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

   1 // $Id$
   2 /**
   3 * Copyright (C) 2016 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10 package eu.etaxonomy.cdm.io.specimen;
  11
  12 import java.net.URI;
  13 import java.util.HashMap;
  14 import java.util.Map;
  15 import java.util.UUID;
  16
  17 import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
  18 import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;
  19 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  20 import eu.etaxonomy.cdm.model.agent.Person;
  21 import eu.etaxonomy.cdm.model.agent.Team;
  22
  23 /**
  24  * @author k.luther
  25  * @date 15.07.2016
  26  *
  27  */
  28 public abstract class SpecimenImportConfiguratorBase<STATE extends SpecimenImportStateBase, InputStream>  extends ImportConfiguratorBase<STATE, InputStream> {
  29
  30     /**
  31      * @param transformer
  32      */
  33     public SpecimenImportConfiguratorBase(IInputTransformer transformer) {
  34         super(transformer);
  35
  36     }
  37
  38     private boolean ignoreImportOfExistingSpecimen = true;
  39     private boolean reuseExistingTaxaWhenPossible = true;
  40     private final Map<UUID, UUID> taxonToDescriptionMap = new HashMap<UUID, UUID>();
  41
  42     private Map<String, Team> titleCacheTeam;
  43     private Map<String, Person> titleCachePerson;
  44     private boolean ignoreAuthorship = false;
  45     private boolean removeCountryFromLocalityText = false;
  46     protected OccurenceQuery query ;
  47
  48     private boolean addMediaAsMediaSpecimen = false;
  49     private boolean reuseExistingMetaData = true;
  50
  51     private static String sourceReferenceTitle = null;
  52
  53     private String taxonReference = null;
  54     private boolean addIndividualsAssociationsSuchAsSpecimenAndObservations = true;
  55     private boolean reuseExistingDescriptiveGroups = false;
  56
  57
  58     private String defaultAuthor="";
  59     private boolean allowReuseOtherClassifications =true;
  60
  61     private boolean deduplicateReferences = false;
  62     private boolean deduplicateClassifications = false;
  63
  64     private boolean moveNewTaxaToDefaultClassification = true;
  65
  66     private boolean mapUnitIdToCatalogNumber = true;
  67     private boolean mapUnitIdToAccessionNumber = false;
  68     private boolean mapUnitIdToBarcode = false;
  69
  70     private boolean overwriteExistingSpecimens = false;
  71
  72
  73     private final SpecimenUserInteraction specimenUserInteraction = new SpecimenUserInteraction();
  74
  75     protected Map<String,UUID> namedAreaDecisions = new HashMap<String,UUID>();
  76
  77     private URI reportUri;
  78
  79
  80     public boolean isIgnoreImportOfExistingSpecimen() {
  81         return ignoreImportOfExistingSpecimen;
  82     }
  83
  84     public void setIgnoreImportOfExistingSpecimen(boolean ignoreImportOfExistingSpecimen) {
  85         this.ignoreImportOfExistingSpecimen = ignoreImportOfExistingSpecimen;
  86     }
  87
  88     public Map<String, Team> getTitleCacheTeam() {
  89         return titleCacheTeam;
  90     }
  91
  92     public void setTitleCacheTeam(Map<String, Team> titleCacheTeam) {
  93         this.titleCacheTeam = titleCacheTeam;
  94     }
  95
  96     public Map<String, Person> getTitleCachePerson() {
  97         return titleCachePerson;
  98     }
  99
 100     public void setTitleCachePerson(Map<String, Person> titleCachePerson) {
 101         this.titleCachePerson = titleCachePerson;
 102     }
 103
 104     public OccurenceQuery getQuery() {
 105         return query;
 106     }
 107
 108     public void setQuery(OccurenceQuery query) {
 109         this.query = query;
 110     }
 111
 112
 113
 114
 115
 116     public String getTaxonReference() {
 117         return taxonReference;
 118     }
 119
 120     public void setTaxonReference(String taxonReference) {
