Cannot start openspecimen app after upgrade attempt from 4 to 6.1

kunleoyafajo · June 6, 2019, 3:27pm

Hello,

I cannot start the openspecimen app after upgrade attempt from version master Nov 2017 to 6.1

The error
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 java.lang.ArrayIndexOutOfBoundsException: 1
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1631)
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$1.getObject(AbstractBeanFactory.java:312)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5157)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5680)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1018)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:994)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2021)
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: java.lang.ArrayIndexOutOfBoundsException: 1
at liquibase.datatype.DataTypeFactory.fromDescription(DataTypeFactory.java:251)
at liquibase.change.core.CreateTableChange.generateStatements(CreateTableChange.java:70)
at liquibase.change.AbstractChange.generateStatementsVolatile(AbstractChange.java:287)
at liquibase.change.AbstractChange.warn(AbstractChange.java:358)
at liquibase.changelog.visitor.ValidatingVisitor.visit(ValidatingVisitor.java:109)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:83)
at liquibase.changelog.DatabaseChangeLog.validate(DatabaseChangeLog.java:269)
at liquibase.Liquibase.update(Liquibase.java:198)
at liquibase.Liquibase.update(Liquibase.java:179)
at liquibase.integration.spring.SpringLiquibase.performUpdate(SpringLiquibase.java:353)
at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:305)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1689)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1627)
… 25 more

Krishna_Waidande · June 4, 2019, 12:01pm

Hi @kunleoyafajo,

OpenSpecimen v6.1 supports only MySQL and Oracle databases. Our assumption is above error is occurring due to OpenSpecimen is running on the MariaDB database.

OpenSpecimen v6.0 and prior versions used to work on MariaDB. In v6.1, we upgraded the Liquibase library to v3.6.3. In this version, Liquibase uses a different name for MariaDB. Earlier aliases for MySQL and MariaDB worked the same way. With the latest Liquibase, they are treated as different. Since then MariaDB and MySQL have diverged and now are not compatible with OpenSpecimen.

You will need to migrate date from MariaDB to MySQL.
Below are steps to switch to MySQL from MariaDB.

Take a backup of the existing database.
Uninstall/Remove MariaDB. (Which includes removing data directory and MariaDB configuration files)
Install MySQL 5.7.
Configure the MySQL as mentioned on below wiki-pages.
MySQL pre-requisites
Database configuration
Import the database dump taken at #1 into MySQL.
Stop the running instance of Tomcat.
Edit new database values inside the tag in the context.xml file. ($Tomcat_path/conf/context.xml)
Start the Tomcat service.
Monitor the log files.

Note: Please make sure #4 is followed properly before moving forward.

Let us know if you have any questions.

Thanks,
Krishna

kunleoyafajo · June 6, 2019, 6:47am

Oh thank you, this very useful.
Our server only use MariaDB for now. I will try to use compile to pull version 6 since you confirmed that it works with MariaDB.

kunleoyafajo · June 6, 2019, 12:12pm

Hello

I decided to deploy build v6.0.RC4

Here is the error I am getting now;

OpenSpecimen, a Krishagni Product
Build Version :
Build Date : Thu Jun 06 05:28:33 EDT 2019
Commit :
Present Time : Thu Jun 06 08:08:07 EDT 2019

