merge minor conflict

.Rbuildignore

@@ -2,3 +2,4 @@
 .gitignore
 ^.*\.Rproj$
 ^\.Rproj\.user$
+man-roxygen

R/authenticate_sb.R

@@ -52,6 +52,7 @@ authenticate_sb = function(username, password){
 
 readPassword <- function(prompt) {
 	# found this cool function in rstudio
+	.rs.askForPassword <- '.global_def'
 	if (exists(".rs.askForPassword")) {
 		pass <- .rs.askForPassword(prompt)
 	} else {

R/folder_create.R

@@ -1,12 +1,8 @@
 #' Create a folder
 #' 
 #' @export
-#' @param id A ScienceBase ID or something that can be coerced to a SB item ID
-#' by \code{\link{as.sbitem}}
+#' @template manipulate_item
 #' @param name (character) the folder name
-#' @param ... Additional parameters are passed on to \code{\link[httr]{GET}} and
-#'   \code{\link[httr]{DELETE}}
-#' @param session Session object from \code{\link{authenticate_sb}}
 #' @return A \code{\link[httr]{response}} object
 #' @examples \dontrun{
 #' folder_create(user_id(), "foobar345")

R/item_append_files.R

@@ -1,11 +1,8 @@
 #' @title Upload File to Item
 #' @description Adds a file to an item
 #'
-#' @param id A ScienceBase ID or something that can be coerced to a SB item ID
-#' by \code{\link{as.sbitem}}
+#' @template manipulate_item
 #' @param files A file path to upload.
-#' @param ... Additional parameters are passed on to \code{\link[httr]{POST}}
-#' @param session A ScienceBase session object from authenticate_sb.
 #'
 #' @return An object of class \code{sbitem}
 #'

R/item_create.R

@@ -1,11 +1,8 @@
 #' @title Create a new SB item
 #'
-#' @param id A ScienceBase ID or something that can be coerced to a SB item ID
-#' by \code{\link{as.sbitem}}
+#' @template manipulate_item
 #' @param title The title of the new SB item
-#' @param ... Additional parameters are passed on to \code{\link[httr]{POST}}
 #' @param info (optional) list of metadata info for the new item
-#' @param session Authenticated session object (from \link{authenticate_sb})
 #' @return An object of class \code{sbitem}
 #'
 #' @export

R/item_file_download.R

@@ -5,15 +5,13 @@
 #' or a \code{dest_dir} can be supplied where all attached files will be written
 #' with the names as stored on SB.
 #'
-#' @param id SB item ID
-#' @param ... Additional parameters are passed on to \code{\link[httr]{GET}}
+#' @template manipulate_item
 #' @param names String vector list of file names attached to item that you wish
 #'   to download.
 #' @param destinations String vector list of destinations for requested files.
 #'   Must be same length as \code{names}
 #' @param dest_dir A directory path for saving files when \code{names} parameter
 #'   is omitted
-#' @param session Session object from \code{\link{authenticate_sb}}
 #' @param overwrite_file Boolean indicating if file should be overwritten if it
 #'   already exists locally
 #'   

R/item_get.R

@@ -1,9 +1,7 @@
 #' @title Retrieve SB item
 #'  
 #' @export
-#' @param id (character) A ScienceBase ID
-#' @param ... Additional parameters are passed on to \code{\link[httr]{GET}}
-#' @param session Session object from \code{\link{authenticate_sb}}
+#' @template manipulate_item
 #' @return An object of class \code{sbitem}
 #' @examples \dontrun{
 #' # Get an item

R/item_get_fields.R

@@ -1,11 +1,9 @@
 #' Retrieve specific fields from an SB item
 #' 
-#' @param id SB item ID
+#' @template manipulate_item
 #' @param fields a vector of fields
-#' @param ... Additional parameters are passed on to \code{\link[httr]{GET}}
 #' @param drop logical. If only one field is selected, should the
 #'   list format be dropped?
-#' @param session Session object from \code{\link{authenticate_sb}}
 #' @return List serialization of chosen metadata for an SB item
 #' @import httr
 #' @export

R/item_get_parent.R

@@ -1,8 +1,6 @@
 #' @title Get an item's parent ID
 #'
-#' @param id ID of SB item
-#' @param ... Additional parameters are passed on to \code{\link[httr]{GET}}
-#' @param session SB session object from \code{\link{authenticate_sb}}
+#' @template manipulate_item
 #' @return The parent ID of an item.
 #' @export
 #' @examples \dontrun{

R/item_list_children.R

@@ -2,10 +2,7 @@
 #'
 #' Returns a list of child IDs for a ScienceBase item
 #'
-#' @param id A ScienceBase ID or something that can be coerced to a SB item ID
-#' by \code{\link{as.sbitem}}
-#' @param ... Additional parameters are passed on to \code{\link[httr]{GET}}
-#' @param session (optional) SB session from \link{authenticate_sb}
+#' @template manipulate_item
 #' @param limit Max children returned
 #'
 #' @return \code{data.frame} with a row for each child item

R/item_list_files.R

@@ -1,9 +1,7 @@
 #' @title Get list of files attached to SB item
 #'
-#' @param id item ID
+#' @template manipulate_item
 #' @param recursive (logical) List files recursively. Default: \code{FALSE}
-#' @param session Session object from \link{authenticate_sb}
-#' @param ... Additional parameters are passed on to \link[httr]{GET}
 #'
 #' @return 
 #' A data.frame with columns fname, size, and url. 

