EDIT

import org.springframework.beans.factory.annotation.Autowired;

import eu.etaxonomy.cdm.api.service.IClassificationService;

import eu.etaxonomy.cdm.api.service.ITaxonNodeService;

    @Autowired

    private IClassificationService classificationService;

    @Autowired

    private ITaxonNodeService taxonNodeService;

        try {

            boolean doSynonyms = false;

            boolean recursive = true;

            Set<UUID> uuidSet = new HashSet<>();

            for (UUID subtreeUuid : subtreeSet){

                UUID tnUuuid = taxonNodeUuid(subtreeUuid);

                uuidSet.add(tnUuuid);

                List<TaxonNodeDto> records = getTaxonNodeService().pageChildNodesDTOs(tnUuuid,

                        recursive, doSynonyms, null, null, null).getRecords();

                for (TaxonNodeDto dto : records){

                    uuidSet.add(dto.getUuid());

                }

            }

            List<TaxonNode> allNodes =  getTaxonNodeService().find(uuidSet);

            List<TaxonNode> result = new ArrayList<>();

            for (TaxonNode node : allNodes){

                if(node.getParent()== null){  //root (or invalid) node

                    continue;

                }

                node = CdmBase.deproxy(node);

                Taxon taxon = CdmBase.deproxy(node.getTaxon());

                if (taxon == null){

                    String message = "There is a taxon node without taxon. id=" + node.getId();

                    state.getResult().addWarning(message);

                    continue;

                }

                result.add(node);

            state.setAllNodes(result);

        } catch (Exception e) {

            String message = "Unexpected exception when trying to compute all taxon nodes";

            state.getResult().addException(e, message);

    }

    /**

     * @param subtreeUuid

     * @return

     */

    private UUID taxonNodeUuid(UUID subtreeUuid) {

        TaxonNode node = taxonNodeService.find(subtreeUuid);

        if (node == null){

            Classification classification = classificationService.find(subtreeUuid);

            if (classification != null){

                node = classification.getRootNode();

            }else{

                throw new IllegalArgumentException("Subtree identifier does not exist: " + subtreeUuid);

        return node.getUuid();

        secUuid = taxon.getSec() != null ? taxon.getSec().getUuid() : null;

        titleCache = taxon.getName() != null ? taxon.getName().getTitleCache() : taxon.getTitleCache();

        taggedTitle = taxon.getName() != null? taxon.getName().getTaggedName() : taxon.getTaggedTitle();

        rankLabel = taxon.getNullSafeRank() != null ? taxon.getNullSafeRank().getLabel() : null;

/*

* Copyright  EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.remote.controller.checklist;

import java.io.File;

import java.io.IOException;

import java.io.InputStream;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import javax.servlet.http.HttpServletRequest;

import javax.servlet.http.HttpServletResponse;

import org.apache.log4j.Logger;

import org.springframework.beans.factory.annotation.Autowired;

import org.springframework.context.ApplicationContext;

import org.springframework.context.ResourceLoaderAware;

import org.springframework.core.io.Resource;

import org.springframework.core.io.ResourceLoader;

import org.springframework.stereotype.Controller;

import org.springframework.web.bind.WebDataBinder;

import org.springframework.web.bind.annotation.InitBinder;

import org.springframework.web.bind.annotation.RequestMapping;

import org.springframework.web.bind.annotation.RequestMethod;

import org.springframework.web.bind.annotation.RequestParam;

import org.springframework.web.servlet.ModelAndView;

import eu.etaxonomy.cdm.api.service.IClassificationService;

import eu.etaxonomy.cdm.api.service.IService;

import eu.etaxonomy.cdm.api.service.ITaxonNodeService;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.common.DocUtils;

import eu.etaxonomy.cdm.common.monitor.IRestServiceProgressMonitor;

import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultExport;

import eu.etaxonomy.cdm.io.dwca.out.DwcaEmlRecord;

import eu.etaxonomy.cdm.io.dwca.out.DwcaTaxExportConfigurator;

import eu.etaxonomy.cdm.model.description.Feature;

import eu.etaxonomy.cdm.model.taxon.Classification;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonNode;

import eu.etaxonomy.cdm.remote.controller.AbstractController;

import eu.etaxonomy.cdm.remote.controller.ProgressMonitorController;

import eu.etaxonomy.cdm.remote.controller.util.ProgressMonitorUtil;

import eu.etaxonomy.cdm.remote.editor.UUIDListPropertyEditor;

import eu.etaxonomy.cdm.remote.editor.UuidList;

import eu.etaxonomy.cdm.remote.view.FileDownloadView;

import eu.etaxonomy.cdm.remote.view.HtmlView;

/**

 * @author a.mueller

 * @created 28.06.2017

 * <p>

 *  This controller exports taxonomies via Darwin Core Archive

 *  (https://en.wikipedia.org/wiki/Darwin_Core_Archive).

