def main(args, stdout, 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
if install_sig_handlers:
arv_cmd.install_signal_handlers()
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:
logger.error(str(u'--update-workflow arg {!r} uses {!r} API, but --api={!r} specified').format(
arvargs.update_workflow, want_api, arvargs.work_api))
return 1
arvargs.work_api = want_api
if (arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
job_order_object = ({}, "")
add_arv_hints()
for key, val in viewitems(cwltool.argparser.get_default_args()):
if not hasattr(arvargs, key):
setattr(arvargs, key, val)
try:
if api_client is None:
api_client = arvados.safeapi.ThreadSafeApiCache(
api_params={"model": OrderedJsonModel(), "timeout": arvargs.http_timeout},
keep_params={"num_retries": 4})
keep_client = api_client.keep
# 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)
except Exception:
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().
if arvargs.debug:
logger.setLevel(logging.DEBUG)
logging.getLogger('arvados').setLevel(logging.DEBUG)
if arvargs.quiet:
logger.setLevel(logging.WARN)
logging.getLogger('arvados').setLevel(logging.WARN)
logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
if arvargs.metrics:
metrics.setLevel(logging.DEBUG)
logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
if arvargs.log_timestamps:
arvados.log_handler.setFormatter(logging.Formatter(
'%(asctime)s %(name)s %(levelname)s: %(message)s',
'%Y-%m-%d %H:%M:%S'))
else:
arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
return cwltool.main.main(args=arvargs,
stdout=stdout,
stderr=stderr,
executor=executor.arv_executor,
versionfunc=versionstring,
job_order_object=job_order_object,
logger_handler=arvados.log_handler,
custom_schema_callback=add_arv_hints,
loadingContext=executor.loadingContext,
runtimeContext=executor.runtimeContext)
def main(args, stdout, 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
if install_sig_handlers:
arv_cmd.install_signal_handlers()
if arvargs.update_workflow:
if arvargs.update_workflow.find('-7fd4e-') == 5:
want_api = 'containers'
else:
want_api = None
if want_api and arvargs.work_api and want_api != arvargs.work_api:
logger.error(str(u'--update-workflow arg {!r} uses {!r} API, but --api={!r} specified').format(
arvargs.update_workflow, want_api, arvargs.work_api))
return 1
arvargs.work_api = want_api
if (arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
job_order_object = ({}, "")
add_arv_hints()
for key, val in viewitems(cwltool.argparser.get_default_args()):
if not hasattr(arvargs, key):
setattr(arvargs, key, val)
try:
if api_client is None:
api_client = arvados.safeapi.ThreadSafeApiCache(
api_params={"model": OrderedJsonModel(), "timeout": arvargs.http_timeout},
keep_params={"num_retries": 4})
keep_client = api_client.keep
# 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)
except Exception:
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.
if arvargs.debug:
logger.setLevel(logging.DEBUG)
logging.getLogger('arvados').setLevel(logging.DEBUG)
if arvargs.quiet:
logger.setLevel(logging.WARN)
logging.getLogger('arvados').setLevel(logging.WARN)
logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
if arvargs.metrics:
metrics.setLevel(logging.DEBUG)
logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
if arvargs.log_timestamps:
arvados.log_handler.setFormatter(logging.Formatter(
'%(asctime)s %(name)s %(levelname)s: %(message)s',
'%Y-%m-%d %H:%M:%S'))
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,
executor=executor.arv_executor,
versionfunc=versionstring,
job_order_object=job_order_object,
logger_handler=arvados.log_handler,
custom_schema_callback=add_arv_hints,
loadingContext=executor.loadingContext,
runtimeContext=executor.runtimeContext,
input_required=not (arvargs.create_workflow or arvargs.update_workflow))
def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr,
install_sig_handlers=True):
global api_client
args = parse_arguments(arguments)
logger = logging.getLogger('arvados.arv_put')
if args.silent:
logger.setLevel(logging.WARNING)
else:
logger.setLevel(logging.INFO)
status = 0
request_id = arvados.util.new_request_id()
formatter = ArvPutLogFormatter(request_id)
logging.getLogger('arvados').handlers[0].setFormatter(formatter)
if api_client is None:
api_client = arvados.api('v1', request_id=request_id)
if install_sig_handlers:
arv_cmd.install_signal_handlers()
# Determine the name to use
if args.name:
if args.stream or args.raw:
logger.error("Cannot use --name with --stream or --raw")
sys.exit(1)
elif args.update_collection:
logger.error("Cannot use --name with --update-collection")
sys.exit(1)
collection_name = args.name
else:
collection_name = "Saved at {} by {}@{}".format(
datetime.datetime.utcnow().strftime("%Y-%m-%d %H:%M:%S UTC"),
pwd.getpwuid(os.getuid()).pw_name,
socket.gethostname())
if args.project_uuid and (args.stream or args.raw):
logger.error("Cannot use --project-uuid with --stream or --raw")
sys.exit(1)
# Determine the parent project
try:
project_uuid = desired_project_uuid(api_client, args.project_uuid,
args.retries)
except (apiclient_errors.Error, ValueError) as error:
logger.error(error)
sys.exit(1)
if args.progress:
reporter = progress_writer(human_progress)
elif args.batch_progress:
reporter = progress_writer(machine_progress)
else:
reporter = None
# Split storage-classes argument
storage_classes = None
if args.storage_classes:
storage_classes = args.storage_classes.strip().split(',')
if len(storage_classes) > 1:
logger.error("Multiple storage classes are not supported currently.")
