Document export

src/PamController/PamController.java

@@ -2598,7 +2598,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 			if (dbc == null) {
 				return null;
 			}
-			return dbc.getDatabaseName();
+			return dbc.getLongDatabaseName();
 		}
 		return null;
 	}

src/tethys/TethysControl.java

@@ -3,6 +3,10 @@ package tethys;
 import java.awt.Desktop;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.Serializable;
 import java.net.MalformedURLException;
@@ -10,9 +14,11 @@ import java.net.URISyntaxException;
 import java.net.URL;
 import java.util.ArrayList;
 
+import javax.swing.JFileChooser;
 import javax.swing.JFrame;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
 import javax.swing.Timer;
 
@@ -20,8 +26,11 @@ import PamController.PamControlledUnit;
 import PamController.PamControlledUnitSettings;
 import PamController.PamController;
 import PamController.PamControllerInterface;
+import PamController.PamFolders;
 import PamController.PamSettingManager;
 import PamController.PamSettings;
+import PamUtils.PamFileChooser;
+import PamUtils.PamFileFilter;
 import PamView.PamTabPanel;
 import PamView.dialog.warn.WarnOnce;
 import PamguardMVC.PamDataBlock;
@@ -43,6 +52,7 @@ import tethys.output.TethysExporter;
 import tethys.output.swing.TethysExportDialog;
 import tethys.swing.ProjectDeploymentsDialog;
 import tethys.swing.TethysTabPanel;
+import tethys.swing.XMLStringView;
 
 /**
  * Quick play with a simple system for outputting data to Tethys. At it's start
@@ -539,4 +549,70 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 		WarnOnce.showWarning(title, msg, WarnOnce.WARNING_MESSAGE);
 	}
 
+	/**
+	 * Load a document from the database and display it in a popup window
+	 * @param collection
+	 * @param documentId
+	 */
+	public void displayDocument(String collection, String documentId) {
+		String doc = getDbxmlQueries().getDocument(collection, documentId);
+		if (doc == null | doc.length() == 0) {
+			doc = String.format("Unable to retrieve document %s/%s from database\n", collection, documentId);
+			
+		}
+		XMLStringView.showDialog(getGuiFrame(), collection, documentId, doc);
+	}
+
+	/**
+	 * Load a document from the database and write to a file selected by the user
+	 * @param collection
+	 * @param documentId
+	 */
+	public void exportDocument(String collection, String documentId) {
+		String doc = getDbxmlQueries().getDocument(collection, documentId);
+		if (doc == null | doc.length() == 0) {
+			String msg = String.format("Unable to retrieve document %s/%s from database\n", collection, documentId);
+			WarnOnce.showWarning("Error", msg, WarnOnce.WARNING_MESSAGE);			
+		}
+		
+		PamFileFilter fileFilter = new PamFileFilter("XML documents", ".xml");
+//		fileFilter
+		JFileChooser fileChooser = new PamFileChooser();
+		fileChooser.setFileFilter(fileFilter);
+		fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
+		// make a default name based on the document id and the dataset directory. 
+		String defFolder = PamFolders.getDefaultProjectFolder();
+		if (defFolder != null) {
+			defFolder = String.format("%s%s%s.xml", defFolder,File.separator,documentId);
+			File defFile = new File(defFolder);
+			fileChooser.setSelectedFile(defFile);
+			fileChooser.setAcceptAllFileFilterUsed(true);
+			
+		}
+		int state = fileChooser.showSaveDialog(getGuiFrame());
+		if (state != JFileChooser.APPROVE_OPTION) return;
+		File newFile = fileChooser.getSelectedFile();
+		if (newFile == null) return;
+		newFile = PamFileFilter.checkFileEnd(newFile, "xml", true);
+		if (newFile == null) {
+			return;
+		}
+		if (newFile.exists()) {
+			int ans2 = WarnOnce.showWarning(newFile.getAbsolutePath(), 
+					"The file already exists. Do you want to overwrite it ?", WarnOnce.OK_CANCEL_OPTION);
+			if (ans2 == WarnOnce.CANCEL_OPTION) {
+				return;
+			}
+		}
+		try {
+			BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(newFile));
+			bos.write(doc.getBytes());
+			bos.close();
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+
 }

