--enable-reuse", action="store_true", default=True, dest="enable_reuse", - help="Enable job or container reuse (default)") + help="Enable container reuse (default)") exgroup.add_argument("--disable-reuse", action="store_false", default=True, dest="enable_reuse", - help="Disable job or container reuse") + help="Disable container reuse") - parser.add_argument("--project-uuid", metavar="UUID", help="Project that will own the workflow jobs, if not provided, will go to home project.") + parser.add_argument("--project-uuid", metavar="UUID", help="Project that will own the workflow containers, if not provided, will go to home project.") parser.add_argument("--output-name", help="Name to use for collection that stores the final output.", default=None) parser.add_argument("--output-tags", help="Tags for the final output collection separated by commas, e.g., '--output-tags tag0,tag1,tag2'.", default=None) parser.add_argument("--ignore-docker-for-reuse", action="store_true", - help="Ignore Docker image version when deciding whether to reuse past jobs.", + help="Ignore Docker image version when deciding whether to reuse past containers.", default=False) exgroup = parser.add_mutually_exclusive_group() exgroup.add_argument("--submit", action="store_true", help="Submit workflow to run on Arvados.", default=True, dest="submit") - exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits jobs to Arvados).", + exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits containers to Arvados).", default=True, dest="submit") exgroup.add_argument("--create-template", action="store_true", help="(Deprecated) synonym for --create-workflow.", dest="create_workflow") - exgroup.add_argument("--create-workflow", action="store_true", help="Create an Arvados workflow (if using the 'containers' API) or pipeline template (if using the 'jobs' API). See --api.") - exgroup.add_argument("--update-workflow", metavar="UUID", help="Update an existing Arvados workflow or pipeline template with the given UUID.") + exgroup.add_argument("--create-workflow", action="store_true", help="Register an Arvados workflow that can be run from Workbench") + exgroup.add_argument("--update-workflow", metavar="UUID", help="Update an existing Arvados workflow with the given UUID.") exgroup = parser.add_mutually_exclusive_group() - exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.", + exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner, wait for completion.", default=True, dest="wait") - exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner job and exit.", + exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner and exit.", default=True, dest="wait") exgroup = parser.add_mutually_exclusive_group() @@ -133,8 +132,8 @@ def arg_parser(): # type: () -> argparse.ArgumentParser parser.add_argument("--api", default=None, dest="work_api", - choices=("jobs", "containers"), - help="Select work submission API. Default is 'jobs' if that API is available, otherwise 'containers'.") + choices=("containers",), + help="Select work submission API. Only supports 'containers'") parser.add_argument("--compute-checksum", action="store_true", default=False, help="Compute checksum of contents while collecting outputs", @@ -155,10 +154,10 @@ def arg_parser(): # type: () -> argparse.ArgumentParser exgroup = parser.add_mutually_exclusive_group() exgroup.add_argument("--submit-request-uuid", default=None, - help="Update and commit to supplied container request instead of creating a new one (containers API only).", + help="Update and commit to supplied container request instead of creating a new one.", metavar="UUID") exgroup.add_argument("--submit-runner-cluster", - help="Submit workflow runner to a remote cluster (containers API only)", + help="Submit workflow runner to a remote cluster", default=None, metavar="CLUSTER_ID") @@ -177,7 +176,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser parser.add_argument("--enable-dev", action="store_true", help="Enable loading and running development versions " - "of CWL spec.", default=False) + "of the CWL standards.", default=False) parser.add_argument('--storage-classes', default="default", help="Specify comma separated list of storage classes to be used when saving workflow output to Keep.") @@ -186,7 +185,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser default=0) parser.add_argument("--priority", type=int, - help="Workflow priority (range 1..1000, higher has precedence over lower, containers api only)", + help="Workflow priority (range 1..1000, higher has precedence over lower)", default=DEFAULT_PRIORITY) parser.add_argument("--disable-validate", dest="do_validate", @@ -219,9 +218,15 @@ def arg_parser(): # type: () -> argparse.ArgumentParser def add_arv_hints(): cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*") cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE - res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml') - use_custom_schema("v1.0", "http://arvados.org/cwl", res.read()) - res.close() + res10 = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.0.yml') + res11 = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.1.yml') + customschema10 = res10.read().decode('utf-8') + customschema11 = res11.read().decode('utf-8') + use_custom_schema("v1.0", "http://arvados.org/cwl", customschema10) + use_custom_schema("v1.1.0-dev1", "http://arvados.org/cwl", customschema11) + use_custom_schema("v1.1", "http://arvados.org/cwl", customschema11) + res10.close() + res11.close() cwltool.process.supportedProcessRequirements.extend([ "http://arvados.org/cwl#RunInSingleContainer", "http://arvados.org/cwl#OutputDirType", @@ -259,8 +264,6 @@ def main(args, stdout, stderr, api_client=None, keep_client=None, if arvargs.update_workflow: if arvargs.update_workflow.find('-7fd4e-') == 5: want_api = 'containers' - elif arvargs.update_workflow.find('-p5p6p-') == 5: - want_api = 'jobs' else: want_api = None if want_api and arvargs.work_api and want_api != arvargs.work_api: @@ -293,8 +296,8 @@ def main(args, stdout, stderr, api_client=None, keep_client=None, logger.exception("Error creating the Arvados CWL Executor") return 1 - # Note that unless in debug mode, some stack traces related to user - # workflow errors may be suppressed. See ArvadosJob.done(). + # Note that unless in debug mode, some stack traces related to user + # workflow errors may be suppressed. if arvargs.debug: logger.setLevel(logging.DEBUG) logging.getLogger('arvados').setLevel(logging.DEBUG) @@ -315,6 +318,15 @@ def main(args, stdout, stderr, api_client=None, keep_client=None, else: arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s')) + if stdout is sys.stdout: + # cwltool.main has code to work around encoding issues with + # sys.stdout and unix pipes (they default to ASCII encoding, + # we want utf-8), so when stdout is sys.stdout set it to None + # to take advantage of that. Don't override it for all cases + # since we still want to be able to capture stdout for the + # unit tests. + stdout = None + return cwltool.main.main(args=arvargs, stdout=stdout, stderr=stderr, @@ -324,4 +336,5 @@ def main(args, stdout, stderr, api_client=None, keep_client=None, logger_handler=arvados.log_handler, custom_schema_callback=add_arv_hints, loadingContext=executor.loadingContext, - runtimeContext=executor.runtimeContext) + runtimeContext=executor.runtimeContext, + input_required=not (arvargs.create_workflow or arvargs.update_workflow))