Hi Everyone,
I am new to the OHDSI platform and I am trying to setup a local OHDSI stack environment using BroadSea via postgresql database. I am following the instructions for installing Broadsea, I have an Azure postgresql server (cloud) and docker running on my local machine. However, I am seeing the error:
"Application initialization failed
Unable to connect to an instance of the WebAPI.
Please contact your administrator to resolve this issue."
when I log I navigate to http://localhost:8080/atlas/.
In the logs, I am seeing:
21-Jun-2021 23:34:40.671 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/9.0.46
21-Jun-2021 23:34:40.675 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: May 8 2021 17:35:52 UTC
21-Jun-2021 23:34:40.676 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 9.0.46.0
21-Jun-2021 23:34:40.676 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
21-Jun-2021 23:34:40.676 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 5.10.25-linuxkit
21-Jun-2021 23:34:40.676 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
21-Jun-2021 23:34:40.676 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/local/openjdk-8/jre
21-Jun-2021 23:34:40.676 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_292-b10
21-Jun-2021 23:34:40.676 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
21-Jun-2021 23:34:40.677 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/tomcat
21-Jun-2021 23:34:40.677 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/tomcat
21-Jun-2021 23:34:40.681 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties
21-Jun-2021 23:34:40.681 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
21-Jun-2021 23:34:40.681 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
21-Jun-2021 23:34:40.681 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
21-Jun-2021 23:34:40.681 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
21-Jun-2021 23:34:40.681 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
21-Jun-2021 23:34:40.682 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/tomcat
21-Jun-2021 23:34:40.682 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/tomcat
21-Jun-2021 23:34:40.682 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/tomcat/temp
21-Jun-2021 23:34:40.687 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent Loaded Apache Tomcat Native library [1.2.28] using APR version [1.6.5].
21-Jun-2021 23:34:40.687 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR capabilities: IPv6 [true], sendfile [true], accept filters [false], random [true].
21-Jun-2021 23:34:40.688 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR/OpenSSL configuration: useAprConnector [false], useOpenSSL [true]
21-Jun-2021 23:34:40.691 INFO [main] org.apache.catalina.core.AprLifecycleListener.initializeSSL OpenSSL successfully initialized [OpenSSL 1.1.1d 10 Sep 2019]
21-Jun-2021 23:34:41.082 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler [âhttp-nio-8080â]
21-Jun-2021 23:34:41.114 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [709] milliseconds
21-Jun-2021 23:34:41.170 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
21-Jun-2021 23:34:41.170 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/9.0.46]
21-Jun-2021 23:34:41.203 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive [/usr/local/tomcat/webapps/WebAPI.war]
21-Jun-2021 23:34:41.215 WARNING [main] org.apache.tomcat.util.digester.SetPropertiesRule.begin Match [Context] failed to set property [antiJARLocking] to [true]
21-Jun-2021 23:34:48.872 INFO [main] org.apache.jasper.servlet.TldScanner.scanJars 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.
21-Jun-2021 23:35:34.639 SEVERE [main] org.apache.catalina.startup.HostConfig.deployWAR Error deploying web application archive [/usr/local/tomcat/webapps/WebAPI.war]
java.lang.IllegalStateException: Error starting child
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:720)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:690)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:692)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1023)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1903)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:824)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:474)
at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1611)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:319)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:423)
at org.apache.catalina.util.LifecycleBase.setState(LifecycleBase.java:366)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:936)
at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:829)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1384)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1374)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:909)
at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:262)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.StandardService.startInternal(StandardService.java:433)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:930)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.startup.Catalina.start(Catalina.java:772)
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.apache.catalina.startup.Bootstrap.start(Bootstrap.java:342)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:473)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/WebAPI]]
at org.apache.catalina.util.LifecycleBase.handleSubClassException(LifecycleBase.java:440)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:198)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:717)
⌠37 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name âflywayInitializerâ defined in class path resource [org/ohdsi/webapi/FlywayConfig.class]: Invocation of init method failed; nested exception is org.flywaydb.core.api.FlywayException: Migration failed !
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1630)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:756)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:542)
at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.refresh(EmbeddedWebApplicationContext.java:123)
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:666)
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:353)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:300)
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:91)
at org.springframework.web.SpringServletContainerInitializer.onStartup(SpringServletContainerInitializer.java:169)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5161)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
⌠38 more
Caused by: org.flywaydb.core.api.FlywayException: Migration failed !
