test coverage

R/subset_nhdplus.R

@@ -220,7 +220,7 @@ intersection_write <- function(layer_name, data_path, envelope,
   if (nrow(out) > 0) {
     if (status) message(paste("Writing", layer_name))
     if(is.null(output_file)) {
-      return(layer)
+      return(out)
     } else {
       sf::write_sf(out, output_file, layer_name)
       return(layer_name)
@@ -433,9 +433,6 @@ get_catchment_subset <- function(nhdplus_data, comids, output_file,
     if (grepl("*.rds$", catchment_path)) {
       catchment <- readRDS(catchment_path)
     } else {
-      if(!layer_name %in% st_layers(catchment_path)$name) {
-        layer_name <- "NHDPlusCatchment"
-      }
       catchment <- sf::read_sf(catchment_path, layer_name)
       catchment <- rename_nhdplus(catchment)
     }

tests/testthat/test_plot_nhdplus.R

@@ -1,7 +1,22 @@
 context("plot tests")
 
 test_that("basics work", {
+  skip_on_cran()
   site <- "USGS-05428500"
   d <-  nhdplusTools:::get_plot_data(site)
   expect_equal(names(d), c("plot_bbox", "sites", "flowline", "basin"))
+
+  p_ready <- nhdplusTools:::gt(d$flowline)
+  expect_equal(st_crs(p_ready), st_crs(3857))
+  expect_s3_class(p_ready, "sfc_LINESTRING")
+
+  pdf(NULL)
+  tempd <- tempdir()
+  dir.create(tempd, recursive = TRUE)
+  tempf <- file.path(tempd, "temp.png")
+  png(file.path(tempd, "temp.png"))
+  plot_nhdplus("USGS-05428500")
+  dev.off()
+
+  expect_true(file.exists(tempf))
 })

tests/testthat/test_subset.R

@@ -1,7 +1,6 @@
 context("subset")
 
-
-test_that("subset runs as expected", {
+test_that("subset errors", {
 
   temp_dir <- tempdir()
 
@@ -11,23 +10,42 @@ test_that("subset runs as expected", {
                               output_file = tempfile(fileext = ".gpkg")),
                "couldn't find nhdplus data")
 
+  expect_error(subset_nhdplus(comids = "dud",
+                              output_file = "test",
+                              "output_file must end in '.gpkg'"))
+
+  expect_error(subset_nhdplus(output_file = "test",
+                              "must provide comids or bounding box"))
+
+  nhdplus_path("../NHDPlusV21_National_Seamless.gdb")
+})
+
+test_that("subset runs as expected", {
+
+  temp_dir <- tempdir()
+  dir.create(temp_dir, recursive = TRUE, showWarnings = FALSE)
+
   sample_data <- system.file("extdata/sample_natseamless.gpkg",
                              package = "nhdplusTools")
 
+  expect_equal(nhdplusTools:::get_catchment_layer_name(TRUE, sample_data), "CatchmentSP")
+
+  nc <- read_sf(system.file("shape/nc.shp", package="sf"))
+  tempf <- file.path(temp_dir, "temp.geojson")
+  write_sf(nc, tempf, "Catchment")
+  expect_equal(nhdplusTools:::get_catchment_layer_name(FALSE, tempf), "Catchment")
+
   nhdplus_path(sample_data)
 
   if (!dir.exists(temp_dir)) dir.create(temp_dir)
 
   staged_nhdplus <- stage_national_data(output_path = temp_dir)
 
-  start_comid <- 13293392
-
-  sample_flines <- readRDS(staged_nhdplus$flowline)
-
-  comids <- get_UM(sample_flines, start_comid)
+  comids <- get_UM(readRDS(staged_nhdplus$flowline), 13293392)
 
   out_file <- tempfile(fileext = ".gpkg")
 
+  # No output file
   fi <- subset_nhdplus(comids = comids,
                        output_file = NULL,
                        nhdplus_data = sample_data,
@@ -36,14 +54,18 @@ test_that("subset runs as expected", {
   expect_equal(names(fi), c("NHDFlowline_Network", "CatchmentSP", "NHDArea",
                             "NHDWaterbody", "Gage", "Sink",
                             "NHDFlowline_NonNetwork"))
+  expect_equal(nrow(fi$CatchmentSP), 4)
+  expect_equal(nrow(fi$NHDWaterbody), 1)
 
+  # write to output file
   fi <- subset_nhdplus(comids = comids,
                  output_file = out_file,
                  nhdplus_data = sample_data,
                  status = FALSE)
 
   expect_equal(fi, out_file)
 
+  # don't overwrite
   expect_error(
     subset_nhdplus(comids = comids,
                    output_file = out_file,
@@ -52,6 +74,7 @@ test_that("subset runs as expected", {
                    status = FALSE),
     "output_file exists and overwrite is false.")
 
