How to use the biothings.utils.common.setup_logfile function in biothings

def main(no_confirm=True):

    src_dump = get_src_dump()
    download_list = get_file_list_for_download()
    if len(download_list) == 0:
        logging.info("No newer file found. Abort now.")
        sys.exit(0)

    doc = src_dump.find_one({'_id': 'ucsc'})
    if not os.path.exists(DATA_FOLDER):
        os.makedirs(DATA_FOLDER)

    logfile = os.path.join(DATA_FOLDER, 'ucsc_dump.log')
    setup_logfile(logfile)

    # mark the download starts
    doc = {'_id': 'ucsc',
           'timestamp': timestamp,
           'data_folder': DATA_FOLDER,
           'lastmodified': latest_lastmodified,
           'logfile': logfile,
           'status': 'downloading'}
    src_dump.save(doc)
    t0 = time.time()
    download(download_list, no_confirm)
    # mark the download finished successfully
    _updates = {
        'status': 'success',
        'time': timesofar(t0),
        'pending_to_upload': True    # a flag to trigger data uploading

def main():
    no_confirm = True   # set it to True for running this script automatically without intervention.

    if not ARCHIVE_DATA:
        rmdashfr(DATA_FOLDER)

    if not os.path.exists(DATA_FOLDER):
        os.makedirs(DATA_FOLDER)
    else:
        if not (no_confirm or len(os.listdir(DATA_FOLDER)) == 0 or ask('DATA_FOLDER (%s) is not empty. Continue?' % DATA_FOLDER) == 'Y'):
            sys.exit()

    logfile = os.path.join(DATA_FOLDER, 'entrez_dump.log')
    setup_logfile(logfile)

    #mark the download starts
    src_dump = get_src_dump()
    doc = {'_id': 'entrez',
           'timestamp': TIMESTAMP,
           'data_folder': DATA_FOLDER,
           'logfile': logfile,
           'status': 'downloading'}
    src_dump.save(doc)
    t0 = time.time()
    download(DATA_FOLDER, no_confirm=no_confirm)
    t_download = timesofar(t0)
    t1 = time.time()
    #mark parsing starts
    src_dump.update({'_id': 'entrez'}, {'$set': {'status': 'parsing'}})
    parse_gbff(DATA_FOLDER)

doc = src_dump.find_one({'_id': 'exac'})
    if doc and 'lastmodified' in doc and lastmodified <= doc['lastmodified']:
        path, filename = os.path.split(DATAFILES_PATH[0])
        data_file = os.path.join(doc['data_folder'], filename)
        if os.path.exists(data_file):
            logging.info("No newer file found. Abort now.")
            sys.exit(0)

    if not os.path.exists(DATA_FOLDER):
        os.makedirs(DATA_FOLDER)
    else:
        if not (no_confirm or len(os.listdir(DATA_FOLDER)) == 0 or ask('DATA_FOLDER (%s) is not empty. Continue?' % DATA_FOLDER) == 'Y'):
            sys.exit(0)

    logfile = os.path.join(DATA_FOLDER, 'exac_dump.log')
    setup_logfile(logfile)

    #mark the download starts
    doc = {'_id': 'exac',
           'timestamp': timestamp,
           'data_folder': DATA_FOLDER,
           'lastmodified': lastmodified,
           'logfile': logfile,
           'status': 'downloading'}
    src_dump.save(doc)
    t0 = time.time()
    download(no_confirm)
    #mark the download finished successfully
    _updates = {
        'status': 'success',
        'time': timesofar(t0),
        'pending_to_upload': True    # a flag to trigger data uploading

data_file = os.path.join(doc['data_folder'], 'genes.zip')
        if os.path.exists(data_file):
            logging.info("No newer file found. Abort now.")
            sys.exit(0)

    if not ARCHIVE_DATA:
        rmdashfr(DATA_FOLDER)

    if not os.path.exists(DATA_FOLDER):
        os.makedirs(DATA_FOLDER)
    else:
        if not (no_confirm or len(os.listdir(DATA_FOLDER)) == 0 or ask('DATA_FOLDER (%s) is not empty. Continue?' % DATA_FOLDER) == 'Y'):
            sys.exit(0)

    logfile = os.path.join(DATA_FOLDER, 'pharmgkb_dump.log')
    setup_logfile(logfile)

