afs commented on code in PR #3027:
URL: https://github.com/apache/jena/pull/3027#discussion_r2063785721
##########
jena-arq/src/main/java/org/apache/jena/sparql/util/Context.java:
##########
@@ -387,6 +389,11 @@ public void clear() {
context.clear();
}
+ /** Atomic compute. */
+ public <V> Object compute(Symbol key, BiFunction<Symbol, Object, V>
remappingFunction) {
Review Comment:
This does mot seem to be used anywhere.
##########
jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/SpatialIndexFindUtils.java:
##########
@@ -0,0 +1,189 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.jena.geosparql.spatial;
+
+import java.lang.invoke.MethodHandles;
+import java.util.Iterator;
+import java.util.List;
Review Comment:
Not used?
##########
jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/index/v2/STRtreePerGraphSerializer.java:
##########
@@ -0,0 +1,49 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.jena.geosparql.spatial.index.v2;
+
+import java.util.Map;
+
+import org.apache.jena.graph.Node;
+import org.locationtech.jts.index.strtree.STRtree;
+
+import com.esotericsoftware.kryo.Kryo;
+import com.esotericsoftware.kryo.Serializer;
+import com.esotericsoftware.kryo.io.Input;
+import com.esotericsoftware.kryo.io.Output;
+
+public class STRtreePerGraphSerializer
+ extends Serializer<STRtreePerGraph>
+{
+ @Override
+ public void write(Kryo kryo, Output output, STRtreePerGraph index) {
+ kryo.writeClassAndObject(output, index.getInternalTreeMap());
+ output.writeBoolean(index.isBuilt());
+ }
+
+ @Override
+ public STRtreePerGraph read(Kryo kryo, Input input, Class<STRtreePerGraph>
type) {
+ Map<Node, STRtree> treeMap = (Map<Node,
STRtree>)kryo.readClassAndObject(input);
Review Comment:
Add `@SuppressWarnings("unchecked")`
##########
jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/index/v1/SpatialIndexV1.java:
##########
@@ -0,0 +1,577 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.jena.geosparql.spatial.index.v1;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.lang.invoke.MethodHandles;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.jena.atlas.RuntimeIOException;
+import org.apache.jena.atlas.io.IOX;
+import org.apache.jena.geosparql.configuration.GeoSPARQLOperations;
+import org.apache.jena.geosparql.implementation.GeometryWrapper;
+import org.apache.jena.geosparql.implementation.SRSInfo;
+import org.apache.jena.geosparql.implementation.registry.SRSRegistry;
+import org.apache.jena.geosparql.implementation.vocabulary.Geo;
+import org.apache.jena.geosparql.implementation.vocabulary.SRS_URI;
+import org.apache.jena.geosparql.implementation.vocabulary.SpatialExtension;
+import org.apache.jena.geosparql.spatial.ConvertLatLon;
+import org.apache.jena.geosparql.spatial.SpatialIndex;
+import org.apache.jena.geosparql.spatial.SpatialIndexException;
+import org.apache.jena.geosparql.spatial.SpatialIndexItem;
+import org.apache.jena.geosparql.spatial.SpatialIndexStorage;
+import org.apache.jena.geosparql.spatial.index.v2.SpatialIndexUtils;
+import org.apache.jena.query.Dataset;
+import org.apache.jena.query.DatasetFactory;
+import org.apache.jena.query.ReadWrite;
+import org.apache.jena.rdf.model.Literal;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.NodeIterator;
+import org.apache.jena.rdf.model.RDFNode;
+import org.apache.jena.rdf.model.ResIterator;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.Statement;
+import org.apache.jena.rdf.model.StmtIterator;
+import org.apache.jena.sparql.engine.ExecutionContext;
+import org.apache.jena.sparql.util.Context;
+import org.apache.jena.sparql.util.ModelUtils;
+import org.apache.jena.util.iterator.ExtendedIterator;
+import org.locationtech.jts.geom.Envelope;
+import org.locationtech.jts.index.strtree.STRtree;
+import org.opengis.geometry.MismatchedDimensionException;
+import org.opengis.referencing.operation.TransformException;
+import org.opengis.util.FactoryException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * SpatialIndex for testing bounding box collisions between geometries within a
+ * Dataset.<br>
+ * Queries must be performed using the same SRS URI as the SpatialIndex.<br>
+ * The SpatialIndex is added to the Dataset Context when it is built.<br>
+ * QueryRewriteIndex is also stored in the SpatialIndex as its content is
+ * Dataset specific.
+ */
+@Deprecated /** Superseded by {@link SpatialIndex} and {@link
SpatialIndexPerGraph}. */
Review Comment:
Should this be `@Deprecated(forRemoval = true)`?
##########
jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/index/v1/SpatialIndexAdapterV1.java:
##########
@@ -0,0 +1,83 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.jena.geosparql.spatial.index.v1;
+
+import java.io.File;
+import java.nio.file.Path;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Optional;
+import java.util.stream.Collectors;
+
+import org.apache.jena.geosparql.implementation.SRSInfo;
+import org.apache.jena.geosparql.spatial.SpatialIndex;
+import org.apache.jena.graph.Node;
+import org.apache.jena.rdf.model.RDFNode;
+import org.apache.jena.rdf.model.Resource;
+import org.locationtech.jts.geom.Envelope;
+
+/** Adapter class for spatial index v1. */
+public class SpatialIndexAdapterV1
Review Comment:
Several deprecation warnings.
Maybe add `@SuppressWarnings("deprecation")` to the class.
