Fixed queries

Also added internal display of existing docuemtns (so they can be
deleted)

src/PamView/PamGui.java

@@ -61,6 +61,7 @@ import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
+import javax.swing.JRootPane;
 import javax.swing.SwingConstants;
 import javax.swing.SwingUtilities;
 import javax.swing.Timer;
@@ -234,6 +235,14 @@ public class PamGui extends PamView implements WindowListener, PamSettings {
 			boolean posOK = true;
 			try {
 				posOK = ScreenSize.isPointOnScreen(topCorner);
+				// some weird stuff going down whereby the screen position is
+				// given as -8 from the corner where it really it. this can return 
+				// false and then push the display onto a different monitor, so alow for this. 
+				if (posOK == false) {
+					topCorner.x += 10;
+					topCorner.y += 10;
+					posOK = ScreenSize.isPointOnScreen(topCorner);
+				}
 			} catch (Exception e) {
 			}
 			if (!posOK) {
@@ -1657,10 +1666,10 @@ public class PamGui extends PamView implements WindowListener, PamSettings {
 	protected void getGuiParameters() {
 		guiParameters.extendedState = frame.getExtendedState();
 		guiParameters.state = frame.getState();
-		if (guiParameters.state != Frame.MAXIMIZED_BOTH) {
+//		if (guiParameters.state != Frame.MAXIMIZED_BOTH) {
 			guiParameters.size = frame.getSize();
 			guiParameters.bounds = frame.getBounds();
-		}
+//		}
 	}
 
 	/**
@@ -1976,5 +1985,29 @@ public class PamGui extends PamView implements WindowListener, PamSettings {
 		return this.mainTab;
 	}
 	
+	/**
+	 * find a parent window for a JComponent. This can be useful in 
+	 * finding windows to open child dialogs when the object holding 
+	 * the component may not have a direct reference back to it's dialog. 
+	 * @param component any Swing component
+	 * @return parent Window (or frame) if it can be found
+	 */
+	public static Window findComponentWindow(JComponent component) {
+		if (component == null) {
+			return null;
+		}
+		JRootPane root = component.getRootPane();
+		if (root == null) {
+			return null;
+		}
+		Container rootP = root.getParent();
+		if (rootP instanceof Window) {
+			return (Window) rootP;
+		}
+		else {
+			return null;
+		}
+	}
+
 
 }

src/RightWhaleEdgeDetector/RWEDataBlock.java

@@ -6,16 +6,20 @@ import PamguardMVC.PamProcess;
 import PamguardMVC.dataOffline.OfflineDataLoadInfo;
 import PamguardMVC.dataSelector.DataSelectorCreator;
 import RightWhaleEdgeDetector.datasel.RWDataSelCreator;
+import RightWhaleEdgeDetector.species.RWSpeciesManager;
 import pamScrollSystem.ViewLoadObserver;
+import tethys.species.DataBlockSpeciesManager;
 import whistlesAndMoans.AbstractWhistleDataBlock;
 
-public class RWEDataBlock extends AbstractWhistleDataBlock implements GroupedDataSource {
+public class RWEDataBlock extends AbstractWhistleDataBlock<RWEDataUnit> implements GroupedDataSource {
 	
 	private double[] rwFreqRange = {50., 250.};
 	private RWEControl rweControl;
 	private RWEProcess rweProcess;
 	private RWDataSelCreator dataSelCreator;
 	
+	private RWSpeciesManager rwSpeciesManager;
+
 	public RWEDataBlock(RWEControl rweControl, String dataName,
 			RWEProcess rweProcess, int channelMap) {
 		super(RWEDataUnit.class, dataName, rweProcess, channelMap);
@@ -53,4 +57,12 @@ public class RWEDataBlock extends AbstractWhistleDataBlock implements GroupedDat
 		return dataSelCreator;
 	}
 
+	@Override
+	public DataBlockSpeciesManager<RWEDataUnit> getDatablockSpeciesManager() {
+		if (rwSpeciesManager == null) {
+			rwSpeciesManager = new RWSpeciesManager(this);
+		}
+		return rwSpeciesManager;
+	}
+
 }

src/RightWhaleEdgeDetector/species/RWSpeciesManager.java

@@ -0,0 +1,26 @@
+package RightWhaleEdgeDetector.species;
+
+import PamguardMVC.PamDataBlock;
+import RightWhaleEdgeDetector.RWEDataUnit;
+import tethys.species.DataBlockSpeciesManager;
+import tethys.species.DataBlockSpeciesTypes;
+
+public class RWSpeciesManager extends DataBlockSpeciesManager<RWEDataUnit> {
+	
+	private RWSpeciesTypes rwSpeciesTypes = new RWSpeciesTypes();
+
+	public RWSpeciesManager(PamDataBlock<RWEDataUnit> dataBlock) {
+		super(dataBlock);
+	}
+
+	@Override
+	public DataBlockSpeciesTypes getSpeciesTypes() {
+		return rwSpeciesTypes;
+	}
+
+	@Override
+	public String getSpeciesString(RWEDataUnit dataUnit) {
+		return RWSpeciesTypes.onlyType;
+	}
+
+}

src/RightWhaleEdgeDetector/species/RWSpeciesTypes.java

@@ -0,0 +1,15 @@
+package RightWhaleEdgeDetector.species;
+
+import tethys.species.DataBlockSpeciesTypes;
+
+public class RWSpeciesTypes extends DataBlockSpeciesTypes {
+	
+	public static final String onlyType = "Up call";
+	
+	private static final int glacialis = 180536;
+
+	public RWSpeciesTypes() {
+		super(glacialis, onlyType);
+	}
+
+}

src/clickDetector/ClickClassifiers/ClickBlockSpeciesManager.java

@@ -5,6 +5,8 @@ import clickDetector.ClickDataBlock;
 import clickDetector.ClickDetection;
 import tethys.species.DataBlockSpeciesManager;
 import tethys.species.DataBlockSpeciesTypes;
+import tethys.species.ITISTypes;
+import tethys.species.SpeciesMapItem;
 
 public class ClickBlockSpeciesManager extends DataBlockSpeciesManager<ClickDetection> {
 
