R/data.R

In ChristopherBarrington/datarepository: handles saving and loading project data

#' Load objects from a data repository
#' 
#' @description
#' A copy of the `utils::data` (4.1.0) function, copied into this namespace to use the `datarepository:::find.package()` function instead of `base::find.package`.
#' 
#' @param ... Object(s) to load from data repository _or_ loaded package
#' 
#' @seealso utils::data
#' @inherit utils::data
#'  
#' @export
#' 
data <- function(..., list=character(), package=NULL, lib.loc=NULL, verbose=getOption("verbose"), envir=.GlobalEnv, overwrite=TRUE, paths) {
    fileExt <- function(x) {
        db <- grepl("\\.[^.]+\\.(gz|bz2|xz)$", x)
        ans <- sub(".*\\.", "", x)
        ans[db] <- sub(".*\\.([^.]+\\.)(gz|bz2|xz)$", "\\1\\2",
            x[db])
        ans
    }
    my_read_table <- function(...) {
        lcc <- Sys.getlocale("LC_COLLATE")
        on.exit(Sys.setlocale("LC_COLLATE", lcc))
        Sys.setlocale("LC_COLLATE", "C")
        read.table(...)
    }
    names <- c(as.character(substitute(list(...))[-1L]), list)
    if (!is.null(package)) {
        if (!is.character(package))
            stop("'package' must be a character string or NULL")
        if (FALSE) {
            if (any(package %in% "base"))
                warning("datasets have been moved from package 'base' to package 'datasets'")
            if (any(package %in% "stats"))
                warning("datasets have been moved from package 'stats' to package 'datasets'")
            package[package %in% c("base", "stats")] <- "datasets"
        }
    }
    paths <- find.package(package, lib.loc, verbose = verbose)
    if (is.null(lib.loc))
        paths <- c(path.package(package, TRUE), if (!length(package)) getwd(), paths)
    paths <- unique(normalizePath(paths[file.exists(paths)]))
    paths <- paths[dir.exists(file.path(paths, "data"))]
    dataExts <- tools:::.make_file_exts("data")
    if (length(names) == 0L) {
        db <- matrix(character(), nrow = 0L, ncol = 4L)
        for (path in paths) {
            entries <- NULL
            packageName <- if (file_test("-f", file.path(path,
                "DESCRIPTION")))
                basename(path)
            else "."
            if (file_test("-f", INDEX <- file.path(path, "Meta",
                "data.rds"))) {
                entries <- readRDS(INDEX)
            }
            else {
                dataDir <- file.path(path, "data")
                entries <- tools::list_files_with_type(dataDir,
                  "data")
                if (length(entries)) {
                  entries <- unique(tools::file_path_sans_ext(basename(entries)))
                  entries <- cbind(entries, "")
                }
            }
            if (NROW(entries)) {
                if (is.matrix(entries) && ncol(entries) == 2L)
                  db <- rbind(db, cbind(packageName, dirname(path),
                    entries))
                else warning(gettextf("data index for package %s is invalid and will be ignored",
                  sQuote(packageName)), domain = NA, call. = FALSE)
            }
        }
        colnames(db) <- c("Package", "LibPath", "Item", "Title")
        footer <- if (missing(package))
            paste0("Use ", sQuote(paste("data(package =", ".packages(all.available = TRUE))")),
                "\n", "to list the data sets in all *available* packages.")
        else NULL
        y <- list(title = "Data sets", header = NULL, results = db,
            footer = footer)
        class(y) <- "packageIQR"
        return(y)
    }
    paths <- file.path(paths, "data")
    for (name in names) {
        found <- FALSE
        for (p in paths) {
            tmp_env <- if (overwrite)
                envir
            else new.env()
            if (file_test("-f", file.path(p, "Rdata.rds"))) {
                rds <- readRDS(file.path(p, "Rdata.rds"))
                if (name %in% names(rds)) {
                  found <- TRUE
                  if (verbose)
                    message(sprintf("name=%s:\t found in Rdata.rds",
                      name), domain = NA)
                  thispkg <- sub(".*/([^/]*)/data$", "\\1", p)
                  thispkg <- sub("_.*$", "", thispkg)
                  thispkg <- paste0("package:", thispkg)
                  objs <- rds[[name]]
                  lazyLoad(file.path(p, "Rdata"), envir = tmp_env,
                    filter = function(x) x %in% objs)
                  break
                }
                else if (verbose)
