sdk/R/R/ArvadosFile.R

   1 #' ArvadosFile Object
   2 #'
   3 #' Update description
   4 #'
   5 #' @export ArvadosFile
   6 ArvadosFile <- R6::R6Class(
   7
   8     "ArvadosFile",
   9
  10     public = list(
  11
  12         initialize = function(name)
  13         {
  14             private$name             <- name
  15             private$http             <- HttpRequest$new()
  16             private$httpParser       <- HttpParser$new()
  17         },
  18
  19         getName = function() private$name,
  20
  21         getFileList = function(fullpath = TRUE)
  22         {
  23             self$getName()
  24         },
  25
  26         getSizeInBytes = function()
  27         {
  28             collectionURL <- URLencode(paste0(private$collection$api$getWebDavHostName(),
  29                                               "c=", private$collection$uuid))
  30             fileURL <- paste0(collectionURL, "/", self$getRelativePath());
  31
  32             headers = list("Authorization" = paste("OAuth2", private$collection$api$getToken()))
  33
  34             propfindResponse <- private$http$PROPFIND(fileURL, headers)
  35
  36             sizes <- private$httpParser$extractFileSizeFromWebDAVResponse(propfindResponse, collectionURL)
  37             as.numeric(sizes)
  38         },
  39
  40         removeFromCollection = function()
  41         {
  42             if(is.null(private$collection))
  43                 stop("ArvadosFile doesn't belong to any collection.")
  44
  45             private$collection$.__enclos_env__$private$deleteFromREST(self$getRelativePath())
  46
  47             private$addToCollection(NULL)
  48             private$detachFromParent()
  49
  50             "Content removed successfully."
  51         },
  52
  53         getRelativePath = function()
  54         {
  55             relativePath <- c(private$name)
  56             parent <- private$parent
  57
  58             while(!is.null(parent))
  59             {
  60                 relativePath <- c(parent$getName(), relativePath)
  61                 parent <- parent$getParent()
  62             }
  63
  64             relativePath <- relativePath[relativePath != ""]
  65             paste0(relativePath, collapse = "/")
  66         },
  67
  68         getParent = function() private$parent,
  69
  70         read = function(contentType = "raw", offset = 0, length = 0)
  71         {
  72             if(is.null(private$collection))
  73                 stop("ArvadosFile doesn't belong to any collection.")
  74
  75             if(offset < 0 || length < 0)
  76                 stop("Offset and length must be positive values.")
  77
  78             if(!(contentType %in% private$http$validContentTypes))
  79                 stop("Invalid contentType. Please use text or raw.")
  80
  81             range = paste0("bytes=", offset, "-")
  82
  83             if(length > 0)
  84                 range = paste0(range, offset + length - 1)
  85
  86             fileURL = paste0(private$collection$api$getWebDavHostName(),
  87                              "c=", private$collection$uuid, "/", self$getRelativePath());
  88
  89             if(offset == 0 && length == 0)
  90             {
  91                 headers <- list(Authorization = paste("OAuth2",
  92                                                       private$collection$api$getToken()))
  93             }
  94             else
  95             {
  96                 headers <- list(Authorization = paste("OAuth2", private$collection$api$getToken()),
  97                                 Range = range)
  98             }
  99
 100             serverResponse <- private$http$GET(fileURL, headers)
 101
 102             if(serverResponse$status_code < 200 || serverResponse$status_code >= 300)
 103                 stop(paste("Server code:", serverResponse$status_code))
 104
 105             parsedServerResponse <- httr::content(serverResponse, contentType)
 106             parsedServerResponse
 107         },
 108
 109         write = function(content, contentType = "text/html")
 110         {
 111             if(is.null(private$collection))
 112                 stop("ArvadosFile doesn't belong to any collection.")
 113
 114             fileURL = paste0(private$collection$api$getWebDavHostName(),
 115                              "c=", private$collection$uuid, "/", self$getRelativePath());
 116             headers <- list(Authorization = paste("OAuth2", private$collection$api$getToken()),
 117                             "Content-Type" = contentType)
 118             body <- content
 119
 120             serverResponse <- private$http$PUT(fileURL, headers, body)
 121
 122             if(serverResponse$status_code < 200 || serverResponse$status_code >= 300)
 123                 stop(paste("Server code:", serverResponse$status_code))
 124
 125             parsedServerResponse <- httr::content(serverResponse, "text")
 126             parsedServerResponse
 127         },
 128
 129         move = function(newLocation)
 130         {
 131             if(is.null(private$collection))
 132                 stop("ArvadosFile doesn't belong to any collection.")
 133
 134             if(endsWith(newLocation, paste0(private$name, "/")))
 135             {
 136                 newLocation <- substr(newLocation, 0,
 137                                       nchar(newLocation) - nchar(paste0(private$name, "/")))
 138             }
 139             else if(endsWith(newLocation, private$name))
 140             {
 141                 newLocation <- substr(newLocation, 0, nchar(newLocation) - nchar(private$name))
 142             }
 143             else
 144             {
 145                 stop("Destination path is not valid.")
 146             }
 147
 148             newParent <- private$collection$get(newLocation)
 149
 150             if(is.null(newParent))
 151             {
 152                 stop("Unable to get destination subcollection.")
 153             }
 154
 155             status <- private$collection$.__enclos_env__$private$moveOnREST(self$getRelativePath(),
 156                                                                             paste0(newParent$getRelativePath(), "/", self$getName()))
 157
 158             private$attachToParent(newParent)
 159
 160             "Content moved successfully."
 161         }
 162     ),
 163
 164     private = list(
 165
 166         name       = NULL,
 167         size       = NULL,
 168         parent     = NULL,
 169         collection = NULL,
 170         http       = NULL,
 171         httpParser = NULL,
 172
 173         getChild = function(name)
 174         {
 175             return(NULL)
 176         },
 177
 178         getFirstChild = function()
 179         {
 180             return(NULL)
 181         },
 182
 183         addToCollection = function(collection)
 184         {
 185             private$collection <- collection
 186         },
 187
 188         detachFromParent = function()
 189         {
 190             if(!is.null(private$parent))
 191             {
 192                 private$parent$.__enclos_env__$private$removeChild(private$name)
 193                 private$parent <- NULL
 194             }
 195         },
 196
 197         attachToParent = function(parent)
 198         {
 199             parent$.__enclos_env__$private$children <- c(parent$.__enclos_env__$private$children, self)
 200             private$parent <- parent
 201         }
 202     ),
 203
 204     cloneable = FALSE
 205 )