-#' ArvadosFile Object
-#'
-#' Update description
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+#' R6 Class Representing a ArvadosFile
#'
-#' @export ArvadosFile
+#' @description
+#' ArvadosFile class represents a file inside Arvados collection.
+
+#' @export
ArvadosFile <- R6::R6Class(
"ArvadosFile",
public = list(
- initialize = function(name, relativePath, api, collection)
+ #' @description
+ #' Initialize new enviroment.
+ #' @param name Name of the new enviroment.
+ #' @return A new `ArvadosFile` object.
+ #' @examples
+ #' \dontrun{
+ #' myFile <- ArvadosFile$new("myFile")
+ #' }
+ initialize = function(name)
{
- private$name <- name
- private$relativePath <- relativePath
- private$api <- api
- private$collection <- collection
- private$http <- HttpRequest$new()
- private$httpParser <- HttpParser$new()
+ if(name == "")
+ stop("Invalid name.")
+
+ private$name <- name
},
+ #' @description
+ #' Returns name of the file.
+ #' @examples
+ #' \dontrun{
+ #' arvadosFile$getName()
+ #' }
getName = function() private$name,
- getRelativePath = function() private$relativePath,
+ #' @description
+ #' Returns collections file content as character vector.
+ #' @param fullPath Checking if TRUE.
+ #' @examples
+ #' \dontrun{
+ #' arvadosFile$getFileListing()
+ #' }
+ getFileListing = function(fullpath = TRUE)
+ {
+ self$getName()
+ },
+
+ #' @description
+ #' Returns collections content size in bytes.
+ #' @examples
+ #' \dontrun{
+ #' arvadosFile$getSizeInBytes()
+ #' }
+ getSizeInBytes = function()
+ {
+ if(is.null(private$collection))
+ return(0)
+
+ REST <- private$collection$getRESTService()
+
+ fileSize <- REST$getResourceSize(self$getRelativePath(),
+ private$collection$uuid)
+ fileSize
+ },
+
+ get = function(fileLikeObjectName)
+ {
+ return(NULL)
+ },
+
+ getFirst = function()
+ {
+ return(NULL)
+ },
+
+ #' @description
+ #' Returns collection UUID.
+ getCollection = function() private$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)
+ parent <- private$parent
+
+ while(!is.null(parent))
+ {
+ relativePath <- c(parent$getName(), relativePath)
+ parent <- parent$getParent()
+ }
+
+ relativePath <- relativePath[relativePath != ""]
+ paste0(relativePath, collapse = "/")
+ },
+
+ #' @description
+ #' Returns project UUID.
+ getParent = function() private$parent,
+
+ #' @description
+ #' Sets project collection.
+ setParent = function(newParent) private$parent <- newParent,
- read = function(offset = 0, length = 0)
+ #' @description
+ #' Read file content.
+ #' @param contentType Type of content. Possible is "text", "raw".
+ #' @param offset Describes the location of a piece of data compared to another location
+ #' @param length Length of content
+ #' @examples
+ #' \dontrun{
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' arvadosFile <- collection$get(fileName)
+ #' fileContent <- arvadosFile$read("text")
+ #' }
+ read = function(contentType = "raw", offset = 0, length = 0)
{
+ if(is.null(private$collection))
+ stop("ArvadosFile doesn't belong to any collection.")
+
if(offset < 0 || length < 0)
- stop("Offset and length must be positive values.")
+ stop("Offset and length must be positive values.")
+
+ REST <- private$collection$getRESTService()
- range = paste0("bytes=", offset, "-")
+ fileContent <- REST$read(self$getRelativePath(),
+ private$collection$uuid,
+ contentType, offset, length)
+ fileContent
+ },
+
+ #' @description
+ #' Get connection opened in "read" or "write" mode.
+ #' @param rw Type of connection.
+ #' @examples
+ #' \dontrun{
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' arvadosFile <- collection$get(fileName)
+ #' arvConnection <- arvadosFile$connection("w")
+ #' }
+ connection = function(rw)
+ {
+ if (rw == "r" || rw == "rb")
+ {
+ REST <- private$collection$getRESTService()
+ return(REST$getConnection(self$getRelativePath(),
+ private$collection$uuid,
+ rw))
+ }
+ else if (rw == "w")
+ {
+ private$buffer <- textConnection(NULL, "w")
+
+ return(private$buffer)
+ }
+ },
- if(length > 0)
- range = paste0(range, offset + length - 1)
-
- fileURL = paste0(private$api$getWebDavHostName(), "c=", private$collection$uuid, "/", private$relativePath);
- headers <- list(Authorization = paste("OAuth2", private$api$getToken()),
- Range = range)
+ #' @description
+ #' Write connections content to a file or override current content of the file.
+ #' @examples
+ #' \dontrun{
+ #' collection <- Collection$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'))
+ },
- #TODO(Fudo): Move this to HttpRequest.R
- # serverResponse <- httr::GET(url = fileURL,
- # config = httr::add_headers(unlist(headers)))
- serverResponse <- private$http$GET(fileURL, headers)
- parsed_response <- httr::content(serverResponse, "raw")
+ #' @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
+ #' \dontrun{
+ #' 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))
+ stop("ArvadosFile doesn't belong to any collection.")
+ REST <- private$collection$getRESTService()
+
+ writeResult <- REST$write(self$getRelativePath(),
+ private$collection$uuid,
+ content, contentType)
+ writeResult
+ },
+
+ #' @description
+ #' Moves file to a new location inside collection.
+ #' @param destination Path to new folder.
+ #' @examples
+ #' \dontrun{
+ #' arvadosFile$move(newPath)
+ #' }
+ move = function(destination)
+ {
+ if(is.null(private$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$getRESTService()
+ REST$move(self$getRelativePath(),
+ paste0(newParent$getRelativePath(), "/", nameAndPath$name),
+ private$collection$uuid)
+
+ private$dettachFromCurrentParent()
+ private$attachToNewParent(self, newParent)
+
+ private$parent <- newParent
+ private$name <- nameAndPath$name
+
+ self
+ },
+
+ #' @description
+ #' Copies file to a new location inside collection.
+ #' @param destination Path to new folder.
+ #' @examples
+ #' \dontrun{
+ #' 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$new(name)
+ newFile
}
),
private = list(
- name = NULL,
- relativePath = NULL,
- parent = NULL,
- api = NULL,
- collection = NULL,
- http = NULL,
- httpParser = NULL
+ name = NULL,
+ size = NULL,
+ parent = NULL,
+ collection = NULL,
+ buffer = NULL,
+
+ attachToNewParent = function(content, newParent)
+ {
+ # We temporary set parents collection to NULL. This will ensure that
+ # add method doesn't post this file on REST.
+ # We also need to set content's collection to NULL because
+ # add method throws exception if we try to add content that already
+ # belongs to a collection.
+
+ parentsCollection <- newParent$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(content)
+ content$setCollection(parentsCollection, setRecursively = FALSE)
+ newParent$setCollection(parentsCollection, setRecursively = FALSE)
+ },
+
+ dettachFromCurrentParent = function()
+ {
+ # 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)
+ }
),
-
+
cloneable = FALSE
)
+
+#' print.ArvadosFile
+#'
+#' Custom print function for ArvadosFile class
+#'
+#' @param x Instance of ArvadosFile class
+#' @param ... Optional arguments.
+#' @export
+print.ArvadosFile = function(x, ...)
+{
+ collection <- NULL
+ relativePath <- x$getRelativePath()
+
+ if(!is.null(x$getCollection()))
+ {
+ collection <- x$getCollection()$uuid
+ 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")
+}
projects / arvados.git / blobdiff