Playing with export options

This commit is contained in:
Douglas Gillespie 2023-05-06 19:26:04 +01:00
parent 38b05b13c5
commit 71c8415bc8
9 changed files with 386 additions and 70 deletions

View File

@ -0,0 +1,20 @@
package PamController;
/**
* Interface to define modules which can be considered as sensors of some sort.
* e.g. depth and orientation modules and the SoundTrap clickdetecotr
* @author dg50
*
*/
public interface PamSensor {
public String getUnitName();
public String getUnitType();
public String getSensorDescription();
public String getSensorId();
}

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@ -47,7 +47,7 @@ public class PamCalendar {
public static TimeZone defaultTimeZone = TimeZone.getTimeZone("UTC");
private static TimeZone localTimeZone = TimeZone.getDefault();
private static TimeZone localTimeZone = defaultTimeZone;// TimeZone.getDefault();
public static final long millisPerDay = 1000L*24L*3600L;

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@ -747,9 +747,9 @@ public class DataStreamPanel extends JPanel implements DataMapObserver {
String tipText;
if (startTimeArrow != null && startTimeArrow.contains(me.getPoint())) {
tipText = "Data Start: " + PamCalendar.formatDateTime(dataBlock.getCurrentViewDataStart(), true);
tipText = "Data Start: " + PamCalendar.formatDateTime(dataBlock.getCurrentViewDataStart(), false);
} else if (endTimeArrow != null && endTimeArrow.contains(me.getPoint())) {
tipText = "Data End: " + PamCalendar.formatDateTime(dataBlock.getCurrentViewDataEnd(), true);
tipText = "Data End: " + PamCalendar.formatDateTime(dataBlock.getCurrentViewDataEnd(), false);
} else {
tipText = "Cursor: " + PamCalendar.formatDateTime(tm, true);
}

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@ -37,6 +37,7 @@ import javax.swing.JSeparator;
import org.pamguard.x3.sud.SUDClickDetectorInfo;
import Acquisition.AcquisitionControl;
import PamController.PamSensor;
import PamController.PamControlledUnitSettings;
import PamController.PamController;
import PamguardMVC.PamRawDataBlock;
@ -51,7 +52,7 @@ import soundtrap.sud.SudFileDWVHandler;
* @author mo55
*
*/
public class STClickControl extends ClickControl {
public class STClickControl extends ClickControl implements PamSensor {
private SUDClickDetectorInfo sudClickDetectorInfo;
@ -218,5 +219,16 @@ public class STClickControl extends ClickControl {
this.sudClickDetectorInfo = sudClickDetectorInfo;
}
@Override
public String getSensorDescription() {
String desc = String.format("SoundTrap Click Detector at %dHz", (int) getClickDataBlock().getSampleRate());
return desc;
}
@Override
public String getSensorId() {
return null;
}
}

View File

@ -264,6 +264,9 @@ public class DBXMLQueries {
e.printStackTrace();
return null;
}
if (doc == null) {
return null;
}
ArrayList<String> detectionsNames = new ArrayList();
int count = 0;
NodeList returns = doc.getElementsByTagName("Detections");

