ccda_to_omop

• 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()