@Override
public void process(ProcessletInputs in, ProcessletOutputs out, ProcessletExecutionInfo info)
throws ProcessletException {
try {
WHSServiceVO vo = new WHSServiceVO();
URL processDefinitionUrl =
this.getClass().getResource("/" + this.getClass().getSimpleName() + ".xml");
DataInputHandler dataInputHandler =
new DataInputHandler(new File(processDefinitionUrl.toURI()));
String srsName = dataInputHandler.getValidatedStringValue(in, "srsName");
String x = String.valueOf(DataInputHandler.getDoubleInputValue(in, "x"));
String y = String.valueOf(DataInputHandler.getDoubleInputValue(in, "y"));
String z = String.valueOf(DataInputHandler.getDoubleInputValue(in, "z"));
String tolerance = dataInputHandler.getValidatedStringValue(in, "tolerance");
String filter = dataInputHandler.getValidatedStringValue(in, "filter");
vo.setFromSRSCodeOne(srsName);
vo.setFromSRSCode(srsName);
// vo.setToSRSCodeOne(agea);
// vo.setToSRSCode(agea);
vo.setTolerance(tolerance);
vo.setFilter(filter);
if (vo.getFilter().toLowerCase().startsWith("filepath:")) {
vo.setFilter(vo.getFilter().replaceAll("filePath:", ""));
}
LOG.debug("From SRS Code: {}", vo.getFromSRSCodeOne());
LOG.debug("Filter: {}", vo.getFilter());
// validate data inputs
vo.setOriginalCoordinateX(x);
vo.setOriginalCoordinateY(y);
vo.setOriginalCoordinateZ(z);
String transformedCoordinatesString = "";
if (vo.getFromSRSCode().equalsIgnoreCase("image")) {
vo.setTransformedCoordinateX(vo.getOriginalCoordinateX());
vo.setTransformedCoordinateY(vo.getOriginalCoordinateY());
vo.setTransformedCoordinateZ(vo.getOriginalCoordinateZ());
} else if (vo.getFromSRSCode().equalsIgnoreCase(abaReference)) {
vo.setTransformedCoordinateX(vo.getOriginalCoordinateX());
vo.setTransformedCoordinateY(vo.getOriginalCoordinateY());
vo.setTransformedCoordinateZ(vo.getOriginalCoordinateZ());
} else {
// Call getTransformationChain method here...
// ABAVoxel
vo.setOriginalCoordinateX(";x=" + vo.getOriginalCoordinateX());
vo.setOriginalCoordinateY(";y=" + vo.getOriginalCoordinateY());
vo.setOriginalCoordinateZ(";z=" + vo.getOriginalCoordinateZ());
vo.setToSRSCode(abaReference);
vo.setToSRSCodeOne(abaReference);
// Construct GetTransformationChain URL
// http://132.239.131.188:8080/atlas-ucsd?service=WPS&version=1.0.0&request=Execute&Identifier=GetTransformationChain&DataInputs=inputSrsName=Mouse_Paxinos_1.0;outputSrsName=Mouse_ABAreference_1.0;filter=Cerebellum
// Start - FIXME - Uncomment below two lines and comment the
// other three lines
// String hostName = uri.getHost();
// String portNumber = delimitor + uri.getPort();
String delimitor = config.getValue("incf.deploy.port.delimitor");
hostName = config.getValue("incf.deploy.host.name");
portNumber = config.getValue("incf.aba.port.number");
portNumber = delimitor + portNumber;
// End - FIXME
// central/atlas
String servicePath =
"/central/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=GetTransformationChain&DataInputs=inputSrsName="
+ vo.getFromSRSCode()
+ ";outputSrsName="
+ vo.getToSRSCode()
+ ";filter=NONE";
String transformationChainURL = "http://" + hostName + portNumber + servicePath;
XMLUtilities xmlUtilities = new XMLUtilities();
transformedCoordinatesString =
xmlUtilities.coordinateTransformation(
transformationChainURL,
vo.getOriginalCoordinateX(),
vo.getOriginalCoordinateY(),
vo.getOriginalCoordinateZ());
// Start - exception handling
if (transformedCoordinatesString.startsWith("Error:")) {
throw new OWSException("Transformed Coordinates Error: ", transformedCoordinatesString);
}
// End - exception handling
WHSUtil util = new WHSUtil();
String[] tempArray = util.getTabDelimNumbers(transformedCoordinatesString);
vo.setTransformedCoordinateX(tempArray[0]);
vo.setTransformedCoordinateY(tempArray[1]);
vo.setTransformedCoordinateZ(tempArray[2]);
}
// End
AnnotationResponseDocument document = completeResponse(vo);
ArrayList errorList = new ArrayList();
// opt.setErrorListener(errorList);
// boolean isValid = document.validate(opt);
// If the XML isn't valid, loop through the listener's contents,
// printing contained messages.
/* if (!isValid) {
for (int i = 0; i < errorList.size(); i++) {
XmlError error = (XmlError) errorList.get(i);
LOG.debug("\n");
LOG.debug("Message: {}" , error.getMessage() + "\n");
LOG.debug("Location of invalid XML: {}"
, error.getCursorLocation().xmlText() + "\n");
}
}
*/
ComplexOutput complexOutput = (ComplexOutput) out.getParameter("GetAnnotationsByPOIOutput");
// get reader on document; reader --> writer
XMLStreamReader reader = document.newXMLStreamReader();
XMLStreamWriter writer = complexOutput.getXMLStreamWriter();
XMLAdapter.writeElement(writer, reader);
} catch (MissingParameterException e) {
LOG.error(e.getMessage(), e);
throw new ProcessletException(new OWSException(e));
} catch (InvalidParameterValueException e) {
LOG.error(e.getMessage(), e);
throw new ProcessletException(new OWSException(e));
} catch (Throwable e) {
String message = "Unexpected exception occured";
LOG.error(message, e);
OWSException owsException =
new OWSException(message, e, ControllerException.NO_APPLICABLE_CODE);
throw new ProcessletException(owsException);
}
}
public AnnotationResponseDocument completeResponse(WHSServiceVO vo) {
LOG.debug("X1: " + vo.getTransformedCoordinateX());
LOG.debug("Y1: " + vo.getTransformedCoordinateY());
LOG.debug("Z1: " + vo.getTransformedCoordinateZ());
String x1 = vo.getTransformedCoordinateX();
String x2 =
String.valueOf(
Double.parseDouble(vo.getTransformedCoordinateX())
+ Double.parseDouble(vo.getTolerance()));
String x3 =
String.valueOf(
Double.parseDouble(vo.getTransformedCoordinateX())
+ Double.parseDouble(vo.getTolerance()));
String x4 = vo.getTransformedCoordinateX();
String y1 = vo.getTransformedCoordinateY();
String y2 = vo.getTransformedCoordinateY();
String y3 =
String.valueOf(
Double.parseDouble(vo.getTransformedCoordinateY())
- Double.parseDouble(vo.getTolerance()));
String y4 =
String.valueOf(
Double.parseDouble(vo.getTransformedCoordinateY())
- Double.parseDouble(vo.getTolerance()));
AnnotationResponseDocument doc = AnnotationResponseDocument.Factory.newInstance();
AnnotationResponse annResp = doc.addNewAnnotationResponse();
String polygonString =
x1 + " " + y1 + "," + x2 + " " + y2 + "," + x3 + " " + y3 + "," + x4 + " " + y4 + "," + x1
+ " " + y1;
LOG.debug("Artibrary polygon string - {}", polygonString);
ArrayList annotationDataList = new ArrayList();
WHSServiceDAOImpl daoImpl = new WHSServiceDAOImpl();
LOG.debug("*********************************SRSName outside: " + vo.getFromSRSCode());
LOG.debug("*********************************filter outside: " + vo.getFilter());
if (!vo.getFromSRSCode().equalsIgnoreCase("image")) {
LOG.debug("*********************************SRSName inside Image: " + vo.getSrsName());
annotationDataList = daoImpl.getAnnotationData(vo, polygonString);
} else if (vo.getFromSRSCode().equalsIgnoreCase("image")) {
LOG.debug(
"*********************************SRSName inside Not Actual SRSName: "
+ vo.getFromSRSCode());
annotationDataList = daoImpl.getAnnotationData(vo);
} else {
// FIXME - Put some exception code here to throw an exception
LOG.debug("SRS TYPE NOT SUPPORTED");
}
Iterator iterator0 = annotationDataList.iterator();
String id = "";
String path = "";
HashMap map = new HashMap();
while (iterator0.hasNext()) {
vo = (WHSServiceVO) iterator0.next();
id = vo.getUniqueID();
path = vo.getOntoFilePath();
map.put(id, path);
}
LOG.debug("Map Size: " + map.size());
Iterator annotationsIterator = map.keySet().iterator();
String key = "";
while (annotationsIterator.hasNext()) {
key = annotationsIterator.next().toString();
LOG.debug("*****************New Annotation*****************");
AnnotationType ann = annResp.addNewAnnotation();
