arglist_parse: Normalise arguments for docker container

In outsider.base: Base Package for 'Outsider'

Description

Utility function for parsing the arguments provided by a user. Drop any specified key:value pairs with keyvals_to_drop or drop any specific values vals_to_drop. With normalise_paths as TRUE, all filepaths in the arglist will be converted to basenames.

Usage

arglist_parse(
  arglist,
  keyvals_to_drop = NULL,
  vals_to_drop = NULL,
  normalise_paths = TRUE
)

Arguments

arglist	Arguments as character vector
keyvals_to_drop	Argument keys to drop, e.g. -wd.
vals_to_drop	Specific values to drop, e.g. –verbose.
normalise_paths	Reduce paths to basenames? Default, TRUE.

Details

It is important the file paths are normalised, because they will not be available to the Docker container. The only files available will be those that have been transferred to the container as determined through the outsider_init. These files will be located in the same directory as where the function is called and require no absolute file path.

Value

Character vector

Examples

library(outsider.base)
wd <- file.path(tempdir(), 'results')
dir.create(wd)
arglist <- c('-a', 10, '-b', 'model2', '-wd', wd, '--unwanted')
# drop unwanted key:value pairs
(arglist_parse(arglist = arglist, keyvals_to_drop = '-wd',
               normalise_paths = FALSE))
# drop unwanted argument values
(arglist_parse(arglist = arglist, vals_to_drop = '--unwanted',
               normalise_paths = FALSE))
# make paths relative, necessary for Docker:
#   paths must be relative to the working directory in the container
(arglist_parse(arglist = arglist, normalise_paths = TRUE))


# clean-up
unlink(wd, recursive = TRUE)

outsider.base documentation built on April 19, 2021, 1:06 a.m.