@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;
}
void parse(String layerName, XMLAdapter adapter, List<SLDStyleType> styles) {
File stylesDir = new File(workspace.getLocation(), "styles");
for (SLDStyleType sty : styles) {
try {
File file = new File(adapter.resolve(sty.getFile()).toURI());
String namedLayer = sty.getNamedLayer();
LOG.debug("Will read styles from SLD '{}', for named layer '{}'.", file, namedLayer);
Map<String, String> map = new HashMap<String, String>();
Map<String, Pair<File, URL>> legends = new HashMap<String, Pair<File, URL>>();
Map<String, Boolean> glgUrls = new HashMap<String, Boolean>();
extractFromSld(sty, adapter, stylesDir, layerName, legends, glgUrls, map);
if (file.getParentFile().equals(stylesDir)) {
handleSldFromStyleStore(file, namedLayer, map, layerName, legends, glgUrls);
}
handleExternalSld(file, namedLayer, layerName, map, legends, glgUrls);
} catch (Throwable e) {
LOG.trace("Stack trace", e);
LOG.info(
"Style file '{}' for layer '{}' could not be parsed: '{}'.",
new Object[] {sty.getFile(), layerName, e.getLocalizedMessage()});
}
}
}
private void extractFromSld(
SLDStyleType sty,
XMLAdapter adapter,
File stylesDir,
String layerName,
Map<String, Pair<File, URL>> legends,
Map<String, Boolean> glgUrls,
Map<String, String> map)
throws Throwable {
String name = null, lastName = null;
for (JAXBElement<?> elem : sty.getNameAndUserStyleAndLegendConfigurationFile()) {
if (elem.getName().getLocalPart().equals("Name")) {
name = elem.getValue().toString();
} else if (elem.getName().getLocalPart().equals("LegendConfigurationFile")) {
File legendFile = new File(adapter.resolve(elem.getValue().toString()).toURI());
Style style = findStyle(legendFile, stylesDir, layerName);
if (style != null) {
if (name != null) {
style.setName(name);
}
registry.putLegend(layerName, style, false);
}
} else if (elem.getName().getLocalPart().equals("LegendGraphicFile")) {
LegendGraphicFile lgf = (LegendGraphicFile) elem.getValue();
URL url = adapter.resolve(lgf.getValue());
if (url.toURI().getScheme().equals("file")) {
File legend = new File(url.toURI());
legends.put(lastName, new Pair<File, URL>(legend, null));
} else {
legends.put(lastName, new Pair<File, URL>(null, url));
}
glgUrls.put(lastName, lgf.isOutputGetLegendGraphicUrl());
} else if (elem.getName().getLocalPart().equals("UserStyle")) {
if (name == null) {
name = elem.getValue().toString();
}
LOG.debug(
"Will load user style with name '{}', it will be known as '{}'.",
elem.getValue(),
name);
map.put(elem.getValue().toString(), name);
lastName = name;
name = null;
}
}
}
protected static Pair<Filter, ConstraintLanguage> parseConstraint(
XMLAdapter adapter, OMElement omQueryElement) {
Pair<Filter, ConstraintLanguage> pc = null;
if (omQueryElement != null
&& new QName(CSWConstants.CSW_202_NS, "Constraint").equals(omQueryElement.getQName())) {
Version versionConstraint =
adapter.getRequiredNodeAsVersion(omQueryElement, new XPath("@version", nsContext));
OMElement filterEl = omQueryElement.getFirstChildWithName(new QName(OGCNS, "Filter"));
OMElement cqlTextEl = omQueryElement.getFirstChildWithName(new QName("", "CQLTEXT"));
if ((filterEl != null) && (cqlTextEl == null)) {
ConstraintLanguage constraintLanguage = ConstraintLanguage.FILTER;
Filter constraint;
try {
// TODO remove usage of wrapper (necessary at the moment to work around problems
// with AXIOM's
XMLStreamReader xmlStream =
new XMLStreamReaderWrapper(filterEl.getXMLStreamReaderWithoutCaching(), null);
// skip START_DOCUMENT
xmlStream.nextTag();
