using hoardr for cache path setup, rework pg_data to use hoardr object

DESCRIPTION

@@ -4,7 +4,7 @@ Description: Tools to interact with the 'Pangaea' Database
     (<https://www.pangaea.de>), including functions for searching for data,
     fetching 'datasets' by 'dataset' 'ID', and working with the 'Pangaea'
     'OAI-PMH' service.
-Version: 0.6.1.9100
+Version: 0.6.2.9100
 Authors@R: c(person("Scott", "Chamberlain",
 		email = "myrmecocystus@gmail.com", role = c("aut","cre")),
     person("Kara", "Woo", email = "woo.kara@gmail.com", role = "aut"),
@@ -22,10 +22,10 @@ Language: en-US
 Imports:
     crul (>= 0.4.0),
     jsonlite (>= 1.5),
-    rappdirs (>= 0.3.1),
     xml2 (>= 1.1.1),
     oai (>= 0.2.2),
     tibble (>= 1.1),
+    hoardr (>= 0.2.0),
     png
 Suggests:
     knitr,

NAMESPACE

@@ -2,6 +2,7 @@
 
 S3method(print,pangaea)
 S3method(print,pg_identify)
+export(pg_cache)
 export(pg_cache_clear)
 export(pg_cache_list)
 export(pg_data)
@@ -14,12 +15,12 @@ export(pg_list_sets)
 export(pg_search)
 export(pg_search_es)
 importFrom(crul,HttpClient)
+importFrom(hoardr,hoard)
 importFrom(oai,get_records)
 importFrom(oai,id)
 importFrom(oai,list_identifiers)
 importFrom(oai,list_metadataformats)
 importFrom(oai,list_sets)
-importFrom(rappdirs,user_cache_dir)
 importFrom(tibble,as_data_frame)
 importFrom(xml2,read_html)
 importFrom(xml2,xml_attr)

R/caching.R

@@ -1,6 +1,45 @@
-env <- new.env(parent = emptyenv())
-
-.onLoad <- function(libname, pkgname) {
-  path <- rappdirs::user_cache_dir("pangaear")
-  env$path <- path
-}
+#' @title Caching
+#'
+#' @description Manage cached `pangaear` files with \pkg{hoardr}
+#'
+#' @export
+#' @name pg_cache
+#'
+#' @details The dafault cache directory is
+#' `paste0(rappdirs::user_cache_dir(), "/R/pangaear")`, but you can set
+#' your own path using `cache_path_set()`
+#'
+#' `cache_delete` only accepts 1 file name, while
+#' `cache_delete_all` doesn't accept any names, but deletes all files.
+#' For deleting many specific files, use `cache_delete` in a [lapply()]
+#' type call
+#'
+#' @section Useful user functions:
+#' \itemize{
+#'  \item `pg_cache$cache_path_get()` get cache path
+#'  \item `pg_cache$cache_path_set()` set cache path
+#'  \item `pg_cache$list()` returns a character vector of full
+#'  path file names
+#'  \item `pg_cache$files()` returns file objects with metadata
+#'  \item `pg_cache$details()` returns files with details
+#'  \item `pg_cache$delete()` delete specific files
+#'  \item `pg_cache$delete_all()` delete all files, returns nothing
+#' }
+#'
+#' @examples \dontrun{
+#' pg_cache
+#'
+#' # list files in cache
+#' pg_cache$list()
+#'
+#' # delete certain database files
+#' # pg_cache$delete("file path")
+#' # pg_cache$list()
+#'
+#' # delete all files in cache
+#' # pg_cache$delete_all()
+#' # pg_cache$list()
+#'
+#' # set a different cache path from the default
+#' }
+NULL

R/onload.R

@@ -0,0 +1,8 @@
+# env <- new.env(parent = emptyenv())
+pg_cache <- NULL # nocov start
+
+.onLoad <- function(libname, pkgname) {
+  x <- hoardr::hoard()
+  x$cache_path_set("pangaear")
+  pg_cache <<- x
+} # nocov start

R/pangaear-package.R

@@ -13,7 +13,7 @@
 #' @importFrom xml2 read_html xml_find_all xml_attr xml_text xml_find_first
 #' xml_parent
 #' @importFrom tibble as_data_frame
-#' @importFrom rappdirs user_cache_dir
+#' @importFrom hoardr hoard
 #' @name pangaear-package
 #' @aliases pangaear
 #' @docType package

R/pg_cache.R

@@ -1,21 +1,13 @@
+#' cache path clear
 #' @export
-#' @rdname pg_data
-pg_cache_clear <- function(doi = NULL, prompt = TRUE) {
-  if (is.null(doi)) {
-    files <- list.files(env$path, full.names = TRUE)
-    resp <- if (prompt) {
-      readline(sprintf("Sure you want to clear all %s files? [y/n]:  ",
-                       length(files)))
-    } else {
-      "y"
-    }
-    if (resp == "y") unlink(files, force = TRUE) else NULL
-  } else {
-    files <- file.path(env$path, rdoi(doi))
-    unlink(files, force = TRUE)
-  }
+#' @rdname pg_cache_clear-defunct
+#' @param ... ignored
+pg_cache_clear <- function(...) {
+  .Defunct(msg = "defunct, see pg_cache$delete() and pg_cache$delete_all()")
 }
 
