Hi,
I am new to the OHDSI platform and I am trying to setup a OHDSI stack environment using BroadSea and SQL Server 2016 database.I have followed the guide provided in the BroadSea documentation page(https://github.com/OHDSI/Broadsea) for setup.
I run “source_source_daimon.sql” and started the containers again (docker-compose up -d).
When I opened tomcat logs I saw following errors:
Nov 06, 2017 8:37:06 AM org.apache.catalina.core.ContainerBase addChildInternal
SEVERE: ContainerBase.addChild: start:
org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/WebAPI]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:162)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2020)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'webApi': Invocation of init method failed; nested exception is javax.ws.rs.WebApplicationException: HTTP 500 Internal Server Error
at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:137)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:866)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:542)
at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.refresh(EmbeddedWebApplicationContext.java:122)
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:737)
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:370)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:314)
at org.springframework.boot.web.support.SpringBootServletInitializer.run(SpringBootServletInitializer.java:151)
at org.springframework.boot.web.support.SpringBootServletInitializer.createRootApplicationContext(SpringBootServletInitializer.java:131)
at org.springframework.boot.web.support.SpringBootServletInitializer.onStartup(SpringBootServletInitializer.java:86)
at org.springframework.web.SpringServletContainerInitializer.onStartup(SpringServletContainerInitializer.java:169)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5623)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
... 10 more
Caused by: javax.ws.rs.WebApplicationException: HTTP 500 Internal Server Error
at org.ohdsi.webapi.job.JobTemplate.launchTasklet(JobTemplate.java:75)
at org.ohdsi.webapi.service.CDMResultsService.warmCache(CDMResultsService.java:143)
at org.ohdsi.webapi.WebApi.lambda$warmCaches$2(WebApi.java:41)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)
at org.ohdsi.webapi.WebApi.warmCaches(WebApi.java:38)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
... 31 more
Nov 06, 2017 8:37:06 AM org.apache.catalina.startup.HostConfig deployWAR
SEVERE: Error deploying web application archive /usr/local/tomcat/webapps/WebAPI.war
java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/WebAPI]]
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:903)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2020)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
If I remove results record from source_daimon table. This error disappears.
-- RESULTS daimon
INSERT INTO ohdsi.source_daimon( source_daimon_id, source_id, daimon_type, table_qualifier, priority) VALUES (3, 1, 2, 'ohdsi', 2);
Not sure what’s relation of this record with error, Am I missing something?
Thanks,
Rohan