add get.cdm functions - Githubissues

#' @title
#' Get OMOP Metadata
#'
#' @description
#' Get metadata for the OMOP CDM Tables, the OMOP Vocabulary Tables, or Both. All functions return built-in values with the exception of \code{\link{get.field_names}}, which returns the field names in real-time.
#'
#' @name get
NULL

#' @title
#' Get Fields
#'
#' @importFrom pg13 lsFields
#' @export
#' @rdname get.field_names
#' @family get functions

get.field_names <-
        function(omop_table,
                 omop_schema,
                 verbose = TRUE) {
                        conn <- connectOMOP(verbose = verbose)
                        on.exit(dcOMOP(conn = conn,
                                        verbose = verbose))
                        pg13::lsFields(conn = conn,
                                       tableName = omop_table,
                                       schema = omop_schema)
        }

#' @title
#' Get CDM Tables
#'
#' @return
#' Vector of names of CDM Tables
#'
#' @export
#' @rdname get.cdm_tables
#' @family get functions

get.cdm_tables <-
        function() {

                c('ATTRIBUTE_DEFINITION',
                  'CARE_SITE',
                  'CDM_SOURCE',
                  'COHORT',
                  'COHORT_ATTRIBUTE',
                  'COHORT_DEFINITION',
                  'CONDITION_ERA',
                  'CONDITION_OCCURRENCE',
                  'COST',
                  'DEATH',
                  'DEVICE_EXPOSURE',
                  'DOSE_ERA',
                  'DRUG_ERA',
                  'DRUG_EXPOSURE',
                  'EPISODE',
                  'EPISODE_EVENT',
                  'FACT_RELATIONSHIP',
                  'LK_PERSON_KEYS',
                  'LOCATION',
                  'MEASUREMENT',
                  'METADATA',
                  'NOTE',
                  'NOTE_NLP',
                  'OBSERVATION',
                  'OBSERVATION_PERIOD',
                  'PAYER_PLAN_PERIOD',
                  'PERSON',
                  'PROCEDURE_OCCURRENCE',
                  'PROVIDER',
                  'REGIMEN',
                  'SOURCE_TO_CONCEPT_MAP',
                  'SPECIMEN',
                  'VISIT_DETAIL',
                  'VISIT_OCCURRENCE')
        }

#' @title
#' Get OMOP Table Abbreviations
#'
#' @return
#' Named vector of abbreviations for all OMOP Tables generated by  \code{\link[base]{abbreviate}}.
#'
#' @export
#' @rdname get.omop_table_abbr
#' @family get functions

get.omop_table_abbr <-
        function() {
                allTables <- c(get.cdm_tables(),
                               get.vocab_tables())
                allTableNames <- stringr::str_replace_all(
                                                      allTables,
                                                      pattern = "[_]{1}",
                                                      replacement = " "
                                                      )
                tolower(abbreviate(allTableNames, minlength = 1L)) %>%
                        as.list() %>%
                        purrr::set_names(allTables)
        }

#' @title
#' Get Vocabulary Tables
#'
#' @return
#' Vector of names of Vocabulary Tables
#'
#' @export
#' @rdname get.vocab_tables
#' @family get functions

get.vocab_tables <-
        function() {
                c('CONCEPT',
                  'CONCEPT_ANCESTOR',
                  'CONCEPT_CLASS',
                  'CONCEPT_RELATIONSHIP',
                  'CONCEPT_SYNONYM',
                  'DOMAIN',
                  'DRUG_STRENGTH',
                  'RELATIONSHIP',
                  'VOCABULARY')
        }

