public String AsXml() {
XmlOptions opt = (new XmlOptions()).setSavePrettyPrint();
opt.setSaveSuggestedPrefixes(Utilities.SuggestedNamespaces());
opt.setSaveNamespacesFirst();
opt.setSaveAggressiveNamespaces();
opt.setUseDefaultNamespace();
DescribeSRSResponseDocument document = completeResponse();
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);
System.out.println("\n");
System.out.println("Message: " + error.getMessage() + "\n");
System.out.println(
"Location of invalid XML: " + error.getCursorLocation().xmlText() + "\n");
}
}
return document.xmlText(opt);
}
private byte[] generateXml(
Integer demographicNo, Integer rourkeFdid, Integer nddsFdid, Integer report18mFdid) {
HashMap<String, String> suggestedPrefixes = new HashMap<String, String>();
suggestedPrefixes.put("http://www.w3.org/2001/XMLSchema-instance", "xsi");
XmlOptions opts = new XmlOptions();
opts.setSaveSuggestedPrefixes(suggestedPrefixes);
opts.setSavePrettyPrint();
opts.setSaveNoXmlDecl();
opts.setUseDefaultNamespace();
opts.setSaveNamespacesFirst();
ByteArrayOutputStream os = null;
PrintWriter pw = null;
boolean xmlCreated = false;
BORN18MFormToXML xml = new BORN18MFormToXML(demographicNo);
try {
os = new ByteArrayOutputStream();
pw = new PrintWriter(os, true);
pw.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
xmlCreated = xml.addXmlToStream(pw, opts, rourkeFdid, nddsFdid, report18mFdid);
pw.close();
if (xmlCreated) return os.toByteArray();
} catch (Exception e) {
logger.warn("Unable to add record", e);
}
return null;
}
/**
* Generate the ExceptionReport as an XML string.
*
* @return the ExceptionReport as an XML string
*/
public String getXMLExceptionReport() {
Map<String, String> suggestedPrefixes = new HashMap<String, String>();
suggestedPrefixes.put("http://www.opengis.net/ows/2.0", "ows");
XmlOptions opts = new XmlOptions();
opts.setSavePrettyPrint();
opts.setSaveSuggestedPrefixes(suggestedPrefixes);
opts.setSaveNamespacesFirst();
opts.setSaveAggressiveNamespaces();
opts.setUseDefaultNamespace();
return exceptionReportDoc.xmlText(opts);
}
@Override
protected void commit() throws IOException {
XmlOptions xmlOptions = new XmlOptions(DEFAULT_XML_OPTIONS);
Map<String, String> map = new HashMap<String, String>();
map.put(STRelationshipId.type.getName().getNamespaceURI(), "r");
xmlOptions.setSaveSuggestedPrefixes(map);
PackagePart part = getPackagePart();
OutputStream out = part.getOutputStream();
_presentation.save(out, xmlOptions);
out.close();
}
@Test
public void validFullResponse() {
XmlOptions opt = (new XmlOptions()).setSavePrettyPrint();
opt.setSaveSuggestedPrefixes(Utilities.SuggestedNamespaces());
opt.setSaveNamespacesFirst();
opt.setSaveAggressiveNamespaces();
opt.setUseDefaultNamespace();
XmlObject co = completeResponse();
ArrayList errorList = new ArrayList();
boolean validXml = Utilities.validateXml(opt, co, errorList);
assertTrue(errorList.toString(), validXml);
}
private File createXMLMetadata(HashMap<String, Object> inputs) {
ArrayList<?> validationErrors = new ArrayList<Object>();
XmlOptions options;
options = new XmlOptions();
options.setSavePrettyPrint();
options.setSaveAggressiveNamespaces();
HashMap<String, String> suggestedPrefixes = new HashMap<String, String>();
suggestedPrefixes.put("http://www.geoviqua.org/QualityInformationModel/4.0", "gvq");
options.setSaveSuggestedPrefixes(suggestedPrefixes);
options.setErrorListener(validationErrors);
GVQMetadataDocument doc = GVQMetadataDocument.Factory.newInstance();
GVQMetadataType gvqMetadata = doc.addNewGVQMetadata();
gvqMetadata.addNewLanguage().setCharacterString("en");
gvqMetadata.addNewMetadataStandardName().setCharacterString("GVQ");
gvqMetadata.addNewMetadataStandardVersion().setCharacterString("1.0.0");
gvqMetadata.addNewDateStamp().setDate(Calendar.getInstance());
DQDataQualityType quality = gvqMetadata.addNewDataQualityInfo2().addNewDQDataQuality();
GVQDataQualityType gvqQuality =
(GVQDataQualityType)
quality.substitute(
