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Creating any project fails after linux upgrade from 7.3.5 to 7.13.0

Nodirbek Husainov

Hi,

I've just upgraded Jira on a local server (CentOS Linux release 7.2.1511) from 7.3.5 to 7.13.0 by executing

atlassian-jira-core-7.13.0-x64.bin.zip since the upgrade via web-gui was not possible.

The upgrade process did not show any issues.

But now I can't create any projects.

The logs are hinting at missing RIGHTS column on sharepermissions table.

Am I missing any schema ugprades?

java.lang.RuntimeException: com.atlassian.cache.CacheException: com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: SQL Exception while executing the following:SELECT ID, entityid, entitytype, sharetype, PARAM1, PARAM2, RIGHTS FROM jira.sharepermissions WHERE entityid=? AND entitytype=? (Unknown column 'RIGHTS' in 'field list')

    java.lang.RuntimeException: com.atlassian.cache.CacheException: com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: SQL Exception while executing the following:SELECT ID, entityid, entitytype, sharetype, PARAM1, PARAM2, RIGHTS FROM jira.sharepermissions WHERE entityid=? AND entitytype=? (Unknown column 'RIGHTS' in 'field list')
        at com.atlassian.web.servlet.plugin.DynamicAuthorizationServletForwarder.forward(DynamicAuthorizationServletForwarder.java:55) [?:?]
        at com.atlassian.web.servlet.plugin.DynamicAuthorizationServletForwarder.forwardSafely(DynamicAuthorizationServletForwarder.java:83) [?:?]
        at com.atlassian.web.servlet.plugin.SanitizingServletForwarder.forwardSafely(SanitizingServletForwarder.java:48) [?:?]
        at com.atlassian.web.servlet.plugin.RememberingServletForwarder.forwardSafely(RememberingServletForwarder.java:75) [?:?]
        at com.atlassian.web.servlet.plugin.ResolvingServletForwarder.forwardSafely(ResolvingServletForwarder.java:50) [?:?]
        at com.atlassian.web.servlet.plugin.request.RedirectInterceptingResponse.lambda$null$0(RedirectInterceptingResponse.java:50) [?:?]
        at java.util.Optional.map(Optional.java:215) [?:1.8.0_181]
        at com.atlassian.web.servlet.plugin.request.RedirectInterceptingResponse.lambda$forward$1(RedirectInterceptingResponse.java:50) [?:?]
        at java.util.Optional.flatMap(Optional.java:241) [?:1.8.0_181]
        ....
     at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) [tomcat-coyote.jar:8.5.32]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_181]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_181]
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-util.jar:8.5.32]
        at java.lang.Thread.run(Thread.java:748) [?:1.8.0_181]
    Caused by: com.atlassian.cache.CacheException: com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: SQL Exception while executing the following:SELECT ID, entityid, entitytype, sharetype, PARAM1, PARAM2, RIGHTS FROM jira.sharepermissions WHERE entityid=? AND entitytype=? (Unknown column 'RIGHTS' in 'field list')
        at com.atlassian.cache.memory.DelegatingCache.get(DelegatingCache.java:211) [atlassian-cache-memory-3.2.0.jar:?]
        at com.atlassian.cache.memory.DelegatingCache.get(DelegatingCache.java:162) [atlassian-cache-memory-3.2.0.jar:?]
        at com.atlassian.jira.sharing.CachingSharePermissionStore.getSharePermissions(CachingSharePermissionStore.java:47) [classes/:?]
        at com.atlassian.jira.sharing.DefaultShareManager.getSharePermissions(DefaultShareManager.java:37) [classes/:?]
        at com.atlassian.jira.issue.search.DefaultSearchRequestManager.setSharePermissions(DefaultSearchRequestManager.java:307) [classes/:?]
        at com.atlassian.jira.issue.search.DefaultSearchRequestManager.getSearchRequestById(DefaultSearchRequestManager.java:148) [classes/:?]
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [?:1.8.0_181]
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) [?:1.8.0_181]
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [?:1.8.0_181]
        at java.lang.reflect.Method.invoke(Method.java:498) [?:1.8.0_181]
        at com.atlassian.plugin.util.ContextClassLoaderSettingInvocationHandler.invoke(ContextClassLoaderSettingInvocationHandler.java:26) [atlassian-plugins-core-4.5.1.jar:?]
        at com.sun.proxy.$Proxy233.getSearchRequestById(Unknown Source) [?:?]
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [?:1.8.0_181]
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) [?:1.8.0_181]
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [?:1.8.0_181]
        at java.lang.reflect.Method.invoke(Method.java:498) [?:1.8.0_181]
        at com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean$DynamicServiceInvocationHandler.invoke(HostComponentFactoryBean.java:136) [?:?]
        at com.sun.proxy.$Proxy233.getSearchRequestById(Unknown Source) [?:?]
        ....
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [catalina.jar:8.5.32]
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [catalina.jar:8.5.32]
        at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:728) [catalina.jar:8.5.32]
        at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:470) [catalina.jar:8.5.32]
        at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:395) [catalina.jar:8.5.32]
        at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:316) [catalina.jar:8.5.32]
