R/classConceptSetExpression.R

In omopgenerics: Methods and Classes for the OMOP Common Data Model

# Copyright 2023 DARWIN EU (C)
#
# This file is part of omopgenerics
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.


#' 'conceptSetExpression' object constructor
#'
#' @param x a named list of tibbles, each of which containing concept set
#' definitions
#'
#' @return A conceptSetExpression
#' @export
#'
newConceptSetExpression <- function(x) {
  # constructor
  x <- constructConceptSetExpression(x)

  # validate
  x <- validateConceptSetExpression(x)

  return(x)
}

constructConceptSetExpression <- function(x) {
  x <- x |> addClass("conceptSetExpression")

  return(x)
}

validateConceptSetExpression <- function(x, call = parent.frame()) {
  assertList(x, named = TRUE, class = c("tbl"), call = call)

  for (i in seq_along(x)) {
    assertTable(
      x = x[[i]], class = "data.frame",
      columns = c("concept_id", "excluded", "descendants", "mapped"),
      call = call
    )
    assertNumeric(x[[i]]$concept_id, integerish = TRUE, call = call)
    assertLogical(x[[i]]$excluded, call = call)
    assertLogical(x[[i]]$descendants, call = call)
    assertLogical(x[[i]]$mapped, call = call)
  }

  x <- x |>
    purrr::map(\(x) {
      x |>
        dplyr::relocate(c("concept_id", "excluded", "descendants", "mapped")) |>
        dplyr::mutate(x, concept_id = as.integer(.data$concept_id))
    })

  # alphabetical order
  if (length(x) > 0) {
    x <- x[order(names(x))] |>
      addClass("conceptSetExpression")
  }

  return(x)
}


#' Print a concept set expression
#'
#' @param x A concept set expression
#' @param ...  Included for compatibility with generic. Not used.
#'
#' @return  Invisibly returns the input
#' @export
#'
#' @examples
#' asthma_cs <- list(
#'   "asthma_narrow" = dplyr::tibble(
#'     "concept_id" = 1,
#'     "excluded" = FALSE,
#'     "descendants" = TRUE,
#'     "mapped" = FALSE
#'   ),
#'   "asthma_broad" = dplyr::tibble(
#'     "concept_id" = c(1, 2),
#'     "excluded" = FALSE,
#'     "descendants" = TRUE,
#'     "mapped" = FALSE
#'   )
#' )
#' asthma_cs <- newConceptSetExpression(asthma_cs)
#' print(asthma_cs)
print.conceptSetExpression <- function(x, ...) {
  cli::cli_h1("{length(x)} conceptSetExpression{?s}")
  cli::cat_line("")
  if (length(x) <= 6) {
    for (i in seq_along(x)) {
      cli::cat_line(paste0("- ", names(x)[i], " (", nrow(x[[i]]), " concept criteria)"))
    }
  } else {
    for (i in seq_along(x[1:10])) {
      cli::cat_line(paste0("- ", names(x[1:10])[i], " (", nrow(x[[i]]), " concept criteria)"))
    }
    cli::cat_line(paste0("along with ", length(x) - 10, " more concept sets"))
  }
  invisible(x)
}