sys.exit(1)
# Setup exclude regex from all the --exclude arguments provided
name_patterns = []
exclude_paths = []
exclude_names = None
if len(args.exclude) > 0:
# We're supporting 2 kinds of exclusion patterns:
# 1) --exclude '*.jpg' (file/dir name patterns, will only match
# the name, wherever the file is on the tree)
# 2.1) --exclude 'foo/bar' (file/dir path patterns, will match the
# entire path, and should be relative to
# any input dir argument)
# 2.2) --exclude './*.jpg' (Special case for excluding files/dirs
# placed directly underneath the input dir)
for p in args.exclude:
# Only relative paths patterns allowed
if p.startswith(os.sep):
logger.error("Cannot use absolute paths with --exclude")
sys.exit(1)
if os.path.dirname(p):
# We don't support of path patterns with '..'
p_parts = p.split(os.sep)
if '..' in p_parts:
logger.error(
"Cannot use path patterns that include or '..'")
sys.exit(1)
# Path search pattern
exclude_paths.append(p)
else:
# Name-only search pattern
name_patterns.append(p)
# For name only matching, we can combine all patterns into a single
# regexp, for better performance.
exclude_names = re.compile('|'.join(
[fnmatch.translate(p) for p in name_patterns]
)) if len(name_patterns) > 0 else None
# Show the user the patterns to be used, just in case they weren't
# specified inside quotes and got changed by the shell expansion.
logger.info("Exclude patterns: {}".format(args.exclude))
# If this is used by a human, and there's at least one directory to be
# uploaded, the expected bytes calculation can take a moment.
if args.progress and any([os.path.isdir(f) for f in args.paths]):
logger.info("Calculating upload size, this could take some time...")
try:
writer = ArvPutUploadJob(paths = args.paths,
resume = args.resume,
use_cache = args.use_cache,
filename = args.filename,
reporter = reporter,
api_client = api_client,
num_retries = args.retries,
replication_desired = args.replication,
put_threads = args.threads,
name = collection_name,
owner_uuid = project_uuid,
ensure_unique_name = True,
update_collection = args.update_collection,
storage_classes=storage_classes,
logger=logger,
dry_run=args.dry_run,
follow_links=args.follow_links,
exclude_paths=exclude_paths,
exclude_names=exclude_names)
except ResumeCacheConflict:
logger.error("\n".join([
"arv-put: Another process is already uploading this data.",
" Use --no-cache if this is really what you want."]))
sys.exit(1)
except ResumeCacheInvalidError:
logger.error("\n".join([
"arv-put: Resume cache contains invalid signature: it may have expired",
" or been created with another Arvados user's credentials.",
" Switch user or use one of the following options to restart upload:",
" --no-resume to start a new resume cache.",
" --no-cache to disable resume cache."]))
sys.exit(1)
except CollectionUpdateError as error:
logger.error("\n".join([
"arv-put: %s" % str(error)]))
sys.exit(1)
except ArvPutUploadIsPending:
# Dry run check successful, return proper exit code.
sys.exit(2)
except ArvPutUploadNotPending:
# No files pending for upload
sys.exit(0)
except PathDoesNotExistError as error:
logger.error("\n".join([
"arv-put: %s" % str(error)]))
sys.exit(1)
if not args.dry_run and not args.update_collection and args.resume and writer.bytes_written > 0:
logger.warning("\n".join([
"arv-put: Resuming previous upload from last checkpoint.",
" Use the --no-resume option to start over."]))
if not args.dry_run:
writer.report_progress()
output = None
try:
writer.start(save_collection=not(args.stream or args.raw))
except arvados.errors.ApiError as error:
logger.error("\n".join([
"arv-put: %s" % str(error)]))
sys.exit(1)
if args.progress: # Print newline to split stderr from stdout for humans.
