ExperimentSetupController.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.LibrarySelectionService;
import net.sourceforge.seqware.common.business.LibrarySourceService;
import net.sourceforge.seqware.common.business.LibraryStrategyService;
import net.sourceforge.seqware.common.business.PlatformService;
import net.sourceforge.seqware.common.business.StudyService;
import net.sourceforge.seqware.common.model.Experiment;
import net.sourceforge.seqware.common.model.Registration;
import net.sourceforge.solexatools.Security;
import net.sourceforge.solexatools.util.SetNodeIdInSession;

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

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

    private StudyService studyService;
    private ExperimentService experimentService;
    private PlatformService platformService;
    private LibrarySelectionService librarySelectionService;
    private LibrarySourceService librarySourceService;
    private LibraryStrategyService libraryStrategyService;

    /**
     * <p>
     * Constructor for ExperimentSetupController.
     * </p>
     */
    public ExperimentSetupController() {
        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<>();
        Experiment experiment = getRequestedExperiment(request);
        boolean isReport = request.getParameter("report") != null;

        model.put("platformList", getPlatformService().list(registration));
        model.put("expLibDesignSelectionList", getLibrarySelectionService().list(registration));
        model.put("expLibDesignSourceList", getLibrarySourceService().list(registration));
        model.put("expLibDesignStrategyList", getLibraryStrategyService().list(registration));
        if (experiment != null) {

            request.setAttribute(getCommandName(), experiment);
            request.setAttribute("studyId", experiment.getStudy().getStudyId());
            request.setAttribute("swid", experiment.getSwAccession());
            model.put("strategy", "update");

            // now fill in some variables that will setup the pulldowns
            // these are all non-persisted fields in the experiment object
            /*
             * model.put("platformId", experiment.getPlatform().getPlatformId()); model.put("expLibDesignSelectionId",
             * experiment.getExpLibDesignSelection()); model.put("expLibDesignSourceId", experiment.getExpLibDesignSource());
             * model.put("expLibDesignStrategyId", experiment.getExpLibDesignStrategy());
             */
            experiment.setPlatformInt(experiment.getPlatform().getPlatformId());
            experiment.setExpLibDesignName(experiment.getExperimentLibraryDesign().getName());
            experiment.setExpLibDesignDesc(experiment.getExperimentLibraryDesign().getDescription());
            experiment.setExpLibDesignProtocol(experiment.getExperimentLibraryDesign().getConstructionProtocol());
            experiment.setExpLibDesignStrategy(experiment.getExperimentLibraryDesign().getStrategy().getLibraryStrategyId());
            experiment.setExpLibDesignSource(experiment.getExperimentLibraryDesign().getSource().getLibrarySourceId());
            experiment.setExpLibDesignSelection(experiment.getExperimentLibraryDesign().getSelection().getLibrarySelectionId());
            experiment.setSpotDesignReadSpec(experiment.getExperimentSpotDesign().getReadSpec());

        } else {
            experiment = new Experiment();
            experiment.setOwner(registration);
            Integer studyId = Integer.parseInt(request.getParameter("studyId"));
            experiment.setStudy(getStudyService().findByID(studyId));
            request.setAttribute(getCommandName(), experiment);
            request.setAttribute("studyId", studyId);
            model.put("strategy", "submit");
        }
        if (!isReport) {
            modelAndView = new ModelAndView("Experiment", model);
        } else {
            modelAndView = new ModelAndView("ExperimentReport", model);
        }

        // add study id
        setOpenNode(request);

        return modelAndView;
    }

    private void setOpenNode(HttpServletRequest request) {
        String studyId = request.getParameter("studyId");
        if (studyId != null) {
            SetNodeIdInSession.setStudy(Integer.parseInt(studyId), request);
        }
    }

    private Experiment getRequestedExperiment(HttpServletRequest request) {
        HttpSession session = request.getSession(false);
        Experiment experiment = null;
        String id = (String) request.getParameter("experimentId");
        session.removeAttribute("experiment");

        if (id != null) {
            Integer expID = Integer.parseInt(id);
            experiment = getExperimentService().findByID(expID);
            session.setAttribute("experiment", experiment);
        }

        return experiment;
    }

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

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

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

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

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

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

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

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

    /**
     * <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>studyService</code>.
     * </p>
     * 
     * @return a {@link net.sourceforge.seqware.common.business.StudyService} object.
     */
    public StudyService getStudyService() {
        return studyService;
    }

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

}