applying the same changes to getICD10Codes

darwin-eu · Jun 14, 2024 · 763a16c · 763a16c
1 parent a80bd38
commit 763a16c
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Showing 2 changed files with 21 additions and 5 deletions.
diff --git a/R/getICD10StandardCodes.R b/R/getICD10StandardCodes.R
@@ -141,7 +141,12 @@ getICD10StandardCodes <- function(cdm,
                        by = "concept_id")
     # split into list
     ICD10StandardCodes <- ICD10MapsTo %>%
-      dplyr::collect()
+      dplyr::collect() %>%
+      dplyr::left_join(cdm[["concept"]] %>% dplyr::select(.data$concept_id, .data$concept_code),
+                       by = "concept_id",
+                       copy = T) %>%
+      dplyr::mutate(name = paste0(.data$concept_code,"_", .data$name))
+
     ICD10StandardCodes <- split(
       x = ICD10StandardCodes,
       f = as.factor(ICD10StandardCodes$name),
@@ -150,14 +155,17 @@ getICD10StandardCodes <- function(cdm,
   } else {
     # split into list (only returning vector of concept ids)
     ICD10StandardCodes <- ICD10MapsTo %>%
-      dplyr::collect()
+      dplyr::collect() %>%
+      dplyr::left_join(cdm[["concept"]] %>% dplyr::select(.data$concept_id, .data$concept_code),
+                       by = "concept_id",
+                       copy = T) %>%
+      dplyr::mutate(name = paste0(.data$concept_code,"_", .data$name))
     ICD10StandardCodes <- split(
       x = ICD10StandardCodes$concept_id,
       f = ICD10StandardCodes$name
     )
   }
 
-
   if(isFALSE(withConceptDetails)){
     ICD10StandardCodes <- omopgenerics::newCodelist(ICD10StandardCodes)
   }

diff --git a/tests/testthat/test-getICD10StandardCodes.R b/tests/testthat/test-getICD10StandardCodes.R
@@ -8,8 +8,8 @@ test_that("db without icd10 codes loaded", {
                                    "ICD10 SubChapter"
                                  ))
   expect_true(length(codes) == 2)
-  expect_true("arthropathies" %in% names(codes))
-  expect_true("diseases_of_the_musculoskeletal_system_and_connective_tissue" %in%
+  expect_true("1234_arthropathies" %in% names(codes))
+  expect_true("1234_diseases_of_the_musculoskeletal_system_and_connective_tissue" %in%
                 names(codes))
   # we should pick up mapping and descendants
   expect_true(all(c(3,4,5) %in% codes[[1]]))
@@ -79,3 +79,11 @@ test_that("expected errors", {
   )))
 
 })
+
+test_that("change of name", {
+  skip_on_cran()
+  cdm <- mockVocabRef()
+  code_icd10 <- getICD10StandardCodes(cdm = cdm)
+
+  expect_true(all(startsWith(names(code_icd10), "1234_")))
+})