Changes for Tethys integration

.classpath

@@ -6,7 +6,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jdk-16.0.2">
 		<attributes>
 			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
@@ -17,5 +17,10 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="lib" path="C:/Users/dg50/Tethys/NilusXMLGenerator/target/nilus-1.5.jar">
+		<attributes>
+			<attribute name="javadoc_location" value="jar:file:/C:/Users/dg50/Tethys/NilusXMLGenerator/target/nilus-1.5-javadoc.jar!/"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

pom.xml

@@ -555,8 +555,29 @@
 	    <groupId>com.sun.xml.bind</groupId>
  	   <artifactId>jaxb-impl</artifactId>
     	<version>2.3.2</version>
+	</dependency>-->
+<!-- From NilusXMLGenerator POM at https://bitbucket.org/tethysacousticmetadata/nilusxmlgenerator/src/master/-->
+    <dependency>
+        <groupId>org.eclipse.persistence</groupId>
+        <artifactId>org.eclipse.persistence.moxy</artifactId>
+        <version>2.5.0</version>
     </dependency>
-	 -->
+	<dependency>
+	    <groupId>javax.xml.bind</groupId>
+	    <artifactId>jaxb-api</artifactId>
+	    <version>2.4.0-b180830.0359</version> 
+	</dependency>
+	<dependency>
+	    <groupId>org.glassfish.jaxb</groupId>
+	    <artifactId>jaxb-runtime</artifactId>
+	    <version>2.4.0-b180830.0438</version> 
+	</dependency>
+	<dependency>
+        <groupId>org.glassfish.jaxb</groupId>
+        <artifactId>jaxb-xjc</artifactId>
+        <version>2.4.0-b180830.0438</version>
+    </dependency>
+	 
 	 
 	 <!-- https://mvnrepository.com/artifact/org.jflac/jflac-codec -->
 	<dependency>

src/PamModel/PamModel.java

@@ -44,6 +44,7 @@ import whistlesAndMoans.AbstractWhistleDataUnit;
 import fftManager.FFTDataUnit;
 import fftManager.PamFFTControl;
 import group3dlocaliser.Group3DLocaliserControl;
+import metadata.MetaDataContol;
 import meygenturbine.MeygenTurbine;
 import networkTransfer.receive.BuoyStatusDataUnit;
 import networkTransfer.receive.NetworkReceiver;
@@ -461,6 +462,12 @@ final public class PamModel implements PamModelInterface, PamSettings {
 		mi.setModulesMenuGroup(utilitiesGroup);
 		mi.setMaxNumber(1);
 
+
+		mi = PamModuleInfo.registerControlledUnit(MetaDataContol.class.getName(), MetaDataContol.unitType);
+		mi.setToolTipText("Deployment Meta Data");
+		mi.setModulesMenuGroup(utilitiesGroup);
+		mi.setMaxNumber(1); 
+		
 		if (isViewer) {
 			mi = PamModuleInfo.registerControlledUnit(TethysControl.class.getName(), TethysControl.defaultName);
 			mi.setToolTipText("Interface to Tethys Database");

src/PamModel/parametermanager/PamParameterData.java

@@ -34,6 +34,11 @@ abstract public class PamParameterData {
 	 */
 	private String postTitle;
 	
+	/**
+	 * field length for automatic dialogs. 
+	 */
+	private int fieldLength;
+	
 
 	/**
 	 * @param parentObject
@@ -45,6 +50,21 @@ abstract public class PamParameterData {
 		this.field = field;
 	}
 
+	/**
+	 * @param parentObject
+	 * @param field
+	 * @param shortName
+	 * @param toolTip
+	 * @param fieldLength length of text in automatic dialogs. 
+	 */
+	public PamParameterData(Object parentObject, Field field, String shortName, String toolTip, int fieldLength) {
+		super();
+		this.field = field;
+		this.shortName = shortName;
+		this.toolTip = toolTip;
+		this.fieldLength = fieldLength;
+	}
+
 	/**
 	 * @param parentObject
 	 * @param field
@@ -58,7 +78,6 @@ abstract public class PamParameterData {
 		this.toolTip = toolTip;
 	}
 
-
 	/**
 	 * @param shortName the shortName to set
 	 */
@@ -66,6 +85,20 @@ abstract public class PamParameterData {
 		this.shortName = shortName;
 	}
 	
