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.hibernate.HibernateProxyHelper;
  24 import eu.etaxonomy.cdm.io.common.DbImportBase;
  25 import eu.etaxonomy.cdm.io.common.IPartitionedIO;
  26 import eu.etaxonomy.cdm.io.common.ImportHelper;
  27 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  28 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  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
  35 /**
  36  *
  37  * @author pplitzner
  38  * @date Mar 1, 2016
  39  *
  40  */
  41
  42 @Component
  43 @SuppressWarnings("serial")
  44 public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
  45     /**
  46      *
  47      */
  48     private static final String EX = " ex ";
  49
  50     private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportNames.class);
  51
  52     private static final String tableName = "Rote Liste Gefäßpflanzen";
  53
  54     private static final String pluralString = "names";
  55
  56     private static final String NAME_NAMESPACE = "name";
  57
  58     public RedListGefaesspflanzenImportNames() {
  59         super(tableName, pluralString);
  60     }
  61
  62     @Override
  63     protected String getIdQuery(RedListGefaesspflanzenImportState state) {
  64         return "SELECT NAMNR "
  65                 + "FROM V_TAXATLAS_D20_EXPORT t "
  66                 + " ORDER BY NAMNR";
  67     }
  68
  69     @Override
  70     protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {
  71         String result = " SELECT * "
  72                 + " FROM V_TAXATLAS_D20_EXPORT t "
  73                 + " WHERE t.NAMNR IN (@IDSET)";
  74         result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
  75         return result;
  76     }
  77
  78     @Override
  79     protected void doInvoke(RedListGefaesspflanzenImportState state) {
  80         super.doInvoke(state);
  81     }
  82
  83
  84     @Override
  85     public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
  86         ResultSet rs = partitioner.getResultSet();
  87         Set<TaxonNameBase> namesToSave = new HashSet<TaxonNameBase>();
  88         try {
  89             while (rs.next()){
  90                 makeSingleName(state, rs, namesToSave);
  91
  92             }
  93         } catch (SQLException e) {
  94             e.printStackTrace();
  95         }
  96
  97         getNameService().saveOrUpdate(namesToSave);
  98         return true;
  99     }
 100
 101     private void makeSingleName(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave)
 102             throws SQLException {
 103         long id = rs.getLong("NAMNR");
 104         String taxNameString = rs.getString("TAXNAME");
 105         String rangString = rs.getString("RANG");
 106         String ep1String = rs.getString("EPI1");
 107         String ep2String = rs.getString("EPI2");
 108         String ep3String = rs.getString("EPI3");
 109         String nomZusatzString = rs.getString("NOM_ZUSATZ");
 110         String zusatzString = rs.getString("ZUSATZ");
 111         String authorKombString = rs.getString("AUTOR_KOMB");
 112         String authorBasiString = rs.getString("AUTOR_BASI");
 113
 114         if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){
 115             logger.error("NAMNR: "+id+" No name found!");
 116         }
 117
 118         Rank rank = makeRank(state, rangString);
 119         if(rank==null){
 120             logger.error("NAMNR: "+id+" Rank could not be resolved.");
 121             return;
 122         }
 123         BotanicalName name = BotanicalName.NewInstance(rank);
 124
 125         //ep1 should always be present
 126         if(CdmUtils.isBlank(ep1String)){
 127             logger.error("NAMNR: "+id+" EPI1 is empty!");
 128         }
 129         name.setGenusOrUninomial(ep1String);
 130 //        if(CdmUtils.isBlank(ep2String)){
 131 //            name.setSpecificEpithet(ep2String);
 132 //        }
 133 //        if(CdmUtils.isBlank(ep3String)){
 134 //        }
 135         if(rank.isSpecies()){
 136             if(!CdmUtils.isBlank(ep2String)){
 137                 name.setSpecificEpithet(ep2String);
 138             }
 139         }
 140         else if(rank.isLower(Rank.SPECIES())){
 141             if(!CdmUtils.isBlank(ep3String)){
 142                 name.setSpecificEpithet(ep3String);
 143             }
 144         }
 145
 146         //--- AUTHORS ---
 147         //combination author
 148         if(authorKombString.contains(EX)){
 149             //TODO: what happens with multiple ex authors??
