public boolean checkEvents(BundleEvent[] expevents) {
boolean res = true;
for (int i = 0; i < 20; i++) {
try {
Thread.sleep(100);
} catch (InterruptedException ignore) {
}
if (events.size() == expevents.length) {
break;
}
}
if (events.size() == expevents.length) {
for (int i = 0; i < events.size(); i++) {
BundleEvent be = (BundleEvent) events.elementAt(i);
if (!(be.getBundle().equals(expevents[i].getBundle())
&& be.getType() == expevents[i].getType())) {
res = false;
}
}
} else {
res = false;
}
if (!res) {
out.println("Real events");
for (int i = 0; i < events.size(); i++) {
BundleEvent be = (BundleEvent) events.elementAt(i);
out.println("Event " + be.getBundle() + ", Type " + be.getType());
}
out.println("Expected events");
for (int i = 0; i < expevents.length; i++) {
out.println("Event " + expevents[i].getBundle() + ", Type " + expevents[i].getType());
}
}
return res;
}
/**
* Remove the first null element found in the specified vector. Return true if a null element was
* found and removed. Return false if a null element was not found.
*/
private boolean removeNullElement(Vector v) {
for (int i = 0; i < v.size(); i++) {
if (v.elementAt(i) == null) {
v.removeElementAt(i);
return true;
}
}
return false;
}
protected void fireHPubReqCompleteEvent(RequestCompleteEvent evt) {
Vector currentListenerList = null;
synchronized (this) {
currentListenerList = (Vector) listenerList.clone();
}
for (int i = 0; i < currentListenerList.size(); i++) {
HPubReqCompleteListener listener = (HPubReqCompleteListener) currentListenerList.elementAt(i);
listener.hPubReqComplete(evt);
}
}
/**
* Assert that the elements in two vectors are equal. If they are not, throw an
* AssertionFailedError. Order of the elements is significant.
*
* @param message the error message
* @param expected the expected value of an vector
* @param actual the actual value of an vector
*/
protected void assertElementsEqual(String message, Vector expected, Vector actual) {
if (expected == actual) {
return;
}
if (expected.size() != actual.size()) {
this.assertTrue(this.notEqualsMessage(message, expected, actual), false);
}
for (int i = 0; i < expected.size(); i++) {
Object e1 = expected.elementAt(i);
Object e2 = actual.elementAt(i);
if (e1 == null) { // avoid null pointer exception
if (e2 != null) {
this.assertTrue(this.notEqualsMessage(message, expected, actual), false);
}
} else {
if (!e1.equals(e2)) {
this.assertTrue(this.notEqualsMessage(message, expected, actual), false);
}
}
}
}
public Class[] getClassesFromClass(Class c) {
Vector cList = new Vector();
Class cTemp;
Class[] aList;
cTemp = c;
while ((cTemp = cTemp.getSuperclass()) != null) {
cList.addElement(cTemp);
}
aList = new Class[cList.size()];
for (int i = 0; i < cList.size(); i++) {
aList[i] = (Class) cList.elementAt(i);
}
return aList;
}
public CompositeData getNextEntry(Object[] indexObjects) {
// User code starts here
if (!agentName.initAlert()) return null;
String previousKeys[] = {indexObjects[0].toString(), indexObjects[1].toString()};
String keys[] = getNextAlert(previousKeys);
if (keys == null) return null;
String source = keys[0];
// String ownerName = keys[1];
String entity = keys[1];
Alert alert1 = new Alert();
alert1.setSource(source);
// alert1.setOwnerName(ownerName);
alert1.setEntity(entity);
Alert alert2 = new Alert();
alert2.setModTime(System.currentTimeMillis());
Vector alerts = null;
try {
alerts = agentName.alertAPI.getAlerts(alert1, alert2);
if (alerts != null) return makeComData((Alert) alerts.elementAt(0));
} catch (Exception e) {
return null;
}
// User code ends here
return null;
}
/**
* Assert that the elements in two vectors are equal. If they are not, throw an
* AssertionFailedError. The order of the elements is ignored.
*
* @param message the error message
* @param expected the expected value of an vector
* @param actual the actual value of an vector
*/
protected void assertUnorderedElementsEqual(String message, Vector expected, Vector actual) {
if (expected == actual) {
return;
}
if (expected.size() != actual.size()) {
this.assertTrue(this.notEqualsMessage(message, expected, actual), false);
}
Vector temp = (Vector) actual.clone();
for (int i = 0; i < expected.size(); i++) {
Object e1 = expected.elementAt(i);
if (e1 == null) { // avoid null pointer exception
if (!this.removeNullElement(temp)) {
this.assertTrue(this.notEqualsMessage(message, expected, actual), false);
}
} else {
if (!temp.removeElement(e1)) {
this.assertTrue(this.notEqualsMessage(message, expected, actual), false);
}
}
}
}
/**
* ************************************************************************* * * Method:
* performGet * Input: CMIRequest theRequest - tokenized LMSGetValue() request * DMErrorManager
* dmErrorMgr - Error manager * * Output: String - the value portion of the element for the
* LMSGetValue() * * Description: This method takes the necessary steps to process * an
* LMSGetValue() request *
* *************************************************************************
*/
public String performGet(CMIRequest theRequest, DMErrorManager dmErrorMgr) {
if (true) {
System.out.println("CMIObjectives::performGet()");
}
// Resultant value to return
String result = new String("");
// Check to make sure this is a valid LMSGetValue() request
if (isValidObjRequest(theRequest) == true) {
// Get the next token off of the request
String token = theRequest.getNextToken();
if (true) {
System.out.println("Token being processed: " + token);
}
// Check to see if the Request has more tokens to process
if (theRequest.hasMoreTokensToProcess()) {
// Token has to be an array index
try {
// Convert the string integer to a number
Integer tmpInt = new Integer(token);
int indexOfArr = tmpInt.intValue();
try {
// Get the Objective Data that is positioned at the input index
CMIObjectiveData objData = (CMIObjectiveData) objectives.elementAt(indexOfArr);
// Invoke the performGet on the Objective Data returned.
