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Glassfish 5.1 missing modules from previous versions

We have an application running on Glassfish 5.0.1 and before that 4.1.1 versions. Recently server is updated to Glassfish 5.1.0 and our application can not be compiled due to the missing of javax.inject.Inject. This relevant jar was in the previous Glassfish versions (in the module folder).
So I'd like to hear that in glassfish 5.1 should we add this jar as an external library or is there a way to make this work in the latest glassfish ?

For GlassFish 5.1 the maven coordinates of dependencies are now jakarta.* instead of javax.*. So for the javax.inject.Inject annotation use the maven dependency
<dependency>
<groupId>jakarta.inject</groupId>
<artifactId>jakarta.inject-api</artifactId>
<version>1.0.3</version>
</dependency>

Liberty Websphere cannot load javax.transaction.Transactional when using java 11

After updating to Java 11 we get the following message:
[4/3/20, 11:47:09:184 CEST] 0000002d com.ibm.ws.classloading.internal.util.FeatureSuggestion I CWWKL0084W: The javax.transaction.TransactionManager class could not be loaded. Try enabling the jdbc-4.0 feature or a newer version of the feature in the server.xml file.
We are already using jdbc-4.3 (had the same message on 4.2 as well). The application itself does not give any errors that I can see. The application is made with maven that has the compile plugin configured with 11.
There are no problems when compiling and running tests for the application on java 11, and this only appears when deployed to liberty. Should we explicitly include a dependency for this in the war, or is this an issue that should be fixed in liberty?

From later releases on, Java EE is not included any more. The transaction classes are in the javax.transaction package.
Adding the following dependency should solve it:
<dependency>
<groupId>javax.transaction</groupId>
<artifactId>jta</artifactId>
<version>1.1</version>
</dependency>
(Not sure if it helps with your deployment, but it works with Spring Boot 2)

java.lang.IllegalArgumentException: Jetty ALPN/NPN has not been properly configured

Getting java.lang.IllegalArgumentException: Jetty ALPN/NPN has not been properly configured, while using gRPC(google pub/sub) to publish/consumes messages from Kafka.

Try adding a runtime dependency on netty-tcnative-boringssl-static. See gRPC's SECURITY.md. Note that the version of netty-tcnative necessary changes over time; you should look at the version of the document for a particular release (e.g., this is for 1.2.0).

Finally, went back to boot class class path approach. Prefixed the jetty-alpn.jar to boot class path and it starts working fine in cloud foundry now.

Adding the ALPN client JAR which matches my JDK version fixed this issue for me. In eclipse, you need to set up the jar as a bootstrap entry for the tomcat server.
You can find more info about it here : https://medium.com/#Parithi/jetty-alpn-npn-has-not-been-properly-configured-solution-418417ee6502

As suggested by google, use jetty container instead of tomcat, this solution works, but in our production, applications deployed on tomcat container, but of course I need it to work on tomcat in production.
On debugging the gRPC code, found that guava version causing the issue, updated the guava version 18.0, (where in some classes missed in previous versions), solved the problem , but failed while deploying in CF
Customized emebed-tomcat-core, and it works fine consistently, but again, team say no to custom tomcat container.
Java –jar apm-asset-xxxx.jar – works fine locally, but need to provide a custom command to CF start, didn’t have luxury to change the CF start process.
Finally, trick, the class loader to use tcnative-boring-ssl, library instead of tomcat-core library at runtime, by providing the following dependency in pom.xml. For the past 3 days, this solution is working CF.
org.springframework.boot
spring-boot-starter-web
org.hibernate
*
org.apache.tomcat.embed
tomcat-embed-core
org.apache.tomcat.embed
tomcat-embed-core
provided
Maven manifest plugin to promote the tc-native library to the top in the classloader.

