testthat::test_that("Function check_tags throws an error if the provided tags argument is not a list", { # nolint start testthat::expect_error( check_tags(tags = "test_tag"), regexp = "Tags parameter must be an unnamed list of tags. For example: tags <- list('my_tag_1', 'my_tag_2')", fixed = TRUE ) # nolint end }) testthat::test_that("Function check_settings throws error when expected", { # Check if the function throws an error if settings argument is not a list testthat::expect_error( check_settings(settings = "test_string"), regexp = "Settings must be provided as a list.", fixed = TRUE ) # Check if it throws an appropriate error if the provided settings list # contains an element with invalid name testthat::expect_error( check_settings(settings = list( locked = FALSE, controlled = FALSE, width = 10L )), regexp = "Argument width is not a valid settings field.", fixed = TRUE ) # Check if the function check_settings throws an error when settings list # elements have invalid types valid_input_names <- c( "locked", "controlled", "use_interruptible_instances", "use_memoization", "allow_network_access", "use_elastic_disk", "location", "intermediate_files" ) settings_field_types <- list( locked = "logical", controlled = "logical", use_interruptible_instances = "logical", use_memoization = "logical", allow_network_access = "logical", location = "character", intermediate_files = "list" ) for (field in names(settings_field_types)) { # provide settings as a list with a field containing some invalid value # (for example, integer) input_list <- list() input_list[[field]] <- 10L # nolint start testthat::expect_error( check_settings(settings = input_list), regexp = glue::glue("Assertion on '{field}' failed: Must be of type '{settings_field_types[field]}' (or 'NULL'), not 'integer'."), fixed = TRUE ) # nolint end if (field == "intermediate_files") { # check error message if retention field is not valid (not character) input_intermediate_files <- list( intermediate_files = list(retention = 15L) ) # nolint start testthat::expect_error( check_settings(settings = input_intermediate_files), regexp = glue::glue("Assertion on 'intermediate_files$retention' failed: Must be of type 'character' (or 'NULL'), not '{typeof(input_intermediate_files$intermediate_files$retention)}'."), fixed = TRUE ) # nolint end # check error message if duration field is not valid (not character) input_intermediate_files <- list( intermediate_files = list(duration = "24") ) # nolint start testthat::expect_error( check_settings(settings = input_intermediate_files), regexp = glue::glue("Assertion on 'intermediate_files$duration' failed: Must be of type 'integer' (or 'NULL'), not '{typeof(input_intermediate_files$intermediate_files$duration)}'."), fixed = TRUE ) # nolint end } } }) test_that("check_limit function passes when limit is valid", { testthat::expect_silent(check_limit(limit = 5L)) testthat::expect_silent(check_limit(limit = 56)) }) test_that("check_limit function throws error when limit is not valid", { negative_limit <- list(limit = -1) string_limit <- list(limit = "limit") big_limit <- list(limit = 1500) testthat::expect_error( do.call(check_limit, negative_limit), regexp = "Limit must be integer number between 1 and 100.", fixed = TRUE ) testthat::expect_error( do.call(check_limit, string_limit), regexp = "Limit must be integer number between 1 and 100.", fixed = TRUE ) testthat::expect_error( do.call(check_limit, big_limit), regexp = "Limit must be integer number between 1 and 100.", fixed = TRUE ) }) test_that("check_offset function passes when offset is valid", { testthat::expect_silent(check_offset(offset = 1L)) testthat::expect_silent(check_offset(offset = 90)) }) test_that("check_offset function throws error when offset is not valid", { negative_offset <- list(offset = -10) string_offset <- list(offset = "offset") testthat::expect_error( do.call(check_offset, negative_offset), regexp = "Offset must be integer number >= 0.", fixed = TRUE ) testthat::expect_error( do.call(check_offset, string_offset), regexp = "Offset must be integer number >= 0.", fixed = TRUE ) }) test_that("check_folder_name function works", { testthat::expect_silent(check_folder_name(name = "New_folder")) testthat::expect_silent(check_folder_name(name = "MyFolder")) }) test_that("check_folder_name function throws error when expected", { missing_name <- list(name = NULL) int_name <- list(name = 123) invalid_start_name <- list(name = "__inputs") spaces_in_name <- list(name = "Another new folder") testthat::expect_error( do.call(check_folder_name, missing_name), regexp = "Please, provide the folder's name.", fixed = TRUE ) testthat::expect_error( do.call(check_folder_name, int_name), regexp = "Assertion on 'name' failed: Must be of type 'string', not 'double'.", # nolint fixed = TRUE ) testthat::expect_error( do.call(check_folder_name, invalid_start_name), regexp = "The folder name cannot start with \"__\"", fixed = TRUE ) testthat::expect_error( do.call(check_folder_name, spaces_in_name), regexp = "The folder name cannot contain spaces in the name.", fixed = TRUE ) }) test_that("check_metadata function throws error when metadata is not valid", { missing_metadata <- list(metadata = list(NULL)) string_metadata <- list(metadata = "test") int_metadata <- list(metadata = 123) # nolint start msg <- "Metadata parameter must be a named list of key-value pairs. For example: metadata <- list(metadata_key_1 = 'metadata_value_1', metadata_key_2 = 'metadata_value_2')" # nolint end testthat::expect_error( do.call(check_metadata, missing_metadata), regexp = msg, fixed = TRUE ) testthat::expect_error( do.call(check_metadata, string_metadata), regexp = msg, fixed = TRUE ) testthat::expect_error( do.call(check_metadata, int_metadata), regexp = msg, fixed = TRUE ) }) test_that("transform_multiple_vals function works", { # Test with metadata example metadata_values <- list( metadata.disease_type = "Acute Myeloma", metadata.sample_id = "some-id", metadata.metadata_field = c("some other value1", "some-value2") ) transformed_metadata <- transform_multiple_vals(metadata_values) testthat::expect_equal(length(names(transformed_metadata)), 4) testthat::expect_true(names(transformed_metadata)[3] == names(transformed_metadata)[4]) # nolint testthat::expect_equal(transformed_metadata[[1]], "Acute%20Myeloma") testthat::expect_equal(transformed_metadata[[2]], metadata_values[[2]]) testthat::expect_equal(transformed_metadata[[3]], "some%20other%20value1") # Test with tags example tags_values <- list(tags = list("index files", "suggested")) transformed_tags <- transform_multiple_vals(tags_values) testthat::expect_equal(length(names(transformed_tags)), 2) testthat::expect_equal(transformed_tags[[1]], "index%20files") testthat::expect_equal(transformed_tags[[2]], "suggested") }) test_that("check_download_path function throws error when parameters are not valid", { # nolint # Negative test use case for directory_path parameter testthat::expect_error( check_download_path( directory_path = "non-existent-directory" ), "Destination directory non-existent-directory does not exist." ) # Negative test use cases for filename parameter # 1) is_missing returns TRUE filename_invalid_values <- c(NA, NULL) for (filename in filename_invalid_values) { testthat::expect_error( check_download_path(directory_path = getwd(), filename = filename), "The filename parameter is missing." ) } # 2) is_missing returns FALSE, but the filename parameter value is not valid filename_invalid_values <- list( 15L, c("test_file_1.txt", "test_file_2.txt"), list("test_file.txt") ) for (filename in filename_invalid_values) { testthat::expect_error( check_download_path(directory_path = getwd(), filename = filename), "The filename parameter should be a length-one string." ) } }) test_that("check_retry_count function throws error when count is invalid", { # Negative test use cases for count parameter invalid_retry_count <- c(-1, "retry", 0, FALSE) for (retry_count in invalid_retry_count) { testthat::expect_error( check_retry_params( input = retry_count, parameter_to_validate = "count" ), "retry_count parameter must be a positive integer number." ) } }) test_that("check_retry_params function throws error when timeout is not valid", { # nolint # Negative test use cases for timeout parameter invalid_retry_timeout <- c(-1, "retry", 0, FALSE) for (retry_timeout in invalid_retry_timeout) { testthat::expect_error( check_retry_params( input = retry_timeout, parameter_to_validate = "timeout" ), "retry_timeout parameter must be a positive integer