cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/abcd206/AbcdIO.java

   1 package eu.etaxonomy.cdm.io.abcd206;
   2
   3 import java.io.File;
   4 import java.util.ArrayList;
   5 import java.util.List;
   6 import java.util.Map;
   7
   8 import javax.xml.parsers.DocumentBuilder;
   9 import javax.xml.parsers.DocumentBuilderFactory;
  10
  11 import org.apache.log4j.Logger;
  12 import org.springframework.transaction.TransactionStatus;
  13 import org.w3c.dom.Document;
  14 import org.w3c.dom.Element;
  15 import org.w3c.dom.Node;
  16 import org.w3c.dom.NodeList;
  17
  18 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  19 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  20 import eu.etaxonomy.cdm.io.common.ICdmIO;
  21 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  22 import eu.etaxonomy.cdm.model.agent.Institution;
  23 import eu.etaxonomy.cdm.model.location.NamedArea;
  24 import eu.etaxonomy.cdm.model.media.Media;
  25 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  26 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  27 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  28 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  29 import eu.etaxonomy.cdm.model.occurrence.Collection;
  30 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  31 import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;
  32 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  33 import eu.etaxonomy.cdm.model.occurrence.FieldObservation;
  34 import eu.etaxonomy.cdm.model.occurrence.LivingBeing;
  35 import eu.etaxonomy.cdm.model.occurrence.Observation;
  36 import eu.etaxonomy.cdm.model.occurrence.Specimen;
  37 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  38 import eu.etaxonomy.cdm.model.reference.Generic;
  39 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  40 import eu.etaxonomy.cdm.model.taxon.Taxon;
  41 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  42
  43 public class AbcdIO  extends SpecimenIoBase  implements ICdmIO {
  44
  45
  46         private static final Logger logger = Logger.getLogger(AbcdIO.class);
  47
  48         protected String fullScientificNameString;
  49         protected String nomenclatureCode;
  50         protected String institutionCode;
  51         protected String collectionCode;
  52         protected String unitID;
  53         protected String recordBasis;
  54         protected String accessionNumber;
  55         protected String collectorsNumber;
  56         protected String fieldNumber;
  57         protected Double longitude;
  58         protected Double latitude;
  59         protected String locality;
  60         protected String languageIso = null;
  61         protected String country;
  62         protected String isocountry;
  63         protected int depth;
  64         protected int altitude;
  65         protected ArrayList<String> gatheringAgentList;
  66         protected ArrayList<String> identificationList;
  67         protected ArrayList<String> namedAreaList;
  68         protected ArrayList<String> referenceList;
  69         protected ArrayList<String> multimediaObjects;
  70
  71
  72         protected ArrayList<String> knownABCDelements = new ArrayList<String>();
  73
  74
  75         public AbcdIO() {
  76                 super();
  77                 knownABCDelements.add("Identifications");
  78                 knownABCDelements.add("Identification");
  79                 knownABCDelements.add("Result");
  80                 knownABCDelements.add("TaxonIdentified");
  81                 knownABCDelements.add("ScientificName");
  82                 knownABCDelements.add("FullScientificNameString");
  83                 knownABCDelements.add("NameAtomised");
  84                 knownABCDelements.add("SourceInstitutionID");
  85                 knownABCDelements.add("SourceID");
  86                 knownABCDelements.add("UnitID");
  87                 knownABCDelements.add("RecordBasis");
  88                 knownABCDelements.add("AccessionNumber");
  89                 knownABCDelements.add("LocalityText");
  90                 knownABCDelements.add("LongitudeDecimal");
  91                 knownABCDelements.add("Country");
  92                 knownABCDelements.add("ISO3166Code");
  93                 knownABCDelements.add("CollectorsFieldNumber");
  94                 knownABCDelements.add("CollectorsNumber");
  95                 knownABCDelements.add("AccessionNumber");
  96                 knownABCDelements.add("Altitude_MeasurementOrFactText");
  97                 knownABCDelements.add("Depth");
  98                 knownABCDelements.add("NamedArea_AreaName");
  99                 knownABCDelements.add("GatheringAgent_Person_FullName");
 100         }
 101
 102         /*
 103          * Return the list of root nodes for an ABCD 2.06 XML file
 104          * @param fileName: the file's location
 105          * @return the list of root nodes ("Unit")
 106          */
 107         private static NodeList getUnitsNodeList(String fileName){
