Index

A

assign_visit_detail_ids_to_events() (in module ccda_to_omop.visit_reconciliation)

assign_visit_occurrence_ids_to_events() (in module ccda_to_omop.visit_reconciliation)

B

build_file_to_domain_dict() (in module ccda_to_omop.layer_datasets)

C

cast_as_concept_id() (in module ccda_to_omop.value_transformations) cast_as_number() (in module ccda_to_omop.value_transformations) cast_as_string() (in module ccda_to_omop.value_transformations) cast_to_date() (in module ccda_to_omop.util) cast_to_datetime() (in module ccda_to_omop.util) ccda_to_omop module ccda_to_omop.code_hunt module ccda_to_omop.constants module ccda_to_omop.data_driven_parse module ccda_to_omop.ddl module ccda_to_omop.domain_dataframe_column_types module ccda_to_omop.find_paths module ccda_to_omop.layer_datasets module ccda_to_omop.load_duck_db module

ccda_to_omop.package_constant_access module ccda_to_omop.util module ccda_to_omop.value_transformations module ccda_to_omop.visit_reconciliation module check_PK() (in module ccda_to_omop.load_duck_db) codemap_xwalk_concept_id() (in module ccda_to_omop.value_transformations) codemap_xwalk_domain_id() (in module ccda_to_omop.value_transformations) codemap_xwalk_source_concept_id() (in module ccda_to_omop.value_transformations) combine_datasets() (in module ccda_to_omop.layer_datasets) concat_field_list_names() (in module ccda_to_omop.value_transformations) concat_field_list_values() (in module ccda_to_omop.value_transformations) concat_fields() (in module ccda_to_omop.value_transformations) create_codemap_dict() (in module ccda_to_omop.util) create_codemap_dict_from_csv() (in module ccda_to_omop.util) create_hash() (in module ccda_to_omop.data_driven_parse) create_hash_too_long() (in module ccda_to_omop.data_driven_parse) create_omop_domain_dataframes() (in module ccda_to_omop.layer_datasets) create_visit_detail_record() (in module ccda_to_omop.visit_reconciliation)

D

dict_summary() (in module ccda_to_omop.layer_datasets) do_basic_fields() (in module ccda_to_omop.data_driven_parse) do_constant_fields() (in module ccda_to_omop.data_driven_parse) do_derived2_fields() (in module ccda_to_omop.data_driven_parse) do_derived_fields() (in module ccda_to_omop.data_driven_parse) do_filename_fields() (in module ccda_to_omop.data_driven_parse)

do_foreign_key_fields() (in module ccda_to_omop.data_driven_parse) do_hash_fields() (in module ccda_to_omop.data_driven_parse) do_none_fields() (in module ccda_to_omop.data_driven_parse) do_priority_fields() (in module ccda_to_omop.data_driven_parse) DO_VISIT_DETAIL (in module ccda_to_omop.layer_datasets) do_write_csv_files() (in module ccda_to_omop.layer_datasets)

E

extract_day_of_birth() (in module ccda_to_omop.value_transformations)

extract_month_of_birth() (in module ccda_to_omop.value_transformations) extract_year_of_birth() (in module ccda_to_omop.value_transformations)

F

find_max_columns() (in module ccda_to_omop.layer_datasets)

find_most_specific_parent() (in module ccda_to_omop.visit_reconciliation)

G

generate_cfg_name_to_domain_map() (in module ccda_to_omop.ddl) get_allow_no_matching_concept() (in module ccda_to_omop.package_constant_access) get_base_elements() (in module ccda_to_omop.find_paths) get_codemap_dict() (in module ccda_to_omop.value_transformations) get_data_partner_id() (in module ccda_to_omop.value_transformations) get_derived_fields() (in module ccda_to_omop.find_paths)

get_extract_order_fn() (in module ccda_to_omop.data_driven_parse) get_filter_fn() (in module ccda_to_omop.data_driven_parse) get_hash_fields() (in module ccda_to_omop.find_paths) get_mspi_map() (in module ccda_to_omop.value_transformations) get_partner_map() (in module ccda_to_omop.value_transformations) get_visit_detail_duration() (in module ccda_to_omop.visit_reconciliation) get_visit_duration_days() (in module ccda_to_omop.visit_reconciliation)