result = objData.performGet(theRequest, dmErrorMgr);
} catch (ArrayIndexOutOfBoundsException e) {
if (true) {
System.out.println("Element does not exist at the given index");
System.out.println("Index: " + indexOfArr);
}
// if element has not been initialized, return Invalid
// Argument Error
dmErrorMgr.SetCurrentErrorCode("201");
}
} catch (NumberFormatException nfe) {
if (true) {
// Invalid parameter passed to LMSGetValue()
System.out.println("Error - Data Model Element not implemented");
System.out.println(
"Invalid data model element: "
+ theRequest.getRequest()
+ " passed to LMSGetValue()");
System.out.println("Array index required");
}
// Notify error manager
dmErrorMgr.SetCurrentErrorCode("401");
}
} else {
// No more tokens to process
// Check to see if the request is for the children of Core Data
if (theRequest.isAChildrenRequest()) {
// Set result to the string of children
result = getChildren();
} else if (theRequest.isACountRequest()) {
int count = 0;
count = objectives.size();
System.out.println("Count: " + count);
Integer tmpInt = new Integer(count);
result = tmpInt.toString();
} else {
if (true) {
System.out.println("Error - Data Model Element not implemented");
System.out.println("Invalid request: " + theRequest.getRequest());
}
dmErrorMgr.recNotImplementedError(theRequest);
}
}
} else {
if (true) {
// Error - Data Model Element not implemented
System.out.println("Error - Data Model Element not implemented");
System.out.println("Invalid request: " + theRequest.getRequest());
}
dmErrorMgr.SetCurrentErrorCode("401");
}
// Done processing. Let CMIRequest object know the processing
// of the LMSGetValue() is done.
theRequest.done();
if (true) {
System.out.println("Returning from CMIObjectives::performGet()");
System.out.println("Value returned: " + result);
}
return result;
} // end of performGet()
/**
* ************************************************************************ * * Method: performSet
* * Input: CMIRequest theRequest - tokenized LMSSetValue() request * DMErrorManager dmErroMgr -
* Error Manager * Output: none * * Description: This method takes the necessary steps to process
* * an LMSSetValue() request *
* *************************************************************************
*/
public void performSet(CMIRequest theRequest, DMErrorManager dmErrorMgr) {
if (true) {
System.out.println("CMIObjectives::performSet()");
}
// The next token must be an array. If not throw
// an exception for this request.
int index = -1;
// Get the next token off of the request
String token = theRequest.getNextToken();
if (true) {
System.out.println("Token being processed: " + token);
}
// Check to see if next token is an array index. For
// a LMSSetValue() this is true
try {
// Try to convert the token to the index
Integer tmpInt = new Integer(token);
index = tmpInt.intValue();
// Get the Objective Data at position of the index
CMIObjectiveData tmpObj = (CMIObjectiveData) objectives.elementAt(index);
// An objective existed at the given index.
// Invoke the performSet() on the Objective Data
tmpObj.performSet(theRequest, dmErrorMgr);
// replace the old ObjectiveData with the newly set Objective
// Data.
objectives.set(index, tmpObj);
} catch (NumberFormatException nfe) {
if (theRequest.isAKeywordRequest() == true) {
dmErrorMgr.recKeyWordError(token);
} else {
if (true) {
// Invalid parameter passed to LMSSetValue()
System.out.println("Error - Data Model Element not implemented");
System.out.println(
"Invalid data model element: "
+ theRequest.getRequest()
+ " passed to LMSSetValue()");
}
// Notify error manager
dmErrorMgr.recNotImplementedError(theRequest);
}
} catch (ArrayIndexOutOfBoundsException e) {
if (true) {
System.out.println("First time setting the Objective Data");
}
if (index <= objectives.size()) {
// A new Objective Data.
CMIObjectiveData objData = new CMIObjectiveData();
// Invoke performSet() on the new Objective Data
objData.performSet(theRequest, dmErrorMgr);
// Place the Objective data into the vector at the
// index position
objectives.add(index, objData);
} else {
dmErrorMgr.SetCurrentErrorCode("201");
}
}
// Done processing. Let CMIRequest object know the processing
// of the LMSGetValue() is done.
theRequest.done();
return;
} // end of performSet
/**
* Parse the section file and fill in the Dbase.
