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