From 11223c93b4cd6107c298d5fd5751c445d0ca12fe Mon Sep 17 00:00:00 2001
From: edward-burn <9583964+edward-burn@users.noreply.github.com>
Date: Sat, 9 Mar 2024 09:29:42 +0000
Subject: [PATCH] codelist class

---
 DESCRIPTION                     |  2 +-
 R/drugCodes.R                   | 12 ++++++++++++
 R/getICD10StandardCodes.R       |  5 +++++
 tests/testthat/test-drugCodes.R |  1 +
 4 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1f2bb08..0a50850 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -12,7 +12,7 @@ Description: Generate a candidate code list for the Observational Medical Outcom
 License: Apache License (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends:
     R (>= 3.5.0)
 Imports:
diff --git a/R/drugCodes.R b/R/drugCodes.R
index efc937b..8d4dc15 100644
--- a/R/drugCodes.R
+++ b/R/drugCodes.R
@@ -144,6 +144,7 @@ getATCCodes <- function(cdm,
         dplyr::select("concept_id") %>%
         dplyr::distinct() %>%
         dplyr::pull()
+
       } else {
         atc_descendants[[i]] <- atc_descendants[[i]] %>%
           dplyr::select(!"ancestor_concept_id")
@@ -152,6 +153,11 @@ getATCCodes <- function(cdm,
       names(atc_descendants)[i] <- workingName
     }
   }
+
+  if(isFALSE(withConceptDetails)){
+  atc_descendants <- omopgenerics::newCodelist(atc_descendants)
+  }
+
   return(atc_descendants)
 }
 
@@ -278,6 +284,7 @@ getDrugIngredientCodes <- function(cdm,
           dplyr::select("concept_id") %>%
           dplyr::distinct() %>%
           dplyr::pull()
+
       } else {
         ingredientCodes[[i]] <- ingredientCodes[[i]] %>%
           dplyr::select(!"ancestor_concept_id")
@@ -285,6 +292,11 @@ getDrugIngredientCodes <- function(cdm,
 
       names(ingredientCodes)[[i]] <- workingName
     }
+
+    if(isFALSE(withConceptDetails)){
+    ingredientCodes <- omopgenerics::newCodelist(ingredientCodes)
+    }
+
     return(ingredientCodes)
 }
 
diff --git a/R/getICD10StandardCodes.R b/R/getICD10StandardCodes.R
index 11e9f83..6ec139b 100644
--- a/R/getICD10StandardCodes.R
+++ b/R/getICD10StandardCodes.R
@@ -141,6 +141,11 @@ getICD10StandardCodes <- function(cdm,
     )
   }
 
+
+  if(isFALSE(withConceptDetails)){
+    ICD10StandardCodes <- omopgenerics::newCodelist(ICD10StandardCodes)
+  }
+
   return(ICD10StandardCodes)
 }
 
diff --git a/tests/testthat/test-drugCodes.R b/tests/testthat/test-drugCodes.R
index 0dc8e81..3b135b7 100644
--- a/tests/testthat/test-drugCodes.R
+++ b/tests/testthat/test-drugCodes.R
@@ -4,6 +4,7 @@ test_that("getATCCodes working", {
   for (i in seq_along(backends)) {
   cdm <- mockVocabRef(backend = backends[i])
   atcCodes <- getATCCodes(cdm, level = "ATC 1st")
+  expect_true("codelist" %in% class(atcCodes))
   expect_true(all(atcCodes[[1]] == c(12,13)))
   expect_true(c("alimentary_tract_and_metabolism") %in%
                 names(atcCodes))