*
* @return Success code
*/
public void parse() throws Exception {
JOAParameter tempProperties[] = new JOAParameter[100];
FileInputStream in = null;
DataInputStream inData = null;
short inShort = 0;
long bytesRead = 0;
long bytesInFile = mFile.length();
short[] sarray = new short[1];
int mTotalStns = 0;
EPSProgressDialog mProgress = new EPSProgressDialog(new Frame(), mProgressStr, Color.blue);
mProgress.setVisible(true);
// Get an epic key database specific to JOA
EPIC_Key_DB mEpicKeyDB = new EPIC_Key_DB("joa_epic.key");
// Get an epic key database specific to JOA
EPIC_Key_DB mOrigEpicKeyDB = new EPIC_Key_DB("epic.key");
// create a vector for temporary storage of the dbases
Vector dBases = new Vector(100);
try {
in = new FileInputStream(mFile);
BufferedInputStream bis = new BufferedInputStream(in, 1000000);
inData = new DataInputStream(bis);
// read version
short vers = inData.readShort();
bytesRead += 2;
if (vers < 2) {
FileImportException fiex = new FileImportException();
String errStr = "Invalid version for a JOA binary file";
fiex.setErrorType(errStr);
throw fiex;
}
// read number of bytes in file description string
inShort = inData.readShort();
bytesRead += 2;
// read the file description String
byte buf[] = new byte[inShort];
inData.read(buf, 0, inShort);
String fileDescrip = new String(buf);
bytesRead += inShort;
// create a new open file object
JOADataFile of = new JOADataFile(fileDescrip);
// read the number of sections
int numSections = inData.readShort();
bytesRead += 2;
// read each section
JOASection sech;
int ord = 0;
for (int s = 0; s < numSections; s++) {
mProgress.setPercentComplete(100.0 * ((double) bytesRead / (double) bytesInFile));
// read the section header
inShort = inData.readShort();
bytesRead += 2;
byte buf1[] = new byte[inShort];
inData.read(buf1, 0, inShort);
String sectionDescrip = new String(buf1);
bytesRead += inShort;
// read the ship code
byte bufsc[] = new byte[2];
bufsc[0] = inData.readByte();
bufsc[1] = inData.readByte();
String shipCode = new String(bufsc);
bytesRead += 2;
// read num casts
int numCasts = inData.readShort();
bytesRead += 2;
// read num parameters
int numVars = inData.readShort();
bytesRead += 2;
// quality code
int qcStd = 1;
if (vers == 4) {
qcStd = inData.readShort();
bytesRead += 2;
}
// create a new section
of.mNumSections++;
sech = new JOASection(of.mNumSections, sectionDescrip, shipCode, numCasts, numVars);
if (vers == 2) {
// read the properties
byte bufv[] = new byte[4];
for (int p = 0; p < numVars; p++) {
// parameter name
inData.read(bufv, 0, 4);
String tempVar = new String(bufv);
bytesRead += 4;
// units
inShort = inData.readShort();
bytesRead += 2;
String units = null;
if (inShort > 0) {
byte buf11[] = new byte[inShort];
inData.read(buf11, 0, inShort);
units = new String(buf11);
bytesRead += inShort;
}
// convert varnames to UC
tempVar.toUpperCase();
// create new property
tempProperties[p] = new JOAParameter(tempVar, units);
// add this property to the section property list
if (tempProperties[p].mUnits == null) {
tempProperties[p].mUnits =
EPS_Util.paramNameToJOAUnits(false, tempProperties[0].mVarLabel);
}
if (tempProperties[p].mUnits == null) {
tempProperties[p].mUnits = new String("na");
}
tempProperties[p].mCastOrObs = EPSConstants.ALL_OBS;
// read the actual scale
int actScale = inData.readShort();
bytesRead += 2;
if (actScale != 0) tempProperties[p].mActScale = 1.0 / (double) actScale;
else tempProperties[p].mActScale = 1.0;
// read the actual origin
int actOrigin = inData.readShort();
tempProperties[p].mActOrigin = (double) actOrigin * tempProperties[p].mActScale;
// read reverse y
int reverseY = inData.readShort();
bytesRead += 2;
if (reverseY == 0) tempProperties[p].mReverseY = false;
else tempProperties[p].mReverseY = true;
tempProperties[p].mWasCalculated = false;
}
} else {
// read the properties
String tempVar = null;
for (int p = 0; p < numVars; p++) {
// length of parameter name
inShort = inData.readShort();
bytesRead += 2;
// parameter name
if (inShort > 0) {
byte buf13[] = new byte[inShort];
inData.read(buf13, 0, inShort);
tempVar = new String(buf13);
bytesRead += inShort;
}
// units
inShort = inData.readShort();
bytesRead += 2;
String units = null;
if (inShort > 0) {
byte buf11[] = new byte[inShort];
inData.read(buf11, 0, inShort);
units = new String(buf11);
bytesRead += inShort;
}
// convert varnames to UC
tempVar = tempVar.toUpperCase();
// create new property
tempProperties[p] = new JOAParameter(tempVar, units);
// add this property to the section property list
if (tempProperties[p].mUnits == null) {
tempProperties[p].mUnits =
EPS_Util.paramNameToJOAUnits(false, tempProperties[0].mVarLabel);
}
if (tempProperties[p].mUnits == null) {
