#
# SPDX-License-Identifier: Apache-2.0
-#' ArvadosFile
+#' R6 Class Representing a ArvadosFile
#'
+#' @description
#' ArvadosFile class represents a file inside Arvados collection.
-#'
-#' @section Usage:
-#' \preformatted{file = ArvadosFile$new(name)}
-#'
-#' @section Arguments:
-#' \describe{
-#' \item{name}{Name of the file.}
-#' }
-#'
-#' @section Methods:
-#' \describe{
-#' \item{getName()}{Returns name of the file.}
-#' \item{getRelativePath()}{Returns file path relative to the root.}
-#' \item{read(contentType = "raw", offset = 0, length = 0)}{Read file content.}
-#' \item{write(content, contentType = "text/html")}{Write to file (override current content of the file).}
-#' \item{connection(rw)}{Get connection opened in "read" or "write" mode.}
-#' \item{flush()}{Write connections content to a file (override current content of the file).}
-#' \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
-#' \item{getSizeInBytes()}{Returns file size in bytes.}
-#' \item{move(destination)}{Moves file to a new location inside collection.}
-#' \item{copy(destination)}{Copies file to a new location inside collection.}
-#' }
-#'
-#' @name ArvadosFile
-#' @examples
-#' \dontrun{
-#' myFile <- ArvadosFile$new("myFile")
-#'
-#' myFile$write("This is new file content")
-#' fileContent <- myFile$read()
-#' fileContent <- myFile$read("text")
-#' fileContent <- myFile$read("raw", offset = 8, length = 4)
-#'
-#' #Write a table:
-#' arvConnection <- myFile$connection("w")
-#' write.table(mytable, arvConnection)
-#' arvadosFile$flush()
-#'
-#' #Read a table:
-#' arvConnection <- myFile$connection("r")
-#' mytable <- read.table(arvConnection)
-#'
-#' myFile$move("newFolder/myFile")
-#' myFile$copy("newFolder/myFile")
-#' }
-NULL
#' @export
ArvadosFile <- R6::R6Class(
public = list(
+ #' @description
+ #' Initialize new enviroment.
+ #' @param name Name of the new enviroment.
+ #' @return A new `ArvadosFile` object.
+ #' @examples
+ #' myFile <- ArvadosFile$new("myFile")
initialize = function(name)
{
if(name == "")
private$name <- name
},
+ #' @description
+ #' Returns name of the file.
+ #' @examples
+ #' arvadosFile$getName()
getName = function() private$name,
+ #' @description
+ #' Returns collections file content as character vector.
+ #' @param fullPath Checking if TRUE.
+ #' @examples
+ #' arvadosFile$getFileListing()
getFileListing = function(fullpath = TRUE)
{
self$getName()
},
+ #' @description
+ #' Returns collections content size in bytes.
+ #' @examples
+ #' arvadosFile$getSizeInBytes()
getSizeInBytes = function()
{
if(is.null(private$collection))
return(NULL)
},
+ #' @description
+ #' Returns collection UUID.
getCollection = function() private$collection,
+ #' @description
+ #' Sets new collection.
setCollection = function(collection, setRecursively = TRUE)
{
private$collection <- collection
},
+ #' @description
+ #' Returns file path relative to the root.
getRelativePath = function()
{
relativePath <- c(private$name)
paste0(relativePath, collapse = "/")
},
+ #' @description
+ #' Returns project UUID.
getParent = function() private$parent,
+ #' @description
+ #' Sets project collection.
setParent = function(newParent) private$parent <- newParent,
+ #' @description
+ #' Read file content.
+ #' @param contentType Type of content. Possible is "text", "raw".
+ #' @param offset Describes the location of a piece of data compared to another location
+ #' @param length Length of content
+ #' @examples
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' arvadosFile <- collection$get(fileName)
+ #' fileContent <- arvadosFile$read("text")
read = function(contentType = "raw", offset = 0, length = 0)
{
if(is.null(private$collection))
fileContent
},
+ #' @description
+ #' Get connection opened in "read" or "write" mode.
+ #' @param rw Type of connection.
+ #' @examples
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' arvadosFile <- collection$get(fileName)
+ #' arvConnection <- arvadosFile$connection("w")
connection = function(rw)
{
if (rw == "r" || rw == "rb")
}
},
+ #' @description
+ #' Write connections content to a file or override current content of the file.
+ #' @examples
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' arvadosFile <- collection$get(fileName)
+ #' myFile$write("This is new file content")
+ #' arvadosFile$flush()
flush = function()
{
v <- textConnectionValue(private$buffer)
self$write(paste(v, collapse='\n'))
},
+ #' @description
+ #' Write to file or override current content of the file.
+ #' @param content File to write.
+ #' @param contentType Type of content. Possible is "text", "raw".
+ #' @examples
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' arvadosFile <- collection$get(fileName)
+ #' myFile$write("This is new file content")
write = function(content, contentType = "text/html")
{
if(is.null(private$collection))
writeResult
},
+ #' @description
+ #' Moves file to a new location inside collection.
+ #' @param destination Path to new folder.
+ #' @examples
+ #' arvadosFile$move(newPath)
move = function(destination)
{
if(is.null(private$collection))
self
},
+ #' @description
+ #' Copies file to a new location inside collection.
+ #' @param destination Path to new folder.
+ #' @examples
+ #' arvadosFile$copy("NewName.format")
copy = function(destination)
{
if(is.null(private$collection))
newFile
},
+ #' @description
+ #' Duplicate file and gives it a new name.
+ #' @param newName New name for duplicated file.
duplicate = function(newName = NULL)
{
name <- if(!is.null(newName)) newName else private$name
# We also need to set content's collection to NULL because
# add method throws exception if we try to add content that already
# belongs to a collection.
+
parentsCollection <- newParent$getCollection()
+ #parent$.__enclos_env__$private$children <- c(parent$.__enclos_env__$private$children, self)
+ #private$parent <- parent
content$setCollection(NULL, setRecursively = FALSE)
newParent$setCollection(NULL, setRecursively = FALSE)
newParent$add(content)
{
# We temporary set parents collection to NULL. This will ensure that
# remove method doesn't remove this file from REST.
+
+ #private$parent$.__enclos_env__$private$removeChild(private$name)
+ #private$parent <- NULL
parent <- private$parent
parentsCollection <- parent$getCollection()
parent$setCollection(NULL, setRecursively = FALSE)
projects / arvados.git / blobdiff