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$uuid,
  89                                      contentType, offset, length)
  90             fileContent
  91         },
  92
  93         connection = function(rw)
  94         {
  95             if (rw == "r" || rw == "rb")
  96             {
  97                 REST <- private$collection$getRESTService()
  98                 return(REST$getConnection(private$collection$uuid,
  99                                           self$getRelativePath(),
 100                                           rw))
 101             }
 102             else if (rw == "w")
 103             {
 104                 private$buffer <- textConnection(NULL, "w")
 105
 106                 return(private$buffer)
 107             }
 108         },
 109
 110         flush = function()
 111         {
 112             v <- textConnectionValue(private$buffer)
 113             close(private$buffer)
 114             self$write(paste(v, collapse='\n'))
 115         },
 116
 117         write = function(content, contentType = "text/html")
 118         {
 119             if(is.null(private$collection))
 120                 stop("ArvadosFile doesn't belong to any collection.")
 121
 122             REST <- private$collection$getRESTService()
 123
 124             writeResult <- REST$write(self$getRelativePath(),
 125                                       private$collection$uuid,
 126                                       content, contentType)
 127             writeResult
 128         },
 129
 130         move = function(newLocation)
 131         {
 132             if(is.null(private$collection))
 133                 stop("ArvadosFile doesn't belong to any collection")
 134
 135
 136             newLocation <- trimFromEnd(newLocation, "/")
 137             nameAndPath <- splitToPathAndName(newLocation)
 138
 139             newParent <- private$collection$get(nameAndPath$path)
 140
 141             if(is.null(newParent))
 142             {
 143                 stop("Unable to get destination subcollection")
 144             }
 145
 146             childWithSameName <- newParent$get(nameAndPath$name)
 147
 148             if(!is.null(childWithSameName))
 149                 stop("Destination already contains content with same name.")
 150
 151             REST <- private$collection$getRESTService()
 152             REST$move(self$getRelativePath(),
 153                       paste0(newParent$getRelativePath(), "/", nameAndPath$name),
 154                       private$collection$uuid)
 155
 156             private$dettachFromCurrentParent()
 157             private$attachToNewParent(newParent)
 158
 159             private$name <- nameAndPath$name
 160
 161             "Content moved successfully."
 162         }
 163     ),
 164
 165     private = list(
 166
 167         name       = NULL,
 168         size       = NULL,
 169         parent     = NULL,
 170         collection = NULL,
 171         http       = NULL,
 172         httpParser = NULL,
 173         buffer     = NULL,
 174
 175         attachToNewParent = function(newParent)
 176         {
 177             #Note: We temporary set parents collection to NULL. This will ensure that
 178             #      add method doesn't post file on REST.
 179             parentsCollection <- newParent$getCollection()
 180             newParent$setCollection(NULL, setRecursively = FALSE)
 181
 182             newParent$add(self)
 183
 184             newParent$setCollection(parentsCollection, setRecursively = FALSE)
 185
 186             private$parent <- newParent
 187         },
 188
 189         dettachFromCurrentParent = function()
 190         {
 191             #Note: We temporary set parents collection to NULL. This will ensure that
 192             #      remove method doesn't remove this subcollection from REST.
 193             parent <- private$parent
 194             parentsCollection <- parent$getCollection()
 195             parent$setCollection(NULL, setRecursively = FALSE)
 196
 197             parent$remove(private$name)
 198
 199             parent$setCollection(parentsCollection, setRecursively = FALSE)
 200         }
 201     ),
 202
 203     cloneable = FALSE
 204 )