R/importCodelist.R

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

# Copyright 2024 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.

#' Import a codelist.
#'
#' @param path Path to where files will be created.
#' @param type Type of files to export. Currently 'json' and 'csv' are
#' supported.
#'
#' @return A codelist
#' @export
importCodelist <- function(path, type = "json") {
  assertChoice(type, choices = c("json", "csv"))
  files <- findFiles(path, type)

  # read content
  codelist <- purrr::map(files, \(x) readConceptSetExpression(x, type)) |>
    purrr::compact() |>
    purrr::imap(\(x, nm) {
      cols <- colnames(x)
      if ("descendants" %in% cols) {
        if (any(as.logical(x$descendants))) {
          cli::cli_warn("skipping: {.pkg {nm}} because descendants = TRUE is not supported in codelists.")
          return(NULL)
        }
      }
      if ("codelist_name" %in% cols) {
        res <-  x |>
          dplyr::select(c("codelist_name", "concept_id"))
      } else if ("concept_set_expression_name" %in% cols) {
        res <- x |>
          dplyr::select(c("codelist_name" = "concept_set_expression_name", "concept_id"))
      } else {
        res <- dplyr::tibble(codelist_name = nm, concept_id = x$concept_id)
      }
      res |>
        dplyr::mutate(
          codelist_name = as.character(.data$codelist_name),
          concept_id = as.integer(.data$concept_id)
        ) |>
        dplyr::select("codelist_name", "concept_id")
    }) |>
    purrr::compact() |>
    dplyr::bind_rows() |>
    newCodelist()

  cli::cli_inform("{.pkg {length(codelist)}} codelist{?s} imported.")

  return(codelist)
}