cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenImportConfiguratorBase.java

   1 /**
   2 * Copyright (C) 2016 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 package eu.etaxonomy.cdm.io.specimen;
  10
  11 import java.net.URI;
  12 import java.util.HashMap;
  13 import java.util.Map;
  14 import java.util.UUID;
  15
  16 import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
  17 import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;
  18 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  19 import eu.etaxonomy.cdm.model.agent.Person;
  20 import eu.etaxonomy.cdm.model.agent.Team;
  21 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  22
  23 /**
  24  * @author k.luther
  25  * @since 15.07.2016
  26  *
  27  */
  28 public abstract class SpecimenImportConfiguratorBase<CONFIG extends SpecimenImportConfiguratorBase, STATE extends SpecimenImportStateBase<CONFIG,STATE>, InputStream>
  29         extends ImportConfiguratorBase<STATE, InputStream> {
  30
  31     private static final long serialVersionUID = 4741134251527063988L;
  32
  33     /**
  34      * @param transformer
  35      */
  36     public SpecimenImportConfiguratorBase(IInputTransformer transformer) {
  37         super(transformer);
  38
  39     }
  40
  41     private boolean ignoreImportOfExistingSpecimen = true;
  42     private boolean reuseExistingTaxaWhenPossible = true;
  43     private final Map<UUID, UUID> taxonToDescriptionMap = new HashMap<UUID, UUID>();
  44
  45     private Map<String, Team> titleCacheTeam;
  46     private Map<String, Person> titleCachePerson;
  47     private boolean ignoreAuthorship = false;
  48     private boolean removeCountryFromLocalityText = false;
  49     protected OccurenceQuery query ;
  50
  51     private boolean addMediaAsMediaSpecimen = false;
  52     private boolean reuseExistingMetaData = true;
  53
  54     private String sourceReferenceTitle = null;
  55
  56     private String taxonReference = null;
  57     private boolean addIndividualsAssociationsSuchAsSpecimenAndObservations = true;
  58     private boolean reuseExistingDescriptiveGroups = false;
  59
  60
  61     private String defaultAuthor="";
  62     private boolean allowReuseOtherClassifications =true;
  63
  64     private boolean deduplicateReferences = false;
  65     private boolean deduplicateClassifications = false;
  66
  67     private boolean moveNewTaxaToDefaultClassification = true;
  68
  69     private boolean mapUnitIdToCatalogNumber = true;
  70     private boolean mapUnitIdToAccessionNumber = false;
  71     private boolean mapUnitIdToBarcode = false;
  72
  73     private boolean overwriteExistingSpecimens = false;
  74     private boolean downloadSequenceData = false;
  75
  76     private SpecimenOrObservationType type;
  77
  78
  79     /**
  80      * @return the type
  81      */
  82     public SpecimenOrObservationType getType() {
  83         return type;
  84     }
  85
  86     /**
  87      * @param type the type to set
  88      */
  89     public void setType(SpecimenOrObservationType type) {
  90         this.type = type;
  91     }
  92
  93     private final SpecimenUserInteraction specimenUserInteraction = new SpecimenUserInteraction();
  94
  95     protected Map<String,UUID> namedAreaDecisions = new HashMap<String,UUID>();
  96
  97     private URI reportUri;
  98
  99
 100     public boolean isIgnoreImportOfExistingSpecimen() {
 101         return ignoreImportOfExistingSpecimen;
 102     }
 103
 104     public void setIgnoreImportOfExistingSpecimen(boolean ignoreImportOfExistingSpecimen) {
 105         this.ignoreImportOfExistingSpecimen = ignoreImportOfExistingSpecimen;
 106     }
 107
 108     public Map<String, Team> getTitleCacheTeam() {
 109         return titleCacheTeam;
 110     }
 111
 112     public void setTitleCacheTeam(Map<String, Team> titleCacheTeam) {
 113         this.titleCacheTeam = titleCacheTeam;
 114     }
 115
 116     public Map<String, Person> getTitleCachePerson() {
 117         return titleCachePerson;
 118     }
 119
 120     public void setTitleCachePerson(Map<String, Person> titleCachePerson) {
 121         this.titleCachePerson = titleCachePerson;
 122     }
 123
 124     public OccurenceQuery getQuery() {
