Added unit tests for utility, data loading, plot, and UI functions.

tests/testthat/test-data_helpers.R

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+## Tests for internal data helper functions
+
+# ── .normalize_results_root ──────────────────────────────────────────────────
+
+test_that(".normalize_results_root returns NULL for invalid inputs", {
+  expect_null(.normalize_results_root(NULL))
+  expect_null(.normalize_results_root(NA))
+  expect_null(.normalize_results_root(""))
+  expect_null(.normalize_results_root(character(0)))
+  # Multiple values
+  expect_null(.normalize_results_root(c("/a", "/b")))
+})
+
+test_that(".normalize_results_root normalizes a valid path", {
+  tmp <- tempdir()
+  result <- .normalize_results_root(tmp)
+  expect_type(result, "character")
+  expect_equal(nchar(result) > 0, TRUE)
+  # Should be an absolute path
+  expect_true(startsWith(result, "/") || grepl("^[A-Z]:", result))
+})
+
+# ── .read_parquet_safe ───────────────────────────────────────────────────────
+
+test_that(".read_parquet_safe returns empty tibble for missing file", {
+  result <- suppressMessages(
+    .read_parquet_safe("/nonexistent/path.parquet", verbose = FALSE)
+  )
+  expect_s3_class(result, "tbl_df")
+  expect_equal(nrow(result), 0)
+})
+
+test_that(".read_parquet_safe returns empty tibble for NULL path", {
+  result <- suppressMessages(
+    .read_parquet_safe(NULL, verbose = FALSE)
+  )
+  expect_s3_class(result, "tbl_df")
+  expect_equal(nrow(result), 0)
+})
+
+test_that(".read_parquet_safe reads a valid parquet file", {
+  extdata <- system.file("extdata", package = "amRshiny")
+  perf_files <- list.files(
+    extdata,
+    pattern = "_ML_perf\\.parquet$",
+    recursive = TRUE, full.names = TRUE
+  )
+  skip_if(length(perf_files) == 0, "No demo parquet files found")
+
+  result <- .read_parquet_safe(perf_files[1], verbose = FALSE)
+  expect_s3_class(result, "tbl_df")
+  expect_gt(nrow(result), 0)
+})

tests/testthat/test-data_loading.R

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+## Tests for data loading functions: loadMLResults, loadTopFeat,
+## listAmRmlSpeciesFolders, get_metadata_path, loadDrugClassMap
+
+# ── listAmRmlSpeciesFolders ──────────────────────────────────────────────────
+
+test_that("listAmRmlSpeciesFolders returns empty for NULL/invalid root", {
+  expect_equal(listAmRmlSpeciesFolders(NULL), character(0))
+  expect_equal(listAmRmlSpeciesFolders(""), character(0))
+  expect_equal(
+    listAmRmlSpeciesFolders("/nonexistent/path"),
+    character(0)
+  )
+})
+
+test_that("listAmRmlSpeciesFolders discovers species dirs in extdata", {
+  extdata <- system.file("extdata", package = "amRshiny")
+  skip_if(!nzchar(extdata), "No extdata directory found")
+
+  result <- listAmRmlSpeciesFolders(extdata, verbose = FALSE)
+  expect_type(result, "character")
+  expect_true(length(result) > 0)
+  expect_true(all(nzchar(names(result))))
+})
+
+test_that("listAmRmlSpeciesFolders ignores dirs without perf parquets", {
+  tmp <- tempfile("test_species_")
+  dir.create(tmp)
+  on.exit(unlink(tmp, recursive = TRUE))
+
+  empty_dir <- file.path(tmp, "Empty_species")
+  dir.create(empty_dir)
+
+  result <- listAmRmlSpeciesFolders(tmp, verbose = FALSE)
+  expect_equal(length(result), 0)
+})
+
+# ── loadMLResults ────────────────────────────────────────────────────────────
+
+test_that("loadMLResults returns empty tibble when results_root given but no species_dirs", {
+  tmp <- tempdir()
+  result <- suppressMessages(
+    loadMLResults(
+      results_root = tmp,
+      species_dirs = NULL,
+      verbose = FALSE
+    )
+  )
+  expect_s3_class(result, "tbl_df")
+  expect_equal(nrow(result), 0)
+})
+
+test_that("loadMLResults loads demo data in fallback mode", {
+  result <- suppressMessages(loadMLResults(verbose = FALSE))
+  expect_s3_class(result, "tbl_df")
+  expect_gt(nrow(result), 0)
+  expect_true("species" %in% names(result))
+})
+
+test_that("loadMLResults loads from specific species_dirs", {
+  extdata <- system.file("extdata", package = "amRshiny")
+  skip_if(!nzchar(extdata), "No extdata directory found")
+
+  folders <- listAmRmlSpeciesFolders(extdata, verbose = FALSE)
+  skip_if(
+    length(folders) == 0,
+    "No species dirs with baseline perf in extdata"
+  )
+
+  result <- suppressMessages(
+    loadMLResults(
+      results_root = extdata,
+      species_dirs = folders[1],
+      verbose = FALSE
+    )
+  )
+  expect_s3_class(result, "tbl_df")
+  expect_gt(nrow(result), 0)
+  expect_true("species_label" %in% names(result))
+})
+
+# ── loadTopFeat ──────────────────────────────────────────────────────────────
+
+test_that("loadTopFeat returns empty tibble when results_root given but no species_dirs", {
+  tmp <- tempdir()
+  result <- suppressMessages(
+    loadTopFeat(
+      results_root = tmp,
+      species_dirs = NULL,
+      verbose = FALSE
+    )
+  )
+  expect_s3_class(result, "tbl_df")
+  expect_equal(nrow(result), 0)
+})
+
+test_that("loadTopFeat loads demo data in fallback mode", {
+  result <- suppressMessages(loadTopFeat(verbose = FALSE))
+  expect_s3_class(result, "tbl_df")
+  expect_gt(nrow(result), 0)
+  expect_true("Variable" %in% names(result))
+  expect_true("Importance" %in% names(result))
+})
+
+# ── get_metadata_path ────────────────────────────────────────────────────────
+
+test_that("get_metadata_path returns NULL for nonexistent species code", {
+  result <- get_metadata_path("Zzz")
+  expect_null(result)
+})
+
+test_that("get_metadata_path finds demo metadata parquet", {
+  extdata <- system.file("extdata", package = "amRshiny")
+  skip_if(!nzchar(extdata), "No extdata directory found")
+
+  result <- get_metadata_path("Sfl")
+  if (!is.null(result)) {
+    expect_true(file.exists(result))
+    expect_true(grepl("Sfl_metadata\\.parquet$", result))
+  }
+})
+
+# ── loadDrugClassMap ─────────────────────────────────────────────────────────
+
+test_that("loadDrugClassMap returns a tibble with expected columns", {
+  result <- suppressMessages(loadDrugClassMap())
+  expect_s3_class(result, "tbl_df")
+  expect_true("drug.antibiotic_name" %in% names(result))
+  expect_true("drug_class" %in% names(result))
+  expect_gt(nrow(result), 0)
+})
+
+test_that("loadDrugClassMap returns distinct rows", {
+  result <- suppressMessages(loadDrugClassMap())
+  expect_equal(nrow(result), nrow(dplyr::distinct(result)))
+})