src/tethys/dbxml/DBXMLConnect.java

@@ -85,6 +85,44 @@ public class DBXMLConnect {
 		return queries;
 	}
 
+	/**
+	 * Convert a nilus Object into a file
+	 * @param nilusObject nilus object
+	 * @param file file (should not exist)
+	 * @return file (will be the same as input file)
+	 * @throws TethysException
+	 */
+	public File createXMLDocument(Object nilusObject, File file) throws TethysException {
+		Class objClass = nilusObject.getClass();
+		try {
+			MarshalXML marshal = new MarshalXML();
+			marshal.createInstance(objClass);
+			marshal.marshal(nilusObject, file.toString());
+		} catch(IllegalArgumentException e) {
+			throw new TethysException("IllegalArgumentException posting to Tethys: " + e.getMessage(), null);
+		} catch (IOException e) {
+			throw new TethysException("IOException posting to Tethys: " + e.getMessage(), null);
+		} catch (JAXBException e) {
+			throw new TethysException("JAXBException posting to Tethys: " + e.getMessage(), null);
+		}
+		return file;
+	}
+	
+	/**
+	 * Create a temporary nilus file. 
+	 * @param nilusObject
+	 * @return
+	 * @throws TethysException
+	 */
+	public File createTempXMLDocument(Object nilusObject) throws TethysException {
+		String tempName = getTempFileName(nilusObject);
+		tempName = tempDirectory.getAbsolutePath() + File.separator + tempName + ".xml";
+		File tempFile = new File(tempName);
+		File retFile = createXMLDocument(nilusObject, tempFile);	
+		retFile.deleteOnExit();
+		return retFile;
+	}
+	
 	/**
 	 * take a nilus object loaded with PamGuard data and post it to the Tethys database
 	 *
@@ -162,7 +200,7 @@ public class DBXMLConnect {
 		String docId = getDocumentId(nilusDocument);
 		String result = null;
 		try {
-			result = jerseyClient.removeDocument(collection+" uio", docId );
+			result = jerseyClient.removeDocument(collection, docId );
 			/**
 			 * Return from a sucessful delete is something like
 			 *

src/tethys/dbxml/DBXMLQueries.java

@@ -440,6 +440,37 @@ public class DBXMLQueries {
 		return count;
 	}
 
+	public String getDocument(String collection, String documentId) {
+//		String queryBase = "return:(collection(\"replaceCollectionName\")/Detections[Id=\"ReplaceDocumentId\"])";
+//		queryBase = queryBase.replace("replaceCollectionName", collection);
+//		queryBase = queryBase.replace("ReplaceDocumentId", documentId);
+//
+//		String result = null;
+//		try {
+//			Queries queries = dbXMLConnect.getTethysQueries();
+//			result = queries.QueryTethys(queryBase);
+////			System.out.println(result);
+//		}
+//		catch (Exception e) {
+//			System.out.println("Error executing " + queryBase);
+////			e.printStackTrace();
+//			return null;
+//		}
+//		return result;
+
+		Queries queries = dbXMLConnect.getTethysQueries();
+		String result = null;
+		try {
+			result = queries.getDocument(collection, documentId);
+		} catch (Exception e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return result;
+
+//		String queryBase = "{\"return\":[\"Deployment/Project\"],\"select\":[],\"enclose\":1}";
+	}
+	
 	/**
 	 * Count on effort detections in a Detections document
 	 * @param docName

src/tethys/detection/DetectionsHandler.java

@@ -5,11 +5,20 @@ import java.util.ArrayList;
 import java.util.List;
 
 import javax.swing.SwingWorker;
+import javax.xml.XMLConstants;
+import javax.xml.bind.JAXBException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.pamguard.x3.sud.SUDClickDetectorInfo;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
 
