@Override
public void setDefaultGeometry(Object newGeometry) {
Property p = getDefaultGeometryProperty();
if (p != null) {
p.setValue(newGeometry);
}
}
@Override
public void setAttribute(int index, Object newValue) throws IndexOutOfBoundsException {
Property p = getProperties().get(index);
if (p != null) {
p.setValue(newValue);
}
}
@Override
public void setAttribute(Name eName, Object newValue) {
Property p = getProperty(eName);
if (p != null) {
p.setValue(newValue);
}
}
/**
* Helper method for subclasses to reduce null checks
*
* @param expression
* @param object
* @return value or null
*/
protected Object eval(org.opengis.filter.expression.Expression expression, Object object) {
if (expression == null) return null;
Object value = expression.evaluate(object);
// NC - HACK (similar to below), but for complex features
if (value instanceof org.opengis.feature.ComplexAttribute) {
Property simpleContent =
((org.opengis.feature.ComplexAttribute) value).getProperty(new NameImpl("simpleContent"));
if (simpleContent == null) {
value = null;
} else {
value = simpleContent.getValue();
}
}
// HACK as this method is used internally for filter
// evaluation comparisons, etc, they work over the
// contents (i.e. comparing an attexpresion with a literal)
// so, lacking a better way of doing so, I'm putting this
// check here
if (value instanceof org.opengis.feature.Attribute) {
value = ((org.opengis.feature.Attribute) value).getValue();
}
return value;
}
@Override
public void setValue(Collection<Property> values) {
for (Property it : values) {
EAttribute eAttr = eStructure().eGetAttribute(it.getName().getURI());
eFeature().eSet(eAttr, it.getValue());
}
}
/**
* Return the simple content of a {@link ComplexAttribute} if it represents a complexType with
* simpleContent, otherwise null.
*
* @param complex
* @return
*/
public static Object getSimpleContent(ComplexAttribute complex) {
Property simpleContent = complex.getProperty(new NameImpl("simpleContent"));
if (simpleContent == null) {
return null;
} else {
return simpleContent.getValue();
}
}
/** @param args */
public static void main(String[] args) {
// TODO Auto-generated method stub
String networkPath = args[0];
String newNetworkPath = args[1];
String shapeFilePath = args[2];
// String shapeFile = "C:/Work/Roadpricing Scenarios/SiouxFalls/Network/SiouxFalls_nodes.shp";
Scenario scenario = ScenarioUtils.createScenario(ConfigUtils.createConfig());
new NetworkReaderMatsimV1(scenario).parse(networkPath);
Network network = scenario.getNetwork();
Map<Id<Node>, ? extends Node> nodes = network.getNodes();
Double x = 0.0;
Double y = 0.0;
System.out.println(shapeFilePath);
ShapeFileReader shapeFileReader = new ShapeFileReader();
Collection<SimpleFeature> fts = shapeFileReader.readFileAndInitialize(shapeFilePath);
log.info("Shape file contains " + fts.size() + " features!");
for (SimpleFeature ft : fts) {
Geometry geo = (Geometry) ft.getDefaultGeometry();
Coordinate[] coordinates = geo.getCoordinates();
Collection<Property> properties = ft.getProperties("Id");
System.out.println(
"Feature: "
+ ft.getID()
+ ","
+ ft.getIdentifier().toString()
+ ","
+ ft.getName().toString());
for (int i = 0; i < coordinates.length; i++) {
System.out.print(coordinates[i].x + "," + coordinates[i].y + " ");
x = coordinates[i].x;
y = coordinates[i].y;
}
for (Property p : properties) {
System.out.println("Value: " + p.getValue().toString());
Node node = nodes.get(Id.create(p.getValue().toString(), Node.class));
node.getCoord().setXY(x, y);
System.out.println("Name: " + p.getName().toString());
System.out.println("Descriptor: " + p.getDescriptor().toString());
}
System.out.println();
System.out.println();
NetworkWriter writer = new NetworkWriter(network);
writer.write(newNetworkPath);
}
}
@Override
public Collection<Property> getProperties(Name eName) {
Set<Property> eItems = new HashSet<Property>();
for (Property it : getProperties()) {
if (it.getName().equals(eName)) {
eItems.add(it);
}
}
return eItems;
}
@Test
public void testImageReaderPolyphemusSimple() throws Exception {
final File file = TestData.file(this, "O3-NO2.nc");
final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
assertTrue(unidataImageReaderSpi.canDecodeInput(file));
NetCDFImageReader reader = null;
try {
// checking low level
reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
reader.setInput(file);
int numImages = reader.getNumImages(true);
LOGGER.info("Found " + numImages + " images.");
for (int i = 0; i < numImages; i++) {
Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
assertNotNull(sliceIndex);
spitOutSliceInformation(i, sliceIndex);
}
// checking slice catalog
final CoverageSlicesCatalog cs = reader.getCatalog();
assertNotNull(cs);
// get typenames
final String[] typeNames = cs.getTypeNames();
for (String typeName : typeNames) {
