Merge branch 'main' of https://github.com/douggillespie/PAMGuardTethys

src/tethys/dbxml/DBXMLConnect.java

@@ -1,6 +1,21 @@
 package tethys.dbxml;
 
+import java.io.IOException;
+import java.nio.file.Files;
+import java.util.List;
+
+import javax.xml.bind.JAXBException;
+
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import dbxml.uploader.Importer;
+import nilus.Deployment;
+import nilus.MarshalXML;
 import tethys.TethysControl;
+import tethys.output.TethysExportParams;
+import tethys.output.StreamExportParams;
+import PamguardMVC.PamDataBlock;
 
 /**
  * Class containing functions for managing the database connection. Opening, closing,
@@ -16,6 +31,80 @@ public class DBXMLConnect {
 		this.tethysControl = tethysControl;
 	}
 	
+	
+	/**
+	 * take list of nilus objects loaded with PamGuard data and post them to the Tethys database
+	 * all objects must be of the same nilus object
+	 * TethysExportParams obj used from UI inputs  
+	 * 
+	 * @param pamGuardObjs all nilus objects loaded with PamGuard data
+	 * @return error string, null string means there are no errors
+	 */
+	public String postToTethys(List<?> pamGuardObjs) 
+	{
+		Class objClass = pamGuardObjs.get(0).getClass();
+		String collection = getTethysCollection(objClass.getName());
+		PamDataBlock defaultPamBlock = null;
+		TethysExportParams params = new TethysExportParams();
+		String fileError = null;
+		try {
+			MarshalXML marshal = new MarshalXML();
+			marshal.createInstance(objClass);			
+			for (Object obj : pamGuardObjs ) 
+			{				
+				Path tempFile = Files.createTempFile("pamGuardToTethys", ".xml");
+				marshal.marshal(obj, tempFile.toString());
+				fileError = Importer.ImportFiles(params.getFullServerName(), collection,
+						new String[] { tempFile.toString() }, "", "", false);
+
+				System.out.println(fileError);
+				
+				tempFile.toFile().deleteOnExit();
+			}
+		} catch(IllegalArgumentException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		} catch (JAXBException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}	
+		
+		return fileError;
+	}
+	
+	/**
+	 * get tethys collection name from nilus collection objects
+	 * @param className nilus object Class Name
+	 * @return name of Tethys collection
+	 */
+	private String getTethysCollection(String className) {
+		switch(className) {
+			case "nilus.Deployment": 
+				return "Deployments";				
+			case "nilus.Detections": 
+				return "Detections";
+			case "nilus.Calibration": 
+				return "Calibrations";				
+			case "nilus.Ensemble": 
+				return "Ensembles";			
+			case "nilus.Localization": 
+				return "Localizations";				
+			case "nilus.SpeciesAbbreviation": 
+				return "SpeciesAbbreviations";				
+			case "nilus.SourceMap": 
+				return "SourceMaps";				
+			case "nilus.ITIS": 
+				return "ITIS";							
+			case "nilus.ranks": 
+				return "ITIS_ranks";
+			default: 
+				return "";									
+		}
+	}
+	
 	public boolean openDatabase() {
 		
 		return true;

src/tethys/deployment/DeploymentHandler.java

@@ -22,6 +22,7 @@ import Array.ThreadingHydrophoneLocator;
 import PamController.PamControlledUnit;
 import PamController.PamController;
 import PamguardMVC.PamDataBlock;
+import javafx.scene.chart.PieChart.Data;
 import metadata.MetaDataContol;
 import metadata.deployment.DeploymentData;
 import nilus.Audio;
@@ -143,7 +144,7 @@ public class DeploymentHandler {
 		}
 		double[] ons = new double[n-1]; // ignore the last one since it may be artificially shortened which is OK
 		double[] gaps = new double[n-1];
-		for (int i = 0; i < n; i++) {
+		for (int i = 0; i < n-1; i++) {
 			ons[i] = tempPeriods.get(i).getDuration();
 		}
 		return null;
@@ -283,13 +284,25 @@ public class DeploymentHandler {
 
 	public Deployment createDeploymentDocument(int i, DeploymentRecoveryPair drd) {
 		Deployment deployment = new Deployment();
+		try {
+			nilus.Helper.createRequiredElements(deployment);
+		} catch (IllegalArgumentException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		} catch (IllegalAccessException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		} catch (InstantiationException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
 		String id = String.format("%d", i);
 		deployment.setId(id);
 		deployment.setDeploymentId(i);
 		deployment.setDeploymentDetails(drd.deploymentDetails);
 		deployment.setRecoveryDetails(drd.recoveryDetails);
 
-		TethysLocationFuncs.getTrackAndPositionData(deployment);
+		TethysLocationFuncs.getTrackAndPositionData(deployment);			
 
 		getProjectData(deployment);
 