R/item_move.R

@@ -1,12 +1,9 @@
 #' Move item from one folder to another
 #'
 #' @export
-#' @param id A ScienceBase ID or something that can be coerced to a SB item ID
-#' by \code{\link{as.sbitem}} 
+#' @template manipulate_item
 #' @param id_new Folder/item to move \code{id} to. A ScienceBase ID or something 
 #' that can be coerced to a SB item ID by \code{\link{as.sbitem}} 
-#' @param ... Additional parameters are passed on to \code{\link[httr]{PUT}}
-#' @param session Authenticated session object (from \link{authenticate_sb})
 #'
 #' @return An object of class \code{sbitem}. Same as \code{id}, but with new 
 #' parent id

R/item_replace_files.R

@@ -1,9 +1,6 @@
 #' @title Replace files associated with an item
-#' @param id a sciencebase item identifier
+#' @template manipulate_item
 #' @param files a character vector of file paths
-#' @param ... Additional parameters are passed on to \code{\link[httr]{PUT}}
-#'   and \code{\link[httr]{POST}}
-#' @param session Authenticated session object (from \link{authenticate_sb})
 #' @description replaces existing files associated with an item with a new one. 
 #'   (Currently does not support multi-file uploads.) This function will not
 #'   append an existing collection of files. If that is desired, use

R/item_rm.R

@@ -1,13 +1,9 @@
 #' @title Remove item from SB
 #'   
-#' @param id A ScienceBase ID or something that can be coerced to a SB item ID
-#' by \code{\link{as.sbitem}}
-#' @param ... Additional parameters are passed on to \code{\link[httr]{GET}} and
-#'   \code{\link[httr]{DELETE}}
+#' @template manipulate_item
 #' @param recursive logical, FALSE by default. CAUTION: setting recursive=TRUE
 #'   means that not only will this item be deleted, but so will all its child
 #'   items and their child items and so on.
-#' @param session Session object from \code{\link{authenticate_sb}}
 #'   
 #' @return \pkg{httr} \code{\link[httr]{response}} object
 #'   

R/item_rm_files.R

@@ -1,9 +1,6 @@
 #' @title Remove all files associated with an item
 #' 
-#' @param id A ScienceBase ID or something that can be coerced to a SB item ID
-#' by \code{\link{as.sbitem}}
-#' @param ... Additional parameters are passed on to \code{\link[httr]{PUT}}
-#' @param session Authenticated session object (from \link{authenticate_sb})
+#' @template manipulate_item
 #' @description Removes existing files associated with an item.
 #' @return An object of class \code{sbitem}
 #' @export

R/item_rm_recursive.R

@@ -1,10 +1,7 @@
 #' @title Remove an item completely by recursively removing its child items
 #' 
 #' @keywords internal
-#' @param id A ScienceBase ID or something that can be coerced to a SB item ID
-#' @param ... Additional parameters are passed on to \code{\link[httr]{GET}} and
-#'   \code{\link[httr]{DELETE}}
-#' @param session Session object from \code{\link{authenticate_sb}}
+#' @template manipulate_item
 #' @return \code{TRUE} to indicate success
 #' @details BEWARE: This completely removes ALL CHILD ITEMS AND THEIR CHILDREN
 #'   as well as the item itself.

R/item_update.R

@@ -1,10 +1,7 @@
 #' @title Update a SB item with new metadata
 #'
-#' @param id A ScienceBase ID or something that can be coerced to a SB item ID
-#' by \code{\link{as.sbitem}}
+#' @template manipulate_item
 #' @param info list of metadata info (key-value pairs) to change on the item
-#' @param ... Additional parameters are passed on to \code{\link[httr]{PUT}}
-#' @param session Authenticated session object (from \link{authenticate_sb})
 #'
 #' @return An object of class \code{sbitem}
 #'

R/item_update_identifier.R

@@ -1,12 +1,9 @@
 #'@title Add custom identifier to an existing item
 #'  
-#'@param id SB item ID
+#' @template manipulate_item
 #'@param scheme The identifier scheme
 #'@param type The identifier type
 #'@param key The identifier key
-#'@param ... Additional parameters are passed on to \code{\link[httr]{GET}} and
-#'  \code{\link[httr]{PUT}}
-#'@param session SB session from \code{\link{authenticate_sb}}
 #'  
 #'@author Luke Winslow
 #'  

R/user_id.R

@@ -4,7 +4,7 @@
 #' 
 #' @export
 #' @param ... Additional parameters are passed on to \code{\link[httr]{POST}}
-#' @param session Session object from authenticate_sb
+#' @param session Session object from \code{\link{authenticate_sb}}
 #' @return A single character string, your user id
 #' @examples \dontrun{
 #' user_id()

man-roxygen/manipulate_item.R

@@ -0,0 +1,5 @@
+#' @param id A ScienceBase ID or something that can be coerced to a SB item ID
+#' by \code{\link{as.sbitem}}
+#' @param ... Additional parameters are passed on to \code{\link[httr]{GET}}, \code{\link[httr]{POST}},
+#' \code{\link[httr]{HEAD}}, \code{\link[httr]{PUT}}, or \code{\link[httr]{DELETE}}
+#' @param session Session object from \code{\link{authenticate_sb}}