final List<CoverageSlice> granules = cs.getGranules(new Query(typeName, Filter.INCLUDE));
assertNotNull(granules);
assertFalse(granules.isEmpty());
for (CoverageSlice slice : granules) {
final SimpleFeature sf = slice.getOriginator();
if (TestData.isInteractiveTest()) {
LOGGER.info(DataUtilities.encodeFeature(sf));
}
// checks
for (Property p : sf.getProperties()) {
assertNotNull("Property " + p.getName() + " had a null value!", p.getValue());
}
}
}
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
}
protected void cleanEmptyElements(Feature target) throws DataSourceException {
try {
ArrayList values = new ArrayList<Property>();
for (Iterator i = target.getValue().iterator(); i.hasNext(); ) {
Property p = (Property) i.next();
if (hasChild(p) || p.getDescriptor().getMinOccurs() > 0 || getEncodeIfEmpty(p)) {
values.add(p);
}
}
target.setValue(values);
} catch (DataSourceException e) {
throw new DataSourceException("Unable to clean empty element", e);
}
}
public BugInfo(SimpleFeature next, long idx) throws IndexOutOfBoundsException, ParseException {
bugId = idx;
attributes = new HashMap<>();
Collection<Property> properties = next.getProperties();
Iterator<Property> it = properties.iterator();
while (it.hasNext()) {
Property p = it.next();
attributes.put(p.getName().toString(), p.getValue().toString());
}
this.geom = (Geometry) next.getAttribute(0);
this.desc = (String) next.getAttribute("error_desc");
this.id = next.getID();
name = next.getName();
}
private boolean getEncodeIfEmpty(Property p) {
Object o = ((p.getDescriptor()).getUserData().get("encodeIfEmpty"));
if (o == null) {
return false;
}
return (Boolean) o;
}
/**
* Parses SimpleFeature typed object recursively to Map - field names (keys) are combined with
* parent sub property names, if properties in property
*
* @param feature
* @return feature all properties as a HashMap
*/
private static void parseFeatureProperties(Map result, SimpleFeature feature) {
for (Property prop : feature.getProperties()) {
String field = prop.getName().toString();
Object value = feature.getAttribute(field);
if (value != null) { // hide null properties
if (value instanceof Map) {
parseFeaturePropertiesMap(result, (Map) value, field);
} else if (value instanceof List) {
parseFeaturePropertiesMapList(result, (List) value, field);
} else {
result.put(field, value.toString());
}
}
}
}
@Override
public String[] encode(SimpleFeature feature) {
List<String> csvRecord = new ArrayList<String>();
for (Property property : feature.getProperties()) {
Object value = property.getValue();
if (value == null) {
csvRecord.add("");
} else if (value instanceof Point) {
Point point = (Point) value;
csvRecord.add(Double.toString(point.getY()));
csvRecord.add(Double.toString(point.getX()));
} else {
String txt = value.toString();
csvRecord.add(txt);
}
}
return csvRecord.toArray(new String[csvRecord.size() - 1]);
}
/**
* Set xlink:href client property for multi-valued chained features. This has to be specially
* handled because we don't want to encode the nested features attributes, since it's already an
* xLink. Also we need to eliminate duplicates.
*
* @param target The target attribute
* @param clientPropsMappings Client properties mappings
* @param value Nested features
* @param xpath Attribute xPath where the client properties are to be set
* @param targetNodeType Target node type
*/
protected void setXlinkReference(
Attribute target,
Map<Name, Expression> clientPropsMappings,
Object value,
StepList xpath,
AttributeType targetNodeType) {
Expression linkExpression = clientPropsMappings.get(XLINK_HREF_NAME);
for (Object singleVal : (Collection) value) {
// Make sure the same value isn't already set
// in case it comes from a denormalized view for many-to-many relationship.
// (1) Get the first existing value
Collection<Property> existingAttributes = getProperties((ComplexAttribute) target, xpath);
boolean exists = false;
if (existingAttributes != null) {
for (Property existingAttribute : existingAttributes) {
Object existingValue = existingAttribute.getUserData().get(Attributes.class);
if (existingValue != null) {
assert existingValue instanceof HashMap;
existingValue = ((Map) existingValue).get(XLINK_HREF_NAME);
}
if (existingValue != null) {
Object hrefValue = linkExpression.evaluate(singleVal);
if (hrefValue != null && hrefValue.equals(existingValue)) {
// (2) if one of the new values matches the first existing value,
// that means this comes from a denormalized view,
// and this set has already been set
exists = true;
// stop looking once found
break;
}
}
}
}
if (!exists) {
Attribute instance =
xpathAttributeBuilder.set(target, xpath, null, null, targetNodeType, true, null);
setClientProperties(instance, singleVal, clientPropsMappings);
}
}
}
/**
* Constructs a new {@link RevFeature} from the provided {@link Feature}.
