-#' ArvadosFile Object
+source("./R/util.R")
+
+#' ArvadosFile
+#'
+#' ArvadosFile class represents a file inside Arvados collection.
+#'
+#' @section Usage:
+#' \preformatted{file = ArvadosFile$new(name)}
+#'
+#' @section Arguments:
+#' \describe{
+#' \item{name}{Name of the file.}
+#' }
+#'
+#' @section Methods:
+#' \describe{
+#' \item{getName()}{Returns name of the file.}
+#' \item{getRelativePath()}{Returns file path relative to the root.}
+#' \item{read(contentType = "raw", offset = 0, length = 0)}{Read file content.}
+#' \item{write(content, contentType = "text/html")}{Write to file (override current content of the file).}
+#' \item{connection(rw)}{Get connection opened in "read" or "write" mode.}
+#' \item{flush()}{Write connections content to a file (override current content of the file).}
+#' \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
+#' \item{getSizeInBytes()}{Returns file size in bytes.}
+#' \item{move(newLocation)}{Moves file to a new location inside collection.}
+#' }
+#'
+#' @name ArvadosFile
+#' @examples
+#' \dontrun{
+#' myFile <- ArvadosFile$new("myFile")
+#'
+#' myFile$write("This is new file content")
+#' fileContent <- myFile$read()
+#' fileContent <- myFile$read("text")
+#' fileContent <- myFile$read("raw", offset = 8, length = 4)
#'
-#' Update description
+#' #Write a table:
+#' arvConnection <- myFile$connection("w")
+#' write.table(mytable, arvConnection)
+#' arvadosFile$flush()
#'
-#' @export ArvadosFile
+#' #Read a table:
+#' arvConnection <- myFile$connection("r")
+#' mytable <- read.table(arvConnection)
+#'
+#' myFile$move("newFolder/myFile")
+#' }
+NULL
+
+#' @export
ArvadosFile <- R6::R6Class(
"ArvadosFile",
public = list(
- initialize = function(name, relativePath, size, api, collection)
+ initialize = function(name)
{
- private$name <- name
- private$size <- size
- private$relativePath <- relativePath
- private$api <- api
- private$collection <- collection
- private$http <- HttpRequest$new()
- private$httpParser <- HttpParser$new()
+ if(name == "")
+ stop("Invalid name.")
+
+ private$name <- name
},
getName = function() private$name,
- getRelativePath = function() private$relativePath,
+ getFileListing = function(fullpath = TRUE)
+ {
+ self$getName()
+ },
+
+ getSizeInBytes = function()
+ {
+ if(is.null(private$collection))
+ return(0)
+
+ REST <- private$collection$getRESTService()
+
+ fileSize <- REST$getResourceSize(self$getRelativePath(),
+ private$collection$uuid)
+
+ fileSize
+ },
+
+ get = function(fileLikeObjectName)
+ {
+ return(NULL)
+ },
+
+ getFirst = function()
+ {
+ return(NULL)
+ },
+
+ getCollection = function() private$collection,
+
+ setCollection = function(collection)
+ {
+ private$collection <- collection
+ },
+
+ 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 = "/")
+ },
+
+ getParent = function() private$parent,
- getSizeInBytes = function() private$size,
+ setParent = function(newParent) private$parent <- newParent,
- read = function(offset = 0, length = 0)
+ read = function(contentType = "raw", offset = 0, length = 0)
{
+ if(is.null(private$collection))
+ stop("ArvadosFile doesn't belong to any collection.")
+
if(offset < 0 || length < 0)
- stop("Offset and length must be positive values.")
+ stop("Offset and length must be positive values.")
