Fix to netcdf read process

.github/actions/r_build/action.yml

@@ -7,6 +7,18 @@ runs:
       shell: bash
       run: |
         sudo apt-get update && sudo apt-get install -y curl libcurl4-openssl-dev pkg-config libharfbuzz-dev libfribidi-dev
+    - name: Configure python interpreter
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python }}
+    - name: Install python dependencies
+      shell: bash
+      run: |
+        # - install pip libs
+        #   note: gdal requires the extra args
+        cd python
+        pip install build wheel pyspark==${{ matrix.spark }} numpy==${{ matrix.numpy }}
+        pip install --no-build-isolation --no-cache-dir --force-reinstall gdal==${{ matrix.gdal }}
     - name: Create download location for Spark
       shell: bash
       run: |

R/generate_R_bindings.R

@@ -214,7 +214,7 @@ main <- function(scala_file_path){
   closeAllConnections()
 
   # supplementary files
-  sparkr_supplementary_files <- c("sparkR-mosaic/enableMosaic.R")
+  sparkr_supplementary_files <- c("sparkR-mosaic/enableMosaic.R", "sparkR-mosaic/enableGDAL.R")
   copy_supplementary_file(sparkr_supplementary_files, "sparkR-mosaic/sparkrMosaic/R")
 
   ##########################
@@ -226,8 +226,8 @@ main <- function(scala_file_path){
   closeAllConnections()
 
   # supplementary files
-  sparkr_supplementary_files <- c("sparklyr-mosaic/enableMosaic.R", "sparklyr-mosaic/sparkFunctions.R")
-  copy_supplementary_file(sparkr_supplementary_files, "sparklyr-mosaic/sparklyrMosaic/R/")
+  sparklyr_supplementary_files <- c("sparklyr-mosaic/enableMosaic.R", "sparklyr-mosaic/sparkFunctions.R", "sparklyr-mosaic/enableGDAL.R")
+  copy_supplementary_file(sparklyr_supplementary_files, "sparklyr-mosaic/sparklyrMosaic/R/")
 }
 
 

R/install_deps.R

@@ -1,3 +1,3 @@
 options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest"))
 
-install.packages(c("pkgbuild", "testthat", "roxygen2", "sparklyr"))
+install.packages(c("pkgbuild", "testthat", "roxygen2", "sparklyr", "readr", "sparklyr.nested"))

R/sparkR-mosaic/enableGDAL.R

@@ -0,0 +1,14 @@
+#' enableGDAL
+#' 
+#' @description enableGDAL activates GDAL extensions for Mosaic
+#' @name enableGDAL
+#' @rdname enableGDAL
+#' @return None
+#' @export enableGDAL
+#' @examples
+#' \dontrun{
+#' enableGDAL() }
+enableGDAL <- function(
+){
+  sparkR.callJStatic(x="com.databricks.labs.mosaic.gdal.MosaicGDAL", methodName="enableGDAL", sparkR.session())
+}

R/sparkR-mosaic/sparkrMosaic/.Rbuildignore

@@ -1,2 +1,2 @@
 ^sparkrMosaic\.Rproj$
-^\.Rproj\.user$
+^\.Rproj\.user$

R/sparkR-mosaic/sparkrMosaic/DESCRIPTION

@@ -1,21 +1,23 @@
 Package: sparkrMosaic
 Title: SparkR bindings for Databricks Mosaic
 Version: 0.4.0
-Authors@R: 
+Authors@R:
     person("Robert", "Whiffin", , "[email protected]", role = c("aut", "cre")
            )
 Description: This package extends SparkR to bring the Databricks Mosaic for geospatial processing APIs into SparkR.
 License: Databricks
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Collate: 
+Collate:
+    'enableGDAL.R'
     'enableMosaic.R'
     'generics.R'
     'functions.R'
 Imports:
   SparkR,
   methods
-Suggests: 
-    testthat (>= 3.0.0)
-Config/testthat/edition: 3
+Suggests:
+    testthat (>= 3.0.0),
+    readr (>= 2.1.5)
+Config/testthat/edition: 3

R/sparkR-mosaic/sparkrMosaic/sparkrMosaic.Rproj → R/sparkR-mosaic/sparkrMosaic/sparkrMosaic.rproj

@@ -14,4 +14,4 @@ LineEndingConversion: Posix
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd,collate,namespace

R/sparkR-mosaic/sparkrMosaic/tests/testthat/data.R → R/sparkR-mosaic/sparkrMosaic/tests/testthat/data/boroughs.geojson

@@ -1,4 +1,4 @@
-inputGJ = '{
+{
    "type":"Feature",
    "properties":{
       "shape_area":"0.0000607235737749",
@@ -225,4 +225,4 @@ inputGJ = '{
          ]
       ]
    }
-}'
+}

