cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelImportConfigurator.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.berlinModel.in;
  11
  12 import java.io.File;
  13 import java.lang.reflect.Method;
  14 import java.net.MalformedURLException;
  15 import java.net.URL;
  16 import java.util.HashSet;
  17 import java.util.Set;
  18
  19 import org.apache.log4j.Logger;
  20
  21 import eu.etaxonomy.cdm.database.ICdmDataSource;
  22 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport.PublishMarkerChooser;
  23 import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelGeneralImportValidator;
  24 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  25 import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;
  26 import eu.etaxonomy.cdm.io.common.ImportStateBase;
  27 import eu.etaxonomy.cdm.io.common.Source;
  28 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  29 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  30 import eu.etaxonomy.cdm.model.reference.Reference;
  31 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  32 import eu.etaxonomy.cdm.model.taxon.Synonym;
  33
  34 /**
  35  * @author a.mueller
  36  * @created 20.03.2008
  37  * @version 1.0
  38  */
  39 public class BerlinModelImportConfigurator extends ImportConfiguratorBase<BerlinModelImportState, Source> implements IImportConfigurator{
  40         private static Logger logger = Logger.getLogger(BerlinModelImportConfigurator.class);
  41
  42         public static BerlinModelImportConfigurator NewInstance(Source berlinModelSource, ICdmDataSource destination){
  43                         return new BerlinModelImportConfigurator(berlinModelSource, destination);
  44         }
  45
  46         private PublishMarkerChooser taxonPublishMarker = PublishMarkerChooser.ALL;
  47
  48         //TODO
  49         private static IInputTransformer defaultTransformer = null;
  50
  51         private boolean doNameStatus = true;
  52         private boolean doRelNames = true;
  53         private boolean doCommonNames = true;
  54         private boolean doOccurrence = true;
  55         private boolean doMarker = true;
  56         private boolean doUser = true;
  57         private boolean doFacts = true;
  58         private boolean doNameFacts = true;
  59         private boolean doAuthors = true;
  60         private DO_REFERENCES doReferences = DO_REFERENCES.ALL;
  61         private boolean doTaxonNames = true;
  62         private boolean doTypes = true;
  63
  64         //taxa
  65         private boolean doTaxa = true;
  66         private boolean doRelTaxa = true;
  67
  68         private boolean useSingleClassification = false;
  69
  70         //occurrences
  71         private boolean isSplitTdwgCodes = true;
  72
  73         /* Max number of records to be saved with one service call */
  74         private int recordsPerTransaction = 1000;
  75
  76         private Method namerelationshipTypeMethod;
  77         private Method uuidForDefTermMethod;
  78         private Method userTransformationMethod;
  79         private Method nameTypeDesignationStatusMethod;
  80
  81         private Set<Synonym> proParteSynonyms = new HashSet<Synonym>();
  82         private Set<Synonym> partialSynonyms = new HashSet<Synonym>();
  83
  84         // NameFact stuff
  85         private URL mediaUrl;
  86         private File mediaPath;
  87         private int maximumNumberOfNameFacts;
  88         private boolean isIgnore0AuthorTeam = false;
  89
  90         private boolean switchSpeciesGroup = false;
  91
  92         //Term labels
  93         private String infrGenericRankAbbrev = null;
  94         private String infrSpecificRankAbbrev = null;
  95
  96         private boolean removeHttpMapsAnchor = false;
  97
  98         //Data Filter
  99
 100         private String taxonTable = "PTaxon";
 101         private String classificationQuery = null;
 102         private String relTaxaIdQuery = null;
 103         private String nameIdTable = null;
 104         private String referenceIdTable = null;
 105         private String authorTeamFilter = null;
 106         private String authorFilter = null;
 107         private String factFilter = null;
 108         private String commonNameFilter = null;
 109         private String occurrenceFilter = null;
 110         private String occurrenceSourceFilter = null;
 111         private String webMarkerFilter = null;
 112
 113         //specific functions
 114         private Method  makeUrlForTaxon = null;
 115
 116         protected void makeIoClassList(){
 117                 ioClassList = new Class[]{
 118                                 BerlinModelGeneralImportValidator.class
 119                                 , BerlinModelUserImport.class
 120                                 , BerlinModelAuthorImport.class
