X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/3facf89bf048487ee718fe15d012b489f2d407b7..HEAD:/sdk/R/R/ArvadosFile.R diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R index fb1d3b335c..f585d1f946 100644 --- a/sdk/R/R/ArvadosFile.R +++ b/sdk/R/R/ArvadosFile.R @@ -2,55 +2,10 @@ # # SPDX-License-Identifier: Apache-2.0 -#' ArvadosFile +#' R6 Class Representing a ArvadosFile #' +#' @description #' 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") -#' -#' 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") -#' myFile$copy("newFolder/myFile") -#' } -NULL #' @export ArvadosFile <- R6::R6Class( @@ -59,6 +14,14 @@ ArvadosFile <- R6::R6Class( public = list( + #' @description + #' Initialize new enviroment. + #' @param name Name of the new enviroment. + #' @return A new `ArvadosFile` object. + #' @examples + #' \dontrun{ + #' myFile <- ArvadosFile$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$collection)) @@ -96,13 +78,19 @@ ArvadosFile <- R6::R6Class( return(NULL) }, + #' @description + #' Returns collection UUID. getCollection = function() private$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) @@ -118,10 +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)) @@ -138,6 +141,15 @@ 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$connection("w") + #' } connection = function(rw) { if (rw == "r" || rw == "rb") @@ -155,6 +167,15 @@ ArvadosFile <- R6::R6Class( } }, + #' @description + #' Write connections content to a file or override current content of the file. + #' @examples + #' \dontrun{ + #' collection <- Collection$new(arv, collectionUUID) + #' arvadosFile <- collection$get(fileName) + #' myFile$write("This is new file content") + #' arvadosFile$flush() + #' } flush = function() { v <- textConnectionValue(private$buffer) @@ -162,6 +183,16 @@ ArvadosFile <- R6::R6Class( 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$collection)) @@ -175,6 +206,13 @@ ArvadosFile <- R6::R6Class( writeResult }, + #' @description + #' Moves file to a new location inside collection. + #' @param destination Path to new folder. + #' @examples + #' \dontrun{ + #' arvadosFile$move(newPath) + #' } move = function(destination) { if(is.null(private$collection)) @@ -207,6 +245,13 @@ ArvadosFile <- R6::R6Class( self }, + #' @description + #' Copies file to a new location inside collection. + #' @param destination Path to new folder. + #' @examples + #' \dontrun{ + #' arvadosFile$copy("NewName.format") + #' } copy = function(destination) { if(is.null(private$collection)) @@ -238,6 +283,9 @@ ArvadosFile <- R6::R6Class( newFile }, + #' @description + #' Duplicate file and gives it a new name. + #' @param newName New name for duplicated file. duplicate = function(newName = NULL) { name <- if(!is.null(newName)) newName else private$name @@ -261,7 +309,10 @@ ArvadosFile <- R6::R6Class( # 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$add(content) @@ -273,6 +324,9 @@ ArvadosFile <- R6::R6Class( { # We temporary set parents collection to NULL. This will ensure that # remove method doesn't remove this file from REST. + + #private$parent$.__enclos_env__$private$removeChild(private$name) + #private$parent <- NULL parent <- private$parent parentsCollection <- parent$getCollection() parent$setCollection(NULL, setRecursively = FALSE)