tempProperties[p].mUnits = new String("na");
}
tempProperties[p].mCastOrObs = EPSConstants.ALL_OBS;
// read the actual scale
int actScale = inData.readShort();
bytesRead += 2;
if (actScale != 0) tempProperties[p].mActScale = 1.0 / (double) actScale;
else tempProperties[p].mActScale = 1.0;
// read the actual origin
int actOrigin = inData.readShort();
tempProperties[p].mActOrigin = (double) actOrigin * tempProperties[p].mActScale;
// read reverse y
int reverseY = inData.readShort();
bytesRead += 2;
if (reverseY == 0) tempProperties[p].mReverseY = false;
else tempProperties[p].mReverseY = true;
tempProperties[p].mWasCalculated = false;
}
}
// read the cast headers
for (int c = 0; c < numCasts; c++) {
// read station number
inShort = inData.readShort();
bytesRead += 2;
byte bufx[] = new byte[inShort];
inData.read(bufx, 0, inShort);
String stnNum = new String(bufx);
bytesRead += inShort;
// read cast number
int castNum = inData.readShort();
bytesRead += 2;
double myLat = 0.0;
double myLon = 0.0;
if (vers == 2) {
// read latitude/lon
int lat = inData.readInt();
bytesRead += 4;
int lon = inData.readInt();
bytesRead += 4;
myLat = lat * 0.001;
myLon = lon * 0.001;
} else if (vers > 2) {
// read latitude/lon
myLat = inData.readDouble();
bytesRead += 8;
myLon = inData.readDouble();
bytesRead += 4;
}
// read number of bottles
int numBottles = inData.readShort();
bytesRead += 2;
// read the date
int year = inData.readInt();
bytesRead += 4;
int month = inData.readInt();
bytesRead += 4;
int day = inData.readInt();
bytesRead += 4;
int hour = inData.readInt();
bytesRead += 4;
double min = inData.readDouble();
bytesRead += 8;
// read bottom
int bottomdbar = inData.readInt();
// read station quality
int stnQual = inData.readShort();
bytesRead += 2;
ord++;
JOAStation sh =
new JOAStation(
ord,
shipCode,
stnNum,
castNum,
myLat,
myLon,
numBottles,
year,
month,
day,
hour,
min,
bottomdbar,
stnQual);
sech.mStations.addElement(sh);
sh.setType("JOA BOTTLE");
// make a DBase object
Dbase db = new Dbase();
// add the global attributes
db.addEPSAttribute(
"CRUISE", EPCHAR, sech.mSectionDescription.length(), sech.mSectionDescription);
db.addEPSAttribute("CAST", EPCHAR, sh.mStnNum.length(), sh.mStnNum);
sarray[0] = (short) sh.mBottomDepthInDBARS;
db.addEPSAttribute("WATER_DEPTH", EPSHORT, 1, sarray);
db.addEPSAttribute("DATA_ORIGIN", EPCHAR, sech.mShipCode.length(), sech.mShipCode);
String dType = sh.getType();
if (dType == null) dType = "UNKN";
db.addEPSAttribute("DATA_TYPE", EPCHAR, dType.length(), dType);
sarray[0] = (short) stnQual;
db.addEPSAttribute("STN_QUALITY", EPSHORT, 1, sarray);
db.setDataType("JOA BOTTLE");
// add to temporary collection
dBases.addElement(db);
}
int start = mTotalStns;
int end = sech.mStations.size() + mTotalStns;
for (int sc = start; sc < end; sc++) {
mProgress.setPercentComplete(100.0 * ((double) bytesRead / (double) bytesInFile));
// get a dBase
Dbase db = (Dbase) dBases.elementAt(sc);
// get a station
JOAStation sh = (JOAStation) sech.mStations.elementAt(sc - start);
// create an array of arrays to store the data
double[][] va = new double[sech.mNumVars][sh.mNumBottles];
int[][] qc = new int[sech.mNumVars][sh.mNumBottles];
short[] bqc = new short[sh.mNumBottles];
int presPos = 0;
// read the bottles
for (int b = 0; b < sh.mNumBottles; b++) {
// read the bottle quality code
bqc[b] = inData.readShort();
bytesRead += 2;
for (int v = 0; v < sech.mNumVars; v++) {
// store the position of the PRES variable
if (tempProperties[v].mVarLabel.equals("PRES")) presPos = v;
// get the measured parameter
double dVarVal = EPSConstants.MISSINGVALUE;
try {
dVarVal = inData.readDouble();
} catch (IOException e) {
FileImportException fiex = new FileImportException();
String errStr =
"Error reading the parameter data. "
+ "\n"
+ "Bottle #"
+ b
+ " Parameter #"
+ v;
fiex.setErrorType(errStr);
throw fiex;
}
bytesRead += 8;
// store the value in the multidimensional array
va[v][b] = dVarVal;
// get the quality flag
short flag = (short) EPSConstants.MISSINGVALUE;
try {
flag = inData.readShort();
} catch (IOException e) {
FileImportException fiex = new FileImportException();
String errStr =
"Error reading the parameter quality code. "
+ "\n"
+ "Bottle #"
+ b
+ " Parameter #"
+ v;
fiex.setErrorType(errStr);
throw fiex;
}
bytesRead += 2;
qc[v][b] = flag;
} // for v
} // for b
// add the bottle quality codes as an attribute
db.addEPSAttribute("BOTTLE_QUALITY_CODES", EPSHORT, sh.mNumBottles, bqc);
// create the axes time = 0, depth = 1, lat = 2, lon = 3
Axis timeAxis = new Axis();
Axis zAxis = new Axis();
Axis latAxis = new Axis();
Axis lonAxis = new Axis();
// time axis
timeAxis.setName("time");
timeAxis.setTime(true);
timeAxis.setUnlimited(false);
timeAxis.setAxisType(EPTAXIS);
