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Adding comments to table definitions.

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Update tabledefs so tableitems can have descriptions. Useful to the
coder, but can also export formal xms schema for each table.
This commit is contained in:
Douglas Gillespie 2022-11-07 17:15:04 +00:00
parent 3e717bd207
commit a72e68c26a
16 changed files with 386 additions and 59 deletions
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34
src/Acquisition/AcquisitionLogging.java
View File

@ -33,23 +33,23 @@ public class AcquisitionLogging extends SQLLogging {
this.acquisitionControl = acquisitionControl;
tableDef = new PamTableDefinition(pamDataBlock.getDataName(), UPDATE_POLICY_OVERWRITE);
tableDef.addTableItem(adcClockTime = new PamTableItem("ADC Clock", Types.TIMESTAMP));
tableDef.addTableItem(adcClockMillis = new PamTableItem("ADC Clock millis", Types.INTEGER));
tableDef.addTableItem(rawADCTime = new PamTableItem("RAW ADC Clock", Types.TIMESTAMP));
tableDef.addTableItem(gSamples = new PamTableItem("GigaSamples", Types.INTEGER));
tableDef.addTableItem(samples = new PamTableItem("Samples", Types.INTEGER));
tableDef.addTableItem(GPSPPSTime = new PamTableItem("GPSPPSTime", Types.TIMESTAMP));
tableDef.addTableItem(status = new PamTableItem("Status", Types.CHAR, 20));
tableDef.addTableItem(reason = new PamTableItem("Reason", Types.CHAR, 50));
tableDef.addTableItem(daqSystemType = new PamTableItem("SystemType", Types.CHAR, 50));
tableDef.addTableItem(daqSystemName = new PamTableItem("SystemName", Types.CHAR, 50));
tableDef.addTableItem(sampleRate = new PamTableItem("sampleRate", Types.INTEGER));
tableDef.addTableItem(nChannels = new PamTableItem("nChannels", Types.INTEGER));
tableDef.addTableItem(voltsPeak2Peak = new PamTableItem("voltsPeak2Peak", Types.DOUBLE));
tableDef.addTableItem(gain = new PamTableItem("gain", Types.REAL));
tableDef.addTableItem(duration = new PamTableItem("duration", Types.DOUBLE));
tableDef.addTableItem(clockError = new PamTableItem("clockError", Types.DOUBLE));
tableDef.addTableItem(serverTime = new PamTableItem("Server Time", Types.TIMESTAMP));
tableDef.addTableItem(adcClockTime = new PamTableItem("ADC Clock", Types.TIMESTAMP, "Time based on PC clock and samples since last PC clock read"));
tableDef.addTableItem(adcClockMillis = new PamTableItem("ADC Clock millis", Types.INTEGER, "Millis for adcClockTime if not supported by database"));
tableDef.addTableItem(rawADCTime = new PamTableItem("RAW ADC Clock", Types.TIMESTAMP, "Time based on start time and number of samples acquired"));
tableDef.addTableItem(gSamples = new PamTableItem("GigaSamples", Types.INTEGER, "Billions of samples. Add this*1e9 to samples"));
tableDef.addTableItem(samples = new PamTableItem("Samples", Types.INTEGER, "Samples. Add this to GigaSamples*1e9"));
tableDef.addTableItem(GPSPPSTime = new PamTableItem("GPSPPSTime", Types.TIMESTAMP, "Time derived from a GPS with PPS output"));
tableDef.addTableItem(status = new PamTableItem("Status", Types.CHAR, 20, "Acquisition Status: 'Start', 'Stop', 'Continue'"));
tableDef.addTableItem(reason = new PamTableItem("Reason", Types.CHAR, 50, "Reason for status change"));
tableDef.addTableItem(daqSystemType = new PamTableItem("SystemType", Types.CHAR, 50, "Type of acquisition system"));
tableDef.addTableItem(daqSystemName = new PamTableItem("SystemName", Types.CHAR, 50, "Specific acquistision system"));
tableDef.addTableItem(sampleRate = new PamTableItem("sampleRate", Types.INTEGER, "Sample rate (samples per second)"));
tableDef.addTableItem(nChannels = new PamTableItem("nChannels", Types.INTEGER, "Total number of channels"));
tableDef.addTableItem(voltsPeak2Peak = new PamTableItem("voltsPeak2Peak", Types.DOUBLE, "Peak to peak input voltage of ADC"));
tableDef.addTableItem(gain = new PamTableItem("gain", Types.REAL, "Additional amplifier gain"));
tableDef.addTableItem(duration = new PamTableItem("duration", Types.DOUBLE, "Time since start in seconds"));
tableDef.addTableItem(clockError = new PamTableItem("clockError", Types.DOUBLE, "Clock error in milliseconds"));
tableDef.addTableItem(serverTime = new PamTableItem("Server Time", Types.TIMESTAMP, "Time taken from an Internet time server"));
setTableDefinition(tableDef);
}

