Merge branch 'experimental/picocli' into develop

.gitignore

@@ -272,3 +272,4 @@ $RECYCLE.BIN/
 *.lnk
 
 # End of https://www.gitignore.io/api/java,maven,macos,linux,eclipse,windows,netbeans,intellij
+/-

src/main/java/eu/simstadt/regionchooser/RegionChooserCLI.java

+package eu.simstadt.regionchooser;
+
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Scanner;
+import java.util.concurrent.Callable;
+import org.osgeo.proj4j.CoordinateReferenceSystem;
+import picocli.CommandLine;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Model.CommandSpec;
+import picocli.CommandLine.Option;
+import picocli.CommandLine.Spec;
+
+
+/**
+ * Command Line Interface for RegionChooser. Could be useful to extract large regions on server, or automate the process
+ * from batch/python scripts.
+ * 
+ */
+
+// Usage: region_chooser [-hlV] [-e=31467] -o=output.gml -w=polygon.wkt -i=input.
+//                       gml[,input.gml...] [-i=input.gml[,input.gml...]]...
+// Extracts a region from one or more citygmls.
+//   -i, --input=input.gml[,input.gml...]
+//                             Citygml files to extract from
+//   -o, --output=output.gml   Output file
+//   -e, --epsg=31467          EPSG id for coordinate reference system
+//    -l, --local               Are WKT coordinates in local CRS?
+//   -w, --wkt=polygon.wkt     File containing WKT polygon, or - for stdin
+//   -h, --help                Show this help message and exit.
+//   -V, --version             Print version information and exit.
+
+
+// Example:
+// --input CGSC_Repository/Würzburg.proj/LoD2_566_5516_2_BY.gml,CGSC_Repository/Würzburg.proj/LoD2_568_5516_2_BY.gml
+// --output ./output.gml
+// --wkt ./grombuhl.txt
+
+
+@Command(name = "region_chooser", mixinStandardHelpOptions = true, version = "regionChooser x.x", description = "Extracts a region from one or more citygmls.", sortOptions = false)
+class RegionChooserCLI implements Callable<Integer>
+{
+	@Spec
+	CommandSpec spec;
+
+	//TODO: Add --gui?
+
+	@Option(names = { "-i",
+			"--input" }, required = true, split = ",", description = "Citygml files to extract from", paramLabel = "input.gml")
+	//TODO: Allow folders too?
+	Path[] citygmls;
+
+	@Option(names = { "-o",
+			"--output" }, required = true, description = "Output file", paramLabel = "output.gml")
+	Path outputCityGML;
+
+	@Option(names = { "-e", "--epsg" }, description = "EPSG id for coordinate reference system", paramLabel = "31467")
+	Integer espgId;
+
+	@Option(names = { "-l",
+			"--local" }, description = "Are WKT coordinates in local CRS?", paramLabel = "local_coordinates?")
+	boolean localCoordinates;
+
+	@Option(names = { "-w",
+			"--wkt" }, required = true, description = "File containing WKT polygon, or - for stdin", paramLabel = "polygon.wkt")
+	String wktFile = "-";
+
+	@Override
+	public Integer call() throws Exception {
+		CoordinateReferenceSystem localCRS;
+
+		if (espgId == null) {
+			localCRS = RegionChooserUtils.crsFromCityGMLHeader(citygmls[0]);
+		} else {
+			localCRS = RegionChooserUtils.crsFromSrsName("EPSG:" + espgId);
+		}
+		logInfo("Coordinate system: " + localCRS);
+
+		String wktPolygon;
+
+		if (wktFile.equals("-")) {
+			if (System.in.available() == 0) {
+				throw new IllegalArgumentException("Please provide \"POLYGON((x1 y1, x2 y2, ...))\" to standard input.");
+			} else {
+				wktPolygon = getInput();
+			}
+		} else {
+			wktPolygon = new String(Files.readAllBytes(Paths.get(wktFile)), StandardCharsets.UTF_8);
+			if (wktPolygon.isEmpty()) {
+				throw new IllegalArgumentException("Please write \"POLYGON((x1 y1, x2 y2, ...))\" inside " + wktFile);
+			}
+		}
+
+		if (!localCoordinates) {
+			// WKT coordinates are in WGS84, so should be first converted to srsName
+			wktPolygon = RegionChooserUtils.wktPolygonToLocalCRS(wktPolygon, localCRS);
+		}
+
+		logInfo("WKT Polygon expressed in local coordinates: " + wktPolygon);
+
+		StringBuilder sb = RegionExtractor.selectRegionDirectlyFromCityGML(wktPolygon, localCRS.toString(), citygmls);
+
+		RegionChooserUtils.writeStringBuilderToFile(sb, outputCityGML);
+
+		return 0;
+	}
+
+	private void logInfo(String message) {
+		spec.commandLine().getErr().println(message);
+	}
+
+	private static String getInput() {
+		try (Scanner myObj = new Scanner(System.in)) {
+			return myObj.nextLine();
+		}
+	}
+
+	// this example implements Callable, so parsing, error handling and handling user
+	// requests for usage help or version help can be done with one line of code.
+	public static void main(String... args) {
+		int exitCode = new CommandLine(new RegionChooserCLI()).execute(args);
+		System.exit(exitCode);
+	}
+}
\ No newline at end of file

