System to search species codes

Search the ITIS species codes in Tethys to find ITIS codes. Search can
be on a common or scientific name.

src/tethys/species/ITISFunctions.java

@@ -1,14 +1,23 @@
 package tethys.species;
 
+import java.io.StringReader;
+import java.util.ArrayList;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
 
 import PamController.settings.output.xml.PAMGuardXMLPreview;
 import PamController.settings.output.xml.PamguardXMLWriter;
+import dbxml.Queries;
 import tethys.TethysControl;
 import tethys.dbxml.DBQueryResult;
+import tethys.dbxml.DBXMLConnect;
 import tethys.dbxml.DBXMLQueries;
 import tethys.dbxml.TethysQueryException;
 
@@ -81,4 +90,83 @@ public class ITISFunctions {
 		
 		return new TethysITISResult(itisCode, taxunit, latin, vernacular);
 	}
+	
+	public ArrayList<SpeciesMapItem> searchSpecies(String searchTerm) {
+		ArrayList<SpeciesMapItem> items = new ArrayList<SpeciesMapItem>();		
+		String xQ = "let $target := \"thespeciessearchterm\" \r\n"
+				+ "return\r\n"
+				+ "<Result xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"> {\r\n"
+				+ "\r\n"
+				+ "  for $ranks0 in collection(\"ITIS_ranks\")/ranks/rank[\r\n"
+				+ "          dbxml:contains(completename, $target) or \r\n"
+				+ "                 vernacular[dbxml:contains(name,$target)]]\r\n"
+				+ "return\r\n"
+				+ "  <Record> {\r\n"
+				+ "    $ranks0/tsn,\r\n"
+				+ "            $ranks0/completename,\r\n"
+				+ "            <vernacular>\r\n"
+				+ "              {string-join($ranks0/vernacular/name, \", \")}\r\n"
+				+ "            </vernacular>\r\n"
+				+ "  } </Record>\r\n"
+				+ "} </Result>\r\n"
+				+ "";
+		xQ = xQ.replace("thespeciessearchterm", searchTerm);
+		DBXMLConnect dbXMLConnect = tethysControl.getDbxmlConnect();
+		DBXMLQueries dbxmlQueries = tethysControl.getDbxmlQueries();
+		Queries queries = dbXMLConnect.getTethysQueries();
+
+		String queryResult = null;
+		try {
+			 queryResult = queries.QueryTethys(xQ);
+		} catch (Exception e) {
+			// TODO Auto-generated catch block
+//			e.printStackTrace();
+			return items;
+		}
+		
+
+		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);
+			return items;
+		}
+		// print for now, then comment this out.. 
+//		PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
+//		String fDoc = pamXMLWriter.getAsString(doc, true);
+//		System.out.println(fDoc);
+		// now unpack the xml document. 
+		NodeList els = doc.getElementsByTagName("Record");
+		int n = els.getLength();
+		for (int i = 0; i < n; i++) {
+			Node aNode = els.item(i);
+			if (aNode instanceof Element) {
+				Element anEl = (Element) aNode;
+				String tsn = dbxmlQueries.getElementData(anEl, "tsn");
+				int nTSN = 0;
+				try {
+					nTSN = Integer.valueOf(tsn);
+				}
+				catch (NumberFormatException ex) {
+					System.out.println("Invalid TSN read from Tethys: " + tsn);
+					continue;
+				}
+				
+				String completeName = dbxmlQueries.getElementData(anEl, "completename");
+				String vernacular = dbxmlQueries.getElementData(anEl, "vernacular");
+				SpeciesMapItem mapItem = new SpeciesMapItem(nTSN, "", "", completeName, vernacular);
+				items.add(mapItem);
+			}
+			
+		}
+		return items;
+	}
 }

src/tethys/species/SpeciesTest.java

@@ -21,11 +21,11 @@ public class SpeciesTest {
 	public static void main(String[] args) {
 		
 		SpeciesTest st = new SpeciesTest();
-		st.runJson();
+//		st.runJson();
 		
 //		int spermWhale = 180488;
 //		st.getCodeInfo(spermWhale);
-//		st.runXQuery();
+		st.runXQuery();
 
 	}
 	private  void getCodeInfo(int itisCode) {
@@ -86,15 +86,32 @@ public class SpeciesTest {
 //				+ "    }</Deployment>\r\n"
 //				+ "} </Result>";
 
