cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/in/SDDImport.java

   1 /**
   2  * Copyright (C) 2007 EDIT
   3  * European Distributed Institute of Taxonomy
   4  * http://www.e-taxonomy.eu
   5  *
   6  * The contents of this file are subject to the Mozilla Public License Version 1.1
   7  * See LICENSE.TXT at the top of this package for the full license terms.
   8  */
   9
  10 package eu.etaxonomy.cdm.io.sdd.in;
  11
  12 import java.io.File;
  13 import java.net.MalformedURLException;
  14 import java.net.URL;
  15 import java.text.SimpleDateFormat;
  16 import java.util.ArrayList;
  17 import java.util.Date;
  18 import java.util.HashMap;
  19 import java.util.HashSet;
  20 import java.util.List;
  21 import java.util.Map;
  22 import java.util.Set;
  23
  24 import org.apache.commons.lang.StringUtils;
  25 import org.apache.log4j.Logger;
  26 import org.jdom.Element;
  27 import org.jdom.Namespace;
  28 import org.joda.time.DateTime;
  29 import org.springframework.stereotype.Component;
  30 import org.springframework.transaction.TransactionStatus;
  31
  32 import eu.etaxonomy.cdm.api.service.IDescriptionService;
  33 import eu.etaxonomy.cdm.common.mediaMetaData.ImageMetaData;
  34 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  35 import eu.etaxonomy.cdm.io.common.CdmImportBase;
  36 import eu.etaxonomy.cdm.io.common.ICdmImport;
  37 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  38 import eu.etaxonomy.cdm.io.common.ImportHelper;
  39 import eu.etaxonomy.cdm.io.sdd.SDDTransformer;
  40 import eu.etaxonomy.cdm.model.agent.Person;
  41 import eu.etaxonomy.cdm.model.agent.Team;
  42 import eu.etaxonomy.cdm.model.common.Annotation;
  43 import eu.etaxonomy.cdm.model.common.AnnotationType;
  44 import eu.etaxonomy.cdm.model.common.CdmBase;
  45 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  46 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  47 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  48 import eu.etaxonomy.cdm.model.common.Language;
  49 import eu.etaxonomy.cdm.model.common.LanguageString;
  50 import eu.etaxonomy.cdm.model.common.Marker;
  51 import eu.etaxonomy.cdm.model.common.MarkerType;
  52 import eu.etaxonomy.cdm.model.common.Representation;
  53 import eu.etaxonomy.cdm.model.common.TermBase;
  54 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  55 import eu.etaxonomy.cdm.model.common.VersionableEntity;
  56 import eu.etaxonomy.cdm.model.description.CategoricalData;
  57 import eu.etaxonomy.cdm.model.description.Feature;
  58 import eu.etaxonomy.cdm.model.description.FeatureNode;
  59 import eu.etaxonomy.cdm.model.description.FeatureTree;
  60 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
  61 import eu.etaxonomy.cdm.model.description.Modifier;
  62 import eu.etaxonomy.cdm.model.description.QuantitativeData;
  63 import eu.etaxonomy.cdm.model.description.State;
  64 import eu.etaxonomy.cdm.model.description.StateData;
  65 import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
  66 import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
  67 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  68 import eu.etaxonomy.cdm.model.description.TextData;
  69 import eu.etaxonomy.cdm.model.location.NamedArea;
  70 import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
  71 import eu.etaxonomy.cdm.model.media.ImageFile;
  72 import eu.etaxonomy.cdm.model.media.Media;
  73 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  74 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  75 import eu.etaxonomy.cdm.model.media.Rights;
  76 import eu.etaxonomy.cdm.model.name.NonViralName;
  77 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  78 import eu.etaxonomy.cdm.model.occurrence.Specimen;
  79 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  80 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  81 import eu.etaxonomy.cdm.model.taxon.Synonym;
  82 import eu.etaxonomy.cdm.model.taxon.Taxon;
  83 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  84 import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
  85
  86 /**
  87  * @author h.fradin
  88  * @created 24.10.2008
  89  * @version 1.0
  90  */
  91 @Component("sddImport")
  92 public class SDDImport extends CdmImportBase<SDDImportConfigurator, SDDImportState> implements ICdmImport<SDDImportConfigurator, SDDImportState> {
  93         private static final Logger logger = Logger.getLogger(SDDImport.class);
  94
  95         private static int modCount = 1000;
  96
  97         private Map<String,Person> authors = new HashMap<String,Person>();
  98         private Map<String,String> citations = new HashMap<String,String>();
  99         private Map<String,String> defaultUnitPrefixes = new HashMap<String,String>();
 100         private Map<String,Person> editors = new HashMap<String,Person>();
 101         private Map<String,FeatureNode> featureNodes = new HashMap<String,FeatureNode>();
 102         private Map<String,Feature> features = new HashMap<String,Feature>();
 103         private Map<String,String> locations = new HashMap<String,String>();
 104         private Map<String,List<CdmBase>> mediaObject_ListCdmBase = new HashMap<String,List<CdmBase>>();
 105         private Map<String,String> mediaObject_Role = new HashMap<String,String>();
 106         private Map<String,ReferenceBase> publications = new HashMap<String,ReferenceBase>();
 107         private Map<String,State> states = new HashMap<String,State>();
 108         private Map<String,TaxonDescription> taxonDescriptions = new HashMap<String,TaxonDescription>();
 109         private Map<String,NonViralName> taxonNameBases = new HashMap<String,NonViralName>();
 110         private Map<String,MeasurementUnit> units = new HashMap<String,MeasurementUnit>();
 111         private Map<String,TaxonNode> taxonNodes = new HashMap<String,TaxonNode>();
 112         private Map<String,NamedArea> namedAreas = new HashMap<String,NamedArea>();
 113         private Map<String,Specimen> specimens = new HashMap<String,Specimen>();
 114         private Map<String,Modifier> modifiers = new HashMap<String,Modifier>();
 115
 116         private Set<MarkerType> markerTypes = new HashSet<MarkerType>();
 117
 118         private Set<Feature> descriptiveConcepts = new HashSet<Feature>();
 119         private Set<AnnotationType> annotationTypes = new HashSet<AnnotationType>();
 120         private Set<Feature> featureSet = new HashSet<Feature>();
 121         private ReferenceBase sec = ReferenceFactory.newDatabase();
 122         private ReferenceBase sourceReference = null;
 123
 124         private Language datasetLanguage = null;
 125
 126         private Namespace xmlNamespace = Namespace.getNamespace("xml","http://www.w3.org/XML/1998/namespace");
 127
 128         private String generatorName = "";
 129         private String generatorVersion = "";
 130
 131         private Set<StatisticalMeasure> statisticalMeasures = new HashSet<StatisticalMeasure>();
 132         private Set<VersionableEntity> featureData = new HashSet<VersionableEntity>();
 133         private Set<FeatureTree> featureTrees = new HashSet<FeatureTree>();
 134         private Set<TaxonomicTree> taxonomicTrees = new HashSet<TaxonomicTree>();
 135
 136         private Rights copyright = null;
 137
 138         private int taxonNamesCount = 0; //XIM ajout
 139
 140         public SDDImport(){
 141                 super();
 142         }
 143
 144         @Override
 145         public boolean doCheck(SDDImportState state){
 146                 boolean result = true;
 147                 logger.warn("No check implemented for SDD");
 148                 return result;
 149         }
 150
 151         //      @Override
 152         //      public boolean doInvoke(IImportConfigurator config, Map<String, MapWrapper<? extends CdmBase>> stores){
 153         @Override
 154         public boolean doInvoke(SDDImportState state){
 155                 boolean success = true;
 156
 157                 TransactionStatus ts = startTransaction();
 158                 SDDImportConfigurator sddConfig = state.getConfig();
 159
 160                 logger.info("start Datasets ...");
 161                 // <Datasets xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://rs.tdwg.org/UBIF/2006/" xsi:schemaLocation="http://rs.tdwg.org/UBIF/2006/ ../SDD.xsd">
 162                 Element root = sddConfig.getSourceRoot();
 163                 Namespace sddNamespace = sddConfig.getSddNamespace();
 164
 165                 logger.info("start TechnicalMetadata ...");
 166                 // <TechnicalMetadata created="2006-04-20T10:00:00">
 167                 importTechnicalMetadata(root, sddNamespace, sddConfig);
 168                 List<Element> elDatasets = root.getChildren("Dataset",sddNamespace);
 169                 int i = 0;
 170
 171                 //for each Dataset
 172                 logger.info("start Dataset ...");
 173                 for (Element elDataset : elDatasets){
 174                         success &= importDataset(elDataset, sddNamespace, state);
 175                         if ((++i % modCount) == 0){ logger.info("Datasets handled: " + i);}
 176                         logger.info(i + " Datasets handled");
 177                 }
 178                 commitTransaction(ts);
 179                 return success;
 180         }
 181
 182         /* (non-Javadoc)
 183          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 184          */
 185         protected boolean isIgnore(SDDImportState state){
 186                 return false;
 187         }
 188
 189
 190         // associates the reference of a media object in SDD with a CdmBase Object
 191         protected void associateImageWithCdmBase(String refMO, CdmBase cb){
 192                 if ((refMO != null) && (cb!=null)) {
 193                         if (! refMO.equals("")) {
 194                                 if (! mediaObject_ListCdmBase.containsKey(refMO)) {
 195                                         List<CdmBase> lcb = new ArrayList<CdmBase>();
 196                                         lcb.add(cb);
 197                                         mediaObject_ListCdmBase.put(refMO,lcb);
 198                                 } else {
 199                                         List<CdmBase> lcb = mediaObject_ListCdmBase.get(refMO);
 200                                         lcb.add(cb);
 201                                         mediaObject_ListCdmBase.put(refMO,lcb);
 202                                 }
 203                         }
 204                 }
 205         }
 206
 207         // imports information about the Dataset
 208         protected void importDatasetRepresentation(Element parent, Namespace sddNamespace){
 209                 logger.info("start Representation ...");
 210                 /* <Representation>
 211                         <Label>The Genus Viola</Label>
 212                         <Detail>This is an example for a very simple SDD file, representing a single description with categorical, quantitative, and text character. Compare also the "Fragment*" examples, which contain more complex examples in the form of document fragments. Intended for version="SDD 1.1".</Detail>
 213                </Representation>
 214                  */
 215                 Element elRepresentation = parent.getChild("Representation",sddNamespace);
 216                 String label = (String)ImportHelper.getXmlInputValue(elRepresentation, "Label",sddNamespace);
 217                 String detail = (String)ImportHelper.getXmlInputValue(elRepresentation, "Detail",sddNamespace);
 218
 219                 sec.setTitleCache(label, true);
 220
 221                 if (detail != null) {
 222                         Annotation annotation = Annotation.NewInstance(detail, datasetLanguage);
 223                         annotation.setAnnotationType(AnnotationType.EDITORIAL());
 224                         sec.addAnnotation(annotation);
 225                 }
 226
 227                 List<Element> listMediaObjects = elRepresentation.getChildren("MediaObject",sddNamespace);
 228
 229                 for (Element elMediaObject : listMediaObjects) {
 230                         String ref = null;
 231                         String role = null;
 232                         if (elMediaObject != null) {
 233                                 ref = elMediaObject.getAttributeValue("ref");
 234                                 role = elMediaObject.getAttributeValue("role");
 235                         }
 236                         if (ref != null) {
 237                                 if (!ref.equals("")) {
 238                                         this.associateImageWithCdmBase(ref,sourceReference);
 239                                         this.associateImageWithCdmBase(ref,sec);
 240                                         mediaObject_Role.put(ref,role);
 241                                 }
 242                         }
 243                 }
 244         }
 245
 246         // imports the representation (label, detail, lang) of a particular SDD element
 247         protected void importRepresentation(Element parent, Namespace sddNamespace, VersionableEntity ve, String id, IImportConfigurator config){
 248                 Element elRepresentation = parent.getChild("Representation",sddNamespace);
 249
 250                 Map<Language,List<String>> langLabDet = new HashMap<Language,List<String>>();
 251
 252                 handleRepresentationLabels(sddNamespace, elRepresentation, langLabDet);
 253                 handleRepresentationDetails(sddNamespace, elRepresentation, langLabDet);
 254
 255                 if (ve instanceof TermBase) {
 256                         makeRepresentationForTerms((TermBase)ve, langLabDet);
 257                 }else if (ve instanceof Media) {
 258                         makeRepresentationForMedia((Media)ve, langLabDet);
 259                 }else if (ve instanceof IdentifiableEntity<?>) {
 260                         IdentifiableEntity<?> ie = (IdentifiableEntity<?>)ve;
 261                         makeRepresentationForIdentifiableEntity(sddNamespace, ie, elRepresentation, langLabDet);
 262                         if (ve instanceof IdentifiableMediaEntity<?>){
 263                                 makeRepresentationForIdentifiableMediaEntity(parent, sddNamespace, (IdentifiableMediaEntity<?>)ve);
 264                         }
 265                 }
 266
 267                 makeRepresentationMediaObjects(sddNamespace, ve, elRepresentation);
 268
 269         }
 270
 271
 272         /**
 273          * Handles the "Detail" children of representations. Adds the result to the langLabDet.
