Hi
We are following the instruction here to install OHDSI stack in docker container, we are seeing all the tables created, and we have a backend CDM database, we setup the source and source_domain, all seems to be good, but it Atlas is still not up, due some strange error (see below).
Since our backend CDM is 2.7.4, so we are using 2.7.4 for WebAPI and Atlas. And we really have no idea about the error message here. Also strange is that the log says INFO main org.flywaydb.core.internal.command.DbMigrate - - Current version of schema "webapi": 2.8.0.20190604111801, which strange, since we are using 2.7.4.
Could some one kindly take a look? Thank you in advance!
root@4c18e4365469:/var/log/supervisor# tail -1000 *stdout*
2021-04-30 19:05:08.097 INFO main org.springframework.beans.factory.support.DefaultListableBeanFactory - - Overriding bean definition for bean 'requestContextFilter' with a different definition: replacing [Root bean: class [null]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=org.springframework.boot.autoconfigure.jersey.JerseyAutoConfiguration; factoryMethodName=requestContextFilter; initMethodName=null; destroyMethodName=(inferred); defined in class path resource [org/springframework/boot/autoconfigure/jersey/JerseyAutoConfiguration.class]] with [Root bean: class [org.springframework.boot.autoconfigure.web.WebMvcAutoConfiguration$WebMvcAutoConfigurationAdapter]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=requestContextFilter; initMethodName=null; destroyMethodName=(inferred); defined in class path resource [org/springframework/boot/autoconfigure/web/WebMvcAutoConfiguration$WebMvcAutoConfigurationAdapter.class]]
2021-04-30 19:05:08.379 INFO main org.springframework.integration.config.IntegrationRegistrar - - No bean named 'integrationHeaderChannelRegistry' has been explicitly defined. Therefore, a default DefaultHeaderChannelRegistry will be created.
2021-04-30 19:05:08.799 INFO main org.springframework.integration.config.DefaultConfiguringBeanFactoryPostProcessor - - No bean named 'errorChannel' has been explicitly defined. Therefore, a default PublishSubscribeChannel will be created.
2021-04-30 19:05:08.819 INFO main org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor - - JSR-330 'javax.inject.Inject' annotation found and supported for autowiring
2021-04-30 19:05:08.897 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'converterConfiguration' of type [org.ohdsi.webapi.ConverterConfiguration$$EnhancerBySpringCGLIB$$f2a64de2] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:08.929 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'conversionService' of type [org.springframework.core.convert.support.DefaultConversionService] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:09.200 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'org.springframework.transaction.annotation.ProxyTransactionManagementConfiguration' of type [org.springframework.transaction.annotation.ProxyTransactionManagementConfiguration$$EnhancerBySpringCGLIB$$8c0b2696] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:09.417 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'shiroConfiguration' of type [org.ohdsi.webapi.ShiroConfiguration$$EnhancerBySpringCGLIB$$d0798c91] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:09.432 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'flywayConfig' of type [org.ohdsi.webapi.FlywayConfig$$EnhancerBySpringCGLIB$$8eaed8ea] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:10.244 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'secondaryDataSource' of type [org.apache.tomcat.jdbc.pool.DataSource] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:10.263 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'org.springframework.boot.autoconfigure.jdbc.DataSourceAutoConfiguration' of type [org.springframework.boot.autoconfigure.jdbc.DataSourceAutoConfiguration$$EnhancerBySpringCGLIB$$6dfec9f6] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:10.355 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'spring.datasource-org.springframework.boot.autoconfigure.jdbc.DataSourceProperties' of type [org.springframework.boot.autoconfigure.jdbc.DataSourceProperties] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:10.368 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'dataSourceInitializer' of type [org.springframework.boot.autoconfigure.jdbc.DataSourceInitializer] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:10.485 INFO main org.flywaydb.core.internal.util.VersionPrinter - - Flyway 4.2.0 by Boxfuse
2021-04-30 19:05:10.834 INFO main org.flywaydb.core.internal.dbsupport.DbSupportFactory - - Database: jdbc:postgresql://host.docker.internal:5432/DockerOHDSI (PostgreSQL 13.2)
2021-04-30 19:05:11.048 INFO main org.flywaydb.core.internal.command.DbMigrate - - Current version of schema "webapi": 2.8.0.20190604111801
2021-04-30 19:05:11.048 WARN main org.flywaydb.core.internal.command.DbMigrate - - outOfOrder mode is active. Migration of schema "webapi" may not be reproducible.