 121                                 , BerlinModelAuthorTeamImport.class
 122                                 , BerlinModelRefDetailImport.class
 123                                 , BerlinModelReferenceImport.class
 124                                 , BerlinModelTaxonNameImport.class
 125                                 , BerlinModelTaxonNameRelationImport.class
 126                                 , BerlinModelNameStatusImport.class
 127                                 , BerlinModelNameFactsImport.class
 128                                 , BerlinModelTypesImport.class
 129                                 , BerlinModelTaxonImport.class
 130                                 , BerlinModelTaxonRelationImport.class
 131                                 , BerlinModelCommonNamesImport.class
 132                                 , BerlinModelFactsImport.class
 133                                 , BerlinModelOccurrenceImport.class
 134                                 , BerlinModelOccurrenceSourceImport.class
 135                                 , BerlinModelWebMarkerCategoryImport.class
 136                                 , BerlinModelWebMarkerImport.class
 137                 };
 138         }
 139
 140
 141
 142         /* (non-Javadoc)
 143          * @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getNewState()
 144          */
 145         public ImportStateBase getNewState() {
 146                 return new BerlinModelImportState(this);
 147         }
 148
 149
 150
 151         /**
 152          * @param berlinModelSource
 153          * @param sourceReference
 154          * @param destination
 155          */
 156         private BerlinModelImportConfigurator(Source berlinModelSource, ICdmDataSource destination) {
 157            super(defaultTransformer);
 158            setNomenclaturalCode(NomenclaturalCode.ICBN); //default for Berlin Model
 159            setSource(berlinModelSource);
 160            setDestination(destination);
 161         }
 162
 163
 164         public Source getSource() {
 165                 return (Source)super.getSource();
 166         }
 167         public void setSource(Source berlinModelSource) {
 168                 super.setSource(berlinModelSource);
 169         }
 170
 171         /* (non-Javadoc)
 172          * @see eu.etaxonomy.cdm.io.tcsrdf.IImportConfigurator#getSourceReference()
 173          */
 174         public Reference getSourceReference() {
 175                 if (sourceReference == null){
 176                         sourceReference =  ReferenceFactory.newDatabase();
 177                         if (getSource() != null){
 178                                 sourceReference.setTitleCache(getSource().getDatabase(), true);
 179                         }
 180                         if (getSourceRefUuid() != null){
 181                                 sourceReference.setUuid(getSourceRefUuid());
 182                         }
 183                 }
 184                 return sourceReference;
 185         }
 186
 187
 188         /* (non-Javadoc)
 189          * @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getSourceNameString()
 190          */
 191         public String getSourceNameString() {
 192                 if (this.getSource() == null){
 193                         return null;
 194                 }else{
 195                         return this.getSource().getDatabase();
 196                 }
 197         }
 198
 199         /**
 200          * Import name relationships yes/no?.
 201          * @return
 202          */
 203         public boolean isDoRelNames() {
 204                 return doRelNames;
 205         }
 206         public void setDoRelNames(boolean doRelNames) {
 207                 this.doRelNames = doRelNames;
 208         }
 209
 210
 211
 212         protected void addProParteSynonym(Synonym proParteSynonym){
 213                 this.proParteSynonyms.add(proParteSynonym);
 214         }
 215
 216         protected boolean isProParteSynonym(Synonym synonym){
 217                 return this.proParteSynonyms.contains(synonym);
 218         }
 219
 220         protected void addPartialSynonym(Synonym partialSynonym){
 221                 this.partialSynonyms.add(partialSynonym);
 222         }
 223
 224         protected boolean isPartialSynonym(Synonym synonym){
 225                 return this.partialSynonyms.contains(synonym);
 226         }
 227
 228         /**
 229          * @return the mediaUrl
 230          */
 231         public URL getMediaUrl() {
 232                 return mediaUrl;
 233         }
 234
 235         /**
 236          * @param mediaUrl the mediaUrl to set
 237          */
 238         public void setMediaUrl(URL mediaUrl) {
 239                 this.mediaUrl = mediaUrl;
 240         }
 241
 242         /**
 243          * @return the mediaPath
