app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoTaxonImport.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.caryo;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.HashMap;
  15 import java.util.HashSet;
  16 import java.util.Map;
  17 import java.util.Set;
  18
  19 import org.apache.commons.lang.StringUtils;
  20 import org.apache.log4j.Logger;
  21 import org.springframework.stereotype.Component;
  22
  23 import eu.etaxonomy.cdm.io.common.DbImportBase;
  24 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  25 import eu.etaxonomy.cdm.io.common.Source;
  26 import eu.etaxonomy.cdm.model.agent.Person;
  27 import eu.etaxonomy.cdm.model.agent.Team;
  28 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  29 import eu.etaxonomy.cdm.model.common.Annotation;
  30 import eu.etaxonomy.cdm.model.common.CdmBase;
  31 import eu.etaxonomy.cdm.model.common.Language;
  32 import eu.etaxonomy.cdm.model.common.OriginalSourceType;
  33 import eu.etaxonomy.cdm.model.common.TimePeriod;
  34 import eu.etaxonomy.cdm.model.name.BotanicalName;
  35 import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
  36 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  37 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  38 import eu.etaxonomy.cdm.model.name.Rank;
  39 import eu.etaxonomy.cdm.model.reference.IArticle;
  40 import eu.etaxonomy.cdm.model.reference.IBook;
  41 import eu.etaxonomy.cdm.model.reference.IBookSection;
  42 import eu.etaxonomy.cdm.model.reference.IJournal;
  43 import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
  44 import eu.etaxonomy.cdm.model.reference.Reference;
  45 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  46 import eu.etaxonomy.cdm.model.taxon.Classification;
  47 import eu.etaxonomy.cdm.model.taxon.Synonym;
  48 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  49 import eu.etaxonomy.cdm.model.taxon.Taxon;
  50 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  51 import eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy;
  52 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  53 import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser;
  54 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  55
  56
  57 /**
  58  * @author a.mueller
  59  * @created 20.02.2010
  60  * @version 1.0
  61  */
  62 @Component
  63 public class CaryoTaxonImport  extends DbImportBase<CaryoImportState, CaryoImportConfigurator> {
  64         private static final Logger logger = Logger.getLogger(CaryoTaxonImport.class);
  65
  66         private int modCount = 10000;
  67         private static final String pluralString = "taxa";
  68         private static final String dbTableName = "CARYOPHYLLALES";
  69
  70
  71
  72         private Map<String, Taxon> familyMap = new HashMap<String, Taxon>();
  73         private Map<String, Person> personMap = new HashMap<String, Person>();
  74         private Map<String, Team> teamMap = new HashMap<String, Team>();
  75         private Map<String, TeamOrPersonBase> inAuthorMap = new HashMap<String, TeamOrPersonBase>();
  76         private Map<String, IJournal> journalMap = new HashMap<String, IJournal>();
  77         private Map<String, IBook> bookMap = new HashMap<String, IBook>();
  78
  79
  80         private Classification classification;
  81
  82
  83
  84         public CaryoTaxonImport(){
  85                 super(dbTableName, pluralString);
  86         }
  87
  88
  89
  90
  91         /* (non-Javadoc)
  92          * @see eu.etaxonomy.cdm.io.common.DbImportBase#getIdQuery(eu.etaxonomy.cdm.io.common.DbImportStateBase)
  93          */
  94         @Override
  95         protected String getIdQuery(CaryoImportState state) {
  96                 String strRecordQuery =
  97                         " SELECT ID " +
  98                         " FROM " + dbTableName +
  99                         " ORDER BY id ";
 100                 return strRecordQuery;
 101         }
 102
 103
 104         /* (non-Javadoc)
 105          * @see eu.etaxonomy.cdm.io.common.DbImportBase#getRecordQuery(eu.etaxonomy.cdm.io.common.DbImportConfiguratorBase)
 106          */
 107         @Override
 108         protected String getRecordQuery(CaryoImportConfigurator config) {
 109                 String strRecordQuery =
 110                         " SELECT t.* " +
 111                         " FROM " + getTableName() + " t " +
 112                         " WHERE ( t.ID IN (" + ID_LIST_TOKEN + ") )";
 113                 return strRecordQuery;
 114         }
 115
 116
 117
 118         /* (non-Javadoc)
 119          * @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#doPartition(eu.etaxonomy.cdm.io.common.ResultSetPartitioner, eu.etaxonomy.cdm.io.globis.GlobisImportState)
 120          */
 121         @Override
 122         public boolean doPartition(ResultSetPartitioner partitioner, CaryoImportState state) {
