more changes to make pipeline run offline

inst/tinytest/test_functions.R

@@ -23,19 +23,6 @@ if (test_file_exists(Sys.which("mp"), access = "x")) {
   unlink(dir, recursive = TRUE)
 }
 
-# test URL assertion
-expect_silent(assert_url("https://www.usa.gov/"))
-expect_error(assert_url("https://fail/on/bad/url/"))
-expect_error(assert_url("https://anyapi.io/api/v1/exchange/rates?base=NAN&apiKey=123"))
-
-# test downloading file
-if (curl::has_internet()) {
-  url <- "https://code.usgs.gov/inl/inldata/-/raw/main/CODE_OF_CONDUCT.md"
-  file <- download_file(url, cachedir = tempdir(), quiet = TRUE)
-  expect_file_exists(file, access = "rw")
-  unlink(file)
-}
-
 # test cleaning simple feature
 x <- clean_sf(cities,
   cols = c("key" = "id", "geometry" = "geometry"),
@@ -72,3 +59,19 @@ unlink(destdir, recursive = TRUE)
 # test cleaning a simple feature
 x <- clean_sf(inl, cols = "geometry", crs = sf::st_crs(3857))
 expect_multi_class(x, classes = c("sf", "data.frame"))
+
+# require internet connection
+if (curl::has_internet()) {
+
+  # test URL assertion
+  expect_silent(assert_url("https://www.usa.gov/"))
+  expect_error(assert_url("https://fail/on/bad/url/"))
+  expect_error(assert_url("https://anyapi.io/api/v1/exchange/rates?base=NAN&apiKey=123"))
+
+  # test downloading file
+  url <- "https://code.usgs.gov/inl/inldata/-/raw/main/CODE_OF_CONDUCT.md"
+  file <- download_file(url, cachedir = tempdir(), quiet = TRUE)
+  expect_file_exists(file, access = "rw")
+  unlink(file)
+
+}

inst/tinytest/test_make_datasets.R

@@ -3,113 +3,118 @@ library("tinytest")
 library("checkmate")
 using("checkmate")
 
-# test existence of data-raw folder
-destdir <- tempfile("")
-expect_error(
-  current = make_datasets(path = tempdir(), destdir = destdir),
-  pattern = "does not exist"
-)
-unlink(destdir)
+# require internet connection
+if (curl::has_internet()) {
 
-# test making parameters
-pcodes <- "07000"
-n <- length(pcodes)
-x <- inldata:::mds_parameters(pcodes)
-expect_data_frame(x, nrows = n, col.names = "named")
-x <- inldata:::tabulate_parm_data(x, samples)
-expect_data_frame(x, nrows = n, col.names = "named")
+  # test existence of data-raw folder
+  destdir <- tempfile("")
+  expect_error(
+    current = make_datasets(path = tempdir(), destdir = destdir),
+    pattern = "does not exist"
+  )
+  unlink(destdir)
 
-# test making detection limits
-data <- data.frame(
-  "srsname" = c("Tritium", "Tritium"),
-  "pcode" = c("07000", "07000"),
-  "unit_cd" = c("pCi/L", "pCi/L"),
-  "lab_det_lim_va" = c("500", "200"),
-  "min_dt" = c("1949-01-16", "2003-04-01"),
-  "reference" = c("Bartholomay", "Bartholomay")
-)
-x <- inldata:::mds_dl(data, parameters)
-expect_data_frame(x, nrows = nrow(data), col.names = "named")
+  # test making parameters
+  pcodes <- "07000"
+  n <- length(pcodes)
+  x <- inldata:::mds_parameters(pcodes)
+  expect_data_frame(x, nrows = n, col.names = "named")
+  x <- inldata:::tabulate_parm_data(x, samples)
+  expect_data_frame(x, nrows = n, col.names = "named")
 
-# test making benchmarks
-bm <- data.frame(
-  "Chemical Name" = "trans-1,3-Dichloropropene",
-  "CAS Registry Number" = "10061-02-6",
-  "USGS Parameter Code" = "34699",
-  "Chemical Class" = "VOC",
-  "MCL (micrograms/L)" = NA_character_,
-  "Chronic Noncancer HHBP (micrograms/L)" = NA_character_,
-  "Carcinogenic HHBP (micrograms/L)" = NA_character_,
-  "Noncancer HBSL (micrograms/L)" = "200",
-  "Cancer HBSL (micrograms/L)" = "0.3-30",
-  "Benchmark Remarks" = NA_character_,
-  check.names = FALSE
-)
-mcl_extras <- data.frame(
-  "srsname" = "Tritium",
-  "pcode" = "07000",
-  "mcl" = "20000",
-  "unit_cd" = "pCi/L"
-)
-n <- nrow(bm) + nrow(mcl_extras)
-x <- inldata:::mds_benchmarks(bm, mcl_extras, parameters)
-expect_data_frame(x, nrows = n, col.names = "named")
+  # test making detection limits
+  data <- data.frame(
+    "srsname" = c("Tritium", "Tritium"),
+    "pcode" = c("07000", "07000"),
+    "unit_cd" = c("pCi/L", "pCi/L"),
+    "lab_det_lim_va" = c("500", "200"),
+    "min_dt" = c("1949-01-16", "2003-04-01"),
+    "reference" = c("Bartholomay", "Bartholomay")
+  )
+  x <- inldata:::mds_dl(data, parameters)
+  expect_data_frame(x, nrows = nrow(data), col.names = "named")
 
