sdk/R/R/CollectionTree.R

   1 source("./R/Subcollection.R")
   2 source("./R/ArvadosFile.R")
   3 source("./R/util.R")
   4
   5 #' Arvados Collection Object
   6 #'
   7 #' Update description
   8 #'
   9 #' @examples arv = Collection$new(api, uuid)
  10 CollectionTree <- R6::R6Class(
  11     "CollectionTree",
  12     public = list(
  13
  14         pathsList = NULL,
  15
  16         initialize = function(fileContent, collection)
  17         {
  18             self$pathsList <- fileContent
  19
  20             treeBranches <- sapply(fileContent, function(filePath)
  21             {
  22                 splitPath <- unlist(strsplit(filePath, "/", fixed = TRUE))
  23                 branch <- private$createBranch(splitPath)
  24             })
  25
  26             root <- Subcollection$new("")
  27
  28             sapply(treeBranches, function(branch)
  29             {
  30                 private$addBranch(root, branch)
  31             })
  32
  33             root$setCollection(collection)
  34             private$tree <- root
  35         },
  36
  37         getElement = function(relativePath)
  38         {
  39             relativePath <- trimFromStart(relativePath, "./")
  40             relativePath <- trimFromEnd(relativePath, "/")
  41
  42             if(endsWith(relativePath, "/"))
  43                 relativePath <- substr(relativePath, 0, nchar(relativePath) - 1)
  44
  45             splitPath <- unlist(strsplit(relativePath, "/", fixed = TRUE))
  46             returnElement <- private$tree
  47
  48             for(pathFragment in splitPath)
  49             {
  50                 returnElement <- returnElement$get(pathFragment)
  51
  52                 if(is.null(returnElement))
  53                     return(NULL)
  54             }
  55
  56             returnElement
  57         },
  58
  59         getTree = function() private$tree
  60     ),
  61
  62     private = list(
  63
  64         tree = NULL,
  65
  66         createBranch = function(splitPath)
  67         {
  68             branch <- NULL
  69             lastElementIndex <- length(splitPath)
  70
  71             for(elementIndex in lastElementIndex:1)
  72             {
  73                 if(elementIndex == lastElementIndex)
  74                 {
  75                     branch <- ArvadosFile$new(splitPath[[elementIndex]])
  76                 }
  77                 else
  78                 {
  79                     newFolder <- Subcollection$new(splitPath[[elementIndex]])
  80                     newFolder$add(branch)
  81                     branch <- newFolder
  82                 }
  83             }
  84
  85             branch
  86         },
  87
  88         addBranch = function(container, node)
  89         {
  90             child <- container$get(node$getName())
  91
  92             if(is.null(child))
  93             {
  94                 container$add(node)
  95             }
  96             else
  97             {
  98                 # Note: REST always returns folder name alone before other folder
  99                 # content, so in first iteration we don't know if it's a file
 100                 # or folder since its just a name, so we assume it's a file.
 101                 # If we encounter that same name again we know
 102                 # it's a folder so we need to replace ArvadosFile with Subcollection.
 103                 if("ArvadosFile" %in% class(child))
 104                 {
 105                     child = private$replaceFileWithSubcollection(child)
 106                 }
 107
 108                 private$addBranch(child, node$getFirst())
 109             }
 110         },
 111
 112         replaceFileWithSubcollection = function(arvadosFile)
 113         {
 114             subcollection <- Subcollection$new(arvadosFile$getName())
 115             fileParent <- arvadosFile$getParent()
 116             fileParent$remove(arvadosFile$getName())
 117             fileParent$add(subcollection)
 118
 119             arvadosFile$setParent(NULL)
 120
 121             subcollection
 122         }
 123     )
 124 )