Refactor kNNClusterer for serialization

main/src/com/google/refine/clustering/knn/kNNClusterer.java

@@ -51,10 +51,12 @@ import org.json.JSONWriter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import com.google.refine.Jsonizable;
 import com.google.refine.browsing.Engine;
 import com.google.refine.browsing.FilteredRows;
 import com.google.refine.browsing.RowVisitor;
 import com.google.refine.clustering.Clusterer;
+import com.google.refine.clustering.ClustererConfig;
 import com.google.refine.model.Cell;
 import com.google.refine.model.Project;
 import com.google.refine.model.Row;
@@ -73,7 +75,83 @@ import edu.mit.simile.vicino.distances.PPMDistance;
 
 public class kNNClusterer extends Clusterer {
     
+    public static class kNNClustererConfig extends ClustererConfig {
+        private String _distanceStr;
+        private Distance _distance;
+        private kNNClustererConfigParameters _parameters;
+        
+        @Override
+        public void write(JSONWriter writer, Properties options)
+                throws JSONException {
+            writer.object();
+            writer.key("function"); writer.value(_distanceStr);
+            writer.key("type"); writer.value("knn");
+            writer.key("column"); writer.value(getColumnName());
+            if(_parameters != null) {
+                writer.key("params");
+                _parameters.write(writer, options);
+            }
+            writer.endObject();
+        }
+        
+        public void initializeFromJSON(JSONObject o) {
+            super.initializeFromJSON(o);
+            _distanceStr = o.getString("function");
+            _distance = _distances.get(_distanceStr.toLowerCase());
+            if(o.has("params")) {
+                _parameters = kNNClustererConfigParameters.reconstruct(o.getJSONObject("params"));
+            } else {
+                _parameters = null;
+            }
+        }
+        
+        public Distance getDistance() {
+            return _distance;
+        }
+        
+        public kNNClustererConfigParameters getParameters() {
+            return _parameters;
+        }
+
+        @Override
+        public kNNClusterer apply(Project project) {
+            kNNClusterer clusterer = new kNNClusterer();
+            clusterer.initializeFromConfig(project, this);
+            return clusterer;
+        }
+        
+    }
+    
+    public static class kNNClustererConfigParameters implements Jsonizable {
+        public static final double defaultRadius = 1.0d;
+        public static final int defaultBlockingNgramSize = 6;
+        public double radius = defaultRadius;
+        public int blockingNgramSize = defaultBlockingNgramSize;
+        
+        @Override
+        public void write(JSONWriter writer, Properties options)
+                throws JSONException {
+            writer.object();
+            writer.key("radius"); writer.value(radius);
+            writer.key("blocking-ngram-size");
+            writer.value(blockingNgramSize);
+            writer.endObject();
+        }
+        
+        public static kNNClustererConfigParameters reconstruct(JSONObject o) {
+            kNNClustererConfigParameters params = new kNNClustererConfigParameters();
+            if(o.has("radius")) {
+                params.radius = o.getDouble("radius");
+            }
+            if(o.has("blocking-ngram-size")) {
+                params.blockingNgramSize = o.getInt("blocking-ngram-size");
+            }
+            return params;
+        }
+    }
+
     private Distance _distance;
+    private kNNClustererConfigParameters _params;
     
     static final protected Map<String, Distance> _distances = new HashMap<String, Distance>();
 
@@ -97,20 +175,13 @@ public class kNNClusterer extends Clusterer {
     class VPTreeClusteringRowVisitor implements RowVisitor {
 
         Distance _distance;
-        JSONObject _config;
+        kNNClustererConfigParameters _params;
         VPTreeClusterer _clusterer;
-        double _radius = 1.0f;
         
-        public VPTreeClusteringRowVisitor(Distance d, JSONObject o) {
+        public VPTreeClusteringRowVisitor(Distance d, kNNClustererConfigParameters params) {
             _distance = d;
-            _config = o;
             _clusterer = new VPTreeClusterer(_distance);
-            try {
+            _params = params;
-                JSONObject params = o.getJSONObject("params");
-                _radius = params.getDouble("radius");
-            } catch (JSONException e) {
-                //Refine.warn("No parameters found, using defaults");
-            }
         }
         
