first attempt at automatic deletion taking into account contained ref…

…erences.

* necessary to delete the referrers first, as JPA ordering is not guaranteed
* does not deal with the case that the referrer is at different level.

doc/guide/modelling/TransformingToVODML.md

@@ -4,9 +4,12 @@ Creating VO-DML from other Data Models
 It is possible to start with an XML schema that can be transferred to VODSL with 
 
 ```shell
-gradle vodmlXsdToVodsl --xsd mymodel.xsd --dsl mymodel.vodsl
+gradle vodmlXsdToVodsl --xsd `pwd`/mymodel.xsd --dsl mymodel.vodsl
 ```
 
+Note that it is necessary to use the full path for the input file.
+
+
 The transformation does not cope with all of the "styles" XML schema that are possible, so that it is likely that
 the generated VODSL will need further hand editing.
 

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

@@ -9,7 +9,7 @@
       <title></title>
       <author>pharriso</author>
       <version>0.1</version>
-      <lastModified>2024-10-19T13:44:44Z</lastModified>
+      <lastModified>2024-11-21T13:44:44Z</lastModified>
       <import>
         <name>null</name><!--should not be needed in modern vo-dml -->
         <url>IVOA-v1.0.vo-dml.xml</url>
@@ -196,7 +196,7 @@
                    <vodml-ref>lifecycleTest:ReferredLifeCycle</vodml-ref>
                  </datatype>
                  <multiplicity>
-                   <minOccurs>1</minOccurs>
+                   <minOccurs>0</minOccurs>
                    <maxOccurs>1</maxOccurs>
                  </multiplicity>
                </reference>

models/sample/test/lifecycleTest.vodsl

@@ -43,7 +43,7 @@ otype ATest3 { /*  fails the "unique composition rule" in schematron if the one
  *  but this should be unlikely if a contained type instance is created at the same time as its container instance.
 	*/
 	contained : Contained @+ as composition ""; //vodsl tooling does not flag this- but the vodml schematron does.
-	refBad references ReferredLifeCycle ""; //this should be lifecycle warning
+	refBad @? references ReferredLifeCycle ""; //this should be lifecycle warning
 }
 
 otype ATest4 {

runtime/java/build.gradle.kts

@@ -6,7 +6,7 @@ plugins {
     signing
 }
 group = "org.javastro.ivoa.vo-dml"
-version = "0.8.2"
+version = "0.8.3"
 
 
 dependencies {
@@ -25,7 +25,7 @@ dependencies {
 
     testImplementation("org.junit.jupiter:junit-jupiter-api:5.9.2")
     testRuntimeOnly("org.junit.jupiter:junit-jupiter-engine:5.9.2")
-    testRuntimeOnly("ch.qos.logback:logback-classic:1.4.7")
+    testRuntimeOnly("ch.qos.logback:logback-classic:1.4.12")
 }
 
 

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

@@ -3,8 +3,11 @@
  * Created on 29/03/2022 by Paul Harrison ([email protected]).
  */
 
+import jakarta.persistence.EntityManager;
+
 /**
  * Interface to implement some common manipulations in JPA.
+ * This interface will be implemented on ObjectTypes.
  */
 public interface JPAManipulationsForObjectType <ID> extends JPAManipulations {
 
@@ -13,7 +16,13 @@ public interface JPAManipulationsForObjectType <ID> extends JPAManipulations {
     * @return the database ID.
     */
    ID getId();
-
-
+
+   /**
+    * Delete the entity from the database. This will take into account any ordering necessary because of any contained references.
+    * If there are no contained references - then this will be equivalent to em.delete(this), however there might be some efficiency built in via bulk deletion.
+    * @param em the entity manager
+    */
+   void delete(EntityManager em);
+
 
 }

tools/Developing.md

@@ -18,6 +18,7 @@ of useful functions that can answer model questions such as "has subtypes" defin
 * 
 There is a [sample](./gradletooling/sample) project that acts as a test bench for the plugin.
 
+http://dh.obdurodon.org/xslt3.xhtml is a good summary of the new features in XSLT 3.0.
 
 ## Local testing
 

tools/gradletooling/TODO.md

@@ -127,4 +127,8 @@ VODML Tooling TODO
 * using dataclasses - need python 3.10 for the kw_only field specifier - might do better just generating multiple  `__init__()` rather than relying on the dataclass generation.
 
