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# Copyright 2024 DARWIN EU (C)
#
# This file is part of CodelistGenerator
#
# 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.
#' Subset a codelist to only those codes from a particular domain.
#'
#' @inheritParams xDoc
#' @inheritParams cdmDoc
#' @inheritParams domainDoc
#' @param negate If FALSE, only concepts with the domain specified will be
#' returned. If TRUE, concepts with the domain specified will be excluded.
#'
#' @return The codelist with only those concepts associated with the domain
#' (if negate = FALSE) or the codelist without those concepts associated with
#' the domain (if negate = TRUE).
#' @export
#'
#' @examples
#' \donttest{
#' library(CodelistGenerator)
#' cdm <- mockVocabRef()
#' codes <- subsetOnDomain(
#' x = list("codes" = c(10,13,15)),
#' cdm = cdm,
#' domain = "Drug")
#' codes
#' }
subsetOnDomain <- function(x,
cdm,
domain,
negate = FALSE){
omopgenerics::validateCdmArgument(cdm)
omopgenerics::assertCharacter(domain)
omopgenerics::assertLogical(negate)
x <- omopgenerics::newCodelist(x)
tableCodelist <- paste0(omopgenerics::uniqueTableName(),
omopgenerics::uniqueId())
for(i in seq_along(x)){
cdm <- omopgenerics::insertTable(cdm = cdm,
name = tableCodelist,
table = dplyr::tibble(concept_id = x[[i]]),
overwrite = TRUE,
temporary = FALSE)
x[[i]] <- cdm[[tableCodelist]] |>
dplyr::inner_join(cdm[["concept"]] ,
by = "concept_id") |>
dplyr::select("concept_id",
"domain_id") |>
dplyr::distinct() |>
dplyr::collect()
if(isTRUE(negate)){
x[[i]] <- x[[i]] |>
dplyr::filter(!tolower(.data$domain_id) %in% tolower(.env$domain))
}else{
x[[i]] <- x[[i]] |>
dplyr::filter(tolower(.data$domain_id) %in% tolower(.env$domain))
}
x[[i]] <- x[[i]] |>
dplyr::pull("concept_id")
x[[i]] <- sort(unique(x[[i]]))
}
x <- x |>
vctrs::list_drop_empty()
if(length(x) == 0){
x <- omopgenerics::emptyCodelist()
}
CDMConnector::dropTable(cdm = cdm, name = tableCodelist)
return(x)
}
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