ccda_to_omop package

Submodules

• ccda_to_omop.code_hunt module
  • main()
• ccda_to_omop.constants module
• ccda_to_omop.data_driven_parse module
  • create_hash()
  • create_hash_too_long()
  • do_basic_fields()
  • do_constant_fields()
  • do_derived2_fields()
  • do_derived_fields()
  • do_filename_fields()
  • do_foreign_key_fields()
  • do_hash_fields()
  • do_none_fields()
  • do_priority_fields()
  • get_extract_order_fn()
  • get_filter_fn()
  • main()
  • make_distinct()
  • parse_config_for_single_root()
  • parse_config_from_xml_file()
  • parse_doc()
  • parse_field_from_dict()
  • parse_string()
  • print_omop_structure()
  • process_and_save_file()
  • process_file()
  • process_single_file_single_config()
  • sort_output_and_omit_dict()
  • str2bool()
  • validate_ccda_document()
  • write_all_csv_files()
  • write_individual_csv_files()
• ccda_to_omop.ddl module
  • generate_cfg_name_to_domain_map()
• ccda_to_omop.domain_dataframe_column_types module
• ccda_to_omop.find_paths module
  • get_base_elements()
  • get_derived_fields()
  • get_hash_fields()
  • main()
  • merge_second_level_dict()
  • print_data_hash()
  • strip_detail()
• ccda_to_omop.layer_datasets module
  • DO_VISIT_DETAIL
  • build_file_to_domain_dict()
  • combine_datasets()
  • create_omop_domain_dataframes()
  • dict_summary()
  • do_write_csv_files()
  • find_max_columns()
  • main()
  • process_directory()
  • process_file()
  • process_string()
  • process_string_to_dict()
  • show_column_dict()
  • write_csvs_from_dataframe_dict()
• ccda_to_omop.load_duck_db module
  • check_PK()
  • main()
• ccda_to_omop.package_constant_access module
  • get_allow_no_matching_concept()
  • set_allow_no_matching_concept()
• ccda_to_omop.util module
  • cast_to_date()
  • cast_to_datetime()
  • create_codemap_dict()
  • create_codemap_dict_from_csv()
  • logger
• ccda_to_omop.value_transformations module
  • VocabContext
  • cast_as_concept_id()
  • cast_as_number()
  • cast_as_string()
  • codemap_xwalk_concept_id()
  • codemap_xwalk_domain_id()
  • codemap_xwalk_source_concept_id()
  • concat_field_list_names()
  • concat_field_list_values()
  • concat_fields()
  • extract_day_of_birth()
  • extract_month_of_birth()
  • extract_year_of_birth()
  • get_codemap_dict()
  • get_data_partner_id()
  • get_mspi_map()
  • get_partner_map()
  • map_filename_to_mspi()
  • reset_context()
  • set_codemap_dict()
  • set_mspi_map()
  • set_partner_map()
  • transform_datetime_high()
  • transform_datetime_low()
• ccda_to_omop.visit_reconciliation module
  • assign_visit_detail_ids_to_events()
  • assign_visit_occurrence_ids_to_events()
  • create_visit_detail_record()
  • find_most_specific_parent()
  • get_visit_detail_duration()
  • get_visit_duration_days()
  • identify_inpatient_parents()
  • is_temporally_contained()
  • reclassify_nested_visit_occurrences_as_detail()
  • reconcile_visit_FK_with_specific_domain()
  • reconcile_visit_detail_FK_with_specific_domain()
  • strip_tz()