 121         this.taxonReference = taxonReference;
 122     }
 123
 124     public boolean isAddIndividualsAssociationsSuchAsSpecimenAndObservations() {
 125         return addIndividualsAssociationsSuchAsSpecimenAndObservations;
 126     }
 127
 128     public void setAddIndividualsAssociationsSuchAsSpecimenAndObservations(
 129             boolean addIndividualsAssociationsSuchAsSpecimenAndObservations) {
 130         this.addIndividualsAssociationsSuchAsSpecimenAndObservations = addIndividualsAssociationsSuchAsSpecimenAndObservations;
 131     }
 132
 133     public boolean isReuseExistingDescriptiveGroups() {
 134         return reuseExistingDescriptiveGroups;
 135     }
 136
 137     public void setReuseExistingDescriptiveGroups(boolean reuseExistingDescriptiveGroups) {
 138         this.reuseExistingDescriptiveGroups = reuseExistingDescriptiveGroups;
 139     }
 140
 141     public String getDefaultAuthor() {
 142         return defaultAuthor;
 143     }
 144
 145     public void setDefaultAuthor(String defaultAuthor) {
 146         this.defaultAuthor = defaultAuthor;
 147     }
 148
 149     public boolean isAllowReuseOtherClassifications() {
 150         return allowReuseOtherClassifications;
 151     }
 152
 153     public void setAllowReuseOtherClassifications(boolean allowReuseOtherClassifications) {
 154         this.allowReuseOtherClassifications = allowReuseOtherClassifications;
 155     }
 156
 157     public boolean isDeduplicateReferences() {
 158         return deduplicateReferences;
 159     }
 160
 161     public void setDeduplicateReferences(boolean deduplicateReferences) {
 162         this.deduplicateReferences = deduplicateReferences;
 163     }
 164
 165     public boolean isDeduplicateClassifications() {
 166         return deduplicateClassifications;
 167     }
 168
 169     public void setDeduplicateClassifications(boolean deduplicateClassifications) {
 170         this.deduplicateClassifications = deduplicateClassifications;
 171     }
 172
 173     public boolean isMoveNewTaxaToDefaultClassification() {
 174         return moveNewTaxaToDefaultClassification;
 175     }
 176
 177     public void setMoveNewTaxaToDefaultClassification(boolean moveNewTaxaToDefaultClassification) {
 178         this.moveNewTaxaToDefaultClassification = moveNewTaxaToDefaultClassification;
 179     }
 180
 181     public boolean isMapUnitIdToCatalogNumber() {
 182         return mapUnitIdToCatalogNumber;
 183     }
 184
 185     public void setMapUnitIdToCatalogNumber(boolean mapUnitIdToCatalogNumber) {
 186         this.mapUnitIdToCatalogNumber = mapUnitIdToCatalogNumber;
 187     }
 188
 189     public boolean isMapUnitIdToAccessionNumber() {
 190         return mapUnitIdToAccessionNumber;
 191     }
 192
 193     public void setMapUnitIdToAccessionNumber(boolean mapUnitIdToAccessionNumber) {
 194         this.mapUnitIdToAccessionNumber = mapUnitIdToAccessionNumber;
 195     }
 196
 197     public boolean isMapUnitIdToBarcode() {
 198         return mapUnitIdToBarcode;
 199     }
 200
 201     public void setMapUnitIdToBarcode(boolean mapUnitIdToBarcode) {
 202         this.mapUnitIdToBarcode = mapUnitIdToBarcode;
 203     }
 204
 205     public Map<String, UUID> getNamedAreaDecisions() {
 206         return namedAreaDecisions;
 207     }
 208
 209
 210     public void setNamedAreaDecisions(Map<String,UUID> namedAreaDecisions) {
 211         this.namedAreaDecisions = namedAreaDecisions;
 212     }
 213
 214     public void putNamedAreaDecision(String areaStr,UUID uuid){
 215         this.namedAreaDecisions.put(areaStr,uuid);
 216     }
 217
 218     public UUID getNamedAreaDecision(String areaStr){
 219         return namedAreaDecisions.get(areaStr);
 220     }
 221
 222     public Map<UUID, UUID> getTaxonToDescriptionMap() {
 223         return taxonToDescriptionMap;
 224     }
 225
 226
 227
 228     public SpecimenUserInteraction getSpecimenUserInteraction() {
