Log Tethys output and include instrumentid in Deployment queries

src/tethys/database/TethysActions.java

@@ -0,0 +1,27 @@
+package tethys.database;
+
+/**
+ * Possible document actions
+ * @author dg50
+ *
+ */
+public enum TethysActions {
+  
+	ADDDOCUMENT, DELETEDOCUMENT, UPDATEDOCUMENT;
+
+//	@Override
+//	public String toString() {
+//		switch (this) {
+//		case ADDDOCUMENT:
+//			return "Add document";
+//		case DELETEDOCUMENT:
+//			return "Delete document";
+//		case UPDATEDOCUMENT:
+//			return "Update document";
+//		default:
+//			return null;
+//		}
+//	}
+  
+  
+}

src/tethys/database/TethysLogDataBlock.java

@@ -0,0 +1,16 @@
+package tethys.database;
+
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.PamProcess;
+import tethys.TethysControl;
+
+public class TethysLogDataBlock extends PamDataBlock<TethysLogDataUnit> {
+
+	private TethysControl tethysControl;
+
+	public TethysLogDataBlock(TethysControl tethysControl) {
+		super(TethysLogDataUnit.class, "Tethys Log", null, 0);
+		this.tethysControl = tethysControl;
+	}
+
+}

src/tethys/database/TethysLogDataUnit.java

@@ -0,0 +1,59 @@
+package tethys.database;
+
+import PamguardMVC.PamDataUnit;
+
+public class TethysLogDataUnit extends PamDataUnit {
+
+	private String collection;
+	private String documentId;
+	private TethysActions action;
+	private String comment;
+	private boolean success;
+
+	public TethysLogDataUnit(long timeMilliseconds, String collection, String documentId, TethysActions action, boolean success, String comment) {
+		super(timeMilliseconds);
+		this.collection = collection;
+		this.documentId = documentId;
+		this.action = action;
+		this.success = success;
+		this.comment = comment;
+				
+	}
+
+	/**
+	 * @return the collection
+	 */
+	public String getCollection() {
+		return collection;
+	}
+
+	/**
+	 * @return the documentId
+	 */
+	public String getDocumentId() {
+		return documentId;
+	}
+
+	/**
+	 * @return the action
+	 */
+	public TethysActions getAction() {
+		return action;
+	}
+
+	/**
+	 * @return the comment
+	 */
+	public String getComment() {
+		return comment;
+	}
+
+	/**
+	 * @return the success
+	 */
+	public boolean isSuccess() {
+		return success;
+	}
+
+
+}

