R/misc-handler.R

In sbg/sevenbridges-r: Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R

#' Handler instance
#'
#' Create Handler instance
#'
#' Used for parse R Markdown and lift into command line interface,
#' Dockerfile, Docker container, and cwl json.
#'
#' @field dockerfileHandler a function or NULL, how you handle Dockefile,
#' for example, push it to GitHub.
#' @field dockerHandler a function or NULL, how you handle local docker
#' container, for example, push it to DockerHub.
#' @field cwlHandler a function or NULL, how you handle cwl json file or
#' yaml file, for example, push it to SevenBridges platform as an app.
#'
#' @return a Handler object
Handler <- setRefClass(
  "Handler",
  fields = list(
    dockerfileHandler = "functionORNULL",
    dockerHandler = "functionORNULL",
    cwlHandler = "functionORNULL"
  )
)

gitHandler <- function(token = NULL) {

}

dockerhubHandler <- function(token = NULL) {
  # first login as DockerHub
  # then push Docker from Dockerfile
}

sevendockerHandler <- function(token = NULL) {

}

SevenHandler <- function(input = NULL, token = NULL, platform = NULL,
                         dockerReg = NULL, dockerfile = NULL) {

  # CGC handler
  dockerfileHandler <- function() {
    message("don't push dockerfile by default")
  }

  dockerHandler <- function() {
    message("do nothing")
  }

  cwlHandler <- function() {
    message("do nothing")
  }

  Handler(
    dockerfileHandler = dockerfileHandler,
    dockerHandler = dockerHandler,
    cwlHandler = cwlHandler
  )
}

# Create CGC handler
# Create SBG handler

# # TODO
# # lift R markdown into everything
# lift = function(input = NULL, output_dir = NULL,
#                 shebang = "#!/usr/local/bin/Rscript") {
#
#     opt_all_list = parse_rmd(input)
#
#     inl <- IPList(lapply(opt_all_list$rabix$inputs, function(i) {
#         do.call(sevenbridges::input, i)
#     }))
#
#     # insert the script
#     docker.fl <- file.path(normalizePath(output_dir), 'Dockerfile')
#     message(docker.fl)
#
#     # add script
#     write(paste("COPY", basename(normalizePath(tmp)), "/usr/local/bin/"),
#           file = docker.fl,
#           append = TRUE)
#     write("RUN mkdir /report/",
#           file = normalizePath(docker.fl),
#           append = TRUE)
#
#     # add report
#     report.file <- file.path(normalizePath(output_dir), basename(input))
#     file.copy(input, report.file)
#     write(paste("COPY", basename(input), "/report/"),
#           file = docker.fl,
#           append = TRUE)
#
# }