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Data export

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A few fixes in Detections export.
This commit is contained in:
Douglas Gillespie 2023-09-07 16:58:38 +01:00
parent 3688719e25
commit fb00a757cd
6 changed files with 115 additions and 28 deletions
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3
src/tethys/dbxml/DBXMLConnect.java
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@ -163,8 +163,9 @@ public class DBXMLConnect {
* Quite hard to see much common structure in this, so just look for
* two words, <Success> and <Error>
*/
boolean error = importReturn.contains("<Error>");
boolean error = importReturn.contains("<Error");
boolean success = importReturn.contains("<Success>");
// error = !success; might be a better options.
if (error) {
throw new TethysException("Error posting to Tethys", importReturn);
}

25
src/tethys/detection/DetectionsHandler.java
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@ -262,30 +262,19 @@ public class DetectionsHandler {
// return false;
// }
private DetectionEffort getDetectorEffort(Deployment deployment, long effortStart, long effortEnd) {
private DetectionEffort getDetectorEffort(PDeployment pDeployment, PamDataBlock dataBlock, StreamExportParams exportParams) {
DetectionEffort effort = new DetectionEffort();
Deployment deployment = pDeployment.deployment;
Long effortStart = pDeployment.getAudioStart();
Long effortEnd = pDeployment.getAudioEnd();
effort.setStart(TethysTimeFuncs.xmlGregCalFromMillis(effortStart));
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);
TethysDataProvider dataProvider = dataBlock.getTethysDataProvider();
dataProvider.getEffortKinds(pDeployment, effortKinds, exportParams);
effortKinds.add(kind);
return effort;
}
@ -508,7 +497,7 @@ public class DetectionsHandler {
supSoft.add(supportSoft);
detections.setAlgorithm(algorithm);
detections.setUserId("Unknown user");
detections.setEffort(getDetectorEffort(deployment.deployment, deployment.getAudioStart(), deployment.getAudioEnd()));
detections.setEffort(getDetectorEffort(deployment, dataBlock, exportParams));
return detections;
}

47
src/tethys/pamdata/AutoTethysProvider.java
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@ -1,6 +1,7 @@
package tethys.pamdata;
import java.math.BigInteger;
import java.util.ArrayList;
import java.util.List;
import org.w3c.dom.Document;
@ -26,12 +27,15 @@ import nilus.AlgorithmType.Parameters;
import nilus.Deployment;
import nilus.DescriptionType;
import nilus.Detection;
import nilus.DetectionEffortKind;
import nilus.SpeciesIDType;
import tethys.TethysControl;
import tethys.TethysTimeFuncs;
import tethys.niluswraps.PDeployment;
import tethys.output.StreamExportParams;
import tethys.output.TethysExportParams;
import tethys.species.DataBlockSpeciesManager;
import tethys.species.DataBlockSpeciesMap;
import tethys.species.ITISTypes;
import tethys.species.SpeciesMapItem;
import whistleClassifier.WhistleContour;
@ -136,7 +140,7 @@ public class AutoTethysProvider implements TethysDataProvider {
// TODO Auto-generated catch block
e.printStackTrace();
}
List<Element> genList = paramPacker.packParameters(settings);
List<Element> genList = paramPacker.packParameters(pamControlledUnit);
if (genList == null || genList.size() == 0) {
return null;
}
@ -389,4 +393,45 @@ public class AutoTethysProvider implements TethysDataProvider {
return species;
}
@Override
public void getEffortKinds(PDeployment pDeployment, List<DetectionEffortKind> effortKinds, StreamExportParams exportParams) {
DataBlockSpeciesManager speciesManager = pamDataBlock.getDatablockSpeciesManager();
if (speciesManager == null) {
return;
}
DataBlockSpeciesMap speciesMap = speciesManager.getDatablockSpeciesMap();
ArrayList<String> speciesCodes = speciesManager.getAllSpeciesCodes();
if (speciesCodes == null || speciesMap == null) {
return;
}
for (String speciesCode : speciesCodes) {
SpeciesMapItem mapItem = speciesMap.getItem(speciesCode);
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(mapItem.getItisCode()));
kind.getGranularity().setValue(exportParams.granularity);
kind.setCall(mapItem.getCallType());
effortKinds.add(kind);
}
}
}