-		String xQ = "<Result xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"> {\r\n"
+//		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"
+//				+ "  for $rank0 in collection(\"ITIS_ranks\")/rank[tsn = \"180488\"]\r\n"
-				+ "  return\r\n"
+//				+ "  return\r\n"
-				+ "    <rank>{\r\n"
+//				+ "    <rank>{\r\n"
-				+ "      $rank0/completename\r\n"
+//				+ "      $rank0/completename\r\n"
-				+ "    }</rank>\r\n"
+//				+ "    }</rank>\r\n"
-				+ "} </Result>";
+//				+ "} </Result>";
+		String xQ = "let $target := \"physeter\" \r\n"
+				+ "return\r\n"
+				+ "<Result xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"> {\r\n"
+				+ "\r\n"
+				+ "  for $ranks0 in collection(\"ITIS_ranks\")/ranks/rank[\r\n"
+				+ "          dbxml:contains(completename, $target) or \r\n"
+				+ "                 vernacular[dbxml:contains(name,$target)]]\r\n"
+				+ "return\r\n"
+				+ "  <Record> {\r\n"
+				+ "    $ranks0/tsn,\r\n"
+				+ "            $ranks0/completename,\r\n"
+				+ "            <vernacular>\r\n"
+				+ "              {string-join($ranks0/vernacular/name, \", \")}\r\n"
+				+ "            </vernacular>\r\n"
+				+ "  } </Record>\r\n"
+				+ "} </Result>\r\n"
+				+ "";
+		System.out.println(xQ);
 		
-
 		JerseyClient jerseyClient = new JerseyClient(uri);
 		Queries queries = new Queries(jerseyClient);
 		

src/tethys/species/swing/SpeciesSearchDialog.java

@@ -0,0 +1,196 @@
+package tethys.species.swing;
+
+import java.awt.BorderLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Window;
+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 javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.border.TitledBorder;
+import javax.swing.table.AbstractTableModel;
+
+import PamView.dialog.PamDialog;
+import PamView.dialog.PamGridBagContraints;
+import PamView.tables.SwingTableColumnWidths;
+import PamView.tables.TableColumnWidthData;
+import tethys.TethysControl;
+import tethys.species.ITISFunctions;
+import tethys.species.SpeciesMapItem;
+
+public class SpeciesSearchDialog extends PamDialog {
+
+	private static final long serialVersionUID = 1L;
+
+	private TethysControl tethysControl;
+	
+	private SpeciesMapItem selectedItem;
+
+	private static SpeciesSearchDialog singleInstance;
+	
+	private JTextField searchText;
+	
+	private JButton searchButton;
+	
+	private JTable resultTable;
+
+	private ArrayList<SpeciesMapItem> speciesMapItems;
+
+	private DataModel tableModel;
+	
+	private int selectedRow = -1;
+	
+
+	private SpeciesSearchDialog(Window parentFrame, TethysControl tethysControl) {
+		super(parentFrame, "Species search", false);
+		this.tethysControl = tethysControl;
+		JPanel mainPanel = new JPanel(new BorderLayout());
+		mainPanel.setBorder(new TitledBorder("Search Term"));
+		JPanel topPanel = new JPanel(new GridBagLayout());
+		GridBagConstraints c = new PamGridBagContraints();
+		topPanel.add(new JLabel("Latin or common name ", JLabel.RIGHT), c);
+		c.gridx++;
+		topPanel.add(searchText = new JTextField(12), c);
+		c.gridx++;
+		topPanel.add(searchButton = new JButton("search"), c);
+		mainPanel.add(BorderLayout.NORTH, topPanel);
+		searchButton.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				searchTethys();
+			}
+
+		});
+		
+		tableModel = new DataModel();
+		resultTable = new JTable(tableModel);
+		JPanel centPanel = new JPanel(new BorderLayout());
+		centPanel.add(BorderLayout.NORTH, new JLabel("Possible matches", JLabel.LEFT));
+		JScrollPane scrollPane = new JScrollPane(resultTable);
+		centPanel.add(BorderLayout.CENTER, scrollPane);
+		mainPanel.add(BorderLayout.CENTER, centPanel);
+		
+		resultTable.addMouseListener(new TableMouse());
+		new SwingTableColumnWidths("Species Search Dialog Table", resultTable);
+		
+		setResizable(true);
+		setDialogComponent(mainPanel);
+	}
+	public static SpeciesMapItem showDialog(Window parentFrame, TethysControl tethysControl) {
+		singleInstance = new SpeciesSearchDialog(parentFrame, tethysControl);
+		singleInstance.setParams();
+		singleInstance.setVisible(true);
+		return singleInstance.selectedItem;
+	}
+
+	
+	private void searchTethys() {
+		clearResults();
+		String str = searchText.getText();
+		if (str == null || str.length() == 0) {
+			return;
+		}
+		ITISFunctions itisFunctions = tethysControl.getItisFunctions();
+		speciesMapItems = itisFunctions.searchSpecies(str);
+		tableModel.fireTableDataChanged();
+	}
+	
+	private void setParams() {
+		searchText.setText(null);
+		clearResults();
+	}
+
+	private void clearResults() {
+		selectedRow = -1;
+		speciesMapItems = null;
+		selectedItem = null;
+	}
+	@Override
+	public boolean getParams() {
+		if (selectedItem == null) {
+			return showWarning("You must select a row from the table of species");
+		}
+		return selectedItem != null;
+	}
+
+	@Override
+	public void cancelButtonPressed() {
+		clearResults();
+	}
+
+	@Override
+	public void restoreDefaultSettings() {
+		// TODO Auto-generated method stub
+
+	}
+	
+	private class TableMouse extends MouseAdapter {
+
+		@Override
+		public void mouseClicked(MouseEvent e) {
+			selectedRow = resultTable.getSelectedRow();
+			if (selectedRow >= 0) {
+				selectedItem = speciesMapItems.get(selectedRow);
+			}
+			tableModel.fireTableDataChanged();
+		}
+		
+	}
+	private class DataModel extends AbstractTableModel {
+		
+		private String[] colNames = {"Select", "TSN", "Name", "Common Name"};
+
+		@Override
+		public int getRowCount() {
+			if (speciesMapItems == null) {
+				return 0;
+			}
+			return speciesMapItems.size();
+		}
+
+		@Override
+		public int getColumnCount() {
+			return colNames.length;
+		}
+
+		@Override
+		public Object getValueAt(int rowIndex, int columnIndex) {
+			SpeciesMapItem mapItem = speciesMapItems.get(rowIndex);
+			switch (columnIndex) {
+			case 0:
+				return rowIndex == selectedRow;
+			case 1:
+				return mapItem.getItisCode();
+			case 2:
+				return mapItem.getLatinName();
+			case 3:
+				return mapItem.getCommonName();
+			}
+			return null;
+		}
+
+		@Override
+		public String getColumnName(int column) {
+			return colNames[column];
+		}
+
+		@Override
+		public Class<?> getColumnClass(int columnIndex) {
+			if (columnIndex == 0) {
+				return Boolean.class;
+			}
+			return super.getColumnClass(columnIndex);
+		}
+		
+	}
+
+}

