# 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))
}
read_data_frame <- function(file_path, kind_string, 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)
tryCatch(
expr = {
my.env$data <- utils::read.delim(
fill = FALSE,
file = file_path,
stringsAsFactors = TRUE
)
my.env$success <- TRUE
}
, error = function(e) {
my.env$ msg <- sprintf("%s read failed", kind_string)
}
)
if (!my.env$success) {
failure_action(my.env$msg)
return ( FALSE )
}
return (my.env)
}
# test matrix outputs and inputs
#' @import testthat w4mclassfilter
#' @export
test_that("io test - matrix", {
# set up variables
out_env <- new.env()
variableMetadata_in <- "input_variableMetadata.tsv"
variableMetadata_out <- out_env
variableMetadata_exp <- "expected_variableMetadata.tsv"
sampleMetadata_in <- "input_sampleMetadata.tsv"
sampleMetadata_out <- out_env
sampleMetadata_exp <- "expected_sampleMetadata.tsv"
dataMatrix_in <- "input_dataMatrix.tsv"
dataMatrix_out <- "output_iotest_dataMatrix.tsv"
dataMatrix_exp <- "expected_filterio_dataMatrix.tsv"
classes_to_filter <- c("M")
class_column <- "gender"
false_to_exclude_classes_in_filter <- TRUE
# test input ...
data_matrix_input_env <- read_data_frame(dataMatrix_in, "data matrix input")
expect_true(data_matrix_input_env$success, info = "read data matrix input")
# dataMatrix_in as data.frame:
dataMatrix_in <- data_matrix_input_env$data
data_matrix_nrow <- nrow(dataMatrix_in)
data_matrix_ncol <- ncol(dataMatrix_in) - 1
rm(data_matrix_input_env)
sample_metadata_input_env <- read_data_frame(sampleMetadata_in, "sample metadata input")
expect_true(sample_metadata_input_env$success, info = "read sample metadata input")
# sampleMetadata_in as list:
sampleMetadata_in <- list(sampleMetadata = sample_metadata_input_env$data)
rm(sample_metadata_input_env)
variable_metadata_input_env <- read_data_frame(variableMetadata_in, "variable metadata input")
expect_true(variable_metadata_input_env$success, info = "read variable metadata input")
# variableMetadata_in as environment:
variableMetadata_in <- list2env(list(variableMetadata = variable_metadata_input_env$data))
rm(variable_metadata_input_env)
# first of two passes: create an unfiltered matrix as output
data_matrix_env <- new.env()
# filter, impute, and write output
filter_result <- w4m_filter_by_sample_class(
dataMatrix_in = dataMatrix_in
, dataMatrix_out = data_matrix_env
, variableMetadata_in = variableMetadata_in
, variableMetadata_out = variableMetadata_out
, sampleMetadata_out = sampleMetadata_out
, sampleMetadata_in = sampleMetadata_in
, classes = c() # no classes to exclude
, include = !false_to_exclude_classes_in_filter # FALSE - exclude only 'no classes to exclude'
, class_column = class_column
)
expect_true(filter_result, info = "filter_result should be true")
expect_equivalent(ls_env <- ls(data_matrix_env), "dataMatrix", info = sprintf("expected ls(data_matrix_env) == 'dataMatrix' but instead was '%s'", ls_env))
expect_true(is.matrix(data_matrix_env$dataMatrix), info = "is.matrix(data_matrix_env$dataMatrix) should be true")
expect_equivalent(nrow(data_matrix_env$dataMatrix), 15, info = "nrow(data_matrix_env$dataMatrix) is not 15 as expected")
expect_equivalent(ncol(data_matrix_env$dataMatrix), 19, info = "ncol(data_matrix_env$dataMatrix) is not 19 as expected")
# first of two passes: read an unfiltered matrix producing a filtered data file for dataMatrix
# filter, impute, and write output
filter_result <- w4m_filter_by_sample_class(
dataMatrix_in = data_matrix_env
, dataMatrix_out = dataMatrix_out
, variableMetadata_in = variableMetadata_in
, variableMetadata_out = variableMetadata_out
, sampleMetadata_out = sampleMetadata_out
, sampleMetadata_in = sampleMetadata_in
, classes = classes_to_filter
, include = false_to_exclude_classes_in_filter
, class_column = class_column
)
expect_true(filter_result, info = "filter_result should be true")
# read actual outputs and compare to expecteds
data_matrix_output_env <- read_data_frame(dataMatrix_out, "data matrix output")
expect_true(data_matrix_output_env$success, info = "read data matrix output")
data_matrix_expected_env <- read_data_frame(dataMatrix_exp, "data matrix expected")
expect_true(data_matrix_expected_env$success, info = "read data matrix expected")
expect_equivalent_length(data_matrix_output_env$data, data_matrix_expected_env$data, info = "validate data matrix")
expect_equivalent(data_matrix_output_env$data, data_matrix_expected_env$data, info = "validate data matrix")
