Merge branch 'refs/heads/dev' into dev_advanced_db_management

# Conflicts:
#	CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/database/EmbeddedDatabaseHandler.java

CHANGELOG.md

@@ -5,6 +5,16 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.18.1] (2025-12-10)
+
+### Hotfix
+
+This hotfix removes the AUTO_SERVER flag from the embedded database, which causes a Firewall popup when the database is 
+started, due to opening local ports for accessing the database while CityDoctor is running.  
+The Firewall request can be safely denied, as CityDoctor uses the database-file for connections to the database.  
+Accepting the request does not open up remote connections to the database, as H2 by default only allows connections from 
+the local machine.
+
 ## [3.18.0] (2025-12-05)
 
 **Semi-breaking change:** This MR introduces breaking changes to the CityDoctorModel and CityObject classes. Usage of the CityDoctorValidation API and CLI remain backwards compatible.

CityDoctorParent/CityDoctorCheckResult/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>de.hft.stuttgart</groupId>
 		<artifactId>CityDoctorParent</artifactId>
-		<version>3.18.0</version>
+		<version>3.18.1</version>
 	</parent>
 	<artifactId>CityDoctorCheckResult</artifactId>
 	<dependencies>

CityDoctorParent/CityDoctorCheckResult/src/main/java/de/hft/stuttgart/citydoctor2/checkresult/CheckReport.java

@@ -22,6 +22,7 @@ import java.io.BufferedReader;
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.nio.file.Path;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -65,7 +66,11 @@ public class CheckReport {
 	private Map<String, FeatureReport> featureReports;
 
 	public static CheckReport load(String file) throws CheckReportParseException {
-		try (BufferedReader reader = new BufferedReader(new FileReader(file))) {
+		return load(Path.of(file));
+	}
+	
+	public static CheckReport load(Path path) throws CheckReportParseException {
+		try (BufferedReader reader = new BufferedReader(new FileReader(path.toFile()))) {
 			CheckReport report = (CheckReport) getContext().createUnmarshaller().unmarshal(new InputSource(reader));
 			enrichReportStructure(report);
 			return report;

CityDoctorParent/CityDoctorEdge/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>de.hft.stuttgart</groupId>
 		<artifactId>CityDoctorParent</artifactId>
-		<version>3.18.0</version>
+		<version>3.18.1</version>
 	</parent>
 	<artifactId>CityDoctorEdge</artifactId>
 	<dependencies>

CityDoctorParent/CityDoctorModel/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>de.hft.stuttgart</groupId>
 		<artifactId>CityDoctorParent</artifactId>
-		<version>3.18.0</version>
+		<version>3.18.1</version>
 	</parent>
 	<properties>
 		<versionString>${project.version}-${git.commit.id.abbrev}</versionString>

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/check/AbstractErrorVisitor.java

@@ -40,6 +40,7 @@ import de.hft.stuttgart.citydoctor2.check.error.SolidSelfIntError;
 import de.hft.stuttgart.citydoctor2.check.error.SurfaceUnfragmentedError;
 import de.hft.stuttgart.citydoctor2.check.error.TooFewPolygonsError;
 import de.hft.stuttgart.citydoctor2.check.error.UnknownCheckError;
+import de.hft.stuttgart.citydoctor2.check.error.XMLValidationError;
 
 public abstract class AbstractErrorVisitor implements ErrorVisitor {
 
@@ -207,4 +208,8 @@ public abstract class AbstractErrorVisitor implements ErrorVisitor {
 	public void visit(SolidError err) {
 	}
 	
+	@Override
+	public void visit(XMLValidationError err) {
+	}
+
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/check/CheckError.java

@@ -83,4 +83,8 @@ public interface CheckError extends Serializable {
 	 */
 	public void report(ErrorReport report);
 
+	public default boolean isParsingError() {
+		return false;
+	}
+
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/check/Checkable.java

@@ -26,7 +26,7 @@ import java.util.Map;
 
 import de.hft.stuttgart.citydoctor2.utils.CheckErrorFound;
 import de.hft.stuttgart.citydoctor2.utils.visitors.CheckableErrorCollector;
-import de.hft.stuttgart.citydoctor2.utils.visitors.ClearVisitorResultsVisitor;
+import de.hft.stuttgart.citydoctor2.utils.visitors.ClearResultsVisitor;
 import de.hft.stuttgart.citydoctor2.utils.visitors.ClearMetaInformationVisitor;
 import de.hft.stuttgart.citydoctor2.utils.visitors.ContainsAnyErrorVisitor;
 import de.hft.stuttgart.citydoctor2.utils.visitors.ContainsErrorVisitor;
@@ -221,18 +221,23 @@ public abstract class Checkable implements Serializable {
 	}
 