+	/**
+	 * Set info about a parameter
+	 * @param shortName short name, e.g. to use in a dialog
+	 * @param postTitle post title, e.g. text coming after a data entry field in a dialog
+	 * @param toolTip tool tip to display over the component in a dialog. 
+	 * @param fieldLength length of text in automatic dialogs. 
+	 */
+	public void setInfo(String shortName, String postTitle, String toolTip, int fieldLength) {
+		this.shortName = shortName;
+		this.postTitle = postTitle;
+		this.toolTip = toolTip;
+		this.fieldLength = fieldLength;
+	}
+	
 	/**
 	 * Set info about a parameter
 	 * @param shortName short name, e.g. to use in a dialog
@@ -136,6 +169,9 @@ abstract public class PamParameterData {
 	 * @return a short name for the field, suitable for use in dialogs.
 	 */
 	public String getShortName() {
+		if (shortName == null) {
+			return getFieldName();
+		}
 		return shortName;
 	}
 	
@@ -166,5 +202,19 @@ abstract public class PamParameterData {
 		return String.format("Param %s class %s", getFieldName(), getDataClass());
 	}
 
+	/**
+	 * @return the fieldLength
+	 */
+	public int getFieldLength() {
+		return fieldLength;
+	}
+
+	/**
+	 * @param fieldLength the fieldLength to set
+	 */
+	public void setFieldLength(int fieldLength) {
+		this.fieldLength = fieldLength;
+	}
+
 	
 }

src/PamModel/parametermanager/PamParameterDataGetter.java

@@ -59,9 +59,12 @@ public class PamParameterDataGetter extends PrivatePamParameterData {
 		if (setter == null) {
 			return false;
 		}
+		// need to convert the type
+		Object convObj = convertStringType(data);
 		try {
-			setter.invoke(getParentObject(), data);
-		} catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
+			Object parentObj = getParentObject();
+			setter.invoke(parentObj, convObj);
+		} catch (InvocationTargetException e) {
 			e.printStackTrace();
 			return false;
 		}

src/PamModel/parametermanager/PamParameterSet.java

@@ -286,4 +286,5 @@ public class PamParameterSet {
 	public PamParameterData removeParameterData(String paramName) {
 		return parameterDatas.remove(paramName);
 	}
+
 }

src/PamModel/parametermanager/ParameterSetManager.java

@@ -0,0 +1,73 @@
+package PamModel.parametermanager;
+
+import java.awt.Window;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JMenuItem;
+
+import PamModel.parametermanager.swing.ManagedParameterDialog;
+import generalDatabase.parameterstore.ParameterDatabaseStore;
+
+/**
+ * Just about everything giving overall control of some managed parameters. 
+ * May be a bit too specific on first cut and need to be abstracted. 
+ * Testing on 'Deployment' data. 
+ * @author dg50
+ *
+ * @param <T>
+ */
+public class ParameterSetManager<T extends ManagedParameters> {
+	
+	private T managedParams;
+	private String name;
+
+	public ParameterSetManager(T defaultParams, String name) {
+		setManagedParams(defaultParams);
+		this.name = name;
+//		if (managedParams == null) {
+//			managedParams = new T();
+//		}
+	}
+
+	/**
+	 * @return the managedParams
+	 */
+	public T getManagedParams() {
+		return managedParams;
+	}
+
+	/**
+	 * @param managedParams the managedParams to set
+	 */
+	public void setManagedParams(T managedParams) {
+		this.managedParams = managedParams;
+	}
+	
+	public JMenuItem getMenuItem(Window parent) {
+		if (managedParams == null) {
+			return null;
+		}
+		JMenuItem menuItem = new JMenuItem(name + " ...");
+		menuItem.addActionListener(new ActionListener() {
+			
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				showDialog(parent);
+			}
+		});
+		
+		return menuItem;
+	}
+
+	protected void showDialog(Window parent) {
+		ManagedParameterDialog<T> dialog = new ManagedParameterDialog<T>(parent, name, managedParams);
+		T newParams = dialog.showDialog(parent, name, managedParams);
+
+		if (newParams != null) {
+		ParameterDatabaseStore paramDatabase = new ParameterDatabaseStore("MetaData");
+		paramDatabase.saveParameterSet(newParams);
+		}
+	}
+
+}

src/PamModel/parametermanager/PrivatePamParameterData.java

@@ -1,6 +1,7 @@
 package PamModel.parametermanager;
 
 import java.lang.reflect.Field;
+import java.lang.reflect.Type;
 
 /**
  * Abstract instance of PamParameterDataInterface which implements everything 
@@ -36,9 +37,48 @@ public abstract class PrivatePamParameterData extends PamParameterData {
 		 * This should really be implemented in every concrete class, but no time to do that now. Aim to delete 
 		 * this function here, then go through and implement everywhere ...
 		 */
-		return false;
+//		return false;
+		Object convData = convertStringType(data);
+		getField().set(this, convData);
+		
+		return true;
+	}
+	
+	/**
+	 * convert a string type to a different type appropriate for the field in
+	 * question. 
+	 * @param value
+	 * @return
+	 */
+	public Object convertStringType(Object value) {
+		if (value == null) {
+			return null;
+		}
+		if (value instanceof String == false) {
+			return value;
+		}
+		String str = (String) value;
+		Type type = getField().getGenericType();
+		Class<?> cls = getField().getType();
+		String clsName = cls.getName();
+		switch (clsName) {
+		case "int":
+		case "Integer":
+			return Integer.valueOf(str);
+		case "double":
+		case "Double":
+			return Double.valueOf(str);
+		case "float":
+		case "Float":
+			return Float.valueOf(str);
+		case "short":
+		case "Short":
+			return Short.valueOf(str);
+			
+		}
+		
+		return value;
 	}
 
