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IHTSDO / snowstorm

Scalable SNOMED CT Terminology Server using Elasticsearch
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Java errors when running SnowStorm image #621

Open paulbuer08 opened 2 months ago

paulbuer08 commented 2 months ago

I am trying to setup and run Hapi FHIR and SnowStorm with ElasticSearch using these images (in wsl2):

ElasticSearch ran okay with: docker run --name elasticsearch --network fhir-network -p 9200:9200 -e "discovery.type=single-node" -e "xpack.security.enabled=false" -e "ES_JAVA_OPTS=-Xms4g -Xmx4g" elasticsearch:8.11.1

I ran SnowStorm with: docker run --name snowstorm --network fhir-network -p 8080:8080 -e "ELASTICSEARCH_HOST=http://localhost:9200" -e "JAVA_OPTS=-Xms2g -Xmx4g" snomedinternational/snowstorm:latest

But SnowStorm is failing with these errors: 

         ____                          _
 __/\__ / ___| _ __   _____      _____| |_ ___  _ __ _ __ ___
 \_\/_/ \___ \| '_ \ / _ \ \ /\ / / __| __/ _ \| '__| '_ ` _ \
 /_/\_\  ___) | | | | (_) \ V  V /\__ \ || (_) | |  | | | | | |
   \/   |____/|_| |_|\___/ \_/\_/ |___/\__\___/|_|  |_| |_| |_|
===============================================================
 :: Snowstorm, SNOMED CT Terminology Server ::

