Merge 2ec850a into 5877e5c

DOI-USGS · Jan 29, 2019 · d03ff06 · d03ff06
2 parents 5877e5c + 2ec850a
commit d03ff06
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: geoknife
 Type: Package
 Title: Web-Processing of Large Gridded Datasets
-Version: 1.6.2
-Date: 2018-08-20
+Version: 1.6.3
+Date: 2019-01-29
 Authors@R: c( person("Jordan", "Read", role = c("aut","cre"),
     email = "jread@usgs.gov"),
     person("Jordan", "Walker", role = c("aut"),
@@ -53,4 +53,4 @@ Suggests:
     rgdal,
     maps
 VignetteBuilder: knitr
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
diff --git a/R/algorithm-webprocess.R b/R/algorithm-webprocess.R
@@ -7,8 +7,10 @@
 #'@param .Object a \linkS4class{webprocess} object
 #'@param value a list with name of algorithm and relative url endpoint
 #'@examples
+#'\dontrun{
 #'wp <- webprocess()
 #'algorithm(wp)
+#'}
 #'@aliases 
 #'algorithm
 #'algorithm<-

diff --git a/R/inputs-webprocess.R b/R/inputs-webprocess.R
@@ -15,13 +15,15 @@
 #'@aliases
 #'inputs<-
 #'@examples
+#'\dontrun{
 #'wp <- webprocess(DELIMITER = 'TAB')
 #'inputs(wp)
 #'
 #'inputs(wp) <- list(DELIMITER = 'COMMA', SUMMARIZE_FEATURE_ATTRIBUTE = 'false')
 #'inputs(wp)
 #'inputs(wp, "DELIMITER")
 #'inputs(wp, "DELIMITER") <- "TAB"
+#'}
 #'@export
 #'@keywords internal
 setGeneric(name="inputs<-",def=function(.Object, ..., value){

diff --git a/tests/testthat/00_create_test_data.R b/tests/testthat/00_create_test_data.R
@@ -1,55 +1,57 @@
 # Run this script in the testthat directory to refresh all the rds files loaded by tests.
 # Try to use RDS files when static objects can be used to keep chattyness of tests down.
-
-library(geoknife)
-
-if(!"geoknife/tests/testthat" == substr(getwd(), nchar(getwd())-22, nchar(getwd()))) {
-  warning("this script assumes it is in the testthat directory of the geoknife package!!!")
-}
-
-gconfig(wps.url = "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
-fabric <- webdata('prism')
-times(fabric)[2] <- "1895-01-01"
-saveRDS(fabric, "data/test_webdata_fabric.rds")
-wp <- webprocess()
-saveRDS(wp, "data/test_webprocess_knife.rds")
-
-default.sleep <- geoknife:::gconfig('sleep.time')
-saveRDS(webprocess(sleep.time = default.sleep+5), "data/test_webprocess_sleep-plus-five.rds")
-saveRDS(query(wp, 'algorithms'), "data/test_webprocess_algorithms.rds")
-
-saveRDS(webprocess(DELIMITER = 'TAB'), "data/test_webprocess_tab.rds")
-
-gconfig('wps.url'="https://cida.usgs.gov/gdp/process/WebProcessingService")
-wp <- webprocess()
-saveRDS(wp, "data/test_webprocess_knife_prod.rds")
-saveRDS(query(wp, 'algorithms'), "data/test_webprocess_algorithms_prod.rds")
-
-gconfig(wps.url = "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
-
-saveRDS(webgeom('HUC8::09020306'), "data/test_webgeom_huc08.rds")
-saveRDS(webgeom('state::Wisconsin'), "data/test_webgeom_WI.rds")
-saveRDS(simplegeom(data.frame(point1 = c(-48.6, 45.2), point2=c(-88.6, 45.2))),
-        "data/test_simplegeom_two_points.rds")
-
-saveRDS(webdata('prism',times = as.POSIXct(c('2001-01-01','2002-02-05'))),
-        "data/test_webdata_prism_year.rds")
-
-# from custom data source vignette
-wg <- webgeom(url="https://www.sciencebase.gov/catalogMaps/mapping/ows/54296bf0e4b0ad29004c2fbb")
-geom(wg) <- "sb:Yahara_River_HRUs_alb_eq"
-attribute(wg) <- "GRIDCODE"
-
-wd <- webdata(url = 'https://cida.usgs.gov/thredds/dodsC/prism_v2', 
-                  variables = c('tmx', 'tmn', 'ppt'),
-                  times = as.POSIXct(c('2000-01-01', '2010-01-01')))
-
-saveRDS(wg, "data/test_XML_no_gmlid_wg.rds")
-saveRDS(wd, "data/test_XML_no_gmlid_wd.rds")
-
-wp <- webprocess(algorithm = list('OPeNDAP Subset'="gov.usgs.cida.gdp.wps.algorithm.FeatureCoverageOPeNDAPIntersectionAlgorithm"))
-inputs(wp, "OUTPUT_TYPE") <- "geotiff"
-saveRDS(wp, "data/test_XML_wp_opendapsubset.rds")
-
-webdata <- query("webdata")
-saveRDS(webdata, "data/test_query_webdata.rds")
+test_that("test data can be created", {
+  testthat::skip_on_cran()
+  library(geoknife)
+
+  if(!"geoknife/tests/testthat" == substr(getwd(), nchar(getwd())-22, nchar(getwd()))) {
+    warning("this script assumes it is in the testthat directory of the geoknife package!!!")
+  }
+  gconfig(wps.url = "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
+  fabric <- webdata('prism')
+  times(fabric)[2] <- "1895-01-01"
+  saveRDS(fabric, "data/test_webdata_fabric.rds")
+  wp <- webprocess()
+  saveRDS(wp, "data/test_webprocess_knife.rds")
+
+  default.sleep <- geoknife:::gconfig('sleep.time')
+  saveRDS(webprocess(sleep.time = default.sleep+5), "data/test_webprocess_sleep-plus-five.rds")
+  saveRDS(query(wp, 'algorithms'), "data/test_webprocess_algorithms.rds")
+
+  saveRDS(webprocess(DELIMITER = 'TAB'), "data/test_webprocess_tab.rds")
+
+  gconfig('wps.url'="https://cida.usgs.gov/gdp/process/WebProcessingService")
+  wp <- webprocess()
+  saveRDS(wp, "data/test_webprocess_knife_prod.rds")
+  saveRDS(query(wp, 'algorithms'), "data/test_webprocess_algorithms_prod.rds")
+
+  gconfig(wps.url = "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
+
+  saveRDS(webgeom('HUC8::09020306'), "data/test_webgeom_huc08.rds")
+  saveRDS(webgeom('state::Wisconsin'), "data/test_webgeom_WI.rds")
+  saveRDS(simplegeom(data.frame(point1 = c(-48.6, 45.2), point2=c(-88.6, 45.2))),
+          "data/test_simplegeom_two_points.rds")
+
+  saveRDS(webdata('prism',times = as.POSIXct(c('2001-01-01','2002-02-05'))),
+          "data/test_webdata_prism_year.rds")
+
+  # from custom data source vignette
+  wg <- webgeom(url="https://www.sciencebase.gov/catalogMaps/mapping/ows/54296bf0e4b0ad29004c2fbb")
+  geom(wg) <- "sb:Yahara_River_HRUs_alb_eq"
+  attribute(wg) <- "GRIDCODE"
+
+  wd <- webdata(url = 'https://cida.usgs.gov/thredds/dodsC/prism_v2', 
+                variables = c('tmx', 'tmn', 'ppt'),
+                times = as.POSIXct(c('2000-01-01', '2010-01-01')))
+
+  saveRDS(wg, "data/test_XML_no_gmlid_wg.rds")
+  saveRDS(wd, "data/test_XML_no_gmlid_wd.rds")
+
+  wp <- webprocess(algorithm = list('OPeNDAP Subset'="gov.usgs.cida.gdp.wps.algorithm.FeatureCoverageOPeNDAPIntersectionAlgorithm"))
+  inputs(wp, "OUTPUT_TYPE") <- "geotiff"
+  saveRDS(wp, "data/test_XML_wp_opendapsubset.rds")
+
+  webdata <- query("webdata")
+  saveRDS(webdata, "data/test_query_webdata.rds")
+  expect_gt(length(list.files('data')), 1)
+})
diff --git a/tests/testthat/test-geoknife_setters.R b/tests/testthat/test-geoknife_setters.R
@@ -75,6 +75,7 @@ test_that("we can set attributes on a webgeom", {
 context("basics of geoknife processing job are as expected")
 
