Merge pull request #68 from PAMGuard/main

Merge from origin

pom.xml

@@ -5,7 +5,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
-  <version>2.02.10aa</version>
+  <version>2.02.10b</version>
   <name>Pamguard Java12+</name>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
 	<url>www.pamguard.org</url>
@@ -748,7 +748,7 @@
 		<dependency>
 			<groupId>net.sf.ucanaccess</groupId>
 			<artifactId>ucanaccess</artifactId>
-			<version>4.0.4</version>
+			<version>5.0.1</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/nz.ac.waikato.cms.weka/weka-dev -->

src/PamController/PamControlledUnitSettings.java

@@ -403,4 +403,9 @@ public class PamControlledUnitSettings implements Serializable, ManagedParameter
 		return ps;
 	}
 
+	@Override
+	public String toString() {
+		return String.format("Type %s; Name %s, Data ", getUnitType(), getUnitName()) + getSettings();
+	}
+
 }

src/PamController/PamSettingManager.java

@@ -384,6 +384,8 @@ public class PamSettingManager {
 			boolean[] usedSettings,	PamSettings user) {
 		if (settingsList == null) return null;
 		// go through the list and see if any match this module. Avoid repeats.
+//		String unitName = user.getUnitName();
+//		String unitType = user.getUnitType();
 		for (int i = 0; i < settingsList.size(); i++) {
 			if (usedSettings != null && usedSettings[i]) continue;
 			if (isSettingsUnit(user, settingsList.get(i))) {
@@ -393,6 +395,7 @@ public class PamSettingManager {
 				return settingsList.get(i);
 			}
 		}
+		
 		/*
 		 * To improve complex module loading where settings may be saved by multiple sub-modules, in
 		 * July 2015 many modules which had fixed settings had their settings names and types changed !
@@ -1482,11 +1485,20 @@ public class PamSettingManager {
 		if (settings.getUnitName() == null || settingsUser.getUnitName() == null) return false;
 		if (settings.getUnitType() == null || settingsUser.getUnitType() == null) return false;
 
-
-		if (settings.getUnitName().equals(settingsUser.getUnitName())
-				&& settings.getUnitType().equals(settingsUser.getUnitType())
-				&& settings.versionNo == settingsUser.getSettingsVersion()){
-			return true;
+		/*
+		 *  some of the settings names used in Viewer mode have become too long, notably
+		 *  in some data selectors which are using a datablocks long data name. This 
+		 *  screws things up, so moving to a begins with rather than equals for the name. 
+		 */
+		String name = settingsUser.getUnitName();
+		String type = settingsUser.getUnitType();
+		long version = settingsUser.getSettingsVersion();
+		
+		if (settings.getUnitType().equals(type)
+				&& settings.versionNo == version){
+			if (name.startsWith(settings.getUnitName())) {
+				return true;
+			}
 		}
 
 		return false;

src/PamController/PamguardVersionInfo.java

@@ -31,7 +31,7 @@ public class PamguardVersionInfo {
 	 * Version number, major version.minorversion.sub-release.
 	 * Note: can't go higher than sub-release 'f'
 	 */
-	static public final String version = "2.02.10aa";
+	static public final String version = "2.02.10b";
 	
 	/**
 	 * Release date

src/PamModel/parametermanager/PamParameterSet.java

@@ -10,7 +10,6 @@ import java.util.Collection;
 import java.util.Hashtable;
 import java.util.List;
 
-import binaryFileStorage.BinaryStoreSettings;
 
 /**
  * Description of the parameters within a class. Primarily holds a list
@@ -51,6 +50,17 @@ public class PamParameterSet {
 		hiddenFields = new ArrayList<>();
 	}
 
