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.NomenclaturalStatus;
  33 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  34 import eu.etaxonomy.cdm.model.name.Rank;
  35 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  36 import eu.etaxonomy.cdm.model.taxon.Synonym;
  37 import eu.etaxonomy.cdm.model.taxon.Taxon;
  38 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  39
  40 /**
  41  *
  42  * @author pplitzner
  43  * @date Mar 1, 2016
  44  *
  45  */
  46
  47 @Component
  48 @SuppressWarnings("serial")
  49 public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
  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(RedListUtil.NAMNR);
 105         String taxNameString = rs.getString(RedListUtil.TAXNAME);
 106         String gueltString = rs.getString(RedListUtil.GUELT);
 107         String rangString = rs.getString(RedListUtil.RANG);
 108         String ep1String = rs.getString(RedListUtil.EPI1);
 109         String ep2String = rs.getString(RedListUtil.EPI2);
 110         String ep3String = rs.getString(RedListUtil.EPI3);
 111         String nomZusatzString = rs.getString(RedListUtil.NOM_ZUSATZ);
 112         String zusatzString = rs.getString(RedListUtil.ZUSATZ);
 113         String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
 114         String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
 115
 116         //---NAME---
 117         if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){
 118             RedListUtil.logMessage(id, "No name found!", logger);
 119         }
 120
 121         Rank rank = makeRank(id, state, rangString);
 122         BotanicalName name = BotanicalName.NewInstance(rank);
 123
 124         //ep1 should always be present
 125         if(CdmUtils.isBlank(ep1String)){
 126             RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger);
 127         }
 128         name.setGenusOrUninomial(ep1String);
 129         if(CdmUtils.isNotBlank(ep2String)){
 130             name.setSpecificEpithet(ep2String);
 131         }
 132         if(CdmUtils.isNotBlank(ep3String)){
 133             if(rank==Rank.SUBSPECIES() ||
 134                     rank==Rank.VARIETY()){
 135                 name.setInfraSpecificEpithet(ep3String);
 136             }
 137         }
 138         //nomenclatural status
 139         if(CdmUtils.isNotBlank(nomZusatzString)){
 140             NomenclaturalStatusType status = makeNomenclaturalStatus(id, state, nomZusatzString);
 141             if(status!=null){
 142                 name.addStatus(NomenclaturalStatus.NewInstance(status));
 143             }
 144         }
 145
 146
 147         //--- AUTHORS ---
 148         //combination author
 149         if(authorKombString.contains(RedListUtil.EX)){
 150             //TODO: what happens with multiple ex authors??
 151             String[] kombSplit = authorKombString.split(RedListUtil.EX);
 152             if(kombSplit.length!=2){
 153                 RedListUtil.logMessage(id, "Multiple ex combination authors found", logger);
 154             }
 155             for (int i = 0; i < kombSplit.length; i++) {
 156                 if(i==0){
 157                     //first author is ex author
 158                     TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);
 159                     name.setExCombinationAuthorship(authorKomb);
 160                 }
 161                 else{
 162                     TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);
 163                     name.setCombinationAuthorship(authorKomb);
 164                 }
 165             }
 166         }
 167         else if(authorKombString.trim().equals(RedListUtil.AUCT)){
 168             RedListUtil.logMessage(id, "AUCT information in "+RedListUtil.AUTOR_KOMB+" column", logger);
 169         }
 170         else if(CdmUtils.isNotBlank(authorKombString)){
 171             TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorKombString);
 172             name.setCombinationAuthorship(authorKomb);
 173         }
 174         //basionym author
 175         if(authorBasiString.contains(RedListUtil.EX)){
 176             String[] basiSplit = authorBasiString.split(RedListUtil.EX);
 177             for (int i = 0; i < basiSplit.length; i++) {
 178                 if(basiSplit.length!=2){
 179                     RedListUtil.logMessage(id, "Multiple ex basionymn authors found", logger);
 180                 }
 181                 if(i==0){
 182                     TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);
 183                     if(CdmUtils.isBlank(authorKombString)){
 184                         name.setExCombinationAuthorship(authorBasi);
 185                     }
 186                     else{
 187                         name.setExBasionymAuthorship(authorBasi);
 188                     }
 189                 }
 190                 else{
 191                     TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);
 192                     if(CdmUtils.isBlank(authorKombString)){
 193                         name.setCombinationAuthorship(authorBasi);
 194                     }
 195                     else{
 196                         name.setBasionymAuthorship(authorBasi);
 197                     }
 198                 }
 199             }
 200         }
 201         else if(CdmUtils.isNotBlank(authorBasiString)){
 202             //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
 203             TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorBasiString);
 204             if(CdmUtils.isBlank(authorKombString)){
