Fix concept-code lookups containing slashes

NEWS.md

@@ -2,6 +2,11 @@
 
 ## Bug Fixes
 
+* `get_by_code()` percent-encodes vocabulary IDs and concept codes as individual
+  path segments, including literal percent sequences and slashes such as ICD-O
+  `8032/3`, with or without hierarchy, synonym, relationship, or vocabulary-release
+  query options.
+
 * HTTP failures now raise the documented OMOPHub condition classes instead of
   only httr2's generic ones (#137): 400 → `omophub_validation_error`, 401 or
   `invalid_api_key` / `missing_api_key` → `omophub_auth_error`, 403 →

R/concepts.R

@@ -88,8 +88,14 @@ ConceptsResource <- R6::R6Class(
 
       perform_get(
         private$.base_req,
-        paste0("concepts/by-code/", vocabulary_id, "/", concept_code),
-        query = if (length(query) > 0) query else NULL
+        paste0(
+          "concepts/by-code/",
+          utils::URLencode(vocabulary_id, reserved = TRUE, repeated = TRUE),
+          "/",
+          utils::URLencode(concept_code, reserved = TRUE, repeated = TRUE)
+        ),
+        query = if (length(query) > 0) query else NULL,
+        endpoint_encoded = TRUE
       )
     },
 

R/request.R

@@ -65,14 +65,18 @@ perform_request <- function(req, endpoint, call = rlang::caller_env()) {
 #' @param base_req Base request object.
 #' @param endpoint API endpoint path.
 #' @param query Named list of query parameters.
+#' @param endpoint_encoded Whether `endpoint` is already percent-encoded.
 #'
 #' @returns Parsed JSON response. For paginated endpoints, returns a list with
 #'   `data` (the results) and `meta` (pagination info). For single-item endpoints,
 #'   returns the unwrapped data directly.
 #' @keywords internal
-perform_get <- function(base_req, endpoint, query = NULL) {
-  req <- base_req |>
-    httr2::req_url_path_append(endpoint)
+perform_get <- function(base_req, endpoint, query = NULL,
+                        endpoint_encoded = FALSE) {
+  req <- base_req
+  if (!isTRUE(endpoint_encoded)) {
+    req <- httr2::req_url_path_append(req, endpoint)
+  }
 
   # Add query parameters, removing NULLs
   if (!is.null(query)) {
@@ -82,6 +86,14 @@ perform_get <- function(base_req, endpoint, query = NULL) {
     }
   }
 
+  if (isTRUE(endpoint_encoded)) {
+    # Query updates parse and rebuild the URL, decoding escaped path separators.
+    # Append the already-encoded endpoint only after all query updates are done.
+    url <- httr2::url_parse(req$url)
+    url$path <- I(paste0(sub("/$", "", url$path), "/", endpoint))
+    req <- httr2::req_url(req, httr2::url_build(url))
+  }
+
   resp <- perform_request(req, endpoint, call = rlang::caller_env())
   body <- httr2::resp_body_json(resp)
 

tests/testthat/test-concepts.R

@@ -108,7 +108,7 @@ test_that("concepts$get_by_code calls correct endpoint", {
 
   called_with <- NULL
   local_mocked_bindings(
-    perform_get = function(req, path, query = NULL) {
+    perform_get = function(req, path, query = NULL, endpoint_encoded = FALSE) {
       called_with <<- list(path = path)
       mock_concept()
     }
@@ -119,13 +119,35 @@ test_that("concepts$get_by_code calls correct endpoint", {
   expect_equal(called_with$path, "concepts/by-code/SNOMED/44054006")
 })
 
+test_that("concepts$get_by_code URL-encodes path segments", {
+  base_req <- httr2::request("https://api.omophub.com/v1")
+  resource <- ConceptsResource$new(base_req)
+
+  request_url <- NULL
+  httr2::local_mocked_responses(function(req) {
+    request_url <<- req$url
+    httr2::response(
+      status_code = 200,
+      headers = list(`content-type` = "application/json"),
+      body = charToRaw(jsonlite::toJSON(mock_concept(), auto_unbox = TRUE))
+    )
+  })
+
+  resource$get_by_code("ICDO3", "8032/3")
+
+  expect_equal(
+    request_url,
+    "https://api.omophub.com/v1/concepts/by-code/ICDO3/8032%2F3"
+  )
+})
+
 test_that("concepts$get_by_code passes include_hierarchy and vocab_release", {
   base_req <- httr2::request("https://api.omophub.com/v1")
   resource <- ConceptsResource$new(base_req)
 
   called_with <- NULL
   local_mocked_bindings(
-    perform_get = function(req, path, query = NULL) {
+    perform_get = function(req, path, query = NULL, endpoint_encoded = FALSE) {
       called_with <<- list(query = query)
       mock_concept()
     }
@@ -469,3 +491,62 @@ test_that("concepts$recommended passes all optional filters", {
   expect_equal(called_with$body$page, 2L)
   expect_equal(called_with$body$page_size, 50L)
 })
+
+test_that("concepts$get_by_code preserves encoded slashes with query options", {
+  base_req <- httr2::request("https://api.omophub.com/v1")
+  resource <- ConceptsResource$new(base_req)
+  request_url <- NULL
+  httr2::local_mocked_responses(function(req) {
+    request_url <<- req$url
+    httr2::response(
+      status_code = 200,
+      headers = list(`content-type` = "application/json"),
+      body = charToRaw(jsonlite::toJSON(mock_concept(), auto_unbox = TRUE))
+    )
+  })
+
+  resource$get_by_code("ICDO3", "8032/3", include_hierarchy = TRUE)
+  expect_identical(
+    request_url,
+    "https://api.omophub.com/v1/concepts/by-code/ICDO3/8032%2F3?include_hierarchy=true"
+  )
+
+  resource$get_by_code(
+    "ICDO3", "8032/3",
+    include_relationships = TRUE,
+    include_synonyms = TRUE,
+    include_hierarchy = TRUE,
+    vocab_release = "2025.1"
+  )
+  expect_identical(
+    strsplit(request_url, "?", fixed = TRUE)[[1]][1],
+    "https://api.omophub.com/v1/concepts/by-code/ICDO3/8032%2F3"
+  )
+  expect_equal(httr2::url_parse(request_url)$query, list(
+    include_relationships = "true",
+    include_synonyms = "true",
+    include_hierarchy = "true",
+    vocab_release = "2025.1"
+  ))
+})
+
+test_that("concepts$get_by_code treats percent sequences as literal segment input", {
+  resource <- ConceptsResource$new(httr2::request("https://api.omophub.com/v1"))
+  request_url <- NULL
+  httr2::local_mocked_responses(function(req) {
+    request_url <<- req$url
+    httr2::response(
+      status_code = 200,
+      headers = list(`content-type` = "application/json"),
+      body = charToRaw(jsonlite::toJSON(mock_concept(), auto_unbox = TRUE))
+    )
+  })
+
+  for (include_hierarchy in c(FALSE, TRUE)) {
+    resource$get_by_code("V%20B/1", "A%20B/1", include_hierarchy = include_hierarchy)
+    expect_identical(
+      strsplit(request_url, "?", fixed = TRUE)[[1]][1],
+      "https://api.omophub.com/v1/concepts/by-code/V%2520B%2F1/A%2520B%2F1"
+    )
+  }
+})