 274          * @param sddNamespace
 275          * @param elRepresentation
 276          * @param langLabDet
 277          */
 278         private void handleRepresentationDetails(Namespace sddNamespace,
 279                         Element elRepresentation, Map<Language, List<String>> langLabDet) {
 280                 List<Element> listDetails = elRepresentation.getChildren("Detail",sddNamespace);
 281                 for (Element elDetail : listDetails){
 282                         Language language = getLanguage(elDetail);
 283                         String role = elDetail.getAttributeValue("role");
 284                         String detail = elDetail.getText();
 285                         List<String> labDet = langLabDet.get(language);
 286                         labDet.add(detail);
 287                         labDet.add(role);
 288                         langLabDet.put(language, labDet);
 289                 }
 290         }
 291
 292         /**
 293          * Handles the "Label" children of representations. Adds the result to the langLabDet.
 294          * @param sddNamespace
 295          * @param elRepresentation
 296          * @param langLabDet
 297          */
 298         private void handleRepresentationLabels(Namespace sddNamespace,
 299                                 Element elRepresentation, Map<Language, List<String>> langLabDet) {
 300                 // <Label xml:lang="la">Viola hederacea Labill.</Label>
 301                 List<Element> listLabels = elRepresentation.getChildren("Label",sddNamespace);
 302                 for (Element elLabel : listLabels){
 303                         Language language = getLanguage(elLabel);
 304                         String label = elLabel.getText();
 305                         List<String> labDet = new ArrayList<String>(3);
 306                         labDet.add(label);
 307                         langLabDet.put(language, labDet);
 308                 }
 309         }
 310
 311         /**
 312          *
 313          * @param ve
 314          * @param langLabDet
 315          */
 316         private void makeRepresentationForMedia(Media m, Map<Language, List<String>> langLabDet) {
 317                 for (Language lang : langLabDet.keySet()){
 318                         List<String> labDet = langLabDet.get(lang);
 319                         if (labDet.get(0) != null){
 320                                 m.addTitle(LanguageString.NewInstance(labDet.get(0), lang));
 321                         }
 322                         if (labDet.size()>1) {
 323                                 m.addDescription(labDet.get(1), lang);
 324                         }
 325                 }
 326         }
 327
 328         /**
 329          * Handles representations for terms. Adds one representation per language in langLabDet.
 330          *
 331          * @param ve
 332          * @param langLabDet
 333          */
 334         private void makeRepresentationForTerms(TermBase tb, Map<Language, List<String>> langLabDet) {
 335                         for (Language lang : langLabDet.keySet()){
 336                                 List<String> labDet = langLabDet.get(lang);
 337                                 if (labDet.size()>0){
 338                                         if (labDet.size()>1) {
 339                                                 tb.addRepresentation(Representation.NewInstance(labDet.get(1), labDet.get(0), labDet.get(0), lang));
 340                                         } else {
 341                                                 tb.addRepresentation(Representation.NewInstance(labDet.get(0), labDet.get(0), labDet.get(0), lang));
 342                                         }
 343                                 }
 344                         }
 345         }
 346
 347
 348         /**
 349          * Handles the "MediaObject" children of representations.
 350          * @param sddNamespace
 351          * @param ve
 352          * @param elRepresentation
 353          */
 354         private void makeRepresentationMediaObjects(Namespace sddNamespace,
 355                         VersionableEntity ve, Element elRepresentation) {
 356                 List <Element> listMediaObjects = elRepresentation.getChildren("MediaObject", sddNamespace);
 357                 for (Element elMediaObject : listMediaObjects) {
 358                         String ref = null;
 359                         //TODO
 360                         String role = null;
 361                         if (elMediaObject != null) {
 362                                 ref = elMediaObject.getAttributeValue("ref");
 363                                 role = elMediaObject.getAttributeValue("role");
 364                         }
 365                         if (StringUtils.isNotBlank(ref)) {
 366                                 if (ve instanceof TaxonDescription) {
 367                                         TaxonDescription td = (TaxonDescription) ve;
 368                                         //TODO: ensure that all images are imported
 369                                         if (td.getDescriptionSources().size() > 0) {
 370                                                 this.associateImageWithCdmBase(ref,(ReferenceBase) td.getDescriptionSources().toArray()[0]);
 371                                         } else {
 372                                                 ReferenceBase descriptionSource = ReferenceFactory.newGeneric();
 373                                                 td.addDescriptionSource(descriptionSource);
 374                                                 this.associateImageWithCdmBase(ref,descriptionSource);
 375                                         }
 376                                 } else {
 377                                         this.associateImageWithCdmBase(ref,ve);
 378                                 }
 379                         }
 380                 }
 381         }
 382
 383         /**
 384          * Handles the "Links" element
 385          * @param parent
 386          * @param sddNamespace
 387          * @param ve
 388          */
 389         private void makeRepresentationForIdentifiableMediaEntity(Element parent,
 390                         Namespace sddNamespace, IdentifiableMediaEntity ime) {
 391                 Element elLinks = parent.getChild("Links",sddNamespace);
 392
 393                 if (elLinks != null) {
 394
 395                         //  <Link rel="Alternate" href="http://www.diversitycampus.net/people/hagedorn"/>
 396                         List<Element> listLinks = elLinks.getChildren("Link", sddNamespace);
 397                         Media link = Media.NewInstance();
 398                         MediaRepresentation mr = MediaRepresentation.NewInstance();
 399                         int k = 0;
 400                         //for each Link
 401                         for (Element elLink : listLinks){
 402
 403                                 try {
 404                                         //TODO
 405                                         String rel = elLink.getAttributeValue("rel");
 406                                         String href = elLink.getAttributeValue("href");
 407
 408                                         mr.addRepresentationPart(MediaRepresentationPart.NewInstance(href, null));
 409                                         link.addRepresentation(mr);
 410                                         ime.addMedia(link);
 411
 412                                 } catch (Exception e) {
 413                                         //FIXME
 414                                         logger.warn("Import of Link " + k + " failed.");
 415                                 }
 416
 417                                 if ((++k % modCount) == 0){ logger.info("Links handled: " + k);}
 418
 419                         }
 420                 }
 421         }
 422
 423         /**
 424          * @param sddNamespace
 425          * @param ve
 426          * @param elRepresentation
 427          * @param langLabDet
 428          * @return
 429          */
 430         private void makeRepresentationForIdentifiableEntity(Namespace sddNamespace, IdentifiableEntity<?> ie,
 431                                         Element elRepresentation, Map<Language, List<String>> langLabDet) {
 432                 List<String> labDet = null;
 433
 434                 if (ie instanceof TaxonNameBase) {
 435                         if (langLabDet.keySet().contains(getTermService().getLanguageByIso("la"))) {
 436                                 labDet = langLabDet.get(getTermService().getLanguageByIso("la"));
 437                         } else if (langLabDet.keySet().contains(datasetLanguage)) {
 438                                 labDet = langLabDet.get(datasetLanguage);
 439                                 logger.info("TaxonName " + (String)ImportHelper.getXmlInputValue(elRepresentation, "Label",sddNamespace) + " is not specified as a latin name.");
 440                         } else {
 441                                 labDet = langLabDet.get(langLabDet.keySet().iterator().next());
 442                                 logger.info("TaxonName " + (String)ImportHelper.getXmlInputValue(elRepresentation, "Label",sddNamespace) + " is not specified as a latin name.");
 443                         }
 444                 } else {
 445                         labDet = langLabDet.get(langLabDet.keySet().iterator().next());
 446                 }
 447
 448                 //FIXME labDet is != null only for TaxonNameBase
 449                 ie.setTitleCache(labDet.get(0), true);
 450
 451                 if (labDet.size()>1) {
 452                         Annotation annotation = null;
 453                         if (labDet.get(1) != null) {
 454                                 if (labDet.get(2) != null) {
 455                                         annotation = Annotation.NewInstance(labDet.get(2) + " - " + labDet.get(1), datasetLanguage);
 456                                 } else {
 457                                         annotation = Annotation.NewInstance(labDet.get(1), datasetLanguage);
 458                                 }
 459                         }
 460                         ie.addAnnotation(annotation);
 461                 }
 462                 return;
 463         }
 464
 465         /**
 466          * @param elLabel
 467          * @return
 468          */
 469         private Language getLanguage(Element elLanguage) {
 470                 String lang = elLanguage.getAttributeValue("lang",xmlNamespace);
 471                 Language language = null;
 472                 if (StringUtils.isNotBlank(lang)) {
 473                         language = getTermService().getLanguageByIso(lang.substring(0, 2));
 474                 } else {
 475                         language = datasetLanguage;
 476                 }
 477                 return language;
 478         }
 479
 480
 481         // imports the representation (label, detail, lang) of a particular SDD element
 482         protected void importTechnicalMetadata(Element root, Namespace sddNamespace, SDDImportConfigurator sddConfig){
 483                 Element elTechnicalMetadata = root.getChild("TechnicalMetadata", sddNamespace);
 484                 String nameCreated = elTechnicalMetadata.getAttributeValue("created");
 485                 sourceReference = sddConfig.getSourceReference();
 486
 487                 if (nameCreated != null) {
 488                         if (!nameCreated.equals("")) {
 489                                 int year = Integer.parseInt(nameCreated.substring(0,4));