 	/**
-	 * Clears the checkResults list of this checkable.
+	 * Clears the checkResults of this checkable unless the error occured during parsing.
 	 */
 	public void clearCheckResults() {
-		setValidated(false);
-		checkResults.clear();
+		checkResults.entrySet().removeIf(e -> {
+			if (e.getValue().getError() == null) {
+				return true;
+			}
+			return !e.getValue().getError().isParsingError();
+		});
+		setValidated(!checkResults.isEmpty());
 	}
 
 	/**
 	 * Clears the checkResults list of this checkable and all child objects in its datastructure.
 	 */
 	public final void clearAllContainedCheckResults() {
-		this.accept(new ClearVisitorResultsVisitor());
+		this.accept(new ClearResultsVisitor());
 	}
 
 	/**

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/check/ErrorId.java

@@ -66,6 +66,7 @@ public record ErrorId(String name) implements Serializable {
 	public static final ErrorId SE_BS_UNFRAGMENTED = new ErrorId("SE_BS_UNFRAGMENTED");
 	public static final ErrorId GE_P_DEGENERATED_RING = new ErrorId("GE_P_DEGENERATED_POLYGON");
 	public static final ErrorId SE_POLYGON_WITHOUT_SURFACE = new ErrorId("SE_POLYGON_WITHOUT_SURFACE");
+	public static final ErrorId SC_SCHEMA_VALIDATION = new ErrorId("SC_SCHEMA_VALIDATION");
 
 
 

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/check/ErrorVisitor.java

@@ -58,6 +58,7 @@ import de.hft.stuttgart.citydoctor2.check.error.SolidSelfIntError;
 import de.hft.stuttgart.citydoctor2.check.error.SurfaceUnfragmentedError;
 import de.hft.stuttgart.citydoctor2.check.error.TooFewPolygonsError;
 import de.hft.stuttgart.citydoctor2.check.error.UnknownCheckError;
+import de.hft.stuttgart.citydoctor2.check.error.XMLValidationError;
 
 /**
  * Visitor pattern interface to access errors. This is to determine the type of
@@ -150,4 +151,6 @@ public interface ErrorVisitor {
 	
 	public void visit(SolidError err);
 	
+	public void visit(XMLValidationError err);
+
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/check/HealingMethod.java

@@ -51,6 +51,7 @@ import de.hft.stuttgart.citydoctor2.check.error.SolidSelfIntError;
 import de.hft.stuttgart.citydoctor2.check.error.SurfaceUnfragmentedError;
 import de.hft.stuttgart.citydoctor2.check.error.TooFewPolygonsError;
 import de.hft.stuttgart.citydoctor2.check.error.UnknownCheckError;
+import de.hft.stuttgart.citydoctor2.check.error.XMLValidationError;
 
 /**
  * Visitor pattern interface used in the healing procedures. The modification
@@ -200,6 +201,10 @@ public interface HealingMethod {
 		return false;
 	}
 	
+	default boolean visit(XMLValidationError err, ModificationListener l) {
+		return false;
+	}
+
 	public HealingMethod createNew();
 
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/check/QualityAdeErrorVisitor.java

@@ -58,6 +58,7 @@ import de.hft.stuttgart.citydoctor2.check.error.SolidSelfIntError;
 import de.hft.stuttgart.citydoctor2.check.error.SurfaceUnfragmentedError;
 import de.hft.stuttgart.citydoctor2.check.error.TooFewPolygonsError;
 import de.hft.stuttgart.citydoctor2.check.error.UnknownCheckError;
+import de.hft.stuttgart.citydoctor2.check.error.XMLValidationError;
 import de.hft.stuttgart.citydoctor2.datastructure.Edge;
 import de.hft.stuttgart.citydoctor2.datastructure.LinearRing;
 import de.hft.stuttgart.citydoctor2.datastructure.Polygon;
@@ -404,4 +405,9 @@ public class QualityAdeErrorVisitor extends AbstractErrorVisitor {
 		// not translated
 	}
 	
+	@Override
+	public void visit(XMLValidationError err) {
+		// not translated
+	}
+
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/check/error/XMLValidationError.java

+package de.hft.stuttgart.citydoctor2.check.error;
+
+import java.io.Serial;
+
+import de.hft.stuttgart.citydoctor2.check.CheckError;
+import de.hft.stuttgart.citydoctor2.check.ErrorId;
+import de.hft.stuttgart.citydoctor2.check.ErrorReport;
+import de.hft.stuttgart.citydoctor2.check.ErrorType;
+import de.hft.stuttgart.citydoctor2.check.ErrorVisitor;
+import de.hft.stuttgart.citydoctor2.check.HealingMethod;
+import de.hft.stuttgart.citydoctor2.check.ModificationListener;
+import de.hft.stuttgart.citydoctor2.datastructure.GmlElement;
+
+public class XMLValidationError implements CheckError {
+
+	@Serial
+	private static final long serialVersionUID = 4002356100680460598L;
+
+	private String message;
+	
+	public XMLValidationError(String message) {
+		this.message = message;
+	}
+
+	@Override
+	public ErrorType getType() {
+		return ErrorType.ERROR;
+	}
+
+	@Override
+	public ErrorId getErrorId() {
+		return ErrorId.SC_SCHEMA_VALIDATION;
+	}
+
+	@Override
+	public GmlElement getFeature() {
+		return null;
+	}
+
+	@Override
+	public void accept(ErrorVisitor errorVisitor) {
+		errorVisitor.visit(this);
+	}
+
+	@Override
+	public boolean accept(HealingMethod method, ModificationListener l) {
+		return method.visit(this, l);
+	}
+	
+	public String getMessage() {
+		return message;
+	}
+
+	@Override
+	public void report(ErrorReport report) {
+		report.add("message", message);
+	}
+	
+	@Override
+	public boolean isParsingError() {
+		return true;
+	}
+
+}

