eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/parser/ParseHandler.java

   1 /**
   2  *
   3  */
   4 package eu.etaxonomy.taxeditor.parser;
   5
   6 import java.util.ArrayList;
   7 import java.util.List;
   8
   9 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  10 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  11 import eu.etaxonomy.cdm.model.name.NonViralName;
  12 import eu.etaxonomy.cdm.model.name.Rank;
  13 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  14 import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
  15 import eu.etaxonomy.cdm.model.reference.Reference;
  16 import eu.etaxonomy.cdm.strategy.match.MatchException;
  17 import eu.etaxonomy.cdm.strategy.match.MatchStrategyConfigurator.MatchStrategy;
  18 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  19 import eu.etaxonomy.taxeditor.model.MessagingUtils;
  20 import eu.etaxonomy.taxeditor.preference.PreferencesUtil;
  21 import eu.etaxonomy.taxeditor.store.CdmStore;
  22
  23 /**
  24  * <p>ParseHandler class.</p>
  25  *
  26  * @author n.hoffmann
  27  * @version $Id: $
  28  */
  29 public class ParseHandler{
  30
  31         private TaxonNameBase taxonNameBase;
  32
  33         private class MatchMatrix {
  34                 List<TaxonNameBase> duplicateNames = new ArrayList<TaxonNameBase>();
  35
  36                 List<INomenclaturalReference> duplicateReferences = new ArrayList<INomenclaturalReference>();
  37                 List<INomenclaturalReference> duplicateInReferences = new ArrayList<INomenclaturalReference>();
  38
  39                 List<TeamOrPersonBase> duplicateCombinationAuthorships = new ArrayList<TeamOrPersonBase>();
  40                 List<TeamOrPersonBase> duplicateExCombinationAuthorships = new ArrayList<TeamOrPersonBase>();
  41                 List<TeamOrPersonBase> duplicateBasionymAuthorships = new ArrayList<TeamOrPersonBase>();
  42                 List<TeamOrPersonBase> duplicateExBasionymAuthorships = new ArrayList<TeamOrPersonBase>();
  43         }
  44
  45         private static NonViralNameParserImpl nonViralNameParser = NonViralNameParserImpl.NewInstance();
  46
  47         /**
  48          * The name that should get parsed
  49          */
  50         private NonViralName name;
  51
  52         private boolean doResolveInReferences;
  53
  54         /**
  55          * Creates a new instance
  56          *
  57          * @param textWidget
  58          * @param name
  59          */
  60         private ParseHandler(TaxonNameBase name){
  61                 if(name == null){
  62                         this.name = nonViralNameParser.getNonViralNameInstance("", PreferencesUtil.getPreferredNomenclaturalCode());
  63                 }else{
  64                         this.name = (NonViralName) HibernateProxyHelper.deproxy(name);
  65                 }
  66         }
  67
  68         /**
  69          * Factory method to create a new instance of the this class
  70          *
  71          * @param textWidget    The text widget where the NonViralName may be entered into
  72          * @param name                  An initial NonViralName or null when creating a new name
  73          * @return                              An instance of this class
  74          */
  75         public static ParseHandler NewInstance(TaxonNameBase name){
  76                 return new ParseHandler(name);
  77
  78         }
  79
  80         /**
  81          * Parses a given string and returns a <code>TaxonNameBase</code> instance with the
  82          * results of the parsing.
  83          *
  84          * This method should be used to quickly create a new name from a string.
  85          * Wherever the string will be parsed again in subsequent editing, an instance
  86          * of <code>ParseHandler</code> should be attached to the text widget.
  87          *
  88          * @param unparsedNameString a {@link java.lang.String} object.
  89          * @return a {@link eu.etaxonomy.cdm.model.name.TaxonNameBase} object.
  90          */
  91         public static NonViralName parseReferencedName(String unparsedNameString, Rank rank){
  92             NonViralName name = nonViralNameParser.parseReferencedName(unparsedNameString,
  93                                 PreferencesUtil.getPreferredNomenclaturalCode(), rank);
  94
  95 //              if (name.hasProblem()) {
  96 //                      name.setFullTitleCache(unparsedNameString);
  97 //              }
  98
  99                 return name;
 100         }
 101
 102         public static NonViralName parseName(String unparsedNameString, Rank rank){
 103                 NonViralName name = nonViralNameParser.parseFullName(unparsedNameString,
 104                                 PreferencesUtil.getPreferredNomenclaturalCode(), rank);
 105
 106                 return name;
 107         }
 108
 109         /**
 110          * Creates an empty <code>TaxonNameBase</code> instance with the nomenclatural code
 111          * currently set in preferences.
 112          *
 113          * @return a {@link eu.etaxonomy.cdm.model.name.TaxonNameBase} object.
 114          */
 115         public static NonViralName createEmptyName(){
 116                 return nonViralNameParser.getNonViralNameInstance("", PreferencesUtil.getPreferredNomenclaturalCode());
 117         }
 118
 119         /**
 120          * Parses the string that was entered into the text widget and returns a
 121          * NonViralName object that resulted from the parsing process.