- range = paste0("bytes=", offset, "-")
+ REST <- private$collection$getRESTService()
- if(length > 0)
- range = paste0(range, offset + length - 1)
-
- fileURL = paste0(private$api$getWebDavHostName(), "c=", private$collection$uuid, "/", private$relativePath);
- headers <- list(Authorization = paste("OAuth2", private$api$getToken()),
- Range = range)
+ fileContent <- REST$read(self$getRelativePath(),
+ private$collection$uuid,
+ contentType, offset, length)
+ fileContent
+ },
- serverResponse <- private$http$GET(fileURL, headers)
+ connection = function(rw)
+ {
+ if (rw == "r" || rw == "rb")
+ {
+ REST <- private$collection$getRESTService()
+ return(REST$getConnection(private$collection$uuid,
+ self$getRelativePath(),
+ rw))
+ }
+ else if (rw == "w")
+ {
+ private$buffer <- textConnection(NULL, "w")
- if(serverResponse$status_code != 206)
- stop(paste("Server code:", serverResponse$status_code))
+ return(private$buffer)
+ }
+ },
- parsedServerResponse <- httr::content(serverResponse, "raw")
- parsedServerResponse
+ flush = function()
+ {
+ v <- textConnectionValue(private$buffer)
+ close(private$buffer)
+ self$write(paste(v, collapse='\n'))
},
-
+
write = function(content, contentType = "text/html")
{
- fileURL = paste0(private$api$getWebDavHostName(), "c=", private$collection$uuid, "/", private$relativePath);
- headers <- list(Authorization = paste("OAuth2", private$api$getToken()),
- "Content-Type" = contentType)
- body <- content
+ if(is.null(private$collection))
+ stop("ArvadosFile doesn't belong to any collection.")
+
+ REST <- private$collection$getRESTService()
+
+ writeResult <- REST$write(self$getRelativePath(),
+ private$collection$uuid,
+ content, contentType)
+ writeResult
+ },
+
+ move = function(newLocation)
+ {
+ if(is.null(private$collection))
+ stop("ArvadosFile doesn't belong to any collection")
+
+ newLocation <- trimFromEnd(newLocation, "/")
+ nameAndPath <- splitToPathAndName(newLocation)
+
+ newParent <- private$collection$get(nameAndPath$path)
- serverResponse <- private$http$PUT(fileURL, headers, body)
+ if(is.null(newParent))
+ {
+ stop("Unable to get destination subcollection")
+ }
- if(serverResponse$status_code != 201)
- stop(paste("Server code:", serverResponse$status_code))
+ childWithSameName <- newParent$get(nameAndPath$name)
- private$notifyCollectionThatFileSizeChanges()
+ if(!is.null(childWithSameName))
+ stop("Destination already contains content with same name.")
- parsedServerResponse <- httr::content(serverResponse, "text")
- parsedServerResponse
+ REST <- private$collection$getRESTService()
+ REST$move(self$getRelativePath(),
+ paste0(newParent$getRelativePath(), "/", nameAndPath$name),
+ private$collection$uuid)
+
+ private$dettachFromCurrentParent()
+ private$attachToNewParent(newParent)
+
+ private$name <- nameAndPath$name
+
+ "Content moved successfully."
}
),
private = list(
- name = NULL,
- relativePath = NULL,
- size = NULL,
- parent = NULL,
- api = NULL,
- collection = NULL,
- http = NULL,
- httpParser = NULL,
+ name = NULL,
+ size = NULL,
+ parent = NULL,
+ collection = NULL,
+ buffer = NULL,
- notifyCollectionThatFileSizeChanges = function()
+ attachToNewParent = function(newParent)
{
- collectionURL <- URLencode(paste0(private$api$getWebDavHostName(), "c=", private$collection$uuid))
- fileURL = paste0(collectionURL, "/", private$relativePath);
- headers = list("Authorization" = paste("OAuth2", private$api$getToken()))
+ #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$parent <- newParent
+ },
- propfindResponse <- private$http$PROPFIND(fileURL, headers)
+ dettachFromCurrentParent = function()
+ {
+ #Note: We temporary set parents collection to NULL. This will ensure that
+ # remove method doesn't remove this subcollection from REST.
+ parent <- private$parent
+ parentsCollection <- parent$getCollection()
+ parent$setCollection(NULL, setRecursively = FALSE)
- fileInfo <- private$httpParser$parseWebDAVResponse(propfindResponse, collectionURL)
+ parent$remove(private$name)
- private$size <- fileInfo[[1]]$fileSize
- private$collection$update(self, "File size changed")
+ 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")
+}