bufix access check at create_raster; refactor BufferedDataOuputStream…

…; update java dependencies; fix for new node.js version

build.gradle

@@ -65,7 +65,7 @@ dependencies {
   	implementation group: 'org.json', name: 'json', version: '20220924'
   	implementation group: 'org.yaml', name: 'snakeyaml', version: '1.33'
   	//implementation group: 'com.opencsv', name: 'opencsv', version: '4.6' // warning: API at v5.0 breaks
-  	implementation group: 'com.opencsv', name: 'opencsv', version: '5.7.0'  	
+  	implementation group: 'com.opencsv', name: 'opencsv', version: '5.7.1'  	
   	implementation group: 'com.github.mreutegg', name: 'laszip4j', version: '0.11'
   	implementation group: 'ar.com.hjg', name: 'pngj', version: '2.1.0'
   	implementation group: 'com.samskivert', name: 'jmustache', version: '1.15'	
@@ -81,19 +81,20 @@ dependencies {
 
   	implementation group: 'org.antlr', name: 'antlr4-runtime', version: '4.9.3' // caution: newer versions may break with generated DSL Java source files
 
-	implementation group: 'org.eclipse.jetty', name: 'jetty-server', version: '11.0.12'
-	implementation group: 'org.eclipse.jetty', name: 'jetty-security', version: '11.0.12'
-	implementation group: 'org.eclipse.jetty.http2', name: 'http2-server', version: '11.0.12'
-	implementation group: 'org.eclipse.jetty', name: 'jetty-alpn-java-server', version: '11.0.12'
-	implementation group: 'org.eclipse.jetty', name: 'jetty-client', version: '11.0.12'
+	implementation group: 'org.eclipse.jetty', name: 'jetty-server', version: '11.0.13'
+	implementation group: 'org.eclipse.jetty', name: 'jetty-security', version: '11.0.13'
+	implementation group: 'org.eclipse.jetty.http2', name: 'http2-server', version: '11.0.13'
+	implementation group: 'org.eclipse.jetty', name: 'jetty-alpn-java-server', version: '11.0.13'
+	implementation group: 'org.eclipse.jetty', name: 'jetty-client', version: '11.0.13'
 
 	implementation 'io.jsonwebtoken:jjwt-api:0.11.5'
     runtimeOnly 'io.jsonwebtoken:jjwt-impl:0.11.5'
     runtimeOnly 'io.jsonwebtoken:jjwt-gson:0.11.5'	
 
 	compileOnly group: 'org.gdal', name: 'gdal', version: '2.2.0' // compileOnly because gdal library from executing system is needed; caution: newer versions may break compatibility
 	implementation group: 'org.locationtech.jts', name: 'jts-core', version: '1.19.0'
-	implementation group: 'org.locationtech.proj4j', name: 'proj4j', version: '1.1.5'	
+	implementation group: 'org.locationtech.proj4j', name: 'proj4j', version: '1.2.2'
+	implementation group: 'org.locationtech.proj4j', name: 'proj4j-epsg', version: '1.2.2'	
 
 	//implementation group: 'org.imintel', name: 'mbtiles4j', version: '1.0.6' // mbtiles currently not used
 

r-package/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: RSDB
 Type: Package
 Title: R to RSDB Server Connection Package
-Version: 1.2.5
+Version: 1.2.6
 Author: woellauer
 Maintainer: woellauer <email@email>
 Description: RSDB (Remote Sensing Database) manages (hyperspectral) rasters and (LiDAR) point-clouds as well as vector data and auxiliary ROIs (regions of interest as named polygons) and POIs (points of interest as named points). Contained data can be queried, processed and analysed. 