sample_metadata_expected_env <- read_data_frame(sampleMetadata_exp, "sample metadata expected")
expect_true(sample_metadata_expected_env$success, info = "read sample metadata expected")
expect_true(all.equal(out_env$sampleMetadata, sample_metadata_expected_env$data), info = {
x <- all.equal(sample_metadata_expected_env$data, out_env$sampleMetadata)
sprintf("all.equal(sample_metadata_expected_env$data, out_env$sampleMetadata) = %s", x)
})
variable_metadata_expected_env <- read_data_frame(variableMetadata_exp, "variable metadata expected")
expect_true(variable_metadata_expected_env$success, info = "read variable metadata expected")
expect_true(all.equal(out_env$variableMetadata, variable_metadata_expected_env$data), info = {
x <- all.equal(variable_metadata_expected_env$data, out_env$variableMetadata)
sprintf("all.equal(variable_metadata_expected_env$data, out_env$variableMetadata) = %s", x)
})
})
# test alternative inputs and outputs
#' @import testthat w4mclassfilter
#' @export
test_that("io test", {
# set up variables
out_env <- new.env()
variableMetadata_in <- "input_variableMetadata.tsv"
variableMetadata_out <- out_env
variableMetadata_exp <- "expected_variableMetadata.tsv"
sampleMetadata_in <- "input_sampleMetadata.tsv"
sampleMetadata_out <- out_env
sampleMetadata_exp <- "expected_sampleMetadata.tsv"
dataMatrix_in <- "input_dataMatrix.tsv"
dataMatrix_out <- "output_iotest2_dataMatrix.tsv"
dataMatrix_exp <- "expected_filterio_dataMatrix.tsv"
classes_to_filter <- c("M")
class_column <- "gender"
false_to_exclude_classes_in_filter <- TRUE
# test input ...
data_matrix_input_env <- read_data_frame(dataMatrix_in, "data matrix input")
expect_true(data_matrix_input_env$success, info = "read data matrix input")
# dataMatrix_in as data.frame:
dataMatrix_in <- data_matrix_input_env$data
rm(data_matrix_input_env)
sample_metadata_input_env <- read_data_frame(sampleMetadata_in, "sample metadata input")
expect_true(sample_metadata_input_env$success, info = "read sample metadata input")
# sampleMetadata_in as list:
sampleMetadata_in <- list(sampleMetadata = sample_metadata_input_env$data)
rm(sample_metadata_input_env)
variable_metadata_input_env <- read_data_frame(variableMetadata_in, "variable metadata input")
expect_true(variable_metadata_input_env$success, info = "read variable metadata input")
# variableMetadata_in as environment:
variableMetadata_in <- list2env(list(variableMetadata = variable_metadata_input_env$data))
rm(variable_metadata_input_env)
# 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
, classes = classes_to_filter # filter out this list of class names
, include = false_to_exclude_classes_in_filter # TRUE - exclude 'classes_to_filter' in previous line
, class_column = class_column
)
expect_true(filter_result, info = "filter_result should be true")
# read actual outputs and compare to expecteds
data_matrix_output_env <- read_data_frame(dataMatrix_out, "data matrix output")
expect_true(data_matrix_output_env$success, info = "read data matrix output")
data_matrix_expected_env <- read_data_frame(dataMatrix_exp, "data matrix expected")
expect_true(data_matrix_expected_env$success, info = "read data matrix expected")
expect_equivalent_length(data_matrix_output_env$data, data_matrix_expected_env$data, info = "validate data matrix")
expect_equivalent(data_matrix_output_env$data, data_matrix_expected_env$data, info = "validate data matrix")
sample_metadata_expected_env <- read_data_frame(sampleMetadata_exp, "sample metadata expected")
expect_true(sample_metadata_expected_env$success, info = "read sample metadata expected")
expect_true(all.equal(out_env$sampleMetadata, sample_metadata_expected_env$data), info = {
x <- all.equal(sample_metadata_expected_env$data, out_env$sampleMetadata)
sprintf("all.equal(sample_metadata_expected_env$data, out_env$sampleMetadata) = %s", x)
})
variable_metadata_expected_env <- read_data_frame(variableMetadata_exp, "variable metadata expected")
expect_true(variable_metadata_expected_env$success, info = "read variable metadata expected")
expect_true(all.equal(out_env$variableMetadata, variable_metadata_expected_env$data), info = {
x <- all.equal(variable_metadata_expected_env$data, out_env$variableMetadata)
sprintf("all.equal(variable_metadata_expected_env$data, out_env$variableMetadata) = %s", x)
})
})
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