Arbiter generic JSON ser/de fixes (#237)

* Arbiter generic JSON ser/de fixes

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* Javadoc fix

Signed-off-by: AlexDBlack <blacka101@gmail.com>

arbiter/arbiter-core/src/main/java/org/deeplearning4j/arbiter/optimize/parameter/FixedValue.java

@@ -17,13 +17,14 @@
 package org.deeplearning4j.arbiter.optimize.parameter;
 
 import lombok.EqualsAndHashCode;
+import lombok.Getter;
 import org.deeplearning4j.arbiter.optimize.api.ParameterSpace;
-import org.deeplearning4j.arbiter.optimize.serde.jackson.GenericDeserializer;
+import org.deeplearning4j.arbiter.optimize.serde.jackson.FixedValueDeserializer;
-import org.deeplearning4j.arbiter.optimize.serde.jackson.GenericSerializer;
+import org.deeplearning4j.arbiter.optimize.serde.jackson.FixedValueSerializer;
 import org.deeplearning4j.arbiter.util.ObjectUtils;
 import org.nd4j.shade.jackson.annotation.JsonCreator;
-import org.nd4j.shade.jackson.annotation.JsonIgnoreProperties;
 import org.nd4j.shade.jackson.annotation.JsonProperty;
+import org.nd4j.shade.jackson.annotation.JsonTypeInfo;
 import org.nd4j.shade.jackson.databind.annotation.JsonDeserialize;
 import org.nd4j.shade.jackson.databind.annotation.JsonSerialize;
 
@@ -37,9 +38,11 @@ import java.util.Map;
  * @param <T> Type of (fixed) value
  */
 @EqualsAndHashCode
+@JsonSerialize(using = FixedValueSerializer.class)
+@JsonDeserialize(using = FixedValueDeserializer.class)
+@JsonTypeInfo(use = JsonTypeInfo.Id.CLASS, include = JsonTypeInfo.As.PROPERTY, property = "@class")
 public class FixedValue<T> implements ParameterSpace<T> {
-    @JsonSerialize(using = GenericSerializer.class)
+    @Getter
-    @JsonDeserialize(using = GenericDeserializer.class)
     private Object value;
     private int index;
 

arbiter/arbiter-core/src/main/java/org/deeplearning4j/arbiter/optimize/serde/jackson/FixedValueDeserializer.java

@@ -0,0 +1,52 @@
+package org.deeplearning4j.arbiter.optimize.serde.jackson;
+
+import org.apache.commons.codec.binary.Base64;
+import org.deeplearning4j.arbiter.optimize.parameter.FixedValue;
+import org.nd4j.shade.jackson.core.JsonParser;
+import org.nd4j.shade.jackson.core.JsonProcessingException;
+import org.nd4j.shade.jackson.databind.DeserializationContext;
+import org.nd4j.shade.jackson.databind.JsonDeserializer;
+import org.nd4j.shade.jackson.databind.JsonNode;
+import org.nd4j.shade.jackson.databind.ObjectMapper;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+
+/**
+ * A custom deserializer to be used in conjunction with {@link FixedValueSerializer}
+ * @author Alex Black
+ */
+public class FixedValueDeserializer extends JsonDeserializer<FixedValue> {
+    @Override
+    public FixedValue deserialize(JsonParser p, DeserializationContext deserializationContext) throws IOException, JsonProcessingException {
+        JsonNode node = p.getCodec().readTree(p);
+        String className = node.get("@valueclass").asText();
+        Class<?> c;
+        try {
+            c = Class.forName(className);
+        } catch (Exception e) {
+            throw new RuntimeException(e);
+        }
+
+        if(node.has("value")){
+            //Number, String, Enum
+            JsonNode valueNode = node.get("value");
+            Object o = new ObjectMapper().treeToValue(valueNode, c);
+            return new FixedValue<>(o);
+        } else {
+            //Everything else
+            JsonNode valueNode = node.get("data");
+            String data = valueNode.asText();
+
+            byte[] b = new Base64().decode(data);
+            ObjectInputStream ois = new ObjectInputStream(new ByteArrayInputStream(b));
+            try {
+                Object o = ois.readObject();
+                return new FixedValue<>(o);
+            } catch (Throwable t) {
+                throw new RuntimeException(t);
+            }
+        }
+    }
+}

arbiter/arbiter-core/src/main/java/org/deeplearning4j/arbiter/optimize/serde/jackson/FixedValueSerializer.java

