get_db

Pipeline to install a pdm_utils MySQL database.

pdm_utils.pipelines.get_db.execute_get_file_db(alchemist, database, filename, config_file=None, schema_version=None, verbose=False)

pdm_utils.pipelines.get_db.execute_get_new_db(alchemist, database, schema_version, config_file=None, verbose=False)

pdm_utils.pipelines.get_db.execute_get_server_db(alchemist, database, url, folder_path=None, folder_name='20220119_get_db', db_name=None, config_file=None, verbose=False, subdirectory=None, download_only=False, get_fastas=False, get_alns=False, force_pull=False, get_version=False, schema_version=None)

pdm_utils.pipelines.get_db.install_db(alchemist, database, db_filepath=None, config_file=None, schema_version=None, verbose=False, pipeline=False)

Install database. If database already exists, it is first removed. :param database: Name of the database to be installed :type database: str :param db_filepath: Directory for installation :type db_filepath: Path

pdm_utils.pipelines.get_db.main(unparsed_args_list)

Run the get_db pipeline.

The database data can be retrieved from three places: The server, which needs to be downloaded to a new folder. A local file, in which no download and no new folder are needed. The empty schema stored within pdm_utils, in which no download, new folder, or local file are needed.

Parameters

unparsed_args_list (list) – list of arguments to run the pipeline unparsed

pdm_utils.pipelines.get_db.parse_args(unparsed_args_list)

Verify the correct arguments are selected for getting a new database. :param unparsed_args_list: arguments in sys.argv format :type unparsed_args_list: list :returns: A parsed list of arguments :rtype: argparse.Namespace

pdm_utils.pipelines.get_db.prepare_download(local_folder, url_folder, db_name, extension, verbose=False)

Construct filepath and check if it already exists, then download. :param local_folder: Working directory where the database is downloaded :type local_folder: Path :param url_folder: Base url where db_files are located. :type url_folder: str :param db_name: Name of the database to be downloaded :type db_name: str :param extension: file extension for the database :type extension: str :returns: Path to the destination directory and the status of the download :rtype: Path, bool