if (versionConstraint.equals(new Version(1, 1, 0))) {
constraint = Filter110XMLDecoder.parse(xmlStream);
} else if (versionConstraint.equals(new Version(1, 0, 0))) {
constraint = Filter100XMLDecoder.parse(xmlStream);
} else {
String msg =
Messages.get(
"CSW_FILTER_VERSION_NOT_SPECIFIED",
versionConstraint,
Version.getVersionsString(new Version(1, 1, 0)),
Version.getVersionsString(new Version(1, 0, 0)));
LOG.info(msg);
throw new InvalidParameterValueException(msg);
}
} catch (XMLStreamException e) {
String msg =
"FilterParsingException: There went something wrong while parsing the filter expression, so please check this!";
LOG.debug(msg);
throw new XMLParsingException(adapter, filterEl, e.getMessage());
}
pc = new Pair<Filter, CSWConstants.ConstraintLanguage>(constraint, constraintLanguage);
} else if ((filterEl == null) && (cqlTextEl != null)) {
String msg = Messages.get("CSW_UNSUPPORTED_CQL_FILTER");
LOG.info(msg);
throw new NotImplementedError(msg);
} else {
String msg = Messages.get("CSW_MISSING_FILTER_OR_CQL");
LOG.debug(msg);
throw new InvalidParameterValueException(msg);
}
}
return pc;
}
/**
* @param datasource
* @param adapter
* @return a corresponding raster, null if files could not be fund
*/
public static AbstractRaster fromDatasource(RasterDataSource datasource, XMLAdapter adapter) {
if (datasource != null) {
String defCRS = datasource.getCrs();
CRS crs = null;
if (defCRS != null) {
crs = new CRS(defCRS);
}
RasterFileSetType directory = datasource.getRasterDirectory();
RasterFileType file = datasource.getRasterFile();
try {
if (directory != null) {
File rasterFiles = new File(adapter.resolve(directory.getValue()).getFile());
boolean recursive = directory.isRecursive() == null ? false : directory.isRecursive();
RasterIOOptions options = new RasterIOOptions();
if (crs != null) {
options.add(RasterIOOptions.CRS, crs.getName());
}
return buildTiledRaster(rasterFiles, directory.getFilePattern(), recursive, options);
}
if (file != null) {
final File loc = new File(adapter.resolve(file.getValue()).getFile());
AbstractRaster raster = loadRasterFromFile(loc);
raster.setCoordinateSystem(crs);
return raster;
}
} catch (MalformedURLException e) {
if (directory != null) {
LOG.warn(
"Could not resolve the file {}, corresponding data will not be available.",
directory.getValue());
} else {
LOG.warn(
"Could not resolve the file {}, corresponding data will not be available.",
file.getValue());
}
} catch (IOException e) {
LOG.warn(
"Could not load the file {}, corresponding data will not be available.",
file.getValue());
}
}
throw new NullPointerException("The configured raster datasource may not be null.");
}
@Override
public GeoCouchFeatureStore create(URL configURL) throws ResourceInitException {
GeoCouchFeatureStore fs = null;
try {
GeoCouchFeatureStoreConfig config =
(GeoCouchFeatureStoreConfig)
JAXBUtils.unmarshall(CONFIG_JAXB_PACKAGE, CONFIG_SCHEMA, configURL, workspace);
XMLAdapter resolver = new XMLAdapter();
resolver.setSystemId(configURL.toString());
String srs = config.getStorageCRS();
srs = srs.trim();
ICRS crs = CRSManager.getCRSRef(srs);
String couchUrl = config.getGeoCouchUrl();
if (!couchUrl.endsWith("/")) {
couchUrl += "/";
}
List<String> configSchemas = config.getGMLSchema();
String[] schemas = new String[configSchemas.size()];
int i = -1;
for (String s : configSchemas) {
schemas[++i] = resolver.resolve(s).toString();
}
GMLAppSchemaReader decoder = new GMLAppSchemaReader(null, null, schemas);
AppSchema schema = decoder.extractAppSchema();
fs = new GeoCouchFeatureStore(crs, schema, couchUrl);
