Use testthat::skip_on_cran #155; closes #127

ncss-tech · Jan 16, 2021 · bcb76c3 · bcb76c3
1 parent b137276
commit bcb76c3
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diff --git a/R/AAAA.R b/R/AAAA.R
@@ -1,27 +1,25 @@
-
-# setup a new environment to store error messages, etc.
-soilDB.env <- new.env(hash=TRUE, parent = parent.frame())
-
-# safely register some options at package load time
-.onLoad <- function(libname, pkgname) {
-
-  ## TODO: normalize these option names
-  # set to FALSE at CRAN submission time: do not test APIs, this protects from API failures
-  # set to TRUE for testing non-NASIS components on machines that don't have local ODBC connection setup
-  options(.soilDB_testNetworkFunctions=TRUE)
-
-  # function verbosity
-  options(soilDB.verbose=FALSE)
-
-  # set default local nasis authentication
-  options(soilDB.NASIS.credentials="DSN=nasis_local;UID=NasisSqlRO;PWD=nasisRe@d0n1y")
-
-  # update according to win 7 or 10
-  si <- Sys.info()
-  if( grepl('windows', si['sysname'], ignore.case = TRUE) & grepl('8|10', si['release'], ignore.case = TRUE) ) {
-    options(soilDB.NASIS.credentials="DSN=nasis_local;UID=NasisSqlRO;PWD=nasisRe@d0n1y365")
-  }
-}
-
-
-
+
+# setup a new environment to store error messages, etc.
+soilDB.env <- new.env(hash=TRUE, parent = parent.frame())
+
+# safely register some options at package load time
+.onLoad <- function(libname, pkgname) {
+
+  # deprecated: soilDB 2.5.9 CRAN release
+  options(.soilDB_testNetworkFunctions=TRUE)
+
+  # function verbosity
+  options(soilDB.verbose=FALSE)
+
+  # set default local nasis authentication
+  options(soilDB.NASIS.credentials="DSN=nasis_local;UID=NasisSqlRO;PWD=nasisRe@d0n1y")
+
+  # update according to win 7 or 10
+  si <- Sys.info()
+  if( grepl('windows', si['sysname'], ignore.case = TRUE) & grepl('8|10', si['release'], ignore.case = TRUE) ) {
+    options(soilDB.NASIS.credentials="DSN=nasis_local;UID=NasisSqlRO;PWD=nasisRe@d0n1y365")
+  }
+}
+
+
+
diff --git a/tests/testthat/test-OSDquery.R b/tests/testthat/test-OSDquery.R
@@ -1,38 +1,30 @@
 context("OSDquery() -- requires internet connection")
 
 test_that("OSDquery() works", {
-  
+
   skip_if_offline()
-
-  # hack for in-house testing only
-  # WWW services aren't always available and will cause CRAN to drop our package if tests fail
-  if( ! getOption('.soilDB_testNetworkFunctions') )  {
-    skip("in-house testing only")
-  }
-
+
+  skip_on_cran()
+
   # a message is printed and NULL returned when no results
   res <- suppressMessages(OSDquery(geog_assoc_soils = 'pardee'))
-  
+
   # standard request
   expect_true(inherits(res, 'data.frame'))
-  
+
 })
 
 
 test_that("OSDquery() returns NULL with bogus query", {
-  
+
   skip_if_offline()
-
-  # hack for in-house testing only
-  # WWW services aren't always available and will cause CRAN to drop our package if tests fail
-  if( ! getOption('.soilDB_testNetworkFunctions') )  {
-    skip("in-house testing only")
-  }
-
+
+  skip_on_cran()
+
   # a message is printed and NULL returned when no results
   res <- suppressMessages(OSDquery(geog_assoc_soils = 'XXX'))
   expect_null(res)
-  
+
 })
 
