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