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)
if "custom_options" in job_details["transform"]["handler_options"]:
for c in job_details["transform"]["handler_options"]["custom_options"]:
transformation_args[c["name"]] = c["value"]
if "working_directory" in transformation_args:
logger.debug(os.path.abspath(os.getcwd()))
transformation_args["working_directory"] = os.path.abspath(os.getcwd())
# check that we are not missing any required arguments
for k in job_details["transform"]["handler_options"]["required_fields"]:
if transformation_args[k] is None:
raise Exception("Missing required field {0}, please provide using optional_arguments.".format(k))
logger.debug(transformation_args)
task_output = handler_utils.run_task(logger, transformation_args, debug=debug)
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"]))
os.chdir(current_directory)
except Exception, e:
logger.debug("Caught exception during transformation step!")
os.chdir(current_directory)
if ujs_job_id is not None:
error_object["status"] = "ERROR : Transformation from KBase type to External type failed - {0}".format(e.message)[:handler_utils.UJS_STATUS_MAX]
# 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:
if args.ujs_job_id is not None:
error_object["status"] = "ERROR : Conversion between KBase Types failed - {0}".format(e.message)[:handler_utils.UJS_STATUS_MAX]
error_object["error_message"] = traceback.format_exc()
handler_utils.report_exception(logger, error_object, cleanup_details)
ujs.complete_job(args.ujs_job_id,
kb_token,
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:
if args.ujs_job_id is not None:
error_object[
"status"] = "ERROR : Conversion between KBase Types failed - {0}".format(
e.message)[:handler_utils.UJS_STATUS_MAX]
error_object["error_message"] = traceback.format_exc()
handler_utils.report_exception(logger, error_object,
cleanup_details)
filename = os.path.split(files[0])[-1]
try:
if ujs_job_id is not None:
# Update on validation steps
logger.info(
"UJS message : " +
"Attempting to validate {0}".format(
filename)[:handler_utils.UJS_STATUS_MAX])
ujs.update_job_progress(
ujs_job_id, kb_token,
"Attempting to validate {0}".format(filename)
[:handler_utils.UJS_STATUS_MAX], 1,
est.strftime('%Y-%m-%dT%H:%M:%S+0000'))
task_output = handler_utils.run_task(logger, validation_args, callback=lambda msg: \
ujs.update_job_progress(ujs_job_id, kb_token, msg[:handler_utils.UJS_STATUS_MAX], 1, est.strftime('%Y-%m-%dT%H:%M:%S+0000')))
else:
logger.info(
"Attempting to validate {0}".format(filename))
task_output = handler_utils.run_task(
logger, validation_args)
except Exception, e:
logger.debug("Caught exception while validating!")
if ujs_job_id is not None:
task_output = dict()
task_output["stdout"] = e.args[0]
task_output["stderr"] = e.args[1]
if task_output["stderr"] != None and len(
task_output["stderr"].strip()) > 0:
for k in job_details["validate"]["handler_options"]["required_fields"]:
if k not in validation_args:
raise Exception("Missing required field {0}, please provide using optional_arguments.".format(k))
elif validation_args[k] is None:
raise Exception("Missing value for required field {0}, please provide using optional_arguments.".format(k))
filename = os.path.split(files[0])[-1]
try:
if ujs_job_id is not None:
# Update on validation steps
logger.info("UJS message : " + "Attempting to validate {0}".format(filename)[:handler_utils.UJS_STATUS_MAX])
ujs.update_job_progress(ujs_job_id, kb_token, "Attempting to validate {0}".format(filename)[:handler_utils.UJS_STATUS_MAX],
1, est.strftime('%Y-%m-%dT%H:%M:%S+0000'))
task_output = handler_utils.run_task(logger, validation_args, callback=lambda msg: \
ujs.update_job_progress(ujs_job_id, kb_token, msg[:handler_utils.UJS_STATUS_MAX], 1, est.strftime('%Y-%m-%dT%H:%M:%S+0000')))
else:
logger.info("Attempting to validate {0}".format(filename))
task_output = handler_utils.run_task(logger, validation_args)
except Exception, e:
logger.debug("Caught exception while validating!")
if ujs_job_id is not None:
task_output = dict()
task_output["stdout"] = e.args[0]
task_output["stderr"] = e.args[1]
if task_output["stderr"] != None and len(task_output["stderr"].strip()) > 0:
error_object["status"] = "ERROR : Validation of input data - {0}".format(task_output["stderr"][-handler_utils.UJS_STATUS_MAX:])[:handler_utils.UJS_STATUS_MAX]
error_object["error_message"] = task_output["stderr"]
elif task_output["stdout"] != None and len(task_output["stdout"].strip()) > 0:
