logger.error(
"Transformation from KBaseGenomes.Genome to Genbank.Genome failed on {0}"
.format(object_name))
logger.error(stderr)
sys.exit(1)
logger.info(
"Transformation from KBaseGenomes.Genome to Genbank.Genome completed.")
sys.exit(0)
if __name__ == "__main__":
script_details = script_utils.parse_docs(transform.__doc__)
parser = script_utils.ArgumentParser(
prog=__file__,
description=script_details["Description"],
epilog=script_details["Authors"])
parser.add_argument("--shock_service_url",
help=script_details["Args"]["shock_service_url"],
action="store",
type=str,
nargs='?',
required=False)
parser.add_argument("--workspace_service_url",
help=script_details["Args"]["workspace_service_url"],
action="store",
type=str,
nargs="?",
required=True)
parser.add_argument("--workspace_name",
help=script_details["Args"]["workspace_name"],
def main():
"""
KBase Convert task manager for converting between KBase objects.
Step 1 - Run a converter to pull the source object and save the destination object.
Args:
workspace_service_url: URL for a KBase Workspace service where KBase objects
are stored.
ujs_service_url: URL for a User and Job State service to report task progress
back to the user.
shock_service_url: URL for a KBase SHOCK data store service for storing files
and large reference data.
handle_service_url: URL for a KBase Handle service that maps permissions from
the Workspace to SHOCK for KBase types that specify a Handle
reference instead of a SHOCK reference.
source_workspace_name: The name of the source workspace.
destination_workspace_name: The name of the destination workspace.
source_object_name: The source object name.
destination_object_name: The destination object name.
source_kbase_type: The KBase Workspace type string that indicates the module
and type of the object being created.
destination_kbase_type: The KBase Workspace type string that indicates the module
and type of the object being created.
optional_arguments: This is a JSON string containing optional parameters that can
be passed in for custom behavior per conversion.
ujs_job_id: The job id from the User and Job State service that can be used to
report status on task progress back to the user.
job_details: This is a JSON string that passes in the script specific command
line options for a given conversion type. The service pulls
these config settings from a script config created by the developer
of the conversion script and passes that into the AWE job that
calls this script.
working_directory: The working directory on disk where files can be created and
will be cleaned when the job ends with success or failure.
keep_working_directory: A flag to tell the script not to delete the working
directory, which is mainly for debugging purposes.
debug: Run the taskrunner in debug mode for local execution in a virtualenv.
Returns:
Literal return value is 0 for success and 1 for failure.
Actual data output is one or more Workspace objects saved to a user's workspace.
Authors:
Matt Henderson, Gavin Price
"""
logger = script_utils.stderrlogger(__file__, level=logging.DEBUG)
logger.info("Executing KBase Convert tasks")
script_details = script_utils.parse_docs(main.__doc__)
logger.debug(script_details["Args"])
parser = script_utils.ArgumentParser(
description=script_details["Description"],
epilog=script_details["Authors"])
# provided by service config
parser.add_argument('--workspace_service_url',
help=script_details["Args"]["workspace_service_url"],
action='store',
required=True)
parser.add_argument('--ujs_service_url',
help=script_details["Args"]["ujs_service_url"],
action='store',
required=True)
# optional because not all KBase Workspace types contain a SHOCK or Handle reference
parser.add_argument('--shock_service_url',
help=script_details["Args"]["shock_service_url"],
action='store',
default=None)
parser.add_argument('--handle_service_url',
help=script_details["Args"]["handle_service_url"],
action='store',
default=None)
# workspace info for pulling the data
parser.add_argument('--source_workspace_name',
help=script_details["Args"]["source_workspace_name"],
action='store',
required=True)
parser.add_argument('--source_object_name',
help=script_details["Args"]["source_object_name"],
action='store',
required=True)
# workspace info for saving the data
parser.add_argument(
'--destination_workspace_name',
help=script_details["Args"]["destination_workspace_name"],
action='store',
required=True)
parser.add_argument('--destination_object_name',
help=script_details["Args"]["destination_object_name"],
action='store',
required=True)
# the types that we are transforming between, currently assumed one to one
parser.add_argument('--source_kbase_type',
help=script_details["Args"]["source_kbase_type"],
action='store',
required=True)
parser.add_argument('--destination_kbase_type',
help=script_details["Args"]["destination_kbase_type"],
action='store',
required=True)
# any user options provided, encoded as a jason string
parser.add_argument('--optional_arguments',
help=script_details["Args"]["optional_arguments"],
action='store',
default='{}')
# Used if you are restarting a previously executed job?
parser.add_argument('--ujs_job_id',
help=script_details["Args"]["ujs_job_id"],
action='store',
default=None,
required=False)
# config information for running the validate and transform scripts
parser.add_argument('--job_details',
help=script_details["Args"]["job_details"],
action='store',
default=None)
# the working directory is where all the files for this job will be written,
# and normal operation cleans it after the job ends (success or fail)
parser.add_argument('--working_directory',
help=script_details["Args"]["working_directory"],
action='store',
default=None,
required=True)
parser.add_argument('--keep_working_directory',
help=script_details["Args"]["keep_working_directory"],
action='store_true')
# turn on debugging options for script developers running locally
parser.add_argument('--debug',
help=script_details["Args"]["debug"],
action='store_true')
args = None
try:
args = parser.parse_args()
except Exception, e:
logger.debug("Caught exception parsing arguments!")