 490                                 int monthOfYear = Integer.parseInt(nameCreated.substring(5,7));
 491                                 int dayOfMonth = Integer.parseInt(nameCreated.substring(8,10));
 492                                 int hourOfDay = Integer.parseInt(nameCreated.substring(11,13));
 493                                 int minuteOfHour = Integer.parseInt(nameCreated.substring(14,16));
 494                                 int secondOfMinute = Integer.parseInt(nameCreated.substring(17,19));
 495                                 DateTime created = new DateTime(year,monthOfYear,dayOfMonth,hourOfDay,minuteOfHour,secondOfMinute,0);
 496                                 sourceReference.setCreated(created);
 497                                 sec.setCreated(created);
 498                         }
 499                 }
 500
 501                 // <Generator name="n/a, handcrafted instance document" version="n/a"/>
 502                 Element elGenerator = elTechnicalMetadata.getChild("Generator", sddNamespace);
 503                 generatorName = elGenerator.getAttributeValue("name");
 504                 generatorVersion = elGenerator.getAttributeValue("version");
 505
 506                 sec.addAnnotation(Annotation.NewDefaultLanguageInstance(generatorName + " - " + generatorVersion));
 507                 sourceReference.addAnnotation(Annotation.NewDefaultLanguageInstance(generatorName + " - " + generatorVersion));
 508
 509         }
 510
 511         // imports the complete dataset information
 512         protected boolean importDataset(Element elDataset, Namespace sddNamespace, SDDImportState state){                       // <Dataset xml:lang="en-us">
 513                 boolean success = true;
 514                 SDDImportConfigurator sddConfig = state.getConfig();
 515                 importDatasetLanguage(elDataset,sddConfig);
 516                 importDatasetRepresentation(elDataset, sddNamespace);
 517                 importRevisionData(elDataset, sddNamespace);
 518                 importIPRStatements(elDataset, sddNamespace, sddConfig);
 519                 importTaxonNames(elDataset, sddNamespace, sddConfig);
 520                 importDescriptiveConcepts(elDataset, sddNamespace, sddConfig);
 521                 success &= importCharacters(elDataset, sddNamespace, sddConfig);
 522                 importCharacterTrees(elDataset, sddNamespace, sddConfig, success);
 523
 524                 MarkerType editorMarkerType = getMarkerType(state, SDDTransformer.uuidMarkerEditor, "editor", "Editor", "edt");
 525                 MarkerType geographicAreaMarkerType = getMarkerType(state, SDDTransformer.uuidMarkerSDDGeographicArea, "SDDGeographicArea", "SDDGeographicArea", "ga");
 526                 MarkerType descriptiveConceptMarkerType = getMarkerType(state, SDDTransformer.uuidMarkerDescriptiveConcept, "DescriptiveConcept", "Descriptive Concept", "DC");
 527                 markerTypes.add(editorMarkerType);
 528                 markerTypes.add(geographicAreaMarkerType);
 529                 markerTypes.add(descriptiveConceptMarkerType);
 530
 531                 //saving of all imported data into the CDM db
 532                 saveFeatures();
 533                 saveModifiers();
 534                 saveStates();
 535                 saveMarkerType();
 536                 saveAreas(geographicAreaMarkerType);
 537                 saveUnits();
 538                 saveStatisticalMeasure();
 539                 saveAnnotationType();
 540
 541                 success &= importCodedDescriptions(elDataset, sddNamespace, sddConfig);
 542                 importAgents(elDataset, sddNamespace, sddConfig, success);
 543                 importPublications(elDataset, sddNamespace, sddConfig, success);
 544                 importMediaObjects(elDataset, sddNamespace, sddConfig, success);
 545                 importTaxonHierarchies(elDataset, sddNamespace, sddConfig, success);
 546                 importGeographicAreas(elDataset, sddNamespace, sddConfig);
 547                 importSpecimens(elDataset,sddNamespace, sddConfig);
 548
 549
 550
 551                 if ((authors != null)||(editors != null)) {
 552                         Team team = Team.NewInstance();
 553                         if (authors != null) {
 554                                 for (Person author : authors.values()){
 555                                         team.addTeamMember(author);
 556                                 }
 557                         }
 558                         if (editors != null) {
 559                                 Marker marker = Marker.NewInstance();
 560                                 marker.setMarkerType(editorMarkerType);
 561                                 for (Person editor : editors.values()){
 562                                         Person edit = editor;
 563                                         edit.addMarker(marker);
 564                                         team.addTeamMember(edit);
 565                                 }
 566                                 }
 567                         sec.setAuthorTeam(team);
 568                         sourceReference.setAuthorTeam(team);
 569                 }
 570
 571                 if (copyright != null) {
 572                         sourceReference.addRights(copyright);
 573                         sec.addRights(copyright);
 574                 }
 575
 576                 // Returns a CdmApplicationController created by the values of this configuration.
 577                 IDescriptionService descriptionService = getDescriptionService();
 578
 579                 for (TaxonDescription taxonDescription : taxonDescriptions.values()){
 580                         // Persists a Description
 581                         descriptionService.save(taxonDescription);
 582                 }
 583
 584                 for (String ref : taxonDescriptions.keySet()){
 585                         TaxonDescription td = taxonDescriptions.get(ref);
 586                         if (citations.containsKey(ref)) {
 587                                 ReferenceBase publication = publications.get(citations.get(ref));
 588                                 if (locations.containsKey(ref)) {
 589                                         Annotation location = Annotation.NewInstance(locations.get(ref), datasetLanguage);
 590                                         AnnotationType annotationType = AnnotationType.NewInstance("", "location", "");
 591                                         annotationTypes.add(annotationType);
 592                                         location.setAnnotationType(annotationType);
 593                                         (publication).addAnnotation(location);
 594                                 }
 595                                 td.addDescriptionSource(publication);
 596                         }
 597                 }
 598                 logger.info("end makeTaxonDescriptions ...");
 599
 600
 601 //              for (Iterator<TermVocabulary<Modifier>> k = termVocabularyStates.iterator() ; k.hasNext() ;){
 602 //                      TermVocabulary<Modifier> termVocabulary = k.next();
 603 //                      getVocabularyService().save(termVocabulary); //XIM
 604 //              }
 605
 606
 607                 //sddConfig.setSourceReference(sourceReference);
 608
 609
 610                 if (descriptiveConcepts != null) {
 611                         for (Feature feature : descriptiveConcepts) {
 612                                 Marker marker = Marker.NewInstance();
 613                                 marker.setMarkerType(descriptiveConceptMarkerType);
 614                                 feature.addMarker(marker);
 615                         }
 616                 }
 617                 saveFeatures();
 618
 619                 /*Marker markerd = Marker.NewInstance();
 620                 markerd.setMarkerType(descriptiveConceptMarker);
 621                 Feature fiture = Feature.NewInstance("Fitoure","Fitoure","Fitoure");
 622                 fiture.addMarker(markerd);
 623                 TermVocabulary<Modifier> termVocabularyState = new TermVocabulary<Modifier>("test","test","test","test");
 624                 Modifier modif = new Modifier("zoub","zab","zib");
 625                 termVocabularyState.addTerm(modif);
 626                 getVocabularyService().save(termVocabularyState);
 627                 fiture.addRecommendedModifierEnumeration(termVocabularyState);
 628                 termService.save(modif);
 629                 termService.save(fiture);*/
 630
 631                 //XIMtermService.save(editorMarkerType);
 632
 633                 //XIMtermService.save(geographicAreaMarkerType);
 634
 635                 // referenceService.saveReference(sourceReference);
 636                 for (ReferenceBase publication : publications.values()){
 637                         getReferenceService().save(publication);
 638                 }
 639
 640                 for (FeatureTree featureTree : featureTrees) {
 641                         getFeatureTreeService().save(featureTree);
 642                 }
 643                 for (TaxonomicTree taxonomicTree : taxonomicTrees) {
 644                         getTaxonTreeService().save(taxonomicTree);
 645                 }
 646                 for (Specimen specimen : specimens.values()) {
 647                         getOccurrenceService().save(specimen);
 648                 }
 649                 logger.info("end of persistence ...");
 650
 651                 return success;
 652         }
 653
 654         private void saveAnnotationType() {
 655                 for (AnnotationType annotationType: annotationTypes){
 656                         getTermService().save(annotationType);
 657                 }
 658         }
 659
 660         private void saveStatisticalMeasure() {
 661                 for (StatisticalMeasure sm : statisticalMeasures){
 662                         getTermService().save(sm);
 663                 }
 664         }
 665
 666         private void saveUnits() {
 667                 if (units != null) {
 668                         for (MeasurementUnit unit : units.values()){
 669                                 if (unit != null) {
 670                                         getTermService().save(unit);
 671                                 }
 672                         }
 673                 }
 674         }
 675
 676         private void saveAreas(MarkerType geographicAreaMarkerType) {
 677                 for (NamedArea area : namedAreas.values() ){
 678                         Marker marker = Marker.NewInstance();
 679                         marker.setMarkerType(geographicAreaMarkerType);
 680                         area.addMarker(marker);
 681                         getTermService().save(area);
 682                 }
 683         }
 684
 685         private void saveStates() {
 686                 for (State state : states.values() ){
 687                         getTermService().save(state);
 688                 }
 689         }
 690
 691         private void saveMarkerType() {
 692                 for (MarkerType markerType : markerTypes){
 693                         getTermService().save(markerType);
 694                 }
 695         }
 696
 697         private void saveModifiers() {
 698                 for (Modifier modifier : modifiers.values() ){
 699                         getTermService().save(modifier);
 700                 }
 701         }
 702
 703         private void saveFeatures() {
 704                 for (Feature feature : features.values() ){
 705                         getTermService().save(feature);
 706                 }
 707         }
 708
