Errors when deploying WebAPI locally on Tomcat

neslonik · September 26, 2023, 8:46pm

Hi there,
I am trying to deploy WebAPI tp my local Tomcat and I got errors:

2023-09-26 16:24:29.252 ERROR localhost-startStop-1 org.apache.juli.logging.DirectJDKLog - [] - Unable to create initial connections of pool.
org.postgresql.util.PSQLException: The connection attempt failed.
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:331) ~[postgresql-42.3.7.jar:42.3.7]
at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:49) ~[postgresql-42.3.7.jar:42.3.7]
at org.postgresql.jdbc.PgConnection.(PgConnection.java:223) ~[postgresql-42.3.7.jar:42.3.7]
at org.postgresql.Driver.makeConnection(Driver.java:402) ~[postgresql-42.3.7.jar:42.3.7]
at org.postgresql.Driver.connect(Driver.java:261) ~[postgresql-42.3.7.jar:42.3.7]
at org.apache.tomcat.jdbc.pool.PooledConnection.connectUsingDriver(PooledConnection.java:346) ~[tomcat-jdbc.jar:?]
at org.apache.tomcat.jdbc.pool.PooledConnection.connect(PooledConnection.java:227) ~[tomcat-jdbc.jar:?]
at org.apache.tomcat.jdbc.pool.ConnectionPool.createConnection(ConnectionPool.java:763) ~[tomcat-jdbc.jar:?]
at org.apache.tomcat.jdbc.pool.ConnectionPool.borrowConnection(ConnectionPool.java:691) ~[tomcat-jdbc.jar:?]
at org.apache.tomcat.jdbc.pool.ConnectionPool.init(ConnectionPool.java:495) [tomcat-jdbc.jar:?]
at org.apache.tomcat.jdbc.pool.ConnectionPool.(ConnectionPool.java:153) [tomcat-jdbc.jar:?]
at org.apache.tomcat.jdbc.pool.DataSourceProxy.pCreatePool(DataSourceProxy.java:118) [tomcat-jdbc.jar:?]
at org.apache.tomcat.jdbc.pool.DataSourceProxy.createPool(DataSourceProxy.java:107) [tomcat-jdbc.jar:?]
at org.apache.tomcat.jdbc.pool.DataSourceProxy.getConnection(DataSourceProxy.java:131) [tomcat-jdbc.jar:?]
at org.flywaydb.core.internal.util.jdbc.JdbcUtils.openConnection(JdbcUtils.java:51) [flyway-core-4.2.0.jar:?]
at org.flywaydb.core.Flyway.execute(Flyway.java:1418) [flyway-core-4.2.0.jar:?]
at org.flywaydb.core.Flyway.migrate(Flyway.java:971) [flyway-core-4.2.0.jar:?]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_202]
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_202]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_202]
at java.lang.reflect.Method.invoke(Unknown Source) ~[?:1.8.0_202]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1759) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1696) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1626) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:297) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:211) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1131) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1059) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:835) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:741) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:467) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1177) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1072) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) [spring-beans-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.context.support.PostProcessorRegistrationDelegate.registerBeanPostProcessors(PostProcessorRegistrationDelegate.java:237) [spring-context-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:703) [spring-context-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:527) [spring-context-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.refresh(EmbeddedWebApplicationContext.java:123) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE]
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:666) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE]
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:353) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE]
at org.springframework.boot.SpringApplication.run(SpringApplication.java:300) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE]
at org.springframework.boot.web.support.SpringBootServletInitializer.run(SpringBootServletInitializer.java:151) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE]
at org.springframework.boot.web.support.SpringBootServletInitializer.createRootApplicationContext(SpringBootServletInitializer.java:131) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE]
at org.springframework.boot.web.support.SpringBootServletInitializer.onStartup(SpringBootServletInitializer.java:91) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE]
at org.springframework.web.SpringServletContainerInitializer.onStartup(SpringServletContainerInitializer.java:169) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE]
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4889) [catalina.jar:8.5.93]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:171) [catalina.jar:8.5.93]
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:710) [catalina.jar:8.5.93]
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:687) [catalina.jar:8.5.93]
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:661) [catalina.jar:8.5.93]
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1016) [catalina.jar:8.5.93]
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1903) [catalina.jar:8.5.93]
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) [?:1.8.0_202]
at java.util.concurrent.FutureTask.run(Unknown Source) [?:1.8.0_202]
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [?:1.8.0_202]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [?:1.8.0_202]
at java.lang.Thread.run(Unknown Source) [?:1.8.0_202]
Caused by: java.net.SocketTimeoutException: connect timed out
at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method) ~[?:1.8.0_202]
at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source) ~[?:1.8.0_202]
at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source) ~[?:1.8.0_202]
at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source) ~[?:1.8.0_202]
at java.net.AbstractPlainSocketImpl.connect(Unknown Source) ~[?:1.8.0_202]
at java.net.PlainSocketImpl.connect(Unknown Source) ~[?:1.8.0_202]
at java.net.SocksSocketImpl.connect(Unknown Source) ~[?:1.8.0_202]
at java.net.Socket.connect(Unknown Source) ~[?:1.8.0_202]
at org.postgresql.core.PGStream.createSocket(PGStream.java:241) ~[postgresql-42.3.7.jar:42.3.7]
at org.postgresql.core.PGStream.(PGStream.java:98) ~[postgresql-42.3.7.jar:42.3.7]
at org.postgresql.core.v3.ConnectionFactoryImpl.tryConnect(ConnectionFactoryImpl.java:109) ~[postgresql-42.3.7.jar:42.3.7]
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:235) ~[postgresql-42.3.7.jar:42.3.7]
… 68 more
2023-09-26 16:24:29.329 WARN localhost-startStop-1 org.springframework.context.support.AbstractApplicationContext - [] - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name ‘shiroFilter’ defined in class path resource [org/ohdsi/webapi/ShiroConfiguration.class]: Unsatisfied dependency expressed through method ‘shiroFilter’ parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘flyway’ defined in class path resource [org/ohdsi/webapi/FlywayConfig.class]: Invocation of init method failed; nested exception is org.flywaydb.core.internal.dbsupport.FlywaySqlException:
Unable to obtain Jdbc connection from DataSource

