Merge pull request #72 from kbss-cvut/development

[0.15.0] Release

.github/workflows/maven.yml

@@ -12,11 +12,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up JDK 11
-        uses: actions/setup-java@v2
+      - uses: actions/checkout@v4
+      - name: Set up JDK 17
+        uses: actions/setup-java@v3
         with:
           distribution: 'temurin'
-          java-version: '11'
+          java-version: '17'
       - name: Build with Maven
         run: mvn -B package --file pom.xml

CHANGELOG.md

@@ -1,5 +1,11 @@
 # JB4JSON-LD Changelog
 
+## 0.15.0 - 2024-08-26
+- Support deserializing objects containing only identifier when `ASSUME_TARGET_TYPE` is enabled (Enhancement #69).
+- Cache deserialization type map (Enhancement #68).
+- Dependency updates: JOPA 2.0.4, test deps.
+- **Breaking change:** Set Java 17 as minimum Java version.
+
 ## 0.14.3 - 2024-04-16
 - Fix missing context entry when serializing empty collection mapped to data/annotation property.
 

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>cz.cvut.kbss.jsonld</groupId>
     <artifactId>jb4jsonld</artifactId>
-    <version>0.14.3</version>
+    <version>0.15.0</version>
     <name>JB4JSON-LD</name>
     <description>Java Binding for JSON-LD allows serialization and deserialization of Java POJOs to/from JSON-LD.
         This is the core implementation, which has to be integrated with Jackson, Jersey etc.
@@ -15,15 +15,16 @@
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <maven.compiler.source>11</maven.compiler.source>
-        <maven.compiler.target>11</maven.compiler.target>
+        <java.version>17</java.version>
+        <maven.compiler.source>${java.version}</maven.compiler.source>
+        <maven.compiler.target>${java.version}</maven.compiler.target>
 
-        <cz.cvut.kbss.jopa.version>1.2.2</cz.cvut.kbss.jopa.version>
+        <cz.cvut.kbss.jopa.version>2.0.4</cz.cvut.kbss.jopa.version>
 
-        <org.junit.jupiter.version>5.9.2</org.junit.jupiter.version>
-        <org.mockito.version>4.11.0</org.mockito.version>
-        <ch.qos.logback.version>1.4.14</ch.qos.logback.version>
-        <org.eclipse.rdf4j.version>4.3.10</org.eclipse.rdf4j.version>
+        <org.junit.jupiter.version>5.11.0</org.junit.jupiter.version>
+        <org.mockito.version>5.12.0</org.mockito.version>
+        <ch.qos.logback.version>1.5.7</ch.qos.logback.version>
+        <org.eclipse.rdf4j.version>5.0.2</org.eclipse.rdf4j.version>
     </properties>
 
     <dependencies>
@@ -79,13 +80,13 @@
         <dependency>
             <groupId>com.apicatalog</groupId>
             <artifactId>titanium-json-ld</artifactId>
-            <version>1.4.0</version>
+            <version>1.4.1</version>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.eclipse.parsson</groupId>
             <artifactId>jakarta.json</artifactId>
-            <version>1.1.5</version>
+            <version>1.1.7</version>
             <scope>test</scope>
         </dependency>
         <dependency>
@@ -152,18 +153,14 @@
                         </executions>
                     </plugin>
                     <plugin>
-                        <!-- explicitly define maven-deploy-plugin after other to force exec order -->
-                        <artifactId>maven-deploy-plugin</artifactId>
-                        <version>3.0.0</version>
-                        <executions>
-                            <execution>
-                                <id>deploy</id>
-                                <phase>deploy</phase>
-                                <goals>
-                                    <goal>deploy</goal>
-                                </goals>
-                            </execution>
-                        </executions>
+                        <groupId>org.sonatype.central</groupId>
+                        <artifactId>central-publishing-maven-plugin</artifactId>
+                        <version>0.5.0</version>
+                        <extensions>true</extensions>
+                        <configuration>
+                            <publishingServerId>central</publishingServerId>
+                            <autoPublish>true</autoPublish>
+                        </configuration>
                     </plugin>
                 </plugins>
             </build>

src/main/java/cz/cvut/kbss/jsonld/ConfigParam.java

@@ -39,9 +39,9 @@ public enum ConfigParam {
     /**
      * Whether to require an identifier when serializing an object.
      * <p>
-     * If set to {@code true} and no identifier is found (either there is no identifier field or its value is {@code
-     * null}), an exception will be thrown. If configured to {@code false}, a blank node identifier is generated if no
-     * id is present.
+     * If set to {@code true} and no identifier is found (either there is no identifier field or its value is
+     * {@code null}), an exception will be thrown. If configured to {@code false}, a blank node identifier is generated
+     * if no id is present.
      */
     REQUIRE_ID("requireId"),
 