 122          *
 123          * @return      The parsed NonViralName object
 124          */
 125         public NonViralName parse(String unparsedNameString){
 126
 127 //              String unparsedNameString = "";
 128 //              try {
 129 //                      Method getText;
 130 //                      getText = textWidget.getClass().getDeclaredMethod("getText", null);
 131 //                      unparsedNameString = (String) getText.invoke(textWidget, null);
 132 //              } catch (Exception e) {
 133 //                      // we should never get here
 134 //                      StoreUtil.error(this.getClass(), "Error trying to invoke getText method", e);
 135 //              }
 136
 137
 138                 nonViralNameParser.parseReferencedName(name, unparsedNameString,
 139                                 name.getRank(), true);
 140
 141 //              if (name.hasProblem()) {
 142 //                      name.setFullTitleCache(unparsedNameString);
 143 //              }
 144
 145                 return name;
 146         }
 147
 148         /**
 149          * Parses the string that was entered into the text widget and returns a
 150          * NonViralName object that resulted from the parsing process.
 151          *
 152          * The atomized fields (scientific name, author and reference) will be matched
 153          * against the database to find possible duplicates. If duplicates were found
 154          * the respective parts of the NonViralName will be replaced with the found
 155          * objects.
 156          *
 157          * @return      The parsed NonViralName object
 158          */
 159         public NonViralName parseAndResolveDuplicates(String unparsedNameString){
 160
 161                 NonViralName parsedName = parse(unparsedNameString);
 162
 163                 MatchMatrix matchMatrix = findMatches(parsedName);
 164
 165                 resolveDuplicates(parsedName, matchMatrix);
 166
 167                 return parsedName;
 168         }
 169
 170
 171
 172
 173         /**
 174          * @param name The name to resolve duplicates for.
 175          */
 176         private void resolveDuplicates(NonViralName name, MatchMatrix matchMatrix) {
 177                 resolveDuplicateNames(name, matchMatrix);
 178
 179                 resolveAllDuplicateAuthors(name, matchMatrix);
 180
 181                 resolveDuplicateReferences(name, matchMatrix);
 182
 183                 if(matchMatrix.duplicateInReferences != null) {
 184             resolveDuplicateInReferences(name, matchMatrix);
 185         }
 186         }
 187
 188
 189         /**
 190          * @param name The name to resolve duplicates for.
 191          */
 192         private void resolveDuplicateNames(NonViralName name, MatchMatrix matchMatrix) {
 193
 194                 if (matchMatrix.duplicateNames.size() == 1){
 195                         name = (NonViralName) matchMatrix.duplicateNames.iterator().next();
 196                 }else if(matchMatrix.duplicateNames.size() > 1){
 197                         // FIXME TODO resolve multiple duplications. Use first match for a start
 198                         name = (NonViralName) matchMatrix.duplicateNames.iterator().next();
 199                 }
 200         }
 201
 202         /**
 203          * @param name The name to resolve duplicates for.
 204          */
 205         private void resolveDuplicateReferences(NonViralName name, MatchMatrix matchMatrix) {
 206                 if(matchMatrix.duplicateReferences.size() == 1){
 207                         // exactly one match. We assume that the user wants this reference
 208                         INomenclaturalReference duplicate = matchMatrix.duplicateReferences.iterator().next();
 209                         name.setNomenclaturalReference(duplicate);
 210                 }else if(matchMatrix.duplicateReferences.size() > 1){
 211                         // FIXME TODO resolve multiple duplications. Use first match for a start
 212                         INomenclaturalReference duplicate = matchMatrix.duplicateReferences.iterator().next();
 213                         name.setNomenclaturalReference(duplicate);
 214                 }
 215         }
 216
 217         /**
 218          * @param name The name to resolve duplicates for.
 219          */
 220         private void resolveDuplicateInReferences(NonViralName name, MatchMatrix matchMatrix) {
 221                 Reference reference = (Reference) HibernateProxyHelper.deproxy(name.getNomenclaturalReference());
 222
 223                 if(matchMatrix.duplicateInReferences.size() > 0){
 224                         Reference inReference = (Reference) matchMatrix.duplicateInReferences.iterator().next();
 225                         reference.setInReference(inReference);
 226                         MessagingUtils.warn(this.getClass(), reference.generateTitle());
 227                         // FIXME TODO resolve multiple duplications. We use first match for a start
 228                         MessagingUtils.warn(this.getClass(), reference.getTitleCache());
 229                 }
 230         }
 231
 232
 233         /**
 234          * @param name The name to resolve duplicates for.
 235          */
 236         private void resolveAllDuplicateAuthors(NonViralName name, MatchMatrix matchMatrix) {
 237
 238                 if(matchMatrix.duplicateCombinationAuthorships.size() > 0){
 239                         name.setCombinationAuthorship(matchMatrix.duplicateCombinationAuthorships.iterator().next());
 240                         Reference reference = (Reference) name.getNomenclaturalReference();
 241                         if(reference != null){
 242                                 reference.setAuthorship(matchMatrix.duplicateCombinationAuthorships.iterator().next());
 243                         }
 244                         // FIXME TODO resolve multiple duplications. We use first match for a start.
