Business model and data integration tier for the laboratory information management system. See also https://gist.github.com/james-d/e485ac525c71e20bb453

Dao.java

package edu.marshall.genomics.lims.data;

import java.util.List;

import edu.marshall.genomics.lims.entities.Investigator;
import edu.marshall.genomics.lims.entities.Project;
import edu.marshall.genomics.lims.entities.Sample;

public interface Dao {
	public List<Investigator> getAllInvestigators() throws DaoException ;
	public Investigator getInvestigatorById(int id) throws DaoException ;
	public List<Project> getAllProjects() throws DaoException ;
	public List<Project> getProjectsByInvestigator(Investigator investigator) throws DaoException ;
	public Project getProjectById(int id) throws DaoException ;
	public List<Sample> getSamplesByProject(Project project) throws DaoException ;
	public Sample getSampleById(int id) throws DaoException ;
	public void addInvestigators(List<Investigator> investigators) throws DaoException ;
	public void updateInvestigator(Investigator invesitgator) throws DaoException ;
	public void addProjects(List<Project> projects) throws DaoException ;
	public void updateProject(Project project) throws DaoException ;
	public void addSamples(List<Sample> samples) throws DaoException ;
	public void updateSample(Sample sample) throws DaoException ;
}

DaoException.java

package edu.marshall.genomics.lims.data;

public class DaoException extends Exception {

	private static final long serialVersionUID = -25809315466194148L;

	public DaoException() {
	}

	public DaoException(String message, Throwable cause) {
		super(message, cause);
	}

	public DaoException(String message) {
		super(message);
	}

	public DaoException(Throwable cause) {
		super(cause);
	}
	
}

JpaDao.java

package edu.marshall.genomics.lims.data;

import java.util.List;

import javax.inject.Named;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;

import edu.marshall.genomics.lims.entities.Investigator;
import edu.marshall.genomics.lims.entities.Project;
import edu.marshall.genomics.lims.entities.Sample;

@Named("dao")
public class JpaDao implements Dao {

	private EntityManager em ;


	public EntityManager getEntityManager() {
		return em ;
	}
	
	@PersistenceContext
	public void setEntityManager(EntityManager em) {
		this.em = em ;
	}

	@Override
	public List<Investigator> getAllInvestigators() throws DaoException {
		return execute("Investigator.findAll", Investigator.class);
	}

	@Override
	public Investigator getInvestigatorById(int id)
			throws DaoException {
		try {
			return em.find(Investigator.class, id);
		} catch (Exception e) {
			throw new DaoException(e);
		}
	}

	@Override
	public List<Project> getAllProjects() throws DaoException {
		return execute("Project.findAll", Project.class);
	}

	@Override
	public List<Project> getProjectsByInvestigator(Investigator investigator)
			throws DaoException {
		try {
			return em.createNamedQuery("Project.byInvestigator", Project.class)
					.setParameter("investigator", investigator)
					.getResultList();
		} catch (Exception e) {
			throw new DaoException(e);
		}
	}
	
	@Override
	 public Project getProjectById(int id) throws DaoException {
		try {
			return em.find(Project.class, id);
		} catch (Exception e) {
			throw new DaoException(e);
		}
	}

	@Override
	public List<Sample> getSamplesByProject(Project project)
			throws DaoException {
		try {
			return em.createNamedQuery("Sample.byProject", Sample.class)
					.setParameter("project", project)
					.getResultList();
		} catch (Exception e) {
			throw new DaoException(e);
		}
	}

	@Override
	 public Sample getSampleById(int id) throws DaoException {
		try {
			return em.find(Sample.class, id);
		} catch (Exception e) {
			throw new DaoException(e);
		}
	}

	@Override
	public void addInvestigators(List<Investigator> investigators)
			throws DaoException {
		try {
			for (Investigator investigator : investigators) {
				em.persist(investigator);
			}
		} catch (Exception e) {
			throw new DaoException(e);
		}
	}

	@Override
	public void addProjects(List<Project> projects) throws DaoException {
		try {
			for (Project project : projects) 
				em.persist(project);
		} catch (Exception e) {
			throw new DaoException(e);
		}
	}

	@Override
	public void addSamples(List<Sample> samples) throws DaoException {
		try {
			for (Sample sample : samples)
				
				em.persist(sample);
		} catch (Exception e) {
			throw new DaoException(e);
		}
	}
	
	private <T> List<T> execute(String queryName, Class<T> type) throws DaoException {
		try {
			return em.createNamedQuery(queryName, type).getResultList();
		} catch (Exception e) {
			throw new DaoException(e);
		}
	}

	@Override
	public void updateInvestigator(Investigator investigator)
			throws DaoException {
		try {
			em.merge(investigator);
		} catch (Exception e) {
			throw new DaoException(e);
		}
	}

	@Override
	public void updateProject(Project project) throws DaoException {
		try {
			em.merge(project);
		} catch (Exception e) {
			throw new DaoException(e);
		}		
	}

	@Override
	public void updateSample(Sample sample) throws DaoException {
		try {
			em.merge(sample);
		} catch (Exception e) {
			throw new DaoException(e);
		}
	}
}