2021-04-30 19:05:11.049 INFO main org.flywaydb.core.internal.command.DbMigrate - - Schema "webapi" is up to date. No migration necessary.
2021-04-30 19:05:11.052 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'flyway' of type [org.flywaydb.core.Flyway] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:11.062 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'disabledSecurity' of type [org.ohdsi.webapi.shiro.management.DisabledSecurity] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:11.073 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'noLockoutPolicy' of type [org.ohdsi.webapi.shiro.lockout.NoLockoutPolicy] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:11.137 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'securityManager' of type [org.ohdsi.webapi.shiro.lockout.LockoutWebSecurityManager] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:11.208 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'integrationGlobalProperties' of type [org.springframework.beans.factory.config.PropertiesFactoryBean] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:11.209 INFO main org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean 'integrationGlobalProperties' of type [java.util.Properties] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2021-04-30 19:05:11.252 INFO main org.springframework.web.context.ContextLoader - - Root WebApplicationContext: initialization completed in 4853 ms
2021-04-30 19:05:12.027 INFO main org.springframework.jdbc.datasource.DriverManagerDataSource - - Loaded JDBC driver: org.postgresql.Driver
2021-04-30 19:05:12.029 INFO main org.ohdsi.webapi.DataAccessConfig - - driver loaded: org.postgresql.Driver
2021-04-30 19:05:12.050 INFO main org.ohdsi.webapi.DataAccessConfig - - driver loaded: com.microsoft.sqlserver.jdbc.SQLServerDriver
2021-04-30 19:05:12.051 INFO main org.ohdsi.webapi.DataAccessConfig - - error loading oracle.jdbc.driver.OracleDriver driver. oracle.jdbc.driver.OracleDriver
2021-04-30 19:05:12.080 INFO main org.ohdsi.webapi.DataAccessConfig - - driver loaded: com.amazon.redshift.jdbc.Driver
2021-04-30 19:05:12.080 INFO main org.ohdsi.webapi.DataAccessConfig - - error loading com.cloudera.impala.jdbc.Driver driver. com.cloudera.impala.jdbc.Driver
2021-04-30 19:05:12.081 INFO main org.ohdsi.webapi.DataAccessConfig - - error loading net.starschema.clouddb.jdbc.BQDriver driver. net.starschema.clouddb.jdbc.BQDriver
2021-04-30 19:05:12.082 INFO main org.ohdsi.webapi.DataAccessConfig - - error loading org.netezza.Driver driver. org.netezza.Driver
2021-04-30 19:05:12.082 INFO main org.ohdsi.webapi.DataAccessConfig - - error loading com.simba.googlebigquery.jdbc42.Driver driver. com.simba.googlebigquery.jdbc42.Driver
2021-04-30 19:05:12.204 INFO main org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean - - Building JPA container EntityManagerFactory for persistence unit 'default'
2021-04-30 19:05:12.230 INFO main org.hibernate.jpa.internal.util.LogHelper - - HHH000204: Processing PersistenceUnitInfo [name: default]
2021-04-30 19:05:12.379 INFO main org.hibernate.Version - - HHH000412: Hibernate Core {5.4.2.Final}
2021-04-30 19:05:12.670 INFO main org.hibernate.annotations.common.Version - - HCANN000001: Hibernate Commons Annotations {5.1.0.Final}
2021-04-30 19:05:13.127 INFO main org.hibernate.dialect.Dialect - - HHH000400: Using dialect: org.hibernate.dialect.PostgreSQLDialect
