X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/0fab8a581c4a711408150ed64ce909d9afda7829..HEAD:/sdk/R/R/Subcollection.R

diff --git a/sdk/R/R/Subcollection.R b/sdk/R/R/Subcollection.R
index 863e3f768f..752a396655 100644
--- a/sdk/R/R/Subcollection.R
+++ b/sdk/R/R/Subcollection.R
@@ -1,43 +1,12 @@
-source("./R/util.R")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
 
-#' Subcollection
-#' 
-#' Subcollection class represents a folder inside Arvados collection.
-#' It is essentially a composite of ArvadosFiles and other Subcollections.
-#' 
-#' @section Usage:
-#' \preformatted{subcollection = Subcollection$new(name)}
-#'
-#' @section Arguments:
-#' \describe{
-#'   \item{name}{Name of the subcollection.}
-#' }
-#' 
-#' @section Methods:
-#' \describe{
-#'   \item{getName()}{Returns name of the subcollection.}
-#'   \item{getRelativePath()}{Returns subcollection path relative to the root.}
-#'   \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the subcollection.}
-#'   \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
-#'   \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
-#'   \item{getFileListing()}{Returns subcollections file content as character vector.}
-#'   \item{getSizeInBytes()}{Returns subcollections content size in bytes.}
-#'   \item{move(newLocation)}{Moves subcollection to a new location inside collection.}
-#' }
-#'
-#' @name Subcollection
-#' @examples
-#' \dontrun{
-#' myFolder <- Subcollection$new("myFolder")
-#' myFile   <- ArvadosFile$new("myFile")
+#' R6 Class Representing a Subcollection
 #'
-#' myFolder$add(myFile)
-#' myFolder$get("myFile")
-#' myFolder$remove("myFile")
-#'
-#' myFolder$move("newLocation/myFolder")
-#' }
-NULL
+#' @description
+#' Subcollection class represents a folder inside Arvados collection.
+#' It is essentially a composite of arvadosFiles and other subcollections.
 
 #' @export
 Subcollection <- R6::R6Class(
@@ -46,13 +15,21 @@ Subcollection <- R6::R6Class(
 
     public = list(
 
+        #' @description
+        #' Initialize new enviroment.
+        #' @param name Name of the new enviroment.
+        #' @return A new `Subcollection` object.
         initialize = function(name)
         {
             private$name <- name
         },
 
+        #' @description
+        #' Returns name of the file.
         getName = function() private$name,
-        
+
+        #' @description
+        #' Returns Subcollection's path relative to the root.
         getRelativePath = function()
         {
             relativePath <- c(private$name)
@@ -68,11 +45,17 @@ Subcollection <- R6::R6Class(
             paste0(relativePath, collapse = "/")
         },
 
+        #' @description
+        #' Adds ArvadosFile or Subcollection specified by content to the Subcollection.
+        #' @param content Content to be added.
         add = function(content)
         {
             if("ArvadosFile"   %in% class(content) ||
                "Subcollection" %in% class(content))
             {
+                if(!is.null(content$getCollection()))
+                    stop("Content already belongs to a collection.")
+
                 if(content$getName() == "")
                     stop("Content has invalid name.")
 
@@ -83,7 +66,7 @@ Subcollection <- R6::R6Class(
                                "or Subcollection with same name."))
 
                 if(!is.null(private$collection))
-                {       
+                {
                     if(self$getRelativePath() != "")
                         contentPath <- paste0(self$getRelativePath(),
                                               "/", content$getFileListing())
@@ -108,6 +91,9 @@ Subcollection <- R6::R6Class(
             }
         },
 
+        #' @description
+        #' Removes ArvadosFile or Subcollection specified by name from the Subcollection.
+        #' @param name Name of the file to be removed.
         remove = function(name)
         {
             if(is.character(name))
@@ -139,12 +125,17 @@ Subcollection <- R6::R6Class(
             }
         },
 
+        #' @description
+        #' Returns Subcollections file content as character vector.
+        #' @param fullPath Checking if the path to file exists.
         getFileListing = function(fullPath = TRUE)
         {
             content <- private$getContentAsCharVector(fullPath)
             content[order(tolower(content))]
         },
 
+        #' @description
+        #' Returns subcollections content size in bytes.
         getSizeInBytes = function()
         {
             if(is.null(private$collection))
@@ -157,20 +148,21 @@ Subcollection <- R6::R6Class(
             return(sum(fileSizes))
         },
 
-        move = function(newLocation)
+        #' @description
+        #' Moves Subcollection to a new location inside collection.
+        #' @param destination Path to move the file.
+        move = function(destination)
         {
             if(is.null(private$collection))
-                stop("Subcollection doesn't belong to any collection")
+                stop("Subcollection 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)
 
@@ -183,13 +175,64 @@ Subcollection <- R6::R6Class(
                       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 Subcollection to a new location inside collection.
+        #' @param destination Path to copy the file.
+        copy = function(destination)
+        {
+            if(is.null(private$collection))
+                stop("Subcollection doesn't belong to any collection.")
+
+            destination <- trimFromEnd(destination, "/")
+            nameAndPath <- splitToPathAndName(destination)
+
+            newParent <- private$collection$get(nameAndPath$path)
+
+            if(is.null(newParent) || !("Subcollection" %in% class(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)
+
+            newContent <- self$duplicate(nameAndPath$name)
+            newContent$setCollection(self$getCollection(), setRecursively = TRUE)
+            newContent$setParent(newParent)
+            private$attachToNewParent(newContent, newParent)
+
+            newContent
+        },
+
+        #' @description
+        #' Duplicate Subcollection 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$name
+            root <- Subcollection$new(name)
+            for(child in private$children)
+                root$add(child$duplicate())
+
+            root
+        },
+
+        #' @description
+        #' If name is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.
+        #' @param name Name of the file.
         get = function(name)
         {
             for(child in private$children)
@@ -201,14 +244,18 @@ Subcollection <- R6::R6Class(
             return(NULL)
         },
 
+        #' @description
+        #' Returns files in Subcollection.
         getFirst = function()
         {
             if(length(private$children) == 0)
-               return(NULL)
+                return(NULL)
 
             private$children[[1]]
         },
 
+        #' @description
+        #' Sets Collection by its UUID.
         setCollection = function(collection, setRecursively = TRUE)
         {
             private$collection = collection
@@ -220,10 +267,16 @@ Subcollection <- R6::R6Class(
             }
         },
 
+        #' @description
+        #' Returns Collection of Subcollection.
         getCollection = function() private$collection,
 
+        #' @description
+        #' Returns Collection UUID.
         getParent = function() private$parent,
 
+        #' @description
+        #' Sets new Collection.
         setParent = function(newParent) private$parent <- newParent
     ),
 
@@ -250,30 +303,29 @@ Subcollection <- R6::R6Class(
             }
         },
 
-        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 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(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 subcollection from REST.
             parent <- private$parent
             parentsCollection <- parent$getCollection()
             parent$setCollection(NULL, setRecursively = FALSE)
-
             parent$remove(private$name)
-
             parent$setCollection(parentsCollection, setRecursively = FALSE)
         },
 
@@ -298,7 +350,7 @@ Subcollection <- R6::R6Class(
             content
         }
     ),
-    
+
     cloneable = FALSE
 )
 
@@ -308,7 +360,7 @@ Subcollection <- R6::R6Class(
 #'
 #' @param x Instance of Subcollection class
 #' @param ... Optional arguments.
-#' @export 
+#' @export
 print.Subcollection = function(x, ...)
 {
     collection   <- NULL