} catch (Throwable e) {
String msg =
"Error in feature store configuration file '" + configURL + "': " + e.getMessage();
LOG.error(msg);
throw new ResourceInitException(msg, e);
}
return fs;
}
/**
* @param datasource
* @param adapter
* @return a corresponding raster
*/
public static MultiResolutionRaster fromDatasource(
MultiResolutionDataSource datasource, XMLAdapter adapter) {
if (datasource != null) {
String defCRS = datasource.getCrs();
CRS crs = null;
if (defCRS != null) {
crs = new CRS(defCRS);
}
MultiResolutionRaster mrr = new MultiResolutionRaster();
mrr.setCoordinateSystem(crs);
for (Resolution resolution : datasource.getResolution()) {
JAXBElement<? extends AbstractGeospatialDataSourceType> dsElement =
resolution.getAbstractGeospatialDataSource();
RasterDataSource ds = (RasterDataSource) dsElement.getValue();
RasterFileSetType directory = ds.getRasterDirectory();
File resolutionDir;
try {
resolutionDir = new File(adapter.resolve(directory.getValue()).getFile());
RasterIOOptions options = new RasterIOOptions();
if (crs != null) {
options.add(RasterIOOptions.CRS, crs.getName());
}
AbstractRaster rasterLevel =
buildTiledRaster(
resolutionDir, directory.getFilePattern(), directory.isRecursive(), options);
// double res = RasterBuilder.getPixelResolution( resolution.getRes(), resolutionDir );
mrr.addRaster(rasterLevel);
} catch (MalformedURLException e) {
LOG.warn(
"Could not resolve the file {}, corresponding data will not be available.",
directory.getValue());
}
}
return mrr;
}
throw new NullPointerException("The configured multi resolution datasource may not be null.");
}
@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);
}
public static Query getQuery(OMElement omElement) {
if (new QName(CSWConstants.CSW_202_NS, "Query").equals(omElement.getQName())) {
XMLAdapter adapter = new XMLAdapter(omElement);
SortProperty[] sortProps = null;
Filter constraint = null;
ReturnableElement elementSetName = null;
String[] elementName = null;
ConstraintLanguage constraintLanguage = null;
List<OMElement> queryChildElements =
adapter.getRequiredElements(omElement, new XPath("*", nsContext));
String typeQuery =
adapter.getNodeAsString(omElement, new XPath("./@typeNames", nsContext), "");
if ("".equals(typeQuery)) {
String msg =
"ERROR in XML document: Required attribute \"typeNames\" in element \"Query\" is missing!";
throw new MissingParameterException(msg);
}
String[] queryTypeNamesString = StringUtils.split(typeQuery, " ");
QName[] queryTypeNames = new QName[queryTypeNamesString.length];
int counterQName = 0;
for (String s : queryTypeNamesString) {
LOG.debug("Parsing typeName '" + s + "' of Query as QName. ");
QName qname = adapter.parseQName(s, adapter.getRootElement());
queryTypeNames[counterQName++] = qname;
}
elementName = adapter.getNodesAsStrings(omElement, new XPath("./csw:ElementName", nsContext));
QName[] returnTypeNames = null;
for (OMElement omQueryElement : queryChildElements) {
// TODO mandatory exclusiveness between ElementSetName vs. ElementName not implemented yet
if (new QName(CSWConstants.CSW_202_NS, "ElementSetName")
.equals(omQueryElement.getQName())) {
String elementSetNameString = omQueryElement.getText();
elementSetName = ReturnableElement.determineReturnableElement(elementSetNameString);
// elementSetNameTypeNames = getNodesAsQNames( omQueryElement, new XPath( "@typeNames",
// nsContext ) );
String typeElementSetName =
adapter
.getNodeAsString(omQueryElement, new XPath("./@typeNames", nsContext), "")
.trim();
String[] elementSetNameTypeNamesString = StringUtils.split(typeElementSetName, " ");