 229         return specimenUserInteraction;
 230     }
 231
 232     public void setReuseExistingTaxaWhenPossible(boolean reuseExistingTaxaWhenPossible) {
 233         this.reuseExistingTaxaWhenPossible = reuseExistingTaxaWhenPossible;
 234     }
 235
 236     public void setIgnoreAuthorship(boolean ignoreAuthorship) {
 237         this.ignoreAuthorship = ignoreAuthorship;
 238     }
 239
 240     public void setRemoveCountryFromLocalityText(boolean removeCountryFromLocalityText) {
 241         this.removeCountryFromLocalityText = removeCountryFromLocalityText;
 242     }
 243
 244     public void setAddMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen) {
 245         this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;
 246     }
 247
 248     public void setOverwriteExistingSpecimens(boolean overwriteExistingSpecimens) {
 249         this.overwriteExistingSpecimens = overwriteExistingSpecimens;
 250     }
 251
 252     public boolean isOverwriteExistingSpecimens(){
 253         return overwriteExistingSpecimens;
 254     }
 255
 256
 257
 258
 259     /**
 260      * @return
 261      */
 262     public boolean isReuseExistingTaxaWhenPossible() {
 263
 264         return reuseExistingTaxaWhenPossible;
 265     }
 266
 267     /**
 268      * @param titleCacheTeam
 269      */
 270     public void setTeams(Map<String, Team> titleCacheTeam) {
 271        this.titleCacheTeam  = titleCacheTeam;
 272
 273     }
 274
 275     public Team getTeam(String titleCache){
 276         return titleCacheTeam.get(titleCache);
 277     }
 278
 279     public Map<String, Team> getTeams(){
 280         return titleCacheTeam;
 281     }
 282     /**
 283      * @param titleCachePerson
 284      */
 285     public void setPersons(Map<String, Person> titleCachePerson) {
 286         this.titleCachePerson = titleCachePerson;
 287     }
 288
 289     public Map<String, Person> getPersons(){
 290         return titleCachePerson;
 291     }
 292
 293     public Person getPerson(String titleCache){
 294         return titleCachePerson.get(titleCache);
 295     }
 296
 297     public boolean isAddMediaAsMediaSpecimen(){
 298         return addMediaAsMediaSpecimen;
 299     }
 300
 301     public void addMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen){
 302        this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;
 303     }
 304
 305
 306     /**
 307      * @return
 308      */
 309     public boolean isIgnoreAuthorship() {
 310         return ignoreAuthorship;
 311     }
 312
 313     /**
 314      * @return
 315      */
 316     public boolean isRemoveCountryFromLocalityText() {
 317         return removeCountryFromLocalityText;
 318     }
 319
 320     public OccurenceQuery getOccurenceQuery(){
 321         return query;
 322     }
 323
 324     public void setOccurenceQuery(OccurenceQuery query){
 325         this.query = query;
 326     }
 327
 328
 329
 330     /**
 331      * @return the reuseExistingMetaData
 332      */
 333     public boolean isReuseExistingMetaData() {
 334         return reuseExistingMetaData;
 335     }
 336
 337     /**
 338      * @param reuseExistingMetaData the reuseExistingMetaData to set
 339      */
 340     public void setReuseExistingMetaData(boolean reuseExistingMetaData) {
 341         this.reuseExistingMetaData = reuseExistingMetaData;
 342     }
 343
 344     public void setReportUri(URI reportUri) {
 345         this.reportUri = reportUri;
 346     }
 347
 348     public URI getReportUri() {
 349         return reportUri;
 350     }
 351
 352     @Override
 353     public String getSourceReferenceTitle(){
 354         return this.sourceReferenceTitle;
 355     }
 356
 357     @Override
 358     public void setSourceReferenceTitle(String name){
 359         this.sourceReferenceTitle=name;
 360     }
 361
 362     @Override
 363     public boolean isValid(){
 364         return true;
 365     }
 366
 367
 368
 369 }