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                 subcollection$add(content)
  53
  54                 content
  55             }
  56             else
  57             {
  58                 stop(paste0("Expected AravodsFile or Subcollection object, got ",
  59                             paste0("(", paste0(class(content), collapse = ", "), ")"),
  60                             "."))
  61             }
  62         },
  63
  64         create = function(fileNames, relativePath = "")
  65         {
  66             if(relativePath == ""  ||
  67                relativePath == "." ||
  68                relativePath == "./")
  69             {
  70                 subcollection <- private$tree$getTree()
  71             }
  72             else
  73             {
  74                 relativePath  <- trimFromEnd(relativePath, "/")
  75                 subcollection <- self$get(relativePath)
  76             }
  77
  78             if(is.null(subcollection))
  79                 stop(paste("Subcollection", relativePath, "doesn't exist."))
  80
  81             if(is.character(fileNames))
  82             {
  83                 arvadosFiles <- NULL
  84                 sapply(fileNames, function(fileName)
  85                 {
  86                     childWithSameName <- subcollection$get(fileName)
  87                     if(!is.null(childWithSameName))
  88                         stop("Destination already contains file with same name.")
  89
  90                     newFile <- ArvadosFile$new(fileName)
  91                     subcollection$add(newFile)
  92
  93                     arvadosFiles <<- c(arvadosFiles, newFile)
  94                 })
  95
  96                 if(length(arvadosFiles) == 1)
  97                     return(arvadosFiles[[1]])
  98                 else
  99                     return(arvadosFiles)
 100             }
 101             else
 102             {
 103                 stop(paste0("Expected character vector, got ",
 104                             paste0("(", paste0(class(fileNames), collapse = ", "), ")"),
 105                             "."))
 106             }
 107         },
 108
 109         remove = function(paths)
 110         {
 111             if(is.character(paths))
 112             {
 113                 sapply(paths, function(filePath)
 114                 {
 115                     filePath <- trimFromEnd(filePath, "/")
 116                     file <- self$get(filePath)
 117
 118                     if(is.null(file))
 119                         stop(paste("File", filePath, "doesn't exist."))
 120
 121                     parent <- file$getParent()
 122                     parent$remove(file$getName())
 123                 })
 124             }
 125             else
 126             {
 127                 stop(paste0("Expected character vector, got ",
 128                             paste0("(", paste0(class(paths), collapse = ", "), ")"),
 129                             "."))
 130             }
 131         },
 132
 133         move = function(content, newLocation)
 134         {
 135             content <- trimFromEnd(content, "/")
 136
 137             elementToMove <- self$get(content)
 138
 139             if(is.null(elementToMove))
 140                 stop("Element you want to move doesn't exist in the collection.")
 141
 142             elementToMove$move(newLocation)
 143         },
 144
 145         getFileListing = function()
 146         {
 147             content <- private$REST$getCollectionContent(self$uuid)
 148             content[order(tolower(content))]
 149         },
 150
 151         get = function(relativePath)
 152         {
 153             private$tree$getElement(relativePath)
 154         },
 155
 156         getRESTService = function() private$REST,
 157         setRESTService = function(newRESTService) private$REST <- newRESTService
 158     ),
 159
 160     private = list(
 161
 162         REST        = NULL,
 163         tree        = NULL,
 164         fileContent = NULL,
 165
 166         generateTree = function(content)
 167         {
 168             treeBranches <- sapply(collectionContent, function(filePath)
 169             {
 170                 splitPath <- unlist(strsplit(filePath$name, "/", fixed = TRUE))
 171
 172                 branch = private$createBranch(splitPath, filePath$fileSize)
 173             })
 174         }
 175     ),
 176
 177     cloneable = FALSE
 178 )