Custom Field Option Synchroniser
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If you want to use MS SQL with Custom Field Option Synchroniser in a version below 1.1.6 you need to use the JTDS database driver engine. 

The open source JTDS engine does not come bundled with Jira and needs to be installed manually:

  1. Download JTDS: http://jtds.sourceforge.net/
  2. Unzip the file
  3. Move the .jar file to <JIRA installation directory>/atlassian-jira/WEB-INF/lib/
  4. Stop Jira
  5. Add your datasource
  6. Restart Jira

Your datasource should look like this with JTDS:

SQL Server Datasource
<Resource
    name="jdbc/myDS"
    auth="Container"
    type="javax.sql.DataSource"
    driverClassName="net.sourceforge.jtds.jdbc.Driver"
    url="jdbc:jtds:sqlserver://sqlserver:1433/mydatabase"
    username="username"
    password="password"
    maxActive="20"
    maxIdle="10"
    maxWait="-1"
    validationQuery="Select 1"
/>

Compatibility to the with Jira bundled Microsoft JDBC was introduced in Custom Field Option Synchroniser 1.1.6:

CFSYNC-12 - Getting issue details... STATUS