Update MATSim CW20

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/AccessibilityUtils.java

@@ -20,6 +20,7 @@
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.geotools.api.feature.simple.SimpleFeature;
 import org.locationtech.jts.geom.Coordinate;
 import org.locationtech.jts.geom.Geometry;
 import org.locationtech.jts.geom.GeometryFactory;
@@ -41,7 +42,6 @@
 import org.matsim.core.utils.geometry.CoordUtils;
 import org.matsim.core.utils.gis.GeoFileReader;
 import org.matsim.facilities.*;
-import org.opengis.feature.simple.SimpleFeature;
 
 import java.util.*;
 import java.util.concurrent.ConcurrentHashMap;

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/FeatureSHP.java

@@ -24,11 +24,11 @@
 import java.util.HashSet;
 import java.util.Set;
 
-import org.geotools.data.DataStore;
-import org.geotools.data.FileDataStoreFinder;
+import org.geotools.api.data.DataStore;
+import org.geotools.api.data.FileDataStoreFinder;
+import org.geotools.api.data.SimpleFeatureSource;
+import org.geotools.api.feature.simple.SimpleFeature;
 import org.geotools.data.simple.SimpleFeatureIterator;
-import org.geotools.data.simple.SimpleFeatureSource;
-import org.opengis.feature.simple.SimpleFeature;
 
 /**
  * Utility class for reading shape (.shp) files.

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/GridUtils.java

@@ -20,7 +20,6 @@
 import org.matsim.facilities.ActivityFacility;
 import org.matsim.facilities.FacilitiesUtils;
 import org.matsim.utils.gis.shp2matsim.ShpGeometryUtils;
-import org.opengis.feature.simple.SimpleFeature;
 
 public final class GridUtils {
 	// used from outside, e.g. in vsp playgrounds

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/VoronoiExample.java

@@ -22,14 +22,14 @@
 import java.util.Collection;
 import java.util.List;
 
+import org.geotools.api.feature.simple.SimpleFeature;
 import org.locationtech.jts.geom.Coordinate;
 import org.locationtech.jts.geom.Geometry;
 import org.locationtech.jts.geom.GeometryFactory;
 import org.locationtech.jts.geom.Polygon;
 import org.locationtech.jts.triangulate.VoronoiDiagramBuilder;
 import org.matsim.contrib.matrixbasedptrouter.utils.BoundingBox;
 import org.matsim.core.utils.gis.GeoFileWriter;
-import org.opengis.feature.simple.SimpleFeature;
 
 /**
  * @author dziemke

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/VoronoiGeometryUtils.java

@@ -27,6 +27,8 @@
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.geotools.api.feature.simple.SimpleFeature;
+import org.geotools.api.feature.simple.SimpleFeatureType;
 import org.geotools.feature.simple.SimpleFeatureBuilder;
 import org.geotools.feature.simple.SimpleFeatureTypeBuilder;
 import org.locationtech.jts.geom.Coordinate;
@@ -40,8 +42,6 @@
 import org.matsim.core.utils.geometry.CoordUtils;
 import org.matsim.facilities.ActivityFacilities;
 import org.matsim.facilities.ActivityFacility;
-import org.opengis.feature.simple.SimpleFeature;
-import org.opengis.feature.simple.SimpleFeatureType;
 
 /**
  * @author dziemke

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/gis/CRSUtils.java

@@ -24,18 +24,18 @@
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.geotools.api.metadata.Identifier;
+import org.geotools.api.referencing.FactoryException;
+import org.geotools.api.referencing.NoSuchAuthorityCodeException;
+import org.geotools.api.referencing.crs.CRSAuthorityFactory;
+import org.geotools.api.referencing.crs.CoordinateReferenceSystem;
+import org.geotools.api.referencing.operation.MathTransform;
+import org.geotools.api.referencing.operation.TransformException;
 import org.geotools.referencing.CRS;
 import org.locationtech.jts.geom.Coordinate;
 import org.locationtech.jts.geom.Geometry;
 import org.locationtech.jts.geom.GeometryFactory;
 import org.locationtech.jts.geom.Point;
-import org.opengis.metadata.Identifier;
-import org.opengis.referencing.FactoryException;
-import org.opengis.referencing.NoSuchAuthorityCodeException;
-import org.opengis.referencing.crs.CRSAuthorityFactory;
-import org.opengis.referencing.crs.CoordinateReferenceSystem;
-import org.opengis.referencing.operation.MathTransform;
-import org.opengis.referencing.operation.TransformException;
 