*
* @param feature the feature to build from
* @return the newly constructed RevFeature
*/
public RevFeature build(Feature feature) {
if (feature == null) {
throw new IllegalStateException("No feature set");
}
Collection<Property> props = feature.getProperties();
List<Property> list = new ArrayList<Property>(props);
Collections.sort(list, PROPERTY_ORDER);
ImmutableList.Builder<Optional<Object>> valuesBuilder =
new ImmutableList.Builder<Optional<Object>>();
for (Property prop : list) {
valuesBuilder.add(Optional.fromNullable(prop.getValue()));
}
return RevFeature.build(valuesBuilder.build());
}
protected Map getClientProperties(Property attribute) throws DataSourceException {
Map<Object, Object> userData = attribute.getUserData();
Map clientProperties = new HashMap<Name, Expression>();
if (userData != null && userData.containsKey(Attributes.class)) {
Map props = (Map) userData.get(Attributes.class);
if (!props.isEmpty()) {
clientProperties.putAll(props);
}
}
return clientProperties;
}
@Override
public List<Object> getAttributes() {
//
// Get properties
//
List<Property> eList = getProperties();
//
// Initialize value list
//
List<Object> values = EFeatureUtils.newList(eList.size());
//
// Loop over all property instances
//
for (Property it : eList) {
values.add(it.getValue());
}
//
// Finished
//
return values;
}
public static void featureToJson(
org.opengis.feature.Feature feature, JSONBuilder json, boolean returnGeometry) {
GeometryAttribute geometry = feature.getDefaultGeometryProperty();
json.object();
if (returnGeometry) {
json.key("geometry");
GeometryEncoder.toJson((com.vividsolutions.jts.geom.Geometry) geometry.getValue(), json);
}
json.key("attributes");
json.object();
json.key("objectid").value(adaptId(feature.getIdentifier().getID()));
for (Property prop : feature.getProperties()) {
if (geometry == null || !prop.getName().equals(geometry.getName())) {
final Object value;
if (prop.getValue() instanceof java.util.Date) {
value = ((java.util.Date) prop.getValue()).getTime();
} else {
value = prop.getValue();
}
json.key(prop.getName().getLocalPart()).value(value);
}
}
json.endObject();
json.endObject();
}
public ShapeWrappers extractFeatureProperties(Feature f) {
HashMap<String, String> propMap = new HashMap<String, String>();
String shapeText = f.getDefaultGeometryProperty().getValue().toString();
Collection<Property> props = f.getProperties();
Iterator<Property> pi = props.iterator();
while (pi.hasNext()) {
Property p = pi.next();
String name = p.getName().toString();
// System.out.println(name);
if (pattern != null) {
if (propNames.contains(name) || pattern.matcher(name).find()) {
propMap.put(p.getName().toString(), p.getValue().toString());
}
} else {
if (propNames.contains(name)) {
try {
propMap.put(p.getName().toString(), p.getValue().toString());
} catch (Exception e) {
log.log(Level.WARNING, "{0} prop name {1}", new Object[] {e.getMessage(), name});
}
}
}
}
return new ShapeWrappers(shapeText, propMap);
}
/**
* Encode any client properties (XML attributes) found in the UserData map of a ComplexAttribute
* as XML attributes of the element.
*
* @param complex the ComplexAttribute to search for client properties
* @param element the element to which XML attributes should be added
*/
@SuppressWarnings("unchecked")
public static void encodeClientProperties(Property complex, Element element) {
Map<Name, Object> clientProperties =
(Map<Name, Object>) complex.getUserData().get(Attributes.class);
if (clientProperties != null) {
for (Name name : clientProperties.keySet()) {
if (clientProperties.get(name) != null) {
element.setAttributeNS(
name.getNamespaceURI(), name.getLocalPart(), clientProperties.get(name).toString());
}
}
}
}
private boolean hasChild(Property p) throws DataSourceException {
boolean result = false;
if (p.getValue() instanceof Collection) {
Collection c = (Collection) p.getValue();
if (this.getClientProperties(p).containsKey(XLINK_HREF_NAME)) {
return true;
}
ArrayList values = new ArrayList();
for (Object o : c) {
if (o instanceof Property) {
if (hasChild((Property) o)) {
values.add(o);
result = true;
} else if (getEncodeIfEmpty((Property) o)) {
values.add(o);
result = true;
} else if (((Property) o).getDescriptor().getMinOccurs() > 0) {
if (((Property) o).getDescriptor().isNillable()) {
// add nil mandatory property
values.add(o);
}
}
}
}
p.setValue(values);
} else if (p.getName().equals(ComplexFeatureConstants.FEATURE_CHAINING_LINK_NAME)) {
// ignore fake attribute FEATURE_LINK
result = false;
} else if (p.getValue() != null && p.getValue().toString().length() > 0) {
result = true;
}
return result;
}
@Override
/**
* @param inputData a HashMap of the input data: inputObservations: the observations
* inputAuthoritativeData: the authoritative points inputDistance: the distance threshold
* minNumber: the minimum number of named features to pass fieldName: the name of the field
* within the observations to match
* @result results a HashpMap of the results: result: the input data with the polygon attributes
* attached, null values for no match qual_result: the matched input only data with polygon
* attributes attached
*/
public Map<String, IData> run(Map<String, List<IData>> inputData) throws ExceptionReport {
List obsList = inputData.get("inputObservations");
List authList = inputData.get("inputAuthoritativeData");