logger.info("\n")
if args.stream:
if args.normalize:
output = writer.manifest_text(normalize=True)
else:
output = writer.manifest_text()
elif args.raw:
output = ','.join(writer.data_locators())
else:
try:
if args.update_collection:
logger.info(u"Collection updated: '{}'".format(writer.collection_name()))
else:
logger.info(u"Collection saved as '{}'".format(writer.collection_name()))
if args.portable_data_hash:
output = writer.portable_data_hash()
else:
output = writer.manifest_locator()
except apiclient_errors.Error as error:
logger.error(
"arv-put: Error creating Collection on project: {}.".format(
error))
status = 1
# Print the locator (uuid) of the new collection.
if output is None:
status = status or 1
elif not args.silent:
stdout.write(output)
if not output.endswith('\n'):
stdout.write('\n')
if install_sig_handlers:
arv_cmd.restore_signal_handlers()
if status != 0:
sys.exit(status)
# Success!
return output
def main(args,
stdout,
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
if install_sig_handlers:
arv_cmd.install_signal_handlers()
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:
logger.error(
str(u'--update-workflow arg {!r} uses {!r} API, but --api={!r} specified'
).format(arvargs.update_workflow, want_api,
arvargs.work_api))
return 1
arvargs.work_api = want_api
if (arvargs.create_workflow
or arvargs.update_workflow) and not arvargs.job_order:
job_order_object = ({}, "")
add_arv_hints()
for key, val in viewitems(cwltool.argparser.get_default_args()):
if not hasattr(arvargs, key):
setattr(arvargs, key, val)
try:
if api_client is None:
api_client = arvados.safeapi.ThreadSafeApiCache(
api_params={
"model": OrderedJsonModel(),
"timeout": arvargs.http_timeout
},
keep_params={"num_retries": 4})
keep_client = api_client.keep
# 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)
except Exception as e:
logger.error(e)
return 1
if arvargs.debug:
logger.setLevel(logging.DEBUG)
logging.getLogger('arvados').setLevel(logging.DEBUG)
if arvargs.quiet:
logger.setLevel(logging.WARN)
logging.getLogger('arvados').setLevel(logging.WARN)
logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
if arvargs.metrics:
metrics.setLevel(logging.DEBUG)
logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
if arvargs.log_timestamps:
arvados.log_handler.setFormatter(
logging.Formatter(
'%(asctime)s %(name)s %(levelname)s: %(message)s',
'%Y-%m-%d %H:%M:%S'))
else:
arvados.log_handler.setFormatter(
logging.Formatter('%(name)s %(levelname)s: %(message)s'))
return cwltool.main.main(args=arvargs,
stdout=stdout,
stderr=stderr,
executor=executor.arv_executor,
versionfunc=versionstring,
job_order_object=job_order_object,
logger_handler=arvados.log_handler,
custom_schema_callback=add_arv_hints,
loadingContext=executor.loadingContext,
runtimeContext=executor.runtimeContext)
def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr,
install_sig_handlers=True):
global api_client
args = parse_arguments(arguments)
logger = logging.getLogger('arvados.arv_put')
if args.silent:
logger.setLevel(logging.WARNING)
else:
logger.setLevel(logging.INFO)
status = 0
request_id = arvados.util.new_request_id()
formatter = ArvPutLogFormatter(request_id)
logging.getLogger('arvados').handlers[0].setFormatter(formatter)
if api_client is None:
api_client = arvados.api('v1', request_id=request_id)
if install_sig_handlers:
arv_cmd.install_signal_handlers()
# Determine the name to use
if args.name:
if args.stream or args.raw:
logger.error("Cannot use --name with --stream or --raw")
sys.exit(1)
elif args.update_collection:
logger.error("Cannot use --name with --update-collection")
sys.exit(1)
collection_name = args.name
else:
collection_name = "Saved at {} by {}@{}".format(
datetime.datetime.utcnow().strftime("%Y-%m-%d %H:%M:%S UTC"),
pwd.getpwuid(os.getuid()).pw_name,
socket.gethostname())
if args.project_uuid and (args.stream or args.raw):
logger.error("Cannot use --project-uuid with --stream or --raw")
sys.exit(1)
# Determine the parent project
try:
project_uuid = desired_project_uuid(api_client, args.project_uuid,
args.retries)
except (apiclient_errors.Error, ValueError) as error:
logger.error(error)
sys.exit(1)
if args.progress:
reporter = progress_writer(human_progress)
elif args.batch_progress:
reporter = progress_writer(machine_progress)
else:
reporter = None
# Split storage-classes argument
storage_classes = None
if args.storage_classes:
storage_classes = args.storage_classes.strip().split(',')
if len(storage_classes) > 1:
logger.error("Multiple storage classes are not supported currently.")
