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
 166                 if (nonViralName.isProtectedTitleCache()){
 167                         return nonViralName.getTitleCache();
 168                 }
 169                 String result = "";
 170                 //Autonym
 171                 if (isAutonym(nonViralName)){
 172                         String speciesPart = getSpeciesNameCache(nonViralName);
 173                         //TODO should this include basionym authors and ex authors
 174                         INomenclaturalAuthor author = nonViralName.getCombinationAuthorTeam();
 175                         String authorPart = "";
 176                         if (author != null){
 177                                 authorPart = CdmUtils.Nz(author.getNomenclaturalTitle());
 178                         }
 179                         INomenclaturalAuthor basAuthor = nonViralName.getBasionymAuthorTeam();
 180                         String basAuthorPart = "";
 181                         if (basAuthor != null){
 182                                 basAuthorPart = CdmUtils.Nz(basAuthor.getNomenclaturalTitle());
 183                         }
 184                         if (! "".equals(basAuthorPart)){
 185                                 authorPart = "("+ basAuthorPart +")" + authorPart;
 186                         }
 187                         String infraSpeciesPart = (CdmUtils.Nz(nonViralName.getInfraSpecificEpithet()));
 188
 189                         String infraSpeciesSeparator = "";
 190                         if (nonViralName.getRank() == null || !nonViralName.getRank().isInfraSpecific()){
 191                                 //TODO handle exception
 192                                 logger.warn("Rank for autonym does not exist or is not lower than species !!");
 193                         }else{
 194                                 infraSpeciesSeparator = nonViralName.getRank().getAbbreviation();
 195                         }
 196
 197                         result = CdmUtils.concat(" ", new String[]{speciesPart, authorPart, infraSpeciesSeparator, infraSpeciesPart});
 198                         result = result.trim().replace("null", "");
 199                 }else{ //not Autonym
 200                         String nameCache = nonViralName.getNameCache();  //OLD: CdmUtils.Nz(getNameCache(nonViralName));
 201                         if (nameIncludesAuthorship(nonViralName)){
 202                                 String authorCache = CdmUtils.Nz(getAuthorshipCache(nonViralName));
 203                                 result = CdmUtils.concat(NameAuthorSeperator, nameCache, authorCache);
 204                         }else{
 205                                 result = nameCache;
 206                         }
 207                 }
 208                 return result;
 209         }
 210
 211         protected boolean nameIncludesAuthorship(NonViralName nonViralName){
 212                 Rank rank = nonViralName.getRank();
 213                 if (rank != null && rank.isSpeciesAggregate()){
 214                         return false;
 215                 }else{
 216                         return true;
 217                 }
 218         }
 219
 220
 221         @Override
 222         public String getFullTitleCache(T nonViralName) {
 223                 //null
 224                 if (nonViralName == null){
 225                         return null;
 226                 }
 227                 //full title cache
 228                 if (nonViralName.isProtectedFullTitleCache() == true) {
 229                         return nonViralName.getFullTitleCache();
 230                 }
 231
 232                 String result = "";
 233                 //title cache
 234                 String titleCache = getTitleCache(nonViralName);
 235
 236                 String microReference = nonViralName.getNomenclaturalMicroReference();
 237                 ReferenceBase<?> ref = nonViralName.getNomenclaturalReference();
 238                 String referenceBaseCache = null;
 239                 if (ref != null){
 240                         INomenclaturalReference nomRef = HibernateProxyHelper.deproxy(ref, INomenclaturalReference.class);
 241                         referenceBaseCache = nomRef.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                         NomenclaturalStatusType statusType =  ncStatus.getType();
 251                         Language lang = Language.LATIN();
 252                         Representation repr = statusType.getRepresentation(lang);
 253                         ncStatusCache = ", " + repr.getAbbreviatedLabel();
 254                 }
 255                 String refConcat = " ";
 256                 if (referenceBaseCache != null && ! referenceBaseCache.trim().startsWith("in ")){
 257                         refConcat = ", ";
 258                 }
 259                 result = CdmUtils.concat(refConcat, titleCache, referenceBaseCache);
 260                 result = CdmUtils.concat("", result, ncStatusCache);
 261                 return result;
 262         }
 263
 264
 265         /**
 266          * Generates and returns the "name cache" (only scientific name without author teams and year).
