# test-config.R - Test MTaP configuration
context("Configuration functions")

# Create test helper function
create_test_files <- function() {
  # Create temporary OTU table
  otu_temp <- tempfile(fileext = ".csv")
  otu_data <- data.frame(
    OTU_ID = c("OTU1", "OTU2", "OTU3"),
    Sample1 = c(10, 5, 3),
    Sample2 = c(15, 7, 2)
  )
  write.csv(otu_data, otu_temp, row.names = FALSE)
  
  # Create temporary taxonomy table
  tax_temp <- tempfile(fileext = ".csv")
  tax_data <- data.frame(
    OTU_ID = c("OTU1", "OTU2", "OTU3"),
    Kingdom = c("Bacteria", "Bacteria", "Bacteria"),
    Phylum = c("Firmicutes", "Bacteroidetes", "Proteobacteria"),
    Class = c("Clostridia", "Bacteroidia", "Gammaproteobacteria")
  )
  write.csv(tax_data, tax_temp, row.names = FALSE)
  
  return(list(otu_file = otu_temp, tax_file = tax_temp))
}

test_that("mtap_config creates valid configuration with required parameters", {
  # Create test files
  test_files <- create_test_files()
  
  # Test 1: Basic configuration
  config <- mtap_config(
    otu_file = test_files$otu_file,
    tax_file = test_files$tax_file
  )
  
  # Check class
  expect_s3_class(config, "mtap_config")
  expect_s3_class(config, "list")
  
  # Check structure
  expect_true(is.list(config))
  expect_named(config)
  
  # Check required fields
  expect_true("otu_file" %in% names(config))
  expect_true("tax_file" %in% names(config))
  expect_true("output_prefix" %in% names(config))
  expect_true("taxonomy_hierarchy" %in% names(config))
  
  # Check default values
  expect_equal(config$output_prefix, "mtap_result")
  expect_null(config$taxonomy_hierarchy)
  
  # Clean up
  unlink(test_files$otu_file)
  unlink(test_files$tax_file)
})

test_that("mtap_config handles custom output prefix and taxonomy hierarchy", {
  # Create test files
  test_files <- create_test_files()
  
  # Test 2: Custom output prefix
  config1 <- mtap_config(
    otu_file = test_files$otu_file,
    tax_file = test_files$tax_file,
    output_prefix = "my_analysis"
  )
  
  expect_equal(config1$output_prefix, "my_analysis")
  
  # Test 3: Custom taxonomy hierarchy
  config2 <- mtap_config(
    otu_file = test_files$otu_file,
    tax_file = test_files$tax_file,
    taxonomy_hierarchy = c("Phylum", "Class", "Order")
  )
  
  expect_equal(config2$taxonomy_hierarchy, c("Phylum", "Class", "Order"))
  
  # Test 4: Multiple parameters
  config3 <- mtap_config(
    otu_file = test_files$otu_file,
    tax_file = test_files$tax_file,
    output_prefix = "full_analysis",
    taxonomy_hierarchy = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus")
  )
  
  expect_equal(config3$output_prefix, "full_analysis")
  expect_equal(
    config3$taxonomy_hierarchy,
    c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus")
  )
  
  # Clean up
  unlink(test_files$otu_file)
  unlink(test_files$tax_file)
})

test_that("mtap_config handles additional parameters", {
  # Create test files
  test_files <- create_test_files()
  
  # Test 5: Additional parameters
  config <- mtap_config(
    otu_file = test_files$otu_file,
    tax_file = test_files$tax_file,
    threads = 4,
    verbose = TRUE,
    random_seed = 12345
  )
  
  # Check additional parameters
  expect_equal(config$threads, 4)
  expect_true(config$verbose)
  expect_equal(config$random_seed, 12345)
  
  # Clean up
  unlink(test_files$otu_file)
  unlink(test_files$tax_file)
})

test_that("mtap_config validates required parameters", {
  # Test 6: Missing required parameters
  expect_error(
    mtap_config(),
    "Both otu_file and tax_file parameters are required"
  )
  
  expect_error(
    mtap_config(otu_file = "otu.csv"),
    "Both otu_file and tax_file parameters are required"
  )
  
  expect_error(
    mtap_config(tax_file = "tax.csv"),
    "Both otu_file and tax_file parameters are required"
  )
  
  # Test 7: File path normalization
  test_files <- create_test_files()
  
  config <- mtap_config(
    otu_file = test_files$otu_file,
    tax_file = test_files$tax_file
  )
  