 
-
 }

src/PamModel/parametermanager/swing/ManagedParameterDialog.java

@@ -0,0 +1,49 @@
+package PamModel.parametermanager.swing;
+
+import java.awt.Window;
+
+import PamModel.parametermanager.ManagedParameters;
+import PamView.dialog.PamDialog;
+
+public class ManagedParameterDialog<T extends ManagedParameters> extends PamDialog {
+	
+	private T params;
+	
+	private ManagedParameterPanel<T> parameterPanel;
+
+	public ManagedParameterDialog(Window parentFrame, String title, T params) {
+		super(parentFrame, title, false);
+		parameterPanel = new ManagedParameterPanel<T>(params);
+		setDialogComponent(parameterPanel.getPanel());
+	}
+	
+	public T showDialog(Window parentFrame, String title, T parameters) {
+//		ManagedParameterDialog dialog = new ManagedParameterDialog<>(parentFrame, title, parameters);
+		setParams(parameters);
+		setVisible(true);
+		
+		return params;
+	}
+	
+	private void setParams(T params) {
+		this.params = params;
+		this.parameterPanel.setParams(params);
+	}
+
+	@Override
+	public boolean getParams() {
+		return parameterPanel.getParams(params);
+	}
+
+	@Override
+	public void cancelButtonPressed() {
+		params = null;
+	}
+
+	@Override
+	public void restoreDefaultSettings() {
+		// TODO Auto-generated method stub
+
+	}
+
+}

src/PamModel/parametermanager/swing/ManagedParameterPanel.java

@@ -0,0 +1,149 @@
+package PamModel.parametermanager.swing;
+
+import java.awt.Color;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.util.Collection;
+
+import javax.swing.BorderFactory;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.text.JTextComponent;
+
+import PamModel.parametermanager.FieldNotFoundException;
+import PamModel.parametermanager.ManagedParameters;
+import PamModel.parametermanager.PamParameterData;
+import PamModel.parametermanager.PamParameterSet;
+import PamView.dialog.PamDialog;
+import PamView.dialog.PamGridBagContraints;
+
+public class ManagedParameterPanel<T extends ManagedParameters> {
+	
+	private JPanel mainPanel;
+	private Collection<PamParameterData> parameterSet;
+	
+	private static final int DEFAULT_TEXT_LENGTH = 6;
+	private static final int MAX_SINGLE_LINE_LENGTH = 40;
+	
+	private JTextComponent[] textComponents;
+
+	public ManagedParameterPanel(T parameterExample) {
+		
+		mainPanel = new JPanel(new GridBagLayout());
+		GridBagConstraints c = new PamGridBagContraints();
+		PamParameterSet exampleSet = parameterExample.getParameterSet();
+		parameterSet = exampleSet.getParameterCollection();
+		int n = parameterSet.size();
+		textComponents = new JTextComponent[n];
+		int i = 0;
+		for (PamParameterData paramData : parameterSet) {
+			textComponents[i] = createComponent(paramData);
+			c.gridx = 0;
+			c.fill = GridBagConstraints.NONE;
+			c.anchor = GridBagConstraints.NORTHEAST;
+			mainPanel.add(new JLabel(paramData.getShortName(), JLabel.RIGHT), c);
+			c.gridx++;
+			if (textComponents[i] instanceof JTextArea) {
+				c.fill = GridBagConstraints.HORIZONTAL;
+			}
+			else {
+				c.fill = GridBagConstraints.NONE;
+			}
+			c.anchor = GridBagConstraints.WEST;
+			mainPanel.add(textComponents[i], c);
+			
+			textComponents[i].setToolTipText(getTipText(paramData));
+			
+			c.gridy++;
+			i++;
+		}
+	}
+	
+	private String getTipText(PamParameterData paramData) {
+		String tip = paramData.getToolTip();
+		if (tip != null) {
+			return tip;
+		}
+		else {
+			return paramData.getFieldName();
+		}
+	}
+	
+	private JTextComponent createComponent(PamParameterData paramData) {
+		int textLen = paramData.getFieldLength();
+		if (textLen == 0) {
+			textLen = DEFAULT_TEXT_LENGTH;
+		}
+		if (textLen <= MAX_SINGLE_LINE_LENGTH) {
+			return new JTextField(textLen);
+		}
+		else {
+			JTextField dummyField = new JTextField(2);
+//			dummyField.getBorder().
+			JTextArea textArea = new JTextArea(textLen/MAX_SINGLE_LINE_LENGTH+1, MAX_SINGLE_LINE_LENGTH);
+			textArea.setBorder(BorderFactory.createLineBorder(Color.LIGHT_GRAY));
+			return textArea;
+		}
+	}
+	
+	public JComponent getPanel() {
+		return mainPanel;
+	}
+	
+	public void setParams(T params) {
+		int i = 0;
+		PamParameterData newParamData = null;
+		Object data = null;
+		for (PamParameterData paramData : this.parameterSet) {
+			// find the parameter in the new parameters (parameterSet is just a formatting placeholder)
+			try {
+				newParamData = params.getParameterSet().findParameterData(paramData.getFieldName());
+			} catch (FieldNotFoundException e) {
+				e.printStackTrace();
+			}
+			try {
+				data = newParamData.getData();
+			} catch (IllegalArgumentException e) {
+				e.printStackTrace();
+			} catch (IllegalAccessException e) {
+				e.printStackTrace();
+			}
+			if (data != null) {
+				textComponents[i].setText(data.toString());
+			}
+			else {
+				textComponents[i].setText(null);
+			}
+			i++;
+		}
+	}
+	
+	public boolean getParams(T params) {
+		int i = 0;
+		PamParameterData newParamData = null;
+		Object data = null;
+		for (PamParameterData paramData : this.parameterSet) {
+			// find the parameter in the new parameters (parameterSet is just a formatting placeholder)
+			try {
+				newParamData = params.getParameterSet().findParameterData(paramData.getFieldName());
+			} catch (FieldNotFoundException e) {
+				e.printStackTrace();
+			}
+			String txt = textComponents[i].getText();
+			try {
+				newParamData.setData(txt);
+			} catch (IllegalArgumentException | IllegalAccessException e) {
+				String msg = "Invalid parameter. Data type should be " + paramData.getField().getType().getName();
+				return PamDialog.showWarning(null, newParamData.getShortName(), msg);
+			}
+		
+			i++;
+		}
+		
+		return true;
+	}
+
+}