 123                 boolean success = true;
 124
 125                 Set<TaxonBase> objectsToSave = new HashSet<TaxonBase>();
 126
 127 //              Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE);
 128
 129
 130                 classification = getClassification(state);
 131
 132                 try {
 133                         doFamilies(state);
 134                         doAuthors(state);
 135                         doInAuthors(state);
 136                         doJournals(state);
 137                         doBooks(state);
 138
 139                         ResultSet rs = partitioner.getResultSet();
 140
 141                         int i = 0;
 142                 Reference<?> sec = state.getTransactionalSourceReference();
 143
 144                         //for each reference
 145             while (rs.next()){
 146
 147                         if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
 148
 149                         Integer id = rs.getInt("Id");
 150                         Integer taxonId = rs.getInt("NCUGenID");
 151                         String genus = rs.getString("Genus");
 152                         String family = rs.getString("Family");
 153                                 String pages = rs.getString("Pages");
 154                                 String autoren = rs.getString("Autoren");
 155                                 String typeStr = rs.getString("Type");
 156                                 String nomStatusStr = rs.getString("NomenclaturalStatus");
 157                                 String basioStr = rs.getString("Basionym");
 158
 159 //                    ,[EtInCitation]
 160 //                    ,[Gender]
 161
 162 //                    ,[Basionym]
 163 //                    ,[OriginalCitation]
 164
 165
 166                                 BotanicalName name = BotanicalName.NewInstance(Rank.GENUS());
 167                                 name.setGenusOrUninomial(genus);
 168                                 makeAuthors(name, autoren, id);
 169                                 INomenclaturalReference nomRef = makeNomRef(state, rs, id);
 170                         name.setNomenclaturalReference(nomRef);
 171                                 name.setNomenclaturalMicroReference(pages);
 172                                 makeStatus(name, nomStatusStr, id);
 173
 174
 175                                 Taxon taxon = Taxon.NewInstance(name, state.getTransactionalSourceReference());
 176                                 handleTypes(state, rs, taxon, typeStr, id);
 177                                 handleBasionym(state, rs, taxon, basioStr, id);
 178
 179                                 Taxon parent = familyMap.get(family);
 180
 181                                 classification.addParentChild(parent, taxon, sec, null);
 182
 183                                 taxon.addSource(OriginalSourceType.Import, String.valueOf(taxonId), "NCUGenID", sec, null);
 184
 185
 186
 187                                 objectsToSave.add(taxon);
 188
 189             }
 190
 191                         logger.warn(pluralString + " to save: " + objectsToSave.size());
 192                         getTaxonService().save(objectsToSave);
 193
 194                         return success;
 195                 } catch (SQLException e) {
 196                         logger.error("SQLException:" +  e);
 197                         return false;
 198                 }
 199         }
 200
 201         private void handleBasionym(CaryoImportState state, ResultSet rs, Taxon taxon, String basioStr, Integer id) {
 202                 if (StringUtils.isNotBlank(basioStr)){
 203                         BotanicalName name = (BotanicalName) taxon.getName();
 204                         BotanicalName basionym = BotanicalName.PARSED_REFERENCE(basioStr);
 205                         if (basionym.hasProblem()){
 206                                 logger.warn("Problem when parsing basionym ("+id+"): " +  basioStr);
 207                         }
 208                         name.addBasionym(basionym);
 209                         Synonym syn = Synonym.NewInstance(basionym, state.getTransactionalSourceReference());
 210                         taxon.addSynonym(syn, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF());
 211                         getTaxonService().save(syn);
 212                 }
 213
 214         }
 215
 216
 217
 218
 219         private void handleTypes(CaryoImportState state, ResultSet rs, Taxon taxon, String origType, Integer id) {
 220                 NameTypeDesignation desig = NameTypeDesignation.NewInstance();
 221                 String type = origType;
 222                 if (StringUtils.isBlank(type) || "to be designated".equalsIgnoreCase(type)){
 223                         return;