@@ -13,6 +15,8 @@ public class ClickBlockSpeciesManager extends DataBlockSpeciesManager<ClickDetec
 	public ClickBlockSpeciesManager(ClickControl clickControl, ClickDataBlock clickDataBlock) {
 		super(clickDataBlock);
 		this.clickControl = clickControl;
+		setDefaultDefaultSpecies(new SpeciesMapItem(ITISTypes.UNKNOWN, "Unknown", "Unknown"));
+		setDefaultName("Unknown");
 	}
 
 	@Override
@@ -22,14 +26,27 @@ public class ClickBlockSpeciesManager extends DataBlockSpeciesManager<ClickDetec
 			return null;
 		}
 		String[] speciesList = masterManager.getSpeciesList();
+		// add the default
+		String[] fullList = new String[speciesList.length+1];
+		fullList[0] = getDefaultName();
+		for (int i = 0; i < speciesList.length; i++) {
+			fullList[i+1] = speciesList[i];
+		}
 		
-		return new DataBlockSpeciesTypes(speciesList);
+		return new DataBlockSpeciesTypes("Click", fullList);
 	}
 
 	@Override
 	public String getSpeciesString(ClickDetection dataUnit) {
-		// TODO Auto-generated method stub
-		return null;
+		ClickTypeMasterManager masterManager = clickControl.getClickTypeMasterManager();
+		if (masterManager == null) {
+			return null;
+		}
+		int listIndex = masterManager.codeToListIndex(dataUnit.getClickType());
+		if (listIndex < 0) {
+			return null;
+		}
+		return masterManager.getSpeciesList()[listIndex];
 	}
 
 }

src/tethys/TethysControl.java

@@ -54,6 +54,7 @@ import tethys.species.ITISFunctions;
 import tethys.swing.ProjectDeploymentsDialog;
 import tethys.swing.TethysTabPanel;
 import tethys.swing.XMLStringView;
+import tethys.swing.documents.TethysDocumentsFrame;
 
 /**
  * Quick play with a simple system for outputting data to Tethys. At it's start
@@ -284,8 +285,23 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 	 * open client in the default web browser
 	 */
 	public void openTethysCollection(String collectionName) {
+		if (collectionName == null) {
+			return;
+		}
+		if (getTethysExportParams().listDocsInPamguard && collectionName.equals("Client") == false) {
+			openCollectionInPAMGuard(collectionName);
+		}
+		else {
+			openCollectionInBrowser(collectionName);
+		}
+	}
+	public void openCollectionInPAMGuard(String collectionName) {
+		TethysDocumentsFrame.showTable(getGuiFrame(), this, collectionName);
+	}
+	
+	public void openCollectionInBrowser(String collectionName) {
 		String urlString = tethysExportParams.getFullServerName() + "/" + collectionName;
-		System.out.println("Opening url " + urlString);
+//		System.out.println("Opening url " + urlString);
 		URL url = null;
 		try {
 			url = new URL(urlString);

src/tethys/TethysTimeFuncs.java

@@ -67,6 +67,7 @@ public class TethysTimeFuncs {
 		try {
 			date = df.parse(gregorianString);
 		} catch (ParseException e) {
+			System.out.printf("Unparsable date string:\"%s\"", gregorianString);
 			e.printStackTrace();
 			return null;
 		}

src/tethys/dbxml/DBXMLConnect.java

@@ -44,7 +44,6 @@ public class DBXMLConnect {
 		this.tethysControl = tethysControl;
 
 		checkTempFolder();
-
 	}
 
 	/**
@@ -63,6 +62,7 @@ public class DBXMLConnect {
 		return true;
 	}
 	
+
 	/**
 	 * Get the client. The client will only be recreated if the url changes
 	 * @return Jersy client

src/tethys/dbxml/DBXMLQueries.java

@@ -145,6 +145,77 @@ public class DBXMLQueries {
 		return new DBQueryResult(System.currentTimeMillis()-t1, queryResult, schemaPlan);
 	}
 	
