eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/dataimport/SaveImportedSpecimenAction.java

   1 package eu.etaxonomy.taxeditor.view.dataimport;
   2
   3 import java.io.IOException;
   4 import java.net.URI;
   5 import java.util.ArrayList;
   6 import java.util.Collection;
   7 import java.util.Collections;
   8 import java.util.Comparator;
   9 import java.util.HashSet;
  10 import java.util.List;
  11 import java.util.Set;
  12 import java.util.UUID;
  13
  14 import org.apache.http.client.ClientProtocolException;
  15 import org.apache.log4j.Logger;
  16 import org.eclipse.core.runtime.jobs.Job;
  17 import org.eclipse.jface.action.Action;
  18 import org.eclipse.jface.text.source.Annotation;
  19 import org.eclipse.swt.widgets.Event;
  20 import org.eclipse.swt.widgets.Table;
  21 import org.eclipse.swt.widgets.TableItem;
  22 import org.eclipse.ui.IWorkbenchPart;
  23 import org.eclipse.ui.IWorkbenchWindow;
  24 import org.eclipse.ui.PlatformUI;
  25
  26 import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
  27 import eu.etaxonomy.cdm.api.service.IClassificationService;
  28 import eu.etaxonomy.cdm.api.service.IOccurrenceService;
  29 import eu.etaxonomy.cdm.api.service.ITermService;
  30 import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
  31 import eu.etaxonomy.cdm.ext.occurrence.gbif.DataSetResponse;
  32 import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifDataSetProtocol;
  33 import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifQueryServiceWrapper;
  34 import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse;
  35 import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
  36 import eu.etaxonomy.cdm.io.specimen.gbif.in.*;
  37 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  38 import eu.etaxonomy.cdm.model.common.ICdmBase;
  39 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  40 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  41 import eu.etaxonomy.cdm.model.taxon.Classification;
  42 import eu.etaxonomy.taxeditor.store.CdmStore;
  43 import eu.etaxonomy.taxeditor.ui.dialog.selection.SelectionDialogFactory;
  44
  45 public class SaveImportedSpecimenAction extends Action {
  46
  47     private final Logger logger = Logger.getLogger(SaveImportedSpecimenAction.class);
  48
  49     private Comparator<GbifResponse> comparator;
  50
  51     /* (non-Javadoc)
  52      * @see org.eclipse.jface.action.Action#run()
  53      */
  54     @Override
  55     public void run() {
  56         final IWorkbenchWindow window = PlatformUI.getWorkbench().getActiveWorkbenchWindow();
  57         IWorkbenchPart activePart = window.getActivePage().getActivePart();
  58         if(activePart instanceof DataImportView<?>){
  59             DataImportView<?> dataImportView = (DataImportView<?>)activePart;
  60             Table table = dataImportView.getTable();
  61             Collection<GbifResponse> checkedResults = new HashSet<GbifResponse>();
  62             Object data;
  63             Set<String[]> unitIdsGbif = new HashSet<String[]>();
  64             Set<String[]> unitIdsBioCase = new HashSet<String[]>();
  65             List<GbifResponse> biocaseResponses = new ArrayList<GbifResponse>();
  66
  67             for(TableItem item:table.getItems()){
  68                 if(item.getChecked()){
  69                     //Save Specimen
  70                          data = item.getData();
  71                          if(data instanceof GbifResponse){
  72                                  checkedResults.add((GbifResponse)item.getData());
  73                          }
  74                 }
  75             }
  76             String[] tripleId ;
  77                 for (GbifResponse response:checkedResults){
  78                         if (response != null){
  79                                 tripleId = response.getTripleID();
  80
  81                                 if (response.getDataSetProtocol().equals(GbifDataSetProtocol.BIOCASE)){
  82                                         biocaseResponses.add(response);
  83
  84                                 }else{
  85                                         unitIdsGbif.add(tripleId);
  86                                 }
  87
  88
  89                         }
  90                 }
  91                 Collections.sort(biocaseResponses, getComparator());
  92                 URI dataSetUri = null;
  93                 Abcd206ImportConfigurator configuratorAbcd;
  94
  95                 List<Abcd206ImportConfigurator> abcdConfigurators = new ArrayList<Abcd206ImportConfigurator>();
  96                 DataSetResponse dataSetResponse;
  97                 OccurenceQuery bioCaseOccurrenceQuery = null;
  98                 for (GbifResponse response: biocaseResponses){
  99                         try {
 100                                                 dataSetResponse = new GbifQueryServiceWrapper().queryOriginalDataSet(response);
 101                                                 dataSetUri = dataSetResponse.getEndpoint();
 102                                         } catch (ClientProtocolException e) {
 103                                                 // TODO Auto-generated catch block
 104                                                 e.printStackTrace();
 105                                         } catch (IOException e) {
 106                                                 // TODO Auto-generated catch block
 107                                                 e.printStackTrace();
 108                                         }
 109                         if (!response.getDataSetUri().equals(dataSetUri)){
 110                                 configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false);
 111                                 configuratorAbcd.addMediaAsMediaSpecimen(true);
 112                                 if (configuratorAbcd != null){
 113                                         abcdConfigurators.add(configuratorAbcd);
 114                                 }
 115                                 unitIdsBioCase = new HashSet<String[]>();
 116                                 bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);
 117                                 configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);
 118                                 if (dataImportView.getClassification() != null){
 119                                         configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());
 120                                 }
 121
 122                         }
 123                         tripleId = response.getTripleID();
 124                         unitIdsBioCase.add(tripleId);
 125                 }
 126
 127                 OccurenceQuery query = new OccurenceQuery(unitIdsGbif);
 128                 GbifImportConfigurator configurator = GbifImportConfigurator.newInstance(query);
 129                 configurator.setSourceReferenceTitle("Import Gbif data");
 130
 131
 132
 133                 //  configurator.setQuery(query);
 134
 135                Job bioCaseJob = CdmStore.getImportManager().createIOServiceJob(abcdConfigurators);
 136                CdmStore.getImportManager().run(bioCaseJob);
 137
 138                Job gbifJob = CdmStore.getImportManager().createIOServiceJob(configurator);
 139                CdmStore.getImportManager().run(gbifJob);
 140
 141
 142
 143             }
 144         }
 145
 146
 147     private void persistTerm(DefinedTermBase<?> term, ITermService termService, ConversationHolder conversation){
 148         if(term!=null){
 149             //if the term does not exist in the DB save it
 150             if(termService.find(term.getUuid())==null){
 151                 termService.saveOrUpdate(term);
 152             }
 153         }
 154     }
 155
 156     /* (non-Javadoc)
 157      * @see org.eclipse.jface.action.Action#getText()
 158      */
 159     @Override
 160     public String getText() {
 161         return "Import";
 162     }
 163
 164     private Comparator<GbifResponse> getComparator(){
 165         if (comparator == null){
 166                 comparator = new GbifResponseComparator();
 167         }
 168         return comparator;
 169     }
 170
 171
 172 }