datasource.primary.url = <url>
datasource.primary.username = <user>
datasource.primary.password = <password>

datasource.secondary.url = <url>
datasource.secondary.username = <user>
datasource.secondary.password = <pass>

@EnableAutoConfiguration
@Configuration
@EntityScan({"com.example.domain","com.example.common.domain"})
@PropertySource(value = "classpath:application.properties")
@EnableScheduling
    public class MyApplication {

public static void main(String[] args) {
    SpringApplication.run(MyApplication.class, args);
}

  }

@Configuration
@EnableJpaRepositories(basePackages = "com.example.repository",
entityManagerFactoryRef = "primaryEntityManagerFactory",
transactionManagerRef = "primaryTransactionManager")
@EnableTransactionManagement
public class PrimaryConfiguration {

@Bean
@ConfigurationProperties(prefix = "datasource.primary")
@Primary
public DataSource primaryDataSource()
{
    return DataSourceBuilder.create().build();
}

@Bean
@Primary
public LocalContainerEntityManagerFactoryBean primaryEntityManagerFactory(final EntityManagerFactoryBuilder builder)
{
    return builder
            .dataSource(primaryDataSource())
            .packages("uk.gov.dwp.pss.roc.domain")
            .persistenceUnit("primaryPersistenceUnit")
            .build();
}

@Bean
@Primary
public JpaTransactionManager primaryTransactionManager(@Qualifier("primaryEntityManagerFactory") final EntityManagerFactory factory)
{
    return new JpaTransactionManager(factory);
}
}

@Configuration
@EnableJpaRepositories(basePackages = "com.example.common.repository",
entityManagerFactoryRef = "secondaryEntityManagerFactory",
transactionManagerRef = "secondaryTransactionManager")
@EnableTransactionManagement
public class SecondaryConfiguration {

@Bean
@ConfigurationProperties(prefix = "datasource.secondary")
public DataSource secondaryDataSource()
{
    return DataSourceBuilder.create().build();
}

@Bean
public LocalContainerEntityManagerFactoryBean secondaryEntityManagerFactory(final EntityManagerFactoryBuilder builder)
{
    return builder
            .dataSource(secondaryDataSource())
            .packages("uk.gov.dwp.pss.commons.domain.security")
            .persistenceUnit("secondaryPersistenceUnit")
            .build();
}

@Bean
public JpaTransactionManager secondaryTransactionManager(@Qualifier("secondaryEntityManagerFactory") final EntityManagerFactory factory)
{
    return new JpaTransactionManager(factory);
}

}

public interface MyRepository extends JpaRepository<MyObject, String>,JpaSpecificationExecutor<MyObject> {
}

@SpringApplicationConfiguration(classes = MyApplication.class)