app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.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.redlist.gefaesspflanzen;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.HashMap;
  15 import java.util.HashSet;
  16 import java.util.Map;
  17 import java.util.Set;
  18
  19 import org.apache.log4j.Logger;
  20 import org.springframework.stereotype.Component;
  21
  22 import eu.etaxonomy.cdm.common.CdmUtils;
  23 import eu.etaxonomy.cdm.io.common.DbImportBase;
  24 import eu.etaxonomy.cdm.io.common.IPartitionedIO;
  25 import eu.etaxonomy.cdm.io.common.ImportHelper;
  26 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  27 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  28 import eu.etaxonomy.cdm.model.agent.AgentBase;
  29 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  30 import eu.etaxonomy.cdm.model.common.CdmBase;
  31 import eu.etaxonomy.cdm.model.name.BotanicalName;
  32 import eu.etaxonomy.cdm.model.name.Rank;
  33 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  34 import eu.etaxonomy.cdm.model.taxon.Synonym;
  35 import eu.etaxonomy.cdm.model.taxon.Taxon;
  36 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  37
  38 /**
  39  *
  40  * @author pplitzner
  41  * @date Mar 1, 2016
  42  *
  43  */
  44
  45 @Component
  46 @SuppressWarnings("serial")
  47 public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
  48
  49     private static final String EX = " ex ";
  50
  51     private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportNames.class);
  52
  53     private static final String tableName = "Rote Liste Gefäßpflanzen";
  54
  55     private static final String pluralString = "names";
  56
  57     public RedListGefaesspflanzenImportNames() {
  58         super(tableName, pluralString);
  59     }
  60
  61     @Override
  62     protected String getIdQuery(RedListGefaesspflanzenImportState state) {
  63         return "SELECT NAMNR "
  64                 + "FROM V_TAXATLAS_D20_EXPORT t "
  65                 + " ORDER BY NAMNR";
  66     }
  67
  68     @Override
  69     protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {
  70         String result = " SELECT * "
  71                 + " FROM V_TAXATLAS_D20_EXPORT t "
  72                 + " WHERE t.NAMNR IN (@IDSET)";
  73         result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
  74         return result;
  75     }
  76
  77     @Override
  78     protected void doInvoke(RedListGefaesspflanzenImportState state) {
  79         super.doInvoke(state);
  80     }
  81
  82
  83     @Override
  84     public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
  85         ResultSet rs = partitioner.getResultSet();
  86         Set<TaxonNameBase> namesToSave = new HashSet<TaxonNameBase>();
  87         Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
  88         try {
  89             while (rs.next()){
  90                 makeSingleNameAndTaxon(state, rs, namesToSave, taxaToSave);
  91
  92             }
  93         } catch (SQLException e) {
  94             e.printStackTrace();
  95         }
  96
  97         getNameService().saveOrUpdate(namesToSave);
  98         getTaxonService().saveOrUpdate(taxaToSave);
  99         return true;
 100     }
 101
 102     private void makeSingleNameAndTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave, Set<TaxonBase> taxaToSave)
 103             throws SQLException {
 104         long id = rs.getLong("NAMNR");
 105         String taxNameString = rs.getString("TAXNAME");
 106         String gueltString = rs.getString("GUELT");
 107         String rangString = rs.getString("RANG");
 108         String ep1String = rs.getString("EPI1");
 109         String ep2String = rs.getString("EPI2");
 110         String ep3String = rs.getString("EPI3");
 111         String nomZusatzString = rs.getString("NOM_ZUSATZ");
 112         String zusatzString = rs.getString("ZUSATZ");
 113         String authorKombString = rs.getString("AUTOR_KOMB");
 114         String authorBasiString = rs.getString("AUTOR_BASI");
 115
 116         if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){
 117             logger.error("NAMNR: "+id+" No name found!");
 118         }
 119
 120         Rank rank = makeRank(state, rangString);
 121         if(rank==null){
 122             logger.error("NAMNR: "+id+" Rank could not be resolved.");
 123         }
 124         BotanicalName name = BotanicalName.NewInstance(rank);
 125
 126         //ep1 should always be present
 127         if(CdmUtils.isBlank(ep1String)){
 128             logger.error("NAMNR: "+id+" EPI1 is empty!");
 129         }
 130         name.setGenusOrUninomial(ep1String);
 131         if(!CdmUtils.isBlank(ep2String)){
 132             name.setSpecificEpithet(ep2String);
 133         }
 134         if(!CdmUtils.isBlank(ep3String)){
 135             if(rank==Rank.SUBSPECIES() ||
 136                     rank==Rank.VARIETY()){
 137                 name.setInfraSpecificEpithet(ep3String);
 138             }
 139         }
 140
 141         //--- AUTHORS ---
 142         //combination author
 143         if(authorKombString.contains(EX)){
 144             //TODO: what happens with multiple ex authors??