+	/**
+	 * Automatically generate a parameter set for a class. Will include all public fields and 
+	 * any private or protected fields for which a getter can be found that has a similar enough name
+	 * @param parentObject class to generate description for. Exception is anything that's listed 
+	 * in the STANDARD_MODIFIER_EXCLUSIONS list (FINAL or STATIC).
+	 * @return Created parameter set. 
+	 */
+	@Deprecated 
+	public static PamParameterSet autoGenerate(Object parentObject) {
+		return autoGenerate(parentObject, ParameterSetType.DETECTOR);
+	}
 	/**
 	 * Automatically generate a parameter set for a class. Will include all public fields and 
 	 * any private or protected fields for which a getter can be found that has a similar enough name

src/PamguardMVC/dataSelector/CompoundParams.java

@@ -19,4 +19,10 @@ public class CompoundParams extends DataSelectParams {
 	public DataSelectParams getSelectorParams(DataSelector dataSelector) {
 		return selectorParams.get(dataSelector.getLongSelectorName());
 	}
+
+	@Override
+	public int getCombinationFlag() {
+		return DATA_SELECT_AND;
+	}
+	
 }

src/PamguardMVC/dataSelector/DataSelectorCreator.java

@@ -200,7 +200,14 @@ public abstract class DataSelectorCreator implements PamSettings {
 			return allSelectors.get(0);
 		}
 		else {
-			return new CompoundDataSelector(pamDataBlock, allSelectors, selectorName, allowScores, selectorType);
+			CompoundDataSelector selector = new CompoundDataSelector(pamDataBlock, allSelectors, selectorName, allowScores, selectorType);
+			// not needed since it get's done after this call anyway. 
+//			DataSelectParams params = dataSelectorSettings.getParams(selectorName);
+//			if (params instanceof CompoundParams) {
+//				selector.setParams(params);
+//			}
+			
+			return selector;
 		}
 	}
 	

src/binaryFileStorage/BinaryOutputStream.java

@@ -515,7 +515,9 @@ public class BinaryOutputStream {
 	 */
 	public synchronized boolean storeData(DataOutputStream outputStream, int objectId, DataUnitBaseData baseData, BinaryObjectData binaryObjectData) {
 		if (lastObjectType == BinaryTypes.MODULE_FOOTER) {
-			System.out.printf("Storing binary object type %d in file %s with no module header\n", objectId, outputStream == null ? null : outputStream.toString());
+			System.out.printf("Storing binary object at %s from %s in file %s with no module header\n", 
+					PamCalendar.formatDBDateTime(baseData.getTimeMilliseconds()),
+					parentDataBlock.getDataName(), outputStream == null ? null : outputStream.toString());
 		}
 		byte[] data = binaryObjectData.getData();
 		int objectLength = binaryObjectData.getDataLength();

src/generalDatabase/lookupTables/LookUpTables.java

@@ -3,10 +3,13 @@ package generalDatabase.lookupTables;
 import java.awt.Color;
 import java.awt.Window;
 import java.sql.Connection;
+import java.sql.ResultSet;
 import java.sql.SQLException;
+import java.sql.Statement;
 import java.sql.Types;
 import java.util.ArrayList;
 import java.util.ListIterator;
+import java.util.Vector;
 
