Errors while starting the webapp

[Abhishek Reddy]

Hello There! 

I am following your cbioportal document and trying to deploy the web app into an EC2 instance and followed the instructions on document here (http://docs.cbioportal.org/deployment/deploy-without-docker/pre-build-steps/)

We are willing to get this installed without docker. So I am running into an issue  as follows. Please take a look at the logs and let me know if i need to do anything from my end.

Ran this command on my EC2 - java -jar portal/target/dependency/webapp-runner.jar portal/src/main/webapp

Logs from EC2 when I ran the above command. 

Adding Context  for portal/src/main/webapp

Oct 13, 2023 6:41:35 PM org.apache.coyote.AbstractProtocol init

INFO: Initializing ProtocolHandler ["http-nio-8080"]

Oct 13, 2023 6:41:35 PM org.apache.tomcat.util.net.NioSelectorPool getSharedSelector

INFO: Using a shared selector for servlet write/read

Oct 13, 2023 6:41:35 PM org.apache.catalina.core.StandardService startInternal

INFO: Starting service [Tomcat]

Oct 13, 2023 6:41:35 PM org.apache.catalina.core.StandardEngine startInternal

INFO: Starting Servlet Engine: Apache Tomcat/8.5.61

Oct 13, 2023 6:41:35 PM org.apache.catalina.startup.SetContextPropertiesRule begin

WARNING: [SetContextPropertiesRule]{Context} Setting property 'antiJARLocking' to 'true' did not find a matching property.

Oct 13, 2023 6:41:35 PM org.apache.catalina.startup.ContextConfig getDefaultWebXmlFragment

INFO: No global web.xml found

Oct 13, 2023 6:41:37 PM org.apache.jasper.servlet.TldScanner scanJars

INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.

Oct 13, 2023 6:41:38 PM org.apache.catalina.core.StandardContext listenerStart

SEVERE: Error configuring application listener of class [org.springframework.web.context.ContextLoaderListener]

java.lang.ClassNotFoundException: org.springframework.web.context.ContextLoaderListener

        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1358)

        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1180)

        at org.apache.catalina.core.DefaultInstanceManager.loadClass(DefaultInstanceManager.java:545)

        at org.apache.catalina.core.DefaultInstanceManager.loadClassMaybePrivileged(DefaultInstanceManager.java:526)

        at org.apache.catalina.core.DefaultInstanceManager.newInstance(DefaultInstanceManager.java:150)

        at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4613)

        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5155)

        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)

        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1412)

        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1402)

        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)

        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)

        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)

        at java.base/java.lang.Thread.run(Thread.java:829)

Oct 13, 2023 6:41:38 PM org.apache.catalina.core.StandardContext listenerStart

SEVERE: Error configuring application listener of class [org.apache.commons.fileupload.servlet.FileCleanerCleanup]

java.lang.ClassNotFoundException: org.apache.commons.fileupload.servlet.FileCleanerCleanup

        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1358)

        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1180)

        at org.apache.catalina.core.DefaultInstanceManager.loadClass(DefaultInstanceManager.java:545)

        at org.apache.catalina.core.DefaultInstanceManager.loadClassMaybePrivileged(DefaultInstanceManager.java:526)

        at org.apache.catalina.core.DefaultInstanceManager.newInstance(DefaultInstanceManager.java:150)

        at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4613)

        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5155)

        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)

        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1412)

        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1402)

        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)

        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)

        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)

        at java.base/java.lang.Thread.run(Thread.java:829)

Oct 13, 2023 6:41:38 PM org.apache.catalina.core.StandardContext listenerStart

SEVERE: Error configuring application listener of class [org.cbioportal.web.config.WebServletContextListener]

java.lang.ClassNotFoundException: org.cbioportal.web.config.WebServletContextListener

        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1358)

        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1180)

        at org.apache.catalina.core.DefaultInstanceManager.loadClass(DefaultInstanceManager.java:545)

        at org.apache.catalina.core.DefaultInstanceManager.loadClassMaybePrivileged(DefaultInstanceManager.java:526)

        at org.apache.catalina.core.DefaultInstanceManager.newInstance(DefaultInstanceManager.java:150)

        at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4613)

        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5155)

        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)

        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1412)

        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1402)

        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)

        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)

        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)

        at java.base/java.lang.Thread.run(Thread.java:829)

Oct 13, 2023 6:41:38 PM org.apache.catalina.core.StandardContext listenerStart

SEVERE: Skipped installing application listeners due to previous error(s)

Oct 13, 2023 6:41:38 PM org.apache.catalina.core.StandardContext startInternal

SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file

Oct 13, 2023 6:41:38 PM org.apache.catalina.core.StandardContext startInternal

SEVERE: Context [] startup failed due to previous errors

SEVERE: Context [] failed in [org.apache.catalina.core.StandardContext] lifecycle. Allowing Tomcat to shutdown.

