cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/demo/CsvDemoRecordBase.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.csv.redlist.demo;
  10
  11 import java.io.PrintWriter;
  12 import java.net.URI;
  13 import java.net.URISyntaxException;
  14 import java.util.ArrayList;
  15 import java.util.HashMap;
  16 import java.util.HashSet;
  17 import java.util.Map;
  18 import java.util.Set;
  19 import java.util.UUID;
  20
  21 import org.apache.commons.lang.StringUtils;
  22 import org.apache.log4j.Logger;
  23 import org.joda.time.DateTime;
  24 import org.joda.time.Partial;
  25
  26 import eu.etaxonomy.cdm.common.CdmUtils;
  27 import eu.etaxonomy.cdm.io.stream.terms.TermUri;
  28 import eu.etaxonomy.cdm.model.agent.AgentBase;
  29 import eu.etaxonomy.cdm.model.common.Annotation;
  30 import eu.etaxonomy.cdm.model.common.CdmBase;
  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 import eu.etaxonomy.cdm.model.term.DefinedTerm;
  45
  46 /**
  47  * @author a.mueller, a.oppermann
  48  * @since 20.04.2011
  49  */
  50 public abstract class CsvDemoRecordBase {
  51
  52         private static final Logger logger = Logger.getLogger(CsvDemoRecordBase.class);
  53
  54         //TODO Collection_SEPARATOR
  55         protected static final CharSequence COLLECTION_SEPARATOR = "@";
  56 //      protected static final String FIELD_ENCLOSER = "\"";
  57         protected static final boolean IS_FIRST = false;
  58         protected static final boolean IS_NOT_FIRST = true;
  59 //      protected static final String SEP = ",";
  60
  61         protected Map<String, URI> knownFields = new HashMap<String, URI>();
  62         protected Set<TermUri> knownTermFields = new HashSet<TermUri>();
  63
  64         public abstract void write(PrintWriter writer);
  65         protected abstract void registerKnownFields();
  66
  67         protected int count;
  68         private final CsvDemoMetaDataRecord metaDataRecord;
  69         protected CsvDemoExportConfigurator config;
  70
  71         private Integer id;
  72         private UUID uuid;
  73
  74         protected CsvDemoRecordBase(CsvDemoMetaDataRecord metaDataRecord, CsvDemoExportConfigurator config){
  75                 this.metaDataRecord = metaDataRecord;
  76                 this.count = metaDataRecord.inc();
  77                 this.config = config;
  78         }
  79
  80         public void setId(Integer id) {
  81                 this.id = id;
  82         }
  83
  84         public Integer getId() {
  85                 return id;
  86         }
  87
  88         public void setUuid(UUID uuid) {
  89                 this.uuid = uuid;
  90         }
  91
  92 /*      public UUID getUuid() {
  93                 return uuid;
  94         }*/
  95
  96         protected void printNotes(Set<Annotation> notes, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
  97                 printNotes(notes, writer, addSeparator, fieldKey.getUriString());
  98         }
  99         protected void printNotes(Set<Annotation> notes, PrintWriter writer, boolean addSeparator, String fieldKey) {
 100                 //FIXME handles annotations correctly
 101                 String value = null;
 102                 print(value, writer, addSeparator, fieldKey);
 103         }
 104
 105 //      protected void print(Object object, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 106 //              print(object == null ? null : object.toString(), writer, addSeparator, fieldKey);
 107 //      }
 108         protected void print(CsvDemoId dwcaId, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 109                 print(dwcaId == null ? null : dwcaId.getId(), writer, addSeparator, fieldKey);
 110         }
 111         protected void print(UUID uuid, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 112                 print(uuid == null ? null : uuid.toString(), writer, addSeparator, fieldKey);
 113         }
 114         protected void print(AgentBase<?> agent, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 115                 print(agent, writer, addSeparator, fieldKey.getUriString());
 116         }
 117         protected void print(AgentBase<?> agent, PrintWriter writer, boolean addSeparator, String fieldKey) {
 118                 print(agent == null ? null : getAgent(agent), writer, addSeparator, fieldKey);
 119         }
 120
 121         protected void print(Language language, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 122                 print(language, writer, addSeparator, fieldKey.getUriString());
 123         }
 124         protected void print(Language language, PrintWriter writer, boolean addSeparator, String fieldKey) {
 125                 print(language == null ? null : getLanguage(language), writer, addSeparator, fieldKey);
 126         }
 127         protected void print(LSID lsid, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 128                 print(lsid, writer, addSeparator, fieldKey.getUriString());
 129         }
 130         protected void print(LSID lsid, PrintWriter writer, boolean addSeparator, String fieldKey) {
 131                 print(lsid == null ? null : String.valueOf(lsid.toString()), writer, addSeparator, fieldKey);
 132         }
 133
