Added json header to the spatial index. Header is used to configure kyro with geometrySerde.

Author: Aklakan

jena-arq/src/main/java/org/apache/jena/system/TxnCtl.java

@@ -26,7 +26,7 @@
 /**
  * Txn variant for use with try-with-resources. Allows raising
  * checked exceptions in an idiomatic way. Closing the TxnCtl
- * instance will by default abort the transaction unless it
+ * instance will abort the transaction unless it
  * has been manually committed.
  * <p>
  *
@@ -35,15 +35,14 @@
  * public void myMethod() throws IOException {
  *   try (TxnCtl txn = TxnCtl.begin(dataset, TxnType.WRITE)) {
  *     // Do work
+ *     if (someError) {
+ *         throw new IOException();
+ *     }
  *     // Must manually call commit on success.
  *     txn.commit();
  *   }
  * }
  * </pre>
- *
- * @param txn The transactional.
- * @param txnType The transaction type.
- * @return An instance of AutoCloseable that commits the transaction on success.
  */
 public class TxnCtl
     implements AutoCloseable

jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/index/v2/SpatialIndexIoKryo.java

@@ -20,9 +20,11 @@
 import java.io.IOException;
 import java.io.OutputStream;
 import java.lang.invoke.MethodHandles;
+import java.lang.reflect.InvocationTargetException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Map;
+import java.util.Objects;
 
 import org.apache.jena.atlas.RuntimeIOException;
 import org.apache.jena.atlas.io.IOX;
@@ -31,6 +33,8 @@
 import org.apache.jena.geosparql.implementation.registry.SRSRegistry;
 import org.apache.jena.geosparql.implementation.vocabulary.SRS_URI;
 import org.apache.jena.geosparql.spatial.SpatialIndexException;
+import org.apache.jena.geosparql.spatial.serde.GeometrySerdeAdapter;
+import org.apache.jena.geosparql.spatial.serde.GeometrySerdeAdapterJtsWkb;
 import org.apache.jena.geosparql.spatial.serde.JtsKryoRegistrator;
 import org.apache.jena.graph.Node;
 import org.apache.jena.query.Dataset;
@@ -41,6 +45,8 @@
 import com.esotericsoftware.kryo.Kryo;
 import com.esotericsoftware.kryo.io.Input;
 import com.esotericsoftware.kryo.io.Output;
+import com.google.gson.Gson;
+import com.google.gson.JsonObject;
 
 public class SpatialIndexIoKryo {
     private static final Logger LOGGER = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
@@ -137,20 +143,42 @@ public static final void save(Path spatialIndexFile, SpatialIndexPerGraph index)
      * @param index spatial index
      */
     public static void writeToOutputStream(OutputStream os, SpatialIndexPerGraph index) {
+        GeometrySerdeAdapter geometrySerde = new GeometrySerdeAdapterJtsWkb();
+
+        JsonObject header = new JsonObject();
+        header.addProperty("type", "jena-spatial-index");
+        header.addProperty("version", "2.0.0");
+        header.addProperty("geometrySerde", geometrySerde.getClass().getName());
+
         Kryo kryo = new Kryo();
-        JtsKryoRegistrator.registerClasses(kryo);
+        JtsKryoRegistrator.registerClasses(kryo, geometrySerde);
         try (Output output = new Output(os)) {
+            writeJson(output, header);
             writeIndex(kryo, output, index);
             output.flush();
         }
     }
 
+    public static void writeJson(Output output, JsonObject header) {
+        Gson gson = new Gson();
+        String headerStr = gson.toJson(header);
+        output.writeString(headerStr);
+    }
+
     public static void writeIndex(Kryo kryo, Output output, SpatialIndexPerGraph index) {
         kryo.writeObject(output, index.getSrsInfo().getSrsURI());
         kryo.writeObject(output, index.getIndex().getDefaultTree());
         kryo.writeClassAndObject(output, index.getIndex().getNamedTreeMap());
     }
 
+    /** Read a string from input and return it as JSON. */
+    public static JsonObject readHeader(Input input) {
+        String headerStr = input.readString();
+        Gson gson = new Gson();
+        JsonObject obj = gson.fromJson(headerStr, JsonObject.class);
+        return obj;
+    }
+
     /**
      * Load a SpatialIndex from file.<br>
      * Index will be built and empty if file does not exist or is null.
@@ -160,9 +188,6 @@ public static void writeIndex(Kryo kryo, Output output, SpatialIndexPerGraph ind
      * @throws SpatialIndexException
      */
     public static final SpatialIndexPerGraph load(Path spatialIndexFile) throws SpatialIndexException {
-        Kryo kryo = new Kryo();
-        JtsKryoRegistrator.registerClasses(kryo);
-
         String srsUri;
         STRtreePerGraph index;
 
@@ -171,6 +196,33 @@ public static final SpatialIndexPerGraph load(Path spatialIndexFile) throws Spat
             LOGGER.info("Loading Spatial Index - Started: {}", spatialIndexFile);
 
