R/dockerfile.R

In thebioengineer/dockyard: Provide tools for interfacing and building docker containers in R

#' @export
#' @title Describe the base docker image to use
#' @description Creating a docker image in a dockerfile requires specification
#'    of the base image to be creating your new docker image off of. {dockyard}
#'    assumes the user is basing their image off the latest available image
#'    from rocker/r-base, but it can be changed at any time.
#' @param df a dockerfile object from `dockerfile()`
#' @param image Repository address in the format username/image[:tag]
#' @return dockerfile
#' @examples
#' # Start a dockerfile based off of the rocker/shiny image to generate a
#' # shiny server using R version 3.6.1
#' dockerfile() %>%
#'   from("rocker/r-ver:devel")
#' @family dockerfile
#'
from <- function(df, image = "rocker/r-base") {
  if(!check_docker_imagename(image)){
    stop("Enter a valid docker image in the format username/image[:tag]")
  }
  add_base_image(df, image)
}


#' @export
#' @title Run update docker image
#' @description Add command when creating docker image to update installed software
#' @param df a dockerfile object from `dockerfile()`
#' @return dockerfile
#' @examples
#' # Start a dockerfile based off of the rocker/shiny image to generate a
#' # shiny server using R version 3.6.1
#' dockerfile() %>%
#'   from("rocker/r-ver:devel") %>%
#'   update()
#' @family dockerfile
#'
update <- function(df) {
  add_command(df, "RUN apt-get update -qq")
}

#' @export
#' @title Apt-get install software
#' @description Add software to install to docker image via `apt-get`
#' @param df a dockerfile object from `dockerfile()`
#' @param ... The software to install to the docker image
#' @return dockerfile
#' @examples
#' # Start a dockerfile based off of the rocker/shiny image to generate a
#' # shiny server using R version 3.6.1, update all existing software
#' # and install git and curl.
#'
#' dockerfile() %>%
#'   from("rocker/r-ver:devel") %>%
#'   update() %>%
#'   install("sudo","gdebi","pandoc","pandoc-citeproc",
#'           "libcurl4-gnutls-dev","libcairo2-dev",
#'           "libxtdev","wget")
#' @family dockerfile
#'
install <- function(df, ...) {
  to_install <- match.call(expand.dots = FALSE)$`...`
  install_command <- paste(
    "apt-get install -y ",
    paste0(to_install, collapse = " ")
  )
  run(df, install_command)
}

#' @export
#' @title Install packages for R
#' @description install packages from the default CRAN location for R
#' @param df a dockerfile object from `dockerfile()`
#' @param ... The R packages to install to the docker image
#' @param new boolean indicating if the command should be added to the prior `Run`` line.
#'  Useful for when breaking out lines in the docker image to skip time consuming library build steps.
#'  defaults to FALSE.
#' @examples
#' # Start a dockerfile based off of the rocker/shiny image to generate a
#' # shiny server using R version 3.6.1, update all existing software
#' # and install git and curl.
#'
#' dockerfile() %>%
#'  from("rocker/r-ver:devel") %>%
#'  update() %>%
#'  install("sudo","gdebi","pandoc","pandoc-citeproc",
#'          "libcurl4-gnutls-dev","libcairo2-dev",
#'          "libxtdev","wget") %>%
#'   install_r_lib("tidyverse")
#' @family dockerfile
#'
install_r_lib <- function(df, ..., new = FALSE) {
  to_install <- match.call(expand.dots = FALSE)$`...`

  install_command <- paste(
    "R -e \"install.packages(c(",
    paste0("'", to_install, "'", collapse = ", "),
    "))\""
  )

  run(df, install_command, new = new)
}

#' @export
#' @title Install specific package version for R
#' @description install packages from the default CRAN location for R
#' @param df a dockerfile object from `dockerfile()`
#' @param package The R package to install to the docker image as a character.
#' @param version The version R package to install to the docker image as a character.
#' @param new boolean indicating if the command should be added to the prior `Run`` line.
#'  Useful for when breaking out lines in the docker image to skip time consuming library build steps.
#'  defaults to FALSE.
#' @examples
#' # Start a dockerfile based off of the rocker/shiny image to generate a
#' # shiny server using R version 3.6.1, update all existing software
#' # and install git and curl.
#'
#' dockerfile() %>%
#'  from("rocker/r-ver:devel") %>%
#'  update() %>%
#'  install("sudo","gdebi","pandoc","pandoc-citeproc",
#'          "libcurl4-gnutls-dev","libcairo2-dev",
#'          "libxtdev","wget") %>%
#'   install_r_lib("tidyverse") %>%
#'   install_r_lib_version("ggplot2", version = "0.9.1")
#' @family dockerfile
#'
install_r_lib_version <- function(df, package, version, new = FALSE) {

