cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/name/NonViralNameDefaultCacheStrategy.java

   1 /**
   2 * Copyright (C) 2007 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.strategy.cache.name;
  10
  11 import java.util.ArrayList;
  12 import java.util.Iterator;
  13 import java.util.List;
  14 import java.util.Set;
  15 import java.util.UUID;
  16
  17 import org.apache.log4j.Logger;
  18
  19 import eu.etaxonomy.cdm.common.CdmUtils;
  20 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  21 import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;
  22 import eu.etaxonomy.cdm.model.agent.Team;
  23 import eu.etaxonomy.cdm.model.common.Language;
  24 import eu.etaxonomy.cdm.model.common.Representation;
  25 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  26 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  27 import eu.etaxonomy.cdm.model.name.NonViralName;
  28 import eu.etaxonomy.cdm.model.name.Rank;
  29 import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
  30 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  31
  32
  33 /**
  34  * This class is a default implementation for the INonViralNameCacheStrategy<T extends NonViralName> interface.
  35  * The method actually implements a cache strategy for botanical names so no method has to be overwritten by
  36  * a subclass for botanic names.
  37  * Where differing from this Default BotanicNameCacheStrategy other subclasses should overwrite the existing methods
  38  * e.g. a CacheStrategy for zoological names should overwrite getAuthorAndExAuthor
  39  * @author a.mueller
  40  */
  41 /**
  42  * @author AM
  43  *
  44  * @param <T>
  45  */
  46 public class NonViralNameDefaultCacheStrategy<T extends NonViralName> extends NameCacheStrategyBase<T> implements INonViralNameCacheStrategy<T> {
  47         private static final Logger logger = Logger.getLogger(NonViralNameDefaultCacheStrategy.class);
  48
  49         final static UUID uuid = UUID.fromString("1cdda0d1-d5bc-480f-bf08-40a510a2f223");
  50
  51         protected String NameAuthorSeperator = " ";
  52         protected String BasionymStart = "(";
  53         protected String BasionymEnd = ")";
  54         protected String ExAuthorSeperator = " ex ";
  55         protected CharSequence BasionymAuthorCombinationAuthorSeperator = " ";
  56
  57         @Override
  58         public  UUID getUuid(){
  59                 return uuid;
  60         }
  61
  62
  63         /**
  64          * Factory method
  65          * @return NonViralNameDefaultCacheStrategy A new instance of  NonViralNameDefaultCacheStrategy
  66          */
  67         public static NonViralNameDefaultCacheStrategy NewInstance(){
  68                 return new NonViralNameDefaultCacheStrategy();
  69         }
  70
  71         /**
  72          * Constructor
  73          */
  74         protected NonViralNameDefaultCacheStrategy(){
  75                 super();
  76         }
  77
  78 /* **************** GETTER / SETTER **************************************/
  79
  80         /**
  81          * String that separates the NameCache part from the AuthorCache part
  82          * @return
  83          */
  84         public String getNameAuthorSeperator() {
  85                 return NameAuthorSeperator;
  86         }
  87
  88
  89         public void setNameAuthorSeperator(String nameAuthorSeperator) {
  90                 NameAuthorSeperator = nameAuthorSeperator;
  91         }
  92
  93
  94         /**
  95          * String the basionym author part starts with e.g. '('.
  96          * This should correspond with the {@link NonViralNameDefaultCacheStrategy#getBasionymEnd() basionymEnd} attribute
  97          * @return
  98          */
  99         public String getBasionymStart() {
 100                 return BasionymStart;
 101         }
 102
 103
 104         public void setBasionymStart(String basionymStart) {
 105                 BasionymStart = basionymStart;
 106         }
 107
 108
 109         /**
 110          * String the basionym author part ends with e.g. ')'.
 111          * This should correspond with the {@link NonViralNameDefaultCacheStrategy#getBasionymStart() basionymStart} attribute
 112          * @return
 113          */
 114         public String getBasionymEnd() {
 115                 return BasionymEnd;
 116         }
 117
 118
 119         public void setBasionymEnd(String basionymEnd) {
 120                 BasionymEnd = basionymEnd;
 121         }
 122
 123
 124         /**
 125          * String to seperate ex author from author.
