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Revision bb4d8757

Added by Andreas Müller over 4 years ago

cleanup

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/CaucasusEuroMedActivator.java
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package eu.etaxonomy.cdm.app.berlinModelImport;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.io.Reader;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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......
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import eu.etaxonomy.cdm.api.application.FirstDataInserter;
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import eu.etaxonomy.cdm.api.application.ICdmRepository;
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import eu.etaxonomy.cdm.api.service.IGroupService;
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import eu.etaxonomy.cdm.api.service.description.TransmissionEngineDistribution;
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import eu.etaxonomy.cdm.api.service.description.TransmissionEngineDistribution.AggregationMode;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.app.common.CdmDestinations;
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import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.ext.geo.IEditGeoService;
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import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
......
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
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import eu.etaxonomy.cdm.model.location.NamedAreaType;
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import eu.etaxonomy.cdm.model.metadata.CdmPreference;
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import eu.etaxonomy.cdm.model.metadata.PreferencePredicate;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
......
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import eu.etaxonomy.cdm.model.term.TermTree;
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import eu.etaxonomy.cdm.persistence.hibernate.permission.Role;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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/**
......
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                tree.getRoot().addChild(Feature.IMAGE());
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                tree.getRoot().addChild(Feature.DISTRIBUTION(), 1);
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                tree.getRoot().addChild(Feature.COMMON_NAME(), 2);
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                app.getFeatureTreeService().saveOrUpdate(tree);
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                app.getTermTreeService().saveOrUpdate(tree);
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                app.commitTransaction(tx);
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            } catch (Exception e) {
......
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	    }
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    }
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    //1. run transmission engine #3979
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    private void runTransmissionEngine(BerlinModelImportConfigurator config,
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            CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
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        if (doRunTransmissionEngine && (config.getCheck().isImport()  )  ){
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            try {
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                ICdmRepository app = bmImport.getCdmAppController();
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                final List<String> term_init_strategy = Arrays.asList(new String []{
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                        "representations"
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                });
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                UUID uuidSuperAreaLevel = BerlinModelTransformer.uuidEuroMedAreaLevelFirst;
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                NamedAreaLevel euroMedLevel1 = (NamedAreaLevel)app.getTermService().find(uuidSuperAreaLevel);
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                Pager<NamedArea> areaPager = app.getTermService().list(
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                        euroMedLevel1,
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                        (NamedAreaType) null,
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                        null,
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                        null,
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                        (List<OrderHint>) null,
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                        term_init_strategy);
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                TransmissionEngineDistribution transmissionEngineDistribution = (TransmissionEngineDistribution)app.getBean("transmissionEngineDistribution");
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                transmissionEngineDistribution.accumulate(
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                        AggregationMode.byAreasAndRanks,
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                        areaPager.getRecords(),
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                        Rank.UNRANKED_INFRASPECIFIC(),   //or do we even want to start from lower (UNKNOWN?)
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                        Rank.GENUS(),
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                        null,
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                        DefaultProgressMonitor.NewInstance());
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            } catch (Exception e) {
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                e.printStackTrace();
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                logger.error("Exception in markAreasAsHidden: " + e.getMessage());
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            }
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        }
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    }
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//    //5.Mark areas to be hidden #3979 .5
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//    private void markAreasAsHidden(BerlinModelImportConfigurator config,
......
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//        app.getTermService().saveOrUpdate(area);
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//    }
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    //2. import shapefile attributes #3979 .2
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    private void importShapefile(BerlinModelImportConfigurator config,
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            CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
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        if (config.isDoOccurrence() && (config.getCheck().isImport())){
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	       try {
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	           UUID areaVocabularyUuid = BerlinModelTransformer.uuidVocEuroMedAreas;
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               List<String> idSearchFields = Arrays.asList(new String[]{"EMAREA","PARENT"});
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               String wmsLayerName = "euromed_2013";
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               Set<UUID> areaUuidSet = null;
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               ICdmRepository app = bmImport.getCdmAppController();
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               IEditGeoService geoService = (IEditGeoService)app.getBean("editGeoService");
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               Map<NamedArea, String> resultMap;
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               try {
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                   InputStream in = CaucasusEuroMedActivator.class.getResourceAsStream("/euromed/euromed_2013.csv");
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                   Reader reader = new InputStreamReader(in, "UTF-8");
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                   resultMap = geoService.mapShapeFileToNamedAreas(
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                               reader, idSearchFields , wmsLayerName , areaVocabularyUuid, areaUuidSet);
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                   Map<String, String> flatResultMap = new HashMap<>(resultMap.size());
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                   for(NamedArea area : resultMap.keySet()){
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                       flatResultMap.put(area.getTitleCache() + " [" + area.getUuid() + "]", resultMap.get(area));
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                   }
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               } catch (IOException e) {
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                    String message = "IOException when reading from mapping file or creating result map.";
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                    logger.error(message);
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                    System.out.println(message);
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               }
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            } catch (Exception e) {
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                e.printStackTrace();
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                logger.error("Exception in importShapefile: " + e.getMessage());
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            }
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	    }
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    }
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    //4. Create users and assign roles  #3979
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    private void createUsersAndRoles(BerlinModelImportConfigurator config,
app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/CaryophyllalesCacheUpdater.java
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController;
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
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import eu.etaxonomy.cdm.io.common.ImportResult;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
......
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	                logger.info("Waiting for monitered work to start ..");
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	                monitor = appCtrInit.getProgressMonitorService().getRemotingMonitor(monitUuid);
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				}
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				return result;
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			} catch (ClassNotFoundException e) {
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				logger.error(e);
......
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			}
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		}
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		/**
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		 * @param args
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		 */
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		public static void main(String[] args) {
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			ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
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......
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			me.doInvoke(destination);
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		}
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	}
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	}
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/FauEu2CdmActivator.java
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        IProgressMonitor monitor = config.getProgressMonitor();
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//        config.setDoTaxa(doTaxa);
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        config.setDbSchemaValidation(hbm2dll);
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        config.getTaxonNodeFilter().orSubtree(uuidTaxonNodeFilter);
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        config.getTaxonNodeFilter().setOrder(ORDER.TREEINDEX);

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