sdk/R/R/Arvados.R

   1 source("./R/HttpRequest.R")
   2 source("./R/HttpParser.R")
   3
   4 #' Arvados SDK Object
   5 #'
   6 #' All Arvados logic is inside this class
   7 #'
   8 #' @field token Token represents user authentification token.
   9 #' @field host Host represents server name we wish to connect to.
  10 #' @examples arv = Arvados$new("token", "host_name")
  11 #' @export Arvados
  12 Arvados <- R6::R6Class(
  13
  14     "Arvados",
  15
  16     public = list(
  17
  18         initialize = function(auth_token = NULL, host_name = NULL)
  19         {
  20             if(!is.null(host_name))
  21                Sys.setenv(ARVADOS_API_HOST  = host_name)
  22
  23             if(!is.null(auth_token))
  24                 Sys.setenv(ARVADOS_API_TOKEN = auth_token)
  25
  26             host  <- Sys.getenv("ARVADOS_API_HOST");
  27             token <- Sys.getenv("ARVADOS_API_TOKEN");
  28
  29             if(host == "" | token == "")
  30                 stop("Please provide host name and authentification token or set
  31                      ARVADOS_API_HOST and ARVADOS_API_TOKEN environmental variables.")
  32
  33             discoveryDocumentURL <- paste0("https://", host,
  34                                            "/discovery/v1/apis/arvados/v1/rest")
  35
  36             version <- "v1"
  37             host  <- paste0("https://", host, "/arvados/", version, "/")
  38
  39             private$http       <- HttpRequest$new()
  40             private$httpParser <- HttpParser$new()
  41             private$token      <- token
  42             private$host       <- host
  43
  44             headers <- list(Authorization = paste("OAuth2", private$token))
  45
  46             serverResponse <- private$http$GET(discoveryDocumentURL, headers)
  47
  48             discoveryDocument <- private$httpParser$parseJSONResponse(serverResponse)
  49             private$webDavHostName <- discoveryDocument$keepWebServiceUrl
  50
  51             if(is.null(private$webDavHostName))
  52                 stop("Unable to find WebDAV server.")
  53         },
  54
  55         getToken    = function() private$token,
  56         getHostName = function() private$host,
  57
  58         getWebDavHostName = function() private$webDavHostName,
  59
  60         getCollection = function(uuid)
  61         {
  62             collectionURL <- paste0(private$host, "collections/", uuid)
  63             headers <- list(Authorization = paste("OAuth2", private$token))
  64
  65             serverResponse <- private$http$GET(collectionURL, headers)
  66
  67             collection <- private$httpParser$parseJSONResponse(serverResponse)
  68
  69             if(!is.null(collection$errors))
  70                 stop(collection$errors)
  71
  72             collection
  73         },
  74
  75         listCollections = function(filters = NULL, limit = 100, offset = 0)
  76         {
  77             collectionURL <- paste0(private$host, "collections")
  78             headers <- list(Authorization = paste("OAuth2", private$token))
  79
  80             if(!is.null(filters))
  81                 names(filters) <- c("collection")
  82
  83             serverResponse <- private$http$GET(collectionURL, headers, filters,
  84                                                limit, offset)
  85
  86             collection <- private$httpParser$parseJSONResponse(serverResponse)
  87
  88             if(!is.null(collection$errors))
  89                 stop(collection$errors)
  90
  91             collection
  92         },
  93
  94         deleteCollection = function(uuid)
  95         {
  96             collectionURL <- paste0(private$host, "collections/", uuid)
  97             headers <- list("Authorization" = paste("OAuth2", private$token),
  98                             "Content-Type"  = "application/json")
  99
 100             serverResponse <- private$http$DELETE(collectionURL, headers)
 101
 102             collection <- private$httpParser$parseJSONResponse(serverResponse)
 103
 104             if(!is.null(collection$errors))
 105                 stop(collection$errors)
 106
 107             collection
 108         },
 109
 110         updateCollection = function(uuid, newContent)
 111         {
 112             collectionURL <- paste0(private$host, "collections/", uuid)
 113             headers <- list("Authorization" = paste("OAuth2", private$token),
 114                             "Content-Type"  = "application/json")
 115
 116             body <- list(list())
 117             names(body) <- c("collection")
 118             body$collection <- newContent
 119
 120             body <- jsonlite::toJSON(body, auto_unbox = T)
 121
 122             serverResponse <- private$http$PUT(collectionURL, headers, body)
 123
