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"