 /**
  * Utility-class providing functionality related to coordinate reference
@@ -94,7 +94,7 @@ public static int getSRID(CoordinateReferenceSystem crs) {
 		/*
 		 * Randomly get one identifier.
 		 */
-		Identifier identifier = (Identifier) (crs.getIdentifiers().iterator().next());
+		Identifier identifier = crs.getIdentifiers().iterator().next();
 		if (identifier == null) {
 			return 0;
 		} else {
@@ -118,7 +118,7 @@ public static MathTransform findTransform(Geometry source, Geometry target) {
 		CoordinateReferenceSystem targetCRS = getCRS(target.getSRID());
 
 		try {
-			return CRS.findMathTransform(sourceCRS, targetCRS);
+            return CRS.findMathTransform(sourceCRS, targetCRS);
 		} catch (FactoryException e) {
 			e.printStackTrace();
 			return null;

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/gis/ZoneLayer.java

@@ -24,13 +24,13 @@
 import java.util.List;
 import java.util.Set;
 
+import org.geotools.api.referencing.FactoryException;
+import org.geotools.api.referencing.crs.CoordinateReferenceSystem;
+import org.geotools.api.referencing.operation.MathTransform;
 import org.geotools.referencing.CRS;
 import org.locationtech.jts.geom.Point;
 import org.locationtech.jts.index.SpatialIndex;
 import org.locationtech.jts.index.quadtree.Quadtree;
-import org.opengis.referencing.FactoryException;
-import org.opengis.referencing.crs.CoordinateReferenceSystem;
-import org.opengis.referencing.operation.MathTransform;
 
 /**
  * Representation of a spatial index containing zones backed by a quadtree.

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/osm/CombinedOsmSink.java

@@ -22,6 +22,7 @@
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.geotools.api.feature.simple.SimpleFeature;
 import org.locationtech.jts.geom.Coordinate;
 import org.locationtech.jts.geom.Geometry;
 import org.locationtech.jts.geom.GeometryFactory;
@@ -41,7 +42,6 @@
 import org.matsim.facilities.ActivityOption;
 import org.matsim.facilities.FacilitiesUtils;
 import org.matsim.utils.objectattributes.ObjectAttributes;
-import org.opengis.feature.simple.SimpleFeature;
 import org.openstreetmap.osmosis.core.container.v0_6.BoundContainer;
 import org.openstreetmap.osmosis.core.container.v0_6.EntityContainer;
 import org.openstreetmap.osmosis.core.container.v0_6.EntityProcessor;
@@ -89,7 +89,7 @@ class CombinedOsmSink implements Sink {
 
 	private Map<String, Integer> typeCount = new HashMap<>();
 
-	private List <SimpleFeature> landUseAreas = new ArrayList <SimpleFeature>();
+	private List <SimpleFeature> landUseAreas = new ArrayList<>();
 
 	private int featureErrorCounter = 0;
 	private int buildingErrorCounter = 0;

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/osm/LandUseBuildingSink.java

@@ -22,6 +22,7 @@
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.geotools.api.feature.simple.SimpleFeature;
 import org.locationtech.jts.geom.Coordinate;
 import org.locationtech.jts.geom.Geometry;
 import org.locationtech.jts.geom.GeometryFactory;
@@ -40,7 +41,6 @@
 import org.matsim.facilities.ActivityOption;
 import org.matsim.facilities.FacilitiesUtils;
 import org.matsim.utils.objectattributes.ObjectAttributes;
-import org.opengis.feature.simple.SimpleFeature;
 import org.openstreetmap.osmosis.core.container.v0_6.BoundContainer;
 import org.openstreetmap.osmosis.core.container.v0_6.EntityContainer;
 import org.openstreetmap.osmosis.core.container.v0_6.EntityProcessor;
@@ -69,11 +69,11 @@ class LandUseBuildingSink implements Sink {
 	private Map<Long, RelationContainer> relationMap;
 	private ActivityFacilities facilities;
 	private ObjectAttributes facilityAttributes;
-	private Map<String, String> landUseTypeMap = new HashMap<>();
-	private Map<String, String> buildingTypeMap = new HashMap<>();
+	private final Map<String, String> landUseTypeMap;
+	private Map<String, String> buildingTypeMap;
 	private Map<String, Integer> typeCount = new HashMap<>();
 
