-#' Arvados SubCollection Object
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+source("./R/util.R")
+
+#' Subcollection
+#'
+#' Subcollection class represents a folder inside Arvados collection.
+#' It is essentially a composite of arvadosFiles and other subcollections.
+#'
+#' @section Usage:
+#' \preformatted{subcollection = Subcollection$new(name)}
+#'
+#' @section Arguments:
+#' \describe{
+#' \item{name}{Name of the subcollection.}
+#' }
#'
-#' Update description
+#' @section Methods:
+#' \describe{
+#' \item{getName()}{Returns name of the subcollection.}
+#' \item{getRelativePath()}{Returns subcollection path relative to the root.}
+#' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the subcollection.}
+#' \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
+#' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
+#' \item{getFileListing()}{Returns subcollections file content as character vector.}
+#' \item{getSizeInBytes()}{Returns subcollections content size in bytes.}
+#' \item{move(destination)}{Moves subcollection to a new location inside collection.}
+#' \item{copy(destination)}{Copies subcollection to a new location inside collection.}
+#' }
#'
-#' @export Subcollection
+#' @name Subcollection
+#' @examples
+#' \dontrun{
+#' myFolder <- Subcollection$new("myFolder")
+#' myFile <- ArvadosFile$new("myFile")
+#'
+#' myFolder$add(myFile)
+#' myFolder$get("myFile")
+#' myFolder$remove("myFile")
+#'
+#' myFolder$move("newLocation/myFolder")
+#' myFolder$copy("newLocation/myFolder")
+#' }
+NULL
+
+#' @export
Subcollection <- R6::R6Class(
"Subcollection",
initialize = function(name)
{
- private$name <- name
- private$http <- HttpRequest$new()
- private$httpParser <- HttpParser$new()
+ private$name <- name
},
-
+
+ getName = function() private$name,
+
+ getRelativePath = function()
+ {
+ relativePath <- c(private$name)
+ parent <- private$parent
+
+ while(!is.null(parent))
+ {
+ relativePath <- c(parent$getName(), relativePath)
+ parent <- parent$getParent()
+ }
+
+ relativePath <- relativePath[relativePath != ""]
+ paste0(relativePath, collapse = "/")
+ },
+
add = function(content)
{
if("ArvadosFile" %in% class(content) ||
"Subcollection" %in% class(content))
{
- if(!is.null(content$.__enclos_env__$private$collection))
- stop("ArvadosFile/Subcollection already belongs to a collection.")
+ if(!is.null(content$getCollection()))
+ stop("Content already belongs to a collection.")
+
+ if(content$getName() == "")
+ stop("Content has invalid name.")
+
+ childWithSameName <- self$get(content$getName())
+
+ if(!is.null(childWithSameName))
+ stop(paste("Subcollection already contains ArvadosFile",
+ "or Subcollection with same name."))
if(!is.null(private$collection))
- {
- contentPath <- paste0(self$getRelativePath(), "/", content$getFileList())
- private$collection$.__enclos_env__$private$createFilesOnREST(contentPath)
- content$.__enclos_env__$private$addToCollection(private$collection)
+ {
+ if(self$getRelativePath() != "")
+ contentPath <- paste0(self$getRelativePath(),
+ "/", content$getFileListing())
+ else
+ contentPath <- content$getFileListing()
+
+ REST <- private$collection$getRESTService()
+ REST$create(contentPath, private$collection$uuid)
+ content$setCollection(private$collection)
}
private$children <- c(private$children, content)
- content$.__enclos_env__$private$parent = self
+ content$setParent(self)
+
+ "Content added successfully."
}
else
{
- stop("Expected AravodsFile or Subcollection object, got ...")
+ stop(paste0("Expected AravodsFile or Subcollection object, got ",
+ paste0("(", paste0(class(content), collapse = ", "), ")"),
+ "."))
}
},
- removeFromCollection = function()
+ remove = function(name)
{
- if(is.null(private$collection))
- stop("Subcollection doesn't belong to any collection.")
-
- if(self$name == "")
- stop("Unable to delete root folder.")
-
- collectionList <- paste0(self$getRelativePath(), "/", self$getFileList(fullpath = FALSE))
- sapply(collectionList, function(file)
+ if(is.character(name))
{
- private$collection$.__enclos_env__$private$deleteFromREST(file)
- })
+ child <- self$get(name)
- private$addToCollection(NULL)
- private$dettachFromParent()
- },
+ if(is.null(child))
+ stop(paste("Subcollection doesn't contains ArvadosFile",
+ "or Subcollection with specified name."))
