Merge pull request #39 from kris7t/partial-interpretation

Implement partial interpretation based model generation

2 files changed, 325 insertions, 5 deletions

diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/RuntimeTypeAdapterFactory.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/RuntimeTypeAdapterFactory.java
new file mode 100644
index 00000000..b16cf7df
--- /dev/null
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/RuntimeTypeAdapterFactory.java
@@ -0,0 +1,304 @@
+/*
+ * Copyright (C) 2011 Google Inc.
+ * Copyright (C) 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: Apache-2.0
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://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.
+ *
+ * This file was copied into Refinery according to upstream instructions at
+ * https://github.com/google/gson/issues/1104#issuecomment-309582470.
+ * However, we changed the package name below to avoid potential clashes
+ * with other jars on the classpath.
+ */
+package tools.refinery.language.web.xtext.servlet;
+
+import com.google.errorprone.annotations.CanIgnoreReturnValue;
+import com.google.gson.Gson;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonParseException;
+import com.google.gson.JsonPrimitive;
+import com.google.gson.TypeAdapter;
+import com.google.gson.TypeAdapterFactory;
+import com.google.gson.reflect.TypeToken;
+import com.google.gson.stream.JsonReader;
+import com.google.gson.stream.JsonWriter;
+import java.io.IOException;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+/**
+ * Adapts values whose runtime type may differ from their declaration type. This
+ * is necessary when a field's type is not the same type that GSON should create
+ * when deserializing that field. For example, consider these types:
+ * <pre>   {@code
+ *   abstract class Shape {
+ *     int x;
+ *     int y;
+ *   }
+ *   class Circle extends Shape {
+ *     int radius;
+ *   }
+ *   class Rectangle extends Shape {
+ *     int width;
+ *     int height;
+ *   }
+ *   class Diamond extends Shape {
+ *     int width;
+ *     int height;
+ *   }
+ *   class Drawing {
+ *     Shape bottomShape;
+ *     Shape topShape;
+ *   }
+ * }</pre>
+ * <p>Without additional type information, the serialized JSON is ambiguous. Is
+ * the bottom shape in this drawing a rectangle or a diamond? <pre>   {@code
+ *   {
+ *     "bottomShape": {
+ *       "width": 10,
+ *       "height": 5,
+ *       "x": 0,
+ *       "y": 0
+ *     },
+ *     "topShape": {
+ *       "radius": 2,
+ *       "x": 4,
+ *       "y": 1
+ *     }
+ *   }}</pre>
+ * This class addresses this problem by adding type information to the
+ * serialized JSON and honoring that type information when the JSON is
+ * deserialized: <pre>   {@code
+ *   {
+ *     "bottomShape": {
+ *       "type": "Diamond",
+ *       "width": 10,
+ *       "height": 5,
+ *       "x": 0,
+ *       "y": 0
+ *     },
+ *     "topShape": {
+ *       "type": "Circle",
+ *       "radius": 2,
+ *       "x": 4,
+ *       "y": 1
+ *     }
+ *   }}</pre>
+ * Both the type field name ({@code "type"}) and the type labels ({@code
+ * "Rectangle"}) are configurable.
+ *
+ * <h2>Registering Types</h2>
+ * Create a {@code RuntimeTypeAdapterFactory} by passing the base type and type field
+ * name to the {@link #of} factory method. If you don't supply an explicit type
+ * field name, {@code "type"} will be used. <pre>   {@code
+ *   RuntimeTypeAdapterFactory<Shape> shapeAdapterFactory
+ *       = RuntimeTypeAdapterFactory.of(Shape.class, "type");
+ * }</pre>
+ * Next register all of your subtypes. Every subtype must be explicitly
+ * registered. This protects your application from injection attacks. If you
+ * don't supply an explicit type label, the type's simple name will be used.
+ * <pre>   {@code
+ *   shapeAdapterFactory.registerSubtype(Rectangle.class, "Rectangle");
+ *   shapeAdapterFactory.registerSubtype(Circle.class, "Circle");
+ *   shapeAdapterFactory.registerSubtype(Diamond.class, "Diamond");
+ * }</pre>
+ * Finally, register the type adapter factory in your application's GSON builder:
+ * <pre>   {@code
+ *   Gson gson = new GsonBuilder()
+ *       .registerTypeAdapterFactory(shapeAdapterFactory)
+ *       .create();
+ * }</pre>
+ * Like {@code GsonBuilder}, this API supports chaining: <pre>   {@code
+ *   RuntimeTypeAdapterFactory<Shape> shapeAdapterFactory = RuntimeTypeAdapterFactory.of(Shape.class)
+ *       .registerSubtype(Rectangle.class)
+ *       .registerSubtype(Circle.class)
+ *       .registerSubtype(Diamond.class);
+ * }</pre>
+ *
+ * <h2>Serialization and deserialization</h2>
+ * In order to serialize and deserialize a polymorphic object,
