cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaRecordBase.java

   1 /**
   2 * Copyright (C) 2009 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.dwca.out;
  10
  11 import java.io.PrintWriter;
  12 import java.net.URI;
  13 import java.net.URISyntaxException;
  14 import java.util.HashMap;
  15 import java.util.HashSet;
  16 import java.util.Map;
  17 import java.util.Set;
  18 import java.util.UUID;
  19
  20 import org.apache.commons.lang.StringUtils;
  21 import org.apache.log4j.Logger;
  22 import org.joda.time.DateTime;
  23 import org.joda.time.Partial;
  24
  25 import eu.etaxonomy.cdm.common.CdmUtils;
  26 import eu.etaxonomy.cdm.io.dwca.TermUri;
  27 import eu.etaxonomy.cdm.model.agent.AgentBase;
  28 import eu.etaxonomy.cdm.model.common.Annotation;
  29 import eu.etaxonomy.cdm.model.common.CdmBase;
  30 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  31 import eu.etaxonomy.cdm.model.common.LSID;
  32 import eu.etaxonomy.cdm.model.common.Language;
  33 import eu.etaxonomy.cdm.model.common.TimePeriod;
  34 import eu.etaxonomy.cdm.model.description.Feature;
  35 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  36 import eu.etaxonomy.cdm.model.location.Point;
  37 import eu.etaxonomy.cdm.model.media.Rights;
  38 import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
  39 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  40 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  41 import eu.etaxonomy.cdm.model.name.Rank;
  42 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  43 import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
  44
  45 /**
  46  * @author a.mueller
  47  * @date 20.04.2011
  48  *
  49  */
  50 public abstract class DwcaRecordBase {
  51         private static final Logger logger = Logger.getLogger(DwcaRecordBase.class);
  52
  53         //TODO Collection_SEPARATOR
  54         protected static final CharSequence COLLECTION_SEPARATOR = "@";
  55 //      protected static final String FIELD_ENCLOSER = "\"";
  56         protected static final boolean IS_FIRST = false;
  57         protected static final boolean IS_NOT_FIRST = true;
  58 //      protected static final String SEP = ",";
  59
  60         protected Map<String, URI> knownFields = new HashMap<String, URI>();
  61         protected Set<TermUri> knownTermFields = new HashSet<TermUri>();
  62
  63         public abstract void write(PrintWriter writer);
  64         protected abstract void registerKnownFields();
  65
  66         protected int count;
  67         private DwcaMetaDataRecord metaDataRecord;
  68         protected DwcaTaxExportConfigurator config;
  69
  70         private Integer id;
  71         private UUID uuid;
  72
  73
  74         protected DwcaRecordBase(DwcaMetaDataRecord metaDataRecord, DwcaTaxExportConfigurator config){
  75                 this.metaDataRecord = metaDataRecord;
  76                 this.count = metaDataRecord.inc();
  77                 this.config = config;
  78         }
  79
  80
  81         public void setId(Integer id) {
  82                 this.id = id;
  83         }
  84
  85         public Integer getId() {
  86                 return id;
  87         }
  88
  89         public void setUuid(UUID uuid) {
  90                 this.uuid = uuid;
  91         }
  92
  93         public UUID getUuid() {
  94                 return uuid;
  95         }
  96
  97         protected void printNotes(Set<Annotation> notes, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
  98                 printNotes(notes, writer, addSeparator, fieldKey.getUriString());
  99         }
 100         protected void printNotes(Set<Annotation> notes, PrintWriter writer, boolean addSeparator, String fieldKey) {
 101                 //FIXME handles annotations correctly
 102                 String value = null;
 103                 print(value, writer, addSeparator, fieldKey);
 104         }
 105
 106 //      protected void print(Object object, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 107 //              print(object == null ? null : object.toString(), writer, addSeparator, fieldKey);
 108 //      }
 109         protected void print(DwcaId dwcaId, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 110                 print(dwcaId == null ? null : dwcaId.getId(), writer, addSeparator, fieldKey);
 111         }
 112         protected void print(UUID uuid, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 113                 print(uuid == null ? null : uuid.toString(), writer, addSeparator, fieldKey);
 114         }
 115         protected void print(AgentBase<?> agent, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 116                 print(agent, writer, addSeparator, fieldKey.getUriString());
 117         }
 118         protected void print(AgentBase<?> agent, PrintWriter writer, boolean addSeparator, String fieldKey) {
