add tests for ml processes

DESCRIPTION

@@ -45,3 +45,6 @@ Collate:
     'error.R'
 Depends:
     R (>= 4.3.0)
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

Dockerfile

@@ -14,7 +14,7 @@ RUN R -e "install.packages('gdalcubes')"
 
 # install other necessary packages
 RUN apt-get install -y libsodium-dev libudunits2-dev
-RUN Rscript -e "install.packages(c('plumber', 'useful', 'ids', 'R6', 'sf', 'rstac','bfast'))"
+RUN Rscript -e "install.packages(c('plumber', 'useful', 'ids', 'R6', 'sf', 'rstac','bfast', 'spsUtil'))"
 
 # create directories
 RUN mkdir -p /opt/dockerfiles/ && mkdir -p /var/openeo/workspace/ && mkdir -p /var/openeo/workspace/data/
@@ -26,4 +26,4 @@ RUN Rscript -e "remotes::install_local('/opt/dockerfiles',dependencies=TRUE)"
 # cmd or entrypoint for startup
 CMD ["R", "-q", "--no-save", "-f /opt/dockerfiles/startProduction.R"]
 
-EXPOSE 8000
+EXPOSE 8000

startLocal.R

@@ -1,5 +1,8 @@
 # build and install package locally (use for development)
-remotes::install_local("./", dependencies = TRUE, force = TRUE)
+remotes::install_local("./", dependencies = FALSE, force = TRUE)
+
+# run test for processes of the package
+test_res = devtools::test(stop_on_failure = TRUE)
 
 # Start service
 library(openeocubes)

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(openeocubes)
+
+test_check("openeocubes")

tests/testthat/test-apply_prediction.R

@@ -0,0 +1,23 @@
+test_that("apply prediction works", {
+
+  # create Session-object for testing
+  config <- SessionConfig(api.port = 8000, host = "127.0.0.1")
+
+  # set workspace for testing
+  config$workspace.path = paste0(getwd(),"/", test_path("testData"))
+
+  # this silently returns "Session"
+  createSessionInstance(config)
+
+  expected_bands = c("predicted_class", "class_confidence")
+  expected_classes = c("apply_pixel_cube", "cube", "xptr")
+
+  datacube = test_path("testData", "train_model_test_cube.nc") |> gdalcubes::ncdf_cube()
+
+  # "myModel" must exist in the Session workspace path
+  prediction_datacube = spsUtil::quiet(apply_prediction_opp(datacube, model_id = "myModel"))
+
+
+  expect_equal(class(prediction_datacube), expected_classes)
+  expect_equal(names(prediction_datacube), expected_bands)
+})

tests/testthat/test-train_model.R

@@ -0,0 +1,37 @@
+test_that("train model works", {
+
+  # create Session-object for testing
+  config <- SessionConfig(api.port = 8000, host = "127.0.0.1")
+
+  # set workspace for testing
+  config$workspace.path = base::paste0(base::getwd(),"/", test_path("testData"))
+
+  # this silently returns "Session"
+  createSessionInstance(config)
+
+  datacube = gdalcubes::ncdf_cube(test_path("testData", "train_model_test_cube.nc"))
+
+  training_data_path = test_path("testData", "classes.geojson")
+  training_data = sf::st_read(training_data_path, quiet = TRUE)
+
+  training_data_class_levels = base::unique(training_data$class) |>
+    base::as.numeric() |>
+    base::sort()
+
+  model = spsUtil:::quiet(train_model_opp(
+    data = datacube,
+    model_type = "RF",
+    labeled_polygons = training_data_path,
+    hyperparameters = base::list(mtry = 5, ntree = 50),
+    ))
+
+  # get model class levels and parse Integer value
+  model_class_levels = base::levels(model$finalModel$y) |>
+    base::as.character() |>
+    stringr::str_extract_all("\\d+") |>
+    base::as.numeric() |>
+    base::sort()
+
+  expect_equal(class(model), c("train", "train.formula"))
+  expect_equal(model_class_levels, training_data_class_levels)
+})

tests/testthat/testData/classes.geojson

@@ -0,0 +1,12 @@
+{
+"type": "FeatureCollection",
+"name": "demo_training_data",
+"crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:OGC:1.3:CRS84" } },
+"features": [
+{ "type": "Feature", "properties": { "class": 1 }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 7.689557844550476, 51.949452468942482 ], [ 7.688892820575198, 51.949026810046234 ], [ 7.688995131956011, 51.947686746399938 ], [ 7.690990203881843, 51.948601147109812 ], [ 7.693778189008965, 51.948616912475792 ], [ 7.695517482482767, 51.949956948328605 ], [ 7.695645371708782, 51.950319539382036 ], [ 7.694443212984243, 51.951013183663179 ], [ 7.696003461541622, 51.951943280746399 ], [ 7.695798838779998, 51.952305855739226 ], [ 7.694340901603431, 51.952274327595376 ], [ 7.692499296748817, 51.950792479828458 ], [ 7.693113165033688, 51.950256480278995 ], [ 7.692192362606382, 51.949673179372205 ], [ 7.689660155931289, 51.949531294220662 ], [ 7.689557844550476, 51.949452468942482 ] ] ] } },
+{ "type": "Feature", "properties": { "class": 1 }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 7.689212543640235, 51.95613636025216 ], [ 7.688266163367726, 51.954575823841481 ], [ 7.693023642575478, 51.952400440037813 ], [ 7.693611933015146, 51.95279453913448 ], [ 7.692205151528981, 51.954055632967936 ], [ 7.690619325126397, 51.954292084113142 ], [ 7.690082190377137, 51.954828035425976 ], [ 7.691156459875661, 51.956152122969122 ], [ 7.689212543640235, 51.95613636025216 ] ] ] } },
+{ "type": "Feature", "properties": { "class": 2 }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 7.697320720569576, 51.952416204068179 ], [ 7.695402382179351, 51.951092006198067 ], [ 7.697013786427139, 51.949752004262422 ], [ 7.697397454105184, 51.949893888715664 ], [ 7.697320720569576, 51.952416204068179 ] ] ] } },
+{ "type": "Feature", "properties": { "class": 3 }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 7.689979878996324, 51.952778775237121 ], [ 7.689928723305917, 51.951785638530744 ], [ 7.691898217386547, 51.9512338864117 ], [ 7.692256307219387, 51.952195507138718 ], [ 7.689979878996324, 51.952778775237121 ] ] ] } },
+{ "type": "Feature", "properties": { "class": 4 }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 7.697371876259982, 51.949468234009203 ], [ 7.696860319355923, 51.949231757426539 ], [ 7.695862783393008, 51.949736239295468 ], [ 7.695786049857396, 51.949625884371564 ], [ 7.696783585820314, 51.949089870878382 ], [ 7.697474187640793, 51.949310583092625 ], [ 7.697371876259982, 51.949468234009203 ] ] ] } }
+]
+}