 224                 }else{
 225                         BotanicalName name = (BotanicalName)taxon.getName();
 226                         BotanicalName typeName = BotanicalName.NewInstance(Rank.SPECIES());
 227                         if ("not designated".equalsIgnoreCase(type)){
 228                                 desig.setNotDesignated(true);
 229                         }else{
 230                                 String genus = name.getGenusOrUninomial();
 231                                 typeName.setGenusOrUninomial(genus);
 232                                 if (! type.startsWith(genus.substring(0,1) + ". " )){
 233                                         int i = type.indexOf(" ");
 234                                         String genusOrig = type.substring(0, i);
 235                                         logger.info("First genus letter not recognized: " + genusOrig + "-" + genus + ":"+  id);
 236                                         typeName.setGenusOrUninomial(genusOrig);
 237                                         type = type.substring(i + 1).trim();
 238                                 }else{
 239                                         type = type.substring(3);
 240                                 }
 241                                 int i = type.indexOf(" ");
 242                                 if (i <= 0){
 243                                         logger.warn("No space: " + type +"; " + id);
 244                                 }else{
 245                                         String species = type.substring(0, i);
 246                                         typeName.setSpecificEpithet(species);
 247                                         type = type.substring(i + 1).trim();
 248
 249                                         int posBracket = type.indexOf("(", 2);
 250                                         if (posBracket > 0){
 251                                                 String bracket = type.substring(posBracket);
 252 //                                              logger.warn("Type has bracket("+id+"): " + bracket);
 253                                                 taxon.addAnnotation(Annotation.NewInstance("Type-bracket: " + bracket, Language.DEFAULT()));
 254                                                 type = type.substring(0, posBracket).trim();
 255                                         }else{
 256                                                 Taxon speciesTaxon = Taxon.NewInstance(typeName, state.getTransactionalSourceReference());
 257                                                 classification.addParentChild(taxon, speciesTaxon, null, null);
 258                                         }
 259                                         type = makeTypeNomStatus(typeName, type);
 260
 261
 262                                         makeAuthors(typeName, type, id);
 263                                 }
 264
 265                                 desig.setTypeName(typeName);
 266                         }
 267                         name.addTypeDesignation(desig, true);
 268                 }
 269
 270
 271         }
 272
 273
 274
 275
 276         private String makeTypeNomStatus(BotanicalName typeName, String type) {
 277                 if (type.endsWith(", nom. illeg.")){
 278                         type = type.replaceAll(", nom. illeg.", "");
 279                         typeName.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ILLEGITIMATE()));
 280                 }
 281                 return type;
 282         }
 283
 284
 285
 286
 287         private void makeStatus(BotanicalName name, String nomStatusStr, Integer id) throws SQLException {
 288 //            ,[NomenclaturalStatus]
 289
 290                 if (StringUtils.isNotBlank(nomStatusStr)){
 291                         NomenclaturalStatusType nomStatusType;
 292                         try {
 293                                 nomStatusType = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(nomStatusStr);
 294                         } catch (UnknownCdmTypeException e) {
 295                                 if (nomStatusStr.startsWith("nom. rej. prop.")){
 296                                         nomStatusType = NomenclaturalStatusType.REJECTED_PROP();
 297                                         logger.info("in favour not supported ("+id+"): " + nomStatusStr);
 298                                 }else if (nomStatusStr.startsWith("nom. rej. in favour")){
 299                                         nomStatusType = NomenclaturalStatusType.REJECTED();
 300                                         logger.info("in favour not supported ("+id+"): " + nomStatusStr);
 301                                 }else if (nomStatusStr.startsWith("nom. cons. against")){
 302                                         nomStatusType = NomenclaturalStatusType.CONSERVED();