 119                 print(agent == null ? null : getAgent(agent), writer, addSeparator, fieldKey);
 120         }
 121
 122
 123         protected void print(Language language, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 124                 print(language, writer, addSeparator, fieldKey.getUriString());
 125         }
 126         protected void print(Language language, PrintWriter writer, boolean addSeparator, String fieldKey) {
 127                 print(language == null ? null : getLanguage(language), writer, addSeparator, fieldKey);
 128         }
 129         protected void print(LSID lsid, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 130                 print(lsid, writer, addSeparator, fieldKey.getUriString());
 131         }
 132         protected void print(LSID lsid, PrintWriter writer, boolean addSeparator, String fieldKey) {
 133                 print(lsid == null ? null : String.valueOf(lsid.toString()), writer, addSeparator, fieldKey);
 134         }
 135
 136         protected void print(Set<Rights> rights, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 137                 print(rights, writer, addSeparator, fieldKey.getUriString());
 138         }
 139         protected void print(Set<Rights> rights, PrintWriter writer, boolean addSeparator, String fieldKey) {
 140                 String rightsString = getRights(rights);
 141                 print(rightsString, writer, addSeparator, fieldKey);
 142         }
 143         protected void print(URI uri, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 144                 print(uri, writer, addSeparator, fieldKey.getUriString());
 145         }
 146         protected void print(URI uri, PrintWriter writer, boolean addSeparator, String fieldKey) {
 147                 print(uri == null ? null : String.valueOf(uri), writer, addSeparator, fieldKey);
 148         }
 149
 150         protected void print(Point point, PrintWriter writer, boolean addSeparator, TermUri latitudeKey, TermUri longitudeKey) {
 151                 print(point, writer, addSeparator, latitudeKey.getUriString(), longitudeKey.getUriString());
 152         }
 153
 154         protected void print(Point point, PrintWriter writer, boolean addSeparator, String latitudeKey, String longitudeKey) {
 155                 if (point == null){
 156                         String toPrint = null;
 157                         print(toPrint, writer, addSeparator, latitudeKey);
 158                         print(toPrint, writer, addSeparator, longitudeKey);
 159                 }else{
 160                         String latitude = point.getLatitude().toString();
 161                         String longitude = point.getLongitude().toString();
 162                         print(latitude, writer, addSeparator, latitudeKey);
 163                         print(longitude, writer, addSeparator, longitudeKey);
 164                 }
 165         }
 166         protected void print(Boolean boolValue, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 167                 print(boolValue, writer, addSeparator, fieldKey.getUriString());
 168         }
 169         protected void print(Boolean boolValue, PrintWriter writer, boolean addSeparator, String fieldKey) {
 170                 print(boolValue == null ? null : String.valueOf(boolValue), writer, addSeparator, fieldKey);
 171         }
 172
 173         protected void print(Integer intValue, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 174                 print(intValue, writer, addSeparator, fieldKey.getUriString());
 175         }
 176         protected void print(Integer intValue, PrintWriter writer, boolean addSeparator, String fieldKey) {
 177                 print(intValue == null ? null : String.valueOf(intValue), writer, addSeparator, fieldKey);
 178         }
 179
 180         protected void printId(Integer intValue, PrintWriter writer, boolean addSeparator, String fieldKey) {
 181                 print(intValue == null ? null : String.valueOf(intValue), writer, addSeparator, fieldKey);
 182         }
 183         protected void printId(UUID uuid, PrintWriter writer, boolean addSeparator, String fieldKey) {
 184                 print(uuid == null ? null : String.valueOf(uuid), writer, addSeparator, fieldKey);
 185         }
 186
 187         protected void print(String value, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 188                 print(value, writer, addSeparator, fieldKey, null);
 189         }
 190
 191         protected void print(String value, PrintWriter writer, boolean addSeparator, TermUri fieldKey, String defaultValue) {
 192                 print(value, writer, addSeparator, fieldKey.getUriString(), defaultValue);
 193         }
 194
 195         protected void print(String value, PrintWriter writer, boolean addSeparator, String fieldKey) {
 196                 print(value, writer, addSeparator, fieldKey, null);
