X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/1012f12d29be01b56f2bbbe2e9bd5969d69f7b89..39c17737ac69d7693684fe2f95bef0ec235a28bf:/sdk/R/R/ArvadosFile.R

diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R
index 3437933a73..70bb4450ec 100644
--- a/sdk/R/R/ArvadosFile.R
+++ b/sdk/R/R/ArvadosFile.R
@@ -1,10 +1,60 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
 source("./R/util.R")
 
-#' ArvadosFile Object
+#' ArvadosFile
+#'
+#' ArvadosFile class represents a file inside Arvados collection.
+#'
+#' @section Usage:
+#' \preformatted{file = ArvadosFile$new(name)}
+#'
+#' @section Arguments:
+#' \describe{
+#'   \item{name}{Name of the file.}
+#' }
+#'
+#' @section Methods:
+#' \describe{
+#'   \item{getName()}{Returns name of the file.}
+#'   \item{getRelativePath()}{Returns file path relative to the root.}
+#'   \item{read(contentType = "raw", offset = 0, length = 0)}{Read file content.}
+#'   \item{write(content, contentType = "text/html")}{Write to file (override current content of the file).}
+#'   \item{connection(rw)}{Get connection opened in "read" or "write" mode.}
+#'   \item{flush()}{Write connections content to a file (override current content of the file).}
+#'   \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
+#'   \item{getSizeInBytes()}{Returns file size in bytes.}
+#'   \item{move(destination)}{Moves file to a new location inside collection.}
+#'   \item{copy(destination)}{Copies file to a new location inside collection.}
+#' }
+#'
+#' @name ArvadosFile
+#' @examples
+#' \dontrun{
+#' myFile <- ArvadosFile$new("myFile")
 #'
-#' Update description
+#' myFile$write("This is new file content")
+#' fileContent <- myFile$read()
+#' fileContent <- myFile$read("text")
+#' fileContent <- myFile$read("raw", offset = 8, length = 4)
 #'
-#' @export ArvadosFile
+#' #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",
@@ -35,7 +85,6 @@ ArvadosFile <- R6::R6Class(
 
             fileSize <- REST$getResourceSize(self$getRelativePath(),
                                              private$collection$uuid)
-
             fileSize
         },
 
@@ -51,7 +100,7 @@ ArvadosFile <- R6::R6Class(
 
         getCollection = function() private$collection,
 
-        setCollection = function(collection)
+        setCollection = function(collection, setRecursively = TRUE)
         {
             private$collection <- collection
         },
@@ -93,14 +142,14 @@ ArvadosFile <- R6::R6Class(
 
         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")
 
@@ -108,7 +157,7 @@ ArvadosFile <- R6::R6Class(
             }
         },
 
-        flush = function() 
+        flush = function()
         {
             v <- textConnectionValue(private$buffer)
             close(private$buffer)
@@ -128,20 +177,18 @@ ArvadosFile <- R6::R6Class(
             writeResult
         },
 
-        move = function(newLocation)
+        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)
 
@@ -154,11 +201,50 @@ ArvadosFile <- 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
+        },
+
+        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
+        },
+
+        duplicate = function(newName = NULL)
+        {
+            name <- if(!is.null(newName)) newName else private$name
+            newFile <- ArvadosFile$new(name)
+            newFile
         }
     ),
 
@@ -170,30 +256,29 @@ ArvadosFile <- R6::R6Class(
         collection = 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$getCollection()
+            content$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.
             parent <- private$parent
             parentsCollection <- parent$getCollection()
             parent$setCollection(NULL, setRecursively = FALSE)
-
             parent$remove(private$name)
-
             parent$setCollection(parentsCollection, setRecursively = FALSE)
         }
     ),
@@ -201,20 +286,26 @@ ArvadosFile <- R6::R6Class(
     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$getName(), "\""), sep = "\n")
-    cat(paste0("Relative path: ", "\"", relativePath,          "\""), sep = "\n")
-    cat(paste0("Collection:    ", "\"", collection,            "\""), sep = "\n")
+    cat(paste0("Type:          ", "\"", "ArvadosFile", "\""), sep = "\n")
+    cat(paste0("Name:          ", "\"", x$getName(),   "\""), sep = "\n")
+    cat(paste0("Relative path: ", "\"", relativePath,  "\""), sep = "\n")
+    cat(paste0("Collection:    ", "\"", collection,    "\""), sep = "\n")
 }