 145             String[] kombSplit = authorKombString.split(EX);
 146             if(kombSplit.length!=2){
 147                 logger.error("NAMNR: "+id+" Multiple ex combination authors found");
 148             }
 149             for (int i = 0; i < kombSplit.length; i++) {
 150                 if(i==0){
 151                     //first author is ex author
 152                     TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(Namespace.AUTHOR_NAMESPACE, kombSplit[i]);
 153                     name.setExCombinationAuthorship(authorKomb);
 154                 }
 155                 else{
 156                     TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(Namespace.AUTHOR_NAMESPACE, kombSplit[i]);
 157                     name.setCombinationAuthorship(authorKomb);
 158                 }
 159             }
 160         }
 161         else if(authorKombString.trim().equals("auct.")){
 162             logger.warn("NAMNR: "+id+" AUCT information in AUTOR_KOMB column");
 163         }
 164         else if(!CdmUtils.isBlank(authorKombString)){
 165             TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(Namespace.AUTHOR_NAMESPACE, authorKombString);
 166             name.setCombinationAuthorship(authorKomb);
 167         }
 168         //basionym author
 169         if(authorBasiString.contains(EX)){
 170             String[] basiSplit = authorBasiString.split(EX);
 171             for (int i = 0; i < basiSplit.length; i++) {
 172                 if(basiSplit.length!=2){
 173                     logger.error("NAMNR: "+id+" Multiple ex basionymn authors found");
 174                 }
 175                 if(i==0){
 176                     TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(Namespace.AUTHOR_NAMESPACE, basiSplit[i]);
 177                     if(CdmUtils.isBlank(authorKombString)){
 178                         name.setExCombinationAuthorship(authorBasi);
 179                     }
 180                     else{
 181                         name.setExBasionymAuthorship(authorBasi);
 182                     }
 183                 }
 184                 else{
 185                     TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(Namespace.AUTHOR_NAMESPACE, basiSplit[i]);
 186                     if(CdmUtils.isBlank(authorKombString)){
 187                         name.setCombinationAuthorship(authorBasi);
 188                     }
 189                     else{
 190                         name.setBasionymAuthorship(authorBasi);
 191                     }
 192                 }
 193             }
 194         }
 195         else if(authorBasiString.trim().equals("auct.")){
 196             name.setAppendedPhrase(authorBasiString);
 197         }
 198         else if(!CdmUtils.isBlank(authorBasiString)){
 199             //this seems to be a convention in the source database: When there is only a single author then only the "AUTOR_BASI" column is used
 200             TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(Namespace.AUTHOR_NAMESPACE, authorBasiString);
 201             if(CdmUtils.isBlank(authorKombString)){
 202                 name.setCombinationAuthorship(authorBasi);
 203             }
 204             else{
 205                 name.setBasionymAuthorship(authorBasi);
 206             }
 207         }
 208
 209         //check authorship consistency
 210         String authorString = rs.getString("AUTOR");
 211         String authorshipCache = name.getAuthorshipCache();
 212
 213         if(!CdmUtils.isBlank(zusatzString)){
 214             authorString = authorString.replace(", "+zusatzString, "");
 215         }
 216 //        if(CdmUtils.isBlank(authorKombString) && !CdmUtils.isBlank(authorBasiString)){
 217 //            authorString = "("+authorString+")";
 218 //        }
 219         if(authorString.equals("auct.")){
 220             authorString = "";
 221         }
 222         if(!authorString.equals(authorshipCache)){
 223             logger.warn("NAMNR: "+id+" Authorship inconsistent! name.authorhshipCache <-> Column AUTOR: "+authorshipCache+" <-> "+authorString);
