R/GrapleR.R
In GRAPLE/GRAPLEr: Distributed Computing Made Easy for Lake Ecology Modeling
Defines functions
validate_json
filePresent
filesPresent
getResultsDirName
check_subdirectory
check_graple
validate_url
.onAttach
Documented in
check_graple
check_subdirectory
filePresent
filesPresent
getResultsDirName
validate_json
validate_url
.onAttach <- function(libname, pkgname) {
packageStartupMessage("GRAPLEr has been developed with support from a supplement the PRAGMA award (NSF OCI-1234983) by
Ken Subratie, Saumitra Aditya, Satish Mahesula, Renato J. Figueiredo, Cayelan C. Carey, Paul C. Hanson, and Vahid Daneshmand.
For more information, please visit 'http://graple.org'.")
#' Skip Self-signed SSL Certificate Error
httr::set_config(httr::config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE))
}
#' Validates whether a given url exists
#'
#' @param url Submission URL
#' @return A boolean value indicating whether url exists
#' @export
#' @keywords internal
#' @importFrom httr http_error
#' @examples
#' validate_url('https://graple.acis.ufl.edu')
validate_url <- function(url){
invalid_url = tryCatch({
http_error(url)
}, error = function(e) {
invalid_url <- TRUE
})
return(!invalid_url)
}
#' Checks if the grapleObject is valid
#' by checking if the directories provided exist and valid
#' @param object A Graple Object
#' @return errors if any of the validation fails
#' @export
#' @keywords internal
#' @examples
#' \dontrun{
#' check_graple(grapleExp1)
#' }
check_graple <- function(object) {
errors <- character()
if(length(object@GWSURL) > 0)
{
valid_url <- validate_url(object@GWSURL)
if (!valid_url) {
msg <- paste("Invalid URL")
errors <- c(errors, msg)
}
}
if(length(object@ExpRootDir) > 0)
{
if(!dir.exists(object@ExpRootDir))
{
msg <- paste("Experiment root directory does not exist.")
errors <- c(errors, msg)
}
}
if(length(object@ResultsDir) > 0)
{
if(!dir.exists(object@ResultsDir))
{
msg <- paste("Results directory does not exist.")
errors <- c(errors, msg)
}
}
if(!check_subdirectory(object))
{
msg <- paste("Experiment root directory or result directory are a sub-directory of Result/Input.")
errors <- c(errors, msg)
}
if (length(errors) == 0) TRUE else errors
}
#' Checks if the input/results directory is a sub-directory of
#' results/input directory
#' @param object A Graple Object
#' @return A boolean value indicating whether the directory
#' structure is valid
#' @export
#' @keywords internal
#' @examples
#' \dontrun{
#' check_subdirectory(grapleExp1)
#' }
check_subdirectory <- function(object){
input_dir <- object@ExpRootDir
results_dir <- object@ResultsDir
valid_directories <- FALSE
if(((length(input_dir) > 0 && length(results_dir) > 0) && (length(grep(input_dir,results_dir)) || length(grep(results_dir, input_dir)))>0))
valid_directories <- FALSE
else
valid_directories <- TRUE
return(valid_directories)
}
#' Gets the name for results directory
#' @param object A Graple Object
#' @return ExpName if provided, else the JobID
#' @export
#' @keywords internal
#' @examples
#' \dontrun{
#' getResultsDirName(grapleExp1)
#' }
getResultsDirName <- function(object){
if(length(object@ExpName) > 0)
return(object@ExpName)
else if(length(object@JobID) > 0)
return(object@JobID)
else
return('')
}
#' Checks if there are any files present in ExpRoot Directory
#' @param object A Graple Object
#' @return A boolean value indicating whether files are present or not
#' @export
#' @keywords internal
#' @examples
#' \dontrun{
#' filesPresent(grapleExp1)
#' }
filesPresent <- function(object){
if(length(list.files(path = object@ExpRootDir, recursive = FALSE, all.files = TRUE)) - 2 != length(list.dirs(path = object@ExpRootDir, recursive = FALSE))) # all.files = TRUE for Checking Hidden Files, -2 for Excluding . and ..
return(TRUE)
else
return(FALSE)
}
#' checks if a given file exists in a directory
#' @param dirPath A Directory path
#' @param fileName File name
#' @return A boolean value indicating whether a file is present or not
#' @export
#' @keywords internal
#' @examples
#' filePresent('C:/ExpRoot/Exp1/mySim', 'met_hourly.csv')
filePresent <- function(dirPath, fileName){
filesList <- list.files(path = dirPath, recursive = FALSE)
if(fileName %in% filesList)
return(TRUE)
else
return(FALSE)
}
#' Checks if a json file is valid according to GRAPLEr constraints
#' @param jsonFilePath JSON File path
#' @return A boolean value indicating whether the json file is valid
#' @export
#' @keywords internal
#' @importFrom jsonlite fromJSON
#' @examples
#' \dontrun{
#' validate_json('C:/ExpRoot/Exp3/job_desc.json')
#' }
validate_json <- function(jsonFilePath)
{
valid_JSON <- TRUE
distribution_type <- ''
distribution_types <- list('uniform', 'binomial', 'normal', 'poisson')
jsonFile <- fromJSON(jsonFilePath, simplifyVector = FALSE)
num_iterations <- jsonFile$num_iterations
if(is.null(num_iterations))
distribution_type <- 'linear'
else
distribution_type <- 'non-linear'
if(is.null(jsonFile$ExpFiles))
return(list(valid_JSON, distribution_type))
if(distribution_type == 'linear') {
steps = 1
for (expFile in 1:length(jsonFile$ExpFiles)) {
for (vb in 1:length(jsonFile$ExpFiles[[expFile]]$variables[[1]])) {
distribution = jsonFile$ExpFiles[[expFile]]$variables[[1]][[vb]]$distribution
if(is.null(distribution) || distribution != 'linear'){
valid_JSON <- FALSE
break
}
else if (distribution == 'linear'){
var_steps = jsonFile$ExpFiles[[expFile]]$variables[[1]][[vb]]$steps
if(is.null(steps)){
valid_JSON <- FALSE
break
}
else{
steps = steps * (var_steps + 1)
}
}
}
}
if(steps >= 100000)
valid_JSON <- FALSE
}
else if(distribution_type == 'non-linear'){
for (expFile in 1:length(jsonFile$ExpFiles)) {
for (vb in 1:length(jsonFile$ExpFiles[[expFile]]$variables[[1]])) {
distribution = jsonFile$ExpFiles[[expFile]]$variables[[1]][[vb]]$distribution
if(is.null(distribution) || !(distribution %in% distribution_types)){
valid_JSON <- FALSE
break
}
}
}
}
else
{
valid_JSON <- FALSE
}
return(list(valid_JSON, distribution_type))
}
#' An S4 class to represent a graple object.