  stopifnot(length(package)==length(version))

  install_command <- paste(
    "R -e \"if(!require(remotes)){install.packages('remotes');library(remotes)};",
     paste0("remotes::install_version(package = '",
            package, "', version = '",version,"')", collapse = ";"),
     "))\"")

  run(df, install_command)
}


#' @export
#' @title RUN command in docker image
#' @description Command to be run in the docker image during building the image.
#' @param df a dockerfile object from `dockerfile()`
#' @param cmd command to be run in the docker image during build
#' @param new boolean indicating if the command should be added to the prior line.
#'  Useful for when breaking out lines in the docker image to skip time consuming build steps.
#'   defaults to FALSE.
#' @examples
#' # Start a dockerfile based off of the rocker/shiny image to generate a
#' # shiny server using R version 3.6.1, update all existing software
#' # and install git and curl. Then initialize Rstudio server
#'
#' dockerfile() %>%
#'  from("rocker/r-ver:devel") %>%
#'  update() %>%
#'  install("sudo","gdebi","pandoc","pandoc-citeproc",
#'          "libcurl4-gnutls-dev","libcairo2-dev",
#'          "libxtdev","wget") %>%
#'   run("wget --no-verbose
#'        https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION
#'        -O version.txt") %>%
#'   run("VERSION=$(cat version.txt)") %>%
#'   run("wget --no-verbose
#'        https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$VERSION-amd64.deb
#'        -O ss-latest.deb") %>%
#'   run("gdebi -n ss-latest.deb") %>%
#'   run("rm -f version.txt ss-latest.deb") %>%
#'   run(". /etc/environment") %>%
#'   install_r_lib("shiny","rmarkdown") %>%
#'   run("cp -R /usr/local/lib/R/site-library/shiny/examples/* /srv/shiny-server/")
#'
#' @family dockerfile
#'
run <- function(df, cmd, new = FALSE) {
  if(grepl("^RUN",df[length(df)]) & !new){
    command<-paste(df[[length(df)]], "&&", cmd )
    update_command(df,length(df),command)
  }else{
    command <- paste("RUN", cmd)
    add_command(df, command)
  }
}

#' @export
#' @title EXPOSE a port from the docker image
#' @description Command to expose a port from inside the docker container through
#' @param df a dockerfile object from `dockerfile()`
#' @param port the port to be exposing from the docker container
#' @param type port open type (defaults to null)
#' @examples
#' # Start a dockerfile based off of the rocker/shiny image to generate a
#' # shiny server using R version 3.6.1, update all existing software
#' # and install git and curl. Then initialize Rstudio server, and copy in a config file
#'
#' dockerfile() %>%
#'  from("rocker/r-ver:devel") %>%
#'  update() %>%
#'  install("sudo","gdebi","pandoc","pandoc-citeproc",
#'          "libcurl4-gnutls-dev","libcairo2-dev",
#'          "libxtdev","wget") %>%
#'   run("wget --no-verbose
#'        https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION
#'         -O version.txt") %>%
#'   run("VERSION=$(cat version.txt)") %>%
#'   run("wget --no-verbose
#'        https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$VERSION-amd64.deb
#'        -O ss-latest.deb") %>%
#'   run("gdebi -n ss-latest.deb") %>%
#'   run("rm -f version.txt ss-latest.deb") %>%
#'   run(". /etc/environment") %>%
#'   install_r_lib("shiny","rmarkdown") %>%
#'   run("cp -R /usr/local/lib/R/site-library/shiny/examples/* /srv/shiny-server/") %>%
#'   expose(3838)
#'
#' @family dockerfile
#'
expose <- function(df,port,type=NULL){
  valid_ports<-c(1023,65535)
  if(port<valid_ports[1] | port>valid_ports[2]){
    stop("Enter a valid port number between ",valid_ports[1]," and ",valid_ports[2],".")
  }
  if(!is.null(type)){
    port <- paste0(port,"/",type)
  }
  cmd <- paste("EXPOSE",port)
  add_command(df, cmd)
}

