eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/dataimport/e4/SaveImportedSpecimenActionE4.java

   1 package eu.etaxonomy.taxeditor.view.dataimport.e4;
   2
   3 import java.net.URI;
   4 import java.time.LocalDate;
   5 import java.time.format.DateTimeFormatter;
   6 import java.util.ArrayList;
   7 import java.util.Collection;
   8 import java.util.Collections;
   9 import java.util.Comparator;
  10 import java.util.HashSet;
  11 import java.util.List;
  12 import java.util.Set;
  13
  14 import org.eclipse.core.runtime.jobs.Job;
  15 import org.eclipse.jface.action.Action;
  16 import org.eclipse.swt.widgets.Table;
  17 import org.eclipse.swt.widgets.TableItem;
  18
  19 import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
  20 import eu.etaxonomy.cdm.api.service.ITermService;
  21 import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
  22 import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseResponse;
  23 import eu.etaxonomy.cdm.ext.occurrence.gbif.DataSetResponse;
  24 import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifDataSetProtocol;
  25 import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse;
  26 import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
  27 import eu.etaxonomy.cdm.io.specimen.gbif.in.GbifImportConfigurator;
  28 import eu.etaxonomy.cdm.model.term.DefinedTermBase;
  29 import eu.etaxonomy.taxeditor.preference.PreferencesUtil;
  30 import eu.etaxonomy.taxeditor.store.CdmStore;
  31 import eu.etaxonomy.taxeditor.view.dataimport.GbifResponseComparator;
  32
  33 /**
  34  * @author pplitzner
  35  * @since Oct 4, 2017
  36  */
  37 public class SaveImportedSpecimenActionE4 extends Action {
  38
  39     private Comparator<GbifResponse> comparator;
  40
  41     private DataImportViewE4<?> dataImportView;
  42
  43     public SaveImportedSpecimenActionE4(DataImportViewE4<?> dataImportView) {
  44         super();
  45         this.dataImportView = dataImportView;
  46     }
  47
  48     @Override
  49     public void run() {
  50         Table table = dataImportView.getTable();
  51         Collection<GbifResponse> checkedResults = new HashSet<>();
  52         Collection<BioCaseResponse> checkedAbcdResults = new HashSet<>();
  53         Object data;
  54         Set<String[]> unitIdsGbif = new HashSet<>();
  55         Set<String[]> unitIdsBioCase = new HashSet<>();
  56         List<GbifResponse> biocaseResponses = new ArrayList<>();
  57
  58         for(TableItem item:table.getItems()){
  59             if(item.getChecked()){
  60                 //Save Specimen
  61                 data = item.getData();
  62                 if(data instanceof GbifResponse){
  63                     checkedResults.add((GbifResponse)item.getData());
  64                 }
  65                 if(data instanceof BioCaseResponse){
  66                     checkedAbcdResults.add((BioCaseResponse)data);
  67                 }
  68             }
  69         }
  70         String[] tripleId ;
  71         for (GbifResponse response:checkedResults){
  72             if (response != null){
  73                 tripleId = response.getTripleID();
  74
  75                 if (response.getDataSetProtocol()!=null && response.getDataSetProtocol().equals(GbifDataSetProtocol.BIOCASE)){
  76                     biocaseResponses.add(response);
  77
  78                 }else{
  79                     unitIdsGbif.add(tripleId);
  80                 }
  81             }
  82         }
  83         Collections.sort(biocaseResponses, getComparator());
  84
  85         Abcd206ImportConfigurator configuratorAbcd;
  86         List<Abcd206ImportConfigurator> abcdConfigurators = new ArrayList<>();
  87         DataSetResponse dataSetResponse;
  88         OccurenceQuery bioCaseOccurrenceQuery = null;
  89         URI dataSetUri = null;
  90         for (BioCaseResponse response:checkedAbcdResults){
  91
  92             if (!response.getDataSetUri().equals(dataSetUri)){
  93                 dataSetUri = response.getDataSetUri();
  94                 //configuratorAbcd = Abcd206ImportConfigurator.NewInstance(null, null);
  95                 configuratorAbcd = PreferencesUtil.getLastUsedAbcdImportConfigurator();
  96                 if (configuratorAbcd != null){
  97
  98                     if (configuratorAbcd.getNomenclaturalCode() == null){
  99                         configuratorAbcd.setNomenclaturalCode(PreferencesUtil.getPreferredNomenclaturalCode());
 100                     }
 101                 }else{
 102                     configuratorAbcd = Abcd206ImportConfigurator.NewInstance(null, null);
 103
 104                     if (configuratorAbcd.getNomenclaturalCode() == null){
 105                         configuratorAbcd.setNomenclaturalCode(PreferencesUtil.getPreferredNomenclaturalCode());
 106                     }
 107                 }
 108                 configuratorAbcd.setSourceUri(dataSetUri);
 109                 if (configuratorAbcd.getSourceReference() == null && configuratorAbcd.getSourceRefUuid() == null){
 110                     DateTimeFormatter dtf = DateTimeFormatter.ofPattern("yyyy/MM/dd");
 111                     LocalDate localDate = LocalDate.now();
 112
 113                     String sourceRef ="Specimen Import " + localDate.toString();
 114                     configuratorAbcd.setSourceReferenceTitle(sourceRef);
 115                 }
 116
 117                 unitIdsBioCase = new HashSet<>();
 118                 bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);
 119                 configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);
 120
 121 //                if (dataImportView.getClassification() != null){
