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[BUG] Problem running ML plugins (branch dependency-mgmt) #95

Open
ericmil87 opened this issue Apr 21, 2023 · 0 comments
Open

[BUG] Problem running ML plugins (branch dependency-mgmt) #95

ericmil87 opened this issue Apr 21, 2023 · 0 comments

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@ericmil87
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ericmil87 commented Apr 21, 2023 •
edited

Describe the bug
I'm having some problems on running docker-compose XNAT with ML Plugins and OHIF.
The error occurs when I add datasets-plugin-1.0.0.jar and ml-plugin-1.0.0.jar on xnat-data/plugins folder.
I've followed the tutorial @ https://wiki.xnat.org/ml/installing-the-xnat-ml-docker-compose-release and even updated default-manifest.json with the following content to add the plugins I want:

{
    "version": "1.8.6.1",
    "base": "xnat-data",
    "webapps": "org.nrg.xnat.web:xnat-web:1.8.6.1 -> ROOT.war",
    "plugins": [
        "org.nrg.xnatx.plugins:batch-launch:0.4.0",
        "org.nrg.xnatx.plugins:container-service:3.0.0:fat",
        "org.nrg.xnatx.plugins:ml-plugin:1.0.0",
        "org.nrg.xnatx.plugins:datasets-plugin:1.0.0",
        "org.nrg.xnatx.plugins:ohif-viewer:3.2.0:fat"
    ]
}

I've also tried with only the plugins I really need:

{
    "version": "1.8.6.1",
    "base": "xnat-data",
    "webapps": "org.nrg.xnat.web:xnat-web:1.8.6.1 -> ROOT.war",
    "plugins": [
        "org.nrg.xnatx.plugins:ml-plugin:1.0.0",
        "org.nrg.xnatx.plugins:datasets-plugin:1.0.0",
        "org.nrg.xnatx.plugins:ohif-viewer:3.2.0:fat"
    ]
}

after running:
$ ./gradlew composeBuild
$ docker-compose up --detach

Terminal Output:

sudo docker-compose up -d
Creating xnat-db      ... done
Creating xnat-web     ... done
Creating xnat-traefik ... done

I've got the stack running with the .jar files of the plugins on the xnat-data/plugins/ folder.
But when I try to access I get a 404 error:
error

Below is the containers logs after trying to access the service.
XNAT-WEB:

psql: error: could not connect to server: Connection refused
	Is the server running on host "xnat-db" (172.18.0.5) and accepting
	TCP/IP connections on port 5432?
Postgres is unavailable - sleeping
Postgres is up - executing command "/usr/local/tomcat/bin/catalina.sh run"
Listening for transport dt_socket at address: 8000
21-Apr-2023 19:14:09.529 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name:   Apache Tomcat/9.0.65
21-Apr-2023 19:14:09.531 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built:          Jul 14 2022 12:28:53 UTC
21-Apr-2023 19:14:09.531 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 9.0.65.0
21-Apr-2023 19:14:09.531 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name:               Linux
21-Apr-2023 19:14:09.531 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version:            5.15.0-1033-oracle
21-Apr-2023 19:14:09.531 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture:          aarch64
21-Apr-2023 19:14:09.531 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home:             /usr/local/openjdk-8/jre
21-Apr-2023 19:14:09.531 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version:           1.8.0_342-b07
21-Apr-2023 19:14:09.532 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor:            Oracle Corporation
21-Apr-2023 19:14:09.532 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE:         /usr/local/tomcat
21-Apr-2023 19:14:09.532 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME:         /usr/local/tomcat
21-Apr-2023 19:14:09.533 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties
21-Apr-2023 19:14:09.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
21-Apr-2023 19:14:09.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
21-Apr-2023 19:14:09.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
21-Apr-2023 19:14:09.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
21-Apr-2023 19:14:09.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms256m
21-Apr-2023 19:14:09.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx4g
21-Apr-2023 19:14:09.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dxnat.home=/data/xnat/home
21-Apr-2023 19:14:09.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=0.0.0.0:8000
21-Apr-2023 19:14:09.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
21-Apr-2023 19:14:09.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/tomcat
21-Apr-2023 19:14:09.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/tomcat
21-Apr-2023 19:14:09.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/tomcat/temp
21-Apr-2023 19:14:09.541 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent Loaded Apache Tomcat Native library [1.2.35] using APR version [1.7.0].
21-Apr-2023 19:14:09.541 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR capabilities: IPv6 [true], sendfile [true], accept filters [false], random [true], UDS [true].
21-Apr-2023 19:14:09.542 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR/OpenSSL configuration: useAprConnector [false], useOpenSSL [true]
21-Apr-2023 19:14:09.555 INFO [main] org.apache.catalina.core.AprLifecycleListener.initializeSSL OpenSSL successfully initialized [OpenSSL 1.1.1n  15 Mar 2022]
21-Apr-2023 19:14:09.854 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
21-Apr-2023 19:14:09.877 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [527] milliseconds
21-Apr-2023 19:14:09.908 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
21-Apr-2023 19:14:09.909 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/9.0.65]
21-Apr-2023 19:14:09.931 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive [/usr/local/tomcat/webapps/ROOT.war]
21-Apr-2023 19:14:21.137 INFO [main] org.apache.jasper.servlet.TldScanner.scanJars 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.
21-Apr-2023 19:14:39.140 SEVERE [main] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file
21-Apr-2023 19:14:39.144 SEVERE [main] org.apache.catalina.core.StandardContext.startInternal Context [] startup failed due to previous errors
21-Apr-2023 19:14:39.183 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [/usr/local/tomcat/webapps/ROOT.war] has finished in [29,250] ms
21-Apr-2023 19:14:39.186 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
21-Apr-2023 19:14:39.205 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [29327] milliseconds

