efforts for using the job id for various utility functions

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: geoknife
 Type: Package
 Title: Web-Processing of Large Gridded Datasets
-Version: 1.5.2
-Date: 2016-12-27
+Version: 1.5.3
+Date: 2017-03-03
 Authors@R: c( person("Jordan", "Read", role = c("aut","cre"),
     email = "jread@usgs.gov"),
     person("Jordan", "Walker", role = c("aut"),

R/check.R

@@ -3,7 +3,8 @@
 #' two fields: \code{status} and \code{URL}. If the \linkS4class{geojob} object has not been executed
 #' (see \code{\link{start}}), this method returns \code{status}='none' and \code{URL}=NULL.
 #'
-#'@param .Object a \linkS4class{geojob} object with an active GDP process request.
+#'@param .Object a \linkS4class{geojob} object with an active GDP process request, 
+#' or a \code{character} URL of an existing job
 #'@return \code{process}, a list containing
 #' \code{status} and \code{URL}. 
 #'
@@ -61,4 +62,10 @@ setMethod(f = "check",signature(.Object = "geojob"), definition = function(.Obje
 
   setJobState(process$status)
 	return(process)
-})
+})
+
+#'@rdname check-geojob
+#'@aliases check
+setMethod(f = "check",signature(.Object = "character"), definition = function(.Object){
+  check(geojob(id = .Object))
+})

R/download-geojob.R

@@ -2,10 +2,10 @@
 #' 
 #' download the result of a processing job to a local destination. 
 #' 
-#'@param .Object a \code{\link{geojob}} that has completed
+#'@param .Object a \code{\link{geojob}} or job id that has completed 
 #'@param destination a file destination. If missing, a temp directory will be used
 #'@param ... additional arguments passed to \code{\link[httr]{write_disk}}, such as overwrite = TRUE
-#'@return the file handle
+#'@return the destination of the downloaded file
 #'@author Jordan S Read
 #'@rdname download
 #'@importFrom httr write_disk progress
@@ -17,19 +17,31 @@ setGeneric("download", function(.Object, destination, ...) {
 #'@rdname download
 #'@aliases download
 setMethod("download", signature("geojob",'missing'), function(.Object, destination, ...) {
+  download(id(.Object), ...)
+})
 
+#'@rdname download
+#'@aliases download
+setMethod("download", signature("character",'missing'), function(.Object, destination, ...) {
+
   status <- check(.Object)
   if (is.null(status)) stop('geojob must be completed for download. See "check(geojob)"')
-
+  
   filename <- strsplit(status$URL, '?id=')[[1]][2]
   destination = file.path(tempdir(), filename)
 
-  download(.Object, destination)
+  download(.Object, destination, ...)
 })
 
 #'@rdname download
 #'@aliases download
 setMethod("download", signature("geojob",'character'), function(.Object, destination, ...) {
+  download(id(.Object), destination, ...)
+})
+
+#'@rdname download
+#'@aliases download
+setMethod("download", signature("character",'character'), function(.Object, destination, ...) {
 
   status <- check(.Object)
   gGET(url=status$URL, write_disk(destination, ...))

R/result.R

@@ -2,9 +2,10 @@
 #'
 #' a \code{geojob} method for loading data into R from a completed processing request
 #'
-#' @param .Object a \code{\link{geojob}} object with a successful processID. 
+#' @param .Object a \code{\link{geojob}} object with a successful processID,
+#' or a \code{character} URL of a completed job.
 #' (See \code{\link{check}}).
-#' @param ... additional arguments passed to parsers (e.g., keep.units = TRUE)
+#' @param ... additional arguments passed to parsers (e.g., with.units = TRUE)
 #' @return data.frame of timeseries values. 
 #' @rdname result-methods
 #' @aliases result
@@ -18,6 +19,10 @@
 #' \dontrun{
 #' job <- geoknife(stencil = c(-89,42), fabric = 'prism', wait = TRUE)
 #' result(job, with.units = TRUE) # load and print output
+#' 
+#' # or use the job id:
+#' id <- id(job)
+#' result(id, with.units = TRUE) # load and print output
 #' }
 #'
 setGeneric(name="result",def=function(.Object, ...){standardGeneric("result")})
@@ -26,48 +31,52 @@ setGeneric(name="result",def=function(.Object, ...){standardGeneric("result")})
 #' @aliases result
 setMethod(f = "result",signature="geojob",
   definition = function(.Object, ...){
+    result(id(.Object), ...)
+})
+
+#' @rdname result-methods
+#' @aliases result
+setMethod(f = "result",signature="character",
+          definition = function(.Object, ...){
             if (successful(.Object)){
-              output <- outputParse(.Object, ...)
+              output <- outputParse(job.id = .Object, ...)
               return(output)
             } else {
               stop('processing is incomplete or has failed. See check(). Processing status: ',
                    check(.Object)$statusType)
             }
-
-          }
-  )
-
-outputParse = function(.Object, ...){
-  funcInfo <- algorithmParseDetails(.Object)
-  fileLocation <- check(.Object)$URL
+})
+outputParse = function(job.id, ...){
+  funcInfo <- algorithmParseDetails(job.id)
+  fileLocation <- check(job.id)$URL
   output <- do.call(funcInfo[['function.name']], args = list(file = fileLocation, 'delim' = funcInfo[['delimiter']], ...))
   return(output)
 }
 
