How to use the petab.get_default_sbml_file_name function in petab

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github ICB-DCM / AMICI / python / amici / petab_import.py View on Github external
parser.add_argument('-c', '--conditions', dest='condition_file_name',
                        help='Conditions table')
    parser.add_argument('-p', '--parameters', dest='parameter_file_name',
                        help='Parameter table')

    # or with model name, following default naming
    parser.add_argument('-n', '--model-name', dest='model_name',
                        help='Model name where all files are in the working '
                        'directory and follow PEtab naming convention. '
                        'Specifying -[smcp] will override defaults')

    args = parser.parse_args()

    if args.model_name:
        if not args.sbml_file_name:
            args.sbml_file_name = petab.get_default_sbml_file_name(
                args.model_name)
        if not args.measurement_file_name:
            args.measurement_file_name = \
                petab.get_default_measurement_file_name(args.model_name)
        if not args.condition_file_name:
            args.condition_file_name = petab.get_default_condition_file_name(
                args.model_name)
        if not args.parameter_file_name:
            args.parameter_file_name = petab.get_default_parameter_file_name(
                args.model_name)

    if not args.model_name and \
            (not args.sbml_file_name
             or not args.condition_file_name
             or not args.measurement_file_name):
        parser.error('When not specifying a model name, sbml, '
github ICB-DCM / AMICI / python / bin / amici_import_petab.py View on Github external
parser.add_argument('-c', '--conditions', dest='condition_file_name',
                        help='Conditions table')
    parser.add_argument('-p', '--parameters', dest='parameter_file_name',
                        help='Parameter table')

    # or with model name, following default naming
    parser.add_argument('-n', '--model-name', dest='model_name',
                        help='Model name where all files are in the working '
                        'directory and follow PEtab naming convention. '
                        'Specifying -[smcp] will override defaults')

    args = parser.parse_args()

    if args.model_name:
        if not args.sbml_file_name:
            args.sbml_file_name = petab.get_default_sbml_file_name(
                args.model_name)
        if not args.measurement_file_name:
            args.measurement_file_name = \
                petab.get_default_measurement_file_name(args.model_name)
        if not args.condition_file_name:
            args.condition_file_name = petab.get_default_condition_file_name(
                args.model_name)
        if not args.parameter_file_name:
            args.parameter_file_name = petab.get_default_parameter_file_name(
                args.model_name)

    if not args.model_name and \
            (not args.sbml_file_name
             or not args.condition_file_name
             or not args.measurement_file_name):
        parser.error('When not specifying a model name, sbml, '