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.URISyntaxException;
  13 import java.util.ArrayList;
  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.lang3.StringUtils;
  21 import org.apache.logging.log4j.LogManager;
  22 import org.apache.logging.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.common.URI;
  28 import eu.etaxonomy.cdm.io.stream.terms.TermUri;
  29 import eu.etaxonomy.cdm.model.agent.AgentBase;
  30 import eu.etaxonomy.cdm.model.common.Annotation;
  31 import eu.etaxonomy.cdm.model.common.CdmBase;
  32 import eu.etaxonomy.cdm.model.common.LSID;
  33 import eu.etaxonomy.cdm.model.common.Language;
  34 import eu.etaxonomy.cdm.model.common.TimePeriod;
  35 import eu.etaxonomy.cdm.model.description.Feature;
  36 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  37 import eu.etaxonomy.cdm.model.location.Point;
  38 import eu.etaxonomy.cdm.model.media.Rights;
  39 import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
  40 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  41 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  42 import eu.etaxonomy.cdm.model.name.Rank;
  43 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  44 import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
  45 import eu.etaxonomy.cdm.model.term.DefinedTerm;
  46
  47 /**
  48  * @author a.mueller, a.oppermann
  49  * @since 20.04.2011
  50  */
  51 public abstract class CsvDemoRecordBase {
  52
  53     private static final Logger logger = LogManager.getLogger();
  54
  55         //TODO Collection_SEPARATOR
  56         protected static final CharSequence COLLECTION_SEPARATOR = "@";
  57 //      protected static final String FIELD_ENCLOSER = "\"";
  58         protected static final boolean IS_FIRST = false;
  59         protected static final boolean IS_NOT_FIRST = true;
  60 //      protected static final String SEP = ",";
  61
  62         protected Map<String, URI> knownFields = new HashMap<String, URI>();
  63         protected Set<TermUri> knownTermFields = new HashSet<TermUri>();
  64
  65         public abstract void write(PrintWriter writer);
  66         protected abstract void registerKnownFields();
  67
  68         protected int count;
  69         private final CsvDemoMetaDataRecord metaDataRecord;
  70         protected CsvDemoExportConfigurator config;
  71
  72         private Integer id;
  73         private UUID uuid;
  74
  75         protected CsvDemoRecordBase(CsvDemoMetaDataRecord metaDataRecord, CsvDemoExportConfigurator config){
  76                 this.metaDataRecord = metaDataRecord;
  77                 this.count = metaDataRecord.inc();
  78                 this.config = config;
  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(CsvDemoId 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         protected void print(Language language, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 123                 print(language, writer, addSeparator, fieldKey.getUriString());
 124         }
 125         protected void print(Language language, PrintWriter writer, boolean addSeparator, String fieldKey) {
 126                 print(language == null ? null : getLanguage(language), writer, addSeparator, fieldKey);
 127         }
 128         protected void print(LSID lsid, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 129                 print(lsid, writer, addSeparator, fieldKey.getUriString());
 130         }
 131         protected void print(LSID lsid, PrintWriter writer, boolean addSeparator, String fieldKey) {
 132                 print(lsid == null ? null : String.valueOf(lsid.toString()), writer, addSeparator, fieldKey);
 133         }
 134
 135         protected void print(Set<Rights> rights, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 136                 print(rights, writer, addSeparator, fieldKey.getUriString());
 137         }
 138         protected void print(Set<Rights> rights, PrintWriter writer, boolean addSeparator, String fieldKey) {
 139                 String rightsString = getRights(rights);
 140                 print(rightsString, writer, addSeparator, fieldKey);
 141         }
 142         protected void print(URI uri, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 143                 print(uri, writer, addSeparator, fieldKey.getUriString());
 144         }
 145         protected void print(URI uri, PrintWriter writer, boolean addSeparator, String fieldKey) {
 146                 print(uri == null ? null : String.valueOf(uri), writer, addSeparator, fieldKey);
 147         }
 148
 149         protected void print(Point point, PrintWriter writer, boolean addSeparator, TermUri latitudeKey, TermUri longitudeKey) {
 150                 print(point, writer, addSeparator, latitudeKey.getUriString(), longitudeKey.getUriString());
 151         }
 152
 153         protected void print(Point point, PrintWriter writer, boolean addSeparator, String latitudeKey, String longitudeKey) {
