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APPLICATION FAILED TO START
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Description:

Parameter 0 of method emfb in datasources.Application$PersistenceConfiguration required a single bean, but 2 were found:
        - ds1: defined by method 'ds1' in class path resource [datasources/Application$PersistenceConfiguration.class]
        - ds2: defined by method 'ds2' in class path resource [datasources/Application$PersistenceConfiguration.class]


Action:

Consider marking one of the beans as @Primary, updating the consumer to accept multiple beans, or using @Qualifier to identify the bean that should be consumed

package datasources;

import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.sql.DataSource;
import javax.ws.rs.ApplicationPath;
import javax.ws.rs.GET;
import javax.ws.rs.Path;
import org.apache.log4j.Logger;
import org.glassfish.jersey.server.ResourceConfig;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
import org.springframework.boot.autoconfigure.transaction.jta.JtaAutoConfiguration;
import org.springframework.boot.builder.SpringApplicationBuilder;
import org.springframework.boot.orm.jpa.EntityManagerFactoryBuilder;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Primary;
import org.springframework.jdbc.datasource.embedded.EmbeddedDatabaseBuilder;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.stereotype.Component;

@Configuration
@EnableAutoConfiguration(exclude = {
//      HibernateJpaAutoConfiguration.class,
//      DataSourceAutoConfiguration.class
        JtaAutoConfiguration.class
})
@ComponentScan
public class Application {

    public static void main(String[] args) {

        new SpringApplicationBuilder(Application.class)
            .build()
            .run(args);
    }

    @Component
    @Path("/ds")
    public static class DsApi {

        private final static Logger logger = Logger.getLogger(DsApi.class);

        @Autowired(required = false)
        @Qualifier("ds1")
        private DataSource ds;

        @GET
        public String ds() {
            logger.info("ds");
            return ds.toString();
        }
    }

    @Component
    @Path("/em")
    public static class EmApi {

        private final static Logger logger = Logger.getLogger(EmApi.class);

        @PersistenceContext(unitName = "ds2", type = PersistenceContextType.TRANSACTION)
        private EntityManager em;

        @GET
        public String em() {
            logger.info("em");
            return em.toString();
        }
    }

    @Configuration
    @ApplicationPath("/jersey")
    public static class JerseyConfig extends ResourceConfig {
        public JerseyConfig() {
            register(DsApi.class);
            register(EmApi.class);
        }
    }

    @Configuration
    public static class PersistenceConfiguration {

        @Bean
        @Qualifier("ds1")
        public DataSource ds1() {
            return new EmbeddedDatabaseBuilder().build();
        }

        @Bean
        @Qualifier("ds2")
        public DataSource ds2() {
            return new EmbeddedDatabaseBuilder().build();
        }

        @Bean
        @Primary
        @Autowired
        public LocalContainerEntityManagerFactoryBean emfb(@Qualifier("ds1") DataSource ds, EntityManagerFactoryBuilder emfb) {
            return emfb.dataSource(ds)
                    .packages(Application.class)
                    .persistenceUnit("ds1")
                    .build();
        }

        @Bean
        @Autowired
        public LocalContainerEntityManagerFactoryBean emfb2(@Qualifier("ds2") DataSource ds, EntityManagerFactoryBuilder emfb) {
            return emfb.dataSource(ds)
                    .packages(Application.class)
                    .persistenceUnit("ds2")
                    .build();
        }
    }
}

@Configuration
public static class PersistenceConfiguration {

        @Bean
        @Primary
        public DataSource ds1() {
            return new EmbeddedDatabaseBuilder().build();
        }

        @Bean
        public DataSource ds2() {
            return new EmbeddedDatabaseBuilder().build();
        }

        @Bean
        @Primary
        @Autowired
        public LocalContainerEntityManagerFactoryBean emfb(@Qualifier("ds1") DataSource ds, EntityManagerFactoryBuilder emfb) {
            return emfb.dataSource(ds)
                    .packages(DemoApplication.class)
                    .persistenceUnit("ds1")
                    .build();
        }

        @Bean
        @Autowired
        public LocalContainerEntityManagerFactoryBean emfb2(@Qualifier("ds2") DataSource ds, EntityManagerFactoryBuilder emfb) {
            return emfb.dataSource(ds)
                    .packages(DemoApplication.class)
                    .persistenceUnit("ds2")
                    .build();
        }
 }