 */

@Controller

@RequestMapping(value = { "/dwca" })

public class DwcaExportController extends AbstractController implements ResourceLoaderAware{

    private static final String DWCA_TAX_EXPORT_DOC_RESSOURCE = "classpath:eu/etaxonomy/cdm/doc/remote/apt/dwca-tax-export-default.apt";

    @Autowired

    private ApplicationContext appContext;

    @Autowired

    private IClassificationService classificationService;

    @Autowired

    private ITaxonNodeService taxonNodeService;

    @Autowired

    public ProgressMonitorController progressMonitorController;

    private ResourceLoader resourceLoader;

    /**

     * There should only be one processes operating on the export

     * therefore the according progress monitor uuid is stored in this static

     * field.

     */

    private static UUID indexMonitorUuid = null;

    private final static long DAY_IN_MILLIS = 86400000;

    private static final Logger logger = Logger.getLogger(DwcaExportController.class);

    /**

     * Helper method, which allows to convert strings directly into uuids.

     *

     * @param binder Special DataBinder for data binding from web request parameters to JavaBean objects.

     */

    @InitBinder

    public void initBinder(WebDataBinder binder) {

        binder.registerCustomEditor(UuidList.class, new UUIDListPropertyEditor());

//        binder.registerCustomEditor(NamedArea.class, new TermBaseListPropertyEditor<>(termService));

//        binder.registerCustomEditor(UUID.class, new UUIDEditor());

    }

    /**

     * Documentation webservice for this controller.

     *

     * @param response unused

     * @param request unused

     * @return

     * @throws IOException

     */

    @RequestMapping(value = {""}, method = { RequestMethod.GET})

    public ModelAndView exportGetExplanation(HttpServletResponse response,

            HttpServletRequest request) throws IOException{

        ModelAndView mv = new ModelAndView();

        // Read apt documentation file.

        Resource resource = resourceLoader.getResource(DWCA_TAX_EXPORT_DOC_RESSOURCE);

        // using input stream as this works for both files in the classes directory

        // as well as files inside jars

        InputStream aptInputStream = resource.getInputStream();

        // Build Html View

        Map<String, String> modelMap = new HashMap<>();

        // Convert Apt to Html

        modelMap.put("html", DocUtils.convertAptToHtml(aptInputStream));

        mv.addAllObjects(modelMap);

        HtmlView hv = new HtmlView();

        mv.setView(hv);

        return mv;

    }

    /**

     * This service endpoint is for generating the documentation site.

     * If any request of the other endpoint below is incomplete or false

     * then this method will be triggered.

     *

     * @param response

     * @param request

     * @return

     * @throws IOException

     */

    public ModelAndView exportGetExplanation(HttpServletResponse response,

            HttpServletRequest request, Resource res) throws IOException{

        ModelAndView mv = new ModelAndView();

        // Read apt documentation file.

        Resource resource = (res!= null) ? res : resourceLoader.getResource(DWCA_TAX_EXPORT_DOC_RESSOURCE);

        // using input stream as this works for both files in the classes directory

        // as well as files inside jars

        InputStream aptInputStream = resource.getInputStream();

        // Build Html View

        Map<String, String> modelMap = new HashMap<>();

        // Convert Apt to Html

        modelMap.put("html", DocUtils.convertAptToHtml(aptInputStream));

        mv.addAllObjects(modelMap);

        HtmlView hv = new HtmlView();

        mv.setView(hv);

        return mv;

    }

    /**

     *

     * This Service endpoint will offer a csv file. It caches the csv-file in the system temp directory

     * and will only generate a new one after 24 hours. Or if explicitly triggerd by noCache parameter.