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@ -15,21 +15,24 @@ import Acquisition.AcquisitionControl;
import Acquisition.AcquisitionParameters;
import Acquisition.DaqStatusDataUnit;
import Acquisition.DaqSystem;
import Acquisition.FolderInputSystem;
import Array.ArrayManager;
import Array.Hydrophone;
import Array.HydrophoneLocator;
import Array.PamArray;
import Array.Streamer;
import Array.ThreadingHydrophoneLocator;
import PamController.PamSensor;
import PamController.PamControlledUnit;
import PamController.PamController;
import PamUtils.LatLong;
import PamUtils.PamCalendar;
import PamUtils.PamUtils;
import PamguardMVC.PamDataBlock;
import SoundRecorder.RecordingInfo;
import javafx.scene.chart.PieChart.Data;
import metadata.MetaDataContol;
import PamguardMVC.PamRawDataBlock;
import binaryFileStorage.BinaryStore;
import dataMap.OfflineDataMap;
import dataMap.OfflineDataMapPoint;
import generalDatabase.DBControlUnit;
import metadata.deployment.DeploymentData;
import nilus.Audio;
import nilus.ChannelInfo;
@ -39,12 +42,14 @@ import nilus.ChannelInfo.DutyCycle.Regimen.RecordingIntervalS;
import nilus.ChannelInfo.Sampling;
import nilus.ChannelInfo.Sampling.Regimen;
import nilus.Deployment;
import nilus.Deployment.Data;
import nilus.Deployment.Instrument;
import nilus.Deployment.SamplingDetails;
import nilus.Deployment.Sensors;
import nilus.DeploymentRecoveryDetails;
import nilus.GeometryTypeM;
import nilus.Helper;
import nilus.UnknownSensor;
import pamMaths.PamVector;
import pamMaths.STD;
import tethys.TethysControl;
@ -52,7 +57,10 @@ import tethys.TethysLocationFuncs;
import tethys.TethysState;
import tethys.TethysStateObserver;
import tethys.TethysTimeFuncs;
import tethys.TethysState.StateType;
import tethys.dbxml.DBXMLConnect;
import tethys.niluswraps.PDeployment;
import tethys.output.TethysExportParams;
/**
* Functions to gather data for the deployment document from all around PAMGuard.
@ -66,6 +74,13 @@ public class DeploymentHandler implements TethysStateObserver {
private TethysControl tethysControl;
/**
* @return the tethysControl
*/
public TethysControl getTethysControl() {
return tethysControl;
}
private DeploymentOverview deploymentOverview;
private ArrayList<PDeployment> projectDeployments;
@ -184,6 +199,10 @@ public class DeploymentHandler implements TethysStateObserver {
else {
tempPeriods = extractTimesFromStatus(allStatusData);
}
if (tempPeriods == null || tempPeriods.size() == 0) {
System.out.println("Data appear to have no logged recording periods available either from the database or the raw recordings.");
tempPeriods = extractTimesFromOutputMaps();
}
if (tempPeriods == null || tempPeriods.size() == 0) {
System.out.println("Data appear to have no logged recording periods available either from the database or the raw recordings.");
return null;
@ -255,6 +274,123 @@ public class DeploymentHandler implements TethysStateObserver {
}
/**
* Exprt deployments docs. Playing with a couple of different ways of doing this.
* @param selectedDeployments
*/
public void exportDeployments(ArrayList<RecordingPeriod> selectedDeployments) {
if (false) {
exportSeparateDeployments(selectedDeployments);
}
else {
exportOneDeploymnet(selectedDeployments);
}
}
/**
* Make one big deployment document with all the recording periods in it.
*/
private void exportOneDeploymnet(ArrayList<RecordingPeriod> selectedDeployments) {
// do the lot, whatever ...
selectedDeployments = getDeploymentOverview().getRecordingPeriods();
int freeId = getTethysControl().getDeploymentHandler().getFirstFreeDeploymentId();
RecordingPeriod onePeriod = new RecordingPeriod(selectedDeployments.get(freeId).getRecordStart(),
selectedDeployments.get(selectedDeployments.size()-1).getRecordStop());
Deployment deployment = createDeploymentDocument(freeId, onePeriod);
// fill in a few things from here
DeploymentData globalMeta = getTethysControl().getGlobalDeplopymentData();
deployment.setCruise(globalMeta.getCruise());
deployment.setSite(globalMeta.getSite());
if (selectedDeployments.size() > 1) {
// now need to remove the
SamplingDetails samplingDetails = deployment.getSamplingDetails();
samplingDetails.getChannel().clear();
for (int i = 0; i < selectedDeployments.size(); i++) {
addSamplingDetails(deployment, selectedDeployments.get(i));
}
}
DBXMLConnect dbxmlConnect = getTethysControl().getDbxmlConnect();
PDeployment exDeploymnet = onePeriod.getMatchedTethysDeployment();
if (exDeploymnet != null) {
deployment.setId(exDeploymnet.deployment.getId());
dbxmlConnect.updateDocument(deployment);
}
else {
dbxmlConnect.postToTethys(deployment);
}
getTethysControl().sendStateUpdate(new TethysState(StateType.UPDATESERVER));
}
/**
* Make a separate deployment document for every recording period.
*/
private void exportSeparateDeployments(ArrayList<RecordingPeriod> selectedDeployments) {
int freeId = getTethysControl().getDeploymentHandler().getFirstFreeDeploymentId();
for (int i = 0; i < selectedDeployments.size(); i++) {
RecordingPeriod recordPeriod = selectedDeployments.get(i);
PDeployment exDeploymnet = recordPeriod.getMatchedTethysDeployment();
Deployment deployment = null;
if (exDeploymnet != null) {
deployment = createDeploymentDocument(freeId, recordPeriod);
deployment.setId(exDeploymnet.deployment.getId());
}
if (deployment == null) {
deployment = createDeploymentDocument(freeId++, recordPeriod);
}
// fill in a few things from here
DeploymentData globalMeta = getTethysControl().getGlobalDeplopymentData();
deployment.setCruise(globalMeta.getCruise());
deployment.setSite(globalMeta.getSite());
// also need to sort out track data here, etc.
DBXMLConnect dbxmlConnect = getTethysControl().getDbxmlConnect();
if (exDeploymnet != null) {
dbxmlConnect.updateDocument(deployment);
}
else {
dbxmlConnect.postToTethys(deployment);
}
}
getTethysControl().sendStateUpdate(new TethysState(StateType.UPDATESERVER));
}
/**
* Get data times from any other datamap, since this will generally match the acquisition anyway
* @return
*/
private ArrayList<RecordingPeriod> extractTimesFromOutputMaps() {
OfflineDataMap bestMap = null;
PamDataBlock bestBlock = null;
long firstStart = Long.MAX_VALUE;
long lastEnd = Long.MIN_VALUE;