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/BridgeConstructiveElement.java

@@ -18,13 +18,10 @@
  */
 package de.hft.stuttgart.citydoctor2.datastructure;
 
-import de.hft.stuttgart.citydoctor2.check.CheckableVisitor;
-import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
-import de.hft.stuttgart.citydoctor2.utils.CityGmlUtils;
-import javafx.scene.paint.Color;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.citygml4j.core.model.core.AbstractSpaceBoundaryProperty;
+import java.io.Serial;
+import java.util.ArrayList;
+import java.util.List;
+
 import org.citygml4j.core.model.deprecated.bridge.DeprecatedPropertiesOfBridgeConstructiveElement;
 import org.citygml4j.core.util.geometry.GeometryFactory;
 import org.xmlobjects.gml.model.geometry.GeometryProperty;
@@ -34,14 +31,13 @@ import org.xmlobjects.gml.model.geometry.complexes.CompositeSurface;
 import org.xmlobjects.gml.model.geometry.primitives.Solid;
 import org.xmlobjects.gml.model.geometry.primitives.SolidProperty;
 
-import java.io.Serial;
-import java.util.ArrayList;
-import java.util.List;
+import de.hft.stuttgart.citydoctor2.check.CheckableVisitor;
+import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
+import de.hft.stuttgart.citydoctor2.utils.CityGmlUtils;
+import javafx.scene.paint.Color;
 
 public class BridgeConstructiveElement extends CityObject {
 
-    private static final Logger logger = LogManager.getLogger(BridgeConstructiveElement.class);
-
     private static final String CANNOT_ADD = "Cannot add ";
 
     @Serial
@@ -105,20 +101,6 @@ public class BridgeConstructiveElement extends CityObject {
         }
     }
 
-    private void reCreateBoundarySurface(GeometryFactory factory, ParserConfiguration config, BoundarySurface bs) {
-        if (bs.getGeometries().isEmpty()) {
-            for (AbstractSpaceBoundaryProperty bsp : gmlBridgeElement.getBoundaries()) {
-                if (bsp.getObject() != null && bsp.getObject() == bs.getGmlObject()) {
-                    logger.warn("Found empty boundary surface: {}, removing from BridgeConstructiveElement", bs.getGmlId());
-                    gmlBridgeElement.getBoundaries().remove(bsp);
-                    break;
-                }
-            }
-            return;
-        }
-        bs.reCreateGeometries(factory, config);
-    }
-
     private void setCompositeSurfaceAccordingToLod(Geometry geom, CompositeSurface cs) {
         switch (geom.getLod()) {
             case LOD1:

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/mapper/citygml3/Citygml3FeatureMapper.java

@@ -23,6 +23,8 @@ import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.StringJoiner;
+import java.util.function.Function;
 
 import de.hft.stuttgart.citydoctor2.database.FeatureCache;
 import de.hft.stuttgart.citydoctor2.database.UnconnectedCache;
@@ -172,10 +174,13 @@ public class Citygml3FeatureMapper extends ObjectWalker {
 	private final Path directory;
     private final double neighborDistance;
 	private Map<String, ConcretePolygon> polygonMap = new HashMap<>();
-	private Map<String, CompositeCollection> compositeMap = new HashMap<>();
+	private Map<String, CompositeCollection> compositeMap = new HashMap<>();;
 	private List<ResolvableReference> references = new ArrayList<>();
 	private Map<Vertex, Vertex> vertexMap = new HashMap<>();
 
+	private Map<String, List<GmlId>> unresolvedPolyRefIDMap = new HashMap<>();
+	private Map<String, GmlId> parsedPolygonsIdMap = new HashMap<>();
+
     public Citygml3FeatureMapper(ParserConfiguration config, Path path, boolean unconnected) {
         this.config = config;
         this.directory = path.getParent();
@@ -197,6 +202,37 @@ public class Citygml3FeatureMapper extends ObjectWalker {
 		}
 	}
 
