Enhance get_by_code() with include_synonyms and include_relationships parameters; update User-Agent header to OMOPHub-SDK-R/1.0.0; add rate limit delay in integration tests.

Author: alex-omophub

NEWS.md

@@ -1,3 +1,13 @@
+# omophub 1.1.0
+
+## New Features
+
+* Added `include_synonyms` and `include_relationships` parameters to `get_by_code()` for retrieving concept synonyms and relationships in a single request.
+
+## Changes
+
+* User-Agent header updated to `OMOPHub-SDK-R/{version}`.
+
 # omophub 1.0.0
 
 ## Initial CRAN Release

R/concepts.R

@@ -47,15 +47,29 @@ ConceptsResource <- R6::R6Class(
     #'
     #' @param vocabulary_id The vocabulary ID (e.g., "SNOMED", "ICD10CM").
     #' @param concept_code The concept code within the vocabulary.
+    #' @param include_relationships Include related concepts. Default `FALSE`.
+    #' @param include_synonyms Include concept synonyms. Default `FALSE`.
     #'
-    #' @returns A list containing the concept data with mappings.
-    get_by_code = function(vocabulary_id, concept_code) {
+    #' @returns A list containing the concept data with optional relationships and synonyms.
+    get_by_code = function(vocabulary_id,
+                           concept_code,
+                           include_relationships = FALSE,
+                           include_synonyms = FALSE) {
       checkmate::assert_string(vocabulary_id, min.chars = 1)
       checkmate::assert_string(concept_code, min.chars = 1)
 
+      query <- list()
+      if (isTRUE(include_relationships)) {
+        query$include_relationships <- "true"
+      }
+      if (isTRUE(include_synonyms)) {
+        query$include_synonyms <- "true"
+      }
+
       perform_get(
         private$.base_req,
-        paste0("concepts/by-code/", vocabulary_id, "/", concept_code)
+        paste0("concepts/by-code/", vocabulary_id, "/", concept_code),
+        query = if (length(query) > 0) query else NULL
       )
     },
 

R/request.R

@@ -20,7 +20,7 @@ build_request <- function(base_url, api_key, timeout = 30, max_retries = 3,
       "Content-Type" = "application/json",
       "Accept" = "application/json"
     ) |>
-    httr2::req_user_agent("omophub-R/1.0.0 (https://github.com/omopHub/omophub-R)") |>
+    httr2::req_user_agent("OMOPHub-SDK-R/1.0.0") |>
     httr2::req_timeout(timeout) |>
     httr2::req_throttle(
       rate = .omophub_env$rate_limit_capacity / .omophub_env$rate_limit_fill_time

tests/testthat/helper-integration.R

@@ -51,6 +51,7 @@ get_integration_api_key <- function() {
 integration_client <- function() {
   skip_if_no_integration_key()
   key <- get_integration_api_key()
+  Sys.sleep(1)  # Rate limit delay between tests
   OMOPHubClient$new(api_key = key)
 }