R/sparkR-mosaic/sparkrMosaic/tests/testthat/testRasterFunctions.R

@@ -0,0 +1,140 @@
+generate_singleband_raster_df <- function() {
+  read.df(
+    path = "sparkrMosaic/tests/testthat/data/MCD43A4.A2018185.h10v07.006.2018194033728_B04.TIF",
+    source = "gdal",
+    raster.read.strategy = "in_memory"
+    )
+}
+
+test_that("mosaic can read single-band GeoTiff", {
+  sdf <- generate_singleband_raster_df()
+  row <- first(sdf)
+  expect_equal(row$length, 1067862L)
+  expect_equal(row$x_size, 2400)
+  expect_equal(row$y_size, 2400)
+  expect_equal(row$srid, 0)
+  expect_equal(row$bandCount, 1)
+  expect_equal(row$metadata[[1]]$LONGNAME, "MODIS/Terra+Aqua BRDF/Albedo Nadir BRDF-Adjusted Ref Daily L3 Global - 500m")
+  expect_equal(row$tile[[1]]$driver, "GTiff")
+
+})
+
+test_that("scalar raster functions behave as intended", {
+  sdf <- generate_singleband_raster_df()
+  sdf <- withColumn(sdf, "rst_rastertogridavg", rst_rastertogridavg(column("tile"), lit(9L)))
+  sdf <- withColumn(sdf, "rst_rastertogridcount", rst_rastertogridcount(column("tile"), lit(9L)))
+  sdf <- withColumn(sdf, "rst_rastertogridmax", rst_rastertogridmax(column("tile"), lit(9L)))
+  sdf <- withColumn(sdf, "rst_rastertogridmedian", rst_rastertogridmedian(column("tile"), lit(9L)))
+  sdf <- withColumn(sdf, "rst_rastertogridmin", rst_rastertogridmin(column("tile"), lit(9L)))
+  sdf <- withColumn(sdf, "rst_rastertoworldcoordx", rst_rastertoworldcoordx(column("tile"), lit(1200L), lit(1200L)))
+  sdf <- withColumn(sdf, "rst_rastertoworldcoordy", rst_rastertoworldcoordy(column("tile"), lit(1200L), lit(1200L)))
+  sdf <- withColumn(sdf, "rst_rastertoworldcoord", rst_rastertoworldcoord(column("tile"), lit(1200L), lit(1200L)))
+  sdf <- withColumn(sdf, "rst_rotation", rst_rotation(column("tile")))
+  sdf <- withColumn(sdf, "rst_scalex", rst_scalex(column("tile")))
+  sdf <- withColumn(sdf, "rst_scaley", rst_scaley(column("tile")))
+  sdf <- withColumn(sdf, "rst_srid", rst_srid(column("tile")))
+  sdf <- withColumn(sdf, "rst_summary", rst_summary(column("tile")))
+  sdf <- withColumn(sdf, "rst_upperleftx", rst_upperleftx(column("tile")))
+  sdf <- withColumn(sdf, "rst_upperlefty", rst_upperlefty(column("tile")))
+  sdf <- withColumn(sdf, "rst_width", rst_width(column("tile")))
+  sdf <- withColumn(sdf, "rst_worldtorastercoordx", rst_worldtorastercoordx(column("tile"), lit(0.0), lit(0.0)))
+  sdf <- withColumn(sdf, "rst_worldtorastercoordy", rst_worldtorastercoordy(column("tile"), lit(0.0), lit(0.0)))
+  sdf <- withColumn(sdf, "rst_worldtorastercoord", rst_worldtorastercoord(column("tile"), lit(0.0), lit(0.0)))
+
+  expect_no_error(write.df(sdf, source = "noop", mode = "overwrite"))
+})
+
+test_that("raster flatmap functions behave as intended", {
+  retiled_sdf <- generate_singleband_raster_df()
+  retiled_sdf <- withColumn(retiled_sdf, "rst_retile", rst_retile(column("tile"), lit(1200L), lit(1200L)))
+
+  expect_no_error(write.df(retiled_sdf, source = "noop", mode = "overwrite"))
+  expect_equal(nrow(retiled_sdf), 4)
+
+  subdivide_sdf <- generate_singleband_raster_df()
+  subdivide_sdf <- withColumn(subdivide_sdf, "rst_subdivide", rst_subdivide(column("tile"), lit(1L)))
+
+  expect_no_error(write.df(subdivide_sdf, source = "noop", mode = "overwrite"))
+  expect_equal(nrow(subdivide_sdf), 4)
+
+  tessellate_sdf <- generate_singleband_raster_df()
+  tessellate_sdf <- withColumn(tessellate_sdf, "rst_tessellate", rst_tessellate(column("tile"), lit(3L)))
+
+  expect_no_error(write.df(tessellate_sdf, source = "noop", mode = "overwrite"))
