disease.etl.base#

Provides abstract base classes for source ETL procedures.

Generally, users shouldn’t ever have to work directly with the classes contained within.

class disease.etl.base.Base(database, data_path=None, silent=True)[source]#

The ETL base class.

__init__(database, data_path=None, silent=True)[source]#

Extract from sources.

Parameters:

  • database (AbstractDatabase) – database client

  • data_path (Optional[Path]) – location of data directory

  • silent (bool) – if True, don’t print ETL results to console

perform_etl(use_existing=False)[source]#

Public-facing method to begin ETL procedures on given data.

Parameters:

use_existing (bool) – if True, use local data instead of retrieving most recent version

Return type:

List

Returns:

List of concept IDs to be added to merge generation.

class disease.etl.base.OWLBase(database, data_path=None, silent=True)[source]#

Base class for sources that use OWL files.

__init__(database, data_path=None, silent=True)[source]#

Extract from sources.

Parameters:

  • database (AbstractDatabase) – database client

  • data_path (Optional[Path]) – location of data directory

  • silent (bool) – if True, don’t print ETL results to console

perform_etl(use_existing=False)[source]#

Public-facing method to begin ETL procedures on given data.

Parameters:

use_existing (bool) – if True, use local data instead of retrieving most recent version

Return type:

List

Returns:

List of concept IDs to be added to merge generation.