 108                 NodeList unitList = null;
 109                 try {
 110                         DocumentBuilderFactory fabrique = DocumentBuilderFactory.newInstance();
 111                         DocumentBuilder constructeur = fabrique.newDocumentBuilder();
 112                         File xml = new File(fileName);
 113                         Document document = constructeur.parse(xml);
 114                         Element racine = document.getDocumentElement();
 115                         unitList = racine.getElementsByTagName("Unit");
 116                 }catch(Exception e){
 117                         System.out.println(e);
 118                 }
 119                 return unitList;
 120         }
 121
 122
 123         public void afficherInfos(Node noeud, int niv) {
 124                 short type = noeud.getNodeType();
 125                 String nom = noeud.getNodeName();
 126                 String valeur = noeud.getNodeValue();
 127
 128                 indenter(niv, type == Node.TEXT_NODE);
 129                 if(!knownABCDelements.contains(nom)){
 130                         System.out.print(nom + " (" + type + ") = '");
 131                         if(valeur != null && !valeur.matches("^\\s+$")){
 132                                 System.out.print(valeur);
 133                                 System.out.println("'");
 134                         }
 135                 }
 136                 if ((type == Node.DOCUMENT_NODE
 137                                 || type == Node.ELEMENT_NODE)
 138                                 && noeud.hasChildNodes()) {
 139                         NodeList liste = noeud.getChildNodes();
 140                         for(int i = 0; i < liste.getLength(); i++)
 141                                 afficherInfos(liste.item(i), niv + 1);
 142                 }
 143         }
 144         public void indenter(int n, boolean texte){
 145                 String tab = "\t";
 146                 for(int i = 0; i < n; i++){
 147                         System.out.print(tab);
 148                 }
 149                 if(texte){
 150                         System.out.print(" - ");
 151                 }
 152                 else
 153                         System.out.print(" + ");
 154         }
 155
 156         /*
 157          * Store the unit's properties into variables
 158          * Look which unit is the preferred one
 159          * Look what kind of name it is supposed to be, for the parsing (Botanical, Zoological)
 160          * @param racine: the root node for a single unit
 161          */
 162         private void setUnitPropertiesXML(Element racine){
 163                 try{
 164                         NodeList group,childs,person;
 165
 166 //                      try{afficherInfos(racine, 0);}catch (Exception e) {System.out.println(e);}
 167                         group = racine.getChildNodes();
 168 //                      logger.info("ABCD ELEMENT not stored: "+group.item(i).getNodeName().toString()+" - value: "+group.item(i).getTextContent());
 169                         for (int i=0; i< group.getLength(); i++){
 170                                 if (group.item(i).getNodeName() == "Identifications"){
 171                                         group = group.item(i).getChildNodes();
 172                                         break;
 173                                 }
 174                         }
 175                         this.identificationList = new ArrayList<String>();
 176                         this.referenceList = new ArrayList<String>();
 177                         this.multimediaObjects = new ArrayList<String>();
 178
 179                         this.getScientificNames(group);
 180
 181 //                      System.out.println("this.identificationList "+this.identificationList.toString());
 182                         this.getIDs(racine);
 183                         this.getRecordBasis(racine);
 184                         this.getMultimedia(racine);
 185                         this.getNumbers(racine);
 186                         this.getGeolocation(racine);
 187                         this.getGatheringPeople(racine);
 188
 189                 } catch (Exception e) {
 190                         logger.info("Error occured while parsing XML file"+e);
 191                 }
 192         }
 193
 194
 195         private void getScientificNames(NodeList group){
 196                 NodeList identifications,results;
 197                 String tmpName = null;
 198                 for (int j=0; j< group.getLength(); j++){
 199                         if(group.item(j).getNodeName() == "Identification"){
 200                                 this.nomenclatureCode ="";
 201                                 identifications = group.item(j).getChildNodes();
 202                                 for (int m=0; m<identifications.getLength();m++){
 203                                         if(identifications.item(m).getNodeName() == "Result"){