#'
#' @slot GWSURL A SubmissionURL for the experiment having a default value of https://graple.acis.ufl.edu
#' @slot ExpRootDir Experiment Root Directory path
#' @slot ResultsDir Directory path for storing the results
#' @slot JobID Unique identifier for the experiment
#' @slot Email Email address to send notifications
#' @slot APIKey API Key to authenticate a user
#' @slot SimsPerJob A number indicating the number of simulations bundled into a worker job
#' @slot StatusCode Integer value indicating the status of an operation
#' @slot StatusMsg A brief text message indicating the status of an operation
#' @slot ExpName A name for the experiment
#' @slot TempDir Temporary Directory path for temporary storage of files
#' @slot Retention A user provided request to the GRAPLEr cluster on duration for which experiment results should be retained
#' @slot Client_Version_ID The version of GRAPLEr package being used
#' @importFrom methods new
#' @exportClass Graple
Graple <- setClass("Graple", slots = c(GWSURL = "character", ExpRootDir="character", ResultsDir="character", JobID="character", Email="character",
APIKey="character", SimsPerJob="numeric", StatusCode="numeric", StatusMsg="character", ExpName="character", TempDir="character",
Retention ="numeric", Client_Version_ID="character"), prototype = list(GWSURL="https://graple.acis.ufl.edu", Email='', APIKey="0",
SimsPerJob=5, TempDir=tempdir(), Retention = 10, Client_Version_ID = toString(packageVersion("GRAPLEr"))), validity = check_graple)
#' Set the Temporary Directory to given directory path for the Graple Object
#' @param grapleObject A Graple Object
#' @param path Path to a directory to be set as Temporary directory for the experiment
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setTempDir(grapleObject, 'C:/TempDir')
#' }
setGeneric(name="setTempDir",
def=function(grapleObject,path)
{
standardGeneric("setTempDir")
}
)
#' Sets the submission URL in the Graple object
#' @param grapleObject A Graple Object
#' @param url A Submission URL
#' @return The Graple object with updated submissionURL
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setSubmissionURL(grapleObject, 'https://graple.acis.ufl.edu')
#' }
setGeneric(name="setSubmissionURL",
def=function(grapleObject,url)
{
standardGeneric("setSubmissionURL")
}
)
#' Sets the name of the experiment in the Graple object
#' @param grapleObject A Graple Object
#' @param expName A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setExpName(grapleObject, 'SweepExperiment')
#' }
setGeneric(name="setExpName",
def=function(grapleObject,expName)
{
standardGeneric("setExpName")
}
)
#' Set the Experiment root directory in the Graple object
#' @param grapleObject A Graple Object
#' @param path Directory path for the experiment root directory
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setExperimentDir(grapleObject, 'C:/ExpRoot/Exp1')
#' }
setGeneric(name="setExperimentDir",
def=function(grapleObject,path)
{
standardGeneric("setExperimentDir")
}
)
#' Sets the results directory for the experiment in the Graple object
#' @param grapleObject A Graple Object
#' @param path Directory path for the results to be downloaded
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setResultsDir(grapleObject, 'C:/ExpRoot/Results/Exp1')
#' }
setGeneric(name="setResultsDir",
def=function(grapleObject,path)
{
standardGeneric("setResultsDir")
}
)
#' Sets the API key in the grapleObject
#' @param grapleObject A Graple Object
#' @param path Path to the a text file containing the security key
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setAPIKey(grapleObject, 'C:/ExpRoot/KeyFiles/myKey.txt')
#' }
setGeneric(name="setAPIKey",
def=function(grapleObject,path)
{
standardGeneric("setAPIKey")
}
)
#' Checks if the graple service is up and running on the submission URL provided
#' @param grapleObject A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleCheckService(grapleObject)
#' }
setGeneric(name="GrapleCheckService",
def=function(grapleObject)
{
standardGeneric("GrapleCheckService")
}
)
#' Used to run a batch experiment with mutiple simulations in the root directory
#' also, an optional filter can be run on the results generated
#' @param grapleObject A Graple Object
#' @param filterName An optional post-process filter name
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr upload_file POST
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleRunExperiment(grapleObject, 'ExtractVariables')
#' }
setGeneric(name="GrapleRunExperiment",
def=function(grapleObject, filterName)
{
standardGeneric("GrapleRunExperiment")
}
)
#' Checks the status of an experiment
#' @param grapleObject A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleCheckExperimentCompletion(grapleObject)
#' }
setGeneric(name="GrapleCheckExperimentCompletion",
def=function(grapleObject)
{
standardGeneric("GrapleCheckExperimentCompletion")
}
)
#' Downloads the results to the results directory path with exp name/job id as the directory name
#' @param grapleObject A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleGetExperimentResults(grapleObject)
#' }
setGeneric(name="GrapleGetExperimentResults",
def=function(grapleObject)
{
standardGeneric("GrapleGetExperimentResults")
}
)
#' Used to run a sweep experiment with a json file providing job description
#' also, an optional filter can be run on the results generated
#' @param grapleObject A Graple Object
#' @param filterName An optional post-process filter name
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr upload_file POST
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleRunSweepExperiment(grapleObject)
#' GrapleRunSweepExperiment(grapleObject, 'ExtractVariables')
#' }
setGeneric(name="GrapleRunSweepExperiment",
def=function(grapleObject, filterName)
{
standardGeneric("GrapleRunSweepExperiment")
}
)
#' A method to abort an experiment
#' @param grapleObject A Graple Object
#' @return A text message with the status of the operation
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleEndExperiment(grapleObject)
#' }
setGeneric(name="GrapleEndExperiment",
def=function(grapleObject)
{
standardGeneric("GrapleEndExperiment")
}
)
#' Checks if the GRAPLEr pacakge being used is compatible with GWS Service being used
#' @param grapleObject A Graple Object
#' @return A status msg indicating whether Web service and GRAPLEr are compatible
#' and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleChkVersionCompatibility(grapleObject)
#' }
setGeneric(name="GrapleChkVersionCompatibility",
def=function(grapleObject)
{
standardGeneric("GrapleChkVersionCompatibility")
}
)
#' Provides a list of post processing operations/ filters available
#' @param grapleObject A Graple Object
#' @return Adds the list of filters to StatusMsg and returns the Graple object
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleListPostProcessFilters(grapleObject)
#' }
setGeneric(name="GrapleListPostProcessFilters",
def=function(grapleObject)
{
standardGeneric("GrapleListPostProcessFilters")
}
)
#' Set the Temporary Directory to given directory path for the Graple Object
#' @param grapleObject A Graple Object
#' @param path Path to a directory to be set as Temporary directory for the experiment
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setTempDir(grapleExp1, 'C:/TempDir')
#' }
setMethod(f="setTempDir",
signature="Graple",
definition=function(grapleObject,path)
{
if(dir.exists(path)){
grapleObject@TempDir <- path
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- "Temporary directory set to directory provided"
}
else{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Temporary directory provided does not exist"
}
return(grapleObject)
}
)
#' Sets the submission URL in the Graple object
#' @param grapleObject A Graple Object
#' @param url A Submission URL
#' @return The Graple object with updated submissionURL
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setSubmissionURL(grapleExp1, 'https://graple.acis.ufl.edu')
#' }
setMethod(f="setSubmissionURL",
signature="Graple",