2021-04-30 19:05:13.897 WARN main org.hibernate.mapping.RootClass - - HHH000038: Composite-id class does not override equals(): org.ohdsi.webapi.conceptset.ConceptSetGenerationInfoKey
2021-04-30 19:05:13.898 WARN main org.hibernate.mapping.RootClass - - HHH000039: Composite-id class does not override hashCode(): org.ohdsi.webapi.conceptset.ConceptSetGenerationInfoKey
2021-04-30 19:05:15.324 INFO main org.hibernate.engine.transaction.jta.platform.internal.JtaPlatformInitiator - - HHH000490: Using JtaPlatform implementation: [org.hibernate.engine.transaction.jta.platform.internal.NoJtaPlatform]
2021-04-30 19:05:15.327 INFO main org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean - - Initialized JPA EntityManagerFactory for persistence unit 'default'
2021-04-30 19:05:16.871 INFO main org.springframework.boot.web.servlet.ServletRegistrationBean - - Mapping servlet: 'org.ohdsi.webapi.JerseyConfig' to [/*]
2021-04-30 19:05:16.872 INFO main org.springframework.boot.web.servlet.ServletRegistrationBean - - Mapping servlet: 'dispatcherServlet' to [/]
2021-04-30 19:05:16.873 INFO main org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: 'errorPageFilter' to: [/*]
2021-04-30 19:05:16.873 INFO main org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: 'characterEncodingFilter' to: [/*]
2021-04-30 19:05:16.873 INFO main org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: 'hiddenHttpMethodFilter' to: [/*]
2021-04-30 19:05:16.873 INFO main org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: 'httpPutFormContentFilter' to: [/*]
2021-04-30 19:05:16.873 INFO main org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: 'requestContextFilter' to: [/*]
2021-04-30 19:05:16.873 INFO main org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: 'exceptionHandlerFilter' to: [/*]
2021-04-30 19:05:16.873 INFO main org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: 'cacheFilter' to: [/*]
2021-04-30 19:05:16.873 INFO main org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: 'corsFilter' to: [/*]
2021-04-30 19:05:16.873 INFO main org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: 'shiroFilter' to: [/*]
2021-04-30 19:05:17.115 INFO main org.springframework.batch.core.repository.support.JobRepositoryFactoryBean - - No database type set, using meta data indicating: POSTGRES
2021-04-30 19:05:17.442 INFO main org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor - - Initializing ExecutorService
2021-04-30 19:05:17.462 INFO main org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor - - Initializing ExecutorService 'taskExecutor'
2021-04-30 19:05:17.620 INFO main org.ehcache.xml.XmlConfiguration - - Loading Ehcache XML configuration from /usr/local/tomcat/webapps/WebAPI/WEB-INF/classes/config/ehcache.xml.
2021-04-30 19:05:18.420 INFO main org.ehcache.core.EhcacheManager - - Cache 'datasources.dashboard' created in EhcacheManager.
2021-04-30 19:05:18.423 INFO main org.ehcache.core.EhcacheManager - - Cache 'datasources.domain' created in EhcacheManager.
2021-04-30 19:05:18.426 INFO main org.ehcache.core.EhcacheManager - - Cache 'datasources.dataDensity' created in EhcacheManager.
2021-04-30 19:05:18.429 INFO main org.ehcache.core.EhcacheManager - - Cache 'datasources.person' created in EhcacheManager.
2021-04-30 19:05:18.431 INFO main org.ehcache.core.EhcacheManager - - Cache 'datasources.drilldown' created in EhcacheManager.
