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Change CodeStar Spring MVC project to Spring Boot

I have a Spring Boot project that works perfectly when run in IDE. I would like to run this via AWS CodeStar. Unfortunately, the default Spring template created by CodeStar uses Spring MVC.
I cannot just overwrite the default Spring MVC project with my Spring Boot project (it doesn't work). I can copy some of my resources to the MVC project, for example index.html and that works. But then features like Thymeleaf don't work. For this and other reasons, I would like to change the provided Spring MVC into the Spring Boot structure I already have.
I followed the instructions here: https://www.baeldung.com/spring-boot-migration
Unfortunately, this doesn't help. I can create Application Entry Point and add Spring Boot dependencies without the app breaking. But when I remove the default dependencies or the configuration associated with the MVC, the app breaks. When trying to reach the URL, I get a 404 error with description:
The origin server did not find a current representation for the target resource or is not willing to disclose that one exists.
Debugging this error message (e.g. https://www.codejava.net/java-ee/servlet/solved-tomcat-error-http-status-404-not-found) didn't help.
The message seems like it's connected to the web resource. I have my web resources in folder resources as well as webapp/resources. And Spring Boot doesn't need any location configuration, right? It uses this location by default.
Can somebody tell me what things to remove and what to add to be able to use my existing Spring Boot project?
EDIT:
This is a link to a default template for AWS CodeStar Spring web application: https://github.com/JanHorcicka/AWS-codestar-template
And this is my Spring Boot project structure:

I realize that you indicated that previously you tried to use your Spring Boot project with some modifications without success, but I think it could be actually a possibility to successfully deploy your application on AWS CodeStar, and it will be my advice.
I also realized that in your screenshot you included several of the required artifacts and classes, but please, double check that you followed these steps when you deployed your application to AWS CodeStar.
Let's start with a pristine version of your Spring Boot project running locally, without any modification, and then, perform the following changes.
First, as indicated in the GitHub link you shared, be sure that you include the following files in your project. They are required for the deployment infrastructure of AWS:
appspec.yml
buildspec.yml
template.yml
template-configuration.json
The whole scripts directory
Please, adapt any necessary configuration to your specific needs, especially, template-configuration.json.
Then, perform the following modifications in your pom.xml. Some of them are required for Spring Boot to work as a traditional deployment and others are required by the deployment in AWS CodeStar.
Be sure that you indicate packaging as war:
<packaging>war</packaging>
To ensure that the embedded servlet container does not interfere with the Tomcat to which the war file is deployed, either mark the Tomcat dependency as being provided as suggested in the above-mentioned documentation:
<dependencies>
<!-- … -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
<scope>provided</scope>
</dependency>
<!-- … -->
</dependencies>
Or exclude the Tomcat dependency in your pom.xml:
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
<exclusions>
<exclusion>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
</exclusion>
</exclusions>
</dependency>
If necessary, apply this exclusion using some kind of profile that allows you to boot Spring Boot locally and in an external servlet container at the same time.
Next, parameterize the maven war plugin to conform to the AWS CodeStar deployment needs:
<build>
<pluginManagement>
<plugins>
<!-- ... -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>3.2.2</version>
<configuration>
<warSourceDirectory>src/main/webapp</warSourceDirectory>
<warName>ROOT</warName>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin>
<!-- ... -->
<plugins>
</pluginManagement>
</build>
I do not consider it necessary, but just to avoid any kind of problem, adjust the name of your final build:
<finalName>ROOT</finalName>
Lastly, as also indicated in the Spring documentation, be sure that your MyProjectApplication - I assume this class is your main entry point subclass SpringBootServletInitializer and override the configure accordingly, something like:
#SpringBootApplication
public class MyProjectApplication extends SpringBootServletInitializer {
#Override
protected SpringApplicationBuilder configure(SpringApplicationBuilder application) {
return application.sources(MyProjectApplication.class);
}
public static void main(String[] args) {
SpringApplication.run(MyProjectApplication.class, args);
}
}
Please, feel free to adapt the class to your specific use case.
With this setup, try to deploy your application and see if it works: perhaps you can find some kind of library dependencies problem, but I think for the most part it should work fine.
At a first step, you can try to deploy locally the version of the application you will later deploy to AWS CodeStar following the instructions you provided in your project template, basically, once configured with the necessary changes described in the answer, by running:
mvn clean package
And deploying the generated war on your local tomcat environment. Please, be aware that probably the ROOT application already exists in a standard tomcat installation (you can verify it by inspecting the webapps folder): you can override that war file.
For local testing you can even choose a different application name (configuring build.finalName and the warName in your pom.xml file): the important thing is verify if locally the application runs successfully.
If you prefer to, you can choose to deploy the app directly to AWS CodeStar and inspect the logs later it necessary.
In any case, please, pay attention on two things: on one hand, if you have any absolute path configured in your application, it can be the cause of the 404 issue you mention in the comments. Be aware that your application will be deployed in Tomcat with context root '/'.
On the other hand, review how you configured your database access.
Probably you used application.properties and it is fine, but please, be aware that when employing the application the database must be reachable: perhaps Spring is unable to create the necessary datasources, and the persistence manager or related stuff associated with and, as a consequence, the application is not starting. Again, it may be the reason of the 404 error code.
To simplify database connectivity, for testing, at first glance, I recommend you to use simple properties for configuring your datasource, namely the driver class, connection string, username and password. If that setup works properly, you can later enable JNDI or what deemed necessary.
Remember that if you need to change your context name and/or define a datasource pool in Tomcat you can place a context.xml file under a META-INF directory in your web app root path.
This context.xml should look like something similar to:
<?xml version="1.0" encoding="UTF-8"?>
<Context path="/">
<Resource name="jdbc/myDS"
type="javax.sql.DataSource"
maxActive="100"
maxIdle="30"
maxWait="10000"
url="jdbc:mysql://localhost:3306/myds"
driverClassName="com.mysql.jdbc.Driver"
username="root"
password="secret"
/>
</Context>