src/generalDatabase/parameterstore/ParameterDatabaseStore.java

@@ -0,0 +1,187 @@
+package generalDatabase.parameterstore;
+
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Statement;
+import java.sql.Types;
+import java.util.Arrays;
+import java.util.Collection;
+
+import PamModel.parametermanager.ManagedParameters;
+import PamModel.parametermanager.PamParameterData;
+import PamModel.parametermanager.PamParameterSet;
+import generalDatabase.DBControlUnit;
+import generalDatabase.EmptyTableDefinition;
+import generalDatabase.PamConnection;
+import generalDatabase.PamTableItem;
+import generalDatabase.SQLTypes;
+
+/**
+ * Store parameters from a managed parameter set in the PAMGuard database. These go into a dead simple table, which has
+ * two columns. The first is a name, the second a string value. Each parameter can only appear once. 
+ * This works with ManagedParameters using the same names and field names that go into the xml output. 
+ * @author dg50
+ *
+ */
+public class ParameterDatabaseStore {
+
+	
+	private EmptyTableDefinition tableDef;
+	private PamTableItem nameItem, dataItem;
+	
+	public ParameterDatabaseStore(String tableName) {
+		tableDef = new EmptyTableDefinition(tableName);
+		tableDef.addTableItem(nameItem = new PamTableItem("ParameterName", Types.VARCHAR));
+		tableDef.addTableItem(dataItem = new PamTableItem("Value", Types.VARCHAR));
+	}
+	
+	public boolean saveParameterSet(ManagedParameters managedParameters) {
+		if (managedParameters == null) {
+			return false;
+		}
+		return saveParameterSet(managedParameters.getClass().getSimpleName(), managedParameters);
+	}
+
+	private boolean saveParameterSet(String name, ManagedParameters managedParameters) {
+		DBControlUnit dbControl = DBControlUnit.findDatabaseControl();
+		if (dbControl == null) {
+			return false;
+		}
+		PamConnection con = dbControl.getConnection();
+		if (checkTable(con) == false) {
+			return false;
+		}
+		
+		String prefix;
+		if (name == null) {
+			prefix = "";
+		}
+		else {
+			prefix = name + ".";
+		}
+		PamParameterSet paramSet = managedParameters.getParameterSet();
+		Collection<PamParameterData> params = paramSet.getParameterCollection();
+		for (PamParameterData paramData : params) {
+			String paramName = paramData.getFieldName();
+			paramName = prefix + paramName;
+			Object data = null;
+			try {
+				data = paramData.getData();// .getField().get(managedParameters);
+			} catch (IllegalArgumentException | IllegalAccessException e) {
+				e.printStackTrace();
+			}
+//			System.out.printf("Store param \"%s\" as \"%s\"\n", paramName, data);
+			saveToDatabase(con, paramName, data);
+		}
+		dbControl.commitChanges();
+		
+		return true;
+	}
+	
+	private boolean saveToDatabase(PamConnection con, String name, Object data) {
+		int[] existing = findExistingRows(con, name);
+		boolean ok = true;
+		if (existing == null || existing.length == 0) {
+			ok |= newRecord(con, name, data);
+		}
+		else {
+			ok |= updateRecord(con, existing[0], name, data);
+			if (existing.length > 1) {
+				for (int i = 1; i < existing.length; i++) {
+					ok |= deleteDuplicateRow(con, existing[i]);
+				}
+			}
+		}
+		return true;
+	}
+	
+	private int[] findExistingRows(PamConnection con, String name) {