- getFileList = function(fullpath = TRUE)
- {
- content <- NULL
+ if(!is.null(private$collection))
+ {
+ REST <- private$collection$getRESTService()
+ REST$delete(child$getRelativePath(), private$collection$uuid)
- if(fullpath)
- {
- for(child in private$children)
- content <- c(content, child$getFileList())
+ child$setCollection(NULL)
+ }
- if(private$name != "")
- content <- unlist(paste0(private$name, "/", content))
+ private$removeChild(name)
+ child$setParent(NULL)
+
+ "Content removed"
}
else
{
- for(child in private$children)
- content <- c(content, child$getName())
+ stop(paste0("Expected character, got ",
+ paste0("(", paste0(class(name), collapse = ", "), ")"),
+ "."))
}
+ },
- content
+ getFileListing = function(fullPath = TRUE)
+ {
+ content <- private$getContentAsCharVector(fullPath)
+ content[order(tolower(content))]
},
getSizeInBytes = function()
{
- collectionURL <- URLencode(paste0(private$collection$api$getWebDavHostName(), "c=", private$collection$uuid))
- subcollectionURL <- paste0(collectionURL, "/", self$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(subcollectionURL, headers)
+ fileSizes <- REST$getResourceSize(paste0(self$getRelativePath(), "/"),
+ private$collection$uuid)
+ return(sum(fileSizes))
+ },
- sizes <- private$httpParser$extractFileSizeFromWebDAVResponse(propfindResponse, collectionURL)
- sizes <- as.numeric(sizes[-1])
+ move = function(destination)
+ {
+ if(is.null(private$collection))
+ stop("Subcollection doesn't belong to any collection.")
- sum(sizes)
- },
+ destination <- trimFromEnd(destination, "/")
+ nameAndPath <- splitToPathAndName(destination)
- getName = function() private$name,
+ newParent <- private$collection$get(nameAndPath$path)
- getRelativePath = function()
- {
- relativePath <- c(private$name)
- parent <- private$parent
+ if(is.null(newParent))
+ stop("Unable to get destination subcollection.")
- #Recurse back to root
- while(!is.null(parent))
- {
- relativePath <- c(parent$getName(), relativePath)
- parent <- parent$getParent()
- }
+ childWithSameName <- newParent$get(nameAndPath$name)
- relativePath <- relativePath[relativePath != ""]
- paste0(relativePath, collapse = "/")
+ if(!is.null(childWithSameName))
+ stop("Destination already contains content with same name.")
+
+ REST <- private$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
},
- move = function(newLocation)
+ copy = function(destination)
{
- if(endsWith(newLocation, paste0(private$name, "/")))
- {
- newLocation <- substr(newLocation, 0, nchar(newLocation) - nchar(paste0(private$name, "/")))
- }
- else if(endsWith(newLocation, private$name))
- {
- newLocation <- substr(newLocation, 0, nchar(newLocation) - nchar(private$name))
- }
- else
- {
- stop("Destination path is not valid.")
- }
+ if(is.null(private$collection))
+ stop("Subcollection doesn't belong to any collection.")
- newParent <- private$collection$get(newLocation)
+ destination <- trimFromEnd(destination, "/")
+ nameAndPath <- splitToPathAndName(destination)
- if(is.null(newParent))
- {
- stop("Unable to get destination subcollectin")
- }
+ newParent <- private$collection$get(nameAndPath$path)
- status <- private$collection$.__enclos_env__$private$moveOnRest(self$getRelativePath(), paste0(newParent$getRelativePath(), "/", self$getName()))
+ if(is.null(newParent) || !("Subcollection" %in% class(newParent)))
+ stop("Unable to get destination subcollection.")
- private$attachToParent(newParent)
+ childWithSameName <- newParent$get(nameAndPath$name)
- paste("Status code :", status$status_code)
- },
+ if(!is.null(childWithSameName))
+ stop("Destination already contains content with same name.")
