sdk/R/R/ArvadosFile.R

   1 source("./R/util.R")
   2
   3 #' ArvadosFile Object
   4 #'
   5 #' Update description
   6 #'
   7 #' @export ArvadosFile
   8 ArvadosFile <- R6::R6Class(
   9
  10     "ArvadosFile",
  11
  12     public = list(
  13
  14         initialize = function(name)
  15         {
  16             private$name             <- name
  17             private$http             <- HttpRequest$new()
  18             private$httpParser       <- HttpParser$new()
  19         },
  20
  21         getName = function() private$name,
  22
  23         getFileListing = function(fullpath = TRUE)
  24         {
  25             self$getName()
  26         },
  27
  28         getSizeInBytes = function()
  29         {
  30             if(is.null(private$collection))
  31                 return(0)
  32
  33             REST <- private$collection$getRESTService()
  34
  35             fileSize <- REST$getResourceSize(self$getRelativePath(),
  36                                              private$collection$uuid)
  37
  38             fileSize
  39         },
  40
  41         get = function(fileLikeObjectName)
  42         {
  43             return(NULL)
  44         },
  45
  46         getFirst = function()
  47         {
  48             return(NULL)
  49         },
  50
  51         getCollection = function() private$collection,
  52
  53         setCollection = function(collection)
  54         {
  55             private$collection <- collection
  56         },
  57
  58         getRelativePath = function()
  59         {
  60             relativePath <- c(private$name)
  61             parent <- private$parent
  62
  63             while(!is.null(parent))
  64             {
  65                 relativePath <- c(parent$getName(), relativePath)
  66                 parent <- parent$getParent()
  67             }
  68
  69             relativePath <- relativePath[relativePath != ""]
  70             paste0(relativePath, collapse = "/")
  71         },
  72
  73         getParent = function() private$parent,
  74
  75         setParent = function(newParent) private$parent <- newParent,
  76
  77         read = function(contentType = "raw", offset = 0, length = 0)
  78         {
  79             if(is.null(private$collection))
  80                 stop("ArvadosFile doesn't belong to any collection.")
  81
  82             if(offset < 0 || length < 0)
  83                 stop("Offset and length must be positive values.")
  84
  85             REST <- private$collection$getRESTService()
  86
  87             fileContent <- REST$read(self$getRelativePath(),
  88                                      private$collection$uuid,
  89                                      contentType, offset, length)
  90             fileContent
  91         },
  92
  93         connection = function(rw)
  94         {
  95             if (rw == "r")
  96             {
  97                 return(textConnection(self$read("text")))
  98             }
  99             else if (rw == "w")
 100             {
 101                 private$buffer <- textConnection(NULL, "w")
 102
 103                 return(private$buffer)
 104             }
 105         },
 106
 107         flush = function()
 108         {
 109             v <- textConnectionValue(private$buffer)
 110             close(private$buffer)
 111             self$write(paste(v, collapse='\n'))
 112         },
 113
 114         write = function(content, contentType = "text/html")
 115         {
 116             if(is.null(private$collection))
 117                 stop("ArvadosFile doesn't belong to any collection.")
 118
 119             REST <- private$collection$getRESTService()
 120
 121             writeResult <- REST$write(self$getRelativePath(),
 122                                       private$collection$uuid,
 123                                       content, contentType)
 124             writeResult
 125         },
 126
 127         move = function(newLocationInCollection)
 128         {
 129             if(is.null(private$collection))
 130                 stop("ArvadosFile doesn't belong to any collection")
 131
 132             newLocationInCollection <- trimFromEnd(newLocationInCollection, "/")
 133             newParentLocation <- trimFromEnd(newLocationInCollection, private$name)
 134
 135             newParent <- private$collection$get(newParentLocation)
 136
 137             if(is.null(newParent))
 138             {
 139                 stop("Unable to get destination subcollection")
 140             }
 141
 142             childWithSameName <- newParent$get(private$name)
 143
 144             if(!is.null(childWithSameName))
 145                 stop("Destination already contains content with same name.")
 146
 147             REST <- private$collection$getRESTService()
 148             REST$move(self$getRelativePath(),
 149                       paste0(newParent$getRelativePath(), "/", self$getName()),
 150                       private$collection$uuid)
 151
 152             private$dettachFromCurrentParent()
 153             private$attachToNewParent(newParent)
 154
 155             "Content moved successfully."
 156         }
 157     ),
 158
 159     private = list(
 160
 161         name       = NULL,
 162         size       = NULL,
 163         parent     = NULL,
 164         collection = NULL,
 165         http       = NULL,
 166         httpParser = NULL,
 167         buffer     = NULL,
 168
 169         attachToNewParent = function(newParent)
 170         {
 171             #Note: We temporary set parents collection to NULL. This will ensure that
 172             #      add method doesn't post file on REST.
 173             parentsCollection <- newParent$getCollection()
 174             newParent$setCollection(NULL, setRecursively = FALSE)
 175
 176             newParent$add(self)
 177
 178             newParent$setCollection(parentsCollection, setRecursively = FALSE)
 179
 180             private$parent <- newParent
 181         },
 182
 183         dettachFromCurrentParent = function()
 184         {
 185             #Note: We temporary set parents collection to NULL. This will ensure that
 186             #      remove method doesn't remove this subcollection from REST.
 187             parent <- private$parent
 188             parentsCollection <- parent$getCollection()
 189             parent$setCollection(NULL, setRecursively = FALSE)
 190
 191             parent$remove(private$name)
 192
 193             parent$setCollection(parentsCollection, setRecursively = FALSE)
 194         }
 195     ),
 196
 197     cloneable = FALSE
 198 )