API Reference

• Query API
  • QueryHandler
    • QueryHandler.__init__()
    • QueryHandler.normalize()
    • QueryHandler.normalize_unmerged()
    • QueryHandler.search()
  • InvalidParameterException
• Database Main API
  • AbstractDatabase
    • AbstractDatabase.__init__()
    • AbstractDatabase.add_merged_record()
    • AbstractDatabase.add_record()
    • AbstractDatabase.add_source_metadata()
    • AbstractDatabase.check_schema_initialized()
    • AbstractDatabase.check_tables_populated()
    • AbstractDatabase.close_connection()
    • AbstractDatabase.complete_write_transaction()
    • AbstractDatabase.delete_normalized_concepts()
    • AbstractDatabase.delete_source()
    • AbstractDatabase.drop_db()
    • AbstractDatabase.export_db()
    • AbstractDatabase.get_all_concept_ids()
    • AbstractDatabase.get_record_by_id()
    • AbstractDatabase.get_refs_by_type()
    • AbstractDatabase.get_source_metadata()
    • AbstractDatabase.initialize_db()
    • AbstractDatabase.list_tables()
    • AbstractDatabase.load_from_remote()
    • AbstractDatabase.update_merge_ref()
  • AwsEnvName
    • AwsEnvName.DEVELOPMENT
    • AwsEnvName.PRODUCTION
    • AwsEnvName.STAGING
  • DatabaseException
  • DatabaseInitializationException
  • DatabaseReadException
  • DatabaseWriteException
  • confirm_aws_db_use()
  • create_db()
• DynamoDB Handler API
  • DynamoDbDatabase
    • DynamoDbDatabase.__init__()
    • DynamoDbDatabase.add_merged_record()
    • DynamoDbDatabase.add_record()
    • DynamoDbDatabase.add_source_metadata()
    • DynamoDbDatabase.check_schema_initialized()
    • DynamoDbDatabase.check_tables_populated()
    • DynamoDbDatabase.close_connection()
    • DynamoDbDatabase.complete_write_transaction()
    • DynamoDbDatabase.delete_normalized_concepts()
    • DynamoDbDatabase.delete_source()
    • DynamoDbDatabase.drop_db()
    • DynamoDbDatabase.export_db()
    • DynamoDbDatabase.get_all_concept_ids()
    • DynamoDbDatabase.get_record_by_id()
    • DynamoDbDatabase.get_refs_by_type()
    • DynamoDbDatabase.get_source_metadata()
    • DynamoDbDatabase.initialize_db()
    • DynamoDbDatabase.list_tables()
    • DynamoDbDatabase.load_from_remote()
    • DynamoDbDatabase.update_merge_ref()
• PostgreSQL Handler API
  • PostgresDatabase
    • PostgresDatabase.__init__()
    • PostgresDatabase.add_merged_record()
    • PostgresDatabase.add_record()
    • PostgresDatabase.add_source_metadata()
    • PostgresDatabase.check_schema_initialized()
    • PostgresDatabase.check_tables_populated()
    • PostgresDatabase.close_connection()
    • PostgresDatabase.complete_write_transaction()
    • PostgresDatabase.delete_normalized_concepts()
    • PostgresDatabase.delete_source()
    • PostgresDatabase.drop_db()
    • PostgresDatabase.export_db()
    • PostgresDatabase.get_all_concept_ids()
    • PostgresDatabase.get_record_by_id()
    • PostgresDatabase.get_refs_by_type()
    • PostgresDatabase.get_source_metadata()
    • PostgresDatabase.initialize_db()
    • PostgresDatabase.list_tables()
    • PostgresDatabase.load_from_remote()
    • PostgresDatabase.update_merge_ref()
• Source ETL API
  • Base
    • Base
      • Base.__init__()
      • Base.get_seqrepo()
      • Base.perform_etl()
  • NCBI
    • NCBI
      • NCBI.__init__()
      • NCBI.perform_etl()
  • HGNC
    • HGNC
      • HGNC.__init__()
      • HGNC.perform_etl()
  • Ensembl
    • Ensembl
      • Ensembl.__init__()
      • Ensembl.perform_etl()
  • Normalized Records
    • Merge
      • Merge.__init__()
      • Merge.create_merged_concepts()
  • Chromosome Location
    • ChromosomeLocation
      • ChromosomeLocation.get_location()
      • ChromosomeLocation.set_interval_range()
  • Sequence Location
    • SequenceLocation
      • SequenceLocation.add_location()
      • SequenceLocation.get_aliases()