 709         // imports the default language of the dataset
 710         protected void importDatasetLanguage(Element elDataset, SDDImportConfigurator sddConfig){
 711                 String nameLang = elDataset.getAttributeValue("lang",xmlNamespace);
 712
 713                 if (!nameLang.equals("")) {
 714                         String iso = nameLang.substring(0, 2);
 715                         datasetLanguage = getTermService().getLanguageByIso(iso);
 716                 } else {
 717                         datasetLanguage = Language.DEFAULT();
 718                 }
 719                 if (datasetLanguage == null) {
 720                         datasetLanguage = Language.DEFAULT();
 721                 }
 722         }
 723
 724         // imports the specimens
 725         protected void importSpecimens(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig) {
 726                 logger.info("start Specimens ...");
 727                 /*      <Specimens>
 728                         <Specimen id="sp1">
 729                                 <Representation>
 730                                 <Label>TJM45337</Label>
 731                                 </Representation>
 732                         </Specimen>
 733                 </Specimens>
 734                  */
 735                 Element elSpecimens = elDataset.getChild("Specimens",sddNamespace);
 736                 if (elSpecimens != null){
 737                         List<Element> listSpecimens = elSpecimens.getChildren("Specimen", sddNamespace);
 738                         int j = 0;
 739                         for (Element elSpecimen : listSpecimens) {
 740                                 String id = elSpecimen.getAttributeValue("id");
 741                                 Specimen specimen = null;
 742                                 if (!id.equals("")) {
 743                                         specimen = Specimen.NewInstance();
 744                                         specimens.put(id,specimen);
 745                                         importRepresentation(elSpecimen, sddNamespace, specimen, id, sddConfig);
 746                                 }
 747                         }
 748
 749                 }
 750         }
 751
 752         // imports the revision data associated with the Dataset (authors, modifications)
 753         protected void importRevisionData(Element elDataset, Namespace sddNamespace){
 754                 // <RevisionData>
 755                 logger.info("start RevisionData ...");
 756                 Element elRevisionData = elDataset.getChild("RevisionData",sddNamespace);
 757                 if (elRevisionData != null){
 758                         // <Creators>
 759                         Element elCreators = elRevisionData.getChild("Creators",sddNamespace);
 760
 761                         // <Agent role="aut" ref="a1"/>
 762                         List<Element> listAgents = elCreators.getChildren("Agent", sddNamespace);
 763
 764                         int j = 0;
 765                         //for each Agent
 766                         for (Element elAgent : listAgents){
 767
 768                                 String role = elAgent.getAttributeValue("role");
 769                                 String ref = elAgent.getAttributeValue("ref");
 770                                 if (role.equals("aut")) {
 771                                         if(!ref.equals("")) {
 772                                                 authors.put(ref, null);
 773                                         }
 774                                 }
 775                                 if (role.equals("edt")) {
 776                                         if(!ref.equals("")) {
 777                                                 editors.put(ref, null);
 778                                         }
 779                                 }
 780                                 if ((++j % modCount) == 0){ logger.info("Agents handled: " + j);}
 781
 782                         }
 783
 784                         // <DateModified>2006-04-08T00:00:00</DateModified>
 785                         String stringDateModified = (String)ImportHelper.getXmlInputValue(elRevisionData, "DateModified",sddNamespace);
 786
 787                         if (stringDateModified != null) {
 788                                 SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ss");
 789                                 Date d = null;
 790                                 try {
 791                                         d = sdf.parse(stringDateModified);
 792                                 } catch(Exception e) {
 793                                         System.err.println("Exception :");
 794                                         e.printStackTrace();
 795                                 }
 796
 797                                 DateTime updated = null;
 798                                 if (d != null) {
 799                                         updated = new DateTime(d);
 800                                         sourceReference.setUpdated(updated);
 801                                         sec.setUpdated(updated);
 802                                 }
 803                         }
 804                 }
 805         }
 806
 807         // imports ipr statements associated with a dataset
 808         protected void importIPRStatements(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig){
 809                 // <IPRStatements>
 810                 logger.info("start IPRStatements ...");
 811                 Element elIPRStatements = elDataset.getChild("IPRStatements",sddNamespace);
 812                 // <IPRStatement role="Copyright">
 813                 if (elIPRStatements != null) {
 814                         List<Element> listIPRStatements = elIPRStatements.getChildren("IPRStatement", sddNamespace);
 815                         int j = 0;
 816                         //for each IPRStatement
 817
 818                         for (Element elIPRStatement : listIPRStatements){
 819
 820                                 String role = elIPRStatement.getAttributeValue("role");
 821                                 // <Label xml:lang="en-au">(c) 2003-2006 Centre for Occasional Botany.</Label>
 822                                 Element elLabel = elIPRStatement.getChild("Label",sddNamespace);
 823                                 String lang = "";
 824                                 if (elLabel != null) {
 825                                         lang = elLabel.getAttributeValue("lang",xmlNamespace);
 826                                 }
 827                                 String label = (String)ImportHelper.getXmlInputValue(elIPRStatement, "Label",sddNamespace);
 828
 829                                 if (role.equals("Copyright")) {
 830                                         Language iprLanguage = null;
 831                                         if (lang != null) {
 832                                                 if (!lang.equals("")) {
 833                                                         iprLanguage = getTermService().getLanguageByIso(lang.substring(0, 2));
 834                                                 } else {
 835                                                         iprLanguage = datasetLanguage;
 836                                                 }
 837                                         }
 838                                         if (iprLanguage == null) {
 839                                                 iprLanguage = datasetLanguage;
 840                                         }
 841                                         copyright = Rights.NewInstance(label, iprLanguage);
 842                                 }
 843
 844                                 if (copyright != null) {
 845                                         sourceReference.addRights(copyright);
 846                                         sec.addRights(copyright);
 847                                 }
 848
 849                                 if ((++j % modCount) == 0){ logger.info("IPRStatements handled: " + j);}
 850
 851                         }
 852                 }
 853         }
 854
 855         // imports the taxon names
 856         protected void importTaxonNames(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig){
 857                 // <TaxonNames>
 858                 logger.info("start TaxonNames ...");
 859                 Element elTaxonNames = elDataset.getChild("TaxonNames",sddNamespace);
 860                 // <TaxonName id="t1" uri="urn:lsid:authority:namespace:my-own-id">
 861                 if (elTaxonNames != null) {
 862                         List<Element> listTaxonNames = elTaxonNames.getChildren("TaxonName", sddNamespace);
 863                         int j = 0;
 864                         //for each TaxonName
 865                         for (Element elTaxonName : listTaxonNames){
 866
 867                                 String id = elTaxonName.getAttributeValue("id");
 868                                 String uri = elTaxonName.getAttributeValue("uri");
 869
 870                                 NonViralName tnb = null;
 871                                 if (!id.equals("")) {
 872                                         tnb = NonViralName.NewInstance(null);
 873                                         IdentifiableSource source = null;
 874                                         if (uri != null) {
 875                                                 if (!uri.equals("")) {
 876                                                         source = IdentifiableSource.NewInstance(id, "TaxonName", ReferenceFactory.newGeneric(), uri);
 877                                                 }
 878                                         } else {
 879                                                 source = IdentifiableSource.NewInstance(id, "TaxonName");
 880                                         }
 881                                         tnb.addSource(source);
 882                                         taxonNameBases.put(id,tnb);
 883                                 }
 884
 885                                 // <Representation>
 886                                 // <Label xml:lang="la">Viola hederacea Labill.</Label>
 887                                 importRepresentation(elTaxonName, sddNamespace, tnb, id, sddConfig);
 888
 889                                 if ((++j % modCount) == 0){ logger.info("TaxonNames handled: " + j);}
 890
 891                         }
 892                 }
 893         }
 894
 895         // imports the characters (categorical, quantitative and text ; sequence characters not supported) which correspond to CDM Features
 896         protected boolean importCharacters(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig){
 897                 boolean success = true;
 898                 // <Characters>
 899                 logger.info("start Characters ...");
 900                 Element elCharacters = elDataset.getChild("Characters", sddNamespace);
 901
 902                 // <CategoricalCharacter id="c1">
 903                 if (elCharacters != null) {
 904                         success &= handleCategoricalData(sddNamespace, sddConfig, elCharacters);
 905                         success &= handleQuantitativeData(sddNamespace, sddConfig, elCharacters);
 906                         success &= handleTextCharacters(sddNamespace, sddConfig, elCharacters);
 907                 }
 908
 909                 /*for (Iterator<Feature> f = features.values().iterator() ; f.hasNext() ;){
 910                         featureSet.add(f.next()); //XIM Why this line ?