-	private List <SimpleFeature> features = new ArrayList <SimpleFeature>();
+	private List <SimpleFeature> features = new ArrayList<>();
 
 	private double buildingTypeFromVicinityRange;
 	private String[] tagsToIgnoreBuildings;

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/utils/GeoserverUpdater.java

@@ -28,9 +28,11 @@
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.geotools.data.DataStore;
-import org.geotools.data.DataStoreFinder;
-import org.geotools.data.simple.SimpleFeatureStore;
+import org.geotools.api.data.DataStore;
+import org.geotools.api.data.DataStoreFinder;
+import org.geotools.api.data.SimpleFeatureStore;
+import org.geotools.api.feature.simple.SimpleFeature;
+import org.geotools.api.feature.simple.SimpleFeatureType;
 import org.geotools.feature.DefaultFeatureCollection;
 import org.geotools.feature.simple.SimpleFeatureBuilder;
 import org.geotools.feature.simple.SimpleFeatureTypeBuilder;
@@ -49,8 +51,6 @@
 import org.matsim.core.utils.geometry.transformations.TransformationFactory;
 import org.matsim.core.utils.gis.GeoFileWriter;
 import org.matsim.facilities.ActivityFacility;
-import org.opengis.feature.simple.SimpleFeature;
-import org.opengis.feature.simple.SimpleFeatureType;
 
 public class GeoserverUpdater implements FacilityDataExchangeInterface {
 

contribs/accidents/src/main/java/org/matsim/contrib/accidents/runExample/AccidentsNetworkModification.java

@@ -28,10 +28,11 @@
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.geotools.data.DataStore;
-import org.geotools.data.FileDataStoreFinder;
+import org.geotools.api.data.DataStore;
+import org.geotools.api.data.FileDataStoreFinder;
+import org.geotools.api.data.SimpleFeatureSource;
+import org.geotools.api.feature.simple.SimpleFeature;
 import org.geotools.data.simple.SimpleFeatureIterator;
-import org.geotools.data.simple.SimpleFeatureSource;
 import org.locationtech.jts.geom.Coordinate;
 import org.locationtech.jts.geom.Geometry;
 import org.locationtech.jts.geom.GeometryFactory;
@@ -45,7 +46,6 @@
 import org.matsim.core.utils.geometry.geotools.MGC;
 import org.matsim.core.utils.geometry.transformations.TransformationFactory;
 import org.matsim.core.utils.gis.GeoFileReader;
-import org.opengis.feature.simple.SimpleFeature;
 
 /**
 * @author mmayobre, ikaddoura

contribs/analysis/pom.xml

@@ -23,7 +23,7 @@
 		<dependency>
 			<groupId>com.google.code.gson</groupId>
 			<artifactId>gson</artifactId>
-			<version>2.10.1</version>
+			<version>2.11.0</version>
 		</dependency>
 		<dependency>
             <groupId>org.apache.commons</groupId>

contribs/analysis/src/main/java/org/matsim/contrib/analysis/christoph/TravelTimesWriter.java

@@ -28,6 +28,8 @@
 import java.util.Map;
 import java.util.Map.Entry;
 
+import org.geotools.api.feature.simple.SimpleFeature;
+import org.geotools.api.referencing.crs.CoordinateReferenceSystem;
 import org.locationtech.jts.geom.Coordinate;
 import org.matsim.api.core.v01.Coord;
 import org.matsim.api.core.v01.network.Link;
@@ -43,8 +45,6 @@
 import org.matsim.core.utils.gis.PolylineFeatureFactory;
 import org.matsim.core.utils.gis.GeoFileWriter;
 import org.matsim.core.utils.io.IOUtils;
-import org.opengis.feature.simple.SimpleFeature;
-import org.opengis.referencing.crs.CoordinateReferenceSystem;
 
 /**
  * Analyzes the average link travel times and writes them to files (absolute and

contribs/application/pom.xml

@@ -87,7 +87,7 @@
 		<dependency>
 			<groupId>com.github.matsim-org</groupId>
 			<artifactId>gtfs2matsim</artifactId>
-			<version>master-33809c4f0f-1</version>
+			<version>fc8b13954d</version>
 			<exclusions>
 				<!-- Exclude unneeded dependencies and these with known CVE -->
 				<exclusion>
@@ -117,7 +117,7 @@
 		<dependency>
 			<groupId>info.picocli</groupId>
 			<artifactId>picocli</artifactId>
-			<version>4.7.5</version>
+			<version>4.7.6</version>
 		</dependency>
 		<dependency>
 			<groupId>it.unimi.dsi</groupId>

contribs/application/src/main/java/org/matsim/application/options/CsvOptions.java

