ITIS Codes GUI

Basic system in place for handling ITIS species codes.

src/tethys/TethysControl.java

@@ -50,6 +50,7 @@ import tethys.output.DatablockSynchInfo;
 import tethys.output.TethysExportParams;
 import tethys.output.TethysExporter;
 import tethys.output.swing.TethysExportDialog;
+import tethys.species.ITISFunctions;
 import tethys.swing.ProjectDeploymentsDialog;
 import tethys.swing.TethysTabPanel;
 import tethys.swing.XMLStringView;
@@ -85,6 +86,8 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 
 	private DeploymentHandler deploymentHandler;
 	private DetectionsHandler detectionsHandler;
+	
+	private ITISFunctions itisFunctions;
 
 	public TethysControl(String unitName) {
 		super(unitType, unitName);
@@ -615,4 +618,14 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 		}
 	}
 
+	/**
+	 * @return the itisFunctions
+	 */
+	public ITISFunctions getItisFunctions() {
+		if (itisFunctions == null) {
+			itisFunctions = new ITISFunctions(this);
+		}
+		return itisFunctions;
+	}
+
 }

src/tethys/dbxml/DBXMLQueries.java

@@ -61,7 +61,7 @@ public class DBXMLQueries {
 	 * @return query result
 	 * @throws TethysQueryException 
 	 */
-	private DBQueryResult executeQuery(String jsonQueryString) throws TethysQueryException {
+	public DBQueryResult executeQuery(String jsonQueryString) throws TethysQueryException {
 		long t1 = System.currentTimeMillis();
 		DBQueryResult result = null;
 		TethysQueryException tException = null;
@@ -636,7 +636,7 @@ public class DBXMLQueries {
 		return blockCounts;
 	}
 
-	private String getElementData(Element root, String elName) {
+	public String getElementData(Element root, String elName) {
 		String[] tree = elName.split("\\.");
 		for (String element : tree) {
 			NodeList nodeList = root.getElementsByTagName(element);
@@ -647,12 +647,13 @@ public class DBXMLQueries {
 			Node firstNode = nodeList.item(0);
 			if (firstNode instanceof Element) {
 				root = (Element) firstNode;
+				break;
 			}
 		}
 		return root.getTextContent();
 	}
 
-	private Document convertStringToXMLDocument(String xmlString) {
+	public Document convertStringToXMLDocument(String xmlString) {
 		//Parser that produces DOM object trees from XML content
 		DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
 

src/tethys/species/DataBlockSpeciesManager.java

@@ -23,6 +23,7 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
 	public DataBlockSpeciesManager(PamDataBlock<T> dataBlock) {
 		super();
 		this.dataBlock = dataBlock;
+		datablockSpeciesMap = SpeciesMapManager.getInstance().getSpeciesMap(dataBlock);
 	}
 	
 	public SpeciesMapItem getSpeciesItem(T dataUnit) {
@@ -38,6 +39,9 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
 	}
 	
 	public DataBlockSpeciesMap getDatablockSpeciesMap() {
+		if (datablockSpeciesMap == null) {
+			datablockSpeciesMap = new DataBlockSpeciesMap();
+		}
 		return datablockSpeciesMap;
 	}
 

src/tethys/species/GlobalSpeciesMap.java

@@ -0,0 +1,32 @@
+package tethys.species;
+
+import java.io.Serializable;
+import java.util.HashMap;
+
+import PamguardMVC.PamDataBlock;
+
+public class GlobalSpeciesMap implements Serializable {
+
+	public static final long serialVersionUID = 1L;
+	
+	private HashMap<String, DataBlockSpeciesMap> datablockMaps;
+
+	/**
+	 * @return the datablockMaps
+	 */
+	private synchronized HashMap<String, DataBlockSpeciesMap> getDatablockMaps() {
+		if (datablockMaps == null) {
+			datablockMaps = new HashMap<>();
+		}
+		return datablockMaps;
+	}
+	
+	public void put(PamDataBlock pamDataBlock, DataBlockSpeciesMap dataBlockSpeciesMap) {
+		getDatablockMaps().put(pamDataBlock.getLongDataName(), dataBlockSpeciesMap);
+	}
+
+	public DataBlockSpeciesMap get(PamDataBlock pamDataBlock) {
+		return getDatablockMaps().get(pamDataBlock.getLongDataName());
+	}
+
+}

