Merge pull request #106 from OxfordIHTM/dev

refactor check functions to fix #105

.github/workflows/test-coverage.yaml

@@ -13,6 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
       - uses: actions/checkout@v4

DESCRIPTION

@@ -22,6 +22,7 @@ Depends:
 Imports: 
     dplyr,
     httr2,
+    rlang,
     tibble,
     tidyr
 Suggests: 

NAMESPACE

@@ -25,6 +25,7 @@ export(icd_structure_foundation)
 export(icd_structure_search)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
+importFrom(dplyr,filter)
 importFrom(dplyr,pull)
 importFrom(httr2,oauth_client)
 importFrom(httr2,req_headers)
@@ -34,5 +35,7 @@ importFrom(httr2,req_url_path)
 importFrom(httr2,req_url_query)
 importFrom(httr2,request)
 importFrom(httr2,resp_body_json)
+importFrom(rlang,.data)
 importFrom(tibble,tibble)
 importFrom(tidyr,unnest)
+importFrom(utils,head)

R/codigo.R

@@ -14,7 +14,9 @@
 #' @importFrom httr2 oauth_client request req_url_query req_headers
 #'   req_oauth_client_credentials req_perform resp_body_json req_url_path
 #' @importFrom tibble tibble
-#' @importFrom dplyr bind_cols bind_rows pull
+#' @importFrom dplyr bind_cols bind_rows pull filter
 #' @importFrom tidyr unnest
+#' @importFrom rlang .data
+#' @importFrom utils head
 #'
 "_PACKAGE"

R/icd_10_get.R

@@ -14,6 +14,8 @@
 #'   languages will vary. Default is English ("en"). Note that language support
 #'   for ICD-10 is limited to English (`en`).
 #' @param category ICD-10 category code or for blocks, the code range.
+#' @param verbose Logical. Should non-warning and non-error messages be
+#'   printed? Default is TRUE.
 #' @param base_url The base URL of the API. Default uses the WHO API server at
 #'   https://id.who.int. If you are using a locally deployed server or hosting
 #'   your own ICD API server, you should specify the URL of your instance here.
@@ -72,6 +74,7 @@ icd_10_get_releases <- function(api_version = c("v2", "v1"),
 icd_10_get_chapters <- function(release = NULL,
                                 api_version = c("v2", "v1"),
                                 language = "en",
+                                verbose = TRUE,
                                 base_url = "https://id.who.int",
                                 client = icd_oauth_client(),
                                 scope = "icdapi_access") {
@@ -80,13 +83,15 @@ icd_10_get_chapters <- function(release = NULL,
 
   ## Check release identifier ----
   if (!is.null(release))
-    icd_check_release(release)
+    icd_check_release(release = release, icd = "icd10", verbose = verbose)
   else
     release <- icd_get_releases(icd = "icd10", latest = TRUE) |> dplyr::pull()
 
   ## Check language ----
   if (!is.null(language))
-    icd_check_language(release = release, language = language)
+    language <- icd_check_language(
+      release = release, language = language, icd = "icd10", verbose = verbose
+    )
 
   ## Make base request ----
   req <- httr2::request(base_url) |>
@@ -150,6 +155,7 @@ icd_10_get_info <- function(release = NULL,
                             category,
                             api_version = c("v2", "v1"),
                             language = "en",
+                            verbose = TRUE,
                             base_url = "https://id.who.int",
                             client = icd_oauth_client(),
                             scope = "icdapi_access") {
@@ -158,13 +164,15 @@ icd_10_get_info <- function(release = NULL,
 
   ## Check release identifier ----
   if (!is.null(release))
-    icd_check_release(release)
+    icd_check_release(release = release, icd = "icd10", verbose = verbose)
   else
     release <- icd_get_releases(icd = "icd10", latest = TRUE) |> dplyr::pull()
 
   ## Check language ----
   if (!is.null(language))
-    icd_check_language(release = release, language = language)
+    language <- icd_check_language(
+      release = release, language = language, icd = "icd10", verbose = verbose
+    )
 
   ## Make base request ----
   req <- httr2::request(base_url) |>

R/icd_autocode.R

@@ -61,11 +61,14 @@ icd_autocode_foundation <- function(q,
   api_version <- match.arg(api_version)
 
