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https://github.com/snystrom/cmdfun
Framework for building R interfaces to shell commands
https://github.com/snystrom/cmdfun
Last synced: 8 days ago
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Framework for building R interfaces to shell commands
- Host: GitHub
- URL: https://github.com/snystrom/cmdfun
- Owner: snystrom
- License: other
- Created: 2020-03-24T20:12:24.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2020-10-12T21:58:04.000Z (about 4 years ago)
- Last Synced: 2024-11-13T14:54:06.108Z (29 days ago)
- Language: R
- Homepage: https://snystrom.github.io/cmdfun
- Size: 897 KB
- Stars: 15
- Watchers: 1
- Forks: 1
- Open Issues: 13
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
Awesome Lists containing this project
- jimsghstars - snystrom/cmdfun - Framework for building R interfaces to shell commands (R)
README
---
title: "cmdfun"
output: github_document
---
[](https://www.tidyverse.org/lifecycle/#maturing)
[](https://www.repostatus.org/#active)
[](https://github.com/snystrom/cmdfun/actions)
[](https://codecov.io/gh/snystrom/cmdfun?branch=master)
## A simple framework for building shell interfaces
The purpose of `cmdfun` is to significantly reduce the overhead involved in
wrapping shell programs in R. The tools are intended to be intuitive and
lightweight enough to use for data scientists trying to get things done quickly,
but robust and full-fledged enough for developers to extend them to more
advanced use cases.
## Installation
Install the development version of `cmdfun` with:
```{r, eval=F}
if (!requireNamespace("remotes"))
install.packages("remotes")
remotes::install_github("snystrom/cmdfun")
```
## Quick Overview
The `cmdfun` framework provides mechanisms for capturing function arguments:
- `cmd_args_dots()` captures all arguments passed to `...`
- `cmd_args_named()` captures all keyword arguments defined by the user
- `cmd_args_all()` captures both named + dot arguments
```{r}
library(cmdfun)
myFunction <- function(input, ...){
cmd_args_all()
}
(argsList <- myFunction(input = "test", boolean_flag = TRUE))
```
`cmd_list_interp` converts the captured argument list to a parsed list of
flag/value pairs.
```{r}
(flagsList <- cmd_list_interp(argsList))
```
`cmd_list_to_flags` converts a list to a vector of
commandline-style flags using the list names as flag names and the list values
as the flag values (empty values return only the flag). This output can be
directly fed to `system2` or `processx`.
```{r}
cmd_list_to_flags(flagsList)
```
`cmd_path_search()` allows package builders to search default locations for installed tools.
```{r}
bin_path <- cmd_path_search(default_path = "/bin", utils = c("ls", "cut"))
bin_path(util = "ls")
```
## Introduction
`cmdfun` attempts to solve the problem of wrapping external software in R.
Calling external software is done with `system2` or `processx`.
For example, calling `ls -l *.md` using `system2`.
```{r}
system2("ls", "-l *.md", stdout = TRUE)
```
However, when using multiple commandline flags each flag should be passed as a
member of a character vector as follows:
When calling `ls -l -i`
```{r}
system2("ls", c("-l", "-i", "*.md"), stdout = TRUE)
```
This becomes even more difficult if trying to support user input, as a
significant amount of overhead is required to parse user inputs and optional
flags into these vectors.
`cmdfun` provides utilities for converting **function arguments** into **lists**
which can easily convert to **character vectors** suitable for use with
`system2` or `processx`.
```{r}
library(cmdfun)
myFunction <- function(input, option1){
# Grabs named arguments as key/value pairs
cmd_args_named()
}
(argsList <- myFunction("myInput.txt", "foo"))
```
```{r}
# Converts list to character vector of flags & values
cmd_list_to_flags(argsList)
```
### Wrapping `ls` with cmdfun
These tools can be used to easily wrap `ls`
```{r}
library(magrittr)
shell_ls <- function(dir = ".", ...){
# grab arguments passed to "..." in a list
flags <- cmd_args_dots() %>%
# prepare list for conversion to vector
cmd_list_interp() %>%
# Convert the list to a flag vector
cmd_list_to_flags()
# Run ls shell command
system2("ls", c(flags, dir), stdout = TRUE)
}
```
```{r}
shell_ls("*.md")
```
#### Boolean flags are passed as bool operators
`ls -l` can be mimicked by passing `l = TRUE` to '...'.
```{r}
shell_ls("*.md", l = TRUE)
```
### Named vectors can be used to provide user-friendly aliases for single-letter flags
Commandline tools can have hundreds of arguments, many with uninformative, often
single-letter, names. To prevent developers from having to write aliased
function arguments for all, often conflicting flags, `cmd_list_interp` can
additionally use a lookup table to allow developers to provide informative
function argument names for unintuitive flags.
For example, allowing `long` to act as `-l` in `ls`.
```{r}
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 renames
cmd_list_interp(names_arg_to_flag) %>%
cmd_list_to_flags()
system2("ls", c(flags, dir), stdout = TRUE)
}
```
```{r}
shell_ls_alias("*.md", long = TRUE)
```
### Wrapping `cut` with cmdfun
Here is another example wrapping `cut` which separates text on a delimiter (set
with `-d`) and returns selected fields (set with `-f`) from the separation.
```{r}
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)
}
```
```{r}
shell_cut("hello_world", fields = 2, sep = "_")
```
#### Multiple values are passed as vectors
```{r}
shell_cut("hello_world_hello", fields = c(1,3), sep = "_")
```
Additionally, `cmdfun` provides utilites for searching & checking valid tool
installs, expecting system behavior, and helpful error handling to allow simple
construction of external tool wrappers (see
[vignette](https://snystrom.github.io/cmdfun/articles/cmdfun.html) for details).
## More Details
See [https://snystrom.github.io/cmdfun/articles/cmdfun.html](https://snystrom.github.io/cmdfun/articles/cmdfun.html)
for the most recent documentation and to learn about all `cmdfun` features.
To file bug reports, please visit
[https://github.com/snystrom/cmdfun/issues](https://github.com/snystrom/cmdfun/issues)
while providing a [reproducible example](https://reprex.tidyverse.org/) of your
issue.