Tethys working again

And a bit more playing around with metadata handling for Deploymnet
documents

.classpath

@@ -6,7 +6,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/Java 17">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
 		<attributes>
 			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
@@ -17,7 +17,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry combineaccessrules="false" kind="src" path="/TethysJavaClient"/>
 	<classpathentry combineaccessrules="false" kind="src" path="/nilusxmlgenerator"/>
+	<classpathentry combineaccessrules="false" kind="src" path="/TethysJavaClient"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

src/Array/Hydrophone.java

@@ -158,7 +158,7 @@ public class Hydrophone implements Serializable, Cloneable, ManagedParameters {
 		return sensitivity;
 	}
 
-	protected void setSensitivity(double sensitivity) {
+	public void setSensitivity(double sensitivity) {
 		this.sensitivity = sensitivity;
 	}
 	
@@ -364,7 +364,7 @@ public class Hydrophone implements Serializable, Cloneable, ManagedParameters {
 	/**
 	 * @param preampGain The preampGain to set.
 	 */
-	protected void setPreampGain(double preampGain) {
+	public void setPreampGain(double preampGain) {
 		this.preampGain = preampGain;
 	}
 

src/PamModel/PamModel.java

@@ -46,8 +46,6 @@ import fftManager.PamFFTControl;
 import group3dlocaliser.Group3DLocaliserControl;
 import metadata.MetaDataContol;
 import meygenturbine.MeygenTurbine;
-import networkTransfer.receive.BuoyStatusDataUnit;
-import networkTransfer.receive.NetworkReceiver;
 import printscreen.PrintScreenControl;
 import rockBlock.RockBlockControl;
 import tethys.TethysControl;
@@ -1098,6 +1096,7 @@ final public class PamModel implements PamModelInterface, PamSettings {
 		 * PamModel !
 		 */
 		
+//		pluginList.add(new MorlaisWP1aPlugin());
 
 		// Load up whatever default classloader was used to create this class.  Must use the same classloader
 		// for all plugins, or else we will not be able to create proper dependencies between them or be able

src/generalDatabase/sqlite/SqliteSQLTypes.java

@@ -10,7 +10,7 @@ import PamUtils.PamCalendar;
 
 public class SqliteSQLTypes extends SQLTypes {
 	
-	protected static final SQLiteConfig.DateClass dateClass = SQLiteConfig.DateClass.TEXT;
+	public static final SQLiteConfig.DateClass dateClass = SQLiteConfig.DateClass.TEXT;
 
 	@Override
 	public String typeToString(int sqlType, int length, boolean counter) {

src/metadata/deployment/DeploymentData.java

@@ -5,6 +5,7 @@ import java.io.Serializable;
 import PamModel.parametermanager.FieldNotFoundException;
 import PamModel.parametermanager.ManagedParameters;
 import PamModel.parametermanager.PamParameterSet;
+import PamUtils.LatLong;
 
 /**
  * Class to hold Deployment data in a form consistent with the ANSI PAM
@@ -65,6 +66,46 @@ public class DeploymentData implements Serializable, Cloneable, ManagedParameter
 	 * Name of geographic region.
 	 */
 	private String region;
+	
+	/**
+	 * time of instrument deployment (different to recording start);
+	 */
+	private Long deploymentMillis;
+
+	/**
+	 * time of actual recovery (different to recording end);
+	 */
+	private Long recoveryMillis;
+
+	private LatLong recoverLatLong;
+	
+	/**
+	 * @return the deploymentMillis
+	 */
+	public Long getDeploymentMillis() {
+		return deploymentMillis;
+	}
+
+	/**
+	 * @param deploymentMillis the deploymentMillis to set
+	 */
+	public void setDeploymentMillis(Long deploymentMillis) {
+		this.deploymentMillis = deploymentMillis;
+	}
+
+	/**
+	 * @return the recoveryMillis
+	 */
+	public Long getRecoveryMillis() {
+		return recoveryMillis;
+	}
+
+	/**
+	 * @param recoveryMillis the recoveryMillis to set
+	 */
+	public void setRecoveryMillis(Long recoveryMillis) {
+		this.recoveryMillis = recoveryMillis;
+	}
 