8
src/Acquisition/AcquisitionProcess.java
View File

@ -254,9 +254,11 @@ public class AcquisitionProcess extends PamProcess {
bufferOverflow = false;
// daqCheckTime = PamCalendar.getTimeInMillis();
Timer t = new Timer(1, new ReallyStart());
t.setRepeats(false);
t.start();
if (!netRX) {
Timer t = new Timer(1, new ReallyStart());
t.setRepeats(false);
t.start();
}
}
private boolean addServerTime(DaqStatusDataUnit daqStatusDataUnit) {

3
src/Array/ThreadingHydrophoneLocator.java
View File

@ -77,6 +77,9 @@ public class ThreadingHydrophoneLocator extends StraightHydrophoneLocator implem
*/
while (gpsIt.hasPrevious()) {
gpsUnit = gpsIt.previous();
if (gpsUnit == null) {
continue;
}
gpsData = gpsUnit;
if (gpsUnit.getTimeInMillis() < timeMilliseconds) {
break;

4
src/PamController/command/SummaryCommand.java
View File

@ -1,6 +1,5 @@
package PamController.command;
import Map.GetMapFile;
import PamController.PamControlledUnit;
import PamController.PamController;
import PamUtils.PamCalendar;
@ -56,6 +55,9 @@ public class SummaryCommand extends ExtCommand {
totalString += String.format("\n<%s>%s:%s<\\%s>", aModule.getShortUnitType(),
aModule.getUnitName(), aString, aModule.getShortUnitType());
}
if (clear) {
lastCallTime = nowTime;
}
return totalString;
}

46
src/PamUtils/XMLUtils.java
View File

@ -1,7 +1,9 @@
package PamUtils;
import java.io.BufferedWriter;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.StringWriter;
@ -9,6 +11,7 @@ import java.io.StringWriter;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
@ -183,4 +186,47 @@ public class XMLUtils {
}
return doc;
}
/**
* Write to the given file.
* @param doc xml document
* @param outFile file
* @throws IOException
*/
public static void writeToFile(Document doc, File outFile) throws IOException {
String asString = getAsString(doc);
if (asString!=null) {
try {
BufferedWriter out = new BufferedWriter(new FileWriter(outFile, false));
out.write(asString);
out.close();
} catch (IOException e) {
e.printStackTrace();
}
}
}
/**
* Get the xml document as a String.
* @param doc xml document
* @return xml content as a a string.
*/
public static String getAsString(Document doc) {
try {
DOMSource domSource = new DOMSource(doc);
StringWriter writer = new StringWriter();
StreamResult result = new StreamResult(writer);
TransformerFactory tf = TransformerFactory.newInstance();
Transformer transformer = tf.newTransformer();
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
transformer.setOutputProperty(OutputKeys.ENCODING, "ISO-8859-1");
// transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
transformer.transform(domSource, result);
return writer.toString();
} catch (TransformerException e) {
e.printStackTrace();
return null;
}
}
}

