comparison data_manager/data_manager_eggnog.py @ 1:269f0970d762 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"

0:9d5f039c637f

import sys
from sqlite3 import OperationalError


def _get_db_version(sqlitedb_path):
    version = '4.5'
    try:
        query = 'select version from version'
        conn = sqlite3.connect(sqlitedb_path)
        cur = conn.cursor()
        cur.execute(query)

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('--config_file')
    parser.add_argument('--install_path')
    parser.add_argument('--dbs', default='')
    args = parser.parse_args()

    eggnog_db_path = os.path.join(args.install_path, 'eggnog.db')
    if not os.path.exists(eggnog_db_path):
        print('Can not open: %s' % eggnog_db_path, file=sys.stderr)

    dm_dict['data_tables'][data_table]\
        = dm_dict['data_tables'].get(data_table, [])
    data_table_entry = dict(value=db_version, name=db_version,
                            path=args.install_path)
    dm_dict['data_tables'][data_table].append(data_table_entry)
    data_table = 'eggnog_mapper_hmm_dbs'
    dm_dict['data_tables'][data_table]\
        = dm_dict['data_tables'].get(data_table, [])
    if args.dbs:
        dbs = [x.strip() for x in args.dbs.split(',')]
        for db in dbs:
            key = '%s_%s' % (db_version, db)
            data_table_entry = dict(key=key, db_version=db_version,
                                    value=db, name=db, path=db)
            dm_dict['data_tables'][data_table].append(data_table_entry)

    # save info to json file
    open(args.config_file, 'wb').write(json.dumps(dm_dict))


if __name__ == "__main__":
    main()

1:269f0970d762

import sys
from sqlite3 import OperationalError


def _get_db_version(sqlitedb_path):
    version = '5.0'
    try:
        query = 'select version from version'
        conn = sqlite3.connect(sqlitedb_path)
        cur = conn.cursor()
        cur.execute(query)

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('--config_file')
    parser.add_argument('--install_path')
    args = parser.parse_args()

    eggnog_db_path = os.path.join(args.install_path, 'eggnog.db')
    if not os.path.exists(eggnog_db_path):
        print('Can not open: %s' % eggnog_db_path, file=sys.stderr)

    dm_dict['data_tables'][data_table]\
        = dm_dict['data_tables'].get(data_table, [])
    data_table_entry = dict(value=db_version, name=db_version,
                            path=args.install_path)
    dm_dict['data_tables'][data_table].append(data_table_entry)

    # save info to json file
    open(args.config_file, 'w').write(json.dumps(dm_dict))


if __name__ == "__main__":
    main()