 126          * @return
 127          */
 128         public String getExAuthorSeperator() {
 129                 return ExAuthorSeperator;
 130         }
 131
 132
 133         public void setExAuthorSeperator(String exAuthorSeperator) {
 134                 ExAuthorSeperator = exAuthorSeperator;
 135         }
 136
 137
 138         /**
 139          * String that seperates the basionym/original_combination author part from the combination author part
 140          * @return
 141          */
 142         public CharSequence getBasionymAuthorCombinationAuthorSeperator() {
 143                 return BasionymAuthorCombinationAuthorSeperator;
 144         }
 145
 146
 147         public void setBasionymAuthorCombinationAuthorSeperator(
 148                         CharSequence basionymAuthorCombinationAuthorSeperator) {
 149                 BasionymAuthorCombinationAuthorSeperator = basionymAuthorCombinationAuthorSeperator;
 150         }
 151
 152
 153 //** *****************************************************************************************/
 154
 155
 156         /* (non-Javadoc)
 157          * @see eu.etaxonomy.cdm.strategy.INameCacheStrategy#getNameCache()
 158          */
 159         @Override
 160         public String getTitleCache(T nonViralName) {
 161                 if (nonViralName == null){
 162                         return null;
 163                 }
 164
 165                 if (nonViralName.isProtectedTitleCache()){
 166                         return nonViralName.getTitleCache();
 167                 }
 168                 String result = "";
 169                 //Autonym
 170                 if (isAutonym(nonViralName)){
 171                         String speciesPart = getSpeciesNameCache(nonViralName);
 172                         //TODO should this include basionym authors and ex authors
 173                         INomenclaturalAuthor author = nonViralName.getCombinationAuthorTeam();
 174                         String authorPart = "";
 175                         if (author != null){
 176                                 authorPart = CdmUtils.Nz(author.getNomenclaturalTitle());
 177                         }
 178                         INomenclaturalAuthor basAuthor = nonViralName.getBasionymAuthorTeam();
 179                         String basAuthorPart = "";
 180                         if (basAuthor != null){
 181                                 basAuthorPart = CdmUtils.Nz(basAuthor.getNomenclaturalTitle());
 182                         }
 183                         if (! "".equals(basAuthorPart)){
 184                                 authorPart = "("+ basAuthorPart +")" + authorPart;
 185                         }
 186                         String infraSpeciesPart = (CdmUtils.Nz(nonViralName.getInfraSpecificEpithet()));
 187
 188                         String infraSpeciesSeparator = "";
 189                         if (nonViralName.getRank() == null || !nonViralName.getRank().isInfraSpecific()){
 190                                 //TODO handle exception
 191                                 logger.warn("Rank for autonym does not exist or is not lower than species !!");
 192                         }else{
 193                                 infraSpeciesSeparator = nonViralName.getRank().getAbbreviation();
 194                         }
 195
 196                         result = CdmUtils.concat(" ", new String[]{speciesPart, authorPart, infraSpeciesSeparator, infraSpeciesPart});
 197                         result = result.trim().replace("null", "");
 198                 }else{ //not Autonym
 199                         String nameCache = nonViralName.getNameCache();  //OLD: CdmUtils.Nz(getNameCache(nonViralName));
 200                         if (nameIncludesAuthorship(nonViralName)){
 201                                 String authorCache = CdmUtils.Nz(getAuthorshipCache(nonViralName));
 202                                 result = CdmUtils.concat(NameAuthorSeperator, nameCache, authorCache);
 203                         }else{
 204                                 result = nameCache;
 205                         }
 206                 }
 207                 return result;
 208         }
 209
 210         protected boolean nameIncludesAuthorship(NonViralName nonViralName){
 211                 Rank rank = nonViralName.getRank();
 212                 if (rank != null && rank.isSpeciesAggregate()){
 213                         return false;
 214                 }else{
 215                         return true;
 216                 }
 217         }
 218
 219
 220         @Override
 221         public String getFullTitleCache(T nonViralName) {
 222                 //null
 223                 if (nonViralName == null){
 224                         return null;
 225                 }
 226                 //full title cache
 227                 if (nonViralName.isProtectedFullTitleCache() == true) {
 228                         return nonViralName.getFullTitleCache();
 229                 }
 230
 231                 String result = "";
 232                 //title cache
 233                 String titleCache = nonViralName.getTitleCache();   // OLD: getTitleCache(nonViralName);
 234
 235                 String microReference = nonViralName.getNomenclaturalMicroReference();
 236                 INomenclaturalReference ref = nonViralName.getNomenclaturalReference();
 237                 String referenceBaseCache = null;
 238                 if (ref != null){
 239                         INomenclaturalReference nomenclaturalReference = HibernateProxyHelper.deproxy(ref, INomenclaturalReference.class);
 240                         nomenclaturalReference.setCacheStrategy(nomenclaturalReference.getType().getCacheStrategy());
 241                         referenceBaseCache = nomenclaturalReference.getNomenclaturalCitation(microReference);
 242                 }
 243