LimsService.java

package edu.marshall.genomics.lims.service;

import java.util.List;

import edu.marshall.genomics.lims.entities.Investigator;
import edu.marshall.genomics.lims.entities.Project;
import edu.marshall.genomics.lims.entities.Sample;

public interface LimsService {
	public List<Investigator> getAllInvestigators() throws ServiceException ;
	public Investigator getInvestigatorById(int id) throws ServiceException ;
	public List<Project> getAllProjects() throws ServiceException ;
	public List<Project> getProjectsByInvestigator(Investigator investigator) throws ServiceException ;
	public Project getProjectById(int id) throws ServiceException ;
	public List<Sample> getSamplesByProject(Project project) throws ServiceException ;
	public Sample getSampleById(int id) throws ServiceException ;
	public void addInvestigators(List<Investigator> investigators) throws ServiceException ;
	public void updateInvestigator(Investigator invesitgator) throws ServiceException ;
	public void addProjects(List<Project> projects) throws ServiceException ;
	public void updateProject(Project project) throws ServiceException ;
	public void addSamples(List<Sample> samples) throws ServiceException ;
	public void updateSample(Sample sample) throws ServiceException ;

}

ServiceException.java

package edu.marshall.genomics.lims.service;

public class ServiceException extends RuntimeException {

	private static final long serialVersionUID = -5739815078288882145L;

	public ServiceException() {
	}

	public ServiceException(String message) {
		super(message);
	}

	public ServiceException(Throwable cause) {
		super(cause);
	}

	public ServiceException(String message, Throwable cause) {
		super(message, cause);
	}


}

ServiceImpl.java

package edu.marshall.genomics.lims.service;

import java.util.List;

import javax.inject.Inject;
import javax.inject.Named;

import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;

import edu.marshall.genomics.lims.data.Dao;
import edu.marshall.genomics.lims.data.DaoException;
import edu.marshall.genomics.lims.entities.Investigator;
import edu.marshall.genomics.lims.entities.Project;
import edu.marshall.genomics.lims.entities.Sample;

@Named("limsService")
@Transactional(propagation=Propagation.REQUIRED, readOnly=false, rollbackFor=ServiceException.class)
public class ServiceImpl implements LimsService {
	
	private Dao dao ;
	
	public Dao getDao() {
		return dao;
	}

	@Inject
	public void setDao(Dao dao) {
		this.dao = dao;
	}

	@Override
	@Transactional(readOnly=true)
	public List<Investigator> getAllInvestigators() throws ServiceException {
		try {
			return dao.getAllInvestigators();
		} catch (DaoException exc) {
			throw new ServiceException(exc);
		}
	}

	@Override
	@Transactional(readOnly=true)
	public Investigator getInvestigatorById(int id)
			throws ServiceException {
		try {
			return dao.getInvestigatorById(id);
		} catch (DaoException exc) {
			throw new ServiceException(exc);
		}
	}

	@Override
	@Transactional(readOnly=true)
	public List<Project> getAllProjects() throws ServiceException {
		try {
			return dao.getAllProjects() ;
		} catch (DaoException e) {
			throw new ServiceException(e);
		}
	}

	@Override
	@Transactional(readOnly=true)
	public List<Project> getProjectsByInvestigator(Investigator investigator)
			throws ServiceException {
		try {
			return dao.getProjectsByInvestigator(investigator);
		} catch (DaoException e) {
			throw new ServiceException(e);
		}
	}
	
	@Override
	@Transactional(readOnly=true) 
	public Project getProjectById(int id) throws ServiceException {
		try {
			return dao.getProjectById(id);
		} catch (DaoException e) {
			throw new ServiceException(e);
		}
	}

	@Override
	@Transactional(readOnly=true)
	public List<Sample> getSamplesByProject(Project project)
			throws ServiceException {
		try {
			return dao.getSamplesByProject(project);
		} catch (DaoException e) {
			throw new ServiceException(e);
		}
	}
	
	@Override
	@Transactional(readOnly=true)
	public Sample getSampleById(int id) {
		try {
			return dao.getSampleById(id);
		} catch (DaoException e) {
			throw new ServiceException(e);
		}
	}

	@Override
	public void addInvestigators(List<Investigator> investigators)
			throws ServiceException {
		try {
			dao.addInvestigators(investigators);
		} catch (DaoException e) {
			throw new ServiceException(e);
		}
	}

	@Override
	public void addProjects(List<Project> projects) throws ServiceException {
		try {
			dao.addProjects(projects);
		} catch (DaoException e) {
			throw new ServiceException(e);
		}
	}

	@Override
	public void addSamples(List<Sample> samples) throws ServiceException {
		try {
			dao.addSamples(samples);
		} catch (DaoException e) {
			throw new ServiceException(e);
		}
	}

	@Override
	public void updateInvestigator(Investigator investigator)
			throws ServiceException {
		try {
			dao.updateInvestigator(investigator);
		} catch (DaoException e) {
			throw new ServiceException(e);
		}
	}

	@Override
	public void updateProject(Project project) throws ServiceException {
		try {
			dao.updateProject(project);
		} catch (DaoException e) {
			throw new ServiceException(e);
		}
	}

	@Override
	public void updateSample(Sample sample) throws ServiceException {
		try {
			dao.updateSample(sample);
		} catch (DaoException e) {
			throw new ServiceException(e);
		}
	}
	
	

}