+		/**
+		 * Find existing rows with that name. 
+		 */
+		int[] rows = new int[0];
+		if (con == null) {
+			return rows;
+		}
+		String qStr = String.format("SELECT Id FROM %s WHERE %s='%s'", tableDef.getTableName(), nameItem.getName(), name);
+		try {
+			Statement stmt = con.getConnection().createStatement();
+			ResultSet res = stmt.executeQuery(qStr);
+			while (res.next()) {
+				int rowId = res.getInt(1);
+				rows = Arrays.copyOf(rows, rows.length+1);
+				rows[rows.length-1] = rowId;
+			}
+			res.close();
+			stmt.close();
+		} catch (SQLException e) {
+			e.printStackTrace();
+		}
+		return rows;
+	}
+
+	private boolean newRecord(PamConnection con, String name, Object data) {
+		
+		String insertStr = tableDef.getSQLInsertString(con.getSqlTypes());
+		try {
+			PreparedStatement stmt = con.getConnection().prepareStatement(insertStr);
+			stmt.setString(1, name);
+			if (data == null) {
+				stmt.setNull(2, Types.VARCHAR);
+			}
+			else {
+				stmt.setString(2, data.toString());
+			}
+			stmt.executeUpdate();
+
+		} catch (SQLException e) {
+			e.printStackTrace();
+			return false;
+		}
+		
+		return true;
+	}
+
+	private boolean updateRecord(PamConnection con, int iRow, String name, Object data) {
+		SQLTypes st = con.getSqlTypes();
+		String updateString = String.format("UPDATE %s SET %s = '%s' WHERE Id = %d", tableDef.getTableName(), 
+			st.formatColumnName(dataItem.getName()), data, iRow);
+
+		try {
+			PreparedStatement stmt = con.getConnection().prepareStatement(updateString);
+			stmt.executeUpdate();
+
+		} catch (SQLException e) {
+			e.printStackTrace();
+			return false;
+		}
+		
+		return true;
+	}
+
+	private boolean deleteDuplicateRow(PamConnection con, int rowId) {
+		
+		String delStr = String.format("DELETE FROM %s WHERE Id=%d", tableDef.getTableName(), rowId);
+
+		try {
+			PreparedStatement stmt = con.getConnection().prepareStatement(delStr);
+			stmt.executeUpdate();
+
+		} catch (SQLException e) {
+			e.printStackTrace();
+			return false;
+		}
+		return true;
+	}
+
+	private boolean checkTable(PamConnection con) {
+		DBControlUnit dbControl = DBControlUnit.findDatabaseControl();
+		if (dbControl == null) {
+			return false;
+		}
+		dbControl.commitChanges();
+		return dbControl.getDbProcess().checkTable(tableDef);
+	}
+
+}

src/metadata/MetaDataContol.java

@@ -0,0 +1,30 @@
+package metadata;
+
+import javax.swing.JFrame;
+import javax.swing.JMenuItem;
+
+import PamController.PamControlledUnit;
+import PamModel.parametermanager.ParameterSetManager;
+import generalDatabase.parameterstore.ParameterDatabaseStore;
+import metadata.deployment.DeploymentData;
+
+public class MetaDataContol extends PamControlledUnit {
+
+	public static final String unitType = "Meta Data";
+	
+	private DeploymentData deploymentData = new DeploymentData();
+	
+	private ParameterSetManager<DeploymentData> deploymentSetManager;
+	
+	
+	public MetaDataContol(String unitName) {
+		super(unitType, unitName);
+		deploymentSetManager = new ParameterSetManager<DeploymentData>(deploymentData, "Deployment Data");
+	}
+
+	@Override
+	public JMenuItem createFileMenu(JFrame parentFrame) {
+		return deploymentSetManager.getMenuItem(parentFrame);
+	}
+
+}

