Validations and tests RE: #149 #146

misc/validate-NASIS-results.R

@@ -0,0 +1,67 @@
+## validation of NASIS-functionality for nasisDBI PR
+## git shell command to list files changed in the PR
+
+# git diff --name-only master...nasisDBI | grep -E get\\|NASIS\\|fetch
+
+f <- read.table(text = "R/fetchNASIS.R
+                        R/fetchNASIS_pedons.R
+                        R/getHzErrorsNASIS.R
+                        R/get_RMF_from_NASIS_db.R
+                        R/get_colors_from_NASIS_db.R
+                        R/get_component_data_from_NASIS_db.R
+                        R/get_concentrations_from_NASIS_db.R
+                        R/get_cosoilmoist_from_NASIS.R
+                        R/get_extended_data_from_NASIS_db.R
+                        R/get_hz_data_from_NASIS_db.R
+                        R/get_lablayer_data_from_NASIS_db.R
+                        R/get_labpedon_data_from_NASIS_db.R
+                        R/get_phfmp_from_NASIS_db.R
+                        R/get_phlabresults_data_from_NASIS_db.R
+                        R/get_projectmapunit_from_NASIS.R
+                        R/get_site_data_from_NASIS_db.R
+                        R/get_text_notes_from_NASIS_db.R
+                        R/get_veg_data_from_NASIS_db.R
+                        R/get_vegplot_data_from_NASIS_db.R 
+                        R/openNASISchannel.R")$V1
+                        # R/dbQueryNASIS.R
+                        # R/get_soilseries_from_NASIS.R
+                        # man/dbConnectNASIS.Rd
+                        # man/dbQueryNASIS.Rd
+                        # man/fetchNASIS.Rd
+                        # man/getHzErrorsNASIS.Rd
+                        # misc/man-deprecated/fetchNASIS.Rd
+                        # 
+library(soilDB)
+
+fnames <- sapply(f, function(x) { 
+  spv <- evalSource(x, package = "soilDB")
+  # source(x)
+  names(as.list(spv)) 
+})
+
+test <- lapply(fnames, function(fname) {
+    lapply(fname, function(FUN) {
+      message(sprintf("Testing: %s", FUN))
+      try(get(FUN, envir = as.environment("package:soilDB"))())
+    })
+  })
+
+res <- unlist(lapply(names(test), function(x) lapply(seq_along(test[[x]]), function(y) {
+      res <- inherits(test[[x]][[y]], 'try-error')
+      names(res) <- fnames[[x]][y]
+      res
+    })))
+
+res[which(res)]
+
+# Fixed: Text fields must come at end of query per MSSQL specs
+# get_text_notes_from_NASIS_db()
+
+# Fixed: same as above
+# get_vegplot_location_from_NASIS_db()
+
+# Fixed: 
+# get_vegplot_textnote_from_NASIS_db()
+
+# Relatively rare data  update soon with input from Jay
+# get_vegplot_transpecies_from_NASIS_db()

tests/testthat/test-getHzErrorsNASIS.R

@@ -1,3 +1,3 @@
 test_that("getHzErrorsNASIS works", {
-    expect_silent({test <- getHzErrorsNASIS()})
+    expect_silent({suppressMessages(getHzErrorsNASIS())})
   })

tests/testthat/test-get_text_notes_from_NASIS_db.R

@@ -0,0 +1,3 @@
+test_that("get_text_notes_from_NASIS_db works", {
+  expect_silent({get_text_notes_from_NASIS_db()})
+})