src/main/java/eu/simstadt/regionchooser/RegionChooserCommandLineInterface.java

-package eu.simstadt.regionchooser;
-
-import java.nio.file.Path;
-import java.util.List;
-import java.util.concurrent.Callable;
-import picocli.CommandLine;
-import picocli.CommandLine.Command;
-import picocli.CommandLine.Parameters;
-
-
-@Command(name = "region_chooser", mixinStandardHelpOptions = true, version = "regionChooser x.x", description = "Extracts a region from one or more citygmls.")
-class RegionChooserCommandLineInterface implements Callable<Integer>
-{
-	@Parameters(index = "0", description = "SRS Name : 'EPSG:31467' or just 31467")
-	String srsName;
-
-	@Parameters(index = "1", description = "Output file : output.gml")
-	Path outputCityGML;
-
-	@Parameters(index = "2..*", arity = "1..*", description = "The citygml files to extract from : input1.gml input2.gml")
-	List<Path> citygmls;
-
-	@Override
-	public Integer call() throws Exception { // your business logic goes here...
-		for (Path file : citygmls) {
-			System.out.println(file);
-		}
-		return 0;
-	}
-
-	// this example implements Callable, so parsing, error handling and handling user
-	// requests for usage help or version help can be done with one line of code.
-	public static void main(String... args) {
-		int exitCode = new CommandLine(new RegionChooserCommandLineInterface()).execute(args);
-		System.exit(exitCode);
-	}
-}
\ No newline at end of file

src/main/java/eu/simstadt/regionchooser/RegionChooserUtils.java

@@ -13,6 +13,9 @@
 import org.locationtech.jts.geom.Coordinate;
 import org.locationtech.jts.geom.GeometryFactory;
 import org.locationtech.jts.geom.Polygon;
+import org.locationtech.jts.io.ParseException;
+import org.locationtech.jts.io.WKTReader;
+import org.locationtech.jts.io.WKTWriter;
 import org.osgeo.proj4j.BasicCoordinateTransform;
 import org.osgeo.proj4j.CRSFactory;
 import org.osgeo.proj4j.CoordinateReferenceSystem;
@@ -47,7 +50,7 @@ private RegionChooserUtils() {
 	 * @param srsName
 	 * @return CoordinateReferenceSystem
 	 */
-	private static CoordinateReferenceSystem crsFromSrsName(String srsName) {
+	public static CoordinateReferenceSystem crsFromSrsName(String srsName) {
 		// EPSG:31467
 		Pattern pEPSG = Pattern.compile("^(EPSG:\\d+)$");
 		Matcher mEPSG = pEPSG.matcher(srsName);
@@ -111,6 +114,15 @@ public static Polygon changePolygonCRS(Polygon polygonInOriginalCRS, CoordinateR
 		return geometryFactory.createPolygon(convexHullcoordinates);
 	}
 
