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  *
  35  * @author pplitzner
  36  * @since Oct 4, 2017
  37  *
  38  */
  39 public class SaveImportedSpecimenActionE4 extends Action {
  40
  41     private Comparator<GbifResponse> comparator;
  42
  43     private DataImportViewE4<?> dataImportView;
  44
  45     public SaveImportedSpecimenActionE4(DataImportViewE4<?> dataImportView) {
  46         super();
  47         this.dataImportView = dataImportView;
  48     }
  49
  50     @Override
  51     public void run() {
  52         Table table = dataImportView.getTable();
  53         Collection<GbifResponse> checkedResults = new HashSet<GbifResponse>();
  54         Collection<BioCaseResponse> checkedAbcdResults = new HashSet<BioCaseResponse>();
  55         Object data;
  56         Set<String[]> unitIdsGbif = new HashSet<String[]>();
  57         Set<String[]> unitIdsBioCase = new HashSet<String[]>();
  58         List<GbifResponse> biocaseResponses = new ArrayList<GbifResponse>();
  59
  60         for(TableItem item:table.getItems()){
  61             if(item.getChecked()){
  62                 //Save Specimen
  63                 data = item.getData();
  64                 if(data instanceof GbifResponse){
  65                     checkedResults.add((GbifResponse)item.getData());
  66                 }
  67                 if(data instanceof BioCaseResponse){
  68                     checkedAbcdResults.add((BioCaseResponse)data);
  69                 }
  70             }
  71         }
  72         String[] tripleId ;
  73         for (GbifResponse response:checkedResults){
  74             if (response != null){
  75                 tripleId = response.getTripleID();
  76
  77                 if (response.getDataSetProtocol()!=null && response.getDataSetProtocol().equals(GbifDataSetProtocol.BIOCASE)){
  78                     biocaseResponses.add(response);
  79
  80                 }else{
  81                     unitIdsGbif.add(tripleId);
  82                 }
  83
  84
  85             }
  86         }
  87         Collections.sort(biocaseResponses, getComparator());
  88
  89         Abcd206ImportConfigurator configuratorAbcd;
  90         List<Abcd206ImportConfigurator> abcdConfigurators = new ArrayList<Abcd206ImportConfigurator>();
  91         DataSetResponse dataSetResponse;
  92         OccurenceQuery bioCaseOccurrenceQuery = null;
  93         URI dataSetUri = null;
  94         for (BioCaseResponse response:checkedAbcdResults){
  95
  96             if (!response.getDataSetUri().equals(dataSetUri)){
  97                 dataSetUri = response.getDataSetUri();
  98                 //configuratorAbcd = Abcd206ImportConfigurator.NewInstance(null, null);
  99                 configuratorAbcd = PreferencesUtil.getLastUsedAbcdImportConfigurator();
 100                 if (configuratorAbcd != null){
 101
 102                     if (configuratorAbcd.getNomenclaturalCode() == null){
 103                         configuratorAbcd.setNomenclaturalCode(PreferencesUtil.getPreferredNomenclaturalCode());
 104                     }
 105                 }else{
 106                     configuratorAbcd = Abcd206ImportConfigurator.NewInstance(null, null);
 107
 108                     if (configuratorAbcd.getNomenclaturalCode() == null){
 109                         configuratorAbcd.setNomenclaturalCode(PreferencesUtil.getPreferredNomenclaturalCode());
 110                     }
 111                 }
 112                 configuratorAbcd.setSourceUri(dataSetUri);
 113                 if (configuratorAbcd.getSourceReference() == null && configuratorAbcd.getSourceRefUuid() == null){
 114                     DateTimeFormatter dtf = DateTimeFormatter.ofPattern("yyyy/MM/dd");
 115                     LocalDate localDate = LocalDate.now();
 116
 117                     String sourceRef ="Specimen Import " + localDate.toString();
 118                     configuratorAbcd.setSourceReferenceTitle(sourceRef);
 119                 }
 120
 121                 unitIdsBioCase = new HashSet<String[]>();
 122                 bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);
 123                 configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);
 124
 125 //                if (dataImportView.getClassification() != null){
 126 //                    configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());
 127 //                }
 128 //                if (dataImportView.getReferenceString() != null){
 129 //                    configuratorAbcd.setSourceReferenceTitle(dataImportView.getReferenceString());
 130 //                }
 131                 abcdConfigurators.add(configuratorAbcd);
 132
 133
 134             }
 135             tripleId = response.getTripleID();
 136             unitIdsBioCase.add(tripleId);
 137
 138         }
 139
 140
 141         //                if (!unitIdsBioCase.isEmpty()){
 142         //                    configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false);