   ## Check release identifier ----
-  if (!is.null(release)) icd_check_release(release, verbose = verbose)
+  if (!is.null(release))
+    icd_check_release(release, verbose = verbose)
 
   ## Check language ----
   if (!is.null(language))
-    language <- icd_check_language(release, language, verbose = verbose)
+    language <- icd_check_language(
+      release = release, language = language, verbose = verbose
+    )
 
   ## Make base request ----
   req <- httr2::request(file.path(base_url, "icd/entity/autocode")) |>
@@ -131,13 +134,15 @@ icd_autocode <- function(q,
 
   ## Check release identifier ----
   if (!is.null(release))
-    icd_check_release(release, verbose = verbose)
+    icd_check_release(release = release, verbose = verbose)
   else
     release <- icd_get_releases(latest = TRUE) |> dplyr::pull()
 
   ## Check language ----
   if (!is.null(language))
-    language <- icd_check_language(release, language, verbose = verbose)
+    language <- icd_check_language(
+      release = release, language = language, verbose = verbose
+    )
 
   ## Make base request ----
   req <- httr2::request(base_url) |>

R/icd_check.R

@@ -3,6 +3,8 @@
 #' functions
 #'
 #' @param release A string specifying the release version of the ICD-11.
+#' @param icd A character string of available ICD classifications. Currently,
+#'   this can be either "icd10" or "icd11". Default is "icd11".
 #' @param language language codes such as en, es, zh, etc.
 #' @param verbose Logical. Should non-warning and non-error messages be
 #'   printed? Default is TRUE.
@@ -22,29 +24,36 @@
 #' @rdname icd_check
 #' @export
 #'
-icd_check_release <- function(release, verbose = TRUE) {
-  release_check <- release %in% codigo::icd_versions$`Release ID`
+icd_check_release <- function(release,
+                              icd = c("icd11", "icd10"),
+                              verbose = TRUE) {
+  icd <- match.arg(icd)
+
+  icd <- ifelse(icd == "icd11", "ICD-11", "ICD-10")
+
+  release_check <- release %in%
+    codigo::icd_versions$`Release ID`[codigo::icd_versions$Classification == icd]
 
   if (release_check) {
-    icd_set <- with(
-      codigo::icd_versions,
-      Classification[`Release ID` == release]
-    )
+    # icd_set <- with(
+    #   codigo::icd_versions,
+    #   Classification[`Release ID` == release]
+    # )
 
     if (verbose)
       message(
         paste0(
           "Release `", release, "` matches a known release for ",
-          icd_set, "."
+          icd, "."
         ) |>
           strwrap(width = 80)
       )
   } else {
     stop(
       paste0(
         "Release `", release,
-        "` does not match any known release for ICD-11 or ICD-10.",
-        " Please verify and check with `icd_versions` and try again."
+        "` does not match any known release for ", icd,
+        ". Please check `icd_versions`."
       ) |>
         strwrap(width = 80)
     )
@@ -56,12 +65,23 @@ icd_check_release <- function(release, verbose = TRUE) {
 #' @rdname icd_check
 #' @export
 #'
-icd_check_language <- function(release = NULL, language, verbose = TRUE) {
+icd_check_language <- function(release = NULL, language,
+                               icd = c("icd11", "icd10"),
+                               verbose = TRUE) {
+  icd <- match.arg(icd)
+
+  #icd <- ifelse(icd == "icd11", "ICD-11", "ICD-10")
+
   ## Check if release is NULL ----
-  if (is.null(release)) release <- codigo::icd_versions$`Release ID`[1]
+  if (is.null(release)) release <- codigo::icd_versions |>
+    dplyr::filter(
+      .data$Classification == ifelse(icd == "icd11", "ICD-11", "ICD-10")
+    ) |>
+    dplyr::pull(.data$`Release ID`) |>
+    head(1)
 
   ## Check whether release is specified correctly ----
-  icd_check_release(release, verbose = verbose)
+  icd_check_release(release = release, icd = icd, verbose = verbose)
 
   ## Get languages available for release provided ----
   languages_available <- with(

R/icd_get.R

@@ -60,10 +60,13 @@ icd_get_foundation <- function(release = NULL,
   api_version <- match.arg(api_version)
 