+	public static String wktPolygonToLocalCRS(String wktPolygonInWGS84, CoordinateReferenceSystem localCRS)
+			throws ParseException {
+		final WKTReader wktReader = new WKTReader();
+		final WKTWriter wktWriter = new WKTWriter();
+		// WKT coordinates are in WGS84, so should be first converted to srsName
+		Polygon wgs84Polygon = (Polygon) wktReader.read(wktPolygonInWGS84);
+		return wktWriter.write(changePolygonCRS(wgs84Polygon, WGS84, localCRS));
+	}
+
 	/**
 	 *
 	 * Fast scan of the 50 first lines of a Citygml file to look for srsName. It might not be as reliable as parsing the

src/main/java/eu/simstadt/regionchooser/RegionExtractor.java

@@ -21,10 +21,10 @@
 
 public class RegionExtractor
 {
-	private static final WKTReader wktReader = new WKTReader();
+	private static final WKTReader WKT_READER = new WKTReader();
 
 	private static final Logger LOGGER = Logger.getLogger(RegionExtractor.class.getName());
-	private static final GeometryFactory gf = new GeometryFactory();
+	private static final GeometryFactory GEOMETRY_FACTORY = new GeometryFactory();
 
 	/**
 	 * Main method behind RegionChooser. Given CityGMLs (as Path[]) and a geometry (as Well-known text POLYGON, in the
@@ -48,10 +48,13 @@
 	static StringBuilder selectRegionDirectlyFromCityGML(String wktPolygon, String srsName, Path... citygmlPaths)
 			throws ParseException, XPathParseException, NavException, IOException {
 
+		//TODO: Should actually write directly to a bufferedwriter
+		//TODO: Should return the number of found buildings.
+
 		int buildingsCount = 0;
 		int foundBuildingsCount = 0;
 		StringBuilder sb = new StringBuilder();
-		Geometry poly = wktReader.read(wktPolygon);
+		Geometry poly = WKT_READER.read(wktPolygon);
 
 		CityGmlIterator citygml = null;
 		for (int i = 0; i < citygmlPaths.length; i++) {
@@ -65,7 +68,7 @@ static StringBuilder selectRegionDirectlyFromCityGML(String wktPolygon, String s
 				buildingsCount += 1;
 				if (buildingXmlNode.hasCoordinates()) {
 					Coordinate coord = new Coordinate(buildingXmlNode.x, buildingXmlNode.y);
-					Point point = gf.createPoint(coord);
+					Point point = GEOMETRY_FACTORY.createPoint(coord);
 					if (point.within(poly)) {
 						foundBuildingsCount++;
 						sb.append(buildingXmlNode.toString());
@@ -75,13 +78,16 @@ static StringBuilder selectRegionDirectlyFromCityGML(String wktPolygon, String s
 					LOGGER.info("1000 buildings parsed");
 				}
 			}
-
 		}
 
 		if (citygml == null) {
 			throw new IllegalArgumentException("There should be at least one citygml");
 		}
 
+		if (foundBuildingsCount == 0) {
+			LOGGER.warning("No building found in the selected region.");
+		}
+
 		LOGGER.info("Buildings found in selected region " + foundBuildingsCount);
 		sb.append(citygml.getFooter());
 		return sb;

src/main/java/eu/simstadt/regionchooser/fast_xml_parser/BuildingXmlNode.java

@@ -28,7 +28,8 @@ public BuildingXmlNode(VTDNav navigator, int buildingOffset, int buildingLength)
 		this.coordinatesFinder = new AutoPilot(navigator);
 		this.buildingLength = buildingLength;
 		this.buildingOffset = buildingOffset;
-		extractCoordinates(); //NOTE: Should it be done lazily? Is there any reason to extract a BuildingXmlNode without coordinates?
+		extractCoordinates();
+		//TODO: Get Building ID too, in order to avoid duplicates?
 	}
 
 	public boolean hasCoordinates() {

src/main/java/eu/simstadt/regionchooser/fast_xml_parser/ConvexHullCalculator.java

@@ -92,6 +92,7 @@ public static void extractHullsForEveryCityGML(Path repository, Consumer<String>
 					try {
 						Path kmlPath = getHullPath(repository, gmlPath);
 						if (Files.exists(kmlPath)) {
+							//TODO: Check if size is the same as original. Recreate otherwise.
 							LOGGER.fine("Using cache from " + repository.relativize(kmlPath));
 							return new String(Files.readAllBytes(kmlPath), StandardCharsets.UTF_8);
 						} else {

src/main/resources/eu/simstadt/regionchooser/website/script/simstadt_openlayers.js