22
src/binaryFileStorage/BinaryStorageDialogPanel.java
View File

@ -131,6 +131,17 @@ public class BinaryStorageDialogPanel {
binaryStoreSettings.datedSubFolders = dateSubFolders.isSelected();
binaryStoreSettings.limitFileSize = limitfileSize.isSelected();
if (allowChannelOffsets) {
try {
binaryStoreSettings.channelShift = Integer.valueOf(channelOffset.getText());
}
catch (NumberFormatException e) {
return PamDialog.showWarning(owner, errorTitle, "Invalid channel offset number format");
}
if (binaryStoreSettings.channelShift < 0 || binaryStoreSettings.channelShift > 31) {
return PamDialog.showWarning(owner, errorTitle, "Channel offset bust be between 0 and 31");
}
}
if (PamController.getInstance().getRunMode() == PamController.RUN_PAMVIEW) {
return true;
}
@ -157,17 +168,6 @@ public class BinaryStorageDialogPanel {
return PamDialog.showWarning(owner, errorTitle, "Invalid file size data");
}
}
if (allowChannelOffsets) {
try {
binaryStoreSettings.channelShift = Integer.valueOf(channelOffset.getText());
}
catch (NumberFormatException e) {
return PamDialog.showWarning(owner, errorTitle, "Invalid channel offset number format");
}
if (binaryStoreSettings.channelShift < 0 || binaryStoreSettings.channelShift > 31) {
return PamDialog.showWarning(owner, errorTitle, "Channel offset bust be between 0 and 31");
}
}
NoiseStoreType nst = (NoiseStoreType) noiseStoreType.getSelectedItem();
if (nst == null) {
return PamDialog.showWarning(owner, errorTitle, "You must select a noise storage type");

15
src/generalDatabase/DBControl.java
View File

@ -428,11 +428,26 @@ PamSettingsSource {
JMenuItem speedMenu = new JMenuItem("Test database speed");
speedMenu.addActionListener(new SpeedMenu(parentFrame));
menu.add(speedMenu);
JMenuItem exSchema = new JMenuItem("Export database schema");
exSchema.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
exportDatabaseSchema(parentFrame);
}
});
menu.add(exSchema);
}
return menu;
}
protected void exportDatabaseSchema(JFrame parentFrame) {
dbProcess.exportDatabaseSchema(parentFrame);
}
class DatabaseFileMenuAction implements ActionListener {
private Frame frame;

42
src/generalDatabase/DBProcess.java
View File

@ -22,6 +22,8 @@ import java.sql.Statement;
import java.sql.Types;
import java.util.ArrayList;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;
import javax.swing.Timer;
@ -36,7 +38,9 @@ import loggerForms.UDFTableDefinition;
import loggerForms.formdesign.FormEditor;
import PamController.PamControlledUnit;
import PamController.PamController;
import PamController.PamFolders;
import PamUtils.PamCalendar;
import PamUtils.PamFileChooser;
import PamView.dialog.warn.WarnOnce;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
@ -1393,4 +1397,42 @@ public class DBProcess extends PamProcess {
return logViewerSettings;
}
/**
* Export all available database schema, converting PamTableDefinitions into
* valid xsd documents.
* @param parentFrame
*/
public void exportDatabaseSchema(JFrame parentFrame) {
File startLoc = PamFolders.getFileChooserPath(PamFolders.getDefaultProjectFolder());
PamFileChooser fc = new PamFileChooser();
fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
startLoc = PamFolders.getFileChooserPath(startLoc);
fc.setCurrentDirectory(startLoc);
int ans = fc.showDialog(parentFrame, "Select storage folder");
if (ans == JFileChooser.APPROVE_OPTION) {
startLoc = fc.getSelectedFile();
exportDatabaseSchema(parentFrame, startLoc);
}
}
/**
* Export all table definitions to xsd files in given folder.
* @param parentFrame
* @param folder
*/
private void exportDatabaseSchema(JFrame parentFrame, File folder) {
ArrayList<PamDataBlock> allDataBlocks = PamController.getInstance().getDataBlocks();
DBSchemaWriter schemaWriter = new DBSchemaWriter();
for (PamDataBlock aBlock : allDataBlocks) {
SQLLogging logging = aBlock.getLogging();
if (logging == null) {
continue;
}
schemaWriter.writeSchema(folder, aBlock);
}
}
}