- getParent = function() private$parent
- ),
+ REST <- private$collection$getRESTService()
+ REST$copy(self$getRelativePath(),
+ paste0(newParent$getRelativePath(), "/", nameAndPath$name),
+ private$collection$uuid)
- private = list(
+ newContent <- self$duplicate(nameAndPath$name)
+ newContent$setCollection(self$getCollection(), setRecursively = TRUE)
+ newContent$setParent(newParent)
+ private$attachToNewParent(newContent, newParent)
- name = NULL,
- children = NULL,
- parent = NULL,
- collection = NULL,
- http = NULL,
- httpParser = NULL,
+ newContent
+ },
- getChild = function(name)
+ duplicate = function(newName = NULL)
+ {
+ name <- if(!is.null(newName)) newName else private$name
+ root <- Subcollection$new(name)
+ for(child in private$children)
+ root$add(child$duplicate())
+
+ root
+ },
+
+ get = function(name)
{
for(child in private$children)
{
return(NULL)
},
- getFirstChild = function()
+ getFirst = function()
{
if(length(private$children) == 0)
return(NULL)
private$children[[1]]
},
+ setCollection = function(collection, setRecursively = TRUE)
+ {
+ private$collection = collection
+
+ if(setRecursively)
+ {
+ for(child in private$children)
+ child$setCollection(collection)
+ }
+ },
+
+ getCollection = function() private$collection,
+
+ getParent = function() private$parent,
+
+ setParent = function(newParent) private$parent <- newParent
+ ),
+
+ private = list(
+
+ name = NULL,
+ children = NULL,
+ parent = NULL,
+ collection = NULL,
+
removeChild = function(name)
{
numberOfChildren = length(private$children)
}
},
- addToCollection = function(collection)
+ attachToNewParent = function(content, newParent)
{
- for(child in private$children)
- child$.__enclos_env__$private$addToCollection(collection)
+ # We temporary set parents collection to NULL. This will ensure that
+ # add method doesn't post this subcollection to REST.
+ # We also need to set content's collection to NULL because
+ # add method throws exception if we try to add content that already
+ # belongs to a collection.
+ parentsCollection <- newParent$getCollection()
+ content$setCollection(NULL, setRecursively = FALSE)
+ newParent$setCollection(NULL, setRecursively = FALSE)
+ newParent$add(content)
+ content$setCollection(parentsCollection, setRecursively = FALSE)
+ newParent$setCollection(parentsCollection, setRecursively = FALSE)
+ },
- private$collection = collection
+ dettachFromCurrentParent = function()
+ {
+ # We temporary set parents collection to NULL. This will ensure that
+ # remove method doesn't remove this subcollection from REST.
+ parent <- private$parent
+ parentsCollection <- parent$getCollection()
+ parent$setCollection(NULL, setRecursively = FALSE)
+ parent$remove(private$name)
+ parent$setCollection(parentsCollection, setRecursively = FALSE)
},
- dettachFromParent = function()
+ getContentAsCharVector = function(fullPath = TRUE)
{
- if(!is.null(private$parent))
+ content <- NULL
+
+ if(fullPath)
{
- private$parent$.__enclos_env__$private$removeChild(private$name)
- private$parent <- NULL
+ for(child in private$children)
+ content <- c(content, child$getFileListing())
+
+ if(private$name != "")
+ content <- unlist(paste0(private$name, "/", content))
}
else
- stop("Parent doesn't exists.")
- },
+ {
+ for(child in private$children)
+ content <- c(content, child$getName())
+ }
- attachToParent = function(parent)
- {
- parent$.__enclos_env__$private$children <- c(parent$.__enclos_env__$private$children, self)
- private$parent <- parent
+ content
}
),
-
+
cloneable = FALSE
)
+
+#' print.Subcollection
+#'
+#' Custom print function for Subcollection class
+#'
+#' @param x Instance of Subcollection class
+#' @param ... Optional arguments.
+#' @export
+print.Subcollection = function(x, ...)
+{
+ collection <- NULL
+ relativePath <- x$getRelativePath()
+
+ if(!is.null(x$getCollection()))
+ {
+ collection <- x$getCollection()$uuid
+
+ if(!x$getName() == "")
+ relativePath <- paste0("/", relativePath)
+ }
+
+ cat(paste0("Type: ", "\"", "Arvados Subcollection", "\""), sep = "\n")
+ cat(paste0("Name: ", "\"", x$getName(), "\""), sep = "\n")
+ cat(paste0("Relative path: ", "\"", relativePath, "\""), sep = "\n")
+ cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n")
+}
projects / arvados.git / blobdiff