scijava-persist : persisting objects with Gson and scijava discovery mechanism

.gitignore

@@ -5,3 +5,7 @@ target/
 .classpath
 .project
 .settings/
+
+# IntelliJ #
+.idea/
+.iml

pom.xml

@@ -47,6 +47,7 @@
 	<modules>
 		<module>imagej/imagej-ops2</module>
 		<module>imagej/imagej-testutil</module>
+		<module>scijava/scijava-persist</module>
 		<module>scijava/scijava-ops</module>
 		<module>scijava/scijava-testutil</module>
 		<module>scijava/scijava-types</module>

scijava/scijava-persist/.gitignore

@@ -0,0 +1,6 @@
+/.classpath
+/.project
+/.settings/
+/.idea/
+/target/
+*.iml

scijava/scijava-persist/README.md

@@ -0,0 +1,10 @@
+#Scijava mechanism for object serialization
+
+This incubator contains a mechanism that uses Scijava extensibility mechanism in order to register adapters that can be dispatched in multiple repositories.
+
+Internally the Gson library is used with `RunTimeAdapters`, which allow to serialize interfaces.
+
+TODO:
+* simple examples
+* tests
+* think about safety, or at least debugging ease (put a UUID)

scijava/scijava-persist/pom.xml

@@ -0,0 +1,116 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
+		http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>org.scijava</groupId>
+		<artifactId>scijava-incubator</artifactId>
+		<version>0-SNAPSHOT</version>
+		<relativePath>../..</relativePath>
+	</parent>
+
+	<artifactId>scijava-persist</artifactId>
+
+	<name>SciJava Persist</name>
+	<description>Extensible serialization mechanism for persisting objects.</description>
+	<url>None</url>
+	<inceptionYear>2021</inceptionYear>
+	<organization>
+		<name>SciJava</name>
+		<url>https://scijava.org/</url>
+	</organization>
+	<licenses>
+		<license>
+			<name>Simplified BSD License</name>
+			<distribution>repo</distribution>
+		</license>
+	</licenses>
+
+
+	<developers>
+		<developer>
+			<id>nicokiaru</id>
+			<name>Nicolas Chiaruttini</name>
+			<url>https://www.epfl.ch/research/facilities/ptbiop/staff/</url>
+			<roles>
+				<role>founder</role>
+				<role>lead</role>
+				<role>developer</role>
+				<role>debugger</role>
+				<role>reviewer</role>
+				<role>support</role>
+				<role>maintainer</role>
+			</roles>
+		</developer>
+	</developers>
+	<contributors>
+		<contributor>
+			<name>Nicolas Chiaruttini</name>
+			<url>http://biop.epfl.ch/INFO_Facility.html</url>
+			<roles><role>founder</role></roles>
+			<properties><id>NicoKiaru</id></properties>
+		</contributor>
+	</contributors>
+
+	<mailingLists>
+		<mailingList>
+			<name>Image.sc Forum</name>
+			<archive>https://forum.image.sc/tag/scijava</archive>
+		</mailingList>
+	</mailingLists>
+
+	<scm>
+		<connection>scm:git:git://github.com/scijava/incubator</connection>
+		<developerConnection>scm:git:git@github.com:scijava/incubator</developerConnection>
+		<tag>HEAD</tag>
+		<url>https://github.com/scijava/incubator</url>
+	</scm>
+
+	<issueManagement>
+		<system>GitHub Issues</system>
+		<url>https://github.com/scijava/scijava-testutil/issues</url>
+	</issueManagement>
+	<ciManagement>
+		<system>Travis CI</system>
+		<url>https://travis-ci.org/scijava/incubator</url>
+	</ciManagement>
+
+
+	<properties>
+		<main-class>org.scijava.persist.Main</main-class>
+		<package-name>org.scijava.persist</package-name>
+
+		<license.licenseName>bsd_2</license.licenseName>
+		<license.copyrightOwners>SciJava developers.</license.copyrightOwners>
+	</properties>
+
+	<repositories>
+		<repository>
+			<id>scijava.public</id>
+			<url>https://maven.scijava.org/content/groups/public</url>
+		</repository>
+	</repositories>
+
+	<dependencies>
+		<dependency>
+			<groupId>org.scijava</groupId>
+			<artifactId>scijava-common</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>com.google.code.gson</groupId>
+			<artifactId>gson</artifactId>
+			<version>2.8.6</version>
+		</dependency>
+
+		<!--- Test dependencies -->
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+</project>