tests/testthat/test-getHoldoutsDrugChoices.R

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+## Tests for getHoldoutsDrugChoices
+
+test_that("getHoldoutsDrugChoices returns empty for NULL input", {
+  expect_equal(getHoldoutsDrugChoices(NULL), character(0))
+})
+
+test_that("getHoldoutsDrugChoices returns empty for empty data frame", {
+  expect_equal(getHoldoutsDrugChoices(data.frame()), character(0))
+})
+
+test_that("getHoldoutsDrugChoices returns empty for zero-row tibble", {
+  df <- tibble::tibble(
+    strat_label = character(0),
+    drug_or_class = character(0),
+    species = character(0)
+  )
+  expect_equal(getHoldoutsDrugChoices(df), character(0))
+})
+
+test_that("getHoldoutsDrugChoices filters to stratified rows only", {
+  df <- tibble::tibble(
+    strat_label = c(NA_character_, "", "country", "year"),
+    drug_or_class = c(
+      "amoxicillin", "ampicillin",
+      "ciprofloxacin", "tetracycline"
+    ),
+    species = c("Sau", "Sau", "Sau", "Sau")
+  )
+  result <- getHoldoutsDrugChoices(df)
+  expect_true("ciprofloxacin" %in% result)
+  expect_true("tetracycline" %in% result)
+  expect_false("amoxicillin" %in% result)
+  expect_false("ampicillin" %in% result)
+})
+
+test_that("getHoldoutsDrugChoices returns sorted unique values", {
+  df <- tibble::tibble(
+    strat_label = c("country", "country", "year"),
+    drug_or_class = c("tetracycline", "ampicillin", "tetracycline"),
+    species = c("Sau", "Sau", "Sau")
+  )
+  result <- getHoldoutsDrugChoices(df)
+  expect_equal(result, c("ampicillin", "tetracycline"))
+})
+
+test_that("getHoldoutsDrugChoices filters by bug when provided", {
+  df <- tibble::tibble(
+    strat_label = c("country", "country", "country"),
+    drug_or_class = c(
+      "ampicillin", "ciprofloxacin", "tetracycline"
+    ),
+    species = c("Sau", "Kpn", "Sau")
+  )
+  result <- getHoldoutsDrugChoices(df, bug = "Sau")
+  expect_true("ampicillin" %in% result)
+  expect_true("tetracycline" %in% result)
+  expect_false("ciprofloxacin" %in% result)
+})
+
+test_that("getHoldoutsDrugChoices normalizes species for comparison", {
+  df <- tibble::tibble(
+    strat_label = c("country", "country"),
+    drug_or_class = c("ampicillin", "ciprofloxacin"),
+    species = c("Esp.", "Esp")
+  )
+  result <- getHoldoutsDrugChoices(df, bug = "Esp.")
+  expect_length(result, 2)
+})
+
+test_that("getHoldoutsDrugChoices excludes NA and blank drug_or_class", {
+  df <- tibble::tibble(
+    strat_label = c("country", "country", "country"),
+    drug_or_class = c("ampicillin", NA_character_, "  "),
+    species = c("Sau", "Sau", "Sau")
+  )
+  result <- getHoldoutsDrugChoices(df)
+  expect_equal(result, "ampicillin")
+})