19
src/tethys/pamdata/TethysDataProvider.java
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@ -1,11 +1,15 @@
package tethys.pamdata;
import java.util.List;
import PamguardMVC.PamDataUnit;
import nilus.AlgorithmType;
import nilus.AlgorithmType.Parameters;
import nilus.Deployment;
import nilus.DescriptionType;
import nilus.Detection;
import nilus.DetectionEffortKind;
import tethys.niluswraps.PDeployment;
import tethys.output.StreamExportParams;
import tethys.output.TethysExportParams;
@ -65,7 +69,22 @@ public interface TethysDataProvider {
StreamExportParams streamExportParams);
/**
* Get the algorithm parameters.
* @return
*/
public Parameters getAlgorithmParameters();
/**
* Fill in the effort kind list for the top of a Detections document. This must contain a list
* of every species that's going to be output within this effort period. Any species assigned
* to an actual detection must be in this list, or the document will be rejected.
* @param pDeployment
* @param effortKinds tethys object list to add to.
* @param exportParams
*/
public void getEffortKinds(PDeployment pDeployment, List<DetectionEffortKind> effortKinds, StreamExportParams exportParams);
}

26
src/tethys/pamdata/TethysParameterPacker.java
View File

@ -17,6 +17,8 @@ import javax.xml.transform.dom.DOMResult;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import PamController.PamControlledUnit;
import PamController.PamSettings;
import PamController.settings.output.xml.PamguardXMLWriter;
import PamModel.parametermanager.ManagedParameters;
import PamModel.parametermanager.PamParameterData;
@ -68,6 +70,8 @@ public class TethysParameterPacker {
private MarshalXML marshaller;
private PamguardXMLWriter xmlWriter;
/**
* @throws JAXBException
*
@ -78,11 +82,20 @@ public class TethysParameterPacker {
marshaller = new MarshalXML();
} catch (JAXBException e) {
}
xmlWriter = PamguardXMLWriter.getXMLWriter();
}
public List<Element> packParameters(Object data) {
public List<Element> packParameters(PamControlledUnit pamControlledUnit) {
if (pamControlledUnit instanceof PamSettings == false) {
return null;
}
PamSettings pamSettings = (PamSettings) pamControlledUnit;
// return null;
// }
//
// public List<Element> packParameters(Object data) {
List<Element> elList = new ArrayList<Element>();
Object data = pamSettings.getSettingsReference();
ArrayList<Object> objectHierarchy = new ArrayList<>();
@ -121,15 +134,16 @@ public class TethysParameterPacker {
try {
Object paramData = pamParam.getData();
boolean ok = createElement(doc, el, paramData, pamParam, objectHierarchy);
// if (newEl != null) {
// elList.add(newEl);
// }
} catch (IllegalArgumentException | IllegalAccessException e) {
e.printStackTrace();
}
}
elList.add(el);
Element pgEl = xmlWriter.writeUnitSettings(doc, el, pamSettings);
if (pgEl != null) {
el.appendChild(pgEl);
// elList.add(pgEl);
}
return elList;
}

21
src/tethys/swing/DatablockDetectionsPanel.java
View File

@ -23,6 +23,7 @@ import tethys.TethysControl;
import tethys.dbxml.TethysException;
import tethys.detection.StreamDetectionsSummary;
import tethys.niluswraps.PDetections;
import tethys.niluswraps.TethysCollections;
/**
* Table of Detections documents for a single PAMGuard datablock.
@ -104,6 +105,8 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
return;
}
JPopupMenu popMenu = new JPopupMenu();
JMenuItem menuItem = new JMenuItem("Delete " + pDets.detections.getId());
menuItem.addActionListener(new ActionListener() {
@Override
@ -111,8 +114,19 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
deleteDocument(pDets);
}
});
JPopupMenu popMenu = new JPopupMenu();
popMenu.add(menuItem);
menuItem = new JMenuItem("Display " + pDets.detections.getId());
menuItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
displayDocument(pDets);
}
});
popMenu.add(menuItem);
popMenu.show(e.getComponent(), e.getX(), e.getY());
}
@ -126,6 +140,11 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
selectDataBlock(dataBlock); // force table update.
}
private void displayDocument(PDetections pDets) {
getTethysControl().displayDocument(TethysCollections.Detections.toString(), pDets.detections.getId());
}
private PDetections detectionsForRow(int iRow) {
if (streamDetectionsSummary == null || streamDetectionsSummary.detectionsDocs == null) {
return null;