+ * you must specify the base type explicitly.
+ * <pre>   {@code
+ *   Diamond diamond = new Diamond();
+ *   String json = gson.toJson(diamond, Shape.class);
+ * }</pre>
+ * And then:
+ * <pre>   {@code
+ *   Shape shape = gson.fromJson(json, Shape.class);
+ * }</pre>
+ */
+public final class RuntimeTypeAdapterFactory<T> implements TypeAdapterFactory {
+        private final Class<?> baseType;
+        private final String typeFieldName;
+        private final Map<String, Class<?>> labelToSubtype = new LinkedHashMap<>();
+        private final Map<Class<?>, String> subtypeToLabel = new LinkedHashMap<>();
+        private final boolean maintainType;
+        private boolean recognizeSubtypes;
+
+        private RuntimeTypeAdapterFactory(
+                        Class<?> baseType, String typeFieldName, boolean maintainType) {
+                if (typeFieldName == null || baseType == null) {
+                        throw new NullPointerException();
+                }
+                this.baseType = baseType;
+                this.typeFieldName = typeFieldName;
+                this.maintainType = maintainType;
+        }
+
+        /**
+         * Creates a new runtime type adapter using for {@code baseType} using {@code
+         * typeFieldName} as the type field name. Type field names are case sensitive.
+         *
+         * @param maintainType true if the type field should be included in deserialized objects
+         */
+        public static <T> RuntimeTypeAdapterFactory<T> of(Class<T> baseType, String typeFieldName, boolean maintainType) {
+                return new RuntimeTypeAdapterFactory<>(baseType, typeFieldName, maintainType);
+        }
+
+        /**
+         * Creates a new runtime type adapter using for {@code baseType} using {@code
+         * typeFieldName} as the type field name. Type field names are case sensitive.
+         */
+        public static <T> RuntimeTypeAdapterFactory<T> of(Class<T> baseType, String typeFieldName) {
+                return new RuntimeTypeAdapterFactory<>(baseType, typeFieldName, false);
+        }
+
+        /**
+         * Creates a new runtime type adapter for {@code baseType} using {@code "type"} as
+         * the type field name.
+         */
+        public static <T> RuntimeTypeAdapterFactory<T> of(Class<T> baseType) {
+                return new RuntimeTypeAdapterFactory<>(baseType, "type", false);
+        }
+
+        /**
+         * Ensures that this factory will handle not just the given {@code baseType}, but any subtype
+         * of that type.
+         */
+        @CanIgnoreReturnValue
+        public RuntimeTypeAdapterFactory<T> recognizeSubtypes() {
+                this.recognizeSubtypes = true;
+                return this;
+        }
+
+        /**
+         * Registers {@code type} identified by {@code label}. Labels are case
+         * sensitive.
+         *
+         * @throws IllegalArgumentException if either {@code type} or {@code label}
+         *     have already been registered on this type adapter.
+         */
+        @CanIgnoreReturnValue
+        public RuntimeTypeAdapterFactory<T> registerSubtype(Class<? extends T> type, String label) {
+                if (type == null || label == null) {
+                        throw new NullPointerException();
+                }
+                if (subtypeToLabel.containsKey(type) || labelToSubtype.containsKey(label)) {
+                        throw new IllegalArgumentException("types and labels must be unique");
+                }
+                labelToSubtype.put(label, type);
+                subtypeToLabel.put(type, label);
+                return this;
+        }
+
+        /**
+         * Registers {@code type} identified by its {@link Class#getSimpleName simple
+         * name}. Labels are case sensitive.
+         *
+         * @throws IllegalArgumentException if either {@code type} or its simple name
+         *     have already been registered on this type adapter.
+         */
+        @CanIgnoreReturnValue
+        public RuntimeTypeAdapterFactory<T> registerSubtype(Class<? extends T> type) {
+                return registerSubtype(type, type.getSimpleName());
+        }
+
+        @Override
+        public <R> TypeAdapter<R> create(Gson gson, TypeToken<R> type) {
+                if (type == null) {
+                        return null;
+                }
+                Class<?> rawType = type.getRawType();
+                boolean handle =
+                                recognizeSubtypes ? baseType.isAssignableFrom(rawType) : baseType.equals(rawType);
+                if (!handle) {
+                        return null;
+                }
