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#' Creates the terminal command to validate a BEAST2 input file
#' @inheritParams default_params_doc
#' @return a character vector, of which the first element
#' is the command (\code{java}, in this case),
#' and the others are arguments (\code{-jar}, in this case, followed
#' by more arguments.
#' @examples
#' check_empty_beaustier_folders()
#'
#' if (is_beast2_installed() && beautier::is_on_ci()) {
#' create_beast2_validate_cmd(
#' input_filename = "input.xml"
#' )
#' }
#'
#' check_empty_beaustier_folders()
#' @author Richèl J.C. Bilderbeek
#' @export
create_beast2_validate_cmd <- function(
input_filename,
beast2_path = get_default_beast2_path()
) {
if (is_jar_path(beast2_path)) {
create_beast2_validate_cmd_jar(
input_filename = input_filename,
beast2_jar_path = beast2_path
)
} else {
check_true(is_bin_path(beast2_path))
create_beast2_validate_cmd_bin(
input_filename = input_filename,
beast2_bin_path = beast2_path
)
}
}
#' Creates the terminal command to validate a BEAST2 input file
#' using a call to the \code{launcher.jar} file
#' @inheritParams default_params_doc
#' @return a character vector, of which the first element
#' is the command (\code{java}, in this case),
#' and the others are arguments (\code{-jar}, in this case, followed
#' by more arguments.
#' @examples
#' check_empty_beaustier_folders()
#'
#' if (is_beast2_installed() && beautier::is_on_ci()) {
#' create_beast2_validate_cmd_jar(
#' input_filename = "input.xml"
#' )
#' }
#'
#' check_empty_beaustier_folders()
#' @author Richèl J.C. Bilderbeek
#' @export
create_beast2_validate_cmd_jar <- function(
input_filename,
beast2_jar_path = get_default_beast2_jar_path()
) {
beautier::check_file_exists(beast2_jar_path, "beast2_jar_path")
check_true(is_jar_path(beast2_jar_path))
cmds <- c(
get_default_java_path(),
"-cp",
add_quotes_if_has_spaces(beast2_jar_path),
get_beast2_main_class_name(),
"-validate",
add_quotes_if_has_spaces(input_filename)
)
# The executable must be runnable. This means that it should not have quotes
check_true(file.exists(cmds[1]))
cmds
}
#' Creates the terminal command to validate a BEAST2 input file
#' using a call to the \code{launcher.jar} file
#' @inheritParams default_params_doc
#' @return a character vector, of which the first element
#' is the command (\code{java}, in this case),
#' and the others are arguments (\code{-jar}, in this case, followed
#' by more arguments.
#' @examples
#' check_empty_beaustier_folders()
#'
#' if (is_beast2_installed() && beautier::is_on_ci()) {
#' create_beast2_validate_cmd_bin(
#' input_filename = "input.xml"
#' )
#' }
#'
#' check_empty_beaustier_folders()
#' @author Richèl J.C. Bilderbeek
#' @export
create_beast2_validate_cmd_bin <- function(
input_filename,
beast2_bin_path = get_default_beast2_bin_path()
) {
beautier::check_file_exists(beast2_bin_path, "beast2_bin_path")
check_true(is_bin_path(beast2_bin_path))
cmds <- c(
beast2_bin_path,
"-validate",
add_quotes_if_has_spaces(input_filename)
)
# The executable must be runnable. This means that it should not have quotes
check_true(file.exists(cmds[1]))
cmds
}
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