publishing 0.5.7

.github/workflows/test.yml

@@ -20,10 +20,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
-      - name: Set up JDK 11
+      - name: Set up JDK 17
         uses: actions/setup-java@v2
         with:
-          java-version: '11'
+          java-version: '17'
           distribution: 'temurin'
       - name: Build java runtime with Gradle
         uses: gradle/actions/setup-gradle@v3

doc/guide/Installation.md

@@ -2,8 +2,8 @@ Installation
 ============
 
 The VO-DML tooling is based around [gradle](https://gradle.org) (currently version 8) which itself
-is based on Java. It is recommended that a minimum of JDK 11 is installed 
-(JDK 17 has also been tested) using a package manager for your OS and 
+is based on Java. It is recommended that a minimum of JDK 17 is installed 
+using a package manager for your OS and 
 similarly use a package manager for gradle installation. Although if you are working
 with a repository that already has a `gradelw` file at the top level, then that can be used
 in place of the gradle command, and it will handle the downloading and running of the correct gradle version. 

models/ivoa/build.gradle.kts

@@ -1,5 +1,5 @@
 plugins {
-    id("net.ivoa.vo-dml.vodmltools") version "0.5.6"
+    id("net.ivoa.vo-dml.vodmltools") version "0.5.7"
 //    id ("com.diffplug.spotless") version "5.17.1"
     `maven-publish`
     id("io.github.gradle-nexus.publish-plugin") version "1.3.0"

models/sample/sample/vo-dml/Sample.vo-dml.xml

@@ -330,8 +330,8 @@
                                <maxOccurs>1</maxOccurs>
                              </multiplicity>
         <semanticconcept>
-          <topConcept>http://purl.org/astronomy/vocab/DataObjectTypes/DataObjectType</topConcept>
-          <vocabularyURI>http://purl.org/astronomy/vocab/DataObjectTypes</vocabularyURI>
+          <topConcept>http://www.ivoa.net/rdf/object-type#DataObjectType</topConcept> <!--FIXME - this is probably not correct -->
+          <vocabularyURI>http://www.ivoa.net/rdf/object-type</vocabularyURI>
         </semanticconcept>
                            </attribute>
                         </objectType>

models/sample/test/serializationExample.vo-dml.xml

@@ -8,7 +8,7 @@
       <uri/>
       <title></title>
       <version>1.0</version>
-      <lastModified>2024-05-31T11:12:57Z</lastModified>
+      <lastModified>2024-10-07T08:26:18Z</lastModified>
       <import>
         <name>null</name><!--should not be needed in modern vo-dml -->
         <url>IVOA-v1.0.vo-dml.xml</url>
@@ -127,6 +127,9 @@
                    <minOccurs>1</minOccurs>
                    <maxOccurs>1</maxOccurs>
                  </multiplicity>
+               <semanticconcept>
+                 <vocabularyURI>http://www.ivoa.net/rdf/product-type</vocabularyURI>
+               </semanticconcept>
                </attribute>
             </objectType>
             <objectType>
@@ -166,7 +169,7 @@
                  </datatype>
                  <multiplicity>
                    <minOccurs>1</minOccurs>
-                   <maxOccurs>1</maxOccurs>
+                   <maxOccurs>-1</maxOccurs>
                  </multiplicity>
                </attribute>
                <composition>

models/sample/test/serializationExample.vodsl

@@ -29,12 +29,12 @@ otype Dcont -> BaseC {
 }
 
 otype Econt -> BaseC {
-	evalue: ivoa:string ""; 
+	evalue: ivoa:string "" semantic in "http://www.ivoa.net/rdf/product-type"; 
 }
 otype SomeContent "" {
 	ref1 references Refa "";
 	ref2 references Refb "";
-	zval : ivoa:string "";
+	zval : ivoa:string @+ "";
 	con: BaseC @+ as composition ""; 
 }
 

runtime/java/build.gradle.kts

@@ -6,7 +6,7 @@ plugins {
     signing
 }
 group = "org.javastro.ivoa.vo-dml"
-version = "0.7.1"
+version = "0.7.2"
 
 
 dependencies {
@@ -15,7 +15,7 @@ dependencies {
     implementation("jakarta.xml.bind:jakarta.xml.bind-api:4.0.0")
 //    implementation("org.glassfish.jaxb:jaxb-runtime:2.3.6")
     implementation("jakarta.persistence:jakarta.persistence-api:3.1.0")
-    implementation("com.fasterxml.jackson.core:jackson-databind:2.15.1")
+    implementation("com.fasterxml.jackson.core:jackson-databind:2.17.0")
     implementation("org.hibernate.orm:hibernate-core:6.2.7.Final")
 
     implementation("org.slf4j:slf4j-api:1.7.36")
@@ -40,12 +40,16 @@ dependencies {
 //}
 