@@ -69,7 +69,7 @@ var regionChooser = (function(){
 		dataPanel.append('.');
 		srsName = feature.get("srsName");
 		if (proj4.defs(srsName) === undefined){
-			console.warning(srsName + " isn't defined by Proj4js!")
+			console.warn(srsName + " isn't defined by Proj4js!")
 		}
 	};
 	
@@ -162,7 +162,7 @@ var regionChooser = (function(){
 		var sketch_percentage = Math.round(intersectionArea / polygonArea * 100);
 		intersections.addFeature(intersection);
 		var link = '<li>'
-        // TODO: If possible, highlight the corresponding polygon when hovering above a name.
+		// TODO: If possible, highlight the corresponding polygon when hovering above a name.
 		link += '<input type="checkbox" id="citygml_' + feature.getId() + '" class="select_citygml" onclick="regionChooser.isDownloadPossible();"><label for="citygml_' + feature.getId() + '">' +  feature['name'] + '</label>';
 
 		link += " (" + citygml_percentage + "%";
@@ -194,13 +194,13 @@ var regionChooser = (function(){
 		features_by_project = groupBy(kml_source.getFeatures(), "project");
 		
 		Object.keys(features_by_project).forEach(function(project) {
-		    features = features_by_project[project];
-		    features_and_intersections = features.map(f=> [f, findIntersection(f,polygon)]).filter(l => l[1] !== undefined);
-		    if (features_and_intersections.length > 0){
-		    	intersection_found = true;
+			features = features_by_project[project];
+			features_and_intersections = features.map(f=> [f, findIntersection(f,polygon)]).filter(l => l[1] !== undefined);
+			if (features_and_intersections.length > 0){
+				intersection_found = true;
 				dataPanel.append("<h2 class='info'>" + project);
-		    	features_and_intersections.forEach(l => showLinkToDownload(l[0], l[1], polygonArea));
-		    }
+				features_and_intersections.forEach(l => showLinkToDownload(l[0], l[1], polygonArea));
+			}
 		});
 		
 		if (intersection_found) {
@@ -246,7 +246,7 @@ var regionChooser = (function(){
 					fxapp.downloadRegionFromCityGMLs(sketchAsWKT(srsName), project, citygmlNames.join(";"), srsName);
 					dataPanel.prepend("<h2 class='ok'>Done!</h2><br/>\n");
 				} catch (e) {
-					console.warning("ERROR : " + e);
+					console.warn("ERROR : " + e);
 					dataPanel.prepend("<h2 class='error'>Some problem occured!</h2><br/>\n");
 				}
 				var end = new Date().getTime();
@@ -266,22 +266,9 @@ var regionChooser = (function(){
 
 	function displayInfo() {
 		dataPanel.empty();
-		var geom = /** @type {ol.geom.Polygon} */
-		(sketch.getGeometry().clone().transform(sourceProj, 'EPSG:4326'));
+		var geom = sketch.getGeometry().clone().transform(sourceProj, 'EPSG:4326');
 		var coordinates = geom.getLinearRing(0).getCoordinates();
 		var area = Math.abs(wgs84Sphere.geodesicArea(coordinates));
-		var coords = geom.getLinearRing(0).getCoordinates();
-		if (!fromJavaFX) {
-			var wgs84_coords = "";
-			var n = coords.length;
-			for (var i = 0; i < n; i++) {
-				var wgs84_coord = coords[i];
-				wgs84_coords += "(" + wgs84_coord[1] + "," + wgs84_coord[0] + ")<br/>";
-
-			}
-			dataPanel.append("WGS84 Coordinates<br/>");
-			dataPanel.append(wgs84_coords + "<br/>\n");
-		}
 		//NOTE: Could show m², ha or km² depending on magnitude
 		dataPanel.append("<h3 class='clean'>Area : " + (area / 10000).toFixed(1) + " ha\n");
 		dataPanel.append('<div style="visibility:hidden" id="download_region">' + 
@@ -290,6 +277,7 @@ var regionChooser = (function(){
 			'<a href="#" onclick="regionChooser.checkCityGMLS(false);">(Select None)</a>\n'+
 			'</div>\n');
 		findIntersections();
+		dataPanel.append('<button type="button" onclick="regionChooser.copyCoordinatesToClipboard()" id="get_wgs84">Copy coordinates</button><br/>\n')
 	}
 
 	draw.on('drawend', function() {
@@ -339,7 +327,7 @@ var regionChooser = (function(){
 			fxapp.log(message);
 		}
 		