timeAxis.setLen(1);
int hour = 0;
if (sh.mHour != EPSConstants.MISSINGVALUE) hour = sh.mHour;
double mins = 0;
if (sh.mMinute != EPSConstants.MISSINGVALUE) mins = sh.mMinute;
// make the time axis units
String date = "days since ";
int min = (int) mins;
double fmin = mins - min;
int secs = (int) (fmin * 60.0);
double fsec = (fmin * 60.0) - secs;
int msec = (int) (fsec * 1000.0);
String fs = String.valueOf(fsec);
fs = fs.substring(fs.indexOf(".") + 1, fs.length()).trim();
int f = 0;
if (fs != null && fs.length() > 0) f = Integer.valueOf(fs).intValue();
// sprintf(time_string,"%04d-%02d-%02d %02d:%02d:%02d.%03d",yr,mon,day,hr,min,sec,f);
String frmt =
new String(
"{0,number,####}-{1,number,00}-{2,number,00} {3,number,00}:{4,number,00}:{5,number,00}.{6,number,000}");
MessageFormat msgf = new MessageFormat(frmt);
Object[] objs = {
new Integer(sh.mYear),
new Integer(sh.mMonth),
new Integer(sh.mDay),
new Integer(hour),
new Integer(min),
new Integer(secs),
new Integer(f)
};
StringBuffer out = new StringBuffer();
msgf.format(objs, out, null);
String time_string = new String(out);
date = date + time_string;
timeAxis.addAttribute(0, "units", EPCHAR, date.length(), date);
timeAxis.setUnits(date);
GeoDate gd = null;
try {
gd = new GeoDate(sh.mMonth, sh.mDay, sh.mYear, hour, min, secs, msec);
GeoDate[] ta = {gd};
MultiArray tma = new ArrayMultiArray(ta);
timeAxis.setData(tma);
db.setAxis(timeAxis);
} catch (Exception ex) {
GeoDate[] ta = {new GeoDate()};
MultiArray tma = new ArrayMultiArray(ta);
timeAxis.setData(tma);
db.setAxis(timeAxis);
}
// add the time axes variable
EPSVariable var = new EPSVariable();
var.setOname("time");
var.setDtype(EPDOUBLE);
var.setVclass(Double.TYPE);
var.addAttribute(0, "units", EPCHAR, date.length(), date);
var.setUnits(date);
double[] vta = {0.0};
MultiArray vtma = new ArrayMultiArray(vta);
try {
var.setData(vtma);
} catch (Exception ex) {
}
db.addEPSVariable(var);
// z axis
zAxis.setName("depth");
zAxis.setTime(false);
zAxis.setUnlimited(false);
zAxis.setLen(sh.mNumBottles);
zAxis.setAxisType(EPZAXIS);
zAxis.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.1");
zAxis.addAttribute(1, "units", EPCHAR, 4, "dbar");
zAxis.setUnits("dbar");
zAxis.setFrmt("f10.1");
// zAxis.addAttribute(2, "type", EPCHAR, 0, "");
sarray[0] = 1;
zAxis.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
double[] za = new double[sh.mNumBottles];
for (int b = 0; b < sh.mNumBottles; b++) {
za[b] = va[presPos][b];
}
MultiArray zma = new ArrayMultiArray(za);
zAxis.setData(zma);
db.setAxis(zAxis);
// add the z axes variables
var = new EPSVariable();
var.setOname("depth");
var.setDtype(EPDOUBLE);
var.setVclass(Double.TYPE);
var.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.1");
var.addAttribute(1, "units", EPCHAR, 4, "dbar");
var.setUnits("dbar");
var.setFrmt("f10.1");
// var.addAttribute(2, "type", EPCHAR, 0, "");
sarray[0] = 1;
var.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
MultiArray zvma = new ArrayMultiArray(za);
try {
var.setData(zvma);
} catch (Exception ex) {
}
db.addEPSVariable(var);
// lat axis
latAxis.setName("latitude");
latAxis.setTime(false);
latAxis.setUnlimited(false);
latAxis.setLen(1);
latAxis.setAxisType(EPYAXIS);
latAxis.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4");
latAxis.addAttribute(1, "units", EPCHAR, 7, "degrees");
latAxis.setUnits("degrees");
latAxis.setFrmt("f10.4");
// latAxis.addAttribute(2, "type", EPCHAR, 0, "");
sarray[0] = 500;
latAxis.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
double lat = sh.mLat;
double[] la = {lat};
MultiArray lma = new ArrayMultiArray(la);
latAxis.setData(lma);
db.setAxis(latAxis);
// add the y axes variable
var = new EPSVariable();
var.setOname("latitude");
var.setDtype(EPDOUBLE);
var.setVclass(Double.TYPE);
var.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4");
var.addAttribute(1, "units", EPCHAR, 7, "degrees");
var.setUnits("degrees");
var.setFrmt("f10.4");
// var.addAttribute(2, "type", EPCHAR, 0, "");
sarray[0] = 500;
var.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
MultiArray yvma = new ArrayMultiArray(la);
try {
var.setData(yvma);
} catch (Exception ex) {
}
db.addEPSVariable(var);
// lon axis
lonAxis.setName("longitude");
lonAxis.setTime(false);
lonAxis.setUnlimited(false);
lonAxis.setLen(1);
lonAxis.setAxisType(EPXAXIS);
lonAxis.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4");
lonAxis.addAttribute(1, "units", EPCHAR, 7, "degrees");
lonAxis.setUnits("degrees");
lonAxis.setFrmt("f10.4");
// lonAxis.addAttribute(2, "type", EPCHAR, 0, "");
sarray[0] = 502;
lonAxis.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
double lon = sh.mLon;
double[] lla = {lon};
lma = new ArrayMultiArray(lla);
lonAxis.setData(lma);