     *

     * @param featureUuids List of uuids to download/select {@link Feature feature}features

     * @param clearCache will trigger export and avoids cached file

     * @param classificationUUID Selected {@link Classification classification} to iterate the {@link Taxon}

     * @param response HttpServletResponse which returns the ByteArrayOutputStream

     * @throws Exception

     */

    @RequestMapping(value = { "dwcaTaxExport" }, method = { RequestMethod.GET })

    public synchronized ModelAndView doDwcaTaxExport(

            @RequestParam(value = "subtrees", required = false) final UuidList subtreeUuids,

            @RequestParam(value = "clearCache", required = false) final boolean clearCache,

//            @RequestParam(value = "demoExport", required = false) final boolean demoExport,

//            @RequestParam(value = "conceptExport", required = false) final boolean conceptExport,

//            @RequestParam(value = "classification", required = false) final String classificationUUID,

//            @RequestParam(value = "area", required = false) final UuidList areas,

            @RequestParam(value = "downloadTokenValueId", required = false) final String downloadTokenValueId,

            @RequestParam(value = "priority", required = false) Integer priority,

            final HttpServletResponse response,

            final HttpServletRequest request) throws Exception {

        /**

         * ========================================

         * progress monitor & new thread for export

         * ========================================

         */

        try{

            ModelAndView mv = new ModelAndView();

            String fileName = makeFileName(response, subtreeUuids);

            final File cacheFile = new File(new File(System.getProperty("java.io.tmpdir")), fileName);

            final String origin = request.getRequestURL().append('?')

                    .append(request.getQueryString()).toString();

            Long result = null;

            if(cacheFile.exists()){

                result = System.currentTimeMillis() - cacheFile.lastModified();

            }

            //if file exists return file instantly

            //timestamp older than one day?

            if(clearCache == false && result != null){ //&& result < 7*(DAY_IN_MILLIS)

                logger.info("result of calculation: " + result);

                Map<String, File> modelMap = new HashMap<>();

                modelMap.put("file", cacheFile);

                mv.addAllObjects(modelMap);

                //application/zip

                FileDownloadView fdv = new FileDownloadView("application/octet-stream", fileName, "zip", "UTF-8");

                mv.setView(fdv);

                return mv;

            }else{//trigger progress monitor and performExport()

                String processLabel = "Exporting ...";

                final String frontbaseUrl = null;

                ProgressMonitorUtil progressUtil = new ProgressMonitorUtil(progressMonitorController);

                if (!progressMonitorController.isMonitorRunning(indexMonitorUuid)) {

                    indexMonitorUuid = progressUtil.registerNewMonitor();

                    Thread subThread = new Thread() {

                        @Override

                        public void run() {

                            try {

                                cacheFile.createNewFile();

                            } catch (IOException e) {

                                logger.info("Could not create file "+ e);

                            }

                            performExport(cacheFile, progressMonitorController.getMonitor(indexMonitorUuid),

                                    subtreeUuids, downloadTokenValueId, origin, response);

                        }

                    };

                    if (priority == null) {

                        priority = AbstractController.DEFAULT_BATCH_THREAD_PRIORITY;

                    }

                    subThread.setPriority(priority);

                    subThread.start();

                }

                mv = progressUtil.respondWithMonitorOrDownload(frontbaseUrl, origin, processLabel, indexMonitorUuid, false, request, response);

            }

            return mv;

        }catch(Exception e){

            //TODO: Write an specific documentation for this service endpoint

           Resource resource = resourceLoader.getResource(DWCA_TAX_EXPORT_DOC_RESSOURCE);

           return exportGetExplanation(response, request, resource);

        }

    }

    //=========== Helper Methods ===============//

    /**

     *

     * This private methods finally triggers the export back in the io-package and will create a cache file

     * in system temp directory.

