cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXXMLFieldGetter.java

   1 package eu.etaxonomy.cdm.io.taxonx2013;
   2
   3 import java.net.URI;
   4 import java.util.Map;
   5
   6 import org.apache.log4j.Logger;
   7 import org.w3c.dom.Document;
   8 import org.w3c.dom.Node;
   9 import org.w3c.dom.NodeList;
  10
  11 import eu.etaxonomy.cdm.model.common.CdmBase;
  12 import eu.etaxonomy.cdm.model.description.Feature;
  13 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  14 import eu.etaxonomy.cdm.model.reference.Reference;
  15 import eu.etaxonomy.cdm.model.taxon.Classification;
  16
  17 public class TaxonXXMLFieldGetter {
  18
  19     private static final Logger logger = Logger.getLogger(TaxonXXMLFieldGetter.class);
  20     private final Document doc;
  21
  22
  23     private final NomenclaturalCode nomenclaturalCode;
  24     private Classification classification;
  25     private final TaxonXImport importer;
  26     private final TaxonXImportState taxonXstate;
  27     private TaxonXModsExtractor modsextractor;
  28     private TaxonXTreatmentExtractor treatmentextractor ;
  29
  30     public TaxonXXMLFieldGetter(TaxonXDataHolder dataholder, String prefix,Document document, TaxonXImport taxonXImport,
  31             TaxonXImportState taxonXstate, Classification classif, Map<String,Feature> featuresMap){
  32         this.doc = document;
  33         this.importer = taxonXImport;
  34         this.nomenclaturalCode = taxonXstate.getConfig().getNomenclaturalCode();
  35         this.classification = classif;
  36         logger.info("CLASSIFICATION "+classification);
  37         this.taxonXstate=taxonXstate;
  38         modsextractor = new TaxonXModsExtractor(importer);
  39         Reference<?> originalSourceUrl =taxonXstate.getConfig().getOriginalSourceURL();
  40         treatmentextractor = new TaxonXTreatmentExtractor(nomenclaturalCode,classification,importer, taxonXstate,featuresMap,originalSourceUrl );
  41     }
  42
  43
  44     /**
  45      * parse the Mods from the TaxonX file
  46      *
  47      *@return the created Reference object
  48      **/
  49     public Reference<?> parseMods(){
  50         //        System.out.println("PARSEMODS");
  51         //taxonx
  52         Node root = doc.getFirstChild();
  53
  54
  55         //taxonHeader, taxonBody
  56         NodeList nodes = root.getChildNodes();
  57         Reference<?> ref = null;
  58         for (int i=0; i< nodes.getLength();i++) {
  59             //            System.out.println(nodes.item(i).getNodeName());
  60             if (nodes.item(i).getNodeName().equalsIgnoreCase("tax:taxonxheader")){
  61                 NodeList nodes2 = nodes.item(i).getChildNodes();
  62                 for (int j=0; j< nodes2.getLength();j++){
  63                     if (nodes2.item(j).getNodeName().equalsIgnoreCase("mods:mods")){
  64                         ref = modsextractor.extractMods(nodes2.item(j));
  65                         importer.getReferenceService().saveOrUpdate(ref);
  66                     }
  67                 }
  68             }
  69         }
  70         if (ref!=null) {
  71             taxonXstate.getConfig().setClassificationName(ref.getCitation());
  72         } else {
  73             taxonXstate.getConfig().setClassificationName("no reference title");
  74         }
  75         ref=CdmBase.deproxy(ref, Reference.class);
  76         return ref;
  77     }
  78
  79
  80     /**
  81      * Foreach treatment section, launches the treatment "extractor"
  82      * @param ref : the current reference, extracted from the mods
  83      * @param sourcename: the URI of the TaxonX document
  84      */
  85     public void parseTreatment(Reference<?> ref, URI sourceName){
  86         System.out.println("PARSETREATMENT "+ref);
  87         //taxonx
  88         Node root = doc.getFirstChild();
  89         //taxonHeader, taxonBody
  90         NodeList nodes = root.getChildNodes();
  91
  92         for ( int i=0; i< nodes.getLength();i++) {
  93             //            System.out.println(nodes.item(i).getNodeName());
  94             if (nodes.item(i).getNodeName().equalsIgnoreCase("tax:taxonxBody")){
  95                 NodeList nodes2 = nodes.item(i).getChildNodes();
  96                 for (int j=0; j< nodes2.getLength();j++){
  97                     if (nodes2.item(j).getNodeName().equalsIgnoreCase("tax:treatment")){
  98                         try {
  99                                                         treatmentextractor.extractTreatment(nodes2.item(j), ref,sourceName);
 100                                                 } catch (Exception e) {
 101                                                         logger.error("Unhandled exception occurred in treatment. Treatment not fully imported.");
 102                                                         e.printStackTrace();
 103                                                 }
 104                     }
 105                 }
 106             }
 107         }
 108     }
 109
 110
 111
 112     /**
 113      * updates the classification in the treatment extractor
 114      * @param classification2
 115      */
 116     public void updateClassification(Classification classification2) {
 117         //System.out.println("UPDATECLASSIFICATIONS "+classification2);
 118         classification=classification2;
 119         if (treatmentextractor != null) {
 120             treatmentextractor.updateClassification(classification);
 121         }
 122
 123     }
 124
 125
 126     /**
 127      * @return
 128      */
 129     public Map<String,Feature> getFeaturesUsed() {
 130        return treatmentextractor.getFeaturesUsed();
 131     }
 132
 133
 134 }