 134         protected void print(Set<Rights> rights, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 135                 print(rights, writer, addSeparator, fieldKey.getUriString());
 136         }
 137         protected void print(Set<Rights> rights, PrintWriter writer, boolean addSeparator, String fieldKey) {
 138                 String rightsString = getRights(rights);
 139                 print(rightsString, writer, addSeparator, fieldKey);
 140         }
 141         protected void print(URI uri, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 142                 print(uri, writer, addSeparator, fieldKey.getUriString());
 143         }
 144         protected void print(URI uri, PrintWriter writer, boolean addSeparator, String fieldKey) {
 145                 print(uri == null ? null : String.valueOf(uri), writer, addSeparator, fieldKey);
 146         }
 147
 148         protected void print(Point point, PrintWriter writer, boolean addSeparator, TermUri latitudeKey, TermUri longitudeKey) {
 149                 print(point, writer, addSeparator, latitudeKey.getUriString(), longitudeKey.getUriString());
 150         }
 151
 152         protected void print(Point point, PrintWriter writer, boolean addSeparator, String latitudeKey, String longitudeKey) {
 153                 if (point == null){
 154                         String toPrint = null;
 155                         print(toPrint, writer, addSeparator, latitudeKey);
 156                         print(toPrint, writer, addSeparator, longitudeKey);
 157                 }else{
 158                         String latitude = point.getLatitude().toString();
 159                         String longitude = point.getLongitude().toString();
 160                         print(latitude, writer, addSeparator, latitudeKey);
 161                         print(longitude, writer, addSeparator, longitudeKey);
 162                 }
 163         }
 164         protected void print(Boolean boolValue, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 165                 print(boolValue, writer, addSeparator, fieldKey.getUriString());
 166         }
 167         protected void print(Boolean boolValue, PrintWriter writer, boolean addSeparator, String fieldKey) {
 168                 print(boolValue == null ? null : String.valueOf(boolValue), writer, addSeparator, fieldKey);
 169         }
 170
 171         protected void print(Integer intValue, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 172                 print(intValue, writer, addSeparator, fieldKey.getUriString());
 173         }
 174         protected void print(Integer intValue, PrintWriter writer, boolean addSeparator, String fieldKey) {
 175                 print(intValue == null ? null : String.valueOf(intValue), writer, addSeparator, fieldKey);
 176         }
 177
 178         protected void printId(Integer intValue, PrintWriter writer, boolean addSeparator, String fieldKey) {
 179                 print(intValue == null ? null : String.valueOf(intValue), writer, addSeparator, fieldKey);
 180         }
 181         protected void printId(UUID uuid, PrintWriter writer, boolean addSeparator, String fieldKey) {
 182                 print(uuid == null ? null : String.valueOf(uuid), writer, addSeparator, fieldKey);
 183         }
 184
 185         protected void print(String value, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 186                 print(value, writer, addSeparator, fieldKey, null);
 187         }
 188
 189         protected void print(String value, PrintWriter writer, boolean addSeparator, TermUri fieldKey, String defaultValue) {
 190                 print(value, writer, addSeparator, fieldKey.getUriString(), defaultValue);
 191         }
 192
 193         protected void print(String value, PrintWriter writer, boolean addSeparator, String fieldKey) {
 194                 print(value, writer, addSeparator, fieldKey, null);
 195         }
 196
 197         protected void print(String value, PrintWriter writer, boolean addSeparator, String fieldKey, String defaultValue) {
 198                 if (count == 1 && addSeparator == IS_NOT_FIRST){
 199                         registerFieldKey(URI.create(fieldKey), defaultValue);
 200                 }
 201                 if (StringUtils.isBlank(defaultValue)){
 202                         String strToPrint = addSeparator ? config.getFieldsTerminatedBy() : "";
 203                         if (StringUtils.isNotBlank(value)){
 204                                 //Replace quotes by double quotes
 205                                 value = value.replace("\"", "\"\"");
 206
 207                                 value = value.replace(config.getLinesTerminatedBy(), "\\r");
 208
 209                                 //replace all line brakes according to best practices: http://code.google.com/p/gbif-ecat/wiki/BestPractices
 210                                 value = value.replace("\r\n", "\\r");
 211                                 value = value.replace("\r", "\\r");
 212                                 value = value.replace("\n", "\\r");
 213
 214                                 strToPrint += config.getFieldsEnclosedBy() + value + config.getFieldsEnclosedBy();
 215                         }
 216                         writer.print(strToPrint);
 217                 }
 218         }
 219
 220         /**