returnTypeNames = new QName[elementSetNameTypeNamesString.length];
for (int i = 0; i < elementSetNameTypeNamesString.length; i++) {
returnTypeNames[i] = adapter.parseQName(elementSetNameTypeNamesString[i], omElement);
}
}
Pair<Filter, ConstraintLanguage> parsedConstraint =
parseConstraint(adapter, omQueryElement);
if (parsedConstraint != null) {
constraintLanguage = parsedConstraint.second;
constraint = parsedConstraint.first;
}
if (new QName(OGCNS, "SortBy").equals(omQueryElement.getQName())) {
List<OMElement> sortPropertyElements =
adapter.getRequiredElements(omQueryElement, new XPath("ogc:SortProperty", nsContext));
sortProps = new SortProperty[sortPropertyElements.size()];
int counter = 0;
for (OMElement sortPropertyEl : sortPropertyElements) {
OMElement propNameEl =
adapter.getRequiredElement(
sortPropertyEl, new XPath("ogc:PropertyName", nsContext));
String sortOrder =
adapter.getNodeAsString(
sortPropertyEl, new XPath("ogc:SortOrder", nsContext), "ASC");
SortProperty sortProp =
new SortProperty(
new ValueReference(
propNameEl.getText(), adapter.getNamespaceContext(propNameEl)),
sortOrder.equals("ASC"));
sortProps[counter++] = sortProp;
}
}
}
return new Query(
elementSetName,
elementName,
constraint,
constraintLanguage,
sortProps,
queryTypeNames,
returnTypeNames);
}
return null;
}
@SuppressWarnings("boxing")
private static GetFeature parse110(Map<String, String> kvpParams) throws Exception {
StandardPresentationParams presentationParams =
parseStandardPresentationParameters110(kvpParams);
ResolveParams resolveParams = parseStandardResolveParameters110(kvpParams);
// optional: 'NAMESPACE'
Map<String, String> nsBindings = extractNamespaceBindings110(kvpParams);
if (nsBindings == null) {
nsBindings = Collections.emptyMap();
}
NamespaceBindings nsContext = new NamespaceBindings();
if (nsBindings != null) {
for (String key : nsBindings.keySet()) {
nsContext.addNamespace(key, nsBindings.get(key));
}
}
// optional: SRSNAME
String srsName = kvpParams.get("SRSNAME");
ICRS srs = null;
if (srsName != null) {
srs = CRSManager.getCRSRef(srsName);
}
// optional: 'PROPERTYNAME'
String propertyStr = kvpParams.get("PROPERTYNAME");
PropertyName[][] propertyNames = getPropertyNames(propertyStr, nsContext);
// optional: SORTBY
String sortbyStr = kvpParams.get("SORTBY");
SortProperty[] sortBy = getSortBy(sortbyStr, nsContext);
// optional: FEATUREVERSION
String featureVersion = kvpParams.get("FEATUREVERSION");
// mandatory: TYPENAME, but optional if FEATUREID is specified
String typeStrList = kvpParams.get("TYPENAME");
TypeName[] typeNames = getTypeNames(typeStrList, nsBindings);
// optional: FEATUREID
String featureIdStr = kvpParams.get("FEATUREID");
String[] featureIds = null;
if (featureIdStr != null) {
featureIds = featureIdStr.split(",");
}
// optional: BBOX
String bboxStr = kvpParams.get("BBOX");
// optional: FILTER
String filterStr = kvpParams.get("FILTER");
// optional: 'PROPTRAVXLINKDEPTH'
String propTravXlinkDepth = kvpParams.get("PROPTRAVXLINKDEPTH");
String[][] ptxDepthAr = null;
if (propTravXlinkDepth != null) {
ptxDepthAr = parseParamList(propTravXlinkDepth);
}
// optional: 'PROPTRAVXLINKEXPIRY'
String propTravXlinkExpiry = kvpParams.get("PROPTRAVXLINKEXPIRY");
Integer[][] ptxExpAr = null;
if (propTravXlinkExpiry != null) {
ptxExpAr = parseParamListAsInts(propTravXlinkDepth);
}
propertyNames = getXLinkPropNames(propertyNames, ptxDepthAr, ptxExpAr);
List<Query> queries = new ArrayList<Query>();
if ((featureIdStr != null && bboxStr != null)
|| (featureIdStr != null && filterStr != null)
