@Configuration
public class DataSourceConfiguration {

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

    @Bean(name = "batchDataSource")
    public DataSource batchDataSource( @Value("${batch.datasource.url}") String url ){
        return DataSourceBuilder.create().url( url ).build();
    }
}

# DATASOURCE (DataSourceAutoConfiguration & DataSourceProperties)
spring.datasource.url=jdbc:mariadb://localhost:3306/batch_poc
spring.datasource.username=root
spring.datasource.password=
spring.datasource.driver-class-name=org.mariadb.jdbc.Driver
spring.datasource.max-age=10000

spring.datasource.initialize=false

# JPA (JpaBaseConfiguration, HibernateJpaAutoConfiguration)
spring.jpa.generate-ddl=false
spring.jpa.show-sql=true
spring.jpa.database=MYSQL

# SPRING BATCH (BatchDatabaseInitializer)
spring.batch.initializer.enabled=false

# ----------------------------------------
# PROJECT SPECIFIC PROPERTIES
# ----------------------------------------

# BATCH DATASOURCE
batch.datasource.url=jdbc:hsqldb:file:C:/tmp/hsqldb/batchdb

@Configuration
@EnableBatchProcessing
public class BatchConfiguration {

    private static final Logger LOG = Logger.getLogger( BatchConfiguration.class );

    @Bean
    public BatchConfigurer configurer(){
        return new CustomBatchConfigurer();
    }

    @Bean
    public Job importElementsJob( JobBuilderFactory jobs, Step step1 ){
        return jobs.get("importElementsJob")
                .incrementer( new RunIdIncrementer() )
                .flow( step1 )
                .end()
                .build();
    }

    @Bean
    public Step step1( StepBuilderFactory stepBuilderFactory, ItemReader<InputElement> reader,
            ItemWriter<List<Entity>> writer, ItemProcessor<InputElement, List<Entity>> processor ){

        return stepBuilderFactory.get("step1")
                .<InputElement, List<Entity>> chunk(100)
                .reader( reader )
                .processor( processor )
                .writer( writer )
                .build();
    }

    @Bean
    public ItemReader<InputElement> reader() throws IOException {
        return new CustomItemReader();
    }

    @Bean
    public ItemProcessor<InputElement, List<Entity>> processor(){
        return new CutsomItemProcessor();
    }

    @Bean
    public ItemWriter<List<Entity>> writer(){
        return new CustomItemWriter();
    }

}

public class CustomBatchConfigurer extends DefaultBatchConfigurer {

    @Override
    @Autowired
    public void setDataSource( @Qualifier("batchDataSource") DataSource dataSource) {
        super.setDataSource(dataSource);
    }

}

public class CustomItemWriter implements ItemWriter<List<Entity>> {

    private static final Logger LOG = Logger.getLogger( EntityWriter.class );

    @Autowired
    private EntityRepository entityRepository;

    @Override
    public void write(List<? extends List<Entity>> items)
            throws Exception {
        if( items != null && !items.isEmpty() ){

            for( List<Entity> entities : items ){
                for( Entity entity : entities ){
                    Entity fromDb = entityRepository.findById( entity.getId() );

                    // Insert
                    if( fromDb == null ){
                        entityRepository.save( entity );
                    }

                    // Update
                    else {
                        // TODO : entityManager.merge()
                    }
                }
            }

        }
    }

}

public class CustomBatchConfigurer implements BatchConfigurer {

    private static final Logger LOG = Logger.getLogger( CustomBatchConfigurer.class );

    private final EntityManagerFactory entityManagerFactory;

    private PlatformTransactionManager transactionManager;

    private JobRepository jobRepository;

    private JobLauncher jobLauncher;

    private JobExplorer jobExplorer;

    /**
     * Create a new {@link CustomBatchConfigurer} instance.
     * @param entityManagerFactory the entity manager factory
     */
    public CustomBatchConfigurer( EntityManagerFactory entityManagerFactory ) {
        this.entityManagerFactory = entityManagerFactory;
    }

    @Override
    public JobRepository getJobRepository() {
        return this.jobRepository;
    }

    @Override
    public PlatformTransactionManager getTransactionManager() {
        return this.transactionManager;
    }

    @Override
    public JobLauncher getJobLauncher() {
        return this.jobLauncher;
    }

    @Override
    public JobExplorer getJobExplorer() throws Exception {
        return this.jobExplorer;
    }

    @PostConstruct
    public void initialize() {
        try {
            // transactionManager:
            LOG.info("Forcing the use of a JPA transactionManager");
            if( this.entityManagerFactory == null ){
                throw new Exception("Unable to initialize batch configurer : entityManagerFactory must not be null");
            }
            this.transactionManager = new JpaTransactionManager( this.entityManagerFactory );

            // jobRepository:
            LOG.info("Forcing the use of a Map based JobRepository");
            MapJobRepositoryFactoryBean jobRepositoryFactory = new MapJobRepositoryFactoryBean( this.transactionManager );
            jobRepositoryFactory.afterPropertiesSet();
            this.jobRepository = jobRepositoryFactory.getObject();

            // jobLauncher:
            SimpleJobLauncher jobLauncher = new SimpleJobLauncher();
            jobLauncher.setJobRepository(getJobRepository());
            jobLauncher.afterPropertiesSet();
            this.jobLauncher = jobLauncher;

            // jobExplorer:
            MapJobExplorerFactoryBean jobExplorerFactory = new MapJobExplorerFactoryBean(jobRepositoryFactory);
            jobExplorerFactory.afterPropertiesSet();
            this.jobExplorer = jobExplorerFactory.getObject();
        }
        catch (Exception ex) {
            throw new IllegalStateException("Unable to initialize Spring Batch", ex);
        }
    }

}

@Configuration
@EnableBatchProcessing
public class BatchConfiguration {

    @Bean
    public BatchConfigurer configurer( EntityManagerFactory entityManagerFactory ){
        return new CustomBatchConfigurer( entityManagerFactory );
    }

    [...]

}

# DATASOURCE (DataSourceAutoConfiguration & DataSourceProperties)
spring.datasource.url=jdbc:mariadb://localhost:3306/inotr_poc
spring.datasource.username=root
spring.datasource.password=adsn123
spring.datasource.driver-class-name=org.mariadb.jdbc.Driver
spring.datasource.max-age=10000

spring.datasource.initialize=true

# JPA (JpaBaseConfiguration, HibernateJpaAutoConfiguration)
spring.jpa.generate-ddl=false
spring.jpa.show-sql=true
spring.jpa.database=MYSQL

# SPRING BATCH (BatchDatabaseInitializer)
spring.batch.initializer.enabled=false

@PostConstruct
    public void initialize() {
        try {
            // transactionManager:
            LOGGER.info("Forcing the use of ResourcelessTransactionManager for batch db");

            this.transactionManager = new ResourcelessTransactionManager();
            //the rest of the code follows...
    }