##########
jena-geosparql/src/test/java/org/apache/jena/geosparql/spatial/SpatialIndexTestData.java:
##########
@@ -60,21 +71,28 @@ public class SpatialIndexTestData {
public static final SRSInfo WGS_84_SRS_INFO = new
SRSInfo(SRS_URI.WGS84_CRS);
public static final SRSInfo OSGB_SRS_INFO = new
SRSInfo(SRS_URI.OSGB36_CRS);
- private static SpatialIndex TEST_SPATIAL_INDEX = null;
+ private static SpatialIndexPerGraph TEST_SPATIAL_INDEX = null;
private static Dataset TEST_DATASET = null;
- public static final SpatialIndex createTestIndex() {
+ public static final List<SpatialIndexItem> getTestItems() {
+ List<SpatialIndexItem> items = List.of(
+ SpatialIndexItem.of(LONDON_GEOMETRY_WRAPPER.getEnvelope(),
LONDON_FEATURE),
Review Comment:
5 deprecated functions here. Add `.asNode()` to second argument.
##########
jena-geosparql/src/main/java/org/apache/jena/geosparql/kryo/NodeSerializer.java:
##########
@@ -0,0 +1,346 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.jena.geosparql.kryo;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.stream.Collectors;
+
+import org.apache.jena.datatypes.RDFDatatype;
+import org.apache.jena.datatypes.TypeMapper;
+import org.apache.jena.graph.Graph;
+import org.apache.jena.graph.Node;
+import org.apache.jena.graph.NodeFactory;
+import org.apache.jena.graph.Node_ANY;
+import org.apache.jena.graph.Node_Blank;
+import org.apache.jena.graph.Node_Graph;
+import org.apache.jena.graph.Node_Literal;
+import org.apache.jena.graph.Node_Triple;
+import org.apache.jena.graph.Node_URI;
+import org.apache.jena.graph.Node_Variable;
+import org.apache.jena.graph.TextDirection;
+import org.apache.jena.graph.Triple;
+import org.apache.jena.sparql.core.Quad;
+import org.apache.jena.sparql.core.Var;
+import org.apache.jena.vocabulary.OWL;
+import org.apache.jena.vocabulary.RDF;
+import org.apache.jena.vocabulary.RDFS;
+import org.apache.jena.vocabulary.XSD;
+
+import com.esotericsoftware.kryo.Kryo;
+import com.esotericsoftware.kryo.Serializer;
+import com.esotericsoftware.kryo.io.Input;
+import com.esotericsoftware.kryo.io.Output;
+
+/**
+ * An RDF1.2 node serializer for kryo.
+ */
+public class NodeSerializer
+ extends Serializer<Node>
+{
+ public static void register(Kryo kryo) {
+ register(kryo, new NodeSerializer());
+ }
+
+ /**
+ * Registers serializers for all Jena Node types - except for Node_Ext and
any subclasses.
+ *
+ * For Node_Triple and Node_Graph to function, additional serializers for
+ * Triple and Graph need to be registered.
+ */
+ public static void register(Kryo kryo, Serializer<Node> nodeSerializer) {
+ // Concrete nodes
+ kryo.register(Node.class, nodeSerializer);
+ kryo.register(Node_Blank.class, nodeSerializer);
+ kryo.register(Node_URI.class, nodeSerializer);
+ kryo.register(Node_Literal.class, nodeSerializer);
+ kryo.register(Node_Triple.class, nodeSerializer);
+
+ // Variable nodes
+ kryo.register(Node_Variable.class, nodeSerializer);
+ kryo.register(Var.class, nodeSerializer);
+ kryo.register(Node_ANY.class, nodeSerializer);
+
+ // Extensions
+ kryo.register(Node_Graph.class, nodeSerializer);
+ }
+
+ protected static final byte TYPE_MASK = (byte)0xf0; // 1111 0000
+ protected static final byte TYPE_IRI = 0x10; // 0001 0000
+ protected static final byte TYPE_BNODE = 0x20; // 0010 0000
+ protected static final byte TYPE_LITERAL = 0x30; // 0011 0000
+ protected static final byte TYPE_TRIPLE = 0x40; // 0100 0000
+ protected static final byte TYPE_GRAPH = 0x50; // 0101 0000 -
Delegates back to kryo
+
+ protected static final byte TYPE_VAR = (byte)0x80; // 1000 0000 -
NoteFactory.createVariable
+ protected static final byte TYPE_SVAR = (byte)0x90; // 1001 0000 -
Var.alloc
+ protected static final byte TYPE_ANY = (byte)0xa0; // 1010 0000
+ protected static final byte TYPE_EXT = (byte)0xb0; // 1011 0000 -
Delegates back to kryo
+
+ protected static final byte LITERAL_MASK = 0x03; // 0000 0011
+ protected static final byte LITERAL_STRING = 0x00; // 0000 0000
+ protected static final byte LITERAL_LANG = 0x01; // 0000 0001
+ protected static final byte LITERAL_DTYPE = 0x02; // 0000 0010
+
+ // Iff (TYPE_LITERAL and LITERAL_LANG) the following applies:
+ protected static final byte LITERAL_LANG_MASK = 0x0c; // 0000 1100
+ protected static final byte LITERAL_LANG_LTR = 0x04; // 0000 0100
+ protected static final byte LITERAL_LANG_RTL = 0x08; // 0000 1000
+
+ // Iff (TYPE_IRI) or (TYPE_LITERAL & LITERAL_DYTE): Whether the value
field is abbreviated.
