Fix JAXB unmarshalling error when compiling to native #37643

rysurd · 2023-12-10T16:22:54Z

The root cause was that not all classes annotated with Jaxb annotations were marked for reflection when using native compilation, in case there we have fields that are declared in parent classes. The fix made was to replace the ReflectiveClassBuildItem from JaxbProcessor with ReflectiveHierarchyBuildItem in order to mark inherited fields for native compilation.

There is a warning throw stating that some classes are not indexed via Jandex. If anyone know how to fix this don't hesitate to tell me ! I have added the jandex maven plugins as documented in the Quarkus doc but it changes nothing. For instance :

[WARNING] [io.quarkus.deployment.steps.ReflectiveHierarchyStep] Unable to properly register the hierarchy of the following classes for reflection as they are not in the Jandex index:
        - com.sun.istack.FinalArrayList (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - com.sun.org.apache.xerces.internal.impl.dv.xs.SchemaDVFactoryImpl (source: JaxbProcessor > com.sun.org.apache.xerces.internal.impl.dv.xs.SchemaDVFactoryImpl)
        - com.sun.org.apache.xpath.internal.functions.FuncNot (source: JaxbProcessor > com.sun.org.apache.xpath.internal.functions.FuncNot)
        - com.sun.xml.internal.stream.XMLInputFactoryImpl (source: JaxbProcessor > com.sun.xml.internal.stream.XMLInputFactoryImpl)
        - com.sun.xml.internal.stream.XMLOutputFactoryImpl (source: JaxbProcessor > com.sun.xml.internal.stream.XMLOutputFactoryImpl)
        - jakarta.activation.MimeType (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - javax.xml.namespace.QName (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.annotation.AnnotationReader (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.annotation.Locatable (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.Adapter (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.BuiltinLeafInfo (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.ClassInfo (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.Element (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.ElementInfo (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.ElementPropertyInfo (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.EnumLeafInfo (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.ErrorHandler (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.ID (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.NonElement (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.PropertyInfo (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.PropertyKind (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.TypeInfo (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.TypeInfoSet (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.core.WildcardMode (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.model.nav.Navigator (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.runtime.IllegalAnnotationException (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.runtime.Location (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
        - org.glassfish.jaxb.core.v2.runtime.RuntimeUtil$ToStringAdapter (source: JaxbProcessor > org.glassfish.jaxb.core.v2.runtime.RuntimeUtil$ToStringAdapter)
        - org.xml.sax.Locator (source: JaxbProcessor > jakarta.xml.bind.annotation.XmlAccessorType)
Consider adding them to the index either by creating a Jandex index for your dependency via the Maven plugin, an empty META-INF/beans.xml or quarkus.index-dependency properties.

rysurd · 2023-12-10T19:12:04Z

@gsmet @zakkak Hello ! I have opened the PR for the jaxb unmarshalling error. I included an integration test which reproduce the same issue and check if it works or not.

gsmet

Thanks for having a look at this. I think we need to be more careful about when we use the hierachy feature: it should only be used on domain classes that will be serialized with JAXB, not on everything that was declared for reflection.
That's why you end up with all these warnings.

You can have a closer look if you want or I can have a look if you prefer, let me know.

In any case, it's nice to have a test case as we will be able to test that everything is fine if we make adjustments.

gsmet · 2023-12-11T12:00:52Z

extensions/jaxb/deployment/src/main/java/io/quarkus/jaxb/deployment/JaxbProcessor.java

+            String className = xmlJavaTypeAdapterInstance.value().asClass().name().toString();
+            Type jandexType = Type.create(DotName.createSimple(className), Type.Kind.CLASS);
+            reflectiveClass.produce(new ReflectiveHierarchyBuildItem.Builder()
+                    .type(jandexType)
+                    .index(index)
+                    .source(getClass().getSimpleName() + " > " + jandexType.name().toString())
+                    .build());


My guess is that this change should be reverted and that's probably what causes the warnings.

gsmet · 2023-12-11T12:01:15Z

extensions/jaxb/deployment/src/main/java/io/quarkus/jaxb/deployment/JaxbProcessor.java

@@ -274,7 +288,7 @@ void ignoreWarnings(BuildProducer<ReflectiveHierarchyIgnoreWarningBuildItem> ign
    void registerClasses(
            BuildProducer<NativeImageSystemPropertyBuildItem> nativeImageProps,
            BuildProducer<ServiceProviderBuildItem> providerItem,
-            BuildProducer<ReflectiveClassBuildItem> reflectiveClass,
+            BuildProducer<ReflectiveHierarchyBuildItem> reflectiveClass,


My guess is that this change should be reverted and that's probably what causes the warnings.

gsmet · 2023-12-11T12:49:19Z

extensions/jaxb/deployment/src/main/java/io/quarkus/jaxb/deployment/JaxbProcessor.java