In POM, try to place the gRPC dependency before the spring boot dependency (the order of dependencies matters). I did that and the issue was solved. For example:
<dependency>
<groupId>com.google.cloud</groupId>
<artifactId>google-cloud-language</artifactId>
<version>0.13.0-beta</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>

Jython 2.7.0 with jersey

I was using Jython standalone version 2.5.3 in my REST application. It was working fine. When I upgraded to Jython 2.7.0, I am getting the following exception,
javax.servlet.ServletException: org.glassfish.jersey.server.ContainerException: javax.xml.transform.TransformerFactoryConfigurationError: Provider org.python.apache.xalan.processor.TransformerFactoryImpl not found

Java xml classes were packaged and distributed with version 2.7.0. But if I understand it correctly Java SE comes with these classes. This issue is raised as a bug here. In order to avoid this exception add the xalan processor dependency in your pom.xml
<dependency>
<groupId>xalan</groupId>
<artifactId>xalan</artifactId>
<version>2.7.1</version>
</dependency>
Another solution would be to upgrade to the latest version of the jython-standalone jar. This issue is fixed in the latest release 2.7.1

NoSuchMethodError in javax.persistence.Table.indexes()[Ljavax/persistence/Index

I have a Play Framework application and I was using Hibernate 4.2.5.Final (which is retrieved via the Maven dependency manager). I decided to upgrade to Hibernate 4.3.0.Final, recompile my application successfully, and ran it.
I got the exception below, and haven't been able to figure out why. I downgraded back to 4.2.5 and this issue did not occur. I then, tried upgrading Hibernate with each Final release after 4.2.5. That is, I went from 4.2.5.Final to 4.2.6.Final, to 4.2.7.Final, to 4.2.8.Final and then to 4.3.Final. The issue does not occur until I upgrade to 4.3.0.Final.
Java version information
java version "1.7.0_45"
Java(TM) SE Runtime Environment (build 1.7.0_45-b18)
Java HotSpot(TM) 64-Bit Server VM (build 24.45-b08, mixed mode)
And exception:
play.api.UnexpectedException: Unexpected exception[NoSuchMethodError: javax.persistence.Table.indexes()[Ljavax/persistence/Index;]
at play.core.ReloadableApplication$$anonfun$get$1$$anonfun$apply$1$$anonfun$1.apply(ApplicationProvider.scala:152) ~[play_2.10.jar:2.2.1]
at play.core.ReloadableApplication$$anonfun$get$1$$anonfun$apply$1$$anonfun$1.apply(ApplicationProvider.scala:112) ~[play_2.10.jar:2.2.1]
at scala.Option.map(Option.scala:145) ~[scala-library.jar:na]
at play.core.ReloadableApplication$$anonfun$get$1$$anonfun$apply$1.apply(ApplicationProvider.scala:112) ~[play_2.10.jar:2.2.1]
at play.core.ReloadableApplication$$anonfun$get$1$$anonfun$apply$1.apply(ApplicationProvider.scala:110) ~[play_2.10.jar:2.2.1]
at scala.util.Success.flatMap(Try.scala:200) ~[scala-library.jar:na]
Caused by: java.lang.NoSuchMethodError: javax.persistence.Table.indexes()[Ljavax/persistence/Index;
at org.hibernate.cfg.annotations.EntityBinder.processComplementaryTableDefinitions(EntityBinder.java:936) ~[hibernate-core-4.3.0.Final.jar:4.3.0.Final]
at org.hibernate.cfg.AnnotationBinder.bindClass(AnnotationBinder.java:781) ~[hibernate-core-4.3.0.Final.jar:4.3.0.Final]
at org.hibernate.cfg.Configuration$MetadataSourceQueue.processAnnotatedClassesQueue(Configuration.java:3762) ~[hibernate-core-4.3.0.Final.jar:4.3.0.Final]
at org.hibernate.cfg.Configuration$MetadataSourceQueue.processMetadata(Configuration.java:3716) ~[hibernate-core-4.3.0.Final.jar:4.3.0.Final]
at org.hibernate.cfg.Configuration.secondPassCompile(Configuration.java:1410) ~[hibernate-core-4.3.0.Final.jar:4.3.0.Final]
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1844) ~[hibernate-core-4.3.0.Final.jar:4.3.0.Final]

