FileReportDAOHibernate.java

package net.sourceforge.seqware.common.dao.hibernate;

import java.math.BigInteger;
import java.util.ArrayList;
import java.util.List;
import net.sourceforge.seqware.common.dao.FileReportDAO;
import net.sourceforge.seqware.common.model.FileReportRow;
import net.sourceforge.seqware.common.model.SequencerRun;
import net.sourceforge.seqware.common.model.Study;
import org.springframework.orm.hibernate3.support.HibernateDaoSupport;

/**
 * <p>
 * FileReportDAOHibernate class.
 * </p>
 * 
 * @author boconnor
 * @version $Id: $Id
 */
public class FileReportDAOHibernate extends HibernateDaoSupport implements FileReportDAO {

    /** {@inheritDoc} */
    @SuppressWarnings("rawtypes")
    @Override
    public List<FileReportRow> getReportForStudy(Study study) {
        String query = "from FileReportRow as row where row.study.studyId = ?";
        List<FileReportRow> fileReport = new ArrayList<>();
        Object[] parameters = { study.getStudyId() };
        List list = this.getHibernateTemplate().find(query, parameters);
        for (Object obj : list) {
            fileReport.add((FileReportRow) obj);
        }
        return fileReport;
    }

    /** {@inheritDoc} */
    @SuppressWarnings("rawtypes")
    @Override
    public List<FileReportRow> getReportForStudy(Study study, String orderField, String sortOrder, int offset, int limit) {
        String query = "from FileReportRow as row where row.study.studyId = ? order by row." + orderField + " " + sortOrder;
        List<FileReportRow> fileReport = new ArrayList<>();
        List list = this.getSession().createQuery(query).setFirstResult(offset).setMaxResults(limit).setInteger(0, study.getStudyId())
                .list();
        for (Object obj : list) {
            fileReport.add((FileReportRow) obj);
        }
        return fileReport;
    }

    /** {@inheritDoc} */
    @SuppressWarnings("rawtypes")
    @Override
    public List<FileReportRow> getReportForSequencerRun(SequencerRun seqRun, String orderField, String sortOrder, int offset, int limit) {
        String query = "from FileReportRow as row where row.lane.sequencerRun.sequencerRunId = ? order by row." + orderField + " "
                + sortOrder;
        List<FileReportRow> fileReport = new ArrayList<>();
        List list = this.getSession().createQuery(query).setFirstResult(offset).setMaxResults(limit)
                .setInteger(0, seqRun.getSequencerRunId()).list();
        for (Object obj : list) {
            fileReport.add((FileReportRow) obj);
        }
        return fileReport;
    }

    /** {@inheritDoc} */
    @SuppressWarnings("rawtypes")
    @Override
    public List<FileReportRow> getReportForSequencerRuns(String orderField, String sortOrder, int offset, int limit) {
        String query = "from FileReportRow as row where row.lane.sequencerRun.sequencerRunId != null order by row." + orderField + " "
                + sortOrder;
        List<FileReportRow> fileReport = new ArrayList<>();
        List list = this.getSession().createQuery(query).setFirstResult(offset).setMaxResults(limit).list();
        for (Object obj : list) {
            fileReport.add((FileReportRow) obj);
        }
        return fileReport;
    }

    /** {@inheritDoc} */
    @SuppressWarnings("rawtypes")
    @Override
    public List<FileReportRow> getReportForSequencerRun(SequencerRun seqRun) {
        if (seqRun == null) {
            String query = "from FileReportRow as row where row.lane.sequencerRun.sequencerRunId != null ";
            List<FileReportRow> fileReport = new ArrayList<>();
            List list = this.getSession().createQuery(query).list();
            for (Object obj : list) {
                fileReport.add((FileReportRow) obj);
            }
            return fileReport;
        } else {
            String query = "from FileReportRow as row where row.lane.sequencerRun.sequencerRunId = ? ";
            List<FileReportRow> fileReport = new ArrayList<>();
            List list = this.getSession().createQuery(query).setInteger(0, seqRun.getSequencerRunId()).list();
            for (Object obj : list) {
                fileReport.add((FileReportRow) obj);
            }
            return fileReport;
        }
    }

    /** {@inheritDoc} */
    @SuppressWarnings("rawtypes")
    @Override
    public int countOfRows(Study study) {
        String query = "select count(*) from file_report where study_id = ?";
        List result = this.getSession().createSQLQuery(query).setInteger(0, study.getStudyId()).list();
        int count = 0;
        if (result.size() > 0) {
            count = ((BigInteger) result.get(0)).intValue();
        }
        return count;
    }

    /** {@inheritDoc} */
    @SuppressWarnings("rawtypes")
    @Override
    public int countOfRows(SequencerRun sr) {
        String query = null;
        List result = null;
        if (sr != null) {
            query = "select count(*) from file_report as fr cross join lane as la "
                    + "where fr.lane_id=la.lane_id and (la.sequencer_run_id = ?)";
            result = this.getSession().createSQLQuery(query).setInteger(0, sr.getSequencerRunId()).list();
        } else {
            query = "select count(*) from file_report as fr cross join lane as la "
                    + "where fr.lane_id=la.lane_id and (la.sequencer_run_id is not null)";
            result = this.getSession().createSQLQuery(query).list();

        }
        int count = 0;
        if (result.size() > 0) {
            count = ((BigInteger) result.get(0)).intValue();
        }
        return count;
    }

}