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Merge branch 'scijava/scijava-persist/init'
From @NicoKiaru: This PR brings a scijava service DefaultScijavaAdapterService which provides a way to serialize and deserialize java objects. Vocabulary : adapter = serializer (object to text) + deserializer (text to object) The most meaningful demo is in SerializationTests.java. A test is included, which basically makes a loop: object -> serialization -> string1 -> deserialization -> object -> serialization -> string2, and checks that string1.equals(string2) Scijava persist uses Gson serialization ( with RunTime adapters, which provide a way to serialize/deserialize objects extending abstract class or implements interface, see javadoc of RuntimeTypeAdapterFactory), and discovers and registers adapters at runtime. The adapters which are autodiscovered are of two kinds: IClassAdapter IClassRuntimeAdapter for adapters which require runtime adaptation (is this RealTransform object an affine transform ? or a sequence of transform, or a thinplateSplineTransform ? One runtime adapter needs to be registered per class) See #30
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‎.gitignore‎

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.classpath
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.project
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.settings/
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# IntelliJ #
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.idea/
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.iml

‎pom.xml‎

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<modules>
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<module>imagej/imagej-ops2</module>
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<module>imagej/imagej-testutil</module>
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<module>scijava/scijava-persist</module>
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<module>scijava/scijava-ops</module>
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<module>scijava/scijava-testutil</module>
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<module>scijava/scijava-types</module>

‎scijava/scijava-persist/.gitignore‎

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/.classpath
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/.project
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/.settings/
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/.idea/
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/target/
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*.iml

‎scijava/scijava-persist/README.md‎

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

‎scijava/scijava-persist/pom.xml‎

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

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

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open module org.scijava.persist {
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exports org.scijava.persist;
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requires transitive com.google.gson;
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requires org.scijava;
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}

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

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

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

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

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

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

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

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

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