Grouper Users - Open Discussion List

[Baron Fujimoto <>]

Just to follow up on this for the sake of posterity in case someone else 
searches the mailing list for a solution. Michael Gettes provided the lead 
for this. It appears that an updating the mysql-connector jar file is the 
solution.

The MySQL docs at 
<https://dev.mysql.com/doc/connector-j/8.0/en/connector-j-versions.html> 
suggests that a 5.1.x connector should have worked, but it failed where we appeared 
to have 5.1.5. Updated it to the latest mysql-connector-java-5.1.49-bin.jar and was 
able to successfully connect once again. FWIW, I also tried the latest 
mysql-connector-java-8.0.21-bin.jar, which also worked, but resulted in a 
deprecation warning:

Loading class 'com.mysql.jdbc.Driver'. This is deprecated. The new driver 
class is 'com.mysql.cj.jdbc.Driver'. The driver is automatically registered 
via the SPI and manual loading of the driver class is generally unnecessary.

This warning can be resolved by setting the following in the 
grouper.hibernate.properties overlay config file:
hibernate.connection.driver_class = com.mysql.cj.jdbc.Driver

Michael Gettes recommends using the 8.0 connector.

Finally, I empirically determined that copying the updated mysql-connector 
jar to
grouper.apiBinary-2.2.2/lib/jdbcSamples/mysql-connector-java-bin.jar
then rebuilding and redeploying was sufficient to update my UI and WS 
components as well.