 221          * @param writer
 222          * @param list
 223          * @param termUri
 224          */
 225         protected void printHeadline(PrintWriter writer, ArrayList<String> list, TermUri termUri){
 226                 for(String element:list){
 227                         if(list.get(0).equals(element)){
 228                                 print(element, writer, IS_FIRST, termUri);
 229                         }
 230                         else{
 231                                 print(element, writer, IS_NOT_FIRST, termUri);
 232                         }
 233                 }
 234                 writer.println();
 235         }
 236
 237         /**
 238          * @param list
 239          * @param termUri
 240          * @param writer
 241          *
 242          * Method for concatenating strings, especially for the red list use case
 243          */
 244         protected void print(ArrayList<String> list, TermUri termUri, PrintWriter writer){
 245                 if(list == null||list.isEmpty()){
 246                         print("", writer, IS_NOT_FIRST, termUri);
 247                 }else{
 248                         for (String element:list){
 249                                 if(list.get(0).equals(element)){
 250                                         writer.write("\t");
 251                                         print(element, writer, IS_FIRST, termUri);
 252                                         if(list.size()>1){
 253                                                 writer.write(",");
 254                                                 logger.info(element);
 255                                         }
 256                                 }else if(list.get(list.size()-1).equals(element)){
 257                                         print(element, writer, IS_FIRST, termUri);
 258                                 }else{
 259                                         print(element, writer, IS_FIRST, termUri);
 260                                         writer.write(",");
 261                                         logger.info(element);
 262
 263                                 }
 264                         }
 265                 }
 266         }
 267
 268
 269         private void registerFieldKey(URI key, String defaultValue) {
 270                 this.metaDataRecord.addFieldEntry(key, defaultValue);
 271         }
 272
 273
 274         protected String getRights(Rights rights) {
 275                 if (rights == null){
 276                         return "";
 277                 }else{
 278                         //TODO
 279                         return rights.getAbbreviatedText();
 280                 }
 281         }
 282
 283         protected String getLanguage(Language language) {
 284                 if (language == null){
 285                         return "";
 286                 }else{
 287                         //TODO
 288                         return language.getIso639_2();
 289                 }
 290         }
 291
 292         protected String getDate(DateTime date) {
 293                 if (date == null){
 294                         return "";
 295                 }else{
 296                         //TODO
 297                         return date.toString();
 298                 }
 299         }
 300
 301         protected String getNomStatus(NomenclaturalStatusType nomStatus) {
 302                 String result = CsvDemoExportTransformer.transformToGbifNomStatus(nomStatus);
 303                 if (result == null){
 304                         if (nomStatus == null){
 305                                 return "";
 306                         }else{
 307                                 return nomStatus.getLabel();
 308                         }
 309                 }else{
 310                         return result;
 311                 }
 312         }
 313
 314         protected String getNomCode(NomenclaturalCode nomCode) {
 315                 if (nomCode == null){
 316                         return "";
 317                 }else{
 318                         //TODO
 319                         return nomCode.getTitleCache();
 320                 }
 321         }
 322
 323         protected String getRank(Rank rank) {
 324                 String result = CsvDemoExportTransformer.transformToGbifRank(rank);
 325                 if (result == null){
 326                         if (rank == null){
 327                                 return "";
 328                         }else{
 329                                 return rank.getLabel();
 330                         }
 331                 }else{
 332                         return result;
 333                 }
 334         }
 335
 336         protected String getSex(DefinedTerm sex) {
 337                 String result = CsvDemoExportTransformer.transformToGbifSex(sex);
 338                 if (result == null){
 339                         if (sex == null){
 340                                 return "";
 341                         }else{
 342                                 return sex.getLabel();
 343                         }
 344                 }else{
 345                         return result;
 346                 }
 347         }
 348
 349         protected String getLifeStage(DefinedTerm stage) {