+
+                final TypeAdapter<JsonElement> jsonElementAdapter = gson.getAdapter(JsonElement.class);
+                final Map<String, TypeAdapter<?>> labelToDelegate = new LinkedHashMap<>();
+                final Map<Class<?>, TypeAdapter<?>> subtypeToDelegate = new LinkedHashMap<>();
+                for (Map.Entry<String, Class<?>> entry : labelToSubtype.entrySet()) {
+                        TypeAdapter<?> delegate = gson.getDelegateAdapter(this, TypeToken.get(entry.getValue()));
+                        labelToDelegate.put(entry.getKey(), delegate);
+                        subtypeToDelegate.put(entry.getValue(), delegate);
+                }
+
+                return new TypeAdapter<R>() {
+                        @Override public R read(JsonReader in) throws IOException {
+                                JsonElement jsonElement = jsonElementAdapter.read(in);
+                                JsonElement labelJsonElement;
+                                if (maintainType) {
+                                        labelJsonElement = jsonElement.getAsJsonObject().get(typeFieldName);
+                                } else {
+                                        labelJsonElement = jsonElement.getAsJsonObject().remove(typeFieldName);
+                                }
+
+                                if (labelJsonElement == null) {
+                                        throw new JsonParseException("cannot deserialize " + baseType
+                                                        + " because it does not define a field named " + typeFieldName);
+                                }
+                                String label = labelJsonElement.getAsString();
+                                @SuppressWarnings("unchecked") // registration requires that subtype extends T
+                                TypeAdapter<R> delegate = (TypeAdapter<R>) labelToDelegate.get(label);
+                                if (delegate == null) {
+                                        throw new JsonParseException("cannot deserialize " + baseType + " subtype named "
+                                                        + label + "; did you forget to register a subtype?");
+                                }
+                                return delegate.fromJsonTree(jsonElement);
+                        }
+
+                        @Override public void write(JsonWriter out, R value) throws IOException {
+                                Class<?> srcType = value.getClass();
+                                String label = subtypeToLabel.get(srcType);
+                                @SuppressWarnings("unchecked") // registration requires that subtype extends T
+                                TypeAdapter<R> delegate = (TypeAdapter<R>) subtypeToDelegate.get(srcType);
+                                if (delegate == null) {
+                                        throw new JsonParseException("cannot serialize " + srcType.getName()
+                                                        + "; did you forget to register a subtype?");
+                                }
+                                JsonObject jsonObject = delegate.toJsonTree(value).getAsJsonObject();
+
+                                if (maintainType) {
+                                        jsonElementAdapter.write(out, jsonObject);
+                                        return;
+                                }
+
+                                JsonObject clone = new JsonObject();
+
+                                if (jsonObject.has(typeFieldName)) {
+                                        throw new JsonParseException("cannot serialize " + srcType.getName()
+                                                        + " because it already defines a field named " + typeFieldName);
+                                }
+                                clone.add(typeFieldName, new JsonPrimitive(label));
+
+                                for (Map.Entry<String, JsonElement> e : jsonObject.entrySet()) {
+                                        clone.add(e.getKey(), e.getValue());
+                                }
+                                jsonElementAdapter.write(out, clone);
+                        }
+                }.nullSafe();
+        }
+}
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextWebSocket.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextWebSocket.java
index 043d318c..1fde1be5 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextWebSocket.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextWebSocket.java
@@ -6,6 +6,7 @@
 package tools.refinery.language.web.xtext.servlet;
 
