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