@@ -0,0 +1,51 @@
+package org.deeplearning4j.arbiter.optimize.serde.jackson;
+
+import org.apache.commons.net.util.Base64;
+import org.deeplearning4j.arbiter.optimize.parameter.FixedValue;
+import org.nd4j.shade.jackson.core.JsonGenerator;
+import org.nd4j.shade.jackson.core.type.WritableTypeId;
+import org.nd4j.shade.jackson.databind.JsonSerializer;
+import org.nd4j.shade.jackson.databind.SerializerProvider;
+import org.nd4j.shade.jackson.databind.jsontype.TypeSerializer;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.ObjectOutputStream;
+
+import static org.nd4j.shade.jackson.core.JsonToken.START_OBJECT;
+
+/**
+ * A custom serializer to handle arbitrary object types
+ * Uses standard JSON where safe (number, string, enumerations) or Java object serialization (bytes -> base64)
+ * The latter is not an ideal approach, but Jackson doesn't support serialization/deserialization of arbitrary
+ * objects very well
+ *
+ * @author Alex Black
+ */
+public class FixedValueSerializer extends JsonSerializer<FixedValue> {
+    @Override
+    public void serialize(FixedValue fixedValue, JsonGenerator j, SerializerProvider serializerProvider) throws IOException {
+        Object o = fixedValue.getValue();
+
+        j.writeStringField("@valueclass", o.getClass().getName());
+        if(o instanceof Number || o instanceof String || o instanceof Enum){
+            j.writeObjectField("value", o);
+        } else {
+            ByteArrayOutputStream baos = new ByteArrayOutputStream();
+            ObjectOutputStream oos = new ObjectOutputStream(baos);
+            oos.writeObject(o);
+            baos.close();
+            byte[] b = baos.toByteArray();
+            String base64 = new Base64().encodeToString(b);
+            j.writeStringField("data", base64);
+        }
+    }
+
+    @Override
+    public void serializeWithType(FixedValue value, JsonGenerator gen, SerializerProvider serializers, TypeSerializer typeSer) throws IOException {
+        WritableTypeId typeId = typeSer.typeId(value, START_OBJECT);
+        typeSer.writeTypePrefix(gen, typeId);
+        serialize(value, gen, serializers);
+        typeSer.writeTypeSuffix(gen, typeId);
+    }
+}

arbiter/arbiter-core/src/main/java/org/deeplearning4j/arbiter/optimize/serde/jackson/GenericDeserializer.java

@@ -1,46 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2015-2018 Skymind, Inc.
- *
- * This program and the accompanying materials are made available under the
- * terms of the Apache License, Version 2.0 which is available at
- * https://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.
- *
- * SPDX-License-Identifier: Apache-2.0
- ******************************************************************************/
-
-package org.deeplearning4j.arbiter.optimize.serde.jackson;
-
-import org.nd4j.shade.jackson.core.JsonParser;
-import org.nd4j.shade.jackson.databind.DeserializationContext;
-import org.nd4j.shade.jackson.databind.JsonDeserializer;
-import org.nd4j.shade.jackson.databind.JsonNode;
-import org.nd4j.shade.jackson.databind.ObjectMapper;
-
-import java.io.IOException;
-
-/**
- * Created by Alex on 15/02/2017.
- */
-public class GenericDeserializer extends JsonDeserializer<Object> {
-    @Override
-    public Object deserialize(JsonParser p, DeserializationContext ctxt) throws IOException {
-        JsonNode node = p.getCodec().readTree(p);
-        String className = node.get("@class").asText();
-        Class<?> c;
-        try {
-            c = Class.forName(className);
-        } catch (Exception e) {
-            throw new RuntimeException(e);
-        }
-
-        JsonNode valueNode = node.get("value");
-        Object o = new ObjectMapper().treeToValue(valueNode, c);
-        return o;
-    }
-}

arbiter/arbiter-core/src/main/java/org/deeplearning4j/arbiter/optimize/serde/jackson/GenericSerializer.java

