-#' ArvadosFile Object
+# 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$new(name)}
+#'
+#' @section Arguments:
+#' \describe{
+#' \item{name}{Name of the file.}
+#' }
+#'
+#' @section Methods:
+#' \describe{
+#' \item{getName()}{Returns name of the file.}
+#' \item{getRelativePath()}{Returns file path relative to the root.}
+#' \item{read(contentType = "raw", offset = 0, length = 0)}{Read file content.}
+#' \item{write(content, contentType = "text/html")}{Write to file (override current content of the file).}
+#' \item{connection(rw)}{Get connection opened in "read" or "write" mode.}
+#' \item{flush()}{Write connections content to a file (override current content of the file).}
+#' \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
+#' \item{getSizeInBytes()}{Returns file size in bytes.}
+#' \item{move(destination)}{Moves file to a new location inside collection.}
+#' \item{copy(destination)}{Copies file to a new location inside collection.}
+#' }
#'
-#' Update description
+#' @name ArvadosFile
+#' @examples
+#' \dontrun{
+#' myFile <- ArvadosFile$new("myFile")
#'
-#' @export ArvadosFile
+#' 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$copy("newFolder/myFile")
+#' }
+NULL
+
+#' @export
ArvadosFile <- R6::R6Class(
"ArvadosFile",
initialize = function(name)
{
- private$name <- name
- private$http <- HttpRequest$new()
- private$httpParser <- HttpParser$new()
+ if(name == "")
+ stop("Invalid name.")
+
+ private$name <- name
},
getName = function() private$name,
- getFileList = function(fullpath = TRUE)
+ getFileListing = function(fullpath = TRUE)
{
self$getName()
},
getSizeInBytes = function()
{
- collectionURL <- URLencode(paste0(private$collection$api$getWebDavHostName(), "c=", private$collection$uuid))
- fileURL <- paste0(collectionURL, "/", self$getRelativePath());
+ if(is.null(private$collection))
+ return(0)
- headers = list("Authorization" = paste("OAuth2", private$collection$api$getToken()))
+ REST <- private$collection$getRESTService()
- propfindResponse <- private$http$PROPFIND(fileURL, headers)
+ fileSize <- REST$getResourceSize(self$getRelativePath(),
+ private$collection$uuid)
+ fileSize
+ },
- sizes <- private$httpParser$extractFileSizeFromWebDAVResponse(propfindResponse, collectionURL)
- as.numeric(sizes)
+ get = function(fileLikeObjectName)
+ {
+ return(NULL)
},
- removeFromCollection = function()
+ getFirst = function()
{
- if(is.null(private$collection))
- stop("Subcollection doesn't belong to any collection.")
-
- private$collection$.__enclos_env__$private$deleteFromREST(self$getRelativePath())
+ return(NULL)
+ },
+
+ getCollection = function() private$collection,
- #todo rename this add to a collection
- private$addToCollection(NULL)
- private$detachFromParent()
+ setCollection = function(collection, setRecursively = TRUE)
+ {
+ private$collection <- collection
},
getRelativePath = function()
relativePath <- c(private$name)
parent <- private$parent
- #Recurse back to root
while(!is.null(parent))
{
relativePath <- c(parent$getName(), relativePath)
getParent = function() private$parent,
- read = function(offset = 0, length = 0)
+ setParent = function(newParent) private$parent <- newParent,
+
+ read = function(contentType = "raw", offset = 0, length = 0)
{
- #todo range is wrong fix it
+ if(is.null(private$collection))
+ stop("ArvadosFile doesn't belong to any collection.")
+
if(offset < 0 || length < 0)
- stop("Offset and length must be positive values.")
+ stop("Offset and length must be positive values.")
