cbioportal_container exited with code 0 cbioportal_container | db.host=cbioportal_database_container:3306 cbioportal_container | db.user=cbio_user cbioportal_container | db.portal_db_name=cbioportal cbioportal_container | db.password=Mesa420 '@'172.19.0.1' (using password: YES)1-06-18T14:53:04.140652Z 8 [Note] Access denied for user 'cbio_user cbioportal_container | Database connection success cbioportal_container | Migrating database if necessary... cbioportal_container | Everything up to date, nothing to migrate. cbioportal_container | Finished. cbioportal_container | Running: /bin/sh -c java -Xms32g -Xmx32g -Dauthenticate=saml -Dsession.service.url=http://cbioportal_session:5000/api/sessions/my_portal/ -jar webapp-runner.jar -AmaxHttpHeaderSize=16384 -AconnectionTimeout=20000 --enable-compression /cbioportal-webapp cbioportal_container | Connector attributes cbioportal_container | property: maxHttpHeaderSize - 16384(OK) cbioportal_container | property: connectionTimeout - 20000(OK) cbioportal_container | Adding Context for /cbioportal-webapp cbioportal_container | Jun 18, 2021 2:53:06 PM org.apache.coyote.AbstractProtocol init cbioportal_container | INFO: Initializing ProtocolHandler ["http-nio-8080"] cbioportal_container | Jun 18, 2021 2:53:06 PM org.apache.tomcat.util.net.NioSelectorPool getSharedSelector cbioportal_container | INFO: Using a shared selector for servlet write/read cbioportal_container | Jun 18, 2021 2:53:06 PM org.apache.catalina.core.StandardService startInternal cbioportal_container | INFO: Starting service [Tomcat] cbioportal_container | Jun 18, 2021 2:53:06 PM org.apache.catalina.core.StandardEngine startInternal cbioportal_container | INFO: Starting Servlet Engine: Apache Tomcat/8.5.61 cbioportal_container | Jun 18, 2021 2:53:07 PM org.apache.catalina.startup.SetContextPropertiesRule begin cbioportal_container | WARNING: [SetContextPropertiesRule]{Context} Setting property 'antiJARLocking' to 'true' did not find a matching property. cbioportal_container | Jun 18, 2021 2:53:08 PM org.apache.catalina.startup.ContextConfig getDefaultWebXmlFragment cbioportal_container | INFO: No global web.xml found cbioportal_container | Jun 18, 2021 2:53:23 PM org.apache.jasper.servlet.TldScanner scanJars cbioportal_container | 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. cbioportal_container | Jun 18, 2021 2:53:24 PM org.apache.catalina.core.ApplicationContext log cbioportal_container | INFO: No Spring WebApplicationInitializer types detected on classpath cbioportal_container | Jun 18, 2021 2:53:24 PM org.apache.catalina.core.ApplicationContext log cbioportal_container | INFO: Initializing Spring root WebApplicationContext cbioportal_container | Jun 18, 2021 2:53:28 PM org.apache.catalina.core.StandardContext listenerStart cbioportal_container | SEVERE: Exception sending context initialized event to listener instance of class [org.springframework.web.context.ContextLoaderListener] cbioportal_container | org.springframework.beans.factory.BeanDefinitionStoreException: Invalid bean definition with name 'metadataGeneratorFilter' defined in class path resource [applicationContext-security.xml]: Could not resolve placeholder 'saml.sp.metadata.entitybaseurl' in value "${saml.sp.metadata.entitybaseurl}"; nested exception is java.lang.IllegalArgumentException: Could not resolve placeholder 'saml.sp.metadata.entitybaseurl' in value "${saml.sp.metadata.entitybaseurl}" cbioportal_container | at org.springframework.beans.factory.config.PlaceholderConfigurerSupport.doProcessProperties(PlaceholderConfigurerSupport.java:228) cbioportal_container | at org.springframework.beans.factory.config.PropertyPlaceholderConfigurer.processProperties(PropertyPlaceholderConfigurer.java:211) cbioportal_container | at org.springframework.beans.factory.config.PropertyResourceConfigurer.postProcessBeanFactory(PropertyResourceConfigurer.java:86) cbioportal_container | at org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanFactoryPostProcessors(PostProcessorRegistrationDelegate.java:291) cbioportal_container | at org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanFactoryPostProcessors(PostProcessorRegistrationDelegate.java:167) cbioportal_container | at org.springframework.context.support.AbstractApplicationContext.invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:706) cbioportal_container | at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:532) cbioportal_container | at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:401) cbioportal_container | at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:292) cbioportal_container | at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:103) cbioportal_container | at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4689) cbioportal_container | at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5155) cbioportal_container | at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183) cbioportal_container | at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1412) cbioportal_container | at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1402) cbioportal_container | at java.base/java.util.concurrent.FutureTask.run(Unknown Source) cbioportal_container | at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) cbioportal_container | at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) cbioportal_container | at java.base/java.lang.Thread.run(Unknown Source) cbioportal_container | Caused by: java.lang.IllegalArgumentException: Could not resolve placeholder 'saml.sp.metadata.entitybaseurl' in value "${saml.sp.metadata.entitybaseurl}" cbioportal_container | at org.springframework.util.PropertyPlaceholderHelper.parseStringValue(PropertyPlaceholderHelper.java:178) cbioportal_container | at org.springframework.util.PropertyPlaceholderHelper.replacePlaceholders(PropertyPlaceholderHelper.java:124) cbioportal_container | at org.springframework.beans.factory.config.PropertyPlaceholderConfigurer$PlaceholderResolvingStringValueResolver.resolveStringValue(PropertyPlaceholderConfigurer.java:230) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.resolveStringValue(BeanDefinitionVisitor.java:296) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.resolveValue(BeanDefinitionVisitor.java:217) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.visitPropertyValues(BeanDefinitionVisitor.java:147) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.visitBeanDefinition(BeanDefinitionVisitor.java:85) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.resolveValue(BeanDefinitionVisitor.java:179) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.visitGenericArgumentValues(BeanDefinitionVisitor.java:165) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.visitBeanDefinition(BeanDefinitionVisitor.java:90) cbioportal_container | at org.springframework.beans.factory.config.PlaceholderConfigurerSupport.doProcessProperties(PlaceholderConfigurerSupport.java:225) cbioportal_container | ... 18 more cbioportal_container | cbioportal_container | 2021-06-18 14:53:28 [localhost-startStop-1] ERROR org.springframework.web.context.ContextLoader - Context initialization failed cbioportal_container | org.springframework.beans.factory.BeanDefinitionStoreException: Invalid bean definition with name 'metadataGeneratorFilter' defined in class path resource [applicationContext-security.xml]: Could not resolve placeholder 'saml.sp.metadata.entitybaseurl' in value "${saml.sp.metadata.entitybaseurl}"; nested exception is java.lang.IllegalArgumentException: Could not resolve placeholder 'saml.sp.metadata.entitybaseurl' in value "${saml.sp.metadata.entitybaseurl}" cbioportal_container | at org.springframework.beans.factory.config.PlaceholderConfigurerSupport.doProcessProperties(PlaceholderConfigurerSupport.java:228) cbioportal_container | at org.springframework.beans.factory.config.PropertyPlaceholderConfigurer.processProperties(PropertyPlaceholderConfigurer.java:211) cbioportal_container | at org.springframework.beans.factory.config.PropertyResourceConfigurer.postProcessBeanFactory(PropertyResourceConfigurer.java:86) cbioportal_container | at org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanFactoryPostProcessors(PostProcessorRegistrationDelegate.java:291) cbioportal_container | at org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanFactoryPostProcessors(PostProcessorRegistrationDelegate.java:167) cbioportal_container | at org.springframework.context.support.AbstractApplicationContext.invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:706) cbioportal_container | at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:532) cbioportal_container | at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:401) cbioportal_container | at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:292) cbioportal_container | at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:103) cbioportal_container | at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4689) cbioportal_container | at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5155) cbioportal_container | at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183) cbioportal_container | at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1412) cbioportal_container | at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1402) cbioportal_container | at java.base/java.util.concurrent.FutureTask.run(Unknown Source) cbioportal_container | at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) cbioportal_container | at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) cbioportal_container | at java.base/java.lang.Thread.run(Unknown Source) cbioportal_container | Caused