definition=function(grapleObject,url)
{
grapleObject@GWSURL <- url
return(grapleObject)
}
)
#' Sets the name of the experiment in the Graple object
#' @param grapleObject A Graple Object
#' @param expName A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setExpName(grapleObject, 'SweepExperiment')
#' }
setMethod(f="setExpName",
signature="Graple",
definition=function(grapleObject,expName)
{
if(length(expName) > 0)
{
grapleObject@ExpName <- expName
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- "Experiment name set to the name provided"
}
else
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Invalid Experiment Name"
}
return(grapleObject)
}
)
#' Set the Experiment root directory in the Graple object
#' @param grapleObject A Graple Object
#' @param path Directory path for the experiment root directory
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setExperimentDir(grapleObject, 'C:/ExpRoot/Exp1')
#' }
setMethod(f="setExperimentDir",
signature="Graple",
definition=function(grapleObject,path)
{
if(length(path) > 0)
{
grapleObject@ExpRootDir <- path
if(!dir.exists(grapleObject@ExpRootDir))
{
grapleObject@ExpRootDir <- character(0)
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory provided does not exist"
}
else if(length(grapleObject@ResultsDir) > 0 && !check_subdirectory(grapleObject))
{
grapleObject@ExpRootDir <- character(0)
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Exp Root Dir/Result directory is a sub-directory of Result/Input"
}
else
{
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- "Experiment root directory has been set to directory provided"
}
}
return(grapleObject)
}
)
#' Sets the results directory for the experiment in the Graple object
#' @param grapleObject A Graple Object
#' @param path Directory path for the results to be downloaded
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setResultsDir(grapleObject, 'C:/ExpRoot/Results/Exp1')
#' }
setMethod(f="setResultsDir",
signature="Graple",
definition=function(grapleObject,path)
{
if(length(path) > 0)
{
grapleObject@ResultsDir <- path
if(!dir.exists(grapleObject@ResultsDir))
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Results directory provided does not exist"
}
else if(length(grapleObject@ExpRootDir) > 0 && !check_subdirectory(grapleObject))
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Exp Root Dir/Result directory is a sub-directory of Result/Input"
}
else
{
grapleObject@ResultsDir <- path
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- "Experiment results directory has been set to directory provided"
}
}
return(grapleObject)
}
)
#' Sets the API key in the grapleObject
#' @param grapleObject A Graple Object
#' @param path Path to the a text file containing the API key
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setAPIKey(grapleExp1, 'C:/ExpRoot/KeyFiles/myKey.txt')
#' }
setMethod(f="setAPIKey",
signature="Graple",
definition=function(grapleObject,path)
{
if(length(path) > 0)
{
if(!file.exists(path))
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "File provided does not exist"
}
else
{
grapleObject@APIKey <- readLines(path)
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- "API Key has been successfully set"
}
}
return(grapleObject)
}
)
#' Checks if the graple service is up and running on the submission URL provided
#' @param grapleObject A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleCheckService(grapleExp1)
#' }
setMethod(f="GrapleCheckService",
signature="Graple",
definition=function(grapleObject)
{
qurl<-paste(grapleObject@GWSURL, "service_status", sep="/")
status<- GET(qurl)
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- paste(content(status)$status,content(status)$time)
return(grapleObject)
}
)
#' Used to run a batch experiment with mutiple simulations in the root directory
#' also, an optional filter can be run on the results generated
#' @param grapleObject A Graple Object
#' @param filterName An optional post-process filter name
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr upload_file POST
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleRunExperiment(grapleExp1, 'ExtractVariables')
#' }
setMethod(f="GrapleRunExperiment",
signature="Graple",
definition=function(grapleObject, filterName)
{
if(length(grapleObject@ExpRootDir)<=0 || !dir.exists(grapleObject@ExpRootDir)){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory provided does not exist"
}
else if(filesPresent(grapleObject)){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory should contain only directories (no files) for this experiment. Check for any files/hidden files there."
}
else if(!missing(filterName) && !dir.exists(paste(grapleObject@ExpRootDir, "FilterParams", sep="/"))){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment Root Directory should consist of FilterParams Directory"
}
else if(!missing(filterName) && dir.exists(paste(grapleObject@ExpRootDir, "FilterParams", sep="/")) && !filePresent(paste(grapleObject@ExpRootDir, "FilterParams", sep = "/"), "FilterParams.json")){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "The Filter Params directory does not contain FilterParams.json"
}
else
{
if(length(grapleObject@TempDir)<=0 || !dir.exists(grapleObject@TempDir)){
grapleObject@TempDir <- tempdir()
}
td<-getwd()
setwd(grapleObject@TempDir)
if(file.exists("sim.tar.gz")) file.remove("sim.tar.gz")
tarfile = file.path(getwd(), "sim.tar.gz")
setwd(grapleObject@ExpRootDir)
tar(tarfile, ".", compression="gz", compression_level = 6, tar="internal")
qurl <- paste(grapleObject@GWSURL, "GrapleRun", sep="/")
if(!missing(filterName))
postresp <- POST(qurl, body = list(retention = grapleObject@Retention, expname = getResultsDirName(grapleObject), email = grapleObject@Email, apikey = grapleObject@APIKey, simsperjob = grapleObject@SimsPerJob, filter = filterName, files = upload_file(tarfile)), encode = "multipart")
else
postresp <- POST(qurl, body = list(retention = grapleObject@Retention, expname = getResultsDirName(grapleObject), email = grapleObject@Email, apikey = grapleObject@APIKey, simsperjob = grapleObject@SimsPerJob, files = upload_file(tarfile)), encode = "multipart")
response <- content(postresp)
grapleObject@JobID <- ''
grapleObject@StatusCode <- -1
if(nchar(response$errors) > 0) {
grapleObject@StatusMsg <- response$errors
} else if(nchar(response$uid) == 40) {
grapleObject@JobID <- toString(response$uid)
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- paste("The simulation was submitted successfully. JobID: ", grapleObject@JobID, sep = '')
} else {
grapleObject@StatusMsg <- "Unknown error"
}
if(nchar(response$warnings) > 0)
grapleObject@StatusMsg <- paste(grapleObject@StatusMsg, "\nWARNING:", response$warnings)
if (file.exists(tarfile)) file.remove(tarfile)
setwd(td)
}
return (grapleObject)
}
)
#' Checks the status of an experiment
#' @param grapleObject A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleCheckExperimentCompletion(grapleExp1)
#' }
setMethod(f="GrapleCheckExperimentCompletion",
signature="Graple",
definition=function(grapleObject)
{
qurl <- paste(grapleObject@GWSURL, "GrapleRunStatus", grapleObject@JobID, sep="/")
grapleObject@StatusCode <- -1
status <- content(GET(qurl, query = list(apikey = grapleObject@APIKey)))
if(nchar(status$errors) > 0)
grapleObject@StatusMsg <- status$errors
else {
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- status$curr_status
}
return (grapleObject)
}
)
#' Downloads the results to the results directory path with exp name/job id as the directory name
#' @param grapleObject A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleGetExperimentResults(grapleExp1)
#' }
setMethod(f="GrapleGetExperimentResults",
signature="Graple",
definition=function(grapleObject)
{
if(length(grapleObject@ResultsDir)<=0 || !dir.exists(grapleObject@ResultsDir))
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Results directory provided does not exist."
}
else if(length(grapleObject@JobID) <= 0)
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "No JobID, Experiment Job ID not provided."