        at com.atlassian.web.servlet.plugin.DynamicAuthorizationServletForwarder.forward(DynamicAuthorizationServletForwarder.java:53) [?:?]
        ... 142 more
    Caused by: com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: SQL Exception while executing the following:SELECT ID, entityid, entitytype, sharetype, PARAM1, PARAM2, RIGHTS FROM jira.sharepermissions WHERE entityid=? AND entitytype=? (Unknown column 'RIGHTS' in 'field list')
        at com.atlassian.jira.ofbiz.DefaultOfBizDelegator.findByAnd(DefaultOfBizDelegator.java:85) [classes/:?]
        at com.atlassian.jira.ofbiz.WrappingOfBizDelegator.findByAnd(WrappingOfBizDelegator.java:62) [classes/:?]
        at com.atlassian.jira.sharing.OfBizSharePermissionStore.getSharePermissions(OfBizSharePermissionStore.java:49) [classes/:?]
        at com.atlassian.jira.sharing.CachingSharePermissionStore.loadSharePermissions(CachingSharePermissionStore.java:156) [classes/:?]
        at com.atlassian.cache.memory.MemoryCacheManager$3$1.load(MemoryCacheManager.java:207) [atlassian-cache-memory-3.2.0.jar:?]
        at com.atlassian.cache.memory.DelegatingCache.lambda$get$0(DelegatingCache.java:162) [atlassian-cache-memory-3.2.0.jar:?]
        at com.atlassian.cache.memory.DelegatingCache.lambda$get$1(DelegatingCache.java:190) [atlassian-cache-memory-3.2.0.jar:?]
        at com.google.common.cache.LocalCache$LocalManualCache$1.load(LocalCache.java:4742) [closure-compiler-v20151216.jar:?]
        at com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3527) [closure-compiler-v20151216.jar:?]
        at com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2319) [closure-compiler-v20151216.jar:?]
        at com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2282) [closure-compiler-v20151216.jar:?]
        at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2197) [closure-compiler-v20151216.jar:?]
        at com.google.common.cache.LocalCache.get(LocalCache.java:3937) [closure-compiler-v20151216.jar:?]
        at com.google.common.cache.LocalCache$LocalManualCache.get(LocalCache.java:4739) [closure-compiler-v20151216.jar:?]
        at com.atlassian.cache.memory.DelegatingCache.get(DelegatingCache.java:177) [atlassian-cache-memory-3.2.0.jar:?]
        ... 400 more
    Caused by: org.ofbiz.core.entity.GenericDataSourceException: SQL Exception while executing the following:SELECT ID, entityid, entitytype, sharetype, PARAM1, PARAM2, RIGHTS FROM jira.sharepermissions WHERE entityid=? AND entitytype=? (Unknown column 'RIGHTS' in 'field list')
        at org.ofbiz.core.entity.jdbc.SQLProcessor.executeQuery(SQLProcessor.java:533) [entityengine-1.3.10.jar:?]
        at org.ofbiz.core.entity.GenericDAO.createEntityListIterator(GenericDAO.java:877) [entityengine-1.3.10.jar:?]
        at org.ofbiz.core.entity.GenericDAO.selectListIteratorByCondition(GenericDAO.java:857) [entityengine-1.3.10.jar:?]
        at org.ofbiz.core.entity.GenericDAO.selectByAnd(GenericDAO.java:729) [entityengine-1.3.10.jar:?]
        at org.ofbiz.core.entity.GenericHelperDAO.findByAnd(GenericHelperDAO.java:166) [entityengine-1.3.10.jar:?]
        at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:909) [entityengine-1.3.10.jar:?]
        at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:887) [entityengine-1.3.10.jar:?]
        at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:856) [entityengine-1.3.10.jar:?]
        at com.atlassian.jira.ofbiz.DefaultOfBizDelegator.findByAnd(DefaultOfBizDelegator.java:83) [classes/:?]
        ... 414 more
    Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'RIGHTS' in 'field list'
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [?:1.8.0_181]
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) [?:1.8.0_181]
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) [?:1.8.0_181]
        at java.lang.reflect.Constructor.newInstance(Constructor.java:423) [?:1.8.0_181]
        at com.mysql.jdbc.Util.handleNewInstance(Util.java:425) [mysql-connector-java-5.1.40-bin.jar:5.1.40]
        at com.mysql.jdbc.Util.getInstance(Util.java:408) [mysql-connector-java-5.1.40-bin.jar:5.1.40]
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943) [mysql-connector-java-5.1.40-bin.jar:5.1.40]
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3970) [mysql-connector-java-5.1.40-bin.jar:5.1.40]
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3906) [mysql-connector-java-5.1.40-bin.jar:5.1.40]
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2524) [mysql-connector-java-5.1.40-bin.jar:5.1.40]
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2677) [mysql-connector-java-5.1.40-bin.jar:5.1.40]
        at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2549) [mysql-connector-java-5.1.40-bin.jar:5.1.40]
        at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1861) [mysql-connector-java-5.1.40-bin.jar:5.1.40]
        at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1962) [mysql-connector-java-5.1.40-bin.jar:5.1.40]
        at org.apache.commons.dbcp2.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:83) [commons-dbcp2-2.1.jar:2.1]
        at org.apache.commons.dbcp2.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:83) [commons-dbcp2-2.1.jar:2.1]
        at org.ofbiz.core.entity.jdbc.SQLProcessor.executeQuery(SQLProcessor.java:527) [entityengine-1.3.10.jar:?]
        ... 422 more

