*#*
.DS_Store
.vscode
+.Rproj.user
--- /dev/null
+^.*\.Rproj$
+^\.Rproj\.user$
--- /dev/null
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 4
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
--- /dev/null
+Package: ArvadosSDK
+Type: Package
+Title: What the Package Does (Title Case)
+Version: 0.1.0
+Author: Who wrote it
+Maintainer: The package maintainer <yourself@somewhere.net>
+Description: More about what it does (maybe more than one line)
+ Use four spaces when indenting paragraphs within the Description.
+License: What license is it under?
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 6.0.1.9000
+Imports:
+ httr,
+ stringr,
+ jsonlite,
+ curl,
+ XML
--- /dev/null
+# Generated by roxygen2: do not edit by hand
+
+export(Arvados)
+exportClasses(Collection)
--- /dev/null
+source("./R/HttpRequest.R")
+source("./R/HttpParser.R")
+source("./R/custom_classes.R")
+
+#' Arvados SDK Object
+#'
+#' All Arvados logic is inside this class
+#'
+#' @field token Token represents user authentification token.
+#' @field host Host represents server name we wish to connect to.
+#' @examples arv = Arvados("token", "host_name")
+#' @export Arvados
+Arvados <- setRefClass(
+
+ "Arvados",
+
+ fields = 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"
+ ),
+
+ methods = list(
+
+ initialize = function(auth_token = NULL, host_name = NULL)
+ {
+ # Private state
+ if(!is.null(host_name))
+ Sys.setenv(ARVADOS_API_HOST = host_name)
+
+ if(!is.null(auth_token))
+ Sys.setenv(ARVADOS_API_TOKEN = auth_token)
+
+ host <- Sys.getenv("ARVADOS_API_HOST");
+ token <- Sys.getenv("ARVADOS_API_TOKEN");
+
+ if(host == "" | token == "")
+ stop("Please provide host name and authentification token or set ARVADOS_API_HOST and ARVADOS_API_TOKEN environmental variables.")
+
+ version <- "v1"
+ host <- paste0("https://", host, "/arvados/", version, "/")
+
+ # Public methods
+ getToken <<- function() { token }
+ getHostName <<- function() { host }
+
+ #Todo(Fudo): Hardcoded credentials to WebDAV server. Remove them later
+ getWebDavToken <<- function() { "4invqy35tf70t7hmvdc83ges8ug9cklhgqq1l8gj2cjn18teuq" }
+ getWebDavHostName <<- function() { "https://collections.4xphq.arvadosapi.com/c=4xphq-4zz18-9d5b0qm4fgijeyi/_/" }
+
+ collection_get <<- function(uuid)
+ {
+ collection_url <- paste0(host, "collections/", uuid)
+ headers <- list(Authorization = paste("OAuth2", token))
+
+ http <- HttpRequest()
+ serverResponse <- http$GET(collection_url, headers)
+
+ httpParser <- HttpParser()
+ collection <- httpParser$parseJSONResponse(serverResponse)
+
+ if(!is.null(collection$errors))
+ stop(collection$errors)
+
+ collection
+ }
+
+ collection_list <<- function(filters = NULL, limit = 100, offset = 0)
+ {
+ collection_url <- paste0(host, "collections")
+ headers <- list(Authorization = paste("OAuth2", token))
+
+ http <- HttpRequest()
+ serverResponse <- http$GET(collection_url, headers, NULL, filters, limit, offset)
+
+ httpParser <- HttpParser()
+ collection <- httpParser$parseJSONResponse(serverResponse)
+
+ if(!is.null(collection$errors))
+ stop(collection$errors)
+
+ collection
+ }
+
+ collection_delete <<- function(uuid)
+ {
+ collection_url <- paste0(host, "collections/", uuid)
+ headers <- list("Authorization" = paste("OAuth2", token),
+ "Content-Type" = "application/json")
+
+ http <- HttpRequest()
+ serverResponse <- http$DELETE(collection_url, headers)
+
+ httpParser <- HttpParser()
+ collection <- httpParser$parseJSONResponse(serverResponse)
+
+ if(!is.null(collection$errors))
