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  * @date 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 static 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
  75     private SpecimenOrObservationType type;
  76
  77
  78     /**
  79      * @return the type
  80      */
  81     public SpecimenOrObservationType getType() {
  82         return type;
  83     }
  84
  85     /**
  86      * @param type the type to set
  87      */
  88     public void setType(SpecimenOrObservationType type) {
  89         this.type = type;
  90     }
  91
  92     private final SpecimenUserInteraction specimenUserInteraction = new SpecimenUserInteraction();
  93
  94     protected Map<String,UUID> namedAreaDecisions = new HashMap<String,UUID>();
  95
  96     private URI reportUri;
  97
  98
  99     public boolean isIgnoreImportOfExistingSpecimen() {
 100         return ignoreImportOfExistingSpecimen;
 101     }
 102
 103     public void setIgnoreImportOfExistingSpecimen(boolean ignoreImportOfExistingSpecimen) {
 104         this.ignoreImportOfExistingSpecimen = ignoreImportOfExistingSpecimen;
 105     }
 106
 107     public Map<String, Team> getTitleCacheTeam() {
 108         return titleCacheTeam;
 109     }
 110
 111     public void setTitleCacheTeam(Map<String, Team> titleCacheTeam) {
 112         this.titleCacheTeam = titleCacheTeam;
 113     }
 114
 115     public Map<String, Person> getTitleCachePerson() {
 116         return titleCachePerson;
 117     }
 118
 119     public void setTitleCachePerson(Map<String, Person> titleCachePerson) {
 120         this.titleCachePerson = titleCachePerson;
 121     }
 122
 123     public OccurenceQuery getQuery() {
 124         return query;
 125     }
 126
 127     public void setQuery(OccurenceQuery query) {
 128         this.query = query;
 129     }
 130
 131
 132
 133
 134
 135     public String getTaxonReference() {
 136         return taxonReference;
 137     }
 138
 139     public void setTaxonReference(String taxonReference) {
 140         this.taxonReference = taxonReference;
 141     }
 142
 143     public boolean isAddIndividualsAssociationsSuchAsSpecimenAndObservations() {
 144         return addIndividualsAssociationsSuchAsSpecimenAndObservations;
 145     }
 146
 147     public void setAddIndividualsAssociationsSuchAsSpecimenAndObservations(
 148             boolean addIndividualsAssociationsSuchAsSpecimenAndObservations) {
 149         this.addIndividualsAssociationsSuchAsSpecimenAndObservations = addIndividualsAssociationsSuchAsSpecimenAndObservations;
 150     }
 151
 152     public boolean isReuseExistingDescriptiveGroups() {
 153         return reuseExistingDescriptiveGroups;
 154     }
 155
 156     public void setReuseExistingDescriptiveGroups(boolean reuseExistingDescriptiveGroups) {
 157         this.reuseExistingDescriptiveGroups = reuseExistingDescriptiveGroups;
 158     }
 159
 160     public String getDefaultAuthor() {
 161         return defaultAuthor;
 162     }
 163
 164     public void setDefaultAuthor(String defaultAuthor) {
 165         this.defaultAuthor = defaultAuthor;
 166     }
 167
 168     public boolean isAllowReuseOtherClassifications() {
 169         return allowReuseOtherClassifications;
 170     }
 171
 172     public void setAllowReuseOtherClassifications(boolean allowReuseOtherClassifications) {
 173         this.allowReuseOtherClassifications = allowReuseOtherClassifications;
 174     }
 175
 176     public boolean isDeduplicateReferences() {
 177         return deduplicateReferences;
 178     }
 179
 180     public void setDeduplicateReferences(boolean deduplicateReferences) {
 181         this.deduplicateReferences = deduplicateReferences;
 182     }
 183
 184     public boolean isDeduplicateClassifications() {
 185         return deduplicateClassifications;
 186     }
 187
 188     public void setDeduplicateClassifications(boolean deduplicateClassifications) {
 189         this.deduplicateClassifications = deduplicateClassifications;
 190     }
 191
 192     public boolean isMoveNewTaxaToDefaultClassification() {
 193         return moveNewTaxaToDefaultClassification;
 194     }
 195
 196     public void setMoveNewTaxaToDefaultClassification(boolean moveNewTaxaToDefaultClassification) {
 197         this.moveNewTaxaToDefaultClassification = moveNewTaxaToDefaultClassification;
 198     }
 199
 200     public boolean isMapUnitIdToCatalogNumber() {
 201         return mapUnitIdToCatalogNumber;
 202     }
 203
 204     public void setMapUnitIdToCatalogNumber(boolean mapUnitIdToCatalogNumber) {
 205         this.mapUnitIdToCatalogNumber = mapUnitIdToCatalogNumber;
 206     }
 207
 208     public boolean isMapUnitIdToAccessionNumber() {
 209         return mapUnitIdToAccessionNumber;
 210     }
 211
 212     public void setMapUnitIdToAccessionNumber(boolean mapUnitIdToAccessionNumber) {
 213         this.mapUnitIdToAccessionNumber = mapUnitIdToAccessionNumber;
