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