number." ) } }) test_that("check_app_copy_strategy function throws error when provided strategy is invalid", { # nolint # Negative test use cases for missing strategy parameter testthat::expect_error( check_app_copy_strategy( strategy = NULL ), "Please provide the copy strategy" ) # Negative test use case for invalid strategy parameter # Valid values: clone, direct_clone, direct, transient supported_app_copy_strategies <- getOption("sevenbridges2")$APP_COPY_STRATEGIES # nolint invalid_strategy_param <- "test_strategy" testthat::expect_error( check_app_copy_strategy( strategy = invalid_strategy_param ), label = "The provided copy strategy (test_strategy) is not supported. Please use one of the following strategies: clone, direct, clone_direct, transient" # nolint ) }) test_that("check_file_path function throws error when provided file_path parameter is not valid", { # nolint # Negative test use case for invalid file_path parameter invalid_file_path <- "/path/to/nonexisting-file.cwl" testthat::expect_error( check_file_path( file_path = invalid_file_path ), label = "File {magenta /path/to/nonexisting-file.cwl} does not exist." ) }) test_that("check_volume_params works", { # Pass invalid args, volume_type testthat::expect_error(check_volume_params(args = NULL)) testthat::expect_error(check_volume_params( args = list("arg1" = "arg1"), volume_type = "some-other-type" )) # Test with valid params valid_args <- list( name = "volume_name", bucket = "bucket_name", prefix = "", access_mode = "RW", description = NULL, properties = list("some-property" = "value"), endpoint = "some-endpoint", root_url = "some-url", credentials = list("key" = "just-string") ) testthat::expect_no_error(check_volume_params(args = valid_args)) # Create invalid params list invalid_args <- list( name = 123, bucket = list("some-name"), container = list("some-container"), prefix = NA, access_mode = "some-other", description = FALSE, properties = c("some-property" = "value"), endpoint = list("some-endpoint"), root_url = TRUE, credentials = "just-string" ) # Pass invalid name testthat::expect_error(check_volume_params(args = invalid_args["name"])) # Pass invalid bucket (volume_type = s3) testthat::expect_error( check_volume_params(args = c(valid_args["name"], invalid_args["bucket"])) ) # Pass invalid container (volume_type = azure) testthat::expect_error( check_volume_params( volume_type = "azure", args = c(valid_args["name"], invalid_args["container"]) ) ) # Pass invalid prefix testthat::expect_error( check_volume_params(args = c( valid_args["name"], valid_args["bucket"], invalid_args["prefix"] )) ) # Pass invalid access_mode testthat::expect_error( check_volume_params(args = c( valid_args["name"], valid_args["bucket"], invalid_args["access_mode"] )) ) # Pass invalid description testthat::expect_error( check_volume_params(args = c( valid_args["name"], valid_args["bucket"], invalid_args["description"] )) ) # Pass invalid properties testthat::expect_error( check_volume_params(args = c( valid_args["name"], valid_args["bucket"], invalid_args["properties"] )) ) # Pass invalid endpoint testthat::expect_error( check_volume_params(args = c( valid_args["name"], valid_args["bucket"], invalid_args["endpoint"] )) ) # Pass invalid root_url testthat::expect_error( check_volume_params(args = c( valid_args["name"], valid_args["bucket"], invalid_args["root_url"] )) ) }) test_that("transform_configuration_param works", { # Provide configuration as valid list config_list <- list( "field1" = "value1", "field2" = 123, "field3" = list( "subfield" = "subfield-value" ), "field4" = "something" ) transformed_str <- transform_configuration_param(configuration = config_list) testthat::expect_type(transformed_str, "character") testthat::expect_true(startsWith(transformed_str, prefix = "{\n")) # Provide configuration as path to JSON file config_json_path <- testthat::test_path( file.path("test_data", "volumes_configuration_params.json") ) testthat::skip_on_ci() transformed_str <- transform_configuration_param(configuration = config_json_path) # nolint testthat::expect_type(transformed_str, "character") testthat::expect_true(startsWith(transformed_str, prefix = "{\n")) }) test_that("transform_configuration_param throws error when needed", { # Provide configuration as NULL