r-package/R/RSDB-package.R

@@ -3,7 +3,7 @@
 #'
 #' Central class is \code{\link{RemoteSensing}} that connects to remote sensing database.
 #' Methods of \code{\link{RemoteSensing}} provide access to raster (\code{\link{RasterDB}}),
-#' to point clouds (\code{\link{PointCloud}}), (deprecated \code{\link{PointDB}}), to vector (\code{\link{VectorDB}}), to region of interest (ROI) and to poin of interest (POI) (at \code{\link{RemoteSensing}}) layers and meta data.
+#' to point clouds (\code{\link{PointCloud}}), to voxels (\code{\link{VoxelDB}}), (deprecated \code{\link{PointDB}}), to vector (\code{\link{VectorDB}}), to region of interest (ROI) and to poin of interest (POI) (at \code{\link{RemoteSensing}}) layers and meta data.
 #'
 #' @name RSDB-package
 #' @docType package

src/broker/Broker.java

@@ -131,7 +131,7 @@ public synchronized void refreshPoiGroupMap() {
 				PoiGroup poiGroup = new PoiGroup(vectordb.getName(), vectordb.informal(), acl_read, details.epsg, details.proj4, pois);
 				map.put(poiGroup.name, poiGroup);
 			} catch(Exception e) {
-				Logger.warn(e);
+				Logger.warn(e.getMessage());
 			}
 		});
 
@@ -161,7 +161,7 @@ public synchronized void refreshRoiGroupMap() {
 				RoiGroup roiGroup = new RoiGroup(vectordb.getName(), vectordb.informal(), acl_read, details.epsg, details.proj4, rois);
 				map.put(roiGroup.name, roiGroup);
 			} catch(Exception e) {
-				Logger.warn(e);
+				Logger.warn(e.getMessage());
 			}
 		});
 

src/pointcloud/LasWriter.java

@@ -5,6 +5,7 @@
 import java.time.LocalDate;
 import java.util.Arrays;
 
+import util.BufferedDataOuputStreamLE;
 import util.LittleEndianDataOutputStream;
 import util.Receiver;
 
@@ -89,68 +90,65 @@ public static void writePoints(PointTable[] pointTables, Receiver receiver, LAS_
 		double yoff = ((int)ymin);
 		double zoff = ((int)zmin);		
 