  # Check if paths are normalized
  expect_true(is.character(config$otu_file))
  expect_true(is.character(config$tax_file))
  
  # Clean up
  unlink(test_files$otu_file)
  unlink(test_files$tax_file)
})

test_that("print.mtap_config method works correctly", {
  # Create test files
  test_files <- create_test_files()
  
  config <- mtap_config(
    otu_file = test_files$otu_file,
    tax_file = test_files$tax_file,
    output_prefix = "test_print",
    taxonomy_hierarchy = c("Phylum", "Class")
  )
  
  # Test 8: Print method
  expect_output(
    print(config),
    "MTaP Analysis Configuration"
  )
  
  expect_output(
    print(config),
    "OTU table file:"
  )
  
  expect_output(
    print(config),
    "Taxonomy table file:"
  )
  
  expect_output(
    print(config),
    "Output prefix: test_print"
  )
  
  expect_output(
    print(config),
    "Taxonomy hierarchy: Phylum -> Class"
  )
  
  # Test 9: Print without taxonomy hierarchy
  config_no_hierarchy <- mtap_config(
    otu_file = test_files$otu_file,
    tax_file = test_files$tax_file
  )
  
  expect_output(
    print(config_no_hierarchy),
    "Taxonomy hierarchy: Auto-detection"
  )
  
  # Clean up
  unlink(test_files$otu_file)
  unlink(test_files$tax_file)
})

test_that("mtap_validate_config validates configuration correctly", {
  # Create test files
  test_files <- create_test_files()
  
  # Test 10: Valid configuration
  config <- mtap_config(
    otu_file = test_files$otu_file,
    tax_file = test_files$tax_file
  )
  
  # Core functionality test: function should return TRUE
  result <- suppressMessages(mtap_validate_config(config))
  expect_true(result)
  
  # Test 11: Invalid configuration object
  expect_error(
    mtap_validate_config(list(otu_file = "test.csv")),
    "config must be a mtap_config object"
  )
  
  # Test 12: Non-existent file
  config_bad <- mtap_config(
    otu_file = "/path/to/nonexistent/otu.csv",
    tax_file = test_files$tax_file
  )
  
  expect_error(
    mtap_validate_config(config_bad),
    "OTU table file does not exist"
  )
  
  # Test 13: Invalid output prefix
  config_invalid_prefix <- mtap_config(
    otu_file = test_files$otu_file,
    tax_file = test_files$tax_file,
    output_prefix = ""
  )
  
  expect_error(
    mtap_validate_config(config_invalid_prefix),
    "output_prefix must be a non-empty string"
  )
  
  # Test 14: Invalid taxonomy hierarchy
  config_invalid_hierarchy <- mtap_config(
    otu_file = test_files$otu_file,
    tax_file = test_files$tax_file,
    taxonomy_hierarchy = c("Phylum", "", "Class")
  )
  
  expect_error(
    mtap_validate_config(config_invalid_hierarchy),
    "taxonomy_hierarchy cannot contain empty strings"
  )
  
  # Clean up
  unlink(test_files$otu_file)
  unlink(test_files$tax_file)
})

test_that("mtap_config with sample data works", {
  ## Test 15: Using package example data
  otu_file <- system.file("extdata", "example_otu_table.csv",
                          package = "MTaP", mustWork = TRUE)
  tax_file <- system.file("extdata", "example_taxonomy_table.csv",
                          package = "MTaP", mustWork = TRUE)
  
  # Check if example files exist
  skip_if_not(file.exists(otu_file), "Example OTU file not found")
  skip_if_not(file.exists(tax_file), "Example taxonomy file not found")
  
  config <- mtap_config(otu_file, tax_file)
  
  expect_s3_class(config, "mtap_config")
  expect_true(file.exists(config$otu_file))
  expect_true(file.exists(config$tax_file))
})

# Additional: Test other functionality of configuration objects能
test_that("mtap_config objects have expected structure", {
  # Create test files
  test_files <- create_test_files()
  
  config <- mtap_config(
    otu_file = test_files$otu_file,
    tax_file = test_files$tax_file,
    output_prefix = "analysis1"
  )
  
  # Test class structure
  expect_equal(class(config), c("mtap_config", "list"))
  
  # Test list structure
  expect_type(config, "list")
  expect_length(config, 4)  # otu_file, tax_file, output_prefix, taxonomy_hierarchy
  
  # Clean up
  unlink(test_files$otu_file)
  unlink(test_files$tax_file)
})