List distList = inputData.get("inputDistance");
List minList = inputData.get("minNumber");
List fieldList = inputData.get("fieldName");
FeatureCollection obsFc = ((GTVectorDataBinding) obsList.get(0)).getPayload();
FeatureCollection authFc = ((GTVectorDataBinding) authList.get(0)).getPayload();
double dist = ((LiteralDoubleBinding) distList.get(0)).getPayload();
int minNum = ((LiteralIntBinding) minList.get(0)).getPayload();
String fieldName = ((LiteralStringBinding) fieldList.get(0)).getPayload();
ArrayList<SimpleFeature> resultFeatures = new ArrayList<SimpleFeature>();
ArrayList<SimpleFeature> returnFeatures = new ArrayList<SimpleFeature>();
SimpleFeatureIterator obsIt = (SimpleFeatureIterator) obsFc.features();
SimpleFeatureIterator authIt = (SimpleFeatureIterator) authFc.features();
SimpleFeatureIterator sfi = (SimpleFeatureIterator) obsFc.features();
SimpleFeatureType fType = null;
SimpleFeature tempPropFeature = sfi.next();
CoordinateReferenceSystem inputObsCrs = obsFc.getSchema().getCoordinateReferenceSystem();
Collection<Property> obsProp = tempPropFeature.getProperties();
SimpleFeatureTypeBuilder resultTypeBuilder = new SimpleFeatureTypeBuilder();
resultTypeBuilder.setName("typeBuilder");
resultTypeBuilder.setCRS(inputObsCrs);
Iterator<Property> pItObs = obsProp.iterator();
sfi.close();
while (pItObs.hasNext() == true) {
try {
Property tempProp = pItObs.next();
PropertyType type = tempProp.getDescriptor().getType();
String name = type.getName().getLocalPart();
Class<String> valueClass = (Class<String>) tempProp.getType().getBinding();
resultTypeBuilder.add(name, valueClass);
// LOG.warn ("Obs property " + name + " " + valueClass + " " +type.toString());
} catch (Exception e) {
LOG.error("property error " + e);
}
}
// add DQ_Field
resultTypeBuilder.add("DQ_SA_SimilarF", Double.class);
SimpleFeatureType typeF = resultTypeBuilder.buildFeatureType();
// LOG.warn("Get Spatial Accuracy Feature Type " + typeF.toString());
SimpleFeatureBuilder resultFeatureBuilder = new SimpleFeatureBuilder(typeF);
obsIt.close();
SimpleFeatureIterator obsIt2 = (SimpleFeatureIterator) obsFc.features();
while (obsIt2.hasNext()) {
SimpleFeature tempFeature = obsIt2.next();
fType = tempFeature.getType();
// LOG.warn("fieldName " + fieldName + " featureName " + featureN + " tempFeature Type " +
// fType);
// LOG.warn("TableFeatureName " + tempFeature.getProperty(fieldName).getValue());
String tempFeatureName = (String) tempFeature.getProperty(fieldName).getValue();
Geometry geom = (Geometry) tempFeature.getDefaultGeometry();
for (Property obsProperty : tempFeature.getProperties()) {
String name = obsProperty.getName().toString();
Object value = obsProperty.getValue();
resultFeatureBuilder.set(name, value);
}
Geometry bufferGeom = geom.buffer(dist);
SimpleFeatureIterator authIt2 = (SimpleFeatureIterator) authFc.features();
int count = 0;
int within = 0;
while (authIt2.hasNext() && count <= minNum) {
SimpleFeature tempAuth = authIt2.next();
String featureN = (String) tempAuth.getProperty(fieldName).getValue();
Geometry tempGeom = (Geometry) tempAuth.getDefaultGeometry();
String authProperty = (String) tempAuth.getProperty(fieldName).getValue();
if (tempGeom.within(bufferGeom) && authProperty.equalsIgnoreCase(featureN)) {
count++;
if (count >= minNum) {
within = 1;
}
}
}
LOG.warn("HERE " + within);
resultFeatureBuilder.set("DQ_SA_SimilarF", within);
SimpleFeature result = resultFeatureBuilder.buildFeature(tempFeature.getID());
result.setDefaultGeometry(geom);
LOG.warn("HERE " + result);
returnFeatures.add(result);
if (within == 1) {
resultFeatures.add(result);
}
authIt2.close();
}
obsIt2.close();
ListFeatureCollection qualResult = new ListFeatureCollection(fType, resultFeatures);
ListFeatureCollection returns = new ListFeatureCollection(fType, returnFeatures);
LOG.warn("HERE 2 " + qualResult.size() + " " + returns.size());
Map<String, IData> results = new HashMap<String, IData>();
results.put("qual_result", new GTVectorDataBinding(qualResult));
results.put("result", new GTVectorDataBinding(returns));
return results;
}
@Override
/**
* inputData a HashMap of the input data:
*
* @param inputObservations: the observations
* @param inputAuthoritativeData: the polygons
* @param bufferSize: the size of the buffer around the polygons results a HashpMap of the
* results:
* @result result: the input data with the polygon attributes attached, null values for no match
* @result qual_result: the matched input only data with polygon attributes attached
*/
public Map<String, IData> run(Map<String, List<IData>> inputData) throws ExceptionReport {
HashMap<String, Object> metadataMap = new HashMap<String, Object>();
ArrayList<SimpleFeature> list = new ArrayList<SimpleFeature>();
List<IData> inputObs = inputData.get("inputObservations");
List<IData> inputAuth = inputData.get("inputAuthoritativeData");
List<IData> inputLit = inputData.get("bufferSize");
IData observations = inputObs.get(0);
IData authoritative = inputAuth.get(0);
IData buffersize = inputLit.get(0);
double doubleB = (Double) buffersize.getPayload();
FeatureCollection obsFC = ((GTVectorDataBinding) observations).getPayload();
FeatureCollection authFC = ((GTVectorDataBinding) authoritative).getPayload();
SimpleFeatureIterator obsIt = (SimpleFeatureIterator) obsFC.features();
