+source("./R/RESTService.R")
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$new("token", "host_name")
#' @export Arvados
-Arvados <- setRefClass(
+Arvados <- R6::R6Class(
"Arvados",
- fields = list(
+ public = list(
- getToken = "function",
- getHostName = "function",
-
- #Todo(Fudo): These are hardcoded and for debug only. Remove them later on.
- getWebDavToken = "function",
- getWebDavHostName = "function",
-
- collection_get = "function",
- collection_list = "function",
- collection_create = "function",
- collection_update = "function",
- collection_delete = "function"
- ),
+ initialize = function(authToken = NULL, hostName = NULL, numRetries = 0)
+ {
+ if(!is.null(hostName))
+ Sys.setenv(ARVADOS_API_HOST = hostName)
- methods = list(
+ if(!is.null(authToken))
+ Sys.setenv(ARVADOS_API_TOKEN = authToken)
- initialize = function(auth_token = NULL, host_name = NULL, webDavToken = NULL, webDavHostName = NULL)
- {
- # Private state
- if(!is.null(host_name))
- Sys.setenv(ARVADOS_API_HOST = host_name)
+ hostName <- Sys.getenv("ARVADOS_API_HOST");
+ token <- Sys.getenv("ARVADOS_API_TOKEN");
- if(!is.null(auth_token))
- Sys.setenv(ARVADOS_API_TOKEN = auth_token)
+ if(hostName == "" | token == "")
+ stop(paste("Please provide host name and authentification token",
+ "or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
+ "environment variables."))
- host <- Sys.getenv("ARVADOS_API_HOST");
- token <- Sys.getenv("ARVADOS_API_TOKEN");
+ private$numRetries <- numRetries
+ private$REST <- RESTService$new(token, hostName,
+ HttpRequest$new(), HttpParser$new(),
+ numRetries)
- if(host == "" | token == "")
- stop("Please provide host name and authentification token or set ARVADOS_API_HOST and ARVADOS_API_TOKEN environmental variables.")
+ private$token <- private$REST$token
+ private$host <- private$REST$hostName
+ },
- version <- "v1"
- host <- paste0("https://", host, "/arvados/", version, "/")
+ getToken = function() private$REST$token,
+ getHostName = function() private$REST$hostName,
+ getWebDavHostName = function() private$REST$getWebDavHostName(),
+ getRESTService = function() private$REST,
+ setRESTService = function(newRESTService) private$REST <- newRESTService,
- # Public methods
- getToken <<- function() { token }
- getHostName <<- function() { host }
+ getNumRetries = function() private$REST$numRetries,
+ setNumRetries = function(newNumOfRetries)
+ {
+ private$REST$setNumRetries(newNumOfRetries)
+ },
- #Todo(Fudo): Hardcoded credentials to WebDAV server. Remove them later
- getWebDavToken <<- function() { webDavToken }
- getWebDavHostName <<- function() { webDavHostName }
+ getCollection = function(uuid)
+ {
+ collection <- private$REST$getResource("collections", uuid)
+ collection
+ },
- collection_get <<- function(uuid)
- {
- collection_url <- paste0(host, "collections/", uuid)
- headers <- list(Authorization = paste("OAuth2", token))
+ listCollections = function(filters = NULL, limit = 100, offset = 0)
+ {
+ if(!is.null(filters))
+ names(filters) <- c("collection")
- http <- HttpRequest()
- serverResponse <- http$GET(collection_url, headers)
+ collections <- private$REST$listResources("collections", filters,
+ limit, offset)
+ collections
+ },
- httpParser <- HttpParser()
- collection <- httpParser$parseJSONResponse(serverResponse)
+ listAllCollections = function(filters = NULL)
+ {
+ if(!is.null(filters))
+ names(filters) <- c("collection")
- if(!is.null(collection$errors))
- stop(collection$errors)
+ collectionURL <- paste0(private$host, "collections")
+ allCollection <- private$REST$fetchAllItems(collectionURL, filters)
+ allCollection
+ },
- collection
- }
+ deleteCollection = function(uuid)
+ {
+ removedCollection <- private$REST$deleteResource("collections", uuid)
+ removedCollection
+ },
- collection_list <<- function(filters = NULL, limit = 100, offset = 0)
- {
- collection_url <- paste0(host, "collections")