+ stop(collection$errors)
+
+ collection
+ }
+
+ 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)
+
+ http <- HttpRequest()
+ serverResponse <- http$PUT(collection_url, headers, body)
+
+ httpParser <- HttpParser()
+ collection <- httpParser$parseJSONResponse(serverResponse)
+
+ if(!is.null(collection$errors))
+ stop(collection$errors)
+
+ collection
+ }
+
+ 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)
+
+ http <- HttpRequest()
+ serverResponse <- http$POST(collection_url, headers, body)
+
+ httpParser <- HttpParser()
+ collection <- httpParser$parseJSONResponse(serverResponse)
+
+ if(!is.null(collection$errors))
+ stop(collection$errors)
+
+ collection
+ }
+ }
+ )
+)
--- /dev/null
+source("./R/Arvados.R")
+source("./R/HttpParser.R")
+
+#' Collection Object
+#'
+#' @details
+#' Todo: Update description
+#' Collection
+#'
+#' @param uuid Object ID
+#' @param etag Object version
+#' @param owner_uuid No description
+#' @param created_at No description
+#' @param modified_by_client_uuid No description
+#' @param modified_by_user_uuid No description
+#' @param modified_at No description
+#' @param portable_data_hash No description
+#' @param replication_desired No description
+#' @param replication_confirmed_at No description
+#' @param replication_confirmed No description
+#' @param updated_at No description
+#' @param manifest_text No description
+#' @param name No description
+#' @param description No description
+#' @param properties No description
+#' @param delete_at No description
+#' @param file_names No description
+#' @param trash_at No description
+#' @param is_trashed No description
+#'
+#' @export
+Collection <- setRefClass(
+
+ "Collection",
+
+ fields = list(uuid = "ANY",
+ items = "ANY",
+ etag = "ANY",
+ owner_uuid = "ANY",
+ created_at = "ANY",
+ modified_by_client_uuid = "ANY",
+ modified_by_user_uuid = "ANY",
+ modified_at = "ANY",
+ portable_data_hash = "ANY",
+ replication_desired = "ANY",
+ replication_confirmed_at = "ANY",
+ replication_confirmed = "ANY",
+ updated_at = "ANY",
+ manifest_text = "ANY",
+ name = "ANY",
+ description = "ANY",
+ properties = "ANY",
+ delete_at = "ANY",
+ file_names = "ANY",
+ trash_at = "ANY",
+ is_trashed = "ANY",
+
+ getCollectionContent = "function"
+ ),
+
+ methods = list(
+
+ initialize = function(api, uuid)
+ {
+
+ result <- api$collection_get(uuid)
+
+ # Private members
+ uuid <<- result$uuid
+ etag <<- result$etag
+ owner_uuid <<- result$owner_uuid
+ created_at <<- result$created_at
+ modified_by_client_uuid <<- result$modified_by_client_uuid
+ modified_by_user_uuid <<- result$modified_by_user_uuid
+ modified_at <<- result$modified_at
+ portable_data_hash <<- result$portable_data_hash
+ replication_desired <<- result$replication_desired
+ replication_confirmed_at <<- result$replication_confirmed_at
+ replication_confirmed <<- result$replication_confirmed
+ updated_at <<- result$updated_at
+ manifest_text <<- result$manifest_text
+ name <<- result$name
+ description <<- result$description
+ properties <<- result$properties
+ delete_at <<- result$delete_at
+ file_names <<- result$file_names
+ trash_at <<- result$trash_at
+ is_trashed <<- result$is_trashed
+
+
+ #Public methods
+
+ # Private methods
+ getCollectionContent <<- function()
+ {
+ #TODO(Fudo): Use proper URL here.
+ uri <- URLencode(api$getWebDavHostName())
+
+ # fetch directory listing via curl and parse XML response
+ h <- curl::new_handle()
+ curl::handle_setopt(h, customrequest = "PROPFIND")
+
+ #TODO(Fudo): Use proper token here.