On Mon, Aug 03, 2020 at 11:59:26AM -1000, Baron Fujimoto wrote:
> We currently have Grouper 2.2.2 using MySQL 5.7.x as its registry. Our 
> database admins want to ugrade MySQL to 8.0.x. When I try to point one of our 
> Grouper instances to a copy of a registry on an 8.0.x db though, I get the 
> errors below if I try to, for example, run gsh.
>
> I can generally connect to the registry db ok using MySQL clients such as 
> MySQL Workbench, and from the grouper host itself using the command line 
> version of mysql. Other simple connectivity tests using nc or telnet are also 
> successful.
>
> Is this a known incompatibility? Any suggestions?
>
> ----- >8 gsh startup errors 8<-----
> Using GROUPER_HOME: /home/grouper/grouper/grouper-api/bin/..
> Using GROUPER_CONF: /home/grouper/grouper/grouper-api/bin/../conf
> Using JAVA: /usr/java/latest/bin/java
> using MEMORY: 64m-750m
> log4j:WARN No such property [maxBackupIndex] in org.apache.log4j.FileAppender.
> log4j:WARN No such property [maxFileSize] in org.apache.log4j.FileAppender.
> log4j:WARN No such property [maxFileSize] in org.apache.log4j.FileAppender.
> log4j:WARN No such property [maxBackupIndex] in org.apache.log4j.FileAppender.
> Grouper starting up: version: 2.2.2, build date: null, env: grouper-future
> grouper.properties read from: 
> /home/grouper/grouper/grouper.apiBinary-2.2.2/conf/grouper.properties
> Grouper current directory is: 
> /home/grouper/grouper/grouper.apiBinary-2.2.2/bin
> log4j.properties read from:   
> /home/grouper/grouper/grouper.apiBinary-2.2.2/conf/log4j.properties
> Grouper is logging to file:   
> /home/grouper/grouper/logs/grouper-api_error.log, at min level WARN for 
> package: edu.internet2.middleware.grouper, based on log4j.properties
> grouper.hibernate.properties: 
> /home/grouper/grouper/grouper.apiBinary-2.2.2/conf/grouper.hibernate.properties
> grouper.hibernate.properties: 
> grpr_admin@jdbc:mysql://mysqldb..example.edu:3306/grprtst?CharSet=utf8&useUnicode=true&characterEncoding=utf8&useSSL=false
> sources.xml read from:        
> /home/grouper/grouper/grouper.apiBinary-2.2.2/conf/sources.xml
> sources.xml groupersource id: g:gsa
> sources.xml groupersource id: grouperEntities
> sources.xml ldap source id:   UH core LDAP: 
> cn=grouper,ou=specials,dc=example,dc=edu@ldaps://ldap.example.edu:636
> Grouper ddl object type 'Grouper' has dbVersion: 0 and java version: 29
> Couldnt startup grouper: Problem in HibernateSession: null
> edu.internet2.middleware.grouper.internal.dao.GrouperDAOException: Problem in 
> HibernateSession: null
>    at 
> edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_hibernateSessionCatch(HibernateSession.java:575)
>    at 
> edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:697)
>    at 
> edu.internet2.middleware.grouper.hibernate.BySqlStatic.select(BySqlStatic.java:141)
>    at 
> edu.internet2.middleware.grouper.hibernate.BySqlStatic.select(BySqlStatic.java:126)
>    at 
> edu.internet2.middleware.grouper.ddl.GrouperDdl.addTableIndices(GrouperDdl.java:12801)
>    at 
> edu.internet2.middleware.grouper.ddl.GrouperDdl.access$3700(GrouperDdl.java:100)
>    at 
> edu.internet2.middleware.grouper.ddl.GrouperDdl$25.updateVersionFromPrevious(GrouperDdl.java:1834)
>    at 
> edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.upgradeDatabaseVersion(GrouperDdlUtils.java:2056)
>    at 
> edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.bootstrapHelper(GrouperDdlUtils.java:619)
>    at 
> edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.bootstrap(GrouperDdlUtils.java:328)
>    at 
> edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperStartup.java:251)
>    at 
> edu.internet2.middleware.grouper.app.gsh.GrouperShell.main(GrouperShell.java:151)
>    at 
> edu.internet2.middleware.grouper.app.gsh.GrouperShellWrapper.main(GrouperShellWrapper.java:31)
> Caused by: org.hibernate.exception.GenericJDBCException: Cannot open 
> connection
>    at 
> org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:140)
>    at 
> org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:128)
>    at 
> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
>    at 
> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:52)
>    at 
> org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:449)
>    at 
> org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:167)
>    at org.hibernate.jdbc.JDBCContext.connection(JDBCContext.java:160)
>    at org.hibernate.transaction.JDBCTransaction.begin(JDBCTransaction.java:81)
>    at org.hibernate.impl.SessionImpl.beginTransaction(SessionImpl.java:1473)
>    at 
> edu.internet2.middleware.grouper.hibernate.HibernateSession.<init>(HibernateSession.java:244)
>    at 
> edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_hibernateSession(HibernateSession.java:457)
>    at 
> edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:646)
>    ... 11 more
> Caused by: java.sql.SQLException: An SQLException was provoked by the 
> following failure: com.mchange.v2.resourcepool.ResourcePoolException: A 
> ResourcePool cannot acquire a new resource -- the factory or source appears 
> to be down.
>    at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:106)
>    at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:65)
>    at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:62)
>    at 
> com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPooledConnection(C3P0PooledConnectionPool.java:531)
>    at 
> com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource.getConnection(AbstractPoolBackedDataSource.java:128)
>    at 
> org.hibernate.connection.C3P0ConnectionProvider.getConnection(C3P0ConnectionProvider.java:78)
>    at 
> org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:446)
>    ... 18 more
> Caused by: com.mchange.v2.resourcepool.ResourcePoolException: A ResourcePool 
> cannot acquire a new resource -- the factory or source appears to be down.
>    at 
> com.mchange.v2.resourcepool.BasicResourcePool.awaitAvailable(BasicResourcePool.java:1279)
>    at 
> com.mchange.v2.resourcepool.BasicResourcePool.prelimCheckoutResource(BasicResourcePool.java:557)
>    at 
> com.mchange.v2.resourcepool.BasicResourcePool.checkoutResource(BasicResourcePool.java:477)
>    at 
> com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPooledConnection(C3P0PooledConnectionPool.java:525)
>    ... 21 more
> Exception in thread "main" 
> edu.internet2.middleware.grouper.internal.dao.GrouperDAOException: Problem in 
> HibernateSession: null
>    at 
> edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_hibernateSessionCatch(HibernateSession.java:575)
>    at 
> edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:697)
>    at 
> edu.internet2.middleware.grouper.hibernate.BySqlStatic.select(BySqlStatic.java:141)
>    at 
> edu.internet2.middleware.grouper.hibernate.BySqlStatic.select(BySqlStatic.java:126)
>    at 
> edu.internet2.middleware.grouper.ddl.GrouperDdl.addTableIndices(GrouperDdl.java:12801)
>    at 
> edu.internet2.middleware.grouper.ddl.GrouperDdl.access$3700(GrouperDdl.java:100)
>    at 
> edu.internet2.middleware.grouper.ddl.GrouperDdl$25.updateVersionFromPrevious(GrouperDdl.java:1834)
>    at 
> edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.upgradeDatabaseVersion(GrouperDdlUtils.java:2056)
>    at 
> edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.bootstrapHelper(GrouperDdlUtils.java:619)
>    at 
> edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.bootstrap(GrouperDdlUtils.java:328)
>    at 
> edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperStartup.java:251)
>    at 
> edu.internet2.middleware.grouper.app.gsh.GrouperShell.main(GrouperShell.java:151)
>    at 
> edu.internet2.middleware.grouper.app.gsh.GrouperShellWrapper.main(GrouperShellWrapper.java:31)
> Caused by: org.hibernate.exception.GenericJDBCException: Cannot open 
> connection
>    at 
> org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:140)
>    at 
> org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:128)
>    at 
> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
>    at 
> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:52)
>    at 
> org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:449)
>    at 
> org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:167)
>    at org.hibernate.jdbc.JDBCContext.connection(JDBCContext.java:160)
>    at org.hibernate.transaction.JDBCTransaction.begin(JDBCTransaction.java:81)
>    at org.hibernate.impl.SessionImpl.beginTransaction(SessionImpl.java:1473)
>    at 
> edu.internet2.middleware.grouper.hibernate.HibernateSession.<init>(HibernateSession.java:244)
>    at 
> edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_hibernateSession(HibernateSession.java:457)
>    at 
> edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:646)
>    ... 11 more
> Caused by: java.sql.SQLException: An SQLException was provoked by the 
> following failure: com.mchange.v2.resourcepool.ResourcePoolException: A 
> ResourcePool cannot acquire a new resource -- the factory or source appears 
> to be down.
>    at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:106)
>    at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:65)
>    at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:62)
>    at 
> com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPooledConnection(C3P0PooledConnectionPool.java:531)
>    at 
> com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource.getConnection(AbstractPoolBackedDataSource.java:128)
>    at 
> org.hibernate.connection.C3P0ConnectionProvider.getConnection(C3P0ConnectionProvider.java:78)
>    at 
> org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:446)
>    ... 18 more
> Caused by: com.mchange.v2.resourcepool.ResourcePoolException: A ResourcePool 
> cannot acquire a new resource -- the factory or source appears to be down.
>    at 
> com.mchange.v2.resourcepool.BasicResourcePool.awaitAvailable(BasicResourcePool.java:1279)
>    at 
> com.mchange.v2.resourcepool.BasicResourcePool.prelimCheckoutResource(BasicResourcePool.java:557)
>    at 
> com.mchange.v2.resourcepool.BasicResourcePool.checkoutResource(BasicResourcePool.java:477)
>    at 
> com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPooledConnection(C3P0PooledConnectionPool.java:525)
>    ... 21 more
>
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