 143         //                    configuratorAbcd.addMediaAsMediaSpecimen(true);
 144         //                    configuratorAbcd.setIgnoreAuthorship(true);
 145         //                    configuratorAbcd.setMoveNewTaxaToDefaultClassification(false);
 146         //                    if (configuratorAbcd != null){
 147         //                        abcdConfigurators.add(configuratorAbcd);
 148         //                    }
 149         ////                    unitIdsBioCase = new HashSet<String[]>();
 150         //                    bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);
 151         //                    configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);
 152         //                    configuratorAbcd.setGetSiblings(true);
 153         //                    if (dataImportView.getClassification() != null){
 154         //                        configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());
 155         //                    }
 156         //                }
 157
 158         //                for (GbifResponse response: biocaseResponses){
 159         //                      try {
 160         //                                              dataSetResponse = new GbifQueryServiceWrapper().queryOriginalDataSet(response);
 161         //                                              dataSetUri = dataSetResponse.getEndpoint();
 162         //                                      } catch (ClientProtocolException e) {
 163         //                                              // TODO Auto-generated catch block
 164         //                                              e.printStackTrace();
 165         //                                      } catch (IOException e) {
 166         //                                              // TODO Auto-generated catch block
 167         //                                              e.printStackTrace();
 168         //                                      }
 169         //                      if (!response.getDataSetUri().equals(dataSetUri)){
 170         //                              configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false);
 171         //                              configuratorAbcd.addMediaAsMediaSpecimen(true);
 172         //                              configuratorAbcd.setIgnoreAuthorship(true);
 173         //                              configuratorAbcd.setMoveNewTaxaToDefaultClassification(false);
 174         //                              if (configuratorAbcd != null){
 175         //                                      abcdConfigurators.add(configuratorAbcd);
 176         //                              }
 177         //                              unitIdsBioCase = new HashSet<String[]>();
 178         //                              bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);
 179         //                              configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);
 180         //                              configuratorAbcd.setGetSiblings(true);
 181         //                              if (dataImportView.getClassification() != null){
 182         //                                      configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());
 183         //                              }
 184         //
 185         //                      }
 186         //                      tripleId = response.getTripleID();
 187         //                      unitIdsBioCase.add(tripleId);
 188         //                }
 189
 190
 191         //  configurator.setQuery(query);
 192         if (!checkedAbcdResults.isEmpty()){
 193             Job bioCaseJob = CdmStore.getImportManager().createIOServiceJob(abcdConfigurators);
 194             CdmStore.getImportManager().run(bioCaseJob);
 195         }
 196
 197         if (!unitIdsGbif.isEmpty()){
 198             OccurenceQuery query = new OccurenceQuery(unitIdsGbif);
 199             GbifImportConfigurator configurator = GbifImportConfigurator.newInstance(query);
 200             configurator.setSourceReferenceTitle("Import Gbif data");
 201
 202             Job gbifJob = CdmStore.getImportManager().createIOServiceJob(configurator);
 203             CdmStore.getImportManager().run(gbifJob);
 204         }
 205
 206     }
 207
 208     private void persistTerm(DefinedTermBase<?> term, ITermService termService, ConversationHolder conversation){
 209         if(term!=null){
 210             //if the term does not exist in the DB save it
 211             if(termService.find(term.getUuid())==null){
 212                 termService.saveOrUpdate(term);
 213             }
 214         }
 215     }
 216
 217     @Override
 218     public String getText() {
 219         return "Import";
 220     }
 221
 222     private Comparator<GbifResponse> getComparator(){
 223         if (comparator == null){
 224             comparator = new GbifResponseComparator();
 225         }
 226         return comparator;
 227     }
 228
 229 }