 #' @importFrom utils tail
-algorithmParseDetails <- function(job){
+algorithmParseDetails <- function(job.id){
   function.handlers <- list("FeatureWeightedGridStatisticsAlgorithm" = c('function.name'='parseTimeseries'),
                             "FeatureGridStatisticsAlgorithm" = c('function.name'='parseTimeseries'),
                             "FeatureCategoricalGridCoverageAlgorithm" = c('function.name'='parseCategorical'))
-  doc <- xmlParse(xml(job))
-  algorithm <- xmlValue(getNodeSet(doc,"/wps:Execute/ows:Identifier")[[1]])
+  xmlProcess <- gcontent(gGET(job.id))
+  algorithm <- xmlValue(getNodeSet(xmlProcess,"/wps:ExecuteResponse/wps:Process/ows:Identifier")[[1]])
+
   algorithm.name <- tail(strsplit(algorithm, '[.]')[[1]], 1)
-  rm(doc) # is this necessary w/ XML package?
 
   if (!algorithm.name %in% names(function.handlers)){
     stop('parser for ',algorithm.name, 
          ' not currently supported. Create an issue to suggest it: https://github.com/USGS-R/geoknife/issues/new', call. = FALSE)
   }
-  parse.details <- c(function.handlers[[algorithm.name]], 'delimiter'=outputDelimiter(job))
+  parse.details <- c(function.handlers[[algorithm.name]], 'delimiter'=outputDelimiter(job.id))
   return(parse.details)
 }
 
-outputDelimiter <- function(job){
+outputDelimiter <- function(job.id){
   delimiters <- c("text/tab-separated-values" = '\t',
                   "text/csv" = ',',
                   'text/plain' = ' ')
   # find output type
-  resp <- rawToChar(GET(id(job))$content)
+  resp <- rawToChar(GET(job.id)$content)
   doc <-  htmlParse(resp, useInternalNodes = TRUE)
   type <- xmlGetAttr(getNodeSet(doc,"//reference[@mimetype]")[[1]],'mimetype')
   if (!type %in% names(delimiters)){

R/successful.R

@@ -35,48 +35,57 @@ setGeneric(name="successful",def=function(.Object, retry){standardGeneric("succe
 #'@rdname successful-methods
 #'@aliases successful
 setMethod(f = "successful",signature(.Object = "geojob"), definition = function(.Object, retry = FALSE){
-
+  successful(id(.Object))
+})
+#'@rdname successful-methods
+#'@aliases successful
+setMethod(f = "successful",signature(.Object = "character"), definition = function(.Object, retry = FALSE){
   process = check(.Object)
   if (process$status == 'unknown' && retry){
     Sys.sleep(gconfig('sleep.time'))
     process = check(.Object)
   }
-
-	return(process$statusType == "ProcessSucceeded")
-
+
+  return(process$statusType == "ProcessSucceeded")
 })
 
-
 #'@export
 setGeneric(name="running",def=function(.Object, retry){standardGeneric("running")})
 
 #'@rdname successful-methods
 #'@aliases running
 setMethod(f = "running",signature(.Object = "geojob"), definition = function(.Object, retry = FALSE){
+  running(id(.Object))
+})
+#'@rdname successful-methods
+#'@aliases running
+setMethod(f = "running",signature(.Object = "character"), definition = function(.Object, retry = FALSE){
 
   process = check(.Object)
   if (process$status == 'unknown' && retry){
     Sys.sleep(gconfig('sleep.time'))
     process = check(.Object)
   }
-
   return(process$statusType == "ProcessStarted" | process$statusType == "ProcessAccepted")
 })
 