+	/**
+	 * Check whether or not to strip of the s of one of the collection names. 
+	 * This is caused by some daft thing whereby the Deployments colleciton is called Deployments
+	 * byt the Detections collection is called Detection
+	 * @param collection
+	 * @return
+	 */
+	public String checkCollectionPlural(String collection) {
+		switch (collection) {
+		case "Deployments":
+			return "Deployment";
+		case "Localizations":
+			return "Localize";
+		case "Calibrations":
+			return "Calibration";
+		case "SpeciesAbbreviations":
+			return "SpeciesAbbreviations";
+		}
+		return collection;
+	}
+	
+	/**
+	 * Get a list of all documents in a collection. 
+	 * @param collection
+	 * @return list of all documents in a collection, or null if no collection. 
+	 */
+	public ArrayList<String> getCollectionDocumentList(String collection) {
+		if (collection == null) {
+			return null;
+		}
+		collection = checkCollectionPlural(collection);
+//		if (collection.endsWith("s")) {
+//			collection = collection.substring(0, collection.length()-1);
+//		}
+		String baseQuery = "{\"return\":[\"COLLECTIONNAME/Id\"],\"select\":[],\"enclose\":1}";
+		baseQuery = baseQuery.replace("COLLECTIONNAME", collection);
+		String tagName = "Id";
+		
+		if (collection.equals("SpeciesAbbreviations")) {
+			baseQuery = "{\"return\":[\"Abbreviations/Name\"],\"select\":[],\"enclose\":1}";
+			tagName = "Name";
+		}
+		
+		DBQueryResult result;
+		try {
+			result = executeQuery(baseQuery);
+		} catch (TethysQueryException e) {
+			System.out.println("Error with query: " + baseQuery);
+			tethysControl.showException(e);
+			return null;
+		}
+
+		if (result == null || result.queryResult == null) {
+			return null;
+		}
+		Document doc = convertStringToXMLDocument(result.queryResult);
+		if (doc == null) {
+			return null;
+		}
+		NodeList returns = doc.getElementsByTagName(tagName);
+		ArrayList<String> docIds = new ArrayList<>();
+		int n = returns.getLength();
+		for (int i = 0; i < n; i++) {
+			Node aNode = returns.item(i);
+			String docId = aNode.getTextContent();
+			docIds.add(docId);
+		}
+		
+		return docIds;
+	}
+
 	public ArrayList<String> getProjectNames() {
 
 		String projectQuery = "{\"return\":[\"Deployment/Project\"],\"select\":[],\"enclose\":1}";
@@ -644,10 +715,13 @@ public class DBXMLQueries {
 			if (nodeList == null || nodeList.getLength() == 0) {
 				return null;
 			}
-			Node firstNode = nodeList.item(0);
-			if (firstNode instanceof Element) {
-				root = (Element) firstNode;
-				break;
+			int count = nodeList.getLength();
+			for (int i = 0; i < count; i++) {
+				Node firstNode = nodeList.item(i);
+				if (firstNode instanceof Element) {
+					root = (Element) firstNode;
+					break;
+				}
 			}
 		}
 		return root.getTextContent();

src/tethys/deployment/DeploymentHandler.java

@@ -455,8 +455,11 @@ public class DeploymentHandler implements TethysStateObserver {
 	public long getDeploymentOverlap(PDeployment aDeployment, RecordingPeriod aPeriod) {
 		long start = aPeriod.getRecordStart(); // recording period. 
 		long stop = aPeriod.getRecordStop();
-		long depStart = aDeployment.getAudioStart();
-		long depStop = aDeployment.getAudioEnd();
+		Long depStart = aDeployment.getAudioStart();
+		Long depStop = aDeployment.getAudioEnd();
+		if (depStart == null || depStop == null) {
+			return -1;
+		}
 		long overlap = (Math.min(stop, depStop)-Math.max(start, depStart));
 		return overlap;
 	}

src/tethys/niluswraps/PDeployment.java

@@ -23,7 +23,7 @@ public class PDeployment {
 	
 	public Long getAudioStart() {
 		DeploymentRecoveryDetails detail = deployment.getDeploymentDetails();
-		if (detail == null) {
+		if (detail == null || detail.getAudioTimeStamp() == null) {
 			return null;
 		}
 		return TethysTimeFuncs.millisFromGregorianXML(detail.getAudioTimeStamp());
@@ -31,7 +31,7 @@ public class PDeployment {
 	
 	public Long getAudioEnd() {
 		DeploymentRecoveryDetails detail = deployment.getRecoveryDetails();
-		if (detail == null) {
+		if (detail == null || detail.getAudioTimeStamp() == null) {
 			return null;
 		}
 		return TethysTimeFuncs.millisFromGregorianXML(detail.getAudioTimeStamp());
@@ -52,7 +52,13 @@ public class PDeployment {
 	}
 
 	public String getShortDescription() {
-		return String.format("%s %s", deployment.getId(), PamCalendar.formatDBDate(getAudioStart()));
+		Long audioStart = getAudioStart();
+		if (audioStart == null) {
+			return String.format("%s %s", deployment.getId(), "unknown start");
+		}
+		else {
+			return String.format("%s %s", deployment.getId(), PamCalendar.formatDBDate(getAudioStart()));
+		}
 	}
 	
 	

src/tethys/output/TethysExportParams.java

@@ -38,6 +38,8 @@ public class TethysExportParams implements Serializable, Cloneable{
 	 */
 	private String datasetName;
 
+	public boolean listDocsInPamguard;
+
 	/**
 	 * @return the datasetName
 	 */

src/tethys/species/DataBlockSpeciesManager.java

@@ -16,6 +16,10 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
 	
 	private PamDataBlock<T> dataBlock;
 	
