test_that("use, v2.4", {
input_filename <- get_fasta_filename()
inference_model <- init_inference_model(
input_filename = input_filename,
create_inference_model()
)
created <- create_screenlog_xml(
inference_model = inference_model
)
expected <- c(
"<logger id=\"screenlog\" logEvery=\"1000\">", # nolint this is no absolute path
" <log idref=\"posterior\"/>", # nolint this is no absolute path
" <log id=\"ESS.0\" spec=\"util.ESS\" arg=\"@posterior\"/>", # nolint this is no absolute path
" <log idref=\"likelihood\"/>", # nolint this is no absolute path
" <log idref=\"prior\"/>", # nolint this is no absolute path
"</logger>"
)
expect_equal(created, expected)
})
test_that("use, v2.6", {
input_filename <- get_fasta_filename()
inference_model <- init_inference_model(
input_filename = input_filename,
create_inference_model(
beauti_options = create_beauti_options_v2_6()
)
)
created <- create_screenlog_xml(
inference_model = inference_model
)
expected <- c(
"<logger id=\"screenlog\" spec=\"Logger\" logEvery=\"1000\">", # nolint
" <log idref=\"posterior\"/>", # nolint
" <log idref=\"likelihood\"/>", # nolint
" <log idref=\"prior\"/>", # nolint
"</logger>" # nolint
)
expect_equal(created, expected)
})
test_that("use", {
input_filename <- get_fasta_filename()
inference_model <- init_inference_model(
input_filename = input_filename,
inference_model = create_inference_model()
)
expect_silent(
create_screenlog_xml(
inference_model = inference_model
)
)
expect_true(
is_xml(
create_screenlog_xml(
inference_model = inference_model
)
)
)
})
test_that("file_name in XML", {
input_filename <- get_fasta_filename()
inference_model <- init_inference_model(
input_filename = input_filename,
inference_model = create_inference_model(
mcmc = create_mcmc(
screenlog = create_screenlog(
filename = "my_file.txt"
)
)
)
)
xml <- create_screenlog_xml(
inference_model = inference_model
)
expect_true(
!is.na(
stringr::str_match(xml, pattern = "fileName=\"my_file.txt\"")[1, 1]
)
)
})
test_that("log_every in XML", {
input_filename <- get_fasta_filename()
inference_model <- init_inference_model(
input_filename = input_filename,
inference_model = create_inference_model(
mcmc = create_mcmc(
screenlog = create_screenlog(
log_every = 1234
)
)
)
)
xml <- create_screenlog_xml(
inference_model = inference_model
)
expect_true(
!is.na(
stringr::str_match(xml, pattern = "logEvery=\"1234\"")[1, 1]
)
)
})
test_that("mode in XML", {
input_filename <- get_fasta_filename()
inference_model <- init_inference_model(
input_filename = input_filename,
inference_model = create_inference_model(
mcmc = create_mcmc(
screenlog = create_screenlog(
mode = "compound"
)
)
)
)
xml <- create_screenlog_xml(
inference_model = inference_model
)
expect_true(
!is.na(
stringr::str_match(xml, pattern = "mode=\"compound\"")[1, 1]
)
)
})
test_that("sanitise_headers in XML", {
input_filename <- get_fasta_filename()
inference_model <- init_inference_model(
input_filename = input_filename,
inference_model = create_inference_model(
mcmc = create_mcmc(
screenlog = create_screenlog(
sanitise_headers = TRUE
)
)
)
)
xml <- create_screenlog_xml(
inference_model = inference_model
)
expect_true(
!is.na(
stringr::str_match(xml, pattern = "sanitiseHeaders=\"true\"")[1, 1]
)
)
})
test_that("sort in XML", {
input_filename <- get_fasta_filename()
inference_model <- init_inference_model(
input_filename = input_filename,
inference_model = create_inference_model(
mcmc = create_mcmc(
screenlog = create_screenlog(
sort = "smart"
)
)
)
)
xml <- create_screenlog_xml(
inference_model = inference_model
)
expect_true(
!is.na(
stringr::str_match(xml, pattern = "sort=\"smart\"")[1, 1]
)
)
})
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