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#' Internal function to extract the treelog filename for a BEAST2 input file
#'
#' Extract the treelog filename from a BEAST2 input file
#' @inheritParams default_params_doc
#' @return the treelog filename for a BEAST2 input file
#' @examples
#' if (beautier::is_on_ci()) {
#'
#' beast2_input_filename <- get_beastier_tempfilename()
#'
#' beautier::create_beast2_input_file_from_model(
#' input_filename = beautier::get_beautier_path("test_output_0.fas"),
#' output_filename = beast2_input_filename
#' )
#' extract_treelog_filename_from_beast2_input_file(
#' input_filename = beast2_input_filename
#' )
#' file.remove(beast2_input_filename)
#'
#' remove_beaustier_folders()
#' }
#' @author Richèl J.C. Bilderbeek
#' @export
extract_treelog_filename_from_beast2_input_file <- function( # nolint indeed a long function name
input_filename
) {
check_true(file.exists(input_filename))
text <- readr::read_lines(input_filename, progress = FALSE)
treelog_line <- stringr::str_subset(
string = text,
pattern = "<logger id=\"treelog.t:"
)
check_true(length(treelog_line) == 1)
treelog_filename <- stringr::str_match(
string = treelog_line,
pattern = "fileName=\\\"([:graph:]+)\\\" "
)[1, 2]
# If there is '$(tree)', replacit by the tree ID
tree_id <- stringr::str_match(
string = treelog_line,
pattern = "id=\\\"treelog.t:([:graph:]+)\\\" "
)[1, 2]
treelog_filename <- stringr::str_replace(
string = treelog_filename,
pattern = "\\$\\(tree\\)",
replacement = tree_id
)
treelog_filename
}
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