 //	/**
 //	 * Instrument type, e.g. HARP, EAR, Popup, DMON, etc.
@@ -235,6 +276,22 @@ public class DeploymentData implements Serializable, Cloneable, ManagedParameter
 		this.region = region;
 	}
 
+	/**
+	 * Set the recovery position latlong for a static recorder. 
+	 * Deployment lat long is in the hydrophone array data. 
+	 * @param recoverLatLong
+	 */
+	public void setRecoveryLatLong(LatLong recoverLatLong) {
+		this.recoverLatLong = recoverLatLong;
+	}
+
+	/**
+	 * @return the recoverLatLong (may often be null)
+	 */
+	public LatLong getRecoverLatLong() {
+		return recoverLatLong;
+	}
+
 //	/**
 //	 * @return the instrumentType
 //	 */

src/tethys/TethysControl.java

@@ -412,7 +412,8 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 	public void notifyModelChanged(int changeType) {
 		super.notifyModelChanged(changeType);
 		switch (changeType) {
-		case PamControllerInterface.INITIALIZATION_COMPLETE:
+		case PamControllerInterface.INITIALIZE_LOADDATA:
+//		case PamControllerInterface.INITIALIZATION_COMPLETE:
 			initializationStuff();
 			break;
 		}

src/tethys/dbxml/DBXMLConnect.java

@@ -1,9 +1,15 @@
 package tethys.dbxml;
 
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
 import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FileWriter;
 import java.io.IOException;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
+import java.nio.file.Files;
 import java.util.ArrayList;
 
 import javax.xml.bind.JAXBException;
@@ -31,6 +37,8 @@ public class DBXMLConnect {
 	private Queries queries;
 
 	private String currentSiteURL;
+	
+	public static String[] collections = {"Deployments", "Detections", "Localizations", "Calibrations", "SpeciesAbbreviations"};
 
 	public DBXMLConnect(TethysControl tethysControl) {
 		this.tethysControl = tethysControl;
@@ -136,13 +144,15 @@ public class DBXMLConnect {
 		String tempName = getTempFileName(nilusObject);
 		tempName = tempDirectory.getAbsolutePath() + File.separator + tempName + ".xml";
 		File tempFile = new File(tempName);
+		String bodgeName = tempName;//"C:\\Users\\dg50\\AppData\\Local\\Temp\\PAMGuardTethys\\Meygen2022_10a.xml";
 		try {
 			MarshalXML marshal = new MarshalXML();
 			marshal.createInstance(objClass);
 //				Path tempFile = Files.createTempFile("pamGuardToTethys", ".xml");
 				marshal.marshal(nilusObject, tempFile.toString());
+//				tempFile = stripXMLHeader(tempFile);
 				fileError = Importer.ImportFiles(params.getFullServerName(), collection,
-						new String[] { tempFile.toString() }, "", "", false);
+						new String[] { bodgeName }, "", "", false);
 
 //				System.out.println(fileError);
 
@@ -157,11 +167,62 @@ public class DBXMLConnect {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}
-//		System.out.println(fileError);
+		System.out.println(fileError);
 		return fileError;
 	}
 
 
+	/**
+	 * Seems we have to get rid of the line <?xml version="1.0" encoding="UTF-8"?>
+	 * which is being put there by the marshaller ? 
+	 * @param tempFile
+	 */
+	private File stripXMLHeader(File tempFile) {
+		// TODO Auto-generated method stub
+
+		File tempTemp = new File(tempFile.getAbsolutePath().replace(".temp.xml", ".xml"));
+		try {
+			BufferedReader reader = new BufferedReader(new FileReader(tempFile));
+			BufferedWriter writer = new BufferedWriter(new FileWriter(tempTemp));
+			String line = reader.readLine(); 
+			while (line != null) {
+				// see if the line has any unicode in it
+				int len = line.length();
+				byte[] bytes = line.getBytes();
+				if (len == bytes.length) {
+					System.out.println(line);
+				}
+				
+				if (line.startsWith("<?xml version=")) {
+					
+				}
+				else {
+					writer.write(line + "\r\n");
+				}
+				line = reader.readLine();
+			}
+			writer.close();
+			reader.close();
+		} catch (FileNotFoundException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+			return tempFile;
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+			return tempFile;
+		}
+		boolean deleted = tempFile.delete();
+		if (deleted) {
+			tempTemp.renameTo(tempFile);
+			return tempFile;
+		}
+		else {
+			return tempTemp;
+		}
+	
+	}
+
 //	/*
 //	 * force a fluch by sending a dummy document to th eimporter which will rail, but ...
 //	 */

