DownloadFileListController.java

package net.sourceforge.solexatools.webapp.controller;

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;

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.FileService;
import net.sourceforge.seqware.common.business.LaneService;
import net.sourceforge.seqware.common.business.ProcessingService;
import net.sourceforge.seqware.common.business.SampleService;
import net.sourceforge.seqware.common.business.StudyService;
import net.sourceforge.seqware.common.business.WorkflowRunService;
import net.sourceforge.seqware.common.model.File;
import net.sourceforge.seqware.common.model.Processing;
import net.sourceforge.seqware.common.model.Registration;
import net.sourceforge.seqware.common.model.WorkflowRun;
import net.sourceforge.seqware.common.util.Log;
import net.sourceforge.solexatools.Security;
import net.sourceforge.solexatools.util.BulkUtil;
import net.sourceforge.solexatools.util.Constant;
import net.sourceforge.solexatools.util.FindChildUtil;
import net.sourceforge.solexatools.util.PageInfo;
import net.sourceforge.solexatools.util.PaginationUtil;
//import net.sourceforge.solexatools.webapp.metamodel.FileMeta;

import org.springframework.context.support.MessageSourceAccessor;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.BaseCommandController;

/**
 * <p>
 * DownloadFileListController class.
 * </p>
 * 
 * @author boconnor
 * @version $Id: $Id
 */
public class DownloadFileListController extends BaseCommandController {
    private StudyService studyService;
    private ExperimentService experimentService;
    private SampleService sampleService;
    private LaneService laneService;
    private ProcessingService processingService;
    private FileService fileService;
    private WorkflowRunService workflowRunService;

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

    private String getRequestedOption(HttpServletRequest request) {
        return request.getParameter("option");
    }

    private String getRequestedTypeNode(HttpServletRequest request) {
        return request.getParameter("typeNode");
    }

    private String[] getRequestedAllSelectIds(HttpServletRequest request) {
        return request.getParameter("allSelectIds").split(",");
    }

    private String[] getRequestedAllSelectStatuses(HttpServletRequest request) {
        return request.getParameter("allSelectStatuses").split(",");
    }

    private boolean getRequestedIsSelect(HttpServletRequest request) {
        return Boolean.parseBoolean(request.getParameter("isSelect"));
    }

    private String getRequestedNodeId(HttpServletRequest request) {
        return request.getParameter("nodeId");
    }

    private String getRequestedTypeBulkTree(HttpServletRequest request) {
        return request.getParameter("typeBulkTree");
    }

    private String getRequestedChildId(HttpServletRequest request) {
        return request.getParameter("childId");
    }

    private String getNameFileListInSession(String typeNode, String option) {
        String nameListInSession = "";
        if (option.equals("getCurrentFileList")) {
            nameListInSession = "unknow";
        }
        if (option.equals("updateFileList")) {
            if (typeNode.equals("study")) {
                nameListInSession = "bulkDownloadFiles";
            }
            if (typeNode.equals("analisys")) {
                nameListInSession = "analysisBulkDownloadFiles";
            }
        }

        return nameListInSession;
    }

    private String getNameSelectedIdsInSession(String typeNode) {
        String nameListInSession = "";
        if (typeNode.equals("study")) {
            nameListInSession = "selectedNodes";
        }
        if (typeNode.equals("analisys")) {
            nameListInSession = "analysisSelectedNodes";
        }

        return nameListInSession;
    }

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

        // Registration registration = Security.requireRegistration(request, response);
        Registration registration = Security.getRegistration(request);
        if (registration == null) {
            // return new ModelAndView("redirect:/login.htm");
            return new ModelAndView("FileList");
        }

        /**
         * Pass registration so that we can filter the list if its appropriate to do so.
         */

        String option = getRequestedOption(request);
        String typeNode = getRequestedTypeNode(request);
        boolean isSelect = getRequestedIsSelect(request);
        String typeBulkTree = getRequestedTypeBulkTree(request);

        String nameFileListInSession = getNameFileListInSession(typeBulkTree, option);

        List<File> listAllFile = BulkUtil.getFiles(request, nameFileListInSession);

        List<File> files = new ArrayList<>();
        if (option.equals("updateFileList")) {
            // update file list
            Integer nodeId = Integer.parseInt(getRequestedNodeId(request));
            List<String> nodeIds = new LinkedList<>();

            switch (typeNode) {
                case "study":
                    files = getStudyService().getFiles(nodeId);
                    nodeIds = FindChildUtil.getNodeIds(getStudyService().findByID(nodeId));
                    break;
                case "exp":
                    files = getExperimentService().getFiles(nodeId);
                    nodeIds = FindChildUtil.getNodeIds(getExperimentService().findByID(nodeId));
                    break;
                case "sam":
                    files = getSampleService().getFiles(nodeId);
                    // nodeIds = FindChildUtil.getNodeIds(getStudyService().findByID(nodeId));
                    nodeIds = FindChildUtil.getNodeIds(getSampleService().findByID(nodeId));
                    break;
                case "lane":
                    files = getLaneService().getFiles(nodeId);
                    nodeIds = FindChildUtil.getNodeIds(getLaneService().findByID(nodeId));
                    // nodeIds.add(nodeId.toString());
                    break;
                case "ae":
                    files = getProcessingService().getFiles(nodeId);
                    nodeIds = FindChildUtil.getNodeIds(getProcessingService().findByID(nodeId));
                    break;
                case "file":
                    files = getFileService().getFiles(nodeId);
                    nodeIds.add(nodeId.toString());
                    break;
            }
            if (typeNode.equals("wfr")) {
                // Integer processingId = getWorkflowRunService().getRootProcessing(nodeId).getProcessingId();
                WorkflowRun wr = getWorkflowRunService().findByID(nodeId);
                String strChildId = getRequestedChildId(request);
                if (strChildId != null && !"".equals(strChildId)) {
                    Log.info("One Proc in Workflow Run");

