Clustering config Jackson deserialization

main/src/com/google/refine/clustering/ClustererConfig.java

@@ -1,8 +1,11 @@
 package com.google.refine.clustering;
 
-import org.json.JSONObject;
-
 import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonSubTypes;
+import com.fasterxml.jackson.annotation.JsonSubTypes.Type;
+import com.fasterxml.jackson.annotation.JsonTypeInfo;
+import com.google.refine.clustering.binning.BinningClusterer.BinningClustererConfig;
+import com.google.refine.clustering.knn.kNNClusterer.kNNClustererConfig;
 import com.google.refine.model.Project;
 
 /**
@@ -10,23 +13,27 @@ import com.google.refine.model.Project;
  * @author Antonin Delpeuch
  *
  */
+@JsonTypeInfo(
+        use=JsonTypeInfo.Id.NAME,
+        include=JsonTypeInfo.As.PROPERTY,
+        property="type")
+@JsonSubTypes({
+    @Type(value = kNNClustererConfig.class, name = "knn"),
+    @Type(value = BinningClustererConfig.class, name = "binning") })
 public abstract class ClustererConfig  {
     
     protected String columnName;
     
-    /**
-     * Reads the configuration from a JSON payload (TODO: delete)
-     * @param o
-     */
-    public void initializeFromJSON(JSONObject o) {
-        columnName = o.getString("column");
-    }
-    
     @JsonProperty("column")
     public String getColumnName() {
         return columnName;
     }
     
+    @JsonProperty("column")
+    public void setColumnName(String name) {
+    	columnName = name;
+    }
+    
     /**
      * Instantiate the configuration on a particular project.
      * @param project

main/src/com/google/refine/clustering/binning/BinningClusterer.java

@@ -44,7 +44,6 @@ import java.util.Map.Entry;
 import java.util.TreeMap;
 import java.util.stream.Collectors;
 
-import org.json.JSONObject;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -67,33 +66,39 @@ public class BinningClusterer extends Clusterer {
     
     public static class BinningClustererConfig extends ClustererConfig {
        
-        @JsonProperty("function")
+        @JsonIgnore
         private String _keyerName;
+        @JsonIgnore
         private Keyer _keyer;
-        private BinningParameters _parameters;
+        @JsonIgnore
-        
+        private BinningParameters _parameters = null;
-        @Override
-        public void initializeFromJSON(JSONObject o) {
-            super.initializeFromJSON(o);
-            _keyerName = o.getString("function");
-            _keyer = _keyers.get(_keyerName.toLowerCase());
-            if(o.has("params")) {
-                _parameters = BinningParameters.reconstruct(o.getJSONObject("params"));
-            } else {
-                _parameters = null;
-            }
-        }
         
         @JsonIgnore
         public Keyer getKeyer() {
             return _keyer;
         }
         
+        @JsonProperty("function")
+        public void setKeyer(String keyerName) {
+        	_keyerName = keyerName;
+        	_keyer = _keyers.get(_keyerName.toLowerCase());
+        }
+        
+        @JsonProperty("function")
+        public String getKeyerName() {
+        	return _keyerName;
+        }
+        
         @JsonProperty("params")
         @JsonInclude(Include.NON_NULL)
         public BinningParameters getParameters() {
             return _parameters;
         }
+        
+        @JsonProperty("params")
+        public void setParameters(BinningParameters params) {
+        	_parameters = params;
+        }
 
         @Override
         public BinningClusterer apply(Project project) {
@@ -112,13 +117,7 @@ public class BinningClusterer extends Clusterer {
     public static class BinningParameters  {
         @JsonProperty("ngram-size")
         @JsonInclude(Include.NON_DEFAULT)
-        public int ngramSize;
+        public int ngramSize = 0;
-        
-        public static BinningParameters reconstruct(JSONObject o) {
-            BinningParameters parameters = new BinningParameters();
-            parameters.ngramSize = o.has("ngram-size") ? o.getInt("ngram-size") : 0;
-            return parameters;
-        }
     }
 
     protected Keyer _keyer;