src/tethys/database/TethysLogger.java

@@ -0,0 +1,128 @@
+package tethys.database;
+
+import java.sql.Types;
+
+import PamguardMVC.PamDataUnit;
+import generalDatabase.DBControlUnit;
+import generalDatabase.DBProcess;
+import generalDatabase.PamConnection;
+import generalDatabase.PamTableDefinition;
+import generalDatabase.PamTableItem;
+import generalDatabase.SQLLogging;
+import generalDatabase.SQLTypes;
+import tethys.TethysControl;
+
+/**
+ * Logging everything we put into Tethys in our own database. 
+ * @author dg50
+ *
+ */
+public class TethysLogger extends SQLLogging {
+	
+	private static TethysLogger tethysLogger;
+
+	private TethysControl tethysControl;
+	
+	private TethysLogDataBlock logDataBlock;
+	
+	private PamTableDefinition tableDefinition;
+	
+	private PamTableItem collection, documentId, action, status, comment;
+	
+	private boolean tableChecked = false;
+
+	private TethysLogger(TethysControl tethysControl, TethysLogDataBlock pamDataBlock) {
+		super(pamDataBlock);
+		this.tethysControl = tethysControl;
+		this.logDataBlock = pamDataBlock;
+		tableDefinition = new PamTableDefinition("TethysLog");
+		tableDefinition.addTableItem(collection = new PamTableItem("Collection", Types.VARCHAR));
+		tableDefinition.addTableItem(documentId = new PamTableItem("DocumentId", Types.VARCHAR));
+		tableDefinition.addTableItem(action = new PamTableItem("Action", Types.VARCHAR));
+		tableDefinition.addTableItem(status = new PamTableItem("Status", Types.VARCHAR));
+		tableDefinition.addTableItem(comment = new PamTableItem("Comment", Types.VARCHAR));
+		tableDefinition.setUpdatePolicy(UPDATE_POLICY_OVERWRITE);
+		setTableDefinition(tableDefinition);
+	}
+	
+	public static TethysLogger getTethysLogger(TethysControl tethysControl) {
+		if (tethysLogger == null) {
+			tethysLogger = createTethysLogger(tethysControl);
+		}
+		return tethysLogger;
+	}
+	
+	private boolean checkTable() {
+		if (tableChecked == true) {
+			return true;
+		}
+		if (findDBProcess() == null) {
+			return false;
+		}
+		else {
+			tableChecked = findDBProcess().checkTable(tableDefinition);
+		}
+		return tableChecked;
+	}
+	
+	public boolean logAction(String collection, String documentId, TethysActions action, boolean success, String comment) {
+		PamConnection con = findDBConnection();
+		if (con == null) {
+			return false;
+		}
+		if (checkTable() == false) {
+			return false;
+		}
+		
+		TethysLogDataUnit dataUnit = new TethysLogDataUnit(System.currentTimeMillis(), collection, documentId, action, success, comment);
+		return this.logData(con, dataUnit);
+	}
+	
+	private PamConnection findDBConnection() {
+		return DBControlUnit.findConnection();	
+	}
+	
+	/**
+	 * Find the database controlled unit. <br>Must exist in viewer mode surely, but perhaps 
+	 * created after the Tethys module if the user is really crafty !
+	 * @return the DB controlled unit.
+	 */
+	private DBControlUnit findDBControl() {
+		return DBControlUnit.findDatabaseControl();
+	}
+	
+	/**
+	 * Fine the database process. Should exist. 
+	 * @return
+	 */
+	private DBProcess findDBProcess() {
+		DBControlUnit dbControl = findDBControl();
+		if (dbControl == null) {
+			return null;
+		}
+		return dbControl.getDbProcess();
+	}
+
+	private static TethysLogger createTethysLogger(TethysControl tethysControl) {
+		TethysLogDataBlock datablock = new TethysLogDataBlock(tethysControl);
+		TethysLogger newLogger = new TethysLogger(tethysControl, datablock);
+		return newLogger;
+	}
+
+
+	@Override
+	public void setTableData(SQLTypes sqlTypes, PamDataUnit pamDataUnit) {
+		TethysLogDataUnit tldu = (TethysLogDataUnit) pamDataUnit;
+		collection.setValue(tldu.getCollection());
+		documentId.setValue(tldu.getDocumentId());
+		action.setValue(tldu.getAction().toString());
+		status.setValue(tldu.isSuccess() ? "Success" : "Fail");
+		comment.setValue(tldu.getComment());
+	}
+	
+//	public TethysLogger(TethysControl tethysControl) {
+//		this.tethysControl = tethysControl;
+//	}
+	
+	
+}

src/tethys/dbxml/DBXMLConnect.java

@@ -19,6 +19,8 @@ import dbxml.Queries;
 import dbxml.uploader.Importer;
 import nilus.MarshalXML;
 import tethys.TethysControl;
+import tethys.database.TethysActions;
+import tethys.database.TethysLogger;
 import tethys.output.TethysExportParams;
 
 /**
@@ -123,6 +125,28 @@ public class DBXMLConnect {
 		return retFile;
 	}
 	
+	
+	public boolean postAndLog(Object nilusObject) throws TethysException
+	{
+		TethysException e = null;
+		boolean success = false;
+		try {
+			success = postToTethys(nilusObject);
+		}
+		catch (TethysException ex) {
+			e = ex;
+		}
+		TethysLogger logger = TethysLogger.getTethysLogger(tethysControl);
+		Class objClass = nilusObject.getClass();
+		String collection = getTethysCollection(objClass.getName());
+		String documentId = getDocumentId(nilusObject);
+		logger.logAction(collection, documentId, TethysActions.ADDDOCUMENT, success, "");
+		if (e != null) {
+			throw (e);
+		}
+		return success;
+	}
+	
 	/**
 	 * take a nilus object loaded with PamGuard data and post it to the Tethys database
 	 *
@@ -130,7 +154,7 @@ public class DBXMLConnect {
 	 * @return error string, null string means there are no errors
 	 * @throws TethysException 
 	 */
-	public boolean postToTethys(Object nilusObject) throws TethysException
+	private boolean postToTethys(Object nilusObject) throws TethysException
 	{
 		Class objClass = nilusObject.getClass();
 		String collection = getTethysCollection(objClass.getName());