 125         return query;
 126     }
 127
 128     public void setQuery(OccurenceQuery query) {
 129         this.query = query;
 130     }
 131
 132
 133
 134
 135
 136     public String getTaxonReference() {
 137         return taxonReference;
 138     }
 139
 140     public void setTaxonReference(String taxonReference) {
 141         this.taxonReference = taxonReference;
 142     }
 143
 144     public boolean isAddIndividualsAssociationsSuchAsSpecimenAndObservations() {
 145         return addIndividualsAssociationsSuchAsSpecimenAndObservations;
 146     }
 147
 148     public void setAddIndividualsAssociationsSuchAsSpecimenAndObservations(
 149             boolean addIndividualsAssociationsSuchAsSpecimenAndObservations) {
 150         this.addIndividualsAssociationsSuchAsSpecimenAndObservations = addIndividualsAssociationsSuchAsSpecimenAndObservations;
 151     }
 152
 153     public boolean isReuseExistingDescriptiveGroups() {
 154         return reuseExistingDescriptiveGroups;
 155     }
 156
 157     public void setReuseExistingDescriptiveGroups(boolean reuseExistingDescriptiveGroups) {
 158         this.reuseExistingDescriptiveGroups = reuseExistingDescriptiveGroups;
 159     }
 160
 161     public String getDefaultAuthor() {
 162         return defaultAuthor;
 163     }
 164
 165     public void setDefaultAuthor(String defaultAuthor) {
 166         this.defaultAuthor = defaultAuthor;
 167     }
 168
 169     public boolean isAllowReuseOtherClassifications() {
 170         return allowReuseOtherClassifications;
 171     }
 172
 173     public void setAllowReuseOtherClassifications(boolean allowReuseOtherClassifications) {
 174         this.allowReuseOtherClassifications = allowReuseOtherClassifications;
 175     }
 176
 177     public boolean isDeduplicateReferences() {
 178         return deduplicateReferences;
 179     }
 180
 181     public void setDeduplicateReferences(boolean deduplicateReferences) {
 182         this.deduplicateReferences = deduplicateReferences;
 183     }
 184
 185     public boolean isDeduplicateClassifications() {
 186         return deduplicateClassifications;
 187     }
 188
 189     public void setDeduplicateClassifications(boolean deduplicateClassifications) {
 190         this.deduplicateClassifications = deduplicateClassifications;
 191     }
 192
 193     public boolean isMoveNewTaxaToDefaultClassification() {
 194         return moveNewTaxaToDefaultClassification;
 195     }
 196
 197     public void setMoveNewTaxaToDefaultClassification(boolean moveNewTaxaToDefaultClassification) {
 198         this.moveNewTaxaToDefaultClassification = moveNewTaxaToDefaultClassification;
 199     }
 200
 201     public boolean isMapUnitIdToCatalogNumber() {
 202         return mapUnitIdToCatalogNumber;
 203     }
 204
 205     public void setMapUnitIdToCatalogNumber(boolean mapUnitIdToCatalogNumber) {
 206         this.mapUnitIdToCatalogNumber = mapUnitIdToCatalogNumber;
 207     }
 208
 209     public boolean isMapUnitIdToAccessionNumber() {
 210         return mapUnitIdToAccessionNumber;
 211     }
 212
 213     public void setMapUnitIdToAccessionNumber(boolean mapUnitIdToAccessionNumber) {
 214         this.mapUnitIdToAccessionNumber = mapUnitIdToAccessionNumber;
 215     }
 216
 217     public boolean isMapUnitIdToBarcode() {
 218         return mapUnitIdToBarcode;
 219     }
 220
 221     public void setMapUnitIdToBarcode(boolean mapUnitIdToBarcode) {
 222         this.mapUnitIdToBarcode = mapUnitIdToBarcode;
 223     }
 224
 225     public Map<String, UUID> getNamedAreaDecisions() {
 226         return namedAreaDecisions;
 227     }
 228
 229
 230     public void setNamedAreaDecisions(Map<String,UUID> namedAreaDecisions) {
 231         this.namedAreaDecisions = namedAreaDecisions;
 232     }
 233
 234     public void putNamedAreaDecision(String areaStr,UUID uuid){
 235         this.namedAreaDecisions.put(areaStr,uuid);
 236     }
 237
 238     public UUID getNamedAreaDecision(String areaStr){
 239         return namedAreaDecisions.get(areaStr);
 240     }
 241
 242     public Map<UUID, UUID> getTaxonToDescriptionMap() {
 243         return taxonToDescriptionMap;
 244     }
 245
 246
 247
