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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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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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import org.apache.log4j.Logger;
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import org.springframework.security.core.GrantedAuthority;
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import org.springframework.transaction.TransactionStatus;
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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.io.common.IImportConfigurator.CHECK;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.GrantedAuthorityImpl;
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import eu.etaxonomy.cdm.model.common.Group;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.User;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureNode;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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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.name.Rank;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.model.term.Representation;
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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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* TODO add the following to a wiki page:
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* HINT: If you are about to import into a mysql data base running under windows and if you wish to
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* dump and restore the resulting data bas under another operation systen
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* you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
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*
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* @author a.mueller
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*/
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public class CaucasusEuroMedActivator {
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private static final Logger logger = Logger.getLogger(CaucasusEuroMedActivator.class);
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//database validation status (create, update, validate ...)
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static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
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static final Source berlinModelSource = BerlinModelSources.euroMed_BGBM42();
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// static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_euromed_caucasus();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_euromed_caucasus();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_euroMed();
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//check - import
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static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
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static final boolean doUser = true;
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// //authors
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static final boolean doAuthors = true;
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//references
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static final DO_REFERENCES doReferences = DO_REFERENCES.ALL;
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//names
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static final boolean doTaxonNames = true;
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static final boolean doRelNames = true;
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static final boolean doNameStatus = true;
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static final boolean doNameFacts = true;
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//taxa
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static final boolean doTaxa = true;
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static final boolean doRelTaxa = true;
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static final boolean doNamedAreas = true;
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//not relevant for caucasus
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static final boolean doFacts = false;
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static final boolean doOccurrences = false;
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static final boolean doOccurrenceSources =false;
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static final boolean doCommonNames = false; //currently takes very long
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//serious types do not exist in E+M except for name types which are handled in name relations
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static final boolean doTypes = false; //serious types do not exist in E+M except for name types which are handled in name relations
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static final boolean doRunTransmissionEngine = false; // (hbm2dll == DbSchemaValidation.VALIDATE);
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//etc.
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static final boolean doMarker = false; //no relevant markers exist
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boolean invers = !(hbm2dll == DbSchemaValidation.CREATE);
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boolean doPreliminaryRefDetailsWithNames = true;
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boolean logNotMatchingOldNames = false;
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boolean logMatchingNotExportedOldNames = false; //true
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boolean checkOldNameIsSynonym = true;
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static final boolean includePesiExport = false;
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static final int sourceSecId = 7000000; //500000
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static final UUID classificationUuid = UUID.fromString("314a68f9-8449-495a-91c2-92fde8bcf344");
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static final boolean useSingleClassification = true;
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static final String classificationName = "Euro+Med (Caucasus) 2018";
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static final UUID featureTreeUuid = UUID.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7");
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static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};
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// set to zero for unlimited nameFacts
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static final int maximumNumberOfNameFacts = 0;
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static final int partitionSize = 2500;
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//editor - import
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static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
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//NomenclaturalCode
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static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
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//ignore null
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static final boolean ignoreNull = false;
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static final boolean switchSpeciesGroup = true;
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static boolean useClassification = true;
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static boolean isSplitTdwgCodes = false;
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static boolean useEmAreaVocabulary = true;
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private final boolean removeHttpMapsAnchor = true;
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static final String infrGenericRankAbbrev = "[unranked]";
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static final String infrSpecificRankAbbrev = "[unranked]";
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static boolean useLastScrutinyAsSec = true;