 911                 }*/
 912
 913                 return success;
 914
 915         }
 916
 917         /**
 918          * @param sddNamespace
 919          * @param sddConfig
 920          * @param success
 921          * @param elCharacters
 922          * @return
 923          */
 924         private boolean handleCategoricalData(Namespace sddNamespace, SDDImportConfigurator sddConfig, Element elCharacters) {
 925                 boolean success = true;
 926                 List<Element> elCategoricalCharacters = elCharacters.getChildren("CategoricalCharacter", sddNamespace);
 927                 int j = 0;
 928                 for (Element elCategoricalCharacter : elCategoricalCharacters){
 929                         try {
 930
 931                                 String idCC = elCategoricalCharacter.getAttributeValue("id");
 932                                 Feature categoricalCharacter = Feature.NewInstance();
 933                                 categoricalCharacter.setKindOf(Feature.DESCRIPTION());
 934                                 importRepresentation(elCategoricalCharacter, sddNamespace, categoricalCharacter, idCC, sddConfig);
 935                                 categoricalCharacter.setSupportsCategoricalData(true);
 936
 937                                 // <States>
 938                                 Element elStates = elCategoricalCharacter.getChild("States",sddNamespace);
 939
 940                                 // <StateDefinition id="s1">
 941                                 List<Element> elStateDefinitions = elStates.getChildren("StateDefinition",sddNamespace);
 942                                 TermVocabulary<State> termVocabularyState = new TermVocabulary<State>();
 943                                 int k = 0;
 944                                 //for each StateDefinition
 945                                 for (Element elStateDefinition : elStateDefinitions){
 946
 947                                         if ((++k % modCount) == 0){ logger.info("StateDefinitions handled: " + (k-1));}
 948
 949                                         String idS = elStateDefinition.getAttributeValue("id");
 950                                         State state = states.get(idS);
 951                                         if (state == null){
 952                                                 state = State.NewInstance();
 953                                         }else{
 954                                                 logger.debug("State duplicate found");
 955                                         }
 956                                         importRepresentation(elStateDefinition, sddNamespace, state, idS, sddConfig);
 957
 958                                         //StateData stateData = StateData.NewInstance();
 959                                         //stateData.setState(state);
 960                                         termVocabularyState.addTerm(state);
 961                                         states.put(idS,state);
 962                                 }
 963                                 categoricalCharacter.addSupportedCategoricalEnumeration(termVocabularyState);
 964                                 features.put(idCC, categoricalCharacter);
 965
 966                         } catch (Exception e) {
 967                                 logger.warn("Import of CategoricalCharacter " + j + " failed.");
 968                                 success = false;
 969                         }
 970
 971                         if ((++j % modCount) == 0){ logger.info("CategoricalCharacters handled: " + j);}
 972
 973                 }
 974                 return success;
 975         }
 976
 977         /**
 978          * @param sddNamespace
 979          * @param sddConfig
 980          * @param elCharacters
 981          */
 982         private boolean handleQuantitativeData(Namespace sddNamespace,  SDDImportConfigurator sddConfig, Element elCharacters) {
 983                 boolean success = true;
 984                 int j;
 985                 // <QuantitativeCharacter id="c2">
 986                 List<Element> elQuantitativeCharacters = elCharacters.getChildren("QuantitativeCharacter", sddNamespace);
 987                 j = 0;
 988                 //for each QuantitativeCharacter
 989                 for (Element elQuantitativeCharacter : elQuantitativeCharacters){
 990
 991                         try {
 992
 993                                 String idQC = elQuantitativeCharacter.getAttributeValue("id");
 994
 995                                 // <Representation>
 996                                 //  <Label>Leaf length</Label>
 997                                 // </Representation>
 998                                 Feature quantitativeCharacter = Feature.NewInstance();
 999                                 quantitativeCharacter.setKindOf(Feature.DESCRIPTION());
1000                                 importRepresentation(elQuantitativeCharacter, sddNamespace, quantitativeCharacter, idQC, sddConfig);
1001
1002                                 quantitativeCharacter.setSupportsQuantitativeData(true);
1003
1004                                 // <MeasurementUnit>
1005                                 //  <Label role="Abbrev">m</Label>
1006                                 // </MeasurementUnit>
1007                                 Element elMeasurementUnit = elQuantitativeCharacter.getChild("MeasurementUnit",sddNamespace);
1008                                 String label = "";
1009                                 String role = "";
1010                                 if (elMeasurementUnit != null) {
1011                                         Element elLabel = elMeasurementUnit.getChild("Label",sddNamespace);
1012                                         role = elLabel.getAttributeValue("role");
1013                                         label = (String)ImportHelper.getXmlInputValue(elMeasurementUnit, "Label",sddNamespace);
1014                                 }
1015
1016                                 MeasurementUnit unit = null;
1017                                 if (!label.equals("")){
1018                                         if (role != null) {
1019                                                 if (role.equals("Abbrev")){
1020                                                         unit = MeasurementUnit.NewInstance(label,label,label);
1021                                                 }
1022                                         } else {
1023                                                 unit = MeasurementUnit.NewInstance(label,label,label);
1024                                         }
1025                                 }
1026
1027                                 if (unit != null) {
1028                                         units.put(idQC, unit);
1029                                 }
1030
1031                                 //<Default>
1032                                 //  <MeasurementUnitPrefix>milli</MeasurementUnitPrefix>
1033                                 //</Default>
1034                                 Element elDefault = elQuantitativeCharacter.getChild("Default",sddNamespace);
1035                                 if (elDefault != null) {
1036                                         String measurementUnitPrefix = (String)ImportHelper.getXmlInputValue(elDefault, "MeasurementUnitPrefix",sddNamespace);
1037                                         if (! measurementUnitPrefix.equals("")){
1038                                                 defaultUnitPrefixes.put(idQC, measurementUnitPrefix);
1039                                         }
1040                                 }
1041
1042                                 features.put(idQC, quantitativeCharacter);
1043
1044                         } catch (Exception e) {
1045                                 //FIXME
1046                                 logger.warn("Import of QuantitativeCharacter " + j + " failed.");
1047                                 success = false;
1048                         }
1049
1050                         if ((++j % modCount) == 0){ logger.info("QuantitativeCharacters handled: " + j);}
1051
1052                 }
1053                 return success;
1054         }
1055
1056         private boolean handleTextCharacters(Namespace sddNamespace, SDDImportConfigurator sddConfig, Element elCharacters) {
1057                 boolean success = true;
1058                 int j;
1059                 // <TextCharacter id="c3">
1060                 List<Element> elTextCharacters = elCharacters.getChildren("TextCharacter", sddNamespace);
1061                 j = 0;
1062                 //for each TextCharacter
1063                 for (Element elTextCharacter : elTextCharacters){
1064
1065                         try {
1066
1067                                 String idTC = elTextCharacter.getAttributeValue("id");
1068
1069                                 // <Representation>
1070                                 //  <Label xml:lang="en">Leaf features not covered by other characters</Label>
1071                                 // </Representation>
1072                                 Feature textCharacter = Feature.NewInstance();
1073                                 textCharacter.setKindOf(Feature.DESCRIPTION());
1074                                 importRepresentation(elTextCharacter, sddNamespace, textCharacter, idTC, sddConfig);
1075
1076                                 textCharacter.setSupportsTextData(true);
1077
1078                                 features.put(idTC, textCharacter);
1079
1080                         } catch (Exception e) {
1081                                 //FIXME
1082                                 logger.warn("Import of TextCharacter " + j + " failed.");
1083                                 success = false;
1084                         }
1085
1086                         if ((++j % modCount) == 0){ logger.info("TextCharacters handled: " + j);}
1087
1088                 }
1089                 return success;
1090         }
1091
1092         // imports the descriptions of taxa
1093         protected boolean importCodedDescriptions(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig){
1094                 boolean success = true;
1095
1096                 // <CodedDescriptions>
1097                 logger.info("start CodedDescriptions ...");
1098                 Element elCodedDescriptions = elDataset.getChild("CodedDescriptions",sddNamespace);
1099
1100                 // <CodedDescription id="D101">
1101                 if (elCodedDescriptions != null) {
1102                         List<Element> listCodedDescriptions = elCodedDescriptions.getChildren("CodedDescription", sddNamespace);
1103                         int j = 0;
1104                         //for each CodedDescription
1105                         for (Element elCodedDescription : listCodedDescriptions){
1106                                 success &= handleCodedDescription(sddNamespace, sddConfig, elCodedDescription, j);
1107                                 if ((++j % modCount) == 0){ logger.info("CodedDescriptions handled: " + j);}
1108                         }
1109                 }
1110                 return success;
1111         }
1112
1113         /**
1114          * @param sddNamespace
1115          * @param sddConfig
1116          * @param j
1117          * @param elCodedDescription
1118          * @return
1119          */
1120         private boolean handleCodedDescription(Namespace sddNamespace, SDDImportConfigurator sddConfig, Element elCodedDescription, int j) {
1121                 boolean success = true ;
1122                 try {
1123
1124                         String idCD = elCodedDescription.getAttributeValue("id");
1125
1126                         // <Representation>
1127                         //  <Label>&lt;i&gt;Viola hederacea&lt;/i&gt; Labill. as revised by R. Morris April 8, 2006</Label>
1128                         // </Representation>
1129                         TaxonDescription taxonDescription = TaxonDescription.NewInstance();
1130                         importRepresentation(elCodedDescription, sddNamespace, taxonDescription, idCD, sddConfig);
1131
1132                         // <Scope>
1133                         //  <TaxonName ref="t1"/>
1134                         //  <Citation ref="p1" location="p. 30"/>
1135                         // </Scope>
1136                         Element elScope = elCodedDescription.getChild("Scope", sddNamespace);
1137                         Taxon taxon;
1138                         if (elScope != null) {
1139                                 taxon = handleCDScope(sddNamespace, sddConfig, idCD, elScope);
1140                         } else {//in case no taxon is linked to the description, a new one is created
1141                                 taxon = handleCDNoScope(sddNamespace, sddConfig, elCodedDescription);
1142                         }
1143
1144                         // <SummaryData>
1145                         Element elSummaryData = elCodedDescription.getChild("SummaryData",sddNamespace);
1146                         if (elSummaryData != null) {
1147                                 handleSummaryCategoricalData(sddNamespace, taxonDescription, elSummaryData);
1148                                 handleSummaryQuantitativeData(sddNamespace, taxonDescription, elSummaryData);
1149                                 handleSummaryTextData(sddNamespace, taxonDescription, elSummaryData);
1150                         }
1151
1152                         if (taxon != null) {
1153                                 taxon.addDescription(taxonDescription);
1154                         }
1155
1156                         taxonDescription.setDescriptiveSystem(featureSet);
1157
1158                         taxonDescriptions.put(idCD, taxonDescription);//FIXME
1159
1160                 } catch (Exception e) {
1161                         //FIXME
1162                         logger.warn("Import of CodedDescription " + j + " failed.", e);
1163                         success = false;
1164                 }
1165                 return success;
1166         }
1167
1168         /**
1169          * @param sddNamespace
1170          * @param sddConfig
1171          * @param elCodedDescription
1172          * @param taxon
1173          * @return
1174          */
1175         private Taxon handleCDNoScope(Namespace sddNamespace,
1176                         SDDImportConfigurator sddConfig, Element elCodedDescription     ) {
1177                 Taxon taxon = null;
1178                 NonViralName nonViralName = NonViralName.NewInstance(null);
1179                 String id = new String("" + taxonNamesCount);
1180                 IdentifiableSource source = IdentifiableSource.NewInstance(id, "TaxonName");
1181                 importRepresentation(elCodedDescription, sddNamespace, nonViralName, id, sddConfig);
1182
1183                 if(sddConfig.isDoMatchTaxa()){
1184                         taxon = getTaxonService().findBestMatchingTaxon(nonViralName.getTitleCache());
1185                 }
1186
1187                 if(taxon != null){
1188                         nonViralName = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class);
1189 //                                                      taxonNameBases.put(id ,tnb);
1190 //                                                      taxonNamesCount++;
1191                         logger.info("using existing Taxon" + taxon.getTitleCache());
1192                 } else {
1193                         nonViralName.addSource(source);
1194                         taxonNameBases.put(id ,nonViralName);
1195                         taxonNamesCount++;
1196                         logger.info("creating new Taxon from TaxonName" + nonViralName.getTitleCache());
1197                         taxon = Taxon.NewInstance(nonViralName, sec);
1198                 }
1199                 return taxon;
1200         }
1201
1202         /**
1203          * @param sddNamespace
1204          * @param sddConfig
1205          * @param idCD
1206          * @param elScope
1207          * @param taxon
1208          * @return
1209          */
1210         private Taxon handleCDScope(Namespace sddNamespace, SDDImportConfigurator sddConfig,
1211                         String idCD, Element elScope) {
1212                 Taxon taxon = null;
1213                 Element elTaxonName = elScope.getChild("TaxonName", sddNamespace);
1214                 String ref = elTaxonName.getAttributeValue("ref");
1215                 NonViralName nonViralName = taxonNameBases.get(ref);
