sdk/R/R/Collection.R

   1 source("./R/Subcollection.R")
   2 source("./R/ArvadosFile.R")
   3 source("./R/HttpRequest.R")
   4 source("./R/HttpParser.R")
   5
   6 #' Arvados Collection Object
   7 #'
   8 #' Update description
   9 #'
  10 #' @examples arv = Collection$new(api, uuid)
  11 #' @export Collection
  12 Collection <- R6::R6Class(
  13
  14     "Collection",
  15
  16     public = list(
  17
  18         api  = NULL,
  19         uuid = NULL,
  20
  21         initialize = function(api, uuid)
  22         {
  23             self$api <- api
  24             private$http <- HttpRequest$new()
  25             private$httpParser <- HttpParser$new()
  26
  27             self$uuid <- uuid
  28             collection <- self$api$getCollection(uuid)
  29
  30             private$fileContent <- private$getCollectionContent()
  31             private$tree <- CollectionTree$new(private$fileContent, self)
  32         },
  33
  34         add = function(content, relativePath = "")
  35         {
  36             if(relativePath == "" ||
  37                relativePath == "." ||
  38                relativePath == "./")
  39             {
  40                 subcollection <- private$tree$.__enclos_env__$private$tree
  41             }
  42             else
  43             {
  44                 if(endsWith(relativePath, "/") && nchar(relativePath) > 0)
  45                     relativePath <- substr(relativePath, 1, nchar(relativePath) - 1)
  46
  47                 subcollection <- self$get(relativePath)
  48             }
  49
  50             if(is.null(subcollection))
  51                 stop(paste("Subcollection", relativePath, "doesn't exist."))
  52
  53             if(is.character(content))
  54             {
  55                 sapply(content, function(fileName)
  56                 {
  57                     subcollection$add(ArvadosFile$new(fileName))
  58                 })
  59             }
  60             else if("ArvadosFile"   %in% class(content) ||
  61                     "Subcollection" %in% class(content))
  62             {
  63                 subcollection$add(content)
  64             }
  65         },
  66
  67         remove = function(content)
  68         {
  69             if(is.character(content))
  70             {
  71                 sapply(content, function(filePath)
  72                 {
  73                     if(endsWith(filePath, "/") && nchar(filePath) > 0)
  74                         filePath <- substr(filePath, 1, nchar(filePath) - 1)
  75
  76                     file <- self$get(filePath)
  77
  78                     if(is.null(file))
  79                         stop(paste("File", filePath, "doesn't exist."))
  80
  81                     file$removeFromCollection()
  82                 })
  83             }
  84             else if("ArvadosFile"   %in% class(content) ||
  85                     "Subcollection" %in% class(content))
  86             {
  87                 if(is.null(content$.__enclos_env__$private$collection) ||
  88                    content$.__enclos_env__$private$collection$uuid != self$uuid)
  89                     stop("Subcollection doesn't belong to this collection.")
  90
  91                 content$removeFromCollection()
  92             }
  93         },
  94
  95         move = function(content, newLocation)
  96         {
  97             if(endsWith(content, "/"))
  98                 content <- substr(content, 0, nchar(content) - 1)
  99
 100             elementToMove <- self$get(content)
 101
 102             if(is.null(elementToMove))
 103                 stop("Element you want to move doesn't exist in the collection.")
 104
 105             elementToMove$move(newLocation)
 106         },
 107
 108         getFileContent = function() private$getCollectionContent(),
 109
 110         get = function(relativePath)
 111         {
 112             private$tree$getElement(relativePath)
 113         }
 114     ),
 115
 116     private = list(
 117
 118         http       = NULL,
 119         httpParser = NULL,
 120         tree       = NULL,
 121
 122         fileContent = NULL,
 123
 124         getCollectionContent = function()
 125         {
 126             collectionURL <- URLencode(paste0(self$api$getWebDavHostName(), "c=", self$uuid))
 127
 128             headers = list("Authorization" = paste("OAuth2", self$api$getToken()))
 129
 130             response <- private$http$PROPFIND(collectionURL, headers)
 131
 132             parsedResponse <- private$httpParser$parseWebDAVResponse(response, collectionURL)
 133             parsedResponse[-1]
 134         },
 135
 136         createFilesOnREST = function(files)
 137         {
 138             sapply(files, function(filePath)
 139             {
 140                 private$createNewFile(filePath, NULL, "text/html")
 141             })
 142         },
 143
 144         generateTree = function(content)
 145         {
 146             treeBranches <- sapply(collectionContent, function(filePath)
 147             {
 148                 splitPath <- unlist(strsplit(filePath$name, "/", fixed = TRUE))
 149
 150                 branch = private$createBranch(splitPath, filePath$fileSize)
 151             })
 152         },
 153
 154         createNewFile = function(relativePath, content, contentType)
 155         {
 156             fileURL <- paste0(self$api$getWebDavHostName(), "c=", self$uuid, "/", relativePath);
 157             headers <- list(Authorization = paste("OAuth2", self$api$getToken()),
 158                             "Content-Type" = contentType)
 159             body <- content
 160
 161             serverResponse <- private$http$PUT(fileURL, headers, body)
 162
 163             if(serverResponse$status_code < 200 || serverResponse$status_code >= 300)
 164                 stop(paste("Server code:", serverResponse$status_code))
 165
 166             print(paste("File created:", relativePath))
 167         },
 168
 169         deleteFromREST = function(relativePath)
 170         {
 171             fileURL <- paste0(self$api$getWebDavHostName(), "c=", self$uuid, "/", relativePath);
 172             headers <- list(Authorization = paste("OAuth2", self$api$getToken()))
 173
 174             serverResponse <- private$http$DELETE(fileURL, headers)
 175
 176             if(serverResponse$status_code < 200 || serverResponse$status_code >= 300)
 177                 stop(paste("Server code:", serverResponse$status_code))
 178
 179             print(paste("File deleted:", relativePath))
 180         },
 181
 182         moveOnREST = function(from, to)
 183         {
 184             collectionURL <- URLencode(paste0(self$api$getWebDavHostName(), "c=", self$uuid, "/"))
 185             fromURL <- paste0(collectionURL, from)
 186             toURL <- paste0(collectionURL, to)
 187
 188             headers = list("Authorization" = paste("OAuth2", self$api$getToken()),
 189                            "Destination" = toURL)
 190
 191             serverResponse <- private$http$MOVE(fromURL, headers)
 192
 193             if(serverResponse$status_code < 200 || serverResponse$status_code >= 300)
 194                 stop(paste("Server code:", serverResponse$status_code))
 195
 196             serverResponse
 197         }
 198     ),
 199
 200     cloneable = FALSE
 201 )