[Bug]: ctakes-web-rest spring version and Docker path issues

[ushahid]

What happened?

Hi,

I compiled the WAR file for ctakes-web-rest. When running the WAR using tomcat, it kept crashing (full exception below) because it was looking for org/springframework/core/NestedIOException which was not found, I learnt later that this class does not exist in spring version 6.x set in pom.xml but spring.version in the following line is still set to 5.3.20.

ctakes/ctakes-web-rest/pom.xml

Line 16 in 0ffcc8f

<spring.version>5.3.20</spring.version>

I was able to fix it by upgrading it to 6.1.11 although I'm not sure if it is the right course of action. After upgrading the spring version and building the docker image, it is still unable to run because it fails to find the piper file. It seems to be looking for piper files in the home directory of tomcat in docker container but they are not there.

I was able to eventually run the pipeline by manually copying the piper files to the Tomcat home directory but I suspect that is not the correct way. Please help me figure out how it should be done. Any help is greatly appreciated.

P.S I also had to change the docker image to khipu/openjdk17-alpine since the original is no longer available.

Thanks!

Relevant log output (from Tomcat)

	java.lang.NoClassDefFoundError: org/springframework/core/NestedIOException
		at org.springframework.context.annotation.ConfigurationClassPostProcessor.processConfigBeanDefinitions(ConfigurationClassPostProcessor.java:323)
		at org.springframework.context.annotation.ConfigurationClassPostProcessor.postProcessBeanDefinitionRegistry(ConfigurationClassPostProcessor.java:247)
		at org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanDefinitionRegistryPostProcessors(PostProcessorRegistrationDelegate.java:311)
		at org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanFactoryPostProcessors(PostProcessorRegistrationDelegate.java:112)
		at org.springframework.context.support.AbstractApplicationContext.invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:746)
		at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:564)
		at org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:706)
		at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:672)
		at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:720)
		at org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:595)
		at org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:537)
		at org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:169)
		at jakarta.servlet.GenericServlet.init(GenericServlet.java:143)
		at jakarta.servlet.http.HttpServlet.init(HttpServlet.java:121)
		at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:837)
		at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:794)
		at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:698)
		at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4172)
		at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4458)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
		at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:599)
		at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:571)
		at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:654)
		at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:969)
		at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1911)
		at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:545)
		at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:328)
		at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
		at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:125)
		at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:771)
		at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:423)
		at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1629)
		at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:303)
		at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:109)
		at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:385)
		at org.apache.catalina.util.LifecycleBase.setState(LifecycleBase.java:332)
		at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:776)
		at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:772)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
		at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1203)
		at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1193)
		at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:328)
		at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
		at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:149)
		at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:749)
		at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:203)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
		at org.apache.catalina.core.StandardService.startInternal(StandardService.java:415)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
		at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:874)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
		at org.apache.catalina.startup.Catalina.start(Catalina.java:757)
		at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
		at java.base/java.lang.reflect.Method.invoke(Method.java:565)
		at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:345)
		at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:473)
	Caused by: java.lang.ClassNotFoundException: org.springframework.core.NestedIOException
		at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1332)
		at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1144)
		... 56 more

cTAKES.error.log contents

Version

7.0.0

What operating system are you seeing the problem on?

Fedora 44, Docker Image khipu/openjdk17-alpine

Contact Details

No response

[seanfinan]

I have reworked some spring dependencies. Please try again and let me know if you still have problems.

[ushahid]

Thanks for the quick response, it fixed that issue but now it generates another exception when the request is received. It's now from spring-beans-6.1.11.

Steps to reproduce:

• Navigate to the docker folder in ctakes-web-rest/docker
• In Dockerfile, change the base image to khipu/openjdk17-alpine (current base image does not exist)
• In Dockerfile, change the tomcat url to https://archive.apache.org/dist/tomcat/tomcat-10/v10.1.26/bin/apache-tomcat-10.1.26.zip (current mirror does not respond)
• Build the image with docker buildx build . -t ctakes-web-rest
• Set env variable ctakes_umls_apikey equal to your UMLS key
• Run start_rest.sh
• Submit a post request to the server:

curl -X POST localhost:8080/ctakes-web-rest/service/analyze?pipeline=Default -d "Patient is hyperventilating"

