add non-generated classes and add maven

pom.xml

@@ -0,0 +1,105 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  ~ Copyright 2023 EBRAINS AISBL
+  ~
+  ~ 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 open source software code was developed in part or in whole in the
+  ~ Human Brain Project, funded from the European Union's Horizon 2020
+  ~ Framework Programme for Research and Innovation under
+  ~ Specific Grant Agreement No. 945539
+  ~ (Human Brain Project SGA3).
+  ~
+  -->
+
+<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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <groupId>org.openmetadatainitiative</groupId>
+    <artifactId>openminds</artifactId>
+    <version>3.0.0-beta1</version>
+    <name>openMINDS</name>
+    <packaging>jar</packaging>
+    <description>A java mapping for openMINDS instances</description>
+    <url>https://openminds-documentation.readthedocs.io</url>
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <maven.compiler.source>17</maven.compiler.source>
+        <maven.compiler.target>17</maven.compiler.target>
+    </properties>
+    <licenses>
+        <license>
+            <name>MIT License</name>
+            <url>http://www.opensource.org/licenses/mit-license.php</url>
+            <distribution>repo</distribution>
+        </license>
+    </licenses>
+    <build>
+        <finalName>${project.artifactId}</finalName>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>2.22.2</version>
+            </plugin>
+            <plugin>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <configuration>
+                    <source>17</source>
+                    <target>17</target>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-source-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>attach-sources</id>
+                        <goals>
+                            <goal>jar-no-fork</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>attach-javadocs</id>
+                        <goals>
+                            <goal>jar</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+
+    </build>
+
+
+    <dependencies>
+        <!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-databind -->
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+            <version>2.15.3</version>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter</artifactId>
+            <version>5.9.3</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+</project>

src/main/java/org/openmetadatainitiative/openminds/utils/Builder.java

@@ -0,0 +1,6 @@
+package org.openmetadatainitiative.openminds.utils;
+
+public interface Builder<T extends Instance> {
+
+    T build();
+}

src/main/java/org/openmetadatainitiative/openminds/utils/ByTypeDeserializer.java

@@ -0,0 +1,57 @@
+package org.openmetadatainitiative.openminds.utils;
+
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.JsonDeserializer;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Optional;
+
+public abstract class ByTypeDeserializer<T extends Entity> extends JsonDeserializer<T> {
+
+    private final Class<? extends T>[] subTypes;
+
+    public ByTypeDeserializer(Class<? extends T>... subTypes) {
+        this.subTypes = subTypes;
+    }
+
+    private T map(JsonNode root, ObjectMapper mapper, Iterable<JsonNode> nodes) throws JsonProcessingException {
+        for (JsonNode type : nodes) {
+            if (type != null) {
+                final String typeString = type.asText();
+                if (typeString != null) {
+                    final Optional<Class<? extends T>> first = Arrays.stream(this.subTypes).filter(t -> {
+                        final InstanceType annotation = t.getAnnotation(InstanceType.class);
+                        if(annotation == null || annotation.value() == null){
+                            throw new RuntimeException("Type {} was mapped as a subtype but doesn't provide the @InstanceType annotation!");
+                        }
+                        return typeString.equals(annotation.value());
+                }).findFirst();
+                    if (first.isPresent()) {
+                        return mapper.treeToValue(root, first.get());
+                    }
+                }
+            }
+        }
+        return null;
+    }
+
+    @Override
+    public T deserialize(JsonParser jsonParser, DeserializationContext deserializationContext) throws IOException {
+        ObjectMapper mapper = (ObjectMapper) jsonParser.getCodec();
+        final JsonNode root = mapper.readTree(jsonParser);
+        final JsonNode typeNode = root.get("@type");
+        if( typeNode.isTextual()){
+            return map(root, mapper, Collections.singleton(typeNode));
+        }
+        if (typeNode.isArray()) {
+            return map(root, mapper, typeNode);
+        }
+        return null;
+    }
+}

src/main/java/org/openmetadatainitiative/openminds/utils/Entity.java

@@ -0,0 +1,8 @@
+package org.openmetadatainitiative.openminds.utils;
+
+public interface Entity {
+
+    InstanceId getId();
+
+
+}

src/main/java/org/openmetadatainitiative/openminds/utils/Instance.java

@@ -0,0 +1,34 @@
+package org.openmetadatainitiative.openminds.utils;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import java.util.List;
+
+public class Instance implements Entity{
+
+    @JsonProperty("@id")
+    protected InstanceId id;
+
+    @JsonProperty("@type")
+    protected List<String> types;
+
+    @JsonIgnore
+    private final LocalId localId;
+
+    public Instance(LocalId localId) {
+        this.localId = localId;
+    }
+
+    @JsonIgnore
+    public LocalId getLocalId() {
+        return localId;
+    }
+
+    public InstanceId getId(){
+        return id;
+    }
+    protected  <T extends Instance> Reference<T> doGetReference(){
+        return new Reference<>(getId());
+    }
+}