+  expect_equal(nrow(tessellate_sdf), 66)
+
+  overlap_sdf <- generate_singleband_raster_df()
+  overlap_sdf <- withColumn(overlap_sdf, "rst_to_overlapping_tiles", rst_to_overlapping_tiles(column("tile"), lit(200L), lit(200L), lit(10L)))
+
+  expect_no_error(write.df(overlap_sdf, source = "noop", mode = "overwrite"))
+  expect_equal(nrow(overlap_sdf), 87)
+})
+
+test_that("raster aggregation functions behave as intended", {
+  collection_sdf <- generate_singleband_raster_df()
+  collection_sdf <- withColumn(collection_sdf, "extent", st_astext(rst_boundingbox(column("tile"))))
+  collection_sdf <- withColumn(collection_sdf, "tile", rst_to_overlapping_tiles(column("tile"), lit(200L), lit(200L), lit(10L)))
+
+  merge_sdf <- summarize(
+    groupBy(collection_sdf, "path"),
+    alias(rst_merge_agg(column("tile")), "tile")
+    )
+  merge_sdf <- withColumn(merge_sdf, "extent", st_astext(rst_boundingbox(column("tile"))))
+
+  expect_equal(nrow(merge_sdf), 1)
+  expect_equal(first(collection_sdf)$extent, first(merge_sdf)$extent)
+
+  combine_avg_sdf <- summarize(
+    groupBy(collection_sdf, "path"),
+    alias(rst_combineavg_agg(column("tile")), "tile")
+  )
+  combine_avg_sdf <- withColumn(combine_avg_sdf, "extent", st_astext(rst_boundingbox(column("tile"))))
+
+  expect_equal(nrow(combine_avg_sdf), 1)
+  expect_equal(first(collection_sdf)$extent, first(combine_avg_sdf)$extent)
+
+})
+
+test_that("the tessellate-join-clip-merge flow works on NetCDF files", {
+  target_resolution <- 1L
+
+  region_keys <- c("NAME", "STATE", "BOROUGH", "BLOCK", "TRACT")
+
+  census_sdf <- read.df(
+    path = "sparkrMosaic/tests/testthat/data/Blocks2020.zip",
+    source = "com.databricks.labs.mosaic.datasource.OGRFileFormat",
+    vsizip = "true",
+    chunkSize = "20"
+  )
+
+  census_sdf <- select(census_sdf, c(region_keys, "geom_0", "geom_0_srid"))
+  census_sdf <- distinct(census_sdf)
+  census_sdf <- withColumn(census_sdf, "geom_0", st_simplify(column("geom_0"), lit(0.001)))
+  census_sdf <- withColumn(census_sdf, "geom_0", st_updatesrid(column("geom_0"), column("geom_0_srid"), lit(4326L)))
+  census_sdf <- withColumn(census_sdf, "chip", grid_tessellateexplode(column("geom_0"), lit(target_resolution)))
+  census_sdf <- select(census_sdf, c(region_keys, "chip.*"))
+
+  raster_sdf <- read.df(
+    path = "sparkrMosaic/tests/testthat/data/prAdjust_day_HadGEM2-CC_SMHI-DBSrev930-GFD-1981-2010-postproc_rcp45_r1i1p1_20201201-20201231.nc",
+    source = "gdal",
+    raster.read.strategy = "retile_on_read"
+  )
+
+  raster_sdf <- withColumn(raster_sdf, "tile", rst_separatebands(column("tile")))
+  raster_sdf <- withColumn(raster_sdf, "timestep", element_at(rst_metadata(column("tile")), "NC_GLOBAL#GDAL_MOSAIC_BAND_INDEX"))
+  raster_sdf <- where(raster_sdf, "timestep = 21")
+  raster_sdf <- withColumn(raster_sdf, "tile", rst_setsrid(column("tile"), lit(4326L)))
+  raster_sdf <- withColumn(raster_sdf, "tile", rst_to_overlapping_tiles(column("tile"), lit(20L), lit(20L), lit(10L)))
+  raster_sdf <- withColumn(raster_sdf, "tile", rst_tessellate(column("tile"), lit(target_resolution)))
+
+  clipped_sdf <- join(raster_sdf, census_sdf, raster_sdf$tile.index_id == census_sdf$index_id)
+  clipped_sdf <- withColumn(clipped_sdf, "tile", rst_clip(column("tile"), column("wkb")))
+
+  merged_precipitation <- summarize(
+    groupBy(clipped_sdf, "timestep"),
+    alias(rst_merge_agg(column("tile")), "tile")
+  )
+
+  expect_equal(nrow(merged_precipitation), 1)
+
+})

