cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaRelShipImport.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
  10 package eu.etaxonomy.cdm.io.faunaEuropaea;
  11
  12 import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.A_AUCT;
  13 import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.P_PARENTHESIS;
  14 import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.Q_NO_RESTRICTION;
  15 import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.R_GENUS;
  16 import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.R_SUBGENUS;
  17 import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.R_SPECIES;
  18 import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.R_SUBSPECIES;
  19 import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.T_STATUS_ACCEPTED;
  20 import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.T_STATUS_NOT_ACCEPTED;
  21
  22 import java.sql.ResultSet;
  23 import java.sql.SQLException;
  24 import java.util.Collection;
  25 import java.util.HashMap;
  26 import java.util.List;
  27 import java.util.Map;
  28 import java.util.Set;
  29 import java.util.UUID;
  30
  31 import org.apache.log4j.Logger;
  32 import org.springframework.stereotype.Component;
  33 import org.springframework.transaction.TransactionStatus;
  34
  35 import eu.etaxonomy.cdm.common.CdmUtils;
  36 import eu.etaxonomy.cdm.io.berlinModel.CdmOneToManyMapper;
  37 import eu.etaxonomy.cdm.io.berlinModel.CdmStringMapper;
  38 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;
  39 import eu.etaxonomy.cdm.io.common.CdmAttributeMapperBase;
  40 import eu.etaxonomy.cdm.io.common.CdmSingleAttributeMapperBase;
  41 import eu.etaxonomy.cdm.io.common.ICdmIO;
  42 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  43 import eu.etaxonomy.cdm.io.common.ImportHelper;
  44 import eu.etaxonomy.cdm.io.common.MapWrapper;
  45 import eu.etaxonomy.cdm.io.common.Source;
  46 import eu.etaxonomy.cdm.io.tcsxml.in.TcsXmlImportState;
  47 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  48 import eu.etaxonomy.cdm.model.common.CdmBase;
  49 import eu.etaxonomy.cdm.model.common.ISourceable;
  50 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  51 import eu.etaxonomy.cdm.model.common.OriginalSource;
  52 import eu.etaxonomy.cdm.model.name.Rank;
  53 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  54 import eu.etaxonomy.cdm.model.name.ZoologicalName;
  55 import eu.etaxonomy.cdm.model.reference.Database;
  56 import eu.etaxonomy.cdm.model.reference.Generic;
  57 import eu.etaxonomy.cdm.model.reference.PublicationBase;
  58 import eu.etaxonomy.cdm.model.reference.Publisher;
  59 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  60 import eu.etaxonomy.cdm.model.taxon.Synonym;
  61 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  62 import eu.etaxonomy.cdm.model.taxon.Taxon;
  63 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  64 import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
  65 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  66
  67
  68 /**
  69  * @author a.babadshanjan
  70  * @created 12.05.2009
  71  * @version 1.0
  72  */
  73 @Component
  74 public class FaunaEuropaeaRelShipImport extends FaunaEuropaeaImportBase  {
  75
  76         public static final String OS_NAMESPACE_TAXON = "Taxon";
  77         private static final Logger logger = Logger.getLogger(FaunaEuropaeaRelShipImport.class);
  78
  79         /* (non-Javadoc)
  80          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  81          */
  82         @Override
  83         protected boolean doCheck(FaunaEuropaeaImportState state) {
  84                 boolean result = true;
  85                 FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
  86                 logger.warn("Checking for Taxa not yet fully implemented");
  87                 result &= checkTaxonStatus(fauEuConfig);
  88
  89                 return result;
  90         }
  91
  92         /* (non-Javadoc)
  93          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  94          */
  95         protected boolean isIgnore(FaunaEuropaeaImportState state) {
  96                 return ! state.getConfig().isDoTaxa();
  97         }
  98
  99         private boolean checkTaxonStatus(FaunaEuropaeaImportConfigurator fauEuConfig) {
 100                 boolean result = true;
 101 //              try {
 102                         Source source = fauEuConfig.getSource();
 103                         String sqlStr = "";
 104                         ResultSet rs = source.getResultSet(sqlStr);
 105                         return result;
 106 //              } catch (SQLException e) {
 107 //                      e.printStackTrace();
 108 //                      return false;
 109 //              }
 110         }
 111
 112
 113         /*
 114          * Import with complete taxon store
 115          */
 116         protected boolean doInvoke(FaunaEuropaeaImportState state) {
 117
 118                 Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();
 119                 MapWrapper<TeamOrPersonBase> authorStore = (MapWrapper<TeamOrPersonBase>)stores.get(ICdmIO.TEAM_STORE);
 120                 authorStore.makeEmpty();
 121                 Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap = state.getFauEuTaxonMap();
 122                 TransactionStatus txStatus = null;
 123                 boolean success = true;
 124
 125                 if(logger.isInfoEnabled()) { logger.info("Start making taxa..."); }
 126
 127                 if (state.getConfig().isUseTransactions()) {
 128                         txStatus = startTransaction();
 129                 }
 130
 131                 success = processTaxa(state, fauEuTaxonMap);
 132                 success = saveTaxa(state, state.getHighestTaxonIndex(), state.getConfig().getLimitSave());
 133
 134                 if (state.getConfig().isUseTransactions()) {
 135                         commitTransaction(txStatus);
 136                 }
 137
 138                 logger.info("End making taxa...");
 139                 return success;
 140         }
 141
 142
 143         /*
 144          * Processes taxa from complete taxon store
 145          */
 146         private boolean processTaxa(FaunaEuropaeaImportState state,