-		console.warning = function(message){
+		console.warn = function(message){
 			fxapp.warning(message);
 		}
 	}
@@ -390,6 +378,48 @@ var regionChooser = (function(){
 		fxapp.selectRepository();
 	}
 	
+	publicScope.copyCoordinatesToClipboard = function(){
+		var geom = sketch.getGeometry().clone().transform(sourceProj, 'EPSG:4326');
+		var wgs84Coords = geom.getLinearRing(0).getCoordinates();
+		var wktPolygon = "POLYGON((";
+		wktPolygon += wgs84Coords.map(lonLat => lonLat.join(" ")).join(", ");
+		publicScope.copyToClipboard(wktPolygon + "))");
+	}
+	
+	// Copies a string to the clipboard. Must be called from within an
+	// event handler such as click. May return false if it failed, but
+	// this is not always possible. Browser support for Chrome 43+,
+	// Firefox 42+, Safari 10+, Edge and Internet Explorer 10+.
+	// Internet Explorer: The clipboard feature may be disabled by
+	// an administrator. By default a prompt is shown the first
+	// time the clipboard is used (per session).
+	// https://stackoverflow.com/a/33928558/6419007
+	publicScope.copyToClipboard = function(text) {
+	if (window.clipboardData && window.clipboardData.setData) {
+		// Internet Explorer-specific code path to prevent textarea being shown while dialog is visible.
+		return window.clipboardData.setData("Text", text);
+	}
+	else if (document.queryCommandSupported && document.queryCommandSupported("copy")) {
+		var textarea = document.createElement("textarea");
+		textarea.textContent = text;
+		textarea.style.position = "fixed";  // Prevent scrolling to bottom of page in Microsoft Edge.
+		document.body.appendChild(textarea);
+		textarea.select();
+		try {
+			document.execCommand("copy");  // Security exception may be thrown by some browsers.
+			dataPanel.append("<h2 class='ok'>Coordinates copied to clipboard!</h2><br/>\n");
+			return;
+		}
+		catch (ex) {
+			console.warn("Copy to clipboard failed.", ex);
+			return prompt("Copy to clipboard: Ctrl+C, Enter", text);
+		}
+		finally {
+			document.body.removeChild(textarea);
+		}
+	}
+}
+	
 	publicScope.showRepositoryName = function(path) {
 		document.getElementById("repo_path").textContent = path;
 	}