 303                                         logger.info("against not supported ("+id+"): " + nomStatusStr);
 304                                 }else if (nomStatusStr.startsWith("nom. cons. prop. against")){
 305                                         nomStatusType = NomenclaturalStatusType.CONSERVED_PROP();
 306                                         logger.info("against not supported ("+id+"): " + nomStatusStr);
 307                                 }else{
 308                                         logger.warn("Unknown status type ("+id+"): " + nomStatusStr);
 309                                         nomStatusType = NomenclaturalStatusType.DOUBTFUL();
 310                                 }
 311                         }
 312
 313                         NomenclaturalStatus status = NomenclaturalStatus.NewInstance(nomStatusType);
 314                         name.addStatus(status);
 315                 }
 316
 317         }
 318
 319
 320
 321
 322         private INomenclaturalReference makeNomRef(CaryoImportState state, ResultSet rs, Integer id) throws SQLException {
 323                 INomenclaturalReference result;
 324                 String periodicalTitle = rs.getString("PeriodicalTitle");
 325                 String volume = rs.getString("PeriodicalVolume");
 326                 String bookTitle = rs.getString("BookTitle");
 327                 String inAutorStr = rs.getString("InAutor");
 328                 String autorenStr = rs.getString("Autoren");
 329
 330                 TeamOrPersonBase<?> author = getNomRefAuthor(autorenStr, id);
 331                 if (StringUtils.isNotBlank(periodicalTitle)){
 332                         IJournal journal = journalMap.get(periodicalTitle);
 333                         if (journal == null){
 334                                 logger.warn("Journal not found: " + periodicalTitle + ";" + id);
 335                         }
 336                         IArticle article = ReferenceFactory.newArticle();
 337                         article.setInJournal(journal);
 338                         article.setVolume(volume);
 339                         result = article;
 340                 }else if (StringUtils.isNotBlank(bookTitle)){
 341                         IBook book = bookMap.get(bookTitle);
 342                         if (inAutorStr != null){
 343                                 IBookSection section = ReferenceFactory.newBookSection();
 344                                 section.setInBook(book);
 345                                 TeamOrPersonBase<?> inAuthor = getInAuthor(inAutorStr);
 346                                 book.setAuthorTeam(inAuthor);
 347                                 result = section;
 348                         }else{
 349                                 result = book;
 350                         }
 351                 }else{
 352                         logger.warn("No nomRef found: " +  id);
 353                         result = null;
 354                 }
 355                 if (result != null){
 356                         result.setAuthorTeam(author);
 357                         makeDate(state, rs, result, id);
 358                 }
 359                 return result;
 360         }
 361
 362         private void makeDate(CaryoImportState state, ResultSet rs, INomenclaturalReference ref, Integer id) throws SQLException {
 363                 TimePeriod tp = TimePeriod.NewInstance();
 364                 String pre1 = rs.getString("DatePre1");
 365                 String pre2 = rs.getString("DatePre2");
 366                 Float year1 = nullSafeFloat(rs, "DateYear1");
 367                 Float year2 = nullSafeFloat(rs, "DateYear2");
 368                 if (year2 == 0.0 ){
 369                         year2 = null;
 370                 }
 371                 String modi1 = rs.getString("DateModi1");
 372                 String modi2 = rs.getString("DateModi2");
 373                 String date = rs.getString("Date");
 374
 375                 tp.setStartYear(year1.intValue());
 376                 Integer[] preDate1 = getDay(pre1,id);
 377 //              tp.setStartMonth(preDate1[1]);
 378 //              tp.setStartDay(preDate1[0]);
 379                 if (year2 != null){
 380                         tp.setEndYear(year2.intValue());
 381                 }
 382                 Integer[] preDate2 = getDay(pre2, id);
 383 //              tp.setEndMonth(preDate2[1]);
 384 //              tp.setEndDay(preDate2[0]);
 385
 386 //              if (StringUtils.isNotBlank(modi1) || StringUtils.isNotBlank(modi2)){
 387 //                      tp.setFreeText(date);
 388 //              }
 389                 ref.setDatePublished(tp);
 390         }
 391
 392
 393
 394
 395         private Integer[] getDay(String pre, Integer id) {
 396                 Integer[] result = new Integer[2];
