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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.

How to do component scanning for sibling package in Spring Boot

Currently I have quite a bit of services written in Spring Boot 2.1.3 (in mono-repo) and I have a common package that's used in most of the services.
So my packages are organized in the following:
root
root.common
root.serviceA
root.serviceA.<subpackages>
root.serviceB
root.serviceB.<subpackages>
...
root.serviceX
root.serviceX.<subpackages>
In each service I have Program.java where it's tagged with #SpringBootApplication (e.g. root/serviceA/Program.java)
The problem now I'm having is that I have a component in root.common (e.g. root/common/JSONSerializer.java) which needs to be loaded in all the services. I tried tagging the file with #JsonComponent but obviously it doesn't work because it's outside root.service* package.
I managed to get it working by manually adding #Import tag in the main file but that means that for each service I have to manually add #Import({root.common.JSONSerializer.class}) which is tedious and error prone. Is there a way to include this file in the component scanning process?

You can set each Program class by following way:
#SpringBootApplication(scanBasePackages = {"root.serviceA", "root.common"})
REFERENCES
SpringBootApplication documentation

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.

How can I redirect to a controller that's in a library?

I have a Spring MVC #Controller in a library project which my main project depends upon. I want to redirect to this from a controller in my main project. How can I do this?
I have a #Configuration in the library with an appropriate #ComponentScan. I tried both putting that #Configuration in my getServletConfigClasses() in my main ApplicationInitializer, and putting it in an #Import tag on my main #Configuration.
When I do a return "redirect:/whateverurl" with either configuration, I just see the redirect string in my browser. It doesn't actually do the redirect.

Is the library a Jar file?
If so, while creating the jar, the directory entries need to be added.
I think this question may have the answer -
Auto-wiring annotations in classes from dependent jars
Thanks,
Paul

Spring Dependency Injection and Plugin Jar

I have web application running with a default impl of a backend service. One should be able to implement the interface and drop the jar into the plugins folder (which is not in the apps classpath). Once the server is restarted, the idea is to load the new jar into the classloader, and have it take part in dependency injection. I am using Spring DI using #Autowired. The new plugin service impl will have #Primary annotation. So given two impls of the interface, the primary should be loaded.
I got the jar loaded into the classloader and can invoke the impl manually. But I haven't been able to get to to participate in the Dependency Injection, and have it replace the default impl.
Here's a simplified example:
#Controller
public class MyController {
#Autowired
Service service;
}
//default.jar
#Service
DefaultService implements Service {
public void print() {
System.out.println("printing DefaultService.print()");
}
}
//plugin.jar not in classpath yet
#Service
#Primary
MyNewService implements Service {
public void print() {
System.out.println("printing MyNewService.print()");
}
}
//For lack of better place, I loaded the plugin jar from the ContextListener
public class PluginContextLoaderListener extends org.springframework.web.context.ContextLoaderListener {
#Override
protected void customizeContext(ServletContext servletContext,
ConfigurableWebApplicationContext wac) {
System.out.println("Init Plugin");
PluginManager pluginManager = PluginManagerFactory.createPluginManager("plugins");
pluginManager.init();
//Prints the MyNewService.print() method
Service service = (Service) pluginManager.getService("service");
service.print();
}
}
<listener>
<listener-class>com.plugin.PluginContextLoaderListener</listener-class>
</listener>
Even after I have loaded the jar into the classloader, DefaultService is still being injected as service. Any idea how I get the plugin jar to participate into the spring's DI lifecycle?
Edited:
To put it simply, I have a war file that has a few plugin jars in a plugins directory inside the war. Based on a value from a configuration file that the app looks at, when the app is started, I want to load that particular plugin jar and run the application with it. That way, I can distribute the war to anyone, and they can choose which plugin to run based on a config value without having to to repackage everything. This is the problem I am trying to solve.

It seems like all You need is to create the Spring ApplicationContext properly. I think it's possible without classpath mingling. What matters most are the locations of the Spring configuration files within the classpath. So put all Your plugin jar's into WEB-INF/lib and read on.
Let's start with the core module. We'll make it to create it's ApplicationContext from files located at classpath*:META-INF/spring/*-corecontext.xml.
Now we'll make all plugins to have their config files elsewhere. I.e. 'myplugin1' will have its config location like this: classpath*:META-INF/spring/*-myplugin1context.xml. And anotherplugin will have the configs at classpath*:META-INF/spring/*-anotherplugincontext.xml.
What You see is a convension. You can also use subdirectiries if You like:
core: classpath*:META-INF/spring/core/*.xml
myplugin1: classpath*:META-INF/spring/myplugin1/*.xml
anotherplugin: classpath*:META-INF/spring/anotherplugin/*.xml
What matters is that the locations have to be disjoint.
All that remains is to pass the right locations to the ApplicationContext creator. For web applications the right place for this would be to extend the ContextLoaderListener and override the method customizeContext(ServletContext, ConfigurableWebApplicationContext).
All that remains is to read Your config file (its location can be passed as servlet init parameter). Than You need to construct the list of config locations:
String locationPrefix = "classpath*:META-INF/spring/";
String locationSiffix = "/*.xml";
List<String> configLocations = new ArrayList<String>();
configLocations.add(locationPrefix + "core" + locationSiffix);
List<String> pluginsTurnedOn = getPluginsTurnedOnFromConfiguration();
for (String pluginName : pluginsTurnedOn) {
configLocations.add(locationPrefix + pluginName + locationSiffix);
}
applicationContext.setConfigLocations(configLocations.toArray(new String[configLocations.size()]));
This way You can easily manage what is and what is not loaded into Spring ApplicationContext.
Update:
To make it work there's one more hidden assumption I made that I'm about to explain now. The base package of the core module and each plugin should also be disjoint. That is i.e.:
com.mycompany.myapp.core
com.mycompany.myapp.myplugin1
com.mycompany.myapp.anotherplugin
This way each module can use <context:componet-scan /> (on equivalent in JavaConfig) easily to add classpath scanning for it's own classes only. The core module should not contain any package scanning of any plugin packages. The plugins should extend configuration of ApplicationContext to add their own packages to classpath scanning.

If you restart the server, I see no reason why you can't just add the JAR to the WEB-INF/lib and have it in the CLASSPATH. All the complication of a custom class loader and context listener goes away, because you treat it just like any other class under Spring's control.
If you do it this way because you don't want to open or modify a WAR, why not put it in the server /lib directory? Let the server class loader pick it up. This makes all plugin classes available to all deployed apps.
The answer depends on how important the separate /plugin directory is. If it's key to the solution, and you can't add the JAR to the server's /lib directory, then that's that. I've got nothing. But I think it'd be worthwhile to at least revisit the solution you have to make sure that it's the only way to accomplish what you want.