             try (Input input = new Input(Files.newInputStream(spatialIndexFile))) {
+                JsonObject header = readHeader(input);
+
+                String type = header.get("type").getAsString();
+                if (!"jena-spatial-index".equals(type)) {
+                    throw new RuntimeException("Type does not indicate a spatial index file.");
+                }
+
+                String version = header.get("version").getAsString();
+                if (!"2.0.0".equals(version)) {
+                    throw new SpatialIndexException("The version of the spatial index does not match the version of this loader class.");
+                }
+
+                // Get the geometrySerializer attribute
+                String geometrySerdeName = header.get("geometrySerde").getAsString();
+                Objects.requireNonNull(geometrySerdeName, "Field 'geometrySerde' not set.");
+
+                GeometrySerdeAdapter geometrySerde;
+                try {
+                    Class<?> geometrySerdeClass = Class.forName(geometrySerdeName);
+                    geometrySerde = (GeometrySerdeAdapter)geometrySerdeClass.getConstructor().newInstance();
+                } catch (ClassNotFoundException | InstantiationException | IllegalAccessException | IllegalArgumentException
+                        | InvocationTargetException | NoSuchMethodException | ClassCastException | SecurityException e) {
+                    throw new SpatialIndexException("Failed to load index", e);
+                }
+
+                Kryo kryo = new Kryo();
+                JtsKryoRegistrator.registerClasses(kryo, geometrySerde);
                 srsUri = kryo.readObject(input, String.class);
                 STRtree defaultGraphTree = kryo.readObject(input, STRtree.class);
                 Map<Node, STRtree> graphToTree = (Map<Node, STRtree>) kryo.readClassAndObject(input);

jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/serde/CustomGeometrySerde.java

@@ -54,9 +54,9 @@ public class CustomGeometrySerde
 
     private GeometrySerdeAdapter geometrySerdeAdapter;
 
-    public CustomGeometrySerde() {
-        this(new GeometrySerdeAdapterJtsWkb(geometryFactory));
-    }
+//    public CustomGeometrySerde() {
+//        this(new GeometrySerdeAdapterJtsWkb(geometryFactory));
+//    }
 
     public CustomGeometrySerde(GeometrySerdeAdapter geometrySerdeAdapter) {
         super();

jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/serde/CustomSpatialIndexSerde.java

@@ -27,8 +27,11 @@
 import com.esotericsoftware.kryo.io.Output;
 
 public class CustomSpatialIndexSerde extends SpatialIndexSerde {
+    protected GeometrySerde geometrySerde;
+
     public CustomSpatialIndexSerde(GeometrySerde geometrySerde) {
         super(geometrySerde);
+        this.geometrySerde = geometrySerde;
     }
 
     @Override
@@ -40,7 +43,8 @@ public void write(Kryo kryo, Output output, Object o) {
             org.locationtech.jts.index.strtree.IndexSerde indexSerde
                     = new org.locationtech.jts.index.strtree.IndexSerde();
             try {
-                FieldUtils.writeField(indexSerde, "geometrySerde", new CustomGeometrySerde(), true);
+                // FieldUtils.writeField(indexSerde, "geometrySerde", new CustomGeometrySerde(), true);
+                FieldUtils.writeField(indexSerde, "geometrySerde", geometrySerde, true);
             } catch (IllegalAccessException e) {
                 throw new RuntimeException(e);
             }
@@ -57,7 +61,8 @@ public Object read(Kryo kryo, Input input, Class aClass) {
             org.locationtech.jts.index.strtree.IndexSerde indexSerde =
                     new org.locationtech.jts.index.strtree.IndexSerde();
             try {
-                FieldUtils.writeField(indexSerde, "geometrySerde", new CustomGeometrySerde(), true);
+                // FieldUtils.writeField(indexSerde, "geometrySerde", new CustomGeometrySerde(), true);
+                FieldUtils.writeField(indexSerde, "geometrySerde", geometrySerde, true);
             } catch (IllegalAccessException e) {
                 throw new RuntimeException(e);
             }

jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/serde/GeometrySerdeAdapterJtsWkb.java

@@ -17,6 +17,8 @@
  */
 package org.apache.jena.geosparql.spatial.serde;
 
+import java.io.Serializable;
+
 import org.locationtech.jts.geom.Geometry;
 import org.locationtech.jts.geom.GeometryFactory;
 import org.locationtech.jts.io.WKBReader;
@@ -28,12 +30,16 @@
 
 /** Geometry de-/serialization via the WKB facilities of JTS. */
 public class GeometrySerdeAdapterJtsWkb
-    implements GeometrySerdeAdapter
+    implements GeometrySerdeAdapter, Serializable
 {
-    private WKBReader geometryReader;
-    private WKBWriter geometryWriter;
+    private transient WKBReader geometryReader;
+    private transient WKBWriter geometryWriter;
+
+    public GeometrySerdeAdapterJtsWkb() {
+        this(new GeometryFactory());
+    }
 
-    public GeometrySerdeAdapterJtsWkb(GeometryFactory geometryFactory) {
+    private GeometrySerdeAdapterJtsWkb(GeometryFactory geometryFactory) {
         super();
         this.geometryReader = new WKBReader(geometryFactory);
         this.geometryWriter = new WKBWriter();

jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/serde/GeometrySerdeAdapterShapeSerde.java

@@ -34,6 +34,10 @@ public class GeometrySerdeAdapterShapeSerde
 {
     protected GeometryFactory geometryFactory;
 
+    public GeometrySerdeAdapterShapeSerde() {
+        this(new GeometryFactory());
+    }
+
     public GeometrySerdeAdapterShapeSerde(GeometryFactory geometryFactory) {
         super();
         this.geometryFactory = geometryFactory;

jena-geosparql/src/main/java/org/apache/jena/geosparql/spatial/serde/JtsKryoRegistrator.java

@@ -49,8 +49,8 @@ public class JtsKryoRegistrator {
 
     final static Logger log = LoggerFactory.getLogger(JtsKryoRegistrator.class);
 
-    public static void registerClasses(Kryo kryo) {
-        GeometrySerde serializer = new CustomGeometrySerde();
+    public static void registerClasses(Kryo kryo, GeometrySerdeAdapter geometrySerde) {
+        GeometrySerde serializer = new CustomGeometrySerde(geometrySerde);
         SpatialIndexSerde indexSerializer = new CustomSpatialIndexSerde(serializer);
 
         log.debug("Registering custom serializers for geometry types");