-# test making sites
-data <- data.frame(
-  "agency_cd" = "USGS",
-  "site_no" = "432700112470801",
-  "station_nm" = "02N 31E 35DCC1 USGS 1",
-  "network_cd" = "A",
-  "pos" = "3"
-)
-x <- inldata:::mds_sites(data, crs)
-expect_multi_class(x, classes = c("sf", "data.frame"))
-expect_set_equal(nrow(x), nrow(data))
-y <- inldata:::tabulate_site_data(x, samples, gwl, swm)
-expect_data_frame(y, nrows = nrow(x), col.names = "named")
+  # test making benchmarks
+  bm <- data.frame(
+    "Chemical Name" = "trans-1,3-Dichloropropene",
+    "CAS Registry Number" = "10061-02-6",
+    "USGS Parameter Code" = "34699",
+    "Chemical Class" = "VOC",
+    "MCL (micrograms/L)" = NA_character_,
+    "Chronic Noncancer HHBP (micrograms/L)" = NA_character_,
+    "Carcinogenic HHBP (micrograms/L)" = NA_character_,
+    "Noncancer HBSL (micrograms/L)" = "200",
+    "Cancer HBSL (micrograms/L)" = "0.3-30",
+    "Benchmark Remarks" = NA_character_,
+    check.names = FALSE
+  )
+  mcl_extras <- data.frame(
+    "srsname" = "Tritium",
+    "pcode" = "07000",
+    "mcl" = "20000",
+    "unit_cd" = "pCi/L"
+  )
+  n <- nrow(bm) + nrow(mcl_extras)
+  x <- inldata:::mds_benchmarks(bm, mcl_extras, parameters)
+  expect_data_frame(x, nrows = n, col.names = "named")
 
-# test making surface-water measurements
-site_no <- "13131000"
-is <- sites$site_no == site_no
-x <- inldata:::mds_swm(sites = sites[is, ], tz = "America/Denver")
-expect_data_frame(x, min.rows = 1, col.names = "named")
+  # test making sites
+  data <- data.frame(
+    "agency_cd" = "USGS",
+    "site_no" = "432700112470801",
+    "station_nm" = "02N 31E 35DCC1 USGS 1",
+    "network_cd" = "A",
+    "pos" = "3"
+  )
+  x <- inldata:::mds_sites(data, crs)
+  expect_multi_class(x, classes = c("sf", "data.frame"))
+  expect_set_equal(nrow(x), nrow(data))
+  y <- inldata:::tabulate_site_data(x, samples, gwl, swm)
+  expect_data_frame(y, nrows = nrow(x), col.names = "named")
 
-# test making groundwater levels
-site_no <- "433500112572501"
-is <- sites$site_no == site_no
-x <- inldata:::mds_gwl(sites = sites[is, ], tz = "America/Denver")
-expect_data_frame(x, min.rows = 1, col.names = "named")
+  # test making surface-water measurements
+  site_no <- "13131000"
+  is <- sites$site_no == site_no
+  x <- inldata:::mds_swm(sites = sites[is, ], tz = "America/Denver")
+  expect_data_frame(x, min.rows = 1, col.names = "named")
 
-# test making units
-data <- data.frame(
-  "unit_cd" = "deg C",
-  "unit_ds" = "degrees Celsius"
-)
-x <- inldata:::mds_units(data)
-expect_data_frame(x, nrows = nrow(data), col.names = "named")
+  # test making groundwater levels
+  site_no <- "433500112572501"
+  is <- sites$site_no == site_no
+  x <- inldata:::mds_gwl(sites = sites[is, ], tz = "America/Denver")
+  expect_data_frame(x, min.rows = 1, col.names = "named")
 
-# test making background concentrations
-data <- data.frame(
-  "srsname" = "Sodium",
-  "pcode" = "00930",
-  "unit_cd" = "mg/L",
-  "bkgrd_min" = "8.3",
-  "bkgrd_max" = "14.8",
-  "reference" = "Bartholomay"
-)
-x <- inldata:::mds_background(data, parameters)
-expect_data_frame(x, nrows = nrow(data), col.names = "named")
+  # test making units
+  data <- data.frame(
+    "unit_cd" = "deg C",
+    "unit_ds" = "degrees Celsius"
+  )
+  x <- inldata:::mds_units(data)
+  expect_data_frame(x, nrows = nrow(data), col.names = "named")
 
-# test unit conversion
-data <- data.frame(
-  "pcode" = c("01065", "00631"),
-  "unit_cd" = c("ug/L", "ug/L")
-)
-x <- inldata:::convert_units(data, parameters)
-expect_data_frame(x,
-  types = c("character", "character", "character", "numeric"),
-  nrows = nrow(data),
-  col.names = "named"
-)
-expect_set_equal(colnames(x), c("pcode", "from", "to", "mult"))
+  # test making background concentrations
+  data <- data.frame(
+    "srsname" = "Sodium",
+    "pcode" = "00930",
+    "unit_cd" = "mg/L",
+    "bkgrd_min" = "8.3",
+    "bkgrd_max" = "14.8",
+    "reference" = "Bartholomay"
+  )
+  x <- inldata:::mds_background(data, parameters)
+  expect_data_frame(x, nrows = nrow(data), col.names = "named")
+
+  # test unit conversion
+  data <- data.frame(
+    "pcode" = c("01065", "00631"),
+    "unit_cd" = c("ug/L", "ug/L")
+  )
+  x <- inldata:::convert_units(data, parameters)
+  expect_data_frame(x,
+    types = c("character", "character", "character", "numeric"),
+    nrows = nrow(data),
+    col.names = "named"
+  )
+  expect_set_equal(colnames(x), c("pcode", "from", "to", "mult"))
+
+}