Can you please help

Accepted answers

Shannon S

Hello Nordirbek,

First you will want to check to make sure that the license you are using for Jira is valid for your version and not expired.
Secondly, it could be an issue with your MySQL encoding.

Have a look here:

Health Check Database Collation

This article can also help you:

SQL Exception while updating data in Jira applications with MySQL due to encoding

Have a look there, and let us know if you have any trouble.

If you do, can you also please confirm your database version?

Regards,

Shannon

All comments

Shannon S

Hello Nordirbek,

First you will want to check to make sure that the license you are using for Jira is valid for your version and not expired.
Secondly, it could be an issue with your MySQL encoding.

Have a look here:

Health Check Database Collation

This article can also help you:

SQL Exception while updating data in Jira applications with MySQL due to encoding

Have a look there, and let us know if you have any trouble.

If you do, can you also please confirm your database version?

Regards,

Shannon

Nodirbek Husainov

Hi Shannon,

Thanks a lot for your response.

1. The server has a valid license (Maintenance expires next year)

2. I've checked the collation and both the Health Check and System Integrity Checker pass without any problems.

The Jira is server is running with MySQL v5.7.14 and Mysql Connector v5.1.40

I've cleaned up the logs and made a clean restart. I realized that the catalina.out log gets spammed with JIRA-Bootstrap errors during table creation with Table '....' already exists error