src/tethys/dbxml/DBXMLQueries.java

@@ -155,6 +155,9 @@ public class DBXMLQueries {
 	 * @return
 	 */
 	public ArrayList<nilus.Deployment> getProjectDeployments(String projectName) {
+		if (projectName == null) {
+			return null;
+		}
 		String qBase = "{\"return\":[\"Deployment\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Deployment/Project\",\"%s\"],\"optype\":\"binary\"}],\"enclose\":1}";
 		String qStr = String.format(qBase, projectName);
 

src/tethys/deployment/DeploymentHandler.java

@@ -2,6 +2,8 @@ package tethys.deployment;
 
 import java.math.BigInteger;
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.List;
 import java.util.ListIterator;
 
@@ -21,6 +23,8 @@ import Array.Streamer;
 import Array.ThreadingHydrophoneLocator;
 import PamController.PamControlledUnit;
 import PamController.PamController;
+import PamUtils.LatLong;
+import PamUtils.PamCalendar;
 import PamUtils.PamUtils;
 import PamguardMVC.PamDataBlock;
 import SoundRecorder.RecordingInfo;
@@ -156,6 +160,20 @@ public class DeploymentHandler implements TethysStateObserver {
 		// just load everything. Probably OK for the acqusition, but will bring down
 		daqInfoDataBlock.loadViewerData(0, Long.MAX_VALUE, null);
 		ArrayList<DaqStatusDataUnit> allStatusData = daqInfoDataBlock.getDataCopy();
+		/**
+		 * Due to seird file overlaps we need to resort this by id if we can.
+		 * 
+		 */
+		Collections.sort(allStatusData, new Comparator<DaqStatusDataUnit>() {
+
+			@Override
+			public int compare(DaqStatusDataUnit o1, DaqStatusDataUnit o2) {
+				if (o1.getDatabaseIndex() == 0) {
+					return (int) (o1.getTimeMilliseconds()-o2.getTimeMilliseconds());
+				}
+				return o1.getDatabaseIndex()-o2.getDatabaseIndex();
+			}
+		});
 
 		ArrayList<RecordingPeriod> tempPeriods = null;
 
@@ -168,8 +186,15 @@ public class DeploymentHandler implements TethysStateObserver {
 		}
 		if (tempPeriods == null || tempPeriods.size() == 0) {
 			System.out.println("Data appear to have no logged recording periods available either from the database or the raw recordings.");
+			return null;
 		}
+
 		int nPeriods = tempPeriods.size();
+//		int i = 0;
+//		for (RecordingPeriod aP : tempPeriods) {
+//			System.out.printf("Pre merge %d : %s to %s\n", i++, PamCalendar.formatDBDateTime(aP.getRecordStart()), 
+//					PamCalendar.formatDBDateTime(aP.getRecordStop()));
+//		}
 		// now go through those and merge into longer periods where there is no gap between files.
 		ListIterator<RecordingPeriod> iterator = tempPeriods.listIterator();
 		RecordingPeriod prevPeriod = null;
@@ -191,6 +216,11 @@ public class DeploymentHandler implements TethysStateObserver {
 			}
 			prevPeriod = nextPeriod;
 		}
+//		i = 0;
+//		for (RecordingPeriod aP : tempPeriods) {
+//			System.out.printf("Post merge %d : %s to %s\n", i++, PamCalendar.formatDBDateTime(aP.getRecordStart()), 
+//					PamCalendar.formatDBDateTime(aP.getRecordStop()));
+//		}
 //		System.out.printf("Data have %d distinct files, but only %d distinct recording periods\n", nPeriods, tempPeriods.size());
 		DutyCycleInfo dutyCycleinfo = assessDutyCycle(tempPeriods);
 		// if it's duty cycles, then we only want a single entry. 
@@ -202,6 +232,17 @@ public class DeploymentHandler implements TethysStateObserver {
 			deploymentPeriods = new ArrayList<>();
 			deploymentPeriods.add(new RecordingPeriod(tempPeriods.get(0).getRecordStart(), tempPeriods.get(tempPeriods.size()-1).getRecordStop()));
 		}
+		/*
+		 * do another sort of the deploymentPeriods. The start stops were in the order they went into the 
+		 * database in the hope that pairs were the right way round. Now check all data are/
+		 */
+		Collections.sort(deploymentPeriods, new Comparator<RecordingPeriod>() {
+			@Override
+			public int compare(RecordingPeriod o1, RecordingPeriod o2) {
+				return (int) (o1.getRecordStart()-o2.getRecordStart());
+			}
+		});
+		
 		DeploymentOverview deploymentOverview = new DeploymentOverview(dutyCycleinfo, deploymentPeriods);
 		matchPamguard2Tethys(deploymentOverview, projectDeployments);
 		this.deploymentOverview = deploymentOverview;
@@ -300,7 +341,6 @@ public class DeploymentHandler implements TethysStateObserver {
 		return cycleInfo;
 	}
 
