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.DerivedUnit;
  32 import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;
  33 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  34 import eu.etaxonomy.cdm.model.occurrence.FieldObservation;
  35 import eu.etaxonomy.cdm.model.occurrence.LivingBeing;
  36 import eu.etaxonomy.cdm.model.occurrence.Observation;
  37 import eu.etaxonomy.cdm.model.occurrence.Specimen;
  38 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  39 import eu.etaxonomy.cdm.model.reference.Generic;
  40 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  41 import eu.etaxonomy.cdm.model.taxon.Taxon;
  42 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  43
  44 public class AbcdIO  extends SpecimenIoBase  implements ICdmIO {
  45
  46
  47         private static final Logger logger = Logger.getLogger(AbcdIO.class);
  48
  49         protected String fullScientificNameString;
  50         protected String nomenclatureCode;
  51         protected String institutionCode;
  52         protected String collectionCode;
  53         protected String unitID;
  54         protected String recordBasis;
  55         protected String accessionNumber;
  56         protected String collectorsNumber;
  57         protected String fieldNumber;
  58         protected Double longitude;
  59         protected Double latitude;
  60         protected String locality;
  61         protected String languageIso = null;
  62         protected String country;
  63         protected String isocountry;
  64         protected int depth;
  65         protected int altitude;
  66         protected ArrayList<String> gatheringAgentList;
  67         protected ArrayList<String> identificationList;
  68         protected ArrayList<String> namedAreaList;
  69         protected ArrayList<String> referenceList;
  70         protected ArrayList<String> multimediaObjects;
  71
  72
  73         protected ArrayList<String> knownABCDelements = new ArrayList<String>();
  74
  75
  76         public AbcdIO() {
  77                 super();
  78                 knownABCDelements.add("Identifications");
  79                 knownABCDelements.add("Identification");
  80                 knownABCDelements.add("Result");
  81                 knownABCDelements.add("TaxonIdentified");
  82                 knownABCDelements.add("ScientificName");
  83                 knownABCDelements.add("FullScientificNameString");
  84                 knownABCDelements.add("NameAtomised");
  85                 knownABCDelements.add("SourceInstitutionID");
  86                 knownABCDelements.add("SourceID");
  87                 knownABCDelements.add("UnitID");
  88                 knownABCDelements.add("RecordBasis");
  89                 knownABCDelements.add("AccessionNumber");
  90                 knownABCDelements.add("LocalityText");
  91                 knownABCDelements.add("LongitudeDecimal");
  92                 knownABCDelements.add("Country");
  93                 knownABCDelements.add("ISO3166Code");
  94                 knownABCDelements.add("CollectorsFieldNumber");
  95                 knownABCDelements.add("CollectorsNumber");
  96                 knownABCDelements.add("AccessionNumber");
  97                 knownABCDelements.add("Altitude_MeasurementOrFactText");
  98                 knownABCDelements.add("Depth");
  99                 knownABCDelements.add("NamedArea_AreaName");
 100                 knownABCDelements.add("GatheringAgent_Person_FullName");
 101         }
 102
 103         /*
 104          * Return the list of root nodes for an ABCD 2.06 XML file
 105          * @param fileName: the file's location
 106          * @return the list of root nodes ("Unit")
 107          */
 108         private static NodeList getUnitsNodeList(String fileName){
 109                 NodeList unitList = null;
 110                 try {
 111                         DocumentBuilderFactory fabrique = DocumentBuilderFactory.newInstance();
 112                         DocumentBuilder constructeur = fabrique.newDocumentBuilder();
 113                         File xml = new File(fileName);
 114                         Document document = constructeur.parse(xml);
 115                         Element racine = document.getDocumentElement();
 116                         unitList = racine.getElementsByTagName("Unit");
 117                 }catch(Exception e){
 118                         System.out.println(e);
 119                 }
 120                 return unitList;
 121         }
 122
 123
 124         public void afficherInfos(Node noeud, int niv) {
 125                 short type = noeud.getNodeType();
 126                 String nom = noeud.getNodeName();
 127                 String valeur = noeud.getNodeValue();
 128
 129                 indenter(niv, type == Node.TEXT_NODE);
 130                 if(!knownABCDelements.contains(nom)){
 131                         System.out.print(nom + " (" + type + ") = '");
 132                         if(valeur != null && !valeur.matches("^\\s+$")){
 133                                 System.out.print(valeur);
 134                                 System.out.println("'");
