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    OS 2.3 Upgrade - issue with JDBC driver class

    Technical Questions
    #1

    we are getting the following error message when we start Catalina

    SEVERE: Exception sending context initialized event to listener instance of class org.springframework.web.context.ContextLoaderListener
    org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘de-liquibase’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is liquibase.exception.DatabaseException: org.apache.tomcat.dbcp.dbcp.SQLNestedException: Cannot load JDBC driver class ‘{{db-driver}}’
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1514)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:521)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:458)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:636)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:934)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:410)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:112)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5016)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5528)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1090)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1900)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
    Caused by: liquibase.exception.DatabaseException: org.apache.tomcat.dbcp.dbcp.SQLNestedException: Cannot load JDBC driver class ‘{{db-driver}}’
    at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:368)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1573)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1511)
    … 25 more
    Caused by: org.apache.tomcat.dbcp.dbcp.SQLNestedException: Cannot load JDBC driver class ‘{{db-driver}}’
    at org.apache.tomcat.dbcp.dbcp.BasicDataSource.createConnectionFactory(BasicDataSource.java:1429)
    at org.apache.tomcat.dbcp.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1371)
    at org.apache.tomcat.dbcp.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
    at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:363)
    … 27 more
    Caused by: java.lang.ClassNotFoundException: {{db-driver}}
    at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1720)
    at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1571)
    at org.apache.tomcat.dbcp.dbcp.BasicDataSource.createConnectionFactory(BasicDataSource.java:1420)
    … 30 more

    Any one ran into similar issue?

    #2

    Looks like in context.xml the tokens for your db driver details didn’t get replaced with the actual values specified to the install.sh script. The attributes in double curly braces probably need to be updated in your $CATALINA_HOME/conf/context.xml

    I ran into this issue on a machine using a non-gnu compiled version of sed which the install script is using to find and replace values in conf files.

    -Randy

    #3

    Hi Randy,

    Do you mean I need to update this
    driverClassName="{{db-driver}}"
    url="{{db-url}}"
    or Just the url?

    #4

    Yes, you will need to update all the values to reflect what your data source is. The install script likely failed to replace them (the tokens that are {{db-attribute}} ) with what was specified when you updated to 2.3. If you are using mysql the driverClassName should be “com.mysql.jdbc.Driver” or for oracle depending on the driver you are using something like “oracle.jdbc.OracleDriver” then your url should follow the jdbc convention. Something like jdbc:mysql://localhost:3306/os_dev.

    -Randy

    #5

    Unable to deploy OS V2.3 when running the CATALINA for a fresh installation.

    EVERE: Exception sending context initialized event to listener instance of class org.springframework.web.context.ContextLoaderListener
    org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘sessionFactory’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is org.hibernate.HibernateException: Dialect class not found: “”
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1514)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:521)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:458)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:618)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:934)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:410)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:112)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5016)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5528)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1090)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1900)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
    Caused by: org.hibernate.HibernateException: Dialect class not found: “”
    at org.hibernate.service.jdbc.dialect.internal.DialectFactoryImpl.constructDialect(DialectFactoryImpl.java:77)
    at org.hibernate.service.jdbc.dialect.internal.DialectFactoryImpl.buildDialect(DialectFactoryImpl.java:65)
    at org.hibernate.engine.jdbc.internal.JdbcServicesImpl.configure(JdbcServicesImpl.java:146)
    at org.hibernate.service.internal.StandardServiceRegistryImpl.configureService(StandardServiceRegistryImpl.java:85)
    at org.hibernate.service.internal.AbstractServiceRegistryImpl.initializeService(AbstractServiceRegistryImpl.java:184)
    at org.hibernate.service.internal.AbstractServiceRegistryImpl.getService(AbstractServiceRegistryImpl.java:156)
    at org.hibernate.cfg.Configuration.buildTypeRegistrations(Configuration.java:1827)
    at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1785)
    at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1870)
    at org.springframework.orm.hibernate4.LocalSessionFactoryBuilder.buildSessionFactory(LocalSessionFactoryBuilder.java:252)
    at org.springframework.orm.hibernate4.LocalSessionFactoryBean.buildSessionFactory(LocalSessionFactoryBean.java:377)
    at org.springframework.orm.hibernate4.LocalSessionFactoryBean.afterPropertiesSet(LocalSessionFactoryBean.java:362)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1573)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1511)
    … 25 more
    Caused by: org.hibernate.service.classloading.spi.ClassLoadingException: Unable to load class [""]
    at org.hibernate.service.classloading.internal.ClassLoaderServiceImpl.classForName(ClassLoaderServiceImpl.java:151)
    at org.hibernate.service.jdbc.dialect.internal.DialectFactoryImpl.constructDialect(DialectFactoryImpl.java:74)
    … 38 more
    Caused by: java.lang.ClassNotFoundException: Could not load requested class : “”
    at org.hibernate.service.classloading.internal.ClassLoaderServiceImpl$AggregatedClassLoader.findClass(ClassLoaderServiceImpl.java:318)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:348)
    at org.hibernate.service.classloading.internal.ClassLoaderServiceImpl.classForName(ClassLoaderServiceImpl.java:148)
    … 39 more

    #6

    I figured out the first problem the second one is this:

    SEVERE: Exception sending context initialized event to listener instance of class org.springframework.web.context.ContextLoaderListener
    org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘deInitializer’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.RuntimeException: Error couldn’t create directory for storing de file data
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1514)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:521)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:458)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:636)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:934)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:410)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:112)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5016)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5528)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1090)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1900)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
    Caused by: java.lang.RuntimeException: Error couldn’t create directory for storing de file data
    at com.krishagni.catissueplus.core.init.DeInitializer.afterPropertiesSet(DeInitializer.java:83)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1573)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1511)

    #7

    Here’s some additonal info about the server environment

    also this is how i’m running the install batch file

    install.bat -dhost localhost -dport 3306 -dname catissueplus42 -duser root -dpass xxxx -dtype mysql -ahome “C:\websites\openspecimen-os_v23” -ahost 111.111.11.111 -aport 8080 -adtype fresh -adatadir “C:\\websites\\openspecimen-os_v23\\os-data” >> install_log2.txt 2>&1

    Another error while recreating the CATISSUEPLUS42 database

    #8

    Hey Rolando

    Do you guys use any printer to print labels from Openspecimen?