src/tethys/dbxml/DBXMLQueries.java

@@ -287,6 +287,23 @@ public class DBXMLQueries {
 		return projectNames;
 	}
 
+	/**
+	 * Get project deployments that use a specific instrument id. More use than the call without this 
+	 * extra clause since it can handle overlapping deployments. 
+	 * @param projectName
+	 * @param instrumentId
+	 * @return
+	 */
+	public ArrayList<nilus.Deployment> getProjectDeployments(String projectName, String instrumentId) {
+		if (projectName == null) {
+			return null;
+		}
+		String qBase = "{\"return\":[\"Deployment\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Deployment/Project\",\"%s\"],\"optype\":\"binary\"},{\"op\":\"=\","
+				+ "\"operands\":[\"Deployment/Instrument/InstrumentId\",\"%s\"],\"optype\":\"binary\"}],\"enclose\":1}";
+		String qStr = String.format(qBase, projectName, instrumentId);
+		
+		return runProjectDeploymentsQuery(projectName, qStr);
+	}
 	/**
 	 * Get some basic (not all) data for deployments associated with a project. Note that
 	 * this may include deployments which are NOT part of the current dataset. That requires
@@ -300,7 +317,16 @@ public class DBXMLQueries {
 		}
 		String qBase = "{\"return\":[\"Deployment\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Deployment/Project\",\"%s\"],\"optype\":\"binary\"}],\"enclose\":1}";
 		String qStr = String.format(qBase, projectName);
+		return runProjectDeploymentsQuery(projectName, qStr);
+	}
 
+	/**
+	 * Run the actual projects query from either of the two above functions. 
+	 * @param projectName
+	 * @param qStr
+	 * @return
+	 */
+	private ArrayList<nilus.Deployment> runProjectDeploymentsQuery(String projectName, String qStr) {
 		DBQueryResult result = null;
 		try {
 			result = executeQuery(qStr);

src/tethys/deployment/DeploymentHandler.java

@@ -123,7 +123,7 @@ public class DeploymentHandler implements TethysStateObserver {
 	 */
 	public boolean updateProjectDeployments() {
 		DeploymentData projData = tethysControl.getGlobalDeplopymentData();
-		ArrayList<Deployment> tethysDocs = tethysControl.getDbxmlQueries().getProjectDeployments(projData.getProject());
+		ArrayList<Deployment> tethysDocs = tethysControl.getDbxmlQueries().getProjectDeployments(projData.getProject(), getInstrumentId());
 		if (tethysDocs == null) {
 			return false;
 		}
@@ -326,7 +326,7 @@ public class DeploymentHandler implements TethysStateObserver {
 				dbxmlConnect.updateDocument(deployment);
 			}
 			else {
-				dbxmlConnect.postToTethys(deployment);
+				dbxmlConnect.postAndLog(deployment);
 			}
 		}
 		catch (TethysException e) {
@@ -363,7 +363,7 @@ public class DeploymentHandler implements TethysStateObserver {
 					dbxmlConnect.updateDocument(deployment);
 				}
 				else {
-					dbxmlConnect.postToTethys(deployment);
+					dbxmlConnect.postAndLog(deployment);
 				}
 			}
 			catch (TethysException e) {

src/tethys/detection/DetectionsHandler.java

@@ -41,9 +41,15 @@ import tethys.output.StreamExportParams;
 import tethys.output.TethysExportParams;
 import tethys.pamdata.TethysDataProvider;
 
+/**
+ * Functions for handling output of Detections documents. 
+ * Works closely with a TethysDataProvider and DataBlockSpeciesManager
+ * to generate Detections elements for an xml doc to export to Tethys. 
+ * @author dg50
+ *
+ */
 public class DetectionsHandler {
 
-
 	private TethysControl tethysControl;
 
 	public int uniqueDetectionsId=1;
@@ -53,6 +59,10 @@ public class DetectionsHandler {
 
 	private ExportWorker exportWorker;
 
+	/**
+	 * 
+	 * @param tethysControl
+	 */
 	public DetectionsHandler(TethysControl tethysControl) {
 		super();
 		this.tethysControl = tethysControl;
@@ -96,159 +106,13 @@ public class DetectionsHandler {
 		return new StreamDetectionsSummary(detectionsDocs);
 	}
 
