Jackson deserialization for PreferenceStore

main/src/com/google/refine/commands/SetPreferenceCommand.java

@@ -42,9 +42,11 @@ import javax.servlet.http.HttpServletResponse;
 import org.json.JSONException;
 import org.json.JSONTokener;
 
+import com.fasterxml.jackson.databind.JsonNode;
 import com.google.refine.ProjectManager;
 import com.google.refine.model.Project;
 import com.google.refine.preference.PreferenceStore;
+import com.google.refine.util.ParsingUtilities;
 
 public class SetPreferenceCommand extends Command {
     @Override
@@ -58,12 +60,12 @@ public class SetPreferenceCommand extends Command {
         String valueString = request.getParameter("value");
         
         try {
-            Object o = valueString == null ? null : new JSONTokener(valueString).nextValue();
+            JsonNode o = valueString == null ? null : ParsingUtilities.mapper.readTree(valueString);
             
             ps.put(prefName, PreferenceStore.loadObject(o));
             
             respond(response, "{ \"code\" : \"ok\" }");
-        } catch (JSONException e) {
+        } catch (IOException e) {
             respondException(response, e);
         }
     }

main/src/com/google/refine/io/FileProjectManager.java

@@ -67,6 +67,7 @@ import com.google.refine.model.metadata.DataPackageMetadata;
 import com.google.refine.model.metadata.IMetadata;
 import com.google.refine.model.metadata.MetadataFormat;
 import com.google.refine.model.metadata.ProjectMetadata;
+import com.google.refine.preference.PreferenceStore;
 import com.google.refine.preference.TopList;
 import com.google.refine.util.ParsingUtilities;
 
@@ -386,7 +387,7 @@ public class FileProjectManager extends ProjectManager  {
                 
                 // load global preferences firstly
                 if (obj.has("preferences") && !obj.isNull("preferences")) {
-                    _preferenceStore.load(obj.getJSONObject("preferences"));
+                    _preferenceStore = ParsingUtilities.mapper.readValue(obj.getJSONObject("preferences").toString(), PreferenceStore.class);
                 }
 
                 JSONArray a = obj.getJSONArray("projectIDs");
@@ -413,8 +414,8 @@ public class FileProjectManager extends ProjectManager  {
                 }
 
                 if (obj.has("expressions") && !obj.isNull("expressions")) { // backward compatibility
-                    ((TopList) _preferenceStore.get("scripting.expressions"))
+                	TopList newExpressions = ParsingUtilities.mapper.readValue(obj.getJSONArray("expressions").toString(), TopList.class);
-                    .load(obj.getJSONArray("expressions"));
+                    this._preferenceStore.put("scripting.expressions", newExpressions);
                 }
 
                 found = true;

main/src/com/google/refine/model/metadata/ProjectMetadata.java

@@ -205,16 +205,17 @@ public class ProjectMetadata  extends AbstractMetadata {
 
         if (obj.has("preferences") && !obj.isNull("preferences")) {
             try {
-                this._preferenceStore.load(obj.getJSONObject("preferences"));
+                this._preferenceStore = ParsingUtilities.mapper.readValue(obj.getJSONObject("preferences").toString(), PreferenceStore.class);
-            } catch (JSONException e) {
+            } catch (IOException e) {
                 logger.error(ExceptionUtils.getStackTrace(e));
             }
         }
 
         if (obj.has("expressions") && !obj.isNull("expressions")) { // backward compatibility
             try {
-                ((TopList) this._preferenceStore.get("scripting.expressions")).load(obj.getJSONArray("expressions"));
+            	TopList newExpressions = ParsingUtilities.mapper.readValue(obj.getJSONArray("expressions").toString(), TopList.class);
-            } catch (JSONException e) {
+                this._preferenceStore.put("scripting.expressions", newExpressions);
+            } catch (IOException e) {
                 logger.error(ExceptionUtils.getStackTrace(e));
             }
         }

main/src/com/google/refine/preference/PreferenceStore.java

@@ -34,7 +34,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 package com.google.refine.preference;
 
 import java.io.IOException;
-import java.lang.reflect.Method;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.Map;
@@ -50,8 +49,9 @@ import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
-
+import com.fasterxml.jackson.databind.node.ArrayNode;
-import com.google.refine.RefineServlet;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.google.refine.util.ParsingUtilities;
 
 public class PreferenceStore  {
     public static final String USER_METADATA_KEY = "userMetadata";
@@ -63,7 +63,6 @@ public class PreferenceStore  {
     protected Map<String, Object> _prefs = new HashMap<>();
     
     // Temporary wrapper while serialization has not been migrated yet.
-    @JsonProperty("entries")
     protected Map<String, Object> _prefsJackson = new HashMap<>();
     
     public void put(String key, Object value) {
@@ -119,39 +118,43 @@ public class PreferenceStore  {
         return null;
     }
     
-    @SuppressWarnings("unchecked")
+    @JsonProperty("entries")
-    public void load(JSONObject obj) throws JSONException {
+    public void setEntries(JsonNode entries) throws JSONException {
-        if (obj.has("entries") && !obj.isNull("entries")) {
+        Iterator<String> i = entries.fieldNames();
-            JSONObject entries = obj.getJSONObject("entries");
-            
-            Iterator<String> i = entries.keys();
         while (i.hasNext()) {
             String key = i.next();
-                if (!entries.isNull(key)) {
+            System.out.println(key);
-                    Object o = entries.get(key), loaded = loadObject(o);
+            if (entries.get(key) != null) {
+                JsonNode o = entries.get(key);
+                Object loaded = loadObject(o);
                 _prefs.put(key, loaded);
                 _prefsJackson.put(key, wrapJSONArray(loaded));
             }
         }
         dirty = false; // internal puts don't count
     }
+    
+    @JsonProperty("entries")
+    public Map<String, Object> getEntries() {
+    	return _prefsJackson;
     }
     