SimpleFeatureIterator authIt = (SimpleFeatureIterator) authFC.features();
// setup result feature
SimpleFeature obsItFeat = obsIt.next();
SimpleFeature obsItAuth = authIt.next();
Collection<Property> property = obsItFeat.getProperties();
Collection<Property> authProperty = obsItAuth.getProperties();
// setup result type builder
SimpleFeatureTypeBuilder resultTypeBuilder = new SimpleFeatureTypeBuilder();
resultTypeBuilder.setName("typeBuilder");
Iterator<Property> pItObs = property.iterator();
Iterator<Property> pItAuth = authProperty.iterator();
metadataMap.put("element", "elementBufferedMetadata");
File metadataFile = createXMLMetadata(metadataMap);
while (pItObs.hasNext() == true) {
try {
Property tempProp = pItObs.next();
PropertyType type = tempProp.getDescriptor().getType();
String name = type.getName().getLocalPart();
Class<String> valueClass = (Class<String>) tempProp.getType().getBinding();
resultTypeBuilder.add(name, valueClass);
} catch (Exception e) {
LOGGER.error("property error " + e);
}
}
int i = 0;
while (pItAuth.hasNext() == true) {
try {
Property tempProp = pItAuth.next();
PropertyType type = tempProp.getDescriptor().getType();
String name = type.getName().getLocalPart();
Class<String> valueClass = (Class<String>) tempProp.getType().getBinding();
if (i > 3) {
resultTypeBuilder.add(name, valueClass);
}
i++;
} catch (Exception e) {
LOGGER.error("property error " + e);
}
}
obsIt.close();
authIt.close();
resultTypeBuilder.add("withinBuffer", Integer.class);
// set up result feature builder
SimpleFeatureType type = resultTypeBuilder.buildFeatureType();
SimpleFeatureBuilder resultFeatureBuilder = new SimpleFeatureBuilder(type);
// process data here:
SimpleFeatureIterator obsIt2 = (SimpleFeatureIterator) obsFC.features();
int within = 0;
FeatureCollection resultFeatureCollection = DefaultFeatureCollections.newCollection();
while (obsIt2.hasNext() == true) {
within = 0;
SimpleFeature tempObs = obsIt2.next();
Geometry obsGeom = (Geometry) tempObs.getDefaultGeometry();
for (Property obsProperty : tempObs.getProperties()) {
String name = obsProperty.getName().getLocalPart();
Object value = obsProperty.getValue();
resultFeatureBuilder.set(name, value);
// LOGGER.warn("obs Property set " + name);
}
double bufferSizeDouble = doubleB;
Geometry bufferGeom = obsGeom.buffer(bufferSizeDouble);
int j = 0;
SimpleFeatureIterator authIt2 = (SimpleFeatureIterator) authFC.features();
while (authIt2.hasNext() == true) {
SimpleFeature tempAuth = authIt2.next();
Geometry authGeom = (Geometry) tempAuth.getDefaultGeometry();
if (bufferGeom.intersects(authGeom) == true) {
within = 1;
j = 0;
LOGGER.warn("Intersection = true");
for (Property authProperty1 : tempAuth.getProperties()) {
String name = authProperty1.getName().getLocalPart();
Object value = authProperty1.getValue();
// Class valueClass = (Class<String>)authProperty1.getType().getBinding();
// LOGGER.warn("Auth property " + name);
if (j > 3) {
resultFeatureBuilder.set(name, value);
// LOGGER.warn("Auth property set " + name);
}
j++;
}
}
}
resultFeatureBuilder.set("withinBuffer", within);
SimpleFeature resultFeature = resultFeatureBuilder.buildFeature(tempObs.getName().toString());
Geometry geom = (Geometry) tempObs.getDefaultGeometry();
resultFeature.setDefaultGeometry(geom);
list.add(resultFeature);
// resultFeatureCollection.add(resultFeature);
// LOGGER.warn("RESULT FEATURE " + resultFeatureCollection.getSchema().toString());
// resultFeatureCollection = obsFC;
}
ListFeatureCollection listFeatureCollection = new ListFeatureCollection(type, list);
LOGGER.warn("Result Feature Size " + listFeatureCollection.size());
// sort HashMap
GenericFileData gf = null;
try {
gf = new GenericFileData(metadataFile, "text/xml");
} catch (IOException e) {
LOGGER.error("GenericFileData " + e);
}
HashMap<String, IData> results = new HashMap<String, IData>();
results.put("result", new GTVectorDataBinding((FeatureCollection) obsFC));
results.put("qual_result", new GTVectorDataBinding((FeatureCollection) listFeatureCollection));
results.put("metadata", new GenericFileDataBinding(gf));
return results;
}
@Test
public void testImageReaderPolyphemunsComplex() throws Exception {
File file = null;
try {
file = TestData.file(this, "polyphemus_20130301.nc");
} catch (IOException e) {
LOGGER.warning("Unable to find file polyphemus_20130301.nc");
return;
}
if (!file.exists()) {
LOGGER.warning("Unable to find file polyphemus_20130301.nc");
return;
}
final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
assertTrue(unidataImageReaderSpi.canDecodeInput(file));
NetCDFImageReader reader = null;
try {
reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
reader.setInput(file);
int numImages = reader.getNumImages(true);
assertEquals(1008, numImages);
for (int i = 0; i < numImages; i++) {
Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
assertNotNull(sliceIndex);
spitOutSliceInformation(i, sliceIndex);
}
// check coverage names
final List<Name> names = reader.getCoveragesNames();
assertNotNull(names);
assertTrue(!names.isEmpty());
assertTrue(3 == names.size());
assertTrue(names.contains(new NameImpl("NO2")));
assertTrue(names.contains(new NameImpl("O3")));
assertTrue(names.contains(new NameImpl("V")));
// checking slice catalog
final CoverageSlicesCatalog cs = reader.getCatalog();