 397                 if (! StringUtils.isBlank(pre)){
 398                         try {
 399                                 String[] split = pre.split("\\s");
 400                                 String monthStr;
 401                                 if (split.length > 2){
 402                                         logger.warn("L > 2: " + pre);
 403                                         monthStr = "";
 404                                 }else if(split.length == 2){
 405                                         result[0] = Integer.valueOf(split[0]);
 406                                         monthStr = split[1];
 407                                 }else{
 408                                         monthStr = split[0];
 409                                 }
 410                                 Integer month;
 411                                 if ("Jan".equalsIgnoreCase(monthStr)){
 412                                         month = 1;
 413                                 }else if ("Feb".equalsIgnoreCase(monthStr)){
 414                                         month = 2;
 415                                 }else if ("Mar".equalsIgnoreCase(monthStr)){
 416                                         month = 3;
 417                                 }else if ("Apr".equalsIgnoreCase(monthStr)){
 418                                         month = 4;
 419                                 }else if ("Mai".equalsIgnoreCase(monthStr)){
 420                                         month = 5;
 421                                 }else if ("Jun".equalsIgnoreCase(monthStr)){
 422                                         month = 6;
 423                                 }else if ("Jul".equalsIgnoreCase(monthStr)){
 424                                         month = 7;
 425                                 }else if ("Aug".equalsIgnoreCase(monthStr)){
 426                                         month = 8;
 427                                 }else if ("Sep".equalsIgnoreCase(monthStr)){
 428                                         month = 9;
 429                                 }else if ("Oct".equalsIgnoreCase(monthStr)){
 430                                         month = 10;
 431                                 }else if ("Nov".equalsIgnoreCase(monthStr)){
 432                                         month = 11;
 433                                 }else if ("Dec".equalsIgnoreCase(monthStr)){
 434                                         month = 12;
 435                                 }else{
 436                                         logger.warn("Unknown month ("+id+"): " + monthStr );
 437                                         month = null;
 438                                 }
 439                                 result[1]= month;
 440                         } catch (Exception e) {
 441                                 e.printStackTrace();
 442                         }
 443                 }
 444                 return result;
 445         }
 446
 447
 448         private TeamOrPersonBase<?> getInAuthor(String inAutorStr) {
 449                 if (StringUtils.isBlank(inAutorStr)){
 450                         return null;
 451                 }
 452                 TeamOrPersonBase<?> inAuthor = inAuthorMap.get(inAutorStr);
 453                 if (inAuthor == null){
 454                         logger.warn("Inauthor not found: " +  inAutorStr);
 455                 }
 456                 return inAuthor;
 457         }
 458
 459
 460
 461         private void makeAuthors(BotanicalName name, String autoren, Integer id) {
 462                 String[] parsedAuthorTeams = getParsedAuthors(autoren);
 463                 name.setBasionymAuthorTeam(getTeam(parsedAuthorTeams[0], id));
 464                 name.setExBasionymAuthorTeam(getTeam(parsedAuthorTeams[1], id));
 465                 name.setCombinationAuthorTeam(getTeam(parsedAuthorTeams[2], id));
 466                 name.setExCombinationAuthorTeam(getTeam(parsedAuthorTeams[3], id));
 467
 468         }
 469
 470         private TeamOrPersonBase<?> getNomRefAuthor(String authorStr, Integer id) {
 471                 String[] parsedAuthorTeams = getParsedAuthors(authorStr);
 472                 TeamOrPersonBase<?> team = getTeam(parsedAuthorTeams[2], id);
 473                 return team;
 474         }
 475
 476
 477         private TeamOrPersonBase<?> getTeam(String author, Integer id) {
 478                 if (StringUtils.isBlank(author)){
 479                         return null;
 480                 }
 481                 TeamOrPersonBase<?> result;
 482                 if (personMap.get(author) != null){
 483                         result = personMap.get(author);
 484                 }else{
 485                         result = teamMap.get(author);
 486                 }
 487                 if (result == null){