Jun 06, 2019 8:08:07 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
INFO 6/6/19 8:08 AM: liquibase: Successfully acquired change log lock
INFO 6/6/19 8:08 AM: liquibase: Reading from openspecimen_db.DATABASECHANGELOG
INFO 6/6/19 8:08 AM: liquibase: Successfully released change log lock
INFO 6/6/19 8:08 AM: liquibase: Successfully acquired change log lock
INFO 6/6/19 8:08 AM: liquibase: Reading from openspecimen_db.DATABASECHANGELOG
WARNING 6/6/19 8:08 AM: liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use and re-specify all configuration if this is the case
INFO 6/6/19 8:08 AM: liquibase: classpath:db/db-os-changelog-master-upgrade.xml: db/db-os-pre-conditions.xml::Pre condition to check the storage engine::slakhani: ChangeSet db/db-os-pre-conditions.xml::Pre condition to check the storage engine::slakhani ran successfully in 0ms
INFO 6/6/19 8:08 AM: liquibase: classpath:db/db-os-changelog-master-upgrade.xml: db/db-os-pre-conditions.xml::Pre condition to check the case sensitivity::nmarwaha: ChangeSet db/db-os-pre-conditions.xml::Pre condition to check the case sensitivity::nmarwaha ran successfully in 0ms
INFO 6/6/19 8:08 AM: liquibase: classpath:db/db-os-changelog-master-upgrade.xml: db/2.0/schema.xml::Drop foreign key from CRG column in CATISSUE_USER::nmarwaha: Change set db/2.0/schema.xml::Drop foreign key from CRG column in CATISSUE_USER::nmarwaha failed, but failOnError was false. Error: java.sql.SQLSyntaxErrorException: (conn=2965) Can’t DROP FOREIGN KEY FKB025CFC7FFA96920; check that it exists
INFO 6/6/19 8:08 AM: liquibase: classpath:db/db-os-changelog-master-upgrade.xml: db/2.0/schema.xml::Drop WUSTLKEY column from CATISSUE_USER::nmarwaha: Change set db/2.0/schema.xml::Drop WUSTLKEY column from CATISSUE_USER::nmarwaha failed, but failOnError was false. Error: java.sql.SQLSyntaxErrorException: (conn=2965) Can’t DROP COLUMN WUSTLKEY; check that it exists
INFO 6/6/19 8:08 AM: liquibase: classpath:db/db-os-changelog-master-upgrade.xml: db/2.0/schema.xml::Drop UK on csm_user_id from catissue user table::vlonushte: Change set db/2.0/schema.xml::Drop UK on csm_user_id from catissue user table::vlonushte failed, but failOnError was false. Error: java.sql.SQLSyntaxErrorException: (conn=2965) Can’t DROP INDEX CSM_USER_ID_UNIQUE_KEY; check that it exists
SEVERE 6/6/19 8:08 AM: liquibase: classpath:db/db-os-changelog-master-upgrade.xml: db/2.0/migration.xml::Script to map departments and institutes::nmarwaha: Change Set db/2.0/migration.xml::Script to map departments and institutes::nmarwaha failed. Error: java.sql.SQLSyntaxErrorException: (conn=2965) Table ‘openspecimen_db.catissue_department’ doesn’t exist
liquibase.exception.DatabaseException: java.sql.SQLSyntaxErrorException: (conn=2965) Table ‘openspecimen_db.catissue_department’ doesn’t exist
at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:316)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:122)
at liquibase.database.AbstractJdbcDatabase.execute(AbstractJdbcDatabase.java:1227)
at liquibase.database.AbstractJdbcDatabase.executeStatements(AbstractJdbcDatabase.java:1210)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:550)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:43)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:73)
at liquibase.Liquibase.update(Liquibase.java:200)
at liquibase.integration.spring.SpringLiquibase.performUpdate(SpringLiquibase.java:402)
at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:366)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1689)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1627)
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$1.getObject(AbstractBeanFactory.java:312)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5157)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5680)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1018)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:994)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2021)
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: java.sql.SQLSyntaxErrorException: (conn=2965) Table ‘openspecimen_db.catissue_department’ doesn’t exist
at org.mariadb.jdbc.internal.util.exceptions.ExceptionMapper.get(ExceptionMapper.java:177)
at org.mariadb.jdbc.internal.util.exceptions.ExceptionMapper.getException(ExceptionMapper.java:110)
at org.mariadb.jdbc.MariaDbStatement.executeExceptionEpilogue(MariaDbStatement.java:235)
at org.mariadb.jdbc.MariaDbStatement.executeInternal(MariaDbStatement.java:332)
at org.mariadb.jdbc.MariaDbStatement.execute(MariaDbStatement.java:383)
at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:314)
… 37 more
Caused by: java.sql.SQLException: Table ‘openspecimen_db.catissue_department’ doesn’t exist
Query is: insert into os_departments
(name, institute_id)
select
distinct d.name, u.institution_id
from
catissue_user u
inner join catissue_department d on d.identifier = u.department_id
at org.mariadb.jdbc.internal.util.LogQueryTool.exceptionWithQuery(LogQueryTool.java:119)
at org.mariadb.jdbc.internal.protocol.AbstractQueryProtocol.executeQuery(AbstractQueryProtocol.java:193)
at org.mariadb.jdbc.MariaDbStatement.executeInternal(MariaDbStatement.java:326)
… 41 more
INFO 6/6/19 8:08 AM: liquibase: db/2.0/migration.xml::Script to map departments and institutes::nmarwaha: Successfully released change log lock
Jun 06, 2019 8:08:15 AM org.apache.catalina.core.StandardContext listenerStart
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 ‘os-liquibase’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is liquibase.exception.MigrationFailedException: Migration failed for change set db/2.0/migration.xml::Script to map departments and institutes::nmarwaha:
Reason: liquibase.exception.DatabaseException: java.sql.SQLSyntaxErrorException: (conn=2965) Table ‘openspecimen_db.catissue_department’ doesn’t exist
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1631)
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$1.getObject(AbstractBeanFactory.java:312)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5157)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5680)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1018)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:994)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2021)
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: liquibase.exception.MigrationFailedException: Migration failed for change set db/2.0/migration.xml::Script to map departments and institutes::nmarwaha:
Reason: liquibase.exception.DatabaseException: java.sql.SQLSyntaxErrorException: (conn=2965) Table ‘openspecimen_db.catissue_department’ doesn’t exist
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:586)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:43)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:73)
at liquibase.Liquibase.update(Liquibase.java:200)
at liquibase.integration.spring.SpringLiquibase.performUpdate(SpringLiquibase.java:402)
at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:366)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1689)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1627)
… 25 more
Caused by: liquibase.exception.DatabaseException: java.sql.SQLSyntaxErrorException: (conn=2965) Table ‘openspecimen_db.catissue_department’ doesn’t exist
at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:316)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:122)
at liquibase.database.AbstractJdbcDatabase.execute(AbstractJdbcDatabase.java:1227)
at liquibase.database.AbstractJdbcDatabase.executeStatements(AbstractJdbcDatabase.java:1210)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:550)
… 32 more
Caused by: java.sql.SQLSyntaxErrorException: (conn=2965) Table ‘openspecimen_db.catissue_department’ doesn’t exist
at org.mariadb.jdbc.internal.util.exceptions.ExceptionMapper.get(ExceptionMapper.java:177)
at org.mariadb.jdbc.internal.util.exceptions.ExceptionMapper.getException(ExceptionMapper.java:110)
at org.mariadb.jdbc.MariaDbStatement.executeExceptionEpilogue(MariaDbStatement.java:235)
at org.mariadb.jdbc.MariaDbStatement.executeInternal(MariaDbStatement.java:332)
at org.mariadb.jdbc.MariaDbStatement.execute(MariaDbStatement.java:383)
at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:314)
… 37 more
Caused by: java.sql.SQLException: Table ‘openspecimen_db.catissue_department’ doesn’t exist
Query is: insert into os_departments
(name, institute_id)
select
distinct d.name, u.institution_id
from
catissue_user u
inner join catissue_department d on d.identifier = u.department_id
at org.mariadb.jdbc.internal.util.LogQueryTool.exceptionWithQuery(LogQueryTool.java:119)
at org.mariadb.jdbc.internal.protocol.AbstractQueryProtocol.executeQuery(AbstractQueryProtocol.java:193)
at org.mariadb.jdbc.MariaDbStatement.executeInternal(MariaDbStatement.java:326)
… 41 more

Krishna_Waidande · June 6, 2019, 1:41pm

Hi @kunleoyafajo,

If datasource.type is set to upgrade into openspecimen.properties file. Please change the value to fresh.

The value ‘upgrade’ is used when migrating/upgrading from caTissue.

Follow the below steps:

Stop running Tomcat.
Change datasource.type=fresh into $Tomcat_path/conf/openspeicmen.properties file.
Start the Tomcat service.

Let us know how it works.

Thanks,
Krishna

kunleoyafajo · June 6, 2019, 2:31pm

Thank you for your reply.

The datatype.type was set as Upgrade; I did so since its an attempt to upgrade existing Openspecimen MariaDB. Based on your advice, I changed to datatype.type to fresh.

Here is the error I am getting now;

OpenSpecimen, a Krishagni Product
Build Version :
Build Date : Thu Jun 06 05:28:33 EDT 2019
Commit :
Present Time : Thu Jun 06 10:24:06 EDT 2019

Jun 06, 2019 10:24:06 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
INFO 6/6/19 10:24 AM: liquibase: Successfully acquired change log lock
INFO 6/6/19 10:24 AM: liquibase: Reading from openspecimen_db.DATABASECHANGELOG
INFO 6/6/19 10:24 AM: liquibase: Successfully released change log lock
INFO 6/6/19 10:24 AM: liquibase: Successfully acquired change log lock
INFO 6/6/19 10:24 AM: liquibase: Reading from openspecimen_db.DATABASECHANGELOG
INFO 6/6/19 10:24 AM: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/db-os-pre-conditions.xml::Pre condition to check the storage engine::slakhani: ChangeSet db/db-os-pre-conditions.xml::Pre condition to check the storage engine::slakhani ran successfully in 0ms
INFO 6/6/19 10:24 AM: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/db-os-pre-conditions.xml::Pre condition to check the case sensitivity::nmarwaha: ChangeSet db/db-os-pre-conditions.xml::Pre condition to check the case sensitivity::nmarwaha ran successfully in 0ms
INFO 6/6/19 10:24 AM: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/2.0/schema.xml::Drop foreign key from CRG column in CATISSUE_USER::nmarwaha: Change set db/2.0/schema.xml::Drop foreign key from CRG column in CATISSUE_USER::nmarwaha failed, but failOnError was false. Error: java.sql.SQLSyntaxErrorException: (conn=4535) Can’t DROP FOREIGN KEY FKB025CFC7FFA96920; check that it exists
INFO 6/6/19 10:24 AM: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/2.0/schema.xml::Drop WUSTLKEY column from CATISSUE_USER::nmarwaha: Change set db/2.0/schema.xml::Drop WUSTLKEY column from CATISSUE_USER::nmarwaha failed, but failOnError was false. Error: java.sql.SQLSyntaxErrorException: (conn=4535) Can’t DROP COLUMN WUSTLKEY; check that it exists
INFO 6/6/19 10:24 AM: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/2.0/schema.xml::Drop UK on csm_user_id from catissue user table::vlonushte: Change set db/2.0/schema.xml::Drop UK on csm_user_id from catissue user table::vlonushte failed, but failOnError was false. Error: java.sql.SQLSyntaxErrorException: (conn=4535) Can’t DROP INDEX CSM_USER_ID_UNIQUE_KEY; check that it exists
SEVERE 6/6/19 10:24 AM: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar: Change Set db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar failed. Error: Migration failed for change set db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar:
Reason:
classpath:db/db-os-changelog-master-fresh.xml : liquibase.precondition.core.ColumnExistsPrecondition@66683af8 : For input string: “NULL”