-
 	private ArrayList<RecordingPeriod> extractTimesFromStatus(ArrayList<DaqStatusDataUnit> allStatusData) {
 		ArrayList<RecordingPeriod> tempPeriods = new ArrayList<>();
 		long dataStart = Long.MAX_VALUE;
@@ -315,14 +355,20 @@ public class DeploymentHandler implements TethysStateObserver {
 				nStart++;
 				dataStart = Math.min(dataStart, daqStatus.getTimeMilliseconds());
 				lastStart = daqStatus.getTimeMilliseconds();
+//				System.out.println("Start at " + PamCalendar.formatDBDateTime(lastStart));
 				break;
 			case "Stop":
 				nStop++;
 				dataEnd = Math.max(dataEnd, daqStatus.getEndTimeInMilliseconds());
 				long lastEnd = daqStatus.getEndTimeInMilliseconds();
 				if (lastStart != null) {
+//					System.out.printf("Adding period %s to %s\n", PamCalendar.formatDBDateTime(lastStart), 
+//							PamCalendar.formatDBDateTime(lastEnd));
 					tempPeriods.add(new RecordingPeriod(lastStart, lastEnd));
 				}
+				else {
+//					System.out.println("Skipping stop at " + PamCalendar.formatDBDateTime(lastEnd));
+				}
 				lastStart = null;
 				break;
 			case "NextFile":
@@ -505,16 +551,23 @@ public class DeploymentHandler implements TethysStateObserver {
 			e.printStackTrace();
 		}
 		DeploymentData globalDeplData = tethysControl.getGlobalDeplopymentData();
-		String id = String.format("%s%d", globalDeplData.getProject(), i);
+		String id = String.format("%s_%d", globalDeplData.getProject(), i);
 		deployment.setId(id);
 		deployment.setDeploymentId(i);
 
-		DeploymentRecoveryDetails deploymentDetails = new DeploymentRecoveryDetails();
-		DeploymentRecoveryDetails recoveryDetails = new DeploymentRecoveryDetails();
-		deploymentDetails.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(recordingPeriod.getRecordStart()));
+		DeploymentRecoveryDetails deploymentDetails = deployment.getDeploymentDetails();
+		if (deploymentDetails == null) {
+			deploymentDetails = new DeploymentRecoveryDetails();
+		}
+		DeploymentRecoveryDetails recoveryDetails = deployment.getRecoveryDetails();
+		if (recoveryDetails == null) {
+			recoveryDetails = new DeploymentRecoveryDetails();
+		}
 		deploymentDetails.setAudioTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(recordingPeriod.getRecordStart()));
-		recoveryDetails.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(recordingPeriod.getRecordStop()));
 		recoveryDetails.setAudioTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(recordingPeriod.getRecordStop()));
+
+		deploymentDetails.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(recordingPeriod.getRecordStart()));
+		recoveryDetails.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(recordingPeriod.getRecordStop()));
 		