- range = paste0("bytes=", offset, "-")
+ REST <- private$collection$getRESTService()
- if(length > 0)
- range = paste0(range, offset + length - 1)
-
- fileURL = paste0(private$collection$api$getWebDavHostName(), "c=", private$collection$uuid, "/", self$getRelativePath());
- headers <- list(Authorization = paste("OAuth2", private$collection$api$getToken()),
- Range = range)
+ fileContent <- REST$read(self$getRelativePath(),
+ private$collection$uuid,
+ contentType, offset, length)
+ fileContent
+ },
- serverResponse <- private$http$GET(fileURL, headers)
+ 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$buffer <- textConnection(NULL, "w")
- if(serverResponse$status_code != 206)
- stop(paste("Server code:", serverResponse$status_code))
+ return(private$buffer)
+ }
+ },
- parsedServerResponse <- httr::content(serverResponse, "raw")
- parsedServerResponse
+ flush = function()
+ {
+ v <- textConnectionValue(private$buffer)
+ close(private$buffer)
+ self$write(paste(v, collapse='\n'))
},
-
+
write = function(content, contentType = "text/html")
{
- fileURL = paste0(private$collection$api$getWebDavHostName(), "c=", private$collection$uuid, "/", self$getRelativePath());
- headers <- list(Authorization = paste("OAuth2", private$collection$api$getToken()),
- "Content-Type" = contentType)
- body <- content
+ if(is.null(private$collection))
+ stop("ArvadosFile doesn't belong to any collection.")
- serverResponse <- private$http$PUT(fileURL, headers, body)
+ REST <- private$collection$getRESTService()
- if(serverResponse$status_code != 201)
- stop(paste("Server code:", serverResponse$status_code))
+ writeResult <- REST$write(self$getRelativePath(),
+ private$collection$uuid,
+ content, contentType)
+ writeResult
+ },
- parsedServerResponse <- httr::content(serverResponse, "text")
- parsedServerResponse
- }
- ),
+ move = function(destination)
+ {
+ if(is.null(private$collection))
+ stop("ArvadosFile doesn't belong to any collection.")
- private = list(
+ destination <- trimFromEnd(destination, "/")
+ nameAndPath <- splitToPathAndName(destination)
- name = NULL,
- size = NULL,
- parent = NULL,
- collection = NULL,
- http = NULL,
- httpParser = NULL,
+ newParent <- private$collection$get(nameAndPath$path)
- getChild = function(name)
- {
- return(NULL)
+ if(is.null(newParent))
+ stop("Unable to get destination subcollection.")
+
+ childWithSameName <- newParent$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
},
- getFirstChild = function()
+ copy = function(destination)
{
- return(NULL)
+ 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
},
- addToCollection = function(collection)
+ duplicate = function(newName = NULL)
+ {
+ name <- if(!is.null(newName)) newName else private$name
+ newFile <- ArvadosFile$new(name)
+ newFile
+ }
+ ),
+
+ private = list(
+
+ name = NULL,
+ size = NULL,
+ parent = NULL,
+ collection = NULL,
+ buffer = NULL,
+
+ attachToNewParent = function(content, newParent)
{
- private$collection = collection
+ # We temporary set parents collection to NULL. This will ensure that
+ # add method doesn't post this file on REST.
+ # We also need to set content's collection to NULL because
+ # add method throws exception if we try to add content that already
+ # belongs to a collection.
+ parentsCollection <- newParent$getCollection()
+ content$setCollection(NULL, setRecursively = FALSE)
+ newParent$setCollection(NULL, setRecursively = FALSE)
+ newParent$add(content)
+ content$setCollection(parentsCollection, setRecursively = FALSE)
+ newParent$setCollection(parentsCollection, setRecursively = FALSE)
},
- detachFromParent = function()
+ dettachFromCurrentParent = function()
{
- if(!is.null(private$parent))
- {
- private$parent$.__enclos_env__$private$removeChild(private$name)
- private$parent <- NULL
- }
+ # We temporary set parents collection to NULL. This will ensure that
+ # remove method doesn't remove this file from REST.
+ 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