SampleReportDAO.java

package net.sourceforge.seqware.common.dao;

import java.util.List;
import net.sourceforge.seqware.common.business.SampleReportService.Status;
import net.sourceforge.seqware.common.model.IUS;
import net.sourceforge.seqware.common.model.Lane;
import net.sourceforge.seqware.common.model.Sample;
import net.sourceforge.seqware.common.model.SampleReportRow;
import net.sourceforge.seqware.common.model.SequencerRun;
import net.sourceforge.seqware.common.model.SequencerRunReportId;
import net.sourceforge.seqware.common.model.Study;
import net.sourceforge.seqware.common.model.Workflow;

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

    /**
     * <p>
     * getStatusesForStudy.
     * </p>
     * 
     * @param study
     *            a {@link net.sourceforge.seqware.common.model.Study} object.
     * @return a {@link java.util.List} object.
     */
    List<Status> getStatusesForStudy(Study study);

    /**
     * <p>
     * getWorkflowsForStudy.
     * </p>
     * 
     * @param study
     *            a {@link net.sourceforge.seqware.common.model.Study} object.
     * @return a {@link java.util.List} object.
     */
    List<Workflow> getWorkflowsForStudy(Study study);

    /**
     * <p>
     * countOfStatus.
     * </p>
     * 
     * @param study
     *            a {@link net.sourceforge.seqware.common.model.Study} object.
     * @param status
     *            a {@link java.lang.String} object.
     * @return a int.
     */
    int countOfStatus(Study study, Status status);

    /**
     * <p>
     * countOfStatus.
     * </p>
     * 
     * @param seqRun
     *            a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     * @param status
     *            a {@link java.lang.String} object.
     * @return a int.
     */
    int countOfStatus(SequencerRun seqRun, Status status);

    /**
     * <p>
     * getChildSamples.
     * </p>
     * 
     * @param study
     *            a {@link net.sourceforge.seqware.common.model.Study} object.
     * @return a {@link java.util.List} object.
     */
    List<Sample> getChildSamples(Study study);

    /**
     * <p>
     * getStatus.
     * </p>
     * 
     * @param study
     *            a {@link net.sourceforge.seqware.common.model.Study} object.
     * @param childSample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     * @param workflow
     *            a {@link net.sourceforge.seqware.common.model.Workflow} object.
     * @return a {@link java.lang.String} object.
     */
    Status getStatus(Study study, Sample childSample, Workflow workflow);

    /**
     * <p>
     * getStatus.
     * </p>
     * 
     * @param study
     *            a {@link net.sourceforge.seqware.common.model.Study} object.
     * @param sample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     * @param ius
     *            a {@link net.sourceforge.seqware.common.model.IUS} object.
     * @param lane
     *            a {@link net.sourceforge.seqware.common.model.Lane} object.
     * @param seqRun
     *            a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     * @param workflow
     *            a {@link net.sourceforge.seqware.common.model.Workflow} object.
     * @return a {@link java.lang.String} object.
     */
    Status getStatus(Study study, Sample sample, IUS ius, Lane lane, SequencerRun seqRun, Workflow workflow);

    /**
     * <p>
     * countOfStatus.
     * </p>
     * 
     * @param study
     *            a {@link net.sourceforge.seqware.common.model.Study} object.
     * @param workflow
     *            a {@link net.sourceforge.seqware.common.model.Workflow} object.
     * @param status
     *            a {@link java.lang.String} object.
     * @return a int.
     */
    int countOfStatus(Study study, Workflow workflow, Status status);

    /**
     * <p>
     * getStatusesForWorkflow.
     * </p>
     * 
     * @param study
     *            a {@link net.sourceforge.seqware.common.model.Study} object.
     * @param workflow
     *            a {@link net.sourceforge.seqware.common.model.Workflow} object.
     * @return a {@link java.util.List} object.
     */
    List<Status> getStatusesForWorkflow(Study study, Workflow workflow);

    /**
     * <p>
     * getRowsForSequencerRun.
     * </p>
     * 
     * @param sr
     *            a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     * @return a {@link java.util.List} object.
     */
    List<SampleReportRow> getRowsForSequencerRun(SequencerRun sr);

    /**
     * <p>
     * getRowsWithSequencerRuns.
     * </p>
     * 
     * @return a {@link java.util.List} object.
     */
    List<SampleReportRow> getRowsWithSequencerRuns();

    /**
     * <p>
     * getStatusesForSequencerRun.
     * </p>
     * 
     * @param seqRun
     *            a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     * @return a {@link java.util.List} object.
     */
    List<Status> getStatusesForSequencerRun(SequencerRun seqRun);

    /**
     * <p>
     * getStatusesForWorkflow.
     * </p>
     * 
     * @param seqRun
     *            a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     * @param workflow
     *            a {@link net.sourceforge.seqware.common.model.Workflow} object.
     * @return a {@link java.util.List} object.
     */
    List<Status> getStatusesForWorkflow(SequencerRun seqRun, Workflow workflow);

    /**
     * <p>
     * countOfStatus.
     * </p>
     * 
     * @param seqRun
     *            a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     * @param workflow
     *            a {@link net.sourceforge.seqware.common.model.Workflow} object.
     * @param status
     *            a {@link java.lang.String} object.
     * @return a int.
     */
    int countOfStatus(SequencerRun seqRun, Workflow workflow, Status status);

    /**
     * <p>
     * getWorkflows.
     * </p>
     * 
     * @param seqRun
     *            a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     * @return a {@link java.util.List} object.
     */
    List<Workflow> getWorkflows(SequencerRun seqRun);

    /**
     * <p>
     * getSequencerRunReportIds.
     * </p>
     * 
     * @param seqRun
     *            a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     * @param sortField
     *            a {@link java.lang.String} object.
     * @param sortOrder
     *            a {@link java.lang.String} object.
     * @param offset
     *            a int.
     * @param limit
     *            a int.
     * @return a {@link java.util.List} object.
     */
    List<SequencerRunReportId> getSequencerRunReportIds(SequencerRun seqRun, String sortField, String sortOrder, int offset, int limit);

    /**
     * <p>
     * countOfRows.
     * </p>
     * 
     * @param seqRun
     *            a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     * @return a int.
     */
    int countOfRows(SequencerRun seqRun);

    /**
     * <p>
     * getSequencerRunReportIds.
     * </p>
     * 
     * @param seqRun
     *            a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     * @return a {@link java.util.List} object.
     */
    List<SequencerRunReportId> getSequencerRunReportIds(SequencerRun seqRun);
}