tests/testthat/test-ifcb_summarize_biovolumes.R

In iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

# Define paths to the test data
test_data_zip <- test_path("test_data/test_data.zip")
temp_dir <- file.path(tempdir(), "ifcb_summarize_biovolumes")
unzip(test_data_zip, exdir = temp_dir)

feature_folder <- file.path(temp_dir, "test_data", "features")
class_folder <- file.path(temp_dir, "test_data", "class", "class2022_v1")
hdr_folder <- file.path(temp_dir, "test_data", "data")
manual_folder <- file.path(temp_dir, "test_data", "manual")

test_that("ifcb_summarize_biovolumes works correctly", {

  # Call the function with the test data
  result <- ifcb_summarize_biovolumes(feature_folder, class_folder, hdr_folder = hdr_folder)

  # Check if the result is a data frame
  expect_s3_class(result, "data.frame")

  # Check if the result contains the expected columns
  expected_columns <- c("sample", "class", "counts", "biovolume_mm3", "carbon_ug", "ml_analyzed",
                        "counts_per_liter", "biovolume_mm3_per_liter", "carbon_ug_per_liter")
  expect_true(all(expected_columns %in% colnames(result)))

  # Check if the result contains the correct number of rows (adjust this based on your expected output)
  expected_rows <- 1
  expect_equal(nrow(result), expected_rows)

  # Check if the result contains non-NA values in key columns
  expect_true(all(!is.na(result$biovolume_mm3)))
  expect_true(all(!is.na(result$carbon_ug)))
  expect_true(all(!is.na(result$ml_analyzed)))
  expect_true(all(!is.na(result$biovolume_mm3_per_liter)))
  expect_true(all(!is.na(result$carbon_ug_per_liter)))

  # Check if the result values are within expected ranges (adjust based on your expected output)
  expect_equal(result$biovolume_mm3, 1.224387e-05, tolerance = 1e-7)
  expect_equal(result$carbon_ug, 0.001554673, tolerance = 1e-6)
  expect_equal(result$ml_analyzed, 2.9812723)
  expect_equal(result$biovolume_mm3_per_liter, 0.004106928)
  expect_equal(result$carbon_ug_per_liter, 0.52147962)
})

test_that("ifcb_summarize_biovolumes handles empty directories gracefully", {

  temp_dir <- file.path(tempdir(), "ifcb_summarize_biovolumes")

  # Create empty directories
  feature_folder <- file.path(temp_dir, "empty_features")
  mat_folder <- file.path(temp_dir, "empty_mat")
  hdr_folder <- file.path(temp_dir, "empty_hdr")
  dir.create(feature_folder, showWarnings = FALSE)
  dir.create(mat_folder, showWarnings = FALSE)
  dir.create(hdr_folder, showWarnings = FALSE)

  expect_error(ifcb_summarize_biovolumes(feature_folder, mat_folder, hdr_folder = hdr_folder),
               "No MAT files found")
})

test_that("ifcb_summarize_biovolumes works correctly with custom class data", {

  # Define custom list
  classes = c("Mesodinium_rubrum", "Mesodinium_rubrum")
  images <- c("D20220522T003051_IFCB134_00002", "D20220522T003051_IFCB134_00003")

  # Call the function with the test data
  result <- ifcb_summarize_biovolumes(feature_folder,
                                      hdr_folder = hdr_folder,
                                      custom_images = images,
                                      custom_classes = classes)

  # Check if the result is a data frame
  expect_s3_class(result, "data.frame")

  # Check if the result contains the expected columns
  expected_columns <- c("sample", "class", "counts", "biovolume_mm3", "carbon_ug", "ml_analyzed",
                        "counts_per_liter", "biovolume_mm3_per_liter", "carbon_ug_per_liter")
  expect_true(all(expected_columns %in% colnames(result)))

  # Check if the result contains the correct number of rows (adjust this based on your expected output)
  expected_rows <- 1
  expect_equal(nrow(result), expected_rows)

  # Check if the result contains non-NA values in key columns
  expect_true(all(!is.na(result$biovolume_mm3)))
  expect_true(all(!is.na(result$carbon_ug)))
  expect_true(all(!is.na(result$ml_analyzed)))
  expect_true(all(!is.na(result$biovolume_mm3_per_liter)))
  expect_true(all(!is.na(result$carbon_ug_per_liter)))
  expect_true(all(is.na(result$classifier)))

  # Check if the result values are within expected ranges (adjust based on your expected output)
  expect_equal(result$biovolume_mm3, 1.224387e-05, tolerance = 1e-7)
  expect_equal(result$carbon_ug, 0.001554673, tolerance = 1e-6)
  expect_equal(result$ml_analyzed, 2.9812723)
  expect_equal(result$biovolume_mm3_per_liter, 0.004106928)
  expect_equal(result$carbon_ug_per_liter, 0.52147962)
})

test_that("ifcb_summarize_biovolumes handles no class2use file gracefully", {

  expect_error(ifcb_summarize_biovolumes(feature_folder, manual_folder, hdr_folder = hdr_folder),
               "class2use must be specified when extracting manual biovolume data")

  # Cleanup temporary files
  unlink(temp_dir, recursive = TRUE)
})