-		receiver.setContentType("application/octet-stream");		
-		LittleEndianDataOutputStream out = new LittleEndianDataOutputStream(receiver.getOutputStream());
-
-
-
-		out.writeInt(LASF_SIGNATUR); //File Signature (“LASF”) char[4] 4 bytes
-		out.writeShort(0); //File Source ID unsigned short 2 bytes
-		out.writeShort(0); //Global Encoding unsigned short 2 bytes
-		out.writeInt(0);//Project ID - GUID data 1 unsigned long 4 bytes
-		out.writeShort(0);//Project ID - GUID data 2 unsigned short 2 byte
-		out.writeShort(0);//Project ID - GUID data 3 unsigned short 2 byte
-		out.writeLong(0);//Project ID - GUID data 4 unsigned char[8] 8 bytes
-		out.writeByte(header.version_major);//Version Major unsigned char 1 byte
-		out.writeByte(header.version_minor);//Version Minor unsigned char 1 byte
-		out.write(SYSTEM_IDENTIFIER);//System Identifier char[32] 32 bytes
-		out.write(GENERATING_SOFTWARE);//Generating Software char[32] 32 bytes
-		out.writeShort(date.getDayOfYear());//File Creation Day of Year unsigned short 2 bytes
-		out.writeShort(date.getYear());//File Creation Year unsigned short 2 bytes
-		out.writeShort(header.size);//Header Size unsigned short 2 bytes
-		out.writeInt(header.size);//Offset to point data unsigned long 4 bytes 
-		out.writeInt(0);//Number of Variable Length Records unsigned long 4 bytes
-		out.writeByte(pointDataRecord.id);//Point Data Record Format unsigned char 1 byte
-		out.writeShort(pointDataRecord.size);//Point Data Record Length unsigned short 2 bytes
-		out.writeInt(pointCount > Integer.MAX_VALUE ? 0 : (int) pointCount);//Legacy Number of point records unsigned long 4 bytes
-		out.writeUint32OverflowZero(numberOfPointsByReturn, 5);//Legacy Number of points by return unsigned long [5] 20 bytes
-		out.writeDouble(SCALE_FACTOR);//X scale factor double 8 bytes
-		out.writeDouble(SCALE_FACTOR);//Y scale factor double 8 bytes
-		out.writeDouble(SCALE_FACTOR);//Z scale factor double 8 bytes
-		out.writeDouble(xoff);//X offset double 8 bytes
-		out.writeDouble(yoff);//Y offset double 8 bytes
-		out.writeDouble(zoff);//Z offset double 8 bytes
-		out.writeDouble(xmax);//Max X double 8 bytes
-		out.writeDouble(xmin);//Min X double 8 byte
-		out.writeDouble(ymax);//Max Y double 8 bytes
-		out.writeDouble(ymin);//Min Y double 8 bytes
-		out.writeDouble(zmax);//Max Z double 8 bytes
-		out.writeDouble(zmin);//Min Z double 8 bytes
-		if((header.version_major == 1 && header.version_minor >= 3) || header.version_major >= 2) {
-			out.writeLong(0);//Start of Waveform Data Packet Record Unsigned long long 8 bytes
-			if((header.version_major == 1 && header.version_minor >= 4) || header.version_major >= 2) {
-				out.writeLong(0);//Start of first Extended Variable Length Record unsigned long long 8 bytes
-				out.writeInt(0);//Number of Extended Variable Length Records unsigned long 4 bytes
-				out.writeLong(pointCount);//Number of point records unsigned long long 8 bytes
-				out.writeUint64(numberOfPointsByReturn);//Number of points by return unsigned long long [15] 120 bytes
+		receiver.setContentType("application/octet-stream");	
+		//LittleEndianDataOutputStream out = new LittleEndianDataOutputStream(receiver.getOutputStream());
+		try(BufferedDataOuputStreamLE out = new BufferedDataOuputStreamLE(receiver.getOutputStream())) {
+			out.putInt(LASF_SIGNATUR); //File Signature (“LASF”) char[4] 4 bytes
+			out.putShort((short) 0); //File Source ID unsigned short 2 bytes
+			out.putShort((short) 0); //Global Encoding unsigned short 2 bytes
+			out.putInt(0);//Project ID - GUID data 1 unsigned long 4 bytes
+			out.putShort((short) 0);//Project ID - GUID data 2 unsigned short 2 byte
+			out.putShort((short) 0);//Project ID - GUID data 3 unsigned short 2 byte
+			out.putLong(0);//Project ID - GUID data 4 unsigned char[8] 8 bytes
+			out.putByte((byte) header.version_major);//Version Major unsigned char 1 byte
+			out.putByte((byte) header.version_minor);//Version Minor unsigned char 1 byte
+			out.putBytes(SYSTEM_IDENTIFIER);//System Identifier char[32] 32 bytes
+			out.putBytes(GENERATING_SOFTWARE);//Generating Software char[32] 32 bytes
+			out.putShort((short) date.getDayOfYear());//File Creation Day of Year unsigned short 2 bytes
+			out.putShort((short) date.getYear());//File Creation Year unsigned short 2 bytes
+			out.putShort((short) header.size);//Header Size unsigned short 2 bytes
+			out.putInt(header.size);//Offset to point data unsigned long 4 bytes 
+			out.putInt(0);//Number of Variable Length Records unsigned long 4 bytes
+			out.putByte((byte) pointDataRecord.id);//Point Data Record Format unsigned char 1 byte
+			out.putShort((short) pointDataRecord.size);//Point Data Record Length unsigned short 2 bytes
+			out.putInt(pointCount > Integer.MAX_VALUE ? 0 : (int) pointCount);//Legacy Number of point records unsigned long 4 bytes
+			out.putIntsOverflowZero(numberOfPointsByReturn, 5);//Legacy Number of points by return unsigned long [5] 20 bytes
+			out.putDouble(SCALE_FACTOR);//X scale factor double 8 bytes
+			out.putDouble(SCALE_FACTOR);//Y scale factor double 8 bytes
+			out.putDouble(SCALE_FACTOR);//Z scale factor double 8 bytes
+			out.putDouble(xoff);//X offset double 8 bytes
+			out.putDouble(yoff);//Y offset double 8 bytes
+			out.putDouble(zoff);//Z offset double 8 bytes
+			out.putDouble(xmax);//Max X double 8 bytes
+			out.putDouble(xmin);//Min X double 8 byte
+			out.putDouble(ymax);//Max Y double 8 bytes
+			out.putDouble(ymin);//Min Y double 8 bytes
+			out.putDouble(zmax);//Max Z double 8 bytes
+			out.putDouble(zmin);//Min Z double 8 bytes
+			if((header.version_major == 1 && header.version_minor >= 3) || header.version_major >= 2) {
+				out.putLong(0);//Start of Waveform Data Packet Record Unsigned long long 8 bytes
+				if((header.version_major == 1 && header.version_minor >= 4) || header.version_major >= 2) {
+					out.putLong(0);//Start of first Extended Variable Length Record unsigned long long 8 bytes
+					out.putInt(0);//Number of Extended Variable Length Records unsigned long 4 bytes
+					out.putLong(pointCount);//Number of point records unsigned long long 8 bytes
+					out.putLongs(numberOfPointsByReturn);//Number of points by return unsigned long long [15] 120 bytes
+				}
 			}
-		}
 