 245                 }
 246
 247                 if(matchMatrix.duplicateExCombinationAuthorships.size() > 0){
 248                         name.setExCombinationAuthorship(matchMatrix.duplicateExCombinationAuthorships.iterator().next());
 249                         // FIXME TODO resolve multiple duplications. We use first match for a start.
 250                 }
 251
 252                 if(matchMatrix.duplicateBasionymAuthorships.size() > 0){
 253                         name.setBasionymAuthorship(matchMatrix.duplicateBasionymAuthorships.iterator().next());
 254                         // FIXME TODO resolve multiple duplications. We use first match for a start.
 255                 }
 256
 257                 if(matchMatrix.duplicateExBasionymAuthorships.size() > 0){
 258                         name.setExBasionymAuthorship(matchMatrix.duplicateExBasionymAuthorships.iterator().next());
 259                         // FIXME TODO resolve multiple duplications. We use first match for a start.
 260                 }
 261         }
 262
 263         /**
 264          * Splits a NonViralName into its parts and calls methods to find matches for these
 265          * parts in the database.
 266          *
 267          * @param name  The NonViralName to find matches for.
 268          */
 269         private MatchMatrix findMatches(NonViralName name){
 270
 271                 MatchMatrix matchMatrix = new MatchMatrix();
 272
 273                 matchMatrix.duplicateNames = findMatchingLatinNames(name);
 274
 275                 matchMatrix.duplicateCombinationAuthorships = findMatchingAuthors(name.getCombinationAuthorship());
 276                 matchMatrix.duplicateExCombinationAuthorships = findMatchingAuthors(name.getExCombinationAuthorship());
 277                 matchMatrix.duplicateBasionymAuthorships = findMatchingAuthors(name.getBasionymAuthorship());
 278                 matchMatrix.duplicateExBasionymAuthorships = findMatchingAuthors(name.getExBasionymAuthorship());
 279
 280                 INomenclaturalReference nomenclaturalReference = name.getNomenclaturalReference();
 281
 282                 // check if the reference has an inreference and also check if the inReference already exists
 283                 if(nomenclaturalReference != null){
 284                         Reference inReference = ((Reference)nomenclaturalReference).getInReference();
 285                         if(inReference != null){
 286                                 doResolveInReferences = true;
 287                                 matchMatrix.duplicateInReferences = findMatchingNomenclaturalReference(inReference);
 288                         }
 289                 }
 290
 291                 matchMatrix.duplicateReferences = findMatchingNomenclaturalReference(nomenclaturalReference);
 292
 293                 return matchMatrix;
 294         }
 295
 296         /**
 297          * @param nomenclaturalReference        The NomenclaturalReference to find matches for.
 298          * @return      A <code>List</code> of possibly matching NomenclaturalReference's.
 299          */
 300         private List<INomenclaturalReference> findMatchingNomenclaturalReference(INomenclaturalReference nomenclaturalReference) {
 301                 if(nomenclaturalReference == null) {
 302             return new ArrayList<INomenclaturalReference>();
 303         }
 304                 try{
 305
 306                         return CdmStore.getCommonService().findMatching(nomenclaturalReference, MatchStrategy.Reference);
 307
 308                 }catch (MatchException e) {
 309                         MessagingUtils.error(this.getClass(), "Error finding matching references", e);
 310                 }
 311                 return null;
 312         }
 313
 314         /**
 315          * @param authorTeam    The TeamOrPersonBase to find matches for.
 316          * @return      A <code>List</code> of possibly matching TeamOrPersonBase's.
 317          */
 318         private List<TeamOrPersonBase> findMatchingAuthors(TeamOrPersonBase authorTeam) {
 319
 320                 if(authorTeam == null){
 321                         return new ArrayList<TeamOrPersonBase>();
 322                 }
 323
 324                 try{
 325
 326                         return CdmStore.getCommonService().findMatching(authorTeam, MatchStrategy.TeamOrPerson);
 327
 328                 }catch (MatchException e) {
 329                         MessagingUtils.error(this.getClass(), "Error finding matching authors", e);
 330                 }
 331                 return null;
 332         }
 333
 334         /**
 335          * @param taxonNameBase The TaxonNameBase to find matches for.
 336          * @return      A <code>List</code> of possibly matching TaxonNameBase's.
 337          */
 338         private List<TaxonNameBase> findMatchingLatinNames(TaxonNameBase taxonNameBase) {
 339
 340                 try {
 341
 342                         return CdmStore.getCommonService().findMatching(taxonNameBase, MatchStrategy.NonViralName);
 343
 344
 345                 } catch (MatchException e) {
 346                         MessagingUtils.error(this.getClass(), "Error finding matching names", e);
 347                 }
 348                 return null;
 349         }
 350 }