+	public void checkUnresolvedReferences() {
+		if (unresolvedPolyRefIDMap.isEmpty()) {
+			return;
+		}
+		boolean xLinkGlobalError = false;
+		List<String> crossRefs = new ArrayList<>();
+		for (Map.Entry<String, List<GmlId>> entry : unresolvedPolyRefIDMap.entrySet()) {
+			String id = entry.getKey();
+			boolean emptyCrossFeatureReference = parsedPolygonsIdMap.containsKey(id);
+			xLinkGlobalError = xLinkGlobalError || emptyCrossFeatureReference;
+			if (emptyCrossFeatureReference) {
+				List<GmlId> gmlIds = entry.getValue();
+				StringJoiner joiner = new StringJoiner(", ");
+				gmlIds.forEach(gmlId -> joiner.add(gmlId.toString()));
+				GmlId crossFeatureId = parsedPolygonsIdMap.get(id);
+				//TODO: Localize String
+				logger.warn("Polygon {} of Feature {} is being referenced in other Features: {}", id, crossFeatureId, joiner);
+				crossRefs.add(id);
+			}
+		}
+		if (xLinkGlobalError) {
+			//TODO: Localize String
+			logger.warn("Model has Features containing cross-feature references without their own copies of the referenced polygons");
+		}
+		crossRefs.forEach(unresolvedPolyRefIDMap::remove);
+		if(!unresolvedPolyRefIDMap.isEmpty()) {
+			logger.warn("Model contains polygon references that could not be found");
+		}
+	}
+
+
 	@Override
 	public void visit(AbstractSpace space) {
 		// if we are here, an AbstractSpace thing was read that is not handled in the
@@ -903,7 +939,7 @@ public class Citygml3FeatureMapper extends ObjectWalker {
 	private void finishCityObjectConstruction(CityObject co) {
 		parseId(co.getGmlObject(), co);
 		co.clearGmlGeometries();
-		resolveAndClearReferences();
+		resolveAndClearReferences(co);
 		updateEdgesAndVertices(co);
 	}
 
@@ -1092,7 +1128,7 @@ public class Citygml3FeatureMapper extends ObjectWalker {
 		return igh;
 	}
 
-	private void resolveAndClearReferences() {
+	private void resolveAndClearReferences(CityObject co) {
 		for (ResolvableReference ref : references) {
 			String href = ref.href();
 			if (href.startsWith("#")) {
@@ -1107,6 +1143,9 @@ public class Citygml3FeatureMapper extends ObjectWalker {
 				handlePolygonReference(href, geom);
 			}
 		}
+		for(String polygonId: polygonMap.keySet()){
+			parsedPolygonsIdMap.put(polygonId, co.getGmlId());
+		}
 
 		// clear storage for polygons and vertices
 		references = new ArrayList<>();
@@ -1117,9 +1156,12 @@ public class Citygml3FeatureMapper extends ObjectWalker {
 	private void handlePolygonReference(String href, Geometry geom) {
 		ConcretePolygon concPoly = polygonMap.get(href);
 		if (concPoly == null) {
-			if (logger.isWarnEnabled()) {
-				logger.warn(Localization.getText("FeatureMapper.polygonUnreferenced"), href);
-			}
+            List<GmlId> featureList = unresolvedPolyRefIDMap.computeIfAbsent(href, k -> new ArrayList<>());
+			GmlId featureId = geom.getParent().getTopLevelCityObject().getGmlId();
+			featureList.add(featureId);
+//            if (logger.isWarnEnabled()) {
+//				logger.warn(Localization.getText("FeatureMapper.polygonUnreferenced"), href);
+//			}
 		} else {
 			LinkedPolygon lPoly = new LinkedPolygon(concPoly, geom);
 			if (geom.getParent() instanceof BoundarySurface bs) {

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/mapper/citygml3/GMLValidationHandler.java

@@ -28,29 +28,38 @@ import org.xml.sax.SAXParseException;
 
 public class GMLValidationHandler implements ErrorHandler {
 	
+	private static final int MAX_LINE_SIZE = 200;
+	
 	private static final Logger logger = LogManager.getLogger(GMLValidationHandler.class);
 	private final List<String> messages = new ArrayList<>();
 	
 	@Override
 	public void error(SAXParseException exception) {
-		String message = "[" + exception.getLineNumber() + ", " + exception.getColumnNumber() + "] "
-				+ exception.getMessage();
+        String message = constructMessage(exception);
 		logger.error(message);
 		messages.add(message);
 	}
 
+	private String constructMessage(SAXParseException exception) {
+		String exceptionMessage = exception.getMessage();
+		String message = "[line: " + exception.getLineNumber() + "] "
+				+ exceptionMessage.substring(0, Math.min(exceptionMessage.length(), MAX_LINE_SIZE));
+        if (exceptionMessage.length() > MAX_LINE_SIZE) {
+        	message += "...";
+        }
+		return message;
+	}
+
 	@Override
 	public void warning(SAXParseException exception) {
-		String message = "[" + exception.getLineNumber() + ", " + exception.getColumnNumber() + "] "
-				+ exception.getMessage();
+        String message = constructMessage(exception);
 		logger.warn(message);
 		messages.add(message);
 	}
 