 204                                                 results = identifications.item(m).getChildNodes();
 205                                                 for(int k=0; k<results.getLength();k++)
 206                                                         if (results.item(k).getNodeName() == "TaxonIdentified")
 207                                                                 tmpName=this.getScientificName(results.item(k));
 208                                         }
 209                                         else if(identifications.item(m).getNodeName() == "PreferredFlag")
 210                                                 this.identificationList.add(tmpName+"_preferred_"+identifications.item(m).getTextContent()+"_code_"+this.nomenclatureCode);
 211
 212                                         else if (identifications.item(m).getNodeName() == "References")
 213                                                 this.getReferences(identifications.item(m));
 214                                         else
 215                                                 if (tmpName != null)
 216                                                         this.identificationList.add(tmpName+"_preferred_"+"0"+"_code_"+this.nomenclatureCode);
 217                                 }
 218                         }
 219                 }
 220         }
 221
 222         private void getReferences(Node result){
 223                 NodeList results,reference;
 224                 results = result.getChildNodes();
 225                 for(int k=0; k<results.getLength();k++){
 226                         if (results.item(k).getNodeName() == "Reference"){
 227                                 reference = results.item(k).getChildNodes();
 228                                 for(int l=0;l<reference.getLength();l++){
 229                                         if (reference.item(l).getNodeName()=="TitleCitation")
 230                                                 referenceList.add(reference.item(l).getTextContent());
 231                                 }
 232                         }
 233                 }
 234         }
 235
 236         private String getScientificName(Node result){
 237                 NodeList taxonsIdentified, scnames;
 238                 String tmpName = "";
 239                 taxonsIdentified = result.getChildNodes();
 240                 for (int l=0; l<taxonsIdentified.getLength(); l++){
 241                         if (taxonsIdentified.item(l).getNodeName() == "ScientificName"){
 242                                 scnames = taxonsIdentified.item(l).getChildNodes();
 243                                 for (int n=0;n<scnames.getLength();n++){
 244                                         if (scnames.item(n).getNodeName() == "FullScientificNameString")
 245                                                 tmpName = scnames.item(n).getTextContent();
 246                                         if (scnames.item(n).getNodeName() == "NameAtomised"){
 247                                                 try {
 248                                                         if (scnames.item(n).hasChildNodes()){
 249
 250                                                                 this.nomenclatureCode = scnames.item(n).getChildNodes().item(1).getNodeName();
 251                                                         }
 252                                                 } catch (Exception e) {
 253                                                         this.nomenclatureCode ="";
 254                                                 }
 255                                         }
 256                                 }
 257                         }
 258                 }
 259                 return tmpName;
 260         }
 261         private void getIDs(Element racine){
 262                 NodeList group;
 263                 try {
 264                         group = racine.getElementsByTagName("SourceInstitutionID");
 265                         this.institutionCode = group.item(0).getTextContent();
 266                 } catch (NullPointerException e) {
 267                         this.institutionCode= "";
 268                 }
 269                 try {
 270                         group = racine.getElementsByTagName("SourceID");
 271                         this.collectionCode = group.item(0).getTextContent();
 272                 } catch (NullPointerException e) {
 273                         this.collectionCode = "";
 274                 }
 275                 try {
 276                         group = racine.getElementsByTagName("UnitID");
 277                         this.unitID = group.item(0).getTextContent();
 278                 } catch (NullPointerException e) {
 279                         this.unitID = "";
 280                 }
 281         }
 282
 283         private void getRecordBasis(Element racine){
 284                 NodeList group;
 285                 try {
 286                         group = racine.getElementsByTagName("RecordBasis");