src/tethys/species/ITISFunctions.java

@@ -0,0 +1,84 @@
+package tethys.species;
+
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import PamController.settings.output.xml.PAMGuardXMLPreview;
+import PamController.settings.output.xml.PamguardXMLWriter;
+import tethys.TethysControl;
+import tethys.dbxml.DBQueryResult;
+import tethys.dbxml.DBXMLQueries;
+import tethys.dbxml.TethysQueryException;
+
+/**
+ * Functions associated with pulling ITIS information from the databsae. 
+ * @author dg50
+ *
+ */
+public class ITISFunctions {
+
+	private TethysControl tethysControl;
+
+	public ITISFunctions(TethysControl tethysControl) {
+		super();
+		this.tethysControl = tethysControl;
+	}
+	
+	public TethysITISResult getITISInformation(int itisCode) {
+		/*
+		 * hope to get back something like
+		 * 
+<?xml version="1.0" encoding="ISO-8859-1"?><Result xmlns="http://tethys.sdsu.edu/schema/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+    <rank>
+        <tsn>180488</tsn>
+        <taxon_unit>Species</taxon_unit>
+        <completename>Physeter macrocephalus</completename>
+        <vernacular>
+            <name language="English">Sperm Whale</name>
+            <name language="English">cachalot</name>
+        </vernacular>
+    </rank>
+</Result>
+		 */
+
+		String jQ =  "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"=\",\"operands\":[\"ranks/rank/tsn\",\"SPECIESCODE\"],\"optype\":\"binary\"}],\"enclose\":1}";
+		jQ = jQ.replace("SPECIESCODE", String.format("%d", itisCode));
+		
+		DBXMLQueries dbQueries = tethysControl.getDbxmlQueries();
+		DBQueryResult qResult = null;
+		try {
+			qResult = dbQueries.executeQuery(jQ);
+		} catch (TethysQueryException e) {
+			e.printStackTrace();
+			return null;
+		}
+		
+		Document doc = dbQueries.convertStringToXMLDocument(qResult.queryResult);
+		Element docEl = doc.getDocumentElement();
+//		doc.
+//		PAMGuardXMLPreview xmlPreview = new PAMGuardXMLPreview(null, "returned", qResult.queryResult)
+		PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
+		String fDoc = pamXMLWriter.getAsString(doc, true);
+		System.out.println(fDoc);
+		
+		String tsn = dbQueries.getElementData(docEl, "tsn");
+		if (tsn == null) {
+			return null;
+		}
+		String taxunit = dbQueries.getElementData(docEl, "taxon_unit");
+		String latin = dbQueries.getElementData(docEl, "completename");
+		// try to find a vernacular.
+		NodeList vEls = doc.getElementsByTagName("vernacular");
+		String vernacular = null;
+		if (vEls.getLength() > 0) {
+			Node f = vEls.item(0);
+			if (f instanceof Element) {
+				vernacular = dbQueries.getElementData((Element) f, "name");
+			}
+		}
+		
+		return new TethysITISResult(itisCode, taxunit, latin, vernacular);
+	}
+}

src/tethys/species/SpeciesMapManager.java

@@ -1,5 +1,104 @@
 package tethys.species;
 
-public class SpeciesMapManager {
+import java.io.Serializable;
+import java.util.ArrayList;
 
