Return already fetched metadata upon connection error

[adamovanja]

As a plugin user,
in case of a connection error to NCBI (Error with gaierror is not JSON serializable), I want get-metadata to store all already retrieved metadata to an artifact.

Current behaviour

get-metadata fails without outputting any artifact by displaying the following Error: EntrezPy failed to connect to NCBI. Please check your internet connection and try again. It may help to wait a few minutes before retrying.

Expected behaviour

get-metadata should store the already retrieved metadata to an artifact and raise a connection warning for the remaining run IDs.

Note for solving

I believe a change here is needed:

def handle_threaded_exception(args):
    logger = set_up_logger('DEBUG', logger_name='ThreadedErrorsManager')
    msg = 'Data fetching was interrupted by the following error: \n'


    if 'gaierror is not JSON serializable' in str(args.exc_value):
        msg += 'EntrezPy failed to connect to NCBI. Please check your ' \
               'internet connection and try again. It may help to wait ' \
               'a few minutes before retrying.'
    # silence threads exiting correctly
    elif issubclass(args.exc_type, SystemExit) and str(args.exc_value) == '0':
        return
    else:
        msg += f'Caught {args.exc_type} with value "{args.exc_value}" ' \
               f'in thread {args.thread}'


    logger.exception(msg)


    # This will send a SIGINT to the main thread, which will gracefully
    # kill the running Q2 action. No artifacts will be saved.
    os.kill(os.getpid(), signal.SIGINT)