-		switch(pointDataRecord) {
-		case FORMAT_0:
-			writePointDataRecordFormat0(out, pointTables, xoff, yoff, zoff);
-			break;
-		case FORMAT_6:
-			writePointDataRecordFormat6(out, pointTables, xoff, yoff, zoff);
-			break;
-		default:
-			throw new RuntimeException();
+			switch(pointDataRecord) {
+			case FORMAT_0:
+				writePointDataRecordFormat0(out, pointTables, xoff, yoff, zoff);
+				break;
+			case FORMAT_6:
+				writePointDataRecordFormat6(out, pointTables, xoff, yoff, zoff);
+				break;
+			default:
+				throw new RuntimeException();
+			}
 		}
-
-
 	}
 
-	private static void writePointDataRecordFormat0(LittleEndianDataOutputStream out, PointTable[] pointTables, double xoff, double yoff, double zoff) throws IOException {
+	private static void writePointDataRecordFormat0(BufferedDataOuputStreamLE out, PointTable[] pointTables, double xoff, double yoff, double zoff) throws IOException {
 		for(PointTable p:pointTables) {
 			int len = p.rows;
 			double[] xs = p.x == null ? new double[len] : p.x;
@@ -162,19 +160,19 @@ private static void writePointDataRecordFormat0(LittleEndianDataOutputStream out
 			byte[] cs = p.classification == null ? new byte[len] : p.classification;
 			byte[] sars = p.scanAngleRank == null ? new byte[len] : p.scanAngleRank;
 			for (int i = 0; i < len; i++) {
-				out.writeInt((int) ((xs[i] - xoff) * 1000d)); //X long 4 bytes
-				out.writeInt((int) ((ys[i] - yoff) * 1000d)); //Y long 4 bytes
-				out.writeInt((int) ((zs[i] - zoff)  * 1000d)); //Z long 4 bytes
-				out.writeChar(is[i]);//Intensity unsigned short 2 bytes
+				out.putInt((int) ((xs[i] - xoff) * 1000d)); //X long 4 bytes
+				out.putInt((int) ((ys[i] - yoff) * 1000d)); //Y long 4 bytes
+				out.putInt((int) ((zs[i] - zoff)  * 1000d)); //Z long 4 bytes
+				out.putChar(is[i]);//Intensity unsigned short 2 bytes
 				//Return Number 3 bits (bits 0 – 2) 3 bits
 				//Number of Returns (given pulse) 3 bits (bits 3 – 5) 3 bits
 				//Scan Direction Flag 1 bit (bit 6) 1 bit
 				//Edge of Flight Line 1 bit (bit 7) 1 bit
-				out.writeByte(getFormat0Flag(rns[i], rs[i]));
-				out.writeByte(cs[i]);//Classification unsigned char 1 byte
-				out.writeByte(sars[i]);//Scan Angle Rank (-90 to +90) – Left side char 1 byte
-				out.writeByte(0);//User Data unsigned char 1 byte
-				out.writeShort(0);//Point Source ID unsigned short 2 bytes
+				out.putByte((byte) getFormat0Flag(rns[i], rs[i]));
+				out.putByte(cs[i]);//Classification unsigned char 1 byte
+				out.putByte(sars[i]);//Scan Angle Rank (-90 to +90) – Left side char 1 byte
+				out.putByte((byte) 0);//User Data unsigned char 1 byte
+				out.putShort((short) 0);//Point Source ID unsigned short 2 bytes
 			}
 		}
 	}
@@ -185,7 +183,7 @@ private static int getFormat0Flag(int returnNumber, int returns) {
 		return rn & (rs << 3);		
 	}
 