src/test/java/eu/simstadt/regionchooser/RegionChooserTests.java

+package eu.simstadt.regionchooser;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import java.io.BufferedWriter;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.PrintStream;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import org.junit.jupiter.api.AfterEach; // JUnit 5
+import org.junit.jupiter.api.BeforeEach; // JUnit 5
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+import picocli.CommandLine;
+
+
+class RegionChooserTests
+{
+	final PrintStream originalOut = System.out;
+	final PrintStream originalErr = System.err;
+	final ByteArrayOutputStream out = new ByteArrayOutputStream();
+	final ByteArrayOutputStream err = new ByteArrayOutputStream();
+
+	private static final Path TEST_REPOSITORY = Paths.get("src/test/resources/testdata/");
+
+
+	@TempDir
+	Path tempDirectory;
+	Path outGML;
+
+	@BeforeEach
+	public void setUp() {
+		out.reset();
+		err.reset();
+		System.setOut(new PrintStream(out));
+		System.setErr(new PrintStream(err));
+		outGML = tempDirectory.resolve("output.gml");
+	}
+
+	@AfterEach
+	public void restore() throws IOException {
+		System.setOut(originalOut);
+		System.setErr(originalErr);
+		Files.deleteIfExists(outGML);
+	}
+
+	@Test
+	void testNoInput() {
+		new CommandLine(new RegionChooserCLI()).execute("");
+		String expectedErr = "Missing required options: '--input=input.gml', '--output=output.gml', '--wkt=polygon.wkt'";
+		assertTrue(err.toString().contains(expectedErr), err.toString() + " should contain " + expectedErr);
+	}
+
+	@Test
+	void testExtractRegionFromTwoCitygmls() throws IOException {
+		String wktPolygon = "POLYGON((3512984.7003764412 5405148.310572891,3513038.6360455155 5405010.072163861,3513142.7277745553 5405004.02571992,3514204.1661769524 5405563.192081669,3514399.2818417274 5405720.905457244,3514291.6158155007 5405896.706492759,3512984.7003764412 5405148.310572891))";
+		Path citygml1 = TEST_REPOSITORY.resolve("Stuttgart.proj/Stuttgart_LOD0_LOD1_small.gml");
+		Path citygml2 = TEST_REPOSITORY.resolve("Stuttgart.proj/Stöckach_überarbeitete GML-NoBuildingPart.gml");
+		Path inWKT = tempDirectory.resolve("polygon.wkt");
+		try (BufferedWriter wkt = Files.newBufferedWriter(inWKT)) {
+			wkt.write(wktPolygon);
+		}
+		assertFalse(Files.exists(outGML));
+		new CommandLine(new RegionChooserCLI()).execute("--input=" + citygml1 + "," + citygml2,
+				"--output=" + outGML, "--wkt=" + inWKT, "--epsg=31463", "--local");
+		assertTrue(Files.exists(outGML));
+		assertTrue(Files.size(outGML) > 600_000);
+		assertEquals(20, countBuildings(outGML));
+	}
+
+
+	@Test
+	void testExtractRegionFromTwoCitygmlsInWGS84() throws IOException {
+		String wktPolygon = "POLYGON((9.18991539528286 48.79067456353269, 9.195580220722313 48.7873947720947, 9.172062612079735 48.78241812742368, 9.170946813129538 48.78569824412753, 9.18991539528286 48.79067456353269))";
+		Path citygml1 = TEST_REPOSITORY.resolve("Stuttgart.proj/Stuttgart_LOD0_LOD1_small.gml");
+		Path citygml2 = TEST_REPOSITORY.resolve("Stuttgart.proj/Stöckach_überarbeitete GML-NoBuildingPart.gml");
+		Path inWKT = tempDirectory.resolve("polygon.wkt");
+		try (BufferedWriter wkt = Files.newBufferedWriter(inWKT)) {
+			wkt.write(wktPolygon);
+		}
+		assertFalse(Files.exists(outGML));
+		new CommandLine(new RegionChooserCLI()).execute("--input=" + citygml1 + "," + citygml2,
+				"--output=" + outGML, "--wkt=" + inWKT);
+		String expectedLog = "EPSG:31463";
+		assertTrue(err.toString().contains(expectedLog), err.toString() + " should contain " + expectedLog);
+		assertTrue(Files.exists(outGML));
+		assertTrue(Files.size(outGML) > 300_000);
+		assertEquals(22, countBuildings(outGML));
+	}
+
+	private long countBuildings(Path outGML) throws IOException {
+		return Files.readAllLines(outGML).stream().filter(line -> line.contains("bldg:Building gml:id=")).count();
+	}
+
+	@Test
+	void testExtractRegionWithStandardInput() throws IOException {
+		String wktPolygon = "POLYGON((-73.9959209576448 40.73286384885367, -73.996317924579 40.732359794090684, -73.9947515145143 40.7315061442504, -73.99422580154739 40.73214841515045, -73.9959209576448 40.73286384885367))";
+		Path citygml = TEST_REPOSITORY.resolve("NewYork.proj/ManhattanSmall.gml");
+		InputStream stdin = new ByteArrayInputStream(wktPolygon.getBytes(StandardCharsets.UTF_8));
+		System.setIn(stdin);
+		assertFalse(Files.exists(outGML));
+		new CommandLine(new RegionChooserCLI()).execute("--input=" + citygml, "--output=" + outGML,
+				"--wkt=-");
+		String expectedLog = "EPSG:32118";
+		assertTrue(err.toString().contains(expectedLog), err.toString() + " should contain " + expectedLog);
+		assertTrue(Files.exists(outGML));
+		assertEquals(2, countBuildings(outGML));
+	}
+
+	@Test
+	void testExtractRegionWithMissingInput() throws IOException {
+		String wktPolygon = "POLYGON((-73.9959209576448 40.73286384885367, -73.996317924579 40.732359794090684, -73.9947515145143 40.7315061442504, -73.99422580154739 40.73214841515045, -73.9959209576448 40.73286384885367))";
+		Path citygml = TEST_REPOSITORY.resolve("NewYork.proj/ManhattanSmall.gml");
+		Path inWKT = tempDirectory.resolve("polygon.wkt");
+		try (BufferedWriter wkt = Files.newBufferedWriter(inWKT)) {
+			wkt.write(wktPolygon);
+		}
+		new CommandLine(new RegionChooserCLI()).execute("--input=" + citygml, "--output=" + outGML,
+				"--wkt=-");
+		String expectedLog = "EPSG:32118";
+		assertTrue(err.toString().contains(expectedLog), err.toString() + " should contain " + expectedLog);
+		expectedLog = "Please provide \"POLYGON((x1 y1, x2 y2, ...))\" to standard input.";
+		assertTrue(err.toString().contains(expectedLog), err.toString() + " should contain " + expectedLog);
+		assertFalse(Files.exists(outGML));
+	}
+}
+