+ curl::handle_setheaders(h, "Authorization" = paste("OAuth2", api$getWebDavToken()))
+ response <- curl::curl_fetch_memory(uri, h)
+
+ HttpParser()$parseWebDAVResponse(response, uri)
+ }
+
+ items <<- getCollectionContent()
+ }
+ )
+)
--- /dev/null
+#' HttpParser
+#'
+HttpParser <- setRefClass(
+
+ "HttrParser",
+
+ fields = list(
+ ),
+
+ methods = list(
+ initialize = function()
+ {
+ },
+
+ parseCollectionGet = function(server_response)
+ {
+ parsed_response <- httr::content(server_response, as = "parsed", type = "application/json")
+
+ #Todo(Fudo): Create new Collection object and populate it
+ },
+
+ parseJSONResponse = function(server_response)
+ {
+ parsed_response <- httr::content(server_response, as = "parsed", type = "application/json")
+
+ #Todo(Fudo): Create new Collection object and populate it
+ },
+
+ parseWebDAVResponse = function(response, uri)
+ {
+ #Todo(Fudo): Move this to HttpParser.
+ text <- rawToChar(response$content)
+ doc <- XML::xmlParse(text, asText=TRUE)
+
+ # calculate relative paths
+ base <- paste(paste("/", strsplit(uri, "/")[[1]][-1:-3], sep="", collapse=""), "/", sep="")
+ result <- unlist(
+ XML::xpathApply(doc, "//D:response/D:href", function(node) {
+ sub(base, "", URLdecode(XML::xmlValue(node)), fixed=TRUE)
+ })
+ )
+ result[result != ""]
+ }
+
+ )
+)
--- /dev/null
+source("./R/custom_classes.R")
+
+HttpRequest <- setRefClass(
+
+ "HttrRequest",
+
+ fields = list(
+
+ GET = "function",
+ PUT = "function",
+ POST = "function",
+ DELETE = "function"
+ ),
+
+ methods = list(
+ initialize = function()
+ {
+ # Public methods
+ GET <<- function(url, headers = NULL, body = NULL,
+ queryFilters = NULL, limit = 100, offset = 0)
+ {
+ print(limit)
+ headers <- httr::add_headers(unlist(headers))
+ query <- .createQuery(queryFilters, limit, offset)
+ url <- paste0(url, query)
+ print(url)
+
+ serverResponse <- httr::GET(url = url, config = headers)
+ }
+
+ PUT <<- function(url, headers = NULL, body = NULL,
+ queryFilters = NULL, limit = 100, offset = 0)
+ {
+ headers <- httr::add_headers(unlist(headers))
+ query <- .createQuery(queryFilters, limit, offset)
+ url <- paste0(url, query)
+
+ serverResponse <- httr::PUT(url = url, config = headers, body = body)
+ }
+
+ POST <<- function(url, headers = NULL, body = NULL,
+ queryFilters = NULL, limit = 100, offset = 0)
+ {
+ headers <- httr::add_headers(unlist(headers))
+ query <- .createQuery(queryFilters, limit, offset)
+ url <- paste0(url, query)
+
+ serverResponse <- httr::POST(url = url, config = headers, body = body)
+ }
+
+ DELETE <<- function(url, headers = NULL, body = NULL,
+ queryFilters = NULL, limit = 100, offset = 0)
+ {
+ headers <- httr::add_headers(unlist(headers))
+ query <- .createQuery(queryFilters, limit, offset)
+ url <- paste0(url, query)
+
+ serverResponse <- httr::DELETE(url = url, config = headers)
+ }
+
+ # Private methods
+ .createQuery <- function(filters, limit, offset)
+ {
+ finalQuery <- "?alt=json"
+
+ if(!is.null(filters))
+ {
+ filters <- sapply(filters, function(filter)
+ {
+ if(length(filter) != 3)
+ stop("Filter list must have exacthey 3 elements.")
