private void writeTitle(
final XMLStreamWriter writer, final List<LanguageString> titles, final String name)
throws XMLStreamException {
if (titles != null && !titles.isEmpty()) {
writeElement(writer, "Title", titles.get(0).getString());
} else if (name != null) {
writeElement(writer, "Title", name);
}
}
@Override
public ISORecord inspect(ISORecord record, Connection conn, SQLDialect dialect)
throws MetadataInspectorException {
ISORecord result = record;
try {
// create temporary sink for normalized XML
ByteArrayOutputStream bos = new ByteArrayOutputStream();
XMLStreamWriter writer = XMLOutputFactory.newInstance().createXMLStreamWriter(bos);
writer = new NamespaceNormalizingXMLStreamWriter(writer, nsBindings);
// create normalized copy
XMLStreamReader reader = record.getAsXMLStream();
XMLAdapter.writeElement(writer, reader);
reader.close();
writer.close();
InputStream is = new ByteArrayInputStream(bos.toByteArray());
XMLStreamReader xmlStream = XMLInputFactory.newInstance().createXMLStreamReader(is);
result = new ISORecord(xmlStream);
} catch (Throwable t) {
LOG.error(
"Namespace normalization failed. Proceeding with unnormalized record. Error: "
+ t.getMessage());
}
return result;
}
/**
* makes a {@link Document} out of a {@link XMLStreamReader}
*
* @param xmlStreamReader the xmlStreamRader to convert
* @return the xmlStreamRader as {@link Document}
* @throws FactoryConfigurationError
* @throws XMLStreamException
* @throws ParserConfigurationException
* @throws IOException
* @throws SAXException
*/
public static Document getAsDocument(XMLStreamReader xmlStreamReader)
throws XMLStreamException, FactoryConfigurationError, ParserConfigurationException,
SAXException, IOException {
StreamBufferStore store = new StreamBufferStore();
XMLStreamWriter xmlWriter = null;
try {
xmlWriter = XMLOutputFactory.newInstance().createXMLStreamWriter(store);
xmlWriter.writeStartDocument();
XMLAdapter.writeElement(xmlWriter, xmlStreamReader);
} finally {
if (xmlWriter != null) {
try {
xmlWriter.close();
} catch (XMLStreamException e) {
LOG.error("Unable to close xmlwriter.");
}
}
}
store.flush();
DOMParser parser = new DOMParser();
parser.parse(new InputSource(store.getInputStream()));
Document doc = parser.getDocument();
store.close();
return doc;
}
private void writeMetadataUrls(final XMLStreamWriter writer, final List<MetadataUrl> list)
throws XMLStreamException {
if (list == null) {
return;
}
for (final MetadataUrl url : list) {
writer.writeStartElement("MetadataURL");
if (url.getType() == null) {
writer.writeAttribute("type", "TC211");
} else {
writer.writeAttribute("type", url.getType());
}
if (url.getFormat() == null) {
writeElement(writer, "Format", "application/xml");
} else {
writeElement(writer, "Format", url.getFormat());
}
writeOnlineResource(writer, url.getUrl());
writer.writeEndElement();
}
}
private void writeKeywordList(
final XMLStreamWriter writer, final List<Pair<List<LanguageString>, CodeType>> keywordList)
throws XMLStreamException {
if (keywordList != null && !keywordList.isEmpty()) {
writer.writeStartElement("KeywordList");
for (final Pair<List<LanguageString>, CodeType> kws : keywordList) {
for (final LanguageString ls : kws.first) {
// <!ELEMENT Keyword (#PCDATA) >
writeElement(writer, "Keyword", ls.getString());
}
}
writer.writeEndElement();
}
}
@Override
public void process(ProcessletInputs in, ProcessletOutputs out, ProcessletExecutionInfo info)
throws ProcessletException {
try {
// validate against allowed values in process definition file
URL processDefinitionUrl =
this.getClass().getResource("/" + this.getClass().getSimpleName() + ".xml");
// get validated data inputs or default values
DataInputHandler dataInputHandler =
new DataInputHandler(new File(processDefinitionUrl.toURI()));
String srsName = dataInputHandler.getValidatedStringValue(in, "srsName");
String filter = dataInputHandler.getValidatedStringValue(in, "filter");
double x = DataInputHandler.getDoubleInputValue(in, "x");
double y = DataInputHandler.getDoubleInputValue(in, "y");
double z = DataInputHandler.getDoubleInputValue(in, "z");
LOG.debug(
String.format(
"DataInputs: srsName: %s, poi: (%f, %f, %f), filter: %s", srsName, x, y, z, filter));
responseValues = new ResponseValues();
responseValues.clientSrsName = srsName;
// transform non-AGEA coordinates to AGEA
if (!srsName.equals("Mouse_AGEA_1.0")) {
ABAServiceVO vo = getTransformPOI(srsName, x, y, z);
if (vo.getTransformationXMLResponseString().startsWith("Error:")) {
throw new OWSException(
"Transformation Coordinates Error: ", vo.getTransformationXMLResponseString());
}
x = Double.parseDouble(vo.getTransformedCoordinateX());
y = Double.parseDouble(vo.getTransformedCoordinateY());
z = Double.parseDouble(vo.getTransformedCoordinateZ());
}
LOG.debug("X from Transformation Method: " + x);
LOG.debug("Y from Transformation Method: " + y);
LOG.debug("Z from Transformation Method: " + z);
String srsFromClient = srsName;
Point3d poiFromClient = new Point3d(x, y, z);
// get plane; defaults to sagittal
ImageSeriesPlane desiredPlane =
filter.equals("maptype:coronal") ? ImageSeriesPlane.CORONAL : ImageSeriesPlane.SAGITTAL;
// 1. get strong gene(s) at POI