Issues with WAS Liberty classloader

I have an issue with the WAS Liberty classloader, nothing I do seem to fix it. The issue seems to be with log4j2, which I am using.
I'm running 16.0.0.4 (just upgraded from 8.5.5.9 where this issue also exist). I'm trying to create a webapp using Primefaces 6.0 which connects to Elasticsearch 5.1.1.
I have added the following dependency to maven:
<dependency>
<groupId>org.elasticsearch.client</groupId>
<artifactId>transport</artifactId>
<version>${library.elasticsearch.version}</version>
</dependency>
Somewhere along the road I need to do the following:
TransportClient client = new PreBuiltTransportClient(settings)
.addTransportAddress(new InetSocketTransportAddress(InetAddress.getByName(HOST), PORT));
Debugging this line hits the following method call in Elasticsearch (class: org.elasticsearch.threadpool.ThreadPool line 203):
logger.debug("created thread pool: {}", entry.getValue().formatInfo(executorHolder.info));
This throws an java.lang.NoSuchMethodError:
org/apache/logging/log4j/Logger.debug(java/lang/String;java/lang/Object;)
Normally we use log4j 2.2, but I have included log4j2 2.7 as described here (Elasticsearch v5.0 uses 2.6.2, v5.1 uses 2.7): https://discuss.elastic.co/t/issue-with-elastic-search-5-0-0-noclassdeffounderror-org-apache-logging-log4j-logger/64262/2
I have also tried to make it "provided". I'm currently building a war file, but I also tried to do it as an ear, same result.
I came accoss this issue on the Elasticsearch 5-alpha: https://github.com/elastic/elasticsearch/issues/19415 Here they note that they wanted to create a server and therefore did not see log4j2 as a consern, but they suggest that you use the REST API instead (although, at the time of writing, this was not usable for Java developers).
So the question is, what do I do? Should I use the REST API (e.g. Jest (https://github.com/searchbox-io/Jest/tree/master/jest)) or ?...
The code I have works fine when running standalone outside Liberty.
UPDATE:
It seems like parts of Liberty does contain log4j v2.2:
class load: org.apache.logging.log4j.core.appender.routing.Route from: file:/C:/deploy/liberty/workarea/org.eclipse.osgi/60/data/cache/com.ibm.ws.app.manager_0/.cache/lib/log4j-core-2.2.jar
...
It loads a lot of classes from this jar, but not the one that I'm having trouble with - this is loaded from an app we have. I tried to bump the version inside our own app, but same issue.