+	private String defaultName = null;
+	
+	private SpeciesMapItem defaultDefaultSpecies = null;
+
 	public abstract DataBlockSpeciesTypes getSpeciesTypes();
 	
 	public abstract String getSpeciesString(T dataUnit);
@@ -29,7 +33,7 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
 	public SpeciesMapItem getSpeciesItem(T dataUnit) {
 		String speciesString = getSpeciesString(dataUnit);
 		if (speciesString == null) {
-			return null;
+			return getDefaultDefaultSpecies();
 		}
 		DataBlockSpeciesMap speciesMap = getDatablockSpeciesMap();
 		if (speciesMap == null) {
@@ -41,10 +45,18 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
 	public DataBlockSpeciesMap getDatablockSpeciesMap() {
 		if (datablockSpeciesMap == null) {
 			datablockSpeciesMap = new DataBlockSpeciesMap();
+			checkMapDefault();
 		}
 		return datablockSpeciesMap;
 	}
 
+	private void checkMapDefault() {
+		SpeciesMapItem defaultItem = datablockSpeciesMap.getItem(getDefaultName());
+		if (defaultItem == null) {
+			datablockSpeciesMap.putItem(getDefaultName(), getDefaultDefaultSpecies());
+		}
+	}
+
 	public void setDatablockSpeciesMap(DataBlockSpeciesMap datablockSpeciesMap) {
 		this.datablockSpeciesMap = datablockSpeciesMap;
 	}
@@ -59,4 +71,32 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
 	public PamDataBlock<T> getDataBlock() {
 		return dataBlock;
 	}
+
+	/**
+	 * @return the defaultSpecies
+	 */
+	public SpeciesMapItem getDefaultDefaultSpecies() {
+		return defaultDefaultSpecies;
+	}
+
+	/**
+	 * @param defaultSpecies the defaultSpecies to set
+	 */
+	public void setDefaultDefaultSpecies(SpeciesMapItem defaultDefaultSpecies) {
+		this.defaultDefaultSpecies = defaultDefaultSpecies;
+	}
+
+	/**
+	 * @return the defaultName
+	 */
+	public String getDefaultName() {
+		return defaultName;
+	}
+
+	/**
+	 * @param defaultName the defaultName to set
+	 */
+	public void setDefaultName(String defaultName) {
+		this.defaultName = defaultName;
+	}
 }

src/tethys/species/DataBlockSpeciesTypes.java

@@ -12,15 +12,44 @@ import java.util.ArrayList;
 public class DataBlockSpeciesTypes {
 
 	/**
-	 * List of species names / codes associated with this data block. 
+	 * List of species names / codes associated with this data block. These can be translated, 
+	 * via a HashMap to more detailed objects which include an ITIS code. 
 	 */
 	private ArrayList<String> speciesNames;
 	
+	/**
+	 * Probably only to be used when there are no defined names, but helpful if it's set. 
+	 */
+	private int itisDefault = ITISTypes.UNKNOWN;
+	
+	/**
+	 * A default sound type, which can be used for all 'species', but can get 
+	 * overridden in other scenarios. e.g. 'Click', 'Whistle'
+	 */
+	private String defaultType;
+	
+	/**
+	 * @param defaultType
+	 */
+	public DataBlockSpeciesTypes(String defaultType) {
+		this.defaultType = defaultType;
+	}
+
+	/**
+	 * @param itisDefault
+	 * @param defaultType
+	 */
+	public DataBlockSpeciesTypes(int itisDefault, String defaultType) {
+		this.itisDefault = itisDefault;
+		this.defaultType = defaultType;
+	}
+
 	/**
 	 * constructor to use with a array of String names. 
 	 * @param speciesList
 	 */
-	public DataBlockSpeciesTypes(String[] speciesList) {
+	public DataBlockSpeciesTypes(String defaultType, String[] speciesList) {
+		this.defaultType = defaultType;
 		if (speciesList == null) {
 			speciesNames = new ArrayList<>();
 		}
@@ -39,5 +68,40 @@ public class DataBlockSpeciesTypes {
 		return speciesNames;
 	}
 
+	/**
+	 * @return the itisDefault
+	 */
+	public int getItisDefault() {
+		return itisDefault;
+	}
+
+	/**
+	 * @param itisDefault the itisDefault to set
+	 */
+	public void setItisDefault(int itisDefault) {
+		this.itisDefault = itisDefault;
+	}
+
+	/**
+	 * @return the defaultType
+	 */
+	public String getDefaultType() {
+		return defaultType;
+	}
+
+	/**
+	 * @param defaultType the defaultType to set
+	 */
+	public void setDefaultType(String defaultType) {
+		this.defaultType = defaultType;
+	}
+
+	/**
+	 * @param speciesNames the speciesNames to set
+	 */
+	public void setSpeciesNames(ArrayList<String> speciesNames) {
+		this.speciesNames = speciesNames;
+	}
+
 	
 }

src/tethys/species/ITISTypes.java

@@ -0,0 +1,22 @@
+package tethys.species;
+
+/**
+ * Some MR defined ITIS codes for non animal sounds. 
+ * @author dg50
+ *
+ */
+public class ITISTypes {
+
+	public static final int UNKNOWN = 0;
+	public static final int ANTHROPOGENIC = -10;
+	
+	public static final String getName(int code) {
+		switch (code) {
+		case UNKNOWN:
+			return "Unknown";
+		case ANTHROPOGENIC:
+			return "Anthropogenic";
+		}
+		return null;
+	}
+}

src/tethys/species/SpeciesTest.java

@@ -1,5 +1,15 @@
 package tethys.species;
 