-    private void addReflectiveClass(BuildProducer<ReflectiveClassBuildItem> reflectiveClass, boolean methods, boolean fields,
-            String... className) {
-        reflectiveClass.produce(new ReflectiveClassBuildItem(methods, fields, className));
+    private void addReflectiveClass(BuildProducer<ReflectiveHierarchyBuildItem> reflectiveClass, boolean methods,


The call sites of this method would have to checked. I'm really not sure it makes sense to replace it in all cases (and might not even be necessary depending on when it's called).

gsmet · 2023-12-11T12:49:55Z

extensions/jaxb/runtime/pom.xml

+            <!-- The entity classes needs to be indexed -->
+            <plugin>
+                <groupId>io.smallrye</groupId>
+                <artifactId>jandex-maven-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>make-index</id>
+                        <goals>
+                            <goal>jandex</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>


Why is this needed? The entity classes should be in the app, not in the extension, shouldn't they?

That was an attempt to resolve the jandex issue but I think that's not the way to go indeed.

rysurd · 2023-12-12T13:17:45Z

Thanks for having a look at this. I think we need to be more careful about when we use the hierachy feature: it should only be used on domain classes that will be serialized with JAXB, not on everything that was declared for reflection. That's why you end up with all these warnings.

You can have a closer look if you want or I can have a look if you prefer, let me know.

In any case, it's nice to have a test case as we will be able to test that everything is fine if we make adjustments.

Thanks for your review! I did some changes according to your inputs but I still got the warning, even if now there are only jaxb classes involved. If you don't mind I would not say no to a little help to troubleshoot this ... :D Thanks a lot again!

EDIT : Found the issue :) I added a logic to filter out the JAXB classes themselves when looping over annotated classes. This is done so we only use the hierarchybuilditem on domain classes only, excluding JAXB's ones.

gsmet · 2023-12-12T15:27:50Z

I will have a look later this week. Thanks for pursuing this.

rysurd · 2023-12-16T14:40:09Z

@gsmet I think I resolved the issue with the Jandex warning ... Build seems ok now (No specific warnings or errors) so maybe if you have some time could you check on this please ? 😄 The integration test seems to do its job too as it failed (throwing the original issue) when using the main branch codebase and succeed when I use the fix.

Edit : Any chance to check this @gsmet ? (happy new year too 😄)

gsmet

@rysurd sorry for the delay, your latest changes look good.

I made some very small changes to make it more consistent with code we already had in the tree but these were really micro changes.

Let's see what CI has to say and merge!

quarkus-bot · 2024-01-12T18:19:02Z

✔️ The latest workflow run for the pull request has completed successfully.

It should be safe to merge provided you have a look at the other checks in the summary.

You can consult the Develocity build scans.

gsmet · 2024-01-12T18:23:49Z

Merged, thanks for your contribution!

rysurd · 2024-01-12T20:20:46Z

Merged, thanks for your contribution!

Thanks !

ppalaga · 2024-01-16T11:13:48Z

This change breaks both Quarkus CXF and Camel Quarkus - see apache/camel-quarkus#5650
I am checking whether we need to revert or whether there is a some way to keep the test in this PR working.

gsmet · 2024-01-16T12:53:28Z

@ppalaga I created https://github.com/quarkusio/quarkus/pull/38217/files that, I think, should mitigate the issues you're having. Let me know how it goes.

rysurd · 2024-01-16T13:30:53Z

Ah, sorry I should have catched that the extent of these changes would reach also into other libs ...

ppalaga · 2024-01-16T14:04:39Z

#36479 complained about ancestors of a JAXB class not being registered for reflection. The current change does much more, because ReflectiveHierarchyBuildItem does much more: it registers not only ancestors, but also all field types, type parameters, etc.
I'd vote for having a much more conservative fix that just climbs up the supertypes and registers those. A PR follows.

ppalaga · 2024-01-16T14:34:57Z

Here is my proposal: #38221

ppalaga · 2024-01-16T14:35:35Z

@rysurd @turing85 could you perhaps check that #38221 fixes your original issue?

turing85 · 2024-01-16T15:47:27Z

@ppalaga Seems to work 👍

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Fixing Jaxb unmarshalling error with native compilation

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gsmet changed the title ~~Fixing Jaxb unmarshalling error with native compilation~~ Fix JAXB unmarshalling error when compiling to native Jan 12, 2024

gsmet merged commit f3ffc50 into quarkusio:main Jan 12, 2024
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JAXB - Ignore @XmlTransient fields/methods when marking hierarchy for reflection #38217

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Fixup #36479 JAXB unmarshalling fails in native mode #38221

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Fix JAXB unmarshalling error when compiling to native #37643

Fix JAXB unmarshalling error when compiling to native #37643

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Fix JAXB unmarshalling error when compiling to native #37643

Fix JAXB unmarshalling error when compiling to native #37643

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