Merge pull request #87 from CenterForOpenScience/dev

v0.2.2

Author: aaronwolen

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: osfr
 Title: R Interface to OSF
-Version: 0.2.1
+Version: 0.2.2
 Authors@R: c(
     person("Aaron", "Wolen",, "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-2542-2202")),

NAMESPACE

@@ -11,11 +11,13 @@ S3method(osf_ls_nodes,osf_tbl_node)
 S3method(osf_ls_nodes,osf_tbl_user)
 S3method(osf_mkdir,osf_tbl_file)
 S3method(osf_mkdir,osf_tbl_node)
+S3method(osf_mv,osf_tbl_file)
 S3method(osf_open,character)
 S3method(osf_open,default)
 S3method(osf_open,osf_id)
 S3method(osf_open,osf_tbl)
 S3method(osf_open,osf_tbl_file)
+S3method(osf_rm,osf_tbl_file)
 S3method(osf_rm,osf_tbl_node)
 S3method(osf_upload,osf_tbl_file)
 S3method(osf_upload,osf_tbl_node)
@@ -29,6 +31,7 @@ export(osf_download)
 export(osf_ls_files)
 export(osf_ls_nodes)
 export(osf_mkdir)
+export(osf_mv)
 export(osf_open)
 export(osf_retrieve_file)
 export(osf_retrieve_node)

NEWS.md

@@ -1,3 +1,18 @@
+# osfr 0.2.2
+
+## New functions
+
+* `osf_mv()` to move files and directories to a new project, component, or
+subdirectory
+
+## New features
+
+* `osf_rm()` can now delete files and directories
+
+## Minor improvements and fixes
+
+* Restructured tests to better handle environments in which `OSF_PAT` and/or `OSF_SERVER` are not defined
+
 # osfr 0.2.1
 
 * Minor tweaks to the website

R/api-client-osf.R

@@ -26,7 +26,9 @@ user_agent <- function(agent = "osfr") {
 
   headers <- list(
     `User-Agent` = user_agent(),
-    `Accept-Header` = sprintf("application/vnd.api+json;version=%s", .osf_api_version)
+    `Accept-Header` = sprintf(
+      "application/vnd.api+json;version=%s",
+      .osf_api_version)
   )
 
   if (!is.null(pat)) {
@@ -46,15 +48,28 @@ user_agent <- function(agent = "osfr") {
 
 # OSF API request functions -----------------------------------------------
 
-.osf_request <- function(method, path, query = list(), body = NULL, verbose = FALSE, ...) {
+.osf_request <-
+  function(method,
+           path,
+           query = list(),
+           body = NULL,
+           verbose = FALSE,
+           ...) {
+
   method <- match.arg(method, c("get", "put", "patch", "post", "delete"))
   cli <- .osf_cli()
   method <- cli[[method]]
   method(path, query, body = body, ...)
 }
 
 # TODO: .osf_request and .osf_paginated_request returns should be consistent
-.osf_paginated_request <- function(method, path, query = list(), n_max = 100, verbose = FALSE) {
+.osf_paginated_request <-
+  function(method,
+           path,
+           query = list(),
+           n_max = 100,
+           verbose = FALSE) {
+
   items <- list()
   i <- 1
   retrieved <- 0
@@ -72,7 +87,9 @@ user_agent <- function(agent = "osfr") {
     items <- c(items, out$data)
 
     if (verbose && n_max > 10) {
-      if (i == 1) message(sprintf("Retrieving %i of %i available items:", n_max, total))
+      if (i == 1) {
+        message(sprintf("Retrieving %i of %i available items:", n_max, total))
+      }
       message(sprintf("..retrieved %i items", retrieved), appendLF = TRUE)
     }
 

R/api-client-wb.R

@@ -8,7 +8,12 @@
 #'   a trailing flash when referring to a folder
 #'
 #' @noRd
-.wb_api_path <- function(id, fid = NULL, provider = "osfstorage", type = "folder") {
+.wb_api_path <-
+  function(id,
+           fid = NULL,
+           provider = "osfstorage",
+           type = "folder") {
+
   type <- match.arg(type, c("folder", "file"))
   api_v <- floor(.wb_api_version)
   if (is.null(fid)) {
@@ -51,8 +56,15 @@
 
 # Waterbutler request functions -------------------------------------------
 
-.wb_request <- function(method, path, query = list(), body = NULL, verbose = FALSE, ...) {
-  method <- match.arg(method, c("get", "put", "patch", "delete"))
+.wb_request <-
+  function(method,
+           path,
+           query = list(),
+           body = NULL,
+           verbose = FALSE,
+           ...) {
+
+  method <- match.arg(method, c("get", "put", "patch", "post", "delete"))
   cli <- .wb_cli()
   method <- cli[[method]]
   method(path, query, body = body, ...)

