cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206ImportConfigurator.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.specimen.abcd206.in;
  11
  12
  13 import java.io.InputStream;
  14 import java.net.URI;
  15 import java.util.HashMap;
  16 import java.util.Map;
  17 import java.util.UUID;
  18
  19 import org.apache.log4j.Logger;
  20
  21 import eu.etaxonomy.cdm.common.UriUtils;
  22 import eu.etaxonomy.cdm.database.ICdmDataSource;
  23 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  24 import eu.etaxonomy.cdm.io.common.IMatchingImportConfigurator;
  25 import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;
  26 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  27 import eu.etaxonomy.cdm.io.specimen.SpecimenUserInteraction;
  28 import eu.etaxonomy.cdm.model.agent.Person;
  29 import eu.etaxonomy.cdm.model.agent.Team;
  30 import eu.etaxonomy.cdm.model.reference.Reference;
  31
  32 /**
  33  * @author p.kelbert
  34  * @created 20.10.2008
  35  * @version 1.0
  36  */
  37 public class Abcd206ImportConfigurator extends ImportConfiguratorBase<Abcd206ImportState, InputStream> implements IImportConfigurator, IMatchingImportConfigurator {
  38     private static final Logger logger = Logger.getLogger(Abcd206ImportConfigurator.class);
  39
  40     private static String sourceReferenceTitle = null;
  41     @Deprecated
  42     //FIXME what does this do?
  43     private boolean parseNameAutomatically = false;
  44     private boolean reuseExistingMetadata = true;
  45     private String taxonReference = null;
  46     private boolean addIndividualsAssociationsSuchAsSpecimenAndObservations = true;
  47     private boolean reuseExistingDescriptiveGroups = false;
  48     private boolean reuseExistingTaxaWhenPossible = true;
  49     private final Map<UUID, UUID> taxonToDescriptionMap = new HashMap<UUID, UUID>();
  50     private Map<String, Team> titleCacheTeam;
  51     private Map<String, Person> titleCachePerson;
  52     private String defaultAuthor="";
  53     private boolean allowReuseOtherClassifications =true;
  54     private boolean addMediaAsMediaSpecimen = false;
  55     private boolean determinationOnFieldUnitLevel = false;
  56     private boolean deduplicateReferences = false;
  57     private boolean deduplicateClassifications = false;
  58     private boolean ignoreAuthorship = false;
  59     private boolean removeCountryFromLocalityText = false;
  60     private boolean moveNewTaxaToDefaultClassification = false;
  61
  62     private boolean mapUnitIdToCatalogNumber = true;
  63     private boolean mapUnitIdToAccessionNumber = false;
  64     private boolean mapUnitIdToBarcode = false;
  65
  66     private final SpecimenUserInteraction specimenUserInteraction = new SpecimenUserInteraction();
  67
  68     private Map<String,UUID> namedAreaDecisions = new HashMap<String,UUID>();
  69
  70     //TODO
  71     private static IInputTransformer defaultTransformer = null;
  72
  73     private URI sourceUri;
  74     private URI reportUri;
  75
  76
  77     @Override
  78     @SuppressWarnings("unchecked")
  79     protected void makeIoClassList(){
  80         System.out.println("makeIOClassList");
  81         ioClassList = new Class[]{
  82                 Abcd206Import.class,
  83         };
  84     };
  85
  86     public static Abcd206ImportConfigurator NewInstance(URI uri,ICdmDataSource destination){
  87         return new Abcd206ImportConfigurator(null, uri, destination, false);
  88     }
  89
  90     /**
  91      * @param uri
  92      * @param object
  93      * @param b
  94      * @return
  95      */
  96     public static Abcd206ImportConfigurator NewInstance(URI uri, ICdmDataSource destination, boolean interact) {
  97         return new Abcd206ImportConfigurator(null, uri, destination, interact);
  98     }
  99
 100     /**
 101      * @param uri
 102      * @param object
 103      * @param b
 104      * @return
 105      */
 106     public static Abcd206ImportConfigurator NewInstance(InputStream stream, ICdmDataSource destination, boolean interact) {
 107         return new Abcd206ImportConfigurator(stream, null, destination, interact);
 108     }
 109
 110
 111
 112     /**
 113      * @param berlinModelSource
 114      * @param sourceReference
 115      * @param destination
 116      */
 117     private Abcd206ImportConfigurator(InputStream stream, URI uri, ICdmDataSource destination, boolean interact) {
 118         super(defaultTransformer);
 119         if (stream != null){
 120                 setSource(stream);
 121         }else{
 122                 this.sourceUri = uri;
 123         }
 124         setDestination(destination);
 125         setSourceReferenceTitle("ABCD classic");
 126         setInteractWithUser(interact);
 127     }
 128
 129
 130
 131
 132
 133     /* (non-Javadoc)