 
diff --git a/tests/testthat/test-ROSETTA.R b/tests/testthat/test-ROSETTA.R
@@ -3,110 +3,101 @@ context("ROSETTA() -- requires internet connection")
 # example data
 x <<- structure(
   list(
-    musym = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
-              1L), 
-    cokey = c(20392868L, 20392868L, 20392870L, 20392870L, 20392870L, 
-              20392870L, 20393517L, 20394343L, 20394343L, 20394343L), 
-    compname = c("Aluf", 
-                 "Aluf", "Hitilo", "Hitilo", "Hitilo", "Hitilo", "Aransas", "Muskogee", 
-                 "Muskogee", "Muskogee"), 
-    comppct_r = c(47L, 47L, 22L, 22L, 22L, 
-                  22L, 100L, 20L, 20L, 20L), 
-    hzname = c("H1", "H2", "H1", "H2", 
-               "H3", "H4", "H1", "H1", "H2", "H3"), 
-    hzdept_r = c(0L, 127L, 0L, 
-                 117L, 137L, 157L, 0L, 0L, 38L, 64L), 
-    hzdepb_r = c(127L, 203L, 
-                 117L, 137L, 157L, 203L, 152L, 38L, 64L, 203L), 
-    sandtotal_r = c(94.4, 
-                    91, 94.1, 55.4, 59.3, 62.8, 23.3, 11.7, 6.8, 23.3), 
-    silttotal_r = c(0.6, 
-                    1, 1.4, 17.6, 13.7, 19.2, 29.2, 69.8, 63.2, 29.2), 
-    claytotal_r = c(5, 
-                    8, 4.5, 27, 27, 18, 47.5, 18.5, 30, 47.5), 
-    dbthirdbar_r = c(1.6, 
-                     1.55, 1.55, 1.58, 1.58, 1.5, 1.45, 1.38, 1.35, 1.33), 
-    wthirdbar_decimal = c(0.117, 
+    musym = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
+              1L),
+    cokey = c(20392868L, 20392868L, 20392870L, 20392870L, 20392870L,
+              20392870L, 20393517L, 20394343L, 20394343L, 20394343L),
+    compname = c("Aluf",
+                 "Aluf", "Hitilo", "Hitilo", "Hitilo", "Hitilo", "Aransas", "Muskogee",
+                 "Muskogee", "Muskogee"),
+    comppct_r = c(47L, 47L, 22L, 22L, 22L,
+                  22L, 100L, 20L, 20L, 20L),
+    hzname = c("H1", "H2", "H1", "H2",
+               "H3", "H4", "H1", "H1", "H2", "H3"),
+    hzdept_r = c(0L, 127L, 0L,
+                 117L, 137L, 157L, 0L, 0L, 38L, 64L),
+    hzdepb_r = c(127L, 203L,
+                 117L, 137L, 157L, 203L, 152L, 38L, 64L, 203L),
+    sandtotal_r = c(94.4,
+                    91, 94.1, 55.4, 59.3, 62.8, 23.3, 11.7, 6.8, 23.3),
+    silttotal_r = c(0.6,
+                    1, 1.4, 17.6, 13.7, 19.2, 29.2, 69.8, 63.2, 29.2),
+    claytotal_r = c(5,
+                    8, 4.5, 27, 27, 18, 47.5, 18.5, 30, 47.5),
+    dbthirdbar_r = c(1.6,
+                     1.55, 1.55, 1.58, 1.58, 1.5, 1.45, 1.38, 1.35, 1.33),
+    wthirdbar_decimal = c(0.117,
                           0.129, 0.106, 0.252, 0.261, 0.211, 0.369, 0.286, 0.308, 0.399
-    ), 
-    wfifteenbar_decimal = c(0.049, 0.062, 0.039, 0.181, 0.156, 
+    ),
+    wfifteenbar_decimal = c(0.049, 0.062, 0.039, 0.181, 0.156,
                             0.122, 0.285, 0.134, 0.165, 0.255)
-  ), 
-  row.names = c(NA, -10L), 
-  class = "data.frame", 
+  ),
+  row.names = c(NA, -10L),
+  class = "data.frame",
   SDA_id = "Table"
 )
 
 
 
 test_that("ROSETTA() works", {
-  
+
   skip_if_offline()
-
-  # hack for in-house testing only
-  # WWW services aren't always available and will cause CRAN to drop our package if tests fail
-  if( ! getOption('.soilDB_testNetworkFunctions') )  {
-    skip("in-house testing only")
-  }
-
+
+  skip_on_cran()
+
   # attempting to use all possible soil properties
   vars <- c('sandtotal_r', 'silttotal_r', 'claytotal_r', 'dbthirdbar_r', 'wthirdbar_decimal', 'wfifteenbar_decimal')
-  
+
   # submit request
   r <- ROSETTA(x, vars = vars)
-  
+
   # correct object
   expect_true(inherits(r, 'data.frame'))
-  
+
   # input / output are conformal
   expect_true(nrow(r) == nrow(x))
-  
+
   # output contains new columns
   expect_true(all(c('theta_r', 'theta_s', 'alpha', 'npar', 'ksat') %in% names(r)))
-  
+
 })
 