 197         }
 198
 199         protected void print(String value, PrintWriter writer, boolean addSeparator, String fieldKey, String defaultValue) {
 200                 if (count == 1 && addSeparator == IS_NOT_FIRST){
 201                         registerFieldKey(URI.create(fieldKey), defaultValue);
 202                 }
 203                 if (StringUtils.isBlank(defaultValue)){
 204                         String strToPrint = addSeparator ? config.getFieldsTerminatedBy() : "";
 205                         if (StringUtils.isNotBlank(value)){
 206                                 //Replace quotes by double quotes
 207                                 value = value.replace("\"", "\"\"");
 208
 209                                 value = value.replace(config.getLinesTerminatedBy(), "\\r");
 210
 211                                 //replace all line brakes according to best practices: http://code.google.com/p/gbif-ecat/wiki/BestPractices
 212                                 value = value.replace("\r\n", "\\r");
 213                                 value = value.replace("\r", "\\r");
 214                                 value = value.replace("\n", "\\r");
 215
 216                                 strToPrint += config.getFieldsEnclosedBy() + value + config.getFieldsEnclosedBy();
 217                         }
 218                         writer.print(strToPrint);
 219                 }
 220         }
 221
 222         private void registerFieldKey(URI key, String defaultValue) {
 223                 this.metaDataRecord.addFieldEntry(key, defaultValue);
 224         }
 225
 226
 227         protected String getRights(Rights rights) {
 228                 if (rights == null){
 229                         return "";
 230                 }else{
 231                         //TODO
 232                         return rights.getAbbreviatedText();
 233                 }
 234         }
 235
 236         protected String getLanguage(Language language) {
 237                 if (language == null){
 238                         return "";
 239                 }else{
 240                         //TODO
 241                         return language.getIso639_2();
 242                 }
 243         }
 244
 245         protected String getDate(DateTime date) {
 246                 if (date == null){
 247                         return "";
 248                 }else{
 249                         //TODO
 250                         return date.toString();
 251                 }
 252         }
 253
 254         protected String getNomStatus(NomenclaturalStatusType nomStatus) {
 255                 String result = DwcaTaxExportTransformer.transformToGbifNomStatus(nomStatus);
 256                 if (result == null){
 257                         if (nomStatus == null){
 258                                 return "";
 259                         }else{
 260                                 return nomStatus.getLabel();
 261                         }
 262                 }else{
 263                         return result;
 264                 }
 265         }
 266
 267         protected String getNomCode(NomenclaturalCode nomCode) {
 268                 if (nomCode == null){
 269                         return "";
 270                 }else{
 271                         //TODO
 272                         return nomCode.getTitleCache();
 273                 }
 274         }
 275
 276         protected String getRank(Rank rank) {
 277                 String result = DwcaTaxExportTransformer.transformToGbifRank(rank);
 278                 if (result == null){
 279                         if (rank == null){
 280                                 return "";
 281                         }else{
 282                                 return rank.getLabel();
 283                         }
 284                 }else{
 285                         return result;
 286                 }
 287         }
 288
 289         protected String getSex(DefinedTerm sex) {
 290                 String result = DwcaTaxExportTransformer.transformToGbifSex(sex);
 291                 if (result == null){
 292                         if (sex == null){
 293                                 return "";
 294                         }else{
 295                                 return sex.getLabel();
 296                         }
 297                 }else{
 298                         return result;
 299                 }
 300         }
 301
 302         protected String getLifeStage(DefinedTerm stage) {
 303                 String result = DwcaTaxExportTransformer.transformToGbifLifeStage(stage);
 304                 if (result == null){
 305                         if (stage == null){
 306                                 return "";
 307                         }else{
 308                                 return stage.getLabel();
 309                         }
 310                 }else{
