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     private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportNames.class);
  46
  47     private static final String tableName = "Rote Liste Gefäßpflanzen";
  48
  49     private static final String pluralString = "names";
  50
  51     private static final String NAME_NAMESPACE = "name";
  52
  53     public RedListGefaesspflanzenImportNames() {
  54         super(tableName, pluralString);
  55     }
  56
  57     @Override
  58     protected String getIdQuery(RedListGefaesspflanzenImportState state) {
  59         return "SELECT NAMNR "
  60                 + "FROM V_TAXATLAS_D20_EXPORT t "
  61                 + " ORDER BY NAMNR";
  62     }
  63
  64     @Override
  65     protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {
  66         String result = " SELECT * "
  67                 + " FROM V_TAXATLAS_D20_EXPORT t "
  68                 + " WHERE t.NAMNR IN (@IDSET)";
  69         result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
  70         return result;
  71     }
  72
  73     @Override
  74     protected void doInvoke(RedListGefaesspflanzenImportState state) {
  75         super.doInvoke(state);
  76     }
  77
  78
  79     @Override
  80     public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
  81         ResultSet rs = partitioner.getResultSet();
  82         Set<TaxonNameBase> namesToSave = new HashSet<TaxonNameBase>();
  83         try {
  84             while (rs.next()){
  85                 makeSingleName(state, rs, namesToSave);
  86
  87             }
  88         } catch (SQLException e) {
  89             e.printStackTrace();
  90         }
  91
  92         getNameService().saveOrUpdate(namesToSave);
  93         return true;
  94     }
  95
  96     private void makeSingleName(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave)
  97             throws SQLException {
  98         long id = rs.getLong("NAMNR");
  99         String taxNameString = rs.getString("TAXNAME");
 100         String rangString = rs.getString("RANG");
 101         String ep1String = rs.getString("EPI1");
 102         String ep2String = rs.getString("EPI2");
 103         String ep3String = rs.getString("EPI3");
 104         String nomZusatzString = rs.getString("NOM_ZUSATZ");
 105         String zusatzString = rs.getString("ZUSATZ");
 106         String authorKombString = rs.getString("AUTOR_KOMB");
 107         String authorBasiString = rs.getString("AUTOR_BASI");
 108
 109         if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){
 110             logger.error("NAMNR: "+id+" No name found!");
 111         }
 112
 113
 114         Rank rank = makeRank(state, rangString);
 115         BotanicalName name = BotanicalName.NewInstance(rank);
 116
 117         //ep1 should always be present
 118         name.setGenusOrUninomial(ep1String);
 119         if(rank==Rank.SPECIES()){
 120             name.setGenusOrUninomial(ep1String);
 121         }
 122
 123         //add author
 124         TeamOrPersonBase authorKomb = HibernateProxyHelper.deproxy(getAgentService().load(state.getAuthorMap().get(authorKombString)), TeamOrPersonBase.class);
 125         name.setCombinationAuthorship(authorKomb);
 126
 127         //id
 128         ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, NAME_NAMESPACE);
 129
 130         namesToSave.add(name);
 131     }
 132
 133     private Rank makeRank(RedListGefaesspflanzenImportState state, String rankStr) {
 134         Rank rank = null;
 135         try {
 136             rank = state.getTransformer().getRankByKey(rankStr);
 137         } catch (UndefinedTransformerMethodException e) {
 138             e.printStackTrace();
 139         }
 140         if(rank==null){
 141             logger.error(rankStr+" could not be associated to a known rank.");
 142         }
 143         return rank;
 144     }
 145
 146
 147
 148     @Override
 149     public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
 150             RedListGefaesspflanzenImportState state) {
 151         Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 152 //        Map<Long, AgentBase<?>> authorKombMap = new HashMap<>();
 153 //        Map<Long, AgentBase<?>> authorBasiMap = new HashMap<>();
 154 //
 155 //        //load authors
 156 //        for(Entry<Long, UUID> entry:state.getAuthorKombMap().entrySet()){
 157 //            authorKombMap.put(entry.getKey(), getAgentService().load(entry.getValue()));
 158 //        }
 159 //        for(Entry<Long, UUID> entry:state.getAuthorBasiMap().entrySet()){
 160 //            authorBasiMap.put(entry.getKey(), getAgentService().load(entry.getValue()));
 161 //        }
 162 //        try {
 163 //            while (rs.next()){
 164 //                long id = rs.getLong("NAMNR");
 165 //            }
 166 //        } catch (SQLException e) {
 167 //            e.printStackTrace();
 168 //        }
 169 //
 170 //        //Authors
 171 //        Set<UUID> uuidSet = new HashSet<>();
 172 //        for (String authorStr : authorKombSet){
 173 //            UUID uuid = state.getAuthorUuid(authorStr);
 174 //            uuidSet.add(uuid);
 175 //        }
 176 //        List<TeamOrPersonBase<?>> authors = (List)getAgentService().find(uuidSet);
 177 //        Map<UUID, TeamOrPersonBase<?>> authorUuidMap = new HashMap<>();
 178 //        for (TeamOrPersonBase<?> author : authors){
 179 //            authorUuidMap.put(author.getUuid(), author);
 180 //        }
 181 //
 182 //        for (String authorStr : authorKombSet){
 183 //            UUID uuid = state.getAuthorUuid(authorStr);
 184 //            TeamOrPersonBase<?> author = authorUuidMap.get(uuid);
 185 //            authorMap.put(authorStr, author);
 186 //        }
 187 //        result.put(AUTHOR_NAMESPACE, authorMap);
 188 //
 189 //        //reference map
 190 //        String nameSpace = REFERENCE_NAMESPACE;
 191 //        Class<?> cdmClass = Reference.class;
 192 //        Set<String> idSet = referenceIdSet;
 193 //        Map<String, Reference<?>> referenceMap = (Map<String, Reference<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 194 //        result.put(nameSpace, referenceMap);
 195 //
 196 //        //secundum
 197 //        UUID secUuid = state.getConfig().getSecUuid();
 198 //        Reference<?> secRef = getReferenceService().find(secUuid);
 199 //        referenceMap.put(secUuid.toString(), secRef);
 200
 201         return result;
 202     }
 203
 204     @Override
 205     protected boolean doCheck(RedListGefaesspflanzenImportState state) {
 206         return false;
 207     }
 208
 209     @Override
 210     protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
 211         return false;
 212     }
 213
 214 }