# test w4mclassfilter::w4m_filter_by_sample_class
expect_equivalent_length <- function(target, current, info) {
expect_equivalent(length(target), length(current), info = info)
}
expect_all_equal <- function(target, current, info) {
expect_equivalent_length(target = target, current = current, info = info)
expect_true(all.equal(target = target, current = current, info = info))
}
my_read_df <- function(file_path, kind_string, my_failure_action = print) {
# ---
# read in the data frame
my.env <- new.env()
my.env$success <- FALSE
my.env$msg <- sprintf("no message reading %s", kind_string)
if (!file.exists(file_path)) {
my.env$msg <- sprintf("file '%s' not found when trying to read %s", file_path, kind_string)
my_failure_action(my.env$msg)
return ( NULL )
}
tryCatch(
expr = {
my.env$data <- utils::read.delim( fill = FALSE, file = file_path )
my.env$success <- TRUE
}
, error = function(e) {
my.env$ msg <- sprintf("%s read failed", kind_string)
}
)
if (!my.env$success) {
my_failure_action(paste("my_read_df - ", my.env$msg))
return ( NULL )
}
return (my.env)
}
run_nofilter_test <- function(classes_to_filter, class_column, samplename_column = "sampleMetadata", false_to_exclude_classes_in_filter) {
# set up variables
variableMetadata_in <- "bad_input_variableMetadata.tsv"
variableMetadata_out <- "output_variableMetadata.tsv"
variableMetadata_exp <- "expected_nofilter_variableMetadata.tsv"
sampleMetadata_in <- "input_sampleMetadata.tsv"
sampleMetadata_out <- "output_sampleMetadata.tsv"
sampleMetadata_exp <- "expected_nofilter_sampleMetadata.tsv"
dataMatrix_in <- "input_dataMatrix.tsv"
dataMatrix_out <- "output_nofilter_dataMatrix.tsv"
dataMatrix_exp <- "expected_nofilter_dataMatrix.tsv"
# test input files
data_matrix_input_env <- my_read_df(dataMatrix_in, "data matrix input")
expect_true(data_matrix_input_env$success, info = "read data matrix input")
rm(data_matrix_input_env)
sample_metadata_input_env <- my_read_df(sampleMetadata_in, "sample metadata input")
expect_true(sample_metadata_input_env$success, info = "read sample metadata input")
rm(sample_metadata_input_env)
variable_metadata_input_env <- my_read_df(
variableMetadata_in
, "variable metadata input"
, my_failure_action = invisible
)
if (!is.null(variable_metadata_input_env)) {
print(ls(variable_metadata_input_env))
print(variable_metadata_input_env$success)
print(variable_metadata_input_env$msg)
print(variable_metadata_input_env$data)
}
expect_true(is.null(variable_metadata_input_env), info = "read variable metadata input")
rm(variable_metadata_input_env)
error_list <- c("Error list:")
add_error <- function(...) {
error_list <<- c(error_list, paste(...))
}
# filter, impute, and write output
filter_result <- w4m_filter_by_sample_class(
dataMatrix_in = dataMatrix_in
, dataMatrix_out = dataMatrix_out
, variableMetadata_in = variableMetadata_in
, variableMetadata_out = variableMetadata_out
, sampleMetadata_out = sampleMetadata_out
, sampleMetadata_in = sampleMetadata_in
, samplename_column = samplename_column
, classes = classes_to_filter
, include = false_to_exclude_classes_in_filter
, class_column = class_column
, failure_action = add_error
)
expect_false(filter_result, info = "filter_result should be false in the case of a bad file")
expect_equal(length(error_list), 3, info = "error_result should be length 3.")
if (filter_result) {
cat(paste("\n", error_list))
} else if (length(error_list) != 3) {
cat(paste("\n", error_list))
}
}
#' @import testthat w4mclassfilter
#' @export
test_that("bad file test", {
run_nofilter_test(classes_to_filter = c("M"), class_column = "", samplename_column = "sampleMetadata", false_to_exclude_classes_in_filter = TRUE)
})
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