 test_that("correct model selection in the presence of NA", {
-  
+
   skip_if_offline()
-
-  # hack for in-house testing only
-  # WWW services aren't always available and will cause CRAN to drop our package if tests fail
-  if( ! getOption('.soilDB_testNetworkFunctions') )  {
-    skip("in-house testing only")
-  }
-
-
+
+  skip_on_cran()
+
   # sprinkle NA
   x$dbthirdbar_r[1] <- NA
   x$wthirdbar_decimal[2] <- NA
   x$wfifteenbar_decimal[3] <- NA
   x$sandtotal_r[9] <- NA
   x[10, ] <- NA
-  
+
   # attempting to use all possible soil properties
   vars <- c('sandtotal_r', 'silttotal_r', 'claytotal_r', 'dbthirdbar_r', 'wthirdbar_decimal', 'wfifteenbar_decimal')
-  
+
   # submit request
   r <- ROSETTA(x, vars = vars)
-  
+
   # missing 1/3 bar Db -> model 2
   expect_true(r$.rosetta.model[1] == 2)
-  
+
   # missing 1/3 bar WT -> model 3
   expect_true(r$.rosetta.model[2] == 3)
-  
+
   # missing 15 bar WT -> model 4
   expect_true(r$.rosetta.model[3] == 4)
-  
+
   # no records missing -> model 5
   expect_true(all(r$.rosetta.model[4:8] == 5))
-  
+
   # missing sand -> NA
   expect_true(is.na(r$theta_r[9]) & (r$.rosetta.model[9] == -1))
-  
+
   # all NA
   expect_true(all(is.na(r[10, c('theta_r', 'theta_s', 'alpha', 'npar', 'ksat')])))
-  
-  
+
+
 })
diff --git a/tests/testthat/test-SDA_query.R b/tests/testthat/test-SDA_query.R
@@ -5,11 +5,7 @@ test_that("SDA_query() works", {
 
   skip_if_offline()
 
-  # hack for in-house testing only
-  # WWW services aren't always available and will cause CRAN to drop our package if tests fail
-  if( ! getOption('.soilDB_testNetworkFunctions') )  {
-    skip("in-house testing only")
-  }
+  skip_on_cran()
 
   ## sample data
 
@@ -40,11 +36,7 @@ test_that("SDA_query() returns expected result", {
 
   skip_if_offline()
 
-  # hack for in-house testing only
-  # WWW services aren't always available and will cause CRAN to drop our package if tests fail
-  if( ! getOption('.soilDB_testNetworkFunctions') ) {
-    skip("in-house testing only")
-  }
+  skip_on_cran()
 
   # table dimensions
   expect_equal(nrow(x.1), 1)
@@ -61,11 +53,7 @@ test_that("SDA_query() SQL error / no results -> NULL", {
 
   skip_if_offline()
 
-  # hack for in-house testing only
-  # WWW services aren't always available and will cause CRAN to drop our package if tests fail
-  if( ! getOption('.soilDB_testNetworkFunctions') ) {
-    skip("in-house testing only")
-  }
+  skip_on_cran()
 
   # bad SQL should result in a warning and try-error result.
   expect_true(inherits(expect_warning(SDA_query("SELECT this from that")), 'try-error'))
@@ -81,11 +69,7 @@ test_that("SDA_spatialQuery() simple spatial query, tabular results", {
 
   skip_if_offline()
 
-  # hack for in-house testing only
-  # WWW services aren't always available and will cause CRAN to drop our package if tests fail
-  if( ! getOption('.soilDB_testNetworkFunctions') ) {
-    skip("in-house testing only")
-  }
+  skip_on_cran()
 
   res <- suppressWarnings(SDA_spatialQuery(p, what = 'mukey'))
 
@@ -101,11 +85,7 @@ test_that("SDA_spatialQuery() simple spatial query, spatial results", {
 
   skip_if_offline()
 
-  # hack for in-house testing only
-  # WWW services aren't always available and will cause CRAN to drop our package if tests fail
-  if( ! getOption('.soilDB_testNetworkFunctions') ) {
-    skip("in-house testing only")
-  }
+  skip_on_cran()
 
   # test with default db = "SSURGO"
   res <- suppressWarnings(SDA_spatialQuery(p, what = 'geom'))
@@ -128,11 +108,7 @@ test_that("SDA_query() interprets column names", {
 
   skip_if_offline()
 
-  # hack for in-house testing only
-  # WWW services aren't always available and will cause CRAN to drop our package if tests fail
-  if( ! getOption('.soilDB_testNetworkFunctions') ) {
-    skip("in-house testing only")
-  }
+  skip_on_cran()
 
   # x.3 is from the component table
   expect_equal(
@@ -148,11 +124,7 @@ test_that("SDA_query() interprets data type correctly", {
 
   skip_if_offline()
 
-  # hack for in-house testing only
-  # WWW services aren't always available and will cause CRAN to drop our package if tests fail
-  if( ! getOption('.soilDB_testNetworkFunctions') ) {
-    skip("in-house testing only")
-  }
+  skip_on_cran()
 
   # x.3 is from the component table
   expect_true(inherits(x.3$mukey, 'integer'))
@@ -173,11 +145,7 @@ test_that("SDA_query() works with multi-line records", {
 
   skip_if_offline()
 
-  # hack for in-house testing only
-  # WWW services aren't always available and will cause CRAN to drop our package if tests fail
-  if( ! getOption('.soilDB_testNetworkFunctions') ) {
-    skip("in-house testing only")
-  }
+  skip_on_cran()
 
   # https://github.com/ncss-tech/soilDB/issues/28
   expect_true(inherits(x.4, 'data.frame'))