2021-04-30 19:05:18.459 INFO main org.ehcache.jsr107.Eh107CacheManager - - Registering Ehcache MBean javax.cache:type=CacheStatistics,CacheManager=file./usr/local/tomcat/webapps/WebAPI/WEB-INF/classes/config/ehcache.xml,Cache=datasources.dashboard
2021-04-30 19:05:18.461 INFO main org.ehcache.jsr107.Eh107CacheManager - - Registering Ehcache MBean javax.cache:type=CacheStatistics,CacheManager=file./usr/local/tomcat/webapps/WebAPI/WEB-INF/classes/config/ehcache.xml,Cache=datasources.domain
2021-04-30 19:05:18.462 INFO main org.ehcache.jsr107.Eh107CacheManager - - Registering Ehcache MBean javax.cache:type=CacheStatistics,CacheManager=file./usr/local/tomcat/webapps/WebAPI/WEB-INF/classes/config/ehcache.xml,Cache=datasources.dataDensity
2021-04-30 19:05:18.462 INFO main org.ehcache.jsr107.Eh107CacheManager - - Registering Ehcache MBean javax.cache:type=CacheStatistics,CacheManager=file./usr/local/tomcat/webapps/WebAPI/WEB-INF/classes/config/ehcache.xml,Cache=datasources.person
2021-04-30 19:05:18.462 INFO main org.ehcache.jsr107.Eh107CacheManager - - Registering Ehcache MBean javax.cache:type=CacheStatistics,CacheManager=file./usr/local/tomcat/webapps/WebAPI/WEB-INF/classes/config/ehcache.xml,Cache=datasources.drilldown
2021-04-30 19:05:19.716 INFO main org.ohdsi.webapi.executionengine.service.ScriptExecutionServiceImpl - - Invalidating execution engine based analyses
2021-04-30 19:05:21.241 INFO taskExecutor-1 org.springframework.batch.core.launch.support.SimpleJobLauncher - - Job: [SimpleJob: [name=warmCache]] launched with the following parameters: [{jobName=warming omop_noPHI_CDM cache, time=1619809521132, jobAuthor=system}]
2021-04-30 19:05:21.269 INFO main org.ehcache.jsr107.Eh107CacheManager - - Registering Ehcache MBean javax.cache:type=CacheStatistics,CacheManager=file./usr/local/tomcat/webapps/WebAPI/WEB-INF/classes/config/ehcache.xml,Cache=datasources.dashboard
2021-04-30 19:05:21.270 INFO main org.ehcache.jsr107.Eh107CacheManager - - Registering Ehcache MBean javax.cache:type=CacheStatistics,CacheManager=file./usr/local/tomcat/webapps/WebAPI/WEB-INF/classes/config/ehcache.xml,Cache=datasources.domain
2021-04-30 19:05:21.270 INFO main org.ehcache.jsr107.Eh107CacheManager - - Registering Ehcache MBean javax.cache:type=CacheStatistics,CacheManager=file./usr/local/tomcat/webapps/WebAPI/WEB-INF/classes/config/ehcache.xml,Cache=datasources.dataDensity
2021-04-30 19:05:21.270 INFO main org.ehcache.jsr107.Eh107CacheManager - - Registering Ehcache MBean javax.cache:type=CacheStatistics,CacheManager=file./usr/local/tomcat/webapps/WebAPI/WEB-INF/classes/config/ehcache.xml,Cache=datasources.person
2021-04-30 19:05:21.270 INFO main org.ehcache.jsr107.Eh107CacheManager - - Registering Ehcache MBean javax.cache:type=CacheStatistics,CacheManager=file./usr/local/tomcat/webapps/WebAPI/WEB-INF/classes/config/ehcache.xml,Cache=datasources.drilldown
2021-04-30 19:05:21.344 INFO taskExecutor-1 org.springframework.batch.core.job.SimpleStepHandler - - Executing step: [warmCacheStep]
2021-04-30 19:05:21.598 INFO main org.springframework.scheduling.concurrent.ThreadPoolTaskScheduler - - Initializing ExecutorService
2021-04-30 19:05:21.617 INFO main org.springframework.scheduling.concurrent.ThreadPoolTaskScheduler - - Initializing ExecutorService 'taskScheduler'
2021-04-30 19:05:22.057 WARN main org.springframework.aop.framework.CglibAopProxy - - Unable to proxy interface-implementing method [public final void com.odysseusinc.scheduler.service.BaseJobServiceImpl.setApplicationContext(org.springframework.context.ApplicationContext) throws org.springframework.beans.BeansException] because it is marked as final: Consider using interface-based JDK proxies instead!
