ProcessingService.java

package net.sourceforge.seqware.common.business;

import java.util.List;
import java.util.Set;
import net.sourceforge.seqware.common.dao.ProcessingDAO;
import net.sourceforge.seqware.common.model.File;
import net.sourceforge.seqware.common.model.Processing;
import net.sourceforge.seqware.common.model.Registration;
import net.sourceforge.seqware.common.model.Sample;
import net.sourceforge.seqware.common.model.SequencerRun;
import net.sourceforge.seqware.common.model.WorkflowRun;

/**
 * <p>
 * ProcessingService interface.
 * </p>
 * 
 * @author boconnor
 * @version $Id: $Id
 */
public interface ProcessingService {

    /** Constant <code>NAME="processingService"</code> */
    public static final String NAME = "processingService";

    /**
     * <p>
     * setProcessingDAO.
     * </p>
     * 
     * @param processingDAO
     *            a {@link net.sourceforge.seqware.common.dao.ProcessingDAO} object.
     */
    public void setProcessingDAO(ProcessingDAO processingDAO);

    // public void insert(Processing processing);
    /**
     * <p>
     * insert.
     * </p>
     * 
     * @param sequencerRun
     *            a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     * @param processing
     *            a {@link net.sourceforge.seqware.common.model.Processing} object.
     */
    public void insert(SequencerRun sequencerRun, Processing processing);

    /**
     * <p>
     * insert.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @param sequencerRun
     *            a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     * @param processing
     *            a {@link net.sourceforge.seqware.common.model.Processing} object.
     */
    public void insert(Registration registration, SequencerRun sequencerRun, Processing processing);

    /**
     * Inserts a new Processing and returns its sw_accession number.
     * 
     * @param processing
     *            Processing to be inserted.
     * @return The SeqWare Accession number for the newly inserted Processing.
     */
    public Integer insert(Processing processing);

    /**
     * <p>
     * insert.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @param processing
     *            a {@link net.sourceforge.seqware.common.model.Processing} object.
     * @return a {@link java.lang.Integer} object.
     */
    public Integer insert(Registration registration, Processing processing);

    /**
     * <p>
     * update.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @param processing
     *            a {@link net.sourceforge.seqware.common.model.Processing} object.
     */
    public void update(Registration registration, Processing processing);

    /**
     * <p>
     * update.
     * </p>
     * 
     * @param processing
     *            a {@link net.sourceforge.seqware.common.model.Processing} object.
     */
    public void update(Processing processing);

    /**
     * <p>
     * delete.
     * </p>
     * 
     * @param processing
     * @param deleteRealFiles
     */
    public void delete(Processing processing, boolean deleteRealFiles);

    // public List<Processing> list();
    // public Processing findByExperiment(Integer expID);
    /**
     * <p>
     * findByID.
     * </p>
     * 
     * @param processingID
     *            a {@link java.lang.Integer} object.
     * @return a {@link net.sourceforge.seqware.common.model.Processing} object.
     */
    public Processing findByID(Integer processingID);

    /**
     * <p>
     * findByIDOnlyWithRunningWR.
     * </p>
     * 
     * @param processingID
     *            a {@link java.lang.Integer} object.
     * @return a {@link net.sourceforge.seqware.common.model.Processing} object.
     */
    public Processing findByIDOnlyWithRunningWR(Integer processingID);

    /**
     * <p>
     * findBySWAccession.
     * </p>
     * 
     * @param swAccession
     *            a {@link java.lang.Integer} object.
     * @return a {@link net.sourceforge.seqware.common.model.Processing} object.
     */
    public Processing findBySWAccession(Integer swAccession);

    /**
     * <p>
     * getFiles.
     * </p>
     * 
     * @param processingId
     *            a {@link java.lang.Integer} object.
     * @return a {@link java.util.List} object.
     */
    public List<File> getFiles(Integer processingId);

    /**
     * <p>
     * getFiles.
     * </p>
     * 
     * @param processingId
     *            a {@link java.lang.Integer} object.
     * @param metaType
     *            a {@link java.lang.String} object.
     * @return a {@link java.util.List} object.
     */
    public List<File> getFiles(Integer processingId, String metaType);

    /**
     * <p>
     * isHasFile.
     * </p>
     * 
     * @param processingId
     *            a {@link java.lang.Integer} object.
     * @return a boolean.
     */
    public boolean isHasFile(Integer processingId);

    /**
     * <p>
     * setWithHasFile.
     * </p>
     * 
     * @param list
     *            a {@link java.util.Set} object.
     * @return a {@link java.util.Set} object.
     */
    public Set<Processing> setWithHasFile(Set<Processing> list);

    /**
     * <p>
     * setWithHasFile.
     * </p>
     * 
     * @param list
     *            a {@link java.util.Set} object.
     * @param metaType
     *            a {@link java.lang.String} object.
     * @return a {@link java.util.Set} object.
     */
    public Set<Processing> setWithHasFile(Set<Processing> list, String metaType);

    /**
     * <p>
     * updateDetached.
     * </p>
     * 
     * @param processing
     *            a {@link net.sourceforge.seqware.common.model.Processing} object.
     * @return a {@link net.sourceforge.seqware.common.model.Processing} object.
     */
    public Processing updateDetached(Processing processing);

    /**
     * <p>
     * updateDetached.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @param processing
     *            a {@link net.sourceforge.seqware.common.model.Processing} object.
     * @return a {@link net.sourceforge.seqware.common.model.Processing} object.
     */
    public Processing updateDetached(Registration registration, Processing processing);

    /**
     * <p>
     * findByOwnerID.
     * </p>
     * 
     * @param registrationId
     *            a {@link java.lang.Integer} object.
     * @return a {@link java.util.List} object.
     */
    public List<Processing> findByOwnerID(Integer registrationId);

    /**
     * <p>
     * findByCriteria.
     * </p>
     * 
     * @param criteria
     *            a {@link java.lang.String} object.
     * @param isCaseSens
     *            a boolean.
     * @return a {@link java.util.List} object.
     */
    public List<Processing> findByCriteria(String criteria, boolean isCaseSens);

    /**
     * <p>
     * findFor.
     * </p>
     * 
     * @param sample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     * @param workflowRun
     *            a {@link net.sourceforge.seqware.common.model.WorkflowRun} object.
     * @return a {@link java.util.Set} object.
     */
    public Set<Processing> findFor(Sample sample, WorkflowRun workflowRun);

    /**
     * <p>
     * findFor.
     * </p>
     * 
     * @param sample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     * @return a {@link java.util.Set} object.
     */
    public Set<Processing> findFor(Sample sample);

    /**
     * <p>
     * list.
     * </p>
     * 
     * @return a {@link java.util.List} object.
     */
    public List<Processing> list();

}

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