assertNotNull(cs);
// get typenames
final String[] typeNames = cs.getTypeNames();
for (String typeName : typeNames) {
final List<CoverageSlice> granules = cs.getGranules(new Query(typeName, Filter.INCLUDE));
assertNotNull(granules);
assertFalse(granules.isEmpty());
for (CoverageSlice slice : granules) {
final SimpleFeature sf = slice.getOriginator();
if (TestData.isInteractiveTest()) {
LOGGER.info(DataUtilities.encodeFeature(sf));
}
// checks
for (Property p : sf.getProperties()) {
assertNotNull("Property " + p.getName() + " had a null value!", p.getValue());
}
}
}
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
}
@Test
public void testImageReaderPolyphemunsComplex2() throws Exception {
File file = null;
try {
file = TestData.file(this, "polyphemus_20130301.nc");
} catch (IOException e) {
LOGGER.warning("Unable to find file polyphemus_20130301.nc");
return;
}
if (!file.exists()) {
LOGGER.warning("Unable to find file polyphemus_20130301.nc");
return;
}
FileUtils.copyFile(file, new File(TestData.file(this, null), "polyphemus.nc"));
file = TestData.file(this, "polyphemus.nc");
final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
assertTrue(unidataImageReaderSpi.canDecodeInput(file));
NetCDFImageReader reader = null;
try {
reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
reader.setInput(file);
int numImages = reader.getNumImages(true);
assertEquals(1008, numImages);
for (int i = 0; i < numImages; i++) {
Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
assertNotNull(sliceIndex);
spitOutSliceInformation(i, sliceIndex);
}
// check dimensions
CoverageSourceDescriptor cd = reader.getCoverageDescriptor(new NameImpl("NO2"));
final List<AdditionalDomain> additionalDomains = cd.getAdditionalDomains();
assertNull(additionalDomains);
final List<DimensionDescriptor> dimensions = cd.getDimensionDescriptors();
assertNotNull(dimensions);
assertTrue(!dimensions.isEmpty());
assertEquals("wrong dimensions", 2, dimensions.size());
DimensionDescriptor dim = dimensions.get(0);
assertTrue(dim.getName().equals("TIME"));
assertTrue(dim.getStartAttribute().equals("time"));
dim = dimensions.get(1);
assertTrue(dim.getName().equals("ELEVATION"));
assertTrue(dim.getStartAttribute().equals("z"));
// check coverage names
final List<Name> names = reader.getCoveragesNames();
assertNotNull(names);
assertTrue(!names.isEmpty());
assertTrue(3 == names.size());
assertTrue(names.contains(new NameImpl("NO2")));
assertTrue(names.contains(new NameImpl("O3")));
assertTrue(names.contains(new NameImpl("V")));
// checking slice catalog
final CoverageSlicesCatalog cs = reader.getCatalog();
assertNotNull(cs);
// get typenames
final String[] typeNames = cs.getTypeNames();
for (String typeName : typeNames) {
final List<CoverageSlice> granules = cs.getGranules(new Query(typeName, Filter.INCLUDE));
assertNotNull(granules);
assertFalse(granules.isEmpty());
for (CoverageSlice slice : granules) {
final SimpleFeature sf = slice.getOriginator();
if (TestData.isInteractiveTest()) {
LOGGER.info(DataUtilities.encodeFeature(sf));
}
// checks
for (Property p : sf.getProperties()) {
assertNotNull("Property " + p.getName() + " had a null value!", p.getValue());
}
}
}
} finally {
// close reader
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
// specific clean up
FileUtils.deleteDirectory(TestData.file(this, ".polyphemus"));
}
}
@Test
public void testImageReaderAscat() throws Exception {
File file = null;
try {
file = TestData.file(this, "ascatl1.nc");
} catch (IOException e) {
LOGGER.warning("Unable to find file ascatl1.nc");
return;
}
if (!file.exists()) {
LOGGER.warning("Unable to find file ascatl1.nc");
return;
}
final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
assertTrue(unidataImageReaderSpi.canDecodeInput(file));
NetCDFImageReader reader = null;
try {
reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
reader.setInput(file);
int numImages = reader.getNumImages(true);
for (int i = 0; i < numImages; i++) {
Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
assertNotNull(sliceIndex);
spitOutSliceInformation(i, sliceIndex);
}
// check coverage names
final List<Name> names = reader.getCoveragesNames();
assertNotNull(names);
assertTrue(!names.isEmpty());
assertTrue(2 == names.size());
assertEquals("cell_index", names.get(0).toString());
assertEquals("f_land", names.get(1).toString());
// checking slice catalog
final CoverageSlicesCatalog cs = reader.getCatalog();
assertNotNull(cs);
// get typenames
final String[] typeNames = cs.getTypeNames();
for (String typeName : typeNames) {
final List<CoverageSlice> granules = cs.getGranules(new Query(typeName, Filter.INCLUDE));
assertNotNull(granules);
assertFalse(granules.isEmpty());
for (CoverageSlice slice : granules) {
final SimpleFeature sf = slice.getOriginator();
if (TestData.isInteractiveTest()) {
LOGGER.info(DataUtilities.encodeFeature(sf));
}
// checks
for (Property p : sf.getProperties()) {
final String pName = p.getName().toString();
if (!pName.equalsIgnoreCase("time") && !pName.equalsIgnoreCase("elevation")) {
assertNotNull("Property " + p.getName() + " had a null value!", p.getValue());
} else {
assertNull("Property " + p.getName() + " did not have a null value!", p.getValue());
}
}
}
}
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
}
/**
* Write the feature into the stream.
