cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXXMLFieldGetter.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 package eu.etaxonomy.cdm.io.taxonx2013;
  10
  11 import java.util.Map;
  12
  13 import org.apache.logging.log4j.LogManager;
  14 import org.apache.logging.log4j.Logger;
  15 import org.w3c.dom.Document;
  16 import org.w3c.dom.Node;
  17 import org.w3c.dom.NodeList;
  18
  19 import eu.etaxonomy.cdm.common.URI;
  20 import eu.etaxonomy.cdm.model.common.CdmBase;
  21 import eu.etaxonomy.cdm.model.description.Feature;
  22 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  23 import eu.etaxonomy.cdm.model.reference.Reference;
  24 import eu.etaxonomy.cdm.model.taxon.Classification;
  25
  26 public class TaxonXXMLFieldGetter {
  27
  28     private static final Logger logger = LogManager.getLogger();
  29
  30     private final Document doc;
  31
  32     private final NomenclaturalCode nomenclaturalCode;
  33     private Classification classification;
  34     private final TaxonXImport importer;
  35     private final TaxonXImportState taxonXstate;
  36     private TaxonXModsExtractor modsextractor;
  37     private TaxonXTreatmentExtractor treatmentextractor ;
  38
  39     public TaxonXXMLFieldGetter(TaxonXDataHolder dataholder, String prefix,Document document, TaxonXImport taxonXImport,
  40             TaxonXImportState taxonXstate, Classification classif, Map<String,Feature> featuresMap){
  41         this.doc = document;
  42         this.importer = taxonXImport;
  43         this.nomenclaturalCode = taxonXstate.getConfig().getNomenclaturalCode();
  44         this.classification = classif;
  45         logger.info("CLASSIFICATION "+classification);
  46         this.taxonXstate=taxonXstate;
  47         modsextractor = new TaxonXModsExtractor(importer);
  48         Reference originalSourceUrl =taxonXstate.getConfig().getOriginalSourceURL();
  49         treatmentextractor = new TaxonXTreatmentExtractor(nomenclaturalCode,classification,importer, taxonXstate,featuresMap,originalSourceUrl );
  50     }
  51
  52
  53     /**
  54      * parse the Mods from the TaxonX file
  55      *
  56      *@return the created Reference object
  57      **/
  58     public Reference parseMods(){
  59         //        System.out.println("PARSEMODS");
  60         //taxonx
  61         Node root = doc.getFirstChild();
  62
  63
  64         //taxonHeader, taxonBody
  65         NodeList nodes = root.getChildNodes();
  66         Reference ref = null;
  67         for (int i=0; i< nodes.getLength();i++) {
  68             //            System.out.println(nodes.item(i).getNodeName());
  69             if (nodes.item(i).getNodeName().equalsIgnoreCase("tax:taxonxheader")){
  70                 NodeList nodes2 = nodes.item(i).getChildNodes();
  71                 for (int j=0; j< nodes2.getLength();j++){
  72                     if (nodes2.item(j).getNodeName().equalsIgnoreCase("mods:mods")){
  73                         ref = modsextractor.extractMods(nodes2.item(j));
  74                         importer.getReferenceService().saveOrUpdate(ref);
  75                     }
  76                 }
  77             }
  78         }
  79         if (ref!=null) {
  80             taxonXstate.getConfig().setClassificationName(ref.getCitation());
  81         } else {
  82             taxonXstate.getConfig().setClassificationName("no reference title");
  83         }
  84         ref=CdmBase.deproxy(ref, Reference.class);
  85         return ref;
  86     }
  87
  88
  89     /**
  90      * Foreach treatment section, launches the treatment "extractor"
  91      * @param ref : the current reference, extracted from the mods
  92      * @param sourcename: the URI of the TaxonX document
  93      */
  94     public void parseTreatment(Reference ref, URI sourceName){
  95         System.out.println("PARSETREATMENT "+ref);
  96         //taxonx
  97         Node root = doc.getFirstChild();
  98         //taxonHeader, taxonBody
  99         NodeList nodes = root.getChildNodes();
 100
 101         for ( int i=0; i< nodes.getLength();i++) {
 102             //            System.out.println(nodes.item(i).getNodeName());
 103             if (nodes.item(i).getNodeName().equalsIgnoreCase("tax:taxonxBody")){
 104                 NodeList nodes2 = nodes.item(i).getChildNodes();
 105                 for (int j=0; j< nodes2.getLength();j++){
 106                     if (nodes2.item(j).getNodeName().equalsIgnoreCase("tax:treatment")){
 107                         try {
 108                                                         treatmentextractor.extractTreatment(nodes2.item(j), ref,sourceName);
 109                                                 } catch (Exception e) {
 110                                                         logger.error("Unhandled exception occurred in treatment. Treatment not fully imported.");
 111                                                         e.printStackTrace();
 112                                                 }
 113                     }
 114                 }
 115             }
 116         }
 117     }
 118
 119
 120
 121     /**
 122      * updates the classification in the treatment extractor
 123      * @param classification2
 124      */
 125     public void updateClassification(Classification classification2) {
 126         //System.out.println("UPDATECLASSIFICATIONS "+classification2);
 127         classification=classification2;
 128         if (treatmentextractor != null) {
 129             treatmentextractor.updateClassification(classification);
 130         }
 131
 132     }
 133
 134
 135     /**
 136      * @return
 137      */
 138     public Map<String,Feature> getFeaturesUsed() {
 139        return treatmentextractor.getFeaturesUsed();
 140     }
 141
 142
 143 }