src/main/java/org/openmetadatainitiative/openminds/utils/InstanceId.java

@@ -0,0 +1,47 @@
+package org.openmetadatainitiative.openminds.utils;
+
+import com.fasterxml.jackson.core.JacksonException;
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.JsonDeserializer;
+import com.fasterxml.jackson.databind.JsonSerializer;
+import com.fasterxml.jackson.databind.SerializerProvider;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+
+import java.io.IOException;
+
+@JsonSerialize(using = InstanceId.Serializer.class)
+@JsonDeserialize(using = InstanceId.Deserializer.class)
+public record InstanceId(String instanceId) {
+
+    public static InstanceId withPrefix(String id, String prefix){
+        return id!=null ? prefix != null ? new InstanceId(prefix+id) : new InstanceId(id) : null;
+
+    }
+
+    static class Serializer extends JsonSerializer<InstanceId> {
+        @Override
+        public void serialize(InstanceId instanceId, JsonGenerator jsonGenerator, SerializerProvider serializerProvider) throws IOException {
+            if (instanceId.instanceId != null) {
+                jsonGenerator.writeString(instanceId.instanceId);
+            } else {
+                jsonGenerator.writeNull();
+            }
+
+        }
+    }
+
+    static class Deserializer extends JsonDeserializer<InstanceId> {
+        @Override
+        public InstanceId deserialize(JsonParser jsonParser, DeserializationContext deserializationContext) throws IOException, JacksonException {
+            final String value = jsonParser.getText();
+            if (value != null) {
+                return new InstanceId(value);
+            }
+            return null;
+        }
+    }
+
+}

src/main/java/org/openmetadatainitiative/openminds/utils/InstanceType.java

@@ -0,0 +1,12 @@
+package org.openmetadatainitiative.openminds.utils;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+@Target(ElementType.TYPE)
+@Retention(RetentionPolicy.RUNTIME)
+public @interface InstanceType {
+    String value();
+}

src/main/java/org/openmetadatainitiative/openminds/utils/LocalId.java

@@ -0,0 +1,40 @@
+package org.openmetadatainitiative.openminds.utils;
+
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.JsonDeserializer;
+import com.fasterxml.jackson.databind.JsonSerializer;
+import com.fasterxml.jackson.databind.SerializerProvider;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+
+import java.io.IOException;
+
+@JsonSerialize(using = LocalId.Serializer.class)
+@JsonDeserialize(using = LocalId.Deserializer.class)
+public record LocalId(String id) {
+
+    static class Serializer extends JsonSerializer<LocalId> {
+        @Override
+        public void serialize(LocalId localId, JsonGenerator jsonGenerator, SerializerProvider serializerProvider) throws IOException {
+            if (localId.id != null) {
+                jsonGenerator.writeString("_:"+localId.id);
+            } else {
+                jsonGenerator.writeNull();
+            }
+
+        }
+    }
+
+    static class Deserializer extends JsonDeserializer<LocalId> {
+        @Override
+        public LocalId deserialize(JsonParser jsonParser, DeserializationContext deserializationContext) throws IOException {
+            final String value = jsonParser.getText();
+            if (value != null && value.startsWith("_:")) {
+                return new LocalId(value.substring(2));
+            }
+            return null;
+        }
+    }
+}

src/main/java/org/openmetadatainitiative/openminds/utils/OpenMINDSContext.java

@@ -0,0 +1,12 @@
+package org.openmetadatainitiative.openminds.utils;
+
+public record OpenMINDSContext(String idPrefix, boolean autoAssignIdPrefix) {
+
+    public static OpenMINDSContext defaultContext(){
+        return local(true);
+    }
+
+    public static OpenMINDSContext local(boolean autoAssignIdPrefix){
+        return new OpenMINDSContext("_:", autoAssignIdPrefix);
+    }
+}

src/main/java/org/openmetadatainitiative/openminds/utils/ParsingUtils.java

@@ -0,0 +1,9 @@
+package org.openmetadatainitiative.openminds.utils;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+public class ParsingUtils {
+
+    public static ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+}

src/main/java/org/openmetadatainitiative/openminds/utils/Reference.java

@@ -0,0 +1,11 @@
+package org.openmetadatainitiative.openminds.utils;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+public record Reference<T extends Instance>(@JsonProperty("@id") InstanceId id){
+
+    public static <T extends Instance> Reference<T> create(T instance){
+        return instance != null ? new Reference<T>(instance.getId()) : null;
+    }
+
+}