liquibase.exception.MigrationFailedException: Migration failed for change set db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar:
Reason:
classpath:db/db-os-changelog-master-fresh.xml : liquibase.precondition.core.ColumnExistsPrecondition@66683af8 : For input string: “NULL”

    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:514)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:43)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:73)
    at liquibase.Liquibase.update(Liquibase.java:200)
    at liquibase.integration.spring.SpringLiquibase.performUpdate(SpringLiquibase.java:402)
    at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:366)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1689)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1627)
    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$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5157)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5680)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1018)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:994)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2021)
    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: liquibase.exception.PreconditionErrorException: Precondition Error
at liquibase.precondition.core.ColumnExistsPrecondition.check(ColumnExistsPrecondition.java:81)
at liquibase.precondition.core.NotPrecondition.check(NotPrecondition.java:38)
at liquibase.precondition.core.AndPrecondition.check(AndPrecondition.java:43)
at liquibase.precondition.core.PreconditionContainer.check(PreconditionContainer.java:201)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:471)
… 32 more
Caused by: liquibase.exception.DatabaseException: java.lang.NumberFormatException: For input string: “NULL”
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.snapshotObject(ColumnSnapshotGenerator.java:82)
at liquibase.snapshot.jvm.JdbcSnapshotGenerator.snapshot(JdbcSnapshotGenerator.java:60)
at liquibase.snapshot.SnapshotGeneratorChain.snapshot(SnapshotGeneratorChain.java:50)
at liquibase.snapshot.DatabaseSnapshot.include(DatabaseSnapshot.java:164)
at liquibase.snapshot.DatabaseSnapshot.replaceObject(DatabaseSnapshot.java:242)
at liquibase.snapshot.DatabaseSnapshot.includeNestedObjects(DatabaseSnapshot.java:196)
at liquibase.snapshot.DatabaseSnapshot.include(DatabaseSnapshot.java:178)
at liquibase.snapshot.DatabaseSnapshot.replaceObject(DatabaseSnapshot.java:242)
at liquibase.snapshot.DatabaseSnapshot.replaceObject(DatabaseSnapshot.java:264)
at liquibase.snapshot.DatabaseSnapshot.includeNestedObjects(DatabaseSnapshot.java:196)
at liquibase.snapshot.DatabaseSnapshot.include(DatabaseSnapshot.java:178)
at liquibase.snapshot.DatabaseSnapshot.init(DatabaseSnapshot.java:61)
at liquibase.snapshot.DatabaseSnapshot.(DatabaseSnapshot.java:38)
at liquibase.snapshot.JdbcDatabaseSnapshot.(JdbcDatabaseSnapshot.java:25)
at liquibase.snapshot.SnapshotGeneratorFactory.createSnapshot(SnapshotGeneratorFactory.java:126)
at liquibase.snapshot.SnapshotGeneratorFactory.createSnapshot(SnapshotGeneratorFactory.java:119)
at liquibase.snapshot.SnapshotGeneratorFactory.createSnapshot(SnapshotGeneratorFactory.java:107)
at liquibase.snapshot.SnapshotGeneratorFactory.has(SnapshotGeneratorFactory.java:97)
at liquibase.precondition.core.ColumnExistsPrecondition.check(ColumnExistsPrecondition.java:77)
… 36 more
Caused by: java.lang.NumberFormatException: For input string: “NULL”
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.(Integer.java:867)
at liquibase.util.SqlUtil.parseValue(SqlUtil.java:129)
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.readDefaultValue(ColumnSnapshotGenerator.java:358)
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.readColumn(ColumnSnapshotGenerator.java:213)
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.snapshotObject(ColumnSnapshotGenerator.java:45)
… 54 more
INFO 6/6/19 10:24 AM: liquibase: db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar: Successfully released change log lock
Jun 06, 2019 10:24:13 AM org.apache.catalina.core.StandardContext listenerStart
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 ‘os-liquibase’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is liquibase.exception.MigrationFailedException: Migration failed for change set db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar:
Reason:
classpath:db/db-os-changelog-master-fresh.xml : liquibase.precondition.core.ColumnExistsPrecondition@66683af8 : For input string: “NULL”

    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1631)
    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$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5157)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5680)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1018)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:994)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2021)
    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: liquibase.exception.MigrationFailedException: Migration failed for change set db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar:
Reason:
classpath:db/db-os-changelog-master-fresh.xml : liquibase.precondition.core.ColumnExistsPrecondition@66683af8 : For input string: “NULL”

    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:514)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:43)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:73)
    at liquibase.Liquibase.update(Liquibase.java:200)
    at liquibase.integration.spring.SpringLiquibase.performUpdate(SpringLiquibase.java:402)
    at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:366)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1689)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1627)
    ... 25 more

