Unable to browse Jira portal

[Joe Tseung]

Jira service is able to be started without error but got this error when going to browse the portal this morning:

JIRA — Internal Server Error

Error reference: 0d652da6-ee56-41e5-abad-4eee8fadb896

Unable to render full error details at this time. Please consult the error logs for more information.

Found below in the log file atlassian-jira.log:

2018-06-11 03:08:40,105 http-nio-8081-exec-25 WARN [o.a.commons.dbcp2.BasicDataSource] Failed to complete JMX registration
javax.management.InstanceAlreadyExistsException: com.atlassian.jira:name=BasicDataSource
at com.sun.jmx.mbeanserver.Repository.addMBean(Repository.java:437)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerWithRepository(DefaultMBeanServerInterceptor.java:1898)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerDynamicMBean(DefaultMBeanServerInterceptor.java:966)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerObject(DefaultMBeanServerInterceptor.java:900)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerMBean(DefaultMBeanServerInterceptor.java:324)
at com.sun.jmx.mbeanserver.JmxMBeanServer.registerMBean(JmxMBeanServer.java:522)
at org.apache.commons.dbcp2.BasicDataSource.jmxRegister(BasicDataSource.java:2346)
at org.apache.commons.dbcp2.BasicDataSource.createDataSource(BasicDataSource.java:2029)
at org.apache.commons.dbcp2.BasicDataSource.setLogWriter(BasicDataSource.java:1625)
at org.ofbiz.core.entity.transaction.DBCPConnectionFactory.getConnection(DBCPConnectionFactory.java:103)
at org.ofbiz.core.entity.ConnectionFactory.tryGenericConnectionSources(ConnectionFactory.java:69)
at org.ofbiz.core.entity.transaction.JNDIFactory.getConnection(JNDIFactory.java:164)
at org.ofbiz.core.entity.TransactionFactory.getConnection(TransactionFactory.java:136)
at org.ofbiz.core.entity.ConnectionFactory.getConnection(ConnectionFactory.java:59)
at org.ofbiz.core.entity.config.DatasourceInfo.getDatabaseTypeFromJDBCConnection(DatasourceInfo.java:402)
at org.ofbiz.core.entity.GenericDAO.selectListIteratorByCondition(GenericDAO.java:831)
at org.ofbiz.core.entity.GenericDAO.selectByAnd(GenericDAO.java:730)
at org.ofbiz.core.entity.GenericHelperDAO.findByAnd(GenericHelperDAO.java:150)
at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:903)
at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:881)
at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:850)
at com.opensymphony.module.propertyset.ofbiz.OFBizPropertySet.findPropertyEntry(OFBizPropertySet.java:298)
at com.opensymphony.module.propertyset.ofbiz.OFBizPropertySet.exists(OFBizPropertySet.java:170)
at com.atlassian.jira.propertyset.JiraCachingPropertySet.exists(JiraCachingPropertySet.java:566)
at com.atlassian.jira.propertyset.BootstrapOfBizPropertyEntryStore.getType(BootstrapOfBizPropertyEntryStore.java:67)
at com.atlassian.jira.propertyset.CachingOfBizPropertySet.exists(CachingOfBizPropertySet.java:139)
at com.atlassian.jira.config.properties.ApplicationPropertiesStore.getOption(ApplicationPropertiesStore.java:157)
at com.atlassian.jira.config.properties.ApplicationPropertiesImpl.getOption(ApplicationPropertiesImpl.java:85)
... 18 filtered
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
2018-06-11 03:08:40,152 http-nio-8081-exec-25 ERROR [NoModule] Error getting datasource via DBCP: JdbcDatasourceInfo{uri='jdbc:h2:file:C:\Program Files\Atlassian\Application Data\JIRA/database/h2db', driverClassName='org.h2.Driver', username='sa', password='********', isolationLevel='null', connectionProperties=null, connectionPoolInfo=ConnectionPoolInfo{maxSize=20, minSize=20, initialSize=null, maxIdle=20, maxWait=30000, sleepTime=300000, lifeTime=600000, deadLockMaxWait=600000, deadLockRetryWait=10000, validationQuery=null, minEvictableTimeMillis=4000, timeBetweenEvictionRunsMillis=5000, poolPreparedStatements=null, testOnBorrow=null, testOnReturn=null, testWhileIdle=null, maxOpenPreparedStatements=null, numTestsPerEvictionRun=null, removeAbandonedOnBorrow=true, removeAbandonedOnMaintanance=null, removeAbandonedTimeout=300, validationQueryTimeout=null, defaultCatalog=null}}