 		deployment.setDeploymentDetails(deploymentDetails);
 		deployment.setRecoveryDetails(recoveryDetails);
@@ -572,6 +625,22 @@ public class DeploymentHandler implements TethysStateObserver {
 		String geomType = getGeometryType();
 		instrument.setGeometryType(geomType);
 		deployment.setInstrument(instrument);
+		
+		// overwrite the default deployment and recovery times if there is non null data
+		Long depMillis = deploymentData.getDeploymentMillis();
+		if (depMillis != null) {
+			deployment.getDeploymentDetails().setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(depMillis));
+		}
+		Long recMillis = deploymentData.getRecoveryMillis();
+		if (recMillis != null) {
+			deployment.getRecoveryDetails().setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(recMillis));
+		}
+		LatLong recLatLong = deploymentData.getRecoverLatLong();
+		if (recLatLong != null) {
+			deployment.getRecoveryDetails().setLatitude(recLatLong.getLatitude());
+			deployment.getRecoveryDetails().setLongitude(PamUtils.constrainedAngle(recLatLong.getLongitude()));
+		}
+		
 		return true;
 	}
 

src/tethys/deployment/DutyCycleInfo.java

@@ -1,5 +1,7 @@
 package tethys.deployment;
 
+import PamUtils.PamCalendar;
+
 public class DutyCycleInfo {
 
 	public boolean isDutyCycled;
@@ -24,7 +26,8 @@ public class DutyCycleInfo {
 			return "No duty cycle";
 		}
 		else {
-			return String.format("%3.1fs on, %3.1fs off, for %d cycles", meanOnTimeS, meanGapS, nCycles);
+			return String.format("%s on, %s off, for %d cycles", PamCalendar.formatDuration((long) (meanOnTimeS*1000)), 
+					PamCalendar.formatDuration((long) (meanGapS*1000)), nCycles);
 		}
 	}
 	

src/tethys/detection/DetectionsHandler.java

@@ -466,7 +466,7 @@ public class DetectionsHandler {
 		String prefix = deployment.deployment.getId();
 		detections.setId(String.format("%s_%d", prefix, uniqueDetectionsId++));
 //		detections.setDescription(dataProvider.getDescription(deployment, tethysExportParams));
-		detections.setDescription(exportParams.detectionDescription);
+		detections.setDescription(exportParams.getNilusDetectionDescription());
 		DataSourceType dataSource = new DataSourceType();
 		dataSource.setDeploymentId(deployment.deployment.getId());
 //		dataSource.setEnsembleId(""); ToDo

src/tethys/niluswraps/PDescriptionType.java

@@ -0,0 +1,101 @@
+package tethys.niluswraps;
+
+import java.io.Serializable;
+
+import nilus.DescriptionType;
+
+/**
+ * Because we want to save DescriptionType objects in serialised
+ * psfx files and because Nilus description types are not serialised
+ * these have to be wrapped in a total bodge way with reasonably convenient 
+ * constructors and getters for converting back and forth from the nilus object. 
+ * @author dg50
+ *
+ */
+public class PDescriptionType implements Serializable {
+
+	private static final long serialVersionUID = 1L;
+
+	protected String objectives;
+	
+	protected String _abstract;
+	
+	protected String method;
+	
+	/**
+	 * Constructor from a set of strings
+	 * @param objectives
+	 * @param _abstract
+	 * @param method
+	 */
+	public PDescriptionType(String objectives, String _abstract, String method) {
+		super();
+		this.objectives = objectives;
+		this._abstract = _abstract;
+		this.method = method;
+	}
+	
+	/**
+	 * Construct from a nilus object
+	 * @param descriptionType
+	 */
+	public PDescriptionType(DescriptionType descriptionType) {
+		this.objectives = descriptionType.getObjectives();
+		this._abstract = descriptionType.getAbstract();
+		this.method = descriptionType.getMethod();
+	}
+
+	public PDescriptionType() {
+	}
+
+	public String getObjectives() {
+		return objectives;
+	}
+
+	/**
+	 * @return the _abstract
+	 */
+	public String getAbstract() {
+		return _abstract;
+	}
+
+	/**
+	 * @param _abstract the _abstract to set
+	 */
+	public void setAbstract(String _abstract) {
+		this._abstract = _abstract;
+	}
+
+	/**
+	 * @return the method
+	 */
+	public String getMethod() {
+		return method;
+	}
+
+	/**
+	 * @param method the method to set
+	 */
+	public void setMethod(String method) {
+		this.method = method;
+	}
+
+	/**
+	 * @param objectives the objectives to set
+	 */
+	public void setObjectives(String objectives) {
+		this.objectives = objectives;
+	}
+
+	/**
+	 * convert into a nilus object for output. 
+	 * @return
+	 */
+	public DescriptionType getDescription() {
+		DescriptionType descriptionType = new DescriptionType();
+		descriptionType.setAbstract(_abstract);
+		descriptionType.setObjectives(objectives);
+		descriptionType.setMethod(method);
+		return descriptionType;
+	}
+}