 	@Override
 	public void fatalError(SAXParseException exception) {
-		String message = "[" + exception.getLineNumber() + ", " + exception.getColumnNumber() + "] "
-				+ exception.getMessage();
+        String message = constructMessage(exception);
 		logger.fatal(message);
 		messages.add(message);
 	}

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/parser/CityGmlConsumer.java

@@ -32,6 +32,5 @@ public interface CityGmlConsumer {
 		
 	}
 
-//	public void endOfFile();
 
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/parser/CityGmlParser.java

@@ -28,6 +28,7 @@ import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -43,8 +44,6 @@ import javax.xml.validation.Schema;
 import javax.xml.validation.SchemaFactory;
 import javax.xml.validation.Validator;
 
-import de.hft.stuttgart.citydoctor2.datastructure.GmlId;
-import de.hft.stuttgart.citydoctor2.datastructure.ImplicitGeometryHolder;
 import org.apache.logging.log4j.Level;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -84,8 +83,11 @@ import org.xmlobjects.schema.SchemaHandlerException;
 import org.xmlobjects.stream.XMLReader;
 import org.xmlobjects.stream.XMLReaderFactory;
 
+import de.hft.stuttgart.citydoctor2.check.error.XMLValidationError;
 import de.hft.stuttgart.citydoctor2.datastructure.CityDoctorModel;
 import de.hft.stuttgart.citydoctor2.datastructure.CityObject;
+import de.hft.stuttgart.citydoctor2.datastructure.GmlId;
+import de.hft.stuttgart.citydoctor2.datastructure.ImplicitGeometryHolder;
 import de.hft.stuttgart.citydoctor2.mapper.citygml3.Citygml3FeatureMapper;
 import de.hft.stuttgart.citydoctor2.mapper.citygml3.GMLValidationHandler;
 import de.hft.stuttgart.citydoctor2.math.Vector3d;
@@ -129,9 +131,9 @@ public class CityGmlParser {
 	private static CityGMLContext context;
 	private static List<QName> chunkProperties = new ArrayList<>();
 
-
 	static {
-        System.setProperty("javax.xml.transform.TransformerFactory", "com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl");
+		System.setProperty("javax.xml.transform.TransformerFactory",
+				"com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl");
 		FACTORY = SAXParserFactory.newInstance();
 		try {
 			FACTORY.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, false);
@@ -147,7 +149,7 @@ public class CityGmlParser {
 	private CityGmlParser() {
 	}
 
-    public static synchronized CityGMLContext getContext() {
+	public static synchronized CityGMLContext setupContext() {
 		if (context == null) {
 			try {
 				context = CityGMLContext.newInstance(CityGmlParser.class.getClassLoader());
@@ -166,13 +168,17 @@ public class CityGmlParser {
 	}
 
 	/**
-     * Parses a given CityGML file and collects the contained CityObject Features in a {@link CityDoctorModel}.
+	 * Parses a given CityGML file and collects the contained CityObject Features in
+	 * a {@link CityDoctorModel}.
 	 * <p/>
-     * The nested parse uses an {@link de.hft.stuttgart.citydoctor2.database.UnconnectedCache UnconnectedCache}, which
-     * is not connected to the database.
+	 * The nested parse uses an
+	 * {@link de.hft.stuttgart.citydoctor2.database.UnconnectedCache
+	 * UnconnectedCache}, which is not connected to the database.
 	 * <p/>
-     * Nested parsing should only be used for accessing Features in auxiliary, small CityGML files, e.g. parsing of
-     * {@link de.hft.stuttgart.citydoctor2.datastructure.LibraryObject LibraryObject} files.
+	 * Nested parsing should only be used for accessing Features in auxiliary, small
+	 * CityGML files, e.g. parsing of
+	 * {@link de.hft.stuttgart.citydoctor2.datastructure.LibraryObject
+	 * LibraryObject} files.
 	 *
 	 * @param filePath String path to the file
 	 * @param config   Configuration of the parser
@@ -186,10 +192,12 @@ public class CityGmlParser {
 	}
 
 	/**
-     * Parses a given CityGML file and collects the contained CityObject Features in a {@link CityDoctorModel}.
+	 * Parses a given CityGML file and collects the contained CityObject Features in
+	 * a {@link CityDoctorModel}.
 	 * <p/>
-     * Features are held in a non-persistent, embedded Database with an in-memory upstream cache. Thus, strong references
-     * to {@link CityObject} are to be avoided, to allow for the memory management of the cache.
+	 * Features are held in a non-persistent, embedded Database with an in-memory
+	 * upstream cache. Thus, strong references to {@link CityObject} are to be
+	 * avoided, to allow for the memory management of the cache.
 	 *
 	 * @param filePath String path to the file
 	 * @param config   Configuration of the parser
@@ -202,12 +210,13 @@ public class CityGmlParser {
 		return parseCityGmlFile(filePath, config, null, null);
 	}
 