ArrayList<PamDataBlock> dataBlocks = PamController.getInstance().getDetectorDataBlocks();
for (PamDataBlock aBlock : dataBlocks) {
if (aBlock instanceof PamRawDataBlock) {
continue; // don't want acquisition !
}
OfflineDataMap dataMap = aBlock.getPrimaryDataMap();
if (dataMap == null) {
continue;
}
if (dataMap.getFirstDataTime() < firstStart && dataMap.getLastDataTime() > lastEnd) {
bestMap = dataMap;
bestBlock = aBlock;
firstStart = dataMap.getFirstDataTime();
lastEnd = dataMap.getLastDataTime();
}
}
if (bestMap == null) {
return null;
}
// get the times out of it.
ArrayList<RecordingPeriod> recPeriods = new ArrayList<>();
List<OfflineDataMapPoint> mapPoints = bestMap.getMapPoints();
for (OfflineDataMapPoint mapPoint : mapPoints) {
recPeriods.add(new RecordingPeriod(mapPoint.getStartTime(), mapPoint.getEndTime()));
}
return recPeriods;
}
public DeploymentOverview getDeploymentOverview() {
return deploymentOverview;
}
@ -305,7 +441,7 @@ public class DeploymentHandler implements TethysStateObserver {
* @return overlap in milliseconds
*/
public long getDeploymentOverlap(PDeployment aDeployment, RecordingPeriod aPeriod) {
long start = aPeriod.getRecordStart();
long start = aPeriod.getRecordStart(); // recording period.
long stop = aPeriod.getRecordStop();
long depStart = aDeployment.getAudioStart();
long depStop = aDeployment.getAudioEnd();
@ -551,7 +687,8 @@ public class DeploymentHandler implements TethysStateObserver {
e.printStackTrace();
}
DeploymentData globalDeplData = tethysControl.getGlobalDeplopymentData();
String id = String.format("%s_%d", globalDeplData.getProject(), i);
TethysExportParams exportParams = tethysControl.getTethysExportParams();
String id = String.format("%s_%d", exportParams.getDatasetName(), i);
deployment.setId(id);
deployment.setDeploymentId(i);
@ -576,22 +713,113 @@ public class DeploymentHandler implements TethysStateObserver {
getProjectData(deployment);
getSamplingDetails(deployment, recordingPeriod);
addSamplingDetails(deployment, recordingPeriod);
getSensorDetails(deployment);
getSensors(deployment);
/**
* Stuff that may need to be put into the UI:
* Audio: can easily get current loc of raw and binary data, but may need to override these. I think
* this may be for the export UI ?
* Tracks: trackline information. General problem in PAMGUard.
*/
getDataDetails(deployment);
return deployment;
}
public String getBinaryDataURI() {
BinaryStore binStore = BinaryStore.findBinaryStoreControl();
if (binStore != null) {
return binStore.getBinaryStoreSettings().getStoreLocation();
}
return null;
}
public String getDatabaseURI() {
DBControlUnit databaseControl = DBControlUnit.findDatabaseControl();
if (databaseControl != null) {
return databaseControl.getLongDatabaseName();
}
return null;
}
public String getRawDataURI() {
try {
PamControlledUnit daq = PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
if (daq instanceof AcquisitionControl) {
AcquisitionControl daqCtrl = (AcquisitionControl) daq;
DaqSystem system = daqCtrl.findDaqSystem(null);// getAcquisitionProcess().getRunningSystem();
if (system instanceof FolderInputSystem) {
FolderInputSystem fip = (FolderInputSystem) system;
return fip.getFolderInputParameters().recentFiles.get(0);
}
}
}
catch (Exception e) {
}
return "unknown";
}
private void getDataDetails(Deployment deployment) {
Data data = deployment.getData();
if (data == null) {
data = new Data();
deployment.setData(data);
}
nilus.Deployment.Data.Audio audio = data.getAudio();
if (audio == null) {
audio = new nilus.Deployment.Data.Audio();
data.setAudio(audio);
}
audio.setURI(getRawDataURI());
String processed = "Database:"+getDatabaseURI();
String binary = getBinaryDataURI();
if (binary != null) {
binary += ";Binary:"+binary;
}
audio.setProcessed(processed);
}
/**
* Get sensor information. The Soundtrap CTD will count as a sensor.
* Modules that are sensors will have to implement a PAMSensor interface
* @param deployment
*/
private void getSensors(Deployment deployment) {
ArrayList<PamControlledUnit> sensorModules = PamController.getInstance().findControlledUnits(PamSensor.class, true);
if (sensorModules == null || sensorModules.size() == 0) {
return;
}
Sensors sensors = deployment.getSensors();
if (sensors == null) {
sensors = new Sensors();
deployment.setSensors(sensors);
}
List<UnknownSensor> sensorList = sensors.getSensor();
for (PamControlledUnit aUnit : sensorModules) {
PamSensor pamSensor = (PamSensor) aUnit;
UnknownSensor nilusSensor = new UnknownSensor();
try {
Helper.createRequiredElements(nilusSensor);
} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// nilusSensor.setName(pamSensor.getUnitName());
nilusSensor.setType(pamSensor.getUnitType());
nilusSensor.setNumber(BigInteger.ZERO);
nilusSensor.setDescription(pamSensor.getSensorDescription());
nilusSensor.setSensorId(pamSensor.getUnitType());
sensorList.add(nilusSensor);
}
}
/**
* Add project Metadata to a Deploymnet document. This is currently being
* made available in the MetaDataControl module which should be added to PAMGuard
@ -781,10 +1009,18 @@ public class DeploymentHandler implements TethysStateObserver {
* @param deployment
* @param recordingPeriod
*/
private boolean getSamplingDetails(Deployment deployment, RecordingPeriod recordingPeriod) {
SamplingDetails samplingDetails = new SamplingDetails();
private boolean addSamplingDetails(Deployment deployment, RecordingPeriod recordingPeriod) {
SamplingDetails samplingDetails = deployment.getSamplingDetails();
if (samplingDetails == null) {
samplingDetails = new SamplingDetails();
deployment.setSamplingDetails(samplingDetails);
}
// this is basically going to be a list of almost identical channel information
// currently just for the first acquisition. May extend to more.
// see if there is > 1 acquisition. May want to include many.
ArrayList<PamControlledUnit> daqUnits = PamController.getInstance().findControlledUnits(AcquisitionControl.class);
AcquisitionControl daq = (AcquisitionControl) PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
if (daq == null) {
return false;
@ -858,7 +1094,6 @@ public class DeploymentHandler implements TethysStateObserver {
* earlier to a wrapper around the Deployment class.
*/
}
deployment.setSamplingDetails(samplingDetails);
return true;
}

