sdk/R/R/Arvados.R

   1 source("./R/RESTService.R")
   2 source("./R/HttpRequest.R")
   3 source("./R/HttpParser.R")
   4
   5 #' Arvados SDK Object
   6 #'
   7 #' All Arvados logic is inside this class
   8 #'
   9 #' @field token Token represents user authentification token.
  10 #' @field host Host represents server name we wish to connect to.
  11 #' @examples arv = Arvados$new("token", "host_name")
  12 #' @export Arvados
  13 Arvados <- R6::R6Class(
  14
  15     "Arvados",
  16
  17     public = list(
  18
  19         initialize = function(authToken = NULL, hostName = NULL)
  20         {
  21             if(!is.null(hostName))
  22                Sys.setenv(ARVADOS_API_HOST = hostName)
  23
  24             if(!is.null(authToken))
  25                 Sys.setenv(ARVADOS_API_TOKEN = authToken)
  26
  27             hostName  <- Sys.getenv("ARVADOS_API_HOST");
  28             token <- Sys.getenv("ARVADOS_API_TOKEN");
  29
  30             if(hostName == "" | token == "")
  31                 stop(paste0("Please provide host name and authentification token",
  32                             " or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
  33                             " environment variables."))
  34
  35             private$REST  <- RESTService$new(token, hostName, NULL,
  36                                              HttpRequest$new(), HttpParser$new())
  37             private$token <- private$REST$token
  38             private$host  <- private$REST$hostName
  39         },
  40
  41         getToken          = function() private$REST$token,
  42         getHostName       = function() private$REST$hostName,
  43         getWebDavHostName = function() private$REST$getWebDavHostName(),
  44         getRESTService    = function() private$REST,
  45         setRESTService    = function(newRESTService) private$REST <- newRESTService,
  46
  47         getCollection = function(uuid)
  48         {
  49             collection <- private$REST$getResource("collections", uuid)
  50             collection
  51         },
  52
  53         listCollections = function(filters = NULL, limit = 100, offset = 0)
  54         {
  55             if(!is.null(filters))
  56                 names(filters) <- c("collection")
  57
  58             collections <- private$REST$listResources("collections", filters,
  59                                                       limit, offset)
  60             collections
  61         },
  62
  63         listAllCollections = function(filters = NULL)
  64         {
  65             if(!is.null(filters))
  66                 names(filters) <- c("collection")
  67
  68             collectionURL <- paste0(private$host, "collections")
  69             allCollection <- private$REST$fetchAllItems(collectionURL, filters)
  70             allCollection
  71         },
  72
  73         deleteCollection = function(uuid)
  74         {
  75             removedCollection <- private$REST$deleteResource("collections", uuid)
  76             removedCollection
  77         },
  78
  79         updateCollection = function(uuid, newContent)
  80         {
  81             body <- list(list())
  82             names(body) <- c("collection")
  83             body$collection <- newContent
  84
  85             updatedCollection <- private$REST$updateResource("collections",
  86                                                              uuid, body)
  87             updatedCollection
  88         },
  89
  90         createCollection = function(content)
  91         {
  92             body <- list(list())
  93             names(body) <- c("collection")
  94             body$collection <- content
  95
  96             newCollection <- private$REST$createResource("collections", body)
  97             newCollection
  98         },
  99
 100         getProject = function(uuid)
 101         {
 102             project <- private$REST$getResource("groups", uuid)
 103             project
 104         },
 105
 106         createProject = function(content)
 107         {
 108             body <- list(list())
 109             names(body) <- c("group")
 110             body$group <- c("group_class" = "project", content)
 111
 112             newProject <- private$REST$createResource("groups", body)
 113             newProject
 114         },
 115
 116         updateProject = function(uuid, newContent)
 117         {
 118             body <- list(list())
 119             names(body) <- c("group")
 120             body$group <- newContent
 121
 122             updatedProject <- private$REST$updateResource("groups",
 123                                                           uuid, body)
 124             updatedProject
 125         },
 126
 127         listProjects = function(filters = NULL, limit = 100, offset = 0)
 128         {
 129             if(!is.null(filters))
 130                 names(filters) <- c("groups")
 131
 132             filters[[length(filters) + 1]] <- list("group_class", "=", "project")
 133
 134             projects <- private$REST$listResources("groups", filters,
 135                                                    limit, offset)
 136             projects
 137         },
 138
 139         listAllProjects = function(filters = NULL)
 140         {
 141             if(!is.null(filters))
 142                 names(filters) <- c("groups")
 143
 144             filters[[length(filters) + 1]] <- list("group_class", "=", "project")
 145
 146             projectURL <- paste0(private$host, "groups")
 147
 148             result <- private$REST$fetchAllItems(projectURL, filters)
 149             result
 150         },
 151
 152         deleteProject = function(uuid)
 153         {
 154             removedProject <- private$REST$deleteResource("groups", uuid)
 155             removedProject
 156         }
 157     ),
 158
 159     private = list(
 160
 161         token = NULL,
 162         host  = NULL,
 163         REST  = NULL
 164     ),
 165
 166     cloneable = FALSE
 167 )
 168
 169 #' @export print.Arvados
 170 print.Arvados = function(arvados)
 171 {
 172     cat(paste0("Type:  ", "\"", "Arvados", "\""), sep = "\n")
 173     cat(paste0("Host:  ", "\"", arvados$getHostName(), "\""), sep = "\n")
 174     cat(paste0("Token: ", "\"", arvados$getToken(), "\"") , sep = "\n")
 175 }