sdk/R/R/CollectionTree.R

   1 source("./R/Subcollection.R")
   2
   3 source("./R/ArvadosFile.R")
   4
   5 #' Arvados Collection Object
   6 #'
   7 #' Update description
   8 #'
   9 #' @examples arv = Collection$new(api, uuid)
  10 #' @export CollectionTree
  11 CollectionTree <- R6::R6Class(
  12     "CollectionTree",
  13     public = list(
  14
  15         pathsList = NULL,
  16
  17         initialize = function(fileContent, collection)
  18         {
  19             self$pathsList <- fileContent
  20
  21             treeBranches <- sapply(fileContent, function(filePath)
  22             {
  23                 splitPath <- unlist(strsplit(filePath, "/", fixed = TRUE))
  24                 branch = private$createBranch(splitPath)
  25             })
  26
  27             root <- Subcollection$new("")
  28
  29             sapply(treeBranches, function(branch)
  30             {
  31                 private$addBranch(root, branch)
  32             })
  33
  34             root$.__enclos_env__$private$addToCollection(collection)
  35             private$tree <- root
  36         },
  37
  38         getElement = function(relativePath)
  39         {
  40             if(endsWith(relativePath, "/"))
  41                 relativePath <- substr(relativePath, 0, nchar(relativePath) - 1)
  42
  43             splitPath <- unlist(strsplit(relativePath, "/", fixed = TRUE))
  44             returnElement = private$tree
  45
  46             for(pathFragment in splitPath)
  47             {
  48                 returnElement = returnElement$.__enclos_env__$private$getChild(pathFragment)
  49
  50                 if(is.null(returnElement))
  51                     return(NULL)
  52             }
  53
  54             returnElement
  55         }
  56     ),
  57
  58     private = list(
  59
  60         tree = NULL,
  61
  62         createBranch = function(splitPath)
  63         {
  64             branch <- NULL
  65             lastElementIndex <- length(splitPath)
  66
  67             for(elementIndex in lastElementIndex:1)
  68             {
  69                 if(elementIndex == lastElementIndex)
  70                 {
  71                     branch = ArvadosFile$new(splitPath[[elementIndex]])
  72                 }
  73                 else
  74                 {
  75                     newFolder = Subcollection$new(splitPath[[elementIndex]])
  76                     newFolder$add(branch)
  77                     branch = newFolder
  78                 }
  79             }
  80
  81             branch
  82         },
  83
  84         addBranch = function(container, node)
  85         {
  86             child = container$.__enclos_env__$private$getChild(node$getName())
  87
  88             if(is.null(child))
  89             {
  90                 container$add(node)
  91             }
  92             else
  93             {
  94                 if("ArvadosFile" %in% class(child))
  95                 {
  96                     child = private$replaceFileWithSubcollection(child)
  97                 }
  98
  99                 private$addBranch(child, node$.__enclos_env__$private$getFirstChild())
 100             }
 101         },
 102
 103         replaceFileWithSubcollection = function(arvadosFile)
 104         {
 105             subcollection <- Subcollection$new(arvadosFile$getName())
 106             fileParent <- arvadosFile$.__enclos_env__$private$parent
 107             fileParent$.__enclos_env__$private$removeChild(arvadosFile$getName())
 108             fileParent$add(subcollection)
 109
 110             arvadosFile$.__enclos_env__$private$parent <- NULL
 111
 112             subcollection
 113         }
 114     )
 115 )