 # Distribution
-  * need better directory structure on IVOA site....
+  * need better directory structure on IVOA site....
+
+
+
+

tools/gradletooling/gradle-plugin/src/main/kotlin/net/ivoa/vodml/gradle/plugin/VodmlGradlePlugin.kt

@@ -163,7 +163,7 @@ class VodmlGradlePlugin: Plugin<Project> {
 
 
         //add the dependencies for JAXB and JPA - using the hibernate implementation
-       listOf("org.javastro.ivoa.vo-dml:vodml-runtime:0.8.2",
+       listOf("org.javastro.ivoa.vo-dml:vodml-runtime:0.8.3",
             "jakarta.xml.bind:jakarta.xml.bind-api:4.0.0",
             "org.glassfish.jaxb:jaxb-runtime:4.0.2",
 //             "org.eclipse.persistence:org.eclipse.persistence.jpa:2.7.10",  // supports JPA 2.2

tools/gradletooling/sample/build.gradle.kts

@@ -110,7 +110,7 @@ python {
     pip("pytest:7.3.1")
     pip("SQLAlchemy:2.0.30")
     pip("xsdata[lxml,cli]:24.5")
-    pip("pydantic:2.7.1")
+    pip("pydantic:2.9.2")
     pip("sqlmodel:0.0.22")
     pip("xsdata-pydantic:24.5")
 }

tools/gradletooling/sample/src/test/java/org/ivoa/dm/lifecycle/LifeCycleDetailedTest.java

@@ -64,6 +64,8 @@ void setUp() throws Exception {
     model = new LifecycleTestModel();
 //    model.addContent(atest);
     model.addContent(atest2);
+    model.addContent(atest3);
+
   }
 
   /**
@@ -128,7 +130,29 @@ void copyTest() {
     // references
     assertEquals("rc1", atest2prime.refcont.test3); // should be pointing to above
 
-    // assertEquals("rc1" ,atest3.refBad.test3);//TODO not sure which way we want these to work.
+   //  assertEquals("rc1" ,atest3.refBad.test3);//TODO not sure which way we want these to work - it is actually a failure of design
+
+  }
+
+  @Test
+  void deleteTest() {
+       jakarta.persistence.EntityManager em =
+        setupH2Db(SampleModel.pu_name()); // IMPL build means that everything is in one
+    // persistence unit.
+    em.getTransaction().begin();
+    model.management().persistRefs(em);
+    em.persist(atest2);
+    em.getTransaction().commit();
+    Long id = atest2.getId();
 
+    // flush any existing entities
+    em.clear();
+    em.getEntityManagerFactory().getCache().evictAll();
+    ATest2 atest2in = em.createNamedQuery("ATest2.findById", ATest2.class).setParameter("id", id).getSingleResult();
+    assertNotNull(atest2in);
+    em.getTransaction().begin();
+    atest2in.delete(em); //IMPL
+    em.getTransaction().commit();
+
   }
 }

tools/gradletooling/sample/src/test/java/org/ivoa/dm/serializationsample/SerializationExampleVocabTest.java

@@ -3,6 +3,8 @@
 import static org.junit.jupiter.api.Assertions.fail;
 import org.junit.jupiter.api.Test;
 
+import jakarta.persistence.EntityManager;
+
 /*
  * Created on 16/05/2023 by Paul Harrison ([email protected]).
  */
@@ -31,6 +33,13 @@ public BaseC copyMe() {
                         "Type1728055728713.copyMe() not implemented");
 
             }
+
+            @Override
+            public void delete(EntityManager em) {
+                // TODO Auto-generated method stub
+                throw new  UnsupportedOperationException("JPAManipulationsForObjectType<Long>.delete() not implemented");
+
+            }
         }, "eval");
         fail("should have thown exception for value outside vocab");
     } catch (Exception e) {

tools/xslt/common-structure-functions.xsl

@@ -308,11 +308,8 @@ note - only define functions in here as it is included in the schematron rules
         <xsl:param name="vodml-ref" as="xsd:string"/>
         <xsl:choose>
             <xsl:when test="$models/key('ellookup',$vodml-ref)">
-                <xsl:variable name="el" as="element()">
-                    <xsl:copy-of select="$models/key('ellookup',$vodml-ref)" />
-                </xsl:variable>
-                <xsl:sequence select="$el/reference/datatype/vodml-ref"/>
-                <xsl:for-each select="$el/composition/datatype/vodml-ref">
+                <xsl:sequence select="for $t in ($models/key('ellookup',$vodml-ref),vf:baseTypes($vodml-ref)) return $t/reference/datatype/vodml-ref"/>
+                <xsl:for-each select="for $t in ($models/key('ellookup',$vodml-ref),vf:baseTypes($vodml-ref)) return $t/composition/datatype/vodml-ref">
                     <!--                            <xsl:message><xsl:value-of select="concat('subtype of ',$vodml-ref, ' is ', name)" /></xsl:message>-->
                     <xsl:sequence select="vf:referenceTypesInContainmentHierarchy(.)"/>
                 </xsl:for-each>
@@ -544,15 +541,8 @@ note - only define functions in here as it is included in the schematron rules
     <xsl:function name="vf:isTypeContainedBelow" as="xsd:boolean">
         <xsl:param name="type-vodml-ref"  as="xsd:string" />
         <xsl:param name="root-vodml-ref" as="xsd:string"/>
-        <xsl:variable name="root" select="$models/key('ellookup',$root-vodml-ref)"/>
-        <xsl:choose>
-            <xsl:when test="$root/composition">
-                <xsl:sequence  select="$type-vodml-ref = vf:containedTypes($root-vodml-ref)"/>
-            </xsl:when>
-            <xsl:otherwise>
-                <xsl:sequence select="false()"/>
-            </xsl:otherwise>
-        </xsl:choose>
+        <xsl:variable name="ct" select="vf:containedTypes($root-vodml-ref)"/>
+        <xsl:sequence  select="$type-vodml-ref = $ct"/>
     </xsl:function>
 