+#' cache list 
 #' @export
-#' @rdname pg_data
-pg_cache_list <- function() list.files(env$path)
+#' @rdname pg_cache_list-defunct
+#' @param ... ignored
+pg_cache_list <- function(...) .Defunct(msg = "defunct, see pg_cache$list()")

R/pg_data.R

@@ -11,8 +11,6 @@
 #' @param overwrite (logical) Ovewrite a file if one is found with the same name
 #' @param mssgs (logical) print information messages. Default: `TRUE`
 #' @param ... Curl options passed on to [crul::HttpClient]
-#' @param prompt (logical) Prompt before clearing all files in cache? No prompt
-#' used when DOIs passed in. Default: `TRUE`
 #' @return One or more items of class pangaea, each with the doi, parent doi
 #' (if many dois within a parent doi), url, citation, path, and data object.
 #' Data object depends on what kind of file it is. For tabular data, we print
@@ -22,8 +20,9 @@
 #' @author Naupaka Zimmerman, Scott Chamberlain
 #' @references <https://www.pangaea.de>
 #' @details Data files are stored in an operating system appropriate location.
-#' Run `rappdirs::user_cache_dir("pangaear")` to get the storage location
-#' on your machine.
+#' Run `pg_cache$cache_path_get()` to get the storage location
+#' on your machine. See [pg_cache] for more information, including how to 
+#' set a different base path for downloaded files.
 #'
 #' Some files/datasets require the user to be logged in. For now we
 #' just pass on these - that is, give back nothing other than metadata.
@@ -44,23 +43,23 @@
 #'
 #' # Manipulating the cache
 #' ## list files in the cache
-#' pg_cache_list()
+#' pg_cache$list()
 #'
 #' ## clear all data
-#' # pg_cache_clear()
-#' pg_cache_list()
+#' # pg_cache$delete_all()
+#' pg_cache$list()
 #'
 #' ## clear a single dataset by DOI
 #' pg_data(doi='10.1594/PANGAEA.812093')
-#' pg_cache_list()
+#' pg_cache$list()
 #' pg_cache_clear(doi='10.1594/PANGAEA.812093')
-#' pg_cache_list()
+#' pg_cache$list()
 #'
 #' ## clear more than 1 dataset by DOI
 #' lapply(c('10.1594/PANGAEA.746398','10.1594/PANGAEA.746400'), pg_data)
-#' pg_cache_list()
+#' pg_cache$list()
 #' pg_cache_clear(doi=c('10.1594/PANGAEA.746398','10.1594/PANGAEA.746400'))
-#' pg_cache_list()
+#' pg_cache$list()
 #'
 #' # search for datasets, then pass in DOIs
 #' (searchres <- pg_search(query = 'birds', count = 20))
@@ -82,7 +81,7 @@ pg_data <- function(doi, overwrite = TRUE, mssgs = TRUE, ...) {
   citation <- attr(dois, "citation")
   if (mssgs) message("Downloading ", length(dois), " datasets from ", doi)
   invisible(lapply(dois, function(x) {
-    if ( !is_pangaea(env$path, x) ) {
+    if ( !is_pangaea(pg_cache$cache_path_get(), x) ) {
       pang_GET(url = paste0(base(), x), doi = x, overwrite, ...)
     }
   }))
@@ -103,7 +102,8 @@ print.pangaea <- function(x, ...) {
 }
 
 pang_GET <- function(url, doi, overwrite, ...){
-  dir.create(env$path, showWarnings = FALSE, recursive = TRUE)
+  bpath <- pg_cache$cache_path_get()
+  dir.create(bpath, showWarnings = FALSE, recursive = TRUE)
 
   cli <- crul::HttpClient$new(url = url, 
     opts = list(followlocation = TRUE, ...))
@@ -133,12 +133,12 @@ pang_GET <- function(url, doi, overwrite, ...){
   )
   switch(
     res$response_headers$`content-type`,
-    `image/png` = png::writePNG(png::readPNG(res$content), file.path(env$path, fname)),
+    `image/png` = png::writePNG(png::readPNG(res$content), file.path(bpath, fname)),
     `text/tab-separated-values;charset=UTF-8` = {
-      writeLines(res$parse("UTF-8"), file.path(env$path, fname))
+      writeLines(res$parse("UTF-8"), file.path(bpath, fname))
     },
     `application/zip` = {
-      path <- file(file.path(env$path, fname), "wb")
+      path <- file(file.path(bpath, fname), "wb")
       writeBin(res$content, path)
       close(path)
     }
@@ -147,7 +147,7 @@ pang_GET <- function(url, doi, overwrite, ...){
 
 process_pg <- function(x, doi, citation) {
   lapply(x, function(m) {
-    file <- list.files(env$path, pattern = gsub("/|\\.", "_", m),
+    file <- list.files(pg_cache$cache_path_get(), pattern = gsub("/|\\.", "_", m),
                        full.names = TRUE)
     if (length(file) == 0) {
       list(