}
else if(getResultsDirName(grapleObject) %in% list.files(grapleObject@ResultsDir))
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- paste("A directory with the same name as ExpName/JobID found in results directory. Please remove it and try again.", sep ="")
}
else{
if(length(grapleObject@TempDir)<=0 || !dir.exists(grapleObject@TempDir)){
grapleObject@TempDir <- tempdir()
}
td<-getwd()
qurl<-paste(grapleObject@GWSURL, "GrapleRunResults", grapleObject@JobID, sep="/")
grapleObject@StatusCode <- -1
getresp <- GET(qurl, query = list(apikey = grapleObject@APIKey))
status <- fromJSON(content(getresp, "text", encoding = "UTF-8"))
if(nchar(status$errors) > 0)
grapleObject@StatusMsg <- status$errors
else if(status$status == "success"){
qurl <- paste(grapleObject@GWSURL, status$output_url, sep="")
resultfile <- file.path(grapleObject@TempDir, "results.tar.gz")
GET(qurl, write_disk(resultfile, overwrite=TRUE))
setwd(grapleObject@TempDir)
resultPath <- paste(grapleObject@ResultsDir, getResultsDirName(grapleObject), sep="/")
dir.create(resultPath)
file.copy("results.tar.gz", resultPath)
file.remove("results.tar.gz")
setwd(resultPath)
untar("results.tar.gz")
file.remove("results.tar.gz")
setwd(td)
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- paste('The results have been downloaded to: ', resultPath, sep ="")
}
}
return(grapleObject)
}
)
#' Used to run a sweep experiment with a json file providing job description
#' also, an optional filter can be run on the results generated
#' @param grapleObject A Graple Object
#' @param filterName An optional post-process filter name
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr upload_file POST
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleRunSweepExperiment(grapleExp1)
#' GrapleRunSweepExperiment(grapleExp1, 'ExtractVariables')
#' }
setMethod(f="GrapleRunSweepExperiment",
signature="Graple",
definition=function(grapleObject, filterName)
{
if(length(grapleObject@ExpRootDir)<=0 || !dir.exists(grapleObject@ExpRootDir)){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory provided does not exist"
}
else if(!filePresent(grapleObject@ExpRootDir, "job_desc.json")){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "A job description file should be present with name job_desc.json in the ExpRootDir"
}
else if(!as.logical(validate_json(paste(grapleObject@ExpRootDir, "job_desc.json", sep="/"))[1])){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Invalid job_desc file"
}
else if(length(list.dirs(path = grapleObject@ExpRootDir, recursive = FALSE)) > 0 && missing(filterName)){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory should not contain any directories for this experiment"
}
else if(length(list.dirs(path = grapleObject@ExpRootDir, recursive = FALSE)) > 1 && !missing(filterName)){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory should contain only files and FilterParams Directory"
}
else if(length(list.dirs(path = grapleObject@ExpRootDir, recursive = FALSE)) == 1 && !missing(filterName) && list.dirs(path = grapleObject@ExpRootDir, recursive = FALSE, full.names = FALSE)[1] != "FilterParams"){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory should contain directory with name FilterParams"
}
else{
if(length(grapleObject@TempDir)<=0 || !dir.exists(grapleObject@TempDir)){
grapleObject@TempDir <- tempdir()
}
td<-getwd()
setwd(grapleObject@TempDir)
if(file.exists("sweepexp.tar.gz")) file.remove("sweepexp.tar.gz")
tarfile = file.path(getwd(), "sweepexp.tar.gz")
setwd(grapleObject@ExpRootDir)
tar(tarfile, ".", compression="gz", compression_level = 6, tar="internal")
distribution_type <- validate_json(paste(grapleObject@ExpRootDir, "job_desc.json", sep="/"))[2]
if(distribution_type == 'non-linear')
qurl <- paste(grapleObject@GWSURL, "GrapleRunMetSample", sep="/")
else
qurl <- paste(grapleObject@GWSURL, "GrapleRunLinearSweep", sep="/")
grapleObject@JobID <- ''
grapleObject@StatusCode <- -1
if(!missing(filterName))
subresp <- POST(qurl, body = list(retention = grapleObject@Retention, expname = getResultsDirName(grapleObject), email = grapleObject@Email, apikey = grapleObject@APIKey, simsperjob = grapleObject@SimsPerJob, filter = filterName, files = upload_file(tarfile)), encode = "multipart")
else
subresp <- POST(qurl, body = list(retention = grapleObject@Retention, expname = getResultsDirName(grapleObject), email = grapleObject@Email, apikey = grapleObject@APIKey, simsperjob = grapleObject@SimsPerJob, files = upload_file(tarfile)), encode = "multipart")
response <- content(subresp)
if(nchar(response$errors) > 0) {
grapleObject@StatusMsg <- response$errors
} else if(nchar(response$uid) == 40) {
grapleObject@JobID <- toString(response$uid)
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- paste("The simulation was submitted successfully. JobID: ", grapleObject@JobID, sep = '')
} else {
grapleObject@StatusMsg <- "Unknown error"
}
if(nchar(response$warnings) > 0)
grapleObject@StatusMsg <- paste(grapleObject@StatusMsg, "\nWARNING:", response$warnings)
if (file.exists(tarfile)) file.remove(tarfile)
setwd(td)
}
return (grapleObject)
}
)
#' A method to abort an experiment
#' @param grapleObject A Graple Object
#' @return A text message with the status of the operation
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleEndExperiment(grapleExp1)
#' }
setMethod(f="GrapleEndExperiment",
signature="Graple",
definition=function(grapleObject)
{
qurl <- paste(grapleObject@GWSURL, "GrapleEnd", grapleObject@JobID, sep="/")
status<- GET(qurl, query = list(apikey = grapleObject@APIKey))
return (fromJSON(content(status, "text")))
}
)
#' Checks if the GRAPLEr pacakge being used is compatible with GWS Service being used
#' @param grapleObject A Graple Object
#' @return A status msg indicating whether Web service and GRAPLEr are compatible
#' and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleChkVersionCompatibility(grapleExp1)
#' }
setMethod(f="GrapleChkVersionCompatibility",
signature="Graple",
definition=function(grapleObject)
{
if(!length(grapleObject@Client_Version_ID) > 0){
grapleObject@Client_Version_ID <- packageVersion("GRAPLEr")
}
qurl <- paste(grapleObject@GWSURL, "GrapleGetVersion", sep="/")
status <- GET(qurl)
compatibleGRAPLEVersions <- fromJSON(content(status, "text"))
if(grapleObject@Client_Version_ID %in% compatibleGRAPLEVersions){
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- 'GRAPLE Web Service and GRAPLEr are compatible.'
}
else{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- paste('GRAPLE Web Service and GRAPLEr are not compatible. Compatible versions are: ', compatibleGRAPLEVersions, sep="")
}
return(grapleObject)
}
)
#' Provides a list of post processing operations/ filters available
#' @param grapleObject A Graple Object
#' @return Adds the list of filters to StatusMsg and returns the Graple object
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleListPostProcessFilters(grapleExp1)
#' }
setMethod(f="GrapleListPostProcessFilters",
signature="Graple",
definition=function(grapleObject)
{
qurl <- paste(grapleObject@GWSURL, "GrapleListFilters", sep="/")
status <- GET(qurl)
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- paste('Available post-process filters: ', toString(fromJSON(content(status, "text"))), sep = "")
return(grapleObject)
}
)
GRAPLE/GRAPLEr documentation built on Oct. 7, 2020, 4:12 p.m.