 244          */
 245         public File getMediaPath() {
 246                 return mediaPath;
 247         }
 248
 249         /**
 250          * @param mediaPath the mediaPath to set
 251          */
 252         public void setMediaPath(File mediaPath) {
 253                 this.mediaPath = mediaPath;
 254         }
 255
 256         public void setMediaPath(String mediaPathString){
 257                 this.mediaPath = new File(mediaPathString);
 258         }
 259
 260         public void setMediaUrl(String mediaUrlString) {
 261                 try {
 262                         this.mediaUrl = new URL(mediaUrlString);
 263                 } catch (MalformedURLException e) {
 264                         logger.error("Could not set mediaUrl because it was malformed: " + mediaUrlString);
 265                 }
 266         }
 267
 268         /**
 269          * @return the maximumNumberOfNameFacts
 270          */
 271         public int getMaximumNumberOfNameFacts() {
 272                 return maximumNumberOfNameFacts;
 273         }
 274
 275         /**
 276          * set to 0 for unlimited
 277          *
 278          * @param maximumNumberOfNameFacts the maximumNumberOfNameFacts to set
 279          */
 280         public void setMaximumNumberOfNameFacts(int maximumNumberOfNameFacts) {
 281                 this.maximumNumberOfNameFacts = maximumNumberOfNameFacts;
 282         }
 283
 284         /**
 285          * If true, an authorTeam with authorTeamId = 0 is not imported (casus Salvador)
 286          * @return the isIgnore0AuthorTeam
 287          */
 288         public boolean isIgnore0AuthorTeam() {
 289                 return isIgnore0AuthorTeam;
 290         }
 291
 292         /**
 293          * @param isIgnore0AuthorTeam the isIgnore0AuthorTeam to set
 294          */
 295         public void setIgnore0AuthorTeam(boolean isIgnore0AuthorTeam) {
 296                 this.isIgnore0AuthorTeam = isIgnore0AuthorTeam;
 297         }
 298
 299         /**
 300          * @return the namerelationshipTypeMethod
 301          */
 302         public Method getNamerelationshipTypeMethod() {
 303                 return namerelationshipTypeMethod;
 304         }
 305
 306         /**
 307          * @param namerelationshipTypeMethod the namerelationshipTypeMethod to set
 308          */
 309         public void setNamerelationshipTypeMethod(Method namerelationshipTypeMethod) {
 310                 this.namerelationshipTypeMethod = namerelationshipTypeMethod;
 311         }
 312
 313         /**
 314          * @return the taxonPublishMarker
 315          */
 316         public BerlinModelTaxonImport.PublishMarkerChooser getTaxonPublishMarker() {
 317                 return taxonPublishMarker;
 318         }
 319
 320         /**
 321          * @param taxonPublishMarker the taxonPublishMarker to set
 322          */
 323         public void setTaxonPublishMarker(
 324                         BerlinModelTaxonImport.PublishMarkerChooser taxonPublishMarker) {
 325                 this.taxonPublishMarker = taxonPublishMarker;
 326         }
 327
 328
 329
 330         /**
 331          * @return the uuidForDefTermMethod
 332          */
 333         public Method getUuidForDefTermMethod() {
 334                 return uuidForDefTermMethod;
 335         }
 336
 337         /**
 338          * @param uuidForDefTermMethod the uuidForDefTermMethod to set
 339          */
 340         public void setUuidForDefTermMethod(Method uuidForDefTermMethod) {
 341                 this.uuidForDefTermMethod = uuidForDefTermMethod;
 342         }
 343
 344         /**
 345          * @return the userTransformationMethod
 346          */
 347         public Method getUserTransformationMethod() {
 348                 return userTransformationMethod;
 349         }
 350
 351         /**
 352          * @param userTransformationMethod the userTransformationMethod to set
 353          */
 354         public void setUserTransformationMethod(Method userTransformationMethod) {
 355                 this.userTransformationMethod = userTransformationMethod;
 356         }
 357
 358
 359
 360         /**
 361          * @return the nameTypeDesignationStatusMethod
 362          */
 363         public Method getNameTypeDesignationStatusMethod() {
 364                 return nameTypeDesignationStatusMethod;
 365         }
 366
 367
 368         /**
 369          * @param nameTypeDesignationStatusMethod the nameTypeDesignationStatusMethod to set
 370          */
 371         public void setNameTypeDesignationStatusMethod(
 372                         Method nameTypeDesignationStatusMethod) {
 373                 this.nameTypeDesignationStatusMethod = nameTypeDesignationStatusMethod;
 374         }
 375
 376         /**
 377          * @return the limitSave
 378          */
