Updates towards v1 release

DESCRIPTION

@@ -1,19 +1,21 @@
-Package: GrapleR
-Title: Graple Webservice Interface for R
-Version: 15.6.0.8
+Package: GRAPLEr
+Title: Distributed computing made easy for lake ecology modeling
+Version: 1.0.0
 Authors@R: c(person("Ken", "S", role = c("aut", "cre"),
   	     email = "[email protected]"),
 	      person("Renato", "F", role = "cph"),
 	      person("Saumitra", "A", role = "ctb",
-		     email = "[email protected]"))
-Description: What the package does (one paragraph)
+		     email = "[email protected]"))
+Description: GRAPLEr brings the power of distributing computing to the fingertips of lake ecology modelers. It is an R Package for connecting to the GRAPLE Web Service (GWS) and running GRAPLE jobs. Experiments consisting  of thousands of simulations can be evaluated in a fraction of the time by submitting batches of GLM (General Lake Model) simulations to a distributed computing system, directly from your R/RStudio environment.
 Depends:
     R (>= 3.1.3)
 Imports:
+	bitops,
     ncdf,
     RCurl,
-    glmtools
+    GLMr,
+    glmtools,
 License: GPL-3
-URL: https://github.com/Graple/grapler
+URL: http://graple.github.io/
 LazyData: true
 RoxygenNote: 5.0.1

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(GrapleAbortExperiment)
 export(GrapleCheckExperimentCompletion)
 export(GrapleCheckService)
 export(GrapleGetExperimentJobResults)

R/GrapleR.R

@@ -1,12 +1,12 @@
 
 .onAttach <- function(libname, pkgname) {
-  packageStartupMessage("This information is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science.")
+  packageStartupMessage("GRAPLEr has been developed with support from a supplement the the PRAGMA award (NSF OCI-1234983). For more information, please visit graple.org")
 }
 
-#' @title Get the Graple Service Status
+#' @title Get the GRAPLEr Service Status
 #' @description
-#' This function allows you to check the staus of the GrapeR service.
-#' @param submissionURL URL:Port of the GrapeR service
+#' This function allows you to check the staus of the GRAPLEr web service.
+#' @param submissionURL URL:Port of the GRAPLEr web service
 #' @return a string describing service status
 #' @keywords Graple ServiceStatus
 #' @export
@@ -21,17 +21,17 @@ GrapleCheckService<-function(submissionURL)
   return(fromJSON(status))
 }
 
-#' @title Sends the experiment (multiple simulations) to be run on GrapleR
+#' @title Sends the experiment (multiple simulations) to be run on GWS
 #' This function allows you to run graple with an optional post-process filtering of results
-#' @param submissionURL URL:Port of the GrapleR service
+#' @param submissionURL URL:Port of the GRAPLEr web service
 #' @param ExperimentDir the experiment root folder
 #' @param FilterName the name of the post-processing filter script
 #' @keywords Graple RunExperiment
 #' @export
 #' @examples
 #' \dontrun{
-#' graplerURL<-"http://128.227.150.20:80"
-#' expRootDir<-"./Workspace/SimRoot"
+#' graplerURL<-"http://graple-service.cloudapp.net"
+#' expRootDir<-"./Workspace/ExpRoot"
 #' filterName<-"Filter1.R"
 #' GrapleRunExperiment(graplerURL, expRootDir, filterName)
 #' }
@@ -57,18 +57,18 @@ GrapleRunExperiment<-function(submissionURL, ExperimentDir, FilterName)
   return (substr(expid[1], start=13, stop=52))
 }
 
-#' @title Check the Graple Experiment Status
+#' @title Check the GRAPLEr Experiment Status
 #' @description
-#' This function allows you to check the staus of the GrapleR service.
-#' @param submissionURL URL:Port of the GrapleR service
+#' This function allows you to check the staus of the GRAPLEr web service.
+#' @param submissionURL URL:Port of the GRAPLEr web service
 #' @param experimentId Experiment ID returned from GrapleRunExperiment
 #' or GrapleRunExperimentSweep
 #' @return a string describing experiment status
 #' @keywords Graple CheckExperimentCompletion
 #' @export
 #' @examples
 #' \dontrun{
-#' graplerURL<-"http://128.227.150.20:80"
+#' graplerURL<-"http://graple-service.cloudapp.net"
 #' expId<-"7YWMJYAYAR7Y3TNTAKC5801KMN7JHQW8NYBDMKUR"
 #' GrapleCheckExperimentCompletion(graplerURL, expId)
 #' }
@@ -79,24 +79,25 @@ GrapleCheckExperimentCompletion <- function(submissionURL, experimentId)
   return (fromJSON(status))
 }
 
-#' @title Gets the Graple Experiment Results
+#' @title Gets the GRAPLEr Experiment Results
 #' @description
 #' This function allows you to retrieve the complete results
 #' of an experiment.
-#' @param submissionURL URL:Port of the GrapleR service
+#' @param submissionURL URL:Port of the GRAPLEr web service
 #' @param experimentId Experiment ID returned from GrapleRunExperiment
 #' or GrapleRunExperimentSweep
 #' @return a string describing the fully qualified result file name
 #' @keywords Graple GetExperimentResults
 #' @export
 #' @examples
 #' \dontrun{
-#' graplerURL<-"http://128.227.150.20:80"
+#' graplerURL<-"http://graple-service.cloudapp.net"
 #' expId<-"7YWMJYAYAR7Y3TNTAKC5801KMN7JHQW8NYBDMKUR"
 #' GrapleGetExperimentResults(graplerURL, expId)
 #' }
 GrapleGetExperimentResults <- function(submissionURL, experimentId)
 {
+  td<-getwd()
   qurl <- paste(submissionURL, "GrapleRunResults", experimentId, sep="/")
   status<- getURL(qurl)
 