R Package Documentation
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Defines functions validate_json filePresent filesPresent getResultsDirName check_subdirectory check_graple validate_url .onAttach
Documented in check_graple check_subdirectory filePresent filesPresent getResultsDirName validate_json validate_url
.onAttach <- function(libname, pkgname) {
packageStartupMessage("GRAPLEr has been developed with support from a supplement the PRAGMA award (NSF OCI-1234983) by
Ken Subratie, Saumitra Aditya, Satish Mahesula, Renato J. Figueiredo, Cayelan C. Carey, Paul C. Hanson, and Vahid Daneshmand.
For more information, please visit 'http://graple.org'.")
#' Skip Self-signed SSL Certificate Error
httr::set_config(httr::config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE))
}
#' Validates whether a given url exists
#'
#' @param url Submission URL
#' @return A boolean value indicating whether url exists
#' @export
#' @keywords internal
#' @importFrom httr http_error
#' @examples
#' validate_url('https://graple.acis.ufl.edu')
validate_url <- function(url){
invalid_url = tryCatch({
http_error(url)
}, error = function(e) {
invalid_url <- TRUE
})
return(!invalid_url)
}
#' Checks if the grapleObject is valid
#' by checking if the directories provided exist and valid
#' @param object A Graple Object
#' @return errors if any of the validation fails
#' @export
#' @keywords internal
#' @examples
#' \dontrun{
#' check_graple(grapleExp1)
#' }
check_graple <- function(object) {
errors <- character()
if(length(object@GWSURL) > 0)
{
valid_url <- validate_url(object@GWSURL)
if (!valid_url) {
msg <- paste("Invalid URL")
errors <- c(errors, msg)
}
}
if(length(object@ExpRootDir) > 0)
{
if(!dir.exists(object@ExpRootDir))
{
msg <- paste("Experiment root directory does not exist.")
errors <- c(errors, msg)
}
}
if(length(object@ResultsDir) > 0)
{
if(!dir.exists(object@ResultsDir))
{
msg <- paste("Results directory does not exist.")
errors <- c(errors, msg)
}
}
if(!check_subdirectory(object))
{
msg <- paste("Experiment root directory or result directory are a sub-directory of Result/Input.")
errors <- c(errors, msg)
}
if (length(errors) == 0) TRUE else errors
}
#' Checks if the input/results directory is a sub-directory of
#' results/input directory
#' @param object A Graple Object
#' @return A boolean value indicating whether the directory
#' structure is valid
#' @export
#' @keywords internal
#' @examples
#' \dontrun{
#' check_subdirectory(grapleExp1)
#' }
check_subdirectory <- function(object){
input_dir <- object@ExpRootDir
results_dir <- object@ResultsDir
valid_directories <- FALSE
if(((length(input_dir) > 0 && length(results_dir) > 0) && (length(grep(input_dir,results_dir)) || length(grep(results_dir, input_dir)))>0))
valid_directories <- FALSE
else
valid_directories <- TRUE
return(valid_directories)
}
#' Gets the name for results directory
#' @param object A Graple Object
#' @return ExpName if provided, else the JobID
#' @export
#' @keywords internal
#' @examples
#' \dontrun{
#' getResultsDirName(grapleExp1)
#' }
getResultsDirName <- function(object){
if(length(object@ExpName) > 0)
return(object@ExpName)
else if(length(object@JobID) > 0)
return(object@JobID)
else
return('')
}
#' Checks if there are any files present in ExpRoot Directory
#' @param object A Graple Object
#' @return A boolean value indicating whether files are present or not
#' @export
#' @keywords internal
#' @examples
#' \dontrun{
#' filesPresent(grapleExp1)
#' }
filesPresent <- function(object){
if(length(list.files(path = object@ExpRootDir, recursive = FALSE, all.files = TRUE)) - 2 != length(list.dirs(path = object@ExpRootDir, recursive = FALSE))) # all.files = TRUE for Checking Hidden Files, -2 for Excluding . and ..
return(TRUE)
else
return(FALSE)
}
#' checks if a given file exists in a directory
#' @param dirPath A Directory path
#' @param fileName File name
#' @return A boolean value indicating whether a file is present or not
#' @export
#' @keywords internal
#' @examples
#' filePresent('C:/ExpRoot/Exp1/mySim', 'met_hourly.csv')
filePresent <- function(dirPath, fileName){
filesList <- list.files(path = dirPath, recursive = FALSE)
if(fileName %in% filesList)
return(TRUE)
else
return(FALSE)
}
#' Checks if a json file is valid according to GRAPLEr constraints
#' @param jsonFilePath JSON File path
#' @return A boolean value indicating whether the json file is valid
#' @export
#' @keywords internal
#' @importFrom jsonlite fromJSON
#' @examples
#' \dontrun{
#' validate_json('C:/ExpRoot/Exp3/job_desc.json')
#' }
validate_json <- function(jsonFilePath)
{
valid_JSON <- TRUE
distribution_type <- ''
distribution_types <- list('uniform', 'binomial', 'normal', 'poisson')
jsonFile <- fromJSON(jsonFilePath, simplifyVector = FALSE)
num_iterations <- jsonFile$num_iterations
if(is.null(num_iterations))
distribution_type <- 'linear'
else
distribution_type <- 'non-linear'
if(is.null(jsonFile$ExpFiles))
return(list(valid_JSON, distribution_type))
if(distribution_type == 'linear') {
steps = 1
for (expFile in 1:length(jsonFile$ExpFiles)) {
for (vb in 1:length(jsonFile$ExpFiles[[expFile]]$variables[[1]])) {
distribution = jsonFile$ExpFiles[[expFile]]$variables[[1]][[vb]]$distribution
if(is.null(distribution) || distribution != 'linear'){
valid_JSON <- FALSE
break
}
else if (distribution == 'linear'){
var_steps = jsonFile$ExpFiles[[expFile]]$variables[[1]][[vb]]$steps
if(is.null(steps)){
valid_JSON <- FALSE
break
}
else{
steps = steps * (var_steps + 1)
}
}
}
}
if(steps >= 100000)
valid_JSON <- FALSE
}
else if(distribution_type == 'non-linear'){
for (expFile in 1:length(jsonFile$ExpFiles)) {
for (vb in 1:length(jsonFile$ExpFiles[[expFile]]$variables[[1]])) {
distribution = jsonFile$ExpFiles[[expFile]]$variables[[1]][[vb]]$distribution
if(is.null(distribution) || !(distribution %in% distribution_types)){
valid_JSON <- FALSE
break
}
}
}
}
else
{
valid_JSON <- FALSE
}
return(list(valid_JSON, distribution_type))
}
#' An S4 class to represent a graple object.