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@ -3,6 +3,7 @@ package tethys.output;
import java.io.Serializable;
import java.util.HashMap;
import PamguardMVC.PamDataBlock;
import generalDatabase.DBControlUnit;
import metadata.deployment.DeploymentData;
@ -31,6 +32,51 @@ public class TethysExportParams implements Serializable, Cloneable{
private DeploymentData deploymentData;
/**
* PAMGuard HAS to have a dataset name to link to data in Tethys, or it all gets
* very confusing. This will be used in Deployment and Detection document names.
*/
private String datasetName;
/**
* @return the datasetName
*/
public String getDatasetName() {
if (datasetName == null) {
datasetName = getDefaultDatasetName();
}
return datasetName;
}
private String getDefaultDatasetName() {
// get the database name. It must exist in viewer mode !
DBControlUnit dbControl = DBControlUnit.findDatabaseControl();
String dbName = dbControl.getDatabaseName();
// strip off trailing file type.
int dPos = dbName.lastIndexOf('.');
if (dPos > 0) {
dbName = dbName.substring(0, dPos);
}
/*
* if the name ends in database, then remove that too (this is quite
* common since it's the default for batch output
*/
if (dbName.toLowerCase().endsWith("database")) {
dbName = dbName.substring(0, dbName.length()-"database".length());
}
if (dbName.endsWith("_")) {
dbName = dbName.substring(0, dbName.length()-1);
}
return dbName;
}
/**
* @param datasetName the datasetName to set
*/
public void setDatasetName(String datasetName) {
this.datasetName = datasetName;
}
@Override
public TethysExportParams clone() {
try {