 

tools/xslt/common.xsl

@@ -161,7 +161,10 @@
     <xsl:value-of select="concat(./ancestor::vo-dml:model/name,':',.)" />
   </xsl:template>
 
-
+  <xsl:function name="vf:multiple" as="xsd:boolean">
+    <xsl:param name="p" as="element()"/>
+    <xsl:sequence select="xsd:int($p/multiplicity/maxOccurs) ne 1"/>
+  </xsl:function>
 
   <xsl:template match="multiplicity" mode="tostring">
     <xsl:variable name="lower">

tools/xslt/jpa.xsl

@@ -495,7 +495,46 @@
   </xsl:template>
   <xsl:template match="*" mode="jpaConfig"><!-- do nothing --></xsl:template>
 
+  <!-- template to do smart deletion in the case of contained references
+  TODO could also do something better in the case of bulk deletion.-->
+  <xsl:template match="objectType" mode="jpadeleter">
+      <xsl:variable name="vodml-ref" select="vf:asvodmlref(current())"/>
+      <xsl:if test="not(@abstract)">
+    /**
+      * {@inheritDoc}
+      */
+      @Override
+      public void delete(jakarta.persistence.EntityManager em) {
+      <xsl:variable name="crefs" select="distinct-values(vf:containedReferencesInContainmentHierarchy($vodml-ref))"/>
 
+      <xsl:choose>
+          <xsl:when test="count($crefs)> 0">
+              //has contained references <xsl:value-of select="string-join($crefs,',')"/>
+              <xsl:variable name="by" select="distinct-values(for $i in $crefs return vf:referredBy($i))"/>
+              //referred to by <xsl:value-of select="concat(string-join($by,','),$nl)"/>
+              <!-- TODO this only deals with referrers same level of containment.... -->
+              <xsl:for-each select="for $v in (vf:baseTypes($vodml-ref),$models/key('ellookup',$vodml-ref)) return $v/(composition)[datatype/vodml-ref= $by]"> <!--assume JPA will deal with attributes OK... -->
+                  <xsl:choose>
+                      <xsl:when test="vf:multiple(current())">
+                          <!-- IMPL perhaps we could do bulk delete to speed things up -->
+                          <xsl:value-of select="vf:javaMemberName(current()/name)"/>.stream().forEach(i -> em.remove(i));
+                      </xsl:when>
+                      <xsl:otherwise>
+                          em.remove(<xsl:value-of select="vf:javaMemberName(current()/name)"/>);
+                      </xsl:otherwise>
+                  </xsl:choose>
+
+              </xsl:for-each>
+              em.remove(this); // finish up with itself.
+          </xsl:when>
+          <xsl:otherwise>
+              em.remove(this); // nothing special to do
+          </xsl:otherwise>
+      </xsl:choose>
+
+      }
+      </xsl:if>
+  </xsl:template>
 
 
 </xsl:stylesheet>

tools/xslt/vo-dml2java.xsl

@@ -762,6 +762,7 @@
 
       <xsl:apply-templates select="." mode="jpawalker"/>
       <xsl:apply-templates select="." mode="jparefs"/>
+      <xsl:apply-templates select="./self::objectType" mode="jpadeleter"/>
 
 <!--      <xsl:if test="local-name() eq 'dataType'">-->
 <!--          <xsl:apply-templates select="." mode="JPAConverter"/>-->

tools/xslt/vo-dml2md.xsl

@@ -397,7 +397,7 @@ classDiagram
         <xsl:if test="constraint[ends-with(@xsi:type,':NaturalKey')]">
             <xsl:value-of select="concat(' :material-key-variant:{title=',$dq,'natural key',$dq,'}')"/>
         </xsl:if>
-        <xsl:if test="./ancestor-or-self::reference">
+        <xsl:if test="./self::reference">
             <xsl:value-of select="concat(' :material-arrow-top-right:{title=',$dq,'reference',$dq,'}')"/>
         </xsl:if>
 

xsd/vo-dml-binding.xsd

@@ -77,7 +77,12 @@ targetNamespace="http://www.ivoa.net/xml/vodml-binding/v0.9.1" attributeFormDefa
            <xsd:documentation>the list of type mappings for the model.</xsd:documentation>
         </xsd:annotation>
      </xsd:element>
-     <xsd:element name="type-detail" type="TypeDetail" minOccurs="0" maxOccurs="1"></xsd:element>
+     <xsd:element name="type-detail" type="TypeDetail" minOccurs="0" maxOccurs="unbounded">
+         <xsd:annotation>
+             <xsd:documentation>the list of type detail the model.</xsd:documentation>
+         </xsd:annotation>
+
+     </xsd:element>
   </xsd:sequence>
 </xsd:complexType>
   <xsd:complexType name="xmlnsMapping">