 124             collection <- private$httpParser$parseJSONResponse(serverResponse)
 125
 126             if(!is.null(collection$errors))
 127                 stop(collection$errors)
 128
 129             collection
 130         },
 131
 132         createCollection = function(content)
 133         {
 134             collectionURL <- paste0(private$host, "collections")
 135             headers <- list("Authorization" = paste("OAuth2", private$token),
 136                             "Content-Type"  = "application/json")
 137
 138             body <- list(list())
 139             names(body) <- c("collection")
 140             body$collection <- content
 141
 142             body <- jsonlite::toJSON(body, auto_unbox = T)
 143
 144             serverResponse <- private$http$POST(collectionURL, headers, body)
 145
 146             collection <- private$httpParser$parseJSONResponse(serverResponse)
 147
 148             if(!is.null(collection$errors))
 149                 stop(collection$errors)
 150
 151             collection
 152         },
 153
 154         getProject = function(uuid)
 155         {
 156             projectURL <- paste0(private$host, "groups/", uuid)
 157             headers <- list(Authorization = paste("OAuth2", private$token))
 158
 159             serverResponse <- private$http$GET(projectURL, headers)
 160
 161             project <- private$httpParser$parseJSONResponse(serverResponse)
 162
 163             if(!is.null(project$errors))
 164                 stop(project$errors)
 165
 166             project
 167         },
 168
 169         createProject = function(content)
 170         {
 171             projectURL <- paste0(private$host, "groups")
 172             headers <- list("Authorization" = paste("OAuth2", private$token),
 173                             "Content-Type"  = "application/json")
 174
 175             body <- list(list())
 176             names(body) <- c("group")
 177             body$group <- c("group_class" = "project", content)
 178             body <- jsonlite::toJSON(body, auto_unbox = T)
 179
 180             serverResponse <- private$http$POST(projectURL, headers, body)
 181
 182             project <- private$httpParser$parseJSONResponse(serverResponse)
 183
 184             if(!is.null(project$errors))
 185                 stop(project$errors)
 186
 187             project
 188         },
 189
 190         updateProject = function(uuid, newContent)
 191         {
 192             projectURL <- paste0(private$host, "groups/", uuid)
 193             headers <- list("Authorization" = paste("OAuth2", private$token),
 194                             "Content-Type"  = "application/json")
 195
 196             body <- list(list())
 197             names(body) <- c("group")
 198             body$group <- newContent
 199             body <- jsonlite::toJSON(body, auto_unbox = T)
 200
 201             serverResponse <- private$http$PUT(projectURL, headers, body)
 202
 203             project <- private$httpParser$parseJSONResponse(serverResponse)
 204
 205             if(!is.null(project$errors))
 206                 stop(project$errors)
 207
 208             project
 209         },
 210
 211         listProjects = function(filters = NULL, limit = 100, offset = 0)
 212         {
 213             projectURL <- paste0(private$host, "groups")
 214             headers <- list(Authorization = paste("OAuth2", private$token))
 215
 216             if(!is.null(filters))
 217                 names(filters) <- c("groups")
 218
 219             filters[[length(filters) + 1]] <- list("group_class", "=", "project")
 220
 221             serverResponse <- private$http$GET(projectURL, headers, filters,
 222                                                limit, offset)
 223
 224             projects <- private$httpParser$parseJSONResponse(serverResponse)
 225
 226             if(!is.null(projects$errors))
 227                 stop(projects$errors)
 228
 229             projects
 230         },
 231
 232         deleteProject = function(uuid)
 233         {
 234             projectURL <- paste0(private$host, "groups/", uuid)
 235             headers <- list("Authorization" = paste("OAuth2", private$token),
 236                             "Content-Type"  = "application/json")
 237
 238             serverResponse <- private$http$DELETE(projectURL, headers)
 239
 240             project <- private$httpParser$parseJSONResponse(serverResponse)
 241
 242             if(!is.null(project$errors))
 243                 stop(project$errors)
 244
 245             project
 246         }
 247     ),
 248
 249     private = list(
 250
 251         token          = NULL,
 252         host           = NULL,
 253         webDavHostName = NULL,
 254         http           = NULL,
 255         httpParser     = NULL
 256     ),
 257
 258     cloneable = FALSE
 259 )