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.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.ResultSetPartitioner;
  26 import eu.etaxonomy.cdm.model.common.CdmBase;
  27 import eu.etaxonomy.cdm.model.common.Language;
  28 import eu.etaxonomy.cdm.model.common.LanguageString;
  29 import eu.etaxonomy.cdm.model.reference.Reference;
  30 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  31 import eu.etaxonomy.cdm.model.taxon.Classification;
  32 import eu.etaxonomy.cdm.model.taxon.Synonym;
  33 import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
  34 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  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 RedListGefaesspflanzenImportClassification extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
  48
  49     private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportClassification.class);
  50
  51     private static final String tableName = "Rote Liste Gefäßpflanzen";
  52
  53     private static final String pluralString = "classifications";
  54
  55     public RedListGefaesspflanzenImportClassification() {
  56         super(tableName, pluralString);
  57     }
  58
  59     @Override
  60     protected String getIdQuery(RedListGefaesspflanzenImportState state) {
  61         return "SELECT NAMNR "
  62                 + "FROM V_TAXATLAS_D20_EXPORT t "
  63                 + " ORDER BY NAMNR";
  64     }
  65
  66     @Override
  67     protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {
  68         String result = " SELECT * "
  69                 + " FROM V_TAXATLAS_D20_EXPORT t "
  70                 + " WHERE t.NAMNR IN (@IDSET)";
  71         result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
  72         return result;
  73     }
  74
  75     @Override
  76     protected void doInvoke(RedListGefaesspflanzenImportState state) {
  77         makeClassification(state);
  78         super.doInvoke(state);
  79     }
  80
  81
  82     @Override
  83     public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
  84         ResultSet rs = partitioner.getResultSet();
  85         Classification gesamtListeClassification = getClassificationService().load(state.getConfig().getClassificationUuid());
  86         Classification checklistClassification = getClassificationService().load(RedListUtil.checkListClassificationUuid);
  87         try {
  88             while (rs.next()){
  89                 makeSingleTaxonNode(state, rs, gesamtListeClassification, checklistClassification);
  90
  91             }
  92         } catch (SQLException e) {
  93             e.printStackTrace();
  94         }
  95
  96         logger.info("Update classification (1000 nodes)");
  97         getClassificationService().saveOrUpdate(gesamtListeClassification);
  98         getClassificationService().saveOrUpdate(checklistClassification);
  99         return true;
 100     }
 101
 102     private void makeSingleTaxonNode(RedListGefaesspflanzenImportState state, ResultSet rs, Classification gesamtListeClassification, Classification checklistClassification)
 103             throws SQLException {
 104         long id = rs.getLong(RedListUtil.NAMNR);
 105         String parentId = String.valueOf(rs.getLong(RedListUtil.LOWER));
 106         String gueltString = rs.getString(RedListUtil.GUELT);
 107         String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ);
 108
 109         //Gesamtliste
 110         TaxonBase taxonBaseGL = state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);
 111         Taxon parentGL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, parentId, TaxonBase.class);
 112         createParentChildNodes(gesamtListeClassification, id, gueltString, taxZusatzString, taxonBaseGL, parentGL);
 113
 114         //Checkliste
 115         TaxonBase taxonBaseCL = state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);
 116         Taxon parentCL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, parentId, TaxonBase.class);
 117         if(taxonBaseCL!=null){//null check necessary because not all taxa exist in the checklist
 118             createParentChildNodes(checklistClassification, id, gueltString, taxZusatzString, taxonBaseCL, parentCL);
 119         }
 120     }
 121
 122     private void createParentChildNodes(Classification classification, long id, String gueltString,
 123             String taxZusatzString, TaxonBase taxonBase, Taxon parent) {
 124         if(parent==null){
 125             RedListUtil.logMessage(id, "parent taxon of "+taxonBase+"  is null." , logger);
 126             return;
 127         }
 128         if(taxonBase==null){
 129             RedListUtil.logMessage(id, "child taxon/synonym of "+parent+"  is null." , logger);
 130             return;
 131         }
 132         //taxon
 133         if(taxonBase.isInstanceOf(Taxon.class)){
 134             //misapplied name
 135             String appendedPhrase = taxonBase.getAppendedPhrase();
 136             if(appendedPhrase!=null && appendedPhrase.equals(RedListUtil.AUCT)){
 137                 parent.addMisappliedName((Taxon) taxonBase, null, null);
