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