#'
#' @slot GWSURL A SubmissionURL for the experiment having a default value of https://graple.acis.ufl.edu
#' @slot ExpRootDir Experiment Root Directory path
#' @slot ResultsDir Directory path for storing the results
#' @slot JobID Unique identifier for the experiment
#' @slot Email Email address to send notifications
#' @slot APIKey API Key to authenticate a user
#' @slot SimsPerJob A number indicating the number of simulations bundled into a worker job
#' @slot StatusCode Integer value indicating the status of an operation
#' @slot StatusMsg A brief text message indicating the status of an operation
#' @slot ExpName A name for the experiment
#' @slot TempDir Temporary Directory path for temporary storage of files
#' @slot Retention A user provided request to the GRAPLEr cluster on duration for which experiment results should be retained
#' @slot Client_Version_ID The version of GRAPLEr package being used
#' @importFrom methods new
#' @exportClass Graple
Graple <- setClass("Graple", slots = c(GWSURL = "character", ExpRootDir="character", ResultsDir="character", JobID="character", Email="character",
APIKey="character", SimsPerJob="numeric", StatusCode="numeric", StatusMsg="character", ExpName="character", TempDir="character",
Retention ="numeric", Client_Version_ID="character"), prototype = list(GWSURL="https://graple.acis.ufl.edu", Email='', APIKey="0",
SimsPerJob=5, TempDir=tempdir(), Retention = 10, Client_Version_ID = toString(packageVersion("GRAPLEr"))), validity = check_graple)
#' Set the Temporary Directory to given directory path for the Graple Object
#' @param grapleObject A Graple Object
#' @param path Path to a directory to be set as Temporary directory for the experiment
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setTempDir(grapleObject, 'C:/TempDir')
#' }
setGeneric(name="setTempDir",
def=function(grapleObject,path)
{
standardGeneric("setTempDir")
}
)
#' Sets the submission URL in the Graple object
#' @param grapleObject A Graple Object
#' @param url A Submission URL
#' @return The Graple object with updated submissionURL
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setSubmissionURL(grapleObject, 'https://graple.acis.ufl.edu')
#' }
setGeneric(name="setSubmissionURL",
def=function(grapleObject,url)
{
standardGeneric("setSubmissionURL")
}
)
#' Sets the name of the experiment in the Graple object
#' @param grapleObject A Graple Object
#' @param expName A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setExpName(grapleObject, 'SweepExperiment')
#' }
setGeneric(name="setExpName",
def=function(grapleObject,expName)
{
standardGeneric("setExpName")
}
)
#' Set the Experiment root directory in the Graple object
#' @param grapleObject A Graple Object
#' @param path Directory path for the experiment root directory
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setExperimentDir(grapleObject, 'C:/ExpRoot/Exp1')
#' }
setGeneric(name="setExperimentDir",
def=function(grapleObject,path)
{
standardGeneric("setExperimentDir")
}
)
#' Sets the results directory for the experiment in the Graple object
#' @param grapleObject A Graple Object
#' @param path Directory path for the results to be downloaded
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setResultsDir(grapleObject, 'C:/ExpRoot/Results/Exp1')
#' }
setGeneric(name="setResultsDir",
def=function(grapleObject,path)
{
standardGeneric("setResultsDir")
}
)
#' Sets the API key in the grapleObject
#' @param grapleObject A Graple Object
#' @param path Path to the a text file containing the security key
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setAPIKey(grapleObject, 'C:/ExpRoot/KeyFiles/myKey.txt')
#' }
setGeneric(name="setAPIKey",
def=function(grapleObject,path)
{
standardGeneric("setAPIKey")
}
)
#' Checks if the graple service is up and running on the submission URL provided
#' @param grapleObject A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleCheckService(grapleObject)
#' }
setGeneric(name="GrapleCheckService",
def=function(grapleObject)
{
standardGeneric("GrapleCheckService")
}
)
#' Used to run a batch experiment with mutiple simulations in the root directory
#' also, an optional filter can be run on the results generated
#' @param grapleObject A Graple Object
#' @param filterName An optional post-process filter name
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr upload_file POST
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleRunExperiment(grapleObject, 'ExtractVariables')
#' }
setGeneric(name="GrapleRunExperiment",
def=function(grapleObject, filterName)
{
standardGeneric("GrapleRunExperiment")
}
)
#' Checks the status of an experiment
#' @param grapleObject A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleCheckExperimentCompletion(grapleObject)
#' }
setGeneric(name="GrapleCheckExperimentCompletion",
def=function(grapleObject)
{
standardGeneric("GrapleCheckExperimentCompletion")
}
)
#' Downloads the results to the results directory path with exp name/job id as the directory name
#' @param grapleObject A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleGetExperimentResults(grapleObject)
#' }
setGeneric(name="GrapleGetExperimentResults",
def=function(grapleObject)
{
standardGeneric("GrapleGetExperimentResults")
}
)
#' Used to run a sweep experiment with a json file providing job description
#' also, an optional filter can be run on the results generated
#' @param grapleObject A Graple Object
#' @param filterName An optional post-process filter name
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr upload_file POST
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleRunSweepExperiment(grapleObject)
#' GrapleRunSweepExperiment(grapleObject, 'ExtractVariables')
#' }
setGeneric(name="GrapleRunSweepExperiment",
def=function(grapleObject, filterName)
{
standardGeneric("GrapleRunSweepExperiment")
}
)
#' A method to abort an experiment
#' @param grapleObject A Graple Object
#' @return A text message with the status of the operation
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleEndExperiment(grapleObject)
#' }
setGeneric(name="GrapleEndExperiment",
def=function(grapleObject)
{
standardGeneric("GrapleEndExperiment")
}
)
#' Checks if the GRAPLEr pacakge being used is compatible with GWS Service being used
#' @param grapleObject A Graple Object
#' @return A status msg indicating whether Web service and GRAPLEr are compatible
#' and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleChkVersionCompatibility(grapleObject)
#' }
setGeneric(name="GrapleChkVersionCompatibility",
def=function(grapleObject)
{
standardGeneric("GrapleChkVersionCompatibility")
}
)
#' Provides a list of post processing operations/ filters available
#' @param grapleObject A Graple Object
#' @return Adds the list of filters to StatusMsg and returns the Graple object
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleListPostProcessFilters(grapleObject)
#' }
setGeneric(name="GrapleListPostProcessFilters",
def=function(grapleObject)
{
standardGeneric("GrapleListPostProcessFilters")
}
)
#' Set the Temporary Directory to given directory path for the Graple Object
#' @param grapleObject A Graple Object
#' @param path Path to a directory to be set as Temporary directory for the experiment
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setTempDir(grapleExp1, 'C:/TempDir')
#' }
setMethod(f="setTempDir",
signature="Graple",
definition=function(grapleObject,path)
{
if(dir.exists(path)){
grapleObject@TempDir <- path
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- "Temporary directory set to directory provided"
}
else{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Temporary directory provided does not exist"
}
return(grapleObject)
}
)
#' Sets the submission URL in the Graple object
#' @param grapleObject A Graple Object
#' @param url A Submission URL
#' @return The Graple object with updated submissionURL
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setSubmissionURL(grapleExp1, 'https://graple.acis.ufl.edu')
#' }
setMethod(f="setSubmissionURL",
signature="Graple",
definition=function(grapleObject,url)
{
grapleObject@GWSURL <- url