#' @export
#' @title Copy files into docker image
#' @description Command to copy files in the docker image during building the image.
#' @param df a dockerfile object from `dockerfile()`
#' @param source file to be copied from your local computer or URL to use
#' @param dir location the file is to be copied to
#' @examples
#' # Start a dockerfile based off of the rocker/shiny image to generate a
#' # shiny server using R version 3.6.1, update all existing software
#' # and install git and curl. Then initialize Rstudio server, and copy in a config file
#'
#' dockerfile() %>%
#'  from("rocker/r-ver:devel") %>%
#'  update() %>%
#'  install("sudo","gdebi","pandoc","pandoc-citeproc",
#'          "libcurl4-gnutls-dev","libcairo2-dev",
#'          "libxtdev","wget") %>%
#'   run("wget --no-verbose
#'        https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION
#'        -O version.txt") %>%
#'   run("VERSION=$(cat version.txt)") %>%
#'   run("wget --no-verbose
#'        https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$VERSION-amd64.deb
#'         -O ss-latest.deb") %>%
#'   run("gdebi -n ss-latest.deb") %>%
#'   run("rm -f version.txt ss-latest.deb") %>%
#'   run(". /etc/environment") %>%
#'   install_r_lib("shiny","rmarkdown") %>%
#'   run("cp -R /usr/local/lib/R/site-library/shiny/examples/* /srv/shiny-server/") %>%
#'   expose(3838) %>%
#'   copy("shiny-server.sh", "/usr/bin/shiny-server.sh")
#'
#' @family dockerfile
#'
copy <- function(df, source, dir) {
  install_command <- paste("COPY", source, dir)
  add_command(df, install_command)
}

#' @export
#' @title Copy files from a URL into docker image
#' @description Command to copy files from a URL into the docker image during building the image.
#' @param  file the output file to save the URL document as
#' @examples
#' # Start a dockerfile based off of the rocker/shiny image to generate a
#' # shiny server using R version 3.6.1, update all existing software
#' # and install git and curl. Then initialize Rstudio server, and copy in a config file
#'
#' dockerfile() %>%
#'  from("rocker/r-ver:devel") %>%
#'  update() %>%
#'  install("sudo","gdebi","pandoc","pandoc-citeproc",
#'          "libcurl4-gnutls-dev","libcairo2-dev",
#'          "libxtdev","wget","curl") %>%
#'   run("wget --no-verbose
#'       https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION
#'        -O version.txt") %>%
#'   run("VERSION=$(cat version.txt)") %>%
#'   run("wget --no-verbose
#'        https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$VERSION-amd64.deb
#'        -O ss-latest.deb") %>%
#'   run("gdebi -n ss-latest.deb") %>%
#'   run("rm -f version.txt ss-latest.deb") %>%
#'   run(". /etc/environment") %>%
#'   install_r_lib("shiny","rmarkdown") %>%
#'   run("cp -R /usr/local/lib/R/site-library/shiny/examples/* /srv/shiny-server/") %>%
#'   expose(3838) %>%
#'   copy_from_url("https://raw.githubusercontent.com/rocker-org/shiny/master/shiny-server.sh",
#'                 "/usr/bin/shiny-server.sh")
#'
#' @family dockerfile
#' @rdname copy
#'
copy_from_url<-function(df,source,file){
  copy_command <- paste("curl", source,">", file)
  run(df, copy_command)
}

#' @export
#' @title Add files from local computerinto docker image
#' @description Command to ADd files from local computer into the docker image during building the image.
#' @examples
#' # Start a dockerfile based off of the rocker/shiny image to generate a
#' # shiny server using R version 3.6.1, update all existing software
#' # and install git and curl. Then initialize Rstudio server, and copy in a config file
#'
#' dockerfile() %>%
#'  from("rocker/r-ver:devel") %>%
#'  update() %>%
#'  install("sudo","gdebi","pandoc","pandoc-citeproc",
#'          "libcurl4-gnutls-dev","libcairo2-dev",
#'          "libxtdev","wget","curl") %>%
#'   run("wget --no-verbose
#'        https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION
#'        -O version.txt") %>%
#'   run("VERSION=$(cat version.txt)") %>%
#'   run("wget --no-verbose
#'        https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$VERSION-amd64.deb
#'        -O ss-latest.deb") %>%
#'   run("gdebi -n ss-latest.deb") %>%
#'   run("rm -f version.txt ss-latest.deb") %>%
#'   run(". /etc/environment") %>%
#'   install_r_lib("shiny","rmarkdown") %>%
#'   run("cp -R /usr/local/lib/R/site-library/shiny/examples/* /srv/shiny-server/") %>%
#'   expose(3838) %>%
#'   copy_from_url("https://raw.githubusercontent.com/rocker-org/shiny/master/shiny-server.sh",
#'                 "/usr/bin/shiny-server.sh") %>%
#'   add("/my/local/shiny/folder/","/srv/shiny-server/")
#'
#' @family dockerfile
#' @rdname copy
#'
add <- function(df, source, dir) {
  # if(!(dir.exists(source)|file.exists(source))){
  #   stop("`source` not found. Please supply a valid source.")
  # }
  Add_command <- paste("ADD", source, dir)
  add_command(df, Add_command)
}