src/metadata/deployment/DeploymentData.java

@@ -0,0 +1,266 @@
+package metadata.deployment;
+
+import java.io.Serializable;
+
+import PamModel.parametermanager.FieldNotFoundException;
+import PamModel.parametermanager.ManagedParameters;
+import PamModel.parametermanager.PamParameterSet;
+
+/**
+ * Class to hold Deployment data in a form consistent with the ANSI PAM
+ * Standard. This has been keep separate from the Tethys Interface to keep it
+ * easy to benefit from these data without using Tethys itself.
+ * 
+ * @author dg50
+ *
+ */
+public class DeploymentData implements Serializable, Cloneable, ManagedParameters {
+
+	public static final long serialVersionUID = 1L;
+
+	/**
+	 * String that uniquely identifies this deployment.
+	 */
+	private String id;
+
+	/**
+	 * Name of project associated with this deployment. Can be related to a
+	 * geographic region, funding source, etc
+	 */
+	private String project;
+
+	/**
+	 * Deployment identifier, a number related to either the Nth deployment
+	 * operation in a series of deployments or the Nth deployment at a specific
+	 * site. This is different from Id which is unique across all deployments
+	 */
+	private int deploymentId;
+
+	/**
+	 * Alternative deployment description.
+	 */
+	private String deploymentAlias;
+
+	/**
+	 * Name for current location.
+	 */
+	private String site;
+
+	/**
+	 * Alternative names for the deployment location
+	 */
+	private String siteAliases;
+
+	/**
+	 * Name of deployment cruise.
+	 */
+	private String cruise;
+
+	/**
+	 * On what platform is the instrument deployed? (e.g. mooring, tag)
+	 */
+	private String platform = "Unknown";
+
+	/**
+	 * Name of geographic region.
+	 */
+	private String region;
+
+	/**
+	 * Instrument type, e.g. HARP, EAR, Popup, DMON, etc.
+	 */
+	private String instrumentType;
+
+	/**
+	 * Instrument identifier, e.g. serial number
+	 */
+	private String instrumentId;
+
+	public DeploymentData() {
+	}
+
+	@Override
+	protected DeploymentData clone() {
+		try {
+			return (DeploymentData) super.clone();
+		} catch (CloneNotSupportedException e) {
+			e.printStackTrace();
+			return null;
+		}
+	}
+
+	@Override
+	public PamParameterSet getParameterSet() {
+		PamParameterSet ps = PamParameterSet.autoGenerate(this);
+		try {
+			ps.findParameterData("id").setInfo("Unique Id", null, "String that uniquely identifies this deployment", 128);
+//			ps.setOrder("id", 0);
+			ps.findParameterData("project").setInfo("Project Name", null, "Name of project associated with this deployment. Can be related to a geographic region, funding source, etc", 200);
+			ps.findParameterData("deploymentId").setInfo("Deployment Identifier", null, "Deployment identifier, a number related to either the Nth deployment operation in a series of deployments or the Nth deployment at a specific site.  This is different from Id which is unique across all deployments");
+			ps.findParameterData("deploymentAlias").setInfo("Alternative deployment description", null, "Alternative deployment description", 20);
+			ps.findParameterData("site").setInfo("Site name", null, "Name for current location", 40);
+			ps.findParameterData("siteAliases").setInfo("Alternative site name", null, "Alternative site description", 40);
+			ps.findParameterData("cruise").setInfo("Deployment cruise", null, "Name of deployment cruise");
+			ps.findParameterData("platform").setInfo("Platform type", null, "On what platform is the instrument deployed? (e.g. mooring, tag)", 20);
+			ps.findParameterData("region").setInfo("Geographic Region", "", "Name of geographic region", 40);
+		} catch (FieldNotFoundException e) {
+			e.printStackTrace();
+		}
+		return ps;
+	}
+
+	/**
+	 * @return the id
+	 */
+	public String getId() {
+		return id;
+	}
+
+	/**
+	 * @param id the id to set
+	 */
+	public void setId(String id) {
+		this.id = id;
+	}
+
+	/**
+	 * @return the project
+	 */
+	public String getProject() {
+		return project;
+	}
+
+	/**
+	 * @param project the project to set
+	 */
+	public void setProject(String project) {
+		this.project = project;
+	}
+
+	/**
+	 * @return the deploymentId
+	 */
+	public int getDeploymentId() {
+		return deploymentId;
+	}
+
+	/**
+	 * @param deploymentId the deploymentId to set
+	 */
+	public void setDeploymentId(int deploymentId) {
+		this.deploymentId = deploymentId;
+	}
+
+	/**
+	 * @return the deplomentAlias
+	 */
+	public String getDeploymentAlias() {
+		return deploymentAlias;
+	}
+
+	/**
+	 * @param deplomentAlias the deplomentAlias to set
+	 */
+	public void setDeploymentAlias(String deplomentAlias) {
+		this.deploymentAlias = deplomentAlias;
+	}
+
+	/**
+	 * @return the site
+	 */
+	public String getSite() {
+		return site;
+	}
+
+	/**
+	 * @param site the site to set
+	 */
+	public void setSite(String site) {
+		this.site = site;
+	}
+
+	/**
+	 * @return the siteAliases
+	 */
+	public String getSiteAliases() {
+		return siteAliases;
+	}
+
+	/**
+	 * @param siteAliases the siteAliases to set
+	 */
+	public void setSiteAliases(String siteAliases) {
+		this.siteAliases = siteAliases;
+	}
+
+	/**
+	 * @return the cruise
+	 */
+	public String getCruise() {
+		return cruise;
+	}
+
+	/**
+	 * @param cruise the cruise to set
+	 */
+	public void setCruise(String cruise) {
+		this.cruise = cruise;
+	}
+
+	/**
+	 * @return the platform
+	 */
+	public String getPlatform() {
+		return platform;
+	}
+
+	/**
+	 * @param platform the platform to set
+	 */
+	public void setPlatform(String platform) {
+		this.platform = platform;
+	}
+
+	/**
+	 * @return the region
+	 */
+	public String getRegion() {
+		return region;
+	}
+
+	/**
+	 * @param region the region to set
+	 */
+	public void setRegion(String region) {
+		this.region = region;
+	}
+
+	/**
+	 * @return the instrumentType
+	 */
+	public String getInstrumentType() {
+		return instrumentType;
+	}
+
+	/**
+	 * @param instrumentType the instrumentType to set
+	 */
+	public void setInstrumentType(String instrumentType) {
+		this.instrumentType = instrumentType;
+	}
+
+	/**
+	 * @return the instrumentId
+	 */
+	public String getInstrumentId() {
+		return instrumentId;
+	}
+
+	/**
+	 * @param instrumentId the instrumentId to set
+	 */
+	public void setInstrumentId(String instrumentId) {
+		this.instrumentId = instrumentId;
+	}
+
+}

