app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportClassification.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.io.common.DbImportBase;
  23 import eu.etaxonomy.cdm.io.common.IPartitionedIO;
  24 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  25 import eu.etaxonomy.cdm.model.common.CdmBase;
  26 import eu.etaxonomy.cdm.model.taxon.Classification;
  27 import eu.etaxonomy.cdm.model.taxon.Synonym;
  28 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  29 import eu.etaxonomy.cdm.model.taxon.Taxon;
  30 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  31
  32 /**
  33  *
  34  * @author pplitzner
  35  * @date Mar 1, 2016
  36  *
  37  */
  38
  39 @Component
  40 @SuppressWarnings("serial")
  41 public class RedListGefaesspflanzenImportClassification extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
  42
  43     private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportClassification.class);
  44
  45     private static final String tableName = "Rote Liste Gefäßpflanzen";
  46
  47     private static final String pluralString = "classifications";
  48
  49     public RedListGefaesspflanzenImportClassification() {
  50         super(tableName, pluralString);
  51     }
  52
  53     @Override
  54     protected String getIdQuery(RedListGefaesspflanzenImportState state) {
  55         return "SELECT NAMNR "
  56                 + "FROM V_TAXATLAS_D20_EXPORT t "
  57                 + " ORDER BY NAMNR";
  58     }
  59
  60     @Override
  61     protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {
  62         String result = " SELECT * "
  63                 + " FROM V_TAXATLAS_D20_EXPORT t "
  64                 + " WHERE t.NAMNR IN (@IDSET)";
  65         result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
  66         return result;
  67     }
  68
  69     @Override
  70     protected void doInvoke(RedListGefaesspflanzenImportState state) {
  71         makeClassification(state);
  72         super.doInvoke(state);
  73     }
  74
  75
  76     @Override
  77     public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
  78         ResultSet rs = partitioner.getResultSet();
  79         Classification classification = getClassificationService().load(state.getConfig().getClassificationUuid());
  80         try {
  81             while (rs.next()){
  82                 makeSingleTaxonNode(state, rs, classification);
  83
  84             }
  85         } catch (SQLException e) {
  86             e.printStackTrace();
  87         }
  88
  89         logger.info("Update classification (1000 nodes)");
  90         getClassificationService().saveOrUpdate(classification);
  91         return true;
  92     }
  93
  94     private void makeSingleTaxonNode(RedListGefaesspflanzenImportState state, ResultSet rs, Classification classification)
  95             throws SQLException {
  96         String id = String.valueOf(rs.getLong("NAMNR"));
  97         String parentId = String.valueOf(rs.getLong("LOWER"));
  98         String gueltString = rs.getString("GUELT");
  99
 100         TaxonBase taxonBase = state.getRelatedObject(Namespace.TAXON_NAMESPACE, id, TaxonBase.class);
 101         Taxon parent = (Taxon) state.getRelatedObject(Namespace.TAXON_NAMESPACE, parentId, TaxonBase.class);
 102
 103         //misapplied name
 104         if(taxonBase.getName().getAppendedPhrase().contains("auct.")){
 105             //TODO why can't I add synonymy as misapplications
 106 //            parent.addMisappliedName(misappliedNameTaxon, citation, microcitation)
 107         }
 108         //taxon
 109         else if(taxonBase.isInstanceOf(Taxon.class)){
 110             classification.addParentChild(parent, (Taxon)taxonBase, null, null);
 111         }
 112         else if(taxonBase.isInstanceOf(Synonym.class)){
 113             //basionym
 114             if(gueltString.equals("b")){
 115                 parent.addHomotypicSynonym((Synonym) taxonBase, null, null);
 116                 parent.getName().addBasionym(taxonBase.getName());
 117             }
 118             //regular synonym
 119             else{
 120                 //TODO: how to correctly add a synonym?
 121                 parent.addSynonym((Synonym) taxonBase, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), null, null);
 122 //                parent.addSynonym((Synonym) taxonBase, SynonymRelationshipType.SYNONYM_OF(), null, null);
 123             }
 124         }
 125     }
 126
 127     @Override
 128     public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
 129             RedListGefaesspflanzenImportState state) {
 130         Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 131
 132         Set<String> idSet = new HashSet<String>();
 133         try {
 134             while (rs.next()){
 135                 idSet.add(String.valueOf(rs.getLong("NAMNR")));
 136                 idSet.add(String.valueOf(rs.getLong("LOWER")));
 137             }
 138         } catch (SQLException e) {
 139             e.printStackTrace();
 140         }
 141         Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, Namespace.TAXON_NAMESPACE);
 142         result.put(Namespace.TAXON_NAMESPACE, taxonMap);
 143         return result;
 144     }
 145
 146     private void makeClassification(RedListGefaesspflanzenImportState state) {
 147         Classification classification = Classification.NewInstance(state.getConfig().getClassificationName());
 148         classification.setUuid(state.getConfig().getClassificationUuid());
 149         getClassificationService().save(classification);
 150     }
 151
 152     @Override
 153     protected boolean doCheck(RedListGefaesspflanzenImportState state) {
 154         return false;
 155     }
 156
 157     @Override
 158     protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
 159         return false;
 160     }
 161
 162 }