*
* @param feature The feature
* @param root
* @throws XMLStreamException
*/
public Element writeFeature(final Feature feature, final Document rootDocument, boolean fragment)
throws ParserConfigurationException {
final Document document;
if (rootDocument == null) {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
// then we have to create document-loader:
factory.setNamespaceAware(false);
DocumentBuilder loader = factory.newDocumentBuilder();
// creating a new DOM-document...
document = loader.newDocument();
} else {
document = rootDocument;
}
// the root element of the xml document (type of the feature)
final FeatureType type = feature.getType();
final Name typeName = type.getName();
final String namespace = typeName.getNamespaceURI();
final String localPart = typeName.getLocalPart();
final Element rootElement;
final Prefix prefix;
if (namespace != null) {
prefix = getPrefix(namespace);
rootElement = document.createElementNS(namespace, localPart);
rootElement.setPrefix(prefix.prefix);
} else {
rootElement = document.createElement(localPart);
prefix = null;
}
// if main document set the xmlns
if (!fragment) {
rootElement.setAttributeNS(
"http://www.w3.org/2000/xmlns/", "xmlns:gml", "http://www.opengis.net/gml");
}
final Attr idAttr = document.createAttributeNS(Namespaces.GML, "id");
idAttr.setValue(feature.getIdentifier().getID());
idAttr.setPrefix("gml");
rootElement.setAttributeNodeNS(idAttr);
if (rootDocument == null) {
document.appendChild(rootElement);
}
// write properties in the type order
for (final PropertyDescriptor desc : type.getDescriptors()) {
final Collection<Property> props = feature.getProperties(desc.getName());
for (Property a : props) {
final Object valueA = a.getValue();
final PropertyType typeA = a.getType();
final Name nameA = a.getName();
final String nameProperty = nameA.getLocalPart();
String namespaceProperty = nameA.getNamespaceURI();
if (valueA instanceof Collection && !(typeA instanceof GeometryType)) {
for (Object value : (Collection) valueA) {
final Element element;
if (namespaceProperty != null) {
element = document.createElementNS(namespaceProperty, nameProperty);
} else {
element = document.createElement(nameProperty);
}
element.setTextContent(Utils.getStringValue(value));
if (prefix != null) {
element.setPrefix(prefix.prefix);
}
rootElement.appendChild(element);
}
} else if (valueA instanceof Map && !(typeA instanceof GeometryType)) {
final Map<?, ?> map = (Map) valueA;
for (Entry<?, ?> entry : map.entrySet()) {
final Element element;
if (namespaceProperty != null) {
element = document.createElementNS(namespaceProperty, nameProperty);
} else {
element = document.createElement(nameProperty);
}
final Object key = entry.getKey();
if (key != null) {
element.setAttribute("name", (String) key);
}
element.setTextContent(Utils.getStringValue(entry.getValue()));
if (prefix != null) {
element.setPrefix(prefix.prefix);
}
rootElement.appendChild(element);
}
} else if (!(typeA instanceof GeometryType)) {
String value = Utils.getStringValue(valueA);
if (value != null || (value == null && !a.isNillable())) {
if ((nameProperty.equals("name") || nameProperty.equals("description"))
&& !Namespaces.GML.equals(namespaceProperty)) {
namespaceProperty = Namespaces.GML;
LOGGER.warning(
"the property name and description of a feature must have the GML namespace");
}
final Element element;
if (namespaceProperty != null) {
element = document.createElementNS(namespaceProperty, nameProperty);
} else {
element = document.createElement(nameProperty);
}
if (value != null) {
element.setTextContent(value);
}
if (prefix != null) {
element.setPrefix(prefix.prefix);
}
rootElement.appendChild(element);
}
// we add the geometry
} else {
if (valueA != null) {
final Element element;
if (namespaceProperty != null) {
element = document.createElementNS(namespaceProperty, nameProperty);
} else {
element = document.createElement(nameProperty);
}
if (prefix != null) {
element.setPrefix(prefix.prefix);
}
Geometry isoGeometry =
JTSUtils.toISO(
(com.vividsolutions.jts.geom.Geometry) valueA,
type.getCoordinateReferenceSystem());
Marshaller marshaller = null;
try {
marshaller = POOL.acquireMarshaller();
marshaller.setProperty(Marshaller.JAXB_FRAGMENT, true);
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, false);
marshaller.marshal(OBJECT_FACTORY.buildAnyGeometry(isoGeometry), element);
} catch (JAXBException ex) {
LOGGER.log(
Level.WARNING,
"JAXB Exception while marshalling the iso geometry: " + ex.getMessage(),
ex);
} finally {
if (marshaller != null) {
POOL.release(marshaller);
}
}
rootElement.appendChild(element);
}
}
}
}
// writer.writeEndElement();
return rootElement;
}
@Override
public int compare(Property left, Property right) {
return RevFeatureType.PROPERTY_ORDER.compare(left.getDescriptor(), right.getDescriptor());
}
/**
* Write SQL string to create tables in the test database based on the property files.
*
* @param propertyFiles Property files from app-schema-test suite.