2024-09-03T19:18:23.476Z  INFO 1 --- [           main] o.snomed.snowstorm.SnowstormApplication  : Starting SnowstormApplication using Java 17.0.12 with PID 1 (/app/classes started by root in /app)
2024-09-03T19:18:23.480Z  INFO 1 --- [           main] o.snomed.snowstorm.SnowstormApplication  : No active profile set, falling back to 1 default profile: "default"
2024-09-03T19:18:25.511Z  INFO 1 --- [           main] .s.d.r.c.RepositoryConfigurationDelegate : Multiple Spring Data modules found, entering strict repository configuration mode
2024-09-03T19:18:25.513Z  INFO 1 --- [           main] .s.d.r.c.RepositoryConfigurationDelegate : Bootstrapping Spring Data Elasticsearch repositories in DEFAULT mode.
2024-09-03T19:18:25.796Z  INFO 1 --- [           main] .s.d.r.c.RepositoryConfigurationDelegate : Finished Spring Data repository scanning in 276 ms. Found 26 Elasticsearch repository interfaces.
2024-09-03T19:18:26.457Z  INFO 1 --- [           main] .s.d.r.c.RepositoryConfigurationDelegate : Multiple Spring Data modules found, entering strict repository configuration mode
2024-09-03T19:18:26.457Z  INFO 1 --- [           main] .s.d.r.c.RepositoryConfigurationDelegate : Bootstrapping Spring Data Reactive Elasticsearch repositories in DEFAULT mode.
2024-09-03T19:18:26.472Z  INFO 1 --- [           main] .s.d.r.c.RepositoryConfigurationDelegate : Finished Spring Data repository scanning in 14 ms. Found 0 Reactive Elasticsearch repository interfaces.
2024-09-03T19:18:26.958Z  INFO 1 --- [           main] o.s.cloud.context.scope.GenericScope     : BeanFactory id=f9691893-b605-3f9b-9a2b-6c513415780c
2024-09-03T19:18:27.187Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'permissionEvaluator' of type [org.snomed.snowstorm.config.MethodSecurityConfig$1] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [healthEndpointGroupsBeanPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.187Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'methodSecurityConfig' of type [org.snomed.snowstorm.config.MethodSecurityConfig$$SpringCGLIB$$0] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [healthEndpointGroupsBeanPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.232Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'org.springframework.cloud.client.loadbalancer.LoadBalancerAutoConfiguration$RetryInterceptorAutoConfiguration' of type [org.springframework.cloud.client.loadbalancer.LoadBalancerAutoConfiguration$RetryInterceptorAutoConfiguration] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). The currently created BeanPostProcessor [lbRestClientPostProcessor] is declared through a non-static factory method on that class; consider declaring it as static instead.
2024-09-03T19:18:27.237Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'org.springframework.cloud.loadbalancer.config.BlockingLoadBalancerClientAutoConfiguration' of type [org.springframework.cloud.loadbalancer.config.BlockingLoadBalancerClientAutoConfiguration] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.240Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'org.springframework.cloud.loadbalancer.config.LoadBalancerAutoConfiguration' of type [org.springframework.cloud.loadbalancer.config.LoadBalancerAutoConfiguration] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.252Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'org.springframework.cloud.commons.config.CommonsConfigAutoConfiguration' of type [org.springframework.cloud.commons.config.CommonsConfigAutoConfiguration] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.256Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'org.springframework.cloud.client.loadbalancer.LoadBalancerDefaultMappingsProviderAutoConfiguration' of type [org.springframework.cloud.client.loadbalancer.LoadBalancerDefaultMappingsProviderAutoConfiguration] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.258Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'loadBalancerClientsDefaultsMappingsProvider' of type [org.springframework.cloud.client.loadbalancer.LoadBalancerDefaultMappingsProviderAutoConfiguration$$Lambda$715/0x00007fe11c5304b0] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.260Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'defaultsBindHandlerAdvisor' of type [org.springframework.cloud.commons.config.DefaultsBindHandlerAdvisor] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.271Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'spring.cloud.loadbalancer-org.springframework.cloud.client.loadbalancer.LoadBalancerClientsProperties' of type [org.springframework.cloud.client.loadbalancer.LoadBalancerClientsProperties] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.278Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'default.org.springframework.cloud.loadbalancer.config.LoadBalancerAutoConfiguration.LoadBalancerClientSpecification' of type [org.springframework.cloud.loadbalancer.annotation.LoadBalancerClientSpecification] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.280Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'default.org.springframework.cloud.loadbalancer.config.BlockingLoadBalancerClientAutoConfiguration.LoadBalancerClientSpecification' of type [org.springframework.cloud.loadbalancer.annotation.LoadBalancerClientSpecification] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.282Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'loadBalancerClientFactory' of type [org.springframework.cloud.loadbalancer.support.LoadBalancerClientFactory] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.289Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'blockingLoadBalancerClient' of type [org.springframework.cloud.loadbalancer.blocking.client.BlockingLoadBalancerClient] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.302Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'loadBalancerServiceInstanceCookieTransformer' of type [org.springframework.cloud.loadbalancer.core.LoadBalancerServiceInstanceCookieTransformer] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.305Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'xForwarderHeadersTransformer' of type [org.springframework.cloud.loadbalancer.blocking.XForwardedHeadersTransformer] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.306Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'org.springframework.cloud.client.loadbalancer.LoadBalancerAutoConfiguration' of type [org.springframework.cloud.client.loadbalancer.LoadBalancerAutoConfiguration] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.310Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'loadBalancerRequestFactory' of type [org.springframework.cloud.client.loadbalancer.LoadBalancerRequestFactory] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.313Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'org.springframework.cloud.loadbalancer.config.BlockingLoadBalancerClientAutoConfiguration$BlockingLoadBalancerRetryConfig' of type [org.springframework.cloud.loadbalancer.config.BlockingLoadBalancerClientAutoConfiguration$BlockingLoadBalancerRetryConfig$$SpringCGLIB$$0] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.318Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'loadBalancedRetryFactory' of type [org.springframework.cloud.loadbalancer.blocking.retry.BlockingLoadBalancedRetryFactory] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.324Z  WARN 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'loadBalancerInterceptor' of type [org.springframework.cloud.client.loadbalancer.RetryLoadBalancerInterceptor] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). Is this bean getting eagerly injected into a currently created BeanPostProcessor [lbRestClientPostProcessor]? Check the corresponding BeanPostProcessor declaration and its dependencies.
2024-09-03T19:18:27.833Z  WARN 1 --- [           main] ConfigServletWebServerApplicationContext : Exception encountered during context initialization - cancelling refresh attempt: org.springframework.context.ApplicationContextException: Unable to start web server
2024-09-03T19:18:27.853Z  INFO 1 --- [           main] .s.b.a.l.ConditionEvaluationReportLogger :

Error starting ApplicationContext. To display the condition evaluation report re-run your application with 'debug' enabled.
2024-09-03T19:18:27.876Z ERROR 1 --- [           main] o.s.boot.SpringApplication               : Application run failed

