Merge branch 'main' into Tethys

src/PamController/PamController.java

@@ -196,7 +196,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 
 	private Timer diagnosticTimer;
 	
-	private boolean debugDumpBufferAtRestart = true;
+	private boolean debugDumpBufferAtRestart = false;
 
 	private NetworkController networkController;
 	private int nNetPrepared;

src/PamController/PamguardVersionInfo.java

@@ -16,7 +16,7 @@ public class PamguardVersionInfo {
 	 * @return release type 
 	 */
 	static public ReleaseType getReleaseType() {
-		return ReleaseType.OTHER; 
+		return ReleaseType.BETA; 
 	}
 	
 	/**

src/PamguardMVC/PamDataBlock.java

@@ -636,7 +636,7 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
 
 	/**
 	 * Find a dataunit based on it's database index. If there have been no updates,
-	 * then database indexes should be in order and a fast find canbe used. If
+	 * then database indexes should be in order and a fast find can be used. If
 	 * however, there have been updates, then things will not be in order so it's
 	 * necessary to go through everything from start to end.
 	 * 

src/PamguardMVC/superdet/SubdetectionInfo.java

@@ -63,6 +63,13 @@ public class SubdetectionInfo<T extends PamDataUnit> implements Comparable<Subde
 	 */
 	private int childDatabaseIndex;
 	
+	private int binaryFileIndex;
+
+	/**
+	 * Only exists for click data. 
+	 */
+	private Integer clickNumber;
+	
 	
 	/**
 	 * @param subDetection2
@@ -106,6 +113,7 @@ public class SubdetectionInfo<T extends PamDataUnit> implements Comparable<Subde
 		binaryFilename = subTableData.getBinaryFilename();
 		parentID = subTableData.getParentID();
 		parentUID = subTableData.getParentUID();
+		clickNumber = subTableData.getClickNumber();
 	}
 	
 	public T getSubDetection() {
@@ -210,4 +218,32 @@ public class SubdetectionInfo<T extends PamDataUnit> implements Comparable<Subde
 		this.childDatabaseIndex = childDatabaseIndex;
 	}
 
+	/**
+	 * @return the binaryFileIndex
+	 */
+	public int getBinaryFileIndex() {
+		return binaryFileIndex;
+	}
+
+	/**
+	 * @param binaryFileIndex the binaryFileIndex to set
+	 */
+	public void setBinaryFileIndex(int binaryFileIndex) {
+		this.binaryFileIndex = binaryFileIndex;
+	}
+
+	/**
+	 * @return the clickNumber
+	 */
+	public Integer getClickNumber() {
+		return clickNumber;
+	}
+
+	/**
+	 * @param childUID the childUID to set
+	 */
+	public void setChildUID(long childUID) {
+		this.childUID = childUID;
+	}
+
 }

src/PamguardMVC/superdet/SuperDetDataBlock.java

@@ -1,5 +1,6 @@
 package PamguardMVC.superdet;
 
+import java.io.File;
 import java.lang.reflect.Method;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -15,6 +16,7 @@ import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
 import PamguardMVC.PamProcess;
 import PamguardMVC.debug.Debug;
+import binaryFileStorage.DataUnitFileInformation;
 import clickDetector.offlineFuncs.OfflineEventDataUnit;
 import generalDatabase.PamSubtableData;
 import generalDatabase.SQLLogging;
@@ -514,7 +516,46 @@ public class SuperDetDataBlock<Tunit extends SuperDetection, TSubDet extends Pam
 				return Long.signum(comp);
 			}
 			comp = subTableData.getChildUID() - dataUnit.getUID();
-			return Long.signum(comp);
+			if (comp == 0) {
+				return 0; 
+			}
+			/**
+			 * Some problems in some datasets where the uid is corrupt. So also check 
+			 * on binary file information. This is slower, but since we've already matched on 
+			 * time, it doesn't get called very often. 
+			 */
+			String dbBin = subTableData.getBinaryFilename();
+			DataUnitFileInformation duFileInfo = dataUnit.getDataUnitFileInformation();
+			if (dbBin == null || duFileInfo == null) {
+				return Long.signum(comp);
+			}
+//			String duBin = duFileInfo.get
+			/*
+			 * Note that some bin names are truncated, so need to match on startswith. 
+			 */
+			File binFile = duFileInfo.getFile();
+			if (binFile == null) {
+				return Long.signum(comp);
+			}
+			String fName = binFile.getName();
+			if (fName.startsWith(dbBin) == false) {
+				return Long.signum(comp);
+			}
+			/*
+			 *  hope for a non null click number. If there isn't onw, then we'll just have to
+			 *  go with the bin file being the same and the millis being the same. It's important
+			 *  for clicks though since there can be >1 in a millisecond.  
+			 */
+			Integer clickNo = subTableData.getClickNumber();
+			if (clickNo == null) {
+				return 0;
+			}
+			else {
+				subTableData.setChildUID(dataUnit.getUID());
+				dataUnit.updateDataUnit(System.currentTimeMillis());
+				return (int) (clickNo - duFileInfo.getIndexInFile());
+			}
+			
 		}
 		
 	}

src/generalDatabase/PamSubtableData.java

@@ -81,6 +81,11 @@ public class PamSubtableData {
 	 * subdetection table, and not the index from the Click_Detector_Clicks table)
 	 */
 	private long dbIndex;
+
+	/**
+	 * Click number. only exists for clicks table, but needed for corrupt database. 
+	 */
+	private Integer clickNumber;
 	
 	/**
 	 * 
@@ -158,5 +163,18 @@ public class PamSubtableData {
 		this.childUTC = childUTC;
 	}
 
+	/**
+	 * @return the clickNumber
+	 */
+	public Integer getClickNumber() {
+		return clickNumber;
+	}
+
+	/**
+	 * @param clickNumber the clickNumber to set
+	 */
+	public void setClickNumber(Integer clickNumber) {
+		this.clickNumber = clickNumber;
+	}
 	
 }

src/generalDatabase/SQLLogging.java

@@ -2077,8 +2077,9 @@ public abstract class SQLLogging {
 		ArrayList<PamSubtableData> tableList = new ArrayList<PamSubtableData>();
 		int n = 0;
 		try {
+			PamSubtableDefinition subtableTableDef = (PamSubtableDefinition) getTableDefinition();
+			PamTableItem clickNoItem = subtableTableDef.findTableItem("ClickNo");
 			while (subtableResults.next()) {
-				PamSubtableDefinition subtableTableDef = (PamSubtableDefinition) getTableDefinition();
 				PamTableItem tableItem;
 //				transferDataFromResult(con.getSqlTypes(), subtableResults);
 				for (int i = 0; i < subtableTableDef.getTableItemCount(); i++) {
@@ -2102,6 +2103,9 @@ public abstract class SQLLogging {
 				subtableData.setLongName(subtableTableDef.getLongName().getStringValue());
 				subtableData.setBinaryFilename(subtableTableDef.getBinaryfile().getStringValue());
 				subtableData.setDbIndex(subtableTableDef.getIndexItem().getIntegerValue());
+				if (clickNoItem != null) {
+					subtableData.setClickNumber(clickNoItem.getIntegerValue());
+				}
 				try {
 					subtableData.setChildUID(subtableTableDef.getUidItem().getLongObject());
 				}