-
 	/**
-     * Parses a given CityGML file and collects the contained CityObject Features in a {@link CityDoctorModel}.
+	 * Parses a given CityGML file and collects the contained CityObject Features in
+	 * a {@link CityDoctorModel}.
 	 * <p/>
-     * Features are held in a non-persistent, embedded Database with an in-memory upstream cache. Thus, strong references
-     * to {@link CityObject} are to be avoided, to allow for the memory management of the cache.
+	 * Features are held in a non-persistent, embedded Database with an in-memory
+	 * upstream cache. Thus, strong references to {@link CityObject} are to be
+	 * avoided, to allow for the memory management of the cache.
 	 *
 	 * @param filePath String path to the file
 	 * @param config   Configuration of the parser
@@ -222,10 +231,12 @@ public class CityGmlParser {
 	}
 
 	/**
-     * Parses a given CityGML file and collects the contained CityObject Features in a {@link CityDoctorModel}.
+	 * Parses a given CityGML file and collects the contained CityObject Features in
+	 * a {@link CityDoctorModel}.
 	 * <p/>
-     * Features are held in a non-persistent, embedded Database with an in-memory upstream cache. Thus, strong references
-     * to {@link CityObject} are to be avoided, to allow for the memory management of the cache.
+	 * Features are held in a non-persistent, embedded Database with an in-memory
+	 * upstream cache. Thus, strong references to {@link CityObject} are to be
+	 * avoided, to allow for the memory management of the cache.
 	 *
 	 * @param filePath String path to the file
 	 * @param config   Configuration of the parser
@@ -241,18 +252,22 @@ public class CityGmlParser {
 	}
 
 	/**
-     * Parses a given CityGML file and collects the contained CityObject Features in a {@link CityDoctorModel}.
+	 * Parses a given CityGML file and collects the contained CityObject Features in
+	 * a {@link CityDoctorModel}.
 	 * <p/>
-     * Features are held in a non-persistent, embedded Database with an in-memory upstream cache. Thus, strong references
-     * to {@link CityObject} are to be avoided, to allow for the memory management of the cache.
+	 * Features are held in a non-persistent, embedded Database with an in-memory
+	 * upstream cache. Thus, strong references to {@link CityObject} are to be
+	 * avoided, to allow for the memory management of the cache.
 	 *
 	 * @param filePath    String path to the file
 	 * @param config      Configuration of the parser
 	 * @param l           Listener hook for tracking of parsing progress
 	 * @param handler     Validation handler for GML-file validation
-     * @param verbose If verbosity is enabled the parser will write info logs to the logger
-     * @param unconnected If true the parser will use an {@link de.hft.stuttgart.citydoctor2.database.UnconnectedCache UnconnectedCache}
-     *                    to collect the parsed CityObjects
+	 * @param verbose     If verbosity is enabled the parser will write info logs to
+	 *                    the logger
+	 * @param unconnected If true the parser will use an
+	 *                    {@link de.hft.stuttgart.citydoctor2.database.UnconnectedCache
+	 *                    UnconnectedCache} to collect the parsed CityObjects
 	 * @return A {@link CityDoctorModel} object with the parsed Features
 	 * @throws CityGmlParseException   if parsing of the CityGML-file failed
 	 * @throws InvalidGmlFileException if the GMLValidationHandler found an error
@@ -260,15 +275,12 @@ public class CityGmlParser {
 	private static CityDoctorModel parseCityGmlFile(String filePath, ParserConfiguration config, ProgressListener l,
 			GMLValidationHandler handler, boolean verbose, boolean unconnected)
 			throws CityGmlParseException, InvalidGmlFileException {
-        CityGMLContext context = getContext();
+		CityGMLContext context = setupContext();
 		Path file = Paths.get(filePath);
+		List<String> validationIssues = Collections.emptyList();
 		if (config.getValidate()) {
-            List<String> messages = validateFile(context, handler, file);
-            if (!messages.isEmpty()) {
-                throw new InvalidGmlFileException("Invalid GML File. First error: \n" + messages.get(0));
+			validationIssues = validateFile(handler, file);
 		}
-        }
-
 		try {
 			parseEpsgCodeFromFile(file, config, verbose);
 			CityGMLInputFactory in = context.createCityGMLInputFactory()
@@ -277,15 +289,17 @@ public class CityGmlParser {
 				if (l != null) {
 					ois.addListener(l::updateProgress);
 				}
-                return readAndKeepFeatures(config, file, in, ois, verbose, unconnected);
+				CityDoctorModel model = readAndKeepFeatures(config, file, in, ois, verbose, unconnected);
+				for (String xmlError : validationIssues) {
+					model.addGlobalError(new XMLValidationError(xmlError));
+				}
+				return model;
 			}
 		} catch (CityGMLReadException | IOException e) {
 			throw new CityGmlParseException("Failed to read CityGML file", e);
 		}
 	}
 