Caused by: liquibase.exception.PreconditionErrorException: Precondition Error
at liquibase.precondition.core.ColumnExistsPrecondition.check(ColumnExistsPrecondition.java:81)
at liquibase.precondition.core.NotPrecondition.check(NotPrecondition.java:38)
at liquibase.precondition.core.AndPrecondition.check(AndPrecondition.java:43)
at liquibase.precondition.core.PreconditionContainer.check(PreconditionContainer.java:201)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:471)
… 32 more
Caused by: liquibase.exception.DatabaseException: java.lang.NumberFormatException: For input string: “NULL”
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.snapshotObject(ColumnSnapshotGenerator.java:82)
at liquibase.snapshot.jvm.JdbcSnapshotGenerator.snapshot(JdbcSnapshotGenerator.java:60)
at liquibase.snapshot.SnapshotGeneratorChain.snapshot(SnapshotGeneratorChain.java:50)
at liquibase.snapshot.DatabaseSnapshot.include(DatabaseSnapshot.java:164)
at liquibase.snapshot.DatabaseSnapshot.replaceObject(DatabaseSnapshot.java:242)
at liquibase.snapshot.DatabaseSnapshot.includeNestedObjects(DatabaseSnapshot.java:196)
at liquibase.snapshot.DatabaseSnapshot.include(DatabaseSnapshot.java:178)
at liquibase.snapshot.DatabaseSnapshot.replaceObject(DatabaseSnapshot.java:242)
at liquibase.snapshot.DatabaseSnapshot.replaceObject(DatabaseSnapshot.java:264)
at liquibase.snapshot.DatabaseSnapshot.includeNestedObjects(DatabaseSnapshot.java:196)
at liquibase.snapshot.DatabaseSnapshot.include(DatabaseSnapshot.java:178)
at liquibase.snapshot.DatabaseSnapshot.init(DatabaseSnapshot.java:61)
at liquibase.snapshot.DatabaseSnapshot.(DatabaseSnapshot.java:38)
at liquibase.snapshot.JdbcDatabaseSnapshot.(JdbcDatabaseSnapshot.java:25)
at liquibase.snapshot.SnapshotGeneratorFactory.createSnapshot(SnapshotGeneratorFactory.java:126)
at liquibase.snapshot.SnapshotGeneratorFactory.createSnapshot(SnapshotGeneratorFactory.java:119)
at liquibase.snapshot.SnapshotGeneratorFactory.createSnapshot(SnapshotGeneratorFactory.java:107)
at liquibase.snapshot.SnapshotGeneratorFactory.has(SnapshotGeneratorFactory.java:97)
at liquibase.precondition.core.ColumnExistsPrecondition.check(ColumnExistsPrecondition.java:77)
… 36 more
Caused by: java.lang.NumberFormatException: For input string: “NULL”
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.(Integer.java:867)
at liquibase.util.SqlUtil.parseValue(SqlUtil.java:129)
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.readDefaultValue(ColumnSnapshotGenerator.java:358)
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.readColumn(ColumnSnapshotGenerator.java:213)
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.snapshotObject(ColumnSnapshotGenerator.java:45)
… 54 more

kunleoyafajo · June 11, 2019, 12:21pm

Hello,

I tried lower version (v5.2.RC5) again and still got similar error, please I am counting on support from this forum to complete this upgrade

OpenSpecimen, a Krishagni Product
Build Version : heads/v5.2.RC5
Build Date : Mon Jun 10 10:27:18 EDT 2019
Commit : 029daedce2
Present Time : Tue Jun 11 08:19:43 EDT 2019

Jun 11, 2019 8:19:43 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
INFO 6/11/19 8:19 AM: liquibase: Successfully acquired change log lock
INFO 6/11/19 8:19 AM: liquibase: Reading from openspecimen_db.DATABASECHANGELOG
INFO 6/11/19 8:19 AM: liquibase: Successfully released change log lock
INFO 6/11/19 8:19 AM: liquibase: Successfully acquired change log lock
INFO 6/11/19 8:19 AM: liquibase: Reading from openspecimen_db.DATABASECHANGELOG
INFO 6/11/19 8:19 AM: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/db-os-pre-conditions.xml::Pre condition to check the storage engine::slakhani: ChangeSet db/db-os-pre-conditions.xml::Pre condition to check the storage engine::slakhani ran successfully in 0ms
INFO 6/11/19 8:19 AM: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/db-os-pre-conditions.xml::Pre condition to check the case sensitivity::nmarwaha: ChangeSet db/db-os-pre-conditions.xml::Pre condition to check the case sensitivity::nmarwaha ran successfully in 0ms
INFO 6/11/19 8:19 AM: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/2.0/schema.xml::Drop foreign key from CRG column in CATISSUE_USER::nmarwaha: Change set db/2.0/schema.xml::Drop foreign key from CRG column in CATISSUE_USER::nmarwaha failed, but failOnError was false. Error: java.sql.SQLSyntaxErrorException: (conn=15638) Can’t DROP FOREIGN KEY FKB025CFC7FFA96920; check that it exists
INFO 6/11/19 8:19 AM: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/2.0/schema.xml::Drop WUSTLKEY column from CATISSUE_USER::nmarwaha: Change set db/2.0/schema.xml::Drop WUSTLKEY column from CATISSUE_USER::nmarwaha failed, but failOnError was false. Error: java.sql.SQLSyntaxErrorException: (conn=15638) Can’t DROP COLUMN WUSTLKEY; check that it exists
INFO 6/11/19 8:19 AM: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/2.0/schema.xml::Drop UK on csm_user_id from catissue user table::vlonushte: Change set db/2.0/schema.xml::Drop UK on csm_user_id from catissue user table::vlonushte failed, but failOnError was false. Error: java.sql.SQLSyntaxErrorException: (conn=15638) Can’t DROP INDEX CSM_USER_ID_UNIQUE_KEY; check that it exists
SEVERE 6/11/19 8:19 AM: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar: Change Set db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar failed. Error: Migration failed for change set db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar:
Reason:
classpath:db/db-os-changelog-master-fresh.xml : liquibase.precondition.core.ColumnExistsPrecondition@36a4651e : For input string: “NULL”

liquibase.exception.MigrationFailedException: Migration failed for change set db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar:
Reason:
classpath:db/db-os-changelog-master-fresh.xml : liquibase.precondition.core.ColumnExistsPrecondition@36a4651e : For input string: “NULL”