+ protected static final byte ABBREV_IRI = 0x08; // 0000 1000
+
+ private static Map<String, String> globalPrefixToIri = new HashMap<>();
+
+ private Map<String, String> prefixToIri = new HashMap<>();
+ private Map<String, String> iriToPrefix = new HashMap<>();
+
+ static {
+ globalPrefixToIri.put("a", RDF.type.getURI());
+ globalPrefixToIri.put("d", Quad.defaultGraphIRI.getURI());
+ globalPrefixToIri.put("g", Quad.defaultGraphNodeGenerated.getURI());
+ globalPrefixToIri.put("x", XSD.NS);
+ globalPrefixToIri.put("r", RDF.uri);
+ globalPrefixToIri.put("s", RDFS.uri);
+ globalPrefixToIri.put("o", OWL.NS);
+ }
+
+ /**
+ * Takes a guess for the namespace URI string to use in abbreviation.
+ * Finds the part of the IRI string before the last '#', '/', ':' or '.'.
+ *
+ * @param iriString String string
+ * @return String or null
+ */
+ // XXX Should use a trie instead.
+ private static String getCandidateNamespaceIri(String iriString) {
+ int n = iriString.length();
+ int i;
+ loop: for (i = n - 1; i >= 0; --i) {
+ char c = iriString.charAt(i);
+ switch(c) {
+ case '#':
+ case '/':
+ case ':':
+ case '.':
+ break loop;
+ default:
+ // continue
+ }
+ }
+ String result = i >= 0 ? iriString.substring(0, i + 1) : null;
+ return result;
+ }
+
+ private static String encode(Map<String, String> iriToPrefix, String iri) {
+ String result = iriToPrefix.get(iri);
+ if (result == null) {
+ String nsIri = getCandidateNamespaceIri(iri);
+ if (nsIri != null) {
+ String prefix = iriToPrefix.get(nsIri);
+ if (prefix != null) {
+ result = prefix + ":" + iri.substring(nsIri.length());
+ }
+ }
+ }
+ return result;
+ }
+
+ private static String decode(Map<String, String> prefixToIri, String
curie) {
+ String result;
+ int idx = curie.indexOf(':');
+ if (idx < 0) {
+ result = prefixToIri.get(curie);
+ } else {
+ String prefix = curie.substring(0, idx);
+ String iri = prefixToIri.get(prefix);
+ result = iri + curie.substring(idx + 1);
+ }
+ return result;
+ }
+
+ protected TypeMapper typeMapper;
+
+ public NodeSerializer() {
+ this(TypeMapper.getInstance());
+ }
+
+ public NodeSerializer(TypeMapper typeMapper) {
+ this(typeMapper, globalPrefixToIri);
+ }
+
+ public NodeSerializer(TypeMapper typeMapper, Map<String, String>
prefixToIri) {
+ super();
+ this.typeMapper = typeMapper;
+ this.prefixToIri = new HashMap<>(prefixToIri);
+
+ this.iriToPrefix = prefixToIri.entrySet().stream()
+ .collect(Collectors.toMap(Entry::getValue, Entry::getKey));
+ }
+
+ @Override
+ public void write(Kryo kryo, Output output, Node node) {
+ if (node.isURI()) {
+ String uri = node.getURI();
+ String curie = encode(iriToPrefix, uri);
+ if (curie != null) {
+ output.writeByte(TYPE_IRI | ABBREV_IRI);
+ output.writeString(curie);
+ } else {
+ output.writeByte(TYPE_IRI);
+ output.writeString(uri);
+ }
+ } else if (node.isLiteral()) {
+ String lex = node.getLiteralLexicalForm();
+ String lang = node.getLiteralLanguage();
+ String dt = node.getLiteralDatatypeURI();
+ TextDirection dir = node.getLiteralBaseDirection();
+
+ if (lang != null && !lang.isEmpty()) {
+ byte langDirBits = dir == null ? (byte)0 : switch(dir) {
+ case LTR -> LITERAL_LANG_LTR;
+ case RTL -> LITERAL_LANG_RTL;
+ };
+ output.writeByte(TYPE_LITERAL | LITERAL_LANG | langDirBits);
+ output.writeString(lex);
+ output.writeString(lang);
+ } else if (dt != null && !dt.isEmpty() &&
!dt.equals(XSD.xstring.getURI())) {
+ String dtCurie = encode(iriToPrefix, dt);
+ if (dtCurie != null) {
+ output.writeByte(TYPE_LITERAL | LITERAL_DTYPE |
ABBREV_IRI);
+ output.writeString(lex);
+ output.writeString(dtCurie);
+ } else {
+ output.writeByte(TYPE_LITERAL | LITERAL_DTYPE);
+ output.writeString(lex);
+ output.writeString(dt);
+ }
+ } else {
+ output.writeByte(TYPE_LITERAL);
+ output.writeString(lex);
+ }
+ } else if (node.isBlank()) {
+ output.writeByte(TYPE_BNODE);
+ output.writeString(node.getBlankNodeLabel());
+ } else if (Node.ANY.equals(node)) {
+ output.writeByte(TYPE_ANY);
+ } else if (node.isVariable()) {
+ if (node instanceof Var) {
+ output.writeByte(TYPE_SVAR);
+ } else {
+ output.writeByte(TYPE_VAR);
+ }
+ output.writeString(node.getName());
+ } else if (node.isTripleTerm()) {
+ output.writeByte(TYPE_TRIPLE);
+ kryo.writeObject(output, node.getTriple());
+ } else if (node.isNodeGraph()) {
+ output.writeByte(TYPE_GRAPH);
+ kryo.writeObject(output, node.getGraph());
+ } else if (node.isExt()) {
+ output.writeByte(TYPE_EXT);
+ kryo.writeClassAndObject(output, node);
+ } else {
+ throw new RuntimeException("Unknown node type: " + node);
+ }
+ }
+
+ @Override
+ public Node read(Kryo kryo, Input input, Class<Node> cls) {
+ Node result;