-
-//	/**
-//	 * Here is where we export data for a specific data stream to Tethys.
-//	 *
-//	 * @param aDataBlock
-//	 * @param aDeployment
-//	 * @param tethysExportParams
-//	 * @param streamExportParams
-//	 */
-//	public boolean exportDetections(PamDataBlock aDataBlock, Deployment deployment, DetectionGranularity granularity, TethysExportParams tethysExportParams,
-//			StreamExportParams streamExportParams) {
-//		if (granularity == null || granularity.granularity == null) {
-//			granularity = new DetectionGranularity(GRANULARITY.TIME, 3600);
-//		}
-//		switch (granularity.granularity) {
-//		case BINARYFILE:
-//			return exportByBinaryFile(aDataBlock, deployment, tethysExportParams, streamExportParams);
-//		case NONE:
-//			return exportEverything(aDataBlock, deployment, tethysExportParams, streamExportParams);
-//		case TIME:
-//			return exportByTimeChunk(aDataBlock, deployment, granularity.granularityIntervalSeconds, tethysExportParams, streamExportParams);
-//		default:
-//			break;
-//		}
-//
-//		return false;
-//
-//
-//	}
-//
-//	private boolean exportByBinaryFile(PamDataBlock dataBlock, Deployment deployment,
-//			TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
-//		long deploymentStart = TethysTimeFuncs.millisFromGregorianXML(deployment.getDeploymentDetails().getAudioTimeStamp());
-//		long deploymentStop = TethysTimeFuncs.millisFromGregorianXML(deployment.getRecoveryDetails().getAudioTimeStamp());
-//		/*
-//		 *  there should be a pretty good correspondence between the start of a binary file and the deploymentStart
-//		 *  since they all derived from the same start clock.
-//		 */
-//		OfflineDataMap dataMap = dataBlock.getPrimaryDataMap();
-//		if (dataMap == null) {
-//			return false;
-//		}
-//		List<OfflineDataMapPoint> mapPoints = dataMap.getMapPoints();
-//		boolean ok = true;
-//		for (OfflineDataMapPoint mapPoint : mapPoints) {
-//			if (mapPoint.getEndTime() < deploymentStart) {
-//				continue;
-//			}
-//			if (mapPoint.getStartTime() >= deploymentStop) {
-//				continue;
-//			}
-//			ok &= loadAndExport(dataBlock, deployment, Math.max(deploymentStart, mapPoint.getStartTime()),
-//					Math.min(deploymentStop, mapPoint.getEndTime()), tethysExportParams, streamExportParams);
-//		}
-//
-//
-//		return ok;
-//	}
-//
-//	private boolean exportEverything(PamDataBlock dataBlock, Deployment deployment,
-//			TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
-//		long deploymentStart = TethysTimeFuncs.millisFromGregorianXML(deployment.getDeploymentDetails().getAudioTimeStamp());
-//		long deploymentStop = TethysTimeFuncs.millisFromGregorianXML(deployment.getRecoveryDetails().getAudioTimeStamp());
-//		return loadAndExport(dataBlock, deployment, deploymentStart, deploymentStop, tethysExportParams, streamExportParams);
-//	}
-//
-//	private boolean exportByTimeChunk(PamDataBlock dataBlock, Deployment deployment, long granularityIntervalSeconds,
-//			TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
-//
-//		long deploymentStart = TethysTimeFuncs.millisFromGregorianXML(deployment.getDeploymentDetails().getAudioTimeStamp());
-//		long deploymentStop = TethysTimeFuncs.millisFromGregorianXML(deployment.getRecoveryDetails().getAudioTimeStamp());
-//		long chunkMillis = granularityIntervalSeconds*1000;
-//		long exportStart = deploymentStart / chunkMillis;
-//		exportStart *= chunkMillis;
-//		boolean ok = true;
-//		while (exportStart < deploymentStop) {
-//			ok &= loadAndExport(dataBlock, deployment, Math.max(deploymentStart, exportStart),
-//					Math.min(deploymentStop, exportStart + chunkMillis), tethysExportParams, streamExportParams);
-//			exportStart += chunkMillis;
-//		}
-//
-//		return ok;
-//	}
-//
-///**
-//	 * Load and export data for a given time period. This may be a complete deployment, it may be a short section. Do as told !
