sdk/R/R/Collection.R

   1 source("./R/Arvados.R")
   2 source("./R/HttpParser.R")
   3 source("./R/Subcollection.R")
   4 source("./R/ArvadosFile.R")
   5
   6 #' Collection Class
   7 #'
   8 #' @details
   9 #' Todo: Update description
  10 #' Collection
  11 #'
  12 #' @param uuid Object ID
  13 #' @param etag Object version
  14 #' @param owner_uuid No description
  15 #' @param created_at No description
  16 #' @param modified_by_client_uuid No description
  17 #' @param modified_by_user_uuid No description
  18 #' @param modified_at No description
  19 #' @param portable_data_hash No description
  20 #' @param replication_desired No description
  21 #' @param replication_confirmed_at No description
  22 #' @param replication_confirmed No description
  23 #' @param updated_at No description
  24 #' @param manifest_text No description
  25 #' @param name No description
  26 #' @param description No description
  27 #' @param properties No description
  28 #' @param delete_at No description
  29 #' @param file_names No description
  30 #' @param trash_at No description
  31 #' @param is_trashed No description
  32 #'
  33 #' @export Collection
  34
  35 #' @exportClass Collection
  36 Collection <- setRefClass(
  37
  38     "Collection",
  39
  40     fields = list(uuid                     = "ANY",
  41                   items                    = "ANY",
  42                   etag                     = "ANY",
  43                   owner_uuid               = "ANY",
  44                   created_at               = "ANY",
  45                   modified_by_client_uuid  = "ANY",
  46                   modified_by_user_uuid    = "ANY",
  47                   modified_at              = "ANY",
  48                   portable_data_hash       = "ANY",
  49                   replication_desired      = "ANY",
  50                   replication_confirmed_at = "ANY",
  51                   replication_confirmed    = "ANY",
  52                   updated_at               = "ANY",
  53                   manifest_text            = "ANY",
  54                   name                     = "ANY",
  55                   description              = "ANY",
  56                   properties               = "ANY",
  57                   delete_at                = "ANY",
  58                   file_names               = "ANY",
  59                   trash_at                 = "ANY",
  60                   is_trashed               = "ANY",
  61
  62                   getCollectionContent = "function"
  63     ),
  64
  65     methods = list(
  66
  67         initialize = function(api, uuid)
  68         {
  69             result <- api$collection_get(uuid)
  70
  71             # Private members
  72             uuid                     <<- result$uuid
  73             etag                     <<- result$etag
  74             owner_uuid               <<- result$owner_uuid
  75             created_at               <<- result$created_at
  76             modified_by_client_uuid  <<- result$modified_by_client_uuid
  77             modified_by_user_uuid    <<- result$modified_by_user_uuid
  78             modified_at              <<- result$modified_at
  79             portable_data_hash       <<- result$portable_data_hash
  80             replication_desired      <<- result$replication_desired
  81             replication_confirmed_at <<- result$replication_confirmed_at
  82             replication_confirmed    <<- result$replication_confirmed
  83             updated_at               <<- result$updated_at
  84             manifest_text            <<- result$manifest_text
  85             name                     <<- result$name
  86             description              <<- result$description
  87             properties               <<- result$properties
  88             delete_at                <<- result$delete_at
  89             file_names               <<- result$file_names
  90             trash_at                 <<- result$trash_at
  91             is_trashed               <<- result$is_trashed
  92
  93             # Private methods
  94             getCollectionContent <<- function()
  95             {
  96                 #TODO(Fudo): Use proper URL here.
  97                 uri <- URLencode(api$getWebDavHostName())
  98
  99                 # fetch directory listing via curl and parse XML response
 100                 h <- curl::new_handle()
 101                 curl::handle_setopt(h, customrequest = "PROPFIND")
 102
 103                 #TODO(Fudo): Use proper token here.
 104                 curl::handle_setheaders(h, "Authorization" = paste("OAuth2", api$getWebDavToken()))
 105                 response <- curl::curl_fetch_memory(uri, h)
 106
 107                 HttpParser()$parseWebDAVResponse(response, uri)
 108             }
 109
 110             createCollectionContentTree <- function(fileStructure)
 111             {
 112                 #Todo(Fudo): Refactor this.
 113                 treeBranches <- sapply(fileStructure, function(filePath)
 114                 {
 115                     fileWithPath <- unlist(stringr::str_split(filePath, "/"))
 116
 117                     file <- fileWithPath[length(fileWithPath), drop = T]
 118                     file <- ArvadosFile(file)
 119
 120                     folders <- fileWithPath[-length(fileWithPath)]
 121
 122                     subcollections <- sapply(folders, function(folder)
 123                     {
 124                         folder <- Subcollection(folder)
 125                     })
 126
 127                     if(length(subcollections) > 0)
 128                     {
 129                         bottomFolder <- subcollections[[length(subcollections)]]
 130                         bottomFolder$add(file)
 131
 132                         if(length(subcollections) == 1)
 133                         {
 134                             return(bottomFolder)
 135                         }
 136                         else
 137                         {
 138                             # Link folders in hierarchy. At the bottom will always be a file.
 139                             for(subcollectionIndex in 1:(length(subcollections) - 1))
 140                             {
 141                                 subcollections[[subcollectionIndex]]$add(subcollections[[subcollectionIndex + 1]])
 142                             }
 143
 144                             subcollections[[1]]
 145                         }
 146                     }
 147                     else
 148                     {
 149                         file
 150                     }
 151                 })
 152
 153                 root <- Subcollection(".")
 154
 155                 addIfExists <- function(firstNode, secondNode)
 156                 {
 157                     firstNodeContent <- sapply(firstNode$content, function(node) {node$name})
 158                     if(length(firstNodeContent) == 0)
 159                     {
 160                         firstNode$add(secondNode)
 161                         return()
 162                     }
 163
 164                     matchPosition <- match(secondNode$name, firstNodeContent, -1)
 165                     if(matchPosition != -1)
 166                     {
 167                         addIfExists(firstNode$content[[matchPosition]], secondNode$content[[1]])
 168                     }
 169                     else
 170                     {
 171                         firstNode$add(secondNode)
 172                     }
 173                 }
 174
 175                 sapply(treeBranches, function(branch)
 176                 {
 177                     addIfExists(root, branch)
 178                 })
 179
 180                 root
 181             }
 182
 183             #Todo(Fudo): This is dummy data. Real content will come from WebDAV server.
 184             testFileStructure <- c("math.h", "main.cpp",
 185                                    "java/render.java", "java/test/observer.java",
 186                                    "java/test/observable.java",
 187                                    "csharp/this.cs", "csharp/is.cs",
 188                                    "csharp/dummy.cs", "csharp/file.cs")
 189             #items  <<- getCollectionContent()
 190             items  <<- createCollectionContentTree(testFileStructure)
 191         }
 192     )
 193 )