\r
import org.apache.commons.lang.StringUtils;\r
import org.apache.log4j.Logger;\r
+import org.springframework.beans.factory.annotation.Autowired;\r
\r
+import eu.etaxonomy.cdm.api.service.IClassificationService;\r
+import eu.etaxonomy.cdm.api.service.ITaxonNodeService;\r
import eu.etaxonomy.cdm.common.CdmUtils;\r
import eu.etaxonomy.cdm.io.common.CdmExportBase;\r
import eu.etaxonomy.cdm.io.common.ICdmExport;\r
\r
protected static final boolean IS_CORE = true;\r
\r
+ @Autowired\r
+ private IClassificationService classificationService;\r
+\r
+ @Autowired\r
+ private ITaxonNodeService taxonNodeService;\r
+\r
\r
@Override\r
public int countSteps(DwcaTaxExportState state) {\r
\r
private void makeAllNodes(DwcaTaxExportState state, Set<UUID> subtreeSet) {\r
\r
- boolean doSynonyms = false;\r
- boolean recursive = true;\r
- Set<UUID> uuidSet = new HashSet<>();\r
+ try {\r
+ boolean doSynonyms = false;\r
+ boolean recursive = true;\r
+ Set<UUID> uuidSet = new HashSet<>();\r
+\r
+ for (UUID subtreeUuid : subtreeSet){\r
+ UUID tnUuuid = taxonNodeUuid(subtreeUuid);\r
+ uuidSet.add(tnUuuid);\r
+ List<TaxonNodeDto> records = getTaxonNodeService().pageChildNodesDTOs(tnUuuid,\r
+ recursive, doSynonyms, null, null, null).getRecords();\r
+ for (TaxonNodeDto dto : records){\r
+ uuidSet.add(dto.getUuid());\r
+ }\r
+ }\r
+ List<TaxonNode> allNodes = getTaxonNodeService().find(uuidSet);\r
\r
- for (UUID subtreeUuid : subtreeSet){\r
- uuidSet.add(subtreeUuid);\r
- List<TaxonNodeDto> records = getTaxonNodeService().pageChildNodesDTOs(subtreeUuid,\r
- recursive, doSynonyms, null, null, null).getRecords();\r
- for (TaxonNodeDto dto : records){\r
- uuidSet.add(dto.getUuid());\r
+ List<TaxonNode> result = new ArrayList<>();\r
+ for (TaxonNode node : allNodes){\r
+ if(node.getParent()== null){ //root (or invalid) node\r
+ continue;\r
+ }\r
+ node = CdmBase.deproxy(node);\r
+ Taxon taxon = CdmBase.deproxy(node.getTaxon());\r
+ if (taxon == null){\r
+ String message = "There is a taxon node without taxon. id=" + node.getId();\r
+ state.getResult().addWarning(message);\r
+ continue;\r
+ }\r
+ result.add(node);\r
}\r
+ state.setAllNodes(result);\r
+ } catch (Exception e) {\r
+ String message = "Unexpected exception when trying to compute all taxon nodes";\r
+ state.getResult().addException(e, message);\r
}\r
- List<TaxonNode> allNodes = getTaxonNodeService().find(uuidSet);\r
+ }\r
\r
- List<TaxonNode> result = new ArrayList<>();\r
- for (TaxonNode node : allNodes){\r
- if(node.getParent()== null){ //root (or invalid) node\r
- continue;\r
- }\r
- node = CdmBase.deproxy(node);\r
- Taxon taxon = CdmBase.deproxy(node.getTaxon());\r
- if (taxon == null){\r
- String message = "There is a taxon node without taxon. id=" + node.getId();\r
- state.getResult().addWarning(message);\r
- continue;\r
+\r
+ /**\r
+ * @param subtreeUuid\r
+ * @return\r
+ */\r
+ private UUID taxonNodeUuid(UUID subtreeUuid) {\r
+ TaxonNode node = taxonNodeService.find(subtreeUuid);\r
+ if (node == null){\r
+ Classification classification = classificationService.find(subtreeUuid);\r
+ if (classification != null){\r
+ node = classification.getRootNode();\r
+ }else{\r
+ throw new IllegalArgumentException("Subtree identifier does not exist: " + subtreeUuid);\r
}\r
- result.add(node);\r
}\r
- state.setAllNodes(result);\r
+ return node.getUuid();\r
}\r
\r
-\r
/**\r
* Creates the locationId, locality, countryCode triple\r
* @param record\r
--- /dev/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;
+ }
+
+}
BGBM BDI Projects / cdmlib.git / commitdiff