    #mark the download starts
    doc = {'_id': 'pharmgkb',
           'timestamp': TIMESTAMP,
           'data_folder': DATA_FOLDER,
           'lastmodified': lastmodified,
           'logfile': logfile,
           'status': 'downloading'}
    src_dump.save(doc)
    t0 = time.time()
    download(no_confirm)
    #mark the download finished successfully
    _updates = {
        'status': 'success',
        'time': timesofar(t0),
        'pending_to_upload': True    # a flag to trigger data uploading

data_file = os.path.join(doc['data_folder'], filename)
        if os.path.exists(data_file):
            logging.info("No newer file found. Abort now.")
            sys.exit(0)

    if not ARCHIVE_DATA:
        rmdashfr(DATA_FOLDER)

    if not os.path.exists(DATA_FOLDER):
        os.makedirs(DATA_FOLDER)
    else:
        if not (no_confirm or len(os.listdir(DATA_FOLDER)) == 0 or ask('DATA_FOLDER (%s) is not empty. Continue?' % DATA_FOLDER) == 'Y'):
            sys.exit(0)

    logfile = os.path.join(DATA_FOLDER, 'uniprot_dump.log')
    setup_logfile(logfile)

    #mark the download starts
    doc = {'_id': 'uniprot',
           'timestamp': TIMESTAMP,
           'data_folder': DATA_FOLDER,
           'lastmodified': lastmodified,
           'logfile': logfile,
           'status': 'downloading'}
    src_dump.save(doc)
    t0 = time.time()
    download(no_confirm)
    #mark the download finished successfully
    _updates = {
        'status': 'success',
        'time': timesofar(t0),
        'pending_to_upload': True    # a flag to trigger data uploading

doc = src_dump.find_one({'_id': 'ensembl'})
    if doc and 'release' in doc and mart_version <= doc['release']:
        data_file = os.path.join(doc['data_folder'], 'gene_ensembl__gene__main.txt')
        if os.path.exists(data_file):
            logging.info("No newer release found. Abort now.")
            sys.exit(0)

    DATA_FOLDER = os.path.join(ENSEMBL_FOLDER, str(mart_version))
    if not os.path.exists(DATA_FOLDER):
        os.makedirs(DATA_FOLDER)
    else:
        if not (no_confirm or len(os.listdir(DATA_FOLDER)) == 0 or ask('DATA_FOLDER (%s) is not empty. Continue?' % DATA_FOLDER) == 'Y'):
            sys.exit(0)

    logfile = os.path.join(DATA_FOLDER, 'ensembl_mart_%s.log' % mart_version)
    setup_logfile(logfile)

    #mark the download starts
    doc = {'_id': 'ensembl',
           'release': mart_version,
           'timestamp': time.strftime('%Y%m%d'),
           'data_folder': DATA_FOLDER,
           'logfile': logfile,
           'status': 'downloading'}
    src_dump.save(doc)
    t0 = time.time()

    try:
        BM = BioMart()
        BM.species_li = get_all_species(mart_version)
        BM.get_gene__main(os.path.join(DATA_FOLDER, 'gene_ensembl__gene__main.txt'))
        BM.get_translation__main(os.path.join(DATA_FOLDER, 'gene_ensembl__translation__main.txt'))

def update_from_temp_collections(config,no_confirm=False,use_parallel=False):
    t0 = time.time()
    sc = GeneDocSyncer(config)
    new_src_li = sc.get_new_source_list()
    if not new_src_li:
        logging.info("No new source collections need to update. Abort now.")
        return

    logging.info("Found {} new source collections need to update:".format(len(new_src_li)))
    logging.info("\n".join(['\t' + x for x in new_src_li]))

    if no_confirm or ask('Continue?') == 'Y':
        logfile = 'databuild_sync_{}_{}.log'.format(config, time.strftime('%Y%m%d'))
        logfile = os.path.join(LOG_FOLDER, logfile)
        setup_logfile(logfile)

        for src in new_src_li:
            t0 = time.time()
            logging.info("Current source collection: %s" % src)
            ts = _get_timestamp(src, as_str=True)
            logging.info("Calculating changes... ")
            changes = sc.get_changes(src, use_parallel=use_parallel)
            logging.info("Done")
            get_changes_stats(changes)
            if no_confirm or ask("Continue to save changes...") == 'Y':
                if config == 'genedoc_mygene':
                    dumpfile = 'changes_{}.pyobj'.format(ts)
                else:
                    dumpfile = 'changes_{}_allspecies.pyobj'.format(ts)
                dump(changes, dumpfile)
                dumpfile_key = 'genedoc_changes/' + dumpfile