                  message(sprintf("name=%s:\t NOT found in names() of Rdata.rds, i.e.,\n\t%s\n",
                    name, paste(names(rds), collapse = ",")),
                    domain = NA)
            }
            if (file_test("-f", file.path(p, "Rdata.zip"))) {
                warning("zipped data found for package ", sQuote(basename(dirname(p))),
                  ".\nThat is defunct, so please re-install the package.",
                  domain = NA)
                if (file_test("-f", fp <- file.path(p, "filelist")))
                  files <- file.path(p, scan(fp, what = "", quiet = TRUE))
                else {
                  warning(gettextf("file 'filelist' is missing for directory %s",
                    sQuote(p)), domain = NA)
                  next
                }
            }
            else {
                files <- list.files(p, full.names = TRUE)
            }
            files <- files[grep(name, files, fixed = TRUE)]
            if (length(files) > 1L) {
                o <- match(fileExt(files), dataExts, nomatch = 100L)
                paths0 <- dirname(files)
                paths0 <- factor(paths0, levels = unique(paths0))
                files <- files[order(paths0, o)]
            }
            if (length(files)) {
                for (file in files) {
                  if (verbose)
                    message("name=", name, ":\t file= ...", .Platform$file.sep,
                      basename(file), "::\t", appendLF = FALSE,
                      domain = NA)
                  ext <- fileExt(file)
                  if (basename(file) != paste0(name, ".", ext))
                    found <- FALSE
                  else {
                    found <- TRUE
                    zfile <- file
                    zipname <- file.path(dirname(file), "Rdata.zip")
                    if (file.exists(zipname)) {
                      Rdatadir <- tempfile("Rdata")
                      dir.create(Rdatadir, showWarnings = FALSE)
                      topic <- basename(file)
                      rc <- .External(C_unzip, zipname, topic,
                        Rdatadir, FALSE, TRUE, FALSE, FALSE)
                      if (rc == 0L)
                        zfile <- file.path(Rdatadir, topic)
                    }
                    if (zfile != file)
                      on.exit(unlink(zfile))
                    switch(ext, R = , r = {
                      library("utils")
                      sys.source(zfile, chdir = TRUE, envir = tmp_env)
                    }, RData = , rdata = , rda = load(zfile,
                      envir = tmp_env), TXT = , txt = , tab = ,
                      tab.gz = , tab.bz2 = , tab.xz = , txt.gz = ,
                      txt.bz2 = , txt.xz = assign(name, my_read_table(zfile,
                        header = TRUE, as.is = FALSE), envir = tmp_env),
                      CSV = , csv = , csv.gz = , csv.bz2 = ,
                      csv.xz = assign(name, my_read_table(zfile,
                        header = TRUE, sep = ";", as.is = FALSE),
                        envir = tmp_env), found <- FALSE)
                  }
                  if (found)
                    break
                }
                if (verbose)
                  message(if (!found)
                    "*NOT* ", "found", domain = NA)
            }
            if (found)
                break
        }
        if (!found) {
            warning(gettextf("data set %s not found", sQuote(name)),
                domain = NA)
        }
        else if (!overwrite) {
            for (o in ls(envir = tmp_env, all.names = TRUE)) {
                if (exists(o, envir = envir, inherits = FALSE))
                  warning(gettextf("an object named %s already exists and will not be overwritten",
                    sQuote(o)))
                else assign(o, get(o, envir = tmp_env, inherits = FALSE),
                  envir = envir)
            }
            rm(tmp_env)
        }
    }
    invisible(names)
}

#' Find paths to loaded packages
#' 
#' @description
#' Prepends `data_repository_path()` to the result of the `base::find_package` function.
#' 
#' @return
#' Paths to all loaded packages (prepended with the data repository path) or the path to the specified `package`.
#' 
#' @importFrom magrittr %<>%
#' 
find.package <- function(...) {
  pkgs <- base::find.package(...)
  if(! 'package' %in% names(match.call(expand.dots=FALSE)$...))
    pkgs %<>% c(data_repository_path(), .)
  invisible(pkgs)
}