 import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
 import com.google.gson.JsonIOException;
 import com.google.gson.JsonParseException;
 import org.eclipse.jetty.websocket.api.Callback;
@@ -16,6 +17,7 @@ import org.eclipse.xtext.resource.IResourceServiceProvider;
 import org.eclipse.xtext.web.server.ISession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import tools.refinery.language.semantics.metadata.*;
 import tools.refinery.language.web.xtext.server.ResponseHandler;
 import tools.refinery.language.web.xtext.server.ResponseHandlerException;
 import tools.refinery.language.web.xtext.server.TransactionExecutor;
@@ -28,7 +30,15 @@ import java.io.Reader;
 public class XtextWebSocket implements ResponseHandler {
         private static final Logger LOG = LoggerFactory.getLogger(XtextWebSocket.class);
 
-        private final Gson gson = new Gson();
+        private final Gson gson = new GsonBuilder()
+                        .disableJdkUnsafe()
+                        .registerTypeAdapterFactory(RuntimeTypeAdapterFactory.of(RelationDetail.class, "type")
+                                        .registerSubtype(ClassDetail.class, "class")
+                                        .registerSubtype(ReferenceDetail.class, "reference")
+                                        .registerSubtype(OppositeReferenceDetail.class, "opposite")
+                                        .registerSubtype(PredicateDetail.class, "predicate")
+                                        .registerSubtype(BuiltInDetail.class, "builtin"))
+                        .create();
 
         private final TransactionExecutor executor;
 
@@ -70,10 +80,11 @@ public class XtextWebSocket implements ResponseHandler {
 
         @OnWebSocketError
         public void onError(Throwable error) {
+                executor.dispose();
                 if (webSocketSession == null) {
                         return;
                 }
-                LOG.error("Internal websocket error in connection from" + webSocketSession.getRemoteSocketAddress(), error);
+                LOG.error("Internal websocket error in connection from " + webSocketSession.getRemoteSocketAddress(), error);
         }
 
         @OnWebSocketMessage
@@ -86,14 +97,18 @@ public class XtextWebSocket implements ResponseHandler {
                 try {
                         request = gson.fromJson(reader, XtextWebRequest.class);
                 } catch (JsonIOException e) {
-                        LOG.error("Cannot read from websocket from" + webSocketSession.getRemoteSocketAddress(), e);
+                        LOG.error("Cannot read from websocket from " + webSocketSession.getRemoteSocketAddress(), e);
                         if (webSocketSession.isOpen()) {
+                                executor.dispose();
                                 webSocketSession.close(StatusCode.SERVER_ERROR, "Cannot read payload", Callback.NOOP);
                         }
                         return;
                 } catch (JsonParseException e) {
-                        LOG.warn("Malformed websocket request from" + webSocketSession.getRemoteSocketAddress(), e);
-                        webSocketSession.close(XtextStatusCode.INVALID_JSON, "Invalid JSON payload", Callback.NOOP);
+                        LOG.warn("Malformed websocket request from " + webSocketSession.getRemoteSocketAddress(), e);
+                        if (webSocketSession.isOpen()) {
+                                executor.dispose();
+                                webSocketSession.close(XtextStatusCode.INVALID_JSON, "Invalid JSON payload", Callback.NOOP);
+                        }
                         return;
                 }
                 try {
@@ -101,6 +116,7 @@ public class XtextWebSocket implements ResponseHandler {
                 } catch (ResponseHandlerException e) {
                         LOG.warn("Cannot write websocket response", e);
                         if (webSocketSession.isOpen()) {
+                                executor.dispose();
                                 webSocketSession.close(StatusCode.SERVER_ERROR, "Cannot write response", Callback.NOOP);
                         }
                 }