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@ -34,6 +34,7 @@ import tethys.TethysControl;
import tethys.TethysState;
import tethys.TethysState.StateType;
import tethys.dbxml.DBXMLConnect;
import tethys.deployment.DeploymentHandler;
import tethys.deployment.RecordingPeriod;
import tethys.niluswraps.PDeployment;
@ -94,7 +95,7 @@ public class DeploymentExportPanel extends TethysGUIPanel implements DeploymentT
addPair("Cruise ", cruise, c);
addPair("Raw data URI ", rawURI, c);
addPair("Binary data URI ", binaryURI, c);
addPair("Datbase URI ", databaseURI, c);
addPair("Database URI ", databaseURI, c);
addPair("Contact ", contact, c);
addPair("Date ", date, c);
addPair("Set from ", projectDeployments, c);
@ -197,31 +198,35 @@ public class DeploymentExportPanel extends TethysGUIPanel implements DeploymentT
private void setDefaultStores() {
DeploymentHandler deploymentHandler = getTethysControl().getDeploymentHandler();
binaryURI.setText(deploymentHandler.getBinaryDataURI());
databaseURI.setText(deploymentHandler.getDatabaseURI());
rawURI.setText(deploymentHandler.getRawDataURI());
BinaryStore binStore = BinaryStore.findBinaryStoreControl();
if (binStore != null) {
binaryURI.setText(binStore.getBinaryStoreSettings().getStoreLocation());
}
DBControlUnit databaseControl = DBControlUnit.findDatabaseControl();
if (databaseControl != null) {
databaseURI.setText(databaseControl.getLongDatabaseName());
}
try {
PamControlledUnit daq = PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
if (daq instanceof AcquisitionControl) {
AcquisitionControl daqCtrl = (AcquisitionControl) daq;
DaqSystem system = daqCtrl.findDaqSystem(null);// getAcquisitionProcess().getRunningSystem();
if (system instanceof FolderInputSystem) {
FolderInputSystem fip = (FolderInputSystem) system;
rawURI.setText(fip.getFolderInputParameters().recentFiles.get(0));
}
}
}
catch (Exception e) {
rawURI.setText("unknown");
}
// BinaryStore binStore = BinaryStore.findBinaryStoreControl();
// if (binStore != null) {
// binaryURI.setText(binStore.getBinaryStoreSettings().getStoreLocation());
// }
//
// DBControlUnit databaseControl = DBControlUnit.findDatabaseControl();
// if (databaseControl != null) {
// databaseURI.setText(databaseControl.getLongDatabaseName());
// }
//
// try {
// PamControlledUnit daq = PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
// if (daq instanceof AcquisitionControl) {
// AcquisitionControl daqCtrl = (AcquisitionControl) daq;
// DaqSystem system = daqCtrl.findDaqSystem(null);// getAcquisitionProcess().getRunningSystem();
// if (system instanceof FolderInputSystem) {
// FolderInputSystem fip = (FolderInputSystem) system;
// rawURI.setText(fip.getFolderInputParameters().recentFiles.get(0));
// }
// }
// }
// catch (Exception e) {
// rawURI.setText("unknown");
// }
}
@ -235,37 +240,10 @@ public class DeploymentExportPanel extends TethysGUIPanel implements DeploymentT
if (selectedDeployments == null || selectedDeployments.size() == 0) {
return;
};
int freeId = getTethysControl().getDeploymentHandler().getFirstFreeDeploymentId();
for (int i = 0; i < selectedDeployments.size(); i++) {
RecordingPeriod recordPeriod = selectedDeployments.get(i);
PDeployment exDeploymnet = recordPeriod.getMatchedTethysDeployment();
Deployment deployment = null;
if (exDeploymnet != null) {
deployment = getTethysControl().getDeploymentHandler().createDeploymentDocument(freeId, recordPeriod);
deployment.setId(exDeploymnet.deployment.getId());
}
if (deployment == null) {
deployment = getTethysControl().getDeploymentHandler().createDeploymentDocument(freeId++, recordPeriod);
}
// fill in a few things from here
deployment.setCruise(cruise.getText());
deployment.setSite(site.getText());
// also need to sort out track data here, etc.
// Should really tidy this up a lot and move functionality to DeploymentHandler with all
// the metadata in a object ?
// Data data = new nilus.Deployment.Data();
// d
DBXMLConnect dbxmlConnect = getTethysControl().getDbxmlConnect();
if (exDeploymnet != null) {
dbxmlConnect.updateDocument(deployment);
}
else {
dbxmlConnect.postToTethys(deployment);
}
}
getTethysControl().sendStateUpdate(new TethysState(StateType.UPDATESERVER));
getTethysControl().getDeploymentHandler().exportDeployments(selectedDeployments);
}
private void enableControls() {
boolean enable = selectedDeployments != null && selectedDeployments.size() > 0;
bigExportButton.setEnabled(enable);