|| (bboxStr != null && filterStr != null)) {
// TODO make new exception
throw new Exception("The FEATUREID, BBOX and FILTER keywords are mutually exclusive!");
}
if (featureIdStr != null) {
if (typeStrList == null && propertyNames == null) {
queries.add(new FeatureIdQuery(null, null, featureVersion, srs, null, sortBy, featureIds));
} else {
for (int i = 0; i < featureIds.length; i++) {
String[] fid = new String[] {featureIds[i]};
TypeName[] typeName = new TypeName[0];
if (typeStrList != null) {
typeName = new TypeName[] {typeNames[i]};
}
PropertyName[] projectionClauses = null;
if (propertyNames != null) {
projectionClauses = propertyNames[i];
}
queries.add(
new FeatureIdQuery(
null, typeName, featureVersion, srs, projectionClauses, sortBy, fid));
}
}
} else if (bboxStr != null) {
if (typeNames == null) {
// TODO make new exception
throw new Exception("The TYPENAME keyword is mandatory if BBOX is present!");
}
String[] coordList = bboxStr.split(",");
// NOTE: Contradiction between spec and CITE tests (for omitted crsUri)
// - WFS 1.1.0 spec, 14.3.3: coordinates should be in WGS84
// - CITE tests, wfs:wfs-1.1.0-Basic-GetFeature-tc8.1: If no CRS reference is provided, a
// service-defined
// default value must be assumed.
ICRS bboxCrs = null;
if (coordList.length % 2 == 1) {
bboxCrs = CRSManager.getCRSRef(coordList[coordList.length - 1]);
}
Envelope bbox = createEnvelope(bboxStr, bboxCrs);
for (int i = 0; i < typeNames.length; i++) {
TypeName typeName = typeNames[i];
PropertyName[] projectionClauses = null;
if (propertyNames != null) {
projectionClauses = propertyNames[i];
}
queries.add(
new BBoxQuery(
null,
new TypeName[] {typeName},
featureVersion,
srs,
projectionClauses,
sortBy,
bbox));
}
} else if (filterStr != null || typeNames != null) {
if (typeNames == null) {
// TODO make new exception
throw new Exception("The FILTER element requires the TYPENAME element");
}
int length = typeNames.length;
String[] filters = getFilters(filterStr);
for (int i = 0; i < length; i++) {
Filter filter = null;
if (filters != null) {
StringReader sr = new StringReader(filters[i]);
XMLAdapter adapter = new XMLAdapter(sr);
XMLStreamReaderWrapper streamWrapper =
new XMLStreamReaderWrapper(
adapter.getRootElement().getXMLStreamReaderWithoutCaching(),
adapter.getSystemId());
try {
streamWrapper.nextTag();
filter = Filter110XMLDecoder.parse(streamWrapper);
} catch (XMLParsingException e) {
e.printStackTrace();
// TODO raise exception
} catch (XMLStreamException e) {
e.printStackTrace();
// TODO raise exception
}
}
if (propertyNames != null) {
queries.add(
new FilterQuery(
null,
new TypeName[] {typeNames[i]},
featureVersion,
srs,
propertyNames[i],
sortBy,
filter));
} else {
queries.add(
new FilterQuery(
null, new TypeName[] {typeNames[i]}, featureVersion, srs, null, sortBy, filter));
}
}
}
return new GetFeature(VERSION_110, null, presentationParams, resolveParams, queries);
}
@SuppressWarnings("boxing")
private static GetFeature parse100(Map<String, String> kvpParams, Map<String, String> nsMap)
throws Exception {
NamespaceBindings nsContext = new NamespaceBindings();
if (nsMap != null) {
for (String key : nsMap.keySet()) {
nsContext.addNamespace(key, nsMap.get(key));
}
}
StandardPresentationParams presentationParams =
parseStandardPresentationParameters100(kvpParams);
// optional: 'PROPERTYNAME'
String propertyStr = kvpParams.get("PROPERTYNAME");
PropertyName[][] propertyNames = getPropertyNames(propertyStr, nsContext);
// optional: FEATUREVERSION
String featureVersion = kvpParams.get("FEATUREVERSION");