-	private static void writePointDataRecordFormat6(LittleEndianDataOutputStream out, PointTable[] pointTables, double xoff, double yoff, double zoff) throws IOException {
+	private static void writePointDataRecordFormat6(BufferedDataOuputStreamLE out, PointTable[] pointTables, double xoff, double yoff, double zoff) throws IOException {
 		for(PointTable p:pointTables) {
 			int len = p.rows;
 			double[] xs = p.x == null ? new double[len] : p.x;
@@ -197,23 +195,23 @@ private static void writePointDataRecordFormat6(LittleEndianDataOutputStream out
 			byte[] cs = p.classification == null ? new byte[len] : p.classification;
 			byte[] sars = p.scanAngleRank == null ? new byte[len] : p.scanAngleRank;
 			for (int i = 0; i < len; i++) {
-				out.writeInt((int) ((xs[i] - xoff) * 1000d)); //X long 4 bytes
-				out.writeInt((int) ((ys[i] - yoff) * 1000d)); //Y long 4 bytes
-				out.writeInt((int) ((zs[i] - zoff)  * 1000d)); //Z long 4 bytes
-				out.writeChar(is[i]);//Intensity unsigned short 2 bytes
+				out.putInt((int) ((xs[i] - xoff) * 1000d)); //X long 4 bytes
+				out.putInt((int) ((ys[i] - yoff) * 1000d)); //Y long 4 bytes
+				out.putInt((int) ((zs[i] - zoff)  * 1000d)); //Z long 4 bytes
+				out.putChar(is[i]);//Intensity unsigned short 2 bytes
 				//Return Number 4 bits (bits 0 - 3) 4 bits
 				//Number of Returns (given pulse) 4 bits (bits 4 - 7) 4 bits
-				out.writeByte(getFormat6ReturnFlag(rns[i], rs[i]));
+				out.putByte((byte) getFormat6ReturnFlag(rns[i], rs[i]));
 				//Classification Flags 4 bits (bits 0 - 3) 4 bits
 				//Scanner Channel 2 bits (bits 4 - 5) 2 bits
 				//Scan Direction Flag 1 bit (bit 6) 1 bit
 				//Edge of Flight Line 1 bit (bit 7) 1 bit
-				out.writeByte(0);
-				out.writeByte(cs[i]);//Classification unsigned char 1 byte
-				out.writeByte(0);//User Data unsigned char 1 byte
-				out.writeShort((int) (sars[i] / 0.006d));//Scan Angle short 2 bytes
-				out.writeShort(0);//Point Source ID unsigned short 2 bytes
-				out.writeDouble(0);//GPS Time double 8 bytes			
+				out.putByte((byte) 0);
+				out.putByte(cs[i]);//Classification unsigned char 1 byte
+				out.putByte((byte) 0);//User Data unsigned char 1 byte
+				out.putShort((short) (sars[i] / 0.006d));//Scan Angle short 2 bytes
+				out.putShort((short) 0);//Point Source ID unsigned short 2 bytes
+				out.putDouble(0);//GPS Time double 8 bytes			
 			}
 		}
 	}