1216
1217                 if(sddConfig.isDoMatchTaxa()){
1218                         taxon = getTaxonService().findBestMatchingTaxon(nonViralName.getTitleCache());
1219                 }
1220
1221                 if(taxon != null){
1222                         logger.info("using existing Taxon" + taxon.getTitleCache());
1223                         if(!nonViralName.getUuid().equals(taxon.getName().getUuid())){
1224                                 logger.warn("TaxonNameBase entity of existing taxon does not match Name in list -> replacing Name in list");
1225                                 nonViralName = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class);
1226                         }
1227                 } else {
1228                         logger.info("creating new Taxon from TaxonName" + nonViralName.getTitleCache());
1229                         taxon = Taxon.NewInstance(nonViralName, sec);
1230                 }
1231
1232                 //citation
1233                 Element elCitation = elScope.getChild("Citation",sddNamespace);
1234                 if (elCitation != null) {
1235                         String refCitation = elCitation.getAttributeValue("ref");
1236                         if (! refCitation.equals("")){
1237                                 citations.put(idCD, refCitation);
1238                         }
1239                         String location = elCitation.getAttributeValue("location");
1240                         if (! location.equals("")){
1241                                 locations.put(idCD, location);
1242                         }
1243                 }
1244                 return taxon;
1245         }
1246
1247         /**
1248          * @param sddNamespace
1249          * @param taxonDescription
1250          * @param elSummaryData
1251          */
1252         private void handleSummaryTextData(Namespace sddNamespace,
1253                         TaxonDescription taxonDescription, Element elSummaryData) {
1254                 String ref;
1255                 int k;
1256                 // <TextChar ref="c3">
1257                 List<Element> elTextChars = elSummaryData.getChildren("TextChar", sddNamespace);
1258                 k = 0;
1259                 //for each TextChar
1260                 for (Element elTextChar : elTextChars){
1261                         if ((++k % modCount) == 0){ logger.info("TextChar handled: " + (k-1));}
1262                         ref = elTextChar.getAttributeValue("ref");
1263                         Feature feature = features.get(ref);
1264                         TextData textData = TextData.NewInstance();
1265                         textData.setFeature(feature);
1266
1267                         // <Content>Free form text</Content>
1268                         String content = (String)ImportHelper.getXmlInputValue(elTextChar, "Content",sddNamespace);
1269                         textData.putText(content, datasetLanguage);
1270                         taxonDescription.addElement(textData);
1271                 }
1272         }
1273
1274         /**
1275          * @param sddNamespace
1276          * @param taxonDescription
1277          * @param elSummaryData
1278          */
1279         private void handleSummaryQuantitativeData(Namespace sddNamespace,
1280                         TaxonDescription taxonDescription, Element elSummaryData) {
1281                 String ref;
1282                 int k;
1283                 // <Quantitative ref="c2">
1284                 List<Element> elQuantitatives = elSummaryData.getChildren("Quantitative", sddNamespace);
1285                 k = 0;
1286                 //for each Quantitative
1287                 for (Element elQuantitative : elQuantitatives){
1288                         if ((++k % modCount) == 0){ logger.warn("Quantitative handled: " + (k-1));}
1289                         ref = elQuantitative.getAttributeValue("ref");
1290                         Feature feature = features.get(ref);
1291                         QuantitativeData quantitativeData = QuantitativeData.NewInstance();
1292                         quantitativeData.setFeature(feature);
1293
1294                         MeasurementUnit unit = units.get(ref);
1295                         String prefix = defaultUnitPrefixes.get(ref);
1296                         if (unit != null) {
1297                                 String u = unit.getLabel();
1298                                 if (prefix != null) {
1299                                         u = prefix + u;
1300                                 }
1301                                 unit.setLabel(u);
1302                                 quantitativeData.setUnit(unit);
1303                         }
1304
1305                         // <Measure type="Min" value="2.3"/>
1306                         List<Element> elMeasures = elQuantitative.getChildren("Measure", sddNamespace);
1307                         int l = 0;
1308
1309                         //for each State
1310                         for (Element elMeasure : elMeasures){
1311                                 if ((++l % modCount) == 0){ logger.info("States handled: " + (l-1));}
1312                                 String type = elMeasure.getAttributeValue("type");
1313                                 String value = elMeasure.getAttributeValue("value");
1314                                 if (value.contains(",")) {
1315                                         value = value.replace(',', '.');
1316                                 }
1317                                 Float v = Float.parseFloat(value);
1318                                 //Float v = new Float(0);
1319                                 StatisticalMeasure t = null;
1320                                 if (type.equals("Min")) {
1321                                         t = StatisticalMeasure.MIN();
1322                                 } else if (type.equals("Mean")) {
1323                                         t = StatisticalMeasure.AVERAGE();
1324                                 } else if (type.equals("Max")) {
1325                                         t = StatisticalMeasure.MAX();
1326                                 } else if (type.equals("SD")) {
1327                                         t = StatisticalMeasure.STANDARD_DEVIATION();
1328                                 } else if (type.equals("N")) {
1329                                         t = StatisticalMeasure.SAMPLE_SIZE();
1330                                 } else if (type.equals("UMethLower")) {
1331                                         t = StatisticalMeasure.TYPICAL_LOWER_BOUNDARY();
1332                                 } else if (type.equals("UMethUpper")) {
1333                                         t = StatisticalMeasure.TYPICAL_UPPER_BOUNDARY();
1334                                 } else if (type.equals("Var")) {
1335                                         t = StatisticalMeasure.VARIANCE();
1336                                 } else {
1337                                         t = StatisticalMeasure.NewInstance(type,type,type);
1338                                         statisticalMeasures.add(t);
1339                                 }
1340
1341                                 StatisticalMeasurementValue statisticalValue = StatisticalMeasurementValue.NewInstance();
1342                                 statisticalValue.setValue(v);
1343                                 statisticalValue.setType(t);
1344                                 quantitativeData.addStatisticalValue(statisticalValue);
1345                                 featureData.add(statisticalValue);
1346                         }
1347                         taxonDescription.addElement(quantitativeData);
1348                 }
1349         }
1350
1351         /**
1352          * @param sddNamespace
1353          * @param taxonDescription
1354          * @param elSummaryData
1355          */
1356         private void handleSummaryCategoricalData(Namespace sddNamespace,
1357                         TaxonDescription taxonDescription, Element elSummaryData) {
1358                 String ref;
1359                 // <Categorical ref="c4">
1360                 List<Element> elCategoricals = elSummaryData.getChildren("Categorical", sddNamespace);
1361                 int k = 0;
1362                 //for each Categorical
1363                 for (Element elCategorical : elCategoricals){
1364                         if ((++k % modCount) == 0){ logger.warn("Categorical handled: " + (k-1));}
1365                         ref = elCategorical.getAttributeValue("ref");
1366                         Feature feature = features.get(ref);
1367                         CategoricalData categoricalData = CategoricalData.NewInstance();
1368                         categoricalData.setFeature(feature);
1369
1370                         // <State ref="s3"/>
1371                         List<Element> elStates = elCategorical.getChildren("State", sddNamespace);
1372                         int l = 0;
1373
1374                         //for each State
1375                         for (Element elState : elStates){
1376                                 if ((++l % modCount) == 0){ logger.info("States handled: " + (l-1));}
1377                                 ref = elState.getAttributeValue("ref");
1378                                 State state = states.get(ref);
1379                                 if (state != null) {
1380                                         StateData stateData = StateData.NewInstance();
1381                                         stateData.setState(state);
1382                                         List<Element> elModifiers = elState.getChildren("Modifier", sddNamespace);
1383                                         for (Element elModifier : elModifiers){
1384                                                 ref = elModifier.getAttributeValue("ref");
1385                                                 Modifier modifier = modifiers.get(ref);
1386                                                 if (modifier != null) {
1387                                                         stateData.addModifier(modifier);
1388                                                 }
1389                                         }
1390                                         categoricalData.addState(stateData);
1391                                 }
1392                                 taxonDescription.addElement(categoricalData);
1393                         }
1394                 }
1395         }
1396
1397         // imports the persons associated with the dataset creation, modification, related publications
1398         protected void importAgents(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig, boolean success){
1399                 // <Agents>
1400                 logger.info("start Agents ...");
1401                 Element elAgents = elDataset.getChild("Agents",sddNamespace);
1402                 if (elAgents != null) {
1403                         // <Agent id="a1">
1404                         List <Element> listAgents = elAgents.getChildren("Agent", sddNamespace);
1405                         int j = 0;
1406                         //for each Agent
1407                         for (Element elAgent : listAgents){
1408
1409                                 try {
1410
1411                                         String idA = elAgent.getAttributeValue("id");
1412
1413                                         //  <Representation>
1414                                         //   <Label>Kevin Thiele</Label>
1415                                         //   <Detail role="Description">Ali Baba is also known as r.a.m.</Detail>
1416                                         //  </Representation>
1417                                         Person person = Person.NewInstance();
1418                                         importRepresentation(elAgent, sddNamespace, person, idA, sddConfig);
1419                                         person.addSource(IdentifiableSource.NewInstance(idA, "Agent"));
1420
1421                                         /*XIM <Links>
1422                                         Element elLinks = elAgent.getChild("Links",sddNamespace);
1423
1424                                         if (elLinks != null) {
1425
1426                                                 //  <Link rel="Alternate" href="http://www.diversitycampus.net/people/hagedorn"/>
1427                                                 List<Element> listLinks = elLinks.getChildren("Link", sddNamespace);
1428                                                 int k = 0;
1429                                                 //for each Link
1430                                                 for (Element elLink : listLinks){
1431
1432                                                         try {
1433
1434                                                                 String rel = elLink.getAttributeValue("rel");
1435                                                                 String href = elLink.getAttributeValue("href");
1436
1437                                                                 Media link = Media.NewInstance();
1438                                                                 MediaRepresentation mr = MediaRepresentation.NewInstance();
1439                                                                 mr.addRepresentationPart(MediaRepresentationPart.NewInstance(href, null));
1440                                                                 link.addRepresentation(mr);
1441                                                                 person.addMedia(link);
1442
1443                                                         } catch (Exception e) {
1444                                                                 //FIXME
1445                                                                 logger.warn("Import of Link " + k + " failed.");
1446                                                                 success = false;
1447                                                         }
1448
1449                                                         if ((++k % modCount) == 0){ logger.info("Links handled: " + k);}
1450
1451                                                 }
1452                                         }
1453                                         */
1454                                         if (authors.containsKey(idA)) {
1455                                                 authors.put(idA,person);
1456                                         }
1457
1458                                         if (editors.containsKey(idA)) {
1459                                                 editors.put(idA, person);
1460                                         }
1461
1462                                 } catch (Exception e) {
1463                                         //FIXME
1464                                         logger.warn("Import of Agent " + j + " failed.");
1465                                         success = false;
1466                                 }
1467
1468                                 if ((++j % modCount) == 0){ logger.info("Agents handled: " + j);}
1469
1470                         }
1471                 }
1472         }
1473
1474         // imports publications related with the data set
1475         protected void importPublications(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig, boolean success){
1476                 /* <Publications>
1477                           <Publication id="p112">
1478                             <Representation>
1479                               <Label>Gee, X. & Haa, Y. (2003). How to be happy in five minutes. Instant Gratifications, Palm Beach.</Label>
1480                             </Representation>
1481                             <Links>
1482                             <Link rel="BasedOn" href="doi:10.1992/32311"/>
1483                             <Link rel="Alternate" href="http://some.service.net/providing/bibliographic.data"/>
1484                             </Links>
1485                         </Publications>
1486 */
1487                 logger.info("start Publications ...");
1488                 Element elPublications = elDataset.getChild("Publications",sddNamespace);
1489
1490                 if (elPublications != null) {
1491                         List<Element> listPublications = elPublications.getChildren("Publication", sddNamespace);
1492                         int j = 0;
1493                         for (Element elPublication : listPublications){
1494
