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 only "json" is supported.
#'
#' @return A codelist
#' @export
importCodelist <- function(path, type = "json") {

 cse <- importConceptSetExpression(path = path,
                                   type = type)

 for(i in seq_along(cse)){
   if(any(cse[[i]]$excluded == TRUE)){
     cli::cli_abort("Not all excluded set to FALSE in {names(cse)[i]}. Use importConceptSetExpression instead.")
   }
   if(any(cse[[i]]$descendants == TRUE)){
     cli::cli_abort("Not all descendants set to FALSE in {names(cse)[i]}. Use importConceptSetExpression instead.")
   }
   if(any(cse[[i]]$mapped == TRUE)){
     cli::cli_abort("Not all mapped set to FALSE in {names(cse)[i]}. Use importConceptSetExpression instead.")
   }

   cse[[i]] <- cse[[i]] |>
     dplyr::pull("concept_id")

 }

 newCodelist(cse)

}