I

identify_inpatient_parents() (in module ccda_to_omop.visit_reconciliation)

is_temporally_contained() (in module ccda_to_omop.visit_reconciliation)

L

logger (in module ccda_to_omop.util)

M

main() (in module ccda_to_omop.code_hunt) (in module ccda_to_omop.data_driven_parse) (in module ccda_to_omop.find_paths) (in module ccda_to_omop.layer_datasets) (in module ccda_to_omop.load_duck_db) make_distinct() (in module ccda_to_omop.data_driven_parse) map_filename_to_mspi() (in module ccda_to_omop.value_transformations) merge_second_level_dict() (in module ccda_to_omop.find_paths) module ccda_to_omop ccda_to_omop.code_hunt ccda_to_omop.constants ccda_to_omop.data_driven_parse ccda_to_omop.ddl ccda_to_omop.domain_dataframe_column_types ccda_to_omop.find_paths ccda_to_omop.layer_datasets ccda_to_omop.load_duck_db ccda_to_omop.package_constant_access ccda_to_omop.util ccda_to_omop.value_transformations ccda_to_omop.visit_reconciliation

P

parse_config_for_single_root() (in module ccda_to_omop.data_driven_parse) parse_config_from_xml_file() (in module ccda_to_omop.data_driven_parse) parse_doc() (in module ccda_to_omop.data_driven_parse) parse_field_from_dict() (in module ccda_to_omop.data_driven_parse) parse_string() (in module ccda_to_omop.data_driven_parse) print_data_hash() (in module ccda_to_omop.find_paths) print_omop_structure() (in module ccda_to_omop.data_driven_parse)

process_and_save_file() (in module ccda_to_omop.data_driven_parse) process_directory() (in module ccda_to_omop.layer_datasets) process_file() (in module ccda_to_omop.data_driven_parse) (in module ccda_to_omop.layer_datasets) process_single_file_single_config() (in module ccda_to_omop.data_driven_parse) process_string() (in module ccda_to_omop.layer_datasets) process_string_to_dict() (in module ccda_to_omop.layer_datasets)

R

reclassify_nested_visit_occurrences_as_detail() (in module ccda_to_omop.visit_reconciliation) reconcile_visit_detail_FK_with_specific_domain() (in module ccda_to_omop.visit_reconciliation)

reconcile_visit_FK_with_specific_domain() (in module ccda_to_omop.visit_reconciliation) reset_context() (in module ccda_to_omop.value_transformations)

S

set_allow_no_matching_concept() (in module ccda_to_omop.package_constant_access) set_codemap_dict() (in module ccda_to_omop.value_transformations) set_mspi_map() (in module ccda_to_omop.value_transformations) set_partner_map() (in module ccda_to_omop.value_transformations)

show_column_dict() (in module ccda_to_omop.layer_datasets) sort_output_and_omit_dict() (in module ccda_to_omop.data_driven_parse) str2bool() (in module ccda_to_omop.data_driven_parse) strip_detail() (in module ccda_to_omop.find_paths) strip_tz() (in module ccda_to_omop.visit_reconciliation)

T

transform_datetime_high() (in module ccda_to_omop.value_transformations)

transform_datetime_low() (in module ccda_to_omop.value_transformations)

V

validate_ccda_document() (in module ccda_to_omop.data_driven_parse)

VocabContext (class in ccda_to_omop.value_transformations)

W

write_all_csv_files() (in module ccda_to_omop.data_driven_parse)

write_csvs_from_dataframe_dict() (in module ccda_to_omop.layer_datasets) write_individual_csv_files() (in module ccda_to_omop.data_driven_parse)