Here is the xnat-data/tomcat/localhost.2023-04-21.log

21-Apr-2023 19:14:21.430 INFO [main] org.apache.catalina.core.ApplicationContext.log 2 Spring WebApplicationInitializers detected on classpath
21-Apr-2023 19:14:21.664 INFO [main] org.apache.catalina.core.ApplicationContext.log Initializing Spring root WebApplicationContext
21-Apr-2023 19:14:39.139 SEVERE [main] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class [org.springframework.web.context.ContextLoaderListener]
	org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'updateSecurityFilterHandlerMethod' defined in file [/usr/local/tomcat/webapps/ROOT/WEB-INF/classes/org/nrg/xnat/event/listeners/methods/UpdateSecurityFilterHandlerMethod.class]: Unsatisfied dependency expressed through constructor parameter 1; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'appInfo' defined in org.nrg.xnat.initialization.RootConfig: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.nrg.xnat.services.XnatAppInfo]: Factory method 'appInfo' threw exception; nested exception is java.lang.NoSuchMethodError: com.fasterxml.jackson.dataformat.yaml.YAMLFactory._createContentReference(Ljava/lang/Object;)Lcom/fasterxml/jackson/core/io/ContentReference;
		at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749)
		at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:189)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1196)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1098)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
		at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
		at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
		at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
		at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
		at org.springframework.context.support.PostProcessorRegistrationDelegate.registerBeanPostProcessors(PostProcessorRegistrationDelegate.java:237)
		at org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:703)
		at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:527)
		at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
		at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
		at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
		at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4766)
		at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5230)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
		at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:726)
		at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:698)
		at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:696)
		at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1024)
		at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1911)
		at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
		at java.util.concurrent.FutureTask.run(FutureTask.java:266)
		at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
		at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
		at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:825)
		at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:475)
		at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1618)
		at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:319)
		at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
		at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:423)
		at org.apache.catalina.util.LifecycleBase.setState(LifecycleBase.java:366)
		at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:946)
		at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:835)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
		at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1396)
		at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1386)
		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:919)
		at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:265)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
		at org.apache.catalina.core.StandardService.startInternal(StandardService.java:432)
		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:345)
		at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:476)
	Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'appInfo' defined in org.nrg.xnat.initialization.RootConfig: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.nrg.xnat.services.XnatAppInfo]: Factory method 'appInfo' threw exception; nested exception is java.lang.NoSuchMethodError: com.fasterxml.jackson.dataformat.yaml.YAMLFactory._createContentReference(Ljava/lang/Object;)Lcom/fasterxml/jackson/core/io/ContentReference;
		at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:599)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1176)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1071)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
		at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
		at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
		at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
		at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
		at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:211)
		at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1134)
		at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1062)
		at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:835)
		at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:741)
		... 56 more
	Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.nrg.xnat.services.XnatAppInfo]: Factory method 'appInfo' threw exception; nested exception is java.lang.NoSuchMethodError: com.fasterxml.jackson.dataformat.yaml.YAMLFactory._createContentReference(Ljava/lang/Object;)Lcom/fasterxml/jackson/core/io/ContentReference;
		at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:189)
		at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:588)
		... 69 more
	Caused by: java.lang.NoSuchMethodError: com.fasterxml.jackson.dataformat.yaml.YAMLFactory._createContentReference(Ljava/lang/Object;)Lcom/fasterxml/jackson/core/io/ContentReference;
		at com.fasterxml.jackson.dataformat.yaml.YAMLFactory.createParser(YAMLFactory.java:367)
		at com.fasterxml.jackson.dataformat.yaml.YAMLFactory.createParser(YAMLFactory.java:15)
		at com.fasterxml.jackson.databind.ObjectMapper.readTree(ObjectMapper.java:2211)
		at org.nrg.framework.services.SerializerService.deserializeYaml(SerializerService.java:198)
		at org.nrg.xnat.services.XnatAppInfo.<init>(XnatAppInfo.java:94)
		at org.nrg.xnat.initialization.RootConfig.appInfo(RootConfig.java:71)
		at org.nrg.xnat.initialization.RootConfig$$EnhancerBySpringCGLIB$$5a228f4b.CGLIB$appInfo$3(<generated>)
		at org.nrg.xnat.initialization.RootConfig$$EnhancerBySpringCGLIB$$5a228f4b$$FastClassBySpringCGLIB$$6594a7f.invoke(<generated>)
		at org.springframework.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:228)
		at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:358)
		at org.nrg.xnat.initialization.RootConfig$$EnhancerBySpringCGLIB$$5a228f4b.appInfo(<generated>)