+ String v1, v2;
+ Triple t;
+
+ byte type = input.readByte();
+
+ int typeVal = type & TYPE_MASK;
+ switch (typeVal) {
+ case TYPE_IRI:
+ v1 = input.readString();
+ if ((type & ABBREV_IRI) != 0) {
+ v1 = decode(prefixToIri, v1);
+ }
+ result = NodeFactory.createURI(v1);
+ break;
+ case TYPE_LITERAL:
+ int subTypeVal = type & LITERAL_MASK;
+ switch (subTypeVal) {
+ case LITERAL_STRING:
+ v1 = input.readString();
+ result = NodeFactory.createLiteralString(v1);
+ break;
+ case LITERAL_LANG:
+ int langDirBits = type & LITERAL_LANG_MASK;
+
+ TextDirection textDir = switch(langDirBits) {
+ case LITERAL_LANG_LTR -> TextDirection.LTR;
+ case LITERAL_LANG_RTL -> TextDirection.RTL;
+ default -> Node.noTextDirection;
+ };
+
+ v1 = input.readString();
+ v2 = input.readString();
+ result = NodeFactory.createLiteralDirLang(v1, v2,
textDir);
+ break;
+ case LITERAL_DTYPE:
+ v1 = input.readString();
+ v2 = input.readString();
+ if ((type & ABBREV_IRI) != 0) {
+ v2 = decode(prefixToIri, v2);
+ }
+ RDFDatatype dtype = typeMapper.getSafeTypeByName(v2);
+ result = NodeFactory.createLiteralDT(v1, dtype);
+ break;
+ default:
+ throw new RuntimeException("Unknown literal sub-type:
" + subTypeVal);
+ }
+ break;
+ case TYPE_BNODE:
+ v1 = input.readString();
+ result = NodeFactory.createBlankNode(v1);
+ break;
+ case TYPE_TRIPLE:
+ t = kryo.readObject(input, Triple.class);
+ result = NodeFactory.createTripleNode(t);
Review Comment:
```suggestion
result = NodeFactory.createTripleTerm(t);
```
`createTripleNode` is deprecated.
##########
jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/SpatialIndexFindUtils.java:
##########
@@ -0,0 +1,189 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.jena.geosparql.spatial;
+
+import java.lang.invoke.MethodHandles;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.jena.atlas.iterator.Iter;
+import org.apache.jena.atlas.iterator.IteratorCloseable;
+import org.apache.jena.geosparql.implementation.GeometryWrapper;
+import org.apache.jena.geosparql.implementation.vocabulary.Geo;
+import org.apache.jena.geosparql.implementation.vocabulary.SpatialExtension;
+import org.apache.jena.graph.Graph;
+import org.apache.jena.graph.Node;
+import org.apache.jena.graph.Triple;
+import org.apache.jena.sparql.core.DatasetGraph;
+import org.apache.jena.system.G;
+import org.locationtech.jts.geom.Envelope;
+import org.opengis.geometry.MismatchedDimensionException;
+import org.opengis.referencing.operation.TransformException;
+import org.opengis.util.FactoryException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class SpatialIndexFindUtils {
+ private static final Logger LOGGER =
LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
+
+ /**
+ * Find Spatial Index Items from all graphs in Dataset.<br>
+ *
+ * @param datasetGraph
+ * @param srsURI
+ * @return SpatialIndexItems found.
+ * @throws SpatialIndexException
Review Comment:
This causes a javadoc warning because there isn't a `throws` for
`SpatialIndexException` (3 occurrences of same situation).
##########
jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/task/AbortableThread.java:
##########
@@ -0,0 +1,200 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.jena.geosparql.spatial.task;
+
+import java.time.Instant;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Objects;
+import java.util.concurrent.atomic.AtomicBoolean;
+import java.util.function.BiConsumer;
+
+import org.apache.jena.geosparql.spatial.task.TaskControl.Registration;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Thread base class that provides {@link #cancel()} and {@link
#requestingCancel} methods
+ * that can run a custom action (in addition to setting the interrupted flag)
+ * as well as a {@link #doAfterRun()} method for cleaning up after execution
+ * (only called if there is a prior call to run).
+ */
+public abstract class AbortableThread<T>
+ extends Thread
+{
+ private static final Logger logger =
LoggerFactory.getLogger(AbortableThread.class);
+
+ private final AtomicBoolean requestingCancel;
+ private volatile boolean cancelOnce = false;
+ private Object cancelLock = new Object();
+
+ protected List<BiConsumer<? super T, Throwable>> completionHandlers = new
ArrayList<>();
+
+ private boolean isComplete = false;
+ private T value = null;
+ private Throwable throwable;
+
+ private Instant startTime;
+ private String statusMessage;
+
+ /**
+ * Time of the first abort request; null if there is none.
+ * Cancel time will not be set if cancel is called after a task's
completion.
+ */
+ private Instant cancelTime;
+ private Instant endTime;
+
+ // XXX Add native support for CompletableFuture?
