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