Merge pull request #129 from pharmaverse/122_increase_test_supp

Closes #122 increase test supp

Author: LiamHobby

tests/testthat/test-supp.R

@@ -300,6 +300,91 @@ test_that("combine_supp() does not create an IDVARVAL column (#78)", {
   expect_false("IDVARVAL" %in% names(noidvarval))
 })
 
+test_that("make_supp_qual handles deprecated dataset_name parameter", {
+  load(metacore::metacore_example("pilot_SDTM.rda"))
+  ae <- combine_supp(safetyData::sdtm_ae, safetyData::sdtm_suppae)
+
+  # Test that dataset_name is deprecated and shows guidance
+  suppressWarnings({
+    result <- make_supp_qual(ae, metacore, dataset_name = "AE")
+  })
+
+  expect_s3_class(result, "data.frame")
+})
+
+test_that("combine_supp handles QNAM not in dataset columns", {
+  simple_ae <- safetyData::sdtm_ae[1:5, ]
+  simple_suppae <- safetyData::sdtm_suppae[1, ]
+  simple_suppae$QNAM <- "NEWCOL" # A new column to add
+
+  # Should successfully add the new column
+  result <- combine_supp(simple_ae, simple_suppae)
+  expect_true("NEWCOL" %in% names(result))
+})
+
+test_that("combine_supp errors when QNAM already exists in dataset", {
+  simple_ae <- safetyData::sdtm_ae[1:5, ]
+  simple_ae$AETRTEM <- "existing" # Add column that matches QNAM
+  simple_suppae <- safetyData::sdtm_suppae[1, ]
+
+  expect_error(
+    combine_supp(simple_ae, simple_suppae),
+    "already in the original dataset"
+  )
+})
+
+test_that("combine_supp handles IDVAR not in dataset", {
+  simple_ae <- safetyData::sdtm_ae[1:5, ]
+  simple_suppae <- safetyData::sdtm_suppae[1, ]
+  simple_suppae$IDVAR <- "FAKEIDVAR" # IDVAR that doesn't exist
+
+  expect_error(
+    combine_supp(simple_ae, simple_suppae),
+    "replacement has 0 rows"
+  )
+})
+
+test_that("combine_supp_by_idvar detects conflicting replacements across IDVARs", {
+  simple_ae <- safetyData::sdtm_ae %>%
+    filter(USUBJID %in% c("01-701-1015", "01-701-1023")) %>%
+    mutate(NEWID = dplyr::row_number())
+
+  # Create supp with same QNAM but different IDVARs that would cause conflicts
+  suppae_conflict <- bind_rows(
+    data.frame(
+      STUDYID = "CDISCPILOT01",
+      RDOMAIN = "AE",
+      USUBJID = "01-701-1015",
+      IDVAR = "AESEQ",
+      IDVARVAL = "1",
+      QNAM = "TESTVAR",
+      QLABEL = "Test Variable",
+      QVAL = "ValueA",
+      QORIG = "CRF",
+      QEVAL = "",
+      stringsAsFactors = FALSE
+    ),
+    data.frame(
+      STUDYID = "CDISCPILOT01",
+      RDOMAIN = "AE",
+      USUBJID = "01-701-1015",
+      IDVAR = "NEWID",
+      IDVARVAL = "1",
+      QNAM = "TESTVAR",
+      QLABEL = "Test Variable",
+      QVAL = "ValueB", # Different value for same subject/QNAM
+      QORIG = "CRF",
+      QEVAL = "",
+      stringsAsFactors = FALSE
+    )
+  )
+
+  expect_error(
+    combine_supp(simple_ae, suppae_conflict),
+    "unexpected number of rows"
+  )
+})
+
 test_that("combine_supp: all SUPP rows merge cleanly (#98)", {
   pc <- tibble::tibble(
     STUDYID = "STUDY123",