java.sql.SQLException: Cannot create PoolableConnectionFactory (General error: "java.lang.IllegalStateException: File corrupted in chunk 4327619, expected page length =< 768, got 875565105 [1.4.185/6]" [50000-185])
at org.apache.commons.dbcp2.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:2291)
at org.apache.commons.dbcp2.BasicDataSource.createDataSource(BasicDataSource.java:2038)
at org.apache.commons.dbcp2.BasicDataSource.setLogWriter(BasicDataSource.java:1625)
at org.ofbiz.core.entity.transaction.DBCPConnectionFactory.getConnection(DBCPConnectionFactory.java:103)
at org.ofbiz.core.entity.ConnectionFactory.tryGenericConnectionSources(ConnectionFactory.java:69)
at org.ofbiz.core.entity.transaction.JNDIFactory.getConnection(JNDIFactory.java:164)
at org.ofbiz.core.entity.TransactionFactory.getConnection(TransactionFactory.java:136)
at org.ofbiz.core.entity.ConnectionFactory.getConnection(ConnectionFactory.java:59)
at org.ofbiz.core.entity.config.DatasourceInfo.getDatabaseTypeFromJDBCConnection(DatasourceInfo.java:402)
at org.ofbiz.core.entity.GenericDAO.selectListIteratorByCondition(GenericDAO.java:831)
at org.ofbiz.core.entity.GenericDAO.selectByAnd(GenericDAO.java:730)
at org.ofbiz.core.entity.GenericHelperDAO.findByAnd(GenericHelperDAO.java:150)
at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:903)
at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:881)
at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:850)
at com.opensymphony.module.propertyset.ofbiz.OFBizPropertySet.findPropertyEntry(OFBizPropertySet.java:298)
at com.opensymphony.module.propertyset.ofbiz.OFBizPropertySet.exists(OFBizPropertySet.java:170)
at com.atlassian.jira.propertyset.JiraCachingPropertySet.exists(JiraCachingPropertySet.java:566)
at com.atlassian.jira.propertyset.BootstrapOfBizPropertyEntryStore.getType(BootstrapOfBizPropertyEntryStore.java:67)
at com.atlassian.jira.propertyset.CachingOfBizPropertySet.exists(CachingOfBizPropertySet.java:139)
at com.atlassian.jira.config.properties.ApplicationPropertiesStore.getOption(ApplicationPropertiesStore.java:157)
at com.atlassian.jira.config.properties.ApplicationPropertiesImpl.getOption(ApplicationPropertiesImpl.java:85)
... 18 filtered
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.h2.jdbc.JdbcSQLException: General error: "java.lang.IllegalStateException: File corrupted in chunk 4327619, expected page length =< 768, got 875565105 [1.4.185/6]" [50000-185]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:345)
at org.h2.message.DbException.get(DbException.java:168)
at org.h2.message.DbException.convert(DbException.java:295)
at org.h2.engine.Database.openDatabase(Database.java:297)
at org.h2.engine.Database.<init>(Database.java:260)
at org.h2.engine.Engine.openSession(Engine.java:167)
at org.h2.engine.Engine.createSessionAndValidate(Engine.java:145)
at org.h2.engine.Engine.createSession(Engine.java:128)
at org.h2.engine.Engine.createSession(Engine.java:26)
at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:347)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:108)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:92)
at org.h2.Driver.connect(Driver.java:72)
at org.apache.commons.dbcp2.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:39)
at org.apache.commons.dbcp2.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:256)
at org.apache.commons.dbcp2.BasicDataSource.validateConnectionFactory(BasicDataSource.java:2301)
at org.apache.commons.dbcp2.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:2287)
... 43 more
Caused by: java.lang.IllegalStateException: File corrupted in chunk 4327619, expected page length =< 768, got 875565105 [1.4.185/6]
at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:773)
at org.h2.mvstore.Page.read(Page.java:640)
at org.h2.mvstore.Page.read(Page.java:194)
at org.h2.mvstore.MVStore.readPage(MVStore.java:1830)
at org.h2.mvstore.MVMap.readPage(MVMap.java:736)
at org.h2.mvstore.MVMap.binarySearch(MVMap.java:468)