Iterator dataIterator = annotationDataList.iterator();
GEOMETRYTYPE geom1 = null;
AnnPolygonType polygon1 = null;
GEOMETRIES geometries = null;
geometries = ann.addNewGEOMETRIES();
geom1 = geometries.addNewGEOMETRY();
// Resource and Geometries should be only one time
RESOURCE res = ann.addNewRESOURCE();
/* CentralServiceVO vo1 = null;
while (dataIterator.hasNext()) {
vo1 = (CentralServiceVO)dataIterator.next();
LOG.debug("**Key from Hash Map:**" + key );
LOG.debug("**Key from Collection:**" + vo1.getUniqueID() );
if (key.equals(vo1.getUniqueID())){
*/
LOG.debug("*****************New Data Inside Annotation*****************");
// Loop here - New Annotation
Iterator iterator1 = annotationDataList.iterator();
WHSServiceVO vo2 = null;
// Delete this loop
while (iterator1.hasNext()) {
vo2 = (WHSServiceVO) iterator1.next();
LOG.debug("##Original Key MAP INSIDEPOLYGON:##" + key);
LOG.debug("##Key from Collection INSIDE POLYGON:##" + vo2.getUniqueID());
if (vo2.getUniqueID().equals(key)) {
polygon1 = geom1.addNewPOLYGON();
LOG.debug("##Inside POLYGON:##");
/* LOG.debug("Date is: " + date );
LOG.debug("Time is: " + date.getTime() );
LOG.debug("Day is: " + date.getDate() );
*/
// FIXME - update the unique url below from the db
res.setFilepath(vo2.getOntoFilePath());
geom1.setUserName(vo2.getUserName());
if (vo2.getSrsName() == null || vo2.getSrsName().equals("")) {
polygon1.setSrsName("Undefined");
} else {
polygon1.setSrsName(vo2.getSrsName());
}
polygon1.setId(gmlId(vo2.getPolygonID()));
// date = vo.getUpdatedTime();
// FIXME
Calendar cal = Calendar.getInstance();
cal.setTime(vo.getUpdatedTime());
ann.setMODIFIEDDATE(cal);
// FIXME - modifiedTime
// long modifiedTime = Long.parseLong(vo1.getUpdatedTime());
Date date = null;
// FIXME
geom1.setModifiedTime(vo.getUpdatedTime().getTime());
AbstractRingPropertyType poly1exterior = polygon1.addNewExterior();
XmlObject ring = poly1exterior.addNewAbstractRing();
XmlObject linearRing =
ring.substitute(
new QName("http://www.opengis.net/gml/3.2", "LinearRing"), LinearRingType.type);
DirectPositionType pos1 = ((LinearRingType) linearRing).addNewPos();
pos1.setStringValue(vo2.getTransformedCoordinates().replaceAll(",", " "));
}
}
GENERALONTOMODEL model1 = ann.addNewGENERALONTOMODEL();
RELATIONSTYPE relations = model1.addNewRELATIONS();
Iterator iterator2 = annotationDataList.iterator();
WHSServiceVO vo3 = null;
while (iterator2.hasNext()) {
vo3 = (WHSServiceVO) iterator2.next();
if (vo3.getUniqueID().equals(key)) {
ONTOPROPERTYTYPE prop2 = relations.addNewONTOPROPERTY();
prop2.setTitle("has_geometry");
// Below URL never changes
prop2.setHref(
"http://ontology.neuinfo.org/NIF/Backend/NIFSTD_Datatype_properties.owl#hasGeometry");
prop2.setUserName(vo3.getUserName());
// FIXME - modifiedTime
prop2.setModifiedTime(vo.getUpdatedTime().getTime());
SUBJECTTYPE subj2 = prop2.addNewSUBJECT();
ONTOTERMTYPE term2_1 = subj2.addNewONTOTERM();
term2_1.setTitle(vo3.getOntoName());
term2_1.setHref(vo3.getOntoURI());
term2_1.setId(gmlId(vo3.getPolygonID()));
// term2_1.newCursor().insertComment(" title = onto_name, href = onto_url gml:id=
// instance_id");
OBJECTTYPE obj2 = prop2.addNewOBJECT();
GEOMETRYTYPE term2_2 = obj2.addNewGEOMETRY();
term2_2.setHref(gmlIdInteralReference(gmlId(vo3.getPolygonID())));
}
}
ONTOTERMS terms = ann.addNewONTOTERMS();
Iterator iterator3 = annotationDataList.iterator();
WHSServiceVO vo4 = null;
while (iterator3.hasNext()) {
vo4 = (WHSServiceVO) iterator3.next();
if (vo4.getUniqueID().equals(key)) {
ONTOTERMTYPE term2 = terms.addNewONTOTERM();
term2.setId(gmlId(vo4.getPolygonID()));
term2.setHref(vo4.getOntoURI());
term2.setTitle(vo4.getOntoName());
}
}
// }
// }
}
return doc;
}