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cmdfun

A simpleframework for building shell interfaces

The purpose ofcmdfun is to significantly reduce theoverhead involved in wrapping shell programs in R. The tools areintended to be intuitive and lightweight enough to use for datascientists trying to get things done quickly, but robust andfull-fledged enough for developers to extend them to more advanced usecases.

Installation

Install the development version ofcmdfun with:

if (!requireNamespace("remotes"))install.packages("remotes")remotes::install_github("snystrom/cmdfun")

Quick Overview

Thecmdfun framework provides mechanisms for capturingfunction arguments:

• cmd_args_dots() captures all arguments passed to...
• cmd_args_named() captures all keyword arguments definedby the user
• cmd_args_all() captures both named + dot arguments

library(cmdfun)myFunction<-function(input, ...){cmd_args_all()}(argsList<-myFunction(input ="test",boolean_flag =TRUE))

## $input## [1] "test"## ## $boolean_flag## [1] TRUE

cmd_list_interp converts the captured argument list to aparsed list of flag/value pairs.

(flagsList<-cmd_list_interp(argsList))

## $input## [1] "test"## ## $boolean_flag## [1] ""

cmd_list_to_flags converts a list to a vector ofcommandline-style flags using the list names as flag names and the listvalues as the flag values (empty values return only the flag). Thisoutput can be directly fed tosystem2 orprocessx.

cmd_list_to_flags(flagsList)

## [1] "-input"        "test"          "-boolean_flag"

cmd_path_search() allows package builders to searchdefault locations for installed tools.

bin_path<-cmd_path_search(default_path ="/bin",utils =c("ls","cut"))bin_path(util ="ls")

## [1] "//bin/ls"

Introduction

cmdfun attempts to solve the problem of wrappingexternal software in R. Calling external software is done withsystem2 orprocessx.

For example, callingls -l *.md usingsystem2.

system2("ls","-l *.md",stdout =TRUE)

## [1] "-rw-r--r-- 1 snystrom its_employee_psx 1077 Aug 20 19:20 LICENSE.md"      ## [2] "-rw-r--r-- 1 snystrom its_employee_psx  837 Aug 26 21:51 NEWS.md"         ## [3] "-rw-r--r-- 1 snystrom its_employee_psx 7718 Aug 26 20:14 README.md"       ## [4] "-rw-r--r-- 1 snystrom its_employee_psx  744 Aug 26 21:35 cran-comments.md"

However, when using multiple commandline flags each flag should bepassed as a member of a character vector as follows:

When callingls -l -i

system2("ls",c("-l","-i","*.md"),stdout =TRUE)

## [1] "1163031755 -rw-r--r-- 1 snystrom its_employee_psx 1077 Aug 20 19:20 LICENSE.md"      ## [2] "1163031757 -rw-r--r-- 1 snystrom its_employee_psx  837 Aug 26 21:51 NEWS.md"         ## [3] "1163031758 -rw-r--r-- 1 snystrom its_employee_psx 7718 Aug 26 20:14 README.md"       ## [4] "1163031762 -rw-r--r-- 1 snystrom its_employee_psx  744 Aug 26 21:35 cran-comments.md"

This becomes even more difficult if trying to support user input, asa significant amount of overhead is required to parse user inputs andoptional flags into these vectors.

cmdfun provides utilities for convertingfunction arguments intolists whichcan easily convert tocharacter vectors suitable foruse withsystem2 orprocessx.

library(cmdfun)myFunction<-function(input, option1){# Grabs named arguments as key/value pairscmd_args_named()}(argsList<-myFunction("myInput.txt","foo"))

## $input## [1] "myInput.txt"## ## $option1## [1] "foo"

# Converts list to character vector of flags & valuescmd_list_to_flags(argsList)

## [1] "-input"      "myInput.txt" "-option1"    "foo"

Wrappingls withcmdfun

These tools can be used to easily wrapls

library(magrittr)shell_ls<-function(dir =".", ...){# grab arguments passed to "..." in a list  flags<-cmd_args_dots()%>%# prepare list for conversion to vectorcmd_list_interp()%>%# Convert the list to a flag vectorcmd_list_to_flags()# Run ls shell commandsystem2("ls",c(flags, dir),stdout =TRUE)}

shell_ls("*.md")

## [1] "LICENSE.md"       "NEWS.md"          "README.md"        "cran-comments.md"

Boolean flags arepassed as bool operators

ls -l can be mimicked by passingl = TRUEto ‘…’.

shell_ls("*.md",l =TRUE)

## [1] "-rw-r--r-- 1 snystrom its_employee_psx 1077 Aug 20 19:20 LICENSE.md"      ## [2] "-rw-r--r-- 1 snystrom its_employee_psx  837 Aug 26 21:51 NEWS.md"         ## [3] "-rw-r--r-- 1 snystrom its_employee_psx 7718 Aug 26 20:14 README.md"       ## [4] "-rw-r--r-- 1 snystrom its_employee_psx  744 Aug 26 21:35 cran-comments.md"

shell_ls_alias<-function(dir =".", ...){# Named vector acts as lookup table# name = function argument# value = flag name  names_arg_to_flag<-c("long"="l")  flags<-cmd_args_dots()%>%# Use lookup table to manage renamescmd_list_interp(names_arg_to_flag)%>%cmd_list_to_flags()system2("ls",c(flags, dir),stdout =TRUE)}

shell_ls_alias("*.md",long =TRUE)

## [1] "-rw-r--r-- 1 snystrom its_employee_psx 1077 Aug 20 19:20 LICENSE.md"      ## [2] "-rw-r--r-- 1 snystrom its_employee_psx  837 Aug 26 21:51 NEWS.md"         ## [3] "-rw-r--r-- 1 snystrom its_employee_psx 7718 Aug 26 20:14 README.md"       ## [4] "-rw-r--r-- 1 snystrom its_employee_psx  744 Aug 26 21:35 cran-comments.md"

shell_cut<-function(text, ...){  names_arg_to_flag<-c("sep"="d","fields"="f")    flags<-cmd_args_dots()%>%cmd_list_interp(names_arg_to_flag)%>%cmd_list_to_flags()system2("cut", flags,stdout = T,input = text)}

shell_cut("hello_world",fields =2,sep ="_")

## [1] "world"

shell_cut("hello_world_hello",fields =c(1,3),sep ="_")

## [1] "hello_hello"