 135                         }
 136                 }
 137                 if ((type == Node.DOCUMENT_NODE
 138                                 || type == Node.ELEMENT_NODE)
 139                                 && noeud.hasChildNodes()) {
 140                         NodeList liste = noeud.getChildNodes();
 141                         for(int i = 0; i < liste.getLength(); i++)
 142                                 afficherInfos(liste.item(i), niv + 1);
 143                 }
 144         }
 145         public void indenter(int n, boolean texte){
 146                 String tab = "\t";
 147                 for(int i = 0; i < n; i++){
 148                         System.out.print(tab);
 149                 }
 150                 if(texte){
 151                         System.out.print(" - ");
 152                 }
 153                 else
 154                         System.out.print(" + ");
 155         }
 156
 157         /*
 158          * Store the unit's properties into variables
 159          * Look which unit is the preferred one
 160          * Look what kind of name it is supposed to be, for the parsing (Botanical, Zoological)
 161          * @param racine: the root node for a single unit
 162          */
 163         private void setUnitPropertiesXML(Element racine){
 164                 try{
 165                         NodeList group,childs,person;
 166
 167 //                      try{afficherInfos(racine, 0);}catch (Exception e) {System.out.println(e);}
 168                         group = racine.getChildNodes();
 169 //                      logger.info("ABCD ELEMENT not stored: "+group.item(i).getNodeName().toString()+" - value: "+group.item(i).getTextContent());
 170                         for (int i=0; i< group.getLength(); i++){
 171                                 if (group.item(i).getNodeName() == "Identifications"){
 172                                         group = group.item(i).getChildNodes();
 173                                         break;
 174                                 }
 175                         }
 176                         this.identificationList = new ArrayList<String>();
 177                         this.referenceList = new ArrayList<String>();
 178                         this.multimediaObjects = new ArrayList<String>();
 179
 180                         this.getScientificNames(group);
 181
 182 //                      System.out.println("this.identificationList "+this.identificationList.toString());
 183                         this.getIDs(racine);
 184                         this.getRecordBasis(racine);
 185                         this.getMultimedia(racine);
 186                         this.getNumbers(racine);
 187                         this.getGeolocation(racine);
 188                         this.getGatheringPeople(racine);
 189
 190                 } catch (Exception e) {
 191                         logger.info("Error occured while parsing XML file"+e);
 192                 }
 193         }
 194
 195
 196         private void getScientificNames(NodeList group){
 197                 NodeList identifications,results;
 198                 String tmpName = null;
 199                 for (int j=0; j< group.getLength(); j++){
 200                         if(group.item(j).getNodeName() == "Identification"){
 201                                 this.nomenclatureCode ="";
 202                                 identifications = group.item(j).getChildNodes();
 203                                 for (int m=0; m<identifications.getLength();m++){
 204                                         if(identifications.item(m).getNodeName() == "Result"){
 205                                                 results = identifications.item(m).getChildNodes();
 206                                                 for(int k=0; k<results.getLength();k++)
 207                                                         if (results.item(k).getNodeName() == "TaxonIdentified")
 208                                                                 tmpName=this.getScientificName(results.item(k));
 209                                         }
 210                                         else if(identifications.item(m).getNodeName() == "PreferredFlag")
 211                                                 this.identificationList.add(tmpName+"_preferred_"+identifications.item(m).getTextContent()+"_code_"+this.nomenclatureCode);
 212
 213                                         else if (identifications.item(m).getNodeName() == "References")
 214                                                 this.getReferences(identifications.item(m));
 215                                         else
 216                                                 if (tmpName != null)
 217                                                         this.identificationList.add(tmpName+"_preferred_"+"0"+"_code_"+this.nomenclatureCode);
 218                                 }
 219                         }
 220                 }
 221         }
 222
 223         private void getReferences(Node result){
 224                 NodeList results,reference;
 225                 results = result.getChildNodes();
