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How to overwrite config in a Quarkus extension

Is there a way to overwrite a configuration in a Quarkus extension with a hard-coded value?
What I'm trying to do: I am creating a custom Quarkus extension for JSON logging, based on quarkus-logging-json but with additional (non static) fields. I reuse some classes from the extension's runtime library, so it is a Maven dependency of the runtime module of the extension (and the deployment also needs to be declared as a dependency to my deployment module, because the quarkus extension plugin checks this).
It seems to work fine, except that I now have 2 formatters, and the following line is logged:
LogManager error of type GENERIC_FAILURE: Multiple console formatters were activated
I would like to disable the quarkus-logging-json extension completely by hard-coding these values:
quarkus.console.json.enable=false
quarkus.file.json.enable=false.
Is there a way to do this?
Thank you.

An extension cannot override runtime configuration values, it can however set a default value using io.quarkus.deployment.builditem.RunTimeConfigurationDefaultBuildItem

Possible to ignore configuration classes on the classpath?

I have a Spring Boot application that works as expected when ran with embedded tomcat, but I noticed that if I try to run it from an existing tomcat instance that I'm using with a previous project then it fails with a NoClassDefFoundError for a class that I don't use anywhere in my application.
I noticed in the /lib directory I had a single jar that contained a few Spring annotated classes, so as a test I cleaned out the /lib directory which resolved the issue. My assumption is that Spring is seeing some of the configurations/beans/imports on the classpath due to them existing in the /lib directory and either trying to autoconfigure something on its own, or is actually trying to instantiate some of these classes.
So then my question is - assuming I can't always fully control the contents of everything on the classpath, how can I prevent errors like this from occurring?
EDIT
For a little more detail - the class not being found is DefaultCookieSerializer which is part of the spring-session-implementation dependency. It is pulled into one of the classes in the jar located in /lib, but it is not any part of my application.

Check for features provided by #EnableAutoConfiguration. You can explicitly configure set of auto-configuration classes for your application. This tutorial can be a good starting point.

You can remove the #SpringBootApplication annotation from the main class and replace it with an #ComponentScan annotation and an #Import annotation that explicitly lists only the configuration classes you want to load. For example, in a Spring boot MVC app that uses metrics, web client, rest template, Jackson, etc, I was able to replace the #SpringBootApplication annotation with below code and get it working exactly as it was before, with all functional tests passing:
#Import({ MetricsAutoConfiguration.class,
InfluxMetricsExportAutoConfiguration.class,
ServletWebServerFactoryAutoConfiguration.class,
DispatcherServletAutoConfiguration.class,
WebMvcAutoConfiguration.class,
JacksonAutoConfiguration.class,
WebClientAutoConfiguration.class,
RestTemplateAutoConfiguration.class,
RefreshAutoConfiguration.class,
ValidationAutoConfiguration.class
})
#ComponentScan

The likely culprit of mentioned exception are incompatible jars on the classpath.
As we don't know with what library you have the issue we cant tell you the exact reason, but the situation looks like that:
One of Spring-Boot autoconfiguration classes is being triggered by the presence of class on the classpath
Trigerred configuration tries to create some bean of class that is not present in the jar you have (but it is in the specific version mentioned in the Spring BOM)
Version incompatibilities may also cause MethodNotFound exceptions.
That's one of the reasons why it is good practice not to run Spring Boot applications inside the container (make jar not war), but as a runnable jar with an embedded container.
Even before Spring Boot it was preferred to take account of libraries being present on runtime classpath and mark them as provided inside your project. Having different versions of the library on a classpath may cause weird ClassCastExceptions where on both ends names match, but the rest doesn't.
You could resolve specific cases by disabling autoconfiguration that causes your issue. You can do that either by adding exclude to your #SpringBootApplication or using a property file.
Edit:
If you don't use very broad package scan (or use package name from outside of your project in package scan) in your Spring Boot application it is unlikely that Spring Boot simply imports configuration from the classpath.
As I have mentioned before it is rather some autoconfiguration that is being triggered by existence of a class in the classpath.
Theoretical solution:
You could use maven shade plugin to relocate all packages into your own package space: see docs.
The problems is you'd have face:
Defining very broad relocation pattern that would exclude JEE classes that need to be used so that container would know how to run your application.
Relocation most likely won't affect package names used as strings in the Spring Boot annotations (like annotations #PackageScan or #ConditionalOnClass). As far as I know it is not implemented yet. You'd have to implement that by yourself - maybe as some kind of shade plugin resource processor.
When relocating classes you'd have to replace package names in all relevant configuration located in the jars. Possibly also merge some of those.
You'd also have to take into account how libraries that you use, or spring uses use package names or files.
This is definitely not a trivial tasks with many traps ahead. But if done right, then it would possibly allow you to disregard what is on the containers classpath. Spring Boot would also look for classes in relocated packages, and you wouldn't have those in ordinary jars.