src/metadata/deployment/QAData.java

@@ -0,0 +1,40 @@
+package metadata.deployment;
+
+import java.io.Serializable;
+
+import PamModel.parametermanager.ManagedParameters;
+import PamModel.parametermanager.PamParameterSet;
+
+/**
+ * Largely the content of the Tethys QualityAssurance schema
+ * @author dg50
+ *
+ */
+public class QAData  implements Serializable, Cloneable, ManagedParameters {
+
+	public static final long serialVersionUID = 1L;
+	
+	private String objectives;
+	
+	private String qaAbstract;
+	
+	private String method;
+	
+	private String responsibleName;
+	private String responsibleOrganisation;
+	private String responsiblePosition;
+	private String responsiblePhone;
+	private String responsibleAddress;
+	private String responsibleEmail;
+	
+	public QAData() {
+		// TODO Auto-generated constructor stub
+	}
+	
+	@Override
+	public PamParameterSet getParameterSet() {
+		PamParameterSet ps = PamParameterSet.autoGenerate(this);
+		return ps;
+	}
+
+}

src/tethys/TethysControl.java

@@ -11,6 +11,8 @@ import javax.swing.JMenuItem;
 import PamController.PamControlledUnit;
 import PamController.PamController;
 import PamguardMVC.PamDataBlock;
+import nilus.Deployment;
+import nilus.Deployment.Instrument;
 import tethys.output.StreamExportParams;
 import tethys.output.TethysExportParams;
 import tethys.output.swing.TethysExportDialog;
@@ -57,6 +59,19 @@ public class TethysControl extends PamControlledUnit {
 		return tethysExportParams;
 	}
 	
+	/**
+	 * Get a nilus deployment document, as full populated as possible. 
+	 * @return
+	 */
+	public Deployment getDeployment() {
+		Deployment deployment = new Deployment();
+		Deployment.Instrument instrument = new Instrument();
+//		instrument.
+//		deployment.
+		
+		return null;
+	}
+
 	/**
 	 * We'll probably want to 
 	 * @param parentFrame