 226                 for(int k=0; k<results.getLength();k++){
 227                         if (results.item(k).getNodeName() == "Reference"){
 228                                 reference = results.item(k).getChildNodes();
 229                                 for(int l=0;l<reference.getLength();l++){
 230                                         if (reference.item(l).getNodeName()=="TitleCitation")
 231                                                 referenceList.add(reference.item(l).getTextContent());
 232                                 }
 233                         }
 234                 }
 235         }
 236
 237         private String getScientificName(Node result){
 238                 NodeList taxonsIdentified, scnames;
 239                 String tmpName = "";
 240                 taxonsIdentified = result.getChildNodes();
 241                 for (int l=0; l<taxonsIdentified.getLength(); l++){
 242                         if (taxonsIdentified.item(l).getNodeName() == "ScientificName"){
 243                                 scnames = taxonsIdentified.item(l).getChildNodes();
 244                                 for (int n=0;n<scnames.getLength();n++){
 245                                         if (scnames.item(n).getNodeName() == "FullScientificNameString")
 246                                                 tmpName = scnames.item(n).getTextContent();
 247                                         if (scnames.item(n).getNodeName() == "NameAtomised"){
 248                                                 try {
 249                                                         if (scnames.item(n).hasChildNodes()){
 250
 251                                                                 this.nomenclatureCode = scnames.item(n).getChildNodes().item(1).getNodeName();
 252                                                         }
 253                                                 } catch (Exception e) {
 254                                                         this.nomenclatureCode ="";
 255                                                 }
 256                                         }
 257                                 }
 258                         }
 259                 }
 260                 return tmpName;
 261         }
 262         private void getIDs(Element racine){
 263                 NodeList group;
 264                 try {
 265                         group = racine.getElementsByTagName("SourceInstitutionID");
 266                         this.institutionCode = group.item(0).getTextContent();
 267                 } catch (NullPointerException e) {
 268                         this.institutionCode= "";
 269                 }
 270                 try {
 271                         group = racine.getElementsByTagName("SourceID");
 272                         this.collectionCode = group.item(0).getTextContent();
 273                 } catch (NullPointerException e) {
 274                         this.collectionCode = "";
 275                 }
 276                 try {
 277                         group = racine.getElementsByTagName("UnitID");
 278                         this.unitID = group.item(0).getTextContent();
 279                 } catch (NullPointerException e) {
 280                         this.unitID = "";
 281                 }
 282         }
 283
 284         private void getRecordBasis(Element racine){
 285                 NodeList group;
 286                 try {
 287                         group = racine.getElementsByTagName("RecordBasis");
 288                         this.recordBasis = group.item(0).getTextContent();
 289                 } catch (NullPointerException e) {
 290                         this.recordBasis = "";
 291                 }
 292         }
 293
 294         private void getMultimedia(Element racine){
 295                 NodeList group, multimedias, multimedia;
 296                 try {
 297                         group = racine.getElementsByTagName("MultiMediaObjects");
 298                         for(int i=0;i<group.getLength();i++){
 299                                 multimedias = group.item(i).getChildNodes();
 300                                 for (int j=0;j<multimedias.getLength();j++){
 301                                         if (multimedias.item(j).getNodeName() == "MultiMediaObject"){
 302                                                 multimedia = multimedias.item(j).getChildNodes();
 303                                                 for (int k=0;k<multimedia.getLength();k++){
 304                                                         if(multimedia.item(k).getNodeName() == "FileURI")
 305                                                                 this.multimediaObjects.add(multimedia.item(k).getTextContent());
 306                                                 }
 307                                         }
 308                                 }
 309                         }
 310                 } catch (NullPointerException e) {
 311                         System.out.println(e);
 312                 }
 313         }
 314
 315         private void getNumbers(Element racine){