return(grapleObject)
}
)
#' Sets the name of the experiment in the Graple object
#' @param grapleObject A Graple Object
#' @param expName A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setExpName(grapleObject, 'SweepExperiment')
#' }
setMethod(f="setExpName",
signature="Graple",
definition=function(grapleObject,expName)
{
if(length(expName) > 0)
{
grapleObject@ExpName <- expName
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- "Experiment name set to the name provided"
}
else
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Invalid Experiment Name"
}
return(grapleObject)
}
)
#' Set the Experiment root directory in the Graple object
#' @param grapleObject A Graple Object
#' @param path Directory path for the experiment root directory
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setExperimentDir(grapleObject, 'C:/ExpRoot/Exp1')
#' }
setMethod(f="setExperimentDir",
signature="Graple",
definition=function(grapleObject,path)
{
if(length(path) > 0)
{
grapleObject@ExpRootDir <- path
if(!dir.exists(grapleObject@ExpRootDir))
{
grapleObject@ExpRootDir <- character(0)
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory provided does not exist"
}
else if(length(grapleObject@ResultsDir) > 0 && !check_subdirectory(grapleObject))
{
grapleObject@ExpRootDir <- character(0)
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Exp Root Dir/Result directory is a sub-directory of Result/Input"
}
else
{
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- "Experiment root directory has been set to directory provided"
}
}
return(grapleObject)
}
)
#' Sets the results directory for the experiment in the Graple object
#' @param grapleObject A Graple Object
#' @param path Directory path for the results to be downloaded
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setResultsDir(grapleObject, 'C:/ExpRoot/Results/Exp1')
#' }
setMethod(f="setResultsDir",
signature="Graple",
definition=function(grapleObject,path)
{
if(length(path) > 0)
{
grapleObject@ResultsDir <- path
if(!dir.exists(grapleObject@ResultsDir))
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Results directory provided does not exist"
}
else if(length(grapleObject@ExpRootDir) > 0 && !check_subdirectory(grapleObject))
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Exp Root Dir/Result directory is a sub-directory of Result/Input"
}
else
{
grapleObject@ResultsDir <- path
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- "Experiment results directory has been set to directory provided"
}
}
return(grapleObject)
}
)
#' Sets the API key in the grapleObject
#' @param grapleObject A Graple Object
#' @param path Path to the a text file containing the API key
#' @return The status message is updated on Graple object and the Graple object is returned
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' setAPIKey(grapleExp1, 'C:/ExpRoot/KeyFiles/myKey.txt')
#' }
setMethod(f="setAPIKey",
signature="Graple",
definition=function(grapleObject,path)
{
if(length(path) > 0)
{
if(!file.exists(path))
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "File provided does not exist"
}
else
{
grapleObject@APIKey <- readLines(path)
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- "API Key has been successfully set"
}
}
return(grapleObject)
}
)
#' Checks if the graple service is up and running on the submission URL provided
#' @param grapleObject A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleCheckService(grapleExp1)
#' }
setMethod(f="GrapleCheckService",
signature="Graple",
definition=function(grapleObject)
{
qurl<-paste(grapleObject@GWSURL, "service_status", sep="/")
status<- GET(qurl)
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- paste(content(status)$status,content(status)$time)
return(grapleObject)
}
)
#' Used to run a batch experiment with mutiple simulations in the root directory
#' also, an optional filter can be run on the results generated
#' @param grapleObject A Graple Object
#' @param filterName An optional post-process filter name
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr upload_file POST
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleRunExperiment(grapleExp1, 'ExtractVariables')
#' }
setMethod(f="GrapleRunExperiment",
signature="Graple",
definition=function(grapleObject, filterName)
{
if(length(grapleObject@ExpRootDir)<=0 || !dir.exists(grapleObject@ExpRootDir)){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory provided does not exist"
}
else if(filesPresent(grapleObject)){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory should contain only directories (no files) for this experiment. Check for any files/hidden files there."
}
else if(!missing(filterName) && !dir.exists(paste(grapleObject@ExpRootDir, "FilterParams", sep="/"))){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment Root Directory should consist of FilterParams Directory"
}
else if(!missing(filterName) && dir.exists(paste(grapleObject@ExpRootDir, "FilterParams", sep="/")) && !filePresent(paste(grapleObject@ExpRootDir, "FilterParams", sep = "/"), "FilterParams.json")){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "The Filter Params directory does not contain FilterParams.json"
}
else
{
if(length(grapleObject@TempDir)<=0 || !dir.exists(grapleObject@TempDir)){
grapleObject@TempDir <- tempdir()
}
td<-getwd()
setwd(grapleObject@TempDir)
if(file.exists("sim.tar.gz")) file.remove("sim.tar.gz")
tarfile = file.path(getwd(), "sim.tar.gz")
setwd(grapleObject@ExpRootDir)
tar(tarfile, ".", compression="gz", compression_level = 6, tar="internal")
qurl <- paste(grapleObject@GWSURL, "GrapleRun", sep="/")
if(!missing(filterName))
postresp <- POST(qurl, body = list(retention = grapleObject@Retention, expname = getResultsDirName(grapleObject), email = grapleObject@Email, apikey = grapleObject@APIKey, simsperjob = grapleObject@SimsPerJob, filter = filterName, files = upload_file(tarfile)), encode = "multipart")
else
postresp <- POST(qurl, body = list(retention = grapleObject@Retention, expname = getResultsDirName(grapleObject), email = grapleObject@Email, apikey = grapleObject@APIKey, simsperjob = grapleObject@SimsPerJob, files = upload_file(tarfile)), encode = "multipart")
response <- content(postresp)
grapleObject@JobID <- ''
grapleObject@StatusCode <- -1
if(nchar(response$errors) > 0) {
grapleObject@StatusMsg <- response$errors
} else if(nchar(response$uid) == 40) {
grapleObject@JobID <- toString(response$uid)
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- paste("The simulation was submitted successfully. JobID: ", grapleObject@JobID, sep = '')
} else {
grapleObject@StatusMsg <- "Unknown error"
}
if(nchar(response$warnings) > 0)
grapleObject@StatusMsg <- paste(grapleObject@StatusMsg, "\nWARNING:", response$warnings)
if (file.exists(tarfile)) file.remove(tarfile)
setwd(td)
}
return (grapleObject)
}
)
#' Checks the status of an experiment
#' @param grapleObject A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleCheckExperimentCompletion(grapleExp1)
#' }
setMethod(f="GrapleCheckExperimentCompletion",
signature="Graple",
definition=function(grapleObject)
{
qurl <- paste(grapleObject@GWSURL, "GrapleRunStatus", grapleObject@JobID, sep="/")
grapleObject@StatusCode <- -1
status <- content(GET(qurl, query = list(apikey = grapleObject@APIKey)))
if(nchar(status$errors) > 0)
grapleObject@StatusMsg <- status$errors
else {
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- status$curr_status
}
return (grapleObject)
}
)
#' Downloads the results to the results directory path with exp name/job id as the directory name
#' @param grapleObject A Graple Object
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleGetExperimentResults(grapleExp1)
#' }
setMethod(f="GrapleGetExperimentResults",
signature="Graple",
definition=function(grapleObject)
{
if(length(grapleObject@ResultsDir)<=0 || !dir.exists(grapleObject@ResultsDir))
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Results directory provided does not exist."
}
else if(length(grapleObject@JobID) <= 0)
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "No JobID, Experiment Job ID not provided."