new QName("http://www.geoviqua.org/QualityInformationModel/4.0", "GVQ_DataQuality"),
GVQDataQualityType.type);
GVQDiscoveredIssueType issue = gvqQuality.addNewDiscoveredIssue().addNewGVQDiscoveredIssue();
issue.addNewKnownProblem().setCharacterString(inputs.get("element").toString());
issue.addNewWorkAround().setCharacterString("solution");
// validate schema conformity
boolean isValid = doc.validate();
if (!isValid) System.out.println(Arrays.toString(validationErrors.toArray()));
// print out as XML
System.out.println(doc.xmlText(options));
try {
File tempFile = File.createTempFile("wpsMetdataTempFile", "xml");
doc.save(tempFile);
return tempFile;
} catch (Exception e) {
LOGGER.error("createXMLMetadataError " + e);
}
return null;
}
/**
* Returns an XMLBeans document as a String with full Fedora/RDF namespace support
*
* @param doc The document to parse to a String
* @return String version of the document. This will contain prefixes for rdf and myns
*/
public static String xmlToString(XmlObject doc) {
HashMap<String, String> namespaces = new HashMap<String, String>();
namespaces.put("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
namespaces.put("http://www.nsdl.org/ontologies/relationships#", "myns");
XmlOptions xmlOptions = new XmlOptions();
xmlOptions.setSaveSuggestedPrefixes(namespaces);
xmlOptions.setSaveAggressiveNamespaces();
StringWriter out = new StringWriter();
try {
doc.save(out, xmlOptions);
return out.toString();
} catch (Exception e) {
return null;
}
}
@Override
protected void commit() throws IOException {
XmlOptions xmlOptions = new XmlOptions(DEFAULT_XML_OPTIONS);
xmlOptions.setSaveSyntheticDocumentElement(
new QName(CTSettings.type.getName().getNamespaceURI(), "settings"));
Map<String, String> map = new HashMap<String, String>();
map.put("http://schemas.openxmlformats.org/wordprocessingml/2006/main", "w");
xmlOptions.setSaveSuggestedPrefixes(map);
PackagePart part = getPackagePart();
OutputStream out = part.getOutputStream();
ctSettings.save(out, xmlOptions);
out.close();
}
/**
* Dumps an XML document to disk.
*
* @param doc The document to dump to disk
* @param filePath The full path and name of the file
*/
public static void dumpXML(XmlObject doc, String filePath) {
HashMap<String, String> namespaces = new HashMap<String, String>();
namespaces.put("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
namespaces.put("http://www.nsdl.org/ontologies/relationships#", "myns");
XmlOptions xmlOptions = new XmlOptions();
xmlOptions.setSavePrettyPrint();
xmlOptions.setSavePrettyPrintIndent(2);
// xmlOptions.setUseDefaultNamespace();
// xmlOptions.setSaveAggressiveNamespaces();
xmlOptions.setSaveSuggestedPrefixes(namespaces);
// xmlOptions.setSaveNamespacesFirst();
try {
doc.save(new File(filePath), xmlOptions);
} catch (Exception e) {
}
}
/** save and commit numbering */
@Override
protected void commit() throws IOException {
XmlOptions xmlOptions = new XmlOptions(DEFAULT_XML_OPTIONS);
xmlOptions.setSaveSyntheticDocumentElement(
new QName(CTNumbering.type.getName().getNamespaceURI(), "numbering"));
Map map = new HashMap();
map.put("http://schemas.openxmlformats.org/markup-compatibility/2006", "ve");
map.put("urn:schemas-microsoft-com:office:office", "o");
map.put("http://schemas.openxmlformats.org/officeDocument/2006/relationships", "r");
map.put("http://schemas.openxmlformats.org/officeDocument/2006/math", "m");
map.put("urn:schemas-microsoft-com:vml", "v");
map.put("http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing", "wp");
map.put("urn:schemas-microsoft-com:office:word", "w10");
map.put("http://schemas.openxmlformats.org/wordprocessingml/2006/main", "w");
map.put("http://schemas.microsoft.com/office/word/2006/wordml", "wne");
xmlOptions.setSaveSuggestedPrefixes(map);
PackagePart part = getPackagePart();
OutputStream out = part.getOutputStream();
ctNumbering.save(out, xmlOptions);
out.close();
}
@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));
}
}
