source("./R/HttpRequest.R")
source("./R/HttpParser.R")
-source("./R/custom_classes.R")
#' Arvados SDK Object
#'
#'
#' @field token Token represents user authentification token.
#' @field host Host represents server name we wish to connect to.
-#' @examples arv = Arvados("token", "host_name")
+#' @examples arv = Arvados$new("token", "host_name")
#' @export Arvados
-Arvados <- setRefClass(
+Arvados <- R6::R6Class(
"Arvados",
- fields = list(
-
- getToken = "function",
- getHostName = "function",
-
- #Todo(Fudo): This is for debug only. Remove it.
- getWebDavToken = "function",
- getWebDavHostName = "function",
- setWebDavToken = "function",
- setWebDavHostName = "function",
-
- collection_get = "function",
- collection_list = "function",
- collection_create = "function",
- collection_update = "function",
- collection_delete = "function"
- ),
-
- methods = list(
+ public = list(
initialize = function(auth_token = NULL, host_name = NULL)
{
- # Private state
if(!is.null(host_name))
Sys.setenv(ARVADOS_API_HOST = host_name)
if(host == "" | token == "")
stop("Please provide host name and authentification token or set ARVADOS_API_HOST and ARVADOS_API_TOKEN environmental variables.")
+ discoveryDocumentURL <- paste0("https://", host, "/discovery/v1/apis/arvados/v1/rest")
+
version <- "v1"
host <- paste0("https://", host, "/arvados/", version, "/")
- # Public methods
- getToken <<- function() { token }
- getHostName <<- function() { host }
+ private$http <- HttpRequest$new()
+ private$httpParser <- HttpParser$new()
+ private$token <- token
+ private$host <- host
+
+ headers <- list(Authorization = paste("OAuth2", private$token))
+
+ serverResponse <- private$http$GET(discoveryDocumentURL, headers)
+
+ discoveryDocument <- private$httpParser$parseJSONResponse(serverResponse)
+ private$webDavHostName <- discoveryDocument$keepWebServiceUrl
+ print(private$webDavHostName)
+ },
+
+ getToken = function() private$token,
+ getHostName = function() private$host,
- #Todo(Fudo): Hardcoded credentials to WebDAV server. Remove them later
- getWebDavToken <<- function() { webDavToken }
- getWebDavHostName <<- function() { webDavHostName }
- setWebDavToken <<- function(token) { webDavToken <<- token }
- setWebDavHostName <<- function(hostName) { webDavHostName <<- hostName }
+ #Todo(Fudo): Hardcoded credentials to WebDAV server. Remove them later
+ getWebDavHostName = function() private$webDavHostName,
- collection_get <<- function(uuid)
- {
- collectionURL <- paste0(host, "collections/", uuid)
- headers <- list(Authorization = paste("OAuth2", token))
+ getCollection = function(uuid)
+ {
+ collectionURL <- paste0(private$host, "collections/", uuid)
+ headers <- list(Authorization = paste("OAuth2", private$token))
- http <- HttpRequest()
- serverResponse <- http$GET(collectionURL, headers)
+ serverResponse <- private$http$GET(collectionURL, headers)
- httpParser <- HttpParser()
- collection <- httpParser$parseJSONResponse(serverResponse)
+ collection <- private$httpParser$parseJSONResponse(serverResponse)
- if(!is.null(collection$errors))
- stop(collection$errors)
+ if(!is.null(collection$errors))
+ stop(collection$errors)
- collection
- }
+ collection
+ },
- collection_list <<- function(filters = NULL, limit = 100, offset = 0)
- {
- collectionURL <- paste0(host, "collections")
- headers <- list(Authorization = paste("OAuth2", token))
+ listCollections = function(filters = NULL, limit = 100, offset = 0)
+ {
+ collectionURL <- paste0(private$host, "collections")