JPA/EclipseLink: Understanding ClassLoader issues

EDIT: Although a (good) answer was given and awarded, this only covers a rather unimportant part of my question. The main parts of this question are still open.
I use EclipseLink (2.6.2) in a cloud project. The project is a web application packaged as a WAR file and deployed on Apache Tomcat 8. The persistence context is set up using Java code, where I specify the entities to use using entityManagerFactoryBean.setPackagesToScan(packagesToScan). This configuration normally works as expected, where exactly the entity classes in the specified packages are found.
I now fail to understand when to use which classloader, especially when considering Tomcat, running tests, and using different connection pool implementations.
When running on Apache Tomcat including Tomcat's connection pool, the DataSource instance is created using the spring-cloud-connector plugin (spring-cloud-spring-service-connector).
In this setting everything works as expected, as long as I don't change the classloader as described below (otherwise I face ClassNotFoundExceptions for the entity classes).
When running unit tests with the help of JUnit and spring-test, the DataSource instance is created using the in-memory database H2 (using EmbeddedDatabaseBuilder from spring-jdbc). In this setting I have to specify JPA to use the classloader used for the DataSource instance (key eclipselink.classloader in the JPA properties map), otherwise I get "Object ... is not a known Entity type".
When running tests in an embedded Apache Tomcat 8, I don't see any message indicating the connection pool in use. In this setting I also have to set the classloader as for the unit tests.
If I add commons-dbcp (2.1.1) to my project and explicitly configure the spring-cloud-connector plugin to use it instead of Tomcat's connection pool, I can run the application on Tomcat without configuring the classloader, but it also works with the classloader specification described above.
For the tests the commons-dbcp does not change anything compared to the scenarios outlined above (as the corresponding configuration is not used).
Summary:
Tomcat (Tomcat CP): only using the unmodified classloader for JPA
Tomcat (DBCP): both variants
Tests: only using DataSource's classloader for JPA
Could you help me understand the differences here, and suggest a simple solution suitable for all cases? I assume that DBCP and Spring use a different classloader than Tomcat (and Tomcat's connection pool).
If you need further information, I will happily add it.
EDIT: I added an example project with a big README on how to reproduce.
https://github.com/C-Otto/classloaderexample

"I get another error when I start using mvn tomcat7:run, use Tomcat's
connection pool (CloudDatabaseConfig) and do not re-configure the
classloder (JpaConfig):"
You must configure the PostreSQL dependency on the maven plugin. You are getting ClassNot found because the PostgreSQL JAR is not in the path:
<plugin>
<groupId>org.apache.tomcat.maven</groupId>
<artifactId>tomcat7-maven-plugin</artifactId>
<version>2.2</version>
<configuration>
<port>8080</port>
<path>/</path>
</configuration>
<!-- For any extra dependencies needed when running embedded Tomcat (not WAR dependencies) add them below -->
<dependencies>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>9.4-1206-jdbc41</version>
<scope>runtime</scope>
</dependency>
</dependencies>
</plugin>
Also have a look at https://tomcat.apache.org/maven-plugin-2.2/run-mojo-features.html
I forgot to include the class loader change on (JpaConfigWithDatasourceClassloader.getJPAProperties):
properties.put(CLASSLOADER, new java.net.URLClassLoader(
((java.net.URLClassLoader)classLoader).getURLs(), JpaConfigWithDatasourceClassloader.class.getClassLoader() )
) ;
With this you can run all variants using tomcat7:run