-
 #'@export
 setGeneric(name="error",def=function(.Object, retry){standardGeneric("error")})
 
 #'@rdname successful-methods
 #'@aliases error
 setMethod(f = "error",signature = "geojob", definition = function(.Object, retry = FALSE){
+  error(id(.Object))
+})
+
+#'@rdname successful-methods
+#'@aliases error
+setMethod(f = "error",signature = "character", definition = function(.Object, retry = FALSE){
 
   process = check(.Object)
   if (process$status == 'unknown' && retry){
     Sys.sleep(gconfig('sleep.time'))
     process = check(.Object)
   }
-
-
   return(process$statusType == "ProcessFailed")
 })

README.md

@@ -1,4 +1,4 @@
-`geoknife` package version 1.5.0
+`geoknife` package version 1.5.2
 ================================
 
 [![Build status](https://ci.appveyor.com/api/projects/status/0iacmg82mp50426o/branch/master)](https://ci.appveyor.com/project/jread-usgs/geoknife/branch/master) [![Build Status](https://travis-ci.org/USGS-R/geoknife.svg)](https://travis-ci.org/USGS-R/geoknife) [![Coverage Status](https://coveralls.io/repos/USGS-R/geoknife/badge.svg)](https://coveralls.io/r/USGS-R/geoknife) [![Download Count](http://cranlogs.r-pkg.org/badges/geoknife)](https://cran.r-project.org/package=geoknife)
@@ -87,7 +87,7 @@ check(job)
     ## [1] "Process successful"
     ## 
     ## $URL
-    ## [1] "https://cida.usgs.gov:443/gdp/process/RetrieveResultServlet?id=056d8e89-6d18-418f-b62c-af76ded6b83dOUTPUT"
+    ## [1] "https://cida.usgs.gov:443/gdp/process/RetrieveResultServlet?id=289eb8f9-858a-4234-b19c-cf0d6a6ba505OUTPUT"
     ## 
     ## $statusType
     ## [1] "ProcessSucceeded"

cran-comments.md

@@ -1,5 +1,5 @@
 ## Resubmission
 This is a resubmission. In this version I have:
 
-* removed a test that used a service that now requires authentication (Errors on CRAN checks were the result of these service changes)
+* added the ability to download, check, and load results based on job id (in addition to the geojob object)
 