List<ABAGene> strongGenes = ABAUtil.retrieveStrongGenesAtAGEAPOI(x, y, z, NBR_STRONG_GENES);
// make sure we have something
if (strongGenes.size() == 0) {
throw new OWSException(
"No 'strong genes' found at " + "coordinates, hence no images to return.",
ControllerException.NO_APPLICABLE_CODE);
}
if (LOG.isDebugEnabled()) {
StringBuilder buf = new StringBuilder();
for (ABAGene gene : strongGenes) {
buf.append(gene.getGenesymbol()).append(", ");
}
LOG.debug("Strong genes: {}", buf.toString());
}
// 2. get image series'es for strong genes and desired plane
List<ImageSeries> imageSerieses = new ArrayList<ImageSeries>();
for (ABAGene gene : strongGenes) {
ImageSeries imageSeries = retrieveImagesSeriesForGene(gene.getGenesymbol(), desiredPlane);
if (imageSeries != null) {
imageSerieses.add(imageSeries);
}
}
// make sure we have something
if (imageSerieses.size() == 0) {
throw new OWSException(
"No image series found for 'strong "
+ "genes' and desired plane, hence no images to "
+ "return.",
ControllerException.NO_APPLICABLE_CODE);
}
if (LOG.isDebugEnabled()) {
StringBuilder buf = new StringBuilder();
for (ImageSeries is : imageSerieses) {
buf.append(is.imageSeriesId).append(':');
buf.append(is.imageSeriesPlane).append(", ");
}
LOG.debug("Image Serieses id:plane: {}", buf.toString());
}
Point3d poiForProximity = new Point3d(poiFromClient);
// divide POI coords by 100
Point3d poi100 = new Point3d();
poi100.scale(0.01, poiForProximity);
LOG.debug("POI for closest position (srs, xyz): {}, {}", srsFromClient, poi100.toString());
// 3. get ......... for each image series
for (ImageSeries imageSeries : imageSerieses) {
// begin to add values to image
Image image = new Image(imageSeries.imageSeriesId);
// get atlas map
// find closest point, get other values including position
// add more (atlas map) values to image
getClosestPosition(imageSeries, poi100, image);
LOG.debug("Position: {}", image.abaImagePosition);
// get best image id in image series based on position
// add more (image elements) values to image
// match position to find image in series, get imageid
// /image-series/images/image/position
// /image-series/images/image/imageid
retrieveImageForPosition(imageSeries.imageSeriesId, image.abaImagePosition, image);
LOG.debug("Image id: {}", image.imageId);
// zoom level not applicable
// image.zoomLevel = zoomLevel;
// assemble aba view image uri
image.imageURI = assembleImageURI(image.downloadImagePath, HI_RES, MIME);
image.thumbnailurl = assembleImageURI(image.downloadImagePath, THUMB, MIME);
LOG.debug("Image URI: {}", image.imageURI.toString());
responseValues.images.add(image);
} // for
// ImagesResponseDocument 'is a' org.apache.xmlbeans.XmlObject
// 'is a' org.apache.xmlbeans.XmlTokenSource
ImagesResponseDocument document = completeResponse();
if (LOG.isDebugEnabled()) {
XmlOptions opt = (new XmlOptions()).setSavePrettyPrint();
opt.setSaveSuggestedPrefixes(Utilities.SuggestedNamespaces());
opt.setSaveNamespacesFirst();
opt.setSaveAggressiveNamespaces();
opt.setUseDefaultNamespace();
LOG.debug("Xml:\n{}", document.xmlText(opt));
}
// 4. Send it
// get reader on document
XMLStreamReader reader = document.newXMLStreamReader();
// get ComplexOutput object from ProcessletOutput...
ComplexOutput complexOutput = (ComplexOutput) out.getParameter("Get2DImagesByPOIOutput");
LOG.debug("Setting complex output (requested=" + complexOutput.isRequested() + ")");
// ComplexOutput objects can be huge so stream it
XMLStreamWriter writer = complexOutput.getXMLStreamWriter();
XMLAdapter.writeElement(writer, reader);
// transform any exceptions into ProcessletException wrapping
// OWSException
} 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 (InvalidDataInputValueException e) {
LOG.error(e.getMessage(), e);
throw new ProcessletException(e); // is already OWSException
} catch (OWSException e) {
LOG.error(e.getMessage(), e);
throw new ProcessletException(e); // is already OWSException
} catch (Throwable e) {
String message = "Unexpected exception occurred: " + e.getMessage();
LOG.error(message, e);
throw new ProcessletException(
new OWSException(message, e, ControllerException.NO_APPLICABLE_CODE));
}
}
/**
* Copies an XML element (including all attributes and subnodes) from the given {@link
* XMLStreamReader} to the given {@link XMLStreamWriter}.
*
* @param writer {@link XMLStreamWriter} that the xml is appended to
* @param reader cursor must point at a <code>START_ELEMENT</code> event and points at the
* corresponding <code>END_ELEMENT</code> event afterwards
* @throws XMLStreamException
*/
public static void copy(XMLStreamWriter writer, XMLStreamReader reader)
throws XMLStreamException {
skipStartDocument(reader);
XMLAdapter.writeElement(writer, reader);
}
private void writeAbstract(final XMLStreamWriter writer, final List<LanguageString> abstracts)
throws XMLStreamException {
if (abstracts != null && !abstracts.isEmpty()) {
writeElement(writer, "Abstract", abstracts.get(0).getString());
}
}
private void writeName(final XMLStreamWriter writer, final String name)
throws XMLStreamException {
if (name != null) {
writeElement(writer, "Name", name);
}
}
@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);
}
}