 316                 NodeList group;
 317                 try {
 318                         group = racine.getElementsByTagName("AccessionNumber");
 319                         this.accessionNumber = group.item(0).getTextContent();
 320                 } catch (NullPointerException e) {
 321                         this.accessionNumber = "";
 322                 }
 323                 try {
 324                         group = racine.getElementsByTagName("CollectorsFieldNumber");
 325                         this.fieldNumber = group.item(0).getTextContent();
 326                 } catch (NullPointerException e) {
 327                         this.fieldNumber = "";
 328                 }
 329
 330                 try {
 331                         group = racine.getElementsByTagName("CollectorsNumber");
 332                         this.collectorsNumber = group.item(0).getTextContent();
 333                 } catch (NullPointerException e) {
 334                         this.collectorsNumber = "";
 335                 }
 336
 337                 try {
 338                         group = racine.getElementsByTagName("AccessionNumber");
 339                         this.accessionNumber = group.item(0).getTextContent();
 340                 } catch (NullPointerException e) {
 341                         this.accessionNumber = "";
 342                 }
 343         }
 344
 345         private void getGeolocation(Element racine){
 346                 NodeList group, childs;
 347                 try {
 348                         group = racine.getElementsByTagName("LocalityText");
 349                         this.locality = group.item(0).getTextContent();
 350                         if (group.item(0).hasAttributes())
 351                                 if (group.item(0).getAttributes().getNamedItem("lang") != null)
 352                                         this.languageIso = group.item(0).getAttributes().getNamedItem("lang").getTextContent();
 353                 } catch (NullPointerException e) {
 354                         this.locality = "";
 355                 }
 356                 try {
 357                         group = racine.getElementsByTagName("LongitudeDecimal");
 358                         this.longitude = Double.valueOf(group.item(0).getTextContent());
 359                 } catch (NullPointerException e) {
 360                         this.longitude=0.0;
 361                 }
 362                 try {
 363                         group = racine.getElementsByTagName("LatitudeDecimal");
 364                         this.latitude = Double.valueOf(group.item(0).getTextContent());
 365                 } catch (NullPointerException e) {
 366                         this.latitude=0.0;
 367                 }
 368                 try {
 369                         group = racine.getElementsByTagName("Country");
 370                         this.country = group.item(0).getTextContent();
 371                 } catch (NullPointerException e) {
 372                         this.country = "";
 373                 }
 374                 try {
 375                         group = racine.getElementsByTagName("ISO3166Code");
 376                         this.isocountry = group.item(0).getTextContent();
 377                 } catch (NullPointerException e) {
 378                         this.isocountry = "";
 379                 }
 380                 try {
 381                         group = racine.getElementsByTagName("Altitude");
 382                         for (int i=0;i<group.getLength();i++){
 383                                 childs = group.item(i).getChildNodes();
 384                                 for (int j=0;j<childs.getLength();j++){
 385                                         if (childs.item(j).getNodeName() == "MeasurementOrFactText")
 386                                                 this.altitude = Integer.valueOf(childs.item(j).getTextContent());
 387                                 }
 388                         }
 389                 } catch (NullPointerException e) {
 390                         this.altitude = -9999;
 391                 }
 392
 393                 try {
 394                         group = racine.getElementsByTagName("Depth");
 395                         this.depth = Integer.valueOf(group.item(0).getTextContent());
 396                 } catch (NullPointerException e) {
 397                         this.depth = -9999;
 398                 }
 399
 400                 try{
 401                         group = racine.getElementsByTagName("NamedArea");
 402                         this.namedAreaList = new ArrayList<String>();
 403                         for (int i=0;i<group.getLength();i++){
 404                                 childs = group.item(i).getChildNodes();
 405                                 for (int j=0; j<childs.getLength();j++){
 406                                         if (childs.item(j).getNodeName() == "AreaName")
 407                                                 this.namedAreaList.add(childs.item(j).getTextContent());
 408                                 }
 409                         }