 154                 if (point == null){
 155                         String toPrint = null;
 156                         print(toPrint, writer, addSeparator, latitudeKey);
 157                         print(toPrint, writer, addSeparator, longitudeKey);
 158                 }else{
 159                         String latitude = point.getLatitude().toString();
 160                         String longitude = point.getLongitude().toString();
 161                         print(latitude, writer, addSeparator, latitudeKey);
 162                         print(longitude, writer, addSeparator, longitudeKey);
 163                 }
 164         }
 165         protected void print(Boolean boolValue, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 166                 print(boolValue, writer, addSeparator, fieldKey.getUriString());
 167         }
 168         protected void print(Boolean boolValue, PrintWriter writer, boolean addSeparator, String fieldKey) {
 169                 print(boolValue == null ? null : String.valueOf(boolValue), writer, addSeparator, fieldKey);
 170         }
 171
 172         protected void print(Integer intValue, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 173                 print(intValue, writer, addSeparator, fieldKey.getUriString());
 174         }
 175         protected void print(Integer intValue, PrintWriter writer, boolean addSeparator, String fieldKey) {
 176                 print(intValue == null ? null : String.valueOf(intValue), writer, addSeparator, fieldKey);
 177         }
 178
 179         protected void printId(Integer intValue, PrintWriter writer, boolean addSeparator, String fieldKey) {
 180                 print(intValue == null ? null : String.valueOf(intValue), writer, addSeparator, fieldKey);
 181         }
 182         protected void printId(UUID uuid, PrintWriter writer, boolean addSeparator, String fieldKey) {
 183                 print(uuid == null ? null : String.valueOf(uuid), writer, addSeparator, fieldKey);
 184         }
 185
 186         protected void print(String value, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
 187                 print(value, writer, addSeparator, fieldKey, null);
 188         }
 189
 190         protected void print(String value, PrintWriter writer, boolean addSeparator, TermUri fieldKey, String defaultValue) {
 191                 print(value, writer, addSeparator, fieldKey.getUriString(), defaultValue);
 192         }
 193
 194         protected void print(String value, PrintWriter writer, boolean addSeparator, String fieldKey) {
 195                 print(value, writer, addSeparator, fieldKey, null);
 196         }
 197
 198         protected void print(String value, PrintWriter writer, boolean addSeparator, String fieldKey, String defaultValue) {
 199                 if (count == 1 && addSeparator == IS_NOT_FIRST){
 200                         registerFieldKey(URI.create(fieldKey), defaultValue);
 201                 }
 202                 if (StringUtils.isBlank(defaultValue)){
 203                         String strToPrint = addSeparator ? config.getFieldsTerminatedBy() : "";
 204                         if (StringUtils.isNotBlank(value)){
 205                                 //Replace quotes by double quotes
 206                                 value = value.replace("\"", "\"\"");
 207
 208                                 value = value.replace(config.getLinesTerminatedBy(), "\\r");
 209
 210                                 //replace all line brakes according to best practices: http://code.google.com/p/gbif-ecat/wiki/BestPractices
 211                                 value = value.replace("\r\n", "\\r");
 212                                 value = value.replace("\r", "\\r");
 213                                 value = value.replace("\n", "\\r");
 214
 215                                 strToPrint += config.getFieldsEnclosedBy() + value + config.getFieldsEnclosedBy();
 216                         }
 217                         writer.print(strToPrint);
 218                 }
 219         }
 220
 221         /**
 222          * @param writer
 223          * @param list
 224          * @param termUri
 225          */
 226         protected void printHeadline(PrintWriter writer, ArrayList<String> list, TermUri termUri){
 227                 for(String element:list){
 228                         if(list.get(0).equals(element)){
 229                                 print(element, writer, IS_FIRST, termUri);
 230                         }
 231                         else{
 232                                 print(element, writer, IS_NOT_FIRST, termUri);
 233                         }
 234                 }
 235                 writer.println();
 236         }
 237
 238         /**
 239          * @param list
 240          * @param termUri
 241          * @param writer
 242          *