 379         public int getRecordsPerTransaction() {
 380                 return recordsPerTransaction;
 381         }
 382
 383         /**
 384          * @param limitSave the limitSave to set
 385          */
 386         public void setRecordsPerTransaction(int recordsPerTransaction) {
 387                 this.recordsPerTransaction = recordsPerTransaction;
 388         }
 389
 390
 391
 392         public boolean isDoNameStatus() {
 393                 return doNameStatus;
 394         }
 395         public void setDoNameStatus(boolean doNameStatus) {
 396                 this.doNameStatus = doNameStatus;
 397         }
 398
 399
 400         public boolean isDoCommonNames() {
 401                 return doCommonNames;
 402         }
 403
 404
 405         /**
 406          * @param doCommonNames
 407          */
 408         public void setDoCommonNames(boolean doCommonNames) {
 409                 this.doCommonNames = doCommonNames;
 410
 411         }
 412
 413         public boolean isDoFacts() {
 414                 return doFacts;
 415         }
 416         public void setDoFacts(boolean doFacts) {
 417                 this.doFacts = doFacts;
 418         }
 419
 420
 421         public boolean isDoOccurrence() {
 422                 return doOccurrence;
 423         }
 424         public void setDoOccurrence(boolean doOccurrence) {
 425                 this.doOccurrence = doOccurrence;
 426         }
 427
 428
 429         public boolean isDoMarker() {
 430                 return doMarker;
 431         }
 432
 433         public void setDoMarker(boolean doMarker) {
 434                 this.doMarker = doMarker;
 435         }
 436
 437         public boolean isDoUser() {
 438                 return doUser;
 439         }
 440
 441         public void setDoUser(boolean doUser) {
 442                 this.doUser = doUser;
 443         }
 444
 445         public boolean isDoNameFacts() {
 446                 return doNameFacts;
 447         }
 448         public void setDoNameFacts(boolean doNameFacts) {
 449                 this.doNameFacts = doNameFacts;
 450         }
 451
 452         public boolean isDoAuthors() {
 453                 return doAuthors;
 454         }
 455         public void setDoAuthors(boolean doAuthors) {
 456                 this.doAuthors = doAuthors;
 457         }
 458
 459         public DO_REFERENCES getDoReferences() {
 460                 return doReferences;
 461         }
 462         public void setDoReferences(DO_REFERENCES doReferences) {
 463                 this.doReferences = doReferences;
 464         }
 465
 466         public boolean isDoTaxonNames() {
 467                 return doTaxonNames;
 468         }
 469         public void setDoTaxonNames(boolean doTaxonNames) {
 470                 this.doTaxonNames = doTaxonNames;
 471         }
 472
 473         public boolean isDoTypes() {
 474                 return doTypes;
 475         }
 476         public void setDoTypes(boolean doTypes) {
 477                 this.doTypes = doTypes;
 478         }
 479
 480         public boolean isDoTaxa() {
 481                 return doTaxa;
 482         }
 483         public void setDoTaxa(boolean doTaxa) {
 484                 this.doTaxa = doTaxa;
 485         }
 486
 487         public boolean isDoRelTaxa() {
 488                 return doRelTaxa;
 489         }
 490         public void setDoRelTaxa(boolean doRelTaxa) {
 491                 this.doRelTaxa = doRelTaxa;
 492         }
 493
 494
 495
 496         public String getTaxonTable() {
 497                 return this.taxonTable ;
 498         }
 499
 500         /**
 501          * @param taxonTable the taxonTable to set
 502          */
 503         public void setTaxonTable(String taxonTable) {
 504                 this.taxonTable = taxonTable;
 505         }
 506
 507
 508
 509         public String getClassificationQuery() {
 510                 return this.classificationQuery ;
 511         }
 512
 513         /**
 514          * @param classificationQuery the classificationQuery to set
 515          */
 516         public void setClassificationQuery(String classificationQuery) {
 517                 this.classificationQuery = classificationQuery;
 518         }
 519
 520         /**
 521          * @param relTaxaIdQuery the relTaxaIdQuery to set
 522          */
 523         public void setRelTaxaIdQuery(String relTaxaIdQuery) {
 524                 this.relTaxaIdQuery = relTaxaIdQuery;
 525         }
 526
 527         public String getRelTaxaIdQuery() {
 528                 return this.relTaxaIdQuery ;
 529         }
 530
 531
 532
 533         /**
 534          * @return the nameIdTable
 535          */
 536         public String getNameIdTable() {
 537                 return nameIdTable;
 538         }
 539
 540
 541
 542         /**
 543          * @param nameIdTable the nameIdTable to set