 287                         this.recordBasis = group.item(0).getTextContent();
 288                 } catch (NullPointerException e) {
 289                         this.recordBasis = "";
 290                 }
 291         }
 292
 293         private void getMultimedia(Element racine){
 294                 NodeList group, multimedias, multimedia;
 295                 try {
 296                         group = racine.getElementsByTagName("MultiMediaObjects");
 297                         for(int i=0;i<group.getLength();i++){
 298                                 multimedias = group.item(i).getChildNodes();
 299                                 for (int j=0;j<multimedias.getLength();j++){
 300                                         if (multimedias.item(j).getNodeName() == "MultiMediaObject"){
 301                                                 multimedia = multimedias.item(j).getChildNodes();
 302                                                 for (int k=0;k<multimedia.getLength();k++){
 303                                                         if(multimedia.item(k).getNodeName() == "FileURI")
 304                                                                 this.multimediaObjects.add(multimedia.item(k).getTextContent());
 305                                                 }
 306                                         }
 307                                 }
 308                         }
 309                 } catch (NullPointerException e) {
 310                         System.out.println(e);
 311                 }
 312         }
 313
 314         private void getNumbers(Element racine){
 315                 NodeList group;
 316                 try {
 317                         group = racine.getElementsByTagName("AccessionNumber");
 318                         this.accessionNumber = group.item(0).getTextContent();
 319                 } catch (NullPointerException e) {
 320                         this.accessionNumber = "";
 321                 }
 322                 try {
 323                         group = racine.getElementsByTagName("CollectorsFieldNumber");
 324                         this.fieldNumber = group.item(0).getTextContent();
 325                 } catch (NullPointerException e) {
 326                         this.fieldNumber = "";
 327                 }
 328
 329                 try {
 330                         group = racine.getElementsByTagName("CollectorsNumber");
 331                         this.collectorsNumber = group.item(0).getTextContent();
 332                 } catch (NullPointerException e) {
 333                         this.collectorsNumber = "";
 334                 }
 335
 336                 try {
 337                         group = racine.getElementsByTagName("AccessionNumber");
 338                         this.accessionNumber = group.item(0).getTextContent();
 339                 } catch (NullPointerException e) {
 340                         this.accessionNumber = "";
 341                 }
 342         }
 343
 344         private void getGeolocation(Element racine){
 345                 NodeList group, childs;
 346                 try {
 347                         group = racine.getElementsByTagName("LocalityText");
 348                         this.locality = group.item(0).getTextContent();
 349                         if (group.item(0).hasAttributes())
 350                                 if (group.item(0).getAttributes().getNamedItem("lang") != null)
 351                                         this.languageIso = group.item(0).getAttributes().getNamedItem("lang").getTextContent();
 352                 } catch (NullPointerException e) {
 353                         this.locality = "";
 354                 }
 355                 try {
 356                         group = racine.getElementsByTagName("LongitudeDecimal");
 357                         this.longitude = Double.valueOf(group.item(0).getTextContent());
 358                 } catch (NullPointerException e) {
 359                         this.longitude=0.0;
 360                 }
 361                 try {
 362                         group = racine.getElementsByTagName("LatitudeDecimal");
 363                         this.latitude = Double.valueOf(group.item(0).getTextContent());
 364                 } catch (NullPointerException e) {
 365                         this.latitude=0.0;
 366                 }
 367                 try {
 368                         group = racine.getElementsByTagName("Country");
 369                         this.country = group.item(0).getTextContent();
 370                 } catch (NullPointerException e) {
 371                         this.country = "";
 372                 }
 373                 try {
 374                         group = racine.getElementsByTagName("ISO3166Code");
 375                         this.isocountry = group.item(0).getTextContent();
 376                 } catch (NullPointerException e) {
 377                         this.isocountry = "";
 378                 }
 379                 try {