#' @title
#' Get CDM Table Concept Id Fields
#'
#' @return
#' Tibble of the concept id fields for each CDM Table
#'
#' @importFrom tibble tribble
#' @export
#' @rdname get.concept_id_fields
#' @family get functions

get.concept_id_fields <-
        function() {
                tibble::tribble(
                        ~CDM_TABLE,~CONCEPT_ID_FIELDS,
                        'ATTRIBUTE_DEFINITION', 'c("attribute_type_concept_id")',
                        'CARE_SITE', 'c("place_of_service_concept_id")',
                        'COHORT', 'c("drug_concept_id")',
                        'COHORT_ATTRIBUTE', 'c("value_as_concept_id")',
                        'COHORT_DEFINITION', 'c("definition_type_concept_id", "subject_concept_id")',
                        'CONDITION_ERA', 'c("condition_concept_id")',
                        'CONDITION_OCCURRENCE', 'c("condition_concept_id", "condition_type_concept_id", "condition_source_concept_id", "condition_status_concept_id")',
                        'COST', 'c("cost_type_concept_id", "currency_concept_id", "revenue_code_concept_id", "drg_concept_id")',
                        'DEATH', 'c("death_type_concept_id", "cause_concept_id", "cause_source_concept_id")',
                        'DEVICE_EXPOSURE', 'c("device_concept_id", "device_type_concept_id", "device_source_concept_id")',
                        'DOSE_ERA', 'c("drug_concept_id", "unit_concept_id")',
                        'DRUG_ERA', 'c("drug_concept_id")',
                        'DRUG_EXPOSURE', 'c("drug_concept_id", "drug_type_concept_id", "route_concept_id", "drug_source_concept_id")',
                        'EPISODE', 'c("episode_concept_id", "episode_object_concept_id", "episode_type_concept_id", "episode_source_concept_id")',
                        'EPISODE_EVENT', 'c("episode_event_field_concept_id")',
                        'FACT_RELATIONSHIP', 'c("domain_concept_id_1", "domain_concept_id_2", "relationship_concept_id")',
                        'MEASUREMENT', 'c("measurement_concept_id", "measurement_type_concept_id", "operator_concept_id", "value_as_concept_id", "unit_concept_id", "measurement_source_concept_id", "modifier_of_field_concept_id")',
                        'METADATA', 'c("metadata_concept_id", "metadata_type_concept_id", "value_as_concept_id")',
                        'NOTE', 'c("note_type_concept_id", "note_class_concept_id", "encoding_concept_id", "language_concept_id")',
                        'NOTE_NLP', 'c("section_concept_id", "note_nlp_concept_id", "note_nlp_source_concept_id")',
                        'OBSERVATION', 'c("observation_concept_id", "observation_type_concept_id", "value_as_concept_id", "qualifier_concept_id", "unit_concept_id", "observation_source_concept_id")',
                        'OBSERVATION_PERIOD', 'c("period_type_concept_id")',
                        'PAYER_PLAN_PERIOD', 'c("payer_concept_id", "payer_source_concept_id", "plan_concept_id", "plan_source_concept_id", "sponsor_concept_id", "sponsor_source_concept_id", "stop_reason_concept_id", "stop_reason_source_concept_id")',
                        'PERSON', 'c("gender_concept_id", "race_concept_id", "ethnicity_concept_id", "gender_source_concept_id", "race_source_concept_id", "ethnicity_source_concept_id")',
                        'PROCEDURE_OCCURRENCE', 'c("procedure_concept_id", "procedure_type_concept_id", "modifier_concept_id", "procedure_source_concept_id")',
                        'PROVIDER', 'c("specialty_concept_id", "gender_concept_id", "specialty_source_concept_id", "gender_source_concept_id")',
                        'REGIMEN', 'c("drug_concept_id")',
                        'SOURCE_TO_CONCEPT_MAP', 'c("source_concept_id", "target_concept_id")',
                        'SPECIMEN', 'c("specimen_concept_id", "specimen_type_concept_id", "unit_concept_id", "anatomic_site_concept_id", "disease_status_concept_id")',
                        'VISIT_DETAIL', 'c("visit_detail_concept_id", "visit_detail_type_concept_id", "admitting_source_concept_id", "discharge_to_concept_id", "visit_detail_source_concept_id")',
                        'VISIT_OCCURRENCE', 'c("visit_concept_id", "visit_type_concept_id", "visit_source_concept_id", "admitting_source_concept_id", "discharge_to_concept_id")'
                )

        }
meerapatelmd / chariot

add get.cdm functions #18