 544          */
 545         public void setNameIdTable(String nameIdTable) {
 546                 this.nameIdTable = nameIdTable;
 547         }
 548
 549
 550
 551         public void setReferenceIdTable(String referenceIdTable) {
 552                 this.referenceIdTable = referenceIdTable;
 553         }
 554
 555         public String getReferenceIdTable() {
 556                 return referenceIdTable;
 557         }
 558
 559
 560
 561         public void setFactFilter(String factFilter) {
 562                 this.factFilter = factFilter;
 563         }
 564
 565
 566
 567         public String getFactFilter() {
 568                 return factFilter;
 569         }
 570
 571
 572
 573         public String getOccurrenceFilter() {
 574                 return occurrenceFilter;
 575         }
 576
 577
 578
 579         public void setOccurrenceFilter(String occurrenceFilter) {
 580                 this.occurrenceFilter = occurrenceFilter;
 581         }
 582
 583
 584
 585         public String getCommonNameFilter() {
 586                 return commonNameFilter;
 587         }
 588
 589
 590
 591         public void setCommonNameFilter(String commonNameFilter) {
 592                 this.commonNameFilter = commonNameFilter;
 593         }
 594
 595
 596
 597         public String getOccurrenceSourceFilter() {
 598                 return occurrenceSourceFilter;
 599         }
 600
 601
 602
 603         public void setOccurrenceSourceFilter(String occurrenceSourceFilter) {
 604                 this.occurrenceSourceFilter = occurrenceSourceFilter;
 605         }
 606
 607
 608
 609         public String getWebMarkerFilter() {
 610                 return webMarkerFilter;
 611         }
 612
 613
 614
 615         public void setWebMarkerFilter(String webMarkerFilter) {
 616                 this.webMarkerFilter = webMarkerFilter;
 617         }
 618
 619
 620
 621         public boolean isUseSingleClassification() {
 622                 return useSingleClassification;
 623         }
 624
 625
 626
 627         public void setUseSingleClassification(boolean useSingleClassification) {
 628                 this.useSingleClassification = useSingleClassification;
 629         }
 630
 631
 632         public void setAuthorTeamFilter(String authorTeamFilter) {
 633                 this.authorTeamFilter = authorTeamFilter;
 634         }
 635
 636         public String getAuthorTeamFilter() {
 637                 return authorTeamFilter;
 638         }
 639
 640
 641
 642         public String getAuthorFilter() {
 643                 return authorFilter;
 644         }
 645
 646
 647
 648         public void setAuthorFilter(String authorFilter) {
 649                 this.authorFilter = authorFilter;
 650         }
 651
 652
 653
 654         public boolean isSwitchSpeciesGroup() {
 655                 return switchSpeciesGroup;
 656         }
 657
 658
 659
 660         /**
 661          * If true, the rankId for speicesGroup is changed from 59 to 57 and
 662          * 59 is used for coll. species instead
 663          * @param switchSpeciesGroup
 664          */
 665         public void setSwitchSpeciesGroup(boolean switchSpeciesGroup) {
 666                 this.switchSpeciesGroup = switchSpeciesGroup;
 667         }
 668
 669
 670
 671         public boolean isSplitTdwgCodes() {
 672                 return isSplitTdwgCodes;
 673         }
 674
 675
 676         public void setSplitTdwgCodes(boolean isSplitTdwgCodes) {
 677                 this.isSplitTdwgCodes = isSplitTdwgCodes;
 678         }
 679
 680
 681         public Method getMakeUrlForTaxon() {
 682                 return makeUrlForTaxon;
 683         }
 684
 685         public void setMakeUrlForTaxon(Method makeUrlForTaxon) {
 686                 this.makeUrlForTaxon = makeUrlForTaxon;
 687         }
 688
 689
 690
 691         public String getInfrGenericRankAbbrev() {
 692                 return infrGenericRankAbbrev;
 693         }
 694
 695
 696
 697         public void setInfrGenericRankAbbrev(String infrGenericRankAbbrev) {
 698                 this.infrGenericRankAbbrev = infrGenericRankAbbrev;
 699         }
 700
 701
 702
 703         public String getInfrSpecificRankAbbrev() {
 704                 return infrSpecificRankAbbrev;
 705         }
 706
 707
 708
 709         public void setInfrSpecificRankAbbrev(String infrSpecificRankAbbrev) {
 710                 this.infrSpecificRankAbbrev = infrSpecificRankAbbrev;
 711         }
 712
 713
 714
 715         public boolean isRemoveHttpMapsAnchor() {
 716                 return removeHttpMapsAnchor;
 717         }
 718
 719
 720
 721         public void setRemoveHttpMapsAnchor(boolean removeHttpMapsAnchor) {
 722                 this.removeHttpMapsAnchor = removeHttpMapsAnchor;
 723         }
 724
 725
 726
 727
 728
 729
 730 }