at com.odysseusinc.arachne.commons.config.flyway.ApplicationContextAwareSpringJdbcMigrationExecutor.execute(ApplicationContextAwareSpringJdbcMigrationExecutor.java:55)
at org.flywaydb.core.internal.command.DbMigrate.doMigrateGroup(DbMigrate.java:343)
at org.flywaydb.core.internal.command.DbMigrate.access$900(DbMigrate.java:53)
at org.flywaydb.core.internal.command.DbMigrate$4.call(DbMigrate.java:276)
at org.flywaydb.core.internal.util.jdbc.TransactionTemplate.execute(TransactionTemplate.java:75)
at org.flywaydb.core.internal.command.DbMigrate.applyMigrations(DbMigrate.java:273)
at org.flywaydb.core.internal.command.DbMigrate.access$800(DbMigrate.java:53)
at org.flywaydb.core.internal.command.DbMigrate$2.call(DbMigrate.java:210)
at org.flywaydb.core.internal.command.DbMigrate$2.call(DbMigrate.java:146)
at org.flywaydb.core.internal.dbsupport.postgresql.PostgreSQLAdvisoryLockTemplate.execute(PostgreSQLAdvisoryLockTemplate.java:68)
at org.flywaydb.core.internal.dbsupport.postgresql.PostgreSQLDbSupport.lock(PostgreSQLDbSupport.java:162)
at org.flywaydb.core.internal.metadatatable.MetaDataTableImpl.lock(MetaDataTableImpl.java:174)
at org.flywaydb.core.internal.command.DbMigrate.migrate(DbMigrate.java:146)
at org.flywaydb.core.Flyway$1.execute(Flyway.java:1010)
at org.flywaydb.core.Flyway$1.execute(Flyway.java:971)
at org.flywaydb.core.Flyway.execute(Flyway.java:1464)
at org.flywaydb.core.Flyway.migrate(Flyway.java:971)
at org.springframework.boot.autoconfigure.flyway.FlywayMigrationInitializer.afterPropertiesSet(FlywayMigrationInitializer.java:65)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1688)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1626)
⌠57 more
Caused by: org.springframework.jdbc.BadSqlGrammarException: StatementCallback; bad SQL grammar [UPDATE ohdsi.cc_results
SET fa_type = âCRITERIA_SETâ
WHERE fa_type = âCRITERIAâ]; nested exception is org.postgresql.util.PSQLException: ERROR: relation âohdsi.cc_resultsâ does not exist
Position: 8
at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:230)
at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:73)
at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:418)
at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:444)
at org.ohdsi.webapi.db.migartion.V2_8_0_20191106092815__migrateEventFAType$MigrationDAO.updateColumnValue(V2_8_0_20191106092815__migrateEventFAType.java:69)
at org.ohdsi.webapi.db.migartion.V2_8_0_20191106092815__migrateEventFAType.lambda$migrate$1(V2_8_0_20191106092815__migrateEventFAType.java:47)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1384)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)
at org.ohdsi.webapi.db.migartion.V2_8_0_20191106092815__migrateEventFAType.migrate(V2_8_0_20191106092815__migrateEventFAType.java:43)
at com.odysseusinc.arachne.commons.config.flyway.ApplicationContextAwareSpringJdbcMigrationExecutor.execute(ApplicationContextAwareSpringJdbcMigrationExecutor.java:53)
⌠76 more
Caused by: org.postgresql.util.PSQLException: ERROR: relation âohdsi.cc_resultsâ does not exist
Position: 8
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2553)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2285)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:323)
at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:473)
at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:393)
at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:322)
at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:308)
at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:284)
at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:279)
at org.springframework.jdbc.core.JdbcTemplate$1ExecuteStatementCallback.doInStatement(JdbcTemplate.java:435)
at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:407)
⌠90 more
21-Jun-2021 23:35:34.644 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [/usr/local/tomcat/webapps/WebAPI.war] has finished in [53,439] ms
21-Jun-2021 23:35:34.645 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat/webapps/atlas]
21-Jun-2021 23:35:34.682 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat/webapps/atlas] has finished in [37] ms
21-Jun-2021 23:35:34.691 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler [âhttp-nio-8080â]
21-Jun-2021 23:35:34.706 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [53626] milliseconds
Exception in thread âtaskExecutor-1â org.springframework.transaction.CannotCreateTransactionException: Could not open JPA EntityManager for transaction; nested exception is java.lang.IllegalStateException: EntityManagerFactory is closed
at org.springframework.orm.jpa.JpaTransactionManager.doBegin(JpaTransactionManager.java:431)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:377)
at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:463)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:277)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy234.update(Unknown Source)
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.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.batch.core.configuration.annotation.SimpleBatchConfiguration$PassthruAdvice.invoke(SimpleBatchConfiguration.java:127)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy234.update(Unknown Source)
at org.springframework.batch.core.job.AbstractJob.execute(AbstractJob.java:357)
at org.springframework.batch.core.launch.support.SimpleJobLauncher$1.run(SimpleJobLauncher.java:135)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.IllegalStateException: EntityManagerFactory is closed
at org.hibernate.internal.SessionFactoryImpl.validateNotClosed(SessionFactoryImpl.java:530)
at org.hibernate.internal.SessionFactoryImpl.createEntityManager(SessionFactoryImpl.java:609)
at org.hibernate.internal.SessionFactoryImpl.createEntityManager(SessionFactoryImpl.java:154)
at org.springframework.orm.jpa.JpaTransactionManager.createEntityManagerForTransaction(JpaTransactionManager.java:449)
at org.springframework.orm.jpa.JpaTransactionManager.doBegin(JpaTransactionManager.java:369)
⌠23 more
In postgresql client, I see that the schema created successfully for ohdsi, and I see the source_daimon and source tables.
Any tips on how I can get past this problem?
Thank you in advance,
Yvonne