+
+ public AbortableThread() {
+ this(new AtomicBoolean());
+ }
+
+ public AbortableThread(AtomicBoolean requestingCancel) {
+ super();
+ this.requestingCancel = Objects.requireNonNull(requestingCancel);
+ }
+
+ public final boolean isComplete() {
+ return isComplete;
+ }
+
+ public T getValue() {
+ return value;
+ }
+
+ public Throwable getThrowable() {
+ return throwable;
+ }
+
+ public Instant getStartTime() {
+ return startTime;
+ }
+
+ public Instant getEndTime() {
+ return endTime;
+ }
+
+ public Instant getCancelTime() {
+ return cancelTime;
+ }
+
+ protected void setStatusMessage(String statusMessage) {
+ this.statusMessage = statusMessage;
+ }
+
+ public String getStatusMessage() {
+ return statusMessage;
+ }
+
+ public final void run() {
Review Comment:
```suggestion
@Override
public final void run() {
```
##########
jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/SpatialIndex.java:
##########
@@ -17,530 +17,45 @@
*/
package org.apache.jena.geosparql.spatial;
-import java.io.*;
-import java.lang.invoke.MethodHandles;
-import java.nio.file.Files;
import java.nio.file.Path;
-import java.util.*;
+import java.util.Collection;
-import org.apache.jena.atlas.RuntimeIOException;
-import org.apache.jena.atlas.io.IOX;
-import org.apache.jena.geosparql.configuration.GeoSPARQLOperations;
-import org.apache.jena.geosparql.implementation.GeometryWrapper;
import org.apache.jena.geosparql.implementation.SRSInfo;
-import org.apache.jena.geosparql.implementation.registry.SRSRegistry;
-import org.apache.jena.geosparql.implementation.vocabulary.Geo;
-import org.apache.jena.geosparql.implementation.vocabulary.SRS_URI;
-import org.apache.jena.geosparql.implementation.vocabulary.SpatialExtension;
-import org.apache.jena.query.Dataset;
-import org.apache.jena.query.DatasetFactory;
-import org.apache.jena.query.ReadWrite;
-import org.apache.jena.rdf.model.*;
-import org.apache.jena.sparql.engine.ExecutionContext;
-import org.apache.jena.sparql.util.Context;
-import org.apache.jena.sparql.util.Symbol;
-import org.apache.jena.util.iterator.ExtendedIterator;
+import org.apache.jena.graph.Node;
+import org.apache.jena.sparql.core.Quad;
import org.locationtech.jts.geom.Envelope;
-import org.locationtech.jts.index.strtree.STRtree;
-import org.opengis.geometry.MismatchedDimensionException;
-import org.opengis.referencing.operation.TransformException;
-import org.opengis.util.FactoryException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-/**
- * SpatialIndex for testing bounding box collisions between geometries within a
- * Dataset.<br>
- * Queries must be performed using the same SRS URI as the SpatialIndex.<br>
- * The SpatialIndex is added to the Dataset Context when it is built.<br>
- * QueryRewriteIndex is also stored in the SpatialIndex as its content is
- * Dataset specific.
- *
- */
-public class SpatialIndex {
-
- private static final Logger LOGGER =
LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
-
- public static final Symbol SPATIAL_INDEX_SYMBOL =
Symbol.create("http://jena.apache.org/spatial#index";);
-
- private transient final SRSInfo srsInfo;
- private boolean isBuilt;
- private final STRtree strTree;
- private static final int MINIMUM_CAPACITY = 2;
-
- private SpatialIndex() {
- this.strTree = new STRtree(MINIMUM_CAPACITY);
- this.isBuilt = true;
- this.strTree.build();
- this.srsInfo = SRSRegistry.getSRSInfo(SRS_URI.DEFAULT_WKT_CRS84);
- }
-
- /**
- * Unbuilt Spatial Index with provided capacity.
- *
- * @param capacity
- * @param srsURI
- */
- public SpatialIndex(int capacity, String srsURI) {
- int indexCapacity = capacity < MINIMUM_CAPACITY ? MINIMUM_CAPACITY :
capacity;
- this.strTree = new STRtree(indexCapacity);
- this.isBuilt = false;
- this.srsInfo = SRSRegistry.getSRSInfo(srsURI);
- }
-
- /**
- * Built Spatial Index with provided capacity.
- *
- * @param spatialIndexItems
- * @param srsURI
- * @throws SpatialIndexException
- */
- public SpatialIndex(Collection<SpatialIndexItem> spatialIndexItems, String
srsURI) throws SpatialIndexException {
- int indexCapacity = spatialIndexItems.size() < MINIMUM_CAPACITY ?
MINIMUM_CAPACITY : spatialIndexItems.size();
- this.strTree = new STRtree(indexCapacity);
- insertItems(spatialIndexItems);
- this.strTree.build();
- this.isBuilt = true;
- this.srsInfo = SRSRegistry.getSRSInfo(srsURI);
- }
+public interface SpatialIndex {
/**
*
* @return Information about the SRS used by the SpatialIndex.
*/
- public SRSInfo getSrsInfo() {
- return srsInfo;
- }
+ SRSInfo getSrsInfo();
/**
*
* @return True if the SpatialIndex is empty.
*/
- public boolean isEmpty() {
- return strTree.isEmpty();
- }
-
- /**
- *
- * @return True if the SpatialIndex has been built.
- */
- public boolean isBuilt() {
- return isBuilt;
- }
-
- /**
- * Build the Spatial Index. No more items can be added.
- */
- public void build() {
- if (!isBuilt) {
- strTree.build();
- isBuilt = true;
- }
- }
+ boolean isEmpty();
/**
- * Items to add to an unbuilt Spatial Index.
- *
- * @param indexItems
- * @throws SpatialIndexException
+ * Returns the number of items in the index.
*/
- public final void insertItems(Collection<SpatialIndexItem> indexItems)
throws SpatialIndexException {
-
- for (SpatialIndexItem indexItem : indexItems) {
- insertItem(indexItem.getEnvelope(), indexItem.getItem());
- }
- }
+ long getSize();
/**
- * Item to add to an unbuilt Spatial Index.
+ * Query the index for all matching data in the given graph.