   ## Check release identifier ----
-  if (!is.null(release)) icd_check_release(release, verbose = verbose)
+  if (!is.null(release)) icd_check_release(release = release, verbose = verbose)
 
   ## Check language ----
-  if (!is.null(language)) icd_check_language(release, language, verbose = verbose)
+  if (!is.null(language))
+    language <- icd_check_language(
+      release = release, language = language, verbose = verbose
+    )
 
   ## Make base request ----
   req <- httr2::request(file.path(base_url, "icd/entity"))
@@ -105,17 +108,22 @@ icd_get_entity <- function(id,
                            include = NULL,
                            api_version = c("v2", "v1"),
                            language = "en",
+                           verbose = TRUE,
                            base_url = "https://id.who.int",
                            client = icd_oauth_client(),
                            scope = "icdapi_access") {
   ## Get API version to use ----
   api_version <- match.arg(api_version)
 
   ## Check release identifier ----
-  if (!is.null(release)) icd_check_release(release)
+  if (!is.null(release))
+    icd_check_release(release = release, verbose = verbose)
 
   ## Check language ----
-  if (!is.null(language)) icd_check_language(release, language)
+  if (!is.null(language))
+    language <- icd_check_language(
+      release = release, language = language, verbose = verbose
+    )
 
   ## Make base request ----
   req <- httr2::request(file.path(base_url, "icd/entity", id)) |>
@@ -159,6 +167,7 @@ icd_get_entity <- function(id,
 icd_get_info <- function(linearization = c("mms", "icf"),
                          api_version = c("v2", "v1"),
                          language = "en",
+                         verbose = TRUE,
                          base_url = "https://id.who.int",
                          client = icd_oauth_client(),
                          scope = "icdapi_access") {
@@ -170,9 +179,10 @@ icd_get_info <- function(linearization = c("mms", "icf"),
 
   ## Check language ----
   if (!is.null(language))
-    icd_check_language(
+    language <- icd_check_language(
       release = icd_get_releases(latest = TRUE) |> dplyr::pull(),
-      language
+      language = language,
+      verbose = verbose
     )
 
   ## Make base request ----
@@ -203,6 +213,7 @@ icd_get_chapter <- function(linearization = c("mms", "icf"),
                             release = NULL,
                             api_version = c("v2", "v1"),
                             language = "en",
+                            verbose = TRUE,
                             base_url = "https://id.who.int",
                             client = icd_oauth_client(),
                             scope = "icdapi_access") {
@@ -214,13 +225,15 @@ icd_get_chapter <- function(linearization = c("mms", "icf"),
 
   ## Check release identifier ----
   if (!is.null(release))
-    icd_check_release(release)
+    icd_check_release(release = release, verbose = verbose)
   else
     release <- icd_get_releases(latest = TRUE) |> dplyr::pull()
 
   ## Check language ----
   if (!is.null(language))
-    icd_check_language(release = release, language = language)
+    language <- icd_check_language(
+      release = release, language = language, verbose = verbose
+    )
 
   ## Make base request ----
   req <- httr2::request(base_url) |>

R/icd_search.R

@@ -126,11 +126,14 @@ icd_search_foundation <- function(q,
   api_version <- match.arg(api_version)
 
   ## Check release identifier ----
-  if (!is.null(release)) icd_check_release(release, verbose = verbose)
+  if (!is.null(release))
+    icd_check_release(release = release, icd = "icd11", verbose = verbose)
 
   ## Check language ----
   if (!is.null(language))
-    language <- icd_check_language(release, language, verbose = verbose)
+    language <- icd_check_language(
+      release = release, language = language, icd = "icd11", verbose = verbose
+    )
 
   ## Make base request ----
   req <- httr2::request(base_url) |>
@@ -229,13 +232,15 @@ icd_search <- function(q,
 
   ## Check release identifier ----
   if (!is.null(release))
-    icd_check_release(release, verbose = verbose)
+    icd_check_release(release = release, icd = "icd11", verbose = verbose)
   else
     release <- icd_get_releases(latest = TRUE) |> dplyr::pull()
 
   ## Check language ----
   if (!is.null(language))
-    language <- icd_check_language(release, language, verbose = verbose)
+    language <- icd_check_language(
+      release = release, language = language, icd = "icd11", verbose = verbose
+    )
 
   ## Make base request ----
   req <- httr2::request(base_url) |>