src/test/java/eu/simstadt/regionchooser/RegionExtractorTests.java

@@ -53,8 +53,7 @@ void testExtract3BuildingsFromGSK3Model() throws Throwable {
 	}
 
 	@Test
-	void testExtractBuildingsWithoutCommentsInBetween() throws Throwable {
-		//NOTE: Small region around WashingtonSquare
+	void testExtractBuildingsWithCommentsInBetween() throws Throwable {
 		String wktPolygon = "POLYGON((300259.78663489706 62835.835907766595,300230.33294975647 62792.0482567884,300213.5667431851 62770.83143720031,300183.6592861123 62730.20347659383,300252.9947486632 62676.938468840905,300273.3862256562 62701.767105345614,300257.5250407747 62715.760413539596,300308.2754543957 62805.14198211394,300259.78663489706 62835.835907766595))";
 		Path citygmlPath = TEST_REPOSITORY.resolve("NewYork.proj/ManhattanSmall.gml");
 		String archGMLString = RegionExtractor.selectRegionDirectlyFromCityGML(wktPolygon, EPSG_32118, citygmlPath)
@@ -65,10 +64,6 @@ void testExtractBuildingsWithoutCommentsInBetween() throws Throwable {
 		assertTrue(archGMLString.contains("uuid_0985cebb-922d-4b3e-95e5-15dc6089cd28"));
 		assertTrue(archGMLString.contains(CITY_MODEL_HEADER));
 		assertTrue(archGMLString.contains(CITY_MODEL_FOOTER));
-		assertFalse(archGMLString.contains("comment between buildings"),
-				"Comments between buildings shouldn't be extracted");
-		assertFalse(archGMLString.contains("comment after last building"),
-				"Comments after buildings shouldn't be extracted");
 	}
 
 	@Test

src/test/java/eu/simstadt/regionchooser/RegionExtractorWithDifferentInputTests.java

@@ -7,25 +7,19 @@
 import java.util.Arrays;
 import java.util.stream.Collectors;
 import org.junit.jupiter.api.Test;
-import org.locationtech.jts.geom.Polygon;
 import org.locationtech.jts.io.ParseException;
-import org.locationtech.jts.io.WKTReader;
-import org.locationtech.jts.io.WKTWriter;
 import org.osgeo.proj4j.CoordinateReferenceSystem;
 import com.ximpleware.NavException;
 import com.ximpleware.XPathEvalException;
 import com.ximpleware.XPathParseException;
 
 
-public class RegionExtractorWithDifferentInputTests
+class RegionExtractorWithDifferentInputTests
 {
-	private static final WKTReader WKT_READER = new WKTReader();
-	private static final WKTWriter WKT_WRITER = new WKTWriter();
 	private static final Path TEST_REPOSITORY = Paths.get("src/test/resources/testdata/");
 
