Merge pull request #3 from adamhsparks/example_data

DESCRIPTION

@@ -31,6 +31,7 @@ Imports:
     tidync,
     withr
 Suggests: 
+    httptest2,
     knitr,
     pander,
     rmarkdown,

R/clear_cache.R

@@ -1,7 +1,7 @@
 
 #' Remove Files in Users' Cache Directory
 #'
-#' Removes all files in the \pkg{read.abares} cache if they exist.
+#' Removes all files in the \pkg{read.abares} cache if any exist.
 #'
 #' @examples
 #' # not run because cached files shouldn't exist on CRAN or testing envs
@@ -13,18 +13,14 @@
 #' @export
 
 clear_cache <- function() {
-  f <- list.files(.find_user_cache(),
-                  recursive = TRUE,
-                  full.names = TRUE)
+  f <- .find_user_cache()
 
-  if (length(f > 0)) {
-    unlink(f, recursive = TRUE, force = TRUE)
-  } else {
-    cli::cli_inform(
-      c(
-        "There do not appear to be any files cached for {.pkg {{read.abares}}}
+  if (unlink(f, recursive = TRUE, force = FALSE) == 0)
+    return(invisible(TRUE))
+  cli::cli_inform(
+    c(
+      "There do not appear to be any files cached for {.pkg {{read.abares}}}
         that need to be cleared at this time."
-      )
     )
-  }
+  )
 }

R/get_aagis_regions.R

@@ -1,10 +1,17 @@
+
 #' Get AAGIS Region Mapping Files
 #'
-#' @param cache `Boolean` Cache the \acronym{AAGIS} regions shape files after
-#'  download using `tools::R_user_dir()` to identify the proper directory for
-#'  storing user data in a cache for this package. Defaults to `TRUE`, caching
-#'  the files locally as a native \R object. If `FALSE`, this function uses
-#'  `tempdir()` and the files are deleted upon closing of the \R session.
+#' Download, cache and import the Australian Agricultural and Grazing
+#'  Industries Survey (\acronym{AAGIS} regions geospatial shapefile. Upon
+#'  import, the geometries  are automatically corrected to fix invalid
+#'  geometries that are present in the original shapefile.
+#'
+#' @param cache `Boolean` Cache the \acronym{AAGIS} regions' geospatial file
+#'  after downloading using `tools::R_user_dir("read.abares", "cache")` to
+#'  identify the proper directory for storing user data in a cache for this
+#'  package. Defaults to `TRUE`, caching the files locally as a Geopackage. If
+#'  `FALSE`, this function uses `tempdir()` and the files are deleted upon
+#'  closing of the \R session.
 #'
 #' @examplesIf interactive()
 #' aagis <- get_aagis_regions()
@@ -16,15 +23,16 @@
 #' @family AGFD
 #'
 #' @references <https://www.agriculture.gov.au/abares/research-topics/surveys/farm-definitions-methods#regions>
+#' @source <https://www.agriculture.gov.au/sites/default/files/documents/aagis_asgs16v1_g5a.shp_.zip>
 #' @autoglobal
 #' @export
 
 get_aagis_regions <- function(cache = TRUE) {
-  aagis_sf <- .check_existing_aagis(cache)
-  if (is.null(aagis_sf)) {
-    aagis_sf <- .download_aagis_shp(cache)
+  aagis <- .check_existing_aagis(cache)
+  if (is.null(aagis)) {
+    aagis <- .download_aagis_shp(cache)
   } else {
-    return(aagis_sf)
+    return(aagis)
   }
 }
 
@@ -35,40 +43,43 @@ get_aagis_regions <- function(cache = TRUE) {
 #' cache, but is in `tempdir()`, it is saved to the cache before being returned
 #' in the current session.
 #'
-#'
 #' @return An \cranpkg{sf} object of AAGIS regions
 #' @noRd
 #' @autoglobal
 #' @keywords Internal
 
 .check_existing_aagis <- function(cache) {
-  aagis_rds <- file.path(.find_user_cache(), "aagis_regions_dir/aagis.rds")
+  aagis_gpkg <- file.path(.find_user_cache(), "aagis_regions_dir/aagis.gpkg")
   tmp_shp <- file.path(tempdir(), "aagis_asgs16v1_g5a.shp")
 
-  if (file.exists(aagis_rds)) {
-    return(readRDS(aagis_rds))
+  if (file.exists(aagis_gpkg)) {
+    return(readRDS(aagis_gpkg))
   } else if (file.exists(tmp_shp)) {
-    aagis_sf <- sf::st_read(tmp_shp)
+    aagis_sf <- sf::st_read(tmp_shp, quiet = TRUE)
+    # From checking the unzipped file, some geometries are invalid, this corrects
+    aagis_sf <- sf::st_make_valid(aagis_sf)
     if (cache) {
-      dir.create(dirname(aagis_rds), recursive = TRUE)
-      saveRDS(aagis_sf, file = aagis_rds)
+      dir.create(dirname(aagis_gpkg), recursive = TRUE)
+      sf::st_write(aagis_sf, file = aagis_gpkg, quiet = TRUE)
     }
     return(aagis_sf)
   } else {
-    return(NULL)
+    return(invisible(NULL))
   }
 }
 