         @Override
@@ -136,32 +207,23 @@ public class kNNClusterer extends Clusterer {
         }
         
         public List<Set<Serializable>> getClusters() {
-            return _clusterer.getClusters(_radius);
+            return _clusterer.getClusters(_params.radius);
         }
     }
 
     class BlockingClusteringRowVisitor implements RowVisitor {
 
         Distance _distance;
-        JSONObject _config;
         double _radius = 1.0d;
         int _blockingNgramSize = 6;
         HashSet<String> _data;
         NGramClusterer _clusterer;
         
-        public BlockingClusteringRowVisitor(Distance d, JSONObject o) {
+        public BlockingClusteringRowVisitor(Distance d, kNNClustererConfigParameters params) {
             _distance = d;
-            _config = o;
             _data = new HashSet<String>();
-            try {
+            _blockingNgramSize = params.blockingNgramSize;
-                JSONObject params = o.getJSONObject("params");
+            _radius = params.radius;
-                _radius = params.getDouble("radius");
-                logger.debug("Use radius: {}", _radius);
-                _blockingNgramSize = params.getInt("blocking-ngram-size");
-                logger.debug("Use blocking ngram size: {}",_blockingNgramSize);
-            } catch (JSONException e) {
-                logger.debug("No parameters found, using defaults");
-            }
             _clusterer = new NGramClusterer(_distance, _blockingNgramSize);
         }
         
@@ -192,16 +254,23 @@ public class kNNClusterer extends Clusterer {
         }
     }
         
-    @Override
+    @Deprecated
     public void initializeFromJSON(Project project, JSONObject o) throws Exception {
-        super.initializeFromJSON(project, o);
+        kNNClustererConfig config = new kNNClustererConfig();
-        _distance = _distances.get(o.getString("function").toLowerCase());
+        config.initializeFromJSON(o);
+        initializeFromConfig(project, config);
+    }
+    
+    public void initializeFromConfig(Project project, kNNClustererConfig config) {
+        super.initializeFromConfig(project, config);
+        _distance = config.getDistance();
+        _params = config.getParameters();
     }
 
     @Override
     public void computeClusters(Engine engine) {
         //VPTreeClusteringRowVisitor visitor = new VPTreeClusteringRowVisitor(_distance,_config);
-        BlockingClusteringRowVisitor visitor = new BlockingClusteringRowVisitor(_distance,_config);
+        BlockingClusteringRowVisitor visitor = new BlockingClusteringRowVisitor(_distance,_params);
         FilteredRows filteredRows = engine.getAllFilteredRows();
         filteredRows.accept(_project, visitor);
      

main/tests/server/src/com/google/refine/tests/clustering/kNNClustererTests.java

@@ -0,0 +1,47 @@
+package com.google.refine.tests.clustering;
+
+import org.json.JSONObject;
+import org.testng.annotations.Test;
+
+import com.google.refine.browsing.Engine;
+import com.google.refine.clustering.knn.kNNClusterer;
+import com.google.refine.clustering.knn.kNNClusterer.kNNClustererConfig;
+import com.google.refine.model.Project;
+import com.google.refine.tests.RefineTest;
+import com.google.refine.tests.util.TestUtils;
+
+public class kNNClustererTests extends RefineTest {
+    
+    public static String configJson = "{"
+            + "\"type\":\"knn\","
+            + "\"function\":\"PPM\","
+            + "\"column\":\"values\","
+            + "\"params\":{\"radius\":1,\"blocking-ngram-size\":2}"
+            + "}";
+    public static String clustererJson = "["
+            + "   [{\"v\":\"ab\",\"c\":1},{\"v\":\"abc\",\"c\":1}]"
+            + "]";
+    
+    @Test
+    public void serializekNNClustererConfig() {
+        kNNClustererConfig config = new kNNClustererConfig();
+        config.initializeFromJSON(new JSONObject(configJson));
+        TestUtils.isSerializedTo(config, configJson);
+    }
+    
+    @Test
+    public void serializekNNClusterer() {
+        Project project = createCSVProject("column\n"
+                + "ab\n"
+                + "abc\n"
+                + "c\n"
+                + "ĉ\n");
+        
+        kNNClustererConfig config = new kNNClustererConfig();
+        config.initializeFromJSON(new JSONObject(configJson));
+        kNNClusterer clusterer = config.apply(project);
+        clusterer.computeClusters(new Engine(project));
+        
+        TestUtils.isSerializedTo(clusterer, clustererJson);
+    }
+}