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$new(api, uuid)
  10 #' @export CollectionTree
  11 CollectionTree <- R6::R6Class(
  12     "CollectionTree",
  13     public = list(
  14
  15         pathsList = NULL,
  16
  17         initialize = function(fileContent, collection)
  18         {
  19             self$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$addBranch(root, branch)
  32             })
  33
  34             root$setCollection(collection)
  35             private$tree <- root
  36         },
  37
  38         getElement = function(relativePath)
  39         {
  40             relativePath <- trimFromStart(relativePath, "./")
  41             relativePath <- trimFromEnd(relativePath, "/")
  42
  43             if(endsWith(relativePath, "/"))
  44                 relativePath <- substr(relativePath, 0, nchar(relativePath) - 1)
  45
  46             splitPath <- unlist(strsplit(relativePath, "/", fixed = TRUE))
  47             returnElement <- private$tree
  48
  49             for(pathFragment in splitPath)
  50             {
  51                 returnElement <- returnElement$get(pathFragment)
  52
  53                 if(is.null(returnElement))
  54                     return(NULL)
  55             }
  56
  57             returnElement
  58         },
  59
  60         getTree = function() private$tree
  61     ),
  62
  63     private = list(
  64
  65         tree = NULL,
  66
  67         createBranch = function(splitPath)
  68         {
  69             branch <- NULL
  70             lastElementIndex <- length(splitPath)
  71
  72             for(elementIndex in lastElementIndex:1)
  73             {
  74                 if(elementIndex == lastElementIndex)
  75                 {
  76                     branch <- ArvadosFile$new(splitPath[[elementIndex]])
  77                 }
  78                 else
  79                 {
  80                     newFolder <- Subcollection$new(splitPath[[elementIndex]])
  81                     newFolder$add(branch)
  82                     branch <- newFolder
  83                 }
  84             }
  85
  86             branch
  87         },
  88
  89         addBranch = function(container, node)
  90         {
  91             child <- container$get(node$getName())
  92
  93             if(is.null(child))
  94             {
  95                 container$add(node)
  96             }
  97             else
  98             {
  99                 # Note: REST always returns folder name alone before other folder content
 100                 # (for some reason), so in first iteration we don't know if it's a file
 101                 # or folder since its just a name, so we assume it's a file.
 102                 # If we encounter that same name again we know
 103                 # it's a folder so we need to replace ArvadosFile with Subcollection.
 104                 if("ArvadosFile" %in% class(child))
 105                 {
 106                     child = private$replaceFileWithSubcollection(child)
 107                 }
 108
 109                 private$addBranch(child, node$getFirst())
 110             }
 111         },
 112
 113         replaceFileWithSubcollection = function(arvadosFile)
 114         {
 115             subcollection <- Subcollection$new(arvadosFile$getName())
 116             fileParent <- arvadosFile$getParent()
 117             fileParent$remove(arvadosFile$getName())
 118             fileParent$add(subcollection)
 119
 120             arvadosFile$setParent(NULL)
 121
 122             subcollection
 123         }
 124     )
 125 )