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$new("token", "host_name")
  12 #' @export Arvados
  13 Arvados <- R6::R6Class(
  14
  15     "Arvados",
  16
  17     public = list(
  18
  19         initialize = function(authToken = NULL, hostName = NULL, numRetries = 0)
  20         {
  21             if(!is.null(hostName))
  22                Sys.setenv(ARVADOS_API_HOST = hostName)
  23
  24             if(!is.null(authToken))
  25                 Sys.setenv(ARVADOS_API_TOKEN = authToken)
  26
  27             hostName  <- Sys.getenv("ARVADOS_API_HOST");
  28             token     <- Sys.getenv("ARVADOS_API_TOKEN");
  29
  30             if(hostName == "" | token == "")
  31                 stop(paste("Please provide host name and authentification token",
  32                            "or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
  33                            "environment variables."))
  34
  35             private$numRetries  <- numRetries
  36             private$REST  <- RESTService$new(token, hostName,
  37                                              HttpRequest$new(), HttpParser$new(),
  38                                              numRetries)
  39
  40             private$token <- private$REST$token
  41             private$host  <- private$REST$hostName
  42         },
  43
  44         getToken          = function() private$REST$token,
  45         getHostName       = function() private$REST$hostName,
  46         getWebDavHostName = function() private$REST$getWebDavHostName(),
  47         getRESTService    = function() private$REST,
  48         setRESTService    = function(newRESTService) private$REST <- newRESTService,
  49
  50         getNumRetries = function() private$REST$numRetries,
  51         setNumRetries = function(newNumOfRetries)
  52         {
  53             private$REST$setNumRetries(newNumOfRetries)
  54         },
  55
  56         getCollection = function(uuid)
  57         {
  58             collection <- private$REST$getResource("collections", uuid)
  59             collection
  60         },
  61
  62         listCollections = function(filters = NULL, limit = 100, offset = 0)
  63         {
  64             if(!is.null(filters))
  65                 names(filters) <- c("collection")
  66
  67             collections <- private$REST$listResources("collections", filters,
  68                                                       limit, offset)
  69             collections
  70         },
  71
  72         listAllCollections = function(filters = NULL)
  73         {
  74             if(!is.null(filters))
  75                 names(filters) <- c("collection")
  76
  77             collectionURL <- paste0(private$host, "collections")
  78             allCollection <- private$REST$fetchAllItems(collectionURL, filters)
  79             allCollection
  80         },
  81
  82         deleteCollection = function(uuid)
  83         {
  84             removedCollection <- private$REST$deleteResource("collections", uuid)
  85             removedCollection
  86         },
  87
  88         updateCollection = function(uuid, newContent)
  89         {
  90             body <- list(list())
  91             names(body) <- c("collection")
  92             body$collection <- newContent
  93
  94             updatedCollection <- private$REST$updateResource("collections",
  95                                                              uuid, body)
  96             updatedCollection
  97         },
  98
  99         createCollection = function(content)
 100         {
 101             body <- list(list())
 102             names(body) <- c("collection")
 103             body$collection <- content
 104
 105             newCollection <- private$REST$createResource("collections", body)
 106             newCollection
 107         },
 108
 109         getProject = function(uuid)
 110         {
 111             project <- private$REST$getResource("groups", uuid)
 112             project
 113         },
 114
 115         createProject = function(content)
 116         {
 117             body <- list(list())
 118             names(body) <- c("group")
 119             body$group <- c("group_class" = "project", content)
 120
 121             newProject <- private$REST$createResource("groups", body)
 122             newProject
 123         },
 124
 125         updateProject = function(uuid, newContent)
 126         {
 127             body <- list(list())
 128             names(body) <- c("group")
 129             body$group <- newContent
 130
 131             updatedProject <- private$REST$updateResource("groups", uuid, body)
 132             updatedProject
 133         },
 134
 135         listProjects = function(filters = NULL, limit = 100, offset = 0)
 136         {
 137             if(!is.null(filters))
 138                 names(filters) <- c("groups")
 139
 140             filters[[length(filters) + 1]] <- list("group_class", "=", "project")
 141
 142             projects <- private$REST$listResources("groups", filters, limit, offset)
 143             projects
 144         },
 145
 146         listAllProjects = function(filters = NULL)
 147         {
 148             if(!is.null(filters))
 149                 names(filters) <- c("groups")
 150
 151             filters[[length(filters) + 1]] <- list("group_class", "=", "project")
 152
 153             projectURL <- paste0(private$host, "groups")
 154
 155             result <- private$REST$fetchAllItems(projectURL, filters)
 156             result
 157         },
 158
 159         deleteProject = function(uuid)
 160         {
 161             removedProject <- private$REST$deleteResource("groups", uuid)
 162             removedProject
 163         }
 164     ),
 165
 166     private = list(
 167
 168         token      = NULL,
 169         host       = NULL,
 170         REST       = NULL,
 171         numRetries = NULL
 172     ),
 173
 174     cloneable = FALSE
 175 )
 176
 177 #' @export print.Arvados
 178 print.Arvados = function(arvados)
 179 {
 180     cat(paste0("Type:  ", "\"", "Arvados",             "\""), sep = "\n")
 181     cat(paste0("Host:  ", "\"", arvados$getHostName(), "\""), sep = "\n")
 182     cat(paste0("Token: ", "\"", arvados$getToken(),    "\""), sep = "\n")
 183 }