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# Copyright (c) 2012-2024 Trevor L. Davis <trevor.l.davis@gmail.com>
#
# This file is free software: you may copy, redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation, either version 2 of the License, or (at your
# option) any later version.
#
# This file is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# This file incorporates work from the argparse module in Python 2.7.3.
#
# Copyright (c) 2001-2012 Python Software Foundation; All Rights Reserved
#
# See (inst/)COPYRIGHTS or http://docs.python.org/2/license.html for the full
# Python (GPL-compatible) license stack.
#' Create a command line parser
#'
#' `ArgumentParser()` creates a parser object that acts as
#' a wrapper to Python's `argparse` module
#'
#' @param ... Arguments cleaned and passed to Pythons `argparse.ArgumentParser()`
#' @param python_cmd Python executable for `argparse` to use.
#' Must have `argparse` and `json` modules (automatically bundled with Python 2.7 and 3.2+).
#' If you need Unicode argument support then you must use Python 3.0+.
#' Default will be to use `findpython` package to find suitable Python binary.
#' @return `ArgumentParser()` returns a parser object which contains
#' an `add_argument()` function to add arguments to the parser,
#' a `parse_args()` function to parse command line arguments into
#' a list, a `print_help()` and a `print_usage()` function to print
#' usage information. See code examples, package vignette,
#' and corresponding python module for more information on how to use it.
#'
#' @references Python's `argparse` library, which this package is based on,
#' is described here: \url{https://docs.python.org/3/library/argparse.html}
#'
#' @examples
#'
#' if (argparse:::detects_python()) {
#' parser <- ArgumentParser(description='Process some integers')
#' parser$add_argument('integers', metavar='N', type = "integer", nargs='+',
#' help='an integer for the accumulator')
#' parser$add_argument('--sum', dest='accumulate', action='store_const',
#' const='sum', default='max',
#' help='sum the integers (default: find the max)')
#' parser$print_help()
#' # default args for ArgumentParser()$parse_args are commandArgs(TRUE)
#' # which is what you'd want for an Rscript but not for interactive use
#' args <- parser$parse_args(c("--sum", "1", "2", "3"))
#' accumulate_fn <- get(args$accumulate)
#' print(accumulate_fn(args$integers))
#' }
#' @importFrom R6 R6Class
#' @export
ArgumentParser <- function(..., python_cmd = NULL) { # nolint
python_cmd <- find_python_cmd(python_cmd)
assert_python_cmd(python_cmd)
initial_python_code <- c("import argparse",
"try:",
" import json",
"except ImportError:",
" import simplejson as json",
"",
"def logical(s):",
" if isinstance(s, bool):",
" return s",
" elif s in ('T', 'TRUE', 'True', 'true'):",
" return True",
" elif s in ('F', 'FALSE', 'False', 'false'):",
" return False",
" else:",
" raise ValueError(\"could not convert string to logical: '{}'\".format(s))",
"",
sprintf("parser = argparse.ArgumentParser(%s)",
convert_..._to_arguments("ArgumentParser", ...)),
"")
Parser$new(Code$new(python_cmd, initial_python_code), "parser")
}
Code <- R6Class("Code", # nolint
public = list(
append = function(new_code) {
private$code <- c(private$code, new_code)
},
run = function(new_code) {
code <- c(private$code, new_code)
suppressWarnings(system2(private$cmd, input = code,
stdout = TRUE, stderr = TRUE))
},
initialize = function(cmd, code = character(0)) {
private$cmd <- cmd
private$code <- code
}
),
private = list(code = NULL, cmd = NULL)
)
Group <- R6Class("Group", # nolint
public = list(
initialize = function(python_code, name) {
private$python_code <- python_code
private$name <- name
},
add_argument = function(...) {
private$python_code$append(sprintf("%s.add_argument(%s)",
private$name, convert_..._to_arguments("add_argument", ...)))
return(invisible(NULL))
}
),
private = list(python_code = NULL, name = NULL)
)
Subparsers <- R6Class("Subparsers", # nolint
public = list(
initialize = function(python_code, name) {
private$python_code <- python_code
private$name <- name
},
add_parser = function(...) {
parser_name <- paste0(private$name, "_subparser", private$n_subparsers)
private$n_subparsers <- private$n_subparsers + 1
private$python_code$append(sprintf("%s = %s.add_parser(%s)",
parser_name, private$name,
convert_..._to_arguments("ArgumentParser", ...)))
