+source("./R/RESTService.R")
source("./R/HttpRequest.R")
source("./R/HttpParser.R")
#'
#' All Arvados logic is inside this class
#'
-#' @field token represents user authentification token.
-#' @field host represents server name we wish to connect to.
+#' @field token Token represents user authentification token.
+#' @field host Host represents server name we wish to connect to.
+#' @examples arv = Arvados$new("token", "host_name")
#' @export Arvados
-Arvados <- setRefClass(
+Arvados <- R6::R6Class(
"Arvados",
- fields = list(
- token = "character",
- host = "character"
- ),
+ public = list(
+
+ initialize = function(authToken = NULL, hostName = NULL, numRetries = 0)
+ {
+ if(!is.null(hostName))
+ Sys.setenv(ARVADOS_API_HOST = hostName)
+
+ if(!is.null(authToken))
+ Sys.setenv(ARVADOS_API_TOKEN = authToken)
+
+ hostName <- Sys.getenv("ARVADOS_API_HOST");
+ token <- Sys.getenv("ARVADOS_API_TOKEN");
+
+ if(hostName == "" | token == "")
+ stop(paste("Please provide host name and authentification token",
+ "or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
+ "environment variables."))
+
+ private$numRetries <- numRetries
+ private$REST <- RESTService$new(token, hostName,
+ HttpRequest$new(), HttpParser$new(),
+ numRetries)
- methods = list(
+ private$token <- private$REST$token
+ private$host <- private$REST$hostName
+ },
- initialize = function(auth_token, host_name)
+ 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,
+
+ getNumRetries = function() private$REST$numRetries,
+ setNumRetries = function(newNumOfRetries)
+ {
+ private$REST$setNumRetries(newNumOfRetries)
+ },
+
+ getCollection = function(uuid)
{
- #Todo(Fudo): Validate token
- token <<- auth_token
- host <<- host_name
+ collection <- private$REST$getResource("collections", uuid)
+ collection
+ },
+
+ listCollections = function(filters = NULL, limit = 100, offset = 0)
+ {
+ if(!is.null(filters))
+ names(filters) <- c("collection")
+
+ collections <- private$REST$listResources("collections", filters,
+ limit, offset)
+ collections
+ },
+
+ listAllCollections = function(filters = NULL)
+ {
+ if(!is.null(filters))
+ names(filters) <- c("collection")
+
+ collectionURL <- paste0(private$host, "collections")
+ allCollection <- private$REST$fetchAllItems(collectionURL, filters)
+ allCollection
+ },
+
+ deleteCollection = function(uuid)
+ {
+ removedCollection <- private$REST$deleteResource("collections", uuid)
+ removedCollection
+ },
+
+ updateCollection = function(uuid, newContent)
+ {
+ body <- list(list())
+ names(body) <- c("collection")
+ body$collection <- newContent
+
+ updatedCollection <- private$REST$updateResource("collections",
+ uuid, body)
+ updatedCollection
+ },
+
+ createCollection = function(content)
+ {
+ body <- list(list())
+ names(body) <- c("collection")
+ body$collection <- content
+
+ newCollection <- private$REST$createResource("collections", body)
+ newCollection
+ },
+
+ getProject = function(uuid)
+ {
+ project <- private$REST$getResource("groups", uuid)
+ project
+ },
+
+ createProject = function(content)
+ {
+ body <- list(list())
+ names(body) <- c("group")
+ body$group <- c("group_class" = "project", content)
+
+ newProject <- private$REST$createResource("groups", body)
+ newProject
+ },
+
+ updateProject = function(uuid, newContent)
+ {
+ body <- list(list())
+ names(body) <- c("group")
+ body$group <- newContent
+
+ updatedProject <- private$REST$updateResource("groups", uuid, body)
+ updatedProject
+ },
+
+ listProjects = function(filters = NULL, limit = 100, offset = 0)
+ {
+ if(!is.null(filters))
+ names(filters) <- c("groups")
+
+ filters[[length(filters) + 1]] <- list("group_class", "=", "project")
+
+ projects <- private$REST$listResources("groups", filters, limit, offset)
+ projects
+ },
+
+ listAllProjects = function(filters = NULL)
+ {
+ if(!is.null(filters))
+ names(filters) <- c("groups")
+
+ filters[[length(filters) + 1]] <- list("group_class", "=", "project")
+
+ projectURL <- paste0(private$host, "groups")
+
+ result <- private$REST$fetchAllItems(projectURL, filters)
+ result
+ },
+
+ deleteProject = function(uuid)
+ {
+ removedProject <- private$REST$deleteResource("groups", uuid)
+ removedProject
}
- )
-)
+ ),
-#' collection_get
-#'
-#' Get Arvados collection
-#'
-#' @name collection_get
-#' @field uuid UUID of the given collection
-Arvados$methods(
-
- collection_get = function(uuid)
- {
- collection_relative_url <- paste0("collections/", uuid)
- http_request <- HttpRequest("GET", token, host, collection_relative_url)
- server_response <- http_request$execute()
-
- httpParser <- HttpParser()
- collection <- httpParser$parseCollectionGet(server_response)
- class(collection) <- "ArvadosCollection"
-
- return(collection)
- }
-)
+ private = list(
-#' collection_list
-#'
-#' List Arvados collections based on filter matching
-#'
-#' @name collection_list
-#' @field uuid UUID of the given collection
-Arvados$methods(
-
- collection_list = function(filters = NULL, limit = NULL, offset = NULL)
- {
- #Todo(Fudo): Implement limit and offset
- collection_relative_url <- "collections"
- http_request <- HttpRequest("GET", token, host, collection_relative_url, filters)
- server_response <- http_request$execute()
-
- httpParser <- HttpParser()
- collection <- httpParser$parseCollectionGet(server_response)
- class(collection) <- "ArvadosCollectionList"
-
- return(collection)
- }
+ token = NULL,
+ host = NULL,
+ REST = NULL,
+ numRetries = NULL
+ ),
+
+ 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