 410                 }catch(NullPointerException e){
 411                         this.namedAreaList = new ArrayList<String>();
 412                 }
 413         }
 414
 415         private void getGatheringPeople(Element racine){
 416                 NodeList group, childs, person;
 417                 try {
 418                         group = racine.getElementsByTagName("GatheringAgent");
 419                         this.gatheringAgentList = new ArrayList<String>();
 420                         for (int i=0; i< group.getLength(); i++){
 421                                 childs = group.item(i).getChildNodes();
 422                                 for (int j=0; j<childs.getLength();j++){
 423                                         if (childs.item(j).getNodeName() == "Person"){
 424                                                 person = childs.item(j).getChildNodes();
 425                                                 for (int k=0; k<person.getLength(); k++)
 426                                                         if (person.item(k).getNodeName() == "FullName")
 427                                                                 this.gatheringAgentList.add(person.item(k).getTextContent());
 428                                         }
 429
 430                                 }
 431                         }
 432                 } catch (NullPointerException e) {
 433                         this.gatheringAgentList = new ArrayList<String>();
 434                 }
 435         }
 436
 437         private Institution getInstitution(String institutionCode, SpecimenImportConfigurator config){
 438                 Institution institution;
 439                 List<Institution> institutions;
 440                 try{
 441                         System.out.println(this.institutionCode);
 442                         institutions= config.getCdmAppController().getAgentService().searchInstitutionByCode(this.institutionCode);
 443                 }catch(Exception e){
 444                         System.out.println("BLI "+e);
 445                         institutions=new ArrayList<Institution>();
 446                 }
 447                 if (institutions.size() ==0 || !config.getReUseExistingMetadata()){
 448                         System.out.println("Institution (agent) unknown or not allowed to reuse existing metadata");
 449                         //create institution
 450                         institution = Institution.NewInstance();
 451                         institution.setCode(this.institutionCode);
 452                 }
 453                 else{
 454                         System.out.println("Institution (agent) already in the db");
 455                         institution = institutions.get(0);
 456                 }
 457                 return institution;
 458         }
 459
 460         /*
 461          * Look if the Collection does already exists
 462          * @param collectionCode: a string
 463          * @param institution: the current Institution
 464          * @param app
 465          * @return the Collection (existing or new)
 466          */
 467         private Collection getCollection(String collectionCode, Institution institution, SpecimenImportConfigurator config){
 468                 Collection collection = Collection.NewInstance();
 469                 List<Collection> collections;
 470                 try{
 471                         collections = config.getCdmAppController().getOccurrenceService().searchCollectionByCode(this.collectionCode);
 472                 }catch(Exception e){
 473                         collections=new ArrayList<Collection>();
 474                 }
 475                 if (collections.size() ==0 || !config.getReUseExistingMetadata()){
 476                         System.out.println("Collection not found or do not reuse existing metadata  "+this.collectionCode);
 477                         //create new collection
 478                         collection.setCode(this.collectionCode);
 479                         collection.setCodeStandard("GBIF");
 480                         collection.setInstitute(institution);
 481                 }
 482                 else{
 483                         boolean collectionFound=false;
 484                         for (int i=0; i<collections.size(); i++){
 485                                 collection = collections.get(i);
 486                                 try {
 487                                         if (collection.getInstitute().getCode().equalsIgnoreCase(institution.getCode())){
 488                                                 //found a collection with the same code and the same institution
 489                                                 collectionFound=true;
 490                                         }
 491                                 } catch (NullPointerException e) {}
 492                         }
 493                         if (!collectionFound){
 494                                 collection.setCode(this.collectionCode);
 495                                 collection.setCodeStandard("GBIF");
 496                                 collection.setInstitute(institution);
