v1.9.0 prep

.github/workflows/R-CMD-check.yaml

@@ -38,7 +38,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck, any::urlchecker
+          extra-packages: any::rcmdcheck, any::urlchecker, any::pkgload
           needs: check
           cache-version: 2
 
@@ -57,6 +57,20 @@ jobs:
           }
         shell: Rscript {0}
 
+      # Source-tree lint. `R CMD check` runs the suite against an INSTALLED
+      # package, whose R/ contains omophub.rdb rather than any .R file, so this
+      # guard skips itself there. Running it here against the checkout keeps it
+      # gating every PR instead of only ever running on a developer's machine.
+      - name: Check roxygen @param order against signatures
+        if: matrix.r == 'release'
+        run: |
+          pkgload::load_all(quiet = TRUE)
+          testthat::test_file(
+            "tests/testthat/test-roxygen-param-order.R",
+            stop_on_failure = TRUE
+          )
+        shell: Rscript {0}
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: omophub
 Title: R Client for the 'OMOPHub' Medical Vocabulary API
-Version: 1.8.1
+Version: 1.9.0
 Authors@R: c(
     person("Alex", "Chen", email = "alex@omophub.com", role = c("aut", "cre", "cph")),
     person("Observational Health Data Science and Informatics", role = c("cph"))

NEWS.md

@@ -1,8 +1,44 @@
+# omophub 1.9.0
+
+## New Features
+
+* **Mapping pagination** - `client$mappings$get()` accepts `page` and
+  `page_size`. `GET /v1/concepts/{id}/mappings` became paginated; 
+  `page_size` defaults to 100,
+  matching the old cap, so an existing call returns exactly the page it
+  returned before. Pagination metadata is attached to the result as the
+  `pagination` attribute - read it with `attr(result, "pagination")`.
+
+* **`client$mappings$get_all()`** - walks every page and returns one tibble of
+  all mappings for a concept. Prefer it over `get()` when assembling a code
+  list; a partial code list is wrong in a way nothing in the result reveals.
+  Takes `max_pages` and `progress` like the other `*_all()` methods.
+
+* **`relationship_ids`** on `client$mappings$get()` and `get_all()` - a
+  character vector of relationship types. The server defaults to `"Maps to"`,
+  so a composite concept returns only half its decomposition unless
+  `"Maps to value"` is asked for too: "Allergy to penicillin G" maps to
+  "Allergy to drug" via `Maps to` and to "penicillin G" via `Maps to value`.
+
+## Bug Fixes
+
+* **`client$mappings$get()` returned a different shape once the API added
+  pagination.** `perform_get()` switches its return shape based on whether the
+  response carries `meta.pagination`.
+
+* **`include_invalid = FALSE` never reached the server** on
+  `client$mappings$get()` and `get_all()`. The parameter was only sent when
+  `TRUE`, and this endpoint defaults to *including* deprecated mappings, so
+  asking to exclude them did nothing. The default is now `NULL` (take the
+  server default); pass `FALSE` to exclude. Omitting it behaves exactly as
+  before, so only callers who explicitly passed `FALSE` - and were being
+  ignored - see a change.
+
 # omophub 1.8.1
 
 ## Changed
 
-* **Canonical endpoint path** — `client$search$semantic()` and
+* **Canonical endpoint path** - `client$search$semantic()` and
   `client$search$semantic_all()` now call `GET /v1/search/semantic` instead of
   `GET /v1/concepts/semantic-search`. The legacy path remains a permanent
   server-side alias (emits `Deprecation: true` + `Link: …rel="successor-version"`
@@ -13,21 +49,21 @@
 
 ## New Features
 
-* **FHIR Value-as-Concept** — the `resolve_batch(as_tibble = TRUE)` tibble now
+* **FHIR Value-as-Concept** - the `resolve_batch(as_tibble = TRUE)` tibble now
   includes `value_as_concept_id` and `value_as_concept_name` columns, populated
   when the resolver decomposes a composite concept via the `Maps to value`
-  relationship (HL7 FHIR-to-OMOP IG Value-as-Concept pattern — e.g. "Allergy to
+  relationship (HL7 FHIR-to-OMOP IG Value-as-Concept pattern - e.g. "Allergy to
   penicillin" yields a standard "Allergy to drug" plus a value "Penicillin G").
 
-* **`on_unmapped` for FHIR resolution** — `resolve()`, `resolve_batch()`, and
+* **`on_unmapped` for FHIR resolution** - `resolve()`, `resolve_batch()`, and
   `resolve_codeable_concept()` gained an `on_unmapped` argument (`"error"`
   default / `"sentinel"`). With `"sentinel"` the resolver returns a
   `concept_id` 0 record instead of a 404 when nothing resolves, so ETL
   pipelines always get a row (matches the Python SDK).
 