-
-
 	public static void streamCityGml(String file, ParserConfiguration config, CityGmlConsumer cityObjectConsumer,
 			String outputFile) throws CityGmlParseException {
 		Path f = Paths.get(file);
@@ -338,18 +352,18 @@ public class CityGmlParser {
 	private static void readAndDiscardFeatures(Path file, ParserConfiguration config, ObservedInputStream ois,
 			CityGmlConsumer cityObjectConsumer, String outputFile) throws CityGMLReadException {
 		Citygml3FeatureMapper mapper = new Citygml3FeatureMapper(config, file, false);
-        readAndDiscardModel(mapper, ois, cityObjectConsumer, outputFile);
+		readAndDiscardModel(mapper, ois, cityObjectConsumer, outputFile, config, file);
 
 	}
 
 	private static void readAndDiscardModel(Citygml3FeatureMapper mapper, ObservedInputStream ois,
-                                            CityGmlConsumer cityObjectConsumer, String outputFile) throws CityGMLReadException {
-        getContext();
+			CityGmlConsumer cityObjectConsumer, String outputFile, ParserConfiguration config, Path file)
+			throws CityGMLReadException {
+		setupContext();
 		CityGMLInputFactory inputFactory = context.createCityGMLInputFactory()
 				.withChunking(ChunkOptions.chunkByProperties(chunkProperties).skipCityModel(false));
 		CityGMLChunkWriter writer = null;
 		try (CityGMLReader reader = inputFactory.createCityGMLReader(ois)) {
-
 			CityDoctorModel model = mapper.getModel();
 			boolean isInitialized = false;
 			while (reader.hasNext()) {
@@ -414,7 +428,7 @@ public class CityGmlParser {
 		if (outputFile == null) {
 			return null;
 		}
-        CityGMLContext gmlContext = CityGmlParser.getContext();
+		CityGMLContext gmlContext = CityGmlParser.setupContext();
 		CityGMLVersion version = CityGMLModules.getCityGMLVersion(reader.getName().getNamespaceURI());
 		CityGMLOutputFactory factory = gmlContext.createCityGMLOutputFactory(version);
 		CityGMLChunkWriter writer = factory.createCityGMLChunkWriter(new File(outputFile),
@@ -428,8 +442,8 @@ public class CityGmlParser {
 	}
 
 	private static CityDoctorModel readAndKeepFeatures(ParserConfiguration config, Path file,
-                                                       CityGMLInputFactory inputFactory, ObservedInputStream ois,
-                                                       boolean verbose, boolean unconnected) throws CityGMLReadException {
+			CityGMLInputFactory inputFactory, ObservedInputStream ois, boolean verbose, boolean unconnected)
+			throws CityGMLReadException {
 		return readAndKeepModel(new Citygml3FeatureMapper(config, file, unconnected), inputFactory, ois, verbose);
 	}
 
@@ -444,7 +458,7 @@ public class CityGmlParser {
 			CityModel cgmlModel = null;
 			CityDoctorModel cdModel = mapper.getModel();
 			AutoCloseable parsingContext = cdModel.getCache().startParsingMode();
-            try (parsingContext){
+			try (parsingContext) {
 				List<AbstractCityObject> queuedObjects = new ArrayList<>();
 				while (reader.hasNext()) {
 					AbstractFeature chunk = reader.next();
@@ -469,7 +483,7 @@ public class CityGmlParser {
 						if (cgmlModel == null) {
 							// Add object to queue till the CityModel has been parsed
 							queuedObjects.add(aco);
-                        }else if (!cdModel.containsGmlId(id)){
+						} else if (!cdModel.containsGmlId(id)) {
 							cgmlModel.getCityObjectMembers().add(new AbstractCityObjectProperty(aco));
 						}
 					}
@@ -482,7 +496,8 @@ public class CityGmlParser {
 					mapper.setCityModel(new CityModel());
 					for (AbstractCityObject aco : queuedObjects) {
 						if (!cdModel.containsGmlId(aco.getId())) {
-                            mapper.getModel().getCityModel().getCityObjectMembers().add(new AbstractCityObjectProperty(aco));
+							mapper.getModel().getCityModel().getCityObjectMembers()
+									.add(new AbstractCityObjectProperty(aco));
 						}
 					}
 				}
@@ -492,6 +507,7 @@ public class CityGmlParser {
 					logger.info(Localization.getText("CityGmlParser.parsedObjects"),
 							mapper.getModel().getNumberOfFeatures());
 				}
+				mapper.checkUnresolvedReferences();
 				mapper.setCityGMLVersion(version);
 				return mapper.getModel();
 			} catch (Exception e) {
@@ -501,7 +517,8 @@ public class CityGmlParser {
 		}
 	}
 
