Merge pull request #9 from DPIRD-FSI/devel

Devel
DPIRD-FSI · Apr 10, 2023 · 69d620c · 69d620c
2 parents cd8d196 + afd9177
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: extractOz
 Title: Extract Australian Soil, Weather and GRDC Agro-ecological Zone
         Information from GPS Points
-Version: 0.1.3.9000
+Version: 1.0.0
 Authors@R: c(person(given = "Adam H.", family = "Sparks",
                      email = "[email protected]",
                      role = c("aut", "cre"),
@@ -21,7 +21,7 @@ RoxygenNote: 7.2.3
 Imports:
   curl,
   data.table,
-  httr2,
+  httr,
   methods,
   nasapower,
   purrr,
@@ -45,3 +45,6 @@ Language: en-US
 X-schema.org-applicationCategory: Tools
 X-schema.org-keywords: agriculture, Australia, agroecology, soils, weather, weather-data, soils-data, agriculture-research
 X-schema.org-isPartOf: https://www.dpird.wa.gov.au/
+URL: https://github.com/DPIRD-FSI/extractOz
+BugReports: https://github.com/DPIRD-FSI/extractOz/issues
+LazyData: true
diff --git a/NAMESPACE b/NAMESPACE
@@ -6,6 +6,7 @@ export(extract_area)
 export(extract_daas_soil_order)
 export(extract_power)
 export(extract_silo)
+export(remove_cache)
 importFrom(data.table,":=")
 importFrom(data.table,.BY)
 importFrom(data.table,.EACHI)

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,11 @@
-# extractOz 0.1.3.9000
+# extractOz 1.0.0
 
 ## Major changes
 
+-   All functions related to retrieving or extracting data are now prefixed as `extract_noun()`.
+
+-   Revert using internal data as geopackage, use in examples but use .Rda internally.
+
 -   Add support for extracting weather data from the NASA POWER database, `extract_power()`.
 
 -   Move from {cropgrowdays} to {weatherOz}, this allows for more flexibility in the queries that can be performed in SILO.
@@ -14,6 +18,14 @@ To help users, a new function, `df_to_list()` has been added so that the workflo
 
 -   Enhanced tests.
 
+-   Add ability to manage DAAS soil order cache.
+
+-   Add ability to download DAAS soil order data but not cache locally (default behaviour now).
+
+## Bug fixes
+
+-   Remove several `Warning` messages when performing {sf} operations.
+
 # extractOz 0.1.3
 
 ## Bug fixes

diff --git a/R/aez.R b/R/aez.R
@@ -0,0 +1,14 @@
+#' GRDC Australian Grains Agroecological Zones
+#'
+#' An [sf::sf()] object for displaying GRDC Australian Grains Agroecological
+#'  Zones
+#'
+#' @section Coordinate Reference System:
+#' Geodetic CRS:  WGS 84
+#'
+#' @format An [sf::sf()] polygon object
+#'
+#' @source The Australian Grains Research and Development Corporation,
+#'  \acronym{GRDC}, <https://grdc.com.au/> under CC0 licence.
+#'
+"aez"
diff --git a/R/extract_ae_zone.R b/R/extract_ae_zone.R
@@ -32,8 +32,6 @@ extract_ae_zone <- function(x) {
     crs = sf::st_crs(aez)
   )
 
-
-
   intersection <- as.integer(sf::st_intersects(points_sf, aez))
   zone <- data.table::data.table(ifelse(is.na(intersection), "",
                                         as.character(aez$AEZ[intersection])))

diff --git a/R/extract_power.R b/R/extract_power.R
@@ -37,7 +37,7 @@
 #'   not for use with \dQuote{global} or with a regional request.  If this
 #'   parameter is provided, the `wind-surface` parameter is required with the
 #'   request, see
-#'    \url{https://power.larc.nasa.gov/docs/methodology/meteorology/wind/}.
+#'    <https://power.larc.nasa.gov/docs/methodology/meteorology/wind/>.
 #' @param wind_surface A user-supplied wind surface for which the corrected
 #'   wind-speed is to be supplied.  See `wind-surface` section for more detail.
 #' @param temporal_average Deprecated. This argument has been superseded by