+ headers <- list(Authorization = paste("OAuth2", private$token))
- http <- HttpRequest()
- serverResponse <- http$GET(collectionURL, headers, NULL, filters, limit, offset)
+ serverResponse <- private$http$GET(collectionURL, headers, NULL, filters, limit, offset)
- httpParser <- HttpParser()
- collection <- httpParser$parseJSONResponse(serverResponse)
+ collection <- private$httpParser$parseJSONResponse(serverResponse)
- if(!is.null(collection$errors))
- stop(collection$errors)
+ if(!is.null(collection$errors))
+ stop(collection$errors)
- collection
- }
+ collection
+ },
- collection_delete <<- function(uuid)
- {
- collectionURL <- paste0(host, "collections/", uuid)
- headers <- list("Authorization" = paste("OAuth2", token),
- "Content-Type" = "application/json")
+ deleteCollection = function(uuid)
+ {
+ collectionURL <- paste0(private$host, "collections/", uuid)
+ headers <- list("Authorization" = paste("OAuth2", private$token),
+ "Content-Type" = "application/json")
- http <- HttpRequest()
- serverResponse <- http$DELETE(collectionURL, headers)
+ serverResponse <- private$http$DELETE(collectionURL, headers)
- httpParser <- HttpParser()
- collection <- httpParser$parseJSONResponse(serverResponse)
+ collection <- private$httpParser$parseJSONResponse(serverResponse)
- if(!is.null(collection$errors))
- stop(collection$errors)
+ if(!is.null(collection$errors))
+ stop(collection$errors)
- collection
- }
+ collection
+ },
- collection_update <<- function(uuid, body)
- {
- collectionURL <- paste0(host, "collections/", uuid)
- headers <- list("Authorization" = paste("OAuth2", token),
- "Content-Type" = "application/json")
- body <- jsonlite::toJSON(body, auto_unbox = T)
+ updateCollection = function(uuid, body)
+ {
+ collectionURL <- paste0(private$host, "collections/", uuid)
+ headers <- list("Authorization" = paste("OAuth2", private$token),
+ "Content-Type" = "application/json")
- http <- HttpRequest()
- serverResponse <- http$PUT(collectionURL, headers, body)
+ body <- jsonlite::toJSON(body, auto_unbox = T)
- httpParser <- HttpParser()
- collection <- httpParser$parseJSONResponse(serverResponse)
+ serverResponse <- private$http$PUT(collectionURL, headers, body)
- if(!is.null(collection$errors))
- stop(collection$errors)
+ collection <- private$httpParser$parseJSONResponse(serverResponse)
- collection
- }
+ if(!is.null(collection$errors))
+ stop(collection$errors)
- collection_create <<- function(body)
- {
- collectionURL <- paste0(host, "collections")
- headers <- list("Authorization" = paste("OAuth2", token),
- "Content-Type" = "application/json")
- body <- jsonlite::toJSON(body, auto_unbox = T)
+ collection
+ },
- http <- HttpRequest()
- serverResponse <- http$POST(collectionURL, headers, body)
+ createCollection = function(body)
+ {
+ collectionURL <- paste0(private$host, "collections")
+ headers <- list("Authorization" = paste("OAuth2", private$token),
+ "Content-Type" = "application/json")
+ body <- jsonlite::toJSON(body, auto_unbox = T)
- httpParser <- HttpParser()
- collection <- httpParser$parseJSONResponse(serverResponse)
+ serverResponse <- private$http$POST(collectionURL, headers, body)
- if(!is.null(collection$errors))
- stop(collection$errors)
+ collection <- private$httpParser$parseJSONResponse(serverResponse)
- collection
- }
+ if(!is.null(collection$errors))
+ stop(collection$errors)
+
+ collection
}
- )
+
+ ),
+
+ private = list(
+
+ token = NULL,
+ host = NULL,
+ webDavHostName = NULL,
+ http = NULL,
+ httpParser = NULL
+ ),
+
+ cloneable = FALSE
)
projects / arvados.git / blobdiff