@@ -111,14 +112,15 @@ GrapleGetExperimentResults <- function(submissionURL, experimentId)
   file.remove("results.tar.gz")
   files <- list.files(".")
   lapply(files, function(x){untar(x); file.remove(x)})
+  setwd(td)
   return(resultfile)
 }
 
 #' @title Creates an experiment based on sweep parameters
 #' @description
 #' This function allows you to run an experiment using a single simulation.
 #' The sweep parameters are used to generate the other sims.
-#' @param submissionURL URL:Port of the GrapeR service
+#' @param submissionURL URL:Port of the GRAPLEr web service
 #' @param simDir the simulation folder containing the driver file
 #' @param driverFileName the driver file name
 #' @param parameterName the column name from the driver file to be swept
@@ -131,7 +133,7 @@ GrapleGetExperimentResults <- function(submissionURL, experimentId)
 #' @export
 #' @examples
 #' \dontrun{
-#' simDir="C:/Workspace/SimRoot/Sim0"
+#' simDir="./Workspace/ExpRoot/Exp0"
 #' driverFileName="met_hourly.csv"
 #' parameterName="AirTemp"
 #' startValue=-2
@@ -188,15 +190,15 @@ GrapleRunExperimentSweep <- function(submissionURL, simDir, driverFileName, para
 #' Parametername1, add, uniform, -1, 1
 #' Paramtername2, sub, binomial, 10, 0.5
 
-#' @param submissionURL URL:Port of the GrapleR service
+#' @param submissionURL URL:Port of the GRAPLEr web service
 #' @param simDir the simulation folder containing the driver file
 #' @param FilterName the name of post-process filter
 #' @return the experiment ID
 #' @keywords Graple RunExperimentJob
 #' @export
 #' @examples
 #' \dontrun{
-#' simDir="C:/Workspace/SimRoot"
+#' simDir="./Workspace/ExpRoot/Exp0"
 #' FilterName="Filter1.R"
 #' expId<-GrapleRunExperimentJob(graplerURL, simDir, FilterName)
 #' }
@@ -219,30 +221,33 @@ GrapleRunExperimentJob <- function(submissionURL, simDir, FilterName)
   status <- postForm(qurl, files=fileUpload(tarfile))
   if (file.exists(tarfile)) file.remove(tarfile)
   unlink("../tempGRAPLE", recursive = TRUE)
+
   print(fromJSON(status))
-  expid <- substr(status[1], start=57, stop=96)
-  setwd(td)
+
+  pid <- substr(status[1], start=57, stop=96)
+setwd(td)
   return (expid)
 }
 
-#' @title Gets the Graple Experiment Job Results
+#' @title Gets the GRAPLEr Experiment Job Results
 #' @description
 #' This function allows you to retrieve the complete results
 #' of an sweep job style experiment.
-#' @param submissionURL URL:Port of the GrapeR service
+#' @param submissionURL URL:Port of the GRAPLEr web service
 #' @param experimentId Experiment ID returned from GrapleRunExperiment
 #' or GrapleRunExperimentSweep
 #' @return a string describing the fully qualified result file name
 #' @keywords Graple GetExperimentJobResults
 #' @export
 #' @examples
 #' \dontrun{
-#' graplerURL<-"http://128.227.150.20:80"
+#' graplerURL<-"http://graple-service.cloudapp.net"
 #' expId<-"7YWMJYAYAR7Y3TNTAKC5801KMN7JHQW8NYBDMKUR"
 #' GrapleGetExperimentJobResults(graplerURL, expId)
 #' }
 GrapleGetExperimentJobResults <- function(submissionURL, experimentId)
 {
+  td<-getwd()
   qurl <- paste(submissionURL, "GrapleRunResultsMetSample", experimentId, sep="/")
   status<- getURL(qurl)
 
@@ -257,5 +262,29 @@ GrapleGetExperimentJobResults <- function(submissionURL, experimentId)
   file.remove("results.tar.gz")
   files <- list.files(".", pattern = "\\.bz2\\.tar$")
   lapply(files, function(x){untar(x); file.remove(x)})
+  setwd(td)
   return(resultfile)
 }
+
+#' @title Aborts an existing GRAPLE experiment
+#' @description
+#' This function allows you to terminate a previously submitted experiment using
+#' its experiment identifier. This is useful for aborting stalled or failed experiments.
+#' @param submissionURL URL:Port of the GRAPLEr web service
+#' @param experimentId Experiment ID returned from GrapleRunExperiment
+#' or GrapleRunExperimentSweep
+#' @return a status string
+#' @keywords Graple AbortExperiment
+#' @export
+#' @examples
+#' \dontrun{
+#' graplerURL<-"http://graple-service.cloudapp.net"
+#' expId<-"7YWMJYAYAR7Y3TNTAKC5801KMN7JHQW8NYBDMKUR"
+#' GrapleAbortExperiment(graplerURL, expId)
+#' }
+GrapleAbortExperiment <- function(submissionURL, experimentId)
+{
+  qurl <- paste(submissionURL, "GrapleAbort", experimentId, sep="/")
+  status<- getURL(qurl)
+  return (fromJSON(status))
+}