+import java.io.StringReader;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.xml.sax.InputSource;
+
+import PamController.settings.output.xml.PamguardXMLWriter;
 import dbxml.JerseyClient;
 import dbxml.Queries;
 import tethys.dbxml.DBQueryResult;
@@ -66,26 +76,62 @@ public class SpeciesTest {
 	private void runXQuery() {
 		System.out.println("Running runXQuery()");
 		String queryBase = "count(collection(\"Detections\")/Detections[Id=\"ReplaceDocumentId\"]/OnEffort/Detection)";
-		String xQ = "collection(\"ITIS_ranks\")/ty:ranks/ty:rank[dbxml:contains(ty:completename, \"Physeter\")]";
+//		String xQ = "collection(\"ITIS_ranks\")/ty:ranks/ty:rank[dbxml:contains(ty:completename, \"Physeter\")]";
+		
+//		String xQ = "<Result xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"> {\r\n"
+//				+ "  for $Deployment0 in collection(\"Deployments\")/Deployment[Project = \"BM\"]\r\n"
+//				+ "  return\r\n"
+//				+ "    <Deployment>{\r\n"
+//				+ "      $Deployment0/Id\r\n"
+//				+ "    }</Deployment>\r\n"
+//				+ "} </Result>";
+
+		String xQ = "<Result xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"> {\r\n"
+				+ "  for $rank0 in collection(\"ITIS_ranks\")/rank[tsn = \"180488\"]\r\n"
+				+ "  return\r\n"
+				+ "    <rank>{\r\n"
+				+ "      $rank0/completename\r\n"
+				+ "    }</rank>\r\n"
+				+ "} </Result>";
+		
 
 		JerseyClient jerseyClient = new JerseyClient(uri);
 		Queries queries = new Queries(jerseyClient);
 		
-		String result = null;
+		String queryResult = null;
 		try {
-			 result = queries.QueryTethys(xQ);
+			 queryResult = queries.QueryTethys(xQ);
 		} catch (Exception e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}
-		System.out.println(result);
+		//API to obtain DOM Document instance
+		DocumentBuilder builder = null;
+		Document doc = null;
+		DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+		try {
+			//Create DocumentBuilder with default configuration
+			builder = factory.newDocumentBuilder();
+
+			//Parse the content to Document object
+			doc = builder.parse(new InputSource(new StringReader(queryResult)));
+		} catch (Exception e) {
+//			e.printStackTrace();
+			System.out.println(queryResult);
+		}
+//		PAMGuardXMLPreview xmlPreview = new PAMGuardXMLPreview(null, "returned", qResult.queryResult)
+		PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
+		String fDoc = pamXMLWriter.getAsString(doc, true);
+		System.out.println(fDoc);
+//		System.out.println(queryResult);
 		
 	}
 	private void runJson() {
 //		String jQ = "{\"return\":[\"Deployment\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Deployment/Project\",\"DCLDE2022\"],\"optype\":\"binary\"}],\"enclose\":1}";
-		String jQ =  "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"=\",\"operands\":[\"ranks/rank/tsn\",\"180488\"],\"optype\":\"binary\"}],\"enclose\":1}";
-//		String jQ = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"=\",\"operands\":[\"ranks/rank/completename\",\"Mesoplodon\"],\"optype\":\"binary\"}],\"enclose\":1}";
-//		String jQ = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"dbxml:contains\",\"operands\":[\"ranks/rank/completename\",\"Mesoplodon\"],\"optype\":\"function\"}],\"enclose\":1}";
+//		String jQ = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"=\",\"operands\":[\"ranks/rank/tsn\",\"180488\"],\"optype\":\"binary\"}],\"enclose\":1}";
+		String jQ = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"=\",\"operands\":[\"ranks/rank/tsn\",\"180488\"],\"optype\":\"binary\"}],\"enclose\":1}";
+//		String jQ = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"=\",\"operands\":[\"ranks/rank/completename\",\"Physeter macrocephalus\"],\"optype\":\"binary\"}],\"enclose\":1}";
+//		String jQ = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"dbxml:contains\",\"operands\":[\"ranks/rank/completename\",\"Sperm\"],\"optype\":\"function\"}],\"enclose\":1}";
 
 		System.out.println(jQ);
 
@@ -103,7 +149,26 @@ public class SpeciesTest {
 		}
 		long t2 = System.nanoTime();
 		System.out.printf("Query time was %3.1fms\n" , (double) (t2-t1)/1e6);
-		System.out.println(queryResult);
+		DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+
+		//API to obtain DOM Document instance
+		DocumentBuilder builder = null;
+		Document doc = null;
+		try {
+			//Create DocumentBuilder with default configuration
+			builder = factory.newDocumentBuilder();
+
+			//Parse the content to Document object
+			doc = builder.parse(new InputSource(new StringReader(queryResult)));
+		} catch (Exception e) {
+//			e.printStackTrace();
+			System.out.println(queryResult);
+		}
+//		PAMGuardXMLPreview xmlPreview = new PAMGuardXMLPreview(null, "returned", qResult.queryResult)
+		PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
+		String fDoc = pamXMLWriter.getAsString(doc, true);
+		System.out.println(fDoc);
+//		System.out.println(queryResult);
 		