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

@@ -43,7 +43,6 @@ import java.util.Map.Entry;
 import java.util.Set;
 import java.util.stream.Collectors;
 
-import org.json.JSONObject;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -75,31 +74,38 @@ import edu.mit.simile.vicino.distances.PPMDistance;
 public class kNNClusterer extends Clusterer {
     
     public static class kNNClustererConfig extends ClustererConfig {
-        @JsonProperty("function")
+        @JsonIgnore
         private String _distanceStr;
+        @JsonIgnore
         private Distance _distance;
-        private kNNClustererConfigParameters _parameters;
+        @JsonIgnore
-
+        private kNNClustererConfigParameters _parameters = null;
-        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;
-            }
-        }
         
         @JsonIgnore
         public Distance getDistance() {
             return _distance;
         }
         
+        @JsonProperty("function")
+        public void setDistance(String distanceStr) {
+        	_distanceStr = distanceStr;
+        	_distance = _distances.get(_distanceStr.toLowerCase());
+        }
+        
+        @JsonProperty("function")
+        public String getDistanceStr() {
+        	return _distanceStr;
+        }
+        
         @JsonProperty("params")
         public kNNClustererConfigParameters getParameters() {
             return _parameters;
         }
+        
+        @JsonProperty("params")
+        public void setParameters(kNNClustererConfigParameters params) {
+        	_parameters = params;
+        }
 
         @Override
         public kNNClusterer apply(Project project) {
@@ -122,17 +128,6 @@ public class kNNClusterer extends Clusterer {
         public double radius = defaultRadius;
         @JsonProperty("blocking-ngram-size")
         public int blockingNgramSize = defaultBlockingNgramSize;
-        
-        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;

main/src/com/google/refine/commands/browsing/ComputeClustersCommand.java

@@ -39,17 +39,15 @@ import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.json.JSONObject;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import com.google.refine.browsing.Engine;
 import com.google.refine.clustering.Clusterer;
 import com.google.refine.clustering.ClustererConfig;
-import com.google.refine.clustering.binning.BinningClusterer.BinningClustererConfig;
-import com.google.refine.clustering.knn.kNNClusterer.kNNClustererConfig;
 import com.google.refine.commands.Command;
 import com.google.refine.model.Project;
+import com.google.refine.util.ParsingUtilities;
 
 public class ComputeClustersCommand extends Command {
 
@@ -63,24 +61,15 @@ public class ComputeClustersCommand extends Command {
             long start = System.currentTimeMillis();
             Project project = getProject(request);
             Engine engine = getEngine(request, project);
-            JSONObject clusterer_conf = getJsonParameter(request,"clusterer");
+            String clusterer_conf = request.getParameter("clusterer");
+            ClustererConfig clustererConfig = ParsingUtilities.mapper.readValue(clusterer_conf, ClustererConfig.class);
 
-            String type = clusterer_conf.has("type") ? clusterer_conf.getString("type") : "binning";
-            
-            ClustererConfig clustererConfig = null;
-            if ("knn".equals(type)) {
-                clustererConfig = new kNNClustererConfig();
-            } else  {
-                clustererConfig = new BinningClustererConfig();
-            }
-                
-            clustererConfig.initializeFromJSON(clusterer_conf);
             Clusterer clusterer = clustererConfig.apply(project);
             
             clusterer.computeClusters(engine);
             
             respondJSON(response, clusterer);
-            logger.info("computed clusters [{},{}] in {}ms", new Object[] { type, clusterer_conf.getString("function"), Long.toString(System.currentTimeMillis() - start) });
+            logger.info("computed clusters [{}] in {}ms", new Object[] { clustererConfig.getType(), Long.toString(System.currentTimeMillis() - start) });
         } catch (Exception e) {
             respondException(response, e);
         }

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

@@ -1,14 +1,18 @@
 package com.google.refine.tests.clustering;
 