org.springframework.context.ApplicationContextException: Unable to start web server
        at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.onRefresh(ServletWebServerApplicationContext.java:165)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:618)
        at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:146)
        at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:762)
        at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:464)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:334)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1358)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1347)
        at org.snomed.snowstorm.SnowstormApplication.main(SnowstormApplication.java:63)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'tomcatServletWebServerFactory' defined in class path resource [org/springframework/boot/autoconfigure/web/servlet/ServletWebServerFactoryConfiguration$EmbeddedTomcat.class]: Failed to instantiate [org.springframework.boot.web.embedded.tomcat.TomcatServletWebServerFactory]: Factory method 'tomcatServletWebServerFactory' threw exception with message: Error creating bean with name 'snowstormApplication': Unsatisfied dependency expressed through field 'elasticsearchOperations': Error creating bean with name 'elasticsearchOperations' defined in org.snomed.snowstorm.SnowstormApplication: Unsatisfied dependency expressed through method 'elasticsearchOperations' parameter 0: Error creating bean with name 'elasticsearchEntityMapper' defined in org.snomed.snowstorm.SnowstormApplication: Unsatisfied dependency expressed through method 'elasticsearchEntityMapper' parameter 0: Error creating bean with name 'elasticsearchMappingContext' defined in org.snomed.snowstorm.SnowstormApplication: Unable to make field private java.lang.String java.util.TimeZone.ID accessible: module java.base does not "opens java.util" to unnamed module @1817d444
        at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:648)
        at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:636)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1335)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1165)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:562)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522)
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:326)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:324)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:205)
        at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.getWebServerFactory(ServletWebServerApplicationContext.java:223)
        at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.createWebServer(ServletWebServerApplicationContext.java:186)
        at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.onRefresh(ServletWebServerApplicationContext.java:162)
        ... 8 common frames omitted
Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.boot.web.embedded.tomcat.TomcatServletWebServerFactory]: Factory method 'tomcatServletWebServerFactory' threw exception with message: Error creating bean with name 'snowstormApplication': Unsatisfied dependency expressed through field 'elasticsearchOperations': Error creating bean with name 'elasticsearchOperations' defined in org.snomed.snowstorm.SnowstormApplication: Unsatisfied dependency expressed through method 'elasticsearchOperations' parameter 0: Error creating bean with name 'elasticsearchEntityMapper' defined in org.snomed.snowstorm.SnowstormApplication: Unsatisfied dependency expressed through method 'elasticsearchEntityMapper' parameter 0: Error creating bean with name 'elasticsearchMappingContext' defined in org.snomed.snowstorm.SnowstormApplication: Unable to make field private java.lang.String java.util.TimeZone.ID accessible: module java.base does not "opens java.util" to unnamed module @1817d444
        at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:177)
        at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:644)
        ... 20 common frames omitted
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'snowstormApplication': Unsatisfied dependency expressed through field 'elasticsearchOperations': Error creating bean with name 'elasticsearchOperations' defined in org.snomed.snowstorm.SnowstormApplication: Unsatisfied dependency expressed through method 'elasticsearchOperations' parameter 0: Error creating bean with name 'elasticsearchEntityMapper' defined in org.snomed.snowstorm.SnowstormApplication: Unsatisfied dependency expressed through method 'elasticsearchEntityMapper' parameter 0: Error creating bean with name 'elasticsearchMappingContext' defined in org.snomed.snowstorm.SnowstormApplication: Unable to make field private java.lang.String java.util.TimeZone.ID accessible: module java.base does not "opens java.util" to unnamed module @1817d444
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.resolveFieldValue(AutowiredAnnotationBeanPostProcessor.java:787)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:767)
        at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:145)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessProperties(AutowiredAnnotationBeanPostProcessor.java:508)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1419)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:599)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522)
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:326)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:324)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200)
        at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:409)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1335)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1165)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:562)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522)
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:326)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:324)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200)
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:254)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.addCandidateEntry(DefaultListableBeanFactory.java:1696)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1653)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveMultipleBeans(DefaultListableBeanFactory.java:1470)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1392)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory$DependencyObjectProvider.resolveStream(DefaultListableBeanFactory.java:2198)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory$DependencyObjectProvider.orderedStream(DefaultListableBeanFactory.java:2192)
        at org.springframework.boot.autoconfigure.web.servlet.ServletWebServerFactoryConfiguration$EmbeddedTomcat.tomcatServletWebServerFactory(ServletWebServerFactoryConfiguration.java:74)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:569)
        at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:140)
        ... 21 common frames omitted
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'elasticsearchOperations' defined in org.snomed.snowstorm.SnowstormApplication: Unsatisfied dependency expressed through method 'elasticsearchOperations' parameter 0: Error creating bean with name 'elasticsearchEntityMapper' defined in org.snomed.snowstorm.SnowstormApplication: Unsatisfied dependency expressed through method 'elasticsearchEntityMapper' parameter 0: Error creating bean with name 'elasticsearchMappingContext' defined in org.snomed.snowstorm.SnowstormApplication: Unable to make field private java.lang.String java.util.TimeZone.ID accessible: module java.base does not "opens java.util" to unnamed module @1817d444
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:795)
        at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:542)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1335)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1165)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:562)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522)
