import cwltool.workflow
import cwltool.process
import cwltool.argparser
+from cwltool.errors import WorkflowException
from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing
from .perf import Perf
from ._version import __version__
from .executor import ArvCwlExecutor
+from .fsaccess import workflow_uuid_pattern
# These aren't used directly in this file but
# other code expects to import them from here
help="When invoked with --submit --wait, always submit a runner to manage the workflow, even when only running a single CommandLineTool",
default=False)
+ parser.add_argument("--match-submitter-images", action="store_true",
+ default=False, dest="match_local_docker",
+ help="Where Arvados has more than one Docker image of the same name, use image from the Docker instance on the submitting node.")
+
exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--submit-request-uuid",
default=None,
help="Enable loading and running development versions "
"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.")
+ help="Specify comma separated list of storage classes to be used when saving final workflow output to Keep.")
+ parser.add_argument('--intermediate-storage-classes', default="default",
+ help="Specify comma separated list of storage classes to be used when saving intermediate workflow output to Keep.")
parser.add_argument("--intermediate-output-ttl", type=int, metavar="N",
help="If N > 0, intermediate output collections will be trashed N seconds after creation. Default is 0 (don't trash).",
action="store_false", default=True,
help=argparse.SUPPRESS)
+ parser.add_argument("--disable-git", dest="git_info",
+ action="store_false", default=True,
+ help=argparse.SUPPRESS)
+
parser.add_argument("--disable-color", dest="enable_color",
action="store_false", default=True,
help=argparse.SUPPRESS)
help=argparse.SUPPRESS)
parser.add_argument("--thread-count", type=int,
- default=1, help="Number of threads to use for job submit and output collection.")
+ default=0, help="Number of threads to use for job submit and output collection.")
parser.add_argument("--http-timeout", type=int,
default=5*60, dest="http_timeout", help="API request timeout in seconds. Default is 300 seconds (5 minutes).")
+ parser.add_argument("--defer-downloads", action="store_true", default=False,
+ help="When submitting a workflow, defer downloading HTTP URLs to workflow launch instead of downloading to Keep before submit.")
+
+ parser.add_argument("--varying-url-params", type=str, default="",
+ help="A comma separated list of URL query parameters that should be ignored when storing HTTP URLs in Keep.")
+
+ parser.add_argument("--prefer-cached-downloads", action="store_true", default=False,
+ help="If a HTTP URL is found in Keep, skip upstream URL freshness check (will not notice if the upstream has changed, but also not error if upstream is unavailable).")
+
+ exgroup = parser.add_mutually_exclusive_group()
+ exgroup.add_argument("--enable-preemptible", dest="enable_preemptible", default=None, action="store_true", help="Use preemptible instances. Control individual steps with arv:UsePreemptible hint.")
+ exgroup.add_argument("--disable-preemptible", dest="enable_preemptible", default=None, action="store_false", help="Don't use preemptible instances.")
+
+ exgroup = parser.add_mutually_exclusive_group()
+ exgroup.add_argument("--copy-deps", dest="copy_deps", default=None, action="store_true", help="Copy dependencies into the destination project.")
+ exgroup.add_argument("--no-copy-deps", dest="copy_deps", default=None, action="store_false", help="Leave dependencies where they are.")
+
parser.add_argument(
"--skip-schemas",
action="store_true",
"http://commonwl.org/cwltool#LoadListingRequirement",
"http://arvados.org/cwl#IntermediateOutput",
"http://arvados.org/cwl#ReuseRequirement",
- "http://arvados.org/cwl#ClusterTarget"
+ "http://arvados.org/cwl#ClusterTarget",
+ "http://arvados.org/cwl#OutputStorageClass",
+ "http://arvados.org/cwl#ProcessProperties",
+ "http://commonwl.org/cwltool#CUDARequirement",
+ "http://arvados.org/cwl#UsePreemptible",
+ "http://arvados.org/cwl#OutputCollectionProperties",
])
def exit_signal_handler(sigcode, frame):
logger.error(str(u"Caught signal {}, exiting.").format(sigcode))
sys.exit(-sigcode)
-def main(args, stdout, stderr, api_client=None, keep_client=None,
+def main(args=sys.argv[1:],
+ stdout=sys.stdout,
+ stderr=sys.stderr,
+ api_client=None,
+ keep_client=None,
install_sig_handlers=True):
parser = arg_parser()
job_order_object = None
arvargs = parser.parse_args(args)
- if len(arvargs.storage_classes.strip().split(',')) > 1:
- logger.error(str(u"Multiple storage classes are not supported currently."))
- return 1
-
arvargs.use_container = True
arvargs.relax_path_checks = True
arvargs.print_supported_versions = False
# Make an API object now so errors are reported early.
api_client.users().current().execute()
if keep_client is None:
- keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)
- executor = ArvCwlExecutor(api_client, arvargs, keep_client=keep_client, num_retries=4)
+ block_cache = arvados.keep.KeepBlockCache(disk_cache=True)
+ keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4, block_cache=block_cache)
+ executor = ArvCwlExecutor(api_client, arvargs, keep_client=keep_client, num_retries=4, stdout=stdout)
+ except WorkflowException as e:
+ logger.error(e, exc_info=(sys.exc_info()[1] if arvargs.debug else False))
+ return 1
except Exception:
logger.exception("Error creating the Arvados CWL Executor")
return 1
# unit tests.
stdout = None
+ if arvargs.submit and (arvargs.workflow.startswith("arvwf:") or workflow_uuid_pattern.match(arvargs.workflow)):
+ executor.loadingContext.do_validate = False
+ executor.fast_submit = True
+
return cwltool.main.main(args=arvargs,
stdout=stdout,
stderr=stderr,
logger_handler=arvados.log_handler,
custom_schema_callback=add_arv_hints,
loadingContext=executor.loadingContext,
- runtimeContext=executor.runtimeContext,
+ runtimeContext=executor.toplevel_runtimeContext,
input_required=not (arvargs.create_workflow or arvargs.update_workflow))
projects / arvados.git / blobdiff