 244                 //make nomenclatural status
 245                 String ncStatusCache = "";
 246                 Set<NomenclaturalStatus> ncStati = nonViralName.getStatus();
 247                 Iterator<NomenclaturalStatus> iterator = ncStati.iterator();
 248                 while (iterator.hasNext()) {
 249                         NomenclaturalStatus ncStatus = (NomenclaturalStatus)iterator.next();
 250                         // since the NewInstance method of nomencatural status allows null as parameter
 251                         // we have to check for null values here
 252                         String suffix = "not defined";
 253                         if(ncStatus.getType() != null){
 254                                 NomenclaturalStatusType statusType =  ncStatus.getType();
 255                                 Language lang = Language.LATIN();
 256                                 Representation repr = statusType.getRepresentation(lang);
 257                                 suffix = repr.getAbbreviatedLabel();
 258                         }else if(ncStatus.getRuleConsidered() != null && ! ncStatus.getRuleConsidered().equals("")){
 259                                 suffix = ncStatus.getRuleConsidered();
 260                         }
 261                         ncStatusCache = ", " + suffix;
 262                 }
 263                 String refConcat = " ";
 264                 if (referenceBaseCache != null && ! referenceBaseCache.trim().startsWith("in ")){
 265                         refConcat = ", ";
 266                 }
 267                 result = CdmUtils.concat(refConcat, titleCache, referenceBaseCache);
 268                 result = CdmUtils.concat("", result, ncStatusCache);
 269                 return result;
 270         }
 271
 272
 273         /**
 274          * Generates and returns the "name cache" (only scientific name without author teams and year).
 275          * @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy#getNameCache(eu.etaxonomy.cdm.model.name.TaxonNameBase)
 276          */
 277         public String getNameCache(T nonViralName) {
 278                 if (nonViralName == null){
 279                         return null;
 280                 }
 281                 String result;
 282                 Rank rank = nonViralName.getRank();
 283
 284                 if (nonViralName.isProtectedNameCache()){
 285                         result = nonViralName.getNameCache();
 286                 }else if (rank == null){
 287                         result = getRanklessNameCache(nonViralName);
 288                 }else if (rank.isInfraSpecific()){
 289                         result = getInfraSpeciesNameCache(nonViralName);
 290                 }else if (rank.isSpecies()){
 291                         result = getSpeciesNameCache(nonViralName);
 292                 }else if (rank.isInfraGeneric()){
 293                         result = getInfraGenusNameCache(nonViralName);
 294                 }else if (rank.isGenus()){
 295                         result = getGenusOrUninomialNameCache(nonViralName);
 296                 }else if (rank.isSupraGeneric()){
 297                         result = getGenusOrUninomialNameCache(nonViralName);
 298                 }else{
 299                         logger.warn("Name Strategy for Name (UUID: " + nonViralName.getUuid() +  ") not yet implemented");
 300                         result = "";
 301                 }
 302                 return result;
 303         }
 304
 305
 306         /* (non-Javadoc)
 307          * @see eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy#getAuthorCache(eu.etaxonomy.cdm.model.name.NonViralName)
 308          */
 309         public String getAuthorshipCache(T nonViralName) {
 310                 if (nonViralName == null){
 311                         return null;
 312                 }
 313                 //cache protected
 314                 if (nonViralName.isProtectedAuthorshipCache() == true) {
 315                         return nonViralName.getAuthorshipCache();
 316                 }
 317                 return getNonCacheAuthorshipCache(nonViralName);
 318
 319         }
 320
 321         /**
 322          * Returns the authorshipcache string for the atomized authorship fields. Does not use the authorshipfield.
 323          * @throws NullPointerException if nonViralName is null.
 324          * @param nonViralName
 325          * @return
 326          */
 327         protected String getNonCacheAuthorshipCache(T nonViralName){
 328                 String result = "";
 329                 INomenclaturalAuthor combinationAuthor = nonViralName.getCombinationAuthorTeam();
 330                 INomenclaturalAuthor exCombinationAuthor = nonViralName.getExCombinationAuthorTeam();
 331                 INomenclaturalAuthor basionymAuthor = nonViralName.getBasionymAuthorTeam();
 332                 INomenclaturalAuthor exBasionymAuthor = nonViralName.getExBasionymAuthorTeam();
 333                 String basionymPart = "";
 334                 String authorPart = "";
 335                 //basionym
 336                 if (basionymAuthor != null || exBasionymAuthor != null){
 337                         basionymPart = BasionymStart + getAuthorAndExAuthor(basionymAuthor, exBasionymAuthor) + BasionymEnd;
 338                 }
 339                 if (combinationAuthor != null || exCombinationAuthor != null){
 340                         authorPart = getAuthorAndExAuthor(combinationAuthor, exCombinationAuthor);
 341                 }
 342                 result = CdmUtils.concat(BasionymAuthorCombinationAuthorSeperator, basionymPart, authorPart);
 343                 return result;
 344         }
 345
 346         /**
 347          * Returns the AuthorCache part for a combination of an author and an ex author. This applies on combination authors
 348          * as well as on basionym/orginal combination authors.