 ## Behavior Changes
 
-* **Unmapped rows in the batch tibble** — a coding that resolves to a source
+* **Unmapped rows in the batch tibble** - a coding that resolves to a source
   concept but has no standard `Maps to` target now reports `status = "unmapped"`
   (with `standard_concept_id = 0`) instead of `"resolved"`, matching the OMOP /
   FHIR-to-OMOP IG convention that an unmapped concept is `concept_id 0`. Code

R/mappings.R

@@ -15,38 +15,131 @@ MappingsResource <- R6::R6Class(
     },
 
     #' @description
-    #' Get mappings for a concept.
+    #' Get one page of mappings for a concept.
+    #'
+    #' The endpoint is paginated and a concept can easily have more mappings
+    #' than one page holds, so a full page means "there is probably more",
+    #' not "this is everything". Read the `pagination` attribute on the
+    #' result, or use `get_all()` to walk every page.
     #'
     #' @param concept_id The concept ID.
     #' @param target_vocabulary Filter to a specific target vocabulary (e.g., "ICD10CM").
-    #' @param include_invalid Include invalid/deprecated mappings. Default `FALSE`.
+    #' @param include_invalid Whether to return mappings whose relationship or
+    #'   target concept is deprecated. Default `NULL` takes the server default,
+    #'   which for this endpoint is to *include* them; pass `FALSE` to exclude
+    #'   them. The source concept is never filtered, so a deprecated concept
+    #'   still returns what it maps to.
     #' @param vocab_release Specific vocabulary release version (e.g., "2025.1"). Default `NULL`.
+    #' @param relationship_ids Character vector of relationship types to return.
+    #'   Defaults server-side to `"Maps to"`. Pass `c("Maps to", "Maps to value")`
+    #'   to also get the Value-as-Concept decomposition of composite concepts -
+    #'   "Allergy to penicillin G" maps to "Allergy to drug" via `Maps to` and to
+    #'   "penicillin G" via `Maps to value`, and the default returns only the
+    #'   first of those.
+    #' @param page Page number. Default 1.
+    #' @param page_size Mappings per page. Default 100, maximum 200.
     #'
-    #' @returns Mappings for the concept.
+    #' @returns Mappings for the concept, with pagination metadata attached as
+    #'   the `pagination` attribute.
     get = function(concept_id,
                    target_vocabulary = NULL,
-                   include_invalid = FALSE,
-                   vocab_release = NULL) {
+                   include_invalid = NULL,
+                   vocab_release = NULL,
+                   relationship_ids = NULL,
+                   page = 1,
+                   page_size = 100) {
       concept_id <- validate_concept_id(concept_id)
+      pag <- validate_pagination(page, page_size, max_page_size = 200)
 
-      params <- list()
+      params <- list(
+        page = pag$page,
+        page_size = pag$page_size
+      )
 
       if (!is.null(target_vocabulary)) {
         checkmate::assert_string(target_vocabulary, min.chars = 1)
         params$target_vocabulary <- target_vocabulary
       }
-      if (isTRUE(include_invalid)) {
-        params$include_invalid <- "true"
+      if (!is.null(relationship_ids)) {
+        checkmate::assert_character(
+          relationship_ids,
+          min.len = 1,
+          any.missing = FALSE
+        )
+        params$relationship_ids <- paste(relationship_ids, collapse = ",")
+      }
+      # Tri-state, not a flag. This endpoint defaults to *including* deprecated
+      # mappings, so omitting the parameter and sending "false" are different
+      # requests -- dropping a FALSE would silently return the rows the caller
+      # asked to exclude.
+      if (!is.null(include_invalid)) {
+        checkmate::assert_flag(include_invalid)
+        params$include_invalid <- if (include_invalid) "true" else "false"
       }
       if (!is.null(vocab_release)) {
         checkmate::assert_string(vocab_release, min.chars = 1)
         params$vocab_release <- vocab_release
       }
 