*
- * @param envelope
- * @param item
- * @throws SpatialIndexException
- */
- public final void insertItem(Envelope envelope, Resource item) throws
SpatialIndexException {
- if (!isBuilt) {
- strTree.insert(envelope, item);
- } else {
- throw new SpatialIndexException("SpatialIndex has been built and
cannot have additional items.");
- }
- }
-
- @SuppressWarnings("unchecked")
- public HashSet<Resource> query(Envelope searchEnvelope) {
- if (!strTree.isEmpty()) {
- return new HashSet<>(strTree.query(searchEnvelope));
- } else {
- return new HashSet<>();
- }
- }
-
- @Override
- public String toString() {
- return "SpatialIndex{" + "srsInfo=" + srsInfo + ", isBuilt=" + isBuilt
+ ", strTree=" + strTree + '}';
- }
-
- /**
- * Retrieve the SpatialIndex from the Context.
- *
- * @param execCxt
- * @return SpatialIndex contained in the Context.
- * @throws SpatialIndexException
- */
- public static final SpatialIndex retrieve(ExecutionContext execCxt) throws
SpatialIndexException {
-
- Context context = execCxt.getContext();
- SpatialIndex spatialIndex = (SpatialIndex)
context.get(SPATIAL_INDEX_SYMBOL, null);
-
- if (spatialIndex == null) {
- throw new SpatialIndexException("Dataset Context does not contain
SpatialIndex.");
- }
-
- return spatialIndex;
- }
-
- /**
- *
- * @param execCxt
- * @return True if a SpatialIndex is defined in the ExecutionContext.
- */
- public static final boolean isDefined(ExecutionContext execCxt) {
- Context context = execCxt.getContext();
- return context.isDefined(SPATIAL_INDEX_SYMBOL);
- }
-
- /**
- * Set the SpatialIndex into the Context of the Dataset for later retrieval
- * and use in spatial functions.
- *
- * @param dataset
- * @param spatialIndex
- */
- public static final void setSpatialIndex(Dataset dataset, SpatialIndex
spatialIndex) {
- Context context = dataset.getContext();
- context.set(SPATIAL_INDEX_SYMBOL, spatialIndex);
- }
-
- /**
- * Build Spatial Index from all graphs in Dataset.<br>
- * Dataset contains SpatialIndex in Context.<br>
- * Spatial Index written to file.
- *
- * @param dataset
- * @param srsURI
- * @param spatialIndexFile
- * @return SpatialIndex constructed.
- * @throws SpatialIndexException
- */
- public static SpatialIndex buildSpatialIndex(Dataset dataset, String
srsURI, File spatialIndexFile) throws SpatialIndexException {
-
- SpatialIndex spatialIndex = load(spatialIndexFile);
-
- if (spatialIndex.isEmpty()) {
- Collection<SpatialIndexItem> spatialIndexItems =
findSpatialIndexItems(dataset, srsURI);
- save(spatialIndexFile, spatialIndexItems, srsURI);
- spatialIndex = new SpatialIndex(spatialIndexItems, srsURI);
- spatialIndex.build();
- }
-
- setSpatialIndex(dataset, spatialIndex);
- return spatialIndex;
- }
-
- /**
- * Build Spatial Index from all graphs in Dataset.<br>
- * Dataset contains SpatialIndex in Context.<br>
- * SRS URI based on most frequent found in Dataset.<br>
- * Spatial Index written to file.
- *
- * @param dataset
- * @param spatialIndexFile
- * @return SpatialIndex constructed.
- * @throws SpatialIndexException
- */
- public static SpatialIndex buildSpatialIndex(Dataset dataset, File
spatialIndexFile) throws SpatialIndexException {
- String srsURI = GeoSPARQLOperations.findModeSRS(dataset);
- SpatialIndex spatialIndex = buildSpatialIndex(dataset, srsURI,
spatialIndexFile);
- return spatialIndex;
- }
-
- /**
- * Build Spatial Index from all graphs in Dataset.<br>
- * Dataset contains SpatialIndex in Context.
- *
- * @param dataset
- * @param srsURI
- * @return SpatialIndex constructed.
- * @throws SpatialIndexException
- */
- public static SpatialIndex buildSpatialIndex(Dataset dataset, String
srsURI) throws SpatialIndexException {
- LOGGER.info("Building Spatial Index - Started");
-
- Collection<SpatialIndexItem> items = findSpatialIndexItems(dataset,
srsURI);
- SpatialIndex spatialIndex = new SpatialIndex(items, srsURI);
- spatialIndex.build();
- setSpatialIndex(dataset, spatialIndex);
- LOGGER.info("Building Spatial Index - Completed");
- return spatialIndex;
- }
-
- /**
- * Find Spatial Index Items from all graphs in Dataset.<br>
- *
- * @param dataset
- * @param srsURI
- * @return SpatialIndexItems found.
- * @throws SpatialIndexException
- */
- public static Collection<SpatialIndexItem> findSpatialIndexItems(Dataset
dataset, String srsURI) throws SpatialIndexException {
- //Default Model
- dataset.begin(ReadWrite.READ);
- Model defaultModel = dataset.getDefaultModel();
- Collection<SpatialIndexItem> items =
getSpatialIndexItems(defaultModel, srsURI);
-
- //Named Models
- Iterator<String> graphNames = dataset.listNames();
- while (graphNames.hasNext()) {
- String graphName = graphNames.next();
- Model namedModel = dataset.getNamedModel(graphName);
- Collection<SpatialIndexItem> graphItems =
getSpatialIndexItems(namedModel, srsURI);
- items.addAll(graphItems);
- }
-
- dataset.end();
-
- return items;
- }
-
- /**
- * Build Spatial Index from all graphs in Dataset.<br>
- * Dataset contains SpatialIndex in Context.<br>
- * SRS URI based on most frequent found in Dataset.
- *
- * @param dataset
- * @return SpatialIndex constructed.
