StudyServiceImpl.java

package net.sourceforge.seqware.common.business.impl;

import io.seqware.common.model.WorkflowRunStatus;
import java.util.Date;
import java.util.LinkedList;
import java.util.List;
import net.sourceforge.seqware.common.business.StudyService;
import net.sourceforge.seqware.common.dao.FileDAO;
import net.sourceforge.seqware.common.dao.StudyDAO;
import net.sourceforge.seqware.common.dao.StudyTypeDAO;
import net.sourceforge.seqware.common.model.File;
import net.sourceforge.seqware.common.model.Registration;
import net.sourceforge.seqware.common.model.Study;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

/**
 * <p>
 * StudyServiceImpl class.
 * </p>
 * 
 * @author boconnor
 * @version $Id: $Id
 */
public class StudyServiceImpl implements StudyService {

    private StudyDAO studyDAO = null;
    private StudyTypeDAO studyTypeDAO = null;
    private FileDAO fileDAO = null;
    private static final Log LOG = LogFactory.getLog(StudyServiceImpl.class);

    /**
     * <p>
     * Constructor for StudyServiceImpl.
     * </p>
     */
    public StudyServiceImpl() {
        super();
    }

    /**
     * {@inheritDoc}
     * 
     * Sets a private member variable with an instance of an implementation of StudyDAO. This method is called by the Spring framework at
     * run time.
     * 
     * @see StudyDAO
     */
    @Override
    public void setStudyDAO(StudyDAO studyDAO) {
        this.studyDAO = studyDAO;
    }

    /**
     * Sets a private member variable with an instance of an implementation of FileDAO. This method is called by the Spring framework at run
     * time.
     * 
     * @param fileDAO
     *            implementation of FileDAO
     * @see FileDAO
     */
    public void setFileDAO(FileDAO fileDAO) {
        this.fileDAO = fileDAO;
    }

    /**
     * {@inheritDoc}
     * 
     * Inserts an instance of Study into the database.
     */
    @Override
    public Integer insert(Study study) {

        study.setCreateTimestamp(new Date());

        return (studyDAO.insert(study));
    }

    /**
     * {@inheritDoc}
     * 
     * Updates an instance of Study in the database.
     */
    @Override
    public void update(Study study) {

        studyDAO.update(study);

    }

    /** {@inheritDoc} */
    @Override
    public void merge(Study study) {
        studyDAO.merge(study);
    }

    /**
     * {@inheritDoc}
     * 
     * Updates an instance of Study in the database.
     * 
     * @param study
     * @param deleteRealFiles
     */
    @Override
    public void delete(Study study, boolean deleteRealFiles) {
        List<File> deleteFiles = null;
        if (deleteRealFiles) {
            deleteFiles = studyDAO.getFiles(study.getStudyId());
            fileDAO.deleteAllWithFolderStore(deleteFiles);
        }

        studyDAO.delete(study);

    }

    /** {@inheritDoc} */
    @Override
    public List<File> getFiles(Integer studyId) {
        return studyDAO.getFiles(studyId);
    }

    /** {@inheritDoc} */
    @Override
    public boolean isHasFile(Integer studyId) {
        return studyDAO.isHasFile(studyId);
    }

    /** {@inheritDoc} */
    @Override
    public List<File> getFiles(Integer studyId, String metaType) {
        return studyDAO.getFiles(studyId, metaType);
    }

    /** {@inheritDoc} */
    @Override
    public boolean isHasFile(Integer studyId, String metaType) {
        return studyDAO.isHasFile(studyId, metaType);
    }

    /** {@inheritDoc} */
    @Override
    public List<Study> list(Registration registration) {
        return list(registration, true);
    }

    /** {@inheritDoc} */
    @Override
    public List<Study> list(Registration registration, Boolean isAcs) {
        return studyDAO.list(registration, isAcs);
    }

    /** {@inheritDoc} */
    @Override
    public List<Study> listMyShared(Registration registration, Boolean isAcs) {
        return studyDAO.listMyShared(registration, isAcs);
    }

    /** {@inheritDoc} */
    @Override
    public List<Study> listSharedWithMe(Registration registration) {
        return listSharedWithMe(registration, true);
    }

    /** {@inheritDoc} */
    @Override
    public List<Study> listSharedWithMe(Registration registration, Boolean isAcs) {
        return studyDAO.listSharedWithMe(registration, isAcs);
    }

    /**
     * {@inheritDoc}
     * 
     * Finds an instance of Study in the database by the Study emailAddress, and copies the Study properties to an instance of Study.
     */
    @Override
    public List<Study> findByTitle(String title) {
        List<Study> study = null;
        if (title != null) {
            try {
                study = studyDAO.findByTitle(title.trim());
            } catch (Exception exception) {
                LOG.debug("Cannot find Study by title " + title);
            }
        }
        return study;
    }

    /**
     * {@inheritDoc}
     * 
     * @param studyID
     */
    @Override
    public Study findByID(Integer studyID) {
        Study study = null;
        if (studyID != null) {
            try {
                study = studyDAO.findByID(studyID);
            } catch (Exception exception) {
                LOG.error("Cannot find Study by studyID " + studyID);
                LOG.error(exception.getMessage());
            }
        }
        return study;
    }