at org.h2.mvstore.MVMap.binarySearch(MVMap.java:469)
at org.h2.mvstore.MVMap.get(MVMap.java:450)
at org.h2.mvstore.MVStore.getRootPos(MVStore.java:2227)
at org.h2.mvstore.MVStore.openMap(MVStore.java:461)
at org.h2.mvstore.db.TransactionStore.openMap(TransactionStore.java:373)
at org.h2.mvstore.db.TransactionStore$Transaction.openMap(TransactionStore.java:726)
at org.h2.mvstore.db.MVPrimaryIndex.<init>(MVPrimaryIndex.java:74)
at org.h2.mvstore.db.MVTable.init(MVTable.java:90)
at org.h2.mvstore.db.MVTableEngine.createTable(MVTableEngine.java:130)
at org.h2.mvstore.db.MVTableEngine.createTable(MVTableEngine.java:41)
at org.h2.schema.Schema.createTable(Schema.java:582)
at org.h2.command.ddl.CreateTable.update(CreateTable.java:137)
at org.h2.engine.MetaRecord.execute(MetaRecord.java:58)
at org.h2.engine.Database.open(Database.java:732)
at org.h2.engine.Database.openDatabase(Database.java:266)
... 57 more
2018-06-11 03:08:40,183 http-nio-8081-exec-25 ERROR [NoModule] Could not determine database type.
org.h2.jdbc.JdbcSQLException: General error: "java.lang.IllegalStateException: File corrupted in chunk 4327619, expected page length =< 768, got 875565105 [1.4.185/6]" [50000-185]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:345)
at org.h2.message.DbException.get(DbException.java:168)
at org.h2.message.DbException.convert(DbException.java:295)
at org.h2.engine.Database.openDatabase(Database.java:297)
at org.h2.engine.Database.<init>(Database.java:260)
at org.h2.engine.Engine.openSession(Engine.java:60)
at org.h2.engine.Engine.openSession(Engine.java:167)
at org.h2.engine.Engine.createSessionAndValidate(Engine.java:145)
at org.h2.engine.Engine.createSession(Engine.java:128)
at org.h2.engine.Engine.createSession(Engine.java:26)
at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:347)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:108)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:92)
at org.h2.Driver.connect(Driver.java:72)
at java.sql.DriverManager.getConnection(DriverManager.java:664)
at java.sql.DriverManager.getConnection(DriverManager.java:247)
at org.ofbiz.core.entity.ConnectionFactory.tryGenericConnectionSources(ConnectionFactory.java:87)
at org.ofbiz.core.entity.transaction.JNDIFactory.getConnection(JNDIFactory.java:164)
at org.ofbiz.core.entity.TransactionFactory.getConnection(TransactionFactory.java:136)
at org.ofbiz.core.entity.ConnectionFactory.getConnection(ConnectionFactory.java:59)
at org.ofbiz.core.entity.config.DatasourceInfo.getDatabaseTypeFromJDBCConnection(DatasourceInfo.java:402)
at org.ofbiz.core.entity.GenericDAO.selectListIteratorByCondition(GenericDAO.java:831)
at org.ofbiz.core.entity.GenericDAO.selectByAnd(GenericDAO.java:730)
at org.ofbiz.core.entity.GenericHelperDAO.findByAnd(GenericHelperDAO.java:150)
at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:903)
at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:881)
at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:850)
at com.opensymphony.module.propertyset.ofbiz.OFBizPropertySet.findPropertyEntry(OFBizPropertySet.java:298)
at com.opensymphony.module.propertyset.ofbiz.OFBizPropertySet.exists(OFBizPropertySet.java:170)
at com.atlassian.jira.propertyset.JiraCachingPropertySet.exists(JiraCachingPropertySet.java:566)
at com.atlassian.jira.propertyset.BootstrapOfBizPropertyEntryStore.getType(BootstrapOfBizPropertyEntryStore.java:67)
at com.atlassian.jira.propertyset.CachingOfBizPropertySet.exists(CachingOfBizPropertySet.java:139)
at com.atlassian.jira.config.properties.ApplicationPropertiesStore.getOption(ApplicationPropertiesStore.java:157)
at com.atlassian.jira.config.properties.ApplicationPropertiesImpl.getOption(ApplicationPropertiesImpl.java:85)
... 18 filtered
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalStateException: File corrupted in chunk 4327619, expected page length =< 768, got 875565105 [1.4.185/6]
at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:773)
at org.h2.mvstore.Page.read(Page.java:640)
at org.h2.mvstore.Page.read(Page.java:194)