+import PamController.PamControlledUnitSettings;
+import PamController.PamController;
+import PamController.PamSettingManager;
+import PamController.PamSettings;
+import PamguardMVC.PamDataBlock;
+
+/**
+ * Master manager for species maps which will eventually allow for export and import from XML
+ * documents, databases and other things ...
+ * @author dg50
+ *
+ */
+public class SpeciesMapManager implements PamSettings {
+	
+	private static SpeciesMapManager singleInstance = null;
+	
+	private static Object synch = new Object(); 
+	
+	private GlobalSpeciesMap globalSpeciesMap;
+
+	private SpeciesMapManager() {
+		PamSettingManager.getInstance().registerSettings(this);
+	}
+	
+	/**
+	 * Get an instance of the global species manager. This handles look up tables 
+	 * for each datablock to convert from internal PAMGuard names to ITIS species codes and
+	 * usefully call types for output to Tethys. 
+	 * @return
+	 */
+	public static SpeciesMapManager getInstance() {
+		if (singleInstance == null) {
+			synchronized (synch) {
+				if (singleInstance == null) {
+					singleInstance = new SpeciesMapManager();
+				}
+			}
+		}
+		return singleInstance;
+	}
+
+	@Override
+	public String getUnitName() {
+		return "Global Species Codes";
+	}
+
+	@Override
+	public String getUnitType() {
+		return "Global Species Codes";
+	}
+
+	@Override
+	public Serializable getSettingsReference() {
+		gatherSpeciesMaps();
+		return globalSpeciesMap;
+	}
+
+	/**
+	 * Get species maps from all PAMGuard datablocks which have such a map
+	 */
+	private void gatherSpeciesMaps() {
+		if (globalSpeciesMap == null) {
+			globalSpeciesMap = new GlobalSpeciesMap();
+		}
+		ArrayList<PamDataBlock> allDataBlocks = PamController.getInstance().getDataBlocks();
+		for (PamDataBlock aBlock : allDataBlocks) {
+			DataBlockSpeciesManager spManager = aBlock.getDatablockSpeciesManager();
+			if (spManager == null) {
+				continue;
+			}
+			DataBlockSpeciesMap speciesMap = spManager.getDatablockSpeciesMap();
+			globalSpeciesMap.put(aBlock, speciesMap);
+		}
+	}
+	
+	public DataBlockSpeciesMap getSpeciesMap(PamDataBlock pamDataBlock) {
+		if (globalSpeciesMap == null) {
+			return null;
+		}
+		return globalSpeciesMap.get(pamDataBlock);
+	}
+
+	@Override
+	public long getSettingsVersion() {
+		return GlobalSpeciesMap.serialVersionUID;
+	}
+
+	@Override
+	public boolean restoreSettings(PamControlledUnitSettings pamControlledUnitSettings) {
+		Object obj = pamControlledUnitSettings.getSettings();
+		if (obj instanceof GlobalSpeciesMap) {
+			this.globalSpeciesMap = (GlobalSpeciesMap) obj;
+			return true;
+		}
+		else {
+			return false;
+		}
+	}
 }

src/tethys/species/SpeciesTest.java

@@ -40,7 +40,7 @@ public class SpeciesTest {
 		System.out.printf("Query time was %3.1fms\n" , (double) (t2-t1)/1e6);
 		System.out.println(queryResult);
 		
-		TethysITISResult itisResult = new TethysITISResult(queryResult);
+//		TethysITISResult itisResult = new TethysITISResult(queryResult);
 	}
 	/*
 	 * 
@@ -83,9 +83,9 @@ public class SpeciesTest {
 	}
 	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\",\"624908\"],\"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\":\"dbxml:contains\",\"operands\":[\"ranks/rank/completename\",\"Mesoplodon\"],\"optype\":\"function\"}],\"enclose\":1}";
 
 		System.out.println(jQ);
 

src/tethys/species/TethysITISResult.java

@@ -1,12 +1,5 @@
 package tethys.species;
 
-import java.io.StringReader;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import org.w3c.dom.Document;
-import org.xml.sax.InputSource;
 
 /**
  * Class to hold and unpack a XML string returned from the ITIS_ranks document
@@ -16,22 +9,52 @@ import org.xml.sax.InputSource;
  */
 public class TethysITISResult {
 
+	private int itisCode;
+	private String taxon_unit;
+	private String latin;
+	private String vernacular;
+
 	/**
 	 * Construct a ITIS object from XML data
+	 * @param itisCode 
 	 * @param xmlData
+	 * @param vernacular 
+	 * @param latin 
 	 */
-	public TethysITISResult(String xmlData) {
+	public TethysITISResult(int itisCode, String taxon_unit, String latin, String vernacular) {
 
-		DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
-
-		//API to obtain DOM Document instance
-		DocumentBuilder builder = null;
-
-//		//Create DocumentBuilder with default configuration
-//		builder = factory.newDocumentBuilder();
-//
-//		//Parse the content to Document object
-//		Document doc = builder.parse(new InputSource(new StringReader(xmlData)));
+		this.itisCode = itisCode;
+		this.taxon_unit = taxon_unit;
+		this.latin = latin;
+		this.vernacular = vernacular;
 		
