WorkflowRunService.java

package net.sourceforge.seqware.common.business;

import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
import net.sourceforge.seqware.common.dao.WorkflowRunDAO;
import net.sourceforge.seqware.common.model.File;
import net.sourceforge.seqware.common.model.IUS;
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.Workflow;
import net.sourceforge.seqware.common.model.WorkflowRun;
import net.sourceforge.seqware.common.model.WorkflowRunParam;

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

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

    /**
     * <p>
     * setWorkflowRunDAO.
     * </p>
     * 
     * @param workflowRunDAO
     *            a {@link net.sourceforge.seqware.common.dao.WorkflowRunDAO} object.
     */
    public void setWorkflowRunDAO(WorkflowRunDAO workflowRunDAO);

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

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

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

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

    /**
     * <p>
     * insert.
     * </p>
     * 
     * @param workflowRun
     *            a {@link net.sourceforge.seqware.common.model.WorkflowRun} object.
     * @param workflowRunParams
     *            a {@link java.util.SortedSet} object.
     * @param allSelectedFiles
     *            a {@link java.util.Map} object.
     * @return a {@link java.lang.Integer} object.
     */
    public Integer insert(WorkflowRun workflowRun, SortedSet<WorkflowRunParam> workflowRunParams, Map<String, List<File>> allSelectedFiles);

    /**
     * <p>
     * insert.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @param workflowRun
     *            a {@link net.sourceforge.seqware.common.model.WorkflowRun} object.
     * @param workflowRunParams
     *            a {@link java.util.SortedSet} object.
     * @param allSelectedFiles
     *            a {@link java.util.Map} object.
     * @return a {@link java.lang.Integer} object.
     */
    public Integer insert(Registration registration, WorkflowRun workflowRun, SortedSet<WorkflowRunParam> workflowRunParams,
            Map<String, List<File>> allSelectedFiles);

    /**
     * <p>
     * update.
     * </p>
     * 
     * @param workflowRun
     *            a {@link net.sourceforge.seqware.common.model.WorkflowRun} object.
     * @param laneIds
     *            a {@link java.util.List} object.
     */
    public void update(WorkflowRun workflowRun, List<Integer> laneIds);

    /**
     * <p>
     * update.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @param workflowRun
     *            a {@link net.sourceforge.seqware.common.model.WorkflowRun} object.
     * @param laneIds
     *            a {@link java.util.List} object.
     */
    public void update(Registration registration, WorkflowRun workflowRun, List<Integer> laneIds);

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

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

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

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

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

    /**
     * <p>
     * listSharedWithMeWithSample.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @return a {@link java.util.List} object.
     */
    public List<WorkflowRun> listSharedWithMeWithSample(Registration registration);

    /**
     * <p>
     * listRunning.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @return a {@link java.util.List} object.
     */
    public List<WorkflowRun> listRunning(Registration registration);

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

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

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

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

    /**
     * <p>
     * findByName.
     * </p>
     * 
     * @param name
     *            a {@link java.lang.String} object.
     * @return a {@link net.sourceforge.seqware.common.model.WorkflowRun} object.
     */
    public WorkflowRun findByName(String name);

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

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

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

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

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

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

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

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

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

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

    /**
     * <p>
     * listRelatedWorkflows.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @return a {@link java.util.List} object.
     */
    public List<Workflow> listRelatedWorkflows(Registration registration);

    /**
     * <p>
     * findRunsForIUS.
     * </p>
     * 
     * @param ius
     *            a {@link net.sourceforge.seqware.common.model.IUS} object.
     * @return a {@link java.util.Set} object.
     */
    public Set<WorkflowRun> findRunsForIUS(IUS ius);

    /**
     * Find all the workflow runs for the specific sample. This function doesn't look into the nested samples.
     * 
     * @param sample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     * @return a {@link java.util.Set} object.
     */
    public Set<WorkflowRun> findRunsForSample(Sample sample);

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