2021-04-30 19:05:22.057 INFO main org.springframework.aop.framework.CglibAopProxy - - Final method [public final void com.odysseusinc.scheduler.service.BaseJobServiceImpl.setApplicationContext(org.springframework.context.ApplicationContext) throws org.springframework.beans.BeansException] cannot get proxied via CGLIB: Calls to this method will NOT be routed to the target instance and might lead to NPEs against uninitialized fields in the proxy instance.
2021-04-30 19:05:22.057 INFO main org.springframework.aop.framework.CglibAopProxy - - Final method [protected final com.cronutils.model.time.ExecutionTime com.odysseusinc.scheduler.service.BaseJobServiceImpl.getExecutionTime(com.odysseusinc.scheduler.model.ArachneJob)] cannot get proxied via CGLIB: Calls to this method will NOT be routed to the target instance and might lead to NPEs against uninitialized fields in the proxy instance.
2021-04-30 19:05:22.407 INFO main org.flywaydb.core.internal.command.DbMigrate - - Current version of schema "webapi": 2.8.0.20190604111801
2021-04-30 19:05:22.407 WARN main org.flywaydb.core.internal.command.DbMigrate - - outOfOrder mode is active. Migration of schema "webapi" may not be reproducible.
2021-04-30 19:05:22.408 INFO main org.flywaydb.core.internal.command.DbMigrate - - Schema "webapi" is up to date. No migration necessary.
2021-04-30 19:05:23.235 INFO main org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter - - Looking for @ControllerAdvice: org.springframework.boot.context.embedded.AnnotationConfigEmbeddedWebApplicationContext@1e8e3df8: startup date [Fri Apr 30 19:05:06 UTC 2021]; root of context hierarchy
2021-04-30 19:05:23.415 INFO main org.springframework.web.servlet.handler.SimpleUrlHandlerMapping - - Mapped URL path [/webjars/**] onto handler of type [class org.springframework.web.servlet.resource.ResourceHttpRequestHandler]
2021-04-30 19:05:23.415 INFO main org.springframework.web.servlet.handler.SimpleUrlHandlerMapping - - Mapped URL path [/**] onto handler of type [class org.springframework.web.servlet.resource.ResourceHttpRequestHandler]
2021-04-30 19:05:23.503 INFO main org.springframework.web.servlet.handler.SimpleUrlHandlerMapping - - Mapped URL path [/**/favicon.ico] onto handler of type [class org.springframework.web.servlet.resource.ResourceHttpRequestHandler]
2021-04-30 19:05:23.775 INFO main org.springframework.ldap.core.support.AbstractContextSource - - Property 'userDn' not set - anonymous context will be used for read-write operations
2021-04-30 19:05:24.933 INFO main org.springframework.jmx.export.annotation.AnnotationMBeanExporter - - Registering beans for JMX exposure on startup
2021-04-30 19:05:24.950 INFO main org.springframework.jmx.export.annotation.AnnotationMBeanExporter - - Bean with name 'integrationMbeanExporter' has been autodetected for JMX exposure
2021-04-30 19:05:24.953 INFO main org.springframework.jmx.export.annotation.AnnotationMBeanExporter - - Located managed bean 'integrationMbeanExporter': registering with JMX server as MBean [org.springframework.integration.monitor:name=integrationMbeanExporter,type=IntegrationMBeanExporter]
2021-04-30 19:05:25.009 INFO main org.springframework.integration.monitor.IntegrationMBeanExporter - - Registering beans for JMX exposure on startup
2021-04-30 19:05:25.009 INFO main org.springframework.integration.monitor.IntegrationMBeanExporter - - Registering MessageChannel nullChannel
2021-04-30 19:05:25.014 INFO main org.springframework.integration.monitor.IntegrationMBeanExporter - - Located managed bean 'org.springframework.integration:type=MessageChannel,name=nullChannel': registering with JMX server as MBean [org.springframework.integration:type=MessageChannel,name=nullChannel]
