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Occasional BeanCreationException in Java Spring Boot project built with Gradle

Sometimes I get a BeanCreationException when starting a Java Spring Boot single-JAR application built by Gradle. My investigations show that it depends on the JAR file and how it has been built by Gradle. Most often (but not always) I see the exception when I build the project on a Linux system. But I have never reproduced the issue with a JAR built on Windows or when running from IntelliJ Idea.
I tried to compare the content of a working JAR with the JAR throwing the exception - all the *.class files (including meta and resources) were binary equal, the only difference was in the order the files were stored in the JAR/ZIP archive. I also tried to unpack the failing JAR on Windows and just repack it into a new JAR file (using 7-zip) - the application started without any exceptions. This weird workaround solved the issue, but it's not something I'd like to do after each build on a linux machine.
The exception suggests to check circular references, so I tried replacing #Autowired properties with #Autowired bean constructors to help me to find the problem but that didn't help. The stacktrace does not mention any of my classes, so I don't know what bean could be responsible for the issue. And because of the fact the issue happens only sometimes and is solvable by repacking the JAR file, I'm not sure there are any circular references anyway.
Could you please help me? Any advice or suggestion is welcomed.
JDK: openjdk 8u262
Gradle version 5.6
Spring boot 2.3.1
Exception message:
BeanCreationException: Error creating bean with name 'webConfig':
Invocation of init method failed; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException:
Error creating bean with name 'requestMappingHandlerAdapter' defined in class path resource
[org/springframework/boot/autoconfigure/web/servlet/WebMvcAutoConfiguration$EnableWebMvcConfiguration.class]:
Unsatisfied dependency expressed through method 'requestMappingHandlerAdapter' parameter 0;
nested exception is org.springframework.beans.factory.BeanCurrentlyInCreationException:
Error creating bean with name 'mvcContentNegotiationManager':
Requested bean is currently in creation: Is there an unresolvable circular reference?

By default, Spring manages itself bean's lifecycle and then, arranges their initialization order during the startup.
Here a full example of usage #DependsOn annotation to order the bean instanciation.
You can also found more detail in the official Spring documentation

WebLogic 10.3.7 File Upload returns "Error creating bean with name 'portletMultipartResolver'"

I am using Spring Portlet mvc with file upload. When I was using WebLogic 10.3.0 it was working fine. I am migrating to WebLogic 10.3.7. Here with the same code I am getting below error:
javax.portlet.PortletException:
org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'portletMultipartResolver' defined in
PortletContext resource Instantiation of bean failed; nested exception
is org.springframework.beans.BeanInstantiationException: Could not
instantiate bean class
[org.springframework.web.portlet.multipart.CommonsPortletMultipartResolver]:
Constructor threw exception; nested exception is
java.lang.NoClassDefFoundError: javax/portlet/ActionRequest
WebLogic server is not able to find ActionRequest.class. I have tried several options like placing jar file (netuix_common.jar) which contains ActionRequest.class inside the application war file but still it didn't work.
What can I try to resolve this?

java.lang.NoClassDefFoundError - you get this error when weblogic server finds this class in its classloader but not the one with the correct version.
you did the right thing by adding it to the application war file, you may want to add the flag of " prefer-web-inf-classes "
https://docs.oracle.com/cd/E23943_01/web.1111/e13712/weblogic_xml.htm#WBAPP601

Tomcat work directory empty

My Spring project was successfully deployed on another Linux server. But when I tried deploying it on this Linux server, it won't deploy. When I go to the homepage, I get the error "HTTP Status 404 - The requested resource is not available".
I compared the Tomcat directory of both servers and see only differences in the "work" directory. On this server (the one having problem), under "work\Catalina\localhost\MyProject" directory of Tomcat, I see that it's empty. Turns out that the files got put under "work\Catalina\localhost\_" instead. What's causing Tomcat to do this?
In my tomcat log file, I'm getting this:
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'SampleService': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.wdc.hydra.dao.DatatypeDAO com.wdc.hydra.service.DatatypeServiceImpl.datatypeDAO; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'SampleDAO': Injection of persistence dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'Sample' defined in class path resource [Sample-dao-context.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: javax.persistence.spi.PersistenceUnitInfo.getValidationMode()Ljavax/persistence/ValidationMode;
Does anyone know why this is happening? Thanks.