 380                         group = racine.getElementsByTagName("Altitude");
 381                         for (int i=0;i<group.getLength();i++){
 382                                 childs = group.item(i).getChildNodes();
 383                                 for (int j=0;j<childs.getLength();j++){
 384                                         if (childs.item(j).getNodeName() == "MeasurementOrFactText")
 385                                                 this.altitude = Integer.valueOf(childs.item(j).getTextContent());
 386                                 }
 387                         }
 388                 } catch (NullPointerException e) {
 389                         this.altitude = -9999;
 390                 }
 391
 392                 try {
 393                         group = racine.getElementsByTagName("Depth");
 394                         this.depth = Integer.valueOf(group.item(0).getTextContent());
 395                 } catch (NullPointerException e) {
 396                         this.depth = -9999;
 397                 }
 398
 399                 try{
 400                         group = racine.getElementsByTagName("NamedArea");
 401                         this.namedAreaList = new ArrayList<String>();
 402                         for (int i=0;i<group.getLength();i++){
 403                                 childs = group.item(i).getChildNodes();
 404                                 for (int j=0; j<childs.getLength();j++){
 405                                         if (childs.item(j).getNodeName() == "AreaName")
 406                                                 this.namedAreaList.add(childs.item(j).getTextContent());
 407                                 }
 408                         }
 409                 }catch(NullPointerException e){
 410                         this.namedAreaList = new ArrayList<String>();
 411                 }
 412         }
 413
 414         private void getGatheringPeople(Element racine){
 415                 NodeList group, childs, person;
 416                 try {
 417                         group = racine.getElementsByTagName("GatheringAgent");
 418                         this.gatheringAgentList = new ArrayList<String>();
 419                         for (int i=0; i< group.getLength(); i++){
 420                                 childs = group.item(i).getChildNodes();
 421                                 for (int j=0; j<childs.getLength();j++){
 422                                         if (childs.item(j).getNodeName() == "Person"){
 423                                                 person = childs.item(j).getChildNodes();
 424                                                 for (int k=0; k<person.getLength(); k++)
 425                                                         if (person.item(k).getNodeName() == "FullName")
 426                                                                 this.gatheringAgentList.add(person.item(k).getTextContent());
 427                                         }
 428
 429                                 }
 430                         }
 431                 } catch (NullPointerException e) {
 432                         this.gatheringAgentList = new ArrayList<String>();
 433                 }
 434         }
 435
 436         private Institution getInstitution(String institutionCode, SpecimenImportConfigurator config){
 437                 Institution institution;
 438                 List<Institution> institutions;
 439                 try{
 440                         System.out.println(this.institutionCode);
 441                         institutions= config.getCdmAppController().getAgentService().searchInstitutionByCode(this.institutionCode);
 442                 }catch(Exception e){
 443                         System.out.println("BLI "+e);
 444                         institutions=new ArrayList<Institution>();
 445                 }
 446                 if (institutions.size() ==0 || !config.getReUseExistingMetadata()){
 447                         System.out.println("Institution (agent) unknown or not allowed to reuse existing metadata");
 448                         //create institution
 449                         institution = Institution.NewInstance();
 450                         institution.setCode(this.institutionCode);
 451                 }
 452                 else{
 453                         System.out.println("Institution (agent) already in the db");
 454                         institution = institutions.get(0);
 455                 }
 456                 return institution;
 457         }
 458
 459         /*
 460          * Look if the Collection does already exists
 461          * @param collectionCode: a string
 462          * @param institution: the current Institution
 463          * @param app
 464          * @return the Collection (existing or new)
 465          */
 466         private Collection getCollection(String collectionCode, Institution institution, SpecimenImportConfigurator config){
 467                 Collection collection = Collection.NewInstance();
 468                 List<Collection> collections;
