def wes_get_service_info(self):
logging.debug(f"Call wes_get_service_info")
response = {
"workflow_type_versions": {
"CWL": {"workflow_type_version": ["v1.0"]}
},
"supported_wes_versions": ["1.0.0"],
"supported_filesystem_protocols": ["file"],
"workflow_engine_versions": {
"cwl-airflow": get_version()
}
}
return response
def get_parser():
"""
Defines arguments for parser. Inlcudes two subparsers for
api server and init components.
"""
parent_parser = argparse.ArgumentParser(add_help=False)
general_parser = argparse.ArgumentParser(
description="CWL-Airflow: a lightweight pipeline manager \
supporting Common Workflow Language")
subparsers = general_parser.add_subparsers()
subparsers.required = True
general_parser.add_argument("--version",
action="version",
version=get_version(),
help="Print current version and exit")
# API
api_parser = subparsers.add_parser("api",
parents=[parent_parser],
help="Run API server")
api_parser.set_defaults(func=run_api_server)
api_parser.add_argument(
"--port",
type=int,
default=8081,
help="Set port to run API server. Default: 8081",
)
api_parser.add_argument(
"--host",
type=str,
default="127.0.0.1",
help="Set host to run API server. Default: 127.0.0.1")
api_parser.add_argument(
"--simulation",
type=str,
nargs="?", # 0 or 1 argument
const=path.abspath(
path.join(__file__, "../../data/default_simulation_suite.yaml")),
help="Set path to the test suite file to simulate reports. \
Pipelines won't get triggered in this mode. \
Default: real reports from the star-index workflow")
api_parser.add_argument(
"--replay",
type=int,
help="Retries to post undelivered progress and results reports \
to the process_report connection every N seconds. \
If connection is not set this parameter is ignored. \
Default: do not resend not delivered reports")
# Init
init_parser = subparsers.add_parser("init",
parents=[parent_parser],
help="Run initial configuration")
init_parser.set_defaults(func=run_init_config)
init_parser.add_argument("--home",
type=str,
default=get_airflow_home(),
help="Set path to Airflow home directory. \
Default: first try AIRFLOW_HOME then '~/airflow'")
init_parser.add_argument("--config",
type=str,
help="Set path to Airflow configuration file. \
Default: first try AIRFLOW_CONFIG then '[airflow home]/airflow.cfg'"
)
init_parser.add_argument(
"--upgrade",
action="store_true",
help="Upgrade old CWLDAG files to the latest format. \
Default: False")
# Test (for running conformance tests)
test_parser = subparsers.add_parser("test",
parents=[parent_parser],
help="Run conformance tests")
test_parser.set_defaults(func=run_test_conformance)
test_parser.add_argument("--suite",
type=str,
required=True,
help="Set path to the conformance test suite")
test_parser.add_argument("--tmp",
type=str,
default=mkdtemp(),
help="Set path to the temp folder. Default: /tmp")
test_parser.add_argument(
"--host",
type=str,
default="127.0.0.1",
help="Set host to listen for DAG results and status updates. \
Default: 127.0.0.1")
test_parser.add_argument(
"--port",
type=int,
default=3070,
help="Set port to listen for DAG results and status updates. \
Should correspond to the port from 'process_report' connection. \
Default: 3070")
test_parser.add_argument(
"--api",
type=str,
default="http://127.0.0.1:8081",
help="Set CWL-Airflow API's base url (IP address and port). \
Default: http://127.0.0.1:8081")
test_parser.add_argument("--range",
type=str,
help="Set test range to run, format 1,3-6,9. \
Order corresponds to the tests from --suite file, starting from 1. \
Default: run all tests")
test_parser.add_argument(
"--spin",
action="store_true",
help="Display spinner wher running. Useful for CI that tracks activity. \
Default: do not spin")
test_parser.add_argument(
"--embed",
action="store_true",
help=
"Embed base64 encoded gzip compressed workflow content into the DAG python file. \
Default: False")
test_parser.add_argument(
"--combine",
action="store_true",
help="Create and trigger DAG using a single API call. \
Default: False")
test_parser.add_argument(
"--relative",
action="store_true",
help="Skip relative paths resolution before submitting jobs to API. \
Default: False")
return general_parser
def get_parser():
"""
Defines arguments for parser. Inlcudes two subparsers for
api server and init components.
"""
parent_parser = argparse.ArgumentParser(add_help=False)
general_parser = argparse.ArgumentParser(
description="CWL-Airflow: a lightweight pipeline manager \
supporting Common Workflow Language")
subparsers = general_parser.add_subparsers()
subparsers.required = True
general_parser.add_argument("--version",
action="version",
version=get_version(),
help="Print current version and exit")
# API
api_parser = subparsers.add_parser("api",
parents=[parent_parser],
help="Run API server")
api_parser.set_defaults(func=run_api_server)
api_parser.add_argument(
"--port",
type=int,
default=8081,
help="Set port to run API server. Default: 8081",
)
api_parser.add_argument(
"--host",
type=str,
default="127.0.0.1",
help="Set host to run API server. Default: 127.0.0.1")
# Init
init_parser = subparsers.add_parser("init",
parents=[parent_parser],
help="Run initial configuration")
init_parser.set_defaults(func=run_init_config)
init_parser.add_argument("--home",
type=str,
default=get_airflow_home(),
help="Set path to Airflow home directory. \
Default: first try AIRFLOW_HOME then '~/airflow'")
init_parser.add_argument("--config",
type=str,
help="Set path to Airflow configuration file. \
Default: first try AIRFLOW_CONFIG then '[airflow home]/airflow.cfg'"
)
init_parser.add_argument(
"--upgrade",
action="store_true",
help="Upgrade old CWLDAG files to the latest format. \
Default: False")
# Test (for running conformance tests)
test_parser = subparsers.add_parser("test",
parents=[parent_parser],
help="Run conformance tests")
test_parser.set_defaults(func=run_test_conformance)
test_parser.add_argument("--suite",
type=str,
required=True,
help="Set path to the conformance test suite")
test_parser.add_argument("--tmp",
type=str,
default=mkdtemp(),
help="Set path to the temp folder. Default: /tmp")
test_parser.add_argument(
"--port",
type=int,
default=3070,
help="Set port to listen for DAG results and status updates. \
Should correspond to the port from 'process_report' connection. \
Default: 3070")
test_parser.add_argument(
"--api",
type=str,
default="http://127.0.0.1:8081",
help="Set CWL-Airflow API's base url (IP address and port). \
Default: http://127.0.0.1:8081")
test_parser.add_argument("--range",
type=str,
help="Set test range to run, format 1,3-6,9. \
Order corresponds to the tests from --suite file, starting from 1. \
Default: run all tests")
test_parser.add_argument(
"--spin",
action="store_true",
help="Display spinner wher running. Useful for CI that tracks activity. \
Default: do not spin")
test_parser.add_argument(
"--embed",
action="store_true",
help=
"Embed base64 encoded zlib compressed workflow content into the DAG python file. \
Default: False")
return general_parser