138
src/generalDatabase/DBSchemaWriter.java Normal file
View File

@ -0,0 +1,138 @@
package generalDatabase;
import java.io.File;
import java.io.IOException;
import java.sql.Types;
import javax.xml.parsers.DocumentBuilderFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import PamUtils.XMLUtils;
import PamguardMVC.PamDataBlock;
/**
* Functions for writing database table schema in a format
* compatible with the Tethys schemas.
* @author dg50
*
*/
public class DBSchemaWriter {
public DBSchemaWriter() {
// TODO Auto-generated constructor stub
}
public boolean writeSchema(File outputFolder, PamDataBlock dataBlock) {
if (dataBlock == null) {
return false;
}
SQLLogging logging = dataBlock.getLogging();
if (logging == null) {
return false;
}
PamTableDefinition tableDef = logging.getTableDefinition();
exportDatabaseSchema(outputFolder, dataBlock, tableDef);
return true;
}
private void exportDatabaseSchema(File outputFolder, PamDataBlock dataBlock, PamTableDefinition tableDef) {
String tableName = tableDef.getTableName();
File outputFile = new File(outputFolder, tableName+".xsd");
Document doc = PamUtils.XMLUtils.createBlankDoc();
Element el = doc.createElement("xs:schema");
el.setAttribute("xmlns:xs","http://www.w3.org/2001/XMLSchema");
el.setAttribute("targetNamespace", "http://tethys.sdsu.edu/schema/1.0");
doc.appendChild(el);
for (PamTableItem tableItem : tableDef.pamTableItems) {
Element itemEl = doc.createElement("xs:element");
itemEl.setAttribute("name", tableItem.getName());
itemEl.setAttribute("type", sqlTypeToString(tableItem.getSqlType(), tableItem.getLength()));
String documentation = tableItem.getDescription();
if (documentation != null) {
Element annotation = doc.createElement("xs:annotation");
itemEl.appendChild(annotation);
Element docEl = doc.createElement("xs:documentation");
docEl.setTextContent(documentation);
annotation.appendChild(docEl);
}
el.appendChild(itemEl);
}
try {
XMLUtils.writeToFile(doc, outputFile);
} catch (IOException e) {
e.printStackTrace();
}
}
private String sqlTypeToString(int sqlType, int length) {
switch (sqlType) {
case Types.ARRAY:
return "ARRAY";
case Types.BIGINT:
return "xs:long";
case Types.BINARY:
return "BINARY";
case Types.BIT:
return "BIT";
case Types.BLOB:
return "BLOB";
case Types.BOOLEAN:
return "xs:boolean";
case Types.CHAR:
return "xs:string";
case Types.CLOB:
return "CLOB";
case Types.DATALINK:
return "DATALINK";
case Types.DATE:
return "xs:dateTime";
case Types.DECIMAL:
return "DECIMAL";
case Types.DISTINCT:
return "DISTINCT";
case Types.DOUBLE:
return "xs:double";
case Types.FLOAT:
return "xs:float";
case Types.INTEGER:
return "xs:int";
case Types.JAVA_OBJECT:
return "JAVA_OBJECT";
case Types.LONGVARBINARY:
return "LONGVARBINARY(" + length + ")";
case Types.LONGVARCHAR:
return "LONGVARCHAR(" + length + ")";
case Types.NULL:
return "NULL";
case Types.NUMERIC:
return "NUMERIC";
case Types.OTHER:
return "OTHER";
case Types.REAL:
return "xs:float";
case Types.REF:
return "REF";
case Types.SMALLINT:
return "xs:short";
case Types.STRUCT:
return "STRUCT";
case Types.TIME:
return "TIME";
case Types.TIMESTAMP:
return "xs:dateTime";
case Types.TINYINT:
return "TINYINT";
case Types.VARBINARY:
return "VARBINARY(" + length + ")";
case Types.VARCHAR:
return "VARCHAR(" + length + ")";
}
return null;
}
}