inst/extdata/completed_request.xml

@@ -0,0 +1,102 @@
+<wps:ExecuteResponse xmlns:wps="http://www.opengis.net/wps/1.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" statusLocation="https://cida.usgs.gov:443/gdp/process/RetrieveResultServlet?id=e0577fe5-2690-4140-8e95-7be4fa7ebec7">
+<wps:Process>
+<ows:Identifier>
+gov.usgs.cida.gdp.wps.algorithm.FeatureWeightedGridStatisticsAlgorithm
+</ows:Identifier>
+<ows:Title>Area Grid Statistics (weighted)</ows:Title>
+</wps:Process>
+<wps:Status creationTime="2017-03-03T07:51:54.155-06:00">
+<wps:ProcessSucceeded>Process successful</wps:ProcessSucceeded>
+</wps:Status>
+<wps:DataInputs>
+<wps:Input xmlns:ogc="http://www.opengis.net/ogc" xmlns:xlink="http://www.w3.org/1999/xlink">
+<ows:Identifier>TIME_START</ows:Identifier>
+<wps:Data>
+<wps:LiteralData>1895-01-01T00:00:00.000Z</wps:LiteralData>
+</wps:Data>
+</wps:Input>
+<wps:Input xmlns:ogc="http://www.opengis.net/ogc" xmlns:xlink="http://www.w3.org/1999/xlink">
+<ows:Identifier>TIME_END</ows:Identifier>
+<wps:Data>
+<wps:LiteralData>1899-01-01T00:00:00.000Z</wps:LiteralData>
+</wps:Data>
+</wps:Input>
+<wps:Input xmlns:ogc="http://www.opengis.net/ogc" xmlns:xlink="http://www.w3.org/1999/xlink">
+<ows:Identifier>SUMMARIZE_TIMESTEP</ows:Identifier>
+<wps:Data>
+<wps:LiteralData>false</wps:LiteralData>
+</wps:Data>
+</wps:Input>
+<wps:Input xmlns:ogc="http://www.opengis.net/ogc" xmlns:xlink="http://www.w3.org/1999/xlink">
+<ows:Identifier>SUMMARIZE_FEATURE_ATTRIBUTE</ows:Identifier>
+<wps:Data>
+<wps:LiteralData>false</wps:LiteralData>
+</wps:Data>
+</wps:Input>
+<wps:Input xmlns:ogc="http://www.opengis.net/ogc" xmlns:xlink="http://www.w3.org/1999/xlink">
+<ows:Identifier>DATASET_URI</ows:Identifier>
+<wps:Data>
+<wps:LiteralData>dods://cida.usgs.gov/thredds/dodsC/prism_v2</wps:LiteralData>
+</wps:Data>
+</wps:Input>
+<wps:Input xmlns:ogc="http://www.opengis.net/ogc" xmlns:xlink="http://www.w3.org/1999/xlink">
+<ows:Identifier>REQUIRE_FULL_COVERAGE</ows:Identifier>
+<wps:Data>
+<wps:LiteralData>true</wps:LiteralData>
+</wps:Data>
+</wps:Input>
+<wps:Input xmlns:ogc="http://www.opengis.net/ogc" xmlns:xlink="http://www.w3.org/1999/xlink">
+<ows:Identifier>STATISTICS</ows:Identifier>
+<wps:Data>
+<wps:LiteralData>MEAN</wps:LiteralData>
+</wps:Data>
+</wps:Input>
+<wps:Input xmlns:ogc="http://www.opengis.net/ogc" xmlns:xlink="http://www.w3.org/1999/xlink">
+<ows:Identifier>GROUP_BY</ows:Identifier>
+<wps:Data>
+<wps:LiteralData>STATISTIC</wps:LiteralData>
+</wps:Data>
+</wps:Input>
+<wps:Input xmlns:ogc="http://www.opengis.net/ogc" xmlns:xlink="http://www.w3.org/1999/xlink">
+<ows:Identifier>FEATURE_ATTRIBUTE_NAME</ows:Identifier>
+<wps:Data>
+<wps:LiteralData>STATE</wps:LiteralData>
+</wps:Data>
+</wps:Input>
+<wps:Input xmlns:ogc="http://www.opengis.net/ogc" xmlns:xlink="http://www.w3.org/1999/xlink">
+<ows:Identifier>DELIMITER</ows:Identifier>
+<wps:Data>
+<wps:LiteralData>COMMA</wps:LiteralData>
+</wps:Data>
+</wps:Input>
+<wps:Input xmlns:ogc="http://www.opengis.net/ogc" xmlns:xlink="http://www.w3.org/1999/xlink">
+<ows:Identifier>DATASET_ID</ows:Identifier>
+<wps:Data>
+<wps:LiteralData>ppt</wps:LiteralData>
+</wps:Data>
+</wps:Input>
+<wps:Input xmlns:ogc="http://www.opengis.net/ogc" xmlns:xlink="http://www.w3.org/1999/xlink">
+<ows:Identifier>FEATURE_COLLECTION</ows:Identifier>
+<wps:Reference xlink:href="https://cida.usgs.gov/gdp/geoserver/wfs">
+<wps:Body>
+<wfs:GetFeature xmlns:gml="http://www.opengis.net/gml" xmlns:wfs="http://www.opengis.net/wfs" outputFormat="text/xml; subtype=gml/3.1.1" service="WFS" version="1.1.0">
+<wfs:Query typeName="sample:CONUS_states">
+<wfs:PropertyName>the_geom</wfs:PropertyName>
+<wfs:PropertyName>STATE</wfs:PropertyName>
+<ogc:Filter>
+<ogc:GmlObjectId gml:id="CONUS_states.48"/>
+</ogc:Filter>
+</wfs:Query>
+</wfs:GetFeature>
+</wps:Body>
+</wps:Reference>
+</wps:Input>
+</wps:DataInputs>
+<wps:ProcessOutputs>
+<wps:Output>
+<ows:Identifier>OUTPUT</ows:Identifier>
+<ows:Title>Output File</ows:Title>
+<wps:Reference mimeType="text/csv" href="https://cida.usgs.gov:443/gdp/process/RetrieveResultServlet?id=e0577fe5-2690-4140-8e95-7be4fa7ebec7OUTPUT"/>
+</wps:Output>
+</wps:ProcessOutputs>
+</wps:ExecuteResponse>