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