How does the Spring Container defined? whether its by XmlWebApplicationContext / FileSystemXmlApplicationContext / ClasspathXmlApplicationContext and if its through FileSystemXmlApplicationContext then your directory structure in both the linux servers should be same. like wise others too.

DispatcherServlet - Context initialization failed in Roo project

I develop a Roo project and deploy to a Tomcat 6 server.
Up until now everything was working fine.
I deleted and re-added an entity.
Now everytime when I start Tomcat I get this exception in the Spring Tool Suite:
SEVERE: StandardWrapper.Throwable
Throwable occurred: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.web.servlet.mvc.annotation.DefaultAnnotationHandlerMapping#0': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.web.servlet.handler.MappedInterceptor#0': Cannot create inner bean '(inner bean)' of type [org.springframework.web.servlet.handler.ConversionServiceExposingInterceptor] while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)': Cannot resolve reference to bean 'applicationConversionService' while setting constructor argument; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [myproject.web.ApplicationConversionServiceFactoryBean] for bean with name 'applicationConversionService' defined in ServletContext resource [/WEB-INF/spring/webmvc-config.xml]; nested exception is java.lang.ClassNotFoundException: myproject.web.ApplicationConversionServiceFactoryBean
Related cause: org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [myproject.web.ApplicationConversionServiceFactoryBean] for bean with name 'applicationConversionService' defined in ServletContext resource [/WEB-INF/spring/webmvc-config.xml]; nested exception is java.lang.ClassNotFoundException: myproject.web.ApplicationConversionServiceFactoryBean
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:527)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291)
...
What do I need to do to make it work again?

spring is complainig about a bean not being available (probably the one you say you deleted).
exception is java.lang.ClassNotFoundException: myproject.web.ApplicationConversionServiceFactoryBean
try to search the config xml files & remove the reference made to this class, things should be back after that,

I had the same exact issue.
The problem was that I disabled the "Project > Build Automatically" feature, so I had to manually build the project.
Once I manually built the project everything went back to normal. :)
So, don't forget to build the project before deploying it, or just re-enable the "Project > Build Automatically" feature.
Hope it helps.

Your app deployed to Tomcat doesn't have a jar file in WEB-INF/lib that contains the class myproject.web.ApplicationConversionServiceFactoryBean. I don't know what that class is or where you'd find it, but it's missing.

my workaround (worked with eclipse and roo 1.1.5 as eclipse plugin)
open ApplicationConversionServiceFactoryBean.java class
delete class annotation #RooConversionService
wait for roo update
add back class annotation #RooConversionService
wait for roo update and try again

Inside of STS, click ->project->clean
It clean and discard all build problems and built states, The next time a build occurs the projects will be rebuilt from scratch.

Why do I get this `TypeMismatchException` with Spring

I'm trying to use Hibernate with Spring in Eclipse. I get the following error when I try to run the welcome file on the server:
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'mySessionFactory' defined in ServletContext resource [/WEB-INF/dispatcher-servlet.xml]:
Initialization of bean failed; nested exception is
org.springframework.beans.TypeMismatchException: Failed to convert property value of type 'java.util.ArrayList' to required type 'java.lang.Class[]' for property 'annotatedClasses';
nested exception is java.lang.IllegalArgumentException: Cannot find class [com.vaannila.domain.User]
The class com.vaannila.domain.User is in the Java Resources:src folder of the project in eclipse. Why isn't it being located?

From time to time Eclipse is a bit picky about deploying a project correctly. It seems that it has to do with the installed plugins. When this happens to me in the 'Servers'-view of the 'Debug'-Perspective i click the 'add and remove' menu and remove my project from deployment - save it - add it again and redeploy. Usually this does the trick.
Another try is to start Eclipse with the -clean option.