    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:514)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:43)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:73)
    at liquibase.Liquibase.update(Liquibase.java:200)
    at liquibase.integration.spring.SpringLiquibase.performUpdate(SpringLiquibase.java:402)
    at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:366)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1689)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1627)
    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$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5157)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5680)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1018)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:994)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2021)
    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: liquibase.exception.PreconditionErrorException: Precondition Error
at liquibase.precondition.core.ColumnExistsPrecondition.check(ColumnExistsPrecondition.java:81)
at liquibase.precondition.core.NotPrecondition.check(NotPrecondition.java:38)
at liquibase.precondition.core.AndPrecondition.check(AndPrecondition.java:43)
at liquibase.precondition.core.PreconditionContainer.check(PreconditionContainer.java:201)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:471)
… 32 more
Caused by: liquibase.exception.DatabaseException: java.lang.NumberFormatException: For input string: “NULL”
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.snapshotObject(ColumnSnapshotGenerator.java:82)
at liquibase.snapshot.jvm.JdbcSnapshotGenerator.snapshot(JdbcSnapshotGenerator.java:60)
at liquibase.snapshot.SnapshotGeneratorChain.snapshot(SnapshotGeneratorChain.java:50)
at liquibase.snapshot.DatabaseSnapshot.include(DatabaseSnapshot.java:164)
at liquibase.snapshot.DatabaseSnapshot.replaceObject(DatabaseSnapshot.java:242)
at liquibase.snapshot.DatabaseSnapshot.includeNestedObjects(DatabaseSnapshot.java:196)
at liquibase.snapshot.DatabaseSnapshot.include(DatabaseSnapshot.java:178)
at liquibase.snapshot.DatabaseSnapshot.replaceObject(DatabaseSnapshot.java:242)
at liquibase.snapshot.DatabaseSnapshot.replaceObject(DatabaseSnapshot.java:264)
at liquibase.snapshot.DatabaseSnapshot.includeNestedObjects(DatabaseSnapshot.java:196)
at liquibase.snapshot.DatabaseSnapshot.include(DatabaseSnapshot.java:178)
at liquibase.snapshot.DatabaseSnapshot.init(DatabaseSnapshot.java:61)
at liquibase.snapshot.DatabaseSnapshot.(DatabaseSnapshot.java:38)
at liquibase.snapshot.JdbcDatabaseSnapshot.(JdbcDatabaseSnapshot.java:25)
at liquibase.snapshot.SnapshotGeneratorFactory.createSnapshot(SnapshotGeneratorFactory.java:126)
at liquibase.snapshot.SnapshotGeneratorFactory.createSnapshot(SnapshotGeneratorFactory.java:119)
at liquibase.snapshot.SnapshotGeneratorFactory.createSnapshot(SnapshotGeneratorFactory.java:107)
at liquibase.snapshot.SnapshotGeneratorFactory.has(SnapshotGeneratorFactory.java:97)
at liquibase.precondition.core.ColumnExistsPrecondition.check(ColumnExistsPrecondition.java:77)
… 36 more
Caused by: java.lang.NumberFormatException: For input string: “NULL”
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.(Integer.java:867)
at liquibase.util.SqlUtil.parseValue(SqlUtil.java:129)
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.readDefaultValue(ColumnSnapshotGenerator.java:358)
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.readColumn(ColumnSnapshotGenerator.java:213)
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.snapshotObject(ColumnSnapshotGenerator.java:45)
… 54 more
INFO 6/11/19 8:19 AM: liquibase: db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar: Successfully released change log lock
Jun 11, 2019 8:19:50 AM org.apache.catalina.core.StandardContext listenerStart
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 ‘os-liquibase’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is liquibase.exception.MigrationFailedException: Migration failed for change set db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar:
Reason:
classpath:db/db-os-changelog-master-fresh.xml : liquibase.precondition.core.ColumnExistsPrecondition@36a4651e : For input string: “NULL”

    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1631)
    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$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5157)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5680)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1018)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:994)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2021)
    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: liquibase.exception.MigrationFailedException: Migration failed for change set db/5.2/schema.xml::Anticipated specimens table - event and SR codes::vpawar:
Reason:
classpath:db/db-os-changelog-master-fresh.xml : liquibase.precondition.core.ColumnExistsPrecondition@36a4651e : For input string: “NULL”

    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:514)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:43)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:73)
    at liquibase.Liquibase.update(Liquibase.java:200)
    at liquibase.integration.spring.SpringLiquibase.performUpdate(SpringLiquibase.java:402)
    at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:366)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1689)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1627)
    ... 25 more

Caused by: liquibase.exception.PreconditionErrorException: Precondition Error
at liquibase.precondition.core.ColumnExistsPrecondition.check(ColumnExistsPrecondition.java:81)
at liquibase.precondition.core.NotPrecondition.check(NotPrecondition.java:38)
at liquibase.precondition.core.AndPrecondition.check(AndPrecondition.java:43)
at liquibase.precondition.core.PreconditionContainer.check(PreconditionContainer.java:201)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:471)
… 32 more
Caused by: liquibase.exception.DatabaseException: java.lang.NumberFormatException: For input string: “NULL”
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.snapshotObject(ColumnSnapshotGenerator.java:82)
at liquibase.snapshot.jvm.JdbcSnapshotGenerator.snapshot(JdbcSnapshotGenerator.java:60)
at liquibase.snapshot.SnapshotGeneratorChain.snapshot(SnapshotGeneratorChain.java:50)
at liquibase.snapshot.DatabaseSnapshot.include(DatabaseSnapshot.java:164)
at liquibase.snapshot.DatabaseSnapshot.replaceObject(DatabaseSnapshot.java:242)
at liquibase.snapshot.DatabaseSnapshot.includeNestedObjects(DatabaseSnapshot.java:196)
at liquibase.snapshot.DatabaseSnapshot.include(DatabaseSnapshot.java:178)
at liquibase.snapshot.DatabaseSnapshot.replaceObject(DatabaseSnapshot.java:242)
at liquibase.snapshot.DatabaseSnapshot.replaceObject(DatabaseSnapshot.java:264)
at liquibase.snapshot.DatabaseSnapshot.includeNestedObjects(DatabaseSnapshot.java:196)
at liquibase.snapshot.DatabaseSnapshot.include(DatabaseSnapshot.java:178)
at liquibase.snapshot.DatabaseSnapshot.init(DatabaseSnapshot.java:61)
at liquibase.snapshot.DatabaseSnapshot.(DatabaseSnapshot.java:38)
at liquibase.snapshot.JdbcDatabaseSnapshot.(JdbcDatabaseSnapshot.java:25)
at liquibase.snapshot.SnapshotGeneratorFactory.createSnapshot(SnapshotGeneratorFactory.java:126)
at liquibase.snapshot.SnapshotGeneratorFactory.createSnapshot(SnapshotGeneratorFactory.java:119)
at liquibase.snapshot.SnapshotGeneratorFactory.createSnapshot(SnapshotGeneratorFactory.java:107)
at liquibase.snapshot.SnapshotGeneratorFactory.has(SnapshotGeneratorFactory.java:97)
at liquibase.precondition.core.ColumnExistsPrecondition.check(ColumnExistsPrecondition.java:77)
… 36 more
Caused by: java.lang.NumberFormatException: For input string: “NULL”
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.(Integer.java:867)
at liquibase.util.SqlUtil.parseValue(SqlUtil.java:129)
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.readDefaultValue(ColumnSnapshotGenerator.java:358)
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.readColumn(ColumnSnapshotGenerator.java:213)
at liquibase.snapshot.jvm.ColumnSnapshotGenerator.snapshotObject(ColumnSnapshotGenerator.java:45)
… 54 more

Srikanth_Adiga2 · June 11, 2019, 3:44pm

Hi @kunleoyafajo

Unfortunately, this is also due to MariaDB. Only option is to migrate from MariaDB to MySQL. You anyway have to do it in the future since we dont support MariaDB.

MySQL is free and the migration is very simple.

You can then use v6.1 instead of an older version

~Sri

kunleoyafajo · June 13, 2019, 3:43pm

Thank you.

I have installed a community version of MySQL and already imported data from MariaDB database into the new MySQL DB.