scijava/scijava-persist/src/main/java/module-info.java

@@ -0,0 +1,7 @@
+open module org.scijava.persist {
+
+	exports org.scijava.persist;
+
+	requires transitive com.google.gson;
+	requires org.scijava;
+}

scijava/scijava-persist/src/main/java/org/scijava/persist/DefaultScijavaAdapterService.java

@@ -0,0 +1,60 @@
+package org.scijava.persist;
+
+import org.scijava.Context;
+import org.scijava.Priority;
+import org.scijava.plugin.AbstractPTService;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import org.scijava.plugin.PluginInfo;
+import org.scijava.service.Service;
+
+import java.util.List;
+
+/**
+ * Scijava service which provides the different Scijava Adapters available in the current context.
+ *
+ * {@link IObjectScijavaAdapter} plugins are automatically discovered and accessible in this service.
+ *
+ * In practice, serializer / deserializers are obtained via {@link ScijavaGsonHelper} helper class
+ *
+ * @author Nicolas Chiaruttini, EPFL, 2021
+ *
+ */
+@Plugin(type = Service.class)
+public class DefaultScijavaAdapterService extends AbstractPTService<IObjectScijavaAdapter> implements IObjectScijavaAdapterService {
+
+    @Override
+    public Class<IObjectScijavaAdapter> getPluginType() {
+        return IObjectScijavaAdapter.class;
+    }
+
+    @Parameter
+    Context ctx;
+
+    @Override
+    public Context context() {
+        return ctx;
+    }
+
+    @Override
+    public Context getContext() {
+        return ctx;
+    }
+
+    double priority = Priority.NORMAL;
+
+    @Override
+    public double getPriority() {
+        return priority;
+    }
+
+    @Override
+    public void setPriority(double priority) {
+        this.priority = priority;
+    }
+
+    @Override
+    public <PT extends IObjectScijavaAdapter> List<PluginInfo<PT>> getAdapters(Class<PT> adapterClass) {
+        return pluginService().getPluginsOfType(adapterClass);
+    }
+}

scijava/scijava-persist/src/main/java/org/scijava/persist/IClassAdapter.java

@@ -0,0 +1,11 @@
+package org.scijava.persist;
+
+import com.google.gson.JsonDeserializer;
+import com.google.gson.JsonSerializer;
+
+public interface IClassAdapter<T> extends IObjectScijavaAdapter, JsonSerializer<T>,
+        JsonDeserializer<T> {
+
+    Class<? extends T> getAdapterClass();
+
+}

scijava/scijava-persist/src/main/java/org/scijava/persist/IClassRuntimeAdapter.java

@@ -0,0 +1,33 @@
+package org.scijava.persist;
+
+import com.google.gson.JsonDeserializer;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonSerializer;
+import com.google.gson.JsonSerializationContext;
+import com.google.gson.JsonDeserializationContext;
+import com.google.gson.JsonParseException;
+import com.google.gson.JsonIOException;
+
+import java.lang.reflect.Type;
+
+public interface IClassRuntimeAdapter<B, T extends B> extends IObjectScijavaAdapter, JsonSerializer<T>,
+        JsonDeserializer<T> {
+
+    Class<? extends B> getBaseClass();
+
+    Class<? extends T> getRunTimeClass();
+
+    default boolean useCustomAdapter() {
+        return false;
+    }
+
+    @Override
+    default T deserialize(JsonElement json, Type typeOfT, JsonDeserializationContext context) throws JsonParseException {
+        throw new JsonParseException("Default deserializer for class "+getBaseClass()+" ("+getRunTimeClass()+") should not be used, return false in method useCustomAdapter instead");
+    }
+
+    @Override
+    default JsonElement serialize(T src, Type typeOfSrc, JsonSerializationContext context) {
+        throw new JsonIOException("Default serializer for class "+getBaseClass()+" ("+getRunTimeClass()+") should not be used, should not be used, return false in method useCustomAdapter instead");
+    }
+}

scijava/scijava-persist/src/main/java/org/scijava/persist/IObjectScijavaAdapter.java