src/pointcloud/RdatWriter.java

@@ -245,5 +245,4 @@ public static void writePoints(PointTable[] pointTables, AttributeSelector selec
 		}
 		df.write(receiver, pointTables);
 	}
-
 }

src/server/api/main/APIHandler_create_raster.java

@@ -27,8 +27,8 @@ public APIHandler_create_raster(Broker broker) {
 	@Override
 	protected void handle(String target, Request request, Response response) throws IOException {	
 		UserIdentity userIdentity = Web.getUserIdentity(request);
-		String name = request.getParameter("name");
-		if(name==null) {
+		String rasterdbName = request.getParameter("name");
+		if(rasterdbName==null) {
 			throw new RuntimeException("missing name parameter");
 		}
 		boolean transaction = true;
@@ -54,13 +54,28 @@ protected void handle(String target, Request request, Response response) throws
 		}
 
 		boolean create_new = Web.getBoolean(request, "create_new", true);
+		boolean newRasterdb = true;
 
-		RasterDB rasterdb = create_new ? broker.createNewRasterdb(name, transaction, storage_type): broker.createOrGetRasterdb(name, transaction, storage_type);
-		if(userIdentity != null) {
-			String username = userIdentity.getUserPrincipal().getName();
-			rasterdb.setACL_owner(ACL.ofRole(username));
+		if(broker.hasRasterdb(rasterdbName)) {
+			newRasterdb = false;
+			RasterDB rasterdb = broker.getRasterdb(rasterdbName);
+			rasterdb.checkMod(userIdentity, "task rasterdb create of existing name");
+			rasterdb.close();
 		}
 
+		RasterDB rasterdb;
+		if(create_new) {
+			rasterdb = broker.createNewRasterdb(rasterdbName, transaction, storage_type);
+			newRasterdb = true;
+		} else {
+			rasterdb = broker.createOrGetRasterdb(rasterdbName, transaction, storage_type);
+		}
+		if(newRasterdb) {
+			if(userIdentity != null) {
+				String username = userIdentity.getUserPrincipal().getName();
+				rasterdb.setACL_owner(ACL.ofRole(username));
+			}			
+		}
 		if(proj4 != null && !proj4.isEmpty()) {
 			rasterdb.setProj4(proj4);
 		}
@@ -77,7 +92,7 @@ protected void handle(String target, Request request, Response response) throws
 		JSONWriter json = new JSONWriter(response.getWriter());
 		json.object();
 		json.key("result");
-		json.value("created raster "+name);
+		json.value("created raster "+rasterdbName);
 		json.endObject();
 	}
 }

src/server/api/pointclouds/PointProcessor.java

@@ -1,13 +1,11 @@
 package server.api.pointclouds;
 
 import java.io.IOException;
-import java.util.Arrays;
 import java.util.function.Function;
 import java.util.stream.Stream;
 
-
-import org.tinylog.Logger;
 import org.eclipse.jetty.server.Request;
+import org.tinylog.Logger;
 
 import pointcloud.AttributeSelector;
 import pointcloud.CellTable.ChainedFilterFunc;
@@ -19,7 +17,6 @@
 import pointdb.processing.geopoint.Normalise;
 import pointdb.subsetdsl.Region;
 import util.Receiver;
-import util.Util;
 import util.Web;
 
 public class PointProcessor {