+  # check that status works
   messages <- capture_messages(
     fi <- subset_nhdplus(comids = comids,
                          output_file = out_file,
@@ -67,12 +90,9 @@ test_that("subset runs as expected", {
 
   check_layers()
 
-  expect_error(subset_nhdplus(comids = "dud",
-                              output_file = "test",
-                              "output_file must end in '.gpkg'"))
-
   unlink(file.path(temp_dir, "*"))
 
+  # Make sure passing data directly works
   fi <- subset_nhdplus(comids = comids,
                        output_file = out_file,
                        nhdplus_data = sample_data,
@@ -86,6 +106,8 @@ test_that("subset runs as expected", {
   nhdplus_path("../NHDPlusV21_National_Seamless.gdb")
 
   skip_on_cran()
+
+  # download option
   fi <- subset_nhdplus(comids = comids,
                        output_file = out_file,
                        nhdplus_data = "download",
@@ -96,70 +118,18 @@ test_that("subset runs as expected", {
 
   })
 
-test_that("prep_nhdplus runs as expected", {
-
-  temp_dir <- tempdir()
-
-  if (!dir.exists(temp_dir)) dir.create(temp_dir)
-
-  expect_error(suppressWarnings(stage_national_data()),
-               paste("Didn't find NHDPlus national data in default",
-                     "location: ../NHDPlusV21_National_Seamless.gdb"))
-
-  sample_gpkg <- file.path(temp_dir, "sample_natseamless.gpkg")
-
-  file.copy(system.file("extdata/sample_natseamless.gpkg",
-                        package = "nhdplusTools"), sample_gpkg)
-
-  nhdplus_path(sample_gpkg)
-
-  expect_warning(temp_data <- stage_national_data(),
-                 regexp = paste0("No output path provided, using:.*"))
-
-  temp_data <- lapply(temp_data, unlink)
-
-  temp_data <- stage_national_data(output_path = temp_dir)
-
-  expect_true(suppressWarnings(all(lapply(temp_data, file.exists))))
-
-  temp_data <- lapply(temp_data, unlink)
-
-  nhdplus_path("bogus")
-
-  expect_error(suppressWarnings(stage_national_data()),
-               paste("Didn't find NHDPlus national data in",
-                     "user specified location: bogus"))
-
-  nhdplus_path(sample_gpkg)
-
-  expect_error(stage_national_data(include = c("bogus"),
-                                   output_path = "data/temp"),
-               paste("Got invalid include entries. Expect one",
-                     "or more of: attribute, flowline, catchment."))
-
-  temp_data <- stage_national_data(output_path = temp_dir)
-
-  expect_equal(
-    capture_warnings(
-      temp_data <- stage_national_data(output_path = temp_dir)),
-    c("attributes file exists", "flowline file exists",
-      "catchment already exists."))
-
-  temp_data <- lapply(temp_data, unlink)
-
-  unlink(sample_gpkg)
-
-})
-
 test_that("subset works with HR", {
   work_dir <- tempdir()
 
   skip_on_cran()
   get_test_file(work_dir)
 
   hr <- get_nhdplushr(work_dir, out_gpkg = file.path(work_dir, "temp.gpkg"),
-                       layers = c("NHDFlowline", "NHDPlusCatchment", "NHDWaterbody",
-                                  "NHDArea", "NHDPlusSink"))
+                      layers = c("NHDFlowline", "NHDPlusCatchment", "NHDWaterbody",
+                                 "NHDArea", "NHDPlusSink"))
+
+  expect_equal(nhdplusTools:::get_catchment_layer_name(TRUE, hr), "NHDPlusCatchment")
+  expect_equal(nhdplusTools:::get_catchment_layer_name(FALSE, hr), "NHDPlusCatchment")
 
   flowlines <- sf::read_sf(hr, "NHDFlowline")
 
@@ -207,4 +177,73 @@ test_that("subset by bounding box", {
                        status = FALSE)
 
   check_layers()
+
+  expect_warning(fi <- subset_nhdplus(comids = c(1, 2, 3),
+                       bbox = as.numeric(bbox),
+                       nhdplus_data = sample_data,
+                       overwrite = TRUE,
+                       simplified = TRUE,
+                       status = FALSE),
+                 "using bounding box rather than submitted comids")
+
+  bbox[1] <- -190
+  expect_error(fi <- subset_nhdplus(bbox = as.numeric(bbox),
+                       nhdplus_data = sample_data,
+                       status = FALSE),
+               "invalid bbox entry")
+})
+
+test_that("prep_nhdplus runs as expected", {
+
+  temp_dir <- tempdir()
+
+  if (!dir.exists(temp_dir)) dir.create(temp_dir)
+
+  expect_error(suppressWarnings(stage_national_data()),
+               paste("Didn't find NHDPlus national data in default",
+                     "location: ../NHDPlusV21_National_Seamless.gdb"))
+
+  sample_gpkg <- file.path(temp_dir, "sample_natseamless.gpkg")
+
+  file.copy(system.file("extdata/sample_natseamless.gpkg",
+                        package = "nhdplusTools"), sample_gpkg)
+
+  nhdplus_path(sample_gpkg)
+
+  expect_warning(temp_data <- stage_national_data(),
+                 regexp = paste0("No output path provided, using:.*"))
+
+  temp_data <- lapply(temp_data, unlink)
+
+  temp_data <- stage_national_data(output_path = temp_dir)
+
+  expect_true(suppressWarnings(all(lapply(temp_data, file.exists))))
+
+  temp_data <- lapply(temp_data, unlink)
+
+  nhdplus_path("bogus")
+
+  expect_error(suppressWarnings(stage_national_data()),
+               paste("Didn't find NHDPlus national data in",
+                     "user specified location: bogus"))
+
+  nhdplus_path(sample_gpkg)
+
+  expect_error(stage_national_data(include = c("bogus"),
+                                   output_path = "data/temp"),
+               paste("Got invalid include entries. Expect one",
+                     "or more of: attribute, flowline, catchment."))
+
+  temp_data <- stage_national_data(output_path = temp_dir)
+
+  expect_equal(
+    capture_warnings(
+      temp_data <- stage_national_data(output_path = temp_dir)),
+    c("attributes file exists", "flowline file exists",
+      "catchment already exists."))
+
+  temp_data <- lapply(temp_data, unlink)
+
+  unlink(sample_gpkg)
+
 })