 248     public SpecimenUserInteraction getSpecimenUserInteraction() {
 249         return specimenUserInteraction;
 250     }
 251
 252     public void setReuseExistingTaxaWhenPossible(boolean reuseExistingTaxaWhenPossible) {
 253         this.reuseExistingTaxaWhenPossible = reuseExistingTaxaWhenPossible;
 254     }
 255
 256     public void setIgnoreAuthorship(boolean ignoreAuthorship) {
 257         this.ignoreAuthorship = ignoreAuthorship;
 258     }
 259
 260     public void setRemoveCountryFromLocalityText(boolean removeCountryFromLocalityText) {
 261         this.removeCountryFromLocalityText = removeCountryFromLocalityText;
 262     }
 263
 264     public void setAddMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen) {
 265         this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;
 266     }
 267
 268     public void setOverwriteExistingSpecimens(boolean overwriteExistingSpecimens) {
 269         this.overwriteExistingSpecimens = overwriteExistingSpecimens;
 270     }
 271
 272     public boolean isOverwriteExistingSpecimens(){
 273         return overwriteExistingSpecimens;
 274     }
 275
 276
 277
 278
 279     /**
 280      * @return
 281      */
 282     public boolean isReuseExistingTaxaWhenPossible() {
 283
 284         return reuseExistingTaxaWhenPossible;
 285     }
 286
 287     /**
 288      * @param titleCacheTeam
 289      */
 290     public void setTeams(Map<String, Team> titleCacheTeam) {
 291        this.titleCacheTeam  = titleCacheTeam;
 292
 293     }
 294
 295     public Team getTeam(String titleCache){
 296         return titleCacheTeam.get(titleCache);
 297     }
 298
 299     public Map<String, Team> getTeams(){
 300         return titleCacheTeam;
 301     }
 302     /**
 303      * @param titleCachePerson
 304      */
 305     public void setPersons(Map<String, Person> titleCachePerson) {
 306         this.titleCachePerson = titleCachePerson;
 307     }
 308
 309     public Map<String, Person> getPersons(){
 310         return titleCachePerson;
 311     }
 312
 313     public Person getPerson(String titleCache){
 314         return titleCachePerson.get(titleCache);
 315     }
 316
 317     public boolean isAddMediaAsMediaSpecimen(){
 318         return addMediaAsMediaSpecimen;
 319     }
 320
 321     public void addMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen){
 322        this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;
 323     }
 324
 325
 326     /**
 327      * @return
 328      */
 329     public boolean isIgnoreAuthorship() {
 330         return ignoreAuthorship;
 331     }
 332
 333     /**
 334      * @return
 335      */
 336     public boolean isRemoveCountryFromLocalityText() {
 337         return removeCountryFromLocalityText;
 338     }
 339
 340     public OccurenceQuery getOccurenceQuery(){
 341         return query;
 342     }
 343
 344     public void setOccurenceQuery(OccurenceQuery query){
 345         this.query = query;
 346     }
 347
 348
 349
 350     /**
 351      * @return the reuseExistingMetaData
 352      */
 353     public boolean isReuseExistingMetaData() {
 354         return reuseExistingMetaData;
 355     }
 356
 357     /**
 358      * @param reuseExistingMetaData the reuseExistingMetaData to set
 359      */
 360     public void setReuseExistingMetaData(boolean reuseExistingMetaData) {
 361         this.reuseExistingMetaData = reuseExistingMetaData;
 362     }
 363
 364     public void setReportUri(URI reportUri) {
 365         this.reportUri = reportUri;
 366     }
 367
 368     public URI getReportUri() {
 369         return reportUri;
 370     }
 371
 372     @Override
 373     public String getSourceReferenceTitle(){
 374         return this.sourceReferenceTitle;
 375     }
 376
 377     @Override
 378     public void setSourceReferenceTitle(String name){
 379         this.sourceReferenceTitle=name;
 380     }
 381
 382     @Override
 383     public boolean isValid(){
 384         return true;
 385     }
 386
 387     public boolean isDownloadSequenceData() {
 388         return downloadSequenceData;
 389     }
 390
 391     public void setDownloadSequenceData(boolean downloadSequenceData) {
 392         this.downloadSequenceData = downloadSequenceData;
 393     }
 394
 395
 396
 397 }