@@ -59,8 +59,8 @@ public enum ConfigParam {
      * Enables optimistic target type resolution.
      * <p>
      * This means that when a an ambiguous target type is encountered during deserialization of an object (i.e.,
-     * multiple concrete classes match the data type), instead of throwing an {@link
-     * cz.cvut.kbss.jsonld.exception.AmbiguousTargetTypeException}, one of the classes will be selected for
+     * multiple concrete classes match the data type), instead of throwing an
+     * {@link cz.cvut.kbss.jsonld.exception.AmbiguousTargetTypeException}, one of the classes will be selected for
      * instantiation.
      * <p>
      * Note that enabling this behavior should probably be done together with setting {@link #IGNORE_UNKNOWN_PROPERTIES}
@@ -98,19 +98,34 @@ public enum ConfigParam {
     /**
      * Format string used to serialize and deserialize datetime values.
      * <p>
-     * Note that if {@link #SERIALIZE_DATETIME_AS_MILLIS} is enabled, this parameter has no effect on serialization of datetime.
+     * Note that if {@link #SERIALIZE_DATETIME_AS_MILLIS} is enabled, this parameter has no effect on serialization of
+     * datetime.
      * <p>
-     * Also note that this format applies only to full datetime values. Date or time values have to be formatted per-attribute.
+     * Also note that this format applies only to full datetime values. Date or time values have to be formatted
+     * per-attribute.
      */
     DATE_TIME_FORMAT("datetimeFormat"),
 
     /**
      * Whether to serialize individuals using expanded term definition in context.
-     *
+     * <p>
      * This basically means that the individual's identifier is provided directly as a string and an expanded term
-     * definition (consisting of a {@literal @id} and {@literal @type}) is added into the context, specifying that the string is an identifier.
+     * definition (consisting of a {@literal @id} and {@literal @type}) is added into the context, specifying that the
+     * string is an identifier.
+     */
+    SERIALIZE_INDIVIDUALS_USING_EXPANDED_DEFINITION("serializeIndividualsUsingExpandedDefinition"),
+
+    /**
+     * Whether to disable the type map cache.
+     * <p>
+     * Type map is used to map JSON-LD types to Java classes for deserialization. Since this map is built by scanning
+     * the classpath (see the {@link #SCAN_PACKAGE} parameter), it is cached by default to avoid repeated scanning of
+     * the classpath.
+     * <p>
+     * If every deserializer instance should get a fresh type map based on the current configuration, disable this
+     * cache.
      */
-    SERIALIZE_INDIVIDUALS_USING_EXPANDED_DEFINITION("serializeIndividualsUsingExpandedDefinition");
+    DISABLE_TYPE_MAP_CACHE("disableTypeMapCache");
 
     private final String name;
 

src/main/java/cz/cvut/kbss/jsonld/common/BeanAnnotationProcessor.java

@@ -17,16 +17,31 @@
  */
 package cz.cvut.kbss.jsonld.common;
 
+import cz.cvut.kbss.jopa.model.annotations.Id;
+import cz.cvut.kbss.jopa.model.annotations.Namespace;
+import cz.cvut.kbss.jopa.model.annotations.Namespaces;
+import cz.cvut.kbss.jopa.model.annotations.OWLAnnotationProperty;
+import cz.cvut.kbss.jopa.model.annotations.OWLClass;
+import cz.cvut.kbss.jopa.model.annotations.OWLDataProperty;
+import cz.cvut.kbss.jopa.model.annotations.OWLObjectProperty;
 import cz.cvut.kbss.jopa.model.annotations.Properties;
-import cz.cvut.kbss.jopa.model.annotations.*;
+import cz.cvut.kbss.jopa.model.annotations.Types;
 import cz.cvut.kbss.jsonld.JsonLd;
 import cz.cvut.kbss.jsonld.annotation.JsonLdAttributeOrder;
 import cz.cvut.kbss.jsonld.exception.JsonLdSerializationException;
 
 import java.lang.reflect.AnnotatedElement;
 import java.lang.reflect.Field;
 import java.lang.reflect.Modifier;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.Set;
 import java.util.function.BiPredicate;
 import java.util.function.Function;
 import java.util.stream.Collectors;
@@ -126,7 +141,7 @@ private static Optional<String> expandIri(String iri, Class<?> declaringClass) {
             }
         }
         return declaringClass.getSuperclass() != null ? expandIri(iri, declaringClass.getSuperclass()) :
-                Optional.empty();
+               Optional.empty();
     }
 
     private static Optional<String> resolveNamespace(AnnotatedElement annotated, String prefix) {
@@ -418,6 +433,14 @@ public static String getAttributeIdentifier(Field field) {
         throw new JsonLdSerializationException("Field " + field + " is not JSON-LD serializable.");
     }
 