 349          * @param author the author
 350          * @param exAuthor the ex-author
 351          * @return
 352          */
 353         protected String getAuthorAndExAuthor(INomenclaturalAuthor author, INomenclaturalAuthor exAuthor){
 354                 String result = "";
 355                 String authorString = "";
 356                 String exAuthorString = "";
 357                 if (author != null){
 358                         authorString = CdmUtils.Nz(author.getNomenclaturalTitle());
 359                 }
 360                 if (exAuthor != null){
 361                         exAuthorString = CdmUtils.Nz(exAuthor.getNomenclaturalTitle());
 362                 }
 363                 if (exAuthorString.length() > 0 ){
 364                         exAuthorString = exAuthorString + ExAuthorSeperator;
 365                 }
 366                 result = exAuthorString + authorString;
 367                 return result;
 368
 369         }
 370
 371
 372         /* (non-Javadoc)
 373          * @see eu.etaxonomy.cdm.strategy.INameCacheStrategy#getTaggedName(eu.etaxonomy.cdm.model.common.CdmBase)
 374          */
 375         @Override
 376         public List<Object> getTaggedName(T nonViralName) {
 377                 List<Object> tags = new ArrayList<Object>();
 378                 tags.add(nonViralName.getGenusOrUninomial());
 379                 if (nonViralName.isSpecies() || nonViralName.isInfraSpecific()){
 380                         tags.add(nonViralName.getSpecificEpithet());
 381                 }
 382
 383                 // No autonym
 384                 if (nonViralName.isInfraSpecific() && ! nonViralName.getSpecificEpithet().equals(nonViralName.getInfraSpecificEpithet())){
 385                         tags.add(nonViralName.getRank());
 386                         tags.add(nonViralName.getInfraSpecificEpithet());
 387                 }
 388
 389                 if (nonViralName.isInfraGeneric()){
 390                         //TODO choose right strategy or generic approach?
 391                         // --- strategy 1 ---
 392                         tags.add(nonViralName.getRank());
 393                         tags.add(nonViralName.getInfraGenericEpithet());
 394                         // --- strategy 2 ---
 395 //                      tags.add('('+nvn.getInfraGenericEpithet()+')');
 396                 }
 397                 Team authorTeam = Team.NewInstance();
 398                 authorTeam.setProtectedTitleCache(true);
 399                 authorTeam.setTitleCache(nonViralName.getAuthorshipCache());
 400                 tags.add(authorTeam);
 401
 402                 // Name is an autonym. Rank and infraspecific eitheton follow the author
 403                 if (nonViralName.isInfraSpecific() && nonViralName.getSpecificEpithet().equals(nonViralName.getInfraSpecificEpithet())){
 404                         tags.add(nonViralName.getRank());
 405                         tags.add(nonViralName.getInfraSpecificEpithet());
 406                 }
 407
 408                 if(! "".equals(nonViralName.getAppendedPhrase())){
 409                         tags.add(nonViralName.getAppendedPhrase());
 410                 }
 411
 412                 return tags;
 413         }
 414
 415
 416         /************** PRIVATES ****************/
 417
 418                 protected String getRanklessNameCache(NonViralName nonViralName){
 419                         String result = "";
 420                         result = (result + (nonViralName.getGenusOrUninomial())).trim().replace("null", "");
 421                         result += " " + (CdmUtils.Nz(nonViralName.getSpecificEpithet())).trim();
 422                         result += " " + (CdmUtils.Nz(nonViralName.getInfraSpecificEpithet())).trim();
 423                         result = result.trim().replace("null", "");
 424                         //result += " (rankless)";
 425                         result = addAppendedPhrase(result, nonViralName);
 426                         return result;
 427                 }
 428
 429
 430                 protected String getGenusOrUninomialNameCache(NonViralName nonViralName){
 431                         String result;
 432                         result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
 433                         result = addAppendedPhrase(result, nonViralName).trim();
 434                         return result;
 435                 }
 436
 437                 protected String getInfraGenusNameCache(NonViralName nonViralName){
 438                         String result;
 439                         Rank rank = nonViralName.getRank();
 440                         if (rank.isSpeciesAggregate()){
 441                                 return getSpeciesAggregateCache(nonViralName);
 442                         }
 443                         String infraGenericMarker = "xxx.";
 444                         if (rank != null){
 445                                 try {
 446                                         infraGenericMarker = rank.getInfraGenericMarker();
 447                                 } catch (UnknownCdmTypeException e) {
 448                                         infraGenericMarker = "'unhandled infrageneric rank'";
 449                                 }
 450                         }
 451                         result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