 134      * @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getNewState()
 135      */
 136     @Override
 137     public Abcd206ImportState getNewState() {
 138         return new Abcd206ImportState(this);
 139     }
 140
 141
 142     @Override
 143     public InputStream getSource(){
 144         if (super.getSource() != null){
 145                 return super.getSource();
 146         }else if (this.sourceUri != null){
 147                 try {
 148                                 InputStream is = UriUtils.getInputStream(sourceUri);
 149                                 setSource(is);
 150                                 return is;
 151                         } catch (Exception e) {
 152                                 throw new RuntimeException(e);
 153                         }
 154         }else{
 155                 return null;
 156         }
 157     }
 158
 159     /**
 160      * @param file
 161      */
 162     @Override
 163     public void setSource(InputStream is) {
 164         this.sourceUri = null;
 165         super.setSource(is);
 166     }
 167
 168     public URI getSourceUri(){
 169         return this.sourceUri;
 170     }
 171
 172     /**
 173      * @param file
 174      */
 175     public void setSourceUri(URI sourceUri) {
 176         this.sourceUri = sourceUri;
 177         super.setSource(null);
 178     }
 179
 180
 181     @Override
 182     public String getSourceReferenceTitle(){
 183         return this.sourceReferenceTitle;
 184     }
 185
 186     @Override
 187     public void setSourceReferenceTitle(String name){
 188         this.sourceReferenceTitle=name;
 189     }
 190
 191     /* (non-Javadoc)
 192      * @see eu.etaxonomy.cdm.io.common.ImportConfiguratorBase#getSourceReference()
 193      */
 194     @Override
 195     public Reference getSourceReference() {
 196         //TODO
 197         return sourceReference;
 198     }
 199
 200     public void setTaxonReference(String taxonReference) {
 201         this.taxonReference = taxonReference;
 202     }
 203
 204     public Reference getTaxonReference() {
 205         //TODO
 206         if (this.taxonReference == null){
 207             logger.info("getTaxonReference not yet fully implemented");
 208         }
 209         return sourceReference;
 210     }
 211     @Deprecated
 212     public void setParseNameAutomatically(boolean doParsing){
 213         this.parseNameAutomatically=doParsing;
 214     }
 215     @Deprecated
 216     public boolean isParseNameAutomatically(){
 217         return this.parseNameAutomatically;
 218     }
 219
 220     public void setReuseExistingMetadata(boolean reuseMetadata){
 221         this.reuseExistingMetadata = reuseMetadata;
 222     }
 223
 224     public boolean isReUseExistingMetadata(){
 225         return this.reuseExistingMetadata;
 226     }
 227
 228     public void setAddIndividualsAssociationsSuchAsSpecimenAndObservations(
 229             boolean doCreateIndividualsAssociations) {
 230         this.addIndividualsAssociationsSuchAsSpecimenAndObservations = doCreateIndividualsAssociations;
 231     }
 232
 233     /**
 234      * Create an IndividualsAssociations for each determination element in the ABCD data. ABCD has no such concept as IndividualsAssociations so the only way to
 235      *
 236      * @return
 237      */
 238     public boolean isAddIndividualsAssociationsSuchAsSpecimenAndObservations() {
 239         return addIndividualsAssociationsSuchAsSpecimenAndObservations;
 240     }
 241
 242     /**
 243      * @param doReuseExistingDescription the doReuseExistingDescription to set
 244      * NOT USED YET
 245      */
 246     public void reuseExistingDescriptiveGroups(boolean doReuseExistingDescription) {
 247         this.reuseExistingDescriptiveGroups = doReuseExistingDescription;
 248     }
 249
 250     /**
 251      * @return the doReuseExistingDescription
 252      */
 253     public boolean isReuseExistingDescriptiveGroups() {
 254         return reuseExistingDescriptiveGroups;
 255     }
 256
 257     /* (non-Javadoc)
 258      * @see eu.etaxonomy.cdm.io.common.IMatchingImportConfigurator#isDoMatchTaxa()
 259      */
 260     @Override
 261     public boolean isReuseExistingTaxaWhenPossible() {
 262         return reuseExistingTaxaWhenPossible;
 263     }
 264
 265     /* (non-Javadoc)
 266      * @see eu.etaxonomy.cdm.io.common.IMatchingImportConfigurator#setDoMatchTaxa(boolean)
 267      */
 268     @Override
 269     public void setReuseExistingTaxaWhenPossible(boolean doMatchTaxa) {
 270         this.reuseExistingTaxaWhenPossible = doMatchTaxa;
 271     }
 272
 273     /**
 274      * @return
 275      */
 276     public Map<UUID, UUID> getTaxonToDescriptionMap() {
 277         // TODO Auto-generated method stub
 278         return taxonToDescriptionMap ;
 279     }
 280
 281
 282
 283     public Map<String, Team> getTeams() {
