closes #98 updated combine_supp_join() to return a message when all…

R/supp.R

@@ -278,20 +278,22 @@ combine_supp_join <- function(dataset, supp) {
 
     # Add message for when there are rows in the supp that didn't get merged
     if (nrow(missing) > 0) {
-      missing_txt <-
-        capture.output(
-          missing %>%
-            select(USUBJID, all_of(current_idvar)) %>%
-            print()
-        ) %>%
-        paste0(collapse = "\n")
-      stop(
-        paste0(
-          "Not all rows of the Supp were merged. The following rows are missing:\n",
-          missing_txt
-        ),
-        call. = FALSE
-      )
+      missing_display <- missing %>%
+        dplyr::transmute(
+          USUBJID,
+          !!current_idvar := IDVARVAL
+        )
+      msg <- "Not all rows of SUPP were merged."
+      cli::cli_alert_warning(msg)
+
+      cli::cli_text("")
+      cli::cli_text("The following rows are missing:")
+      cli::cli_rule()
+
+      print(missing_display)
+
+      cli::cli_rule()
+      warning(msg, call. = FALSE)
     }
 
     # join the data

tests/testthat/test-supp.R

@@ -220,14 +220,18 @@ test_that("combine_supp works with without QEVAL", {
   expect_silent(combine_supp(pharmaversesdtm::tr_onco, pharmaversesdtm::supptr_onco))
 })
 
-test_that("supp data that does not match the main data will raise a warning", {
+test_that("supp data that does not match the main data will raise a warning but return a dataset", {
   sdtm_suppae_extra <- safetyData::sdtm_suppae
   sdtm_suppae_extra$IDVARVAL[1] <- 99
-  expect_error(
-    combine_supp(safetyData::sdtm_ae, sdtm_suppae_extra)
+
+  expect_warning(
+    out <- combine_supp(safetyData::sdtm_ae, sdtm_suppae_extra),
+    "Not all rows of SUPP were merged"
   )
+  expect_s3_class(out, "data.frame")
 })
 
+
 test_that("Floating point correction works", {
   fp1 <- 0.1 + 0.1 + 0.1 + 0.1 + 0.1 + 0.1 + 0.1 + 0.1 + 0.1 + 0.1
   sdtm_ae_fp <- safetyData::sdtm_ae %>%
@@ -296,6 +300,105 @@ test_that("combine_supp() does not create an IDVARVAL column (#78)", {
   expect_false("IDVARVAL" %in% names(noidvarval))
 })
 
+test_that("combine_supp: all SUPP rows merge cleanly (#98)", {
+  pc <- tibble::tibble(
+    STUDYID = "STUDY123",
+    DOMAIN = "PC",
+    USUBJID = c("01-001", "01-002", "01-003"),
+    PCSEQ = c(1, 2, 3),
+    PCTESTCD = "CONC",
+    PCTEST = "Concentration",
+    PCORRES = c("5.1", "7.3", "4.8"),
+    PCORRESU = "ng/mL",
+    PCSTRESC = c("5.1", "7.3", "4.8"),
+    PCSTRESN = c(5.1, 7.3, 4.8),
+    PCSTRESU = "ng/mL",
+    PCPOS = "PLASMA",
+    PCDTC = c("2025-07-15T08:00", "2025-07-15T09:00", "2025-07-15T10:00"),
+    VISITNUM = 1,
+    VISIT = "Visit 1",
+    ARM = "Drug A",
+    ACTARM = "Drug A"
+  )
+
+  supppc <- tibble::tibble(
+    STUDYID  = "STUDY123",
+    RDOMAIN  = "PC",
+    USUBJID  = c("01-001", "01-002", "01-003"),
+    IDVAR    = "PCSEQ",
+    IDVARVAL = c(1, 2, 3),
+    QNAM     = "PCREASND",
+    QLABEL   = "Reason Not Done",
+    QVAL     = c("NA", "NA", "NA"),
+    QORIG    = "SPONSOR",
+    QEVAL    = "INVESTIGATOR"
+  )
+  expect_no_warning(
+    out <- combine_supp(pc, supppc)
+  )
+
+  expect_s3_class(out, "data.frame")
+  expect_equal(nrow(out), nrow(pc))
+  expect_true("PCREASND" %in% names(out))
+  expect_equal(
+    unname(as.character(out$PCREASND)),
+    c("NA", "NA", "NA")
+  )
+})
+
+test_that("combine_supp: extra SUPP rows that do not match core raise a warning but return a dataset(#98)", {
+  pc <- tibble::tibble(
+    STUDYID = "STUDY123",
+    DOMAIN = "PC",
+    USUBJID = c("01-001", "01-002", "01-003"),
+    PCSEQ = c(1, 2, 3),
+    PCTESTCD = "CONC",
+    PCTEST = "Concentration",
+    PCORRES = c("5.1", "7.3", "4.8"),
+    PCORRESU = "ng/mL",
+    PCSTRESC = c("5.1", "7.3", "4.8"),
+    PCSTRESN = c(5.1, 7.3, 4.8),
+    PCSTRESU = "ng/mL",
+    PCPOS = "PLASMA",
+    PCDTC = c("2025-07-15T08:00", "2025-07-15T09:00", "2025-07-15T10:00"),
+    VISITNUM = 1,
+    VISIT = "Visit 1",
+    ARM = "Drug A",
+    ACTARM = "Drug A"
+  )
+
+  supppc <- tibble::tibble(
+    STUDYID  = "STUDY123",
+    RDOMAIN  = "PC",
+    USUBJID  = c("01-001", "01-002", "01-003"),
+    IDVAR    = "PCSEQ",
+    IDVARVAL = c(1, 2, 3),
+    QNAM     = "PCREASND",
+    QLABEL   = "Reason Not Done",
+    QVAL     = c("NA", "NA", "NA"),
+    QORIG    = "SPONSOR",
+    QEVAL    = "INVESTIGATOR"
+  )
+  supppc_extra <- dplyr::bind_rows(
+    supppc,
+    dplyr::mutate(supppc[3, ], IDVARVAL = 99),
+    dplyr::mutate(supppc[3, ], IDVARVAL = 101)
+  )
+
+  expect_warning(
+    out <- combine_supp(pc, supppc_extra),
+    "Not all rows of SUPP were merged"
+  )
+  expect_s3_class(out, "data.frame")
+  expect_equal(nrow(out), nrow(pc))
+  expect_true("PCREASND" %in% names(out))
+  expect_equal(
+    unname(as.character(out$PCREASND)),
+    c("NA", "NA", "NA")
+  )
+  expect_false(any(out$PCSEQ %in% c(99, 101)))
+})
+
 test_that("build_qnam verbose parameter", {
   # Create simple test data with a column that will be used as QNAM
   ae <- safetyData::sdtm_ae %>%