by: java.lang.IllegalArgumentException: Could not resolve placeholder 'saml.sp.metadata.entitybaseurl' in value "${saml.sp.metadata.entitybaseurl}" cbioportal_container | at org.springframework.util.PropertyPlaceholderHelper.parseStringValue(PropertyPlaceholderHelper.java:178) cbioportal_container | at org.springframework.util.PropertyPlaceholderHelper.replacePlaceholders(PropertyPlaceholderHelper.java:124) cbioportal_container | at org.springframework.beans.factory.config.PropertyPlaceholderConfigurer$PlaceholderResolvingStringValueResolver.resolveStringValue(PropertyPlaceholderConfigurer.java:230) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.resolveStringValue(BeanDefinitionVisitor.java:296) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.resolveValue(BeanDefinitionVisitor.java:217) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.visitPropertyValues(BeanDefinitionVisitor.java:147) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.visitBeanDefinition(BeanDefinitionVisitor.java:85) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.resolveValue(BeanDefinitionVisitor.java:179) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.visitGenericArgumentValues(BeanDefinitionVisitor.java:165) cbioportal_container | at org.springframework.beans.factory.config.BeanDefinitionVisitor.visitBeanDefinition(BeanDefinitionVisitor.java:90) cbioportal_container | at org.springframework.beans.factory.config.PlaceholderConfigurerSupport.doProcessProperties(PlaceholderConfigurerSupport.java:225) cbioportal_container | ... 18 more cbioportal_container | Jun 18, 2021 2:53:28 PM org.apache.catalina.core.StandardContext startInternal cbioportal_container | SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file cbioportal_container | Jun 18, 2021 2:54:03 PM org.apache.catalina.util.SessionIdGeneratorBase createSecureRandom cbioportal_container | WARNING: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [34,717] milliseconds. cbioportal_container | Jun 18, 2021 2:54:03 PM org.apache.catalina.core.StandardContext startInternal cbioportal_container | SEVERE: Context [] startup failed due to previous errors cbioportal_container | SEVERE: Context [] failed in [org.apache.catalina.core.StandardContext] lifecycle. Allowing Tomcat to shutdown. cbioportal_container | ServletContextListener destroyed cbioportal_container | Jun 18, 2021 2:54:03 PM org.apache.catalina.core.ApplicationContext log cbioportal_container | INFO: Closing Spring root WebApplicationContext cbioportal_container | Jun 18, 2021 2:54:03 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesJdbc cbioportal_container | WARNING: The web application [ROOT] registered the JDBC driver [com.mysql.jdbc.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered. cbioportal_container | Jun 18, 2021 2:54:03 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesJdbc cbioportal_container | WARNING: The web application [ROOT] registered the JDBC driver [com.mysql.fabric.jdbc.FabricMySQLDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered. cbioportal_container | Jun 18, 2021 2:54:03 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads cbioportal_container | WARNING: The web application [ROOT] appears to have started a thread named [mysql-cj-abandoned-connection-cleanup] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread: cbioportal_container | java.base@11.0.10/java.lang.Object.wait(Native Method) cbioportal_container | java.base@11.0.10/java.lang.ref.ReferenceQueue.remove(Unknown Source) cbioportal_container | com.mysql.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:80) cbioportal_container | java.base@11.0.10/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) cbioportal_container | java.base@11.0.10/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) cbioportal_container | java.base@11.0.10/java.lang.Thread.run(Unknown Source) cbioportal_container | WARNING: An illegal reflective access operation has occurred cbioportal_container | WARNING: Illegal reflective access by org.apache.catalina.loader.WebappClassLoaderBase (file:/webapp-runner.jar) to field java.io.ObjectStreamClass$Caches.localDescs cbioportal_container | WARNING: Please consider reporting this to the maintainers of org.apache.catalina.loader.WebappClassLoaderBase cbioportal_container | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations cbioportal_container | WARNING: All illegal access operations will be denied in a future release cbioportal_container | Jun 18, 2021 2:54:03 PM org.apache.coyote.AbstractProtocol start cbioportal_container | INFO: Starting ProtocolHandler ["http-nio-8080"] cbioportal_container | Jun 18, 2021 2:54:04 PM org.apache.coyote.AbstractProtocol pause cbioportal_container | INFO: Pausing ProtocolHandler ["http-nio-8080"] cbioportal_container exited with code 0