#' @export
#' @title Command to exectute on docker image creation
#' @description desctribe the script to be executed on docker image creation
#' @param df a dockerfile object from `dockerfile()`
#' @param ... commands with arguments to be executed as a series of character vectors
#' @examples
#' # Start a dockerfile based off of the rocker/shiny image to generate a
#' # shiny server using R version 3.6.1, update all existing software
#' # and install git and curl. Then initialize Rstudio server, and copy in a config file
#'
#' dockerfile() %>%
#'  from("rocker/r-ver:devel") %>%
#'  update() %>%
#'  install("sudo","gdebi","pandoc","pandoc-citeproc",
#'          "libcurl4-gnutls-dev","libcairo2-dev",
#'          "libxtdev","wget") %>%
#'   run("wget --no-verbose
#'        https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION
#'        -O version.txt") %>%
#'   run("VERSION=$(cat version.txt)") %>%
#'   run("wget --no-verbose
#'        https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$VERSION-amd64.deb
#'         -O ss-latest.deb") %>%
#'   run("gdebi -n ss-latest.deb") %>%
#'   run("rm -f version.txt ss-latest.deb") %>%
#'   run(". /etc/environment") %>%
#'   install_r_lib("shiny","rmarkdown") %>%
#'   run("cp -R /usr/local/lib/R/site-library/shiny/examples/* /srv/shiny-server/") %>%
#'   expose(3838) %>%
#'   copy("shiny-server.sh", "/usr/bin/shiny-server.sh") %>%
#'   cmd("/usr/bin/shiny-server.sh")
#'
#' @family dockerfile
#'
cmd <- function(df, ...) {
  args<-match.call(expand.dots = FALSE)$...
  cmd_run <- paste0("CMD [", paste0("\"",args,"\"",collapse = ", "), "]")
  add_command(df, cmd_run)
}


#' @export
#' @title RUN command in docker image
#' @description Command to cope files  in the docker image during building the image.
#' @param df a dockerfile object from `dockerfile()`
#' @param path path to where the dockerfile will be saved at
#' @param overwrite should the current dockefile be overwritten?
#' @examples
#' # Start a dockerfile based off of the rocker/shiny image to generate a
#' # shiny server using R version 3.6.1, update all existing software
#' # and install git and curl. Then initialize Rstudio server, and copy in a config file
#'
#' new_dockerfile <- tempfile(pattern = "new_dockerfile_", fileext = "")
#'
#'
#' df <- dockerfile() %>%
#'   from("rocker/shiny:3.6.1") %>%
#'   update() %>%
#'   install("git", "libcurl4-openssl-dev") %>%
#'   install_r_lib("rcurl", "dplyr") %>%
#'   run("wget --no-check-certificate
#'    https://raw.githubusercontent.com/rocker-org/rstudio-daily/master/latest.R") %>%
#'   run("Rscript latest.R") %>%
#'   run("dpkg -i rstudio-server-daily-amd64.deb") %>%
#'   copy("userconf.sh", "/etc/cont-init.d/userconf") %>%
#'   write_dockerfile(new_dockerfile)
#' @family dockerfile
write_dockerfile <- function(df, path, overwrite = FALSE) {
  if (file.exists(path) & !overwrite) {
    stop("File already exists. Change overwrite to TRUE to overwrite existing dockerfile")
  }
  writeLines(commands(df), path, sep = "\n")
  attr(df, ".dockerfile") <- path
  class(df) <- "dockerfile"
  invisible(df)
}