I am now attempting deployment of version 6.1 and here is the error I am getting now;

OpenSpecimen, a Krishagni Product
Build Version : v6.1.RC1
Build Date : Fri May 31 10:33:25 EDT 2019
Commit : 6972fe2
Present Time : Thu Jun 13 11:42:01 EDT 2019

Jun 13, 2019 11:42:01 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Thu Jun 13 11:42:02 EDT 2019 WARN: Establishing SSL connection without server’s identity verification is not recommended. According to MySQL 5.5.45+, 5.6.26+ and 5.7.6+ requirements SSL connection must be established by default if explicit option isn’t set. For compliance with existing applications not using SSL the verifyServerCertificate property is set to ‘false’. You need either to explicitly disable SSL by setting useSSL=false, or set useSSL=true and provide truststore for server certificate verification.
Thu Jun 13 11:42:02 EDT 2019 WARN: Establishing SSL connection without server’s identity verification is not recommended. According to MySQL 5.5.45+, 5.6.26+ and 5.7.6+ requirements SSL connection must be established by default if explicit option isn’t set. For compliance with existing applications not using SSL the verifyServerCertificate property is set to ‘false’. You need either to explicitly disable SSL by setting useSSL=false, or set useSSL=true and provide truststore for server certificate verification.
Jun 13, 2019 11:42:06 AM org.apache.catalina.core.StandardContext listenerStart
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 ‘os-liquibase’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is liquibase.exception.MigrationFailedException: Migration failed for change set db/5.2/config.xml::Config setting to specify max. no of retries to process failed external app messages::vpawar:
Reason: liquibase.exception.DatabaseException: Illegal mix of collations (utf8_general_ci,IMPLICIT) and (utf8_unicode_ci,IMPLICIT) for operation ‘=’ [Failed SQL: call add_cfg_prop(
‘common’, ‘max_eapp_msg_retries’,
‘max_eapp_msg_retries’, ‘max_eapp_msg_retries_desc’,
‘INT’, ‘5’
)]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1631)
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$1.getObject(AbstractBeanFactory.java:312)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5157)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5680)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1018)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:994)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2021)
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: liquibase.exception.MigrationFailedException: Migration failed for change set db/5.2/config.xml::Config setting to specify max. no of retries to process failed external app messages::vpawar:
Reason: liquibase.exception.DatabaseException: Illegal mix of collations (utf8_general_ci,IMPLICIT) and (utf8_unicode_ci,IMPLICIT) for operation ‘=’ [Failed SQL: call add_cfg_prop(
‘common’, ‘max_eapp_msg_retries’,
‘max_eapp_msg_retries’, ‘max_eapp_msg_retries_desc’,
‘INT’, ‘5’
)]
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:637)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:53)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:83)
at liquibase.Liquibase.update(Liquibase.java:202)
at liquibase.Liquibase.update(Liquibase.java:179)
at liquibase.integration.spring.SpringLiquibase.performUpdate(SpringLiquibase.java:353)
at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:305)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1689)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1627)
… 25 more
Caused by: liquibase.exception.DatabaseException: Illegal mix of collations (utf8_general_ci,IMPLICIT) and (utf8_unicode_ci,IMPLICIT) for operation ‘=’ [Failed SQL: call add_cfg_prop(
‘common’, ‘max_eapp_msg_retries’,
‘max_eapp_msg_retries’, ‘max_eapp_msg_retries_desc’,
‘INT’, ‘5’
)]
at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:356)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:57)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:125)
at liquibase.database.AbstractJdbcDatabase.execute(AbstractJdbcDatabase.java:1229)
at liquibase.database.AbstractJdbcDatabase.executeStatements(AbstractJdbcDatabase.java:1211)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:600)
… 33 more
Caused by: java.sql.SQLException: Illegal mix of collations (utf8_general_ci,IMPLICIT) and (utf8_unicode_ci,IMPLICIT) for operation ‘=’
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:965)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2480)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2438)
at com.mysql.jdbc.StatementImpl.executeInternal(StatementImpl.java:845)
at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:745)
at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:352)
… 38 more

kunleoyafajo · June 15, 2019, 5:17pm

Hello,

Can anyone help me with latest issue reported above

Swapnil_Ingle · June 16, 2019, 5:53am

Hi kunleoyafajo,

Please make sure the below points are checked:

Change the JDBC URL in the context file ($TOMCAT/conf/context.xml) that conforms to the MySQL database (‘jdbc:mysql://hostname:port/database’).

It might be the case that while migrating from MariaDB to MySQL you forgot to change the JDBC URL in the context.xml file.

Please make sure that you have the MySQL connector JAR in the $TOMCAT/lib folder.

You can download the connector JAR from here

Please make sure that the database/table collation is ‘utf8_unicode_ci’

Follow steps on this wiki page to ensure your MySQL is correctly setup.

Thanks,

kunleoyafajo · June 17, 2019, 8:58am

Thank you for your reply.
Unfortunately, the deployment on existing MySQL database is still failing with the error below.

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 ‘os-liquibase’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is liquibase.exception.MigrationFailedException: Migration failed for change set db/5.2/config.xml::Config setting to specify max. no of retries to process failed external app messages::vpawar:
Reason: liquibase.exception.DatabaseException: Illegal mix of collations (utf8_general_ci,IMPLICIT) and (utf8_unicode_ci,IMPLICIT) for operation ‘=’ [Failed SQL: call add_cfg_prop(
‘common’, ‘max_eapp_msg_retries’,
‘max_eapp_msg_retries’, ‘max_eapp_msg_retries_desc’,
‘INT’, ‘5’
)]

I even changed charset of the procedure in question, and I still stumbled on another error.

I decided to try out fresh deployment on a new database, see error log below. Please note that I tried to follow the recommendation in the previous reply yet the tables were created as utf8_general_ci despite default collation of database and server as utf8_unicode_ci