 350                 String result = CsvDemoExportTransformer.transformToGbifLifeStage(stage);
 351                 if (result == null){
 352                         if (stage == null){
 353                                 return "";
 354                         }else{
 355                                 return stage.getLabel();
 356                         }
 357                 }else{
 358                         return result;
 359                 }
 360         }
 361
 362         protected String getOccurrenceStatus(PresenceAbsenceTerm status) {
 363                 String result = CsvDemoExportTransformer.transformToGbifOccStatus(status);
 364                 if (result == null){
 365                         if (status == null){
 366                                 return "";
 367                         }else{
 368                                 return status.getLabel();
 369                         }
 370                 }else{
 371                         return result;
 372                 }
 373         }
 374
 375         protected String getEstablishmentMeans(PresenceAbsenceTerm status) {
 376                 String result = CsvDemoExportTransformer.transformToGbifEstablishmentMeans(status);
 377                 if (result == null){
 378                         if (status == null){
 379                                 return "";
 380                         }else{
 381                                 return status.getLabel();
 382                         }
 383                 }else{
 384                         return result;
 385                 }
 386         }
 387
 388
 389
 390         protected String getAgent(AgentBase<?> agent) {
 391                 if (agent == null){
 392                         return "";
 393                 }else{
 394                         //TODO
 395                         return agent.getTitleCache();
 396                 }
 397         }
 398
 399
 400         protected String getFeature(Feature feature) {
 401                 if (feature == null){
 402                         return "";
 403                 }else{
 404                         //TODO
 405                         return feature.getTitleCache();
 406                 }
 407         }
 408
 409
 410         protected String getTimePeriod(TimePeriod period) {
 411                 if (period == null){
 412                         return "";
 413                 }else{
 414                         //TODO
 415                         return period.toString();
 416                 }
 417         }
 418
 419         protected String getTimePeriodPart(TimePeriod period, boolean useEnd) {
 420                 if (period == null){
 421                         return "";
 422                 }else{
 423                         Partial date = useEnd? period.getEnd(): period.getStart();
 424                         if (date == null){
 425                                 return "";
 426                         }else{
 427                                 //TODO
 428                                 return date.toString();
 429                         }
 430                 }
 431         }
 432
 433         private String getRights(Set<Rights> rights) {
 434                 if (rights == null || rights.isEmpty()){
 435                         return null;
 436                 }else{
 437                         String result = null;
 438                         for (Rights right: rights){
 439                                 //TODO usi uri if available ??
 440                                 String message = "Rights not yet fully implemented";
 441                                 logger.warn(message);
 442                                 result = CdmUtils.concat(COLLECTION_SEPARATOR, result, right.getAbbreviatedText());
 443                         }
 444                         return result;
 445                 }
 446         }
 447
 448
 449         protected String getDesignationType(TypeDesignationStatusBase<?> status) {
 450                 if (status == null){
 451                         return "";
 452                 }
 453                 String result;
 454                 if (status.isInstanceOf(SpecimenTypeDesignationStatus.class)){
 455                         SpecimenTypeDesignationStatus specStatus = CdmBase.deproxy(status, SpecimenTypeDesignationStatus.class);
 456                         result = CsvDemoExportTransformer.transformSpecimenTypeStatusToGbif(specStatus);
 457                 }else{
 458                         NameTypeDesignationStatus nameStatus = CdmBase.deproxy(status, NameTypeDesignationStatus.class);
 459                         result = CsvDemoExportTransformer.transformNameTypeStatusToGbif(nameStatus);
 460                 }
 461                 if (result == null){
 462                         return status.getLabel();
 463                 }else{
 464                         return result;
 465                 }
 466         }
 467
 468
 469         protected void addKnownField(String string, String uri) throws URISyntaxException {
 470                 this.knownFields.put(string, new URI(uri));
 471         }
 472
 473         protected void addKnownField(TermUri term) throws URISyntaxException {
 474                 this.knownTermFields.add(term);
 475         }
 476 }