 	}
 

src/tethys/species/swing/DataBlockSpeciesDialog.java

@@ -25,13 +25,16 @@ public class DataBlockSpeciesDialog extends PamDialog {
 		speciesPanel = new DataBlockSpeciesPanel(dataBlock);
 		mainPanel.add(BorderLayout.CENTER, speciesPanel.getDialogComponent());
 		JButton itisButton = new JButton("Go to ITIS web site");
+		itisButton.setToolTipText("Go to ITIS website to search for species codes");
 		itisButton.addActionListener(new ActionListener() {
 			@Override
 			public void actionPerformed(ActionEvent e) {
 				gotoITIS();
 			}
 		});
-		mainPanel.add(BorderLayout.NORTH, itisButton);
+		JPanel nPanel = new JPanel(new BorderLayout());
+		nPanel.add(BorderLayout.EAST, itisButton);
+		mainPanel.add(BorderLayout.NORTH, nPanel);
 		setDialogComponent(mainPanel);
 	}
 	

src/tethys/species/swing/SpeciesSubPanel.java

@@ -124,7 +124,7 @@ public class SpeciesSubPanel {
 			commonName.setText(null);
 			return;
 		}
-		pamguardName.setText(speciesMapItem.getPamguardName());
+		pamguardName.setText("\"" + speciesMapItem.getPamguardName() + "\"");
 		itisCode.setText(String.format("%d", speciesMapItem.getItisCode()));
 		callType.setText(speciesMapItem.getCallType());
 		latinName.setText(speciesMapItem.getLatinName());

src/tethys/swing/FancyClientButton.java

@@ -8,9 +8,11 @@ import java.awt.Insets;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 
+import javax.swing.AbstractButton;
 import javax.swing.BoxLayout;
 import javax.swing.ImageIcon;
 import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
@@ -31,11 +33,14 @@ public class FancyClientButton extends JPanel {
 	private JButton dropButton;
 	private JPopupMenu collectionsMenu;
 	private TethysControl tethysControl;
+	private JCheckBoxMenuItem showBrowser;
+	private AbstractButton showPAMGuard;
+
 
 	public FancyClientButton(TethysControl tethysControl) {
 		this.tethysControl = tethysControl;
 		setLayout(new GridBagLayout());
-//		setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
+		//		setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
 		GridBagConstraints c = new GridBagConstraints();
 		c.ipadx = c.ipady = 0;
 		c.insets = new Insets(0,0,0,0);
@@ -44,8 +49,8 @@ public class FancyClientButton extends JPanel {
 		clientButton.setToolTipText("Open Tethys web client in default browser");
 		ImageIcon arrowDown= null;
 		try {
-		arrowDown = new ImageIcon(ClassLoader
-				.getSystemResource("Resources/SidePanelShowH.png"));
+			arrowDown = new ImageIcon(ClassLoader
+					.getSystemResource("Resources/SidePanelShowH.png"));
 		}
 		catch (Exception e) {
 		}
@@ -68,6 +73,32 @@ public class FancyClientButton extends JPanel {
 
 		String[] collections = DBXMLConnect.collections;
 		collectionsMenu = new JPopupMenu();
+		boolean isP = tethysControl.getTethysExportParams().listDocsInPamguard;
+		showBrowser = new JCheckBoxMenuItem("Show in Browser", isP == false);
+		showBrowser.setEnabled(isP);
+		showBrowser.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				tethysControl.getTethysExportParams().listDocsInPamguard = false;
+				enableItems();
+			}
+		});
+		showBrowser.setToolTipText("Show collection in default Web Browser");
+		collectionsMenu.add(showBrowser);
+		showPAMGuard = new JCheckBoxMenuItem("Show in PAMGuard", isP);
+		showPAMGuard.setEnabled(isP == false);
+		showPAMGuard.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				tethysControl.getTethysExportParams().listDocsInPamguard = true;
+				enableItems();
+			}
+		});
+		showPAMGuard.setToolTipText("Show collection in PAMGuard window");
+		collectionsMenu.add(showPAMGuard);
+		
+		collectionsMenu.addSeparator();
+		
 		for (int i = 0; i < collections.length; i++) {
 			JMenuItem menuItem = new JMenuItem(collections[i]);
 			menuItem.addActionListener(new OpenCollection(collections[i]));
@@ -80,6 +111,15 @@ public class FancyClientButton extends JPanel {
 				collectionsMenu.show(dropButton, 0, 0);
 			}
 		});
+		enableItems();
+	}
+
+	protected void enableItems() {
+		boolean isP = tethysControl.getTethysExportParams().listDocsInPamguard;
+		showBrowser.setSelected(!isP);
+		showBrowser.setEnabled(true);
+		showPAMGuard.setSelected(isP);
+		showPAMGuard.setEnabled(true);	
 	}
 