 311                         return result;
 312                 }
 313         }
 314
 315         protected String getOccurrenceStatus(PresenceAbsenceTerm status) {
 316                 String result = DwcaTaxExportTransformer.transformToGbifOccStatus(status);
 317                 if (result == null){
 318                         if (status == null){
 319                                 return "";
 320                         }else{
 321                                 return status.getLabel();
 322                         }
 323                 }else{
 324                         return result;
 325                 }
 326         }
 327
 328         protected String getEstablishmentMeans(PresenceAbsenceTerm status) {
 329                 String result = DwcaTaxExportTransformer.transformToGbifEstablishmentMeans(status);
 330                 if (result == null){
 331                         if (status == null){
 332                                 return "";
 333                         }else{
 334                                 return status.getLabel();
 335                         }
 336                 }else{
 337                         return result;
 338                 }
 339         }
 340
 341
 342
 343         protected String getAgent(AgentBase<?> agent) {
 344                 if (agent == null){
 345                         return "";
 346                 }else{
 347                         //TODO
 348                         return agent.getTitleCache();
 349                 }
 350         }
 351
 352
 353         protected String getFeature(Feature feature) {
 354                 if (feature == null){
 355                         return "";
 356                 }else{
 357                         //TODO
 358                         return feature.getTitleCache();
 359                 }
 360         }
 361
 362
 363         protected String getTimePeriod(TimePeriod period) {
 364                 if (period == null){
 365                         return "";
 366                 }else{
 367                         //TODO
 368                         return period.toString();
 369                 }
 370         }
 371
 372         protected String getTimePeriodPart(TimePeriod period, boolean useEnd) {
 373                 if (period == null){
 374                         return "";
 375                 }else{
 376                         Partial date = useEnd? period.getEnd(): period.getStart();
 377                         if (date == null){
 378                                 return "";
 379                         }else{
 380                                 //TODO
 381                                 return date.toString();
 382                         }
 383                 }
 384         }
 385
 386         private String getRights(Set<Rights> rights) {
 387                 if (rights == null || rights.isEmpty()){
 388                         return null;
 389                 }else{
 390                         String result = null;
 391                         for (Rights right: rights){
 392                                 //TODO usi uri if available ??
 393                                 String message = "Rights not yet fully implemented";
 394                                 logger.warn(message);
 395                                 result = CdmUtils.concat(COLLECTION_SEPARATOR, result, right.getAbbreviatedText());
 396                         }
 397                         return result;
 398                 }
 399         }
 400
 401
 402         protected String getDesignationType(TypeDesignationStatusBase<?> status) {
 403                 if (status == null){
 404                         return "";
 405                 }
 406                 String result;
 407                 if (status.isInstanceOf(SpecimenTypeDesignationStatus.class)){
 408                         SpecimenTypeDesignationStatus specStatus = CdmBase.deproxy(status, SpecimenTypeDesignationStatus.class);
 409                         result = DwcaTaxExportTransformer.transformSpecimenTypeStatusToGbif(specStatus);
 410                 }else{
 411                         NameTypeDesignationStatus nameStatus = CdmBase.deproxy(status, NameTypeDesignationStatus.class);
 412                         result = DwcaTaxExportTransformer.transformNameTypeStatusToGbif(nameStatus);
 413                 }
 414                 if (result == null){
 415                         return status.getLabel();
 416                 }else{
 417                         return result;
 418                 }
 419         }
 420
 421
 422         protected void addKnownField(String string, String uri) throws URISyntaxException {
 423                 this.knownFields.put(string, new URI(uri));
 424         }
 425
 426         protected void addKnownField(TermUri term) throws URISyntaxException {
 427                 this.knownTermFields.add(term);
 428         }
 429 }