Merge pull request #252 from jread-usgs/wait

Wait
DOI-USGS · Feb 11, 2016 · 01f8668 · 01f8668
2 parents 258b38d + 6c1aefe
commit 01f8668
Show file tree

Hide file tree

Showing 15 changed files with 118 additions and 81 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: geoknife
 Type: Package
 Title: Web-Processing of Large Gridded Datasets
-Version: 1.1.6
-Date: 2016-01-15
+Version: 1.2.1
+Date: 2016-02-11
 Authors@R: c( person("Jordan", "Read", role = c("aut","cre"),
     email = "jread@usgs.gov"),
     person("Jordan", "Walker", role = c("aut"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -43,6 +43,7 @@ export(values)
 export(variables)
 export(variables_query)
 export(version)
+export(wait)
 export(webdata)
 export(webgeom)
 export(webprocess)
@@ -94,5 +95,6 @@ importFrom(sp,Polygons)
 importFrom(sp,SpatialPolygons)
 importFrom(sp,coordinates)
 importFrom(utils,lsf.str)
+importFrom(utils,packageName)
 importFrom(utils,packageVersion)
 importFrom(utils,read.table)
diff --git a/R/01-webdata-obj.R b/R/01-webdata-obj.R
@@ -8,7 +8,7 @@ pkg.env$gconfig <- list('wps.url'='http://cida.usgs.gov/gdp/process/WebProcessin
                         'verbose' = FALSE,
                         'version' = '1.0.0')
 
-#' @importFrom utils lsf.str
+#' @importFrom utils lsf.str packageName
 .onLoad <- function(libname, pkgname){
   setJobState()
   funs <- unclass(lsf.str(envir = asNamespace(packageName()), all = TRUE))

diff --git a/R/geoknife-generic.R b/R/geoknife-generic.R
@@ -72,7 +72,7 @@ geoknife <- function(stencil, fabric, knife = webprocess(...), ...){
   }
 
   if (knife@wait){
-    waitUntilFinished(geojob, sleep.time = knife@sleep.time)
+    wait(geojob, sleep.time = knife@sleep.time)
   }
   return(geojob)
 }

diff --git a/R/waitUntilFinished.R b/R/waitUntilFinished.R
@@ -1,13 +1,25 @@
 
-#' @title hold up R while GDP is processing
-#' @description keeps R in a loop while GDP works on the request. 
-#' Checks \code{\link{running}}. Will drop out of loop whenever !running(geojob)
-#' @keywords internal
+#' hold up R while GDP is processing
 #' 
-waitUntilFinished <- function(.Object, sleep.time = gconfig('sleep.time')){
+#' keeps R in a loop while GDP works on the request. Checks \code{\link{running}}. 
+#' Will drop out of loop whenever !running(geojob)
+#' 
+#' @param .Object a geojob
+#' @param sleep.time a number of seconds to wait in between checking the process
+#' @return invisible return of .Object, unaltered
+#' @examples
+#' \dontrun{
+#' job <- geoknife(stencil = c(-89,42), fabric = 'prism')
+#' 2+2
+#' wait(job)
+#' check(job) # should be complete
+#' }
+#' @export
+wait <- function(.Object, sleep.time = gconfig('sleep.time')){
   running <- running(.Object, retry = TRUE)
   while(running){
     Sys.sleep(sleep.time)
     running <- running(.Object, retry = TRUE)
   }
+  invisible(.Object)
 }
diff --git a/README.Rmd b/README.Rmd
@@ -103,10 +103,11 @@ plot(data[,1:2], ylab = variables(fabric))
 job <- geoknife(webgeom('state::New Hampshire'), fabric = 'prism', email = 'fake.email@gmail.com')
 ```
 
-###`geoknife` Functions (as of v0.12.1)
+###`geoknife` Functions (as of v1.1.5)
 | Function       | Title           |
 | ------------- |:-------------|
 | `geoknife` | slice up gridded data according to overlap with feature(s) |
+| `gconfig` | set or query package settings for `geoknife` processing defaults |
 | `algorithm` | the algorithm of a `webprocess` |
 | `attribute` | the attribute of an `webgeom` |
 | `check` | check status of `geojob` |

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-`geoknife` package version 1.1.4
+`geoknife` package version 1.1.6
 ================================
 
 [![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] "http://cida.usgs.gov:80/gdp/process/RetrieveResultServlet?id=0ac86798-7a2f-47c8-b153-3673e77e3e80OUTPUT"
+    ## [1] "http://cida.usgs.gov:80/gdp/process/RetrieveResultServlet?id=3089e8d3-1ce7-4058-aa14-989ee4e67ae1OUTPUT"
     ## 
     ## $statusType
     ## [1] "ProcessSucceeded"
@@ -115,31 +115,32 @@ plot(data[,1:2], ylab = variables(fabric))
 job <- geoknife(webgeom('state::New Hampshire'), fabric = 'prism', email = 'fake.email@gmail.com')
 ```
 