-//	 * Hopefully data interval is small enough to hold all in memory - it needs to be if the document will fit in mempory, so should be OK
-//	 * @param dataBlock
-//	 * @param deployment
-//	 * @param max
-//	 * @param min
-//	 * @param tethysExportParams
-//	 * @param streamExportParams
-//	 */
-//	private boolean loadAndExport(PamDataBlock dataBlock, Deployment deployment, long startTimeMillis, long endTimeMillis,
-//			TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
-//		// load the data
-//		dataBlock.loadViewerData(startTimeMillis, endTimeMillis, null);
-//		DataSelector dataSelector = dataBlock.getDataSelector(tethysControl.getDataSelectName(), false);
-//		/*
-//		 *  for easier synching, get a copy of the data and also apply the data selector right away so that
-//		 *  we've a list of exactly the right data.
-//		 */
-//		ArrayList<PamDataUnit> data = dataBlock.getDataCopy(startTimeMillis, endTimeMillis, true, dataSelector);
-//		/*
-//		 * Here, make Detection object and add the DetectionEffort data.
-//		 */
-//		DeploymentData globalDeplData = tethysControl.getGlobalDeplopymentData();
-//		TethysDataProvider dataProvider = dataBlock.getTethysDataProvider();
-//		Detections detections = new Detections();
-////		String prefix = getDetectionsDocIdPrefix(globalDeplData.getProject(), dataBlock);
-//		String prefix = deployment.getId();
-//		detections.setId(String.format("%s_%d", prefix, uniqueDetectionsId++));
-//		detections.setDescription(dataProvider.getDescription(deployment, tethysExportParams));
-//		DataSourceType dataSource = new DataSourceType();
-//		dataSource.setDeploymentId(deployment.getId());
-////		dataSource.setEnsembleId(""); ToDo
-//		detections.setDataSource(dataSource);
-//		detections.setAlgorithm(dataProvider.getAlgorithm());
-//		detections.setUserId("Unknown user");
-//		detections.setEffort(getDetectorEffort(deployment, startTimeMillis, endTimeMillis));
-//		DetectionGroup detectionGroup = new DetectionGroup();
-//		detections.setOnEffort(detectionGroup);
-//		List<Detection> detectionList = detectionGroup.getDetection();
-//		for (int i = 0; i < data.size(); i++) {
-//			PamDataUnit dataUnit = data.get(i);
-//			Detection detection = dataProvider.createDetection(dataUnit, tethysExportParams, streamExportParams);
-//			if (detection != null) {
-//				detectionList.add(detection);
-//			}
-//		}
-//		System.out.printf("Exporting %d %s detections for time period %s to %s\n", detectionList.size(), dataBlock.getDataName(),
-//				detections.getEffort().getStart().toString(), detections.getEffort().getEnd().toString());
-//		/*
-//		 * We should now have a fully populated Detections object, so write it to the database
-//		 * using functions in DBXMLConnect
-//		 */
-//		ArrayList<Detections> detectionDocuments = new ArrayList();
-//		detectionDocuments.add(detections);
-//
-////		tethysControl.getDbxmlConnect().postToTethys(detectionDocuments); // call whatever you need to call in here to write the Detections.
-//
-//
-//		return true;
-//
-//	}
-
-//	private boolean exportByTimeChunk(PamDataBlock aDataBlock, Deployment deployment, long granularityIntervalSeconds,
-//			TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
-//		// TODO Auto-generated method stub
-//		return false;
-//	}
-
+	/**
+	 * Get the Detection Effort part of a Detections document
+	 * @param pDeployment
+	 * @param dataBlock
+	 * @param exportParams
+	 * @return
+	 */
 	private DetectionEffort getDetectorEffort(PDeployment pDeployment, PamDataBlock dataBlock, StreamExportParams exportParams) {
 		DetectionEffort effort = new DetectionEffort();
 		Deployment deployment = pDeployment.deployment;
@@ -312,25 +176,24 @@ public class DetectionsHandler {
 		}
 	}
 