sys.exit(1)
# Setup exclude regex from all the --exclude arguments provided
name_patterns = []
exclude_paths = []
exclude_names = None
if len(args.exclude) > 0:
# We're supporting 2 kinds of exclusion patterns:
# 1) --exclude '*.jpg' (file/dir name patterns, will only match
# the name, wherever the file is on the tree)
# 2.1) --exclude 'foo/bar' (file/dir path patterns, will match the
# entire path, and should be relative to
# any input dir argument)
# 2.2) --exclude './*.jpg' (Special case for excluding files/dirs
# placed directly underneath the input dir)
for p in args.exclude:
# Only relative paths patterns allowed
if p.startswith(os.sep):
logger.error("Cannot use absolute paths with --exclude")
sys.exit(1)
if os.path.dirname(p):
# We don't support of path patterns with '..'
p_parts = p.split(os.sep)
if '..' in p_parts:
logger.error(
"Cannot use path patterns that include or '..'")
sys.exit(1)
# Path search pattern
exclude_paths.append(p)
else:
# Name-only search pattern
name_patterns.append(p)
# For name only matching, we can combine all patterns into a single
# regexp, for better performance.
exclude_names = re.compile('|'.join(
[fnmatch.translate(p) for p in name_patterns]
)) if len(name_patterns) > 0 else None
# Show the user the patterns to be used, just in case they weren't
# specified inside quotes and got changed by the shell expansion.
logger.info("Exclude patterns: {}".format(args.exclude))
# If this is used by a human, and there's at least one directory to be
# uploaded, the expected bytes calculation can take a moment.
if args.progress and any([os.path.isdir(f) for f in args.paths]):
logger.info("Calculating upload size, this could take some time...")
try:
writer = ArvPutUploadJob(paths = args.paths,
resume = args.resume,
use_cache = args.use_cache,
filename = args.filename,
reporter = reporter,
api_client = api_client,
num_retries = args.retries,
replication_desired = args.replication,
put_threads = args.threads,
name = collection_name,
owner_uuid = project_uuid,
ensure_unique_name = True,
update_collection = args.update_collection,
storage_classes=storage_classes,
logger=logger,
dry_run=args.dry_run,
follow_links=args.follow_links,
exclude_paths=exclude_paths,
exclude_names=exclude_names)
except ResumeCacheConflict:
logger.error("\n".join([
"arv-put: Another process is already uploading this data.",
" Use --no-cache if this is really what you want."]))
sys.exit(1)
except CollectionUpdateError as error:
logger.error("\n".join([
"arv-put: %s" % str(error)]))
sys.exit(1)
except ArvPutUploadIsPending:
# Dry run check successful, return proper exit code.
sys.exit(2)
except ArvPutUploadNotPending:
# No files pending for upload
sys.exit(0)
except PathDoesNotExistError as error:
logger.error("\n".join([
"arv-put: %s" % str(error)]))
sys.exit(1)
if not args.dry_run and not args.update_collection and args.resume and writer.bytes_written > 0:
logger.warning("\n".join([
"arv-put: Resuming previous upload from last checkpoint.",
" Use the --no-resume option to start over."]))
if not args.dry_run:
writer.report_progress()
output = None
try:
writer.start(save_collection=not(args.stream or args.raw))
except arvados.errors.ApiError as error:
logger.error("\n".join([
"arv-put: %s" % str(error)]))
sys.exit(1)
if args.progress: # Print newline to split stderr from stdout for humans.
logger.info("\n")
if args.stream:
if args.normalize:
output = writer.manifest_text(normalize=True)
else:
output = writer.manifest_text()
elif args.raw:
output = ','.join(writer.data_locators())
else:
try:
if args.update_collection:
logger.info("Collection updated: '{}'".format(writer.collection_name()))
else:
logger.info("Collection saved as '{}'".format(writer.collection_name()))
if args.portable_data_hash:
output = writer.portable_data_hash()
else:
output = writer.manifest_locator()
except apiclient_errors.Error as error:
logger.error(
"arv-put: Error creating Collection on project: {}.".format(
error))
status = 1
# Print the locator (uuid) of the new collection.
if output is None:
status = status or 1
elif not args.silent:
stdout.write(output)
if not output.endswith('\n'):
stdout.write('\n')
if install_sig_handlers:
arv_cmd.restore_signal_handlers()
if status != 0:
sys.exit(status)
# Success!
return output
