cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/TcsRdfTaxonNameRelationsImport.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.tcsrdf;
  11
  12 import java.util.HashSet;
  13 import java.util.List;
  14 import java.util.Set;
  15
  16 import org.apache.log4j.Logger;
  17 import org.jdom.Attribute;
  18 import org.jdom.Element;
  19 import org.jdom.Namespace;
  20 import org.springframework.stereotype.Component;
  21
  22 import eu.etaxonomy.cdm.api.service.INameService;
  23 import eu.etaxonomy.cdm.io.common.ICdmIO;
  24 import eu.etaxonomy.cdm.io.common.MapWrapper;
  25 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  26 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  27
  28 /**
  29  * @author a.mueller
  30  * @created 29.05.2008
  31  * @version 1.0
  32  */
  33 @Component
  34 public class TcsRdfTaxonNameRelationsImport extends TcsRdfImportBase implements ICdmIO<TcsRdfImportState> {
  35         private static final Logger logger = Logger.getLogger(TcsRdfTaxonNameRelationsImport.class);
  36
  37         private static int modCount = 5000;
  38
  39         public TcsRdfTaxonNameRelationsImport(){
  40                 super();
  41         }
  42
  43         @Override
  44         public boolean doCheck(TcsRdfImportState state){
  45                 boolean result = true;
  46                 logger.warn("Checking for TaxonNameRelations not yet implemented");
  47                 //result &= checkArticlesWithoutJournal(tcsConfig);
  48                 //result &= checkPartOfJournal(tcsConfig);
  49
  50                 return result;
  51         }
  52
  53         @Override
  54         public boolean doInvoke(TcsRdfImportState state){
  55
  56                 MapWrapper<TaxonNameBase> taxonNameMap = (MapWrapper<TaxonNameBase>)state.getStore(ICdmIO.TAXONNAME_STORE);
  57                 MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)state.getStore(ICdmIO.REFERENCE_STORE);
  58
  59                 String tcsElementName;
  60                 Namespace tcsNamespace;
  61                 String cdmAttrName;
  62                 String value;
  63
  64                 Set<TaxonNameBase> nameStore = new HashSet<TaxonNameBase>();
  65                 TcsRdfImportConfigurator config = state.getConfig();
  66                 Element source = config.getSourceRoot();
  67
  68                 logger.info("start makeNameRelationships ...");
  69                 INameService nameService = getNameService();
  70
  71 //              <tn:hasBasionym rdf:resource="palm_tn_14530"/>
  72
  73                 Element root = config.getSourceRoot();
  74                 boolean success =true;
  75
  76                 Namespace rdfNamespace = config.getRdfNamespace();
  77                 Namespace taxonNameNamespace = config.getTnNamespace();
  78
  79                 List<Element> elTaxonNames = root.getChildren("TaxonName", taxonNameNamespace);
  80
  81                 int i = 0;
  82                 int nameRelCount = 0;
  83                 //for each taxonName
  84                 for (Element elTaxonName : elTaxonNames){
  85
  86                         TaxonNameBase fromName = null;
  87                         if ((++i % modCount) == 0){ logger.info("Names handled: " + (i-1));}
  88
  89                         //Basionyms
  90                         tcsElementName = "hasBasionym";
  91                         tcsNamespace = taxonNameNamespace;
  92                         List<Element> elBasionymList = elTaxonName.getChildren(tcsElementName, tcsNamespace);
  93
  94                         for (Element elBasionym: elBasionymList){
  95                                 nameRelCount++;
  96                                 logger.debug("BASIONYM "+  nameRelCount);
  97                                 tcsElementName = "resource";
  98                                 tcsNamespace = rdfNamespace;
  99                                 Attribute attrResource = elBasionym.getAttribute(tcsElementName, tcsNamespace);
 100                                 if (attrResource == null){
 101                                         logger.warn("Basionym rdf:resource is missing ! Basionym not set!");
 102                                         continue;
 103                                 }
 104                                 String basionymId = attrResource.getValue();
 105                                 TaxonNameBase basionym = taxonNameMap.get(basionymId);
 106                                 if (basionym == null){
 107                                         logger.warn("Basionym name ("+basionymId+") not found in Map! Basionym not set!");
 108                                         continue;
 109                                 }
 110                                 if (fromName == null){
 111                                         Attribute about = elTaxonName.getAttribute("about", rdfNamespace);
 112                                         if (about != null){
 113                                                 fromName = taxonNameMap.get(about.getValue() );
 114                                         }
 115                                         if (fromName == null){
 116                                                 logger.warn("From name ("+about+") not found in Map! Basionym not set!");
 117                                                 continue;
 118                                         }
 119                                 }
 120                                 String ruleConcidered = null; //TODO
 121                                 String microCitation = null; //TODO;
 122                                 ReferenceBase citation = null; //TODO;
 123                                 fromName.addBasionym(basionym, citation, microCitation, ruleConcidered);
 124                                 nameStore.add(fromName);
 125
 126                         }
 127                 }// end Basionyms
 128
 129                 //Other Relations
 130                 //TODO
 131
 132                 logger.info(nameRelCount + " nameRelations handled");
 133                 nameService.save(nameStore);
 134                 logger.info("end makeNameRelationships ...");
 135                 return success;
 136         }
 137
 138         /* (non-Javadoc)
 139          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 140          */
 141         protected boolean isIgnore(TcsRdfImportState state){
 142                 return ! state.getConfig().isDoRelNames();
 143         }
 144
 145 }