Issues Converting Mule Tomcat WAR to Spring Boot

I've been going through the process of converting my Mule project to a Spring Boot application, and have hit a snag I can't seem to figure out.
I'm pretty new to Spring Boot so I'm not sure if my issues lie with it, or with the way I'm doing my mule stuff.
Here is my sample project I've been trying to convert: https://github.com/JustinBell/mule-webapp-example
When I deploy this to a tomcat instance it works great, the issue comes when I try to run it as a Spring Boot application I'm getting this exception:
ApplicationContextException: Unable to start EmbeddedWebApplicationContext due to missing EmbeddedServletContainerFactory bean.
Just as a note I'm moving from mule 3.6.1 to 3.7.0-M1 as that's required (from my understanding) to use Spring Boot.
I've tried looking around for support on this issue which seems to pretty common, but none of the suggestions I've found have solved the issue.
Thanks for any help with these issues!

There are a few things that aren't quite right in your code as it stands.
If you want to build a web app with Spring Boot, you'll typically want to add a dependency on spring-boot-starter-web. This provides, among other things, the embedded servlet container:
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
<version>${spring-boot.version}</version>
</dependency>
Your app's dependency on org.mule.transports:mule-transport-servlet pulls in a very old version of Tomcat's Coyote module. You need to exclude this to avoid it clashing with the up-to-date dependency that's provided by spring-boot-starter-web:
<dependency>
<groupId>org.mule.transports</groupId>
<artifactId>mule-transport-servlet</artifactId>
<version>${mule.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.tomcat</groupId>
<artifactId>coyote</artifactId>
</exclusion>
</exclusions>
</dependency>
Your Application class is trying to run MuleContextInitializer which it also declares as a bean. It should be running Application.class:
#SpringBootApplication
public class Application {
public static void main(String[] args) {
SpringApplication.run(Application.class);
}
// ...
}
Your Application class is also in the default package. You should avoid using the default package as it will cause Spring Boot to scan then entire classpath looking for your application's classes and configuration. Moving it into a package of its own to stop this from happening.
Lastly, the app fails to launch as it's looking for a file named mule-config.xml. Renaming mule-webapp-demo.xml to mule-config.xml addresses this.

I believe autodelete is an Enterprise feature, perhaps you are using ftp rather than ftp-ee.

Error: No class Def found error while setting up Java as a Windows Service

Following is the error log I'm getting:
I'm using
wrapper-windows-x86-32-3.5.25-pro
in order to make my already developed application in Spring-boot. I wanted to execute this application as a windows service but I'm not.
This problem is specific to Tanukisoftware as I'm unable to configure it.
PFB the configuration I'm using for setting up the class path here:
wrapper.java.classpath.1=../lib/wrappertest.jar
wrapper.java.classpath.2=../lib/wrapper.jar
wrapper.java.classpath.3=../lib/slf4j-api-1.7.5
wrapper.java.classpath.4=../lib/myApp.jar
even if myApp.jar contains the slf4j classpath already and its running already. I think this is library specific problem and its not finding up the classpath even if I explicitly set it like did above.
Can you please let me know how it can be solved?

Did you try building a fat jar of your application ? You can add following lines to your Spring Boot project's pom.xml to repackage jar file:
<build>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
</plugins>
</build>
Besides, your following property line seems invalid:
wrapper.java.classpath.3=../lib/slf4j-api-1.7.5
Is it pointing a jar file actually ?

slf4j-api-1.7.5 should have a .jar extension. That is possibly confusing things.

Also, even just as a debugging step, try running your Windows service using Apache ProcRun to see if your results are any different.