# Example data for testing
example_counts <- matrix(1:20, nrow = 4, ncol = 5)
example_pg_ids <- data.frame(id = 1:4)
example_sample_metadata <- data.frame(id = 1:5, replicate = factor(c(1, 1, 2, 2, 3)), timepoint = factor(c("T0", "T0", "T1", "T1", "T2")))

# Test elements inside output list
test_that("setup_data() works correctly", {
  testthat::skip_on_cran()
  result <- setup_data(
    counts = example_counts,
    pg_ids = example_pg_ids,
    sample_metadata = example_sample_metadata
  )

  expect_s3_class(result, "gimap_dataset")
  expect_equal(result$raw_counts, example_counts)
  expect_equal(result$metadata$pg_ids, example_pg_ids)
  expect_equal(result$metadata$sample_metadata, example_sample_metadata)
  expect_equal(result$counts_per_sample, apply(example_counts, 2, sum))


  counts_timepoint <- get_example_data("count")
  counts_treatment <- get_example_data("count_treatment")
  gimap_dataset <- get_example_data("gimap")
  gimap_dataset <- get_example_data("gimap_treatment")
  metadata <- get_example_data("meta")
  annotation <- get_example_data("annotation")

  data_dir <- system.file("extdata", package = "gimap")

  expect_true(file.exists(file.path(data_dir, "PP_pgPEN_HeLa_counts.txt")))
  expect_true(file.exists(file.path(data_dir, "counts_pgPEN_PC9_example.tsv")))
  expect_true(file.exists(file.path(data_dir, "pgRNA_ID_pgPEN_library_comp.csv")))
  expect_true(file.exists(file.path(data_dir, "gimap_dataset_timepoint.RDS")))
  expect_true(file.exists(file.path(data_dir, "gimap_dataset_treatment.RDS")))
  expect_true(file.exists(file.path(data_dir, "pgPEN_annotations.txt")))
})