testthat::expect_error( transform_configuration_param(configuration = NULL), regexp = "Invalid configuration parameter! \n Please, provide a string path to the JSON file or a named list.", # nolint fixed = TRUE ) # Provide configuration as empty list testthat::expect_error( transform_configuration_param(configuration = list()), regexp = "Invalid configuration parameter! \n Please, provide a string path to the JSON file or a named list.", # nolint fixed = TRUE ) # Provide configuration as unnamed list testthat::expect_error( transform_configuration_param(configuration = list("unnamed list")), regexp = "Invalid configuration parameter! \n Please, provide a string path to the JSON file or a named list.", # nolint fixed = TRUE ) # Provide configuration as invalid json path config_path <- file.path("unnoun", "path", "to", "file.json") testthat::expect_error( transform_configuration_param(configuration = config_path) ) # Provide configuration as non-string type testthat::expect_error( transform_configuration_param(configuration = c("field1", "field2")) ) }) test_that("check_upload_params throws error when needed", { too_big_size <- getOption("sevenbridges2")$MAXIMUM_OBJECT_SIZE + 1 too_big_part_size <- getOption("sevenbridges2")$MAXIMUM_PART_SIZE + 1 too_small_part_size <- getOption("sevenbridges2")$MINIMUM_PART_SIZE - 1 # Setup test parameters for test test_no_size <- list(size = NULL, part_size = 1000) test_bad_size <- list(size = "Bad_size", part_size = 1000) test_negative_size <- list(size = -5, part_size = 1000) test_too_big_size <- list(size = too_big_size, part_size = 1000) test_no_part_size <- list(size = 1000, part_size = NULL) test_bad_part_size <- list(size = 1000, part_size = "Bad_size") test_negative_part_size <- list(size = 1000, part_size = -1000) test_too_big_part_size <- list(size = 1000, part_size = too_big_part_size) test_too_small_part_size <- list(size = 1000, part_size = too_small_part_size) # Edge case for part length part_size <- getOption("sevenbridges2")$MINIMUM_PART_SIZE size <- (part_size * getOption("sevenbridges2")$MAXIMUM_TOTAL_PARTS) + getOption("sevenbridges2")$MINIMUM_PART_SIZE # nolint test_bad_part_length <- list(size = size, part_size = part_size) # Fails when no size is provided testthat::expect_error(do.call(check_upload_params, test_no_size)) # Fails when bad size is provided testthat::expect_error(do.call(check_upload_params, test_bad_size)) # Fails when negative size is provided testthat::expect_error(do.call(check_upload_params, test_negative_size)) # Fails when too big size is provided testthat::expect_error( do.call(check_upload_params, test_too_big_size), regexp = "File size must be between 0 - 5497558138880 (5TB), inclusive", fixed = TRUE ) # Fails when no part size is provided testthat::expect_error(do.call(check_upload_params, test_no_part_size)) # Fails when bad part size is provided testthat::expect_error(do.call(check_upload_params, test_bad_part_size)) # Fails when negative part size is provided testthat::expect_error(do.call(check_upload_params, test_negative_part_size)) # Fails when too big part size is provided testthat::expect_error( do.call(check_upload_params, test_too_big_part_size), regexp = "Parameter part_size must be 5 MB to 5 GB, last part can be < 5 MB", # nolint fixed = TRUE ) # Fails when too small part size is provided testthat::expect_error( do.call(check_upload_params, test_too_small_part_size), regexp = "Parameter part_size must be 5 MB to 5 GB, last part can be < 5 MB", # nolint fixed = TRUE ) # Fails when part length is too big testthat::expect_error( do.call(check_upload_params, test_bad_part_length), regexp = "Total number of parts must be from 1 to 10,000 (inclusive). Please, modify part_size.", # nolint fixed = TRUE ) }) test_that("check_and_transform_datetime works as expected", { # Fails when no datetime is provided testthat::expect_error(check_and_transform_datetime(), regexp = "Date is required!", fixed = TRUE ) # Check if character returns character back time <- "2016-04-01 14:25:50" testthat::expect_equal(check_and_transform_datetime(time), expected = "2016-04-01 14:25:50" ) # Check if Date/time returns character back time <- as.POSIXct("2016-04-01 14:25:50", tz = "UTC") testthat::expect_equal(check_and_transform_datetime(time), expected = "2016-04-01 14:25:50" ) })