src/tethys/deployment/DeploymentWrapper.java

@@ -0,0 +1,85 @@
+package tethys.deployment;
+
+import java.io.ByteArrayOutputStream;
+import java.io.Serializable;
+import java.lang.annotation.Annotation;
+import java.lang.reflect.AnnotatedType;
+import java.util.List;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.namespace.QName;
+import javax.xml.validation.Schema;
+
+import nilus.Deployment.Data.Audio;
+import nilus.Deployment;
+import nilus.Deployment.Data;
+import nilus.Deployment.Instrument;
+
+public class DeploymentWrapper<T extends Serializable> {
+
+	public DeploymentWrapper(T tethysObject) {
+		
+	}
+	
+	public List<String> getFieldNames() {
+		return null;
+	}
+	
+	public List<Serializable> getComplexObjects() {
+		
+		return null;
+	}
+
+	public static void main(String[] args) {
+		// quick play with some JAXB objects to see what they can do. 
+		Deployment deployment = new Deployment();
+
+		Class<? extends Deployment> deploymentClass = deployment.getClass();
+		Annotation[] annots = deploymentClass.getAnnotations();
+		AnnotatedType[] annotInterfaces = deploymentClass.getAnnotatedInterfaces();
+		Annotation[] declAnnots = deploymentClass.getDeclaredAnnotations();
+		
+		Instrument instrument = new Instrument();
+		instrument.setID("22");
+		instrument.setType("SoundTrap");
+		QName qName = new QName("Instrument");
+		JAXBElement<Instrument> jInst = new JAXBElement<Deployment.Instrument>(qName, Instrument.class, instrument);
+		deployment.getContent().add(jInst);
+		
+		Deployment.Data data = new Data();
+		Audio audio = new Audio();
+		audio.setProcessed("??");
+		data.setAudio(audio);
+		JAXBElement jData = new JAXBElement<Deployment.Data>(new QName("Data"), Data.class, data);
+		deployment.getContent().add(jData);
+		
+		String project = "Project Name";
+		JAXBElement<String> jProj = new JAXBElement<String>(new QName("Project"), String.class, project);
+		deployment.getContent().add(jProj);
+
+		String aaa = "Project Something else";
+		JAXBElement<String> jProj2 = new JAXBElement<String>(new QName("Region"), String.class, aaa);
+		deployment.getContent().add(jProj2);
+		
+		
+		try {
+			JAXBContext jContext = JAXBContext.newInstance(Deployment.class);
+			Marshaller mar = (Marshaller) jContext.createMarshaller();
+			mar.setProperty(javax.xml.bind.Marshaller.JAXB_FORMATTED_OUTPUT, true);
+			
+			ByteArrayOutputStream bos = new ByteArrayOutputStream();
+			mar.marshal(deployment, bos);
+			String xml = new String(bos.toByteArray());
+			System.out.println(xml);
+//			Schema schema = mar.getSchema(); // is null. Can't generate it's own it seems. 
+			
+		} catch (Exception e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		
+	}
+
+}

src/tethys/deployment/PamDeployment.java

@@ -0,0 +1,64 @@
+package tethys.deployment;
+
+import java.io.Serializable;
+
+import nilus.DeploymentRecoveryDetails;
+
+/**
+ * Wrapper and functions associated with the Tethys Deployment object which can
+ * exchange these with the PAMGuard database and display Everything is just held
+ * within a list, in no particular order, which getContent public
+ * 
+ * This is from the Deployment JavaDoc. TBH it's pretty horrible, since it's possible to have
+ * more than one of each type of object in the list, so not sure what to do about that. Would be nicer
+ * as a HashTable. however we are where we're are for now. Start by focussing on getting the 
+ * content saved for each type 
+ * 
+ * List<Serializable> getContent()
+ * 
+ * Gets the value of the content property. This accessor method returns a
+ * reference to the live list,not a snapshot. Therefore any modification you
+ * make to the returned list will be present inside the JAXB object.This is why
+ * there is not a set method for the content property.
+ * 
+ * For example, to add a new item, do as follows: getContent().add(newItem);
+ * 
+ * 
+ * Objects of the following type(s) are allowed in the list JAXBElement<String>
+ * JAXBElement<String> 
+ * JAXBElement<Integer>
+ * JAXBElement<DeploymentRecoveryDetails> 
+ * JAXBElement<String>
+ * JAXBElement<Deployment.SamplingDetails> 
+ * JAXBElement<Deployment.Sensors>
+ * JAXBElement<Deployment.Instrument> 
+ * JAXBElement<String>
+ * JAXBElement<Deployment.Data> 
+ * JAXBElement<String> String
+ * JAXBElement<AcousticDataQAType> 
+ * JAXBElement<Deployment.SiteAliases>
+ * JAXBElement<String> 
+ * JAXBElement<DeploymentRecoveryDetails>
+ * 
+ * 
+ * @author dg50
+ *
+ */
+public class PamDeployment {
+
+	public PamDeployment() {
+
+	}
+	
+	public DeploymentRecoveryDetails getDeploymentRecoveryDetails() {
+		DeploymentRecoveryDetails drd = new DeploymentRecoveryDetails();
+		
+		return null;
+	}
+	
+	private void ripApart(Serializable object) {
+		Class cls = object.getClass();
+//		cls.get
+	}
+
+}

src/tethys/exchange/TethysExchange.java

@@ -0,0 +1,5 @@
+package tethys.exchange;
+
+public interface TethysExchange {
+//	JAXB
+}