-	//NOTE: This test can be adapted to download a region which is too large for the server. Here with local coordinates
 	@Test
-	public void testExtractRegionWithLocalCRS()
+	void testExtractRegionWithLocalCRS()
 			throws IOException, XPathParseException, NavException, XPathEvalException, ParseException {
 		String citygml = "DA13_DA14_3D_Buildings_Port_Morris.gml";
 		String projectName = "NewYork";
@@ -39,9 +33,8 @@ public void testExtractRegionWithLocalCRS()
 				"One weird shaped roof should be inside the region");
 	}
 
-	//NOTE: This test can be adapted to download a region which is too large for the server. Here with WGS84 coordinates
 	@Test
-	public void testExtractRegionWithWGS84()
+	void testExtractRegionWithWGS84()
 			throws ParseException, IOException, XPathParseException, NavException, XPathEvalException {
 		String wgs84WktPolygon = "POLYGON((-73.91140940026597 40.804246732157196,-73.91424181298568 40.80025100302325,-73.90934946374252 40.79755456207104,-73.90561582879378 40.80116062104605,-73.90960695580794 40.80340212653638,-73.91140940026597 40.804246732157196))";
 		String citygml = "DA13_DA14_3D_Buildings_Port_Morris.gml";
@@ -49,19 +42,16 @@ public void testExtractRegionWithWGS84()
 		Path project = TEST_REPOSITORY.resolve(projectName + ".proj");
 		Path citygmlPath = project.resolve(citygml);
 
-		Polygon wgs84Polygon = (Polygon) WKT_READER.read(wgs84WktPolygon);
 		CoordinateReferenceSystem localCRS = RegionChooserUtils.crsFromCityGMLHeader(citygmlPath);
-		String localWktPolygon = WKT_WRITER
-				.write(RegionChooserUtils.changePolygonCRS(wgs84Polygon, RegionChooserUtils.WGS84, localCRS));
+		String localWktPolygon = RegionChooserUtils.wktPolygonToLocalCRS(wgs84WktPolygon, localCRS);
 		StringBuilder sb = RegionExtractor.selectRegionDirectlyFromCityGML(localWktPolygon, localCRS.getName(),
 				citygmlPath);
 		assertTrue(sb.toString().contains("gml_ZVHMQQ6BZGRT0O3Q6RGXF12BDOV49QIZ58XB"),
 				"One weird shaped roof should be inside the region");
 	}
 
-	//NOTE: This test can be adapted to download a region which is too large for the server. Here with old coordinates from WebSimstadt
 	@Test
-	public void testExtractRegionWithOldCoordinates()
+	void testExtractRegionWithOldCoordinates()
 			throws ParseException, IOException, XPathParseException, NavException, XPathEvalException {
 		String oldFormatPolygon = "(40.81173171854368,-73.93268437431763)\r\n" +
 				"(40.81069231965162,-73.93068165999941)\r\n" +
@@ -98,16 +88,12 @@ public void testExtractRegionWithOldCoordinates()
 		Path project = TEST_REPOSITORY.resolve(projectName + ".proj");
 		Path citygmlPath = project.resolve(citygml);
 
-		Polygon wgs84Polygon = (Polygon) WKT_READER.read(wgs84WktPolygon);
 		CoordinateReferenceSystem localCRS = RegionChooserUtils.crsFromCityGMLHeader(citygmlPath);
-		String localWktPolygon = WKT_WRITER
-				.write(RegionChooserUtils.changePolygonCRS(wgs84Polygon, RegionChooserUtils.WGS84, localCRS));
+		String localWktPolygon = RegionChooserUtils.wktPolygonToLocalCRS(wgs84WktPolygon, localCRS);
 		StringBuilder sb = RegionExtractor.selectRegionDirectlyFromCityGML(localWktPolygon, localCRS.getName(),
 				citygmlPath);
 
 		assertTrue(sb.toString().contains("gml_ZVHMQQ6BZGRT0O3Q6RGXF12BDOV49QIZ58XB"),
 				"One weird shaped roof should be inside the region");
 	}
-
-	//TODO: Write a method to merge RegionChooser results from multiple gmls
 }