 224         }
 225
 226         //id
 227         ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, Namespace.NAME_NAMESPACE);
 228         state.getNameMap().put(id, name.getUuid());
 229
 230         namesToSave.add(name);
 231
 232         //---TAXON---
 233         TaxonBase taxonBase = null;
 234         if(gueltString.equals("1")){
 235             taxonBase = Taxon.NewInstance(name, null);
 236         }
 237         else if(gueltString.equals("x") || gueltString.equals("b")){
 238             taxonBase = Synonym.NewInstance(name, null);
 239         }
 240         if(taxonBase==null){
 241             logger.error("NAMNR: "+id+" Taxon for name "+name+" could not be created.");
 242             return;
 243         }
 244
 245         taxaToSave.add(taxonBase);
 246
 247         //id
 248         ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, Namespace.TAXON_NAMESPACE);
 249         state.getTaxonMap().put(id, taxonBase.getUuid());
 250     }
 251
 252     private Rank makeRank(RedListGefaesspflanzenImportState state, String rankStr) {
 253         Rank rank = null;
 254         try {
 255             rank = state.getTransformer().getRankByKey(rankStr);
 256         } catch (UndefinedTransformerMethodException e) {
 257             e.printStackTrace();
 258         }
 259         if(rank==null){
 260             logger.error(rankStr+" could not be associated to a known rank.");
 261         }
 262         return rank;
 263     }
 264
 265
 266
 267     @Override
 268     public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
 269             RedListGefaesspflanzenImportState state) {
 270         Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 271         Map<String, AgentBase<?>> authorMap = new HashMap<String, AgentBase<?>>();
 272
 273         try {
 274             while (rs.next()){
 275                 String authorKombString = rs.getString("AUTOR_KOMB");
 276
 277                 if(authorKombString.contains(EX)){
 278                     String[] kombSplit = authorKombString.split(EX);
 279                     for (int i = 0; i < kombSplit.length; i++) {
 280                         if(!authorMap.containsKey(kombSplit[i])){
 281                             authorMap.put(kombSplit[i], getAgentService().load(state.getAuthorMap().get(kombSplit[i])));
 282                         }
 283                     }
 284                 }
 285                 else if(!CdmUtils.isBlank(authorKombString) && !authorMap.containsKey(authorKombString)){
 286                     authorMap.put(authorKombString, getAgentService().load(state.getAuthorMap().get(authorKombString)));
 287                 }
 288
 289                 String authorBasiString = rs.getString("AUTOR_BASI");
 290                 //basionym author
 291                 if(authorBasiString.contains(EX)){
 292                     String[] basiSplit = authorBasiString.split(EX);
 293                     for (int i = 0; i < basiSplit.length; i++) {
 294                         if(!authorMap.containsKey(basiSplit[i])){
 295                             authorMap.put(basiSplit[i], getAgentService().load(state.getAuthorMap().get(basiSplit[i])));
 296                         }
 297                     }
 298                 }
 299                 else if(!CdmUtils.isBlank(authorBasiString) && !authorMap.containsKey(authorBasiString)){
 300                     authorMap.put(authorBasiString, getAgentService().load(state.getAuthorMap().get(authorBasiString)));
 301                 }
 302             }
 303         } catch (SQLException e) {
 304             e.printStackTrace();
 305         }
 306         result.put(Namespace.AUTHOR_NAMESPACE, authorMap);
 307
 308         return result;
 309     }
 310
 311     @Override
 312     protected boolean doCheck(RedListGefaesspflanzenImportState state) {
 313         return false;
 314     }
 315
 316     @Override
 317     protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
 318         return false;
 319     }
 320
 321 }