+    /**
+     * Gets the identifier field of the specified class.
+     * <p>
+     * That is, gets the field annotated with {@link Id}, even inherited.
+     *
+     * @param cls Class whose identifier field to retrieve
+     * @return Matching field, optionally empty
+     */
     public static Optional<Field> getIdentifierField(Class<?> cls) {
         return getMarshallableFields(cls, (f, c) -> f.isAnnotationPresent(Id.class)).stream().findFirst();
     }

src/main/java/cz/cvut/kbss/jsonld/deserialization/InstanceBuilder.java

@@ -23,7 +23,6 @@
 import cz.cvut.kbss.jsonld.exception.JsonLdDeserializationException;
 
 import java.util.List;
-import java.util.Optional;
 
 /**
  * Builds instances from parsed JSON-LD.
@@ -58,8 +57,8 @@ public interface InstanceBuilder {
      * <p>
      * The new instance also becomes the currently open object.
      * <p>
-     * This method is intended for creating top level objects or adding objects to collections. Use {@link
-     * #openObject(String, String, List)} for opening objects as values of attributes.
+     * This method is intended for creating top level objects or adding objects to collections. Use
+     * {@link #openObject(String, String, List)} for opening objects as values of attributes.
      *
      * @param <T> The type of the object to open
      * @param id  Identifier of the object being open
@@ -82,8 +81,8 @@ public interface InstanceBuilder {
      * <p>
      * The new collection also becomes the currently open object.
      * <p>
-     * This method should also verify cardinality, i.e. a collection cannot be set as value of a field mapped by {@code
-     * property}, if the field is singular.
+     * This method should also verify cardinality, i.e. a collection cannot be set as value of a field mapped by
+     * {@code property}, if the field is singular.
      * <p>
      * This method assumes that the property is mapped, i.e. that {@link #isPropertyMapped(String)} returned true.
      *
@@ -99,8 +98,8 @@ public interface InstanceBuilder {
      * <p>
      * The new collection also becomes the currently open object.
      * <p>
-     * This method is intended for creating top level collections or nesting collections. Use {@link
-     * #openCollection(String)} for opening collections as values of attributes.
+     * This method is intended for creating top level collections or nesting collections. Use
+     * {@link #openCollection(String)} for opening collections as values of attributes.
      *
      * @param collectionType Type of the JSON collection to instantiate in Java
      * @see #openCollection(String)
@@ -188,8 +187,8 @@ public interface InstanceBuilder {
      * Checks whether the current collection context represents a {@link cz.cvut.kbss.jopa.model.annotations.Properties}
      * attribute.
      *
-     * @return {@code true} if the current context is a collection representing a {@link
-     * cz.cvut.kbss.jopa.model.annotations.Properties} field
+     * @return {@code true} if the current context is a collection representing a
+     * {@link cz.cvut.kbss.jopa.model.annotations.Properties} field
      */
     boolean isCurrentCollectionProperties();
 
@@ -239,11 +238,12 @@ public interface InstanceBuilder {
 
     /**
      * Gets the target type of the specified property.
-     *
-     * That is, it retrieves the type of the field to which the specified property is mapped. If the target field is a collection,
-     * the element type is returned (equivalent to {@link #getCurrentCollectionElementType()}).
-     *
+     * <p>
+     * That is, it retrieves the type of the field to which the specified property is mapped. If the target field is a
+     * collection, the element type is returned (equivalent to {@link #getCurrentCollectionElementType()}).
+     * <p>
      * This method assumes that the property is mapped, i.e. that {@link #isPropertyMapped(String)} returned true.
+     *
      * @param property Property whose target type to resolve
      * @return Target type wrapped in an optional
      */

src/main/java/cz/cvut/kbss/jsonld/deserialization/JsonLdDeserializer.java

@@ -36,6 +36,8 @@
  */
 public abstract class JsonLdDeserializer implements Configured {
 