 import PamController.PamControlledUnit;
 import PamController.PamguardVersionInfo;
+import PamController.settings.output.xml.PamguardXMLWriter;
 import PamModel.PamPluginInterface;
 import PamUtils.PamCalendar;
+import PamUtils.XMLUtils;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
 import PamguardMVC.PamProcess;
@@ -18,6 +27,7 @@ import dataMap.OfflineDataMap;
 import dataMap.OfflineDataMapPoint;
 import metadata.deployment.DeploymentData;
 import nilus.AlgorithmType;
+import nilus.AlgorithmType.Parameters;
 import nilus.AlgorithmType.SupportSoftware;
 import nilus.DataSourceType;
 import nilus.Deployment;
@@ -484,6 +494,69 @@ public class DetectionsHandler {
 		algorithm.setMethod(getMethodString(dataBlock));
 		algorithm.setSoftware(getSoftwareString(dataBlock));
 		algorithm.setVersion(getVersionString(dataBlock));
+		
+		TethysDataProvider dataProvider = dataBlock.getTethysDataProvider();
+		if (dataProvider != null) {
+//			Parameters parameters = dataProvider.getAlgorithmParameters();
+			Parameters parameters = algorithm.getParameters();
+			if (parameters == null) {
+				parameters = new Parameters();
+				algorithm.setParameters(parameters);
+			}
+			List<Element> paramList = parameters.getAny();
+//			algorithm.setParameters(parameters);
+			// make a really simple parameter or two to see if it works with simpler xml than PG generates. 
+			/**
+			 * Parameters should look something like
+			 * 
+  <Algorithm>
+    <Method>Analyst detections</Method>
+    <Software>Triton</Software>
+    <Version>unknown</Version>
+    <Parameters>
+      <LTSA_plot_time_h>0.75</LTSA_plot_time_h>
+      <LTSA_low_Hz>0.0</LTSA_low_Hz>
+      <LTSA_high_Hz>5000.0</LTSA_high_Hz>
+      <LTSA_brightness>30.0</LTSA_brightness>
+    </Parameters>
+  </Algorithm>
+			 */
+			// this works. Can look at the source to see how it's done. 
+			// may have fun making this work for more complex structures. 
+			try {
+				Helper helper = new Helper();
+				helper.AddAnyElement(paramList, "Threshold", "3.5");
+				/*
+				 *  and see Matlab code for dbStruct2DOM for more complex structures
+				 *  This looks like it may be possible to rewrite my functions for 
+				 *  writing structures to XML using the helper.AddAnyElement function as 
+				 *  an example and I should be able to output my complex structures. 
+				 */
+			} catch (JAXBException | ParserConfigurationException e) {
+				e.printStackTrace();
+			}
+
+			Document doc = XMLUtils.createBlankDoc();
+//			PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
+			Element dummyEl = doc.createElement("SomeParam");
+////			dummyEl.setNodeValue("nothing");
+			dummyEl.setTextContent("3.0");
+			/*
+			 * xsl:stylesheet version=\"1.0\" \n"
+				+ "  xmlns:xsl=http://www.w3.org/1999/XSL/Transform\n"
+				+ "  xmlns:ns0=http://mydata.com/H2H/Automation\n"
+			 */
+			dummyEl.setAttribute("xmlns:ns0", TethysControl.xmlNameSpace);
+//			dummyEl.set
+//			paramList.add(dummyEl);
+			
+//			Element mainEl = doc.createElement("CONFIG");
+//			mainEl.appendChild(dummyEl);
+//			doc.appendChild(mainEl);
+//			System.out.println(pamXMLWriter.getAsString(doc));
+		}
+		
+		
 		List<SupportSoftware> supSoft = algorithm.getSupportSoftware();
 		SupportSoftware supportSoft = new SupportSoftware();
 		supportSoft.setSoftware(getSupportSoftware(dataBlock));

src/tethys/niluswraps/TethysCollections.java

@@ -0,0 +1,13 @@
+package tethys.niluswraps;
+
+public enum TethysCollections {
+	
+	Deployments, Detections, Localizations, Calibrations, SpeciesAbreviations;
+
+	@Override
+	public String toString() {
+		return super.toString();
+	}
+
+
+}

src/tethys/pamdata/AutoTethysProvider.java

@@ -112,7 +112,8 @@ public class AutoTethysProvider implements TethysDataProvider {
 		return algorithm;
 	}
 
-	private Parameters getAlgorithmParameters() {
+	@Override
+	public Parameters getAlgorithmParameters() {
 		if (pamControlledUnit instanceof PamSettings == false) {
 			return null;
 		}
@@ -133,7 +134,7 @@ public class AutoTethysProvider implements TethysDataProvider {
 			return null;
 		}
 