 122 //                    configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());
 123 //                }
 124 //                if (dataImportView.getReferenceString() != null){
 125 //                    configuratorAbcd.setSourceReferenceTitle(dataImportView.getReferenceString());
 126 //                }
 127                 abcdConfigurators.add(configuratorAbcd);
 128
 129
 130             }
 131             tripleId = response.getTripleID();
 132             unitIdsBioCase.add(tripleId);
 133
 134         }
 135
 136
 137         //                if (!unitIdsBioCase.isEmpty()){
 138         //                    configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false);
 139         //                    configuratorAbcd.addMediaAsMediaSpecimen(true);
 140         //                    configuratorAbcd.setIgnoreAuthorship(true);
 141         //                    configuratorAbcd.setMoveNewTaxaToDefaultClassification(false);
 142         //                    if (configuratorAbcd != null){
 143         //                        abcdConfigurators.add(configuratorAbcd);
 144         //                    }
 145         ////                    unitIdsBioCase = new HashSet<String[]>();
 146         //                    bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);
 147         //                    configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);
 148         //                    configuratorAbcd.setGetSiblings(true);
 149         //                    if (dataImportView.getClassification() != null){
 150         //                        configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());
 151         //                    }
 152         //                }
 153
 154         //                for (GbifResponse response: biocaseResponses){
 155         //                      try {
 156         //                                              dataSetResponse = new GbifQueryServiceWrapper().queryOriginalDataSet(response);
 157         //                                              dataSetUri = dataSetResponse.getEndpoint();
 158         //                                      } catch (ClientProtocolException e) {
 159         //                                              // TODO Auto-generated catch block
 160         //                                              e.printStackTrace();
 161         //                                      } catch (IOException e) {
 162         //                                              // TODO Auto-generated catch block
 163         //                                              e.printStackTrace();
 164         //                                      }
 165         //                      if (!response.getDataSetUri().equals(dataSetUri)){
 166         //                              configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false);
 167         //                              configuratorAbcd.addMediaAsMediaSpecimen(true);
 168         //                              configuratorAbcd.setIgnoreAuthorship(true);
 169         //                              configuratorAbcd.setMoveNewTaxaToDefaultClassification(false);
 170         //                              if (configuratorAbcd != null){
 171         //                                      abcdConfigurators.add(configuratorAbcd);
 172         //                              }
 173         //                              unitIdsBioCase = new HashSet<String[]>();
 174         //                              bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);
 175         //                              configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);
 176         //                              configuratorAbcd.setGetSiblings(true);
 177         //                              if (dataImportView.getClassification() != null){
 178         //                                      configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());
 179         //                              }
 180         //
 181         //                      }
 182         //                      tripleId = response.getTripleID();
 183         //                      unitIdsBioCase.add(tripleId);
 184         //                }
 185
 186
 187         //  configurator.setQuery(query);
 188         if (!checkedAbcdResults.isEmpty()){
 189             Job bioCaseJob = CdmStore.getImportManager().createIOServiceJob(abcdConfigurators);
 190             CdmStore.getImportManager().run(bioCaseJob);
 191         }
 192
 193         if (!unitIdsGbif.isEmpty()){
 194             OccurenceQuery query = new OccurenceQuery(unitIdsGbif);
 195             GbifImportConfigurator configurator = GbifImportConfigurator.newInstance(query);
 196             configurator.setSourceReferenceTitle("Import Gbif data");
 197
 198             Job gbifJob = CdmStore.getImportManager().createIOServiceJob(configurator);
 199             CdmStore.getImportManager().run(gbifJob);
 200         }
 201     }
 202
 203     private void persistTerm(DefinedTermBase<?> term, ITermService termService, ConversationHolder conversation){
 204         if(term!=null){
 205             //if the term does not exist in the DB save it
 206             if(termService.find(term.getUuid())==null){
 207                 termService.saveOrUpdate(term);
 208             }
 209         }
 210     }
 211
 212     @Override
 213     public String getText() {
 214         return "Import";
 215     }
 216
 217     private Comparator<GbifResponse> getComparator(){
 218         if (comparator == null){
 219             comparator = new GbifResponseComparator();
 220         }
 221         return comparator;
 222     }
 223 }