 488                         logger.warn("Team not found ("+id+"): " + author);
 489                 }
 490                 return result;
 491         }
 492
 493
 494         private void doInAuthors(CaryoImportState state) throws SQLException {
 495                 Source source = state.getConfig().getSource();
 496                 String sql = "SELECT DISTINCT inAutor FROM " + getTableName() + " WHERE inAutor IS NOT NULL AND inAutor <> '' ";
 497                 ResultSet rs = source.getResultSet(sql);
 498                 while (rs.next()){
 499                         String inAutorStr = rs.getString("inAutor");
 500                         if (inAuthorMap.get(inAutorStr) == null){
 501                                 Team team = Team.NewTitledInstance(inAutorStr, inAutorStr);
 502
 503                                 inAuthorMap.put(inAutorStr, team);
 504                                 getAgentService().save(team);
 505                         }
 506                 }
 507
 508         }
 509
 510
 511         private void doAuthors(CaryoImportState state) throws SQLException {
 512                 Source source = state.getConfig().getSource();
 513                 String sql = "SELECT DISTINCT Autoren FROM " + getTableName() + " WHERE Autoren IS NOT NULL AND Autoren <> '' ";
 514                 ResultSet rs = source.getResultSet(sql);
 515                 doTypeAuthors(state);
 516                 while (rs.next()){
 517                         String autorenStr = rs.getString("Autoren");
 518                         String[] parsedAuthorTeams = getParsedAuthors(autorenStr);
 519                         for (String teamStr : parsedAuthorTeams){
 520                                 doTeam(teamStr);
 521                         }
 522                 }
 523         }
 524
 525
 526
 527
 528         private void doTypeAuthors(CaryoImportState state) {
 529                 doTeam("Dinter & Derenb.");
 530                 doTeam("Marloth");
 531                 doTeam("Engl.");
 532                 doTeam("Kensit");
 533                 doTeam("Sond.");
 534                 doTeam("L. f.");
 535                 doTeam("Dinter & A. Berger");
 536                 doTeam("Schltr.");
 537                 doTeam("Dinter & Berger");
 538                 doTeam("Poir.");
 539                 doTeam("J. C. Wendl.");
 540                 doTeam("Baker & Clarke");
 541                 doTeam("Vahl");
 542                 doTeam("Nicolai");
 543                 doTeam("Gürke");
 544                 doTeam("Cels");
 545                 doTeam("Dams");
 546                 doTeam("Coult.");
 547                 doTeam("A. Weber");
 548                 doTeam("Vaupel");
 549                 doTeam("Gay");
 550                 doTeam("Pall.");
 551                 doTeam("Moq. & Coss.");
 552                 doTeam("Durieu & Moq.");
 553                 doTeam("Lag. & Rodrigues");
 554                 doTeam("M. Martens & Galeotti");
 555                 doTeam("Steud.");
 556                 doTeam("Aitch. & Hemsl.");
 557                 doTeam("Ikonn.-Gal.");
 558                 doTeam("Freitag");
 559                 doTeam("Regel");
 560                 doTeam("Ledeb.");
 561                 doTeam("Schur");
 562                 doTeam("Asch.");
 563                 doTeam("G. Forst.");
 564                 doTeam("Gray");
 565                 doTeam("Curran");
 566                 doTeam("Donn. Sm.");
 567                 doTeam("Diels");
 568                 doTeam("Colla");
 569                 doTeam("Miers");
 570                 doTeam("Gillis");
 571                 doTeam("Royle");
 572                 doTeam("Monv.");
 573                 doTeam("Werderm. & Backeb.");
 574                 doTeam("Wright");
 575                 doTeam("Meyen");
 576                 doTeam("Runge");
 577                 doTeam("Böd.");
 578                 doTeam("Rol.-Goss.");
 579                 doTeam("Poselg.");
 580                 doTeam("Andreae & Backeberg");
 581                 doTeam("Miq.");
 582                 doTeam("Rol.");
 583                 doTeam("Backeb. & Voll");
 584                 doTeam("Engelm. & Bigelow");
 585                 doTeam("Pfeiffer & Otto");
 586                 doTeam("Humb. & Bonpl.");
 587                 doTeam("Schmalh.");
 588                 doTeam("Preobr.");
 589                 doTeam("Labill.");
 590                 doTeam("Barkoudah");
 591                 doTeam("Regel & Schmalh.");
 592                 doTeam("Cambess.");
 593                 doTeam("Pax & K. Hoff.");
 594                 doTeam("Bergeret");
 595                 doTeam("Walp.");
 596                 doTeam("Huds.");
 597                 doTeam("Kit.");
 598                 doTeam("Schott, Nymann & Kotschy");
 599                 doTeam("Boiss. & Buhse");