@@ -23,7 +23,7 @@ public final class CsvOptions {
 	@CommandLine.Option(names = "--csv-format", description = "CSV Format", defaultValue = "Default")
 	private CSVFormat.Predefined csvFormat;
 
-	@CommandLine.Option(names = "--csv-delimiter", description = "CSV Delimiter", required = false)
+	@CommandLine.Option(names = "--csv-delimiter", description = "CSV Delimiter")
 	private Character csvDelimiter;
 
 	@CommandLine.Option(names = "--csv-charset", description = "CSV input encoding", defaultValue = "UTF8")
@@ -56,24 +56,48 @@ public CsvOptions(CSVFormat.Predefined csvFormat, Character csvDelimiter, Charse
 	 */
 	public static Character detectDelimiter(String path) throws IOException {
         try (BufferedReader reader = IOUtils.getBufferedReader(path)) {
-			String firstLine = reader.readLine();
+			int[] comma = new int[5];
+			int[] semicolon = new int[5];
+			int[] tab = new int[5];
+			String[] lines = new String[5];
+
+//			check five first lines for separator chars. It might be that the csv file has additional info in the first x lines (e.g. EPSG)
+			for (int i = 0; i < 5; i++) {
+				lines[i] = reader.readLine();
+				if (lines[i] == null) {
+					comma[i] = 0;
+					semicolon[i] = 0;
+					tab[i] = 0;
+				} else {
+					comma[i] = StringUtils.countMatches(lines[i], ",");
+					semicolon[i] = StringUtils.countMatches(lines[i], ";");
+					tab[i] = StringUtils.countMatches(lines[i], "\t");
+				}
+			}
 
-			int comma = StringUtils.countMatches(firstLine, ",");
-			int semicolon = StringUtils.countMatches(firstLine, ";");
-			int tab = StringUtils.countMatches(firstLine, "\t");
+			Integer index = null;
 
-			if (comma == 0 && semicolon == 0 && tab == 0) {
-				throw new IllegalArgumentException("No delimiter found in the first line of the file.");
+			for (int i = 0; i < comma.length - 1; i++) {
+//				only check next index if line with separators was not found
+				if (index == null) {
+					if (!(comma[i] == 0 && semicolon[i] == 0 && tab[i] == 0)) {
+						index = i;
+					}
+				}
 			}
 
-			// Comma is preferred as the more likely format
-			if (comma >= semicolon && comma >= tab) {
-				return ',';
-			} else if (tab >= semicolon)
-				return '\t';
-			else
-				return ';';
-        }
+			if (index == null) {
+				throw new IllegalArgumentException("No delimiter found in the first line of the file.");
+			} else {
+				// Comma is preferred as the more likely format
+				if (comma[index] >= semicolon[index] && comma[index] >= tab[index]) {
+					return ',';
+				} else if (tab[index] >= semicolon[index])
+					return '\t';
+				else
+					return ';';
+			}
+		}
 	}
 
 	/**

contribs/application/src/main/java/org/matsim/application/options/ShpOptions.java

@@ -3,6 +3,11 @@
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.geotools.api.data.*;
+import org.geotools.api.feature.simple.SimpleFeature;
+import org.geotools.api.feature.simple.SimpleFeatureType;
+import org.geotools.api.referencing.FactoryException;
+import org.geotools.api.referencing.crs.CoordinateReferenceSystem;
 import org.geotools.data.*;
 import org.geotools.data.shapefile.ShapefileDataStore;
 import org.geotools.data.shapefile.ShapefileDataStoreFactory;
@@ -21,10 +26,6 @@
 import org.matsim.core.utils.geometry.transformations.TransformationFactory;
 import org.matsim.core.utils.gis.GeoFileReader;
 import org.matsim.core.utils.io.IOUtils;
-import org.opengis.feature.simple.SimpleFeature;
-import org.opengis.feature.simple.SimpleFeatureType;
-import org.opengis.referencing.FactoryException;
-import org.opengis.referencing.crs.CoordinateReferenceSystem;
 import picocli.CommandLine;
 
 import javax.annotation.Nullable;