tar_terra*: Add generic support for storing targets as zip files for n…

…jtierney#37

R/tar-terra-rast.R

@@ -6,8 +6,18 @@
 #'   to [terra::writeRaster()]
 #' @param gdal character. GDAL driver specific datasource creation options
 #'   passed to [terra::writeRaster()]
+#' @param zipfile logical. Should the file in the target store be a ZIP archive?
+#'   Required for `filetype` formats that have sidecar files. Not all GDAL
+#'   drivers support directly generating SOZip-enabled files. Default: `FALSE`.
 #' @param ... Additional arguments not yet used
 #'
+#' @note Although you may pass any supported GDAL vector driver to the
+#'   `filetype` argument, not all formats are guaranteed to work with
+#'   `geotargets`.  At the moment, we have tested `GTiff` and `GPKG` and
+#'    they appear to work generally. Both `GTiff` and `GPKG` rasters can be
+#'    stored as ZIP files by setting `zipfile=TRUE`. To write a SOZip-enabled
+#'    `GTiff` target set `gdal=c("STREAMABLE_OUTPUT=YES", "COMPRESS=NONE")`.
+#'
 #' @inheritParams targets::tar_target
 #' @importFrom rlang %||% arg_match0
 #' @seealso [targets::tar_target_raw()]
@@ -33,6 +43,7 @@ tar_terra_rast <- function(name,
                            pattern = NULL,
                            filetype = geotargets_option_get("gdal.raster.driver"),
                            gdal = geotargets_option_get("gdal.raster.creation.options"),
+                           zipfile = FALSE,
                            ...,
                            tidy_eval = targets::tar_option_get("tidy_eval"),
                            packages = targets::tar_option_get("packages"),
@@ -73,23 +84,40 @@ tar_terra_rast <- function(name,
         tidy_eval = tidy_eval
     )
 
+    .format_terra_rast_read <- eval(substitute(function(path) {
+        path2 <- ifelse(zipfile, paste0("/vsizip/{", path, "}"), path)
+        terra::rast(path2)
+    }, list(zipfile = zipfile)))
+
+    .format_terra_rast_write <- eval(substitute(function(object, path) {
+        path2 <- ifelse(zipfile, paste0("/vsizip/{", path, "}/", basename(path)), path)
+        filetype <- Sys.getenv("GEOTARGETS_GDAL_RASTER_DRIVER")
+        extension <- ""
+        if (filetype == "GPKG") {
+            extension <- ".gpkg.zip"
+            path2 <- paste0(path, extension)
+        }
+        terra::writeRaster(
+            object,
+            path2,
+            filetype = filetype,
+            overwrite = TRUE,
+            gdal = strsplit(Sys.getenv("GEOTARGETS_GDAL_RASTER_CREATION_OPTIONS", unset = ";"), ";")[[1]]
+        )
+        if (extension != "") {
+            file.rename(paste0(path, extension), path)
+        }
+    }, list(zipfile = zipfile)))
+
     targets::tar_target_raw(
         name = name,
         command = command,
         pattern = pattern,
         packages = packages,
         library = library,
         format = targets::tar_format(
-            read = function(path) terra::rast(path),
-            write = function(object, path) {
-                terra::writeRaster(
-                    object,
-                    path,
-                    filetype = Sys.getenv("GEOTARGETS_GDAL_RASTER_DRIVER"),
-                    overwrite = TRUE,
-                    gdal = strsplit(Sys.getenv("GEOTARGETS_GDAL_RASTER_CREATION_OPTIONS", unset = ";"), ";")[[1]]
-                )
-            },
+            read = .format_terra_rast_read,
+            write = .format_terra_rast_write,
             marshal = function(object) terra::wrap(object),
             unmarshal = function(object) terra::unwrap(object)
         ),