 205                 name.setCombinationAuthorship(authorBasi);
 206             }
 207             else{
 208                 name.setBasionymAuthorship(authorBasi);
 209             }
 210         }
 211
 212         //check authorship consistency
 213         String authorString = rs.getString(RedListUtil.AUTOR);
 214         String authorshipCache = name.getAuthorshipCache();
 215
 216         if(CdmUtils.isNotBlank(zusatzString)){
 217             authorString = authorString.replace(", "+zusatzString, "");
 218         }
 219         if(authorString.equals(RedListUtil.AUCT)){
 220             authorString = "";
 221         }
 222         if(!authorString.equals(authorshipCache)){
 223             RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
 224         }
 225
 226         //id
 227         ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, RedListUtil.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(RedListUtil.GUELT_ACCEPTED_TAXON) || (name.getAppendedPhrase()!=null && authorBasiString.trim().equals(RedListUtil.AUCT))){
 235             taxonBase = Taxon.NewInstance(name, null);
 236             taxonBase.setAppendedPhrase(authorBasiString);
 237         }
 238         else if(gueltString.equals(RedListUtil.GUELT_SYNONYM) || gueltString.equals(RedListUtil.GUELT_BASIONYM)){
 239             taxonBase = Synonym.NewInstance(name, null);
 240         }
 241         if(taxonBase==null){
 242             RedListUtil.logMessage(id, "Taxon for name "+name+" could not be created.", logger);
 243             return;
 244         }
 245
 246         taxaToSave.add(taxonBase);
 247
 248         //id
 249         ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_NAMESPACE);
 250         state.getTaxonMap().put(id, taxonBase.getUuid());
 251     }
 252
 253     private Rank makeRank(long id, RedListGefaesspflanzenImportState state, String rankStr) {
 254         Rank rank = null;
 255         try {
 256             rank = state.getTransformer().getRankByKey(rankStr);
 257         } catch (UndefinedTransformerMethodException e) {
 258             e.printStackTrace();
 259         }
 260         if(rank==null){
 261             RedListUtil.logMessage(id, rankStr+" could not be associated to a known rank.", logger);
 262         }
 263         return rank;
 264     }
 265
 266     private NomenclaturalStatusType makeNomenclaturalStatus(long id, RedListGefaesspflanzenImportState state, String nomZusatzString) {
 267         NomenclaturalStatusType status = null;
 268         try {
 269             status = state.getTransformer().getNomenclaturalStatusByKey(nomZusatzString);
 270         } catch (UndefinedTransformerMethodException e) {
 271             e.printStackTrace();
 272         }
 273         if(status==null){
 274             RedListUtil.logMessage(id, nomZusatzString+" could not be associated to a known nomenclatural status.", logger);
 275         }
 276         return status;
 277     }
 278
 279
 280
 281     @Override
 282     public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
 283             RedListGefaesspflanzenImportState state) {
 284         Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 285         Map<String, AgentBase<?>> authorMap = new HashMap<String, AgentBase<?>>();
 286
 287         try {
 288             while (rs.next()){
 289                 String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
 290
 291                 if(authorKombString.contains(RedListUtil.EX)){
 292                     String[] kombSplit = authorKombString.split(RedListUtil.EX);
 293                     for (int i = 0; i < kombSplit.length; i++) {
 294                         if(!authorMap.containsKey(kombSplit[i])){
 295                             authorMap.put(kombSplit[i], getAgentService().load(state.getAuthorMap().get(kombSplit[i])));
 296                         }
 297                     }
 298                 }
 299                 else if(CdmUtils.isNotBlank(authorKombString) && !authorMap.containsKey(authorKombString)){
 300                     authorMap.put(authorKombString, getAgentService().load(state.getAuthorMap().get(authorKombString)));
 301                 }
 302
 303                 String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
 304                 //basionym author
 305                 if(authorBasiString.contains(RedListUtil.EX)){
 306                     String[] basiSplit = authorBasiString.split(RedListUtil.EX);
 307                     for (int i = 0; i < basiSplit.length; i++) {
 308                         if(!authorMap.containsKey(basiSplit[i])){
 309                             authorMap.put(basiSplit[i], getAgentService().load(state.getAuthorMap().get(basiSplit[i])));
 310                         }
 311                     }
 312                 }
 313                 else if(CdmUtils.isNotBlank(authorBasiString) && !authorMap.containsKey(authorBasiString)){
 314                     authorMap.put(authorBasiString, getAgentService().load(state.getAuthorMap().get(authorBasiString)));
 315                 }
 316             }
 317         } catch (SQLException e) {
 318             e.printStackTrace();
 319         }
 320         result.put(RedListUtil.AUTHOR_NAMESPACE, authorMap);
 321
 322         return result;
 323     }
 324
 325     @Override
 326     protected boolean doCheck(RedListGefaesspflanzenImportState state) {
 327         return false;
 328     }
 329
 330     @Override
 331     protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
 332         return false;
 333     }
 334
 335 }