-    private static void parseEpsgCodeFromFile(Path file, ParserConfiguration config, boolean verbose) throws CityGmlParseException {
+	private static void parseEpsgCodeFromFile(Path file, ParserConfiguration config, boolean verbose)
+			throws CityGmlParseException {
 		try (BufferedInputStream bis = new BufferedInputStream(new FileInputStream(file.toFile()))) {
 			parseEpsgCodeFromStream(bis, config, verbose);
 		} catch (ParserConfigurationException | SAXException | IOException e) {
@@ -668,11 +685,12 @@ public class CityGmlParser {
 		return CRS_FACTORY.createFromParameters(crsName, params.toArray(new String[0]));
 	}
 
-    private static List<String> validateFile(CityGMLContext context, GMLValidationHandler handler, Path file)
+	public static List<String> validateFile(GMLValidationHandler handler, Path file)
 			throws CityGmlParseException {
 		if (handler == null) {
 			handler = new GMLValidationHandler();
 		}
+		setupContext();
 		try {
 			SchemaHandler schemaHandler = new ValidationSchemaHandler(context.getDefaultSchemaHandler());
 			readAdditionalSchemaDefinitions(context, file, schemaHandler);
@@ -691,8 +709,7 @@ public class CityGmlParser {
 
 	private static void readAdditionalSchemaDefinitions(CityGMLContext context, Path file, SchemaHandler schemaHandler)
 			throws CityGmlParseException {
-        try (XMLReader reader = XMLReaderFactory.newInstance(context.getXMLObjects())
-                .withSchemaHandler(schemaHandler)
+		try (XMLReader reader = XMLReaderFactory.newInstance(context.getXMLObjects()).withSchemaHandler(schemaHandler)
 				.createReader(file)) {
 			reader.nextTag();
 		} catch (Exception e) {
@@ -710,5 +727,4 @@ public class CityGmlParser {
 
 	}
 
-
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/utils/CityGmlUtils.java

@@ -41,7 +41,6 @@ import java.util.Set;
  */
 public final class CityGmlUtils {
 
-
 	private CityGmlUtils() {
 		// util class
 	}
@@ -91,7 +90,6 @@ public final class CityGmlUtils {
 		return new CompositeSurface(surfaces);
 	}
 
-
 	public static org.xmlobjects.gml.model.geometry.primitives.LinearRing createGmlRing(GeometryFactory factory,
 			ParserConfiguration config, LinearRing lr) {
 
@@ -130,7 +128,8 @@ public final class CityGmlUtils {
 		List<SurfaceProperty> surfaceMember = comp.getSurfaceMembers();
 		for (Polygon cdPoly : geom.getPolygons()) {
 			if (!cdPoly.isLink()) {
-                org.xmlobjects.gml.model.geometry.primitives.Polygon gmlPoly = createGmlPolygon(factory, cdPoly, config);
+				org.xmlobjects.gml.model.geometry.primitives.Polygon gmlPoly = createGmlPolygon(factory, cdPoly,
+						config);
 				if (gmlPoly != null) {
 					surfaceMember.add(new SurfaceProperty(gmlPoly));
 				}
@@ -150,8 +149,7 @@ public final class CityGmlUtils {
 		return solid;
 	}
 
-    public static MultiSurface createMultiSurface(Geometry geom, GeometryFactory factory,
-                                                  ParserConfiguration config) {
+	public static MultiSurface createMultiSurface(Geometry geom, GeometryFactory factory, ParserConfiguration config) {
 		if (geom.getType() != GeometryType.MULTI_SURFACE && geom.getType() != GeometryType.COMPOSITE_SURFACE) {
 			throw new IllegalArgumentException("This can only handle MultiSurfaces");
 		}
@@ -162,7 +160,8 @@ public final class CityGmlUtils {
 				compositeCollections.add(conc.getPartOfComposite());
 			} else if (!cdPoly.isLink()) {
 				// is not part of a boundary surface
-                org.xmlobjects.gml.model.geometry.primitives.Polygon gmlPoly = createGmlPolygon(factory, cdPoly, config);
+				org.xmlobjects.gml.model.geometry.primitives.Polygon gmlPoly = createGmlPolygon(factory, cdPoly,
+						config);
 				if (gmlPoly != null) {
 					surfaces.add(new SurfaceProperty(gmlPoly));
 				}

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/utils/visitors/ClearVisitorResultsVisitor.java → CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/utils/visitors/ClearResultsVisitor.java

@@ -6,7 +6,7 @@ import de.hft.stuttgart.citydoctor2.check.Checkable;
 /**
  * This Visitor removes the check results from a CityObject and the objects in its datastructure.
  */
-public class ClearVisitorResultsVisitor extends CheckableUtilsVisitor {
+public class ClearResultsVisitor extends CheckableUtilsVisitor {
 
     @Override
     public void check(Checkable checkable) {