Parser$new(private$python_code, parser_name)
}
),
private = list(python_code = NULL, name = NULL, n_subparsers = 0)
)
Parser <- R6Class("Parser", # nolint
public = list(
parse_args = function(args = commandArgs(TRUE)) {
new_code <- c(sprintf("args = %s.parse_args([%s])", private$name,
paste(sprintf("'%s'", args), collapse = ", ")),
"print(json.dumps(args.__dict__, sort_keys=True))")
output <- private$python_code$run(new_code)
parse_args_output(output)
},
parse_intermixed_args = function(args = commandArgs(TRUE)) {
new_code <- c(sprintf("args = %s.parse_intermixed_args([%s])", private$name,
paste(sprintf("'%s'", args), collapse = ", ")),
"print(json.dumps(args.__dict__, sort_keys=True))")
output <- private$python_code$run(new_code)
parse_args_output(output)
},
parse_known_args = function(args = commandArgs(TRUE)) {
new_code <- c(sprintf("args_remainder = %s.parse_known_args([%s])", private$name,
paste(sprintf("'%s'", args), collapse = ", ")),
"print(json.dumps((args_remainder[0].__dict__, args_remainder[1])))")
output <- private$python_code$run(new_code)
parse_args_output(output)
},
parse_known_intermixed_args = function(args = commandArgs(TRUE)) {
new_code <- c(sprintf("args_remainder = %s.parse_known_intermixed_args([%s])", private$name,
paste(sprintf("'%s'", args), collapse = ", ")),
"print(json.dumps((args_remainder[0].__dict__, args_remainder[1])))")
output <- private$python_code$run(new_code)
parse_args_output(output)
},
format_help = function() {
paste(private$python_code$run(sprintf("%s.print_help()", private$name)),
collapse = "\n")
},
format_usage = function() {
paste(private$python_code$run(sprintf("%s.print_usage()", private$name)),
collapse = "\n")
},
print_help = function() {
cat(private$python_code$run(sprintf("%s.print_help()", private$name)), sep = "\n")
invisible(NULL)
},
print_usage = function() {
cat(private$python_code$run(sprintf("%s.print_usage()", private$name)), sep = "\n")
invisible(NULL)
},
get_default = function(...) {
stop("We don't currently support `get_default()`")
},
set_defaults = function(...) {
private$python_code$append(sprintf("%s.set_defaults(%s)", private$name,
convert_..._to_arguments("add_argument", ...)))
invisible(NULL)
},
add_argument = function(...) {
private$python_code$append(sprintf("%s.add_argument(%s)", private$name,
convert_..._to_arguments("add_argument", ...)))
invisible(NULL)
},
add_argument_group = function(...) {
group_name <- paste0(private$name, "_group", private$n_groups)
private$n_groups <- private$n_groups + 1
private$python_code$append(sprintf("%s = %s.add_argument_group(%s)",
group_name, private$name,
convert_..._to_arguments("add_argument", ...)))
Group$new(private$python_code, group_name)
},
add_mutually_exclusive_group = function(required = FALSE) {
group_name <- paste0(private$name, "_mutually_exclusive_group",
private$n_mutually_exclusive_groups)
private$n_mutually_exclusive_groups <- private$n_mutually_exclusive_groups + 1
private$python_code$append(sprintf("%s = %s.add_mutually_exclusive_group(%s)",
group_name, private$name,
ifelse(required, "required=True", "")))
Group$new(private$python_code, group_name)
},
add_subparsers = function(...) {
subparsers_name <- paste0(private$name, "_subparsers")
private$python_code$append(sprintf("%s = %s.add_subparsers(%s)",
subparsers_name, private$name,
convert_..._to_arguments("add_argument", ...)))
Subparsers$new(private$python_code, subparsers_name)
},
initialize = function(python_code, name) {
private$python_code <- python_code
private$name <- name
}
),
private = list(python_code = NULL, name = NULL,
n_mutually_exclusive_groups = 0, n_groups = 0)
)
parse_args_output <- function(output) {
if (grepl("^usage:", output[1])) {
has_positional_arguments <- any(grepl("^positional arguments:", output))
has_optional_arguments <- any(grepl("^optional arguments:|^options:", output))
if (has_positional_arguments || has_optional_arguments) {
print_message_and_exit(output, "help requested:")
} else {
pa_stop(output, "parse error:")
}
} else if (grepl("^Traceback", output[1])) {
pa_stop(output, "python error:")
} else if (any(grepl("^SyntaxError: Non-ASCII character", output))) {
message <- paste("Non-ASCII character detected.",
"If you wish to use Unicode arguments/options",
"please upgrade to Python 3.2+",
"Please see file INSTALL for more details.")
pa_stop(message, "non-ascii character error:")
} else if (any(grepl("^SyntaxError: positional argument follows keyword argument", output)) ||
grepl("^SyntaxError: non-keyword arg after keyword arg", output[2])) {
message <- "Positional argument following keyword argument."