WARNING: An illegal reflective access operation has occurred

WARNING: Illegal reflective access by org.apache.catalina.loader.WebappClassLoaderBase (file:/opt/cbioportal/portal/target/dependency/webapp-runner.jar) to field java.io.ObjectStreamClass$Caches.localDescs

WARNING: Please consider reporting this to the maintainers of org.apache.catalina.loader.WebappClassLoaderBase

WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations

WARNING: All illegal access operations will be denied in a future release

Oct 13, 2023 6:41:38 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesObjectStreamClassCaches

WARNING: Failed to clear soft references from ObjectStreamClass$Caches for web application [ROOT]

java.lang.ClassCastException: class java.io.ObjectStreamClass$Caches$1 cannot be cast to class java.util.Map (java.io.ObjectStreamClass$Caches$1 and java.util.Map are in module java.base of loader 'bootstrap')

        at org.apache.catalina.loader.WebappClassLoaderBase.clearCache(WebappClassLoaderBase.java:2258)

        at org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesObjectStreamClassCaches(WebappClassLoaderBase.java:2233)

        at org.apache.catalina.loader.WebappClassLoaderBase.clearReferences(WebappClassLoaderBase.java:1603)

        at org.apache.catalina.loader.WebappClassLoaderBase.stop(WebappClassLoaderBase.java:1548)

        at org.apache.catalina.loader.WebappLoader.stopInternal(WebappLoader.java:452)

        at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:257)

        at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5435)

        at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:257)

        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:187)

        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1412)

        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1402)

        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)

        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)

        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)

        at java.base/java.lang.Thread.run(Thread.java:829)

Oct 13, 2023 6:41:38 PM org.apache.coyote.AbstractProtocol start

INFO: Starting ProtocolHandler ["http-nio-8080"]

Please advise how to resolve this issue..

Thanks,

Abhishek

[Tim Kuijpers]

Dear Abhishek,

Thank you for reaching out!

Unfortunately, it's hard for us to support non-docker-based installations, because of the many ways the servers can be configured. Our current recommendation is to use Docker for deployment.

Regarding the error logs, I assume you successfully executed all previous steps before building from the source. Please check if  the Java and Apache Maven versions are the same version as specified in the official documentation. A wrong version might cause this error.

I hope this helps.

Best,
Tim

[Abhishek Reddy]

Hello Tim, 

Thank you for responding back! And i have validated the versions on both JAVA and Maven. The versions the i am currently using are matching with the documentation. please see the versions below.

openjdk version "11.0.20.1" 2023-08-24

maven version - apache maven 3.6.3.

still iam facing the same issue as mentioned before in the log. please advise the next steps on this for better resolution.

Thanks,

Abhishek

[Abhishek Reddy]

Hello Tim,

Please see the versions below. they are supported as per the documentation. 
/opt/cbioportal# java -version
openjdk version "17.0.8.1" 2023-08-24
OpenJDK Runtime Environment (build 17.0.8.1+1-Ubuntu-0ubuntu122.04)
OpenJDK 64-Bit Server VM (build 17.0.8.1+1-Ubuntu-0ubuntu122.04, mixed mode, sharing)
/opt/cbioportal# mvn -version
Apache Maven 3.6.3
Maven home: /usr/share/maven
Java version: 17.0.8.1, vendor: Private Build, runtime: /usr/lib/jvm/java-17-openjdk-amd64
Default locale: en, platform encoding: UTF-8
OS name: "linux", version: "6.2.0-1013-aws", arch: "amd64", family: "unix"
/opt/cbioportal#

Please advice on the error resolution steps.

Thanks,

Abhishek

On Monday, October 16, 2023 at 11:13:44 AM UTC-4 Tim Kuijpers wrote: