SampleSetupController.java

package net.sourceforge.solexatools.webapp.controller;

import java.util.HashMap;

import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import javax.servlet.http.HttpSession;

import net.sourceforge.seqware.common.business.ExperimentService;
import net.sourceforge.seqware.common.business.LaneService;
import net.sourceforge.seqware.common.business.OrganismService;
import net.sourceforge.seqware.common.business.SampleService;
import net.sourceforge.seqware.common.model.Registration;
import net.sourceforge.seqware.common.model.Sample;
import net.sourceforge.solexatools.Security;

import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.BaseCommandController;

/**
 * RegistrationSetupController
 * 
 * @author boconnor
 * @version $Id: $Id
 */
public class SampleSetupController extends BaseCommandController {

    private ExperimentService experimentService;
    private SampleService sampleService;
    private LaneService laneService;
    private OrganismService organismService;

    /**
     * <p>
     * Constructor for SampleSetupController.
     * </p>
     */
    public SampleSetupController() {
        super();
        setSupportedMethods(new String[] { METHOD_GET });
    }

    /**
     * {@inheritDoc}
     * 
     * @return
     * @throws java.lang.Exception
     */
    @Override
    protected ModelAndView handleRequestInternal(HttpServletRequest request, HttpServletResponse response) throws Exception {

        Registration registration = Security.getRegistration(request);
        if (registration == null) return new ModelAndView("redirect:/login.htm");

        ModelAndView modelAndView = null;
        HashMap<String, Object> model = new HashMap<>();
        Sample sample = getRequestedSample(request);
        boolean isReport = request.getParameter("report") != null;

        model.put("organismList", getOrganismService().list(registration));

        if (sample != null) {
            request.setAttribute(getCommandName(), sample);
            request.setAttribute("experimentId", sample.getExperiment() != null ? sample.getExperiment().getExperimentId() : "");
            request.setAttribute("swid", sample.getSwAccession());
            model.put("strategy", "update");
            sample.setOrganismId(sample.getOrganism() != null ? sample.getOrganism().getOrganismId() : null);
            if (!isReport) {
                modelAndView = new ModelAndView("Sample", model);
            } else {
                modelAndView = new ModelAndView("SampleReport", model);
            }
        } else {
            sample = new Sample();
            sample.setOwner(registration);

            // Integer experimentId = Integer.parseInt(request.getParameter("experimentId"));
            // sample.setExperiment(getExperimentService().findByID(experimentId));

            Integer experimentId = getRequestedExperimentId(request);
            if (experimentId != null) {
                sample.setExperiment(getExperimentService().findByID(experimentId));
                request.setAttribute("experimentId", experimentId);
            } else {
                Integer parentSampleId = getRequestedParentId(request);
                request.setAttribute("parentSampleId", parentSampleId);
            }

            request.setAttribute(getCommandName(), sample);

            model.put("strategy", "submit");
            modelAndView = new ModelAndView("Sample", model);
        }

        String typeTree = request.getParameter("tt");
        request.getSession(false).setAttribute("typeTree", typeTree);
        /*
         * String laneId = request.getParameter("laneId");
         * 
         * Log.info("TYPE TREE Sample Setup = " + typeTree); Log.info("Lane ID = " + laneId);
         * 
         * if(typeTree!= null && typeTree.equals("st")){ Log.info("In Study"); SetNodeIdInSession.setSampleForStudy(sample, request); }else
         * if(typeTree!= null && typeTree.equals("sr")){ if(laneId != null && !laneId.equals("")){ Log.info("In SR"); Integer sequencerId =
         * getLaneService().findByID(Integer.parseInt(laneId)).getSequencerRun().getSequencerRunId();
         * SetNodeIdInSession.setSequencerRun(sequencerId, request); } }else if(typeTree!= null && typeTree.equals("wfr")){
         * Log.info("In wfr"); SetNodeIdInSession.setWorkflowRunWithSample(request); }else if(typeTree!= null && typeTree.equals("wfrr")){
         * Log.info("In wfrr"); SetNodeIdInSession.setWorkflowRunRunningWithSample(request); }else{ Log.info("By DEFAULT");
         * SetNodeIdInSession.setExperiment(sample.getExperiment(), request); }
         */
        return modelAndView;
    }

    private Integer getRequestedExperimentId(HttpServletRequest request) {
        Integer expID = null;
        String strId = (String) request.getParameter("experimentId");
        if (strId != null && !strId.isEmpty()) {
            expID = Integer.parseInt(strId);
        }
        return expID;
    }

    private Integer getRequestedParentId(HttpServletRequest request) {
        Integer parentID = null;
        String strId = (String) request.getParameter("parentSampleId");
        if (strId != null && !strId.isEmpty()) {
            parentID = Integer.parseInt(strId);
        }
        return parentID;
    }

    private Sample getRequestedSample(HttpServletRequest request) {
        HttpSession session = request.getSession(false);
        Sample sample = null;
        String id = (String) request.getParameter("sampleId");
        session.removeAttribute("sample");
        if (id != null) {
            Integer sampleID = Integer.parseInt(id);
            sample = getSampleService().findByID(sampleID);
            session.setAttribute("sample", sample);
        }
        return sample;
    }

    /**
     * <p>
     * Getter for the field <code>organismService</code>.
     * </p>
     * 
     * @return a {@link net.sourceforge.seqware.common.business.OrganismService} object.
     */
    public OrganismService getOrganismService() {
        return organismService;
    }

    /**
     * <p>
     * Setter for the field <code>organismService</code>.
     * </p>
     * 
     * @param organismService
     *            a {@link net.sourceforge.seqware.common.business.OrganismService} object.
     */
    public void setOrganismService(OrganismService organismService) {
        this.organismService = organismService;
    }

    /**
     * <p>
     * Getter for the field <code>sampleService</code>.
     * </p>
     * 
     * @return a {@link net.sourceforge.seqware.common.business.SampleService} object.
     */
    public SampleService getSampleService() {
        return sampleService;
    }

    /**
     * <p>
     * Setter for the field <code>sampleService</code>.
     * </p>
     * 
     * @param sampleService
     *            a {@link net.sourceforge.seqware.common.business.SampleService} object.
     */
    public void setSampleService(SampleService sampleService) {
        this.sampleService = sampleService;
    }

    /**
     * <p>
     * Getter for the field <code>experimentService</code>.
     * </p>
     * 
     * @return a {@link net.sourceforge.seqware.common.business.ExperimentService} object.
     */
    public ExperimentService getExperimentService() {
        return experimentService;
    }

    /**
     * <p>
     * Setter for the field <code>experimentService</code>.
     * </p>
     * 
     * @param experimentService
     *            a {@link net.sourceforge.seqware.common.business.ExperimentService} object.
     */
    public void setExperimentService(ExperimentService experimentService) {
        this.experimentService = experimentService;
    }

    /**
     * <p>
     * Getter for the field <code>laneService</code>.
     * </p>
     * 
     * @return a {@link net.sourceforge.seqware.common.business.LaneService} object.
     */
    public LaneService getLaneService() {
        return laneService;
    }

    /**
     * <p>
     * Setter for the field <code>laneService</code>.
     * </p>
     * 
     * @param laneService
     *            a {@link net.sourceforge.seqware.common.business.LaneService} object.
     */
    public void setLaneService(LaneService laneService) {
        this.laneService = laneService;
    }
}