cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcs/TcsTaxonIO.java

   1 /**
   2  *
   3  */
   4 package eu.etaxonomy.cdm.io.tcs;
   5
   6 import java.util.HashSet;
   7 import java.util.Iterator;
   8 import java.util.List;
   9 import java.util.Map;
  10 import java.util.Set;
  11
  12 import org.apache.log4j.Logger;
  13 import org.jdom.Attribute;
  14 import org.jdom.Element;
  15 import org.jdom.Namespace;
  16 import org.jdom.filter.ElementFilter;
  17 import org.jdom.filter.Filter;
  18
  19 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  20 import eu.etaxonomy.cdm.api.service.INameService;
  21 import eu.etaxonomy.cdm.api.service.ITaxonService;
  22 import eu.etaxonomy.cdm.common.XmlHelp;
  23 import eu.etaxonomy.cdm.io.common.CdmIoBase;
  24 import eu.etaxonomy.cdm.io.common.ICdmIO;
  25 import eu.etaxonomy.cdm.io.common.IIO;
  26 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  27 import eu.etaxonomy.cdm.io.common.MapWrapper;
  28 import eu.etaxonomy.cdm.model.common.CdmBase;
  29 import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
  30 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  31 import eu.etaxonomy.cdm.model.reference.Generic;
  32 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  33 import eu.etaxonomy.cdm.model.taxon.Synonym;
  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 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  38 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  39
  40
  41 /**
  42  * @author a.mueller
  43  *
  44  */
  45 public class TcsTaxonIO  extends CdmIoBase implements ICdmIO {
  46         private static final Logger logger = Logger.getLogger(TcsTaxonIO.class);
  47
  48         private static int modCount = 30000;
  49         private static final String ioNameLocal = "TcsTaxonIO";
  50
  51         public TcsTaxonIO(boolean ignore){
  52                 super(ioNameLocal, ignore);
  53         }
  54
  55
  56         @Override
  57         public boolean doCheck(IImportConfigurator config){
  58                 boolean result = true;
  59                 logger.warn("Checking for Taxa not yet implemented");
  60                 //result &= checkArticlesWithoutJournal(bmiConfig);
  61                 //result &= checkPartOfJournal(bmiConfig);
  62
  63                 return result;
  64         }
  65
  66         @Override
  67         public boolean doInvoke(IImportConfigurator config, CdmApplicationController cdmApp, Map<String, MapWrapper<? extends CdmBase>> stores){
  68
  69                 MapWrapper<TaxonBase> taxonMap = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);
  70                 MapWrapper<TaxonNameBase> taxonNameMap = (MapWrapper<TaxonNameBase>)stores.get(ICdmIO.TAXONNAME_STORE);
  71                 MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.REFERENCE_STORE);
  72
  73                 String xmlElementName;
  74                 String xmlAttributeName;
  75                 Namespace elementNamespace;
  76                 Namespace attributeNamespace;
  77                 String cdmAttrName;
  78                 String value;
  79
  80                 logger.info("start makeTaxa ...");
  81
  82                 TcsImportConfigurator tcsConfig = (TcsImportConfigurator)config;
  83                 Element root = tcsConfig.getSourceRoot();
  84                 boolean success =true;
  85                 INameService nameService = cdmApp.getNameService();
  86
  87                 String prefix;
  88                 Namespace rdfNamespace = root.getNamespace();
  89                 prefix = "tc";
  90                 Namespace taxonConceptNamespace = root.getNamespace(prefix);
  91                 prefix = "tcom";
  92                 Namespace commonNamespace = root.getNamespace(prefix);
  93
  94                 xmlElementName = "TaxonConcept";
  95                 elementNamespace = taxonConceptNamespace;
  96                 List<Element> elTaxonConcepts = root.getChildren(xmlElementName, elementNamespace);
  97
  98                 ITaxonService taxonService = cdmApp.getTaxonService();
  99
 100                 int i = 0;
 101                 //for each taxonName
 102                 for (Element elTaxonConcept : elTaxonConcepts){
 103                         if ((i++ % modCount) == 0){ logger.info("Taxa handled: " + (i-1));}
 104
 105                         //
 106                         String taxonAbout = elTaxonConcept.getAttributeValue("about", rdfNamespace);
 107
 108                         //hasName
 109                         xmlElementName = "hasName";
 110                         elementNamespace = taxonConceptNamespace;
 111                         xmlAttributeName = "resource";
 112                         attributeNamespace = rdfNamespace;
 113                         String strNameResource= XmlHelp.getChildAttributeValue(elTaxonConcept, xmlElementName, elementNamespace, xmlAttributeName, attributeNamespace);
 114                         TaxonNameBase taxonNameBase = taxonNameMap.get(strNameResource);
 115
 116                         //accordingTo
 117                         xmlElementName = "accordingTo";
 118                         elementNamespace = taxonConceptNamespace;
 119                         String strAccordingTo = elTaxonConcept.getChildTextTrim(xmlElementName, elementNamespace);
 120                         //FIXME
 121                         Generic sec = Generic.NewInstance();
 122                         sec.setTitleCache(strAccordingTo);
 123
 124                         //FIXME or synonym
 125                         TaxonBase taxonBase;
 126                         if (hasIsSynonymRelation(elTaxonConcept, rdfNamespace)){
 127                                 taxonBase = Synonym.NewInstance(taxonNameBase, sec);
 128                         }else{
 129                                 taxonBase = Taxon.NewInstance(taxonNameBase, sec);
 130                         }
 131
 132                         //primary
 133 //                      xmlElementName = "primary";
 134 //                      elementNamespace = taxonConceptNamespace;
 135 //                      cdmAttrName = "isPrimary";
 136 //                      Boolean primary = ImportHelper.addXmlBooleanValue(elTaxonConcept, taxon, xmlElementName, elementNamespace, cdmAttrName);
 137
 138                         taxonMap.put(taxonAbout, taxonBase);
 139
 140                 }
 141                 //invokeRelations(source, cdmApp, deleteAll, taxonMap, referenceMap);
 142                 logger.info("saving taxa ...");
 143                 taxonService.saveTaxonAll(taxonMap.objects());
 144                 logger.info("end makeTaxa ...");
 145                 return success;
 146         }
 147
 148
 149         private static boolean hasIsSynonymRelation(Element taxonConcept, Namespace rdfNamespace){
 150                 boolean result = false;
 151                 if (taxonConcept == null || ! "TaxonConcept".equalsIgnoreCase(taxonConcept.getName()) ){
 152                         return false;
 153                 }
 154
 155                 String elName = "relationshipCategory";
 156                 Filter filter = new ElementFilter(elName, taxonConcept.getNamespace());
 157                 Iterator<Element> relationshipCategories = taxonConcept.getDescendants(filter);
 158                 while (relationshipCategories.hasNext()){
 159                         Element relationshipCategory = relationshipCategories.next();
 160                         Attribute resource = relationshipCategory.getAttribute("resource", rdfNamespace);
 161                         String isSynonymFor = "http://rs.tdwg.org/ontology/voc/TaxonConcept#IsSynonymFor";
 162                         if (resource != null && isSynonymFor.equalsIgnoreCase(resource.getValue()) ){
 163                                 return true;
 164                         }
 165                 }
 166                 return result;
 167         }
 168
 169 }