diff --git a/R/extract_soil_order.R b/R/extract_soil_order.R
@@ -4,10 +4,15 @@
 #' Extracts the major soil order at the GPS points provided.
 #'
 #' @inheritParams extract_ae_zone
+#' @param cache `Boolean`.  Store soil data locally for later use?  If `FALSE`,
+#' the downloaded files are removed when \R session is closed. To take advantage
+#' of cached files in future sessions, use `cache = TRUE`.  Defaults to `FALSE`.
+#' Value is optional.  All future requests will use the cached data unless
+#' `remove_cache()` is used to remove the cached file.
 #'
 #' @note The first run will take additional time to download and extract the
-#' soils data and cache it locally for future use.  Any use after this will be
-#' much faster due to the locally cached geospatial soils data.
+#' soils data.  If `cache = TRUE`, any use after this will be much faster due to
+#' the locally cached geospatial soils data.
 #'
 #' @return A `data.table` with the provided \acronym{GPS} coordinates and the
 #'  respective Digital Atlas of Australian Soils (\acronym{DAAS} soil order),
@@ -23,17 +28,25 @@
 #'   "Tamworth" = c(x = 150.84, y = -31.07)
 #'   )
 #'
-#' extract_daas_soil_order(x = locs)
+#' extract_daas_soil_order(x = locs, cache = FALSE)
 #' @export
 
-extract_daas_soil_order <- function(x) {
+extract_daas_soil_order <- function(x, cache = FALSE) {
   # check if the DAAS data exists in the local cache and if not, download and
   # mask it before saving in the user cache
 
-  .check_for_cache()
   .check_lonlat(x)
 
-  load(.get_cache_file())
+  if (file.exists(.get_cache_file())) {
+    load(.get_cache_file())
+  } else {
+    if (isTRUE(cache)) {
+      message("This is the first time using caching, a cache will be created.")
+      daas <- .get_daas_data(.cache = cache)
+    } else {
+      daas <- .get_daas_data(.cache = cache)
+    }
+  }
 
   x <- .create_dt(x)
 
@@ -45,7 +58,7 @@ extract_daas_soil_order <- function(x) {
 
   intersection <- as.integer(sf::st_intersects(points_sf, daas))
   soil <- data.table::data.table(ifelse(is.na(intersection), "",
-                                   as.character(daas$SOIL[intersection])))
+                                        as.character(daas$SOIL[intersection])))
 
   out <- cbind(x, soil)
   data.table::setnames(out, old = "V1", new = "daas_soil_order")
@@ -71,48 +84,65 @@ extract_daas_soil_order <- function(x) {
 
