-source("./R/util.R")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
-#' ArvadosFile Object
+#' R6 Class Representing a ArvadosFile
#'
-#' Update description
-#'
-#' @export ArvadosFile
+#' @description
+#' ArvadosFile class represents a file inside Arvados collection.
+
+#' @export
ArvadosFile <- R6::R6Class(
"ArvadosFile",
public = list(
+ #' @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$http <- HttpRequest$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$name,
+ #' @description
+ #' Returns collections file content as character vector.
+ #' @param fullPath Checking if TRUE.
+ #' @examples
+ #' \dontrun{
+ #' arvadosFile$getFileListing()
+ #' }
getFileListing = function(fullpath = TRUE)
{
self$getName()
},
+ #' @description
+ #' Returns collections content size in bytes.
+ #' @examples
+ #' \dontrun{
+ #' arvadosFile$getSizeInBytes()
+ #' }
getSizeInBytes = function()
{
if(is.null(private$collection))
fileSize <- REST$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
+ #' \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))
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$connection("w")
+ #' }
connection = function(rw)
{
- if (rw == "r" || rw == "rb")
+ if (rw == "r" || rw == "rb")
{
REST <- private$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
+ #' \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$write(paste(v, collapse='\n'))
},
+ #' @description
+ #' Write to file or override current content of the file.
+ #' @param content File to write.
+ #' @param contentType Type of content. Possible is "text", "raw".
+ #' @examples
+ #' \dontrun{
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' arvadosFile <- collection$get(fileName)
+ #' myFile$write("This is new file content")
+ #' }
write = function(content, contentType = "text/html")
{
if(is.null(private$collection))
writeResult
},
- move = function(newLocation)
+ #' @description
+ #' Moves file to a new location inside collection.
+ #' @param destination Path to new folder.
+ #' @examples
+ #' \dontrun{
+ #' arvadosFile$move(newPath)
+ #' }
+ move = function(destination)
{
if(is.null(private$collection))
- stop("ArvadosFile doesn't belong to any collection")
-
+ stop("ArvadosFile doesn't belong to any collection.")
- newLocation <- trimFromEnd(newLocation, "/")
- nameAndPath <- splitToPathAndName(newLocation)
+ destination <- trimFromEnd(destination, "/")
+ nameAndPath <- splitToPathAndName(destination)
newParent <- private$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
+ #' \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$new(name)
+ newFile
}
),
size = NULL,
parent = NULL,
collection = NULL,
- http = NULL,
- httpParser = NULL,
buffer = NULL,
- attachToNewParent = function(newParent)
+ attachToNewParent = function(content, newParent)
{
- #Note: We temporary set parents collection to NULL. This will ensure that
- # add method doesn't post file on REST.
+ # We temporary set parents collection to NULL. This will ensure that
+ # add method doesn't post this file on REST.
+ # We also need to set content's collection to NULL because
+ # add method throws exception if we try to add content that already
+ # belongs to a collection.
+
parentsCollection <- newParent$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)
}
),
cloneable = FALSE
)
-#' @export print.ArvadosFile
-print.ArvadosFile = function(arvadosFile)
+#' 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 <- arvadosFile$getRelativePath()
+ relativePath <- x$getRelativePath()
- if(!is.null(arvadosFile$getCollection()))
+ if(!is.null(x$getCollection()))
{
- collection <- arvadosFile$getCollection()$uuid
+ collection <- x$getCollection()$uuid
relativePath <- paste0("/", relativePath)
}
cat(paste0("Type: ", "\"", "ArvadosFile", "\""), sep = "\n")
- cat(paste0("Name: ", "\"", arvadosFile$getName(), "\""), sep = "\n")
- cat(paste0("Relative path: ", "\"", relativePath, "\"") , sep = "\n")
- cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n")
+ cat(paste0("Name: ", "\"", x$getName(), "\""), sep = "\n")
+ cat(paste0("Relative path: ", "\"", relativePath, "\""), sep = "\n")
+ cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n")
}
projects / arvados.git / blobdiff