R/endpoint.R

In cjvanlissa/worcs: Workflow for Open Reproducible Code in Science

#' @title Add endpoint to WORCS project
#' @description Add a specific endpoint to the WORCS project file. Endpoints are
#' files that are expected to be exactly reproducible (e.g., a manuscript,
#' figure, table, et cetera). Reproducibility is checked by ensuring the
#' endpoint's checksum is unchanged.
#' @param filename Character, indicating the file to be tracked as endpoint.
#' Default: NULL.
#' @param worcs_directory Character, indicating the WORCS project directory
#' to which to save data. The default value "." points to the current directory.
#' Default: '.'
#' @param verbose Logical. Whether or not to print status messages to the
#' console. Default: TRUE
#' @param ... Additional arguments.
#' @return No return value. This function is called for its side effects.
#' @examples
#' # Create directory to run the example
#' old_wd <- getwd()
#' test_dir <- file.path(tempdir(), "add_endpoint")
#' dir.create(test_dir)
#' setwd(test_dir)
#' file.create(".worcs")
#' writeLines("test", "test.txt")
#' add_endpoint("test.txt")
#' # Cleaning example directory
#' setwd(old_wd)
#' unlink(test_dir, recursive = TRUE)
#' @rdname add_endpoint
#' @seealso
#'  \code{\link[worcs]{snapshot_endpoints}}
#'  \code{\link[worcs]{check_endpoints}}
#' @export
#' @importFrom yaml read_yaml
add_endpoint <- function(filename = NULL, worcs_directory = ".", verbose = TRUE, ...){
  dn_worcs <- dirname(check_recursive(file.path(normalizePath(worcs_directory),
                                                        ".worcs")))
  fn_worcs <- file.path(dn_worcs, ".worcs")
  worcsfile <- yaml::read_yaml(fn_worcs)
  endpoints <- worcsfile[["endpoints"]]
  # if(is.null(entry_point)){
  #   if(is.null(worcsfile[["entry_point"]])){
  #     stop("No 'entry_point' specified, and the project contains no existing entry points.")
  #   } else {
  #     if(length(worcsfile[["entry_point"]]) > 1){
  #       stop("No 'entry_point' specified, and the project contains multiple entry points. Specify one of the following: ", paste0("'", names(worcsfile[["entry_point"]])))
  #     }
  #   }
  #
  # }
  fn_endpoint <- path_abs_worcs(filename, dn_worcs)
  if(!file.exists(fn_endpoint)){
    stop("The file does not exist: ", filename)
  }
  endpoints <- append(endpoints, filename)
  endpoints <- unique(endpoints)
  # Append worcsfile
  out <- try({
    write_worcsfile(filename = fn_worcs, endpoints = endpoints, modify = TRUE)
    store_checksum(fn_endpoint, entry_name = filename, worcsfile = fn_worcs)
    })
  if(inherits(out, "try-error")){
    col_message("Could not add endpoint '", filename, "' to '.worcs'.",
                        verbose = verbose, success = FALSE)
  } else {
    col_message("Adding endpoint '", filename, "' to '.worcs'.",
                        verbose = verbose)
  }
}

#' @title Snapshot endpoints in WORCS project
#' @description Update the checksums of all endpoints in a WORCS project.
#' @param worcs_directory Character, indicating the WORCS project directory
#' to which to save data. The default value "." points to the current directory.
#' Default: '.'
#' @param verbose Logical. Whether or not to print status messages to the
#' console. Default: TRUE
#' @param ... Additional arguments.
#' @return No return value. This function is called for its side effects.
#' @examples
#' # Create directory to run the example
#' old_wd <- getwd()
#' test_dir <- file.path(tempdir(), "update_endpoint")
#' dir.create(test_dir)
#' setwd(test_dir)
#' file.create(".worcs")
#' writeLines("test", "test.txt")
#' add_endpoint("test.txt")
#' writeLines("second test", "test.txt")
#' snapshot_endpoints()
#' # Cleaning example directory
#' setwd(old_wd)
#' unlink(test_dir, recursive = TRUE)
#' @seealso
#'  \code{\link[worcs]{add_endpoint}}
#'  \code{\link[worcs]{check_endpoints}}
#' @export
snapshot_endpoints <- function(worcs_directory = ".", verbose = TRUE, ...){
  dn_worcs <- dirname(check_recursive(file.path(normalizePath(worcs_directory),
                                                        ".worcs")))
  fn_worcs <- file.path(dn_worcs, ".worcs")
  worcsfile <- yaml::read_yaml(fn_worcs)
  if(is.null(worcsfile[["endpoints"]])){
    col_message("No endpoints found in WORCS project.", verbose = verbose, success = FALSE)
  }
  endpoints <- worcsfile[["endpoints"]]
  for(ep in endpoints){
    out <- try({
      fn_endpoint <- path_abs_worcs(ep, dn_worcs)
      store_checksum(fn_endpoint, entry_name = ep, worcsfile = fn_worcs)
    })
    if(inherits(out, "try-error")){
      col_message("Could not snapshot endpoint '", ep, "'.",
                          verbose = verbose, success = FALSE)
    } else {
      col_message("Update snapshot of endpoint '", ep, "'.",
                          verbose = verbose)
    }
  }
}

