Dear LabKey support team,
We have upgraded from LabKey 18.1 to 18.2 and the connection to the external data source we had running (a MySQL database), is not working anymore.
I attach the log file for documentation of the error messages.
First of all, the error was clearly stating that it is necessary to change a parameter value in the connection string: from "zeroDateTimeBehavior=convertToNull" to "zeroDateTimeBehavior=CONVERT_TO_NULL", which we did. But that did not solve the issue.
We are running:
jdk1.8.0_40
apache-tomcat-7.0.68
postgres 9.6
MySQL-server-community-5.1.33-0.rhel5 (for the external data source)
Do you know how to restore the external data source connection?
Thank you very much,
Eva |
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| Jon (LabKey DevOps) responded: |
2018-08-03 15:03 |
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| eva pujadas responded: |
2018-08-09 03:14 |
Hi Jon,
Thanks for your answer.
In fact the LabKey update script had already copied all the jars in the tomcat lib directory.
We checked that in fact that happened:
labkey@bc2-labkey-dev ~]$ sha256sum /home/labkey/LabKey18.2-59193.12-community-bin/tomcat-lib/*
aac05ebf5504c91b29420129b02dd878a86c52f8fa6eccf9235e0bfd7a60bef1 /home/labkey/LabKey18.2-59193.12-community-bin/tomcat-lib/jtds.jar
e5b2ad98bc5ff38334fb8f10d20e17f81b4128e98dfc15e1428cbf43ef485216 /home/labkey/LabKey18.2-59193.12-community-bin/tomcat-lib/labkeyBootstrap.jar
5ee49bd9d91b50f7fc426cecb031ba2b516d2744c1b6f42ced9177cbfe52489d /home/labkey/LabKey18.2-59193.12-community-bin/tomcat-lib/mail.jar
0cbe25eb4b4e7a38f52374a46283fc2381c68870581651925db752000c0d053d /home/labkey/LabKey18.2-59193.12-community-bin/tomcat-lib/mysql.jar
1996524026a3027853f3932e8639ef813807d1b63fe14832f410fffa4274fa70 /home/labkey/LabKey18.2-59193.12-community-bin/tomcat-lib/postgresql.jar
[labkey@bc2-labkey-dev ~]$ sha256sum /opt/tomcat/lib/{jtds.jar,labkeyBootstrap.jar,mail.jar,mysql.jar,postgresql.jar}
aac05ebf5504c91b29420129b02dd878a86c52f8fa6eccf9235e0bfd7a60bef1 /opt/tomcat/lib/jtds.jar
e5b2ad98bc5ff38334fb8f10d20e17f81b4128e98dfc15e1428cbf43ef485216 /opt/tomcat/lib/labkeyBootstrap.jar
5ee49bd9d91b50f7fc426cecb031ba2b516d2744c1b6f42ced9177cbfe52489d /opt/tomcat/lib/mail.jar
0cbe25eb4b4e7a38f52374a46283fc2381c68870581651925db752000c0d053d /opt/tomcat/lib/mysql.jar
1996524026a3027853f3932e8639ef813807d1b63fe14832f410fffa4274fa70 /opt/tomcat/lib/postgresql.jar
We also upgraded tomcat and java, having finally the following versions:
java version "1.8.0_181"
apache-tomcat-8.5.32
postgres 9.6
MySQL-server-community-5.1.33-0.rhel5 (for the external data source)
But the problem to connect to the external MySQL data source continues: (see also attached file)
Cannot connect to DataSource "bc2statsDataSource" defined in labkey.xml. This DataSource will not be available during this server session.
java.sql.SQLException: Cannot create PoolableConnectionFactory (Could not create connection to database server. Attempted reconnect 3 times. Giving up.)
Do you have an idea about how that could be solved?
Thanks a lot and best regards,
Eva |
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| Jon (LabKey DevOps) responded: |
2018-08-23 13:39 |
Hi Eva,
That version of MySQL is pretty old and no longer supported. The end of life on that version was back in 2013 ( https://blog.cpanel.com/mysql-5-1-end-of-life).
The MySQL 8.0 JDBC driver that is supplied claims to support MySQL 8.0, 5.7, 5.6, and 5.5. But since your version is 5.1, the likelihood of it supporting that is very low.
Have you looked into upgrading your MySQL instance? Having a current version is ideal due to security, reliability, and the ability to connect to LabKey among many other reasons. If this isn't possible, your only other recourse is to downgrade to an older version of the JDBC driver that supports MySQL 5.1
Regards,
Jon |
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labkey-errors.log
labkey_mysql_error.txt