eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/dataimport/e4/SpecimenImportViewE4.java

   1 /**
   2 * Copyright (C) 2014 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.taxeditor.view.dataimport.e4;
  10
  11 import java.io.IOException;
  12 import java.io.InputStream;
  13 import java.util.ArrayList;
  14 import java.util.Collection;
  15
  16 import org.apache.http.client.ClientProtocolException;
  17 import org.w3c.dom.Element;
  18 import org.w3c.dom.NodeList;
  19
  20 import eu.etaxonomy.cdm.common.URI;
  21 import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper;
  22 import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseResponse;
  23 import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206DataHolder;
  24 import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
  25 import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportParser;
  26 import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportState;
  27 import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206XMLFieldGetter;
  28 import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility;
  29 import eu.etaxonomy.cdm.io.specimen.abcd206.in.Identification;
  30 import eu.etaxonomy.cdm.io.specimen.abcd206.in.UnitAssociationWrapper;
  31 import eu.etaxonomy.taxeditor.model.MessagingUtils;
  32
  33 /**
  34  * @author pplitzner
  35  * @date Sep 3, 2014
  36  */
  37 public class SpecimenImportViewE4 extends DataImportViewE4<BioCaseResponse> {
  38
  39     public static final String ID = "eu.etaxonomy.taxeditor.view.dataimport.SpecimenImportView"; //$NON-NLS-1$
  40
  41     private URI endPoint;
  42
  43     public SpecimenImportViewE4() {
  44
  45     }
  46
  47     public void setEndpoint(URI endPoint) {
  48         this.endPoint = endPoint;
  49     }
  50
  51     @Override
  52     protected String getTextForTableItem(BioCaseResponse item) {
  53         //TODO: could be defined in user preferences...
  54         String name = null;
  55         if(!(((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList() == null) && !((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList().isEmpty()){
  56            Identification identification =  ((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList().iterator().next();
  57            name = identification.getScientificName();
  58         }
  59         if (name != null){
  60             return name +" - "+((Abcd206DataHolder)item.getAbcdDataHolder()).getCollectionCode() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getUnitID() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getKindOfUnit();
  61         }else {
  62             return ((Abcd206DataHolder)item.getAbcdDataHolder()).getCollectionCode() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getUnitID() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getKindOfUnit();
  63         }
  64     }
  65
  66     @Override
  67     public void query() {
  68         String errorMessage = "Could not execute query " + query;
  69
  70         Collection<BioCaseResponse> results = new ArrayList<BioCaseResponse>();
  71         try {
  72             //FIXME move ABCD import to cdmlib -> this will also get rid of the transient services
  73             InputStream resultStream;
  74             resultStream = new BioCaseQueryServiceWrapper().query(query, endPoint);
  75             Abcd206ImportConfigurator configurator = Abcd206ImportConfigurator.NewInstance(null, null);
  76             configurator.setSourceUri(endPoint);
  77
  78             //            TransientCdmRepository repo =
  79 //                    new TransientCdmRepository(CdmStore.getCurrentApplicationConfiguration());
  80             //configurator.setCdmAppController(repo);
  81
  82             //TODO: do not query all data but with the selected triple IDs -> see GbifResponseImportView
  83             configurator.setAddMediaAsMediaSpecimen(true);
  84             configurator.setAllowReuseOtherClassifications(true);
  85             configurator.setMoveNewTaxaToDefaultClassification(false);
  86             UnitAssociationWrapper unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(resultStream, null);
  87             NodeList unitsList = unitAssociationWrapper.getAssociatedUnits();
  88             Abcd206DataHolder dataHolder = new Abcd206DataHolder();
  89             Abcd206XMLFieldGetter abcdFieldGetter = new Abcd206XMLFieldGetter(dataHolder, unitAssociationWrapper.getPrefix());
  90             Abcd206ImportState state = new Abcd206ImportState(configurator);
  91             state.setDataHolder(dataHolder);
  92             BioCaseResponse response = null;
  93             if (unitsList != null){
  94                 for (int i = 0; i <unitsList.getLength(); i++){
  95                     Element item = (Element) unitsList.item(i);
  96                     dataHolder = new Abcd206DataHolder();
  97                     abcdFieldGetter = new Abcd206XMLFieldGetter(dataHolder, unitAssociationWrapper.getPrefix());
  98                     state.setPrefix(unitAssociationWrapper.getPrefix());
  99                     Abcd206ImportParser.setUnitPropertiesXML(item, abcdFieldGetter, state);
 100                     String[] tripleIdBioCase = new String[3];
 101                     tripleIdBioCase[0] =dataHolder.getUnitID();
 102                     tripleIdBioCase[1] = dataHolder.getInstitutionCode();
 103                     tripleIdBioCase[2] = dataHolder.getCollectionCode();
 104
 105                     response = new BioCaseResponse(dataHolder, endPoint, tripleIdBioCase );
 106                     results.add(response);
 107                 }
 108             }
 109
 110 //            Job job = CdmStore.getImportManager().createIOServiceJob(configurator, resultStream, SOURCE_TYPE.INPUTSTREAM);
 111 //            CdmStore.getImportManager().run(job);
 112
 113             setResults(results);
 114
 115         } catch (ClientProtocolException e) {
 116             MessagingUtils.error(getClass(), e);
 117            // logger.error(errorMessage, e);
 118         } catch (IOException e) {
 119             //logger.error(errorMessage, e);
 120             MessagingUtils.error(getClass(), e);
 121         }
 122
 123        // setResults(results);
 124
 125     }
 126 }