logger.exception(e)
sys.exit(1)
def main():
"""
KBase Convert task manager for converting between KBase objects.
Step 1 - Run a converter to pull the source object and save the destination object.
Args:
workspace_service_url: URL for a KBase Workspace service where KBase objects
are stored.
ujs_service_url: URL for a User and Job State service to report task progress
back to the user.
shock_service_url: URL for a KBase SHOCK data store service for storing files
and large reference data.
handle_service_url: URL for a KBase Handle service that maps permissions from
the Workspace to SHOCK for KBase types that specify a Handle
reference instead of a SHOCK reference.
source_workspace_name: The name of the source workspace.
destination_workspace_name: The name of the destination workspace.
source_object_name: The source object name.
destination_object_name: The destination object name.
source_kbase_type: The KBase Workspace type string that indicates the module
and type of the object being created.
destination_kbase_type: The KBase Workspace type string that indicates the module
and type of the object being created.
optional_arguments: This is a JSON string containing optional parameters that can
be passed in for custom behavior per conversion.
ujs_job_id: The job id from the User and Job State service that can be used to
report status on task progress back to the user.
job_details: This is a JSON string that passes in the script specific command
line options for a given conversion type. The service pulls
these config settings from a script config created by the developer
of the conversion script and passes that into the AWE job that
calls this script.
working_directory: The working directory on disk where files can be created and
will be cleaned when the job ends with success or failure.
keep_working_directory: A flag to tell the script not to delete the working
directory, which is mainly for debugging purposes.
Returns:
Literal return value is 0 for success and 1 for failure.
Actual data output is one or more Workspace objects saved to a user's workspace.
Authors:
Matt Henderson, Gavin Price
"""
logger = script_utils.stderrlogger(__file__, level=logging.DEBUG)
logger.info("Executing KBase Convert tasks")
script_details = script_utils.parse_docs(main.__doc__)
logger.debug(script_details["Args"])
parser = script_utils.ArgumentParser(description=script_details["Description"],
epilog=script_details["Authors"])
# provided by service config
parser.add_argument('--workspace_service_url',
help=script_details["Args"]["workspace_service_url"],
action='store',
required=True)
parser.add_argument('--ujs_service_url',
help=script_details["Args"]["ujs_service_url"],
action='store',
required=True)
# optional because not all KBase Workspace types contain a SHOCK or Handle reference
parser.add_argument('--shock_service_url',
help=script_details["Args"]["shock_service_url"],
action='store',
default=None)
parser.add_argument('--handle_service_url',
help=script_details["Args"]["handle_service_url"],
action='store',
default=None)
# workspace info for pulling the data
parser.add_argument('--source_workspace_name',
help=script_details["Args"]["source_workspace_name"],
action='store',
required=True)
parser.add_argument('--source_object_name',
help=script_details["Args"]["source_object_name"],
action='store',
required=True)
# workspace info for saving the data
parser.add_argument('--destination_workspace_name',
help=script_details["Args"]["destination_workspace_name"],
action='store',
required=True)
parser.add_argument('--destination_object_name',
help=script_details["Args"]["destination_object_name"],
action='store',
required=True)
# the types that we are transforming between, currently assumed one to one
parser.add_argument('--source_kbase_type',
help=script_details["Args"]["source_kbase_type"],
action='store',
required=True)
parser.add_argument('--destination_kbase_type',
help=script_details["Args"]["destination_kbase_type"],
action='store',
required=True)
# any user options provided, encoded as a jason string
parser.add_argument('--optional_arguments',
help=script_details["Args"]["optional_arguments"],
action='store',
default='{}')