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@ -1,6 +1,7 @@
package tethys.swing;
import java.awt.BorderLayout;
import java.awt.FlowLayout;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
@ -8,10 +9,12 @@ import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.BoxLayout;
import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.border.EmptyBorder;
import tethys.TethysControl;
import tethys.dbxml.DBXMLConnect;
@ -32,17 +35,36 @@ public class FancyClientButton extends JPanel {
public FancyClientButton(TethysControl tethysControl) {
this.tethysControl = tethysControl;
setLayout(new GridBagLayout());
// setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
GridBagConstraints c = new GridBagConstraints();
c.ipadx = c.ipady = 0;
c.insets = new Insets(0,0,0,0);
c.fill = GridBagConstraints.VERTICAL;
clientButton = new JButton("Open Client");
clientButton.setToolTipText("Open Tethys web client in default browser");
ImageIcon arrowDown= null;
try {
arrowDown = new ImageIcon(ClassLoader
.getSystemResource("Resources/SidePanelShowH.png"));
}
catch (Exception e) {
}
if (arrowDown != null) {
dropButton = new JButton(arrowDown);
}
else {
dropButton = new JButton("v");
}
dropButton.setToolTipText("Open Tethys collections pages in default browser");
c.gridx = 0;
add(clientButton, c);
c.gridx++;
add(dropButton, c);
Insets dInsets = dropButton.getInsets();
if (dInsets != null) {
dInsets.left = dInsets.right = 4;
dropButton.setBorder(new EmptyBorder(dInsets));
}
String[] collections = DBXMLConnect.collections;
collectionsMenu = new JPopupMenu();