R/tar-terra-vect.R

@@ -6,13 +6,18 @@
 #'   to [terra::writeVector()]. See 'Note' for more details
 #' @param gdal character. GDAL driver specific datasource creation options
 #'   passed to [terra::writeVector()].
+#' @param zipfile logical. Should the file in the target store be a ZIP archive?
+#'   Required for `filetype` formats that have sidecar files. Not all GDAL
+#'   drivers support directly generating SOZip-enabled files. Default: `FALSE`.
 #' @param ... Additional arguments not yet used
 #' @inheritParams targets::tar_target
 #'
 #' @note Although you may pass any supported GDAL vector driver to the
 #'   `filetype` argument, not all formats are guaranteed to work with
-#'   `geotargets`.  At the moment, we have tested `GeoJSON` and `ESRI Shapefile`
-#'   which both appear to work generally.
+#'   `geotargets`.  At the moment, we have tested `GeoJSON`, `ESRI Shapefile`,
+#'    `GPKG`, and `Parquet` which all appear to work generally. `ESRI Shapefile`
+#'    targets are always stored as SOZip-enabled Zipfiles (GDAL >= 3.7). `GPKG`
+#'    and `Parquet` can also be stored as ZIP files by setting `zipfile=TRUE`.
 #' @export
 #' @examples
 #' if (Sys.getenv("TAR_LONG_EXAMPLES") == "true") {
@@ -42,6 +47,7 @@ tar_terra_vect <- function(name,
                            pattern = NULL,
                            filetype = geotargets_option_get("gdal.vector.driver"),
                            gdal = geotargets_option_get("gdal.vector.creation.options"),
+                           zipfile = FALSE,
                            ...,
                            packages = targets::tar_option_get("packages"),
                            tidy_eval = targets::tar_option_get("tidy_eval"),
@@ -81,12 +87,16 @@ tar_terra_vect <- function(name,
         tidy_eval = tidy_eval
     )
 
-    format <- ifelse(
-        test = filetype == "ESRI Shapefile",
-        #special handling of ESRI shapefiles because the output is a dir of multiple files.
-        yes = create_format_terra_vect_shz(),
-        no =  create_format_terra_vect()
-    )
+    # special handling of drivers w/ file extension for direct write of SOZIP (GDAL >=3.7)
+    extension <- switch(filetype,
+                        "ESRI Shapefile" = ".shz",
+                        "GPKG" = ".gpkg.zip",
+                        "")
+
+    format <- ifelse(zipfile || filetype == "ESRI Shapefile",
+                     yes = create_format_terra_vect_zip(extension,
+                                                        filetype = filetype),
+                     no = create_format_terra_vect())
 
     targets::tar_target_raw(
         name = name,
@@ -137,24 +147,35 @@ create_format_terra_vect <- function() {
     )
 }
 
-#' Special handling for ESRI Shapefiles
+#' Handling for ZIP files (required for ESRI Shapefile)
 #' @noRd
-create_format_terra_vect_shz <- function() {
+create_format_terra_vect_zip <- function(extension, filetype) {
 
     check_pkg_installed("terra")
 
+    .format_terra_vect_write_zip <- eval(substitute(function(object, path) {
+
+        if (extension == "") {
+            # no extension, use generic "/vsizip/{path to zipfile}/path/in/zipfile"
+            path <- paste0("/vsizip/{", path, "}/", basename(path))
+        }
+
+        terra::writeVector(
+            x = object,
+            filename = paste0(path, extension),
+            filetype = filetype,
+            overwrite = TRUE,
+            options = strsplit(Sys.getenv("GEOTARGETS_GDAL_VECTOR_CREATION_OPTIONS", unset = ";"), ";")[[1]]
+        )
+
+        if (extension != "") {
+            file.rename(paste0(path, extension), path)
+        }
+    }, list(extension = extension, filetype = filetype)))
+
     targets::tar_format(
         read = function(path) terra::vect(paste0("/vsizip/{", path, "}")),
-        write = function(object, path) {
-            terra::writeVector(
-                x = object,
-                filename = paste0(path, ".shz"),
-                filetype = "ESRI Shapefile",
-                overwrite = TRUE,
-                options = strsplit(Sys.getenv("GEOTARGETS_GDAL_VECTOR_CREATION_OPTIONS", unset = ";"), ";")[[1]]
-            )
-            file.rename(paste0(path, ".shz"), path)
-        },
+        write = .format_terra_vect_write_zip,
         marshal = function(object) terra::wrap(object),
         unmarshal = function(object) terra::unwrap(object)
     )

tests/testthat/_snaps/tar-terra.md

@@ -13,6 +13,19 @@
       min value   :       141 
       max value   :       547 
 