 java {
-//    modularity.inferModulePath.set(false) // still can only build on java 1.8
     toolchain {
-        languageVersion.set(JavaLanguageVersion.of(11))
+        languageVersion = JavaLanguageVersion.of(17)
     }
     withJavadocJar()
     withSourcesJar()
+
+}
+
+tasks.javadoc {
+    (options as StandardJavadocDocletOptions).tags("TODO","IMPL")
 }
 
 tasks.test {
@@ -110,6 +114,9 @@ publishing.publications.withType(MavenPublication::class.java).forEach { publica
     }
 }
 println ("java property skipSigning= " + project.hasProperty("skipSigning"))
+repositories {
+    mavenCentral()
+}
 
 
 signing {

runtime/java/src/main/java/org/ivoa/vodml/jpa/AttributeConverters.java

@@ -0,0 +1,128 @@
+/*
+ * Created on 7 Oct 2024 
+ * Copyright 2024 Paul Harrison ([email protected])
+ *
+ * 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 in file LICENSE
+ */ 
+
+package org.ivoa.vodml.jpa;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import jakarta.persistence.AttributeConverter;
+
+/**
+ * Attribute converters to convert lists to comma separated strings.
+ * @author Paul Harrison ([email protected]) 
+ */
+public class AttributeConverters {
+
+    private static final String SPLIT_CHAR = ";";
+    public static class StringListConverter implements AttributeConverter<List<String>, String> {
+
+
+        /**
+         * {@inheritDoc}
+         * overrides @see jakarta.persistence.AttributeConverter#convertToDatabaseColumn(java.lang.Object)
+         */
+        @Override
+        public String convertToDatabaseColumn(List<String> attribute) {
+            return attribute != null ? String.join(SPLIT_CHAR, attribute) : "";
+        }
+
+        /**
+         * {@inheritDoc}
+         * overrides @see jakarta.persistence.AttributeConverter#convertToEntityAttribute(java.lang.Object)
+         */
+        @Override
+        public List<String> convertToEntityAttribute(String dbData) {
+           return dbData != null ? Arrays.asList(dbData.split(SPLIT_CHAR)) : new ArrayList<String>() ;
+        }
+
+    }
+
+    public static abstract class NumberListConverter <T> implements AttributeConverter<List<T>, String> {
+
+        /**
+         * {@inheritDoc}
+         * overrides @see jakarta.persistence.AttributeConverter#convertToDatabaseColumn(java.lang.Object)
+         */
+        @Override
+        public String convertToDatabaseColumn(List<T> attribute) {
+
+            if(attribute!= null)
+            {
+               return attribute.stream().map(T::toString).collect(Collectors.joining (SPLIT_CHAR)); 
+            }
+            else
+            {
+                return "";
+            }
+        }
+
+
+    }
+    public static class IntListConverter extends NumberListConverter<Integer>
+    {
+
+        /**
+         * {@inheritDoc}
+         * overrides @see jakarta.persistence.AttributeConverter#convertToEntityAttribute(java.lang.Object)
+         */
+        @Override
+        public List<Integer> convertToEntityAttribute(String dbData) {
+           if (dbData != null)
+           {
+               return Stream.of(dbData.split(SPLIT_CHAR)).map(Integer::parseInt).toList();
+           }
+           else return new ArrayList<>();
+
+        }
+
+    }
+    public static class DoubleListConverter extends NumberListConverter<Double>
+    {
+
+        /**
+         * {@inheritDoc}
+         * overrides @see jakarta.persistence.AttributeConverter#convertToEntityAttribute(java.lang.Object)
+         */
+        @Override
+        public List<Double> convertToEntityAttribute(String dbData) {
+           if (dbData != null)
+           {
+               return Stream.of(dbData.split(SPLIT_CHAR)).map(Double::parseDouble).toList();
+           }
+           else return new ArrayList<>();
+
+        }
+
+    }
+    public static class BooleanListConverter extends NumberListConverter<Boolean> 
+    {
+
+        /**
+         * {@inheritDoc}
+         * overrides @see jakarta.persistence.AttributeConverter#convertToEntityAttribute(java.lang.Object)
+         */
+        @Override
+        public List<Boolean> convertToEntityAttribute(String dbData) {
+            if (dbData != null)
+           {
+               return Stream.of(dbData.split(SPLIT_CHAR)).map(Boolean::parseBoolean).toList();
+           }
+           else return new ArrayList<>();
+
+
+        }
+
+    }
+}
+
+

runtime/java/src/main/java/org/ivoa/vodml/testing/AutoDBRoundTripTest.java

@@ -33,7 +33,7 @@ public abstract class AutoDBRoundTripTest <M extends VodmlModel<M>, I, T extends
      * @param e the entity to be tested.
      */
     public abstract void testEntity(T e);
-
+    
     @Test
     void testRDBRoundTrip()
     {
@@ -46,7 +46,8 @@ void testRDBRoundTrip()
         testEntity(result.retval);
 