 469                 try{
 470                         collections = config.getCdmAppController().getOccurrenceService().searchCollectionByCode(this.collectionCode);
 471                 }catch(Exception e){
 472                         collections=new ArrayList<Collection>();
 473                 }
 474                 if (collections.size() ==0 || !config.getReUseExistingMetadata()){
 475                         System.out.println("Collection not found or do not reuse existing metadata  "+this.collectionCode);
 476                         //create new collection
 477                         collection.setCode(this.collectionCode);
 478                         collection.setCodeStandard("GBIF");
 479                         collection.setInstitute(institution);
 480                 }
 481                 else{
 482                         boolean collectionFound=false;
 483                         for (int i=0; i<collections.size(); i++){
 484                                 collection = collections.get(i);
 485                                 try {
 486                                         if (collection.getInstitute().getCode().equalsIgnoreCase(institution.getCode())){
 487                                                 //found a collection with the same code and the same institution
 488                                                 collectionFound=true;
 489                                         }
 490                                 } catch (NullPointerException e) {}
 491                         }
 492                         if (!collectionFound){
 493                                 collection.setCode(this.collectionCode);
 494                                 collection.setCodeStandard("GBIF");
 495                                 collection.setInstitute(institution);
 496                         }
 497
 498                 }
 499                 return collection;
 500         }
 501
 502         /*
 503          *
 504          * @param app
 505          * @param derivedThing
 506          * @param sec
 507          */
 508         private void setTaxonNameBase(SpecimenImportConfigurator config, DerivedUnitBase derivedThing, ReferenceBase sec){
 509                 TaxonNameBase taxonName = null;
 510                 String fullScientificNameString;
 511                 Taxon taxon = null;
 512                 DeterminationEvent determinationEvent = null;
 513                 List<TaxonNameBase> names = null;
 514
 515                 String scientificName="";
 516                 boolean preferredFlag=false;
 517
 518                 for (int i = 0; i < this.identificationList.size(); i++) {
 519                         fullScientificNameString = this.identificationList.get(i);
 520                         fullScientificNameString = fullScientificNameString.replaceAll(" et ", " & ");
 521                         if (fullScientificNameString.indexOf("_preferred_") != -1){
 522                                 scientificName = fullScientificNameString.split("_preferred_")[0];
 523                                 String pTmp = fullScientificNameString.split("_preferred_")[1].split("_code_")[0];
 524                                 if (pTmp == "1" || pTmp.toLowerCase().indexOf("true") != -1)
 525                                         preferredFlag=true;
 526                                 else
 527                                         preferredFlag=false;
 528                         }
 529                         else scientificName = fullScientificNameString;
 530
 531                         if (fullScientificNameString.indexOf("_code_") != -1)
 532                                 this.nomenclatureCode = fullScientificNameString.split("_code_")[1];
 533
 534                         if (config.getDoAutomaticParsing())
 535                                 taxonName = this.parseScientificName(scientificName);
 536                         else taxonName.setTitleCache(scientificName);
 537
 538                         if (true){
 539                                 names = config.getCdmAppController().getNameService().getNamesByName(scientificName);
 540                                 if (names.size() == 0){
 541                                         System.out.println("Name not found: " + scientificName);
 542                                 }else{
 543                                         if (names.size() > 1){
 544                                                 System.out.println("More then 1 name found: " + scientificName);
 545                                         }
 546                                         System.out.println("Name found");
 547                                         taxonName = names.get(0);
 548                                 }
 549                         }
 550
 551                         config.getCdmAppController().getNameService().saveTaxonName(taxonName);
 552                         taxon = Taxon.NewInstance(taxonName, sec); //sec set null
 553