 150             String[] kombSplit = authorKombString.split(EX);
 151             for (int i = 0; i < kombSplit.length; i++) {
 152                 if(i==0){
 153                     //first author is ex author
 154                     TeamOrPersonBase authorKomb = HibernateProxyHelper.deproxy(getAgentService().load(state.getAuthorMap().get(kombSplit[i])), TeamOrPersonBase.class);
 155                     name.setExCombinationAuthorship(authorKomb);
 156                 }
 157                 else{
 158                     TeamOrPersonBase authorKomb = HibernateProxyHelper.deproxy(getAgentService().load(state.getAuthorMap().get(kombSplit[i])), TeamOrPersonBase.class);
 159                     name.setCombinationAuthorship(authorKomb);
 160                 }
 161             }
 162         }
 163         else if(!CdmUtils.isBlank(authorKombString)){
 164             TeamOrPersonBase authorKomb = HibernateProxyHelper.deproxy(getAgentService().load(state.getAuthorMap().get(authorKombString)), TeamOrPersonBase.class);
 165             name.setCombinationAuthorship(authorKomb);
 166         }
 167         //basionym author
 168         if(authorBasiString.contains(EX)){
 169             String[] basiSplit = authorBasiString.split(EX);
 170             for (int i = 0; i < basiSplit.length; i++) {
 171                 if(i==0){
 172                     TeamOrPersonBase authorBasi = HibernateProxyHelper.deproxy(getAgentService().load(state.getAuthorMap().get(basiSplit[i])), TeamOrPersonBase.class);
 173                     name.setExBasionymAuthorship(authorBasi);
 174                 }
 175                 else{
 176                     TeamOrPersonBase authorBasi = HibernateProxyHelper.deproxy(getAgentService().load(state.getAuthorMap().get(basiSplit[i])), TeamOrPersonBase.class);
 177                     name.setBasionymAuthorship(authorBasi);
 178                 }
 179             }
 180         }
 181         else if(!CdmUtils.isBlank(authorBasiString)){
 182             TeamOrPersonBase authorBasi = HibernateProxyHelper.deproxy(getAgentService().load(state.getAuthorMap().get(authorBasiString)), TeamOrPersonBase.class);
 183             name.setBasionymAuthorship(authorBasi);
 184         }
 185
 186         //check authorship consistency
 187         String authorString = rs.getString("AUTOR");
 188         String authorshipCache = name.getAuthorshipCache();
 189
 190         if(!CdmUtils.isBlank(zusatzString)){
 191             authorString = authorString.replace(", "+zusatzString, "");
 192         }
 193         if(CdmUtils.isBlank(authorKombString) && !CdmUtils.isBlank(authorBasiString)){
 194             authorString = "("+authorString+")";
 195         }
 196         if(!authorString.equals(authorshipCache)){
 197             logger.warn("NAMNR: "+id+" Authorship inconsistent! name.authorhshipCache <-> Column AUTOR: "+authorshipCache+" <-> "+authorString);
 198         }
 199
 200         //id
 201         ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, NAME_NAMESPACE);
 202
 203         namesToSave.add(name);
 204     }
 205
 206     private Rank makeRank(RedListGefaesspflanzenImportState state, String rankStr) {
 207         Rank rank = null;
 208         try {
 209             rank = state.getTransformer().getRankByKey(rankStr);
 210         } catch (UndefinedTransformerMethodException e) {
 211             e.printStackTrace();
 212         }
 213         if(rank==null){
 214             logger.error(rankStr+" could not be associated to a known rank.");
 215         }
 216         return rank;
 217     }
 218
 219
 220
 221     @Override
 222     public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
 223             RedListGefaesspflanzenImportState state) {
 224         Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 225 //        Map<Long, AgentBase<?>> authorKombMap = new HashMap<>();
 226 //        Map<Long, AgentBase<?>> authorBasiMap = new HashMap<>();
 227 //
 228 //        //load authors
 229 //        for(Entry<Long, UUID> entry:state.getAuthorKombMap().entrySet()){
 230 //            authorKombMap.put(entry.getKey(), getAgentService().load(entry.getValue()));
 231 //        }
 232 //        for(Entry<Long, UUID> entry:state.getAuthorBasiMap().entrySet()){
 233 //            authorBasiMap.put(entry.getKey(), getAgentService().load(entry.getValue()));
 234 //        }
 235 //        try {
 236 //            while (rs.next()){
 237 //                long id = rs.getLong("NAMNR");
 238 //            }
 239 //        } catch (SQLException e) {
 240 //            e.printStackTrace();
 241 //        }
 242 //
 243 //        //Authors
 244 //        Set<UUID> uuidSet = new HashSet<>();
 245 //        for (String authorStr : authorKombSet){
 246 //            UUID uuid = state.getAuthorUuid(authorStr);
 247 //            uuidSet.add(uuid);
 248 //        }
 249 //        List<TeamOrPersonBase<?>> authors = (List)getAgentService().find(uuidSet);
 250 //        Map<UUID, TeamOrPersonBase<?>> authorUuidMap = new HashMap<>();
 251 //        for (TeamOrPersonBase<?> author : authors){
 252 //            authorUuidMap.put(author.getUuid(), author);
 253 //        }
 254 //
 255 //        for (String authorStr : authorKombSet){
 256 //            UUID uuid = state.getAuthorUuid(authorStr);
 257 //            TeamOrPersonBase<?> author = authorUuidMap.get(uuid);
 258 //            authorMap.put(authorStr, author);
 259 //        }
 260 //        result.put(AUTHOR_NAMESPACE, authorMap);
 261 //
 262 //        //reference map
 263 //        String nameSpace = REFERENCE_NAMESPACE;
 264 //        Class<?> cdmClass = Reference.class;
 265 //        Set<String> idSet = referenceIdSet;
 266 //        Map<String, Reference<?>> referenceMap = (Map<String, Reference<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 267 //        result.put(nameSpace, referenceMap);
 268 //
 269 //        //secundum
 270 //        UUID secUuid = state.getConfig().getSecUuid();
 271 //        Reference<?> secRef = getReferenceService().find(secUuid);
 272 //        referenceMap.put(secUuid.toString(), secRef);
 273
 274         return result;
 275     }
 276
 277     @Override
 278     protected boolean doCheck(RedListGefaesspflanzenImportState state) {
 279         return false;
 280     }
 281
 282     @Override
 283     protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
 284         return false;
 285     }
 286
 287 }