db.setAxis(lonAxis);
// add the x axes variable
var = new EPSVariable();
var.setOname("longitude");
var.setDtype(EPDOUBLE);
var.setVclass(Double.TYPE);
var.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4");
var.addAttribute(1, "units", EPCHAR, 7, "degrees");
var.setUnits("degrees");
var.setFrmt("f10.4");
// var.addAttribute(2, "type", EPCHAR, 0, "");
sarray[0] = 502;
var.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
MultiArray xvma = new ArrayMultiArray(lla);
try {
var.setData(xvma);
} catch (Exception ex) {
}
db.addEPSVariable(var);
// add the measured variables
for (int v = 0; v < sech.mNumVars; v++) {
// if (presPos == v)
// continue;
// create an array of measured EPSVariables for this database
EPSVariable epsVar = new EPSVariable();
// initialize the new EPSVariables
// look this variable up in JOA EPIC_Key. find matching entry in original EPIC Key
String oname = tempProperties[v].mVarLabel;
String sname = null;
String lname = null;
String gname = null;
String units = null;
String ffrmt = null;
int keyID = -99;
int type = -99;
try {
keyID = mEpicKeyDB.findKey(tempProperties[v].mVarLabel);
Key key = mOrigEpicKeyDB.findKey(keyID);
gname = key.getGname();
sname = key.getSname();
lname = key.getLname();
units = key.getUnits();
ffrmt = key.getFrmt();
type = key.getType();
} catch (Exception e) {
lname = tempProperties[v].mVarLabel;
gname = tempProperties[v].mVarLabel;
sname = tempProperties[v].mVarLabel;
units = tempProperties[v].mUnits;
}
// make a new variable
epsVar = new EPSVariable();
epsVar.setOname(oname);
epsVar.setSname(sname);
epsVar.setLname(lname);
epsVar.setGname(gname);
epsVar.setDtype(EPDOUBLE);
epsVar.setVclass(Double.TYPE);
int numAttributes = 0;
if (ffrmt != null) {
epsVar.addAttribute(numAttributes++, "FORTRAN_format", EPCHAR, ffrmt.length(), ffrmt);
epsVar.setFrmt(ffrmt);
}
if (units != null && units.length() > 0) {
epsVar.addAttribute(numAttributes++, "units", EPCHAR, units.length(), units);
epsVar.setUnits(units);
}
if (keyID >= 0) {
sarray[0] = (short) type;
// epsVar.addAttribute(numAttributes++, "type", EPSHORT, 1, sarray);
}
if (keyID >= 0) {
sarray[0] = (short) keyID;
epsVar.addAttribute(numAttributes++, "epic_code", EPSHORT, 1, sarray);
}
// add the quality code attribute
String qcVar = oname + "_QC";
epsVar.addAttribute(numAttributes++, "OBS_QC_VARIABLE", EPCHAR, qcVar.length(), qcVar);
// connect variable to axis
epsVar.setDimorder(0, 0);
epsVar.setDimorder(1, 1);
epsVar.setDimorder(2, 2);
epsVar.setDimorder(3, 3);
epsVar.setT(timeAxis);
epsVar.setZ(zAxis);
epsVar.setY(latAxis);
epsVar.setX(lonAxis);
// set the data
// create storage for the measured variables
double[][][][] vaa = new double[1][sh.mNumBottles][1][1];
for (int b = 0; b < sh.mNumBottles; b++) {
vaa[0][b][0][0] = va[v][b];
}
MultiArray mdma = new ArrayMultiArray(vaa);
try {
epsVar.setData(mdma);
} catch (Exception ex) {
System.out.println("throwing");
}
// add the variable to the database
db.addEPSVariable(epsVar);
// create the quality code variable
epsVar = new EPSVariable();
epsVar.setOname(oname + "_QC");
epsVar.setSname(sname + "_QC");
epsVar.setLname(sname + "_QC");
epsVar.setGname(sname + "_QC");
epsVar.setDtype(EPSHORT);
epsVar.setVclass(Short.TYPE);
// connect variable to axis
epsVar.setDimorder(0, 0);
epsVar.setDimorder(1, 1);
epsVar.setDimorder(2, 2);
epsVar.setDimorder(3, 3);
epsVar.setT(timeAxis);
epsVar.setZ(zAxis);
epsVar.setY(latAxis);
epsVar.setX(lonAxis);
// set the data
// create storage for the qc variables
short[][][][] qcaa = new short[1][sh.mNumBottles][1][1];
for (int b = 0; b < sh.mNumBottles; b++) {
qcaa[0][b][0][0] = (short) qc[v][b];
}
MultiArray qcma = new ArrayMultiArray(qcaa);
try {
epsVar.setData(qcma);
} catch (Exception ex) {
System.out.println("throwing");
}
// add the qc variable to the database
db.addEPSVariable(epsVar);
} // for v
}
mTotalStns += numCasts;
} // for sc
// read the file comments
StringBuffer sb = null;
while (true) {
try {
// read continuation line
inShort = inData.readShort();
bytesRead += 2;
if (inShort == 1) {
// read number of bytes in file description string
inShort = inData.readShort();
bytesRead += 2;
// read the file description String
byte buf2[] = new byte[inShort];
inData.read(buf2, 0, inShort);
String commentLine = new String(buf2);
bytesRead += inShort;
if (sb == null) sb = new StringBuffer(commentLine);
else sb.append(commentLine);
}
} catch (IOException e) {
break;
}
} // while true
if (sb != null) {
// make attributes for the comments
mOwnerDBase.setDataComment(new String(sb));
}
// make a sub database in the dbase
mOwnerDBase.createSubEntries(mTotalStns, mFile.getName());
for (int d = 0; d < mTotalStns; d++) {
Dbase db = (Dbase) dBases.elementAt(d);