***************************************************
 OpenSpecimen, a Krishagni Product
 Build Version : v6.1.RC1
 Build Date    : Fri May 31 10:33:25 EDT 2019
 Commit        : 6972fe2
 Present Time  : Mon Jun 17 03:12:20 EDT 2019
 ***************************************************
Jun 17, 2019 3:12:20 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Jun 17, 2019 3:12:25 AM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of clas                                                                                                                                                                       s org.springframework.web.context.ContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean wit                                                                                                                                                                       h name 'sessionFactory': Failed to introspect bean class [org.springframework.or                                                                                                                                                                       m.hibernate5.LocalSessionFactoryBean] for lookup method metadata: could not find                                                                                                                                                                        class that it depends on; nested exception is java.lang.NoClassDefFoundError: j                                                                                                                                                                       avax/persistence/EntityManagerFactory
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanP                                                                                                                                                                       ostProcessor.determineCandidateConstructors(AutowiredAnnotationBeanPostProcessor                                                                                                                                                                       .java:269)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean                                                                                                                                                                       Factory.determineConstructorsFromBeanPostProcessors(AbstractAutowireCapableBeanF                                                                                                                                                                       actory.java:1123)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean                                                                                                                                                                       Factory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1096)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean                                                                                                                                                                       Factory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean                                                                                                                                                                       Factory.createBean(AbstractAutowireCapableBeanFactory.java:481)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getOb                                                                                                                                                                       ject(AbstractBeanFactory.java:312)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistr                                                                                                                                                                       y.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe                                                                                                                                                                       an(AbstractBeanFactory.java:308)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean                                                                                                                                                                       (AbstractBeanFactory.java:197)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.                                                                                                                                                                       preInstantiateSingletons(DefaultListableBeanFactory.java:742)
        at org.springframework.context.support.AbstractApplicationContext.finish                                                                                                                                                                       BeanFactoryInitialization(AbstractApplicationContext.java:867)
        at org.springframework.context.support.AbstractApplicationContext.refres                                                                                                                                                                       h(AbstractApplicationContext.java:543)
        at org.springframework.web.context.ContextLoader.configureAndRefreshWebA                                                                                                                                                                       pplicationContext(ContextLoader.java:443)
        at org.springframework.web.context.ContextLoader.initWebApplicationConte                                                                                                                                                                       xt(ContextLoader.java:325)
        at org.springframework.web.context.ContextLoaderListener.contextInitiali                                                                                                                                                                       zed(ContextLoaderListener.java:107)
        at org.apache.catalina.core.StandardContext.listenerStart(StandardContex                                                                                                                                                                       t.java:5157)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContex                                                                                                                                                                       t.java:5680)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase                                                                                                                                                                       .java:1018)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:99                                                                                                                                                                       4)
        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:                                                                                                                                                                       2021)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:51                                                                                                                                                                       1)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.                                                                                                                                                                       java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor                                                                                                                                                                       .java:624)
        at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoClassDefFoundError: javax/persistence/EntityManagerFactor                                                                                                                                                                       y
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:14                                                                                                                                                                       2)
        at org.apache.catalina.loader.WebappClassLoaderBase.findClassInternal(We                                                                                                                                                                       bappClassLoaderBase.java:3239)
        at org.apache.catalina.loader.WebappClassLoaderBase.findClass(WebappClas                                                                                                                                                                       sLoaderBase.java:1410)
        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClas                                                                                                                                                                       sLoaderBase.java:1914)
        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClas                                                                                                                                                                       sLoaderBase.java:1788)
        at java.lang.Class.getDeclaredMethods0(Native Method)
        at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
        at java.lang.Class.getDeclaredMethods(Class.java:1975)
        at org.springframework.util.ReflectionUtils.getDeclaredMethods(Reflectio                                                                                                                                                                       nUtils.java:613)
        at org.springframework.util.ReflectionUtils.doWithMethods(ReflectionUtil                                                                                                                                                                       s.java:524)
        at org.springframework.util.ReflectionUtils.doWithMethods(ReflectionUtil                                                                                                                                                                       s.java:510)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanP                                                                                                                                                                       ostProcessor.determineCandidateConstructors(AutowiredAnnotationBeanPostProcessor                                                                                                                                                                       .java:247)
        ... 27 more
Caused by: java.lang.ClassNotFoundException: javax.persistence.EntityManagerFact                                                                                                                                                                       ory
        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClas                                                                                                                                                                       sLoaderBase.java:1945)
        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClas                                                                                                                                                                       sLoaderBase.java:1788)
        ... 41 more

Swapnil_Ingle · June 17, 2019, 2:23pm

Hi kunleoyafajo,

I see two errors in the stack trace you shared.

#1 Illegal mix of collations (utf8_general_ci,IMPLICIT) and (utf8_unicode_ci,IMPLICIT) for operation ‘=’

Make sure that the tables ’ os_cfg_settings ', ’ os_cfg_props ', and ’ os_modules ’ have utf8 charset and utf8_unicode_ci collation.

Please run the following SQLs and restart the application:

ALTER TABLE os_cfg_settings CONVERT TO CHARACTER SET utf8 COLLATE utf8_unicode_ci;
ALTER TABLE os_cfg_props CONVERT TO CHARACTER SET utf8 COLLATE utf8_unicode_ci;
ALTER TABLE os_modules CONVERT TO CHARACTER SET utf8 COLLATE utf8_unicode_ci;

#2 java.lang.ClassNotFoundException: javax.persistence.EntityManagerFactory

This is really strange, as the OpenSpecimen web app has this class and it should not have been reported as missing. I’m sorry but we cannot infer (at least remotely) the root cause for this error.

Thanks,

kunleoyafajo · June 18, 2019, 12:31pm

Hi,

Thank you for your guide.

I found my way around the Illegal Mix issue after following your guide. I had to run it for all the tables. Then I changed all input parameters of procedure add_cfg_prop to utf8mb4.

Having passed the first error, the second one surfaced again; referring to the one below. The error now shows up for both upgrades existing database or setup of a fresh one.

Please, what’s your advice on how to move forward?

***************************************************
 OpenSpecimen, a Krishagni Product
 Build Version : v6.1.RC1
 Build Date    : Fri May 31 10:33:25 EDT 2019
 Commit        : 6972fe2
 Present Time  : Tue Jun 18 08:20:50 EDT 2019
 ***************************************************
Jun 18, 2019 8:20:50 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Jun 18, 2019 8:21:49 AM org.apache.catalina.core.StandardContext listenerStart
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 'sessionFactory': Failed to introspect bean class [org.springframework.orm.hibernate5.LocalSessionFactoryBean] for lookup method metadata: could not find class that it depends on; nested exception is java.lang.NoClassDefFoundError: javax/persistence/EntityManagerFactory
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.determineCandidateConstructors(AutowiredAnnotationBeanPostProcessor.java:269)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.determineConstructorsFromBeanPostProcessors(AbstractAutowireCapableBeanFactory.java:1123)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1096)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:742)
        at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
        at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
        at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
        at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
        at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5157)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5680)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1018)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:994)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
        at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)
        at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2021)
        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: java.lang.NoClassDefFoundError: javax/persistence/EntityManagerFactory
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
        at org.apache.catalina.loader.WebappClassLoaderBase.findClassInternal(WebappClassLoaderBase.java:3239)
        at org.apache.catalina.loader.WebappClassLoaderBase.findClass(WebappClassLoaderBase.java:1410)
        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1914)
        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1788)
        at java.lang.Class.getDeclaredMethods0(Native Method)
        at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
        at java.lang.Class.getDeclaredMethods(Class.java:1975)
        at org.springframework.util.ReflectionUtils.getDeclaredMethods(ReflectionUtils.java:613)
        at org.springframework.util.ReflectionUtils.doWithMethods(ReflectionUtils.java:524)
        at org.springframework.util.ReflectionUtils.doWithMethods(ReflectionUtils.java:510)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.determineCandidateConstructors(AutowiredAnnotationBeanPostProcessor.java:247)
        ... 27 more
Caused by: java.lang.ClassNotFoundException: javax.persistence.EntityManagerFactory
        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1945)
        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1788)
        ... 41 more

kunleoyafajo · June 19, 2019, 11:40am

Hi @Swapnil_Ingle,

Do you have any update on this #2 java.lang.ClassNotFoundException: javax.persistence.EntityManagerFactory

It appears I’m now stuck on that now. Is there a way to bypass or add the dependency file?

Krishna_Waidande · June 19, 2019, 2:31pm

Hi @kunleoyafajo,

Please make sure the Tomcat version is >=8. The above errors occur when using Tomcat versions prior to the 7.x

Thanks,
Krishna

kunleoyafajo · June 19, 2019, 3:00pm

Okay, we are currently running Tomcat 7.