- * @throws SpatialIndexException
- */
- public static SpatialIndex buildSpatialIndex(Dataset dataset) throws
SpatialIndexException {
- String srsURI = GeoSPARQLOperations.findModeSRS(dataset);
- SpatialIndex spatialIndex = buildSpatialIndex(dataset, srsURI);
- return spatialIndex;
- }
-
- /**
- * Wrap Model in a Dataset and build SpatialIndex.
- *
- * @param model
- * @param srsURI
- * @return Dataset with default Model and SpatialIndex in Context.
- * @throws SpatialIndexException
- */
- public static final Dataset wrapModel(Model model, String srsURI) throws
SpatialIndexException {
-
- Dataset dataset = DatasetFactory.createTxnMem();
- dataset.setDefaultModel(model);
- buildSpatialIndex(dataset, srsURI);
-
- return dataset;
- }
-
- /**
- * Wrap Model in a Dataset and build SpatialIndex.
- *
- * @param model
- * @return Dataset with default Model and SpatialIndex in Context.
- * @throws SpatialIndexException
- */
- public static final Dataset wrapModel(Model model) throws
SpatialIndexException {
- Dataset dataset = DatasetFactory.createTxnMem();
- dataset.setDefaultModel(model);
- String srsURI = GeoSPARQLOperations.findModeSRS(dataset);
- buildSpatialIndex(dataset, srsURI);
-
- return dataset;
- }
-
- /**
- * Find items from the Model transformed to the SRS URI.
- *
- * @param model
- * @param srsURI
- * @return Items found in the Model in the SRS URI.
- * @throws SpatialIndexException
- */
- public static final Collection<SpatialIndexItem>
getSpatialIndexItems(Model model, String srsURI) throws SpatialIndexException {
-
- List<SpatialIndexItem> items = new ArrayList<>();
-
- //Only add one set of statements as a converted dataset will duplicate
the same info.
- if (model.contains(null, Geo.HAS_GEOMETRY_PROP, (Resource) null)) {
- LOGGER.info("Feature-hasGeometry-Geometry statements found.");
- if (model.contains(null, SpatialExtension.GEO_LAT_PROP, (Literal)
null)) {
- LOGGER.warn("Lat/Lon Geo predicates also found but will not be
added to index.");
- }
- Collection<SpatialIndexItem> geometryLiteralItems =
getGeometryLiteralIndexItems(model, srsURI);
- items.addAll(geometryLiteralItems);
- } else if (model.contains(null, SpatialExtension.GEO_LAT_PROP,
(Literal) null)) {
- LOGGER.info("Geo predicate statements found.");
- Collection<SpatialIndexItem> geoPredicateItems =
getGeoPredicateIndexItems(model, srsURI);
- items.addAll(geoPredicateItems);
- }
-
- return items;
- }
-
- /**
- *
- * @param model
- * @param srsURI
- * @return GeometryLiteral items prepared for adding to SpatialIndex.
- * @throws SpatialIndexException
- */
- private static Collection<SpatialIndexItem>
getGeometryLiteralIndexItems(Model model, String srsURI) throws
SpatialIndexException {
- List<SpatialIndexItem> items = new ArrayList<>();
- StmtIterator stmtIt = model.listStatements(null,
Geo.HAS_GEOMETRY_PROP, (Resource) null);
- while (stmtIt.hasNext()) {
- Statement stmt = stmtIt.nextStatement();
-
- Resource feature = stmt.getSubject();
- Resource geometry = stmt.getResource();
-
- ExtendedIterator<RDFNode> nodeIter =
model.listObjectsOfProperty(geometry, Geo.HAS_SERIALIZATION_PROP);
- if (!nodeIter.hasNext()) {
- NodeIterator wktNodeIter =
model.listObjectsOfProperty(geometry, Geo.AS_WKT_PROP);
- NodeIterator gmlNodeIter =
model.listObjectsOfProperty(geometry, Geo.AS_GML_PROP);
- nodeIter = wktNodeIter.andThen(gmlNodeIter);
- }
-
- while (nodeIter.hasNext()) {
- Literal geometryLiteral = nodeIter.next().asLiteral();
- GeometryWrapper geometryWrapper =
GeometryWrapper.extract(geometryLiteral);
-
- try {
- //Ensure all entries in the target SRS URI.
- GeometryWrapper transformedGeometryWrapper =
geometryWrapper.convertSRS(srsURI);
-
- Envelope envelope =
transformedGeometryWrapper.getEnvelope();
- SpatialIndexItem item = new SpatialIndexItem(envelope,
feature);
- items.add(item);
- } catch (FactoryException | MismatchedDimensionException |
TransformException ex) {
- throw new SpatialIndexException("Transformation Exception:
" + geometryLiteral + ". " + ex.getMessage());
- }
-
- }
- }
- return items;
- }
-
- /**
- *
- * @param model
- * @param srsURI
- * @return Geo predicate objects prepared for adding to SpatialIndex.
- */
- private static Collection<SpatialIndexItem>
getGeoPredicateIndexItems(Model model, String srsURI) throws
SpatialIndexException {
- List<SpatialIndexItem> items = new ArrayList<>();
- ResIterator resIt =
model.listResourcesWithProperty(SpatialExtension.GEO_LAT_PROP);
-
- while (resIt.hasNext()) {
- Resource feature = resIt.nextResource();
-
- Literal lat =
feature.getRequiredProperty(SpatialExtension.GEO_LAT_PROP).getLiteral();
- Literal lon =
feature.getProperty(SpatialExtension.GEO_LON_PROP).getLiteral();
- if (lon == null) {
- LOGGER.warn("Geo predicates: latitude found but not longitude.