-    static public Object loadObject(Object o) {
+    static public Object loadObject(JsonNode o) {
-        if (o instanceof JSONObject) {
+    	System.out.println("loading");
+    	System.out.println(o.toString());
         try {
-                JSONObject obj2 = (JSONObject) o;
+	        if (o instanceof ObjectNode) {
-                String className = obj2.getString("class");
+                ObjectNode obj2 = (ObjectNode) o;
-                Class<?> klass = RefineServlet.getClass(className);
+                return ParsingUtilities.mapper.treeToValue(obj2, PreferenceValue.class);
-                Method method = klass.getMethod("load", JSONObject.class);
+	        } else if (o instanceof ArrayNode) {
-                
+	        	return o;
-                return method.invoke(null, obj2);
+	        } else {
+	        	// basic datatypes (int, double, boolean, string)
+	            return ParsingUtilities.mapper.treeToValue(o, Object.class);
+	        }
         } catch (Exception e) {
             e.printStackTrace();
             return null;
         }
-        } else {
-            return o;
-        }
     }
 }

main/src/com/google/refine/preference/TopList.java

@@ -38,24 +38,32 @@ import java.util.Iterator;
 import java.util.List;
 
 import org.apache.commons.collections.list.UnmodifiableList;
-import org.json.JSONArray;
-import org.json.JSONException;
-import org.json.JSONObject;
 
+import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 
-public class TopList implements Iterable<String> {
+public class TopList implements Iterable<String>, PreferenceValue {
     
     @JsonProperty("top")
-    final protected int          _top;
+    protected int          _top = 10;
-    final protected List<String> _list = new ArrayList<String>();
+    protected List<String> _list = new ArrayList<String>();
 
     public TopList(int top) {
         _top = top;
     }
     
+    @JsonCreator
+    public TopList(
+    		@JsonProperty("top")
+    		int top,
+    		@JsonProperty("list")
+    		List<String> list) {
+    	_top = top;
+    	_list = list;
+    }
+    
     @SuppressWarnings("unchecked")
     @JsonProperty("list")
     public List<String> getList() {
@@ -75,30 +83,6 @@ public class TopList implements Iterable<String> {
         _list.remove(element);
     }
     
-    @JsonProperty("class")
-    public String getClassName() {
-        return this.getClass().getName();
-    }
-    
-    static public TopList load(JSONObject obj) throws JSONException {
-        int top = obj.has("top") && !obj.isNull("top") ? obj.getInt("top") : 10;
-        TopList tl = new TopList(top);
-        
-        if (obj.has("list") && !obj.isNull("list")) {
-            JSONArray a = obj.getJSONArray("list");
-            
-            tl.load(a);
-        }
-        return tl;
-    }
-    
-    public void load(JSONArray a) throws JSONException {
-        int length = a.length();
-        for (int i = 0; i < length && _list.size() < _top; i++) {
-            _list.add(a.getString(i));
-        }
-    }
-    
     @Override
     @JsonIgnore
     public Iterator<String> iterator() {  

main/tests/server/src/com/google/refine/tests/preference/PreferenceStoreTests.java

@@ -3,12 +3,15 @@ package com.google.refine.tests.preference;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertTrue;
 
-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.preference.PreferenceStore;
-import com.google.refine.tests.RefineTest;
 import com.google.refine.tests.util.TestUtils;
+import com.google.refine.util.ParsingUtilities;
 
 public class PreferenceStoreTests {
     public static String json = "{"
@@ -21,7 +24,7 @@ public class PreferenceStoreTests {
             + "}}";
     
     @Test
-    public void serializePreferenceStore() {
+    public void serializePreferenceStore() throws JsonParseException, JsonMappingException, IOException {
  
         String jsonAfter = "{"
                 + "\"entries\":{"
@@ -32,8 +35,7 @@ public class PreferenceStoreTests {
                 + "   \"scripting.expressions\":{\"class\":\"com.google.refine.preference.TopList\",\"top\":100,\"list\":[]},"
                 + "   \"mypreference\":\"myvalue\""
                 + "}}";
-        PreferenceStore prefStore = new PreferenceStore();
+        PreferenceStore prefStore = ParsingUtilities.mapper.readValue(json, PreferenceStore.class);
-        prefStore.load(new JSONObject(json));
         assertFalse(prefStore.isDirty());
         prefStore.put("mypreference", "myvalue");
         assertTrue(prefStore.isDirty());

main/tests/server/src/com/google/refine/tests/preference/TopListTests.java

@@ -1,14 +1,18 @@
 package com.google.refine.tests.preference;
 
-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.preference.TopList;
 import com.google.refine.tests.util.TestUtils;
+import com.google.refine.util.ParsingUtilities;
 
 public class TopListTests {
     @Test
-    public void serializeTopList() {
+    public void serializeTopList() throws JsonParseException, JsonMappingException, IOException {
         String json = "{"
                 + "\"class\":\"com.google.refine.preference.TopList\","
                 + "\"top\":100,"
@@ -21,7 +25,7 @@ public class TopListTests {
                 + "   \"grel:\\\"https://pub.orcid.org/\\\"+value+\\\"/employments\\\"\""
                 + "]}";
         TestUtils.isSerializedTo(
-                TopList.load(new JSONObject(json)),
+                ParsingUtilities.mapper.readValue(json, TopList.class),
                 json);
     }
 }