pa_stop(message, "syntax error:")
} else if (grepl("^\\{|^\\[", output)) {
args <- jsonlite::fromJSON(paste(output, collapse = ""))
return(args)
} else { # presumably version number request
print_message_and_exit(output, "version requested:")
}
}
# @param argument argument to be converted from R to Python
convert_argument <- function(argument, as_list = FALSE) {
if (is.character(argument)) argument <- convert_character(argument)
if (is.numeric(argument)) argument <- as.character(argument)
if (is.logical(argument)) argument <- ifelse(argument, "True", "False")
if (is.null(argument)) argument <- "None"
if (as_list) {
argument <- sprintf("[%s]", paste(argument, collapse = ", "))
} else if (length(argument) > 1) {
argument <- sprintf("(%s)", paste(argument, collapse = ", "))
}
argument
}
convert_character <- function(s) {
bool <- substr(s, nchar(s), nchar(s)) == '"'
ifelse(bool, paste0("r'''", s, "'''"), paste0('r"""', s, '"""'))
}
get_python_type <- function(type, proposed_arguments) {
python_type <- switch(type,
character = "str",
double = "float",
integer = "int",
logical = "logical",
numeric = "float",
stop(paste(sprintf("type %s not supported,", type),
"supported types:",
"'logical', 'integer', 'double' or 'character'")))
sprintf("type=%s", python_type)
}
should_as_list <- function(name, argument_list) {
if (name == "default" &&
(argument_list[["action"]] %||% "store") == "append") {
TRUE
} else {
FALSE
}
}
`%||%` <- function(x, y) if (is.null(x)) y else x # nolint
# @param mode Either "add_argument" or "ArgumentParser"
convert_..._to_arguments <- function(mode, ...) { # nolint
argument_list <- list(...)
argument_names <- names(argument_list)
if (is.null(argument_names))
argument_names <- rep_len("", length(argument_list))
equals <- ifelse(argument_names == "", "", "=")
proposed_arguments <- c()
for (ii in seq_along(argument_list)) {
name <- argument_names[ii]
equal <- equals[ii]
as_list <- should_as_list(name, argument_list)
argument <- convert_argument(argument_list[[ii]], as_list)
proposed_arguments <- append(proposed_arguments,
paste0(name, equal, argument))
}
# Make sure types are what Python wants
if (mode == "add_argument" && any(grepl("type=", proposed_arguments))) {
ii <- grep("type=", proposed_arguments)
type <- argument_list[[ii]]
proposed_arguments[ii] <- get_python_type(type, proposed_arguments)
}
# Don't put quotes around formatter_class argument
if (mode == "ArgumentParser" && any(grepl("formatter_class=", proposed_arguments))) {
ii <- grep("formatter_class=", proposed_arguments)
formatter_class <- argument_list[[ii]]
proposed_arguments[ii] <- sprintf("formatter_class=%s", formatter_class)
}
# Set right default prog name if not specified, if possible
# Do last to not screw up other fixes with prog insertion
if (mode == "ArgumentParser" && needs_prog(argument_names)) {
prog <- get_Rscript_filename()
if (is.na(prog)) prog <- "PROGRAM"
proposed_arguments <- c(sprintf("prog='%s'", prog), proposed_arguments)
}
return(paste(proposed_arguments, collapse = ", "))
}
needs_prog <- function(argument_names) {
if (length(argument_names) == 0L) {
TRUE
} else if (argument_names[1L] == "") {
FALSE
} else if (any(argument_names == "prog")) {
FALSE
} else {
TRUE
}
}
# Manually copied over from getopt to eliminate it as a dependency
get_Rscript_filename <- function() { # nolint
prog <- sub("--file=", "", grep("--file=", commandArgs(), value = TRUE)[1])
if (.Platform$OS.type == "windows") {
prog <- gsub("\\\\", "\\\\\\\\", prog)
}
prog
}
# Internal function to check python cmd is okay
# @param python_cmd Python cmd to use
assert_python_cmd <- function(python_cmd) {
if (!findpython::is_python_sufficient(python_cmd, required_modules = c("argparse", "json | simplejson"))) {
stop(paste(sprintf("python executable %s either is not installed,", python_cmd),
"is not on the path, or does not have argparse, json modules",
"please see INSTALL file"))
}
}
required_modules <- c("argparse", "json | simplejson")
detects_python <- function(...) {
python_cmd <- try(find_python_cmd())
!inherits(python_cmd, "try-error") &&
findpython::is_python_sufficient(python_cmd, ..., required_modules = required_modules)
}
# Internal function to find python cmd
# @param python_cmd Python cmd to use
find_python_cmd <- function(python_cmd = NULL) {
if (is.null(python_cmd)) {
python_cmd <- getOption("python_cmd")
}
if (is.null(python_cmd)) {
did_find_python3 <- findpython::can_find_python_cmd(minimum_version = "3.0",
required_modules = required_modules,
silent = TRUE)
if (did_find_python3) {
python_cmd <- attr(did_find_python3, "python_cmd")
} else {
python_cmd <- findpython::find_python_cmd(required_modules = required_modules)
}
}
python_cmd <- normalizePath(python_cmd, mustWork = FALSE)
python_cmd
}
quieter_error_handler <- function(e) {
quit('no', status = 1, runLast = FALSE)
}
pa_stop <- function(message, r_note) {
msg <- paste(c(r_note, message), collapse = "\n")
cnd <- errorCondition(msg,
call = "argparse::parse_args_output(output)",
class = "argparse_parse_error")
if (interactive()) {
stop(cnd)
} else {
signalCondition(cnd)
cat(message, sep = "\n", file = stderr())
opt <- options(error = getOption("error", quieter_error_handler),
show.error.messages = FALSE)
on.exit(options(opt))
stop(cnd)
}
}
# Internal function to print message
print_message_and_exit <- function(message, r_note) {
if (interactive()) {
pa_stop(message, r_note)
} else {
cat(message, sep = "\n")
quit(status = 0)
}
}
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