+    private static final TypeMap TYPE_MAP = new TypeMap();
+
     private final Configuration configuration;
 
     protected final TargetClassResolver classResolver;
@@ -53,19 +55,33 @@ protected JsonLdDeserializer(Configuration configuration) {
     }
 
     private TargetClassResolver initializeTargetClassResolver() {
-        final TypeMap typeMap = new TypeMap();
         final String scanPath = configuration.get(ConfigParam.SCAN_PACKAGE, "");
+        final TypeMap typeMap = discoverAvailableTypes(scanPath, configuration.is(ConfigParam.DISABLE_TYPE_MAP_CACHE));
+        return new TargetClassResolver(typeMap,
+                                       new TargetClassResolverConfig(
+                                               configuration.is(ConfigParam.ASSUME_TARGET_TYPE),
+                                               configuration().is(ConfigParam.ENABLE_OPTIMISTIC_TARGET_TYPE_RESOLUTION),
+                                               configuration().is(ConfigParam.PREFER_SUPERCLASS)));
+    }
+
+    /**
+     * Finds potential deserialization target types on the classpath.
+     *
+     * @param scanPath Path to scan on classpath
+     * @return Map of types to Java classes
+     */
+    private static TypeMap discoverAvailableTypes(String scanPath, boolean disableCache) {
+        final TypeMap map = disableCache ? new TypeMap() : TYPE_MAP;
+        if (!map.isEmpty()) {
+            return map;
+        }
         new ClasspathScanner(c -> {
             final OWLClass ann = c.getDeclaredAnnotation(OWLClass.class);
             if (ann != null) {
-                typeMap.register(BeanAnnotationProcessor.expandIriIfNecessary(ann.iri(), c), c);
+                map.register(BeanAnnotationProcessor.expandIriIfNecessary(ann.iri(), c), c);
             }
         }).processClasses(scanPath);
-        return new TargetClassResolver(typeMap,
-                new TargetClassResolverConfig(
-                        configuration.is(ConfigParam.ASSUME_TARGET_TYPE),
-                        configuration().is(ConfigParam.ENABLE_OPTIMISTIC_TARGET_TYPE_RESOLUTION),
-                        configuration().is(ConfigParam.PREFER_SUPERCLASS)));
+        return map;
     }
 
     @Override
@@ -78,9 +94,9 @@ public Configuration configuration() {
      * <p>
      * If a deserializer already existed for the type, it is replaced by the new one.
      *
-     * @param type       Target type to register the deserializer for
+     * @param type         Target type to register the deserializer for
      * @param deserializer Deserializer to register
-     * @param <T>        Target type
+     * @param <T>          Target type
      */
     public <T> void registerDeserializer(Class<T> type, ValueDeserializer<T> deserializer) {
         Objects.requireNonNull(type);

src/main/java/cz/cvut/kbss/jsonld/deserialization/expanded/ExpandedJsonLdDeserializer.java

@@ -17,11 +17,13 @@
  */
 package cz.cvut.kbss.jsonld.deserialization.expanded;
 
+import cz.cvut.kbss.jsonld.ConfigParam;
 import cz.cvut.kbss.jsonld.Configuration;
 import cz.cvut.kbss.jsonld.deserialization.DefaultInstanceBuilder;
 import cz.cvut.kbss.jsonld.deserialization.DeserializationContext;
 import cz.cvut.kbss.jsonld.deserialization.InstanceBuilder;
 import cz.cvut.kbss.jsonld.deserialization.JsonLdDeserializer;
+import cz.cvut.kbss.jsonld.deserialization.reference.AssumedTypeReferenceReplacer;
 import cz.cvut.kbss.jsonld.deserialization.reference.PendingReferenceRegistry;
 import cz.cvut.kbss.jsonld.exception.JsonLdDeserializationException;
 import jakarta.json.JsonArray;
@@ -59,6 +61,9 @@ public <T> T deserialize(JsonValue jsonLd, Class<T> resultClass) {
         final InstanceBuilder instanceBuilder = new DefaultInstanceBuilder(classResolver, referenceRegistry);
         new ObjectDeserializer(instanceBuilder, new DeserializerConfig(configuration(), classResolver, deserializers), resultClass)
                 .processValue(root);
+        if (configuration().is(ConfigParam.ASSUME_TARGET_TYPE)) {
+            new AssumedTypeReferenceReplacer().replacePendingReferencesWithAssumedTypedObjects(referenceRegistry);
+        }
         referenceRegistry.verifyNoUnresolvedReferencesExist();
         assert resultClass.isAssignableFrom(instanceBuilder.getCurrentRoot().getClass());
         return resultClass.cast(instanceBuilder.getCurrentRoot());