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