at org.h2.mvstore.MVStore.readPage(MVStore.java:1830)
at org.h2.mvstore.MVMap.readPage(MVMap.java:736)
at org.h2.mvstore.MVMap.binarySearch(MVMap.java:468)
at org.h2.mvstore.MVMap.binarySearch(MVMap.java:469)
at org.h2.mvstore.MVMap.get(MVMap.java:450)
at org.h2.mvstore.MVStore.getRootPos(MVStore.java:2227)
at org.h2.mvstore.MVStore.openMap(MVStore.java:461)
at org.h2.mvstore.db.TransactionStore.openMap(TransactionStore.java:373)
at org.h2.mvstore.db.TransactionStore$Transaction.openMap(TransactionStore.java:726)
at org.h2.mvstore.db.MVPrimaryIndex.<init>(MVPrimaryIndex.java:74)
at org.h2.mvstore.db.MVTable.init(MVTable.java:90)
at org.h2.mvstore.db.MVTableEngine.createTable(MVTableEngine.java:130)
at org.h2.mvstore.db.MVTableEngine.createTable(MVTableEngine.java:41)
at org.h2.schema.Schema.createTable(Schema.java:582)
at org.h2.command.ddl.CreateTable.update(CreateTable.java:137)
at org.h2.engine.MetaRecord.execute(MetaRecord.java:58)
at org.h2.engine.Database.open(Database.java:732)
at org.h2.engine.Database.openDatabase(Database.java:266)
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'javax.servlet.forward.request_uri'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'javax.servlet.forward.context_path'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'javax.servlet.forward.servlet_path'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'javax.servlet.error.status_code'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'jira.request.start.millis'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'javax.servlet.error.message'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'javax.servlet.error.servlet_name'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'jira.webwork.cleanup'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'com.atlassian.gzipfilter.GzipFilter_already_filtered'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'com.atlassian.jira.web.filters.JiraFirstFilter_alreadyfiltered'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'javax.servlet.error.request_uri'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'jira.request.id'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'com.atlassian.core.filters.HeaderSanitisingFilter_already_filtered'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'javax.servlet.error.exception'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'com.atlassian.jira.web.filters.JiraPostEncodingFilter_alreadyfiltered'
2018-06-11 03:08:40,761 http-nio-8081-exec-1 WARN - [c.a.jira.i18n.BootstrapTranslationStore] No bootstrap translation available for 'com.atlassian.jira.web.filters.accesslog.AccessLogRequestInfoexit.called'

 Appreciate for any help to resolve this. Thanks!

[Rambabu Patina _Appfire_]

That usually means there is an error in your config files (dbconfig.xml, server.xml or jira.xml)

Have a look through https://confluence.atlassian.com/display/JIRAKB/JIRA+Functionality+Fails+due+to+InstanceAlreadyExistsException. Hope this helps you.

[Joe Tseung]

I checked but i didn't change any of the config files you mentioned. It has been working fine from day 1 and suddenly not working from this morning.

One of the errors above mentioned "File corrupted in chunk 4327619". Could it be possible that the Jira database is corrupted?

thanks!

[Rambabu Patina _Appfire_]

Yes probably your database is got corrupted and unfortunately it is not fixable.

Are you sure you have no backups?  Have a look under <jira home>/export.

[Joe Tseung]

Yes i have backups.  i have successfully installed a fresh copy on a different server with a  backup imported.. If i need to import the same copy on the server used before, do i have to uninstall and install the exe again?

[Rambabu Patina _Appfire_]

I think not needed to install it again but stop the jira and follow this article. Do not forget to re-index before accessing jira.

[Joe Tseung]

i am using the built-in h2 db. I am not sure how to import the zip file (activeobjects.xml and entities.xml) in the export directory without the jira portal loaded.