def get_args(args):
parser = argparse.ArgumentParser(
description=
'Add a tag to provided items (and optionally their children)',
parents=[scu.create_input_arg_parser(),
scu.create_ff_arg_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument(
'--types2exclude',
nargs='+',
help="List of Item Types to Explicitly Exclude getting - \
by default 'User', 'Lab', 'Award', 'OntologyTerm', 'Ontology', \
and 'Organism' are excluded - add others using this argument"
)
parser.add_argument(
'--types2include',
nargs='+',
help="List of Item Types (that are usually excluded - see \
--types2exclude help) that you want to include")
parser.add_argument('--no_children',
nargs='+',
help="List of Item types not to get children of")
parser.add_argument('--include_released',
default=False,
action='store_true',
help='Normally released items are skipped \
- this flag includes them in the final list')
args = parser.parse_args(args)
if args.key:
args.key = scu.convert_key_arg_to_dict(args.key)
return args
def get_args(): # pragma: no cover
parser = argparse.ArgumentParser(
description='Given a file of item jsons try to load into database',
parents=[create_ff_arg_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument('infile',
help="the datafile containing json formatted items")
parser.add_argument(
'--itypes',
nargs='*',
help=
"The item type(s) to load if not specified in the file by store key(s)"
)
parser.add_argument(
'--id-field',
help=
"Field name to used as identifier for items (all item types in file)")
parser.add_argument(
'--as-file',
default=False,
action='store_true',
help=
"Will attempt to load and process the file directly in the request. "
"This currently only works locally or if the file has been uploaded to "
"the apps file system")
args = parser.parse_args()
if args.key:
args.key = convert_key_arg_to_dict(args.key)
return args
def get_args(args):
parser = argparse.ArgumentParser(
parents=[scu.create_input_arg_parser(),
scu.create_ff_arg_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument('field', help="The field to update.")
parser.add_argument(
'value',
help="The value(s) to update. Array fields need \"''\" surround \
even if only a single value i.e. \"'value here'\" or \"'v1' 'v2'\""
)
parser.add_argument('--isarray',
default=False,
action='store_true',
help="Field is an array. Default is False \
use this so value is correctly formatted even if only a single value"
)
parser.add_argument(
'--numtype',
help=
"options: 'i' or 'f' If the field value is integer or number deal accordingly"
)
args = parser.parse_args(args)
if args.key:
args.key = scu.convert_key_arg_to_dict(args.key)
return args
def test_convert_key_arg_to_dict_good_key():
inkey = "{'key': 'ABCDEF', 'secret': 'supersecret', 'server': 'https://data.4dnucleome.org'}"
outkey = scu.convert_key_arg_to_dict(inkey)
assert outkey == {
'key': 'ABCDEF',
'secret': 'supersecret',
'server': 'https://data.4dnucleome.org'
}
def get_args(args):
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
parents=[scu.create_ff_arg_parser()],
)
args = parser.parse_args()
if args.key:
args.key = scu.convert_key_arg_to_dict(args.key)
return args
def get_args(): # pragma: no cover
parser = argparse.ArgumentParser(
description='Provide a search query suffix and get a list of item uuids',
parents=[scu.create_ff_arg_parser(), scu.create_input_arg_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter,
)
args = parser.parse_args()
if args.key:
args.key = scu.convert_key_arg_to_dict(args.key)
return args
def get_args():
parser = argparse.ArgumentParser(
parents=[scu.create_ff_arg_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument(
'reltag',
help="The release tag to query DataReleaseUpdates and add to items.")
args = parser.parse_args()
if args.key:
args.key = scu.convert_key_arg_to_dict(args.key)
return args
def get_args(): # pragma: no cover
parser = argparse.ArgumentParser(
description=
'Given a file of ontology term jsons (one per line) load into db',
parents=[create_ff_arg_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument('infile',
help="the datafile containing object data to import")
args = parser.parse_args()
if args.key:
args.key = convert_key_arg_to_dict(args.key)
return args
def get_args(args):
parser = argparse.ArgumentParser(
parents=[scu.create_input_arg_parser(),
scu.create_ff_arg_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument(
'--title',
default='Set of preliminary processed files',
help="The title for the group of other processed files.")
args = parser.parse_args()
if args.key:
args.key = scu.convert_key_arg_to_dict(args.key)
return args
def get_args(): # pragma: no cover
parser = argparse.ArgumentParser(
description=
'Provide a search query suffix and get a list of item uuids',
parents=[scu.create_ff_arg_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument('query',
help="A search string \
eg. type=Biosource&biosource_type=primary cell")
args = parser.parse_args()
if args.key:
args.key = scu.convert_key_arg_to_dict(args.key)
return args
def get_args(args):
parser = argparse.ArgumentParser(
parents=[scu.create_ff_arg_parser(),
scu.create_input_arg_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument(
'--workflow',
default="bef50397-4d72-4ed1-9c78-100e14e5c47f",
help="The uuid of the workflow to use to generate the run \
default is File Provenance Workflow")
args = parser.parse_args(args)
if args.key:
args.key = scu.convert_key_arg_to_dict(args.key)
return args
def get_args():
parser = argparse.ArgumentParser(
parents=[scu.create_input_arg_parser(), scu.create_ff_arg_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument('--fields',
nargs='+',
help="The item fields to retrieve/report.")
parser.add_argument('--noid',
action='store_true',
default='False',
help="By default the id provided is the first column of output - this flag removes that column")
args = parser.parse_args()
if args.key:
args.key = scu.convert_key_arg_to_dict(args.key)
return args
def get_args(): # pragma: no cover
parser = argparse.ArgumentParser(
parents=[scu.create_ff_arg_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument('old',
help="The uuid or ID of the Biorxiv publication")
parser.add_argument('new',
help="The uuid or ID of the Published Journal Article")
parser.add_argument(
'--vals2skip',
nargs='+',
help="A list of values or IDs (uuids, accessions ...) to not transfer")
args = parser.parse_args()
if args.key:
args.key = scu.convert_key_arg_to_dict(args.key)
return args
def get_args(): # pragma: no cover
parser = argparse.ArgumentParser(
description=
'Add a tag to provided items (and optionally their children)',
parents=[scu.create_input_arg_parser(),
scu.create_ff_arg_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument('tag',
help="The tag you want to add - eg. '4DN Standard'")
parser.add_argument('--taglinked',
default=False,
action='store_true',
help='Tag items linked to items that are input')
parser.add_argument(
'--types2exclude',
nargs='+',
help="List of Item Types to Explicitly Exclude Tagging - \
you may have some linked items that can get tags but may \
not want to tag them with this tag")
args = parser.parse_args()
if args.key:
args.key = scu.convert_key_arg_to_dict(args.key)
return args
def test_convert_key_arg_to_dict_bad_key(capsys):
inkey = "{'key': 'ABCDEF', 'secret': 'supersecret'}"
with pytest.raises(SystemExit):
scu.convert_key_arg_to_dict(inkey)
out = capsys.readouterr()[0]
assert out == "You included a key argument but it appears to be malformed or missing required info - see --help"