I will setup Tomcat 8 and revert on the outcome

kunleoyafajo · June 19, 2019, 9:24pm

Hello,

I have setup Tomcat 9 but I still encountered some errors,

Error creating bean with name 'importQueryForms' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.RuntimeException: javax.persistence.PersistenceException: org.hibernate.HibernateException: More than one row with the given identifier was found: 1, for class: com.krishagni.catissueplus.core.de.domain.Form

see detail error log below;

***************************************************
 OpenSpecimen, a Krishagni Product
 Build Version : v6.1.RC1
 Build Date    : Fri May 31 10:33:25 EDT 2019
 Commit        : 6972fe2
 Present Time  : Wed Jun 19 16:56:46 EDT 2019
 ***************************************************
19-Jun-2019 16:56:46.383 INFO [Catalina-utility-1] org.apache.catalina.core.ApplicationContext.log Initializing Spring root WebApplicationContext
19-Jun-2019 16:56:57.750 SEVERE [Catalina-utility-1] org.apache.catalina.core.StandardContext.listenerStart 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 'importQueryForms' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.RuntimeException: javax.persistence.PersistenceException: org.hibernate.HibernateException: More than one row with the given identifier was found: 1, for class: com.krishagni.catissueplus.core.de.domain.Form
                at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1631)
                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$1.getObject(AbstractBeanFactory.java:312)
                at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
                at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
                at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
                at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
                at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
                at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
                at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
                at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
                at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
                at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4682)
                at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5143)
                at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
                at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:717)
                at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:690)
                at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:705)
                at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:978)
                at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1849)
                at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
                at java.util.concurrent.FutureTask.run(FutureTask.java:266)
                at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
                at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
                at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:773)
                at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:427)
                at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1620)
                at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:305)
                at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
                at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1151)
                at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1353)
                at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1357)
                at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1335)
                at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
                at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
                at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)
                at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)
                at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
                at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
                at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
                at java.lang.Thread.run(Thread.java:748)
        Caused by: java.lang.RuntimeException: javax.persistence.PersistenceException: org.hibernate.HibernateException: More than one row with the given identifier was found: 1, for class: com.krishagni.catissueplus.core.de.domain.Form
                at com.krishagni.catissueplus.core.init.ImportForms$1.doInTransaction(ImportForms.java:107)
                at com.krishagni.catissueplus.core.init.ImportForms$1.doInTransaction(ImportForms.java:1)
                at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133)
                at com.krishagni.catissueplus.core.init.ImportForms.importForms(ImportForms.java:98)
                at com.krishagni.catissueplus.core.init.ImportForms.afterPropertiesSet(ImportForms.java:86)
                at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1689)
                at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1627)
                ... 41 more
        Caused by: javax.persistence.PersistenceException: org.hibernate.HibernateException: More than one row with the given identifier was found: 1, for class: com.krishagni.catissueplus.core.de.domain.Form
                at org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:154)
                at org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:181)
                at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1514)
                at com.krishagni.catissueplus.core.de.repository.impl.FormDaoImpl.getFormContext(FormDaoImpl.java:318)
                at com.krishagni.catissueplus.core.init.ImportQueryForms.getFormContext(ImportQueryForms.java:64)
                at com.krishagni.catissueplus.core.init.ImportForms.saveOrUpdateFormCtx(ImportForms.java:122)
                at com.krishagni.catissueplus.core.init.ImportForms.importForms(ImportForms.java:161)
                at com.krishagni.catissueplus.core.init.ImportForms.access$1(ImportForms.java:131)
                at com.krishagni.catissueplus.core.init.ImportForms$1.doInTransaction(ImportForms.java:103)
                ... 47 more
        Caused by: org.hibernate.HibernateException: More than one row with the given identifier was found: 1, for class: com.krishagni.catissueplus.core.de.domain.Form
                at org.hibernate.loader.entity.plan.AbstractLoadPlanBasedEntityLoader.extractEntityResult(AbstractLoadPlanBasedEntityLoader.java:251)
                at org.hibernate.loader.entity.plan.AbstractLoadPlanBasedEntityLoader.load(AbstractLoadPlanBasedEntityLoader.java:195)
                at org.hibernate.loader.entity.plan.LegacyBatchingEntityLoaderBuilder$LegacyBatchingEntityLoader.load(LegacyBatchingEntityLoaderBuilder.java:131)
                at org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.java:4269)
                at org.hibernate.event.internal.DefaultLoadEventListener.loadFromDatasource(DefaultLoadEventListener.java:511)
                at org.hibernate.event.internal.DefaultLoadEventListener.doLoad(DefaultLoadEventListener.java:481)
                at org.hibernate.event.internal.DefaultLoadEventListener.load(DefaultLoadEventListener.java:222)
                at org.hibernate.event.internal.DefaultLoadEventListener.proxyOrLoad(DefaultLoadEventListener.java:281)
                at org.hibernate.event.internal.DefaultLoadEventListener.doOnLoad(DefaultLoadEventListener.java:124)
                at org.hibernate.event.internal.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:92)
                at org.hibernate.internal.SessionImpl.fireLoad(SessionImpl.java:1257)
                at org.hibernate.internal.SessionImpl.internalLoad(SessionImpl.java:1140)
                at org.hibernate.type.EntityType.resolveIdentifier(EntityType.java:682)
                at org.hibernate.type.EntityType.resolve(EntityType.java:464)
                at org.hibernate.type.ManyToOneType.resolve(ManyToOneType.java:239)
                at org.hibernate.engine.internal.TwoPhaseLoad.doInitializeEntity(TwoPhaseLoad.java:172)
                at org.hibernate.engine.internal.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:129)
                at org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:1151)
                at org.hibernate.loader.Loader.processResultSet(Loader.java:1010)
                at org.hibernate.loader.Loader.doQuery(Loader.java:948)
                at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:340)
                at org.hibernate.loader.Loader.doList(Loader.java:2689)
                at org.hibernate.loader.Loader.doList(Loader.java:2672)
                at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2506)
                at org.hibernate.loader.Loader.list(Loader.java:2501)
                at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:504)
                at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:395)
                at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:220)
                at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1508)
                at org.hibernate.query.internal.AbstractProducedQuery.doList(AbstractProducedQuery.java:1537)
                at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1505)
                ... 53 more

Krishna_Waidande · June 20, 2019, 1:44pm

Hi @kunleoyafajo,

Could you please share the output of below SQLs with us?

Query 1:

select
identifier, name, caption, created_by, create_time, last_modified_by, last_modify_time, deleted_on
from
dyextn_containers;

Query 2:

select
fc.identifier, fc.entity_type, fc.deleted_on, f.identifier, f.name, f.caption, f.deleted_on
from
catissue_form_context fc
inner join dyextn_containers f on f.identifier = fc.container_id
where
fc.entity_type in (‘SpecimenEvent’, ‘Query’);

Thanks,

kunleoyafajo · June 20, 2019, 3:07pm

Hi @Krishna_Waidande,

See output below;

catissue_form_context.csv (3.8 KB)
dyextn_containers.csv (4.6 KB)