src/tethys/output/StreamExportParams.java

@@ -1,9 +1,11 @@
 package tethys.output;
 
+import java.io.IOException;
 import java.io.Serializable;
 
 import nilus.DescriptionType;
 import nilus.GranularityEnumType;
+import tethys.niluswraps.PDescriptionType;
 
 /**
  * Parameters controlling export of a single stream. 
@@ -32,13 +34,21 @@ public class StreamExportParams implements Serializable {
 	/*
 	 * Can't have this here since it isn't serializable. 
 	 */
-	transient public nilus.DescriptionType detectionDescription;
+	public PDescriptionType detectionDescription;
 
-	public DescriptionType getDetectionDescription() {
+	public PDescriptionType getDetectionDescription() {
 		if (detectionDescription == null) {
-			detectionDescription = new DescriptionType();
+			detectionDescription = new PDescriptionType();
 		}
 		return detectionDescription;
 	}
+	
+	/**
+	 * Get the nilus detection description
+	 * @return
+	 */
+	public DescriptionType getNilusDetectionDescription() {
+		return getDetectionDescription().getDescription();
+	}
 
 }

src/tethys/swing/DeploymentExportPanel.java

@@ -32,6 +32,7 @@ import nilus.Deployment;
 import nilus.Deployment.Data;
 import tethys.TethysControl;
 import tethys.TethysState;
+import tethys.TethysState.StateType;
 import tethys.dbxml.DBXMLConnect;
 import tethys.deployment.RecordingPeriod;
 import tethys.niluswraps.PDeployment;
@@ -149,6 +150,10 @@ public class DeploymentExportPanel extends TethysGUIPanel implements DeploymentT
 		case NEWPROJECTSELECTION:
 			updateDeployments();
 			enableControls();
+			break;
+		case UPDATEMETADATA:
+			setInternal();
+			break;
 		}
 	}
 
@@ -258,6 +263,7 @@ public class DeploymentExportPanel extends TethysGUIPanel implements DeploymentT
 				dbxmlConnect.postToTethys(deployment);
 			}
 		}
+		getTethysControl().sendStateUpdate(new TethysState(StateType.UPDATESERVER));
 	}
 
