sdk/R/R/Collection.R

   1 source("./R/Subcollection.R")
   2 source("./R/ArvadosFile.R")
   3 source("./R/RESTService.R")
   4 source("./R/util.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$REST <- api$getRESTService()
  25
  26             self$uuid <- uuid
  27
  28             private$fileContent <- private$REST$getCollectionContent(uuid)
  29             private$tree <- CollectionTree$new(private$fileContent, self)
  30         },
  31
  32         add = function(content, relativePath = "")
  33         {
  34             if(relativePath == ""  ||
  35                relativePath == "." ||
  36                relativePath == "./")
  37             {
  38                 subcollection <- private$tree$getTree()
  39             }
  40             else
  41             {
  42                 relativePath <- trimFromEnd(relativePath, "/")
  43                 subcollection <- self$get(relativePath)
  44             }
  45
  46             if(is.null(subcollection))
  47                 stop(paste("Subcollection", relativePath, "doesn't exist."))
  48
  49             if("ArvadosFile"   %in% class(content) ||
  50                "Subcollection" %in% class(content))
  51             {
  52
  53                 if(content$getName() == "")
  54                     stop("Content has invalid name.")
  55
  56                 subcollection$add(content)
  57                 content
  58             }
  59             else
  60             {
  61                 stop(paste0("Expected AravodsFile or Subcollection object, got ",
  62                             paste0("(", paste0(class(content), collapse = ", "), ")"),
  63                             "."))
  64             }
  65         },
  66
  67         create = function(fileNames, relativePath = "")
  68         {
  69             if(relativePath == ""  ||
  70                relativePath == "." ||
  71                relativePath == "./")
  72             {
  73                 subcollection <- private$tree$getTree()
  74             }
  75             else
  76             {
  77                 relativePath  <- trimFromEnd(relativePath, "/")
  78                 subcollection <- self$get(relativePath)
  79             }
  80
  81             if(is.null(subcollection))
  82                 stop(paste("Subcollection", relativePath, "doesn't exist."))
  83
  84             if(is.character(fileNames))
  85             {
  86                 arvadosFiles <- NULL
  87                 sapply(fileNames, function(fileName)
  88                 {
  89                     childWithSameName <- subcollection$get(fileName)
  90                     if(!is.null(childWithSameName))
  91                         stop("Destination already contains file with same name.")
  92
  93                     newFile <- ArvadosFile$new(fileName)
  94                     subcollection$add(newFile)
  95
  96                     arvadosFiles <<- c(arvadosFiles, newFile)
  97                 })
  98
  99                 if(length(arvadosFiles) == 1)
 100                     return(arvadosFiles[[1]])
 101                 else
 102                     return(arvadosFiles)
 103             }
 104             else
 105             {
 106                 stop(paste0("Expected character vector, got ",
 107                             paste0("(", paste0(class(fileNames), collapse = ", "), ")"),
 108                             "."))
 109             }
 110         },
 111
 112         remove = function(paths)
 113         {
 114             if(is.character(paths))
 115             {
 116                 sapply(paths, function(filePath)
 117                 {
 118                     filePath <- trimFromEnd(filePath, "/")
 119                     file <- self$get(filePath)
 120
 121                     if(is.null(file))
 122                         stop(paste("File", filePath, "doesn't exist."))
 123
 124                     parent <- file$getParent()
 125
 126                     if(is.null(parent))
 127                         stop("You can't delete root folder.")
 128
 129                     parent$remove(file$getName())
 130                 })
 131
 132                 "Content removed"
 133             }
 134             else
 135             {
 136                 stop(paste0("Expected character vector, got ",
 137                             paste0("(", paste0(class(paths), collapse = ", "), ")"),
 138                             "."))
 139             }
 140         },
 141
 142         move = function(content, newLocation)
 143         {
 144             content <- trimFromEnd(content, "/")
 145
 146             elementToMove <- self$get(content)
 147
 148             if(is.null(elementToMove))
 149                 stop("Content you want to move doesn't exist in the collection.")
 150
 151             elementToMove$move(newLocation)
 152         },
 153
 154         getFileListing = function()
 155         {
 156             content <- private$REST$getCollectionContent(self$uuid)
 157             content[order(tolower(content))]
 158         },
 159
 160         get = function(relativePath)
 161         {
 162             private$tree$getElement(relativePath)
 163         },
 164
 165         getRESTService = function() private$REST,
 166         setRESTService = function(newRESTService) private$REST <- newRESTService
 167     ),
 168
 169     private = list(
 170
 171         REST        = NULL,
 172         tree        = NULL,
 173         fileContent = NULL
 174     ),
 175
 176     cloneable = FALSE
 177 )
 178
 179 #' @export print.Collection
 180 print.Collection = function(collection)
 181 {
 182     cat(paste0("Type: ", "\"", "Arvados Collection", "\""), sep = "\n")
 183     cat(paste0("uuid: ", "\"", collection$uuid,      "\""), sep = "\n")
 184 }