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