 214     }
 215
 216     public boolean isMapUnitIdToBarcode() {
 217         return mapUnitIdToBarcode;
 218     }
 219
 220     public void setMapUnitIdToBarcode(boolean mapUnitIdToBarcode) {
 221         this.mapUnitIdToBarcode = mapUnitIdToBarcode;
 222     }
 223
 224     public Map<String, UUID> getNamedAreaDecisions() {
 225         return namedAreaDecisions;
 226     }
 227
 228
 229     public void setNamedAreaDecisions(Map<String,UUID> namedAreaDecisions) {
 230         this.namedAreaDecisions = namedAreaDecisions;
 231     }
 232
 233     public void putNamedAreaDecision(String areaStr,UUID uuid){
 234         this.namedAreaDecisions.put(areaStr,uuid);
 235     }
 236
 237     public UUID getNamedAreaDecision(String areaStr){
 238         return namedAreaDecisions.get(areaStr);
 239     }
 240
 241     public Map<UUID, UUID> getTaxonToDescriptionMap() {
 242         return taxonToDescriptionMap;
 243     }
 244
 245
 246
 247     public SpecimenUserInteraction getSpecimenUserInteraction() {
 248         return specimenUserInteraction;
 249     }
 250
 251     public void setReuseExistingTaxaWhenPossible(boolean reuseExistingTaxaWhenPossible) {
 252         this.reuseExistingTaxaWhenPossible = reuseExistingTaxaWhenPossible;
 253     }
 254
 255     public void setIgnoreAuthorship(boolean ignoreAuthorship) {
 256         this.ignoreAuthorship = ignoreAuthorship;
 257     }
 258
 259     public void setRemoveCountryFromLocalityText(boolean removeCountryFromLocalityText) {
 260         this.removeCountryFromLocalityText = removeCountryFromLocalityText;
 261     }
 262
 263     public void setAddMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen) {
 264         this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;
 265     }
 266
 267     public void setOverwriteExistingSpecimens(boolean overwriteExistingSpecimens) {
 268         this.overwriteExistingSpecimens = overwriteExistingSpecimens;
 269     }
 270
 271     public boolean isOverwriteExistingSpecimens(){
 272         return overwriteExistingSpecimens;
 273     }
 274
 275
 276
 277
 278     /**
 279      * @return
 280      */
 281     public boolean isReuseExistingTaxaWhenPossible() {
 282
 283         return reuseExistingTaxaWhenPossible;
 284     }
 285
 286     /**
 287      * @param titleCacheTeam
 288      */
 289     public void setTeams(Map<String, Team> titleCacheTeam) {
 290        this.titleCacheTeam  = titleCacheTeam;
 291
 292     }
 293
 294     public Team getTeam(String titleCache){
 295         return titleCacheTeam.get(titleCache);
 296     }
 297
 298     public Map<String, Team> getTeams(){
 299         return titleCacheTeam;
 300     }
 301     /**
 302      * @param titleCachePerson
 303      */
 304     public void setPersons(Map<String, Person> titleCachePerson) {
 305         this.titleCachePerson = titleCachePerson;
 306     }
 307
 308     public Map<String, Person> getPersons(){
 309         return titleCachePerson;
 310     }
 311
 312     public Person getPerson(String titleCache){
 313         return titleCachePerson.get(titleCache);
 314     }
 315
 316     public boolean isAddMediaAsMediaSpecimen(){
 317         return addMediaAsMediaSpecimen;
 318     }
 319
 320     public void addMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen){
 321        this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;
 322     }
 323
 324
 325     /**
 326      * @return
 327      */
 328     public boolean isIgnoreAuthorship() {
 329         return ignoreAuthorship;
 330     }
 331
 332     /**
 333      * @return
 334      */
 335     public boolean isRemoveCountryFromLocalityText() {
 336         return removeCountryFromLocalityText;
 337     }
 338
 339     public OccurenceQuery getOccurenceQuery(){
 340         return query;
 341     }
 342
 343     public void setOccurenceQuery(OccurenceQuery query){
 344         this.query = query;
 345     }
 346
 347
 348
 349     /**
 350      * @return the reuseExistingMetaData
 351      */
 352     public boolean isReuseExistingMetaData() {
 353         return reuseExistingMetaData;
 354     }
 355
 356     /**
 357      * @param reuseExistingMetaData the reuseExistingMetaData to set
 358      */
 359     public void setReuseExistingMetaData(boolean reuseExistingMetaData) {
 360         this.reuseExistingMetaData = reuseExistingMetaData;
 361     }
 362
 363     public void setReportUri(URI reportUri) {
 364         this.reportUri = reportUri;
 365     }
 366
 367     public URI getReportUri() {
 368         return reportUri;
 369     }
 370
 371     @Override
 372     public String getSourceReferenceTitle(){
 373         return this.sourceReferenceTitle;
 374     }
 375
 376     @Override
 377     public void setSourceReferenceTitle(String name){
 378         this.sourceReferenceTitle=name;
 379     }
 380
 381     @Override
 382     public boolean isValid(){
 383         return true;
 384     }
 385
 386
 387
 388 }