 497                         }
 498
 499                 }
 500                 return collection;
 501         }
 502
 503         /*
 504          *
 505          * @param app
 506          * @param derivedThing
 507          * @param sec
 508          */
 509         private void setTaxonNameBase(SpecimenImportConfigurator config, DerivedUnitBase derivedThing, ReferenceBase sec){
 510                 TaxonNameBase taxonName = null;
 511                 String fullScientificNameString;
 512                 Taxon taxon = null;
 513                 DeterminationEvent determinationEvent = null;
 514                 List<TaxonNameBase> names = null;
 515
 516                 String scientificName="";
 517                 boolean preferredFlag=false;
 518
 519                 for (int i = 0; i < this.identificationList.size(); i++) {
 520                         fullScientificNameString = this.identificationList.get(i);
 521                         fullScientificNameString = fullScientificNameString.replaceAll(" et ", " & ");
 522                         if (fullScientificNameString.indexOf("_preferred_") != -1){
 523                                 scientificName = fullScientificNameString.split("_preferred_")[0];
 524                                 String pTmp = fullScientificNameString.split("_preferred_")[1].split("_code_")[0];
 525                                 if (pTmp == "1" || pTmp.toLowerCase().indexOf("true") != -1)
 526                                         preferredFlag=true;
 527                                 else
 528                                         preferredFlag=false;
 529                         }
 530                         else scientificName = fullScientificNameString;
 531
 532                         if (fullScientificNameString.indexOf("_code_") != -1)
 533                                 this.nomenclatureCode = fullScientificNameString.split("_code_")[1];
 534
 535                         if (config.getDoAutomaticParsing())
 536                                 taxonName = this.parseScientificName(scientificName);
 537                         else
 538                                 taxonName.setTitleCache(scientificName);
 539
 540                         if (true){
 541                                 names = config.getCdmAppController().getNameService().getNamesByName(scientificName);
 542                                 if (names.size() == 0){
 543                                         System.out.println("Name not found: " + scientificName);
 544                                 }else{
 545                                         if (names.size() > 1){
 546                                                 System.out.println("More then 1 name found: " + scientificName);
 547                                         }
 548                                         System.out.println("Name found");
 549                                         taxonName = names.get(0);
 550                                 }
 551                         }
 552
 553                         config.getCdmAppController().getNameService().saveTaxonName(taxonName);
 554                         taxon = Taxon.NewInstance(taxonName, sec); //sec set null
 555
 556                         determinationEvent = DeterminationEvent.NewInstance();
 557                         determinationEvent.setTaxon(taxon);
 558                         determinationEvent.setPreferredFlag(preferredFlag);
 559                         for (int l=0;l<this.referenceList.size();l++){
 560                                 ReferenceBase reference = new Generic();
 561                                 reference.setTitleCache(this.referenceList.get(l));
 562                                 determinationEvent.addReference(reference);
 563                         }
 564                         derivedThing.addDetermination(determinationEvent);
 565                 }
 566
 567         }
 568
 569         private TaxonNameBase parseScientificName(String scientificName){
 570                 System.out.println("scientificName");
 571                 TaxonNameBase taxonName = null;
 572                 NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
 573
 574                 System.out.println("nomenclature: "+this.nomenclatureCode);
 575                 if (this.nomenclatureCode == "Zoological"){
 576                         taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICZN(),null);
 577                         if (taxonName.hasProblem())
 578                                 System.out.println("pb ICZN");}
 579                 if (this.nomenclatureCode == "Botanical"){
 580                         taxonName  = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICBN(),null);
 581                         if (taxonName.hasProblem())
 582                                 System.out.println("pb ICBN");}
 583                 if (this.nomenclatureCode == "Bacterial"){
 584                         taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNB(), null);
 585                         if (taxonName.hasProblem())
 586                                 System.out.println("pb ICNB");