		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.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:162)
		... 70 more
21-Apr-2023 19:14:39.140 SEVERE [main] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class [org.nrg.xnat.security.XnatSessionEventPublisher]
	org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'updateSecurityFilterHandlerMethod' defined in file [/usr/local/tomcat/webapps/ROOT/WEB-INF/classes/org/nrg/xnat/event/listeners/methods/UpdateSecurityFilterHandlerMethod.class]: Unsatisfied dependency expressed through constructor parameter 1; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'appInfo' defined in org.nrg.xnat.initialization.RootConfig: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.nrg.xnat.services.XnatAppInfo]: Factory method 'appInfo' threw exception; nested exception is java.lang.NoSuchMethodError: com.fasterxml.jackson.dataformat.yaml.YAMLFactory._createContentReference(Ljava/lang/Object;)Lcom/fasterxml/jackson/core/io/ContentReference;
		at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749)
		at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:189)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1196)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1098)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
		at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
		at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
		at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
		at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
		at org.springframework.context.support.PostProcessorRegistrationDelegate.registerBeanPostProcessors(PostProcessorRegistrationDelegate.java:237)
		at org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:703)
		at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:527)
		at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
		at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
		at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
		at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4766)
		at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5230)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
		at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:726)
		at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:698)
		at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:696)
		at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1024)
		at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1911)
		at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
		at java.util.concurrent.FutureTask.run(FutureTask.java:266)
		at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
		at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
		at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:825)
		at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:475)
		at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1618)
		at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:319)
		at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
		at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:423)
		at org.apache.catalina.util.LifecycleBase.setState(LifecycleBase.java:366)
		at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:946)
		at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:835)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
		at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1396)
		at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1386)
		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:919)
		at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:265)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
		at org.apache.catalina.core.StandardService.startInternal(StandardService.java:432)
		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:345)
		at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:476)
	Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'appInfo' defined in org.nrg.xnat.initialization.RootConfig: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.nrg.xnat.services.XnatAppInfo]: Factory method 'appInfo' threw exception; nested exception is java.lang.NoSuchMethodError: com.fasterxml.jackson.dataformat.yaml.YAMLFactory._createContentReference(Ljava/lang/Object;)Lcom/fasterxml/jackson/core/io/ContentReference;
		at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:599)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1176)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1071)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
		at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
		at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
		at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
		at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
		at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:211)
		at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1134)
		at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1062)
		at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:835)
		at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:741)
		... 56 more
	Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.nrg.xnat.services.XnatAppInfo]: Factory method 'appInfo' threw exception; nested exception is java.lang.NoSuchMethodError: com.fasterxml.jackson.dataformat.yaml.YAMLFactory._createContentReference(Ljava/lang/Object;)Lcom/fasterxml/jackson/core/io/ContentReference;
		at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:189)
		at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:588)
		... 69 more
	Caused by: java.lang.NoSuchMethodError: com.fasterxml.jackson.dataformat.yaml.YAMLFactory._createContentReference(Ljava/lang/Object;)Lcom/fasterxml/jackson/core/io/ContentReference;
		at com.fasterxml.jackson.dataformat.yaml.YAMLFactory.createParser(YAMLFactory.java:367)
		at com.fasterxml.jackson.dataformat.yaml.YAMLFactory.createParser(YAMLFactory.java:15)
		at com.fasterxml.jackson.databind.ObjectMapper.readTree(ObjectMapper.java:2211)
		at org.nrg.framework.services.SerializerService.deserializeYaml(SerializerService.java:198)
		at org.nrg.xnat.services.XnatAppInfo.<init>(XnatAppInfo.java:94)
		at org.nrg.xnat.initialization.RootConfig.appInfo(RootConfig.java:71)
		at org.nrg.xnat.initialization.RootConfig$$EnhancerBySpringCGLIB$$5a228f4b.CGLIB$appInfo$3(<generated>)
		at org.nrg.xnat.initialization.RootConfig$$EnhancerBySpringCGLIB$$5a228f4b$$FastClassBySpringCGLIB$$6594a7f.invoke(<generated>)
		at org.springframework.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:228)
		at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:358)
		at org.nrg.xnat.initialization.RootConfig$$EnhancerBySpringCGLIB$$5a228f4b.appInfo(<generated>)
		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.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:162)
		... 70 more
21-Apr-2023 19:14:39.150 INFO [main] org.apache.catalina.core.ApplicationContext.log Closing Spring root WebApplicationContext

Normally, if I'm running the compose with only with the ohif-viewer plugin, I would get this output from XNAT-WEB container logs:

21-Apr-2023 18:43:31.077 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive [/usr/local/tomcat/webapps/ROOT.war]
21-Apr-2023 18:43:41.964 INFO [main] org.apache.jasper.servlet.TldScanner.scanJars 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.
SOURCE: /usr/local/tomcat/webapps/ROOT/
===========================
New Database -- BEGINNING Initialization
===========================
===========================
Database initialization complete.
===========================
21-Apr-2023 18:44:44.155 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [/usr/local/tomcat/webapps/ROOT.war] has finished in [73,075] ms
21-Apr-2023 18:44:44.159 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
21-Apr-2023 18:44:44.173 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [73174] milliseconds

And I would be able to access the web server.

On all cases, everything looks alright with traefik and tomcat.

To Reproduce
Steps to reproduce the behavior:

$ git clone https://github.com/NrgXnat/xnat-docker-compose.git
$ cd xnat-docker-compose
$ git checkout features/dependency-mgmt

updated default-manifest.json with the following content to add the plugins I want:

{
    "version": "1.8.6.1",
    "base": "xnat-data",
    "webapps": "org.nrg.xnat.web:xnat-web:1.8.6.1 -> ROOT.war",
    "plugins": [
        "org.nrg.xnatx.plugins:batch-launch:0.4.0",
        "org.nrg.xnatx.plugins:container-service:3.0.0:fat",
        "org.nrg.xnatx.plugins:ml-plugin:1.0.0",
        "org.nrg.xnatx.plugins:datasets-plugin:1.0.0",
        "org.nrg.xnatx.plugins:ohif-viewer:3.2.0:fat"
    ]
}

$ ./gradlew composeBuild
$ docker-compose up --detach

Expected behavior
I expect to have the ML Project Dashboard as describe @ https://wiki.xnat.org/ml/using-the-machine-learning-project-dashboard

Docker server environment (please complete the following information):
Ubuntu 20.04.6 LTS (GNU/Linux 5.15.0-1033-oracle aarch64)
System load: 0.22
Usage of /: 9.5% of 193.63GB
Memory usage: 2% of 24GB
** Shape configuration**
Shape:
VM.Standard.A1.Flex
OCPU count:
4
Network bandwidth (Gbps):
4
Memory (GB):
24

system, docker and docker-compose updated.

Can you help me?
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@ericmil87