#' @title Check endpoints in WORCS project
#' @description Check that the checksums of all endpoints in a WORCS project
#' match their snapshots.
#' @param worcs_directory Character, indicating the WORCS project directory
#' to which to save data. The default value "." points to the current directory.
#' Default: '.'
#' @param verbose Logical. Whether or not to print status messages to the
#' console. Default: TRUE
#' @param ... Additional arguments.
#' @return Returns a logical value (TRUE/FALSE) invisibly.
#' @examples
#' # Create directory to run the example
#' old_wd <- getwd()
#' test_dir <- file.path(tempdir(), "check_endpoint")
#' dir.create(test_dir)
#' setwd(test_dir)
#' file.create(".worcs")
#' writeLines("test", "test.txt")
#' add_endpoint("test.txt")
#' check_endpoints()
#' # Cleaning example directory
#' setwd(old_wd)
#' unlink(test_dir, recursive = TRUE)
#' @seealso
#'  \code{\link[worcs]{add_endpoint}}
#'  \code{\link[worcs]{snapshot_endpoints}}
#' @export
check_endpoints <- function(worcs_directory = ".", verbose = TRUE, ...){
  dn_worcs <- dirname(check_recursive(file.path(normalizePath(worcs_directory),
                                                        ".worcs")))
  fn_worcs <- file.path(dn_worcs, ".worcs")
  worcsfile <- yaml::read_yaml(fn_worcs)
  if(is.null(worcsfile[["endpoints"]])){
    if(interactive()){
      col_message("No endpoints found in WORCS project.", verbose = verbose, success = FALSE)
    } else {
      stop("No endpoints found in WORCS project.")
    }

  }
  endpoints <- worcsfile[["endpoints"]]
  replicates <- rep(x = TRUE, times = length(endpoints))
  for(i in seq_along(endpoints)){
    ep <- endpoints[i]
    out <- try({
      #fn_endpoint <- path_abs_worcs(ep, dn_worcs)
      # Use absolute file path here
      check_sum(file.path(dn_worcs, ep), old_cs = worcsfile[["checksums"]][[ep]], worcsfile = fn_worcs, error = TRUE)
    }, silent = TRUE)
    if(inherits(out, "try-error")){
      col_message("Endpoint '", ep, "' did not replicate.",
                          verbose = verbose, success = FALSE)
      replicates[i] <- FALSE
    } else {
      col_message("Endpoint '", ep, "' replicates.",
                          verbose = verbose)
    }
  }
  if(!interactive()){
    if(any(!replicates)){
      # git_record <- system2("git", paste0('-C "', dirname(fn_worcs), '" ls-files --eol'), stdout = TRUE)
      # git_record <- git_record[grepl(endpoints[1], git_record, fixed = TRUE)]
      # stop("Endpoints ", paste0(endpoints[which(!replicates)], collapse = ", "), " did not replicate. Checksum of record: ", worcsfile[["checksums"]][[endpoints[1]]], ", local checksum: ", cs_fun(ep, fn_worcs), ", git ls: ", git_record)
      stop("Endpoints ", paste0(endpoints[which(!replicates)], collapse = ", "), " did not replicate. Make sure that the endpoint snapshot and renv are up to date, and verify that differences are not due to Git changing the line endings of text files.")
    }
  }
  return(invisible(all(replicates)))
}

#' @title Set up GitHub Actions to Check Endpoints
#' @description Sets up a GitHub Action to perform continuous integration (CI)
#' for a WORCS project. CI automatically evaluates `check_endpoints()` or
#' `reproduce(check_endpoints = TRUE)`.
#' at each push or pull request.
#' @param worcs_directory Character, indicating the WORCS project directory
#' to which to save data. The default value "." points to the current directory.
#' Default: '.'
#' @return No return value. This function is called for its side effects.
#' @seealso
#'  \code{\link[usethis]{use_github_action}}
#'  \code{\link[worcs]{add_endpoint}}
#'  \code{\link[worcs]{check_endpoints}}
#' @export
#' @importFrom usethis use_github_action
github_action_check_endpoints <- function(worcs_directory = "."){
  github_action_generic(worcs_directory = worcs_directory, url = "https://github.com/cjvanlissa/actions/blob/main/worcs_endpoints.yaml")
}


#' @rdname github_action_check_endpoints
#' @export
#' @importFrom usethis use_github_action
github_action_reproduce <- function(worcs_directory = "."){
  # Check if all data sources will be available on GitHub
  has_data <- check_data_resources(dn_worcs = worcs_directory,
                                   worcsfile = NULL,
                                   verbose = TRUE)
  gitig <- readLines(file.path(worcs_directory, ".gitignore"))
  if(any(has_data$data_files %in% gitig)){
    col_message(paste0("The following original data sources are not available on GitHub, which could prevent the GitHub action from reproducing your analysis:\n", paste0(has_data$data_files[which(has_data$data_files %in% gitig)], collapse = ", ")), success = FALSE)
  }
  github_action_generic(worcs_directory = worcs_directory, url = "https://github.com/cjvanlissa/actions/blob/main/worcs_reproduce.yaml")
}

github_action_generic <- function(worcs_directory = ".", url = NULL){
  Args <- list(
    url = url
  )
  if(!normalizePath(getwd()) == normalizePath(worcs_directory)){
    usethis::ui_info("The current directory is not the same as 'worcs_directory'. The GitHub action might not install correctly.")
  }

  if("badge" %in% names(formals(usethis::use_github_action))){
    Args$badge <- TRUE
    if(file.exists(file.path(worcs_directory, "README.md"))){
      Args$readme <- file.path(worcs_directory, "README.md")
    }
  } else {
    usethis::ui_oops("Could not add badge to readme.md; consider updating the 'usethis' package by running install.packages('usethis').")
  }
  do.call(usethis::use_github_action, Args)
}