 243          * Method for concatenating strings, especially for the red list use case
 244          */
 245         protected void print(ArrayList<String> list, TermUri termUri, PrintWriter writer){
 246                 if(list == null||list.isEmpty()){
 247                         print("", writer, IS_NOT_FIRST, termUri);
 248                 }else{
 249                         for (String element:list){
 250                                 if(list.get(0).equals(element)){
 251                                         writer.write("\t");
 252                                         print(element, writer, IS_FIRST, termUri);
 253                                         if(list.size()>1){
 254                                                 writer.write(",");
 255                                                 logger.info(element);
 256                                         }
 257                                 }else if(list.get(list.size()-1).equals(element)){
 258                                         print(element, writer, IS_FIRST, termUri);
 259                                 }else{
 260                                         print(element, writer, IS_FIRST, termUri);
 261                                         writer.write(",");
 262                                         logger.info(element);
 263
 264                                 }
 265                         }
 266                 }
 267         }
 268
 269
 270         private void registerFieldKey(URI key, String defaultValue) {
 271                 this.metaDataRecord.addFieldEntry(key, defaultValue);
 272         }
 273
 274
 275         protected String getRights(Rights rights) {
 276                 if (rights == null){
 277                         return "";
 278                 }else{
 279                         //TODO
 280                         return rights.getAbbreviatedText();
 281                 }
 282         }
 283
 284         protected String getLanguage(Language language) {
 285                 if (language == null){
 286                         return "";
 287                 }else{
 288                         //TODO
 289                         return language.getIso639_2();
 290                 }
 291         }
 292
 293         protected String getDate(DateTime date) {
 294                 if (date == null){
 295                         return "";
 296                 }else{
 297                         //TODO
 298                         return date.toString();
 299                 }
 300         }
 301
 302         protected String getNomStatus(NomenclaturalStatusType nomStatus) {
 303                 String result = CsvDemoExportTransformer.transformToGbifNomStatus(nomStatus);
 304                 if (result == null){
 305                         if (nomStatus == null){
 306                                 return "";
 307                         }else{
 308                                 return nomStatus.getLabel();
 309                         }
 310                 }else{
 311                         return result;
 312                 }
 313         }
 314
 315         protected String getNomCode(NomenclaturalCode nomCode) {
 316                 if (nomCode == null){
 317                         return "";
 318                 }else{
 319                         //TODO
 320                         return nomCode.getTitleCache();
 321                 }
 322         }
 323
 324         protected String getRank(Rank rank) {
 325                 String result = CsvDemoExportTransformer.transformToGbifRank(rank);
 326                 if (result == null){
 327                         if (rank == null){
 328                                 return "";
 329                         }else{
 330                                 return rank.getLabel();
 331                         }
 332                 }else{
 333                         return result;
 334                 }
 335         }
 336
 337         protected String getSex(DefinedTerm sex) {
 338                 String result = CsvDemoExportTransformer.transformToGbifSex(sex);
 339                 if (result == null){
 340                         if (sex == null){
 341                                 return "";
 342                         }else{
 343                                 return sex.getLabel();
 344                         }
 345                 }else{
 346                         return result;
 347                 }
 348         }
 349
 350         protected String getLifeStage(DefinedTerm stage) {
 351                 String result = CsvDemoExportTransformer.transformToGbifLifeStage(stage);
 352                 if (result == null){
 353                         if (stage == null){
 354                                 return "";
 355                         }else{
 356                                 return stage.getLabel();
 357                         }
 358                 }else{