- headers <- list(Authorization = paste("OAuth2", token))
+ updateCollection = function(uuid, newContent)
+ {
+ body <- list(list())
+ names(body) <- c("collection")
+ body$collection <- newContent
- http <- HttpRequest()
- serverResponse <- http$GET(collection_url, headers, NULL, filters, limit, offset)
+ updatedCollection <- private$REST$updateResource("collections",
+ uuid, body)
+ updatedCollection
+ },
- httpParser <- HttpParser()
- collection <- httpParser$parseJSONResponse(serverResponse)
+ createCollection = function(content)
+ {
+ body <- list(list())
+ names(body) <- c("collection")
+ body$collection <- content
- if(!is.null(collection$errors))
- stop(collection$errors)
+ newCollection <- private$REST$createResource("collections", body)
+ newCollection
+ },
- collection
- }
+ getProject = function(uuid)
+ {
+ project <- private$REST$getResource("groups", uuid)
+ project
+ },
- collection_delete <<- function(uuid)
- {
- collection_url <- paste0(host, "collections/", uuid)
- headers <- list("Authorization" = paste("OAuth2", token),
- "Content-Type" = "application/json")
+ createProject = function(content)
+ {
+ body <- list(list())
+ names(body) <- c("group")
+ body$group <- c("group_class" = "project", content)
- http <- HttpRequest()
- serverResponse <- http$DELETE(collection_url, headers)
+ newProject <- private$REST$createResource("groups", body)
+ newProject
+ },
- httpParser <- HttpParser()
- collection <- httpParser$parseJSONResponse(serverResponse)
+ updateProject = function(uuid, newContent)
+ {
+ body <- list(list())
+ names(body) <- c("group")
+ body$group <- newContent
- if(!is.null(collection$errors))
- stop(collection$errors)
+ updatedProject <- private$REST$updateResource("groups", uuid, body)
+ updatedProject
+ },
- collection
- }
+ listProjects = function(filters = NULL, limit = 100, offset = 0)
+ {
+ if(!is.null(filters))
+ names(filters) <- c("groups")
- collection_update <<- function(uuid, body)
- {
- collection_url <- paste0(host, "collections/", uuid)
- headers <- list("Authorization" = paste("OAuth2", token),
- "Content-Type" = "application/json")
- body <- jsonlite::toJSON(body, auto_unbox = T)
+ filters[[length(filters) + 1]] <- list("group_class", "=", "project")
- http <- HttpRequest()
- serverResponse <- http$PUT(collection_url, headers, body)
+ projects <- private$REST$listResources("groups", filters, limit, offset)
+ projects
+ },
- httpParser <- HttpParser()
- collection <- httpParser$parseJSONResponse(serverResponse)
+ listAllProjects = function(filters = NULL)
+ {
+ if(!is.null(filters))
+ names(filters) <- c("groups")
- if(!is.null(collection$errors))
- stop(collection$errors)
+ filters[[length(filters) + 1]] <- list("group_class", "=", "project")
- collection
- }
+ projectURL <- paste0(private$host, "groups")
- collection_create <<- function(body)
- {
- collection_url <- paste0(host, "collections")
- headers <- list("Authorization" = paste("OAuth2", token),
- "Content-Type" = "application/json")
- body <- jsonlite::toJSON(body, auto_unbox = T)
+ result <- private$REST$fetchAllItems(projectURL, filters)
+ result
+ },
- http <- HttpRequest()
- serverResponse <- http$POST(collection_url, headers, body)
+ deleteProject = function(uuid)
+ {
+ removedProject <- private$REST$deleteResource("groups", uuid)
+ removedProject
+ }
+ ),
- httpParser <- HttpParser()
- collection <- httpParser$parseJSONResponse(serverResponse)
+ private = list(
- if(!is.null(collection$errors))
- stop(collection$errors)
+ token = NULL,
+ host = NULL,
+ REST = NULL,
+ numRetries = NULL
+ ),
- collection
- }
- }
- )
+ cloneable = FALSE
)
+
+#' @export print.Arvados
+print.Arvados = function(arvados)
+{
+ cat(paste0("Type: ", "\"", "Arvados", "\""), sep = "\n")
+ cat(paste0("Host: ", "\"", arvados$getHostName(), "\""), sep = "\n")
+ cat(paste0("Token: ", "\"", arvados$getToken(), "\""), sep = "\n")
+}
projects / arvados.git / blobdiff