 	public void addActionListener(ActionListener actionListener) {

src/tethys/swing/documents/TethysDocumentTable.java

@@ -0,0 +1,196 @@
+package tethys.swing.documents;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.ArrayList;
+import java.util.Collections;
+
+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.table.AbstractTableModel;
+
+import PamView.dialog.PamDialogPanel;
+import PamView.tables.SwingTableColumnWidths;
+import tethys.TethysControl;
+
+/**
+ * Table view of a collection of Tethys documents. 
+ * @author dg50
+ *
+ */
+public class TethysDocumentTable implements PamDialogPanel {
+
+	private TethysControl tethysControl;
+	
+	private String collectionName;
+	
+	private JTable mainTable;
+	
+	private TableModel tableModel;
+	
+	private ArrayList<String> documentNames;
+	
+	private JPanel mainPanel;
+	
+	private JScrollPane scrollPane;
+
+	/**
+	 * @param tethysControl
+	 * @param collectionName
+	 */
+	public TethysDocumentTable(TethysControl tethysControl, String collectionName) {
+		this.tethysControl = tethysControl;
+		mainPanel = new JPanel(new BorderLayout());
+		tableModel = new TableModel();
+		mainTable = new JTable(tableModel);
+		scrollPane = new JScrollPane(mainTable);
+		mainPanel.add(BorderLayout.CENTER, scrollPane);
+		new SwingTableColumnWidths(tethysControl.getUnitName()+"TethysDocumentsTable", mainTable);
+		this.setCollectionName(collectionName);
+		mainTable.addMouseListener(new TableMouse());		
+	}
+	
+	public void updateTableData() {
+		documentNames = tethysControl.getDbxmlQueries().getCollectionDocumentList(collectionName);
+		if (documentNames != null) {
+			Collections.sort(documentNames);
+		}
+		tableModel.fireTableDataChanged();
+	}
+	
+	private class TableMouse extends MouseAdapter {
+
+		@Override
+		public void mousePressed(MouseEvent e) {
+			if (e.isPopupTrigger()) {
+				showPopupMenu(e);
+			}
+		}
+
+		@Override
+		public void mouseReleased(MouseEvent e) {
+			if (e.isPopupTrigger()) {
+				showPopupMenu(e);
+			}
+		}
+		
+	}
+
+	public void showPopupMenu(MouseEvent e) {
+		if (documentNames == null) {
+			return;
+		}
+		int row = mainTable.getSelectedRow();
+		if (row < 0|| row >= documentNames.size()) {
+			return;
+		}
+		String docName = documentNames.get(row);
+		JPopupMenu popMenu = new JPopupMenu();
+		JMenuItem menuItem = new JMenuItem("Show document " + docName);
+		menuItem.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				showDocument(docName);
+			}
+		});
+		popMenu.add(menuItem);
+		menuItem = new JMenuItem("Delete document " + docName);
+		menuItem.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				deleteDocument(docName);
+			}
+		});
+		popMenu.add(menuItem);
+		
+		popMenu.show(e.getComponent(), e.getX(), e.getY());
+	}
+	
+	private void showDocument(String docName) {
+		tethysControl.displayDocument(collectionName, docName);
+	}
+
+	private void deleteDocument(String docName) {
+		// TODO Auto-generated method stub
+		
+	}
+	
+	private class TableModel extends AbstractTableModel {
+		
+		private String[] columnNames = {"", "Document Id/Name"};
+
+		@Override
+		public int getRowCount() {
+			if (documentNames == null) {
+				return 0;
+			}
+			return documentNames.size();
+		}
+
+		@Override
+		public int getColumnCount() {
+			return columnNames.length;
+		}
+
+		@Override
+		public Object getValueAt(int rowIndex, int columnIndex) {
+			if (documentNames == null) {
+				return null;
+			}
+			switch (columnIndex) {
+			case 0:
+				return rowIndex+1;
+			case 1:
+				return documentNames.get(rowIndex);
+			}
+			return null;
+		}
+
+		@Override
+		public String getColumnName(int column) {
+			return columnNames[column];
+		}
+		
+	}
+
+
+
+	@Override
+	public JComponent getDialogComponent() {
+		return mainPanel;
+	}
+
+	@Override
+	public void setParams() {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public boolean getParams() {
+		// TODO Auto-generated method stub
+		return false;
+	}
+
+	/**
+	 * @return the collectionName
+	 */
+	public String getCollectionName() {
+		return collectionName;
+	}
+
+	/**
+	 * @param collectionName the collectionName to set
+	 */
+	public void setCollectionName(String collectionName) {
+		this.collectionName = collectionName;
+		updateTableData();
+	}
+}

src/tethys/swing/documents/TethysDocumentsFrame.java

@@ -0,0 +1,49 @@
+package tethys.swing.documents;
+
+import java.awt.Window;
+
+import PamView.dialog.PamDialog;
+import tethys.TethysControl;
+
+public class TethysDocumentsFrame extends PamDialog {
+	
+	private static final long serialVersionUID = 1L;
+
+	private static TethysDocumentsFrame singleInstance;
+	
+	private TethysDocumentTable documentsTable;
+
+	private TethysDocumentsFrame(Window parentFrame,TethysControl tethysControl) {
+		super(parentFrame, "Documents", false);
+		documentsTable = new TethysDocumentTable(tethysControl, null);
+		setDialogComponent(documentsTable.getDialogComponent());
+		setModalityType(ModalityType.MODELESS);
+		setResizable(true);
+		getOkButton().setVisible(false);
+		getCancelButton().setText("Close");
+	}
+	
+	public static void showTable(Window parentFrame, TethysControl tethysControl, String collectionName) {
+		if (singleInstance == null) {
+			singleInstance = new TethysDocumentsFrame(parentFrame, tethysControl);
+		}
+		singleInstance.documentsTable.setCollectionName(collectionName);
+		singleInstance.setTitle(collectionName + " Documents");
+		singleInstance.setVisible(true);
+	}
+	
+
+	@Override
+	public boolean getParams() {
+		return true;
+	}
+
+	@Override
+	public void cancelButtonPressed() {
+	}
+
+	@Override
+	public void restoreDefaultSettings() {
+	}
+
+}

src/tethys/swing/export/DescriptionTypePanel.java

@@ -1,15 +1,21 @@
 package tethys.swing.export;
 
