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  • Upgrade from 3.5 to 4.0

    I did run the installer to upgrade from version 3.5 to version 4.0 and tomcat is starting but openspecimen not, I have the following errors in my catalina.out

    Java HotSpot™ 64-Bit Server VM warning: ignoring option PermSize=64m; support was removed in 8.0
    Java HotSpot™ 64-Bit Server VM warning: ignoring option MaxPermSize=512m; support was removed in 8.0
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Server version: Apache Tomcat/7.0.61
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Server built: Mar 27 2015 12:03:56 UTC
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Server number: 7.0.61.0
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: OS Name: Linux
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: OS Version: 3.10.0-327.36.3.el7.x86_64
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Architecture: amd64
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Java Home: /usr/java/jdk1.8.0_45/jre
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: JVM Version: 1.8.0_45-b14
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: JVM Vendor: Oracle Corporation
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: CATALINA_BASE: /opt/openspecimen/tomcat-as
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: CATALINA_HOME: /opt/openspecimen/tomcat-as
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Command line argument: -Djava.util.logging.config.file=/opt/openspecimen/tomcat-as/conf/logging.properties
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Command line argument: -Dfile.encoding=UTF-8
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Command line argument: -Xms128m
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Command line argument: -Xmx2048m
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Command line argument: -XX:PermSize=64m
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Command line argument: -XX:MaxPermSize=512m
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Command line argument: -Djava.endorsed.dirs=/opt/openspecimen/tomcat-as/endorsed
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Command line argument: -Dcatalina.base=/opt/openspecimen/tomcat-as
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Command line argument: -Dcatalina.home=/opt/openspecimen/tomcat-as
    mei 02, 2017 11:12:49 PM org.apache.catalina.startup.VersionLoggerListener log
    INFO: Command line argument: -Djava.io.tmpdir=/opt/openspecimen/tomcat-as/temp
    mei 02, 2017 11:12:49 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
    INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
    mei 02, 2017 11:12:50 PM org.apache.coyote.AbstractProtocol init
    INFO: Initializing ProtocolHandler [“http-bio-80”]
    mei 02, 2017 11:12:50 PM org.apache.coyote.AbstractProtocol init
    INFO: Initializing ProtocolHandler [“ajp-bio-8009”]
    mei 02, 2017 11:12:50 PM org.apache.catalina.startup.Catalina load
    INFO: Initialization processed in 1300 ms
    mei 02, 2017 11:12:50 PM org.apache.catalina.core.StandardService startInternal
    INFO: Starting service Catalina
    mei 02, 2017 11:12:50 PM org.apache.catalina.core.StandardEngine startInternal
    INFO: Starting Servlet Engine: Apache Tomcat/7.0.61
    mei 02, 2017 11:12:50 PM org.apache.catalina.startup.HostConfig deployWAR
    INFO: Deploying web application archive /opt/openspecimen/tomcat-as/webapps/openspecimen.war


    OpenSpecimen, a Krishagni Product
    Build Version : v4.0
    Build Date : Wed Apr 26 14:21:26 CEST 2017
    Commit : 748656d
    Present Time : Tue May 02 23:12:55 CEST 2017


    INFO 2-5-17 23:12: liquibase: Successfully acquired change log lock
    INFO 2-5-17 23:13: liquibase: Reading from openspecimen.DATABASECHANGELOG
    INFO 2-5-17 23:13: liquibase: Successfully released change log lock
    INFO 2-5-17 23:13: liquibase: Successfully acquired change log lock
    INFO 2-5-17 23:13: liquibase: Reading from openspecimen.DATABASECHANGELOG
    INFO 2-5-17 23:13: 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 2ms
    INFO 2-5-17 23:13: 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 1ms
    INFO 2-5-17 23:13: 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: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Can’t DROP ‘FKB025CFC7FFA96920’; check that column/key exists
    INFO 2-5-17 23:13: 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: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Can’t DROP ‘WUSTLKEY’; check that column/key exists
    INFO 2-5-17 23:13: 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: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Can’t DROP ‘CSM_USER_ID_UNIQUE_KEY’; check that column/key exists
    SEVERE 2-5-17 23:13: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/4.0/schema.xml::Flag to specify whether bulk registration of participants is allowed::vgaikwad: Change Set db/4.0/schema.xml::Flag to specify whether bulk registration of participants is allowed::vgaikwad failed. Error: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Duplicate column name ‘BULK_PART_REG_ALLOWED’
    liquibase.exception.DatabaseException: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Duplicate column name ‘BULK_PART_REG_ALLOWED’
    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:1573)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1511)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:521)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:458)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:636)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:934)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:410)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:112)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5016)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5528)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1090)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1900)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
    Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Duplicate column name ‘BULK_PART_REG_ALLOWED’
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
    at com.mysql.jdbc.Util.handleNewInstance(Util.java:408)
    at com.mysql.jdbc.Util.getInstance(Util.java:383)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1062)
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4226)
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4158)
    at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2615)
    at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2776)
    at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2834)
    at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2783)
    at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:908)
    at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:788)
    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
    INFO 2-5-17 23:13: liquibase: db/4.0/schema.xml::Flag to specify whether bulk registration of participants is allowed::vgaikwad: Successfully released change log lock
    mei 02, 2017 11:13:04 PM org.apache.catalina.core.StandardContext startInternal
    SEVERE: Error listenerStart

    Hi @Erik_van_Iperen

    OpenSpecimen v3.5 was an intermediate beta build, which was not distributed for general use. We discarded v3.5 in favor of v4.0. You need to adjust few SQL change log entries in your database. I’ve sent a private email to you with details of SQLs to execute to fix the errors.

    Thanks.