                    Integer processingId = Constant.getId(strChildId);
                    files = getProcessingService().getFiles(processingId);

                    // get Processing
                    SortedSet<Processing> processings = new TreeSet<>();
                    processings.add(getProcessingService().findByID(processingId));

                    // set one Processing in Workflow Run
                    wr.setProcessings(processings);
                } else {
                    Log.info("More One Proc in Workflow Run");
                    files = getWorkflowRunService().getFiles(wr.getWorkflowRunId());
                }
                nodeIds = FindChildUtil.getNodeIds(wr);
            }

            listAllFile = updateFiles(isSelect, files, listAllFile);

            setFiles(request, nameFileListInSession, listAllFile);

            // update Selected nodes in tree view
            // String[] allSelectIds = getRequestedAllSelectIds(request);
            // String[] allSelectStatuses = getRequestedAllSelectStatuses(request);
            String nameSelectedIdsInSession = getNameSelectedIdsInSession(typeBulkTree);
            // BulkUtil.getSelectedIds(request, nameSelectedIdsInSession, allSelectIds, allSelectStatuses);
            BulkUtil.updateSelectedIds(request, nameSelectedIdsInSession, isSelect, nodeIds);

        }

        MessageSourceAccessor ma = this.getMessageSourceAccessor();

        /**
		 * 
		 */
        List<File> listViewFile = null;
        PageInfo pageInfo = null;
        synchronized (listAllFile) {
            // listViewFile = Collections.synchronizedList(PaginationUtil.subListSD(request, "bulkDownloadFilePage", listAllFile));
            listViewFile = Collections.synchronizedList(PaginationUtil.subListSD(request, "bulkDownloadFilePage",
                    Collections.synchronizedList(listAllFile)));
            // listViewFile = PaginationUtil.subListSD(request, "bulkDownloadFilePage", listAllFile);
            pageInfo = PaginationUtil.getPageInfoSD(request, "bulkDownloadFilePage", listViewFile, listAllFile, ma);
        }

        /**
		 * 
		 */

        ModelAndView modelAndView = new ModelAndView("FileList");
        modelAndView.addObject("isSelectedInput", false);
        modelAndView.addObject("files", listViewFile);
        modelAndView.addObject("pageInfo", pageInfo);
        modelAndView.addObject("registration", registration);

        return modelAndView;
    }

    /*
     * private void updateMetaFile(List<FileMeta> metaFiles, List<File> files) { // TODO Auto-generated method stub for (File file: files) {
     * 
     * //FileMeta metaFile = new FileMeta(path, size)); } }
     */

    private synchronized List<File> updateFiles(boolean isSelect, List<File> files, List<File> list) {
        if (isSelect) {
            list = addFiles(list, files);
        } else {
            list = removeFiles(list, files);
        }
        return list;
    }

    private List<File> addFiles(List<File> list, List<File> addList) {
        Set<File> temp = new HashSet<>();
        temp.addAll(list);
        temp.addAll(addList);

        List<File> result = Collections.synchronizedList(new LinkedList<File>());
        result.addAll(temp);

        return result;
        /*
         * for(File addFile: addList){ boolean isAdd = true; for (File file: list) { if(file.equals(addFile)){ isAdd = false; break; } }
         * if(isAdd){ list.add(addFile); } }
         */
        // if(!list.contains(addFile)){
        // list.add(addFile);
        // }
        // return list;
    }

    private List<File> removeFiles(List<File> list, List<File> removeList) {
        // list.removeAll(removeList);
        for (File removefile : removeList) {
            list.remove(removefile);
            /*
             * boolean isRemove = false; for(File file: list){ if(file.equals(removefile)){ isRemove = true; } } if(isRemove){
             * list.remove(removefile); }
             */
        }
        return list;
    }

    private void setSelectedIds(HttpServletRequest request, String typeNode, String selectedIds) {
        HttpSession session = request.getSession(false);
        if (typeNode.equals("study")) {
            session.setAttribute("selectedIds", selectedIds);
        }
        if (typeNode.equals("analisys")) {
            session.setAttribute("analysisSelectedIds", selectedIds);
        }
    }

    private void setFiles(HttpServletRequest request, String nameList, List<File> list) {
        HttpSession session = request.getSession(false);
        session.setAttribute(nameList, list);
    }

    /**
     * <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;
    }

    /**
     * <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>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>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;
    }

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

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

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

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

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

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