 600                 doTeam("Medik.");
 601                 doTeam("Coss. & Germ.");
 602                 doTeam("Moss");
 603                 doTeam("Pax & Hoffm.");
 604                 doTeam("Schischk.");
 605                 doTeam("Lipsch.");
 606                 doTeam("Maerkl.");
 607                 doTeam("Vierh.");
 608                 doTeam("Exell");
 609
 610         }
 611
 612
 613
 614
 615         /**
 616          * @param teamStr
 617          * @return
 618          */
 619         protected void doTeam(String teamStr) {
 620                 if (StringUtils.isBlank(teamStr)){
 621                         return;
 622                 }
 623                 String[] parsedTeam = parseTeam(teamStr);
 624                 if (parsedTeam.length == 1){
 625                         savePerson(parsedTeam[0]);
 626                 }else{
 627                         Team team = teamMap.get(teamStr);
 628                         if (team == null){
 629                                 team = Team.NewInstance();
 630                                 for (String member : parsedTeam){
 631                                         Person person = savePerson(member);
 632                                         team.addTeamMember(person);
 633                                 }
 634                                 teamMap.put(teamStr, team);
 635                                 getAgentService().saveOrUpdate(team);
 636                         }
 637                 }
 638                 return;
 639         }
 640
 641         private String[] parseTeam(String teamStr) {
 642                 String[] split = teamStr.split("[&,]");
 643                 for (int i = 0; i < split.length; i++){
 644                         split[i] = split[i].trim();
 645                 }
 646                 return split;
 647         }
 648
 649         private Person savePerson(String personStr) {
 650                 Person result = personMap.get(personStr);
 651                 if (result == null ){
 652                         Person person = Person.NewTitledInstance(personStr);
 653                         personMap.put(personStr, person);
 654                         getAgentService().save(person);
 655                         result = person;
 656                 }
 657                 return result;
 658         }
 659
 660
 661
 662
 663         private String[] getParsedAuthors(String autorenStr) {
 664                 String[] result = new String[4];
 665                 String basioFull = null;
 666                 String origFull;
 667
 668                         String[]  split = autorenStr.split("\\)");
 669                 if (split.length > 1){
 670                         basioFull = split[0].replace("(", "").trim();
 671                         origFull = split[1].trim();
 672                 }else{
 673                         origFull = split[0].trim();
 674                 }
 675                 String[] splitBasio = splitExAuthors(basioFull);
 676                 String[] splitOrig = splitExAuthors(origFull);
 677                 result[0] = splitBasio[0];
 678                 result[1] = splitBasio[1];
 679                 result[2] = splitOrig[0];
 680                 result[3] = splitOrig[1];
 681
 682                 return result;
 683         }
 684
 685
 686
 687
 688         private String[] splitExAuthors(String author) {
 689                 String[] result = new String[2];
 690                 if (author != null){
 691                         String[]  split = author.split("\\sex\\s");
 692                         if (split.length > 1){
 693                                 result[0] = split[1].trim();
 694                                 result[1] = split[0].trim();
 695                         }else{
 696                                 result[0] = split[0].trim();
 697                         }
 698                 }
 699                 return result;
 700         }
 701
 702
 703
 704
 705         private void doBooks(CaryoImportState state) throws SQLException {
 706                 Source source = state.getConfig().getSource();
 707                 String sql = "SELECT DISTINCT BookTitle FROM " + getTableName() + " WHERE BookTitle IS NOT NULL AND BookTitle <> '' ";
 708                 ResultSet rs = source.getResultSet(sql);
 709                 while (rs.next()){
 710                         String bookStr = rs.getString("BookTitle");
 711                         if (bookMap.get(bookStr) == null ){
 712
 713                                 IBook book = ReferenceFactory.newBook();
 714
 715                                 book.setTitle(bookStr);
 716
 717                                 bookMap.put(bookStr, book);
 718                                 getReferenceService().save((Reference<?>)book);
 719                         }
