X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/c856e47c2a25dc6979ea07f2c3942687687c833a..HEAD:/sdk/R/R/ArvadosFile.R diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R index 8f737831c4..f585d1f946 100644 --- a/sdk/R/R/ArvadosFile.R +++ b/sdk/R/R/ArvadosFile.R @@ -2,55 +2,10 @@ # # SPDX-License-Identifier: Apache-2.0 -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) -#' -#' #Write a table: -#' arvConnection <- myFile$connection("w") -#' write.table(mytable, arvConnection) -#' arvadosFile$flush() +#' R6 Class Representing a ArvadosFile #' -#' #Read a table: -#' arvConnection <- myFile$connection("r") -#' mytable <- read.table(arvConnection) -#' -#' myFile$move("newFolder/myFile") -#' } -NULL +#' @description +#' ArvadosFile class represents a file inside Arvados collection. #' @export ArvadosFile <- R6::R6Class( @@ -59,6 +14,14 @@ ArvadosFile <- R6::R6Class( public = list( + #' @description + #' Initialize new enviroment. + #' @param name Name of the new enviroment. + #' @return A new `ArvadosFile` object. + #' @examples + #' \dontrun{ + #' myFile <- ArvadosFile$new("myFile") + #' } initialize = function(name) { if(name == "") @@ -67,13 +30,32 @@ ArvadosFile <- R6::R6Class( private$name <- name }, + #' @description + #' Returns name of the file. + #' @examples + #' \dontrun{ + #' arvadosFile$getName() + #' } getName = function() private$name, + #' @description + #' Returns collections file content as character vector. + #' @param fullPath Checking if TRUE. + #' @examples + #' \dontrun{ + #' arvadosFile$getFileListing() + #' } getFileListing = function(fullpath = TRUE) { self$getName() }, + #' @description + #' Returns collections content size in bytes. + #' @examples + #' \dontrun{ + #' arvadosFile$getSizeInBytes() + #' } getSizeInBytes = function() { if(is.null(private$collection)) @@ -83,7 +65,6 @@ ArvadosFile <- R6::R6Class( fileSize <- REST$getResourceSize(self$getRelativePath(), private$collection$uuid) - fileSize }, @@ -97,13 +78,19 @@ ArvadosFile <- R6::R6Class( return(NULL) }, + #' @description + #' Returns collection UUID. getCollection = function() private$collection, - setCollection = function(collection) + #' @description + #' Sets new collection. + setCollection = function(collection, setRecursively = TRUE) { private$collection <- collection }, + #' @description + #' Returns file path relative to the root. getRelativePath = function() { relativePath <- c(private$name) @@ -119,10 +106,25 @@ ArvadosFile <- R6::R6Class( paste0(relativePath, collapse = "/") }, + #' @description + #' Returns project UUID. getParent = function() private$parent, + #' @description + #' Sets project collection. setParent = function(newParent) private$parent <- newParent, + #' @description + #' Read file content. + #' @param contentType Type of content. Possible is "text", "raw". + #' @param offset Describes the location of a piece of data compared to another location + #' @param length Length of content + #' @examples + #' \dontrun{ + #' collection <- Collection$new(arv, collectionUUID) + #' arvadosFile <- collection$get(fileName) + #' fileContent <- arvadosFile$read("text") + #' } read = function(contentType = "raw", offset = 0, length = 0) { if(is.null(private$collection)) @@ -139,16 +141,25 @@ ArvadosFile <- R6::R6Class( fileContent }, + #' @description + #' Get connection opened in "read" or "write" mode. + #' @param rw Type of connection. + #' @examples + #' \dontrun{ + #' collection <- Collection$new(arv, collectionUUID) + #' arvadosFile <- collection$get(fileName) + #' arvConnection <- arvadosFile$connection("w") + #' } 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$buffer <- textConnection(NULL, "w") @@ -156,13 +167,32 @@ ArvadosFile <- R6::R6Class( } }, - flush = function() + #' @description + #' Write connections content to a file or override current content of the file. + #' @examples + #' \dontrun{ + #' collection <- Collection$new(arv, collectionUUID) + #' arvadosFile <- collection$get(fileName) + #' myFile$write("This is new file content") + #' arvadosFile$flush() + #' } + flush = function() { v <- textConnectionValue(private$buffer) close(private$buffer) self$write(paste(v, collapse='\n')) }, + #' @description + #' Write to file or override current content of the file. + #' @param content File to write. + #' @param contentType Type of content. Possible is "text", "raw". + #' @examples + #' \dontrun{ + #' collection <- Collection$new(arv, collectionUUID) + #' arvadosFile <- collection$get(fileName) + #' myFile$write("This is new file content") + #' } write = function(content, contentType = "text/html") { if(is.null(private$collection)) @@ -176,20 +206,25 @@ ArvadosFile <- R6::R6Class( writeResult }, - move = function(newLocation) + #' @description + #' Moves file to a new location inside collection. + #' @param destination Path to new folder. + #' @examples + #' \dontrun{ + #' arvadosFile$move(newPath) + #' } + move = function(destination) { if(is.null(private$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$name) @@ -202,11 +237,60 @@ ArvadosFile <- R6::R6Class( private$collection$uuid) private$dettachFromCurrentParent() - private$attachToNewParent(newParent) + private$attachToNewParent(self, newParent) + private$parent <- newParent private$name <- nameAndPath$name - "Content moved successfully." + self + }, + + #' @description + #' Copies file to a new location inside collection. + #' @param destination Path to new folder. + #' @examples + #' \dontrun{ + #' arvadosFile$copy("NewName.format") + #' } + 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 + }, + + #' @description + #' Duplicate file 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$name + newFile <- ArvadosFile$new(name) + newFile } ), @@ -218,30 +302,35 @@ 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$getCollection() + #parent$.__enclos_env__$private$children <- c(parent$.__enclos_env__$private$children, self) + #private$parent <- parent + 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$parent <- newParent }, dettachFromCurrentParent = function() { - #Note: We temporary set parents collection to NULL. This will ensure that - # remove method doesn't remove this subcollection from REST. + # We temporary set parents collection to NULL. This will ensure that + # remove method doesn't remove this file from REST. + + #private$parent$.__enclos_env__$private$removeChild(private$name) + #private$parent <- NULL parent <- private$parent parentsCollection <- parent$getCollection() parent$setCollection(NULL, setRecursively = FALSE) - parent$remove(private$name) - parent$setCollection(parentsCollection, setRecursively = FALSE) } ), @@ -255,7 +344,7 @@ ArvadosFile <- R6::R6Class( #' #' @param x Instance of ArvadosFile class #' @param ... Optional arguments. -#' @export +#' @export print.ArvadosFile = function(x, ...) { collection <- NULL @@ -267,8 +356,8 @@ print.ArvadosFile = function(x, ...) relativePath <- paste0("/", relativePath) } - cat(paste0("Type: ", "\"", "ArvadosFile", "\""), sep = "\n") - cat(paste0("Name: ", "\"", x$getName(), "\""), sep = "\n") - cat(paste0("Relative path: ", "\"", relativePath, "\""), sep = "\n") - cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n") + 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") }