R/fhir_table_list.R

In POLAR-fhiR/fhircrackr: Handling HL7 FHIR® Resources in R

#' Virtual superclass for [fhir_df_list-class] and [fhir_dt_list-class]
#'
#' @slot names A character vector containing the names of the tables.
#' @slot design An object of class [fhir_design-class] that was used to create the table list.
#' @include fhir_design.R
#' @noRd
#'
setClass(
	Class = 'fhir_table_list',
	contains = c('VIRTUAL', 'list'),
	slots = c(
		names = 'character',
		design = 'fhir_design'
	)
)

setValidity(
	Class = 'fhir_table_list',
	function(object) {

		messages <- c()

		if(length(object) != length(object)) {
			messages <- c(messages, 'Slot names has to have the same length as the list.')
		}

		if(length(object) != length(object@design)) {
			messages <- c(
				messages,
				'The number of table_descriptions in the design doesn\'t correspond to the number of tables.'
			)
		}

		if(any(!names(object@design) %in% object@names)) {
			messages <- c(
				messages,
				'The names in the design don\'t correspond to the names of the tables.'
			)
		}

		if(0 < length(messages)) {messages} else {TRUE}
	}
)

#' List of data.frames as returned by [fhir_crack()]
#'
#' Objects of this class are returned by [fhir_crack()] when `data.table=FALSE` (the default).
#' They behave like an ordinary named list of data.frames but have some additional information
#' in the slot `design`.
#'
#' @slot names Character vector containing the names of the data.frames.
#' @slot design An object of class [fhir_design-class] that was used to create the df_list.
#' @export
#'
setClass(
	Class = 'fhir_df_list',
	contains = 'fhir_table_list'
)

setValidity(
	Class = 'fhir_df_list',
	method = function(object) {

		messages <- c()
		if(!all(sapply(object, is.data.frame))){'A fhir_df_list can only contain data.frames.'}
		if(0 < length(messages)) {messages} else {TRUE}

	}
)

#' List of data.tables as returned by [fhir_crack()]
#'
#' Objects of this class are returned by [fhir_crack()] when `data.table=TRUE`.
#' They behave like an ordinary named list of data.tables but have some additional information
#' in the slot `design`.
#'
#' @slot names A character vector containing the names of the data.tables.
#' @slot design An object of class [fhir_design-class] that was used to create the dt_list.
#' @export
setClass(
	Class = 'fhir_dt_list',
	contains = 'fhir_table_list'
)

setValidity(
	Class = 'fhir_dt_list',
	function(object) {
		messages <- c()
		if(!all(sapply(object, is.data.table))) {'A fhir_dt_list can only contain data.tables.'}
		if(0 < length(messages)) {messages} else {TRUE}
	}
)
#' create fhir_df_list
#'
#' This function is only for internal use and should not be exported
#' An object of this class should **only** be created inside of [fhir_crack()]
#' @param df_list A named list of data.frames.
#' @param design The design that was used to create the list.
#' @noRd
#' @examples
#' df_desc1 <- fhir_table_description(
#'     resource = 'Patient',
#'     cols = c(
#'         id     = 'id',
#'         name   = 'name/family',
#'         gender = 'gender'
#'     ),
#'     sep           = '||',
#'     brackets      = c('[', ']'),
#'     rm_empty_cols = FALSE
#' )
#'
#' df_desc2 <- fhir_table_description(
#'     resource = 'Observation',
#'     cols = c(
#'         'code/coding/system',
#'         'code/coding/code'
#'     )
#' )
#'
#' design <- fhir_design(list(Patients = df_desc1, Observations = df_desc2))
#'
#' dt_list <- list(Patients = data.frame(), Observations = data.frame())
#'
#' fhir_df_list(df_list, design)
#' @noRd
fhir_df_list <- function(df_list, design) {
	new(Class = 'fhir_df_list', df_list, design = design)
}
#' create fhir_dt_list
#'
#' This function is only for internal use and should not be exported
#' An object of this class should **only** be created inside of [fhir_crack()]
#' @param dt_list A named list of data.tables.
#' @param design The design that was used to create the list.
#'
#' @examples
#' df_desc1 <- fhir_table_description(
#'     resource = 'Patient',
#'     cols = c(
#'         id     = 'id',
#'         name   = 'name/family',
#'         gender = 'gender'
#'     ),
#'     sep           = '||',
#'     brackets      = c('[', ']'),
#'     rm_empty_cols = FALSE
#' )
#'
#' df_desc2 <- fhir_table_description(
#'     resource = 'Observation',
#'     cols     = c(
#'         'code/coding/system',
#'         'code/coding/code'
#'     )
#' )
#'
#' design <- fhir_design(list(Patients = df_desc1, Observations = df_desc2))
#'
#' dt_list <- list(Patients = data.table(), Observations = data.table())
#'
#' fhir_dt_list(dt_list, design)
#' @noRd
fhir_dt_list <- function(dt_list, design){
	new(Class = 'fhir_dt_list', dt_list, design = design)
}

#corresponding generic in fhir_design.R
#' @rdname fhir_design-methods
#' @aliases fhir_design,fhir_table_list-method
setMethod(
	f = 'fhir_design',
	signature = c(... = 'fhir_table_list'),
	definition = function(...) {
		args <- list(...)
		tab <- args[[1]]
		tab@design
	}
)

setMethod(
	f = 'show',
	signature = 'fhir_dt_list',
	definition = function(object) {
		cat('A fhir_dt_list:\n')
		list <- S3Part(object, strictS3 = TRUE)
		names(list) <- names(object)
		print(list)
	}
)

setMethod(
	f = 'show',
	signature = 'fhir_df_list',
	definition = function(object) {
		cat('A fhir_df_list:\n')
		list <- S3Part(object, strictS3 = TRUE)
		names(list) <- names(object)
		print(list)
	}
)