R/api-endpoints-wb.R

@@ -59,7 +59,8 @@
   type <- match.arg(type, c("file", "folder"))
   query <- list()
   if (zip) query$zip <- ""
-  res <- .wb_request("get", .wb_api_path(id, fid, type = type), query, disk = path)
+  api_path <- .wb_api_path(id, fid, type = type)
+  res <- .wb_request("get", api_path, query, disk = path)
   if (res$status_code == 200) return(TRUE)
   if (res$status_code == 404) {
     msg <- sprintf("The requested %s (%s) could not be found in node `%s`",

R/osf_create.R

@@ -76,7 +76,7 @@ osf_create_component <-
            category = NULL) {
 
   if (missing(x) || !inherits(x, "osf_tbl_node"))
-    abort("`x` must be an `osf_tbl_node` referencing an existing project/component. ")
+    abort("`x` must be an `osf_tbl_node` referencing an existing project/component.")
   if (missing(title)) abort("Must define a title for the new component.")
 
   out <- .osf_node_create(

R/osf_ls_files.R

@@ -53,7 +53,13 @@ osf_ls_files.osf_tbl_node <-
            verbose = FALSE) {
 
   x <- make_single(x)
- .osf_list_files(x, path, type, pattern, n_max, verbose)
+
+  if (!is.null(path) && path != ".") {
+    leaf_dir <- recurse_path(x, path, missing_action = "error", verbose)
+    return(osf_ls_files(leaf_dir, path = ".", type, pattern, n_max, verbose))
+  }
+
+ .osf_list_files(x, type, pattern, n_max, verbose)
 }
 
 #' @export
@@ -69,33 +75,31 @@ osf_ls_files.osf_tbl_file <-
   if (is_osf_file(x)) {
     abort("Listing an `osf_tbl_file` requires a directory\n* `x` contains a file")
   }
- .osf_list_files(x, path, type, pattern, n_max, verbose)
+
+  # walk down path tree and replace x with the leaf directory
+  if (!is.null(path) && path != ".") {
+    x <- recurse_path(x, path, missing_action = "error", verbose = verbose)
+  }
+
+ .osf_list_files(x, type, pattern, n_max, verbose)
 }
 
 
-.osf_list_files <- function(x, path, type, pattern, n_max, verbose) {
+#' Internal list files method
+#'
+#' This requires an API path to more easily support different storage providers
+#' in the future when listing from a node.
+#' @return An `osf_tbl_file`.
+#' @noRd
+.osf_list_files <- function(x, type, pattern, n_max, verbose) {
 
-  # manually construct path for nodes because the provided files endpoint is
-  # for listing storage providers
+  # manually construct the API path because the 'files' endpoint for nodes lists
+  # the enabled storage providers
   api_path <- switch(class(x)[1],
     osf_tbl_node = .osf_api_path(sprintf("nodes/%s/files/osfstorage/", as_id(x))),
     osf_tbl_file = crul::url_parse(get_relation(x, "files"))$path
   )
 
-  # recurse if path contains subdirectories
-  path <- path %||% "."
-  if (path != ".") {
-    path_root <- fs::path_split(path)[[1]][1]
-    root_dir <- find_exact_match(x, name = path_root, type = "folder")
-    if (nrow(root_dir) == 0) {
-      abort(sprintf("Can't find path `%s` within `%s`", path, x$name))
-    }
-
-    next_path <- fs::path_rel(path, path_root)
-    res <- .osf_list_files(root_dir, next_path, type, pattern, n_max, verbose)
-    return(as_osf_tbl(res, "osf_tbl_file"))
-  }
-
   res <- .osf_paginated_request(
     method = "get",
     path = api_path,

R/osf_ls_nodes.R

@@ -41,7 +41,14 @@ osf_ls_nodes.osf_tbl_node <-
            n_max = 10,
            verbose = FALSE) {
   x <- make_single(x)
-  out <- .osf_node_children(as_id(x), n_max, filter_nodes(pattern = pattern), verbose)
+
+  out <- .osf_node_children(
+    id = as_id(x),
+    n_max = n_max,
+    query = filter_nodes(pattern = pattern),
+    verbose = verbose
+  )
+
   raise_error(out)
   as_osf_tbl(out, "osf_tbl_node")
 }
@@ -53,7 +60,14 @@ osf_ls_nodes.osf_tbl_user <-
            n_max = 10,
            verbose = FALSE) {
   x <- make_single(x)
-  out <- .osf_user_nodes(as_id(x), n_max, filter_nodes(pattern = pattern), verbose)
+
+  out <- .osf_user_nodes(
+    id = as_id(x),
+    n_max = n_max,
+    query = filter_nodes(pattern = pattern),
+    verbose = verbose
+  )
+
   raise_error(out)
   as_osf_tbl(out, "osf_tbl_node")
 }

R/osf_mkdir.R

@@ -36,58 +36,74 @@ osf_mkdir <- function(x, path, verbose = FALSE) {
 
 #' @export
 osf_mkdir.osf_tbl_node <- function(x, path, verbose = FALSE) {
-
   x <- make_single(x)
-  id <- as_id(x)
+  recurse_path(x, path, missing_action = "create", verbose)
+}
 