 	private void enableControls() {

src/tethys/swing/FancyClientButton.java

@@ -0,0 +1,84 @@
+package tethys.swing;
+
+import java.awt.BorderLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+
+import tethys.TethysControl;
+import tethys.dbxml.DBXMLConnect;
+
+/**
+ * Fancy button which has a normal button AND a drop down 
+ * for other web client pages. 
+ * @author dg50
+ *
+ */
+public class FancyClientButton extends JPanel {
+
+	private JButton clientButton;
+	private JButton dropButton;
+	private JPopupMenu collectionsMenu;
+	private TethysControl tethysControl;
+	
+	public FancyClientButton(TethysControl tethysControl) {
+		this.tethysControl = tethysControl;
+		setLayout(new GridBagLayout());
+		GridBagConstraints c = new GridBagConstraints();
+		c.ipadx = c.ipady = 0;
+		c.insets = new Insets(0,0,0,0);
+		clientButton = new JButton("Open Client");
+		clientButton.setToolTipText("Open Tethys web client in default browser");
+		dropButton = new JButton("v");
+		dropButton.setToolTipText("Open Tethys collections pages in default browser");
+		c.gridx = 0;
+		add(clientButton, c);
+		c.gridx++;
+		add(dropButton, c);
+		
+		String[] collections = DBXMLConnect.collections;
+		collectionsMenu = new JPopupMenu();
+		for (int i = 0; i < collections.length; i++) {
+			JMenuItem menuItem = new JMenuItem(collections[i]);
+			menuItem.addActionListener(new OpenCollection(collections[i]));
+			collectionsMenu.add(menuItem);
+		}
+		
+		dropButton.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				collectionsMenu.show(dropButton, 0, 0);
+			}
+		});
+	}
+	
+	public void addActionListener(ActionListener actionListener) {
+		clientButton.addActionListener(actionListener);
+	}
+	
+	private class OpenCollection implements ActionListener {
+
+		private String collection;
+		
+		public OpenCollection(String collection) {
+			super();
+			this.collection = collection;
+		}
+
+		@Override
+		public void actionPerformed(ActionEvent e) {
+			tethysControl.openTethysCollection(collection);
+		}
+		
+	}
+	
+	
+}

src/tethys/swing/PAMGuardDeploymentsTable.java

@@ -2,6 +2,8 @@ package tethys.swing;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.util.ArrayList;
@@ -9,7 +11,9 @@ import java.util.Arrays;
 
 import javax.swing.JCheckBox;
 import javax.swing.JComponent;
+import javax.swing.JMenuItem;
 import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
 import javax.swing.JScrollPane;
 import javax.swing.JTable;
 import javax.swing.ListSelectionModel;
@@ -17,10 +21,13 @@ import javax.swing.border.TitledBorder;
 import javax.swing.table.AbstractTableModel;
 
 import PamUtils.PamCalendar;
+import PamView.dialog.warn.WarnOnce;
 import PamView.panel.PamPanel;
 import PamView.tables.SwingTableColumnWidths;
+import nilus.Deployment;
 import tethys.TethysControl;
 import tethys.TethysState;
+import tethys.TethysState.StateType;
 import tethys.deployment.DeploymentHandler;
 import tethys.deployment.DeploymentOverview;
 import tethys.deployment.RecordingPeriod;
@@ -71,14 +78,14 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
 		@Override
 		public void mousePressed(MouseEvent e) {
 			if (e.isPopupTrigger()) {
-				showPopup();
+				showPopup(e);
 			}
 		}
 
 		@Override
 		public void mouseReleased(MouseEvent e) {
 			if (e.isPopupTrigger()) {
-				showPopup();
+				showPopup(e);
 			}
 		}
 
@@ -96,7 +103,7 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
 
 	}
 
-	public void showPopup() {
+	public void showPopup(MouseEvent e) {
 		int aRow = table.getSelectedRow();
 		int[] selRows = table.getSelectedRows();
 		if (selRows == null || selRows.length == 0) {
@@ -111,21 +118,56 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
 		// make a list of RecordingPeriods which don't currently have a Deployment document
 		ArrayList<RecordingPeriod> newPeriods = new ArrayList<>();
 		ArrayList<RecordingPeriod> allPeriods = deploymentOverview.getRecordingPeriods();
+		ArrayList<PDeployment> matchedDeployments = new ArrayList<>();
 		for (int i = 0; i < selRows.length; i++) {
-			if (allPeriods.get(selRows[i]).getMatchedTethysDeployment() == null) {
+			PDeployment tethysDeployment = allPeriods.get(selRows[i]).getMatchedTethysDeployment();
+			if (tethysDeployment == null) {
 				newPeriods.add(allPeriods.get(i));
 			}
+			else {
+				if (matchedDeployments.contains(tethysDeployment) == false) {
+					matchedDeployments.add(tethysDeployment);
+				}
+			}
 		}
-		if (newPeriods.size() == 0) {
-			return;
+		if (matchedDeployments.size() == 1) {
+			JPopupMenu popMenu = new JPopupMenu();
+			JMenuItem menuItem = new JMenuItem("Remove deployment document " + matchedDeployments.get(0));
+			menuItem.addActionListener(new ActionListener() {
+				
+				@Override
+				public void actionPerformed(ActionEvent e) {
+					deleteDeployment(matchedDeployments.get(0));
+				}
+			});
+			popMenu.add(menuItem);
+			popMenu.show(e.getComponent(), e.getX(), e.getY());
 		}
-		/*
-		 *  if we get here, we've one or more rows without a Tethys output, so can have
-		 *  a menu to create them. 
-		 */
+//		if (newPeriods.size() == 0) {
+//			return;
+//		}
+//		/*
+//		 *  if we get here, we've one or more rows without a Tethys output, so can have
+//		 *  a menu to create them. 
+//		 */
+		
 		
