+source("./R/RESTService.R")
source("./R/HttpRequest.R")
source("./R/HttpParser.R")
-source("./R/RESTService.R")
#' Arvados SDK Object
#'
public = list(
- initialize = function(auth_token = NULL, host_name = NULL)
+ initialize = function(authToken = NULL, hostName = NULL, numRetries = 0)
{
- if(!is.null(host_name))
- Sys.setenv(ARVADOS_API_HOST = host_name)
+ if(!is.null(hostName))
+ Sys.setenv(ARVADOS_API_HOST = hostName)
- if(!is.null(auth_token))
- Sys.setenv(ARVADOS_API_TOKEN = auth_token)
+ if(!is.null(authToken))
+ Sys.setenv(ARVADOS_API_TOKEN = authToken)
- host_name <- Sys.getenv("ARVADOS_API_HOST");
- token <- Sys.getenv("ARVADOS_API_TOKEN");
+ hostName <- Sys.getenv("ARVADOS_API_HOST");
+ token <- Sys.getenv("ARVADOS_API_TOKEN");
- if(host_name == "" | token == "")
- stop(paste0("Please provide host name and authentification token",
- " or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
- " environment variables."))
+ if(hostName == "" | token == "")
+ stop(paste("Please provide host name and authentification token",
+ "or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
+ "environment variables."))
- version <- "v1"
- host <- paste0("https://", host_name, "/arvados/", version, "/")
+ private$numRetries <- numRetries
+ private$REST <- RESTService$new(token, hostName,
+ HttpRequest$new(), HttpParser$new(),
+ numRetries)
- private$http <- HttpRequest$new()
- private$httpParser <- HttpParser$new()
- private$REST <- RESTService$new(self)
- private$token <- token
- private$host <- host
- private$rawHost <- host_name
+ private$token <- private$REST$token
+ private$host <- private$REST$hostName
},
- getToken = function() private$token,
- getHostName = function() private$host,
-
- getHttpClient = function() private$http,
- setHttpClient = function(newClient) private$http <- newClient,
-
- getHttpParser = function() private$httpParser,
- setHttpParser = function(newParser) private$httpParser <- newParser,
-
- getRESTService = function() private$REST,
- setRESTService = function(newRESTService) private$REST <- newRESTService,
+ 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,
- getWebDavHostName = function()
+ getNumRetries = function() private$REST$numRetries,
+ setNumRetries = function(newNumOfRetries)
{
- if(is.null(private$webDavHostName))
- {
- discoveryDocumentURL <- paste0("https://", private$rawHost,
- "/discovery/v1/apis/arvados/v1/rest")
-
- headers <- list(Authorization = paste("OAuth2", private$token))
-
- serverResponse <- private$http$GET(discoveryDocumentURL, headers)
-
- discoveryDocument <- private$httpParser$parseJSONResponse(serverResponse)
- private$webDavHostName <- discoveryDocument$keepWebServiceUrl
-
- if(is.null(private$webDavHostName))
- stop("Unable to find WebDAV server.")
- }
-
- private$webDavHostName
+ private$REST$setNumRetries(newNumOfRetries)
},
getCollection = function(uuid)
{
- collectionURL <- paste0(private$host, "collections/", uuid)
- headers <- list(Authorization = paste("OAuth2", private$token))
-
- serverResponse <- private$http$GET(collectionURL, headers)
-
- collection <- private$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(collection$errors))
- stop(collection$errors)
-
+ collection <- private$REST$getResource("collections", uuid)
collection
},
listCollections = function(filters = NULL, limit = 100, offset = 0)
{
- collectionURL <- paste0(private$host, "collections")
- headers <- list(Authorization = paste("OAuth2", private$token))
-
if(!is.null(filters))
names(filters) <- c("collection")
- serverResponse <- private$http$GET(collectionURL, headers, filters,
- limit, offset)
-
- collections <- private$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(collections$errors))
- stop(collections$errors)
-
+ collections <- private$REST$listResources("collections", filters,
+ limit, offset)
collections
},
names(filters) <- c("collection")
collectionURL <- paste0(private$host, "collections")
- private$fetchAllItems(collectionURL, filters)
+ allCollection <- private$REST$fetchAllItems(collectionURL, filters)
+ allCollection
},
deleteCollection = function(uuid)
{
- collectionURL <- paste0(private$host, "collections/", uuid)
- headers <- list("Authorization" = paste("OAuth2", private$token),
- "Content-Type" = "application/json")
-
- serverResponse <- private$http$DELETE(collectionURL, headers)
-
- collection <- private$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(collection$errors))
- stop(collection$errors)
-
- collection
+ removedCollection <- private$REST$deleteResource("collections", uuid)
+ removedCollection
},
updateCollection = function(uuid, newContent)
{
- collectionURL <- paste0(private$host, "collections/", uuid)
- headers <- list("Authorization" = paste("OAuth2", private$token),
- "Content-Type" = "application/json")
-
body <- list(list())
- #test if this is needed
names(body) <- c("collection")
body$collection <- newContent
- body <- jsonlite::toJSON(body, auto_unbox = T)
-