16
src/generalDatabase/PamTableDefinition.java
View File

@ -55,15 +55,15 @@ public class PamTableDefinition extends EmptyTableDefinition implements Cloneabl
*/
public PamTableDefinition(String tableName, int updatePolicy) {
super(tableName, updatePolicy);
pamTableItems.add(uid = new PamTableItem("UID", Types.BIGINT));
pamTableItems.add(timeStampItem = new PamTableItem(utcColName, Types.TIMESTAMP));
pamTableItems.add(timeStampMillis = new PamTableItem("UTCMilliseconds", Types.SMALLINT));
pamTableItems.add(localTime = new PamTableItem("PCLocalTime", Types.TIMESTAMP));
pamTableItems.add(pcTime = new PamTableItem("PCTime", Types.TIMESTAMP));
pamTableItems.add(channelBitmap = new PamTableItem("ChannelBitmap", Types.INTEGER));
pamTableItems.add(sequenceBitmap = new PamTableItem("SequenceBitmap", Types.INTEGER));
pamTableItems.add(uid = new PamTableItem("UID", Types.BIGINT, "Unique Identifier"));
pamTableItems.add(timeStampItem = new PamTableItem(utcColName, Types.TIMESTAMP, "Timestamp UTC"));
pamTableItems.add(timeStampMillis = new PamTableItem("UTCMilliseconds", Types.SMALLINT, "Time milliseconds (for databases which do not support millis)"));
pamTableItems.add(localTime = new PamTableItem("PCLocalTime", Types.TIMESTAMP, "Local time on PC"));
pamTableItems.add(pcTime = new PamTableItem("PCTime", Types.TIMESTAMP, "Time data written, UTC. Same as UTC for real time data, current time for offline file analysis"));
pamTableItems.add(channelBitmap = new PamTableItem("ChannelBitmap", Types.INTEGER, "Bitmap of input channels used"));
pamTableItems.add(sequenceBitmap = new PamTableItem("SequenceBitmap", Types.INTEGER, "Bitmap of beam or channel outputs used"));
if (updatePolicy == SQLLogging.UPDATE_POLICY_WRITENEW) {
addTableItem(updateReference = new PamTableItem("UpdateOf", Types.INTEGER));
addTableItem(updateReference = new PamTableItem("UpdateOf", Types.INTEGER, "Reference to previous value"));
}
}

64
src/generalDatabase/PamTableItem.java
View File

@ -50,6 +50,14 @@ public class PamTableItem implements Cloneable {
*/
private Object value;
/**
* Test description of field. Can be exported to schema and may
* be possible to write into database description fields one day. In any case
* it can be useful to the programmer when looking back to see what on earth
* code is supposed to be doing.
*/
private String description;
/*
* Reference to another PamTableItem in a different
* table. This must be of the same sqlType as this
@ -60,6 +68,11 @@ public class PamTableItem implements Cloneable {
*/
private PamTableItem crossReferenceItem;
/**
* Generate a table item
* @param name name of table item
* @param sqlType SQL Type from java.sql.Types, e.g. Types.INTEGER
*/
public PamTableItem(String name, int sqlType) {
super();
this.name = name;
@ -68,6 +81,27 @@ public class PamTableItem implements Cloneable {
this.required = false;
}
/**
* Generate a table item
* @param name name of table item
* @param sqlType SQL Type from java.sql.Types, e.g. Types.INTEGER
* @param description optional description
*/
public PamTableItem(String name, int sqlType, String description) {
super();
this.name = name;
this.sqlType = sqlType;
this.description = description;
this.length = 0;
this.required = false;
}
/**
* Generate a table item
* @param name name of table item
* @param sqlType SQL Type from java.sql.Types, e.g. Types.INTEGER
* @param length length (only applicable to Types.CHAR types)
*/
public PamTableItem(String name, int sqlType, int length) {
super();
this.name = name;
@ -76,6 +110,22 @@ public class PamTableItem implements Cloneable {
this.required = false;
}
/**
* Generate a table item
* @param name name of table item
* @param sqlType SQL Type from java.sql.Types, e.g. Types.INTEGER
* @param length length (only applicable to Types.CHAR types)
* @param description optional description
*/
public PamTableItem(String name, int sqlType, int length, String description) {
super();
this.name = name;
this.sqlType = sqlType;
this.length = length;
this.description = description;
this.required = false;
}
public PamTableItem(String name, int sqlType, int length, boolean required) {
super();
this.name = name;
@ -501,5 +551,19 @@ public class PamTableItem implements Cloneable {
}
}
/**
* @return the description
*/
public String getDescription() {
return description;
}
/**
* @param description the description to set
*/
public void setDescription(String description) {
this.description = description;
}
}

