tests made robust to failing APIS, #125

DESCRIPTION

@@ -2,7 +2,7 @@ Package: soilDB
 Type: Package
 Title: Soil Database Interface
 Version: 2.5
-Date: 2020-01-23
+Date: 2020-01-27
 Authors@R: c(person(given="Dylan", family="Beaudette", role = c("cre", "aut"), email = "[email protected]"), person(given="Jay", family="Skovlin", role = c("aut")), person(given="Stephen", family="Roecker", role = c("aut")) )
 Author: Dylan Beaudette [cre, aut], Jay Skovlin [aut], Stephen Roecker [aut]
 Maintainer: Dylan Beaudette <[email protected]>

R/openNASISchannel.R

@@ -17,4 +17,15 @@
     stop("no local NASIS database available", call.=FALSE)
 
   return(channel)
-}
+}
+
+# check for presence of `nasis_local` ODBC data source
+# primarily used in test suite
+.local_NASIS_defined <- function() {
+  # check for user-defined
+  if('nasis_local' %in% names(RODBC::odbcDataSources())) {
+    return(TRUE)
+  } else {
+    return(FALSE)
+  }
+}

tests/testthat.R

@@ -3,5 +3,4 @@ library(soilDB)
 
 
 
-
 test_check("soilDB")

tests/testthat/test-OSDquery.R

@@ -4,6 +4,12 @@ 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # a message is printed and NULL returned when no results
   res <- suppressMessages(OSDquery(geog_assoc_soils = 'pardee'))
 
@@ -17,6 +23,12 @@ 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # a message is printed and NULL returned when no results
   res <- suppressMessages(OSDquery(geog_assoc_soils = 'XXX'))
   expect_null(res)

tests/testthat/test-SDA_query.R

@@ -5,6 +5,12 @@ 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   ## sample data
 
   # single-table result
@@ -34,6 +40,12 @@ 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # table dimensions
   expect_equal(nrow(x.1), 1)
   expect_equal(ncol(x.1), 2)
@@ -49,6 +61,12 @@ 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # bad SQL should result in a local error
   expect_error(SDA_query("SELECT this from that"))
 
@@ -63,6 +81,12 @@ 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   res <- SDA_spatialQuery(p, what = 'mukey')
 
   # testing known values
@@ -77,6 +101,12 @@ 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   res <- SDA_spatialQuery(p, what = 'geom')
 
   # testing known values
@@ -89,6 +119,12 @@ 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # x.3 is from the component table
   expect_equal(
     names(x.3), 
@@ -103,6 +139,12 @@ 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # x.3 is from the component table
   expect_true(inherits(x.3$mukey, 'integer'))
   expect_true(inherits(x.3$cokey, 'integer'))
@@ -122,6 +164,12 @@ 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # https://github.com/ncss-tech/soilDB/issues/28
   expect_true(inherits(x.4, 'data.frame'))
   expect_true(nrow(x.4) == 6)

tests/testthat/test-fetchKSSL.R

@@ -4,6 +4,12 @@ test_that("fetchKSSL() 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   ## sample data
   x <<- fetchKSSL(series='sierra')
   x.morph <<- fetchKSSL(series='sierra', returnMorphologicData = TRUE)
@@ -20,6 +26,12 @@ test_that("fetchKSSL() returns an SPC or list", {
 
   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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # SPC + morphologic data
   expect_true(inherits(x.morph, 'list'))
   expect_true(inherits(x.morph$SPC, 'SoilProfileCollection'))
@@ -35,6 +47,12 @@ test_that("fetchKSSL() returns reasonable data", {
 
   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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # standard request
   expect_equal(nrow(site(x)) > 0, TRUE)
   expect_equal(nrow(horizons(x)) > 0, TRUE)
@@ -47,6 +65,12 @@ test_that("fetchKSSL() returns data associated with named series (sierra)", {
 
   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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # all of the results should contain the search term
   f <- grepl('sierra', x$taxonname, ignore.case = TRUE)
   expect_equal(all(f), TRUE)
@@ -58,6 +82,12 @@ test_that("fetchKSSL() 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # a message is printed and NULL returned when no results
   res <- suppressMessages(fetchKSSL(series='XXX'))
   expect_null(res)
@@ -69,6 +99,12 @@ test_that("fetchKSSL() fails gracefully when morphology data are missing", {
 
   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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # pedon_key 37457 is missing:
   # * most lab data
   # * all morphologic data

tests/testthat/test-fetchNASIS.R

@@ -7,14 +7,6 @@ context("fetchNASIS() -- requires local NASIS and ODBC connection")
 # * pedons / component missing from local database
 