-  # does path root already exist?
-  path_root <- fs::path_split(path)[[1]][1]
-  items <- osf_ls_files(x, type = "folder", pattern = path_root)
-  dir_root <- items[which(items$name == path_root), ]
+#' @export
+osf_mkdir.osf_tbl_file <- function(x, path, verbose = FALSE) {
+  if (is_osf_file(x)) abort("Can't create directories within a file.")
+  x <- make_single(x)
+  recurse_path(x, path, missing_action = "create", verbose)
+}
 
-  if (nrow(dir_root) == 0) {
-    res <- .wb_create_folder(id = id, name = path_root)
-    raise_error(res)
-    dir_id <- gsub("/", "", res$data$attributes$path, fixed = TRUE)
-    dir_root <- osf_retrieve_file(dir_id)
-    msg <- sprintf("Created directory '%s/' in node %s", path_root, id)
-  } else {
-    msg <- sprintf("Directory '%s/' already exists in node %s", path_root, id)
-  }
 
-  if (verbose) message(msg)
+#' Create a single folder on OSF
+#'
+#' This wraps the create folder endpoint on Waterbutler but retrieves the newly
+#' created directory from OSF because Waterbutler returns only a subset of the
+#' information provided by OSF.
+#'
+#' @param id GUID for an OSF project or component
+#' @param name Name of the new directory (note: this must be the name of a
+#'   single directory, not a path)
+#' @param fid Optional, provide a Waterbutler folder ID to create the new folder
+#'   within the specified existing folder.
+#' @noRd
 
-  # recurse to the next-level if there is a subfolder
-  path_next <- fs::path_rel(path, path_root)
-  if (path_next == ".") {
-    out <- dir_root
-  } else {
-    out <- osf_mkdir(dir_root, path_next, verbose)
-  }
-  out
+.osf_mkdir <- function(id, name, fid = NULL) {
+  res <- .wb_create_folder(id, name, fid)
+  raise_error(res)
+  dir_id <- gsub("/", "", res$data$attributes$path, fixed = TRUE)
+  osf_retrieve_file(dir_id)
 }
 
-#' @export
-osf_mkdir.osf_tbl_file <- function(x, path, verbose = FALSE) {
-  x <- make_single(x)
-  id <- as_id(x)
-  if (is_osf_file(x)) abort("Can't create directories within a file.")
 
-  # does path root already exist?
+#' Recurse a directory path
+#'
+#' Given a path like 'root/subdir1/subdir2', this will retrieve each directory
+#' level from OSF and return the leaf directory. The `missing_action` argument
+#' determines what happens if an intermediate directory does not exist.
+#'
+#' @param x An `osf_tbl_node` or an `osf_tbl_file` with a directory.
+#' @param path A path of directories.
+#' @param missing_action Either `"error"` or `"create"` to create the missing
+#'   directory.
+#' @noRd
+recurse_path <- function(x, path, missing_action = "error", verbose = FALSE) {
+  missing_action <- match.arg(missing_action, c("error", "create"))
+
   path_root <- fs::path_split(path)[[1]][1]
-  items <- osf_ls_files(x, type = "folder", pattern = path_root)
-  dir_root <- items[which(items$name == path_root), ]
+  root_dir <- osf_ls_files(x, type = "folder", pattern = path_root)
 
-  if (nrow(dir_root) == 0) {
-    res <- .wb_create_folder(id = get_parent_id(x), name = path_root, fid = id)
-    raise_error(res)
+  if (nrow(root_dir) == 0) {
+    if (missing_action == "error") {
+      abort(sprintf("Can't find directory '%s' in `%s`", path_root, x$name))
+    }
 
-    dir_id <- gsub("/", "", res$data$attributes$path, fixed = TRUE)
-    dir_root <- osf_retrieve_file(dir_id)
-    msg <- sprintf("Created sub-directory '%s/' in directory '%s/'",
+    # create the missing directory
+    if (inherits(x, "osf_tbl_node")) {
+      root_dir <- .osf_mkdir(as_id(x), name = path_root)
+      msg <- sprintf("Created directory '%s/' in node %s",
+                     path_root, as_id(x))
+    } else {
+      root_dir <- .osf_mkdir(get_parent_id(x), name = path_root, fid = as_id(x))
+      msg <- sprintf("Created sub-directory '%s/' in directory '%s/'",
                    path_root, x$name)
+    }
+
   } else {
-    msg <- sprintf("Sub-directory '%s/' already exists in directory '%s/'",
+    msg <- sprintf("Navigating to sub-directory '%s/' in '%s'",
                    path_root, x$name)
   }
 
@@ -96,9 +112,9 @@ osf_mkdir.osf_tbl_file <- function(x, path, verbose = FALSE) {
   # recurse to the next-level if there is a subfolder
   path_next <- fs::path_rel(path, path_root)
   if (path_next == ".") {
-    out <- dir_root
+    out <- root_dir
   } else {
-    out <- osf_mkdir(dir_root, path_next, verbose)
+    out <- Recall(root_dir, path_next, missing_action, verbose)
   }
   out
 }