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             if(name == "")
  17                 stop("Invalid name.")
  18
  19             private$name <- name
  20         },
  21
  22         getName = function() private$name,
  23
  24         getFileListing = function(fullpath = TRUE)
  25         {
  26             self$getName()
  27         },
  28
  29         getSizeInBytes = function()
  30         {
  31             if(is.null(private$collection))
  32                 return(0)
  33
  34             REST <- private$collection$getRESTService()
  35
  36             fileSize <- REST$getResourceSize(self$getRelativePath(),
  37                                              private$collection$uuid)
  38
  39             fileSize
  40         },
  41
  42         get = function(fileLikeObjectName)
  43         {
  44             return(NULL)
  45         },
  46
  47         getFirst = function()
  48         {
  49             return(NULL)
  50         },
  51
  52         getCollection = function() private$collection,
  53
  54         setCollection = function(collection)
  55         {
  56             private$collection <- collection
  57         },
  58
  59         getRelativePath = function()
  60         {
  61             relativePath <- c(private$name)
  62             parent <- private$parent
  63
  64             while(!is.null(parent))
  65             {
  66                 relativePath <- c(parent$getName(), relativePath)
  67                 parent <- parent$getParent()
  68             }
  69
  70             relativePath <- relativePath[relativePath != ""]
  71             paste0(relativePath, collapse = "/")
  72         },
  73
  74         getParent = function() private$parent,
  75
  76         setParent = function(newParent) private$parent <- newParent,
  77
  78         read = function(contentType = "raw", offset = 0, length = 0)
  79         {
  80             if(is.null(private$collection))
  81                 stop("ArvadosFile doesn't belong to any collection.")
  82
  83             if(offset < 0 || length < 0)
  84                 stop("Offset and length must be positive values.")
  85
  86             REST <- private$collection$getRESTService()
  87
  88             fileContent <- REST$read(self$getRelativePath(),
  89                                      private$collection$uuid,
  90                                      contentType, offset, length)
  91             fileContent
  92         },
  93
  94         connection = function(rw)
  95         {
  96             if (rw == "r" || rw == "rb")
  97             {
  98                 REST <- private$collection$getRESTService()
  99                 return(REST$getConnection(private$collection$uuid,
 100                                           self$getRelativePath(),
 101                                           rw))
 102             }
 103             else if (rw == "w")
 104             {
 105                 private$buffer <- textConnection(NULL, "w")
 106
 107                 return(private$buffer)
 108             }
 109         },
 110
 111         flush = function()
 112         {
 113             v <- textConnectionValue(private$buffer)
 114             close(private$buffer)
 115             self$write(paste(v, collapse='\n'))
 116         },
 117
 118         write = function(content, contentType = "text/html")
 119         {
 120             if(is.null(private$collection))
 121                 stop("ArvadosFile doesn't belong to any collection.")
 122
 123             REST <- private$collection$getRESTService()
 124
 125             writeResult <- REST$write(self$getRelativePath(),
 126                                       private$collection$uuid,
 127                                       content, contentType)
 128             writeResult
 129         },
 130
 131         move = function(newLocation)
 132         {
 133             if(is.null(private$collection))
 134                 stop("ArvadosFile doesn't belong to any collection")
 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$name
 160
 161             "Content moved successfully."
 162         }
 163     ),
 164
 165     private = list(
 166
 167         name       = NULL,
 168         size       = NULL,
 169         parent     = NULL,
 170         collection = NULL,
 171         buffer     = NULL,
 172
 173         attachToNewParent = function(newParent)
 174         {
 175             #Note: We temporary set parents collection to NULL. This will ensure that
 176             #      add method doesn't post file on REST.
 177             parentsCollection <- newParent$getCollection()
 178             newParent$setCollection(NULL, setRecursively = FALSE)
 179
 180             newParent$add(self)
 181
 182             newParent$setCollection(parentsCollection, setRecursively = FALSE)
 183
 184             private$parent <- newParent
 185         },
 186
 187         dettachFromCurrentParent = function()
 188         {
 189             #Note: We temporary set parents collection to NULL. This will ensure that
 190             #      remove method doesn't remove this subcollection from REST.
 191             parent <- private$parent
 192             parentsCollection <- parent$getCollection()
 193             parent$setCollection(NULL, setRecursively = FALSE)
 194
 195             parent$remove(private$name)
 196
 197             parent$setCollection(parentsCollection, setRecursively = FALSE)
 198         }
 199     ),
 200
 201     cloneable = FALSE
 202 )
 203
 204 #' @export print.ArvadosFile
 205 print.ArvadosFile = function(arvadosFile)
 206 {
 207     collection   <- NULL
 208     relativePath <- arvadosFile$getRelativePath()
 209
 210     if(!is.null(arvadosFile$getCollection()))
 211     {
 212         collection <- arvadosFile$getCollection()$uuid
 213         relativePath <- paste0("/", relativePath)
 214     }
 215
 216     cat(paste0("Type:          ", "\"", "ArvadosFile",         "\""), sep = "\n")
 217     cat(paste0("Name:          ", "\"", arvadosFile$getName(), "\""), sep = "\n")
 218     cat(paste0("Relative path: ", "\"", relativePath,          "\""), sep = "\n")
 219     cat(paste0("Collection:    ", "\"", collection,            "\""), sep = "\n")
 220 }