-import org.json.JSONObject;
+import java.io.IOException;
+
 import org.testng.annotations.Test;
 
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.databind.JsonMappingException;
 import com.google.refine.browsing.Engine;
 import com.google.refine.clustering.binning.BinningClusterer;
 import com.google.refine.clustering.binning.BinningClusterer.BinningClustererConfig;
 import com.google.refine.model.Project;
 import com.google.refine.tests.RefineTest;
 import com.google.refine.tests.util.TestUtils;
+import com.google.refine.util.ParsingUtilities;
 
 public class BinningClustererTests extends RefineTest {
     
@@ -30,28 +34,25 @@ public class BinningClustererTests extends RefineTest {
             + "]";
     
     @Test
-    public void testSerializeBinningClustererConfig() {
+    public void testSerializeBinningClustererConfig() throws JsonParseException, JsonMappingException, IOException {
-        BinningClustererConfig config = new BinningClustererConfig();
+        BinningClustererConfig config = ParsingUtilities.mapper.readValue(configJson, BinningClustererConfig.class);
-        config.initializeFromJSON(new JSONObject(configJson));
         TestUtils.isSerializedTo(config, configJson);
     }
     
     @Test
-    public void testSerializeBinningClustererConfigWithNgrams() {
+    public void testSerializeBinningClustererConfigWithNgrams() throws JsonParseException, JsonMappingException, IOException {
-        BinningClustererConfig config = new BinningClustererConfig();
+        BinningClustererConfig config = ParsingUtilities.mapper.readValue(configNgramJson, BinningClustererConfig.class);
-        config.initializeFromJSON(new JSONObject(configNgramJson));
         TestUtils.isSerializedTo(config, configNgramJson);
     }
 
     @Test
-    public void testSerializeBinningClusterer() {
+    public void testSerializeBinningClusterer() throws JsonParseException, JsonMappingException, IOException {
         Project project = createCSVProject("column\n"
                 + "a\n"
                 + "à\n"
                 + "c\n"
                 + "ĉ\n");
-        BinningClustererConfig config = new BinningClustererConfig();
+        BinningClustererConfig config = ParsingUtilities.mapper.readValue(configJson, BinningClustererConfig.class);
-        config.initializeFromJSON(new JSONObject(configJson));
         BinningClusterer clusterer = config.apply(project);
         clusterer.computeClusters(new Engine(project));
         TestUtils.isSerializedTo(clusterer, clustererJson);

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

@@ -1,14 +1,18 @@
 package com.google.refine.tests.clustering;
 
-import org.json.JSONObject;
+import java.io.IOException;
+
 import org.testng.annotations.Test;
 
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.databind.JsonMappingException;
 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;
+import com.google.refine.util.ParsingUtilities;
 
 public class kNNClustererTests extends RefineTest {
     
@@ -23,22 +27,20 @@ public class kNNClustererTests extends RefineTest {
             + "]";
     
     @Test
-    public void serializekNNClustererConfig() {
+    public void serializekNNClustererConfig() throws JsonParseException, JsonMappingException, IOException {
-        kNNClustererConfig config = new kNNClustererConfig();
+        kNNClustererConfig config = ParsingUtilities.mapper.readValue(configJson, kNNClustererConfig.class);
-        config.initializeFromJSON(new JSONObject(configJson));
         TestUtils.isSerializedTo(config, configJson);
     }
     
     @Test
-    public void serializekNNClusterer() {
+    public void serializekNNClusterer() throws JsonParseException, JsonMappingException, IOException {
         Project project = createCSVProject("column\n"
                 + "ab\n"
                 + "abc\n"
                 + "c\n"
                 + "ĉ\n");
         
-        kNNClustererConfig config = new kNNClustererConfig();
+        kNNClustererConfig config = ParsingUtilities.mapper.readValue(configJson, kNNClustererConfig.class);
-        config.initializeFromJSON(new JSONObject(configJson));
         kNNClusterer clusterer = config.apply(project);
         clusterer.computeClusters(new Engine(project));