 359                         return result;
 360                 }
 361         }
 362
 363         protected String getOccurrenceStatus(PresenceAbsenceTerm status) {
 364                 String result = CsvDemoExportTransformer.transformToGbifOccStatus(status);
 365                 if (result == null){
 366                         if (status == null){
 367                                 return "";
 368                         }else{
 369                                 return status.getLabel();
 370                         }
 371                 }else{
 372                         return result;
 373                 }
 374         }
 375
 376         protected String getEstablishmentMeans(PresenceAbsenceTerm status) {
 377                 String result = CsvDemoExportTransformer.transformToGbifEstablishmentMeans(status);
 378                 if (result == null){
 379                         if (status == null){
 380                                 return "";
 381                         }else{
 382                                 return status.getLabel();
 383                         }
 384                 }else{
 385                         return result;
 386                 }
 387         }
 388
 389
 390
 391         protected String getAgent(AgentBase<?> agent) {
 392                 if (agent == null){
 393                         return "";
 394                 }else{
 395                         //TODO
 396                         return agent.getTitleCache();
 397                 }
 398         }
 399
 400
 401         protected String getFeature(Feature feature) {
 402                 if (feature == null){
 403                         return "";
 404                 }else{
 405                         //TODO
 406                         return feature.getTitleCache();
 407                 }
 408         }
 409
 410
 411         protected String getTimePeriod(TimePeriod period) {
 412                 if (period == null){
 413                         return "";
 414                 }else{
 415                         //TODO
 416                         return period.toString();
 417                 }
 418         }
 419
 420         protected String getTimePeriodPart(TimePeriod period, boolean useEnd) {
 421                 if (period == null){
 422                         return "";
 423                 }else{
 424                         Partial date = useEnd? period.getEnd(): period.getStart();
 425                         if (date == null){
 426                                 return "";
 427                         }else{
 428                                 //TODO
 429                                 return date.toString();
 430                         }
 431                 }
 432         }
 433
 434         private String getRights(Set<Rights> rights) {
 435                 if (rights == null || rights.isEmpty()){
 436                         return null;
 437                 }else{
 438                         String result = null;
 439                         for (Rights right: rights){
 440                                 //TODO usi uri if available ??
 441                                 String message = "Rights not yet fully implemented";
 442                                 logger.warn(message);
 443                                 result = CdmUtils.concat(COLLECTION_SEPARATOR, result, right.getAbbreviatedText());
 444                         }
 445                         return result;
 446                 }
 447         }
 448
 449
 450         protected String getDesignationType(TypeDesignationStatusBase<?> status) {
 451                 if (status == null){
 452                         return "";
 453                 }
 454                 String result;
 455                 if (status.isInstanceOf(SpecimenTypeDesignationStatus.class)){
 456                         SpecimenTypeDesignationStatus specStatus = CdmBase.deproxy(status, SpecimenTypeDesignationStatus.class);
 457                         result = CsvDemoExportTransformer.transformSpecimenTypeStatusToGbif(specStatus);
 458                 }else{
 459                         NameTypeDesignationStatus nameStatus = CdmBase.deproxy(status, NameTypeDesignationStatus.class);
 460                         result = CsvDemoExportTransformer.transformNameTypeStatusToGbif(nameStatus);
 461                 }
 462                 if (result == null){
 463                         return status.getLabel();
 464                 }else{
 465                         return result;
 466                 }
 467         }
 468
 469
 470         protected void addKnownField(String string, String uri) throws URISyntaxException {
 471                 this.knownFields.put(string, new URI(uri));
 472         }
 473
 474         protected void addKnownField(TermUri term) throws URISyntaxException {
 475                 this.knownTermFields.add(term);
 476         }
 477 }