4851692537

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Commit Message

Merge pull request #37 from dbmi-bgm/dmichaels_from_kmp_submit_cgap_for_fourfront_via_s3

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/submit_cgap/scripts/submit_ontology.py

import argparse
import json
import io
import os
from dcicutils.common import APP_FOURFRONT, ORCHESTRATED_APPS
from dcicutils.command_utils import ScriptFailure
from dcicutils.misc_utils import get_error_message
from ..submission import submit_any_ingestion, SubmissionProtocol, SUBMISSION_PROTOCOLS
from ..utils import script_catch_errors, show


EPILOG = __doc__


def main(simulated_args_for_testing=None):
    parser = argparse.ArgumentParser(  # noqa - PyCharm wrongly thinks the formatter_class is invalid
        description="Submits an ontology",
        epilog=EPILOG,
        formatter_class=argparse.RawDescriptionHelpFormatter
    )
    parser.add_argument('ontology_filename', help='a file of ontology data')
    parser.add_argument('--lab', '-l', '-L', help='lab identifier', default=None)
    parser.add_argument('--award', '-a', help='award identifier', default=None)
    parser.add_argument('--server', '-s', help="an http or https address of the server to use", default=None)
    parser.add_argument('--env', '-e', help="a CGAP beanstalk environment name for the server to use", default=None)
    parser.add_argument('--validate-only', '-v', action="store_true",
                        help="whether to stop after validating without submitting", default=False)
    parser.add_argument('--app', choices=ORCHESTRATED_APPS, default=APP_FOURFRONT,
                        help=f"An application (default {APP_FOURFRONT!r}. Only for debugging."
                             f" Normally this should not be given.")
    parser.add_argument('--submission_protocol', '--submission-protocol', '-sp',
                        choices=SUBMISSION_PROTOCOLS, default=SubmissionProtocol.S3,
                        help=f"the submission protocol (default {SubmissionProtocol.S3!r})")
    args = parser.parse_args(args=simulated_args_for_testing)

    with script_catch_errors():

        verify_ontology_file(args.ontology_filename)

        return submit_any_ingestion(
                ingestion_filename=args.ontology_filename,
                ingestion_type='ontology',
                lab=args.lab,
                award=args.award,
                server=args.server,
                env=args.env,
                validate_only=args.validate_only,
                app=args.app,
                submission_protocol=args.submission_protocol,
        )


def verify_ontology_file(ontology_filename: str) -> bool:
    if not os.path.exists(ontology_filename):
        raise ScriptFailure(f"Specified ontology file does not exist: {ontology_filename}")
    try:
        with io.open(ontology_filename, "r") as f:
            ontology_json = json.load(f)
            ontology_term_count = len(ontology_json["ontology_term"])  # xyzzy
    except Exception as e:
        raise ScriptFailure(f"Cannot load specified ontology (JSON) file: {ontology_filename} | {get_error_message(e)}")
    show(f"Verified specified ontology (JSON) file: {ontology_filename} (ontology terms: {ontology_term_count})")
    return True


if __name__ == '__main__':
    main()

1	import argparse	1✔
2	import json	1✔
3	import io	1✔
4	import os	1✔
5	from dcicutils.common import APP_FOURFRONT, ORCHESTRATED_APPS	1✔
6	from dcicutils.command_utils import ScriptFailure	1✔
7	from dcicutils.misc_utils import get_error_message	1✔
8	from ..submission import submit_any_ingestion, SubmissionProtocol, SUBMISSION_PROTOCOLS	1✔
9	from ..utils import script_catch_errors, show	1✔
10
11
12	EPILOG = __doc__	1✔
13
14
15	def main(simulated_args_for_testing=None):	1✔
16	parser = argparse.ArgumentParser( # noqa - PyCharm wrongly thinks the formatter_class is invalid	1✔
17	description="Submits an ontology",
18	epilog=EPILOG,
19	formatter_class=argparse.RawDescriptionHelpFormatter
20	)
21	parser.add_argument('ontology_filename', help='a file of ontology data')	1✔
22	parser.add_argument('--lab', '-l', '-L', help='lab identifier', default=None)	1✔
23	parser.add_argument('--award', '-a', help='award identifier', default=None)	1✔
24	parser.add_argument('--server', '-s', help="an http or https address of the server to use", default=None)	1✔
25	parser.add_argument('--env', '-e', help="a CGAP beanstalk environment name for the server to use", default=None)	1✔
26	parser.add_argument('--validate-only', '-v', action="store_true",	1✔
27	help="whether to stop after validating without submitting", default=False)
28	parser.add_argument('--app', choices=ORCHESTRATED_APPS, default=APP_FOURFRONT,	1✔
29	help=f"An application (default {APP_FOURFRONT!r}. Only for debugging."
30	f" Normally this should not be given.")
31	parser.add_argument('--submission_protocol', '--submission-protocol', '-sp',	1✔
32	choices=SUBMISSION_PROTOCOLS, default=SubmissionProtocol.S3,
33	help=f"the submission protocol (default {SubmissionProtocol.S3!r})")
34	args = parser.parse_args(args=simulated_args_for_testing)	1✔
35
36	with script_catch_errors():	1✔
37
38	verify_ontology_file(args.ontology_filename)	1✔
39
40	return submit_any_ingestion(	1✔
41	ingestion_filename=args.ontology_filename,
42	ingestion_type='ontology',
43	lab=args.lab,
44	award=args.award,
45	server=args.server,
46	env=args.env,
47	validate_only=args.validate_only,
48	app=args.app,
49	submission_protocol=args.submission_protocol,
50	)
51
52
53	def verify_ontology_file(ontology_filename: str) -> bool:	1✔
54	if not os.path.exists(ontology_filename):	1✔
55	raise ScriptFailure(f"Specified ontology file does not exist: {ontology_filename}")	×
56	try:	1✔
57	with io.open(ontology_filename, "r") as f:	1✔
58	ontology_json = json.load(f)	1✔
59	ontology_term_count = len(ontology_json["ontology_term"]) # xyzzy	1✔
60	except Exception as e:	×
61	raise ScriptFailure(f"Cannot load specified ontology (JSON) file: {ontology_filename} \| {get_error_message(e)}")	×
62	show(f"Verified specified ontology (JSON) file: {ontology_filename} (ontology terms: {ontology_term_count})")	1✔
63	return True	1✔
64
65
66	if __name__ == '__main__':
67	main()

dbmi-bgm / SubmitCGAP / 4851692537

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