-source("./R/util.R")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
-#' ArvadosFile
-#'
-#' ArvadosFile class represents a file inside Arvados collection.
-#'
-#' @section Usage:
-#' \preformatted{file = ArvadosFile$new(name)}
-#'
-#' @section Arguments:
-#' \describe{
-#' \item{name}{Name of the file.}
-#' }
-#'
-#' @section Methods:
-#' \describe{
-#' \item{getName()}{Returns name of the file.}
-#' \item{getRelativePath()}{Returns file path relative to the root.}
-#' \item{read(contentType = "raw", offset = 0, length = 0)}{Read file content.}
-#' \item{write(content, contentType = "text/html")}{Write to file (override current content of the file).}
-#' \item{connection(rw)}{Get connection opened in "read" or "write" mode.}
-#' \item{flush()}{Write connections content to a file (override current content of the file).}
-#' \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
-#' \item{getSizeInBytes()}{Returns file size in bytes.}
-#' \item{move(newLocation)}{Moves file to a new location inside collection.}
-#' }
-#'
-#' @name ArvadosFile
-#' @examples
-#' \dontrun{
-#' myFile <- ArvadosFile$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$connection("r")
-#' mytable <- read.table(arvConnection)
+#' R6 Class Representing a ArvadosFile
#'
-#' myFile$move("newFolder/myFile")
-#' }
-NULL
+#' @description
+#' ArvadosFile class represents a file inside Arvados collection.
#' @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))
fileSize <- REST$getResourceSize(self$getRelativePath(),
private$collection$uuid)
-
fileSize
},
return(NULL)
},
+ #' @description
+ #' Returns collection UUID.
getCollection = function() private$collection,
- setCollection = function(collection)
+ #' @description
+ #' Sets new collection.
+ setCollection = function(collection, setRecursively = TRUE)
{
private$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")
+ if (rw == "r" || rw == "rb")
{
REST <- private$collection$getRESTService()
- return(REST$getConnection(private$collection$uuid,
- self$getRelativePath(),
+ return(REST$getConnection(self$getRelativePath(),
+ private$collection$uuid,
rw))
}
- else if (rw == "w")
+ else if (rw == "w")
{
private$buffer <- textConnection(NULL, "w")
}
},
- flush = function()
+ #' @description
+ #' Write connections content to a file or override current content of the file.
+ #' @examples
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' arvadosFile <- collection$get(fileName)
+ #' myFile$write("This is new file content")
+ #' arvadosFile$flush()
+ flush = function()
{
v <- textConnectionValue(private$buffer)
close(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
},
- move = function(newLocation)
+ #' @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))
- stop("ArvadosFile doesn't belong to any collection")
+ stop("ArvadosFile doesn't belong to any collection.")
- newLocation <- trimFromEnd(newLocation, "/")
- nameAndPath <- splitToPathAndName(newLocation)
+ destination <- trimFromEnd(destination, "/")
+ nameAndPath <- splitToPathAndName(destination)
newParent <- private$collection$get(nameAndPath$path)
if(is.null(newParent))
- {
- stop("Unable to get destination subcollection")
- }
+ stop("Unable to get destination subcollection.")
childWithSameName <- newParent$get(nameAndPath$name)
private$collection$uuid)
private$dettachFromCurrentParent()
- private$attachToNewParent(newParent)
+ private$attachToNewParent(self, newParent)
+ private$parent <- newParent
private$name <- nameAndPath$name
- "Content moved successfully."
+ self
+ },
+
+ #' @description
+ #' Copies file to a new location inside collection.
+ #' @param destination Path to new folder.
+ #' @examples
+ #' arvadosFile$copy("NewName.format")
+ copy = function(destination)
+ {
+ if(is.null(private$collection))
+ stop("ArvadosFile doesn't belong to any collection.")
+
+ destination <- trimFromEnd(destination, "/")
+ nameAndPath <- splitToPathAndName(destination)
+
+ newParent <- private$collection$get(nameAndPath$path)
+
+ if(is.null(newParent))
+ stop("Unable to get destination subcollection.")
+
+ childWithSameName <- newParent$get(nameAndPath$name)
+
+ if(!is.null(childWithSameName))
+ stop("Destination already contains content with same name.")
+
+ REST <- private$collection$getRESTService()
+ REST$copy(self$getRelativePath(),
+ paste0(newParent$getRelativePath(), "/", nameAndPath$name),
+ private$collection$uuid)
+
+ newFile <- self$duplicate(nameAndPath$name)
+ newFile$setCollection(self$getCollection())
+ private$attachToNewParent(newFile, newParent)
+ newFile$setParent(newParent)
+
+ 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$name
+ newFile <- ArvadosFile$new(name)
+ newFile
}
),
collection = NULL,
buffer = NULL,
- attachToNewParent = function(newParent)
+ attachToNewParent = function(content, newParent)
{
- #Note: We temporary set parents collection to NULL. This will ensure that
- # add method doesn't post file on REST.
+ # We temporary set parents collection to NULL. This will ensure that
+ # add method doesn't post this file on REST.
+ # 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$add(self)
-
+ newParent$add(content)
+ content$setCollection(parentsCollection, setRecursively = FALSE)
newParent$setCollection(parentsCollection, setRecursively = FALSE)
-
- private$parent <- newParent
},
dettachFromCurrentParent = function()
{
- #Note: We temporary set parents collection to NULL. This will ensure that
- # remove method doesn't remove this subcollection from REST.
+ # We temporary set parents collection to NULL. This will ensure that
+ # remove method doesn't remove this file from REST.
+
+ #private$parent$.__enclos_env__$private$removeChild(private$name)
+ #private$parent <- NULL
parent <- private$parent
parentsCollection <- parent$getCollection()
parent$setCollection(NULL, setRecursively = FALSE)
-
parent$remove(private$name)
-
parent$setCollection(parentsCollection, setRecursively = FALSE)
}
),
#'
#' @param x Instance of ArvadosFile class
#' @param ... Optional arguments.
-#' @export
+#' @export
print.ArvadosFile = function(x, ...)
{
collection <- NULL
relativePath <- paste0("/", relativePath)
}
- cat(paste0("Type: ", "\"", "ArvadosFile", "\""), sep = "\n")
- cat(paste0("Name: ", "\"", x$getName(), "\""), sep = "\n")
- cat(paste0("Relative path: ", "\"", relativePath, "\""), sep = "\n")
- cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n")
+ cat(paste0("Type: ", "\"", "ArvadosFile", "\""), sep = "\n")
+ cat(paste0("Name: ", "\"", x$getName(), "\""), sep = "\n")
+ cat(paste0("Relative path: ", "\"", relativePath, "\""), sep = "\n")
+ cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n")
}