1495                                 try {
1496
1497                                         String idP = elPublication.getAttributeValue("id");
1498                                         ReferenceBase publication = ReferenceFactory.newArticle();
1499                                         importRepresentation(elPublication, sddNamespace, publication, idP, sddConfig);
1500
1501                                         publications.put(idP,publication);
1502
1503                                 } catch (Exception e) {
1504                                         logger.warn("Import of Publication " + j + " failed.");
1505                                         success = false;
1506                                 }
1507
1508                                 if ((++j % modCount) == 0){ logger.info("Publications handled: " + j);}
1509
1510                         }
1511                 }
1512         }
1513
1514         // imports media objects such as images //FIXME check mediaobj
1515         protected void importMediaObjects(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig, boolean success){
1516                 // <MediaObjects>
1517                 logger.info("start MediaObjects ...");
1518                 Element elMediaObjects = elDataset.getChild("MediaObjects",sddNamespace);
1519
1520                 if (elMediaObjects != null) {
1521                         // <MediaObject id="m1">
1522                         List<Element> listMediaObjects = elMediaObjects.getChildren("MediaObject", sddNamespace);
1523                         int j = 0;
1524                         for (Element elMO : listMediaObjects){
1525
1526                                 String id = "";
1527
1528                                 try {
1529                                         String idMO = elMO.getAttributeValue("id");
1530                                         id = idMO;
1531
1532                                         //  <Representation>
1533                                         //   <Label>Image description, e.g. to be used for alt-attribute in html.</Label>
1534                                         //  </Representation>
1535                                         Media media = Media.NewInstance();
1536                                         importRepresentation(elMO, sddNamespace, media, idMO, sddConfig);
1537
1538                                         // <Type>Image</Type>
1539                                         // <Source href="http://test.edu/test.jpg"/>
1540                                         String type = (String)ImportHelper.getXmlInputValue(elMO,"Type",sddNamespace);
1541
1542                                         if ((type != null) && (type.equals("Image"))) {
1543                                                 Element elSource = elMO.getChild("Source",sddNamespace);
1544                                                 String href = elSource.getAttributeValue("href");
1545
1546                                                 ImageMetaData imageMetaData = ImageMetaData.newInstance();
1547                                                 ImageFile image = null;
1548                                                 if (href.substring(0,7).equals("http://")) {
1549                                                         try{
1550                                                                 URL url = new URL(href);
1551
1552                                                                 imageMetaData.readMetaData(url.toURI(), 0);
1553                                                                 image = ImageFile.NewInstance(url.toString(), null, imageMetaData);
1554                                                         } catch (MalformedURLException e) {
1555                                                                 logger.error("Malformed URL", e);
1556                                                         }
1557                                                 } else {
1558                                                         String sns = sddConfig.getSourceNameString();
1559                                                         File f = new File(sns);
1560                                                         File parent = f.getParentFile();
1561                                                         String fi = href;
1562                                                         //String fi = parent.toString() + File.separator + href; //TODO erase file:/
1563                                                         File file = new File(fi);
1564                                                         imageMetaData.readMetaData(file.toURI(), 0);
1565                                                         image = ImageFile.NewInstance(file.toString(), null, imageMetaData);
1566                                                 }
1567                                                 MediaRepresentation representation = MediaRepresentation.NewInstance(imageMetaData.getMimeType(), null);
1568                                                 representation.addRepresentationPart(image);
1569
1570                                                 media.addRepresentation(representation);
1571
1572                                                 ArrayList<CdmBase> lcb = (ArrayList<CdmBase>) mediaObject_ListCdmBase.get(idMO);
1573                                                 if (lcb != null) {
1574                                                         for (int k = 0; k < lcb.size(); k++) {
1575                                                                 if (lcb.get(k) instanceof DefinedTermBase) {
1576                                                                         DefinedTermBase dtb = (DefinedTermBase) lcb.get(k);
1577                                                                         // if (lcb.get(0) instanceof DefinedTermBase) {
1578                                                                         // DefinedTermBase dtb = (DefinedTermBase) lcb.get(0);
1579                                                                         //                                                                      if (dtb!=null) {
1580                                                                         //                                                                              if (k == 0) {
1581                                                                         dtb.addMedia(media);
1582                                                                         //System.out.println(dtb.getLabel());
1583                                                                         //                                                                              } else {
1584                                                                         //                                                                                      Media me = (Media) media.clone();
1585                                                                         //                                                                                      dtb.addMedia(me);
1586                                                                         //                                                                              }
1587                                                                         //                                                                      }
1588                                                                 } else if (lcb.get(k) instanceof ReferenceBase) {
1589                                                                         ReferenceBase rb = (ReferenceBase) lcb.get(k);
1590                                                                         //} else if (lcb.get(0) instanceof ReferenceBase) {
1591                                                                         //ReferenceBase rb = (ReferenceBase) lcb.get(0);
1592                                                                         // rb.setTitleCache(label);
1593                                                                         //                                                                      if (rb!=null) {
1594                                                                         //                                                                              if (k == 0) {
1595                                                                         rb.addMedia(media);
1596                                                                         //System.out.println(rb.getTitle());
1597                                                                         //                                                                              } else {
1598                                                                         //                                                                                      Media me = (Media) media.clone();
1599                                                                         //                                                                                      rb.addMedia(me);
1600                                                                         //                                                                              }
1601                                                                         //                                                                      }
1602                                                                 }/* else if (lcb.get(k) instanceof TaxonNameBase){
1603                                                                         TaxonNameBase tb = (TaxonNameBase) lcb.get(k);
1604                                                                         tb.addMedia(media);
1605                                                         }*/
1606                                                         }
1607                                                 }
1608                                         }
1609
1610                                 } catch (Exception e) {
1611                                         //FIXME
1612                                         logger.warn("Could not attach MediaObject " + j + "(SDD: " + id + ") to several objects.");
1613                                         success = false;
1614                                 }
1615
1616                                 if ((++j % modCount) == 0){ logger.info("MediaObjects handled: " + j);
1617
1618                                 }
1619                         }
1620                 }
1621         }
1622
1623         // imports the <DescriptiveConcepts> block ; DescriptiveConcepts are used as nodes in CharacterTrees and Characters as leaves
1624         // but since Modifiers can be linked to DescriptiveConcepts they are stored as features with a particular Marker
1625         protected void importDescriptiveConcepts(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig){
1626                 /* <DescriptiveConcepts>
1627                       <DescriptiveConcept id="dc0">
1628                                 <Representation>
1629                                   <Label>Fixed set of modifiers supported in Lucid3</Label>
1630                                 </Representation>
1631                                 <Modifiers>
1632                                   <Modifier id="mod1">
1633                                     <Representation>
1634                                       <Label>rarely</Label>
1635                                     </Representation>
1636                                     <ModifierClass>Frequency</ModifierClass>
1637                                     <ProportionRange lowerestimate="0.0" upperestimate="0.25"/>
1638                                   </Modifier>
1639                           </Modifiers>
1640                         </DescriptiveConcept>
1641                  </DescriptiveConcepts>
1642                  */
1643                 logger.info("start DescriptiveConcepts ...");
1644                 Element elDescriptiveConcepts = elDataset.getChild("DescriptiveConcepts",sddNamespace);
1645                 if (elDescriptiveConcepts != null) {
1646                         List<Element> listDescriptiveConcepts = elDescriptiveConcepts.getChildren("DescriptiveConcept", sddNamespace);
1647                         int j = 0;
1648
1649                         for (Element elDescriptiveConcept : listDescriptiveConcepts){
1650                                 try {
1651                                 String id = elDescriptiveConcept.getAttributeValue("id");
1652                                         Feature feature = Feature.NewInstance();
1653                                         feature.setKindOf(Feature.DESCRIPTION());
1654                                         if (!id.equals("")) {
1655                                         //       <Representation>
1656                                         //       <Label>Body</Label>
1657                                         importRepresentation(elDescriptiveConcept, sddNamespace, feature, id, sddConfig);
1658                                                 features.put(id, feature);
1659                                                 getTermService().save(feature);//XIM
1660                                                 descriptiveConcepts.add(feature);
1661                                                 // imports the modifiers
1662                                                 Element elModifiers = elDescriptiveConcept.getChild("Modifiers", sddNamespace);
1663                                         if (elModifiers !=null){
1664                                                 List<Element> listModifiers = elModifiers.getChildren("Modifier", sddNamespace);
1665                                                         TermVocabulary<Modifier> termVocabularyState = new TermVocabulary<Modifier>();
1666                                                 for (Element elModifier : listModifiers) {
1667                                                                 Modifier modif = Modifier.NewInstance();
1668                                                                 String idmod = elModifier.getAttributeValue("id");
1669                                                                 importRepresentation(elModifier, sddNamespace, modif, idmod, sddConfig);
1670                                                                 termVocabularyState.addTerm(modif);
1671                                                                 //termVocabularyStates.add(termVocabularyState);
1672                                                                 getVocabularyService().save(termVocabularyState);//XIM
1673                                                                 modifiers.put(idmod, modif);
1674                                                 }
1675                                                         feature.addRecommendedModifierEnumeration(termVocabularyState);
1676                                 }
1677
1678                                         }
1679                                 }
1680                                 catch (Exception e) {
1681                                         logger.warn("Import of DescriptiveConcept " + j + " failed.");
1682                                 }
1683                                 if ((++j % modCount) == 0){ logger.info("DescriptiveConcepts handled: " + j);}
1684
1685                         }
1686                 }
1687         }
1688
1689         // imports the <CharacterTrees> block
1690         protected void importCharacterTrees(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig, boolean success){
1691                 // <CharacterTrees>
1692                 logger.info("start CharacterTrees ...");
1693                 Element elCharacterTrees = elDataset.getChild("CharacterTrees",sddNamespace);
1694
1695                 if (elCharacterTrees != null) {
1696                         List<Element> listCharacterTrees = elCharacterTrees.getChildren("CharacterTree", sddNamespace);
1697                         int j = 0;
1698                         for (Element elCharacterTree : listCharacterTrees){
1699                                 try {
1700                                         Element elRepresentation = elCharacterTree.getChild("Representation",sddNamespace);
1701                                         String label = (String)ImportHelper.getXmlInputValue(elRepresentation,"Label",sddNamespace);
1702                                         //Element elDesignedFor = elCharacterTree.getChild("DesignedFor",sddNamespace);//TODO ?