+	/**
+	 * 
+	 * @param dataBlock
+	 * @return default value is PAMGuard
+	 */
 	public String getSupportSoftware(PamDataBlock dataBlock) {
 		return "PAMGuard";
 	}
 
+	/**
+	 * 
+	 * @param dataBlock
+	 * @return PAMGuard version
+	 */
 	public String getSupportSoftwareVersion(PamDataBlock dataBlock) {
 //		should try to dig into the binary store and get the version from there.
 		return PamguardVersionInfo.version;
 	}
-//	/**
-//	 * Get a prefix for a id for a Detections document. This is just the project name
-//	 * and the datablock name. Something may need to be added to allow for multiple
-//	 * analysis going into one database.
-//	 * @param project
-//	 * @param dataBlock
-//	 * @return Detections document prefix.
-//	 */
-//	public static final String getDetectionsDocIdPrefix(String project, PamDataBlock dataBlock) {
-//		return project + "_" + dataBlock.getDataName();
-//	}
 
 	/**
 	 * Detections will be exported in a separate worker thread since export may take some time and
@@ -375,7 +238,9 @@ public class DetectionsHandler {
 		streamExportParams.granularity = allowed[0];
 	}
 
-
+	/**
+	 * send a cancel command to export thread if it's running
+	 */
 	public void cancelExport() {
 		activeExport = false;
 	}
@@ -482,18 +347,6 @@ public class DetectionsHandler {
 					break;
 				}
 
-//				if (documentCount > 500000 && mapPoint != dataMap.getLastMapPoint()) {
-//					prog = new DetectionExportProgress(deployment, currentDetections,
-//							lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_WRITING);
-//					exportObserver.update(prog);
-//					closeDetectionsDocument(currentDetections, mapPoint.getEndTime());
-//					try {
-//						dbxmlConnect.postToTethys(currentDetections);
-//					} catch (TethysException e) {
-//						tethysControl.showException(e);
-//					}
-//					currentDetections = null;
-//				}
 			}
 			Detection dets[] = granularityHandler.cleanup(deployment.getAudioEnd());
 			if (dets != null) {
@@ -504,9 +357,6 @@ public class DetectionsHandler {
 
 		}
 
-//		prog = new DetectionExportProgress(null, null,
-//				lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_GATHERING);
-//		exportObserver.update(prog);
 		return exportCount;
 	}/**
 	 * Export detections in all deployments for this PAMGuard dataset.
@@ -601,7 +451,7 @@ public class DetectionsHandler {
 					exportObserver.update(prog);
 					closeDetectionsDocument(currentDetections, mapPoint.getEndTime());
 					try {
-						dbxmlConnect.postToTethys(currentDetections);
+						dbxmlConnect.postAndLog(currentDetections);
 					} catch (TethysException e) {
 						tethysControl.showException(e);
 					}
@@ -627,7 +477,7 @@ public class DetectionsHandler {
 						lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_WRITING);
 				closeDetectionsDocument(currentDetections, deployment.getAudioEnd());
 				try {
-					dbxmlConnect.postToTethys(currentDetections);
+					dbxmlConnect.postAndLog(currentDetections);
 				} catch (TethysException e) {
 					tethysControl.showException(e);
 				}
@@ -640,6 +490,15 @@ public class DetectionsHandler {
 		exportObserver.update(prog);
 		return DetectionExportProgress.STATE_COMPLETE;
 	}
+	
+	/**
+	 * Start a new detections document for the deployment and datablock. <br>
+	 * Add all the standard information to the top of the Document
+	 * @param deployment
+	 * @param dataBlock
+	 * @param exportParams
+	 * @return new Detections document
+	 */
 	private Detections startDetectionsDocument(PDeployment deployment, PamDataBlock dataBlock,
 			StreamExportParams exportParams) {
 		Detections detections = new Detections();
@@ -701,6 +560,14 @@ public class DetectionsHandler {
 		detections.getEffort().setEnd(TethysTimeFuncs.xmlGregCalFromMillis(audioEnd));
 	}
 
+	/**
+	 * Worker thread for exporting detections. 
+	 * Currently, it counts them first, then checks the user wants to export 
+	 * This requires going through the data twice, but may be sensible to avoid
+	 * people outputting stupidly large documents. 
+	 * @author dg50
+	 *
+	 */
 	private class ExportWorker extends SwingWorker<Integer, DetectionExportProgress> implements DetectionExportObserver {
 
 		private PamDataBlock dataBlock;

src/tethys/output/TethysExporter.java

@@ -174,7 +174,7 @@ public class TethysExporter {
 //			System.out.println(deployment.toString());
 			deploymentDocs.add(deployment);
 			try {
-				tethysControl.getDbxmlConnect().postToTethys(deployment);
+				tethysControl.getDbxmlConnect().postAndLog(deployment);
 			} catch (TethysException e) {
 				tethysControl.showException(e);
 			}

src/tethys/pamdata/AutoTethysProvider.java

@@ -60,9 +60,9 @@ import java.io.StringReader;
 import java.net.URISyntaxException;
 