 #' @noRd
 # nocov start
-.check_for_cache <- function() {
-  if (!file.exists(.get_cache_file())) {
-    if (!dir.exists(.get_cache_dir())) {
-      dir.create(path = .get_cache_dir(), recursive = TRUE)
+.get_daas_data <- function(.cache) {
+  u_remote <-
+    "https://data.gov.au/data/"
+  d_remote <-
+    "dataset/5ccb44bf-93f2-4f94-8ae2-4c3f699ea4e7/resource/56ba5f25-2324-43b5-8df8-b9c69ae2ea0b/download/"
+  filename <- "6f804e8b-2de9-4c88-adfa-918ec327c32f.zip"
+
+  url <- paste0(u_remote, d_remote, filename)
+  tryCatch(
+    # check for an http error b4 proceeding
+    if (!httr::http_error(url)) {
+      h <- curl::new_handle()
+      curl::handle_setopt(h, CONNECTTIMEOUT = 120L)
+      curl::curl_download(
+        url = url,
+        destfile = file.path(tempdir(), filename),
+        quiet = FALSE,
+        handle = h,
+        mode = "wb"
+      )
+
+      utils::unzip(file.path(tempdir(), filename), exdir = tempdir())
+
+      x <-
+        sf::st_read(dsn = file.path(tempdir(), "SoilAtlas2M_ASC_Conversion_v01"),
+                    layer = "soilAtlas2M_ASC_Conversion")
+      x <- x[with(x, SOIL != "Nodata" | SOIL != "Lake"),]
+      x <- sf::st_transform(x, crs = sf::st_crs(aez))
+      sf::st_agr(x) = "constant"
+      sf::st_agr(aez) = "constant"
+      daas <- sf::st_intersection(x, aez)
+    },
+    error = function(x)
+      stop(
+        call. = FALSE,
+        "\nThe file download for DAAS has failed. Please try again.\n"
+      )
+  )
+
+  if (isTRUE(.cache)) {
+    if (!file.exists(.get_cache_file())) {
+      if (!dir.exists(.get_cache_dir())) {
+        dir.create(path = .get_cache_dir(), recursive = TRUE)
+      }
+      save(daas, file = .get_cache_file())
     }
-    u_remote <-
-      "https://data.gov.au/data/"
-    d_remote <-
-      "dataset/5ccb44bf-93f2-4f94-8ae2-4c3f699ea4e7/resource/56ba5f25-2324-43b5-8df8-b9c69ae2ea0b/download/"
-    filename <- "6f804e8b-2de9-4c88-adfa-918ec327c32f.zip"
-
-    url <- paste0(u_remote, d_remote, filename)
-    tryCatch(
-      # check for an http error b4 proceeding
-      if (!httr2::req_error(url)) {
-        h <- curl::new_handle()
-        curl::handle_setopt(h, CONNECTTIMEOUT = 120L)
-        curl::curl_download(
-          url = url,
-          destfile = file.path(tempdir(), filename),
-          quiet = FALSE,
-          handle = h,
-          mode = "wb"
-        )
-
-        utils::unzip(file.path(tempdir(), filename), exdir = tempdir())
-
-        x <- sf::st_read(
-          dsn = file.path(tempdir(), "SoilAtlas2M_ASC_Conversion_v01"),
-          layer = "soilAtlas2M_ASC_Conversion"
-        )
-        x <- x[with(x, SOIL != "Nodata" | SOIL != "Lake"), ]
-        x <- sf::st_transform(x, crs = sf::st_crs(aez))
-        daas <- sf::st_intersection(x = x, y = aez)
-        save(daas, file = .get_cache_file())
-      },
-      error = function(x)
-        stop(
-          call. = FALSE,
-          "\nThe file download for DAAS has failed. Please try again.\n"
-        )
-    )
   }
-  return(invisible(NULL))
+  return(daas)
 } #nocov end
+
+#' Remove DAAS Soil Order Cache
+#'
+#' The cache is located at `tools::R_user_dir("extractOz", which = "cache")`
+#'
+#' @return `NULL`, called for its side-effects
+#' @export
+remove_cache = function() {
+  path = .get_cache_file()
+  if (file.exists(path))
+    file.remove(path)
+  return(invisible(NULL))
+}
diff --git a/R/zzz.R b/R/zzz.R
diff --git a/codemeta.json b/codemeta.json
@@ -4,8 +4,10 @@
   "identifier": "extractOz",
   "description": "Extracts point data for a given GPS coordinate that includes major soil order, weather and GRDC agro-ecological zone information at that point.",
   "name": "extractOz: Extract Australian Soil, Weather and GRDC Agro-ecological Zone\n        Information from GPS Points",
+  "codeRepository": "https://github.com/DPIRD-FSI/extractOz",
+  "issueTracker": "https://github.com/DPIRD-FSI/extractOz/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.1.3.9000",
+  "version": "1.0.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -59,6 +61,18 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=knitr"
     },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "readr",
+      "name": "readr",
+      "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=readr"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "rmarkdown",
@@ -107,6 +121,19 @@
         "url": "https://cran.r-project.org"
       },
       "sameAs": "https://CRAN.R-project.org/package=tidyverse"
+    },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "vcr",
+      "name": "vcr",
+      "version": ">= 0.6.0",
+      "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=vcr"
     }
   ],
   "softwareRequirements": {
@@ -147,6 +174,23 @@
       "sameAs": "https://CRAN.R-project.org/package=httr"
     },
     "4": {
+      "@type": "SoftwareApplication",
+      "identifier": "methods",
+      "name": "methods"
+    },
+    "5": {
+      "@type": "SoftwareApplication",
+      "identifier": "nasapower",
+      "name": "nasapower",
+      "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=nasapower"
+    },
+    "6": {
       "@type": "SoftwareApplication",
       "identifier": "purrr",
       "name": "purrr",
@@ -158,7 +202,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=purrr"
     },
-    "5": {
+    "7": {
       "@type": "SoftwareApplication",
       "identifier": "sf",
       "name": "sf",
@@ -170,17 +214,17 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=sf"
     },
-    "6": {
+    "8": {
       "@type": "SoftwareApplication",
       "identifier": "utils",
       "name": "utils"
     },
-    "7": {
+    "9": {
       "@type": "SoftwareApplication",
       "identifier": "weatherOz",
       "name": "weatherOz"
     },
-    "8": {
+    "10": {
       "@type": "SoftwareApplication",
       "identifier": "R",
       "name": "R",
@@ -190,8 +234,9 @@
   },
   "applicationCategory": "Tools",
   "isPartOf": "https://www.dpird.wa.gov.au/",
-  "keywords": ["agriculture", "Australia", "agroecology", "soils", "weather", "weather-data", "soils-data", "agriculture-research"],
-  "fileSize": "3323.622KB",
+  "keywords": ["agriculture", "Australia", "agroecology", "soils", "weather", "weather-data", "soils-data", "agriculture-research", "r-package", "agriculture-data", "australia"],
+  "fileSize": "4562.105KB",
+  "readme": "https://github.com/DPIRD-FSI/extractOz/blob/main/README.md",
   "contIntegration": ["https://github.com/DPIRD-FSI/extractOz/actions", "https://codecov.io/gh/DPIRD-FSI/extractOz"],
   "developmentStatus": "https://www.repostatus.org/#active"
 }
diff --git a/data/aez.rda b/data/aez.rda