sdk/R/R/autoGenAPI.R

   1 #TODO: Some methods do the same thing like collecion.index and collection.list.
   2 #      Make one implementation of the method and make other reference to it.
   3
   4 getAPIDocument <- function(){
   5     url <- "https://4xphq.arvadosapi.com/discovery/v1/apis/arvados/v1/rest"
   6     serverResponse <- httr::RETRY("GET", url = url)
   7
   8     httr::content(serverResponse, as = "parsed", type = "application/json")
   9 }
  10
  11 #' @export
  12 generateAPI <- function()
  13 {
  14     JSONDocument <- getAPIDocument()
  15
  16     generateArvadosClasses(JSONDocument)
  17     generateArvadosAPIClass(JSONDocument)
  18 }
  19
  20 generateArvadosAPIClass <- function(discoveryDocument)
  21 {
  22     classMetaData     <- discoveryDocument$schemas
  23     functionResources <- discoveryDocument$resources
  24     resourceNames     <- names(functionResources)
  25
  26     arvadosAPIHeader <- generateAPIClassHeader()
  27     arvadosAPIFooter <- generateAPIClassFooter()
  28
  29     arvadosMethods <- Map(function(resource, resourceName)
  30     {
  31         methodNames <- names(resource$methods)
  32
  33         functions <- Map(function(methodMetaData, methodName)
  34         {
  35             methodName <- paste0(resourceName, ".", methodName)
  36             createFunction(methodName, methodMetaData, classMetaData)
  37
  38         }, resource$methods, methodNames)
  39
  40         unlist(unname(functions))
  41
  42     }, functionResources, resourceNames)
  43
  44     arvadosClass <- c(arvadosAPIHeader, arvadosMethods, arvadosAPIFooter)
  45
  46     #TODO: Save to a file or load in memory?
  47     fileConn <- file("ArvadosAPI.R", "w")
  48     writeLines(unlist(arvadosClass), fileConn)
  49     close(fileConn)
  50     NULL
  51 }
  52
  53 getFunctionName <- function(functionMetaData)
  54 {
  55     stringr::str_replace(functionMetaData$id, "arvados.", "")
  56 }
  57
  58 #TODO: Make sure that arguments that are required always go first.
  59 #      This is not the case if request$required is false.
  60 getFunctionArguments <- function(functionMetaData)
  61 {
  62     request <- functionMetaData$request
  63     requestArgument <- NULL
  64
  65     if(!is.null(request))
  66         if(request$required)
  67             requestArgument <- names(request$properties)[1]
  68         else
  69             requestArgument <- paste(names(request$properties)[1], "=", "NULL")
  70
  71     argNames <- names(functionMetaData$parameters)
  72
  73     args <- sapply(argNames, function(argName)
  74     {
  75         arg <- functionMetaData$parameters[[argName]]
  76
  77         if(!arg$required)
  78         {
  79             if(!is.null(arg$default))
  80                 return(paste0(argName, " = ", "\"", arg$default, "\""))
  81             else
  82                 return(paste(argName, "=", "NULL"))
  83         }
  84
  85         argName
  86     })
  87
  88     paste0(c(requestArgument, args), collapse = ", ")
  89 }
  90
  91 getFunctionBody <- function(functionMetaData, classMetaData)
  92 {
  93     url  <- getRequestURL(functionMetaData)
  94     headers <- getRequestHeaders()
  95     requestQueryList <- getRequestQueryList(functionMetaData)
  96     requestQueryList <- getRequestQueryList(functionMetaData)
  97     requestBody <- getRequestBody(functionMetaData)
  98     request <- getRequest(functionMetaData)
  99     response <- getResponse(functionMetaData)
 100     returnObject <- getReturnObject(functionMetaData, classMetaData)
 101
 102     body <- c(url, headers, requestQueryList, requestBody, request, response, returnObject)
 103     paste0("\t\t\t", body)
 104 }
 105
 106 getRequestBody <- function(functionMetaData)
 107 {
 108     request <- functionMetaData$request
 109
 110     if(is.null(request) || !request$required)
 111         return("body <- NULL")
 112
 113     requestParameterName <- names(request$properties)[1]
 114     paste0("body <- ", requestParameterName, "$toJSON()")
 115 }
 116
 117 getRequestHeaders <- function()
 118 {
 119     paste0("headers <- list(Authorization = paste(\"OAuth2\", private$token),",
 120                             "\"Content-Type\" = \"application/json\")")
 121 }
 122
 123 getReturnObject <- function(functionMetaData, classMetaData)
 124 {
 125     returnClass <- functionMetaData$response[["$ref"]]
 126     classArguments <- getReturnClassArguments(returnClass, classMetaData)
 127
 128     c(paste0(returnClass, "$new(", classArguments, ")"))
 129 }
 130
 131 getReturnClassArguments <- function(className, classMetaData)
 132 {
 133     classArguments <- unique(names(classMetaData[[className]]$properties))
 134
 135     arguments <- sapply(classArguments, function(arg)
 136     {
 137         paste0(arg, " = resource$", arg)
 138     })
 139
 140     paste0(arguments, collapse = ", ")
 141 }
 142
 143 getRequest <- function(functionMetaData)
 144 {
 145     method <- functionMetaData$httpMethod
 146     paste0("response <- private$http$exec(\"", method, "\", url, headers, body, queryArgs)")
 147 }
 148
 149 getResponse <- function(functionMetaData)
 150 {
 151     "resource <- private$httpParser$parseJSONResponse(response)"
 152 }
 153