 587                 }
 588                 if (this.nomenclatureCode == "Cultivar"){
 589                         taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNCP(), null);
 590                         if (taxonName.hasProblem())
 591                                 System.out.println("pb ICNCP");
 592                 }
 593                 if (this.nomenclatureCode == "Viral"){
 594                         taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICVCN(), null);
 595                         if (taxonName.hasProblem())
 596                                 System.out.println("pb ICVCN");
 597                 }
 598                 try{taxonName.hasProblem();}
 599                 catch (Exception e) {
 600                         taxonName = nvnpi.parseFullName(scientificName);
 601                 }
 602                 if (taxonName.hasProblem())
 603                         taxonName = nvnpi.parseFullName(scientificName);
 604                 return taxonName;
 605         }
 606         /*
 607          * Store the unit with its Gathering informations in the CDM
 608          */
 609         public boolean start(SpecimenImportConfigurator config){
 610                 boolean result = true;
 611                 boolean withCdm = true;
 612                 CdmApplicationController app = null;
 613                 TransactionStatus tx = null;
 614
 615                 app = config.getCdmAppController();
 616 //              try {
 617 //              app = CdmApplicationController.NewInstance(config.getDestination(), config.getDbSchemaValidation());
 618 //              } catch (DataSourceNotFoundException e1) {
 619 //              e1.printStackTrace();
 620 //              System.out.println("DataSourceNotFoundException "+e1);
 621 //              } catch (TermNotFoundException e1) {
 622 //              e1.printStackTrace();
 623 //              System.out.println("TermNotFoundException " +e1);
 624 //              }
 625
 626                 tx = app.startTransaction();
 627                 try {
 628 //                      ReferenceBase sec = Database.NewInstance();
 629 //                      sec.setTitleCache("XML DATA");
 630                         ReferenceBase sec = null;
 631
 632                         /**
 633                          * SPECIMEN OR OBSERVATION OR LIVING
 634                          */
 635                         DerivedUnitBase derivedThing = null;
 636                         //create specimen
 637                         boolean rbFound=false;
 638                         if (this.recordBasis != null){
 639                                 if (this.recordBasis.toLowerCase().startsWith("s")) {//specimen
 640                                         derivedThing = Specimen.NewInstance();
 641                                         rbFound = true;
 642                                 }
 643                                 else if (this.recordBasis.toLowerCase().startsWith("o")) {//observation
 644                                         derivedThing = Observation.NewInstance();
 645                                         rbFound = true;
 646                                 }
 647                                 else if (this.recordBasis.toLowerCase().startsWith("l")) {//living -> fossil, herbarium sheet....???
 648                                         derivedThing = LivingBeing.NewInstance();
 649                                         rbFound = true;
 650                                 }
 651                                 if (! rbFound){
 652                                         logger.info("The basis of record does not seem to be known: "+this.recordBasis);
 653                                         derivedThing = DerivedUnit.NewInstance();
 654                                 }
 655                         }
 656                         else{
 657                                 logger.info("The basis of record is null");
 658                                 derivedThing = DerivedUnit.NewInstance();
 659                         }
 660 //                      if(derivedThing == null)derivedThing=Observation.NewInstance();
 661
 662                         this.setTaxonNameBase(config, derivedThing, sec);
 663
 664
 665                         //set catalogue number (unitID)
 666                         derivedThing.setCatalogNumber(this.unitID);
 667                         derivedThing.setAccessionNumber(this.accessionNumber);
 668                         derivedThing.setCollectorsNumber(this.collectorsNumber);
 669
 670
 671                         /**
 672                          * INSTITUTION & COLLECTION
 673                          */
 674                         //manage institution
 675                         Institution institution = this.getInstitution(this.institutionCode,config);
 676                         //manage collection
 677                         Collection collection = this.getCollection(this.collectionCode, institution, config);
 678                         //link specimen & collection
 679                         derivedThing.setCollection(collection);
 680
 681                         /**
