Indexer needs JAX-B dependencies to work with Java 9+

[Shooter3k]

Greetings,

I keep getting the following error in the log file (many times) when trying to index. The index seems to finish successfully although I don't know what these errors are or what they mean. I've been running opengrok for many years and this is the first time I've run into this sort of error without being able to figure out why it's happening. Any advice is appreciated.

Please note: this is running in a corporate environment and "simple" OS patches may or may not be an option.

Opengrok Version: opengrok-1.1-rc60 (it's been happening at least since rc41)

java --version
java 10.0.2 2018-07-17
Java(TM) SE Runtime Environment 18.3 (build 10.0.2+13)
Java HotSpot(TM) 64-Bit Server VM 18.3 (build 10.0.2+13, mixed mode)

Apache Tomcat/8.5.28

[~]$ uname -a
Linux 2.6.32-754.2.1.el6.x86_64 #1 SMP Tue Jul 3 16:37:52 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux

[~]$ cat /etc/issue.net
Red Hat Enterprise Linux Server release 6.10 (Santiago)
Kernel \r on an \m

Error in log file after running index command(s):

2018-10-16 12:58:33.008 WARNING [org.glassfish.jersey.internal.Errors] - The following warnings have been detected: WARNING: HK2 failure has been detected in a code that does not run in an active Jersey Error scope.
WARNING: HK2 service reification failed for [org.glassfish.jersey.jaxb.internal.XmlRootObjectJaxbProvider$General] with an exception:
MultiException stack 1 of 2
java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
at java.base/java.lang.Class.getDeclaredConstructors0(Native Method)
at java.base/java.lang.Class.privateGetDeclaredConstructors(Unknown Source)
at java.base/java.lang.Class.getDeclaredConstructors(Unknown Source)
at org.jvnet.hk2.internal.Utilities$3.run(Utilities.java:1378)
at org.jvnet.hk2.internal.Utilities$3.run(Utilities.java:1374)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at org.jvnet.hk2.internal.Utilities.getAllConstructors(Utilities.java:1374)
at org.jvnet.hk2.internal.Utilities.findProducerConstructor(Utilities.java:1317)
at org.jvnet.hk2.internal.DefaultClassAnalyzer.getConstructor(DefaultClassAnalyzer.java:83)
at org.glassfish.jersey.inject.hk2.JerseyClassAnalyzer.getConstructor(JerseyClassAnalyzer.java:148)
at org.jvnet.hk2.internal.Utilities.getConstructor(Utilities.java:180)
at org.jvnet.hk2.internal.ClazzCreator.initialize(ClazzCreator.java:129)
at org.jvnet.hk2.internal.ClazzCreator.initialize(ClazzCreator.java:180)
at org.jvnet.hk2.internal.SystemDescriptor.internalReify(SystemDescriptor.java:740)
at org.jvnet.hk2.internal.SystemDescriptor.reify(SystemDescriptor.java:694)
at org.jvnet.hk2.internal.ServiceLocatorImpl.reifyDescriptor(ServiceLocatorImpl.java:464)
at org.jvnet.hk2.internal.ServiceLocatorImpl.narrow(ServiceLocatorImpl.java:2310)
at org.jvnet.hk2.internal.ServiceLocatorImpl.access$1200(ServiceLocatorImpl.java:128)
at org.jvnet.hk2.internal.ServiceLocatorImpl$9.compute(ServiceLocatorImpl.java:1395)
at org.jvnet.hk2.internal.ServiceLocatorImpl$9.compute(ServiceLocatorImpl.java:1390)
at org.glassfish.hk2.utilities.cache.internal.WeakCARCacheImpl.compute(WeakCARCacheImpl.java:128)
at org.jvnet.hk2.internal.ServiceLocatorImpl.internalGetAllServiceHandles(ServiceLocatorImpl.java:1452)
at org.jvnet.hk2.internal.ServiceLocatorImpl.getAllServiceHandles(ServiceLocatorImpl.java:1377)
at org.jvnet.hk2.internal.ServiceLocatorImpl.getAllServiceHandles(ServiceLocatorImpl.java:1366)
at org.glassfish.jersey.inject.hk2.AbstractHk2InjectionManager.getAllServiceHolders(AbstractHk2InjectionManager.java:158)
at org.glassfish.jersey.inject.hk2.ImmediateHk2InjectionManager.getAllServiceHolders(ImmediateHk2InjectionManager.java:54)
at org.glassfish.jersey.internal.inject.Providers.getServiceHolders(Providers.java:337)
at org.glassfish.jersey.internal.inject.Providers.getCustomProviders(Providers.java:175)
at org.glassfish.jersey.message.internal.MessageBodyFactory.initialize(MessageBodyFactory.java:238)
at org.glassfish.jersey.message.internal.MessageBodyFactory$MessageBodyWorkersConfigurator.postInit(MessageBodyFactory.java:136)
at org.glassfish.jersey.client.ClientConfig$State.lambda$initRuntime$2(ClientConfig.java:470)
at java.base/java.util.Arrays$ArrayList.forEach(Unknown Source)
at org.glassfish.jersey.client.ClientConfig$State.initRuntime(ClientConfig.java:470)
at org.glassfish.jersey.internal.util.collection.Values$LazyValueImpl.get(Values.java:341)
at org.glassfish.jersey.client.ClientConfig.getRuntime(ClientConfig.java:826)
at org.glassfish.jersey.client.ClientRequest.getConfiguration(ClientRequest.java:285)
at org.glassfish.jersey.client.JerseyInvocation.validateHttpMethodAndEntity(JerseyInvocation.java:143)
at org.glassfish.jersey.client.JerseyInvocation.(JerseyInvocation.java:112)
at org.glassfish.jersey.client.JerseyInvocation.(JerseyInvocation.java:108)