@@ -0,0 +1,17 @@
+package org.scijava.persist;
+
+import org.scijava.plugin.SciJavaPlugin;
+
+/**
+ * Top level class for plugins which can serialize object using gson and the scijava context.
+ *
+ * The scijava context may provide custom adapters {@link IClassAdapter} and also
+ * runtime adapters, see {@link IClassRuntimeAdapter}) auto-discovered via scijava plugin
+ * extensibility mechanism.
+ *
+ * @author Nicolas Chiaruttini, EPFL, 2021
+ *
+ */
+
+public interface IObjectScijavaAdapter extends SciJavaPlugin {
+}

scijava/scijava-persist/src/main/java/org/scijava/persist/IObjectScijavaAdapterService.java

@@ -0,0 +1,11 @@
+package org.scijava.persist;
+
+import org.scijava.plugin.PTService;
+import org.scijava.plugin.PluginInfo;
+import org.scijava.service.SciJavaService;
+
+import java.util.List;
+
+public interface IObjectScijavaAdapterService extends PTService<IObjectScijavaAdapter>, SciJavaService {
+    <PT extends IObjectScijavaAdapter> List<PluginInfo<PT>> getAdapters(Class<PT> adapterClass);
+}

scijava/scijava-persist/src/main/java/org/scijava/persist/LazilyParsedNumber.java

@@ -0,0 +1,96 @@
+/*
+ * Copyright (C) 2011 Google Inc.
+ *
+ * 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.
+ */
+package org.scijava.persist;
+
+import java.io.ObjectStreamException;
+import java.math.BigDecimal;
+
+/**
+ * This class holds a number value that is lazily converted to a specific number type
+ *
+ * @author Inderjeet Singh
+ */
+public final class LazilyParsedNumber extends Number {
+  private final String value;
+
+  /** @param value must not be null */
+  public LazilyParsedNumber(String value) {
+    this.value = value;
+  }
+
+  @Override
+  public int intValue() {
+    try {
+      return Integer.parseInt(value);
+    } catch (NumberFormatException e) {
+      try {
+        return (int) Long.parseLong(value);
+      } catch (NumberFormatException nfe) {
+        return new BigDecimal(value).intValue();
+      }
+    }
+  }
+
+  @Override
+  public long longValue() {
+    try {
+      return Long.parseLong(value);
+    } catch (NumberFormatException e) {
+      return new BigDecimal(value).longValue();
+    }
+  }
+
+  @Override
+  public float floatValue() {
+    return Float.parseFloat(value);
+  }
+
+  @Override
+  public double doubleValue() {
+    return Double.parseDouble(value);
+  }
+
+  @Override
+  public String toString() {
+    return value;
+  }
+
+  /**
+   * If somebody is unlucky enough to have to serialize one of these, serialize
+   * it as a BigDecimal so that they won't need Gson on the other side to
+   * deserialize it.
+   */
+  private Object writeReplace() throws ObjectStreamException {
+    return new BigDecimal(value);
+  }
+
+  @Override
+  public int hashCode() {
+    return value.hashCode();
+  }
+
+  @Override
+  public boolean equals(Object obj) {
+    if (this == obj) {
+      return true;
+    }
+    if (obj instanceof LazilyParsedNumber) {
+      LazilyParsedNumber other = (LazilyParsedNumber) obj;
+      return value == other.value || value.equals(other.value);
+    }
+    return false;
+  }
+}