 554                         determinationEvent = DeterminationEvent.NewInstance();
 555                         determinationEvent.setTaxon(taxon);
 556                         determinationEvent.setPreferredFlag(preferredFlag);
 557                         for (int l=0;l<this.referenceList.size();l++){
 558                                 ReferenceBase reference = new Generic();
 559                                 reference.setTitleCache(this.referenceList.get(l));
 560                                 determinationEvent.addReference(reference);
 561                         }
 562                         derivedThing.addDetermination(determinationEvent);
 563                 }
 564
 565         }
 566
 567         private TaxonNameBase parseScientificName(String scientificName){
 568                 System.out.println("scientificName");
 569                 TaxonNameBase taxonName = null;
 570                 NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
 571
 572                 System.out.println("nomenclature: "+this.nomenclatureCode);
 573                 if (this.nomenclatureCode == "Zoological"){
 574                         taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICZN(),null);
 575                         if (taxonName.hasProblem())
 576                                 System.out.println("pb ICZN");}
 577                 if (this.nomenclatureCode == "Botanical"){
 578                         taxonName  = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICBN(),null);
 579                         if (taxonName.hasProblem())
 580                                 System.out.println("pb ICBN");}
 581                 if (this.nomenclatureCode == "Bacterial"){
 582                         taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNB(), null);
 583                         if (taxonName.hasProblem())
 584                                 System.out.println("pb ICNB");
 585                 }
 586                 if (this.nomenclatureCode == "Cultivar"){
 587                         taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNCP(), null);
 588                         if (taxonName.hasProblem())
 589                                 System.out.println("pb ICNCP");
 590                 }
 591                 if (this.nomenclatureCode == "Viral"){
 592                         taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICVCN(), null);
 593                         if (taxonName.hasProblem())
 594                                 System.out.println("pb ICVCN");
 595                 }
 596                 try{taxonName.hasProblem();}
 597                 catch (Exception e) {
 598                         taxonName = nvnpi.parseFullName(scientificName);
 599                 }
 600                 if (taxonName.hasProblem())
 601                         taxonName = nvnpi.parseFullName(scientificName);
 602                 return taxonName;
 603         }
 604         /*
 605          * Store the unit with its Gathering informations in the CDM
 606          */
 607         public boolean start(SpecimenImportConfigurator config){
 608                 boolean result = true;
 609                 boolean withCdm = true;
 610                 CdmApplicationController app = null;
 611                 TransactionStatus tx = null;
 612
 613                 app = config.getCdmAppController();
 614 //              try {
 615 //              app = CdmApplicationController.NewInstance(config.getDestination(), config.getDbSchemaValidation());
 616 //              } catch (DataSourceNotFoundException e1) {
 617 //              e1.printStackTrace();
 618 //              System.out.println("DataSourceNotFoundException "+e1);
 619 //              } catch (TermNotFoundException e1) {
 620 //              e1.printStackTrace();
 621 //              System.out.println("TermNotFoundException " +e1);
 622 //              }
 623
 624                 tx = app.startTransaction();
 625                 try {
 626 //                      ReferenceBase sec = Database.NewInstance();
 627 //                      sec.setTitleCache("XML DATA");
 628                         ReferenceBase sec = null;
 629
 630                         /**
 631                          * SPECIMEN OR OBSERVATION OR LIVING
 632                          */
 633                         DerivedUnitBase derivedThing = null;
 634                         //create specimen
 635                         if (this.recordBasis != null){
 636                                 if (this.recordBasis.toLowerCase().startsWith("s")) {//specimen
 637                                         derivedThing = Specimen.NewInstance();
 638                                 }
 639                                 else if (this.recordBasis.toLowerCase().startsWith("o")) {//observation
 640                                         derivedThing = Observation.NewInstance();
 641                                 }
 642                                 else if (this.recordBasis.toLowerCase().startsWith("l")) {//living -> fossil, herbarium sheet....???