Here's a snippet from the catalina.out file

2018-12-10 01:47:34,838 JIRA-Bootstrap INFO      [c.a.jira.startup.JiraStartupLogger] Running JIRA startup checks.
2018-12-10 01:47:34,838 JIRA-Bootstrap INFO      [c.a.jira.startup.JiraStartupLogger] JIRA pre-database startup checks completed successfully.
2018-12-10 01:47:35,141 JIRA-Bootstrap INFO      [o.o.c.entity.jdbc.DatabaseUtil] Database Product Name is MySQL
2018-12-10 01:47:35,141 JIRA-Bootstrap INFO      [o.o.c.entity.jdbc.DatabaseUtil] Database Product Version is 5.7.14
2018-12-10 01:47:35,141 JIRA-Bootstrap INFO      [o.o.c.entity.jdbc.DatabaseUtil] Database Driver Name is MySQL Connector Java
2018-12-10 01:47:35,142 JIRA-Bootstrap INFO      [o.o.c.entity.jdbc.DatabaseUtil] Database Driver Version is mysql-connector-java-5.1.40 ( Revision: 402933ef52cad9aa82624e80acbea46e3a701ce6 )
2018-12-10 01:47:35,422 JIRA-Bootstrap WARN      [o.o.c.entity.jdbc.DatabaseUtil] Entity "Action" has no table in the database
2018-12-10 01:47:35,424 JIRA-Bootstrap ERROR      [o.o.c.entity.jdbc.DatabaseUtil] Could not create table "jira.jiraaction"
2018-12-10 01:47:35,424 JIRA-Bootstrap ERROR      [o.o.c.entity.jdbc.DatabaseUtil] SQL Exception while executing the following:
    CREATE TABLE jira.jiraaction (ID DECIMAL(18,0) NOT NULL, issueid DECIMAL(18,0), AUTHOR VARCHAR(255), actiontype VARCHAR(255), actionlevel VARCHAR(255), rolelevel DECIMAL(18,0), actionbody LONGTEXT, CREATED DATETIME, UPDATEAUTHOR VARCHAR(255), UPDATED DATETIME, actionnum DECIMAL(18,0), CONS
TRAINT PK_jiraaction PRIMARY KEY (ID))
    Error was: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'jiraaction' already exists
2018-12-10 01:47:35,425 JIRA-Bootstrap WARN      [o.o.c.entity.jdbc.DatabaseUtil] Entity "Application" has no table in the database
2018-12-10 01:47:35,425 JIRA-Bootstrap ERROR      [o.o.c.entity.jdbc.DatabaseUtil] Could not create table "jira.cwd_application"
2018-12-10 01:47:35,425 JIRA-Bootstrap ERROR      [o.o.c.entity.jdbc.DatabaseUtil] SQL Exception while executing the following:
    CREATE TABLE jira.cwd_application (ID DECIMAL(18,0) NOT NULL, application_name VARCHAR(255), lower_application_name VARCHAR(255), created_date DATETIME, updated_date DATETIME, active DECIMAL(9,0), description VARCHAR(255), application_type VARCHAR(255), credential VARCHAR(255), CONSTRAINT
PK_cwd_application PRIMARY KEY (ID))
    Error was: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'cwd_application' already exists
2018-12-10 01:47:35,426 JIRA-Bootstrap WARN      [o.o.c.entity.jdbc.DatabaseUtil] Entity "ApplicationUser" has no table in the database
2018-12-10 01:47:35,426 JIRA-Bootstrap ERROR      [o.o.c.entity.jdbc.DatabaseUtil] Could not create table "jira.app_user"
2018-12-10 01:47:35,426 JIRA-Bootstrap ERROR      [o.o.c.entity.jdbc.DatabaseUtil] SQL Exception while executing the following:
    CREATE TABLE jira.app_user (ID DECIMAL(18,0) NOT NULL, user_key VARCHAR(255), lower_user_name VARCHAR(255), CONSTRAINT PK_app_user PRIMARY KEY (ID))
    Error was: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'app_user' already exists
2018-12-10 01:47:35,426 JIRA-Bootstrap WARN      [o.o.c.entity.jdbc.DatabaseUtil] Entity "AuditChangedValue" has no table in the database
2018-12-10 01:47:35,427 JIRA-Bootstrap ERROR      [o.o.c.entity.jdbc.DatabaseUtil] Could not create table "jira.audit_changed_value"
2018-12-10 01:47:35,427 JIRA-Bootstrap ERROR      [o.o.c.entity.jdbc.DatabaseUtil] SQL Exception while executing the following:
    CREATE TABLE jira.audit_changed_value (ID DECIMAL(18,0) NOT NULL, LOG_ID DECIMAL(18,0), NAME VARCHAR(255), DELTA_FROM LONGTEXT, DELTA_TO LONGTEXT, CONSTRAINT PK_audit_changed_value PRIMARY KEY (ID))
    Error was: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'audit_changed_value' already exists
2018-12-10 01:47:35,427 JIRA-Bootstrap WARN      [o.o.c.entity.jdbc.DatabaseUtil] Entity "AuditItem" has no table in the database

best regards,

Nodirbek

Shannon S

Nodirbek,

I think you might be running into this error:

JIRA throws table already exist error due to incorrect MySQL Schema

Cause

JIRA is using a MySQL database and has a schema specified, where it should not.

Resolution

Stop JIRA.
Remove the entire line containing the <schema-name> tag from the dbconfig.xml:
```
<schema-name>jiradb</schema-name>
```
Restart JIRA and confirm the database tables are created successfully by confirming no similar errors are present in the logs during startup.

Could you give that a try and let us know if you have any trouble?

Regards,

Shannon

Nodirbek Husainov

Thanks a million.

This was it. After removing the schema-name and starting the server up, the issues went away. The catalina.log looks error-free now

regards,

Nodirbek

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