 682                          * GATHERING EVENT
 683                          */
 684
 685                         UnitsGatheringEvent unitsGatheringEvent = new UnitsGatheringEvent(config, this.locality, this.languageIso, this.longitude,
 686                                         this.latitude, this.gatheringAgentList);
 687                         UnitsGatheringArea unitsGatheringArea = new UnitsGatheringArea(this.isocountry, this.country, config);
 688                         NamedArea areaCountry = unitsGatheringArea.getArea();
 689                         unitsGatheringEvent.addArea(areaCountry);
 690                         unitsGatheringArea = new UnitsGatheringArea(this.namedAreaList);
 691                         ArrayList<NamedArea> nas = unitsGatheringArea.getAreas();
 692                         for (int i=0; i<nas.size();i++)
 693                                 unitsGatheringEvent.addArea(nas.get(i));
 694
 695
 696                         //create field/observation
 697                         FieldObservation fieldObservation = FieldObservation.NewInstance();
 698                         //add fieldNumber
 699                         fieldObservation.setFieldNumber(this.fieldNumber);
 700                         //join gatheringEvent to fieldObservation
 701                         fieldObservation.setGatheringEvent(unitsGatheringEvent.getGatheringEvent());
 702 //                      //add Multimedia URLs
 703                         if(this.multimediaObjects.size()>0){
 704                                 MediaRepresentationPart part;
 705                                 MediaRepresentation representation;
 706                                 Media media;
 707                                 for (int i=0;i<this.multimediaObjects.size();i++){
 708                                         part= MediaRepresentationPart.NewInstance(this.multimediaObjects.get(i),0);
 709                                         //TODO update the Multimedia Object without size :)
 710                                         representation = MediaRepresentation.NewInstance();
 711                                         representation.addRepresentationPart(part);
 712                                         media = Media.NewInstance();
 713                                         media.addRepresentation(representation);
 714                                         fieldObservation.addMedia(media);
 715                                 }
 716                         }
 717 //                      //link fieldObservation and specimen
 718                         DerivationEvent derivationEvent = DerivationEvent.NewInstance();
 719                         derivationEvent.addOriginal(fieldObservation);
 720                         derivedThing.addDerivationEvent(derivationEvent);
 721
 722                         /**
 723                          * SAVE AND STORE DATA
 724                          */
 725
 726                         app.getTermService().saveTerm(areaCountry);//save it sooner
 727                         for (int i=0; i<nas.size();i++)
 728                                 app.getTermService().saveTerm(nas.get(i));//save it sooner (foreach area)
 729                         app.getTermService().saveLanguageData(unitsGatheringEvent.getLocality());//save it sooner
 730                         app.getOccurrenceService().saveSpecimenOrObservationBase(derivedThing);
 731
 732                         logger.info("saved new specimen ...");
 733
 734
 735                 } catch (Exception e) {
 736                         logger.warn("Error when reading record!!");
 737                         e.printStackTrace();
 738                         result = false;
 739                 }
 740                 app.commitTransaction(tx);
 741                 System.out.println("commit done");
 742                 app.close();
 743                 return result;
 744         }
 745
 746
 747         public boolean invoke(SpecimenImportConfigurator config){
 748                 System.out.println("INVOKE Specimen Import from ABCD2.06 XML File");
 749                 AbcdIO test = new AbcdIO();
 750                 String sourceName = config.getSourceNameString();
 751                 NodeList unitsList = getUnitsNodeList(sourceName);
 752                 if (unitsList != null)
 753                 {
 754                         System.out.println("nb units to insert: "+unitsList.getLength());
 755                         for (int i=0;i<unitsList.getLength();i++){
 756                                 test.setUnitPropertiesXML((Element)unitsList.item(i));
 757                                 test.start(config);
 758                                 config.setDbSchemaValidation(DbSchemaValidation.UPDATE);
 759                         }
 760                 }
 761
 762                 return false;
 763
 764         }
 765
 766
 767         public boolean invoke(IImportConfigurator config, Map stores) {
 768                 System.out.println("invoke de ABCDio");
 769                 invoke((SpecimenImportConfigurator)config);
 770                 return false;
 771         }
 772
 773
 774
 775
 776 }