 720                 }
 721         }
 722
 723
 724
 725
 726         private void doJournals(CaryoImportState state) throws SQLException {
 727                 Source source = state.getConfig().getSource();
 728                 String sqlPeriodical = "SELECT DISTINCT PeriodicalTitle FROM " + getTableName() + " WHERE PeriodicalTitle IS NOT NULL AND PeriodicalTitle <> '' ";
 729                 ResultSet rs = source.getResultSet(sqlPeriodical);
 730                 while (rs.next()){
 731                         String periodical = rs.getString("PeriodicalTitle");
 732                         if (journalMap.get(periodical) == null ){
 733
 734                                 Reference<?> journal = ReferenceFactory.newJournal();
 735
 736                                 journal.setTitle(periodical);
 737
 738                                 journalMap.put(periodical, journal);
 739                                 getReferenceService().save(journal);
 740                         }
 741                 }
 742         }
 743
 744
 745
 746
 747         private void doFamilies(CaryoImportState state) throws SQLException {
 748                 Source source = state.getConfig().getSource();
 749                 String sqlFamily = "SELECT DISTINCT Family FROM " + getTableName() + " WHERE Family IS NOT NULL";
 750                 ResultSet rs = source.getResultSet(sqlFamily);
 751                 while (rs.next()){
 752                         String family = rs.getString("family");
 753                         if (familyMap.get(family) == null ){
 754
 755                                 BotanicalName name = BotanicalName.NewInstance(Rank.FAMILY());
 756                                 name.setGenusOrUninomial(family);
 757                                 Taxon taxon = Taxon.NewInstance(name, state.getTransactionalSourceReference());
 758                                 classification.addChildTaxon(taxon, null, null);
 759         //                      taxon.addSource(id, idNamespace, citation, null);
 760
 761                                 familyMap.put(family, taxon);
 762                                 getTaxonService().save(taxon);
 763                         }
 764                 }
 765
 766         }
 767
 768         private Classification getClassification(CaryoImportState state) {
 769                 if (this.classification == null){
 770                         String name = state.getConfig().getClassificationName();
 771                         Reference<?> reference = state.getTransactionalSourceReference();
 772                         this.classification = Classification.NewInstance(name, reference, Language.DEFAULT());
 773                         if (state.getConfig().getClassificationUuid() != null){
 774                                 classification.setUuid(state.getConfig().getClassificationUuid());
 775                         }
 776                         getClassificationService().save(classification);
 777                 }
 778                 return this.classification;
 779         }
 780
 781
 782
 783
 784
 785         /* (non-Javadoc)
 786          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 787          */
 788         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 789 //              String nameSpace;
 790 //              Class cdmClass;
 791 //              Set<String> idSet;
 792                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 793 //              try{
 794 //                      Set<String> taxonIdSet = new HashSet<String>();
 795 //
 796 //                      while (rs.next()){
 797 ////                            handleForeignKey(rs, taxonIdSet, "taxonId");
 798 //                      }
 799 //
 800 //                      //taxon map
 801 //                      nameSpace = TAXON_NAMESPACE;
 802 //                      cdmClass = Taxon.class;
 803 //                      idSet = taxonIdSet;
 804 //                      Map<String, Taxon> objectMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 805 //                      result.put(nameSpace, objectMap);
 806 //
 807 //
 808 //              } catch (SQLException e) {
 809 //                      throw new RuntimeException(e);
 810 //              }
 811                 return result;
 812         }
 813
 814         /* (non-Javadoc)
 815          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 816          */
 817         @Override
 818         protected boolean doCheck(CaryoImportState state){
 819                 return true;
 820         }
 821
 822
 823         /* (non-Javadoc)
 824          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 825          */
 826         protected boolean isIgnore(CaryoImportState state){
 827                 return ! state.getConfig().isDoTaxa();
 828         }
 829
 830
 831
 832
 833
 834
 835
 836 }