-		settingsEl = addNameSpaceToElements(doc, settingsEl, TethysControl.xmlNameSpace);
+//		settingsEl = addNameSpaceToElements(doc, settingsEl, TethysControl.xmlNameSpace);
 
 
 		dummyEl.appendChild(settingsEl);

src/tethys/pamdata/TethysDataProvider.java

@@ -2,6 +2,7 @@ package tethys.pamdata;
 
 import PamguardMVC.PamDataUnit;
 import nilus.AlgorithmType;
+import nilus.AlgorithmType.Parameters;
 import nilus.Deployment;
 import nilus.DescriptionType;
 import nilus.Detection;
@@ -63,4 +64,7 @@ public interface TethysDataProvider {
 	public Detection createDetection(PamDataUnit dataUnit, TethysExportParams tethysExportParams,
 			StreamExportParams streamExportParams);
 
+
+	public Parameters getAlgorithmParameters();
+	
 }

src/tethys/swing/PAMGuardDeploymentsTable.java

@@ -33,6 +33,7 @@ import tethys.deployment.DeploymentHandler;
 import tethys.deployment.DeploymentOverview;
 import tethys.deployment.RecordingPeriod;
 import tethys.niluswraps.PDeployment;
+import tethys.niluswraps.TethysCollections;
 
 /**
  * Table view of PAMGuard deployments. For a really simple deployment, this may have only
@@ -135,13 +136,30 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
 			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);
+			menuItem = new JMenuItem("Display deployment document " + matchedDeployments.get(0));
+			menuItem.addActionListener(new ActionListener() {
+				@Override
+				public void actionPerformed(ActionEvent e) {
+					displayDeployment(matchedDeployments.get(0));
+				}
+			});
+			popMenu.add(menuItem);
+			menuItem = new JMenuItem("Export deployment document " + matchedDeployments.get(0));
+			menuItem.addActionListener(new ActionListener() {
+				@Override
+				public void actionPerformed(ActionEvent e) {
+					exportDeployment(matchedDeployments.get(0));
+				}
+			});
+			popMenu.add(menuItem);
+			
+			
 			popMenu.show(e.getComponent(), e.getX(), e.getY());
 		}
 //		if (newPeriods.size() == 0) {
@@ -155,6 +173,14 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
 		
 	}
 	
+	protected void exportDeployment(PDeployment pDeployment) {
+		getTethysControl().exportDocument(TethysCollections.Deployments.toString(), pDeployment.deployment.getId());
+	}
+
+	protected void displayDeployment(PDeployment pDeployment) {
+		getTethysControl().displayDocument(TethysCollections.Deployments.toString(), pDeployment.deployment.getId());
+	}
+
 	protected void deleteDeployment(PDeployment pDeployment) {
 		Deployment dep = pDeployment.deployment;
 		if (dep == null) {

src/tethys/swing/XMLStringView.java

@@ -0,0 +1,54 @@
+package tethys.swing;
+
+import java.awt.BorderLayout;
+import java.awt.Window;
+
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+
+import PamView.dialog.PamDialog;
+
+public class XMLStringView extends PamDialog {
+	
+	private JTextArea textArea;
+
+	private XMLStringView(Window parentFrame, String title, String xmlString) {
+		super(parentFrame, title, false);
+		
+		JTextArea textArea = new JTextArea(50, 100);
+		JPanel mainPanel = new JPanel(new BorderLayout());
+		JScrollPane scrollPane = new JScrollPane(textArea, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+		mainPanel.add(scrollPane, BorderLayout.CENTER);
+		setDialogComponent(mainPanel);
+		setResizable(true);
+		textArea.setText(xmlString);
+		
+		getCancelButton().setVisible(false);
+	}
+	
+	public static void showDialog(Window parent, String collection, String documentId, String xmlString) {
+		String title = String.format("\"%s\"/\"%s\"", collection, documentId);
+		XMLStringView view = new XMLStringView(parent, title, xmlString);
+		view.setVisible(true);
+	}
+
+	@Override
+	public boolean getParams() {
+		// TODO Auto-generated method stub
+		return false;
+	}
+
+	@Override
+	public void cancelButtonPressed() {
+		// TODO Auto-generated method stub
+
+	}
+
+	@Override
+	public void restoreDefaultSettings() {
+		// TODO Auto-generated method stub
+
+	}
+
+}