-### `geoknife` Functions (as of v0.12.1)
-
-| Function     | Title                                                        |
-|--------------|:-------------------------------------------------------------|
-| `geoknife`   | slice up gridded data according to overlap with feature(s)   |
-| `algorithm`  | the algorithm of a `webprocess`                              |
-| `attribute`  | the attribute of an `webgeom`                                |
-| `check`      | check status of `geojob`                                     |
-| `download`   | download the results of a `geojob`                           |
-| `error`      | convenience function for state of `geojob`                   |
-| `running`    | convenience function for state of `geojob`                   |
-| `successful` | convenience function for state of `geojob`                   |
-| `start`      | start a `geojob`                                             |
-| `cancel`     | cancel a `geojob`                                            |
-| `geom`       | the geom of a `webgeom`                                      |
-| `inputs`     | the inputs of a `webprocess`                                 |
-| `id`         | the process id of a `geojob`                                 |
-| `values`     | the values of a `webgeom`                                    |
-| `result`     | load the output of a completed `geojob` into data.frame      |
-| `variables`  | the variables for a `webdata` object                         |
-| `times`      | the times of a `webdata` object                              |
-| `url`        | the url of a `webdata`, `webgeom`, `geojob`, or `webprocess` |
-| `version`    | the version of a `webgeom` or `webdata`                      |
-| `xml`        | the xml of a `geojob`                                        |
-| `query`      | query datasets or variables                                  |
+### `geoknife` Functions (as of v1.1.5)
+
+| Function     | Title                                                            |
+|--------------|:-----------------------------------------------------------------|
+| `geoknife`   | slice up gridded data according to overlap with feature(s)       |
+| `gconfig`    | set or query package settings for `geoknife` processing defaults |
+| `algorithm`  | the algorithm of a `webprocess`                                  |
+| `attribute`  | the attribute of an `webgeom`                                    |
+| `check`      | check status of `geojob`                                         |
+| `download`   | download the results of a `geojob`                               |
+| `error`      | convenience function for state of `geojob`                       |
+| `running`    | convenience function for state of `geojob`                       |
+| `successful` | convenience function for state of `geojob`                       |
+| `start`      | start a `geojob`                                                 |
+| `cancel`     | cancel a `geojob`                                                |
+| `geom`       | the geom of a `webgeom`                                          |
+| `inputs`     | the inputs of a `webprocess`                                     |
+| `id`         | the process id of a `geojob`                                     |
+| `values`     | the values of a `webgeom`                                        |
+| `result`     | load the output of a completed `geojob` into data.frame          |
+| `variables`  | the variables for a `webdata` object                             |
+| `times`      | the times of a `webdata` object                                  |
+| `url`        | the url of a `webdata`, `webgeom`, `geojob`, or `webprocess`     |
+| `version`    | the version of a `webgeom` or `webdata`                          |
+| `xml`        | the xml of a `geojob`                                            |
+| `query`      | query datasets or variables                                      |
 
 ### `geoknife` classes (as of v0.12.0)
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,17 +1,10 @@
 ## Resubmission
 This is a resubmission. In this version I have:
 
-* Added a new output type to data subsets (geotiff)
+* Added a new vignette (plotting geotiffs)
 
-* Modified the GET and POST requests to work correctly with the release and dev version of the httr package
+* Modified the GET and POST requests to capture a warning message from the new CRAN version of the httr package
 
-* improved documentation
+* Added a new feature that allows users to turn on a verbose mode for web requests, and also set defaults for a number of variables. 
 
-* Fixed the CITATION file DOI, which was improperly formatted
-
-### a note about geoknife URLs:
-this package has a numer of service URLs that can be found in code, 
-in help text, and in vignettes. Some of these URLs will return 404s 
-without the proper POST body 
-(e.g., http://cida.usgs.gov/gdp/process/WebProcessingService). These 
-should be ignored for the purpose of testing valid urls. 
+* Removed urls in the vignette that cause 404s to url checks (as they are urls that receive POST bodies, not GET/HEAD requests)
diff --git a/inst/doc/geoknife.html b/inst/doc/geoknife.html
@@ -71,7 +71,7 @@
 <div id="header">
 <h1 class="title">geoknife package</h1>
 <h4 class="author"><em>Jordan Read</em></h4>
-<h4 class="date"><em>10 February, 2016</em></h4>
+<h4 class="date"><em>11 February, 2016</em></h4>
 </div>
 