+
+ attributeAndOperator = filter[c(1, 2)]
+ filterList = filter[[3]]
+ filterListIsPrimitive = TRUE
+ if(length(filterList) > 1)
+ filterListIsPrimitive = FALSE
+
+ attributeAndOperator <- sapply(attributeAndOperator, function(component) {
+ component <- paste0("\"", component, "\"")
+ })
+
+ filterList <- sapply(unlist(filterList), function(filter) {
+ filter <- paste0("\"", filter, "\"")
+ })
+
+ filterList <- paste(filterList, collapse = ",+")
+
+ if(!filterListIsPrimitive)
+ filterList <- paste0("[", filterList, "]")
+
+ filter <- c(attributeAndOperator, filterList)
+
+ queryParameter <- paste(filter, collapse = ",+")
+ queryParameter <- paste0("[", queryParameter, "]")
+
+ })
+
+ filters <- paste(filters, collapse = ",+")
+ filters <- paste0("[", filters, "]")
+
+ encodedQuery <- URLencode(filters, reserved = T, repeated = T)
+
+ finalQuery <- paste0(finalQuery, "&filters=", encodedQuery)
+
+ #Todo(Fudo): This is a hack for now. Find a proper solution.
+ finalQuery <- stringr::str_replace_all(finalQuery, "%2B", "+")
+ }
+
+ if(!is.null(limit))
+ {
+ if(!is.numeric(limit))
+ stop("Limit must be a numeric type.")
+
+ finalQuery <- paste0(finalQuery, "&limit=", limit)
+ }
+
+ if(!is.null(offset))
+ {
+ if(!is.numeric(offset))
+ stop("Offset must be a numeric type.")
+
+ finalQuery <- paste0(finalQuery, "&offset=", offset)
+ }
+
+ finalQuery
+ }
+ }
+ )
+)
--- /dev/null
+setClassUnion("characterOrNull", c("character", "NULL"))
+setClassUnion("listOrNull", c("list", "NULL"))
+setClassUnion("numericOrNull", c("numeric", "NULL"))
--- /dev/null
+R SDK for Arvados
\ No newline at end of file
--- /dev/null
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Arvados.R
+\docType{class}
+\name{Arvados-class}
+\alias{Arvados-class}
+\alias{Arvados}
+\title{Arvados SDK Object}
+\description{
+All Arvados logic is inside this class
+}
+\section{Fields}{
+
+\describe{
+\item{\code{token}}{Token represents user authentification token.}
+
+\item{\code{host}}{Host represents server name we wish to connect to.}
+}}
+
+
+\examples{
+arv = Arvados("token", "host_name")
+}
--- /dev/null
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Collection.R
+\docType{class}
+\name{Collection-class}
+\alias{Collection-class}
+\alias{Collection}
+\title{Collection Object}
+\arguments{
+\item{uuid}{Object ID}
+
+\item{etag}{Object version}
+
+\item{owner_uuid}{No description}
+
+\item{created_at}{No description}
+
+\item{modified_by_client_uuid}{No description}
+
+\item{modified_by_user_uuid}{No description}
+
+\item{modified_at}{No description}
+
+\item{portable_data_hash}{No description}
+
+\item{replication_desired}{No description}
+
+\item{replication_confirmed_at}{No description}
+
+\item{replication_confirmed}{No description}
+
+\item{updated_at}{No description}
+
+\item{manifest_text}{No description}
+
+\item{name}{No description}
+
+\item{description}{No description}
+
+\item{properties}{No description}
+
+\item{delete_at}{No description}
+
+\item{file_names}{No description}
+
+\item{trash_at}{No description}
+
+\item{is_trashed}{No description}
+}
+\description{
+Collection Object
+}
+\details{
+Todo: Update description
+Collection
+}
+
--- /dev/null
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/HttpParser.R
+\docType{class}
+\name{HttrParser-class}
+\alias{HttrParser-class}
+\alias{HttpParser}
+\title{HttpParser}
+\description{
+HttpParser
+}
+
projects / arvados.git / commitdiff