+import java.awt.Container;
 import java.awt.Dimension;
+import java.awt.Frame;
 import java.awt.Label;
+import java.awt.Window;
 
 import javax.swing.BoxLayout;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
+import javax.swing.JRootPane;
 import javax.swing.JScrollPane;
 import javax.swing.JTextArea;
+import javax.swing.SwingUtilities;
 import javax.swing.border.TitledBorder;
 
+import PamView.PamGui;
 import PamView.dialog.PamDialog;
 import nilus.DescriptionType;
 import tethys.niluswraps.PDescriptionType;
@@ -75,14 +81,15 @@ public class DescriptionTypePanel {
 	}
 	
 	public boolean getParams(PDescriptionType description) {
+		Window f = PamGui.findComponentWindow(mainPanel);
 		if (checkField(requireObjective, tObjectives) == false) {
-			return PamDialog.showWarning(null, "Objectives", "The objectives field must be competed");
+			return PamDialog.showWarning(f, "Objectives", "The objectives field must be completed");
 		}
 		if (checkField(requireAbstract, tAbstract) == false) {
-			return PamDialog.showWarning(null, "Abstract", "The abstract field must be competed");
+			return PamDialog.showWarning(f, "Abstract", "The abstract field must be completed");
 		}
 		if (checkField(requireMethod, tMethod) == false) {
-			return PamDialog.showWarning(null, "Method", "The method field must be competed");
+			return PamDialog.showWarning(f, "Method", "The method field must be completed");
 		}
 
 		description.setObjectives(tObjectives.getText());

src/whistlesAndMoans/ConnectedRegionDataBlock.java

@@ -2,6 +2,7 @@ package whistlesAndMoans;
 
 import whistlesAndMoans.alarm.WMAlarmCounterProvider;
 import whistlesAndMoans.dataSelector.WMDDataSelectCreator;
+import whistlesAndMoans.species.WhistleSpeciesManager;
 import whistlesAndMoans.toad.WSLToadCalculator;
 import PamView.GroupedDataSource;
 import PamView.GroupedSourceParameters;
@@ -10,14 +11,16 @@ import PamguardMVC.dataSelector.DataSelectorCreator;
 import PamguardMVC.toad.TOADCalculator;
 import alarm.AlarmCounterProvider;
 import alarm.AlarmDataSource;
+import tethys.species.DataBlockSpeciesManager;
 
-public class ConnectedRegionDataBlock extends AbstractWhistleDataBlock implements AlarmDataSource, GroupedDataSource, FFTDataHolderBlock  {
+public class ConnectedRegionDataBlock extends AbstractWhistleDataBlock<ConnectedRegionDataUnit> implements AlarmDataSource, GroupedDataSource, FFTDataHolderBlock  {
 
 	private WhistleToneConnectProcess parentProcess;
 	private WhistleMoanControl whistleMoanControl;
 	private WMAlarmCounterProvider wmAlarmCounterProvider;
 	private WMDDataSelectCreator dataSelectCreator;
 	private WSLToadCalculator wslToadCalculator;
+	private WhistleSpeciesManager whistleSpeciesManager;
 		
 	public ConnectedRegionDataBlock(String dataName,
 			WhistleMoanControl whistleMoanControl, WhistleToneConnectProcess parentProcess, int channelMap) {
@@ -86,6 +89,14 @@ public class ConnectedRegionDataBlock extends AbstractWhistleDataBlock implement
 		return fftParams;
 	}
 
+	@Override
+	public DataBlockSpeciesManager<ConnectedRegionDataUnit> getDatablockSpeciesManager() {
+		if (whistleSpeciesManager == null) {
+			whistleSpeciesManager = new WhistleSpeciesManager(this);
+		}
+		return whistleSpeciesManager;
+	}
+
 	
 
 	

src/whistlesAndMoans/species/WhistleSpeciesManager.java

@@ -0,0 +1,34 @@
+package whistlesAndMoans.species;
+
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.PamDataUnit;
+import tethys.species.DataBlockSpeciesManager;
+import tethys.species.DataBlockSpeciesTypes;
+import tethys.species.ITISTypes;
+import tethys.species.SpeciesMapItem;
+import whistlesAndMoans.ConnectedRegionDataUnit;
+
+public class WhistleSpeciesManager extends DataBlockSpeciesManager<ConnectedRegionDataUnit> {
+	
+	private String defaultName = "Tonal";
+	
+
+	public WhistleSpeciesManager(PamDataBlock<ConnectedRegionDataUnit> dataBlock) {
+		super(dataBlock);
+		setDefaultDefaultSpecies(new SpeciesMapItem(180404, "Tonal", "Odontocete"));
+	}
+
+	@Override
+	public DataBlockSpeciesTypes getSpeciesTypes() {
+		String spList[] = {"Unknown"};
+
+		DataBlockSpeciesTypes whistleSpeciesTypes = new DataBlockSpeciesTypes("Tonal", spList);
+		return whistleSpeciesTypes;
+	}
+
+	@Override
+	public String getSpeciesString(ConnectedRegionDataUnit dataUnit) {
+		return defaultName;
+	}
+
+}