mOwnerDBase.addSubEntry(db);
}
mProgress.setPercentComplete(100.0);
mProgress.setVisible(false);
mProgress.dispose();
in.close();
} catch (IOException e) {
mProgress.setVisible(false);
mProgress.dispose();
throw e;
}
}
/** used by preParse */
private static String preParseOnce(String s, FormulaManager fm) {
// convert to lower case
String l = s.toLowerCase();
// scan entire string
int len = l.length();
boolean letter = false;
String ns = "";
for (int i = 0; i < len; i++) {
if (!letter && i < len - 1 && l.substring(i, i + 2).equals("d(")) {
// convert d(x)/d(y) notation to standard derive(x, y) notation
i += 2;
int s1 = i;
for (int paren = 1; paren > 0; i++) {
// check for correct syntax
if (i >= len) return s;
char c = l.charAt(i);
if (c == '(') paren++;
if (c == ')') paren--;
}
int e1 = i - 1;
// check for correct syntax
if (i > len - 3 || !l.substring(i, i + 3).equals("/d(")) return s;
i += 3;
int s2 = i;
for (int paren = 1; paren > 0; i++) {
// check for correct syntax
if (i >= len) return s;
char c = l.charAt(i);
if (c == '(') paren++;
if (c == ')') paren--;
}
int e2 = i - 1;
ns = ns + "derive(" + s.substring(s1, e1) + "," + s.substring(s2, e2) + ")";
i--;
} else if (!letter && i < len - 4 && l.substring(i, i + 5).equals("link(")) {
// evaluate link(code) notation and replace with link variable
i += 5;
int s1 = i;
try {
while (l.charAt(i) != '(') i++;
} catch (ArrayIndexOutOfBoundsException exc) {
// incorrect syntax
return s;
}
i++;
int e1 = i - 1;
int s2 = i;
for (int paren = 2; paren > 1; i++) {
// check for correct syntax
if (i >= len) return s;
char c = l.charAt(i);
if (c == '(') paren++;
if (c == ')') paren--;
}
int e2 = i - 1;
// check for correct syntax
if (i >= len || l.charAt(i) != ')') return s;
String prestr = s.substring(s1, e1) + "(";
String str = prestr;
// parse method's arguments; determine if they are Data or RealType
String sub = s.substring(s2, e2);
StringTokenizer st = new StringTokenizer(sub, ",", false);
boolean first = true;
Vector v = new Vector();
while (st.hasMoreTokens()) {
String token = st.nextToken();
if (first) first = false;
else str = str + ",";
RealType rt = RealType.getRealTypeByName(token);
String sv = (rt == null ? "visad.Data" : "visad.RealType");
v.add(sv);
str = str + sv;
}
str = str + ")";
// obtain Method object
Method[] meths = FormulaUtil.stringsToMethods(new String[] {str});
if (meths[0] == null) {
// attempt to identify any matching methods by compressing
// some or all of the arguments into array form
int vlen = v.size();
Vector vstrs = new Vector();
for (int iv = 0; iv < vlen; iv++) {
String si = (String) v.elementAt(iv);
int lv = iv;
String sl;
while (lv < vlen) {
sl = (String) v.elementAt(lv++);
if (!sl.equals(si)) {
break;
}
str = prestr;
first = true;
for (int j = 0; j < vlen; j++) {
if (first) first = false;
else str = str + ",";
String sj = (String) v.elementAt(j);
str = str + sj;
if (iv == j) {
str = str + "[]";
j = lv - 1;
}
}
str = str + ")";
vstrs.add(str);
}
}
String[] strlist = new String[vstrs.size()];
vstrs.toArray(strlist);
meths = FormulaUtil.stringsToMethods(strlist);
int found = -1;
for (int j = 0; j < meths.length && found < 0; j++) {
if (meths[j] != null) found = j;
}
if (found >= 0) meths[0] = meths[found];
else {
// could not find a matching method
return s;
}
}
// store method object in a link variable
String link = "link" + (++linkNum);
try {
fm.setThing(link, new VMethod(meths[0]));
}
// catch any errors setting the link variable
catch (FormulaException exc) {
return s;
} catch (VisADException exc) {
return s;
} catch (RemoteException exc) {
return s;
}
ns = ns + "linkx(" + link + "," + s.substring(s2, e2) + ")";
} else if (!letter) {
int j = i;
char c = l.charAt(j++);
while (j < len && ((c >= 'a' && c <= 'z') || (c >= '0' && c <= '9'))) {
c = l.charAt(j++);
}
// check for end-of-string
if (j == len) return ns + s.substring(i, len);
if (c == '[') {
// convert x[y] notation to standard getSample(x, y) notation
int k = j;
for (int paren = 1; paren > 0; k++) {
// check for correct syntax
if (k >= len) return s;
c = l.charAt(k);
if (c == '[') paren++;
if (c == ']') paren--;
}
ns = ns + "getSample(" + s.substring(i, j - 1) + "," + s.substring(j, k - 1) + ")";
i = k - 1;
} else ns = ns + s.charAt(i);
} else {
// append character to new string
ns = ns + s.charAt(i);
}
char c = (i < len) ? l.charAt(i) : '\0';
letter = (c >= 'a' && c <= 'z');
}
return ns;
}
/**
* This method returns a <tt>Class</tt> for a helper which can handle the list of distributions
* specified by <tt>seq1</tt>. We maintain a cache of recently-loaded helpers, so check the cache
* before going to the trouble of searching for a helper. The cache is blown away every
* <tt>HELPER_CACHE_REFRESH</tt> seconds.