2021-04-30 19:05:25.026 INFO main org.springframework.integration.monitor.IntegrationMBeanExporter - - Registering MessageChannel errorChannel
2021-04-30 19:05:25.028 INFO main org.springframework.integration.monitor.IntegrationMBeanExporter - - Located managed bean 'org.springframework.integration:type=MessageChannel,name=errorChannel': registering with JMX server as MBean [org.springframework.integration:type=MessageChannel,name=errorChannel]
2021-04-30 19:05:25.093 INFO main org.springframework.integration.monitor.IntegrationMBeanExporter - - Registering MessageHandler errorLogger
2021-04-30 19:05:25.094 INFO main org.springframework.integration.monitor.IntegrationMBeanExporter - - Located managed bean 'org.springframework.integration:type=MessageHandler,name=errorLogger,bean=internal': registering with JMX server as MBean [org.springframework.integration:type=MessageHandler,name=errorLogger,bean=internal]
2021-04-30 19:05:25.123 INFO main org.springframework.context.support.DefaultLifecycleProcessor - - Starting beans in phase 0
2021-04-30 19:05:25.123 INFO main org.springframework.integration.endpoint.EventDrivenConsumer - - Adding {logging-channel-adapter:_org.springframework.integration.errorLogger} as a subscriber to the 'errorChannel' channel
2021-04-30 19:05:25.123 INFO main org.springframework.integration.channel.PublishSubscribeChannel - - Channel 'application:default:8089.errorChannel' has 1 subscriber(s).
2021-04-30 19:05:25.124 INFO main org.springframework.integration.endpoint.EventDrivenConsumer - - started _org.springframework.integration.errorLogger
2021-04-30 19:05:25.124 INFO main org.springframework.context.support.DefaultLifecycleProcessor - - Starting beans in phase 2147483647
2021-04-30 19:05:25.157 INFO main org.ohdsi.webapi.WebApi - - Started WebApi in 19.466 seconds (JVM running for 26.766)
2021-04-30 19:05:25.191 INFO taskScheduler-2 org.ohdsi.webapi.executionengine.service.ScriptExecutionServiceImpl - - Invalidating execution engine based analyses
2021-04-30 19:08:02.207 INFO taskExecutor-1 org.springframework.beans.factory.xml.XmlBeanDefinitionReader - - Loading XML bean definitions from class path resource [org/springframework/jdbc/support/sql-error-codes.xml]
2021-04-30 19:08:02.257 WARN taskExecutor-1 org.springframework.jdbc.support.SQLErrorCodesFactory - - Error while extracting database name - falling back to empty error codes
org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is org.postgresql.util.PSQLException: This connection has been closed.
at org.springframework.jdbc.support.JdbcUtils.extractDatabaseMetaData(JdbcUtils.java:342)
at org.springframework.jdbc.support.JdbcUtils.extractDatabaseMetaData(JdbcUtils.java:366)
at org.springframework.jdbc.support.SQLErrorCodesFactory.getErrorCodes(SQLErrorCodesFactory.java:212)
at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.setDataSource(SQLErrorCodeSQLExceptionTranslator.java:134)
at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.<init>(SQLErrorCodeSQLExceptionTranslator.java:97)
at org.springframework.jdbc.support.JdbcAccessor.getExceptionTranslator(JdbcAccessor.java:105)
at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:654)
at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:688)
at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:720)
at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:770)
at org.ohdsi.webapi.cdmresults.CDMResultsCacheTasklet.warmCache(CDMResultsCacheTasklet.java:66)
at org.ohdsi.webapi.cdmresults.CDMResultsCacheTasklet.execute(CDMResultsCacheTasklet.java:78)