 
-check_local_NASIS <- function() {
-  # check for connection
-  if(! 'nasis_local' %in% names(RODBC::odbcDataSources())) {
-    skip("local NASIS database not available")
-  }
-}
-
-
 check_local_NASIS_pedons_available <- function() {
 
   # attempt to load pedons
@@ -55,7 +47,11 @@ check_local_NASIS_components_available <- function() {
 test_that("fetchNASIS(from='pedons') returns reasonable data", {
 
   # test for conditions permitting this test to run
-  check_local_NASIS()
+  if(! soilDB:::.local_NASIS_defined()) {
+    skip("local NASIS database not available")
+  }
+
+  # pedons must be present for tests
   check_local_NASIS_pedons_available()
 
   # get data
@@ -79,7 +75,11 @@ test_that("fetchNASIS(from='pedons') returns reasonable data", {
 test_that("fetchNASIS(from='pedons') nullFragsAreZero works as expected", {
 
   # test for conditions permitting this test to run
-  check_local_NASIS()
+  if(! soilDB:::.local_NASIS_defined()) {
+    skip("local NASIS database not available")
+  }
+
+  # components must be present for tests
   check_local_NASIS_pedons_available()
 
   # get data
@@ -94,8 +94,13 @@ test_that("fetchNASIS(from='pedons') nullFragsAreZero works as expected", {
 
 test_that("fetchNASIS(from='components') returns reasonable data", {
 
-  # test for conditions permitting this test to run
-  check_local_NASIS()
+  # hack for in-house testing only
+  # WWW services aren't always available and will cause CRAN to drop our package if tests fail
+  if(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
+  # must have components to complete test
   check_local_NASIS_components_available()
 
   # get data

tests/testthat/test-fetchNASISLabData.R

@@ -7,13 +7,6 @@ context("fetchNASISLabData() -- requires local NASIS and ODBC connection")
 # * pedons / component missing from local database
 
 
-check_local_NASIS <- function() {
-  # check for connection
-  if(! 'nasis_local' %in% names(RODBC::odbcDataSources())) {
-    skip("local NASIS database not available")
-  }
-}
-
 
 check_local_NASIS_labdata_available <- function() {
 
@@ -30,7 +23,11 @@ check_local_NASIS_labdata_available <- function() {
 test_that("fetchNASISLabData returns reasonable data", {
 
   # test for conditions permitting this test to run
-  check_local_NASIS()
+  if(! soilDB:::.local_NASIS_defined()) {
+    skip("local NASIS database not available")
+  }
+
+  # test for lab data to check
   check_local_NASIS_labdata_available()
 
   # get data
@@ -44,4 +41,4 @@ test_that("fetchNASISLabData returns reasonable data", {
   expect_equal(idname(x), 'labpeiid')
   expect_equal(hzidname(x), 'labphiid')
   expect_equal(horizonDepths(x), c("hzdept", "hzdepb"))
-})
+})

tests/testthat/test-fetchNASISWebReport.R

@@ -4,6 +4,12 @@ test_that("fetchNASISWebReport() 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   ## sample data
   pn <- "MLRA 18 - Sierra sandy loam, 2 to 9 percent slopes"
 
@@ -19,6 +25,12 @@ test_that("fetchNASISWebReport() returns an SPC of component/horizon data and da
 
   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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # SPC + morphologic data
   expect_true(inherits(x$spc, 'SoilProfileCollection'))
   expect_true(inherits(x$mapunit, 'data.frame'))
@@ -30,6 +42,12 @@ test_that("fetchNASISWebReport() returns reasonable data", {
 
   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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # standard request
   expect_equal(nrow(site(x$spc)) > 0, TRUE)
   expect_equal(nrow(horizons(x$spc)) > 0, TRUE)
@@ -43,6 +61,12 @@ test_that("fetchNASISWebReport() returns data for component name (Sierra)", {
 
   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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # all major components are Sierra
   f <- grepl('Sierra', x$spc$compname[x$spc$majcompflag == 1], ignore.case = TRUE)
   expect_equal(all(f), TRUE)
@@ -54,6 +78,12 @@ test_that("fetchNASISWebReport() 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(! soilDB:::.local_NASIS_defined()) {
+    skip("in-house testing only")
+  }
+
   # a message is printed and NULL returned when no results
   res <- suppressMessages(fetchNASISWebReport(projectname='XXX'))
   expect_null(res)