// mandatory: TYPENAME, but optional if FEATUREID is specified
String typeStrList = kvpParams.get("TYPENAME");
TypeName[] typeNames = getTypeNames100(typeStrList);
// optional: FEATUREID
String featureIdStr = kvpParams.get("FEATUREID");
String[] featureIds = null;
if (featureIdStr != null) {
featureIds = featureIdStr.split(",");
}
// optional: BBOX
String bboxStr = kvpParams.get("BBOX");
// optional: FILTER
String filterStr = kvpParams.get("FILTER");
// optional: SRSNAME (not specified in WFS 1.0.0, deegree extension)
String srsName = kvpParams.get("SRSNAME");
ICRS srs = null;
if (srsName != null) {
srs = CRSManager.getCRSRef(srsName);
}
List<Query> queries = new ArrayList<Query>();
if ((featureIdStr != null && bboxStr != null)
|| (featureIdStr != null && filterStr != null)
|| (bboxStr != null && filterStr != null)) {
// TODO make new exception
throw new Exception("The FEATUREID, BBOX and FILTER keywords are mutually exclusive!");
}
if (featureIdStr != null) {
if (typeStrList == null && propertyNames == null) {
queries.add(new FeatureIdQuery(null, null, featureVersion, srs, null, null, featureIds));
} else {
for (int i = 0; i < featureIds.length; i++) {
String[] fids = new String[] {featureIds[i]};
TypeName[] typeName = new TypeName[0];
if (typeStrList != null) {
typeName = new TypeName[] {typeNames[i]};
}
PropertyName[] projectionClauses = null;
if (propertyNames != null) {
if (propertyNames.length > 1) {
projectionClauses = propertyNames[i];
} else {
projectionClauses = propertyNames[0];
}
}
queries.add(
new FeatureIdQuery(
null, typeName, featureVersion, srs, projectionClauses, null, fids));
}
}
} else if (bboxStr != null) {
if (typeNames == null) {
// TODO make new exception
throw new Exception("The TYPENAME keyword is mandatory if BBOX is present!");
}
String[] coordList = bboxStr.split(",");
ICRS bboxCrs = null;
if (coordList.length % 2 == 1) {
bboxCrs = CRSManager.getCRSRef(coordList[coordList.length - 1]);
}
Envelope bbox = createEnvelope(bboxStr, bboxCrs);
for (int i = 0; i < typeNames.length; i++) {
TypeName typeName = typeNames[i];
PropertyName[] projectionClauses = null;
if (propertyNames != null) {
projectionClauses = propertyNames[i];
}
queries.add(
new BBoxQuery(
null,
new TypeName[] {typeName},
featureVersion,
srs,
projectionClauses,
null,
bbox));
}
} else if (filterStr != null || typeNames != null) {
if (typeNames == null) {
// TODO make new exception
throw new Exception("The FILTER element requires the TYPENAME element");
}
int length = typeNames.length;
String[] filters = getFilters(filterStr);
for (int i = 0; i < length; i++) {
Filter filter = null;
if (filters != null) {
StringReader sr = new StringReader(filters[i]);
XMLAdapter adapter = new XMLAdapter(sr);
XMLStreamReaderWrapper streamWrapper =
new XMLStreamReaderWrapper(
adapter.getRootElement().getXMLStreamReaderWithoutCaching(),
adapter.getSystemId());
try {
streamWrapper.nextTag();
filter = Filter100XMLDecoder.parse(streamWrapper);
} catch (XMLParsingException e) {
e.printStackTrace();
// TODO raise exception
} catch (XMLStreamException e) {
e.printStackTrace();
// TODO raise exception
}
}
if (propertyNames != null) {
queries.add(
new FilterQuery(
null,
new TypeName[] {typeNames[i]},
featureVersion,
srs,
propertyNames[i],
null,
filter));
} else {
queries.add(
new FilterQuery(
null, new TypeName[] {typeNames[i]}, featureVersion, srs, null, null, filter));
}
}
}
return new GetFeature(VERSION_100, null, presentationParams, null, queries);
}
@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);
}
}