@@ -1,38 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2015-2018 Skymind, Inc.
- *
- * This program and the accompanying materials are made available under the
- * terms of the Apache License, Version 2.0 which is available at
- * https://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.
- *
- * SPDX-License-Identifier: Apache-2.0
- ******************************************************************************/
-
-package org.deeplearning4j.arbiter.optimize.serde.jackson;
-
-import org.nd4j.shade.jackson.core.JsonGenerator;
-import org.nd4j.shade.jackson.core.JsonProcessingException;
-import org.nd4j.shade.jackson.databind.JsonSerializer;
-import org.nd4j.shade.jackson.databind.SerializerProvider;
-
-import java.io.IOException;
-
-/**
- * Created by Alex on 15/02/2017.
- */
-public class GenericSerializer extends JsonSerializer<Object> {
-    @Override
-    public void serialize(Object o, JsonGenerator j, SerializerProvider serializerProvider)
-                    throws IOException, JsonProcessingException {
-        j.writeStartObject();
-        j.writeStringField("@class", o.getClass().getName());
-        j.writeObjectField("value", o);
-        j.writeEndObject();
-    }
-}

arbiter/arbiter-core/src/main/java/org/deeplearning4j/arbiter/optimize/serde/jackson/JsonMapper.java

@@ -24,9 +24,6 @@ import org.nd4j.shade.jackson.databind.SerializationFeature;
 import org.nd4j.shade.jackson.dataformat.yaml.YAMLFactory;
 import org.nd4j.shade.jackson.datatype.joda.JodaModule;
 
-import java.util.Collections;
-import java.util.Map;
-
 /**
  * Created by Alex on 16/11/2016.
  */
@@ -44,6 +41,7 @@ public class JsonMapper {
         mapper.setVisibility(PropertyAccessor.ALL, JsonAutoDetect.Visibility.NONE);
         mapper.setVisibility(PropertyAccessor.FIELD, JsonAutoDetect.Visibility.ANY);
         mapper.setVisibility(PropertyAccessor.CREATOR, JsonAutoDetect.Visibility.ANY);
+        mapper.setVisibility(PropertyAccessor.SETTER, JsonAutoDetect.Visibility.ANY);
         yamlMapper = new ObjectMapper(new YAMLFactory());
         yamlMapper.registerModule(new JodaModule());
         yamlMapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);

arbiter/arbiter-deeplearning4j/src/main/java/org/deeplearning4j/arbiter/layers/BaseOutputLayerSpace.java

@@ -32,7 +32,7 @@ import org.nd4j.linalg.lossfunctions.LossFunctions.LossFunction;
  */
 @Data
 @EqualsAndHashCode(callSuper = true)
-@NoArgsConstructor(access = AccessLevel.PROTECTED) //For Jackson JSON/YAML deserialization
+@NoArgsConstructor(access = AccessLevel.PUBLIC) //For Jackson JSON/YAML deserialization
 public abstract class BaseOutputLayerSpace<L extends BaseOutputLayer> extends FeedForwardLayerSpace<L> {
 
     protected ParameterSpace<ILossFunction> lossFunction;

arbiter/arbiter-ui/src/main/java/org/deeplearning4j/arbiter/ui/data/GlobalConfigPersistable.java

@@ -18,8 +18,11 @@ package org.deeplearning4j.arbiter.ui.data;
 
 import lombok.Getter;
 import org.deeplearning4j.arbiter.optimize.config.OptimizationConfiguration;
-import org.deeplearning4j.arbiter.ui.misc.JsonMapper;
+import org.deeplearning4j.arbiter.optimize.serde.jackson.JsonMapper;
 import org.deeplearning4j.arbiter.ui.module.ArbiterModule;
+import org.deeplearning4j.nn.conf.serde.JsonMappers;
+
+import java.io.IOException;
 
