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