JAX-RS - Loading #Provider classes from a jar file

I have a simple Rest application that is deployed to an IBM MobileFirst 7.1 Liberty Server. (I don't know the implementation of the JAX-RS but it is included with the liberty server runtime I believe)
I have to share some of my common code with other teams, so I moved some of the code into a separate maven project to be jared and added as a server library. This all works great until I had to add some #Provider annotated classes into the separate maven project. Specifically, some ExceptionMapper implementations marked with the #Provider annotation.
I have tried setting the class directly within the Application classes getClasses() method. This seemed to work, but I get a warning message saying that my exception mapper implementations need to be marked with the #Provider or #Path annotations (which they are).
Is there some sort of trick to get JAX-RS to recognize these resource classes from a Jar file?

In order to have the #Provider recognized, please try to put the JAR inside the adapter /lib folder instead of the server/lib folder.

Hibernate and Jersey dependency conflict (javassist) - can anyone explain how this works?

I'm currently using hibernate-4.1.4 and jersey-2.22. These have javassist-3.15 and javassist-3.18 respectively.
I included both hibernate and jersey in my project and to my surprise, there were no dependency conflicts between the said javassists.
I was wondering how Java tells hibernate to use 3.15 and how it tell jersey to use 3.18 since both are in the build path. Is one javassist not being used?
Follow up question: Let's say that javassist-3.15 and javassist-3.18 have a conflict with each other. How do I resolve this? Do I disable both javassists and include one externally?
EDIT: My app is a web app that runs on Tomcat 7. We don't use Maven/Gradle. We just configure the dependencies by putting the jars in the build path using Eclipse.

JAVA loads classes through ClassLoaders ... Many applications servers, as Tomcat or Wildfly, implement and use their own class loaders (not the regular ones of the common JDK) ... So you must check the Tomcat documentation to read about its classloading behaviour...
After saying that, is very likely that Tomcat is loading libraries in alphabetical order. I Explain...
Suppose that you use a class named: Dummy, and this class is contained at the libraries: dummy-1.0.jar and dummy-1.1.jar ... when the class Dummy is requested, the Tomcat ClassLoader search for that class definition, looking first at dummy-1.0.jar and later at dummy-1.1.jar ... given that dummy-1.0.jar contains that class, Tomcat stops looking a returns that class version ... If dummy-1.0.jar would not have the target class, the dummy-1.1.jar class version would be returned instead...
(I suggest to try this to validate the container behaivour, it's not so hard to implement)...
And yes, if javassist-3.15 and javassist-3.18 conflicts with each other, you should remove them and pick the javassist JAR more
suitable for both libraries (jersey and hibernate).
As thumb rule, I tend to pick the newest library (the one with greater version), but this scheme not always work...

Initial SessionFactory creation failed.java.lang.ClassFormatError

Error in Console:-
Initial SessionFactory creation failed.java.lang.ClassFormatError: Absent Code attribute in method that is not native or abstract in class file javax/transaction/SystemException
Hello
I am building a standalone Java Application with Main Method which connects to the database using Hibernate and writes to a file on C drive as well.
I have added all the libraries to the class path using Java Build Path configuration and user libraries. But I keep getting this error ...I have also added the javaee jar from the glassfish server libraries but that has also not solved the problem. I also have the jboss-transaction-api_1.1_spec-1.0.0.Final.Jar added to my class path.
Please advise as I am not using Maven as yet ???
Here are the jars in my build path-
-antlr
-c3p0
-commons-collections
-commons-logging
-commong-logging-api
-dom4j
-hibernate-c3p0
-hibernate-commons-annotation
-hibernate-core
-hibernate-entitymanager
-hibernate-envers
-hibernate-jpa
-javaee-api-6.0jar
-javaassist
-jboss-logging
-jboss-transaction-api
-jms
-log4j
-lucene-core
-MySQL-connector
-slf4j
-javaee.jar
Any help would be truly appreciated .. I am just lost on what is going on ?

I am sure you have 2 different versions for the same class. check your jars.