*
* <p>If we can't find a helper in the cache, we must search through the list of available helpers
* to find an appropriate one. First try to find helper using class sequence as specified by
* <tt>seq</tt>. Whether or not that succeeds, promote any <tt>Gaussian</tt> in the sequence to
* <tt>MixGaussians</tt>, and try again. If we get a better match on the second try, return the
* helper thus found.
*/
public static Class find_helper_class(Vector seq1, String helper_type)
throws ClassNotFoundException {
// Let's see if an appropriate helper is in the cache.
// If the cache is too old, empty it and search for the helper anew.
if (System.currentTimeMillis() - cache_timestamp > HELPER_CACHE_REFRESH) {
helper_cache = new Hashtable();
cache_timestamp = System.currentTimeMillis();
// Go on and search for appropriate helper.
} else {
HelperCacheKey key = new HelperCacheKey(helper_type, seq1);
Class helper_class = (Class) helper_cache.get(key);
if (helper_class != null) {
if (Global.debug > -1)
System.err.println(
"PiHelperLoader.find_helper_class: found helper class: "
+ helper_class
+ "; no need to search.");
return helper_class;
}
// else no luck; we have to search for helper.
}
// Well, we didn't find a helper in the cache, so let's go to work.
if (Global.debug > -1)
System.err.println(
"PiHelperLoader.find_helper_class: DID NOT FIND HELPER CLASS; NOW SEARCH.");
Class c1 = null, c2 = null;
ClassNotFoundException cnfe1 = null, cnfe2 = null;
int[] class_score1 = new int[1], count_score1 = new int[1];
int[] class_score2 = new int[1], count_score2 = new int[1];
try {
c1 = find_helper_class1(seq1, helper_type, class_score1, count_score1);
} catch (ClassNotFoundException e) {
cnfe1 = e;
} // hang on, we may need to re-throw later.
Class gaussian_class = Class.forName("riso.distributions.Gaussian");
MixGaussians mog = new MixGaussians(1, 1);
Vector seq2 = new Vector(seq1.size());
for (int i = 0; i < seq1.size(); i++)
if (gaussian_class.isAssignableFrom((Class) seq1.elementAt(i)))
seq2.addElement(mog.getClass());
else seq2.addElement(seq1.elementAt(i));
try {
c2 = find_helper_class1(seq2, helper_type, class_score2, count_score2);
} catch (ClassNotFoundException e) {
cnfe2 = e;
}
if (cnfe1 == null && cnfe2 == null) {
// Both matched; see which one fits better.
// Break ties in favor of the helper for non-promoted messages.
if (class_score1[0] >= class_score2[0]
|| (class_score1[0] == class_score2[0] && count_score1[0] >= count_score2[0])) {
if (Global.debug > 1)
System.err.println(
"\taccept helper " + c1 + " for non-promoted classes instead of " + c2);
if (Global.debug > 1)
System.err.println(
"\t\t"
+ class_score1[0]
+ ", "
+ class_score2[0]
+ "; "
+ count_score1[0]
+ ", "
+ count_score2[0]);
helper_cache.put(new HelperCacheKey(helper_type, seq1), c1);
return c1;
} else {
if (Global.debug > 1)
System.err.println("\taccept helper " + c2 + " for promoted classes instead of " + c1);
if (Global.debug > 1)
System.err.println(
"\t\t"
+ class_score1[0]
+ ", "
+ class_score2[0]
+ "; "
+ count_score1[0]
+ ", "
+ count_score2[0]);
helper_cache.put(new HelperCacheKey(helper_type, seq1), c2);
return c2;
}
} else if (cnfe1 == null && cnfe2 != null) {
// Only the first try matched, return it.
helper_cache.put(new HelperCacheKey(helper_type, seq1), c1);
return c1;
} else if (cnfe1 != null && cnfe2 == null) {
// Only the second try matched, return it.
helper_cache.put(new HelperCacheKey(helper_type, seq1), c2);
return c2;
} else {
// Neither try matched. Re-throw the exception generated by the first try.
throw cnfe1;
}
}