Unable to deploy spring boot application on external tomcat

Question

I am trying to deploy spring boot application to external tomcat, I am getting the following exception in the catalina.log file as shown below.

The war file name is : com#myApp.war.

I wanted to set the context-path of the application to com/myApp in the url

http://localhost:8080/com/myApp/healthcheck, hence the war file name is com#myApp.war

 java version is : 1.8 (both application and tomcat)
    tomcat is running on linux server.

08-Apr-2021 15:41:20.326 SEVERE [main] org.apache.catalina.startup.HostConfig.deployWAR Error deploying web application archive [/opt/apache/tomcat/base/webapps/com#myApp.war]
    java.lang.IllegalStateException: Error starting child
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:720)
        at org.apache.catalina.core.ContainerBase.access$000(ContainerBase.java:129)
        at org.apache.catalina.core.ContainerBase$PrivilegedAddChild.run(ContainerBase.java:150)
        at org.apache.catalina.core.ContainerBase$PrivilegedAddChild.run(ContainerBase.java:140)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:688)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:706)
        at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:978)
        at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1848)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
        at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
        at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:773)
        at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:427)
        at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1576)
        at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:309)
        at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
        at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:423)
        at org.apache.catalina.util.LifecycleBase.setState(LifecycleBase.java:366)
        at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:936)
        at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:843)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1384)
        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1374)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
        at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)
        at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:909)
        at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:262)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
        at org.apache.catalina.core.StandardService.startInternal(StandardService.java:421)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
        at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:930)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
        at org.apache.catalina.startup.Catalina.start(Catalina.java:772)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:342)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:473)
    Caused by: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/com/myApp]]
        at org.apache.catalina.util.LifecycleBase.handleSubClassException(LifecycleBase.java:440)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:198)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:717)
        ... 41 more
    Caused by: java.lang.IllegalArgumentException: Cannot instantiate interface org.springframework.context.ApplicationContextInitializer : org.springframework.boot.autoconfigure.SharedMetadataReaderFactoryContextInitializer
        at org.springframework.boot.SpringApplication.createSpringFactoriesInstances(SpringApplication.java:467)
        at org.springframework.boot.SpringApplication.getSpringFactoriesInstances(SpringApplication.java:449)
        at org.springframework.boot.SpringApplication.getSpringFactoriesInstances(SpringApplication.java:442)
        at org.springframework.boot.SpringApplication.<init>(SpringApplication.java:284)
        at org.springframework.boot.SpringApplication.<init>(SpringApplication.java:264)
        at org.springframework.boot.builder.SpringApplicationBuilder.createSpringApplication(SpringApplicationBuilder.java:109)
        at org.springframework.boot.builder.SpringApplicationBuilder.<init>(SpringApplicationBuilder.java:97)
        at org.springframework.boot.web.servlet.support.SpringBootServletInitializer.createSpringApplicationBuilder(SpringBootServletInitializer.java:164)
        at org.springframework.boot.web.servlet.support.SpringBootServletInitializer.createRootApplicationContext(SpringBootServletInitializer.java:128)
        at org.springframework.boot.web.servlet.support.SpringBootServletInitializer.onStartup(SpringBootServletInitializer.java:95)
        at org.springframework.web.SpringServletContainerInitializer.onStartup(SpringServletContainerInitializer.java:174)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5166)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
        ... 42 more
    Caused by: java.lang.ExceptionInInitializerError
        at org.springframework.beans.BeanUtils.<clinit>(BeanUtils.java:80)
        at org.springframework.boot.SpringApplication.createSpringFactoriesInstances(SpringApplication.java:463)
        ... 54 more
    Caused by: java.security.AccessControlException: access denied ("java.util.PropertyPermission" "org.graalvm.nativeimage.imagecode" "read")
        at java.security.AccessControlContext.checkPermission(AccessControlContext.java:472)
        at java.security.AccessController.checkPermission(AccessController.java:886)
        at java.lang.SecurityManager.checkPermission(SecurityManager.java:549)
        at java.lang.SecurityManager.checkPropertyAccess(SecurityManager.java:1294)
        at java.lang.System.getProperty(System.java:717)
        at org.springframework.core.DefaultParameterNameDiscoverer.<clinit>(DefaultParameterNameDiscoverer.java:47)
        ... 56 more
08-Apr-2021 15:41:20.329 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [/opt/apache/tomcat/base/webapps/com#myApp.war] has finished in [3,052] ms
08-Apr-2021 15:41:20.331 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
08-Apr-2021 15:41:20.348 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["https-jsse-nio2-8443"]
08-Apr-2021 15:41:20.349 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [21648] milliseconds

pom.xml

<dependencies>
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-data-jpa</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-web</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-devtools</artifactId>
            <scope>runtime</scope>
            <optional>true</optional>
        </dependency>

    
        <dependency>
            <groupId>com.oracle.ojdbc</groupId>
            <artifactId>ojdbc8</artifactId>
            <version>19.3.0.0</version>
<!--            <scope>provided</scope>-->
        </dependency>


        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-test</artifactId>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>org.springframework.security</groupId>
            <artifactId>spring-security-test</artifactId>
            <scope>test</scope>
        </dependency>
        
    </dependencies>

    <build>
<!--        This gives the final war file name-->

        <finalName>${project.artifactId}</finalName>

        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.3</version>
                <configuration>
                    <source>1.8</source>
                    <target>1.8</target>
                </configuration>
            </plugin>


            <plugin>
                <groupId>org.springframework.boot</groupId>
                <artifactId>spring-boot-maven-plugin</artifactId>
                <version>2.4.2</version>

                <executions>
                    <execution>
                        <id>build-info</id>
                        <goals>
                            <goal>build-info</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>

Answer 1

When you start tomcat first thing it does is to search for web.xml file in the classpath. Spring Boot however, comes with an embedded tomcat server to run it on an external server you would need to use ServletInitializer

Answer 2

You problems you are facing running with a security manager are known and best summarized in Tomcat's documentation (emphasis mine):

Tomcat is tested with the security manager enabled; but the majority of Tomcat users do not run with a security manager, so Tomcat is not as well user-tested in this configuration. There have been, and continue to be, bugs reported that are triggered by running under a security manager.

The restrictions imposed by a security manager are likely to break most applications if the security manager is enabled. The security manager should not be used without extensive testing. Ideally, the use of a security manager should be introduced at the start of the development cycle as it can be time-consuming to track down and fix issues caused by enabling a security manager for a mature application.

Your application will break either because of a Tomcat bug, a Spring bug or a bug in your own application. Regarding the problems you found up to now:

• the problem with java.util.PropertyPermission "org.graalvm.nativeimage.imagecode", "read" should probably considered a Spring bug (as stated in Deinum's comment): Spring should probably only issue a warning if it can't access org.graalvm.nativeimage.imagecode property,
• the problem with java.lang.reflect.ReflectPermission "suppressAccessChecks" (in this version of your question) is probably due to your own code. Spring tries to access a private field by reflection, because you didn't provide a public setter (cf. ReflectPermission JavaDoc). The stack trace will tell you, which class is the culprit.

I understand that the choice of running with a security manager isn't yours, but now you have to thoroughly debug your application, check the meaning of the security exceptions and decide whether they are required or you can work around them.