def run():
# Set global debug value and setup application logging.
setup_logging(
_logger, mod_cmd, '--debug' in sys.argv,
'{0}.log'.format(mod_cmd) if '--log-file' in sys.argv else None)
setup_unicode()
# Setup program arguments.
parser = argparse.ArgumentParser(prog=mod_cmd, description=mod_desc)
parser.add_argument('--debug',
help='Enable debug output',
default=False,
action='store_true') # noqa
parser.add_argument('--log-file',
help='write output to a log file',
default=False,
action='store_true') # noqa
parser.add_argument('--project',
help='gcp project name',
default='localhost') # noqa
parser.add_argument('--account', help='pmi-ops account',
default=None) # noqa
parser.add_argument('--service-account',
help='gcp iam service account',
default=None) # noqa
args = parser.parse_args()
with GCPProcessContext(mod_cmd, args.project, args.account,
args.service_account):
process = ProgramTemplateClass(args)
exit_code = process.run()
return exit_code
def run():
# Set global debug value and setup application logging.
setup_logging(_logger, mod_cmd,
'--debug' in sys.argv, '{0}.log'.format(mod_cmd) if '--log-file' in sys.argv else None)
setup_unicode()
# Setup program arguments.
parser = argparse.ArgumentParser(prog=mod_cmd, description=mod_desc)
parser.add_argument('--debug', help='Enable debug output', default=False, action='store_true') # noqa
parser.add_argument('--log-file', help='write output to a log file', default=False, action='store_true') # noqa
parser.add_argument('--project', help='gcp project name', default='localhost') # noqa
parser.add_argument('--account', help='pmi-ops account', default=None) # noqa
parser.add_argument('--service-account', help='gcp iam service account', default=None) # noqa
parser.add_argument('--port', help='alternate ip port to connect to', default=None) # noqa
parser.add_argument('--horiz', help='participant data is horizontal in the spreadsheet',
default=False, action='store_true') # noqa
parser.add_argument('--src-csv', help='participant list csv (file/google doc id)', required=True) # noqa
args = parser.parse_args()
with GCPProcessContext(mod_cmd, args.project, args.account, args.service_account) as env:
# verify we're not getting pointed to production.
if env['project'] == 'all-of-us-rdr-prod':
_logger.error('using spec generator in production is not allowed.')
return 1
process = DataGeneratorClass(args)
exit_code = process.run()
return exit_code
def run():
# Set global debug value and setup application logging.
setup_logging(_logger, mod_cmd,
'--debug' in sys.argv, '{0}.log'.format(mod_cmd) if '--log-file' in sys.argv else None)
setup_unicode()
exit_code = 1
# Setup program arguments.
parser = argparse.ArgumentParser(prog=mod_cmd, description=mod_group)
parser.add_argument('--debug', help='Enable debug output', default=False, action='store_true') # noqa
parser.add_argument('--log-file', help='write output to a log file', default=False, action='store_true') # noqa
parser.add_argument('--project', help='gcp project name', default='localhost') # noqa
parser.add_argument('--account', help='pmi-ops account', default=None) # noqa
parser.add_argument('--service-account', help='gcp iam service account', default=None) # noqa
parser.add_argument('--port', help='alternate ip port to connect to', default=None) # noqa
parser.add_argument('--num_participants', type=int, help='The number of participants to create.', default=0)
parser.add_argument('--include_physical_measurements', action='store_true',
help='True if physical measurements should be created')
parser.add_argument('--include_biobank_orders', action='store_true',
help='True if biobank orders should be created')
parser.add_argument('--hpo', help='The HPO name to assign participants to; defaults to random choice.')
parser.add_argument('--create_biobank_samples', action='store_true',
help='True if biobank samples should be created')
parser.add_argument('--create_samples_from_file',
help='Creates PM&B for existing participants from a csv file; requires path'
' to file. File is expected to contain a single column of ID"s with a '
'leading env. identifier. i.e. P')
args = parser.parse_args()
if args.num_participants == 0 and not args.create_biobank_samples and not args.create_samples_from_file:
parser.error('--num_participants must be nonzero unless --create_biobank_samples is true.')
exit(exit_code)
with GCPProcessContext(mod_cmd, args.project, args.account, args.service_account) as env:
# verify we're not getting pointed to production.
if env['project'] == 'all-of-us-rdr-prod':
_logger.error('using spec generator in production is not allowed.')
return 1
process = RandomGeneratorClass(args)
exit_code = process.run()
return exit_code
def run():
# Set global debug value and setup application logging.
setup_logging(
_logger, tool_cmd, '--debug' in sys.argv,
'{0}.log'.format(tool_cmd) if '--log-file' in sys.argv else None)
setup_unicode()
# Setup program arguments.
parser = argparse.ArgumentParser(prog=tool_cmd, description=tool_desc)
parser.add_argument('--debug',
help='Enable debug output',
default=False,
action='store_true') # noqa
parser.add_argument('--log-file',
help='write output to a log file',
default=False,
action='store_true') # noqa
parser.add_argument('--project',
help='gcp project name',
default='localhost') # noqa
parser.add_argument('--account', help='pmi-ops account',
default=None) # noqa
parser.add_argument('--service-account',
help='gcp iam service account',
default=None) # noqa
parser.add_argument('--delete',
help="a comma delimited list of schema names or 'all'",
default=None,
metavar='SCHEMAS') # noqa
parser.add_argument('--show-schemas',
help='print schemas to stdout',
default=False,
action='store_true') # noqa
args = parser.parse_args()
with GCPProcessContext(tool_cmd, args.project, args.account,
args.service_account) as gcp_env:
process = BQMigration(args, gcp_env)
exit_code = process.run()
return exit_code
def run():
# Set global debug value and setup application logging.
setup_logging(_logger, tool_cmd,
'--debug' in sys.argv, '{0}.log'.format(tool_cmd) if '--log-file' in sys.argv else None)
setup_unicode()
# Setup program arguments.
parser = argparse.ArgumentParser(prog=tool_cmd, description=tool_desc)
parser.add_argument('--debug', help='Enable debug output', default=False, action='store_true') # noqa
parser.add_argument('--log-file', help='write output to a log file', default=False, action='store_true') # noqa
parser.add_argument('--project', help='gcp project name', default='localhost') # noqa
parser.add_argument('--account', help='pmi-ops account', default=None) # noqa
parser.add_argument('--service-account', help='gcp iam service account', default=None) # noqa
parser.add_argument('--org-id', help='organization id', default=None) # noqa
parser.add_argument('--destination_bucket', default=None,
help='Override the destination bucket lookup for the given organization.')
parser.add_argument('--dry_run', action="store_true",
help='Do not copy files, only print the list of files that would be copied')
args = parser.parse_args()
with GCPProcessContext(tool_cmd, args.project, args.account, args.service_account) as gcp_env:
process = SyncConsentClass(args, gcp_env)
exit_code = process.run()
return exit_code