# Used if you are restarting a previously executed job?
parser.add_argument('--ujs_job_id',
help=script_details["Args"]["ujs_job_id"],
action='store',
default=None,
required=False)
# config information for running the validate and transform scripts
parser.add_argument('--job_details',
help=script_details["Args"]["job_details"],
action='store',
default=None)
# the working directory is where all the files for this job will be written,
# and normal operation cleans it after the job ends (success or fail)
parser.add_argument('--working_directory',
help=script_details["Args"]["working_directory"],
action='store',
default=None,
required=True)
parser.add_argument('--keep_working_directory',
help=script_details["Args"]["keep_working_directory"],
action='store_true')
# ignore any extra arguments
args, unknown = parser.parse_known_args()
kb_token = os.environ.get('KB_AUTH_TOKEN')
ujs = UserAndJobState(url=args.ujs_service_url, token=kb_token)
est = datetime.datetime.utcnow() + datetime.timedelta(minutes=3)
if args.ujs_job_id is not None:
ujs.update_job_progress(args.ujs_job_id, kb_token, "KBase Data Convert started",
1, est.strftime('%Y-%m-%dT%H:%M:%S+0000'))
# parse all the json strings from the argument list into dicts
# TODO had issues with json.loads and unicode strings, workaround was using simplejson and base64
args.optional_arguments = simplejson.loads(base64.urlsafe_b64decode(args.optional_arguments))
args.job_details = simplejson.loads(base64.urlsafe_b64decode(args.job_details))
if not os.path.exists(args.working_directory):
os.mkdir(args.working_directory)
if args.ujs_job_id is not None:
ujs.update_job_progress(args.ujs_job_id, kb_token,
"Converting from {0} to {1}".format(args.source_kbase_type,args.destination_kbase_type),
1, est.strftime('%Y-%m-%dT%H:%M:%S+0000') )
# Step 1 : Convert the objects
try:
logger.info(args)
convert_args = args.job_details["transform"]
convert_args["optional_arguments"] = args.optional_arguments
convert_args["working_directory"] = args.working_directory
convert_args["workspace_service_url"] = args.workspace_service_url
convert_args["source_workspace_name"] = args.source_workspace_name
convert_args["source_object_name"] = args.source_object_name
convert_args["destination_workspace_name"] = args.destination_workspace_name
convert_args["destination_object_name"] = args.destination_object_name
logger.info(convert_args)
task_output = handler_utils.run_task(logger, convert_args)
if task_output["stdout"] is not None:
logger.debug("STDOUT : " + str(task_output["stdout"]))
if task_output["stderr"] is not None:
logger.debug("STDERR : " + str(task_output["stderr"]))
except Exception, e:
handler_utils.report_exception(logger,
{"message": 'ERROR : Conversion from {0} to {1}'.format(args.source_kbase_type,args.destination_kbase_type),
"exc": e,
"ujs": ujs,
"ujs_job_id": args.ujs_job_id,
"token": kb_token,
},
{"keep_working_directory": args.keep_working_directory,
"working_directory": args.working_directory})
ujs.complete_job(args.ujs_job_id,
kb_token,
"Convert to {0} failed.".format(
args.destination_workspace_name),
str(e),
None)
def main():
parser = script_utils.ArgumentParser(
prog=SCRIPT_NAME,
description='Converts KBaseFile.AssemblyFile to ' +
'KBaseGenomes.ContigSet.',
epilog='Authors: Jason Baumohl, Matt Henderson, Gavin Price')
# The following 7 arguments should be standard to all uploaders
parser.add_argument('--working_directory',
help='Directory for temporary files',
action='store',
type=str,
required=True)
# Example of a custom argument specific to this uploader
parser.add_argument('--workspace_service_url',
help='workspace service url',
action='store',
type=str,
required=True)
parser.add_argument('--source_workspace_name',
help='name of the source workspace',
action='store',
type=str,
required=True)
parser.add_argument('--destination_workspace_name',
help='name of the target workspace',
action='store',
type=str,
required=True)
parser.add_argument('--source_object_name',
help='name of the workspace object to convert',
action='store',
type=str,
required=True)
parser.add_argument('--destination_object_name',
help='name for the produced ContigSet.',
action='store',
type=str,
required=True)
parser.add_argument(
'--fasta_reference_only',
help='Creates a reference to the fasta file in Shock, but does not ' +
'store the sequences in the workspace object. Not recommended ' +
'unless the fasta file is larger than 1GB. This is the default ' +
'behavior for files that large.',
action='store_true',
required=False)
# ignore unknown arguments for now
args, _ = parser.parse_known_args()
logger = script_utils.stderrlogger(__file__)
try:
# make there's at least something for a token
if not TOKEN:
raise Exception("Unable to retrieve KBase Authentication token!")
shock_url, shock_id, ref, source = download_workspace_data(
args.workspace_service_url, args.source_workspace_name,
args.source_object_name, args.working_directory, logger)
inputfile = os.path.join(args.working_directory,
args.source_object_name)
cs = convert_to_contigs(None,
None,
inputfile,
args.destination_object_name,
args.working_directory,
shock_id,
None,
args.fasta_reference_only,
source,
logger=logger)
upload_workspace_data(cs, args.workspace_service_url, ref,
args.destination_workspace_name,
args.destination_object_name)
except Exception, e:
logger.exception(e)
sys.exit(1)
