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.taxon.Classification;
  30 import eu.etaxonomy.cdm.model.taxon.Synonym;
  31 import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
  32 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  33 import eu.etaxonomy.cdm.model.taxon.Taxon;
  34 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  35
  36 /**
  37  *
  38  * @author pplitzner
  39  * @date Mar 1, 2016
  40  *
  41  */
  42
  43 @Component
  44 @SuppressWarnings("serial")
  45 public class RedListGefaesspflanzenImportClassification extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
  46
  47     private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportClassification.class);
  48
  49     private static final String tableName = "Rote Liste Gefäßpflanzen";
  50
  51     private static final String pluralString = "classifications";
  52
  53     public RedListGefaesspflanzenImportClassification() {
  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         makeClassification(state);
  76         super.doInvoke(state);
  77     }
  78
  79
  80     @Override
  81     public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
  82         ResultSet rs = partitioner.getResultSet();
  83         Classification gesamtListeClassification = getClassificationService().load(state.getConfig().getClassificationUuid());
  84         Classification checklistClassification = getClassificationService().load(RedListUtil.checkListClassificationUuid);
  85         try {
  86             while (rs.next()){
  87                 makeSingleTaxonNode(state, rs, gesamtListeClassification, checklistClassification);
  88
  89             }
  90         } catch (SQLException e) {
  91             e.printStackTrace();
  92         }
  93
  94         logger.info("Update classification (1000 nodes)");
  95         getClassificationService().saveOrUpdate(gesamtListeClassification);
  96         getClassificationService().saveOrUpdate(checklistClassification);
  97         return true;
  98     }
  99
 100     private void makeSingleTaxonNode(RedListGefaesspflanzenImportState state, ResultSet rs, Classification gesamtListeClassification, Classification checklistClassification)
 101             throws SQLException {
 102         long id = rs.getLong(RedListUtil.NAMNR);
 103         String parentId = String.valueOf(rs.getLong(RedListUtil.LOWER));
 104         String gueltString = rs.getString(RedListUtil.GUELT);
 105         String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ);
 106
 107         //Gesamtliste
 108         TaxonBase taxonBaseGL = state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);
 109         Taxon parentGL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, parentId, TaxonBase.class);
 110         createParentChildNodes(gesamtListeClassification, id, gueltString, taxZusatzString, taxonBaseGL, parentGL);
 111
 112         //Checkliste
 113         TaxonBase taxonBaseCL = state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);
 114         Taxon parentCL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, parentId, TaxonBase.class);
 115         if(taxonBaseCL!=null){//null check necessary because not all taxa exist in the checklist
 116             createParentChildNodes(checklistClassification, id, gueltString, taxZusatzString, taxonBaseCL, parentCL);
 117         }
 118     }
 119
 120     private void createParentChildNodes(Classification classification, long id, String gueltString,
 121             String taxZusatzString, TaxonBase taxonBase, Taxon parent) {
 122         if(parent==null){
 123             RedListUtil.logMessage(id, "parent taxon of "+taxonBase+"  is null." , logger);
 124             return;
 125         }
 126         if(taxonBase==null){
 127             RedListUtil.logMessage(id, "child taxon/synonym of "+parent+"  is null." , logger);
 128             return;
 129         }
 130         //taxon
 131         if(taxonBase.isInstanceOf(Taxon.class)){
 132             //misapplied name
 133             String appendedPhrase = taxonBase.getAppendedPhrase();
 134             if(appendedPhrase!=null && appendedPhrase.equals(RedListUtil.AUCT)){
 135                 parent.addMisappliedName((Taxon) taxonBase, null, null);
 136             }
 137             else{
 138                 classification.addParentChild(parent, (Taxon)taxonBase, null, null);
 139             }
 140
 141             if(CdmUtils.isNotBlank(taxZusatzString)){
 142                 if(taxZusatzString.trim().equals("p. p.")){
 143                     RedListUtil.logMessage(id, "pro parte for accepted taxon "+taxonBase, logger);
 144                 }
 145             }
 146         }
 147         //synonym
 148         else if(taxonBase.isInstanceOf(Synonym.class)){
 149             //basionym
 150             if(gueltString.equals(RedListUtil.GUELT_BASIONYM)){
 151                 parent.addHomotypicSynonym((Synonym) taxonBase, null, null);
 152                 parent.getName().addBasionym(taxonBase.getName());
 153             }
 154             //regular synonym
 155             else{
 156                 SynonymRelationship synonymRelationship = parent.addSynonym((Synonym) taxonBase, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), null, null);
 157
 158                 //TAX_ZUSATZ
 159                 if(CdmUtils.isNotBlank(taxZusatzString)){
 160                     if(taxZusatzString.trim().equals("p. p.")){
 161                         synonymRelationship.setProParte(true);
 162                     }
 163                     else if(taxZusatzString.trim().equals("s. l. p. p.")){
 164                         synonymRelationship.setProParte(true);
 165                         taxonBase.setAppendedPhrase("s. l.");
 166                     }
 167                     else if(taxZusatzString.trim().equals("s. str. p. p.")){
 168                         synonymRelationship.setProParte(true);
 169                         taxonBase.setAppendedPhrase("s. str.");
 170                     }
 171                     else if(taxZusatzString.trim().equals("s. l.")
 172                             || taxZusatzString.trim().equals("s. str.")){
 173                         taxonBase.setAppendedPhrase(taxZusatzString);
 174                     }
 175                     else{
 176                         RedListUtil.logMessage(id, "unknown value "+taxZusatzString+" for column "+RedListUtil.TAX_ZUSATZ, logger);
 177                     }
 178                 }
 179             }
 180         }
 181     }
 182
 183     @Override
 184     public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
 185             RedListGefaesspflanzenImportState state) {
 186         Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 187
 188         Set<String> idSet = new HashSet<String>();
 189         try {
 190             while (rs.next()){
 191                 idSet.add(String.valueOf(rs.getLong(RedListUtil.NAMNR)));
 192                 idSet.add(String.valueOf(rs.getLong(RedListUtil.LOWER)));
 193             }
 194         } catch (SQLException e) {
 195             e.printStackTrace();
 196         }
 197         Map<String, TaxonBase> taxonMapGesamtListe = (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE);
 198         result.put(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, taxonMapGesamtListe);
 199         Map<String, TaxonBase> taxonMapCheckliste = (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_CHECKLISTE_NAMESPACE);
 200         result.put(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, taxonMapCheckliste);
 201         return result;
 202     }
 203
 204     private void makeClassification(RedListGefaesspflanzenImportState state) {
 205         //Gesamtliste
 206         Classification classification = Classification.NewInstance(state.getConfig().getClassificationName());
 207         classification.setName(LanguageString.NewInstance("Gesamtliste", Language.DEFAULT()));
 208         classification.setUuid(state.getConfig().getClassificationUuid());
 209         getClassificationService().save(classification);
 210         //checkliste
 211         Classification checklistClassification = Classification.NewInstance("Checkliste");
 212         checklistClassification.setUuid(RedListUtil.checkListClassificationUuid);
 213         getClassificationService().save(checklistClassification);
 214     }
 215
 216     @Override
 217     protected boolean doCheck(RedListGefaesspflanzenImportState state) {
 218         return false;
 219     }
 220
 221     @Override
 222     protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
 223         return false;
 224     }
 225
 226 }