 138             }
 139             else{
 140                 classification.addParentChild(parent, (Taxon)taxonBase, null, null);
 141             }
 142
 143             if(CdmUtils.isNotBlank(taxZusatzString)){
 144                 if(taxZusatzString.trim().equals("p. p.")){
 145                     RedListUtil.logMessage(id, "pro parte for accepted taxon "+taxonBase, logger);
 146                 }
 147             }
 148         }
 149         //synonym
 150         else if(taxonBase.isInstanceOf(Synonym.class)){
 151             //basionym
 152             if(gueltString.equals(RedListUtil.GUELT_BASIONYM)){
 153                 parent.addHomotypicSynonym((Synonym) taxonBase, null, null);
 154                 parent.getName().addBasionym(taxonBase.getName());
 155             }
 156             //regular synonym
 157             else{
 158                 SynonymRelationship synonymRelationship = parent.addSynonym((Synonym) taxonBase, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), null, null);
 159
 160                 //TAX_ZUSATZ
 161                 if(CdmUtils.isNotBlank(taxZusatzString)){
 162                     if(taxZusatzString.trim().equals("p. p.")){
 163                         synonymRelationship.setProParte(true);
 164                     }
 165                     else if(taxZusatzString.trim().equals("s. l. p. p.")){
 166                         synonymRelationship.setProParte(true);
 167                         taxonBase.setAppendedPhrase("s. l.");
 168                     }
 169                     else if(taxZusatzString.trim().equals("s. str. p. p.")){
 170                         synonymRelationship.setProParte(true);
 171                         taxonBase.setAppendedPhrase("s. str.");
 172                     }
 173                     else if(taxZusatzString.trim().equals("s. l.")
 174                             || taxZusatzString.trim().equals("s. str.")){
 175                         taxonBase.setAppendedPhrase(taxZusatzString);
 176                     }
 177                     else{
 178                         RedListUtil.logMessage(id, "unknown value "+taxZusatzString+" for column "+RedListUtil.TAX_ZUSATZ, logger);
 179                     }
 180                 }
 181             }
 182         }
 183         //set sec reference
 184         taxonBase.setSec(classification.getReference());
 185     }
 186
 187     @Override
 188     public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
 189             RedListGefaesspflanzenImportState state) {
 190         Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 191
 192         Set<String> idSet = new HashSet<String>();
 193         try {
 194             while (rs.next()){
 195                 idSet.add(String.valueOf(rs.getLong(RedListUtil.NAMNR)));
 196                 idSet.add(String.valueOf(rs.getLong(RedListUtil.LOWER)));
 197             }
 198         } catch (SQLException e) {
 199             e.printStackTrace();
 200         }
 201         Map<String, TaxonBase> taxonMapGesamtListe = (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE);
 202         result.put(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, taxonMapGesamtListe);
 203         Map<String, TaxonBase> taxonMapCheckliste = (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_CHECKLISTE_NAMESPACE);
 204         result.put(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, taxonMapCheckliste);
 205         return result;
 206     }
 207
 208     private void makeClassification(RedListGefaesspflanzenImportState state) {
 209         //Gesamtliste
 210         Classification classification = Classification.NewInstance(state.getConfig().getClassificationName());
 211         classification.setName(LanguageString.NewInstance("Gesamtliste", Language.DEFAULT()));
 212         classification.setUuid(state.getConfig().getClassificationUuid());
 213         Reference gesamtListeReference = ReferenceFactory.newGeneric();
 214         gesamtListeReference.setUuid(RedListUtil.gesamtListeReferenceUuid);
 215         gesamtListeReference.setTitle("Gesamtliste");
 216         classification.setReference(gesamtListeReference);
 217         getClassificationService().save(classification);
 218         //checkliste
 219         Classification checklistClassification = Classification.NewInstance("Checkliste");
 220         checklistClassification.setUuid(RedListUtil.checkListClassificationUuid);
 221         Reference checklistReference = ReferenceFactory.newGeneric();
 222         checklistReference.setUuid(RedListUtil.checkListClassificationUuid);
 223         checklistReference.setTitle("Gesamtliste");
 224         checklistClassification.setReference(checklistReference);
 225         getClassificationService().save(checklistClassification);
 226     }
 227
 228     @Override
 229     protected boolean doCheck(RedListGefaesspflanzenImportState state) {
 230         return false;
 231     }
 232
 233     @Override
 234     protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
 235         return false;
 236     }
 237
 238 }