Merge pull request #165 from jread-usgs/master

with.units for loadOutput

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: geoknife
 Type: Package
 Title: Geo-web processing of gridded data
-Version: 0.10.2
+Version: 0.10.3
 Date: 2013-05-23
 Author: Jordan S Read
 Maintainer: Jordan S Read <jread@usgs.gov>

R/loadOutput.R

@@ -4,6 +4,7 @@
 #'
 #'@param .Object a \code{\link{geojob}} object with a successful processID. 
 #'(See \code{\link{check}}).
+#'@param ... additional arguments passed to parsers (e.g., keep.units = TRUE)
 #'@return data.frame of timeseries values. 
 #'@rdname loadOutput-methods
 #'@aliases loadOutput
@@ -14,22 +15,18 @@
 #'@export
 #'@examples
 #'\dontrun{
-#'wp <- quick_wp()
-#'job <- geoknife(stencil = c(-89,42), fabric = 'prism', knife = wp)
-#'check(job)
-#'
-#'Sys.sleep(10) # give it some time to process
-#'loadOutput(job) # load and print output
+#'job <- geoknife(stencil = c(-89,42), fabric = 'prism', wait = TRUE)
+#'loadOutput(job, with.units = TRUE) # load and print output
 #'}
 #'
-setGeneric(name="loadOutput",def=function(.Object){standardGeneric("loadOutput")})
+setGeneric(name="loadOutput",def=function(.Object, ...){standardGeneric("loadOutput")})
 
 #'@rdname loadOutput-methods
 #'@aliases loadOutput
 setMethod(f = "loadOutput",signature="geojob",
-  definition = function(.Object){
+  definition = function(.Object, ...){
             if (successful(.Object)){
-              output <- outputParse(.Object)
+              output <- outputParse(.Object, ...)
               return(output)
             } else {
               stop('processing is incomplete or has failed. See checkProcess(). Processing status: ',
@@ -39,10 +36,10 @@ setMethod(f = "loadOutput",signature="geojob",
           }
   )
 
-outputParse = function(.Object){
+outputParse = function(.Object, ...){
   funcInfo <- getParseFunction(id(.Object))
   fileLocation <- check(.Object)$URL
-  output <- do.call(funcInfo$function_name, args = list(file = fileLocation, 'delim' = funcInfo$delim))
+  output <- do.call(funcInfo$function_name, args = list(file = fileLocation, 'delim' = funcInfo$delim, ...))
   return(output)
 }
 

R/parseTimeseries.R

@@ -6,15 +6,15 @@
 #'@param file a \linkS4class{geojob} timeseries processing result file location
 #'(See \code{\link{check}}).
 #'@param delim the file delimiter
-#'@param keep.units boolean for including a units column in returned data.frame
+#'@param with.units boolean for including a units column in returned data.frame
 #'@return a data.frame of timeseries values.
 #'@keywords methods
 #'@author Luke A. Winslow, Jordan S. Read
 #'@export
 #'@examples
 #'local_file <- system.file('extdata','tsv_linear_ring.tsv', package = 'geoknife')
 #'output <- parseTimeseries(local_file, delim = '\t')
-parseTimeseries <- function(file, delim, keep.units = FALSE){
+parseTimeseries <- function(file, delim, with.units = FALSE){
 
   config = parseConfig(file, delim)
 
@@ -53,7 +53,7 @@ parseTimeseries <- function(file, delim, keep.units = FALSE){
         'variable' = rep(as.character(config[['vars']][blk]), length.out = nrow(statData)),
         'statistic' = rep(cleanStat, length.out = nrow(statData)))
       )
-      if (keep.units){
+      if (with.units){
         statData = cbind(statData, data.frame('units'=rep(units, length.out = nrow(statData))))
       }
       dataOut <- rbind(dataOut, statData)

man/loadOutput-methods.Rd

@@ -6,13 +6,15 @@
 \alias{loadOutput,geojob-method}
 \title{parse process output into R environment}
 \usage{
-loadOutput(.Object)
+loadOutput(.Object, ...)
 
-\S4method{loadOutput}{geojob}(.Object)
+\S4method{loadOutput}{geojob}(.Object, ...)
 }
 \arguments{
 \item{.Object}{a \code{\link{geojob}} object with a successful processID.
 (See \code{\link{check}}).}
+
+\item{...}{additional arguments passed to parsers (e.g., keep.units = TRUE)}
 }
 \value{
 data.frame of timeseries values.
@@ -25,12 +27,8 @@ a \code{geojob} method for loading data into R from a completed processing reque
 }
 \examples{
 \dontrun{
-wp <- quick_wp()
-job <- geoknife(stencil = c(-89,42), fabric = 'prism', knife = wp)
-check(job)
-
-Sys.sleep(10) # give it some time to process
-loadOutput(job) # load and print output
+job <- geoknife(stencil = c(-89,42), fabric = 'prism', wait = TRUE)
+loadOutput(job, with.units = TRUE) # load and print output
 }
 }
 \author{

man/parseTimeseries.Rd

@@ -4,15 +4,15 @@
 \alias{parseTimeseries}
 \title{parse timeseries file into R environment}
 \usage{
-parseTimeseries(file, delim, keep.units = FALSE)
+parseTimeseries(file, delim, with.units = FALSE)
 }
 \arguments{
 \item{file}{a \linkS4class{geojob} timeseries processing result file location
 (See \code{\link{check}}).}
 
 \item{delim}{the file delimiter}
 
-\item{keep.units}{boolean for including a units column in returned data.frame}
+\item{with.units}{boolean for including a units column in returned data.frame}
 }
 \value{
 a data.frame of timeseries values.

tests/testthat/test-geoknife_output_parser.R

@@ -9,10 +9,10 @@ test_that("loadOutput fails with no process", {
 
 test_that("timeseries parser works on multi feature, single variable", {
   local_file <- system.file('extdata','tsv_multi_feature.tsv', package = 'geoknife')
-  output <- parseTimeseries(local_file, delim = '\t', keep.units = T)
+  output <- parseTimeseries(local_file, delim = '\t', with.units = T)
   expect_is(output, "data.frame")
   expect_true('units' %in% names(output))
-  output <- parseTimeseries(local_file, delim = '\t', keep.units = F)
+  output <- parseTimeseries(local_file, delim = '\t', with.units = F)
   expect_false('units' %in% names(output))
 })