* @param parser The parser (WKT or an SC4O one for 3D tests)
* @throws IllegalAttributeException
* @throws NoSuchElementException
* @throws IOException
*/
private void createTables(Map<String, File> propertyFiles, String parser)
throws IllegalAttributeException, NoSuchElementException, IOException {
StringBuffer buf = new StringBuffer();
StringBuffer spatialIndex = new StringBuffer();
// drop table procedure I copied from Victor's Oracle_Data_ref_set.sql
buf.append("CREATE OR REPLACE PROCEDURE DROP_TABLE_OR_VIEW(TabName in Varchar2) IS ")
.append("temp number:=0;")
.append(" tes VARCHAR2 (200) := TabName;")
.append(" drp_stmt VARCHAR2 (200):=null;")
.append("BEGIN select count(*) into temp from user_tables where TABLE_NAME = tes;")
.append("if temp = 1 then drp_stmt := 'Drop Table '||tes;")
.append("EXECUTE IMMEDIATE drp_stmt;")
// drop views too
.append("else select count(*) into temp from user_views where VIEW_NAME = tes;")
.append("if temp = 1 then drp_stmt := 'Drop VIEW '||tes;")
.append("EXECUTE IMMEDIATE drp_stmt;end if;end if;")
.append("EXCEPTION WHEN OTHERS THEN ")
.append(
"raise_application_error(-20001,'An error was encountered - '||SQLCODE||' -ERROR- '||SQLERRM);")
.append("END DROP_TABLE_OR_VIEW;\n");
for (String fileName : propertyFiles.keySet()) {
File file = new File(propertyFiles.get(fileName), fileName);
try (PropertyFeatureReader reader = new PropertyFeatureReader("test", file)) {
SimpleFeatureType schema = reader.getFeatureType();
String tableName = schema.getName().getLocalPart().toUpperCase();
// drop table if exists
buf.append("CALL DROP_TABLE_OR_VIEW('").append(tableName).append("')\n");
// create the table
buf.append("CREATE TABLE ").append(tableName).append("(");
// + pkey
int size = schema.getAttributeCount() + 1;
String[] fieldNames = new String[size];
List<String> createParams = new ArrayList<String>();
int j = 0;
String type;
String field;
int spatialIndexCounter = 0;
for (PropertyDescriptor desc : schema.getDescriptors()) {
field = desc.getName().toString().toUpperCase();
fieldNames[j] = field;
if (desc instanceof GeometryDescriptor) {
type = "SDO_GEOMETRY";
// Update spatial index
int srid = getSrid(((GeometryType) desc.getType()));
spatialIndex
.append("DELETE FROM user_sdo_geom_metadata WHERE table_name = '")
.append(tableName)
.append("'\n");
spatialIndex
.append("Insert into user_sdo_geom_metadata ")
.append("(TABLE_NAME,COLUMN_NAME,DIMINFO,SRID)")
.append("values ('")
.append(tableName)
.append("','")
.append(field)
.append("',MDSYS.SDO_DIM_ARRAY(MDSYS.SDO_DIM_ELEMENT('X',140.962,144.909,0.00001),")
.append("MDSYS.SDO_DIM_ELEMENT('Y',-38.858,-33.98,0.00001)")
.append( // support 3d index
((GeometryDescriptor) desc).getCoordinateReferenceSystem() != null
&& ((GeometryDescriptor) desc)
.getCoordinateReferenceSystem()
.getCoordinateSystem()
.getDimension()
== 3
? ", MDSYS.SDO_DIM_ELEMENT('Z',-100000, 100000, 1) ),"
: "),")
.append(srid)
.append(")\n");
// ensure it's <= 30 characters to avoid Oracle exception
String indexName =
(tableName.length() <= 26 ? tableName : tableName.substring(0, 26)) + "_IDX";
if (spatialIndexCounter > 0) {
// to avoid duplicate index name when there are > 1 geometry in the same table
indexName += spatialIndexCounter;
}
spatialIndex
.append("CREATE INDEX \"")
.append(indexName)
.append("\" ON \"")
.append(tableName)
.append("\"(\"")
.append(field)
.append("\") ")
.append("INDEXTYPE IS \"MDSYS\".\"SPATIAL_INDEX\"\n");
spatialIndexCounter++;
} else {
type = Classes.getShortName(desc.getType().getBinding());
if (type.equalsIgnoreCase("String")) {
type = "NVARCHAR2(250)";
} else if (type.equalsIgnoreCase("Double")) {
type = "NUMBER";
}
// etc. assign as required
}
createParams.add(field + " " + type);
j++;
}
// Add numeric PK for sorting
fieldNames[j] = "PKEY";
createParams.add("PKEY VARCHAR2(30)");
buf.append(StringUtils.join(createParams.iterator(), ", "));
buf.append(")\n");
buf.append(
"ALTER TABLE " + tableName + " ADD CONSTRAINT " + tableName + " PRIMARY KEY (PKEY)\n");
// then insert rows
SimpleFeature feature;
FeatureId id;
while (reader.hasNext()) {
buf.append("INSERT INTO ").append(tableName).append("(");
feature = reader.next();
buf.append(StringUtils.join(fieldNames, ", "));
buf.append(") ");
buf.append("VALUES (");
Collection<Property> properties = feature.getProperties();
String[] values = new String[size];
int valueIndex = 0;
for (Property prop : properties) {
Object value = prop.getValue();
if (value instanceof Geometry) {
// use wkt writer to convert geometry to string, so third dimension can be supported
// if present.
Geometry geom = (Geometry) value;
value = new WKTWriter(geom.getCoordinate().z == Double.NaN ? 2 : 3).write(geom);
}
if (value == null || value.toString().equalsIgnoreCase("null")) {
values[valueIndex] = "null";
} else if (prop.getType() instanceof GeometryType) {
int srid = getSrid(((GeometryType) prop.getType()));
StringBuffer geomValue = new StringBuffer(parser + "('");
geomValue.append(value).append("'");
if (srid > -1) {
// attach srid
geomValue.append(", ").append(srid);
}
geomValue.append(")");
values[valueIndex] = geomValue.toString();
} else if (prop.getType().getBinding().getSimpleName().equalsIgnoreCase("DATE")) {
values[valueIndex] = "TO_DATE('" + value + "', 'yyyy-MM-dd')";
} else {
values[valueIndex] = "'" + value + "'";
}
valueIndex++;
}
id = feature.getIdentifier();
// insert primary key
values[valueIndex] = "'" + id.toString() + "'";
buf.append(StringUtils.join(values, ","));
buf.append(")\n");
}
}
buf.append(spatialIndex.toString());
spatialIndex.delete(0, spatialIndex.length());
if (buf.length() > 0) {
this.sql = buf.toString();
}
}
}