 	}
+
+	/**
+	 * @return the itisCode
+	 */
+	public int getItisCode() {
+		return itisCode;
+	}
+
+	/**
+	 * @return the taxon_unit
+	 */
+	public String getTaxon_unit() {
+		return taxon_unit;
+	}
+
+	/**
+	 * @return the latin
+	 */
+	public String getLatin() {
+		return latin;
+	}
+
+	/**
+	 * @return the vernacular
+	 */
+	public String getVernacular() {
+		return vernacular;
+	}
 }

src/tethys/species/swing/DataBlockSpeciesDialog.java

@@ -1,7 +1,15 @@
 package tethys.species.swing;
 
+import java.awt.BorderLayout;
 import java.awt.Window;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 
+import javax.swing.JButton;
+import javax.swing.JPanel;
+
+import PamController.PamController;
+import PamView.PamGui;
 import PamView.dialog.PamDialog;
 import PamguardMVC.PamDataBlock;
 
@@ -9,14 +17,28 @@ public class DataBlockSpeciesDialog extends PamDialog {
 
 	private static final long serialVersionUID = 1L;
 
-	DataBlockSpeciesPanel speciesPanel;
+	private DataBlockSpeciesPanel speciesPanel;
 	
 	private DataBlockSpeciesDialog(Window parentFrame, PamDataBlock dataBlock) {
 		super(parentFrame, dataBlock.getDataName() +  " species", false);
+		JPanel mainPanel = new JPanel(new BorderLayout());
 		speciesPanel = new DataBlockSpeciesPanel(dataBlock);
-		setDialogComponent(speciesPanel.getDialogComponent());
+		mainPanel.add(BorderLayout.CENTER, speciesPanel.getDialogComponent());
+		JButton itisButton = new JButton("Go to ITIS web site");
+		itisButton.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				gotoITIS();
+			}
+		});
+		mainPanel.add(BorderLayout.NORTH, itisButton);
+		setDialogComponent(mainPanel);
 	}
 	
+	protected void gotoITIS() {
+		PamGui.openURL("https://www.itis.gov");
+	}
+
 	public static void showDialog(Window parentFrame, PamDataBlock dataBlock) {
 		DataBlockSpeciesDialog speciesDialog = new DataBlockSpeciesDialog(parentFrame, dataBlock);
 		speciesDialog.setParams();

src/tethys/species/swing/DataBlockSpeciesPanel.java

@@ -22,6 +22,8 @@ public class DataBlockSpeciesPanel implements PamDialogPanel {
 	private PamDataBlock dataBlock;
 	
 	private JPanel speciesPanel;
+	
+	private ArrayList<SpeciesSubPanel> subPanels = new ArrayList<>();
 
 	public DataBlockSpeciesPanel(PamDataBlock dataBlock) {
 		super();
@@ -41,6 +43,7 @@ public class DataBlockSpeciesPanel implements PamDialogPanel {
 	public void setParams() {
 		speciesPanel.removeAll();
 		speciesPanel.setLayout(new BoxLayout(speciesPanel, BoxLayout.Y_AXIS));
+		subPanels.clear();
 		
 		DataBlockSpeciesManager speciesManager = dataBlock.getDatablockSpeciesManager();
 		DataBlockSpeciesTypes speciesTypes = speciesManager.getSpeciesTypes();
@@ -48,6 +51,7 @@ public class DataBlockSpeciesPanel implements PamDialogPanel {
 		DataBlockSpeciesMap speciesMap = speciesManager.getDatablockSpeciesMap();
 		for (String aSpecies : speciesNames) {
 			SpeciesSubPanel subPanel = new SpeciesSubPanel(aSpecies);
+			subPanels.add(subPanel);
 			speciesPanel.add(subPanel.getDialogComponent());
 			if (speciesMap != null) {
 				SpeciesMapItem speciesInfo = speciesMap.getItem(aSpecies);
@@ -58,8 +62,19 @@ public class DataBlockSpeciesPanel implements PamDialogPanel {
 
