Starting to map species codes

src/PamguardMVC/PamDataBlock.java

@@ -3103,6 +3103,16 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
 		this.tethysDataProvider = tethysDataProvider;
 	}
 	
+
+	/**
+	 * Get information about species types that may occur within this data 
+	 * block.  
+	 * @return Types of species information available within this datablock. 
+	 */
+	public tethys.species.SpeciesTypes getSpeciesTypes() {
+		return null;
+	}
+
 	final public boolean getCanLog() {
 		return (logging != null);
 	}

src/tethys/dbxml/DBXMLQueries.java

@@ -129,7 +129,6 @@ public class DBXMLQueries {
 
 		String queryResult = null;
 		String schemaPlan = null;
-		TethysExportParams params = tethysControl.getTethysExportParams();
 
 		try {
 			JerseyClient jerseyClient = dbxmlConnect.getJerseyClient();

src/tethys/pamdata/TethysDataProvider.java

@@ -67,4 +67,5 @@ public interface TethysDataProvider {
 
 	public Parameters getAlgorithmParameters();
 	
+	
 }

src/tethys/species/DatablockSpeciesMap.java

@@ -0,0 +1,12 @@
+package tethys.species;
+
+import java.io.Serializable;
+
+/**
+ * Species map for a specified data block
+ * @author dg50
+ *
+ */
+public class DatablockSpeciesMap implements Serializable {
+
+}

src/tethys/species/SpeciesMapItem.java

@@ -0,0 +1,19 @@
+package tethys.species;
+
+import java.io.Serializable;
+
+public class SpeciesMapItem implements Serializable, Cloneable {
+
+	public static final long serialVersionUID = 1L;
+
+	private int itisCode;
+	
+	private String pamguardName;
+	
+	private String latinName;
+	
+	private String commonName;
+	
+	private String callType;
+	
+}

src/tethys/species/SpeciesMapManager.java

@@ -0,0 +1,5 @@
+package tethys.species;
+
+public class SpeciesMapManager {
+
+}

src/tethys/species/SpeciesTest.java

@@ -0,0 +1,110 @@
+package tethys.species;
+
+import dbxml.JerseyClient;
+import dbxml.Queries;
+import tethys.dbxml.DBQueryResult;
+import tethys.dbxml.TethysQueryException;
+
+public class SpeciesTest extends SpeciesTypes {
+
+	String uri = "http://localhost:9779";
+	public static void main(String[] args) {
+		
+		SpeciesTest st = new SpeciesTest();
+		st.runJson();
+		
+//		int spermWhale = 180488;
+//		st.getCodeInfo(spermWhale);
+//		st.runXQuery();
+
+	}
+	private  void getCodeInfo(int itisCode) {
+		System.out.println("Running getCodeInfo()");
+		String jQBase = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"=\",\"operands\":[\"ranks/rank/tsn\",\"SPECIESTSN\"],\"optype\":\"binary\"}],\"enclose\":1}";
+		String jQ = jQBase.replace("SPECIESTSN", String.format("%d", itisCode));
+		
+
+		DBQueryResult result = null;
+		String queryResult = null;
+		String schemaPlan = null;
+		JerseyClient jerseyClient = new JerseyClient(uri);
+		long t1 = System.nanoTime();
+		try {
+			queryResult = jerseyClient.queryJSON(jQ, 0);
+//			schemaPlan = jerseyClient.queryJSON(jQ, 1);
+		} catch (Exception e1) {
+			e1.printStackTrace();
+			
+		}
+		long t2 = System.nanoTime();
+		System.out.printf("Query time was %3.1fms\n" , (double) (t2-t1)/1e6);
+		System.out.println(queryResult);
+		
+		TethysITISResult itisResult = new TethysITISResult(queryResult);
+	}
+	/*
+	 * 
+<ranks xmlns="http://tethys.sdsu.edu/schema/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://tethys.sdsu.edu/schema/1.0 tethys.xsd">
+  <rank>
+    <tsn>-10</tsn>
+    <completename>Other phenomena</completename>
+    <vernacular>
+      <name language="English">Other</name>
+      <name language="French">Autre</name>
+      <name language="Spanish">Otro</name>
+    </vernacular>
+  </rank>
+  <rank>
+    <tsn>555654</tsn>
+    <completename>Delphinus capensis</completename>
+    <vernacular>
+      <name language="English">Long-beaked Common Dolphin</name>
+    </vernacular>
+  </rank>
+	 */
+	
+	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\")]";
+
+		JerseyClient jerseyClient = new JerseyClient(uri);
+		Queries queries = new Queries(jerseyClient);
+		
+		String result = null;
+		try {
+			 result = queries.QueryTethys(xQ);
+		} catch (Exception e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		System.out.println(result);
+		
+	}
+	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/completename\",\"Mesoplodon\"],\"optype\":\"binary\"}],\"enclose\":1}";
+		String jQ = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"dbxml:contains\",\"operands\":[\"ranks/rank/completename\",\"Mesoplodon\"],\"optype\":\"function\"}],\"enclose\":1}";
+
+		System.out.println(jQ);
+
+		DBQueryResult result = null;
+		String queryResult = null;
+		String schemaPlan = null;
+		JerseyClient jerseyClient = new JerseyClient(uri);
+		long t1 = System.nanoTime();
+		try {
+			queryResult = jerseyClient.queryJSON(jQ, 0);
+//			schemaPlan = jerseyClient.queryJSON(jQ, 1);
+		} catch (Exception e1) {
+			System.out.println("epic fail");
+			e1.printStackTrace();
+		}
+		long t2 = System.nanoTime();
+		System.out.printf("Query time was %3.1fms\n" , (double) (t2-t1)/1e6);
+		System.out.println(queryResult);
+		
+	}
+
+}

src/tethys/species/SpeciesTypes.java

@@ -0,0 +1,20 @@
+package tethys.species;
+
+import java.util.ArrayList;
+
+/**
+ * Class to return lists of species codes or names for a datablock. 
+ * This information will then get incorporated into a more complicated translation table to 
+ * provide PAMGuard data on it's way to Tethys with more rigid species code definitions.  
+ * @author dg50
+ *
+ */
+public class SpeciesTypes {
+
+
+	/**
+	 * List of species names / codes associated with this data block. 
+	 */
+	private ArrayList<String> speciesNames;
+	
+}

src/tethys/species/TethysITISResult.java

@@ -0,0 +1,37 @@
+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
+ * in a Tethys database. 
+ * @author dg50
+ *
+ */
+public class TethysITISResult {
+
+	/**
+	 * Construct a ITIS object from XML data
+	 * @param xmlData
+	 */
+	public TethysITISResult(String xmlData) {
+
+		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)));
+		
+	}
+}