+# tar_terra_rast(zipfile=TRUE) works
+
+    Code
+      x
+    Output
+      class       : SpatRaster 
+      dimensions  : 90, 95, 1  (nrow, ncol, nlyr)
+      resolution  : 0.008333333, 0.008333333  (x, y)
+      extent      : 5.741667, 6.533333, 49.44167, 50.19167  (xmin, xmax, ymin, ymax)
+      coord. ref. : lon/lat WGS 84 (EPSG:4326) 
+      source      : test_terra_rast2} 
+      name        : elevation 
+
 # tar_terra_vect() works
 
     Code
@@ -47,3 +60,20 @@
                          1 Diekirch     2 Diekirch   218 32543
                          1 Diekirch     3  Redange   259 18664
 
+---
+
+    Code
+      z
+    Output
+       class       : SpatVector 
+       geometry    : polygons 
+       dimensions  : 12, 6  (geometries, attributes)
+       extent      : 5.74414, 6.528252, 49.44781, 50.18162  (xmin, xmax, ymin, ymax)
+       source      : test_terra_vect_parquet_zip}
+       coord. ref. : lon/lat WGS 84 (EPSG:4326) 
+       names       :  ID_1   NAME_1  ID_2   NAME_2  AREA   POP
+       type        : <num>    <chr> <num>    <chr> <num> <int>
+       values      :     1 Diekirch     1 Clervaux   312 18081
+                         1 Diekirch     2 Diekirch   218 32543
+                         1 Diekirch     3  Redange   259 18664
+

tests/testthat/test-tar-terra.R

@@ -17,6 +17,32 @@ targets::tar_test("tar_terra_rast() works", {
     )
 })
 
+targets::tar_test("tar_terra_rast(zipfile=TRUE) works", {
+    targets::tar_script({
+        list(
+            geotargets::tar_terra_rast(
+                test_terra_rast2,
+                terra::rast(system.file("ex/elev.tif", package = "terra")),
+                gdal = c("STREAMABLE_OUTPUT=YES", "COMPRESS=NONE"),
+                zipfile = TRUE
+            ),
+            geotargets::tar_terra_rast(
+                test_terra_rast3,
+                terra::rast(system.file("ex/elev.tif", package = "terra")),
+                filetype = "GPKG",
+                zipfile = TRUE
+            )
+        )
+    })
+    targets::tar_make()
+    x <- targets::tar_read(test_terra_rast2)
+    y <- targets::tar_read(test_terra_rast3)
+    expect_s4_class(x, "SpatRaster")
+    expect_snapshot(
+        x
+    )
+})
+
 targets::tar_test("tar_terra_vect() works", {
     targets::tar_script({
         lux_area <- function(projection = "EPSG:4326") {
@@ -36,15 +62,25 @@ targets::tar_test("tar_terra_vect() works", {
                 test_terra_vect_shz,
                 lux_area(),
                 filetype = "ESRI Shapefile"
+            ),
+            geotargets::tar_terra_vect(
+                test_terra_vect_parquet_zip,
+                lux_area(),
+                filetype = "Parquet",
+                zipfile = TRUE
             )
         )
     })
     targets::tar_make()
     x <- targets::tar_read(test_terra_vect)
     y <- targets::tar_read(test_terra_vect_shz)
+    z <- targets::tar_read(test_terra_vect_parquet_zip)
     expect_s4_class(x, "SpatVector")
     expect_s4_class(y, "SpatVector")
+    expect_s4_class(z, "SpatVector")
     expect_snapshot(x)
     expect_snapshot(y)
+    expect_snapshot(z)
     expect_equal(terra::values(x), terra::values(y))
+    expect_equal(terra::values(y), terra::values(z))
 })