1703
1704                                                 FeatureTree feattree =  FeatureTree.NewInstance();
1705                                                 importRepresentation(elCharacterTree, sddNamespace, feattree, "", sddConfig);
1706                                                 FeatureNode root = feattree.getRoot();
1707                                                 List<Element> listelNodes = elCharacterTree.getChildren("Nodes", sddNamespace);
1708
1709                                         //Nodes of CharacterTrees in SDD always refer to DescriptiveConcepts
1710                                                 for (Element elNodes : listelNodes) {
1711                                                         List<Element> listNodes = elNodes.getChildren("Node", sddNamespace);
1712                                                         if (listNodes != null) {
1713                                                                 for (Element elNode : listNodes){
1714                                                                         String idN = elNode.getAttributeValue("id");
1715                                                                         FeatureNode fn = null;
1716                                                                 Feature dc = null;
1717                                                                 if (idN!=null) {
1718                                                                         // DescriptiveConcepts are used as nodes in CharacterTrees
1719                                                                                 Element elDescriptiveConcept = elNode.getChild("DescriptiveConcept", sddNamespace);
1720                                                                                 if (elDescriptiveConcept != null){
1721                                                                                         String refDC = elDescriptiveConcept.getAttributeValue("ref");
1722                                                                                 dc = features.get(refDC);
1723                                                                                 fn = FeatureNode.NewInstance(dc);
1724                                                                                 }
1725                                                                         if (fn==null){
1726                                                                                         fn = FeatureNode.NewInstance();
1727                                                                                 }
1728                                                                                 Element elParent = elNode.getChild("Parent", sddNamespace);
1729                                                                         // in SDD links between Nodes are referenced by the <Parent> tag
1730                                                                                 if (elParent!=null){
1731                                                                                         String refP = elParent.getAttributeValue("ref");
1732                                                                                 if (refP!=null) {
1733                                                                                         FeatureNode parent = featureNodes.get(refP);
1734                                                                                         if (parent==null){
1735                                                                                                 root.addChild(fn); // if no parent found or the reference is broken, add the node to the root of the tree
1736                                                                                         }
1737                                                                                         else {
1738                                                                                                 parent.addChild(fn);
1739                                                                                         }
1740                                                                                 }
1741                                                                         }
1742                                                                                 else {
1743                                                                                 root.addChild(fn); // if no parent found or the reference is broken, add the node to the root of the tree
1744                                                                                 }
1745                                                                         }
1746                                                                 featureNodes.put(idN, fn);
1747                                                                 }
1748                                                 }
1749
1750                                                 // Leaves of CharacterTrees in SDD are always CharNodes (referring to Characters)
1751                                                                 List<Element> listCharNodes = elNodes.getChildren("CharNode", sddNamespace);
1752                                                 if (listCharNodes != null) {
1753                                                                 for (Element elCharNode : listCharNodes){
1754                                                                         Element elParent = elCharNode.getChild("Parent", sddNamespace);
1755                                                                         Element elCharacter = elCharNode.getChild("Character", sddNamespace);
1756                                                                         FeatureNode fn = FeatureNode.NewInstance();
1757                                                                         if (elParent!=null){
1758                                                                                 String refP = elParent.getAttributeValue("ref");
1759                                                                                 if ((refP!=null)&&(!refP.equals(""))) {
1760                                                                                 FeatureNode parent = featureNodes.get(refP);
1761                                                                                         if (parent==null){
1762                                                                                         parent = root; // if no parent found or the reference is broken, add the node to the root of the tree
1763                                                                                         }
1764                                                                                         parent.addChild(fn);
1765                                                                                 }
1766                                                                         }
1767                                                                         String refC = elCharacter.getAttributeValue("ref");
1768                                                                         if ((refC!=null)&&(!refC.equals(""))){
1769                                                                                 Feature character = features.get(refC);
1770                                                                                 fn.setFeature(character);
1771                                                                 featureNodes.put(refC, fn);
1772                                                                         }
1773                                                         }
1774                                                                         }
1775                                                                 }
1776                                                 featureTrees.add(feattree);
1777                                         }
1778
1779                                 catch (Exception e) {
1780                                         logger.warn("Import of Character tree " + j + " failed.");
1781                                         success = false;
1782                                 }
1783                                 if ((++j % modCount) == 0){ logger.info("CharacterTrees handled: " + j);}
1784
1785                         }
1786
1787                 }
1788         }
1789
1790         // imports the <TaxonHierarchies> block
1791         protected void importTaxonHierarchies(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig, boolean success){
1792
1793                 logger.info("start TaxonHierarchies ...");
1794                 Element elTaxonHierarchies = elDataset.getChild("TaxonHierarchies",sddNamespace);
1795
1796                 if (elTaxonHierarchies != null) {
1797                         List<Element> listTaxonHierarchies = elTaxonHierarchies.getChildren("TaxonHierarchy", sddNamespace);
1798                         int j = 0;
1799                         for (Element elTaxonHierarchy : listTaxonHierarchies){
1800                                 try {
1801                                         Element elRepresentation = elTaxonHierarchy.getChild("Representation",sddNamespace);
1802                                         String label = (String)ImportHelper.getXmlInputValue(elRepresentation,"Label",sddNamespace);
1803                                                 TaxonomicTree taxonomicTree =  TaxonomicTree.NewInstance(label);
1804                                                 importRepresentation(elTaxonHierarchy, sddNamespace, taxonomicTree, "", sddConfig);
1805
1806                                                 Set<TaxonNode> root = taxonomicTree.getChildNodes();
1807                                                 Element elNodes = elTaxonHierarchy.getChild("Nodes", sddNamespace); // There can be only one <Nodes> block for TaxonHierarchies
1808                                                 List<Element> listNodes = elNodes.getChildren("Node", sddNamespace);
1809
1810                                                 for (Element elNode : listNodes){
1811                                                         String idN = elNode.getAttributeValue("id");
1812                                                         TaxonNameBase tnb = null;
1813                                                         if (!idN.equals("")) {
1814                                                                 Element elTaxonName = elNode.getChild("TaxonName", sddNamespace);
1815                                                                 String refTN = elTaxonName.getAttributeValue("ref");
1816                                                                 tnb = taxonNameBases.get(refTN);
1817                                                                 Taxon taxon = (Taxon) tnb.getTaxa().iterator().next() ;
1818                                                                 Element elParent = elNode.getChild("Parent", sddNamespace);
1819                                                                 if (elParent!=null){
1820                                                                         String refP = elParent.getAttributeValue("ref");
1821                                                                         if (!refP.equals("")) {
1822                                                                                 TaxonNode parent = taxonNodes.get(refP);
1823                                                                                 TaxonNode child = parent.addChildTaxon(taxon, sec, "", Synonym.NewInstance(tnb, sec));
1824                                                                                 taxonNodes.put(idN,child);
1825                                                                         }
1826                                                                 }
1827                                                                 else {
1828                                                                         TaxonNode tn = taxonomicTree.addChildTaxon(taxon, sec, "", Synonym.NewInstance(tnb, sec)); // if no parent found or the reference is broken, add the node to the root of the tree
1829                                                                         taxonNodes.put(idN,tn);
1830                                                                 }
1831                                                         }
1832                                                 }
1833
1834                                                 taxonomicTrees.add(taxonomicTree);
1835                                         }
1836
1837                                 catch (Exception e) {
1838                                         //FIXME
1839                                         logger.warn("Import of Taxon Hierarchy " + j + " failed.");
1840                                         success = false;
1841                                 }
1842
1843                                 if ((++j % modCount) == 0){ logger.info("TaxonHierarchies handled: " + j);}
1844
1845                         }
1846
1847                 }
1848         }
1849
1850
1851         // imports the <GeographicAreas> block
1852         protected void importGeographicAreas(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig) {
1853                 Element elGeographicAreas = elDataset.getChild("GeographicAreas",sddNamespace);
1854                 if (elGeographicAreas != null) {
1855                         List<Element> listGeographicAreas = elGeographicAreas.getChildren("GeographicArea", sddNamespace);
1856                         int j = 0;
1857
1858                         for (Element elGeographicArea : listGeographicAreas){
1859
1860                                 String id = elGeographicArea.getAttributeValue("id");
1861                                 NamedArea na = new NamedArea();
1862                                 importRepresentation(elGeographicArea, sddNamespace, na, id, sddConfig);
1863                                 namedAreas.put(id,na);
1864                                                                 }
1865                         if ((++j % modCount) == 0){ logger.info("GeographicAreas handled: " + j);}
1866                                                         }
1867                                                         }
1868 }