tests/testthat/test-makeFeatureImportTable.R

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+## Tests for makeFeatureImportTable
+
+test_that("makeFeatureImportTable returns datatable for NULL input", {
+  result <- makeFeatureImportTable(NULL)
+  expect_s3_class(result, "datatables")
+})
+
+test_that("makeFeatureImportTable returns datatable for empty data", {
+  df <- tibble::tibble()
+  result <- makeFeatureImportTable(df)
+  expect_s3_class(result, "datatables")
+})
+
+test_that("makeFeatureImportTable formats numeric columns to scientific notation", {
+  df <- tibble::tibble(
+    species = c("Sau", "Kpn"),
+    drug_or_class = c("ampicillin", "tetracycline"),
+    Variable = c("gene1", "gene2"),
+    Importance = c(0.00123, 0.456)
+  )
+
+  result <- makeFeatureImportTable(df)
+  expect_s3_class(result, "datatables")
+})
+
+test_that("makeFeatureImportTable reorders columns by priority", {
+  df <- tibble::tibble(
+    Variable = c("gene1"),
+    Importance = c(0.5),
+    species = c("Sau"),
+    drug_or_class = c("ampicillin"),
+    feature_type = c("genes"),
+    feature_subtype = c("binary")
+  )
+
+  result <- makeFeatureImportTable(df)
+  expect_s3_class(result, "datatables")
+})
+
+test_that("makeFeatureImportTable adds hyperlinks for accession column", {
+  df <- tibble::tibble(
+    species = c("Sau"),
+    drug_or_class = c("ampicillin"),
+    accession = c("WP_001234567.1"),
+    Importance = c(0.5)
+  )
+
+  result <- makeFeatureImportTable(df)
+  expect_s3_class(result, "datatables")
+  expect_true(any(grepl("href", unlist(result$x$data))))
+})
+
+test_that("makeFeatureImportTable adds hyperlinks for COG_name column", {
+  df <- tibble::tibble(
+    species = c("Sau"),
+    drug_or_class = c("ampicillin"),
+    COG_name = c("COG0001"),
+    Importance = c(0.5)
+  )
+
+  result <- makeFeatureImportTable(df)
+  expect_s3_class(result, "datatables")
+  expect_true(any(grepl("href", unlist(result$x$data))))
+})
+
+test_that("makeFeatureImportTable replaces non-ARG in ARG_name column", {
+  df <- tibble::tibble(
+    species = c("Sau", "Sau"),
+    drug_or_class = c("ampicillin", "tetracycline"),
+    ARG_name = c("non-ARG", "blaOXA-1"),
+    Importance = c(0.5, 0.8)
+  )
+
+  result <- makeFeatureImportTable(df)
+  expect_s3_class(result, "datatables")
+})

tests/testthat/test-makeQuickStats.R

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+## Tests for makeQuickStats
+
+test_that("makeQuickStats returns a tagList with expected structure", {
+  df <- tibble::tibble(
+    genome_drug.genome_id = c("G1", "G1", "G2", "G3"),
+    genome_drug.antibiotic = c(
+      "ampicillin", "tetracycline",
+      "ampicillin", "ciprofloxacin"
+    ),
+    genome_drug.resistant_phenotype = c(
+      "Resistant", "Susceptible",
+      "Resistant", "Susceptible"
+    ),
+    drug_class = c(
+      "penicillins", "tetracyclines",
+      "penicillins", "fluoroquinolones"
+    ),
+    genome.isolation_country = c("USA", "UK", "USA", "Germany"),
+    species = c(
+      "staphylococcus aureus", "staphylococcus aureus",
+      "staphylococcus aureus", "staphylococcus aureus"
+    )
+  )
+
+  result <- makeQuickStats(df)
+  expect_s3_class(result, "shiny.tag.list")
+})
+
+test_that("makeQuickStats handles single-row data", {
+  df <- tibble::tibble(
+    genome_drug.genome_id = "G1",
+    genome_drug.antibiotic = "ampicillin",
+    genome_drug.resistant_phenotype = "Resistant",
+    drug_class = "penicillins",
+    genome.isolation_country = "USA",
+    species = "staphylococcus aureus"
+  )
+
+  result <- makeQuickStats(df)
+  expect_s3_class(result, "shiny.tag.list")
+})