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:326)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:324)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200)
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:254)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1443)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1353)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.resolveFieldValue(AutowiredAnnotationBeanPostProcessor.java:784)
        ... 53 common frames omitted
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'elasticsearchEntityMapper' defined in org.snomed.snowstorm.SnowstormApplication: Unsatisfied dependency expressed through method 'elasticsearchEntityMapper' parameter 0: Error creating bean with name 'elasticsearchMappingContext' defined in org.snomed.snowstorm.SnowstormApplication: Unable to make field private java.lang.String java.util.TimeZone.ID accessible: module java.base does not "opens java.util" to unnamed module @1817d444
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:795)
        at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:542)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1335)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1165)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:562)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522)
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:326)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:324)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200)
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:254)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1443)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1353)
        at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:904)
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:782)
        ... 66 common frames omitted
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'elasticsearchMappingContext' defined in org.snomed.snowstorm.SnowstormApplication: Unable to make field private java.lang.String java.util.TimeZone.ID accessible: module java.base does not "opens java.util" to unnamed module @1817d444
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1786)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:600)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522)
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:326)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:324)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200)
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:254)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1443)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1353)
        at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:904)
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:782)
        ... 80 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.TimeZone.ID accessible: module java.base does not "opens java.util" to unnamed module @1817d444
        at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
        at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
        at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
        at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
        at org.springframework.util.ReflectionUtils.makeAccessible(ReflectionUtils.java:804)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.doWith(AbstractMappingContext.java:540)
        at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:728)
        at org.springframework.data.mapping.context.AbstractMappingContext.doAddPersistentEntity(AbstractMappingContext.java:426)
        at org.springframework.data.mapping.context.AbstractMappingContext.addPersistentEntity(AbstractMappingContext.java:383)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.lambda$createAndRegisterProperty$3(AbstractMappingContext.java:595)
        at java.base/java.lang.Iterable.forEach(Iterable.java:75)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.createAndRegisterProperty(AbstractMappingContext.java:592)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.doWith(AbstractMappingContext.java:546)
        at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:728)
        at org.springframework.data.mapping.context.AbstractMappingContext.doAddPersistentEntity(AbstractMappingContext.java:426)
        at org.springframework.data.mapping.context.AbstractMappingContext.addPersistentEntity(AbstractMappingContext.java:383)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.lambda$createAndRegisterProperty$3(AbstractMappingContext.java:595)
        at java.base/java.lang.Iterable.forEach(Iterable.java:75)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.createAndRegisterProperty(AbstractMappingContext.java:592)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.doWith(AbstractMappingContext.java:546)
        at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:728)
        at org.springframework.data.mapping.context.AbstractMappingContext.doAddPersistentEntity(AbstractMappingContext.java:426)
        at org.springframework.data.mapping.context.AbstractMappingContext.addPersistentEntity(AbstractMappingContext.java:383)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.lambda$createAndRegisterProperty$3(AbstractMappingContext.java:595)
        at java.base/java.lang.Iterable.forEach(Iterable.java:75)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.createAndRegisterProperty(AbstractMappingContext.java:592)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.doWith(AbstractMappingContext.java:546)
        at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:728)
        at org.springframework.data.mapping.context.AbstractMappingContext.doAddPersistentEntity(AbstractMappingContext.java:426)
        at org.springframework.data.mapping.context.AbstractMappingContext.addPersistentEntity(AbstractMappingContext.java:383)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.lambda$createAndRegisterProperty$3(AbstractMappingContext.java:595)
        at java.base/java.lang.Iterable.forEach(Iterable.java:75)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.createAndRegisterProperty(AbstractMappingContext.java:592)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.doWith(AbstractMappingContext.java:546)
        at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:728)
        at org.springframework.data.mapping.context.AbstractMappingContext.doAddPersistentEntity(AbstractMappingContext.java:426)
        at org.springframework.data.mapping.context.AbstractMappingContext.addPersistentEntity(AbstractMappingContext.java:383)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.lambda$createAndRegisterProperty$3(AbstractMappingContext.java:595)
        at java.base/java.lang.Iterable.forEach(Iterable.java:75)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.createAndRegisterProperty(AbstractMappingContext.java:592)
        at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.doWith(AbstractMappingContext.java:546)
        at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:728)
        at org.springframework.data.mapping.context.AbstractMappingContext.doAddPersistentEntity(AbstractMappingContext.java:426)
        at org.springframework.data.mapping.context.AbstractMappingContext.addPersistentEntity(AbstractMappingContext.java:383)
        at org.springframework.data.mapping.context.AbstractMappingContext.addPersistentEntity(AbstractMappingContext.java:343)
        at java.base/java.lang.Iterable.forEach(Iterable.java:75)
        at org.springframework.data.mapping.context.AbstractMappingContext.initialize(AbstractMappingContext.java:488)
        at org.springframework.data.mapping.context.AbstractMappingContext.afterPropertiesSet(AbstractMappingContext.java:480)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1833)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1782)
        ... 91 common frames omitted
kaicode commented 2 months ago