 284         return titleCacheTeam;
 285     }
 286
 287     public void setTeams(Map<String, Team> titleCacheTeam) {
 288         this.titleCacheTeam = titleCacheTeam;
 289     }
 290
 291     public Map<String, Person> getPersons() {
 292         return titleCachePerson;
 293     }
 294
 295     public void setPersons(Map<String, Person> titleCachePerson) {
 296         this.titleCachePerson = titleCachePerson;
 297     }
 298
 299     /**
 300      * @param string
 301      */
 302     public void setDefaultAuthor(String string) {
 303         defaultAuthor=string;
 304
 305     }
 306
 307     public String getDefaultAuthor(){
 308         return defaultAuthor;
 309     }
 310
 311     public Map<String,UUID> getNamedAreaDecisions() {
 312         return namedAreaDecisions;
 313     }
 314
 315     public void setNamedAreaDecisions(Map<String,UUID> namedAreaDecisions) {
 316         this.namedAreaDecisions = namedAreaDecisions;
 317     }
 318
 319     public void putNamedAreaDecision(String areaStr,UUID uuid){
 320         this.namedAreaDecisions.put(areaStr,uuid);
 321     }
 322
 323     public UUID getNamedAreaDecision(String areaStr){
 324         return namedAreaDecisions.get(areaStr);
 325     }
 326
 327     /**
 328      * @return the doAddMediaAsMediaSpecimen
 329      */
 330     public boolean isAddMediaAsMediaSpecimen() {
 331         return addMediaAsMediaSpecimen;
 332     }
 333
 334     public void setAddMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen) {
 335         this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;
 336     }
 337
 338     public boolean isDeterminationOnFieldUnitLevel() {
 339         return determinationOnFieldUnitLevel;
 340     }
 341
 342     public void setDeterminationOnFieldUnitLevel(boolean determinationOnFieldUnitLevel) {
 343         this.determinationOnFieldUnitLevel = determinationOnFieldUnitLevel;
 344     }
 345
 346
 347     public boolean isDeduplicateClassifications() {
 348         return deduplicateClassifications;
 349     }
 350
 351     public void setDeduplicateClassifications(boolean deduplicateClassifications) {
 352         this.deduplicateClassifications = deduplicateClassifications;
 353     }
 354
 355     public boolean isDeduplicateReferences() {
 356         return deduplicateReferences;
 357     }
 358
 359     public void setDeduplicateReferences(boolean deduplicateReferences) {
 360         this.deduplicateReferences = deduplicateReferences;
 361     }
 362
 363     public boolean isAllowReuseOtherClassifications() {
 364         return allowReuseOtherClassifications;
 365     }
 366
 367     public void setAllowReuseOtherClassifications(boolean allowReuseOtherClassifications) {
 368         this.allowReuseOtherClassifications = allowReuseOtherClassifications;
 369     }
 370
 371     public SpecimenUserInteraction getSpecimenUserInteraction() {
 372         return specimenUserInteraction;
 373     }
 374
 375     public void setReportUri(URI reportUri) {
 376         this.reportUri = reportUri;
 377     }
 378
 379     public URI getReportUri() {
 380         return reportUri;
 381     }
 382
 383     public void setIgnoreAuthorship(boolean ignoreAuthorship) {
 384         this.ignoreAuthorship = ignoreAuthorship;
 385     }
 386
 387     public boolean isIgnoreAuthorship() {
 388         return ignoreAuthorship;
 389     }
 390
 391     public boolean isMapUnitIdToAccessionNumber() {
 392         return mapUnitIdToAccessionNumber;
 393     }
 394
 395     public boolean isMapUnitIdToBarcode() {
 396         return mapUnitIdToBarcode;
 397     }
 398
 399     public boolean isMapUnitIdToCatalogNumber() {
 400         return mapUnitIdToCatalogNumber;
 401     }
 402
 403     public void setMapUnitIdToAccessionNumber(boolean mapUnitIdToAccessionNumber) {
 404         this.mapUnitIdToAccessionNumber = mapUnitIdToAccessionNumber;
 405     }
 406
 407     public void setMapUnitIdToBarcode(boolean mapUnitIdToBarcode) {
 408         this.mapUnitIdToBarcode = mapUnitIdToBarcode;
 409     }
 410
 411     public void setMapUnitIdToCatalogNumber(boolean mapUnitIdToCatalogNumber) {
 412         this.mapUnitIdToCatalogNumber = mapUnitIdToCatalogNumber;
 413     }
 414
 415     public void setRemoveCountryFromLocalityText(boolean removeCountryFromLocalityText) {
 416         this.removeCountryFromLocalityText = removeCountryFromLocalityText;
 417     }
 418
 419     public boolean isRemoveCountryFromLocalityText() {
 420         return removeCountryFromLocalityText;
 421     }
 422
 423     public boolean isMoveNewTaxaToDefaultClassification() {
 424         return moveNewTaxaToDefaultClassification;
 425     }
 426
 427     public void setMoveNewTaxaToDefaultClassification(boolean moveNewTaxaToDefaultClassification) {
 428         this.moveNewTaxaToDefaultClassification = moveNewTaxaToDefaultClassification;
 429     }
 430
 431 }