R/sparkR-mosaic/sparkrMosaic/tests/testthat/testVectorFunctions.R

@@ -1,9 +1,7 @@
-source("data.R")
-
 test_that("scalar vector functions behave as intended", {
-  sdf <- SparkR::createDataFrame(
+  sdf <- createDataFrame(
     data.frame(
-      wkt = "POLYGON ((0 0, 0 2, 1 2, 1 0, 0 0))",
+      wkt = "POLYGON ((2 1, 1 2, 2 3, 2 1))",
       point_wkt = "POINT (1 1)"
     )
   )
@@ -52,14 +50,16 @@ test_that("scalar vector functions behave as intended", {
   sdf <- withColumn(sdf, "mosaic_explode", mosaic_explode(column("wkt"), lit(1L)))
   sdf <- withColumn(sdf, "mosaicfill", mosaicfill(column("wkt"), lit(1L)))
 
-  expect_no_error(SparkR::write.df(sdf, source = "noop", mode = "overwrite"))
+  expect_no_error(write.df(sdf, source = "noop", mode = "overwrite"))
   expect_equal(nrow(sdf), 1)
 
 })
 
 test_that("aggregate vector functions behave as intended", {
 
-  sdf <- SparkR::sql("SELECT id as location_id FROM range(1)")
+  sdf <- sql("SELECT id as location_id FROM range(1)")
+
+  inputGJ <- read_file("data/boroughs.geojson")
   sdf <- withColumn(sdf, "geometry", st_geomfromgeojson(lit(inputGJ)))
   expect_equal(nrow(sdf), 1)
 

R/sparkR-mosaic/tests.R

@@ -1,4 +1,6 @@
+options(warn = -1)
 library(testthat)
+library(readr)
 
 spark_location <- Sys.getenv("SPARK_HOME")
 library(SparkR, lib.loc = c(file.path(spark_location, "R", "lib")))
@@ -12,7 +14,7 @@ install.packages(package_file, repos=NULL)
 library(sparkrMosaic)
 
 # find the mosaic jar in staging
-staging_dir <- "/home/runner/work/mosaic/mosaic/staging/"
+staging_dir <- Sys.getenv("MOSAIC_LIB_PATH", "/home/runner/work/mosaic/mosaic/staging/")
 mosaic_jar <- list.files(staging_dir)
 mosaic_jar <- mosaic_jar[grep("jar-with-dependencies.jar", mosaic_jar, fixed=T)]
 print("Looking for mosaic jar in")

R/sparklyr-mosaic/enableGDAL.R

@@ -0,0 +1,17 @@
+#' enableGDAL
+#' 
+#' @description enableGDAL activates GDAL extensions for Mosaic
+#' @param sc sparkContext
+#' @name enableGDAL
+#' @rdname enableGDAL
+#' @return None
+#' @export enableGDAL
+#' @examples
+#' \dontrun{
+#' enableGDAL(sc)}
+
+enableGDAL <- function(
+    sc
+){
+  sparklyr::invoke_static(sc, class="com.databricks.labs.mosaic.gdal.MosaicGDAL", method="enableGDAL", spark_session(sc))
+}

R/sparklyr-mosaic/sparklyrMosaic/.Rbuildignore

@@ -1,2 +1,2 @@
 ^sparkrMosaic\.Rproj$
-^\.Rproj\.user$
+^\.Rproj\.user$

R/sparklyr-mosaic/sparklyrMosaic/DESCRIPTION

@@ -1,20 +1,23 @@
 Package: sparklyrMosaic
 Title: sparklyr bindings for Databricks Mosaic
 Version: 0.4.0
-Authors@R: 
+Authors@R:
     person("Robert", "Whiffin", , "[email protected]", role = c("aut", "cre")
            )
 Description: This package extends sparklyr to bring the Databricks Mosaic for geospatial processing APIs into sparklyr  .
 License: Databricks
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Collate: 
+Collate:
+    'enableGDAL.R'
     'enableMosaic.R'
     'sparkFunctions.R'
-    'functions.R'    
+    'functions.R'
 Imports:
   sparklyr
-Suggests: 
-    testthat (>= 3.0.0)
-Config/testthat/edition: 3
+Suggests:
+    testthat (>= 3.0.0),
+    sparklyr.nested (>= 0.0.4),
+    readr (>= 2.1.5)
+Config/testthat/edition: 3

R/sparklyr-mosaic/sparklyrMosaic/tests/testthat/data.R → R/sparklyr-mosaic/sparklyrMosaic/tests/testthat/data/boroughs.geojson

@@ -1,4 +1,4 @@
-inputGJ = '{
+{
    "type":"Feature",
    "properties":{
       "shape_area":"0.0000607235737749",
@@ -225,4 +225,4 @@ inputGJ = '{
          ]
       ]
    }
-}'
+}