 154 getRequestURL <- function(functionMetaData)
 155 {
 156     endPoint <- functionMetaData$path
 157     endPoint <- stringr::str_replace_all(endPoint, "\\{", "${")
 158     url <- c(paste0("endPoint <- stringr::str_interp(\"", endPoint, "\")"),
 159              paste0("url <- paste0(private$host, endPoint)"))
 160     url
 161 }
 162
 163 getRequestQueryList <- function(functionMetaData)
 164 {
 165     argNames <- names(functionMetaData$parameters)
 166
 167     if(length(argNames) == 0)
 168         return("queryArgs <- NULL")
 169
 170     queryListContent <- sapply(argNames, function(arg) paste0(arg, " = ", arg))
 171
 172     paste0("queryArgs <- list(", paste0(queryListContent, collapse = ', ') , ")")
 173 }
 174
 175 createFunction <- function(functionName, functionMetaData, classMetaData)
 176 {
 177     args <- getFunctionArguments(functionMetaData)
 178     aditionalArgs <-
 179     body <- getFunctionBody(functionMetaData, classMetaData)
 180
 181     functionString <- c(paste0("\t\t", functionName, " = function(", args, ")"),
 182                        "\t\t{",
 183                            body,
 184                        "\t\t},\n")
 185
 186     functionString
 187 }
 188
 189 generateAPIClassHeader <- function()
 190 {
 191     c("#' @export",
 192       "ArvadosAPI <- R6::R6Class(",
 193       "",
 194       "\t\"ArvadosAPI\",",
 195       "",
 196       "\tpublic = list(",
 197       "",
 198       "\t\tinitialize = function(authToken = NULL, hostName = NULL, numRetries = 0)",
 199       "\t\t{",
 200       "\t\t\tif(!is.null(hostName))",
 201       "\t\t\t\tSys.setenv(ARVADOS_API_HOST = hostName)",
 202       "",
 203       "\t\t\tif(!is.null(authToken))",
 204       "\t\t\t\tSys.setenv(ARVADOS_API_TOKEN = authToken)",
 205       "",
 206       "\t\t\tprivate$rawHost <- Sys.getenv(\"ARVADOS_API_HOST\")",
 207       "\t\t\tprivate$host <- paste0(\"https://\", private$rawHost, \"/arvados/v1/\")",
 208       "\t\t\tprivate$token <- Sys.getenv(\"ARVADOS_API_TOKEN\")",
 209       "\t\t\tprivate$numRetries  <- numRetries",
 210       "\t\t\tprivate$http  <- ArvadosR:::HttpRequest$new()",
 211       "\t\t\tprivate$httpParser  <- ArvadosR:::HttpParser$new()",
 212       "",
 213       "\t\t\tif(private$rawHost == \"\" | private$token == \"\")",
 214       "\t\t\t\tstop(paste(\"Please provide host name and authentification token\",",
 215       "\t\t\t\t\t\t   \"or set ARVADOS_API_HOST and ARVADOS_API_TOKEN\",",
 216       "\t\t\t\t\t\t   \"environment variables.\"))",
 217       "\t\t},\n")
 218 }
 219
 220 generateAPIClassFooter <- function()
 221 {
 222     c("\t\tgetHostName = function() private$host,",
 223       "\t\tgetToken = function() private$token",
 224       "\t),",
 225       "",
 226       "\tprivate = list(",
 227       "",
 228       "\t\ttoken = NULL,",
 229       "\t\trawHost = NULL,",
 230       "\t\thost = NULL,",
 231       "\t\thttp = NULL,",
 232       "\t\thttpParser = NULL,",
 233       "\t\tnumRetries = NULL",
 234       "\t),",
 235       "",
 236       "\tcloneable = FALSE",
 237       ")")
 238 }
 239
 240 generateArvadosClasses <- function(resources)
 241 {
 242     classes <- sapply(resources$schemas, function(classSchema)
 243     {
 244         getArvadosClass(classSchema)
 245
 246     }, USE.NAMES = TRUE)
 247
 248     unlist(unname(classes))
 249
 250     fileConn <- file("ArvadosClasses.R", "w")
 251     writeLines(unlist(classes), fileConn)
 252     close(fileConn)
 253     NULL
 254 }
 255
 256 getArvadosClass <- function(classSchema)
 257 {
 258     name   <- classSchema$id
 259     fields <- unique(names(classSchema$properties))
 260     fieldsList <- paste0("c(", paste0("\"", fields, "\"", collapse = ", "), ")")
 261     constructorArgs <- paste0(fields, " = NULL", collapse = ", ")
 262
 263     classString <- c(paste0(name, " <- R6::R6Class("),
 264                      "",
 265               paste0("\t\"", name, "\","),
 266                      "",
 267                      "\tpublic = list(",
 268               paste0("\t\t", fields, " = NULL,"),
 269                      "",
 270               paste0("\t\tinitialize = function(", constructorArgs, ") {"),
 271               paste0("\t\t\tself$", fields, " <- ", fields),
 272                      "\t\t\t",
 273               paste0("\t\t\tprivate$classFields <- ", fieldsList),
 274                      "\t\t},",
 275                      "",
 276                      "\t\ttoJSON = function() {",
 277                      "\t\t\tfields <- sapply(private$classFields, function(field)",
 278                      "\t\t\t{",
 279                      "\t\t\t\tself[[field]]",
 280                      "\t\t\t}, USE.NAMES = TRUE)",
 281                      "\t\t\t",
 282               paste0("\t\t\tjsonlite::toJSON(list(\"", tolower(name), "\" = Filter(Negate(is.null), fields)), auto_unbox = TRUE)"),
 283                      "\t\t}",
 284                      "\t),",
 285                      "",
 286                      "\tprivate = list(",
 287                      "\t\tclassFields = NULL",
 288                      "\t),",
 289                      "",
 290                      "\tcloneable = FALSE",
 291                      ")",
 292                      "")
 293 }