UploadSequenceSetupController.java

package net.sourceforge.solexatools.webapp.controller;

import java.util.HashMap;
import java.util.List;
import java.util.Map;

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

import net.sourceforge.seqware.common.business.FileTypeService;
import net.sourceforge.seqware.common.business.SampleService;
import net.sourceforge.seqware.common.model.FileType;
import net.sourceforge.seqware.common.model.Registration;
import net.sourceforge.seqware.common.model.Sample;
import net.sourceforge.seqware.common.model.UploadSequence;
import net.sourceforge.solexatools.Security;

import org.springframework.validation.BindException;
import org.springframework.validation.BindingResult;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.BaseCommandController;

/**
 * <p>
 * UploadSequenceSetupController class.
 * </p>
 * 
 * @author boconnor
 * @version $Id: $Id
 */
public class UploadSequenceSetupController extends BaseCommandController {
    private SampleService sampleService;
    private FileTypeService fileTypeService;

    /**
     * <p>
     * Constructor for UploadSequenceSetupController.
     * </p>
     */
    public UploadSequenceSetupController() {
        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);

        UploadSequence uploadSequence = new UploadSequence();
        // model.put("organismList", getOrganismService().list(registration));

        List<Sample> listSample = getSampleService().listSample(registration);

        List<FileType> listFileType = getFileTypeService().list();
        model.put("listFileType", listFileType);

        // if operation Upload cant be launch
        if (sample == null && listSample.isEmpty()) {
            BindingResult errors = new BindException(uploadSequence, getCommandName());
            errors.reject("upload.required.sample");
            Map errorModel = errors.getModel();
            errorModel.put("strategy", "any_node");
            errorModel.put("sampleList", listSample);
            modelAndView = new ModelAndView("UploadSequence", errorModel);
        } else {
            if (sample != null) {
                model.put("strategy", "defined_node");
                uploadSequence.setSample(sample);
                model.put("sample", sample);
                // listSample = setEndElement(sample, listSample);
            } else {
                model.put("strategy", "any_node");
                // get list sample for view on the web page
                model.put("sampleList", listSample);
            }
            request.setAttribute(getCommandName(), uploadSequence);
            modelAndView = new ModelAndView("UploadSequence", model);
        }
        String typeTree = request.getParameter("tt");
        request.getSession(false).setAttribute("typeTree", typeTree);
        /*
         * if (sample != null) { request.setAttribute(getCommandName(), sample); model.put("strategy", "update");
         * sample.setOrganismId(sample.getOrganism().getOrganismId()); modelAndView = new ModelAndView("Sample", model); } else { sample =
         * new Sample(); sample.setOwner(registration);
         * sample.setExperiment(getExperimentService().findByID(Integer.parseInt(request.getParameter("experimentId"))));
         * request.setAttribute(getCommandName(), sample); model.put("strategy", "submit"); modelAndView = new ModelAndView("Sample",
         * model); }
         */

        /*
         * String typeTree = request.getParameter("tt"); request.getSession(false).setAttribute("typeTree", typeTree);
         * Log.info("TYPE TREE SETUP UPLOAD = " + typeTree); if(typeTree!= null){ if(typeTree.equals("st")){ if(sample != null){
         * SetNodeIdInSession.setExperiment(sample.getExperiment(), request); } } if(typeTree.equals("wfr")){
         * SetNodeIdInSession.setWorkflowRunWithSample(request); } if(typeTree.equals("wfrr")){
         * SetNodeIdInSession.setWorkflowRunRunningWithSample(request); } }
         */
        return modelAndView;
    }

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

    /**
     * <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>fileTypeService</code>.
     * </p>
     * 
     * @return a {@link net.sourceforge.seqware.common.business.FileTypeService} object.
     */
    public FileTypeService getFileTypeService() {
        return fileTypeService;
    }

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