- serverResponse <- private$http$PUT(collectionURL, headers, body)
-
- collection <- private$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(collection$errors))
- stop(collection$errors)
-
- collection
+ updatedCollection <- private$REST$updateResource("collections",
+ uuid, body)
+ updatedCollection
},
createCollection = function(content)
{
- collectionURL <- paste0(private$host, "collections")
- headers <- list("Authorization" = paste("OAuth2", private$token),
- "Content-Type" = "application/json")
-
body <- list(list())
names(body) <- c("collection")
body$collection <- content
- body <- jsonlite::toJSON(body, auto_unbox = T)
-
- serverResponse <- private$http$POST(collectionURL, headers, body)
-
- collection <- private$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(collection$errors))
- stop(collection$errors)
-
- collection
+ newCollection <- private$REST$createResource("collections", body)
+ newCollection
},
getProject = function(uuid)
{
- projectURL <- paste0(private$host, "groups/", uuid)
- headers <- list(Authorization = paste("OAuth2", private$token))
-
- serverResponse <- private$http$GET(projectURL, headers)
-
- project <- private$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(project$errors))
- stop(project$errors)
-
+ project <- private$REST$getResource("groups", uuid)
project
},
createProject = function(content)
{
- projectURL <- paste0(private$host, "groups")
- headers <- list("Authorization" = paste("OAuth2", private$token),
- "Content-Type" = "application/json")
-
body <- list(list())
names(body) <- c("group")
body$group <- c("group_class" = "project", content)
- body <- jsonlite::toJSON(body, auto_unbox = T)
-
- serverResponse <- private$http$POST(projectURL, headers, body)
-
- project <- private$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(project$errors))
- stop(project$errors)
- project
+ newProject <- private$REST$createResource("groups", body)
+ newProject
},
updateProject = function(uuid, newContent)
{
- projectURL <- paste0(private$host, "groups/", uuid)
- headers <- list("Authorization" = paste("OAuth2", private$token),
- "Content-Type" = "application/json")
-
body <- list(list())
names(body) <- c("group")
body$group <- newContent
- body <- jsonlite::toJSON(body, auto_unbox = T)
-
- serverResponse <- private$http$PUT(projectURL, headers, body)
-
- project <- private$httpParser$parseJSONResponse(serverResponse)
- if(!is.null(project$errors))
- stop(project$errors)
-
- project
+ updatedProject <- private$REST$updateResource("groups", uuid, body)
+ updatedProject
},
listProjects = function(filters = NULL, limit = 100, offset = 0)
{
- projectURL <- paste0(private$host, "groups")
- headers <- list(Authorization = paste("OAuth2", private$token))
-
if(!is.null(filters))
names(filters) <- c("groups")
filters[[length(filters) + 1]] <- list("group_class", "=", "project")
- serverResponse <- private$http$GET(projectURL, headers, filters,
- limit, offset)
-
- projects <- private$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(projects$errors))
- stop(projects$errors)
-
+ projects <- private$REST$listResources("groups", filters, limit, offset)
projects
},
projectURL <- paste0(private$host, "groups")
- private$fetchAllItems(projectURL, filters)
+ result <- private$REST$fetchAllItems(projectURL, filters)
+ result
},
deleteProject = function(uuid)
{
- projectURL <- paste0(private$host, "groups/", uuid)
- headers <- list("Authorization" = paste("OAuth2", private$token),
- "Content-Type" = "application/json")
-
- serverResponse <- private$http$DELETE(projectURL, headers)
-
- project <- private$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(project$errors))
- stop(project$errors)
-
- project
+ removedProject <- private$REST$deleteResource("groups", uuid)
+ removedProject
}
),
private = list(
- token = NULL,
- host = NULL,
- rawHost = NULL,
- webDavHostName = NULL,
- http = NULL,
- httpParser = NULL,
- REST = NULL,
-
- fetchAllItems = function(resourceURL, filters)
- {
- headers <- list(Authorization = paste("OAuth2", private$token))
-
- offset <- 0
- itemsAvailable <- .Machine$integer.max
- items <- c()
- while(length(items) < itemsAvailable)
- {
- serverResponse <- private$http$GET(url = resourceURL,
- headers = headers,
- queryFilters = filters,
- limit = NULL,
- offset = offset)
-
- parsedResponse <- private$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(parsedResponse$errors))
- stop(parsedResponse$errors)
-
- items <- c(items, parsedResponse$items)
- offset <- length(items)
- itemsAvailable <- parsedResponse$items_available
- }
-
- items
- }
+ token = NULL,
+ host = NULL,
+ REST = NULL,
+ numRetries = NULL
),
cloneable = FALSE
)
+
+#' @export print.Arvados
+print.Arvados = function(arvados)
+{
+ cat(paste0("Type: ", "\"", "Arvados", "\""), sep = "\n")
+ cat(paste0("Host: ", "\"", arvados$getHostName(), "\""), sep = "\n")
+ cat(paste0("Token: ", "\"", arvados$getToken(), "\""), sep = "\n")
+}
projects / arvados.git / blobdiff