src/tethys/species/swing/SpeciesSubPanel.java

@@ -85,7 +85,8 @@ public class SpeciesSubPanel {
 		
 		pamguardName.setToolTipText("Internal name within PAMGuard module");
 		itisCode.setToolTipText("ITIS species code");
-		searchButton.setToolTipText("Search for species code");
+		searchButton.setToolTipText("<html>Either enter a code manually and press \"Find\" for additional information,<br>"
+				+ "or leave the code empty and press \"Find\" to search the Tethys database using common or scientific names.</html>" );
 		callType.setToolTipText("Descriptive name for call type or measurement");
 		latinName.setToolTipText("Scientific name");
 		commonName.setToolTipText("Common name");
@@ -112,6 +113,17 @@ public class SpeciesSubPanel {
 			return;
 		}
 		ITISFunctions itisFunctions = tethysControl.getItisFunctions();
+		String itisString = this.itisCode.getText();
+		if (itisString == null || itisString.length() == 0) {
+			searchForCode(tethysControl, itisFunctions);
+		}
+		else {
+			getCodeInformation(tethysControl, itisFunctions, itisString);
+		}
+//		System.out.println(itisInfo);
+	}
+
+	private void getCodeInformation(TethysControl tethysControl, ITISFunctions itisFunctions, String itisString) {
 		int itisCode = 0;
 		try {
 			itisCode = Integer.valueOf(this.itisCode.getText());
@@ -128,8 +140,16 @@ public class SpeciesSubPanel {
 			if (itisInfo.getVernacular() != null) {
 				commonName.setText(itisInfo.getVernacular());
 			}
+		}		
+	}
+
+	private void searchForCode(TethysControl tethysControl, ITISFunctions itisFunctions) {
+		SpeciesMapItem speciesItem = SpeciesSearchDialog.showDialog(tethysControl.getGuiFrame(), tethysControl);
+		if (speciesItem != null) {
+			itisCode.setText(String.format("%d", speciesItem.getItisCode()));
+			latinName.setText(speciesItem.getLatinName());
+			commonName.setText(speciesItem.getCommonName());
 		}
-//		System.out.println(itisInfo);
 	}
 
 	public JComponent getDialogComponent() {