 /**
- * Automatically provides Tethys data based on the SQL database interface 
- * for a data block. does most of what needs to be done, though individual modules
- * may want to override this, call the base createDetection function and then add a 
+ * Automatically provides Tethys data for a PAMGuard datablock. 
+ * Does most of what needs to be done, though individual modules
+ * will want to override this, call the base createDetection function and then add a 
  * few more bespoke elements. 
  * @author dg50
  *
@@ -86,24 +86,6 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 			e.printStackTrace();
 		}
 	}
-//
-//	@Override
-//	public TethysSchema getSchema() {
-//		SQLLogging logging = pamDataBlock.getLogging();
-//		if (logging == null) {
-//			return null;
-//		}
-//		DBSchemaWriter schemaWriter = new DBSchemaWriter();
-//		Document doc = schemaWriter.generateDatabaseSchema(pamDataBlock, logging, logging.getTableDefinition());
-//		TethysSchema schema = new TethysSchema(doc);
-//		return schema;
-//	}
-
-	//	@Override
-	//	public TethysDataPoint getDataPoint(PamDataUnit pamDataUnit) {
-	//		// TODO Auto-generated method stub
-	//		return null;
-	//	}
 	
 	@Override
 	public DescriptionType getDescription(Deployment deployment, TethysExportParams tethysExportParams) {
@@ -155,7 +137,6 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 		try {
 			paramPacker = new TethysParameterPacker(tethysControl);
 		} catch (JAXBException e) {
-			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}
 		List<Element> genList = paramPacker.packParameters(pamDataBlock);
@@ -164,70 +145,17 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 		}
 		paramList.addAll(genList);
 
-		//		Document doc = XMLUtils.createBlankDoc();
-		//		PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
-		//		Element dummyEl = doc.createElement("MODULES");
-		//		doc.appendChild(dummyEl);
-		//		PamSettings[] settingsObjs = getSettingsObjects();
-		//		if (settingsObjs == null) {
-		//			return null;
-		//		}
-		////				pamXMLWriter.setStaticNameSpace(TethysControl.xmlNameSpace);
-		//		Element settingsEl = pamXMLWriter.writeUnitSettings(doc, dummyEl, pamSettings, settingsObjs);
-		//		if (settingsEl == null) {
-		//			return null;
-		//		}
-		//
-		////		settingsEl = addNameSpaceToElements(doc, settingsEl, TethysControl.xmlNameSpace);
-		//
-		//
-		//		dummyEl.appendChild(settingsEl);
-		//		NodeList childs = settingsEl.getChildNodes();
-		//		for (int i = 0; i < childs.getLength(); i++) {
-		//			Node el = childs.item(i);
-		//			//			System.out.println(el.getNodeName());
-		//			if (el instanceof Element) {
-		//				paramList.add((Element) el);
-		//			}
-		//		}
-		//
-		//		//		Document doc = pamXMLWriter.writeOneModule((PamSettings) pamControlledUnit, System.currentTimeMillis());
-		//		//		String moduleXML = null;
-		//		if (doc != null) {
-		//			// this string should be XML of all the settings for the module controlling this
-		//			// datablock.
-		//			//			moduleXML = pamXMLWriter.getAsString(doc, true); // change to false to get smaller xml
-		//			//			System.out.printf("Module settings for datablock %s are:\n", moduleXML);
-		//			//			System.out.println(moduleXML);
-		//			//			Element pamguard = doc.get("PAMGUARD");
-		//			//			Element modules = (Element) pamguard.getElementsByTagName("MODULES");
-		//			//			doc.get
-		//			//			NodeList childs = doc.getChildNodes();
-		//			//			for (int i = 0; i < childs.getLength(); i++) {
-		//			//				Node el = childs.item(i);
-		//			//				System.out.println(el.getNodeName());
-		//			//				if (el instanceof Element) {
-		//			//					paramList.add((Element) el);
-		//			//				}
-		//			//			}
-		//			//			String moduleXML = pamXMLWriter.getAsString(doc, true); // change to false to get smaller xml
-		//			//			System.out.printf("Module settings for datablock %s are:\n%s", this.pamDataBlock.getDataName(), moduleXML);
-		//		}
-		//
-		//		//		// try the old say
-		//		//		Document doc2 = pamXMLWriter.writeOneModule((PamSettings) pamControlledUnit, System.currentTimeMillis());
-		//		//		String moduleXML = null;
-		//		//		if (doc2 != null) {
-		//		//			// this string should be XML of all the settings for the module controlling this
-		//		//			// datablock.
-		//		//			moduleXML = pamXMLWriter.getAsString(doc2, true); // change to false to get smaller xml
-		//		//			System.out.printf("Module settings for datablock %s are:\n%s", pamDataBlock.getDataName(),moduleXML);
-		//		//		}
-		//		//		
-
 		return parameters;
 	}
 