5
src/networkTransfer/receive/BuoyStatusData.java
View File

@ -144,4 +144,9 @@ public class BuoyStatusData implements Serializable, ManagedParameters {
return ps;
}
@Override
public String toString() {
return String.format("Buoy %d(%d) ip %s", buoyId1, buoyId2, ipAddr);
}
}

5
src/networkTransfer/receive/BuoyStatusDataUnit.java
View File

@ -387,6 +387,11 @@ public class BuoyStatusDataUnit extends PamDataUnit {
return buoyStatusData;
}
@Override
public String toString() {
return String.format("Status %s\n", buoyStatusData.toString());
}
// /**
// * @return the genericStringPairsChanged
// */

2
src/networkTransfer/receive/NetworkReceiver.java
View File

@ -770,7 +770,7 @@ public class NetworkReceiver extends PamControlledUnit implements PamSettings, N
}
private NetworkObject interpretPamCommand(NetworkObject receivedData, BuoyStatusDataUnit buoyStatusDataUnit) {
// System.out.println("Network command received: " + getPamCommandString(dataId2));
// System.out.println("Network command received: " + getPamCommandString(dataId2));
buoyStatusDataUnit.setCommandStatus(receivedData.getDataType2());
long time = PamCalendar.getTimeInMillis();
if (receivedData.getData() != null && receivedData.getDataLength() >= 8) {

10
src/whistlesAndMoans/WhistleMoanControl.java
View File

@ -183,11 +183,6 @@ public class WhistleMoanControl extends PamControlledUnit implements PamSettings
return true;
}
@Override
public String getModuleSummary() {
return whistleToneProcess.getModuleSummary();
}
@Override
public Object getShortUnitType() {
return "WMD";
@ -225,4 +220,9 @@ public class WhistleMoanControl extends PamControlledUnit implements PamSettings
}
return null;
}
@Override
public String getModuleSummary(boolean clear) {
return whistleToneProcess.getModuleSummary(clear);
}
}

27
src/whistlesAndMoans/WhistleToneConnectProcess.java
View File

@ -968,17 +968,6 @@ public class WhistleToneConnectProcess extends PamProcess {
}
public String getModuleSummary() {
String sumText = String.format("%d", NSUMMARYPOINTS);
for (int i = 0; i < NSUMMARYPOINTS; i++) {
sumText += String.format(",%d",whistleSummaryCount[i]);
}
clearSummaryData();
return sumText;
}
/**
* When delay data are written to binary files, int16's are used, but these
* must be scaled up to allow for sub-sample timing. How much they can be
@ -1099,4 +1088,20 @@ public class WhistleToneConnectProcess extends PamProcess {
return fftUnitsOut;
}
/*
* replicate Decimus function to give counts of whistles in four evenly spaced frequency
* bins.
*/
public String getModuleSummary(boolean clear) {
String sumText = String.format("%d", NSUMMARYPOINTS);
for (int i = 0; i < NSUMMARYPOINTS; i++) {
sumText += String.format(",%d",whistleSummaryCount[i]);
}
if (clear) {
clearSummaryData();
}
return sumText;
}
}