 	@Override
 	public boolean getParams() {
-		// TODO Auto-generated method stub
-		return false;
+		DataBlockSpeciesManager speciesManager = dataBlock.getDatablockSpeciesManager();
+		DataBlockSpeciesMap speciesMap = speciesManager.getDatablockSpeciesMap();
+		int errors = 0;
+		for (SpeciesSubPanel subPanel : subPanels) {
+			SpeciesMapItem mapItem = subPanel.getParams();
+			if (mapItem == null) {
+				errors++;
+			}
+			else {
+				speciesMap.putItem(mapItem.getPamguardName(), mapItem);
+			}
+		}
+		return errors == 0;
 	}
 
 }

src/tethys/species/swing/SpeciesSubPanel.java

@@ -2,6 +2,8 @@ package tethys.species.swing;
 
 import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 
 import javax.swing.JButton;
 import javax.swing.JComponent;
@@ -10,8 +12,13 @@ import javax.swing.JPanel;
 import javax.swing.JTextField;
 import javax.swing.border.BevelBorder;
 
+import PamController.PamController;
+import PamView.dialog.PamDialog;
 import PamView.dialog.PamGridBagContraints;
+import tethys.TethysControl;
+import tethys.species.ITISFunctions;
 import tethys.species.SpeciesMapItem;
+import tethys.species.TethysITISResult;
 
 public class SpeciesSubPanel {
 	
@@ -31,7 +38,7 @@ public class SpeciesSubPanel {
 		c.gridx++;
 		mainPanel.add(new JLabel(" ITIS code ", JLabel.RIGHT), c);
 		c.gridx++;
-		mainPanel.add(itisCode = new JTextField(3), c);
+		mainPanel.add(itisCode = new JTextField(6), c);
 		c.gridx ++;
 		mainPanel.add(searchButton = new JButton("Find"));
 		
@@ -66,6 +73,43 @@ public class SpeciesSubPanel {
 		latinName.setToolTipText("Scientific name");
 		commonName.setToolTipText("Common name");
 		
+		searchButton.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				searchSpecies(e);
+			}
+		});
+		
+	}
+
+	/**
+	 * Action when 'Find' button is pressed.
+	 * @param e
+	 */
+	protected void searchSpecies(ActionEvent e) {
+		TethysControl tethysControl = (TethysControl) PamController.getInstance().findControlledUnit(TethysControl.unitType);
+		if (tethysControl == null) {
+			return;
+		}
+		ITISFunctions itisFunctions = tethysControl.getItisFunctions();
+		int itisCode = 0;
+		try {
+			itisCode = Integer.valueOf(this.itisCode.getText());
+		}
+		catch (NumberFormatException ex) {
+			PamDialog.showWarning(PamController.getMainFrame(), "No Code", "Enter  avalid ITIS code");
+			return;
+		}
+		TethysITISResult itisInfo = itisFunctions.getITISInformation(itisCode);
+		if (itisInfo != null) {
+			if (itisInfo.getLatin() != null) {
+				latinName.setText(itisInfo.getLatin());
+			}
+			if (itisInfo.getVernacular() != null) {
+				commonName.setText(itisInfo.getVernacular());
+			}
+		}
+//		System.out.println(itisInfo);
 	}
 
 	public JComponent getDialogComponent() {
@@ -88,8 +132,24 @@ public class SpeciesSubPanel {
 	}
 
 	public SpeciesMapItem getParams() {
-		// TODO Auto-generated method stub
-		return null;
+		Integer tsn = null;
+		String vernacular = null;
+		String latin = null;
+		try {
+			tsn = Integer.valueOf(itisCode.getText());
+		}
+		catch (NumberFormatException e) {
+			PamDialog.showWarning(PamController.getMainFrame(), pamguardName.getText(), "You must specified an ITIS taxanomic code");
+			return null;
+		}
+		latin = latinName.getText();
+		vernacular = commonName.getText();
+		String callType = this.callType.getText();
+		if (callType == null || callType.length() == 0) {
+			PamDialog.showWarning(PamController.getMainFrame(), pamguardName.getText(), "You must specified a call type");
+			return null;			
+		}
+		return new SpeciesMapItem(tsn, callType, pamguardName.getText(), latin, vernacular);
 	}
 
 }