 267          * @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy#getNameCache(eu.etaxonomy.cdm.model.name.TaxonNameBase)
 268          */
 269         public String getNameCache(T nonViralName) {
 270                 if (nonViralName == null){
 271                         return null;
 272                 }
 273                 String result;
 274                 Rank rank = nonViralName.getRank();
 275
 276                 if (nonViralName.isProtectedNameCache()){
 277                         result = nonViralName.getNameCache();
 278                 }else if (rank == null){
 279                         result = getRanklessNameCache(nonViralName);
 280                 }else if (rank.isInfraSpecific()){
 281                         result = getInfraSpeciesNameCache(nonViralName);
 282                 }else if (rank.isSpecies()){
 283                         result = getSpeciesNameCache(nonViralName);
 284                 }else if (rank.isInfraGeneric()){
 285                         result = getInfraGenusNameCache(nonViralName);
 286                 }else if (rank.isGenus()){
 287                         result = getGenusOrUninomialNameCache(nonViralName);
 288                 }else if (rank.isSupraGeneric()){
 289                         result = getGenusOrUninomialNameCache(nonViralName);
 290                 }else{
 291                         logger.warn("Name Strategy for Name (UUID: " + nonViralName.getUuid() +  ") not yet implemented");
 292                         result = "";
 293                 }
 294                 return result;
 295         }
 296
 297
 298         /* (non-Javadoc)
 299          * @see eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy#getAuthorCache(eu.etaxonomy.cdm.model.name.NonViralName)
 300          */
 301         public String getAuthorshipCache(T nonViralName) {
 302                 if (nonViralName == null){
 303                         return null;
 304                 }
 305                 //cache protected
 306                 if (nonViralName.isProtectedAuthorshipCache() == true) {
 307                         return nonViralName.getAuthorshipCache();
 308                 }
 309                 return getNonCacheAuthorshipCache(nonViralName);
 310
 311         }
 312
 313         /**
 314          * Returns the authorshipcache string for the atomized authorship fields. Does not use the authorshipfield.
 315          * @throws NullPointerException if nonViralName is null.
 316          * @param nonViralName
 317          * @return
 318          */
 319         protected String getNonCacheAuthorshipCache(T nonViralName){
 320                 String result = "";
 321                 INomenclaturalAuthor combinationAuthor = nonViralName.getCombinationAuthorTeam();
 322                 INomenclaturalAuthor exCombinationAuthor = nonViralName.getExCombinationAuthorTeam();
 323                 INomenclaturalAuthor basionymAuthor = nonViralName.getBasionymAuthorTeam();
 324                 INomenclaturalAuthor exBasionymAuthor = nonViralName.getExBasionymAuthorTeam();
 325                 String basionymPart = "";
 326                 String authorPart = "";
 327                 //basionym
 328                 if (basionymAuthor != null || exBasionymAuthor != null){
 329                         basionymPart = BasionymStart + getAuthorAndExAuthor(basionymAuthor, exBasionymAuthor) + BasionymEnd;
 330                 }
 331                 if (combinationAuthor != null || exCombinationAuthor != null){
 332                         authorPart = getAuthorAndExAuthor(combinationAuthor, exCombinationAuthor);
 333                 }
 334                 result = CdmUtils.concat(BasionymAuthorCombinationAuthorSeperator, basionymPart, authorPart);
 335                 return result;
 336         }
 337
 338         /**
 339          * Returns the AuthorCache part for a combination of an author and an ex author. This applies on combination authors
 340          * as well as on basionym/orginal combination authors.