+	/**
+	 * Not used. Was an attempt to automatically add name spaces to the PAMGuard settings
+	 * XML I generate, but we found a better way. 
+	 * @param doc
+	 * @param settingsEl
+	 * @param xmlNameSpace
+	 * @return
+	 */
 	private Element addNameSpaceToElements(Document doc, Element settingsEl, String xmlNameSpace) {
 
 

src/tethys/pamdata/TethysDataPoint.java

@@ -1,18 +0,0 @@
-package tethys.pamdata;
-
-import PamguardMVC.PamDataUnit;
-
-/**
- * This will be a unit of Tethys Data, e.g. a Detection. 
- * Can it also be used for things like GPS data ? 
- * @author dg50
- *
- */
-public class TethysDataPoint {
-
-	public TethysDataPoint(PamDataUnit dataUnit) {
-		// TODO Auto-generated constructor stub
-	}
-
-
-}

src/tethys/pamdata/TethysParameterPacker.java

@@ -40,40 +40,6 @@ import tethys.TethysControl;
  */
 public class TethysParameterPacker {
 
-//	/**
-//	 * Parameters should look something like below. however, only packing them with a long 
-//	schema name seems to work. 
-//	 * 
-//<Algorithm>
-//<Method>Analyst detections</Method>
-//<Software>Triton</Software>
-//<Version>unknown</Version>
-//<Parameters>
-//<LTSA_plot_time_h>0.75</LTSA_plot_time_h>
-//<LTSA_low_Hz>0.0</LTSA_low_Hz>
-//<LTSA_high_Hz>5000.0</LTSA_high_Hz>
-//<LTSA_brightness>30.0</LTSA_brightness>
-//</Parameters>
-//</Algorithm>
-	/*
-	 * 
-//			// this works. Can look at the source to see how it's done. 
-//			// may have fun making this work for more complex structures. 
-//			try {
-//				Helper helper = new Helper();
-//				helper.AddAnyElement(paramList, "Threshold", "3.5");
-//				
-//				 *  and see Matlab code for dbStruct2DOM at C:\Users\dg50\source\repos\TethysMatlab\db
-//				 *  for more complex structures
-//				 *  This looks like it may be possible to rewrite my functions for 
-//				 *  writing structures to XML using the helper.AddAnyElement function as 
-//				 *  an example and I should be able to output my complex structures. 
-//				 
-//			} catch (JAXBException | ParserConfigurationException e) {
-//				e.printStackTrace();
-//			}
-	 */
-
 	private MarshalXML marshaller;
 	
 	private PamguardXMLWriter xmlWriter;
@@ -94,6 +60,12 @@ public class TethysParameterPacker {
 		xmlWriter = PamguardXMLWriter.getXMLWriter();
 	}
 
+	/**
+	 * Get a list of elements of parameters for all modules feeding 
+	 * the given datablock. These are given in reverse order. 
+	 * @param pamDataBlock output datablock
+	 * @return parameters of all modules feeding that datablock. 
+	 */
 	public List<Element> packParameters(PamDataBlock pamDataBlock) {
 		PamProcess pamProcess = pamDataBlock.getParentProcess();
 		PamControlledUnit pamControlledUnit = pamProcess.getPamControlledUnit();

src/tethys/pamdata/TethysSchema.java

@@ -7,6 +7,7 @@ import org.w3c.dom.Document;
  * wrapper around an XML string, or a JAXB object or something, 
  * but may get more sophisticated. TBD in discussions with SDSU
  */
+@Deprecated
 public class TethysSchema {
 
 	private Document schemaDoc;