at org.springframework.batch.core.step.tasklet.TaskletStep$ChunkTransactionCallback.doInTransaction(TaskletStep.java:406)
at org.springframework.batch.core.step.tasklet.TaskletStep$ChunkTransactionCallback.doInTransaction(TaskletStep.java:330)
at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133)
at org.springframework.batch.core.step.tasklet.TaskletStep$2.doInChunkContext(TaskletStep.java:272)
at org.springframework.batch.core.scope.context.StepContextRepeatCallback.doInIteration(StepContextRepeatCallback.java:81)
at org.springframework.batch.repeat.support.RepeatTemplate.getNextResult(RepeatTemplate.java:374)
at org.springframework.batch.repeat.support.RepeatTemplate.executeInternal(RepeatTemplate.java:215)
at org.springframework.batch.repeat.support.RepeatTemplate.iterate(RepeatTemplate.java:144)
at org.springframework.batch.core.step.tasklet.TaskletStep.doExecute(TaskletStep.java:257)
at org.springframework.batch.core.step.AbstractStep.execute(AbstractStep.java:200)
at org.springframework.batch.core.job.SimpleStepHandler.handleStep(SimpleStepHandler.java:148)
at org.springframework.batch.core.job.AbstractJob.handleStep(AbstractJob.java:392)
at org.springframework.batch.core.job.SimpleJob.doExecute(SimpleJob.java:135)
at org.springframework.batch.core.job.AbstractJob.execute(AbstractJob.java:306)
at org.springframework.batch.core.launch.support.SimpleJobLauncher$1.run(SimpleJobLauncher.java:135)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: org.postgresql.util.PSQLException: This connection has been closed.
at org.postgresql.jdbc.PgConnection.checkClosed(PgConnection.java:885)
at org.postgresql.jdbc.PgConnection.getMetaData(PgConnection.java:1317)
at org.springframework.jdbc.support.JdbcUtils.extractDatabaseMetaData(JdbcUtils.java:331)
... 29 more
2021-04-30 19:08:02.261 ERROR taskExecutor-1 org.ohdsi.webapi.cdmresults.CDMResultsCacheTasklet - - Failed to warm cache for omop_noPHI_CDM. Exception: PreparedStatementCallback; SQL [WITH concepts AS (
SELECT
CAST(ancestor_concept_id AS VARCHAR) ancestor_id,
CAST(descendant_concept_id AS VARCHAR) descendant_id
FROM omop_cdm.concept_ancestor ca
UNION
SELECT
CAST(concept_id AS VARCHAR) ancestor_id,
CAST(concept_id AS VARCHAR) descendant_id
FROM omop_cdm.concept c
), counts AS (
SELECT stratum_1 concept_id, MAX (count_value) agg_count_value
FROM results.achilles_results
WHERE analysis_id IN (2, 4, 5, 201, 225, 301, 325, 401, 425, 501, 505, 525, 601, 625, 701, 725, 801, 825,
826, 827, 901, 1001, 1201, 1425, 1801, 1825, 1826, 1827, 2101, 2125, 2301)
GROUP BY stratum_1
UNION
SELECT stratum_2 AS concept_id, SUM (count_value) AS agg_count_value
FROM results.achilles_results
WHERE analysis_id IN (405, 605, 705, 805, 807, 1805, 1807, 2105)
GROUP BY stratum_2
)
SELECT
concepts.ancestor_id concept_id,
COALESCE(max(c1.agg_count_value),0) record_count,
COALESCE(sum(c2.agg_count_value),0) descendant_record_count
FROM concepts
LEFT JOIN counts c1 ON concepts.ancestor_id = c1.concept_id
LEFT JOIN counts c2 ON concepts.descendant_id = c2.concept_id
GROUP BY concepts.ancestor_id
]; An I/O error occurred while sending to the backend.; nested exception is org.postgresql.util.PSQLException: An I/O error occurred while sending to the backend.
2021-04-30 19:08:02.330 INFO taskExecutor-1 org.springframework.batch.core.launch.support.SimpleJobLauncher - - Job: [SimpleJob: [name=warmCache]] completed with the following parameters: [{jobName=warming omop_noPHI_CDM cache, time=1619809521132, jobAuthor=system}] and the following status: [COMPLETED]
root@4c18e4365469:/var/log/supervisor#