 341          * @param author the author
 342          * @param exAuthor the ex-author
 343          * @return
 344          */
 345         protected String getAuthorAndExAuthor(INomenclaturalAuthor author, INomenclaturalAuthor exAuthor){
 346                 String result = "";
 347                 String authorString = "";
 348                 String exAuthorString = "";
 349                 if (author != null){
 350                         authorString = CdmUtils.Nz(author.getNomenclaturalTitle());
 351                 }
 352                 if (exAuthor != null){
 353                         exAuthorString = CdmUtils.Nz(exAuthor.getNomenclaturalTitle());
 354                 }
 355                 if (exAuthorString.length() > 0 ){
 356                         exAuthorString = exAuthorString + ExAuthorSeperator;
 357                 }
 358                 result = exAuthorString + authorString;
 359                 return result;
 360
 361         }
 362
 363
 364         /* (non-Javadoc)
 365          * @see eu.etaxonomy.cdm.strategy.INameCacheStrategy#getTaggedName(eu.etaxonomy.cdm.model.common.CdmBase)
 366          */
 367         @Override
 368         public List<Object> getTaggedName(T nonViralName) {
 369                 List<Object> tags = new ArrayList<Object>();
 370                 tags.add(nonViralName.getGenusOrUninomial());
 371                 if (nonViralName.isSpecies() || nonViralName.isInfraSpecific()){
 372                         tags.add(nonViralName.getSpecificEpithet());
 373                 }
 374
 375                 // No autonym
 376                 if (nonViralName.isInfraSpecific() && ! nonViralName.getSpecificEpithet().equals(nonViralName.getInfraSpecificEpithet())){
 377                         tags.add(nonViralName.getRank());
 378                         tags.add(nonViralName.getInfraSpecificEpithet());
 379                 }
 380
 381                 if (nonViralName.isInfraGeneric()){
 382                         //TODO choose right strategy or generic approach?
 383                         // --- strategy 1 ---
 384                         tags.add(nonViralName.getRank());
 385                         tags.add(nonViralName.getInfraGenericEpithet());
 386                         // --- strategy 2 ---
 387 //                      tags.add('('+nvn.getInfraGenericEpithet()+')');
 388                 }
 389                 Team authorTeam = Team.NewInstance();
 390                 authorTeam.setProtectedTitleCache(true);
 391                 authorTeam.setTitleCache(nonViralName.getAuthorshipCache());
 392                 tags.add(authorTeam);
 393
 394                 // Name is an autonym. Rank and infraspecific eitheton follow the author
 395                 if (nonViralName.isInfraSpecific() && nonViralName.getSpecificEpithet().equals(nonViralName.getInfraSpecificEpithet())){
 396                         tags.add(nonViralName.getRank());
 397                         tags.add(nonViralName.getInfraSpecificEpithet());
 398                 }
 399
 400                 if(! "".equals(nonViralName.getAppendedPhrase())){
 401                         tags.add(nonViralName.getAppendedPhrase());
 402                 }
 403
 404                 return tags;
 405         }
 406
 407
 408         /************** PRIVATES ****************/
 409
 410                 protected String getRanklessNameCache(NonViralName nonViralName){
 411                         String result = "";
 412                         result = (result + (nonViralName.getGenusOrUninomial())).trim().replace("null", "");
 413                         result += " " + (CdmUtils.Nz(nonViralName.getSpecificEpithet())).trim();
 414                         result += " " + (CdmUtils.Nz(nonViralName.getInfraSpecificEpithet())).trim();
 415                         result = result.trim().replace("null", "");
 416                         //result += " (rankless)";
 417                         result = addAppendedPhrase(result, nonViralName);
 418                         return result;
 419                 }
 420
 421
 422                 protected String getGenusOrUninomialNameCache(NonViralName nonViralName){
 423                         String result;
 424                         result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
 425                         result = addAppendedPhrase(result, nonViralName);
 426                         return result;
 427                 }
 428
 429                 protected String getInfraGenusNameCache(NonViralName nonViralName){
 430                         String result;
 431                         Rank rank = nonViralName.getRank();
 432                         if (rank.isSpeciesAggregate()){
 433                                 return getSpeciesAggregateCache(nonViralName);
 434                         }
 435                         String infraGenericMarker = "xxx.";
 436                         if (rank != null){
 437                                 try {
 438                                         infraGenericMarker = rank.getInfraGenericMarker();
 439                                 } catch (UnknownCdmTypeException e) {
 440                                         infraGenericMarker = "'unhandled infrageneric rank'";
 441                                 }
 442                         }