 643                                         derivedThing = LivingBeing.NewInstance();
 644                                 }
 645                         }
 646                         if (derivedThing == null)
 647                                 derivedThing = Observation.NewInstance();
 648
 649                         this.setTaxonNameBase(config, derivedThing, sec);
 650
 651
 652                         //set catalogue number (unitID)
 653                         derivedThing.setCatalogNumber(this.unitID);
 654                         derivedThing.setAccessionNumber(this.accessionNumber);
 655                         derivedThing.setCollectorsNumber(this.collectorsNumber);
 656
 657
 658                         /**
 659                          * INSTITUTION & COLLECTION
 660                          */
 661                         //manage institution
 662                         Institution institution = this.getInstitution(this.institutionCode,config);
 663                         //manage collection
 664                         Collection collection = this.getCollection(this.collectionCode, institution, config);
 665                         //link specimen & collection
 666                         derivedThing.setCollection(collection);
 667
 668                         /**
 669                          * GATHERING EVENT
 670                          */
 671
 672                         UnitsGatheringEvent unitsGatheringEvent = new UnitsGatheringEvent(config, this.locality, this.languageIso, this.longitude,
 673                                         this.latitude, this.gatheringAgentList);
 674                         UnitsGatheringArea unitsGatheringArea = new UnitsGatheringArea(this.isocountry, this.country, config);
 675                         NamedArea areaCountry = unitsGatheringArea.getArea();
 676                         unitsGatheringEvent.addArea(areaCountry);
 677                         unitsGatheringArea = new UnitsGatheringArea(this.namedAreaList);
 678                         ArrayList<NamedArea> nas = unitsGatheringArea.getAreas();
 679                         for (int i=0; i<nas.size();i++)
 680                                 unitsGatheringEvent.addArea(nas.get(i));
 681
 682
 683                         //create field/observation
 684                         FieldObservation fieldObservation = FieldObservation.NewInstance();
 685                         //add fieldNumber
 686                         fieldObservation.setFieldNumber(this.fieldNumber);
 687                         //join gatheringEvent to fieldObservation
 688                         fieldObservation.setGatheringEvent(unitsGatheringEvent.getGatheringEvent());
 689 //                      //add Multimedia URLs
 690                         if(this.multimediaObjects.size()>0){
 691                                 MediaRepresentationPart part;
 692                                 MediaRepresentation representation;
 693                                 Media media;
 694                                 for (int i=0;i<this.multimediaObjects.size();i++){
 695                                         part= MediaRepresentationPart.NewInstance(this.multimediaObjects.get(i),0);
 696                                         //TODO update the Multimedia Object without size :)
 697                                         representation = MediaRepresentation.NewInstance();
 698                                         representation.addRepresentationPart(part);
 699                                         media = Media.NewInstance();
 700                                         media.addRepresentation(representation);
 701                                         fieldObservation.addMedia(media);
 702                                 }
 703                         }
 704 //                      //link fieldObservation and specimen
 705                         DerivationEvent derivationEvent = DerivationEvent.NewInstance();
 706                         derivationEvent.addOriginal(fieldObservation);
 707                         derivedThing.addDerivationEvent(derivationEvent);
 708
 709                         /**
 710                          * SAVE AND STORE DATA
 711                          */
 712
 713                         app.getTermService().saveTerm(areaCountry);//save it sooner
 714                         for (int i=0; i<nas.size();i++)
 715                                 app.getTermService().saveTerm(nas.get(i));//save it sooner (foreach area)
 716                         app.getTermService().saveLanguageData(unitsGatheringEvent.getLocality());//save it sooner
 717                         app.getOccurrenceService().saveSpecimenOrObservationBase(derivedThing);
 718
 719                         logger.info("saved new specimen ...");
 720
 721
 722                 } catch (Exception e) {
 723                         logger.warn("Error when reading record!!");
 724                         e.printStackTrace();
 725                         result = false;
 726                 }
 727                 app.commitTransaction(tx);
 728                 System.out.println("commit done");
 729                 app.close();
 730                 return result;
 731         }
 732
 733
 734         public boolean invoke(SpecimenImportConfigurator config){
 735                 System.out.println("INVOKE Specimen Import from ABCD2.06 XML File");
 736                 AbcdIO test = new AbcdIO();
 737                 String sourceName = config.getSourceNameString();
 738                 NodeList unitsList = getUnitsNodeList(sourceName);
 739                 if (unitsList != null)
 740                 {
 741                         System.out.println("nb units to insert: "+unitsList.getLength());
 742                         for (int i=0;i<unitsList.getLength();i++){
 743                                 test.setUnitPropertiesXML((Element)unitsList.item(i));
 744                                 test.start(config);
 745                                 config.setDbSchemaValidation(DbSchemaValidation.UPDATE);
 746                         }
 747                 }
 748
 749                 return false;
 750
 751         }
 752
 753
 754         public boolean invoke(IImportConfigurator config, Map stores) {
 755                 System.out.println("invoke de ABCDio");
 756                 invoke((SpecimenImportConfigurator)config);
 757                 return false;
 758         }
 759
 760
 761
 762
 763 }