 #' Download the AAGIS Regions Shapefile
 #'
-#' Handles downloading and caching (if requested) of AAGIS regions geospatial
-#' data.
+#' Handles downloading, caching (if requested) and importing of AAGIS regions
+#'  geospatial data.  The geometries are corrected for validity before returning
+#'  to the user.
 #'
 #' @param cache `Boolean` Cache the \acronym{AAGIS} regions shape files after
-#'  download using `tools::R_user_dir()` to identify the proper directory for
-#'  storing user data in a cache for this package. Defaults to `TRUE`, caching
-#'  the files locally as a native \R object. If `FALSE`, this function uses
-#'  `tempdir()` and the files are deleted upon closing of the \R session.
+#'  download using `tools::R_user_dir("read.abares")` to identify the proper
+#'  directory for storing user data in a cache for this package. Defaults to
+#'  `TRUE`, caching the files locally as a native \R object. If `FALSE`, this
+#'  function uses `tempdir()` and the files are deleted upon closing of the \R
+#'  session.
 #'
 #' @return An \cranpkg{sf} object of AAGIS regions
 #' @noRd
@@ -81,7 +92,7 @@ get_aagis_regions <- function(cache = TRUE) {
   tmp_zip <- file.path(file.path(tempdir(), "aagis.zip"))
   aagis_zip <- data.table::fifelse(cache, cached_zip, tmp_zip)
   aagis_regions_dir <- dirname(aagis_zip)
-  aagis_rds <- file.path(aagis_regions_dir, "aagis.rds")
+  aagis_gpkg <- file.path(aagis_regions_dir, "aagis.gpkg")
 
   # the user-cache may not exist if caching is enabled for the 1st time
   if (cache && !dir.exists(aagis_regions_dir)) {
@@ -95,10 +106,14 @@ get_aagis_regions <- function(cache = TRUE) {
                   utils::unzip(aagis_zip, exdir = aagis_regions_dir))
 
   aagis_sf <- sf::read_sf(dsn = file.path(aagis_regions_dir,
-                                          "aagis_asgs16v1_g5a.shp"))
+                                          "aagis_asgs16v1_g5a.shp"),
+                          quiet = TRUE)
+
+  # From checking the unzipped file, some geometries are invalid, this corrects
+  aagis_sf <- sf::st_make_valid(aagis_sf)
 
   if (cache) {
-    saveRDS(aagis_sf, file = aagis_rds)
+    sf::st_write(obj = aagis_sf, dsn = aagis_gpkg, quiet = TRUE)
     unlink(c(
       aagis_zip,
       file.path(aagis_regions_dir, "aagis_asgs16v1_g5a.*")

codemeta.json

@@ -34,6 +34,18 @@
     }
   ],
   "softwareSuggestions": [
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "httptest2",
+      "name": "httptest2",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=httptest2"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "knitr",
@@ -273,7 +285,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "343.019KB",
+  "fileSize": "344.301KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",

tests/testthat/setup.R

@@ -0,0 +1 @@
+library(httptest2)

tests/testthat/test-get_aagis_regions.R

@@ -3,22 +3,25 @@
 withr::local_envvar(R_USER_CACHE_DIR = file.path(tempdir(), "abares.cache.1"))
 
 # without caching ----
-
-test_that("get_aagis_regions doesn't cache", {
-  skip_if_offline()
-  skip_on_ci()
-  x <- get_aagis_regions(cache = FALSE)
-  expect_s3_class(x, "sf")
-  expect_false(file.exists(
-    file.path(.find_user_cache(), "aagis_regions_dir/aagis.rds")
-  ))
+with_mock_dir("test-get_aagis_regions", {
+  test_that("get_aagis_regions doesn't cache", {
+    skip_if_offline()
+    skip_on_ci()
+    x <- get_aagis_regions(cache = FALSE)
+    expect_s3_class(x, "sf")
+    expect_false(file.exists(
+      file.path(.find_user_cache(), "aagis_regions_dir/aagis.rds")
+    ))
+  })
 })
 
-test_that("get_aagis_regions skips downloading if still in tempdir()", {
-  skip_if_offline()
-  skip_on_ci()
-  x <- .check_existing_aagis(cache = FALSE)
-  expect_s3_class(x, "sf")
+with_mock_dir("test-get_aagis_regions", {
+  test_that("get_aagis_regions skips downloading if still in tempdir()", {
+    skip_if_offline()
+    skip_on_ci()
+    x <- .check_existing_aagis(cache = FALSE)
+    expect_s3_class(x, "sf")
+  })
 })
 
 # with caching ----
@@ -49,6 +52,7 @@ test_that("get_aagis_regions skips downloading if cache is available", {
 # sets up a custom cache environment in `tempdir()` just for testing
 withr::local_envvar(R_USER_CACHE_DIR = file.path(tempdir(), "abares.cache.2"))
 
+
 test_that("get_aagis_regions does cache", {
   skip_if_offline()
   skip_on_ci()
@@ -71,5 +75,6 @@ test_that("get_aagis_regions skips downloading if still in tempdir()", {
   x <- .check_existing_aagis(cache = TRUE)
   expect_s3_class(x, "sf")
 })
+})
 
 withr::deferred_run()