}
else if(getResultsDirName(grapleObject) %in% list.files(grapleObject@ResultsDir))
{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- paste("A directory with the same name as ExpName/JobID found in results directory. Please remove it and try again.", sep ="")
}
else{
if(length(grapleObject@TempDir)<=0 || !dir.exists(grapleObject@TempDir)){
grapleObject@TempDir <- tempdir()
}
td<-getwd()
qurl<-paste(grapleObject@GWSURL, "GrapleRunResults", grapleObject@JobID, sep="/")
grapleObject@StatusCode <- -1
getresp <- GET(qurl, query = list(apikey = grapleObject@APIKey))
status <- fromJSON(content(getresp, "text", encoding = "UTF-8"))
if(nchar(status$errors) > 0)
grapleObject@StatusMsg <- status$errors
else if(status$status == "success"){
qurl <- paste(grapleObject@GWSURL, status$output_url, sep="")
resultfile <- file.path(grapleObject@TempDir, "results.tar.gz")
GET(qurl, write_disk(resultfile, overwrite=TRUE))
setwd(grapleObject@TempDir)
resultPath <- paste(grapleObject@ResultsDir, getResultsDirName(grapleObject), sep="/")
dir.create(resultPath)
file.copy("results.tar.gz", resultPath)
file.remove("results.tar.gz")
setwd(resultPath)
untar("results.tar.gz")
file.remove("results.tar.gz")
setwd(td)
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- paste('The results have been downloaded to: ', resultPath, sep ="")
}
}
return(grapleObject)
}
)
#' Used to run a sweep experiment with a json file providing job description
#' also, an optional filter can be run on the results generated
#' @param grapleObject A Graple Object
#' @param filterName An optional post-process filter name
#' @return The status message is updated on Graple object and the Graple object is returned
#' @importFrom httr upload_file POST
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleRunSweepExperiment(grapleExp1)
#' GrapleRunSweepExperiment(grapleExp1, 'ExtractVariables')
#' }
setMethod(f="GrapleRunSweepExperiment",
signature="Graple",
definition=function(grapleObject, filterName)
{
if(length(grapleObject@ExpRootDir)<=0 || !dir.exists(grapleObject@ExpRootDir)){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory provided does not exist"
}
else if(!filePresent(grapleObject@ExpRootDir, "job_desc.json")){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "A job description file should be present with name job_desc.json in the ExpRootDir"
}
else if(!as.logical(validate_json(paste(grapleObject@ExpRootDir, "job_desc.json", sep="/"))[1])){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Invalid job_desc file"
}
else if(length(list.dirs(path = grapleObject@ExpRootDir, recursive = FALSE)) > 0 && missing(filterName)){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory should not contain any directories for this experiment"
}
else if(length(list.dirs(path = grapleObject@ExpRootDir, recursive = FALSE)) > 1 && !missing(filterName)){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory should contain only files and FilterParams Directory"
}
else if(length(list.dirs(path = grapleObject@ExpRootDir, recursive = FALSE)) == 1 && !missing(filterName) && list.dirs(path = grapleObject@ExpRootDir, recursive = FALSE, full.names = FALSE)[1] != "FilterParams"){
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- "Experiment root directory should contain directory with name FilterParams"
}
else{
if(length(grapleObject@TempDir)<=0 || !dir.exists(grapleObject@TempDir)){
grapleObject@TempDir <- tempdir()
}
td<-getwd()
setwd(grapleObject@TempDir)
if(file.exists("sweepexp.tar.gz")) file.remove("sweepexp.tar.gz")
tarfile = file.path(getwd(), "sweepexp.tar.gz")
setwd(grapleObject@ExpRootDir)
tar(tarfile, ".", compression="gz", compression_level = 6, tar="internal")
distribution_type <- validate_json(paste(grapleObject@ExpRootDir, "job_desc.json", sep="/"))[2]
if(distribution_type == 'non-linear')
qurl <- paste(grapleObject@GWSURL, "GrapleRunMetSample", sep="/")
else
qurl <- paste(grapleObject@GWSURL, "GrapleRunLinearSweep", sep="/")
grapleObject@JobID <- ''
grapleObject@StatusCode <- -1
if(!missing(filterName))
subresp <- POST(qurl, body = list(retention = grapleObject@Retention, expname = getResultsDirName(grapleObject), email = grapleObject@Email, apikey = grapleObject@APIKey, simsperjob = grapleObject@SimsPerJob, filter = filterName, files = upload_file(tarfile)), encode = "multipart")
else
subresp <- POST(qurl, body = list(retention = grapleObject@Retention, expname = getResultsDirName(grapleObject), email = grapleObject@Email, apikey = grapleObject@APIKey, simsperjob = grapleObject@SimsPerJob, files = upload_file(tarfile)), encode = "multipart")
response <- content(subresp)
if(nchar(response$errors) > 0) {
grapleObject@StatusMsg <- response$errors
} else if(nchar(response$uid) == 40) {
grapleObject@JobID <- toString(response$uid)
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- paste("The simulation was submitted successfully. JobID: ", grapleObject@JobID, sep = '')
} else {
grapleObject@StatusMsg <- "Unknown error"
}
if(nchar(response$warnings) > 0)
grapleObject@StatusMsg <- paste(grapleObject@StatusMsg, "\nWARNING:", response$warnings)
if (file.exists(tarfile)) file.remove(tarfile)
setwd(td)
}
return (grapleObject)
}
)
#' A method to abort an experiment
#' @param grapleObject A Graple Object
#' @return A text message with the status of the operation
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleEndExperiment(grapleExp1)
#' }
setMethod(f="GrapleEndExperiment",
signature="Graple",
definition=function(grapleObject)
{
qurl <- paste(grapleObject@GWSURL, "GrapleEnd", grapleObject@JobID, sep="/")
status<- GET(qurl, query = list(apikey = grapleObject@APIKey))
return (fromJSON(content(status, "text")))
}
)
#' Checks if the GRAPLEr pacakge being used is compatible with GWS Service being used
#' @param grapleObject A Graple Object
#' @return A status msg indicating whether Web service and GRAPLEr are compatible
#' and the Graple object is returned
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleChkVersionCompatibility(grapleExp1)
#' }
setMethod(f="GrapleChkVersionCompatibility",
signature="Graple",
definition=function(grapleObject)
{
if(!length(grapleObject@Client_Version_ID) > 0){
grapleObject@Client_Version_ID <- packageVersion("GRAPLEr")
}
qurl <- paste(grapleObject@GWSURL, "GrapleGetVersion", sep="/")
status <- GET(qurl)
compatibleGRAPLEVersions <- fromJSON(content(status, "text"))
if(grapleObject@Client_Version_ID %in% compatibleGRAPLEVersions){
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- 'GRAPLE Web Service and GRAPLEr are compatible.'
}
else{
grapleObject@StatusCode <- -1
grapleObject@StatusMsg <- paste('GRAPLE Web Service and GRAPLEr are not compatible. Compatible versions are: ', compatibleGRAPLEVersions, sep="")
}
return(grapleObject)
}
)
#' Provides a list of post processing operations/ filters available
#' @param grapleObject A Graple Object
#' @return Adds the list of filters to StatusMsg and returns the Graple object
#' @importFrom httr GET
#' @export
#' @examples
#' \dontrun{
#' grapleObject <- Graple(ExpRootDir="C:/InputDirectory", ResultsDir="C:/ResultsDirectory", TempDir = tempdir())
#' GrapleListPostProcessFilters(grapleExp1)
#' }
setMethod(f="GrapleListPostProcessFilters",
signature="Graple",
definition=function(grapleObject)
{
qurl <- paste(grapleObject@GWSURL, "GrapleListFilters", sep="/")
status <- GET(qurl)
grapleObject@StatusCode <- 1
grapleObject@StatusMsg <- paste('Available post-process filters: ', toString(fromJSON(content(status, "text"))), sep = "")
return(grapleObject)
}
)
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