# tests/testthat/test-pca-analysis.R
test_that("perform_mea_pca redirects to pca_analysis_enhanced with helpful message", {
  expect_error(
    perform_mea_pca(data.frame(), variables = NULL),
    regexp = "pca_analysis_enhanced"
  )
})

test_that("null_coalesce is not redefined inside pca_analysis_enhanced body", {
  fn_body <- deparse(body(pca_analysis_enhanced))
  local_def <- any(grepl("null_coalesce\\s*<-\\s*function", fn_body))
  expect_false(local_def,
    info = "null_coalesce should not be locally redefined inside pca_analysis_enhanced")
})

test_that("pca_analysis_enhanced loads from raw_data sheet when normalized_data missing", {
  skip_if_not_installed("writexl")
  skip_if_not_installed("readxl")

  # Build minimal long-format data
  fake_data <- data.frame(
    Variable = rep(paste0("V", 1:5), 2),
    Sample   = rep(c("S1", "S2"), each = 5),
    Value    = rnorm(10),
    stringsAsFactors = FALSE
  )

  tmp <- tempfile(fileext = ".xlsx")
  writexl::write_xlsx(list(raw_data = fake_data), path = tmp)

  # Should NOT throw a scoping-related error
  expect_no_error({
    result <- pca_analysis_enhanced(
      data_path       = tmp,
      value_column    = "Value",
      variable_column = "Variable",
      verbose         = FALSE
    )
  })
  unlink(tmp)
})

# -- trajectory color_by tests ──────────────────────────────────────────────

make_mini_pca <- function() {
  plot_data <- data.frame(
    PC1        = c(-1, 0, 1, -0.8, 0.2, 1.2),
    PC2        = c(-1, 0, 1,  0.8,-0.2,-1.2),
    Timepoint  = rep(c("0min","30min","60min"), 2),
    Treatment  = rep(c("PBS","KA"), each = 3),
    Genotype   = rep(c("WT","KO"), each = 3),
    Experiment = rep(c("Exp1","Exp2"), each = 3),
    stringsAsFactors = FALSE
  )
  list(plot_data = plot_data)
}

test_that("plot_pca_trajectories_general accepts color_by = 'Treatment'", {
  skip_if_not_installed("ggrepel")
  result <- plot_pca_trajectories_general(
    pca_results         = make_mini_pca(),
    trajectory_grouping = c("Treatment","Genotype"),
    color_by            = "Treatment",
    save_plots          = FALSE,
    verbose             = FALSE
  )
  expect_type(result, "list")
})

test_that("color_by = 'group' still works (backward compat)", {
  result <- plot_pca_trajectories_general(
    pca_results         = make_mini_pca(),
    trajectory_grouping = c("Treatment","Genotype"),
    color_by            = "group",
    save_plots          = FALSE,
    verbose             = FALSE
  )
  expect_type(result, "list")
})

test_that("combined averaged plot subtitle contains timepoints", {
  result <- plot_pca_trajectories_general(
    pca_results         = make_mini_pca(),
    trajectory_grouping = c("Treatment","Genotype"),
    save_plots          = FALSE,
    verbose             = FALSE
  )
  comb_avg <- result$plots$combined_average
  subtitle  <- comb_avg$labels$subtitle
  expect_true(!is.null(subtitle) && nchar(subtitle) > 0)
})