 452                         result += " " + infraGenericMarker + " " + (CdmUtils.Nz(nonViralName.getInfraGenericEpithet())).trim().replace("null", "");
 453                         result = addAppendedPhrase(result, nonViralName).trim();
 454                         return result;
 455                 }
 456
 457 //              aggr.|agg.|group
 458                 protected String getSpeciesAggregateCache(NonViralName nonViralName){
 459                         String result;
 460                         result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
 461                         result += " " + CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim().replace("null", "");
 462                         String marker;
 463                         try {
 464                                 marker = nonViralName.getRank().getInfraGenericMarker();
 465                         } catch (UnknownCdmTypeException e) {
 466                                 marker = "'unknown aggregat type'";
 467                         }
 468                         result += " " + marker;
 469                         result = addAppendedPhrase(result, nonViralName).trim();
 470                         return result;
 471                 }
 472
 473                 protected String getSpeciesNameCache(NonViralName nonViralName){
 474                         String result;
 475                         result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
 476                         result += " " + CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim().replace("null", "");
 477                         result = addAppendedPhrase(result, nonViralName).trim();
 478                         result = result.replace("\\s\\", " ");
 479                         return result;
 480                 }
 481
 482
 483                 protected String getInfraSpeciesNameCache(NonViralName nonViralName){
 484                         return getInfraSpeciesNameCache(nonViralName, true);
 485                 }
 486
 487                 protected String getInfraSpeciesNameCache(NonViralName nonViralName, boolean includeMarker){
 488                         String result;
 489                         result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
 490                         result += " " + (CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim()).replace("null", "");
 491                         if (includeMarker){
 492                                 result += " " + (nonViralName.getRank().getAbbreviation()).trim().replace("null", "");
 493                         }
 494                         result += " " + (CdmUtils.Nz(nonViralName.getInfraSpecificEpithet())).trim().replace("null", "");
 495                         result = addAppendedPhrase(result, nonViralName).trim();
 496                         return result;
 497                 }
 498
 499
 500
 501                 /**
 502                  * @param name
 503                  * @return true, if name has Rank, Rank is below species and species epithet equals infraSpeciesEpithtet, else false
 504                  */
 505                 protected boolean isAutonym(NonViralName nonViralName){
 506                         if (nonViralName != null && nonViralName.getRank() != null && nonViralName.getSpecificEpithet() != null && nonViralName.getInfraSpecificEpithet() != null &&
 507                                         nonViralName.getRank().isInfraSpecific() && nonViralName.getSpecificEpithet().trim().equals(nonViralName.getInfraSpecificEpithet().trim())){
 508                                 return true;
 509                         }else{
 510                                 return false;
 511                         }
 512                 }
 513
 514                 protected String addAppendedPhrase(String resultString, NonViralName nonViralName){
 515                         String appendedPhrase = nonViralName ==null ? null : nonViralName.getAppendedPhrase();
 516                         if (resultString == null){
 517                                 return appendedPhrase;
 518                         }else if(appendedPhrase == null || "".equals(appendedPhrase.trim())) {
 519                                 return resultString;
 520                         }else if ("".equals(resultString)){
 521                                 return resultString + appendedPhrase;
 522                         }else {
 523                                 return resultString + " " + appendedPhrase;
 524                         }
 525                 }
 526
 527
 528                 public String getLastEpithet(T taxonNameBase) {
 529                         Rank rank = taxonNameBase.getRank();
 530                         if(rank.isGenus() || rank.isSupraGeneric()) {
 531                                 return taxonNameBase.getGenusOrUninomial();
 532                         } else if(rank.isInfraGeneric()) {
 533                                 return taxonNameBase.getInfraGenericEpithet();
 534                         } else if(rank.isSpecies()) {
 535                                 return taxonNameBase.getSpecificEpithet();
 536                         } else {
 537                                 return taxonNameBase.getInfraSpecificEpithet();
 538                         }
 539                 }
 540 }