My settings file is:

<?xml version="1.0" encoding="UTF-8"?> webapi-postgresql 8080 org.postgresql.Driver jdbc:postgresql://localhost:5432/OHDSI ohdsi_app_user app1 postgresql webapi ${datasource.driverClassName} ${datasource.url} ohdsi_admin_user admin1 classpath:db/migration/postgresql DisabledSecurity 43200 * false true http://localhost/Atlas/#/welcome http://localhost:8080/WebAPI/user/oauth/callback http://localhost/index.html#/welcome/ cn={0},dc=example,dc=org ldap://localhost:389 ldap://localhost:389 CN=Users,DC=example,DC=org @example.org true 30000 public casticket 3 10 10 ${datasource.ohdsi.schema} ${datasource.url} ${datasource.driverClassName} ${datasource.username} ${datasource.password} select password from ${security.db.datasource.schema}.users where lower(email) = lower(?)

I confirm I can connect to this local database using a SQL client.

Any help in resolving the issue is freatly appreciated.

Thank you.
Alla

Chris_Knoll · September 27, 2023, 12:27pm

It’s clearly a connection to database issue. But it’s happening during the db migration which involves Flyway.

I don’t’ see anything in your settings file related to flyway. This should be specified like:

        <flyway.datasource.url>...</flyway.datasource.url>
        <flyway.datasource.username>...</flyway.datasource.username>
        <flyway.datasource.password>...</flyway.datasource.password>

Finally, if you are going to paste formatted text iinto your post, please surroundi it with a formatting block. You can see the formatting on the preview in order to see if you’re done it correctly.

neslonik · December 28, 2023, 6:25pm

I resolved the problem
Thank you for your tips.