-      perform_get(
+      result <- perform_get(
         private$.base_req,
         paste0("concepts/", concept_id, "/mappings"),
-        query = if (length(params) > 0) params else NULL
+        query = params
+      )
+
+      private$.with_pagination(result)
+    },
+
+    #' @description
+    #' Get every mapping for a concept, walking all pages.
+    #'
+    #' Prefer this over `get()` when assembling a code list — `get()` returns
+    #' a single page, and a partial code list is wrong in a way nothing in
+    #' the result reveals.
+    #'
+    #' @param concept_id The concept ID.
+    #' @param target_vocabulary Filter to a specific target vocabulary (e.g., "ICD10CM").
+    #' @param include_invalid Whether to return deprecated mappings. Same
+    #'   semantics as `$get()`, including the include-by-default behaviour.
+    #' @param vocab_release Specific vocabulary release version (e.g., "2025.1"). Default `NULL`.
+    #' @param relationship_ids Relationship types to return. Same semantics as
+    #'   `$get()` -- see there for the Value-as-Concept case.
+    #' @param page_size Mappings fetched per request. Default 100, maximum 200.
+    #' @param max_pages Maximum pages to fetch. Default `Inf`.
+    #' @param progress Show progress bar. Default `TRUE`.
+    #'
+    #' @returns A tibble of all mappings for the concept.
+    get_all = function(concept_id,
+                       target_vocabulary = NULL,
+                       include_invalid = NULL,
+                       vocab_release = NULL,
+                       relationship_ids = NULL,
+                       page_size = 100,
+                       max_pages = Inf,
+                       progress = TRUE) {
+      concept_id <- validate_concept_id(concept_id)
+
+      fetch_fn <- function(page, size) {
+        result <- self$get(
+          concept_id,
+          target_vocabulary = target_vocabulary,
+          relationship_ids = relationship_ids,
+          include_invalid = include_invalid,
+          page = page,
+          page_size = size,
+          vocab_release = vocab_release
+        )
+        list(
+          data = result$mappings %||% list(),
+          meta = attr(result, "pagination") %||% list()
+        )
+      }
+
+      paginate_all(
+        fetch_fn,
+        page_size = page_size,
+        max_pages = max_pages,
+        progress = progress
       )
     },
 
@@ -120,11 +213,31 @@ MappingsResource <- R6::R6Class(
     #' Print resource information.
     print = function() {
       cat("<OMOPHub MappingsResource>\n")
-      cat("  Methods: get, map\n")
+      cat("  Methods: get, get_all, map\n")
       invisible(self)
     }
   ),
   private = list(
-    .base_req = NULL
+    .base_req = NULL,
+
+    # Keep get()'s return shape stable across the API gaining pagination.
+    #
+    # perform_get() switches shape based on the response: without
+    # meta.pagination it unwraps to body$data (so `result$mappings` works),
+    # with it, it returns list(data = <body$data>, meta = <pagination>). When
+    # GET /concepts/{id}/mappings became paginated on 2026-08-04 that flipped
+    # this method's result out from under existing callers — `result$mappings`
+    # started returning NULL against an unchanged SDK, with no error.
+    #
+    # So unwrap back to the documented shape and carry the pagination as an
+    # attribute, which adds the new information without moving the old.
+    .with_pagination = function(result) {
+      if (is.list(result) && !is.null(result$data) && !is.null(result$meta)) {
+        out <- result$data
+        attr(out, "pagination") <- result$meta
+        return(out)
+      }
+      result
+    }
   )
 )

README.md

@@ -75,8 +75,10 @@ results$data
 # Get concept by vocabulary code
 snomed_concept <- client$concepts$get_by_code("SNOMED", "44054006")
 
-# Map to another vocabulary
-mappings <- client$mappings$get(201826, target_vocabulary = "ICD10CM")
+# Map to another vocabulary. `Maps to` points at *standard* concepts, so
+# SNOMED -> ICD10CM returns nothing; look the code up and map it instead.
+icd <- client$concepts$get_by_code("ICD10CM", "E11.9")
+mappings <- client$mappings$get(icd$concept_id, target_vocabulary = "SNOMED")
 
 # Navigate hierarchy
 ancestors <- client$hierarchy$ancestors(201826, max_levels = 3)
@@ -391,7 +393,7 @@ concepts_df %>%
 | `concepts` | Concept lookup and batch operations | `get()`, `get_by_code()`, `batch()`, `suggest()` |
 | `search` | Full-text and semantic search | `basic()`, `advanced()`, `semantic()`, `similar()`, `bulk_basic()`, `bulk_semantic()` |
 | `hierarchy` | Navigate concept relationships | `ancestors()`, `descendants()` |
-| `mappings` | Cross-vocabulary mappings | `get()`, `map()` |
+| `mappings` | Cross-vocabulary mappings | `get()`, `get_all()`, `map()` |
 | `vocabularies` | Vocabulary metadata | `list()`, `get()`, `stats()` |
 | `domains` | Domain information | `list()`, `get()`, `concepts()` |
 | `fhir` | FHIR-to-OMOP resolution | `resolve()`, `resolve_batch()`, `resolve_codeable_concept()` |