     }
-
+
+
 }
 
 

runtime/java/src/main/java/org/ivoa/vodml/validation/AbstractBaseValidation.java

@@ -39,7 +39,17 @@
 import org.ivoa.vodml.jpa.JPAManipulationsForObjectType;
 import org.ivoa.vodml.validation.ModelValidator.ValidationResult;
 
+/**
+ * Base Class for doing validating tests.
+ */
 public abstract class AbstractBaseValidation {
+    /**
+     * Do a JSON round trip of a model instance.
+     * @param m A model instance.
+     * @return The result of the round trip test.
+     * @param <T> The Model class .
+     * @throws JsonProcessingException
+     */
     protected  <T> RoundTripResult<T> roundTripJSON(VodmlModel<T> m) throws JsonProcessingException {
         T model = m.management().theModel();
         if(m.management().hasReferences())
@@ -57,6 +67,10 @@ protected  <T> RoundTripResult<T> roundTripJSON(VodmlModel<T> m) throws JsonProc
 
     }
 
+    /**
+     * The result of doing a round trip test.
+     * @param <T> the model class.
+     */
     public static class RoundTripResult <T>  {
         public final boolean isValid;
         public final T retval;
@@ -66,6 +80,18 @@ public static class RoundTripResult <T>  {
         }
     }
 
+    /**
+     * Do a XML round trip of a model instance.
+     * @param vodmlModel a model instance.
+     * @return the result of doing a round trip.
+     * @param <T> The model class.
+     * @throws ParserConfigurationException
+     * @throws JAXBException
+     * @throws PropertyException
+     * @throws TransformerFactoryConfigurationError
+     * @throws TransformerConfigurationException
+     * @throws TransformerException
+     */
     protected <T extends VodmlModel<T>> RoundTripResult<T> roundtripXML(VodmlModel<T> vodmlModel) throws ParserConfigurationException, JAXBException,
     PropertyException, TransformerFactoryConfigurationError,
     TransformerConfigurationException, TransformerException {
@@ -108,7 +134,16 @@ protected <T extends VodmlModel<T>> RoundTripResult<T> roundtripXML(VodmlModel<T
         T modelin = el.getValue();
         return new RoundTripResult<T>(!vc.hasEvents(), modelin);
     }
-
+
+    /**
+     * Do an RDB round trip of a model instance.
+     * @param modelManagement Then model management
+     * @param entity The entity to round trip.
+     * @return
+     * @param <M> the model class.
+     * @param <I> The type of the identifier for the entity.
+     * @param <T> The type of the entity.
+     */
     protected <M, I, T extends JPAManipulationsForObjectType<I>> RoundTripResult<T> roundtripRDB(ModelManagement<M> modelManagement, T  entity)
     {
 
@@ -118,7 +153,8 @@ protected <M, I, T extends JPAManipulationsForObjectType<I>> RoundTripResult<T>
         em.persist(entity);
         em.getTransaction().commit();
         I id = entity.getId();
-
+        String dumpfile = setDbDumpFile();
+        if(dumpfile!= null) dumpDbData(em, dumpfile);
         //flush any existing entities
         em.clear();
         em.getEntityManagerFactory().getCache().evictAll();
@@ -131,7 +167,12 @@ protected <M, I, T extends JPAManipulationsForObjectType<I>> RoundTripResult<T>
         return new RoundTripResult<T>(true, r);
 
     }
-
+
+    /**
+     * Create an Entity manager for a memory-based test database;
+     * @param puname the persistence unit name of the JPA DB.
+     * @return the EntityManager for the database.
+     */
     protected EntityManager setupH2Db(String puname){
         Map<String, String> props = new HashMap<>();
 
@@ -173,7 +214,14 @@ protected EntityManager setupH2Db(String puname){
         return em;
 
     }
-
+
+    /**
+     * Validate a model instance. This is done via JAXB.
+     * @param m the model instance.
+     * @return result of the validation.
+     * @param <T> the model class.
+     * @throws JAXBException exception when there is a JAXB problem.
+     */
     protected <T> ValidationResult validateModel(VodmlModel<T> m) throws JAXBException {
 
         final ModelDescription desc = m.descriptor();
@@ -198,4 +246,12 @@ protected void dumpDbData(jakarta.persistence.EntityManager em, String filename)
             });
     }
 
+    /**
+     * set the name of the file to which the dbDump is written. The default is null so that no file is written.
+     * @return the filename.
+     */
+    protected String setDbDumpFile() {
+        return  null;
+    }
+
 }