StudyDAO.java

package net.sourceforge.seqware.common.dao;

import io.seqware.common.model.WorkflowRunStatus;
import java.util.List;
import net.sourceforge.seqware.common.model.File;
import net.sourceforge.seqware.common.model.Registration;
import net.sourceforge.seqware.common.model.Study;

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

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

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

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

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

    /**
     * <p>
     * delete.
     * </p>
     * 
     * @param study
     *            a {@link net.sourceforge.seqware.common.model.Study} object.
     */
    public void delete(Study study);

    /**
     * <p>
     * merge.
     * </p>
     * 
     * @param study
     *            a {@link net.sourceforge.seqware.common.model.Study} object.
     */
    void merge(Study study);

    /**
     * <p>
     * list.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @param isAcs
     *            a {@link java.lang.Boolean} object.
     * @return a {@link java.util.List} object.
     */
    public List<Study> list(Registration registration, Boolean isAcs);

    /**
     * <p>
     * listMyShared.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @param isAcs
     *            a {@link java.lang.Boolean} object.
     * @return a {@link java.util.List} object.
     */
    public List<Study> listMyShared(Registration registration, Boolean isAcs);

    /**
     * <p>
     * listSharedWithMe.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @param isAcs
     *            a {@link java.lang.Boolean} object.
     * @return a {@link java.util.List} object.
     */
    public List<Study> listSharedWithMe(Registration registration, Boolean isAcs);

    /**
     * <p>
     * findByTitle.
     * </p>
     * 
     * @param title
     *            a {@link java.lang.String} object.
     * @return a {@link net.sourceforge.seqware.common.model.Study} object.
     */
    public List<Study> findByTitle(String title);

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

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

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

    /**
     * <p>
     * getFiles.
     * </p>
     * 
     * @param studyId
     *            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 studyId, String metaType);

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

    /**
     * <p>
     * listStudyHasFile.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @param metaType
     *            a {@link java.lang.String} object.
     * @param iaAsc
     *            a {@link java.lang.Boolean} object.
     * @return a {@link java.util.List} object.
     */
    public List<Study> listStudyHasFile(Registration registration, String metaType, Boolean iaAsc);

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

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

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

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

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

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

    /**
     * <p>
     * updateOwners.
     * </p>
     * 
     * @param swAccession
     *            a {@link java.lang.Integer} object.
     */
    public void updateOwners(Integer swAccession);

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

    /**
     * <p>
     * Count the number of workflow runs with the given status, under the given study
     * </p>
     * 
     * @param study
     *            the study
     * @param status
     *            the status of the workflow runs to count
     * @return the count
     */
    public int getStatusCount(Study study, WorkflowRunStatus status);

}