org.springframework.beans.factory.BeanDefinitionStoreException: Unexpected exception parsing XML document from ServletContext resource [/WEB-INF/ctakes-rest-service-servlet.xml]
        at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:426) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:347) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:319) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:184) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:220) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:191) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.web.context.support.XmlWebApplicationContext.loadBeanDefinitions(XmlWebApplicationContext.java:125) ~[spring-web-6.1.21.jar:6.1.21]
        at org.springframework.web.context.support.XmlWebApplicationContext.loadBeanDefinitions(XmlWebApplicationContext.java:94) ~[spring-web-6.1.21.jar:6.1.21]
        at org.springframework.context.support.AbstractRefreshableApplicationContext.refreshBeanFactory(AbstractRefreshableApplicationContext.java:131) ~[spring-context-6.1.11.jar:6.1.11]
        at org.springframework.context.support.AbstractApplicationContext.obtainFreshBeanFactory(AbstractApplicationContext.java:714) ~[spring-context-6.1.11.jar:6.1.11]
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:596) ~[spring-context-6.1.11.jar:6.1.11]
        at org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:706) ~[spring-webmvc-6.2.19.jar:6.2.19]
        at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:672) ~[spring-webmvc-6.2.19.jar:6.2.19]
        at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:720) ~[spring-webmvc-6.2.19.jar:6.2.19]
        at org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:595) ~[spring-webmvc-6.2.19.jar:6.2.19]
        at org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:537) [spring-webmvc-6.2.19.jar:6.2.19]
        at org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:172) [spring-webmvc-6.2.19.jar:6.2.19]
        at jakarta.servlet.GenericServlet.init(GenericServlet.java:143) [servlet-api.jar:6.0]
        at jakarta.servlet.http.HttpServlet.init(HttpServlet.java:121) [servlet-api.jar:?]
        at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:837) [catalina.jar:10.1.26]
        at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:794) [catalina.jar:10.1.26]
        at org.apache.catalina.core.StandardWrapper.allocate(StandardWrapper.java:575) [catalina.jar:10.1.26]
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:115) [catalina.jar:10.1.26]
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90) [catalina.jar:10.1.26]
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:483) [catalina.jar:10.1.26]
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:115) [catalina.jar:10.1.26]
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93) [catalina.jar:10.1.26]
        at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:663) [catalina.jar:10.1.26]
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74) [catalina.jar:10.1.26]
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:344) [catalina.jar:10.1.26]
        at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:389) [tomcat-coyote.jar:10.1.26]
        at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63) [tomcat-coyote.jar:10.1.26]
        at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:904) [tomcat-coyote.jar:10.1.26]
        at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1741) [tomcat-coyote.jar:10.1.26]
        at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52) [tomcat-coyote.jar:10.1.26]
        at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1190) [tomcat-util.jar:10.1.26]
        at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659) [tomcat-util.jar:10.1.26]
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:63) [tomcat-util.jar:10.1.26]
        at java.base/java.lang.Thread.run(Thread.java:840) [?:?]
Caused by: java.lang.NoClassDefFoundError: org/springframework/web/cors/PreFlightRequestHandler
        at org.springframework.web.servlet.config.MvcNamespaceUtils.registerHandlerMappingIntrospector(MvcNamespaceUtils.java:286) ~[spring-webmvc-6.2.19.jar:6.2.19]
        at org.springframework.web.servlet.config.MvcNamespaceUtils.registerDefaultComponents(MvcNamespaceUtils.java:81) ~[spring-webmvc-6.2.19.jar:6.2.19]
        at org.springframework.web.servlet.config.AnnotationDrivenBeanDefinitionParser.parse(AnnotationDrivenBeanDefinitionParser.java:329) ~[spring-webmvc-6.2.19.jar:6.2.19]
        at org.springframework.beans.factory.xml.NamespaceHandlerSupport.parse(NamespaceHandlerSupport.java:74) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.BeanDefinitionParserDelegate.parseCustomElement(BeanDefinitionParserDelegate.java:1390) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.BeanDefinitionParserDelegate.parseCustomElement(BeanDefinitionParserDelegate.java:1370) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.parseBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:179) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.doRegisterBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:150) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.registerBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:96) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.registerBeanDefinitions(XmlBeanDefinitionReader.java:520) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:400) ~[spring-beans-6.1.11.jar:6.1.11]
        ... 38 more
Caused by: java.lang.ClassNotFoundException: org.springframework.web.cors.PreFlightRequestHandler
        at org.springframework.web.servlet.config.MvcNamespaceUtils.registerHandlerMappingIntrospector(MvcNamespaceUtils.java:286) ~[spring-webmvc-6.2.19.jar:6.2.19]
        at org.springframework.web.servlet.config.MvcNamespaceUtils.registerDefaultComponents(MvcNamespaceUtils.java:81) ~[spring-webmvc-6.2.19.jar:6.2.19]
        at org.springframework.web.servlet.config.AnnotationDrivenBeanDefinitionParser.parse(AnnotationDrivenBeanDefinitionParser.java:329) ~[spring-webmvc-6.2.19.jar:6.2.19]
        at org.springframework.beans.factory.xml.NamespaceHandlerSupport.parse(NamespaceHandlerSupport.java:74) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.BeanDefinitionParserDelegate.parseCustomElement(BeanDefinitionParserDelegate.java:1390) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.BeanDefinitionParserDelegate.parseCustomElement(BeanDefinitionParserDelegate.java:1370) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.parseBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:179) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.doRegisterBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:150) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.registerBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:96) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.registerBeanDefinitions(XmlBeanDefinitionReader.java:520) ~[spring-beans-6.1.11.jar:6.1.11]
        at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:400) ~[spring-beans-6.1.11.jar:6.1.11]
        ... 38 more

[seanfinan]

I upgraded spring a bit more, Please try again and let me know if it works. Thanks!

[ushahid]

Thank you! That fixed the dependency issues, the following issues remain, I'll try to submit a fix as a pull request.

1. Docker base image is missing on dockerhub
2. Tomcat mirror in Dockerfile does not respond
3. Piper filepath is broken in docker, it expects piper files to be in tomcat root directory