    /** {@inheritDoc} */
    @Override
    public Study findBySWAccession(Integer swAccession) {
        Study study = null;
        if (swAccession != null) {
            try {
                study = studyDAO.findBySWAccession(swAccession);
            } catch (Exception exception) {
                LOG.error("Cannot find Study by swAccession " + swAccession);
                LOG.error(exception.getMessage());
            }
        }
        return study;
    }

    /** {@inheritDoc} */
    @Override
    public List<Study> findByOwnerID(Integer registrationId) {
        List<Study> studies = null;
        if (registrationId != null) {
            try {
                studies = studyDAO.findByOwnerID(registrationId);
            } catch (Exception exception) {
                LOG.error("Cannot find Study by registrationId " + registrationId);
                LOG.error(exception.getMessage());
            }
        }
        return studies;
    }

    /** {@inheritDoc} */
    @Override
    public List<Study> findByCriteria(String criteria, boolean isCaseSens) {
        return studyDAO.findByCriteria(criteria, isCaseSens);
    }

    /** {@inheritDoc} */
    @Override
    public List<Study> findByCriteria(String criteria) {
        return studyDAO.findByCriteria(criteria);
    }

    /**
     * {@inheritDoc}
     * 
     * Determines if an study title has already been used.
     */
    @Override
    public boolean hasTitleBeenUsed(String oldTitle, String newTitle) {
        boolean titleUsed = false;
        boolean checkTitle = true;

        if (newTitle != null) {
            if (oldTitle != null) {
                /*
                 * We do not want to check if an title address has been used if the user is updating an existing sequencer run and has not
                 * changed the titleAddress.
                 */
                checkTitle = !newTitle.trim().equalsIgnoreCase(oldTitle.trim());
            }

            if (checkTitle) {
                List<Study> studies = this.findByTitle(newTitle.trim());
                if (studies != null) {
                    titleUsed = true;
                }
            }
        }
        return titleUsed;
    }

    /** {@inheritDoc} */
    @Override
    public List<Study> listWithHasFile(List<Study> list) {
        for (Study study : list) {
            study.setIsHasFile(isHasFile(study.getStudyId()));
        }
        return list;
    }

    /** {@inheritDoc} */
    @Override
    public List<Study> listWithHasFile(List<Study> list, String metaType) {
        List<Study> result = new LinkedList<>();
        for (Study study : list) {
            if (isHasFile(study.getStudyId(), metaType)) {
                study.setIsHasFile(true);
                result.add(study);
            }
        }
        return result;
    }

    /** {@inheritDoc} */
    @Override
    public List<Study> list() {
        return studyDAO.list();
    }

    /**
     * {@inheritDoc}
     * 
     * @param isAsc
     */
    @Override
    public List<Study> listStudyHasFile(Registration registration, String metaType, Boolean isAsc) {
        return studyDAO.listStudyHasFile(registration, metaType, isAsc);
    }

    /**
     * <p>
     * Getter for the field <code>studyTypeDAO</code>.
     * </p>
     * 
     * @return a {@link net.sourceforge.seqware.common.dao.StudyTypeDAO} object.
     */
    public StudyTypeDAO getStudyTypeDAO() {
        return studyTypeDAO;
    }

    /**
     * <p>
     * Setter for the field <code>studyTypeDAO</code>.
     * </p>
     * 
     * @param studyTypeDAO
     *            a {@link net.sourceforge.seqware.common.dao.StudyTypeDAO} object.
     */
    public void setStudyTypeDAO(StudyTypeDAO studyTypeDAO) {
        this.studyTypeDAO = studyTypeDAO;
    }

    /**
     * <p>
     * Getter for the field <code>studyDAO</code>.
     * </p>
     * 
     * @return a {@link net.sourceforge.seqware.common.dao.StudyDAO} object.
     */
    public StudyDAO getStudyDAO() {
        return studyDAO;
    }

    /** {@inheritDoc} */
    @Override
    public Study updateDetached(Study study) {
        return studyDAO.updateDetached(study);
    }

    /** {@inheritDoc} */
    @Override
    public void updateOwners(Integer swAccession) {
        studyDAO.updateOwners(swAccession);
    }

    /** {@inheritDoc} */
    @Override
    public void update(Registration registration, Study study) {
        studyDAO.update(registration, study);
    }

    /** {@inheritDoc} */
    @Override
    public Integer insert(Registration registration, Study study) {
        study.setCreateTimestamp(new Date());
        return (studyDAO.insert(registration, study));
    }

    /** {@inheritDoc} */
    @Override
    public Study updateDetached(Registration registration, Study study) {
        return studyDAO.updateDetached(registration, study);
    }

    /** {@inheritDoc} */
    @Override
    public int getRunningCount(Study study) {
        return studyDAO.getStatusCount(study, WorkflowRunStatus.running);
    }

    /** {@inheritDoc} */
    @Override
    public int getFinishedCount(Study study) {
        return studyDAO.getStatusCount(study, WorkflowRunStatus.completed);
    }

    /** {@inheritDoc} */
    @Override
    public int getFailedCount(Study study) {
        return studyDAO.getStatusCount(study, WorkflowRunStatus.failed);
    }
}

// ex:sw=4:ts=4: