X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/d246f53c1d991f1572d6701569aa8c7eac4d722d..9bb169138470dbb176af7e891d6da2089950354b:/sdk/R/R/ArvadosFile.R

diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R
index 8c2e9e2547..e28ba9606c 100644
--- a/sdk/R/R/ArvadosFile.R
+++ b/sdk/R/R/ArvadosFile.R
@@ -1,8 +1,54 @@
-#' ArvadosFile Object
+source("./R/util.R")
+
+#' ArvadosFile
+#' 
+#' ArvadosFile class represents a file inside Arvados collection.
+#' 
+#' @section Usage:
+#' \preformatted{file = ArvadosFile$new(name)}
 #'
-#' Update description
+#' @section Arguments:
+#' \describe{
+#'   \item{name}{Name of the file.}
+#' }
+#' 
+#' @section Methods:
+#' \describe{
+#'   \item{getName()}{Returns name of the file.}
+#'   \item{getRelativePath()}{Returns file path relative to the root.}
+#'   \item{read(contentType = "raw", offset = 0, length = 0)}{Read file content.}
+#'   \item{write(content, contentType = "text/html")}{Write to file (override current content of the file).}
+#'   \item{connection(rw)}{Get connection opened in "read" or "write" mode.}
+#'   \item{flush()}{Write connections content to a file (override current content of the file).}
+#'   \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
+#'   \item{getSizeInBytes()}{Returns file size in bytes.}
+#'   \item{move(newLocation)}{Moves file to a new location inside collection.}
+#' }
 #'
-#' @export ArvadosFile
+#' @name ArvadosFile
+#' @examples
+#' \dontrun{
+#' myFile <- ArvadosFile$new("myFile")
+#'
+#' 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")
+#' }
+NULL
+
+#' @export
 ArvadosFile <- R6::R6Class(
 
     "ArvadosFile",
@@ -11,9 +57,10 @@ ArvadosFile <- R6::R6Class(
 
         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,
@@ -25,16 +72,15 @@ ArvadosFile <- R6::R6Class(
 
         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)
 
-            sizes <- private$httpParser$extractFileSizeFromWebDAVResponse(propfindResponse, collectionURL)
-            as.numeric(sizes)
+            fileSize
         },
 
         get = function(fileLikeObjectName)
@@ -81,106 +127,80 @@ ArvadosFile <- R6::R6Class(
             if(offset < 0 || length < 0)
                 stop("Offset and length must be positive values.")
 
-            if(!(contentType %in% private$http$validContentTypes))
-                stop("Invalid contentType. Please use text or raw.")
-
-            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());
+            fileContent <- REST$read(self$getRelativePath(),
+                                     private$collection$uuid,
+                                     contentType, offset, length)
+            fileContent
+        },
 
-            if(offset == 0 && length == 0)
+        connection = function(rw)
+        {
+            if (rw == "r" || rw == "rb") 
             {
-                headers <- list(Authorization = paste("OAuth2",
-                                                      private$collection$api$getToken())) 
+                REST <- private$collection$getRESTService()
+                return(REST$getConnection(private$collection$uuid,
+                                          self$getRelativePath(),
+                                          rw))
             }
-            else
+            else if (rw == "w") 
             {
-                headers <- list(Authorization = paste("OAuth2", private$collection$api$getToken()), 
-                                Range = range)
-            }
-
-            serverResponse <- private$http$GET(fileURL, headers)
+                private$buffer <- textConnection(NULL, "w")
 
-            if(serverResponse$status_code < 200 || serverResponse$status_code >= 300)
-                stop(paste("Server code:", serverResponse$status_code))
+                return(private$buffer)
+            }
+        },
 
-            parsedServerResponse <- httr::content(serverResponse, contentType)
-            parsedServerResponse
+        flush = function() 
+        {
+            v <- textConnectionValue(private$buffer)
+            close(private$buffer)
+            self$write(paste(v, collapse='\n'))
         },
-        
+
         write = function(content, contentType = "text/html")
         {
             if(is.null(private$collection))
                 stop("ArvadosFile doesn't belong to any collection.")
 
-            fileURL = paste0(private$collection$api$getWebDavHostName(), 
-                             "c=", private$collection$uuid, "/", self$getRelativePath());
-            headers <- list(Authorization = paste("OAuth2", private$collection$api$getToken()), 
-                            "Content-Type" = contentType)
-            body <- content
-
-            serverResponse <- private$http$PUT(fileURL, headers, body)
+            REST <- private$collection$getRESTService()
 
-            if(serverResponse$status_code < 200 || serverResponse$status_code >= 300)
-                stop(paste("Server code:", serverResponse$status_code))
-
-            parsedServerResponse <- httr::content(serverResponse, "text")
-            parsedServerResponse
+            writeResult <- REST$write(self$getRelativePath(),
+                                      private$collection$uuid,
+                                      content, contentType)
+            writeResult
         },
 
         move = function(newLocation)
         {
-            #todo test if file can be moved
-
             if(is.null(private$collection))
-                stop("ArvadosFile doesn't belong to any collection.")
+                stop("ArvadosFile doesn't belong to any collection")
 
-            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.")
-            }
+            newLocation <- trimFromEnd(newLocation, "/")
+            nameAndPath <- splitToPathAndName(newLocation)
 
-            newParent <- private$collection$get(newLocation)
+            newParent <- private$collection$get(nameAndPath$path)
 
             if(is.null(newParent))
             {
-                stop("Unable to get destination subcollection.")
+                stop("Unable to get destination subcollection")
             }
 
-            childWithSameName <- newParent$get(private$name)
+            childWithSameName <- newParent$get(nameAndPath$name)
 
             if(!is.null(childWithSameName))
-                stop("Destination already contains file with same name.")
+                stop("Destination already contains content with same name.")
 
-            status <- private$collection$moveOnREST(self$getRelativePath(),
-                                                    paste0(newParent$getRelativePath(),
-                                                           "/", self$getName()))
+            REST <- private$collection$getRESTService()
+            REST$move(self$getRelativePath(),
+                      paste0(newParent$getRelativePath(), "/", nameAndPath$name),
+                      private$collection$uuid)
 
-            #Note: We temporary set parents collection to NULL. This will ensure that
-            #      add method doesn't post file on REST server.
-            parentsCollection <- newParent$getCollection()
-            newParent$setCollection(NULL, setRecursively = FALSE)
+            private$dettachFromCurrentParent()
+            private$attachToNewParent(newParent)
 
-            newParent$add(self)
-
-            newParent$setCollection(parentsCollection, setRecursively = FALSE)
-
-            private$parent <- newParent
+            private$name <- nameAndPath$name
 
             "Content moved successfully."
         }
@@ -192,9 +212,59 @@ ArvadosFile <- R6::R6Class(
         size       = NULL,
         parent     = NULL,
         collection = NULL,
-        http       = NULL,
-        httpParser = NULL
+        buffer     = NULL,
+
+        attachToNewParent = function(newParent)
+        {
+            #Note: We temporary set parents collection to NULL. This will ensure that
+            #      add method doesn't post file on REST.
+            parentsCollection <- newParent$getCollection()
+            newParent$setCollection(NULL, setRecursively = FALSE)
+
+            newParent$add(self)
+
+            newParent$setCollection(parentsCollection, setRecursively = FALSE)
+
+            private$parent <- newParent
+        },
+
+        dettachFromCurrentParent = function()
+        {
+            #Note: We temporary set parents collection to NULL. This will ensure that
+            #      remove method doesn't remove this subcollection from REST.
+            parent <- private$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")
+}