 147                         Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap) {
 148
 149                 if(logger.isInfoEnabled()) { logger.info("Processing taxa second pass..."); }
 150
 151                 Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();
 152                 MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);
 153                 FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
 154                 ReferenceBase<?> sourceRef = fauEuConfig.getSourceReference();
 155
 156                 boolean success = true;
 157
 158                 for (int id : fauEuTaxonMap.keySet())
 159                 //for (int id : taxonStore.keySet())
 160                 {
 161                         TaxonBase<?> taxonBase = taxonStore.get(id);
 162                         TaxonNameBase<?,?> taxonName = taxonBase.getName();
 163                         FaunaEuropaeaTaxon fauEuTaxon = fauEuTaxonMap.get(id);
 164
 165                         if (logger.isDebugEnabled()) { logger.debug("Taxon # " + id); }
 166                         createRelationships(fauEuTaxon, taxonBase, taxonName, fauEuTaxonMap, state);
 167                 }
 168                 return success;
 169         }
 170
 171
 172         /** Creates relationships for existing taxon store in memory */
 173         private boolean createRelationships(FaunaEuropaeaTaxon fauEuTaxon,
 174                         TaxonBase<?> taxonBase, TaxonNameBase<?,?> taxonName,
 175                         Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap, FaunaEuropaeaImportState state) {
 176
 177                 int parentId = fauEuTaxon.getParentId();
 178                 int taxonId = fauEuTaxon.getId();
 179                 Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();
 180                 MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);
 181                 ReferenceBase<?> sourceRef = state.getConfig().getSourceReference();
 182                 TaxonBase<?> parentTaxonBase = taxonStore.get(parentId);
 183                 Taxon parentTaxon = parentTaxonBase.deproxy(parentTaxonBase, Taxon.class);
 184 //              FaunaEuropaeaTaxon parent = fauEuTaxonMap.get(parentId);
 185                 boolean success = true;
 186
 187                 if (!fauEuTaxon.isValid()) { // FauEu Synonym
 188
 189                         if (fauEuTaxon.getAuthor() != null && fauEuTaxon.getAuthor().equals("A_AUCT_NAME")) {
 190                                 try {
 191                                         // add misapplied name relationship from this taxon to parent
 192                                         Taxon taxon = taxonBase.deproxy(taxonBase, Taxon.class);
 193                                         taxon.addMisappliedName(parentTaxon, sourceRef, null);
 194                                         if (logger.isInfoEnabled()) {
 195                                                 logger.info("Misapplied name created " + taxon.getUuid());
 196                                         }
 197
 198                                 } catch (Exception e) {
 199                                         logger.error("Error creating misapplied name relationship for taxon (" +
 200                                                         parentId + ")");
 201                                 }
 202                         }
 203
 204                         else if((fauEuTaxon.getAuthor() == null)
 205                                         || (fauEuTaxon.getAuthor() != null && !fauEuTaxon.getAuthor().equals("A_AUCT_NAME"))) {
 206                                 try {
 207                                         // add this synonym as heterotypic synonym to parent
 208                                         Synonym synonym = taxonBase.deproxy(taxonBase, Synonym.class);
 209                                         parentTaxon.addSynonym(synonym, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
 210                                         if (logger.isDebugEnabled()) {
 211                                                 logger.debug("Heterotypic synonym created " + synonym.getUuid());
 212                                         }
 213
 214                                 } catch (Exception e) {
 215                                         logger.error("Error creating heterotypic synonym for taxon (" + parentId + ")");
 216 //                                      e.printStackTrace();
 217                                 }
 218                         }
 219
 220                 } else if (fauEuTaxon.isValid()) { // FauEu Taxon
 221
 222                         Taxon taxon = taxonBase.deproxy(taxonBase, Taxon.class);
 223
 224                         try {
 225                                 // add this taxon as child to parent
 226                                 if (parentTaxon != null) {
 227                                         makeTaxonomicallyIncluded(state, parentTaxon, taxon, sourceRef, null);
 228                                         if (logger.isDebugEnabled()) {
 229                                                 logger.debug("Parent-child (" + parentId + "-" + taxonId +
 230                                                 ") relationship created");
 231                                         }
 232                                 }
 233
 234                         } catch (Exception e) {
 235                                 logger.error("Error creating taxonomically included relationship Parent-child (" +
 236                                                 parentId + "-" + taxonId + ")");
 237                         }
 238                 }
 239
 240                 return success;
 241         }
 242
 243
 244         private boolean makeTaxonomicallyIncluded(FaunaEuropaeaImportState state, Taxon toTaxon, Taxon fromTaxon, ReferenceBase citation, String microCitation){
 245                 boolean success = true;
 246                 ReferenceBase sec = toTaxon.getSec();
 247                 TaxonomicTree tree = state.getTree(sec);
 248                 if (tree == null){
 249                         tree = makeTree(state, sec);
 250                 }
 251                 success = tree.addParentChild(toTaxon, fromTaxon, citation, microCitation);
 252                 return success;
 253         }
 254
 255 }