 443                         result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
 444                         result += " " + infraGenericMarker + " " + (CdmUtils.Nz(nonViralName.getInfraGenericEpithet())).trim().replace("null", "");
 445                         result = addAppendedPhrase(result, nonViralName);
 446                         return result;
 447                 }
 448
 449 //              aggr.|agg.|group
 450                 protected String getSpeciesAggregateCache(NonViralName nonViralName){
 451                         String result;
 452                         result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
 453                         result += " " + CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim().replace("null", "");
 454                         String marker;
 455                         try {
 456                                 marker = nonViralName.getRank().getInfraGenericMarker();
 457                         } catch (UnknownCdmTypeException e) {
 458                                 marker = "'unknown aggregat type'";
 459                         }
 460                         result += " " + marker;
 461                         result = addAppendedPhrase(result, nonViralName);
 462                         return result;
 463                 }
 464
 465                 protected String getSpeciesNameCache(NonViralName nonViralName){
 466                         String result;
 467                         result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
 468                         result += " " + CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim().replace("null", "");
 469                         result = addAppendedPhrase(result, nonViralName);
 470                         return result;
 471                 }
 472
 473
 474                 protected String getInfraSpeciesNameCache(NonViralName nonViralName){
 475                         return getInfraSpeciesNameCache(nonViralName, true);
 476                 }
 477
 478                 protected String getInfraSpeciesNameCache(NonViralName nonViralName, boolean includeMarker){
 479                         String result;
 480                         result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
 481                         result += " " + (CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim()).replace("null", "");
 482                         if (includeMarker){
 483                                 result += " " + (nonViralName.getRank().getAbbreviation()).trim().replace("null", "");
 484                         }
 485                         result += " " + (CdmUtils.Nz(nonViralName.getInfraSpecificEpithet())).trim().replace("null", "");
 486                         result = addAppendedPhrase(result, nonViralName);
 487                         return result;
 488                 }
 489
 490
 491
 492                 /**
 493                  * @param name
 494                  * @return true, if name has Rank, Rank is below species and species epithet equals infraSpeciesEpithtet, else false
 495                  */
 496                 protected boolean isAutonym(NonViralName nonViralName){
 497                         if (nonViralName != null && nonViralName.getRank() != null && nonViralName.getSpecificEpithet() != null && nonViralName.getInfraSpecificEpithet() != null &&
 498                                         nonViralName.getRank().isInfraSpecific() && nonViralName.getSpecificEpithet().trim().equals(nonViralName.getInfraSpecificEpithet().trim())){
 499                                 return true;
 500                         }else{
 501                                 return false;
 502                         }
 503                 }
 504
 505                 protected String addAppendedPhrase(String resultString, NonViralName nonViralName){
 506                         String appendedPhrase = nonViralName ==null ? null : nonViralName.getAppendedPhrase();
 507                         if (resultString == null){
 508                                 return appendedPhrase;
 509                         }else if(appendedPhrase == null || "".equals(appendedPhrase.trim())) {
 510                                 return resultString;
 511                         }else if ("".equals(resultString)){
 512                                 return resultString + appendedPhrase;
 513                         }else {
 514                                 return resultString + " " + appendedPhrase;
 515                         }
 516                 }
 517
 518
 519                 public String getLastEpithet(T taxonNameBase) {
 520                         Rank rank = taxonNameBase.getRank();
 521                         if(rank.isGenus() || rank.isSupraGeneric()) {
 522                                 return taxonNameBase.getGenusOrUninomial();
 523                         } else if(rank.isInfraGeneric()) {
 524                                 return taxonNameBase.getInfraGenericEpithet();
 525                         } else if(rank.isSpecies()) {
 526                                 return taxonNameBase.getSpecificEpithet();
 527                         } else {
 528                                 return taxonNameBase.getInfraSpecificEpithet();
 529                         }
 530                 }
 531 }