This part of the log looks like a java security issue:

...
Unable to make field private java.lang.String java.util.TimeZone.ID accessible: module java.base does not "opens java.util" to unnamed module
...

Adding these JAVA_OPTS should fix it: --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED

paulbuer08 commented 2 months ago

Thanks @kaicode for the quick response. But still I'm getting the same errors, I have added your suggested options: docker run --name snowstorm --network fhir-network -p 8080:8080 -e "ELASTICSEARCH_HOST=http://localhost:9200" -e "JAVA_OPTS=-Xms2g -Xmx4g --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED" snomedinternational/snowstorm:latest

I have also tried extending the options further to cover more internal packages, but still the same result: 

docker run --name snowstorm --network fhir-network \
  -p 8080:8080 \
  -e "ELASTICSEARCH_HOST=http://localhost:9200" \
  -e "JAVA_OPTS=-Xms2g -Xmx4g -Dspring.profiles.active=debug \
  --add-opens=java.base/java.lang=ALL-UNNAMED \
  --add-opens=java.base/java.util=ALL-UNNAMED \
  --add-opens=java.base/java.util.concurrent=ALL-UNNAMED \
  --add-opens=java.base/sun.nio.ch=ALL-UNNAMED \
  --add-opens=java.base/java.time=ALL-UNNAMED \
  --add-opens=java.base/java.nio=ALL-UNNAMED \
  --add-opens=java.base/java.lang.reflect=ALL-UNNAMED \
  --add-opens=java.base/java.net=ALL-UNNAMED \
  --add-opens=java.base/java.security=ALL-UNNAMED \
  --add-opens=java.base/java.text=ALL-UNNAMED \
  --add-opens=java.base/java.io=ALL-UNNAMED \
  --add-opens=java.base/java.util.stream=ALL-UNNAMED \
  --add-opens=java.base/java.nio.charset=ALL-UNNAMED \
  --add-opens=java.base/java.util.TimeZone=ALL-UNNAMED \
  --add-exports=java.base/sun.nio.cs=ALL-UNNAMED \
  --add-exports=java.base/jdk.internal.reflect=ALL-UNNAMED \
  --add-exports=java.base/sun.security.util=ALL-UNNAMED \
  --add-exports=java.base/sun.security.x509=ALL-UNNAMED" \
  snomedinternational/snowstorm:latest
kaicode commented 2 months ago

After some testing with your approach this seems to work:

docker run --name snowstorm --network fhir-network -p 8080:8080 -e \
-e JAVA_TOOL_OPTIONS="-Xms2g -Xmx4g --add-opens=java.base/java.lang=ALL-UNNAMED \
--add-opens=java.base/java.util=ALL-UNNAMED" snomedinternational/snowstorm:latest \
--elasticsearch.urls=http://elasticsearch:9200

Using JAVA_TOOL_OPTIONS rather than JAVA_OPTS. I removed ELASTICSEARCH_HOST and added --elasticsearch.urls at the end.

paulbuer08 commented 1 month ago

After some testing with your approach this seems to work:

docker run --name snowstorm --network fhir-network -p 8080:8080 -e \
-e JAVA_TOOL_OPTIONS="-Xms2g -Xmx4g --add-opens=java.base/java.lang=ALL-UNNAMED \
--add-opens=java.base/java.util=ALL-UNNAMED" snomedinternational/snowstorm:latest \
--elasticsearch.urls=http://elasticsearch:9200

Using JAVA_TOOL_OPTIONS rather than JAVA_OPTS. I removed ELASTICSEARCH_HOST and added --elasticsearch.urls at the end.

Thanks @kaicode, this is working as well in my end. Nice catch!