     *

     * @param downloadTokenValueId

     * @param response

     * @param byteArrayOutputStream

     * @param config

     * @param defaultExport

     */

    private void performExport(File cacheFile, IRestServiceProgressMonitor progressMonitor,

            UuidList featureUuids, String downloadTokenValueId, String origin,

            HttpServletResponse response

            ) {

        progressMonitor.subTask("configure export");

        DwcaTaxExportConfigurator config = setDwcaTaxExportConfigurator(cacheFile, progressMonitor, featureUuids);

        @SuppressWarnings("unchecked")

        CdmApplicationAwareDefaultExport<DwcaTaxExportConfigurator> defaultExport =

                (CdmApplicationAwareDefaultExport<DwcaTaxExportConfigurator>)appContext.getBean("defaultExport");

        progressMonitor.subTask("invoke export");

        defaultExport.invoke(config);  //triggers export

        progressMonitor.subTask("wrote results to cache");

        progressMonitor.done();

        progressMonitor.setOrigin(origin);

    }

    /**

     * Cofiguration method to set the configuration details for the defaultExport in the application context.

     * @param cacheFile

     *

     * @param classificationUUID pass-through the selected {@link Classification classification}

     * @param featureUuids pass-through the selected {@link Feature feature} of a {@link Taxon}, in order to fetch it.

     * @param areas

     * @param byteArrayOutputStream pass-through the stream to write out the data later.

     * @param progressMonitor

     * @param conceptExport

     * @param demoExport

     * @return the CsvTaxExportConfiguratorRedlist config

     */

    private DwcaTaxExportConfigurator setDwcaTaxExportConfigurator(File cacheFile, IRestServiceProgressMonitor progressMonitor,

            UuidList subtreeUuids) {

        if(cacheFile == null){

            String destination = System.getProperty("java.io.tmpdir");

            cacheFile = new File(destination);

        }

        DwcaEmlRecord emlRecord = null;

        DwcaTaxExportConfigurator config = DwcaTaxExportConfigurator.NewInstance(

                null, cacheFile, emlRecord);

        Set<UUID> subtreeSet = new HashSet<>(subtreeUuids);

        config.setProgressMonitor(progressMonitor);

        config.setSubtreeUuids(subtreeSet);

//        config.setHasHeaderLines(true);

//        config.setFieldsTerminatedBy("\t");

//        config.setClassificationUuids(classificationUUIDS);

//        if(demoExport == false && conceptExport == false){

//        	config.createPreSelectedExport(false, true);

//        }else{

//        	config.createPreSelectedExport(demoExport, conceptExport);

//        }

        return config;

    }

    /**

     * @param response

     * @param subtreeUuids

     * @throws IOException

     */

    private String makeFileName(HttpServletResponse response, UuidList subtreeUuids) throws IOException {

        String fileName;

        if (subtreeUuids != null && ! subtreeUuids.isEmpty()){

            UUID firstUuid = subtreeUuids.get(0);

            TaxonNode node = taxonNodeService.find(firstUuid);

            if (node != null && node.getTaxon() != null){

                if (node.getTaxon().getName() != null){

                    fileName = node.getTaxon().getName().getTitleCache();

                }else{

                    fileName = node.getTaxon().getTitleCache();

                }

            }else if (node != null){

                fileName = node.getClassification().getTitleCache();

            }else{

                Classification classification = classificationService.find(firstUuid);

                if (classification != null){

                    fileName = classification.getTitleCache();

                }else{

                    //handle via repso

                    response.sendError(404, "Subtree uuid does not exist: " + firstUuid);

                    fileName = "Error";

                }

            }

        }else{

            List<Classification> classificationList = classificationService.list(null, 1, null

                    , null, null);

            if (!classificationList.isEmpty()){

                fileName = classificationList.get(0).getTitleCache();

            }else{

               //handle via repso

                response.sendError(404, "No classification found");

                fileName = "Error";

            }

        }

        fileName = fileName + "_" + uuidListToString(subtreeUuids, 40) + ".zip";

        return fileName;

    }

    private String uuidListToString(UuidList uuidList, Integer truncate) {

        String result = null;

        for (UUID uuid : uuidList){

            result = CdmUtils.concat("_", uuid.toString());

        }

        if (result != null && result.length() > truncate){

            result = result.substring(0, truncate);

        }

        return result;

    }

    @Override

    public void setService(IService service) {}

    @Override

    public void setResourceLoader(ResourceLoader resourceLoader) {

        this.resourceLoader = resourceLoader;

    }

}

                                   --------------------------

                                    DWCA TAXON EXPORT API

                                    --------------------------

{CDM DWCA TAXON API}

    TODO

*	The request parameters are :