 	}
 	
+	protected void deleteDeployment(PDeployment pDeployment) {
+		Deployment dep = pDeployment.deployment;
+		if (dep == null) {
+			return;
+		}
+		int ans = WarnOnce.showWarning(getTethysControl().getGuiFrame(), "Delete Deployment document", 
+				"Are you sure you want to delete the deployment document " + dep.getId(), WarnOnce.OK_CANCEL_OPTION);
+		if (ans == WarnOnce.CANCEL_OPTION) {
+			return;
+		}
+		boolean gone = getTethysControl().getDbxmlConnect().deleteDocument(dep);
+		getTethysControl().sendStateUpdate(new TethysState(StateType.UPDATESERVER));
+	}
+
 	/**
 	 * Get a list of selected recording periods. 
 	 * @return list of selected periods. 
@@ -172,6 +214,9 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
 	private void updateDeployments() {
 		DeploymentHandler deploymentHandler = getTethysControl().getDeploymentHandler();
 		deploymentOverview = deploymentHandler.getDeploymentOverview();
+		if (deploymentOverview == null) {
+			return;
+		}
 		int n = deploymentOverview.getRecordingPeriods().size();
 		if (selection.length < n) {
 			selection = Arrays.copyOf(selection, n);

src/tethys/swing/TethysConnectionPanel.java

@@ -62,7 +62,7 @@ public class TethysConnectionPanel extends TethysGUIPanel {
 	
 	private JButton newInstrument;
 	
-	private JButton openClient;
+	private FancyClientButton openClient;
 	
 	public TethysConnectionPanel(TethysControl tethysControl) {
 		super(tethysControl);
@@ -73,8 +73,8 @@ public class TethysConnectionPanel extends TethysGUIPanel {
 		serverSelButton.setToolTipText("Select server");
 		serverStatus = new ScrollingPamLabel(SERVERSTATUSLENGTH);
 		serverName.setEditable(false);
-		openClient = new JButton("Open Client");
-		openClient.setToolTipText("Open Tethys client in web browser");
+		openClient = new FancyClientButton(tethysControl);
+//		openClient.setToolTipText("Open Tethys client in web browser");
 //		serverStatus.setEditable(false);
 		serverSelButton.addActionListener(new ActionListener() {
 			@Override

src/tethys/swing/export/DescriptionTypePanel.java

@@ -12,6 +12,7 @@ import javax.swing.border.TitledBorder;
 
 import PamView.dialog.PamDialog;
 import nilus.DescriptionType;
+import tethys.niluswraps.PDescriptionType;
 
 /**
  * Panel containing the three test entry fields for nilus.DescriptionType
@@ -65,7 +66,7 @@ public class DescriptionTypePanel {
 		return mainPanel;
 	}
 	
-	public void setParams(DescriptionType description) {
+	public void setParams(PDescriptionType description) {
 		if (description == null) {
 			tObjectives.setText(null);
 			tAbstract.setText(null);
@@ -73,7 +74,7 @@ public class DescriptionTypePanel {
 		}
 	}
 	
-	public boolean getParams(DescriptionType description) {
+	public boolean getParams(PDescriptionType description) {
 		if (checkField(requireObjective, tObjectives) == false) {
 			return PamDialog.showWarning(null, "Objectives", "The objectives field must be competed");
 		}