 import PamController.PamController;
 import PamView.dialog.warn.WarnOnce;
@@ -101,9 +104,101 @@ public class LookUpTables {
 		checkedTableConnection = null;
 		if (dbControlUnit.getDbProcess().checkTable(lutTableDef)) {
 			checkedTableConnection = con;
-			return true;
 		}
-		return false;
+		
+		checkTableRepeats(con, lutTableDef);
+		
+		return checkedTableConnection != null;
+	}
+
+	/**
+	 * for some reason some repeats have got into the LUT and need to be removed
+	 * or it really messes stuff up. So check it automatically. 
+	 * @param con
+	 * @param lutTableDef2
+	 */
+	private boolean checkTableRepeats(PamConnection con, EmptyTableDefinition lutTableDef) {
+		/*
+		 * first get a list of unique topics, then check them one at a time. 
+		 */
+		ArrayList<String> topics = getTopicList(con, lutTableDef);
+		if (topics == null) {
+			return false;
+		}
+		
+		for (String topic : topics) {
+			checkTopicRepeats(con, lutTableDef, topic);
+		}
+		return true;
+	}
+	
+	private void checkTopicRepeats(PamConnection con, EmptyTableDefinition lutTableDef2, String topic) {
+		LookupList lutList = getLookupList(topic);
+		Vector<LookupItem> list = lutList.getList();
+		int n = list.size();
+		boolean[] isRepeat = new boolean[n];
+		int nRepeat = 0;
+		// search for repeats.
+		for (int i = 0; i < n-1; i++) {
+			String code = list.get(i).getCode().trim();
+			for (int j = i+1; j < n; j++) {
+				String code2 = list.get(j).getCode().trim();
+				if (code.equals(code2)) {
+					isRepeat[j] = true;
+					nRepeat++;
+				}
+			}
+		}
+		if (nRepeat == 0) {
+			return;
+		}
+		// make a clause to delete the repeats. 
+		String sql = null;
+		for (int i = 0; i < n; i++) {
+			if (isRepeat[i] == false) {
+				continue;
+			}
+			if (sql == null) {
+				sql = String.format("DELETE FROM %s WHERE Id IN (%d", lutTableDef.getTableName(), list.get(i).getDatabaseId());
+			}
+			else {
+				sql = sql + String.format(",%d", list.get(i).getDatabaseId());
+			}
+		}
+		sql += ")";
+		boolean ok = false;
+		try {
+			Statement stmt = con.getConnection().createStatement();
+			ok = stmt.execute(sql);
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+	}
+
+	private ArrayList<String> getTopicList(PamConnection con, EmptyTableDefinition lutTableDef) {
+		if (con == null) {
+			return null;
+		}
+		ArrayList<String> topics = new ArrayList<>();
+		String qStr = "SELECT DISTINCT Topic FROM  " + lutTableDef.getTableName();
+		try {
+			Statement stmt = con.getConnection().createStatement();
+			boolean ok = stmt.execute(qStr);
+			if (ok == false) {
+				return null;
+			}
+			ResultSet results = stmt.getResultSet();
+			while (results.next()) {
+				String topic = results.getString(1);
+				topics.add(topic);
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+			return null;
+		}
+		return topics;
 	}
 
 	public LookupList createLookupList(PamCursor resultSet, String topic) {

src/generalDatabase/ucanAccess/UCanAccessSystem.java

@@ -153,7 +153,7 @@ public class UCanAccessSystem extends BaseAccessSystem implements PamSettings {
 			String conStr = "jdbc:ucanaccess://"
 					+ fl.getAbsolutePath() + passwordEntry+noMem;
 			System.out.println("UCanAccess connection string = " + conStr);
-			conn = DriverManager.getConnection(conStr);
+			conn = DriverManager.getConnection(conStr,"","");
 			conn.setAutoCommit(false);
 		} catch (Exception e) {
 			e.printStackTrace();

src/loggerForms/FormDescription.java

@@ -1598,7 +1598,9 @@ public class FormDescription implements Cloneable, Comparable<FormDescription> {
 			normalForm.destroyForm();
 		}
 		if (hiddenForm != null) {
-			normalForm.destroyForm();
+			if (normalForm != null) {
+				normalForm.destroyForm();
+			}
 		}
 		if (subtabForms != null) {
 			for (LoggerForm aForm:subtabForms) {

src/loggerForms/LoggerForm.java

@@ -21,6 +21,7 @@ import javax.swing.BoxLayout;
 import javax.swing.JButton;
 import javax.swing.JComponent;
 import javax.swing.JOptionPane;
+import javax.swing.JPanel;
 import javax.swing.JRootPane;
 import javax.swing.JScrollPane;
 import javax.swing.Timer;
@@ -529,7 +530,10 @@ public class LoggerForm{
 				innerCenterPanel.add(currentRow);
 				currentRow = new LoggerFormPanel(this, new FlowLayout(FlowLayout.LEFT));
 			}else{
-				currentRow.add(c.makeComponent(this));
+				JPanel component = c.makeComponent(this);
+				if (component != null) {
+					currentRow.add(component);
+				}
 			}
 
 		}