@@ -317,9 +330,16 @@ public class DeploymentHandler {
 	 */
 	private boolean getProjectData(Deployment deployment) {
 		PamControlledUnit aUnit = PamController.getInstance().findControlledUnit(MetaDataContol.class, null);
-		if (aUnit instanceof MetaDataContol == false) {
+		if (aUnit instanceof MetaDataContol == false || true) {
+			deployment.setProject("thisIsAProject");
+			deployment.setPlatform("Yay a platform");
+			Instrument instrument = new Instrument();
+			instrument.setType("machiney");
+			instrument.setInstrumentId("12345555");			
+			deployment.setInstrument(instrument);
 			return false;
 		}
+		
 		MetaDataContol metaControl = (MetaDataContol) aUnit;
 		DeploymentData deploymentData = metaControl.getDeploymentData();
 		deployment.setProject(deploymentData.getProject());

src/tethys/detection/DetectionsHandler.java

@@ -1,5 +1,6 @@
 package tethys.detection;
 
+import java.math.BigInteger;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -166,7 +167,10 @@ public class DetectionsHandler {
 		 * We should now have a fully populated Detections object, so write it to the database
 		 * using functions in DBXMLConnect 
 		 */
-		tethysControl.getDbxmlConnect(); // call whatever you need to call in here to write the Detections. 
+		ArrayList<Detections> detectionDocuments = new ArrayList();
+		detectionDocuments.add(detections);
+		
+		tethysControl.getDbxmlConnect().postToTethys(detectionDocuments); // call whatever you need to call in here to write the Detections. 
 		
 		
 		return true;
@@ -185,6 +189,25 @@ public class DetectionsHandler {
 		effort.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(effortEnd));
 //		effort.set // no setter for DetectionEffortKind
 		List<DetectionEffortKind> effortKinds = effort.getKind();
+		DetectionEffortKind kind = new DetectionEffortKind();
+		try {
+			nilus.Helper.createRequiredElements(kind);
+		} catch (IllegalArgumentException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		} catch (IllegalAccessException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		} catch (InstantiationException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		
+		kind.getSpeciesId().setValue(BigInteger.valueOf(180537));
+		kind.getGranularity().setValue(nilus.GranularityEnumType.CALL);
+		
+		effortKinds.add(kind);		
+				 
 		return effort;
 	}
 

src/tethys/output/StreamExportParams.java

@@ -12,7 +12,7 @@ import java.io.Serializable;
  */
 public class StreamExportParams implements Serializable {
 
-	public static final long serialVersionUID = 1L;
+	public static final long serialVersionUID = 1L;	
 
 	public StreamExportParams(String longDataName, boolean selected) {
 		super();

src/tethys/output/TethysExportParams.java

@@ -2,9 +2,9 @@ package tethys.output;
 
 import java.io.Serializable;
 import java.util.HashMap;
-
 import PamguardMVC.PamDataBlock;
 
+
 /**
  * Parameters for controlling export of Tethys data. 
  * @author dg50
@@ -18,6 +18,13 @@ public class TethysExportParams implements Serializable, Cloneable{
 	 * Need to add lots of other parameters here, such as the connection detils
 	 * for the tethys database. 
 	 */
+	public String serverName = "http://localhost";
+	
+	public String port = "9779";
+	
+	public String getFullServerName() {
+		return serverName + ":" + port;			
+	}
 	
 	private HashMap<String, StreamExportParams> streamParamsMap = new HashMap();
 

src/tethys/output/TethysExporter.java

@@ -1,7 +1,7 @@
 package tethys.output;
 
 import java.io.IOException;
-import java.io.StringWriter;
+import java.io.PrintWriter;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
@@ -82,39 +82,7 @@ public class TethysExporter {
 		 */
 		// return false;
 		// }
-
-		Deployment deployment1 = new Deployment();
-		deployment1.setId("1");
-
-		Path tempFile = null;
-		try {
-
-			JAXBContext jaxB = JAXBContext.newInstance(Deployment.class);
-			Marshaller marshall = jaxB.createMarshaller();
-			marshall.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
-			StringWriter sw = new StringWriter();
-			marshall.marshal(deployment1, sw);
-			tempFile = Files.createTempFile("pamGuardToTethys", ".xml");
-			Files.write(tempFile, sw.toString().getBytes());
-
-			String fileText = Importer.ImportFiles("http://localhost:9779", "Deployment",
-					new String[] { tempFile.toString() }, "", "", false);
-
-			tempFile.toFile().deleteOnExit();
-
-		} catch(IllegalArgumentException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		} catch (IOException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		} catch (JAXBException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-
-		SnapshotGeometry arrayGeometry = findArrayGeometrey();
-
+				
 		/**
 		 * Doug populate instrument fields - may need to add a few things. Marie to
 		 * define what we mean by instrument. Instrument names probably need to be added
@@ -220,7 +188,7 @@ public class TethysExporter {
 
 		}
 
-		
+		tethysControl.getDbxmlConnect().postToTethys(deploymentDocs);
 
 		/*
 		 * go through the export params and call something for every data block that's

src/tethys/pamdata/AutoTethysProvider.java

@@ -249,7 +249,7 @@ public class AutoTethysProvider implements TethysDataProvider {
 
 	private SpeciesIDType getSpeciesIdType() {
 		SpeciesIDType species = new SpeciesIDType();
-//		species.s
+		species.setValue(BigInteger.valueOf(180537));
 		return species;
 	}