I've ran into the same problem. The question here is that play-java-jpa artifact (javaJpa key in the build.sbt file) depends on a different version of the spec (version 2.0 -> "org.hibernate.javax.persistence" % "hibernate-jpa-2.0-api" % "1.0.1.Final").
When you added hibernate-entitymanager 4.3 this brought the newer spec (2.1) and a different factory provider for the entitymanager. Basically you ended up having both jars in the classpath as transitive dependencies.
Edit your build.sbt file like this and it will temporarily fix you problem until play releases a new version of the jpa plugin for the newer api dependency.
libraryDependencies ++= Seq(
javaJdbc,
javaJpa.exclude("org.hibernate.javax.persistence", "hibernate-jpa-2.0-api"),
"org.hibernate" % "hibernate-entitymanager" % "4.3.0.Final"
)
This is for play 2.2.x. In previous versions there were some differences in the build files.

Hibernate 4.3 is the first version to implement the JPA 2.1 spec (part of Java EE 7). And it's thus expecting the JPA 2.1 library in the classpath, not the JPA 2.0 library. That's why you get this exception: Table.indexes() is a new attribute of Table, introduced in JPA 2.1

I update my Hibernate JPA to 2.1 and It works.
<dependency>
<groupId>org.hibernate.javax.persistence</groupId>
<artifactId>hibernate-jpa-2.1-api</artifactId>
<version>1.0.0.Final</version>
</dependency>

You probablly have 2 different versions of hibernate-jpa-api on the classpath. To check that run:
mvn dependency:tree >dep.txt
Then search if there are hibernate-jpa-2.0-api and hibernate-jpa-2.1-api. And exclude the excess one.

I could solve the issue simply by replacing the JPA api jar file which is located jboss7/modules/javax/persistence/api/main with 'hibernate-jpa-2.1-api'. also with updating module.xml in the directory.

Error:
java.lang.NoSuchMethodError: javax.persistence.JoinTable.indexes()[Ljavax/persistence/Index;
The only thing that solved my problem was removing the following dependency in pom.xml:
<dependency>
<groupId>org.hibernate.javax.persistence</groupId>
<artifactId>hibernate-jpa-2.1-api</artifactId>
<version>1.0.0.Final</version>
</dependency>
And replace it for:
<dependency>
<groupId>javax.persistence</groupId>
<artifactId>persistence-api</artifactId>
<version>1.0.2</version>
</dependency>
Hope it helps someone.

i have experienced same issue in my spring boot application. after removing manually javax.persistance.jar file from lib folder. issue was fixed. in pom.xml file i have remained following dependency only
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>

I had the same issue, I fixed it by using org.hibernate.annotations.Table annotation instead of javax.persistence.Table in the Entity class.
import javax.persistence.Entity;
import org.hibernate.annotations.Table;
#Entity
#Table(appliesTo = "my_table")
public class MyTable{
//and rest of the code

There are multiple JPA providers in your classpath. Or atleast in your Application server lib folder.
If you are using Maven
Check for dependencies using command mentioned here https://stackoverflow.com/a/47474708/3333878
Then fix by removing/excluding unwanted dependency.
If you just have one dependecy in your classpath, then the application server's class loader might be the issue.
As JavaEE application servers like Websphere, Wildfly, Tomee etc., have their own implementations of JPA and other EE Standards, The Class loader might load it's own implementation instead of picking from your classpath in WAR/EAR file.
To avoid this, you can try below steps.
Removing the offending jar in Application Servers library path. Proceed with Caution, as it might break other hosted applications.
In Tomee 1.7.5 Plume/ Web it will have bundled eclipselink-2.4.2 in the lib folder using JPA 2.0, but I had to use JPA 2.1 from org.hibernate:hibernate-core:5.1.17, so removed the eclipselink jar and added all related/ transitive dependencies from hibernate core.
Add a shared library. and manually add jars to the app server's path. Websphere has this option.
In Websphere, execution of class loader can be changed. so making it the application server's classpath to load last i.e, parent last and having your path load first. Can solve this.
Check if your appserver has above features, before proceeding with first point.
Ibm websphere References :
https://www.ibm.com/support/knowledgecenter/SSEQTP_9.0.5/com.ibm.websphere.base.doc/ae/trun_classload_server.html
https://www.ibm.com/support/pages/how-create-shared-library-and-associate-it-application-server-or-enterprise-application-websphere-application-server