Fixed control flow bugs : three bugs in how the ML pipeline finds and validates its input files

R/run_ML.R

@@ -201,9 +201,17 @@ createMLinputList <- function(path,
 
   path <- normalizePath(path)
 
-#  if (isTRUE(LOO) && (is.null(stratify_by) || !(stratify_by %in% c("year", "country")))) {
- #   stop("For Leave-One-Out (LOO) models, stratify_by must be 'year' or 'country'.")
- # }
+  # Leave-one-drug-out cross-testing (LOO + cross_test) is a separate mode
+  # that doesn't stratify by year/country - see the `cross_test && LOO`
+  # branch below. Stratified LOO (leave-one-year/country-out) always needs
+  # stratify_by, whether or not it's also cross-tested.
+  if (isTRUE(LOO) && !isTRUE(cross_test) &&
+    (is.null(stratify_by) || !(stratify_by %in% c("year", "country")))) {
+    stop(
+      "For Leave-One-Out (LOO) models without cross-testing, ",
+      "stratify_by must be 'year' or 'country'."
+    )
+  }
 
   if (isTRUE(MDR) && (!is.null(stratify_by) || LOO || cross_test)) {
     stop("MDR can only run when stratify_by = NULL, LOO = FALSE, cross_test = FALSE.")
@@ -579,7 +587,9 @@ parsed_drugs <- parsed |>
     out_top     = paths$ML_top_features,
     out_models  = paths$ML_models,
     out_pred    = paths$ML_prediction
-  ) 
+  )
+
+            return(out)
             }
       # LOO requires special directory structure resolution
       test_path <- file.path(path, stringr::str_remove(basename(paths$matrix_path), "^LOO_"))
@@ -1002,7 +1012,12 @@ runMLmodels <- function(path,
     MDR         = FALSE,
     cross_test  = cross_test
   )
-
+
+  if (nrow(files) == 0) {
+    message("No files found to process. Exiting.")
+    return(invisible(NULL))
+  }
+
 .findNonRanPrefixes <- function(files,
                                 seed,
                                 shuffle_labels = FALSE) {

tests/testthat/test-run-ml-models.R

@@ -0,0 +1,58 @@
+# Regression tests for control-flow bugs in
+# createMLinputList()/runMLmodels().
+
+test_that("runMLmodels() exits cleanly instead of crashing on no files", {
+  tmp <- withr::local_tempdir()
+  # No matrix parquet files are created, so createMLinputList() returns an
+  # empty tibble. runMLmodels() must message and return early instead of
+  # trying to use the empty result (which previously crashed with
+  # "a character vector argument expected").
+  result <- NULL
+  expect_message(
+    result <- runMLmodels(
+      path = tmp, stratify_by = NULL, LOO = FALSE, cross_test = FALSE
+    ),
+    "No files found"
+  )
+  expect_null(result)
+})
+
+test_that("createMLinputList() rejects LOO w/o year/country (no cross-test)", {
+  tmp <- withr::local_tempdir()
+  expect_error(
+    createMLinputList(tmp, LOO = TRUE, cross_test = FALSE, stratify_by = NULL),
+    "stratify_by must be"
+  )
+})
+
+test_that("createMLinputList() allows LOO+cross-test with stratify_by = NULL", {
+  # LOO + cross_test with stratify_by = NULL is a distinct mode
+  # (leave-one-drug-out cross-testing, "Case A" in the cross_test && LOO
+  # branch) and is intentionally exempt from the year/country requirement
+  # above.
+  tmp <- withr::local_tempdir()
+  paths <- createMLResultDir(
+    tmp,
+    stratify_by = NULL, LOO = TRUE, cross_test = TRUE, MDR = FALSE
+  )
+
+  # A single matrix filename that satisfies both the general filename parser
+  # and the LOO-specific parser used inside Case A. File content is
+  # irrelevant - createMLinputList() only inspects filenames.
+  file.create(file.path(
+    paths$matrix_path,
+    "Csp_drug_leaveout_leaveout_genes_binary_sparse.parquet"
+  ))
+
+  out <- createMLinputList(
+    tmp,
+    stratify_by = NULL, LOO = TRUE, cross_test = TRUE, MDR = FALSE
+  )
+
+  # Before the return() fix, Case A built the right result but never
+  # returned it, so execution fell through into the stratify_by != NULL
+  # branch, which self-joins the single file against itself and always
+  # filters it out (ref_file != test_file), silently returning 0 rows.
+  expect_equal(nrow(out), 1)
+  expect_true(grepl("_drug_leaveout_", out$output_prefix))
+})