 <div id="TOC">
@@ -369,20 +369,19 @@ <h3>query function for <code>webgeom</code></h3>
 ##  [4] &quot;derivative:CONUS_States&quot;        
 ##  [5] &quot;sample:CONUS_states&quot;            
 ##  [6] &quot;sample:CSC_Boundaries&quot;          
-##  [7] &quot;upload:E4_UTM&quot;                  
-##  [8] &quot;derivative:FWS_LCC&quot;             
-##  [9] &quot;sample:FWS_LCC&quot;                 
-## [10] &quot;draw:GL&quot;                        
-## [11] &quot;draw:GRSF&quot;                      
-## [12] &quot;derivative:wbdhu8_alb_simp&quot;     
-## [13] &quot;derivative:Level_III_Ecoregions&quot;
-## [14] &quot;derivative:NCA_Regions&quot;         
-## [15] &quot;derivative:US_Counties&quot;         
-## [16] &quot;draw:box&quot;                       
-## [17] &quot;upload:climate_E4&quot;              
-## [18] &quot;upload:layers&quot;                  
-## [19] &quot;sample:nps_boundary_2013&quot;       
-## [20] &quot;sample:simplified_HUC8s&quot;</code></pre>
+##  [7] &quot;derivative:FWS_LCC&quot;             
+##  [8] &quot;sample:FWS_LCC&quot;                 
+##  [9] &quot;draw:GRSF&quot;                      
+## [10] &quot;derivative:wbdhu8_alb_simp&quot;     
+## [11] &quot;derivative:Level_III_Ecoregions&quot;
+## [12] &quot;derivative:NCA_Regions&quot;         
+## [13] &quot;draw:SD&quot;                        
+## [14] &quot;derivative:US_Counties&quot;         
+## [15] &quot;draw:box&quot;                       
+## [16] &quot;upload:haynes_wshed_project&quot;    
+## [17] &quot;upload:layers&quot;                  
+## [18] &quot;sample:nps_boundary_2013&quot;       
+## [19] &quot;sample:simplified_HUC8s&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">query</span>(stencil, <span class="st">'attributes'</span>)</code></pre></div>
 <pre><code>## [1] &quot;STATE&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">query</span>(stencil, <span class="st">'values'</span>)</code></pre></div>
@@ -653,7 +652,7 @@ <h3><code>cancel</code> geojob</h3>
 <p>The <code>geoknife</code> package currently limits the user processing requests to single-running processes, so as to avoid creating thousands of requests in error, which could overwhelm the processing resources. If there is a reason to support additional jobs at one time, please email the package maintainers with your query.</p>
 <p>To cancel and existing job: Cancel a running job but retain the details:</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">id</span>(job)</code></pre></div>
-<pre><code>## [1] &quot;http://cida.usgs.gov:80/gdp/process/RetrieveResultServlet?id=8d6f59b2-09be-4802-ab8a-a2609da1c158&quot;</code></pre>
+<pre><code>## [1] &quot;http://cida.usgs.gov:80/gdp/process/RetrieveResultServlet?id=8ec535ed-711f-4192-b139-e6119fb89154&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">job &lt;-<span class="st"> </span><span class="kw">cancel</span>(job)
 <span class="kw">id</span>(job)</code></pre></div>
 <pre><code>## [1] &quot;&lt;no active job&gt;&quot;</code></pre>

diff --git a/inst/doc/plot_geotiff.html b/inst/doc/plot_geotiff.html
@@ -71,7 +71,7 @@
 <div id="header">
 <h1 class="title">subset gridded data as geotiff and plot</h1>
 <h4 class="author"><em>Jordan Read, Alison Appling</em></h4>
-<h4 class="date"><em>10 February, 2016</em></h4>
+<h4 class="date"><em>11 February, 2016</em></h4>
 </div>
 
 <div id="TOC">

diff --git a/man/wait.Rd b/man/wait.Rd
diff --git a/man/waitUntilFinished.Rd b/man/waitUntilFinished.Rd
diff --git a/tests/testthat/test-download_result.R b/tests/testthat/test-download_result.R
@@ -1,6 +1,6 @@
 context("download and load")
 
-
+gconfig(wps.url = "http://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
 test_that("download works", {
   testthat::skip_on_cran()
   cancel()

diff --git a/tests/testthat/test-gconfig.R b/tests/testthat/test-gconfig.R
@@ -15,6 +15,8 @@ test_that("can set !read.only variables", {
   expect_false(gconfig('wait'))
   gconfig('wait'=TRUE)
   expect_true(gconfig('wait'))
+  gconfig('wait'=FALSE)
+  expect_false(gconfig('wait'))
 })
 
 test_that("can set !read.only variables on webprocess()", {

diff --git a/tests/testthat/test-waitUntilFinished.R b/tests/testthat/test-waitUntilFinished.R
@@ -12,4 +12,16 @@ test_that("creating simple job", {
   expect_true(geoknife:::canStart())
   geoknife(stencil, fabric, wait = FALSE)
   expect_false(geoknife:::getJobState() == "Process successful")
-})
+})
+
+context("Test re-enter wait loop")
+test_that("creation of webprocess object", {
+  testthat::skip_on_cran()
+  fabric <- webdata('prism',times <- c('1895-01-01T00:00:00Z', '1999-01-01T00:00:00Z')) # should take longer than a re-check
+  cancel()
+  job <- geoknife(stencil = c(-89,42), fabric, wait=FALSE)
+  expect_equal(2+2, 4)
+  expect_true(running(job))
+  wait(job)
+  expect_false(running(job))
+})