 test_that("algorithm version works", {
+  testthat::skip_on_cran()
   fabric <- webdata('prism')
   times(fabric)[2] <- as.POSIXct('1895-01-01', tz = "UTC")
   job <- geoknife(stencil = c(-89,42), fabric = fabric)
@@ -83,6 +84,7 @@ test_that("algorithm version works", {
 })
 
 test_that("version method works", {
+  testthat::skip_on_cran()
   stencil <- webgeom()
   version(stencil) <- "2.0.0"
   expect_equal(version(stencil), "2.0.0")

diff --git a/tests/testthat/test-geoknife_utils.R b/tests/testthat/test-geoknife_utils.R
@@ -47,16 +47,15 @@ test_that("check status of an ID that doesn't exist", {
   expect_equal(status$statusType, "unknown")
 })
 
-fabric <- webdata('prism', variables = 'wrong')
-job <- geoknife(c(-89,43), fabric, wait = TRUE)
-failed.id <- id(job)
+
 test_that("check status of an ID that failed", {
+  testthat::skip_on_cran()
+  fabric <- webdata('prism', variables = 'wrong')
+  job <- geoknife(c(-89,43), fabric, wait = TRUE)
+  failed.id <- id(job)
   testthat::skip_on_cran()
   status <- check(failed.id)
   expect_equal(status$statusType, "ProcessFailed")
-})
-
-test_that("result fails with failed job",{
   expect_error(result(failed.id), "processing is incomplete or has failed. See check()")
 })
 

diff --git a/tests/testthat/test-knife_shorthand.R b/tests/testthat/test-knife_shorthand.R
@@ -17,6 +17,7 @@ test_that("built in knifes are algorithms on prod", {
 })
 
 test_that('multi-args work with shorthand knife',{
+  testthat::skip_on_cran()
   wp <- webprocess('subset', OUTPUT_TYPE='geotiff') # this makes two describe process requests!!! HUH?
   expect_is(wp, 'webprocess')
   expect_equal(inputs(wp)$OUTPUT_TYPE, 'geotiff')

diff --git a/tests/testthat/test-webprocess_object.R b/tests/testthat/test-webprocess_object.R
@@ -60,6 +60,7 @@ test_that("error is thrown on job start for read only vars", {
 context("create webprocess from geojob")
 gconfig(wps.url = "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
 test_that("given a geojob, we can create a webprocess", {
+  testthat::skip_on_cran()
   xml <- system.file("extdata/state_webgeom_post.xml", 
                                package = "geoknife")
   geojob <- geojob(xml=xml)