" + feature);
- continue;
- }
-
- Literal latLonPoint = ConvertLatLon.toLiteral(lat.getFloat(),
lon.getFloat());
- GeometryWrapper geometryWrapper =
GeometryWrapper.extract(latLonPoint);
-
- try {
- //Ensure all entries in the target SRS URI.
- GeometryWrapper transformedGeometryWrapper =
geometryWrapper.convertSRS(srsURI);
-
- Envelope envelope = transformedGeometryWrapper.getEnvelope();
- SpatialIndexItem item = new SpatialIndexItem(envelope,
feature);
- items.add(item);
- } catch (FactoryException | MismatchedDimensionException |
TransformException ex) {
- throw new SpatialIndexException("Transformation Exception: " +
geometryWrapper.getLexicalForm() + ". " + ex.getMessage());
- }
- }
- return items;
- }
-
- /**
- * Load a SpatialIndex from file.<br>
- * Index will be built and empty if file does not exist or is null.
- *
- * @param spatialIndexFile
- * @return Built Spatial Index.
- * @throws SpatialIndexException
- */
- public static final SpatialIndex load(File spatialIndexFile) throws
SpatialIndexException {
-
- if (spatialIndexFile != null && spatialIndexFile.exists()) {
- LOGGER.info("Loading Spatial Index - Started: {}",
spatialIndexFile.getAbsolutePath());
- //Cannot directly store the SpatialIndex due to Resources not
being serializable, use SpatialIndexStorage class.
- try (ObjectInputStream in = new ObjectInputStream(new
FileInputStream(spatialIndexFile))) {
- SpatialIndexStorage storage = (SpatialIndexStorage)
in.readObject();
-
- SpatialIndex spatialIndex = storage.getSpatialIndex();
- LOGGER.info("Loading Spatial Index - Completed: {}",
spatialIndexFile.getAbsolutePath());
- return spatialIndex;
- } catch (ClassNotFoundException | IOException ex) {
- throw new SpatialIndexException("Loading Exception: " +
ex.getMessage(), ex);
- }
- } else {
- return new SpatialIndex();
- }
- }
-
- /**
- * Save SpatialIndex contents to file.
- *
- * @param spatialIndexFileURI
- * @param spatialIndexItems
- * @param srsURI
- * @throws SpatialIndexException
- */
- public static final void save(String spatialIndexFileURI,
Collection<SpatialIndexItem> spatialIndexItems, String srsURI) throws
SpatialIndexException {
- save(new File(spatialIndexFileURI), spatialIndexItems, srsURI);
- }
-
- /**
- * Save SpatialIndex contents to file.
+ * The default graph can be referenced with null or any value for which
{@link Quad#isDefaultGraph()} returns true.
+ * The union graph (= all named graphs but not the default graph) can be
referenced with {@link Quad#unionGraph}.
*
- * @param spatialIndexFile
- * @param spatialIndexItems
- * @param srsURI
- * @throws SpatialIndexException
+ * @param searchEnvelope
+ * @param graph
+ * @return
Review Comment:
Incomplete javadoc. `@return` needs a type.
##########
jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/index/v1/SpatialIndexV1.java:
##########
@@ -0,0 +1,577 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.jena.geosparql.spatial.index.v1;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.lang.invoke.MethodHandles;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.jena.atlas.RuntimeIOException;
+import org.apache.jena.atlas.io.IOX;
+import org.apache.jena.geosparql.configuration.GeoSPARQLOperations;
+import org.apache.jena.geosparql.implementation.GeometryWrapper;
+import org.apache.jena.geosparql.implementation.SRSInfo;
+import org.apache.jena.geosparql.implementation.registry.SRSRegistry;
+import org.apache.jena.geosparql.implementation.vocabulary.Geo;
+import org.apache.jena.geosparql.implementation.vocabulary.SRS_URI;
+import org.apache.jena.geosparql.implementation.vocabulary.SpatialExtension;
+import org.apache.jena.geosparql.spatial.ConvertLatLon;
+import org.apache.jena.geosparql.spatial.SpatialIndex;
+import org.apache.jena.geosparql.spatial.SpatialIndexException;
+import org.apache.jena.geosparql.spatial.SpatialIndexItem;
+import org.apache.jena.geosparql.spatial.SpatialIndexStorage;
+import org.apache.jena.geosparql.spatial.index.v2.SpatialIndexUtils;
+import org.apache.jena.query.Dataset;
+import org.apache.jena.query.DatasetFactory;
+import org.apache.jena.query.ReadWrite;
+import org.apache.jena.rdf.model.Literal;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.NodeIterator;
+import org.apache.jena.rdf.model.RDFNode;
+import org.apache.jena.rdf.model.ResIterator;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.Statement;
+import org.apache.jena.rdf.model.StmtIterator;
+import org.apache.jena.sparql.engine.ExecutionContext;
+import org.apache.jena.sparql.util.Context;
+import org.apache.jena.sparql.util.ModelUtils;
+import org.apache.jena.util.iterator.ExtendedIterator;
+import org.locationtech.jts.geom.Envelope;
+import org.locationtech.jts.index.strtree.STRtree;
+import org.opengis.geometry.MismatchedDimensionException;
+import org.opengis.referencing.operation.TransformException;
+import org.opengis.util.FactoryException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * SpatialIndex for testing bounding box collisions between geometries within a
+ * Dataset.<br>
+ * Queries must be performed using the same SRS URI as the SpatialIndex.<br>
+ * The SpatialIndex is added to the Dataset Context when it is built.<br>
+ * QueryRewriteIndex is also stored in the SpatialIndex as its content is
+ * Dataset specific.
+ */
+@Deprecated /** Superseded by {@link SpatialIndex} and {@link
SpatialIndexPerGraph}. */
Review Comment:
There isn't a `SpatialIndexPerGraph`.
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