 /**
  *
@@ -64,7 +67,11 @@ public class GlobalConfigPersistable extends BaseJavaPersistable {
 
 
     public OptimizationConfiguration getOptimizationConfiguration(){
-        return JsonMapper.fromJson(optimizationConfigJson, OptimizationConfiguration.class);
+        try {
+            return JsonMapper.getMapper().readValue(optimizationConfigJson, OptimizationConfiguration.class);
+        } catch (IOException e){
+            throw new RuntimeException(e);
+        }
     }
 
     public int getCandidatesQueued(){

arbiter/arbiter-ui/src/main/java/org/deeplearning4j/arbiter/ui/listener/ArbiterStatusListener.java

@@ -26,13 +26,14 @@ import org.deeplearning4j.arbiter.optimize.api.OptimizationResult;
 import org.deeplearning4j.arbiter.optimize.runner.CandidateInfo;
 import org.deeplearning4j.arbiter.optimize.runner.IOptimizationRunner;
 import org.deeplearning4j.arbiter.optimize.runner.listener.StatusListener;
+import org.deeplearning4j.arbiter.optimize.serde.jackson.JsonMapper;
 import org.deeplearning4j.arbiter.ui.data.GlobalConfigPersistable;
 import org.deeplearning4j.arbiter.ui.data.ModelInfoPersistable;
-import org.deeplearning4j.arbiter.ui.misc.JsonMapper;
 import org.deeplearning4j.nn.graph.ComputationGraph;
 import org.deeplearning4j.nn.multilayer.MultiLayerNetwork;
 import org.nd4j.linalg.primitives.Pair;
 
+import java.io.IOException;
 import java.util.Map;
 import java.util.UUID;
 import java.util.concurrent.ConcurrentHashMap;
@@ -217,7 +218,11 @@ public class ArbiterStatusListener implements StatusListener {
 //        }
         //TODO: cache global config, but we don't want to have outdated info (like uninitialized termination conditions)
 
-        ocJson = JsonMapper.asJson(r.getConfiguration());
+        try {
+            ocJson = JsonMapper.getMapper().writeValueAsString(r.getConfiguration());
+        } catch (IOException e){
+            throw new RuntimeException(e);
+        }
 
         GlobalConfigPersistable p = new GlobalConfigPersistable.Builder()
                 .sessionId(sessionId)

nd4j/nd4j-backends/nd4j-api-parent/nd4j-api/src/main/java/org/nd4j/linalg/lossfunctions/impl/LossL2.java

@@ -27,6 +27,7 @@ import org.nd4j.linalg.primitives.Pair;
 import org.nd4j.serde.jackson.shaded.NDArrayTextDeSerializer;
 import org.nd4j.serde.jackson.shaded.NDArrayTextSerializer;
 import org.nd4j.shade.jackson.annotation.JsonInclude;
+import org.nd4j.shade.jackson.annotation.JsonProperty;
 import org.nd4j.shade.jackson.databind.annotation.JsonDeserialize;
 import org.nd4j.shade.jackson.databind.annotation.JsonSerialize;
 
@@ -58,7 +59,7 @@ public class LossL2 implements ILossFunction {
      *
      * @param weights Weights array (row vector). May be null.
      */
-    public LossL2(INDArray weights) {
+    public LossL2(@JsonProperty("weights") INDArray weights) {
         if (weights != null && !weights.isRowVector()) {
             throw new IllegalArgumentException("Weights array must be a row vector");
         }

nd4j/nd4j-backends/nd4j-api-parent/nd4j-api/src/main/java/org/nd4j/linalg/lossfunctions/impl/LossMSE.java

@@ -19,6 +19,7 @@ package org.nd4j.linalg.lossfunctions.impl;
 import lombok.EqualsAndHashCode;
 import org.nd4j.linalg.activations.IActivation;
 import org.nd4j.linalg.api.ndarray.INDArray;
+import org.nd4j.shade.jackson.annotation.JsonProperty;
 
 /**
  * Mean Squared Error loss function: L = 1/N sum_i (actual_i - predicted)^2
@@ -38,7 +39,7 @@ public class LossMSE extends LossL2 {
      *
      * @param weights Weights array (row vector). May be null.
      */
-    public LossMSE(INDArray weights) {
+    public LossMSE(@JsonProperty("weights") INDArray weights) {
         super(weights);
     }