at org.glassfish.jersey.client.JerseyInvocation.(JerseyInvocation.java:99)
at org.glassfish.jersey.client.JerseyInvocation$Builder.method(JerseyInvocation.java:445)
at org.glassfish.jersey.client.JerseyInvocation$Builder.put(JerseyInvocation.java:334)
at org.opengrok.indexer.index.IndexDatabase.markProjectIndexed(IndexDatabase.java:385)
at org.opengrok.indexer.index.IndexDatabase.update(IndexDatabase.java:522)
at org.opengrok.indexer.index.IndexDatabase$1.run(IndexDatabase.java:226)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.lang.ClassNotFoundException: javax.xml.bind.JAXBException
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(Unknown Source)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(Unknown Source)
at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
... 50 more
MultiException stack 2 of 2
java.lang.IllegalArgumentException: Errors were discovered while reifying SystemDescriptor(
implementation=org.glassfish.jersey.jaxb.internal.XmlRootObjectJaxbProvider$General
contracts={javax.ws.rs.ext.MessageBodyReader}
scope=javax.inject.Singleton
qualifiers={}
descriptorType=CLASS
descriptorVisibility=NORMAL
metadata=
rank=0
loader=null
proxiable=null
proxyForSameScope=null
analysisName=null
id=73
locatorId=2
identityHashCode=1635286880
reified=false)
at org.jvnet.hk2.internal.SystemDescriptor.reify(SystemDescriptor.java:705)
at org.jvnet.hk2.internal.ServiceLocatorImpl.reifyDescriptor(ServiceLocatorImpl.java:464)
at org.jvnet.hk2.internal.ServiceLocatorImpl.narrow(ServiceLocatorImpl.java:2310)
at org.jvnet.hk2.internal.ServiceLocatorImpl.access$1200(ServiceLocatorImpl.java:128)
at org.jvnet.hk2.internal.ServiceLocatorImpl$9.compute(ServiceLocatorImpl.java:1395)
at org.jvnet.hk2.internal.ServiceLocatorImpl$9.compute(ServiceLocatorImpl.java:1390)
at org.glassfish.hk2.utilities.cache.internal.WeakCARCacheImpl.compute(WeakCARCacheImpl.java:128)
at org.jvnet.hk2.internal.ServiceLocatorImpl.internalGetAllServiceHandles(ServiceLocatorImpl.java:1452)
at org.jvnet.hk2.internal.ServiceLocatorImpl.getAllServiceHandles(ServiceLocatorImpl.java:1377)
at org.jvnet.hk2.internal.ServiceLocatorImpl.getAllServiceHandles(ServiceLocatorImpl.java:1366)
at org.glassfish.jersey.inject.hk2.AbstractHk2InjectionManager.getAllServiceHolders(AbstractHk2InjectionManager.java:158)
at org.glassfish.jersey.inject.hk2.ImmediateHk2InjectionManager.getAllServiceHolders(ImmediateHk2InjectionManager.java:54)
at org.glassfish.jersey.internal.inject.Providers.getServiceHolders(Providers.java:337)
at org.glassfish.jersey.internal.inject.Providers.getCustomProviders(Providers.java:175)
at org.glassfish.jersey.message.internal.MessageBodyFactory.initialize(MessageBodyFactory.java:238)
at org.glassfish.jersey.message.internal.MessageBodyFactory$MessageBodyWorkersConfigurator.postInit(MessageBodyFactory.java:136)
at org.glassfish.jersey.client.ClientConfig$State.lambda$initRuntime$2(ClientConfig.java:470)
at java.base/java.util.Arrays$ArrayList.forEach(Unknown Source)
at org.glassfish.jersey.client.ClientConfig$State.initRuntime(ClientConfig.java:470)
at org.glassfish.jersey.internal.util.collection.Values$LazyValueImpl.get(Values.java:341)
at org.glassfish.jersey.client.ClientConfig.getRuntime(ClientConfig.java:826)
at org.glassfish.jersey.client.ClientRequest.getConfiguration(ClientRequest.java:285)
at org.glassfish.jersey.client.JerseyInvocation.validateHttpMethodAndEntity(JerseyInvocation.java:143)
at org.glassfish.jersey.client.JerseyInvocation.(JerseyInvocation.java:112)
at org.glassfish.jersey.client.JerseyInvocation.(JerseyInvocation.java:108)
at org.glassfish.jersey.client.JerseyInvocation.(JerseyInvocation.java:99)
at org.glassfish.jersey.client.JerseyInvocation$Builder.method(JerseyInvocation.java:445)
at org.glassfish.jersey.client.JerseyInvocation$Builder.put(JerseyInvocation.java:334)
at org.opengrok.indexer.index.IndexDatabase.markProjectIndexed(IndexDatabase.java:385)
at org.opengrok.indexer.index.IndexDatabase.update(IndexDatabase.java:522)
at org.opengrok.indexer.index.IndexDatabase$1.run(IndexDatabase.java:226)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)

[vladak]

I think this has to do with the fact that you are running Java 10. The advice from https://stackoverflow.com/questions/43574426/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-j is to run java with --add-modules java.xml.bind. Actually, #2355 displays that someone is already using this workaround.

As for what effect this can have - the project might not be marked as indexed and therefore will not appear in the UI.

[vladak]

According to the above stackoverflow link, the proper solution is to add dependencies on JAX-B APIs in Maven.

[vladak]

Actually, some of the suggested dependencies are already present in opengrok-web Maven module but not in the opengrok-indexer module, hence the failure.