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static boolean warnForDifferingSynonymReference = false;
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static String taxonTable = "v_cdm_exp_taxaAll";
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static String classificationQuery = " SELECT DISTINCT t.PTRefFk, r.RefCache FROM PTaxon t INNER JOIN Reference r ON t.PTRefFk = r.RefId WHERE t.PTRefFk = " + sourceSecId;
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static String relPTaxonIdQuery = " SELECT r.RelPTaxonId "
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+ " FROM RelPTaxon AS r "
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+ " INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk "
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+ " INNER JOIN PTaxon As pt1 ON pt1.PTNameFk = r.PTNameFk1 AND pt1.PTRefFk = r.PTRefFk1 "
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+ " WHERE r.RelPTaxonID NOT IN (1874890,1874959,1874932,1874793,1874956,1874971,1874902,1874696) " //Relations to unpublished Kew genus taxa of Bethulaceae which are not imported anymore, but Bethulaceae is still imported
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+ " AND NOT (pt1.PTRefFk = 8000000 AND pt1.publishFlag = 0) ";
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static String nameIdTable = " v_cdm_exp_namesAll ";
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static String referenceIdTable = " v_cdm_exp_refAll ";
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static String refDetailFilter = " RefDetailID IN (SELECT RefDetailID FROM v_cdm_exp_RefDetail) ";
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static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll WHERE FactCategoryFk NOT IN (12, 14, 249, 251))";
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static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
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static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
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static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";
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static String webMarkerFilter = " TableNameFk <> 500 OR ( RIdentifierFk IN (SELECT RIdentifier FROM v_cdm_exp_taxaAll)) ";
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static String authorTeamFilter = " authorTeamId IN (SELECT drvTab.authorTeamId FROM (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) as drvTab) ";
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static String authorFilter = " authorId IN (SELECT drvTab.authorId FROM (SELECT authorId FROM v_cdm_exp_authorsAll) as drvTab) ";
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// **************** ALL *********************
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public void importEm2CDM (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
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System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
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//make BerlinModel Source
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BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source, destination);
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config.setClassificationName(classificationName);
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config.setClassificationUuid(classificationUuid);
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config.setSourceSecId(sourceSecId);
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config.setNomenclaturalCode(nomenclaturalCode);
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config.setIgnoreNull(ignoreNull);
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config.setDoAuthors(doAuthors ^ invers);
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config.setDoReferences(invers ? doReferences.invers() : doReferences);
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config.setDoTaxonNames(doTaxonNames ^ invers);
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config.setDoRelNames(doRelNames ^ invers);
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config.setDoNameStatus(doNameStatus ^ invers);
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config.setDoTypes(doTypes); //always false
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config.setDoNameFacts(doNameFacts ^ invers);
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config.setDoTaxa(doTaxa ^ invers);
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config.setDoRelTaxa(doRelTaxa ^ invers);
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config.setDoNamedAreas(doNamedAreas ^ invers);
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config.setDoFacts(doFacts);
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config.setDoOccurrence(doOccurrences);
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config.setDoOccurrenceSources(doOccurrenceSources);
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config.setDoCommonNames(doCommonNames);
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config.setDoMarker(doMarker);
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config.setDoUser(doUser ^ invers);
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config.setEuroMed(true);
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config.setDoSourceNumber(true);
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config.setLogNotMatchingOldNames(logNotMatchingOldNames);
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config.setLogMatchingNotExportedOldNames(logMatchingNotExportedOldNames);
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config.setCheckOldNameIsSynonym(checkOldNameIsSynonym);
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config.setUseClassification(useClassification);
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config.setSourceRefUuid(BerlinModelTransformer.uuidSourceRefEuroMed);
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config.setEditor(editor);
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config.setDbSchemaValidation(hbm2dll);
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config.setUseLastScrutinyAsSec(useLastScrutinyAsSec);
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config.setWarnForDifferingSynonymReference(warnForDifferingSynonymReference);
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// maximum number of name facts to import
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config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
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config.setInfrGenericRankAbbrev(infrGenericRankAbbrev);
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config.setInfrSpecificRankAbbrev(infrSpecificRankAbbrev);
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config.setRemoveHttpMapsAnchor(removeHttpMapsAnchor);
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config.setDoPreliminaryRefDetailsWithNames(doPreliminaryRefDetailsWithNames);
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// filter
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config.setTaxonTable(taxonTable);
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config.setClassificationQuery(classificationQuery);
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config.setRelTaxaIdQuery(relPTaxonIdQuery);
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config.setNameIdTable(nameIdTable);
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config.setReferenceIdTable(referenceIdTable);
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config.setAuthorTeamFilter(authorTeamFilter);
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config.setAuthorFilter(authorFilter);
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config.setFactFilter(factFilter);
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config.setRefDetailFilter(refDetailFilter);
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config.setCommonNameFilter(commonNameFilter);
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config.setOccurrenceFilter(occurrenceFilter);
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config.setOccurrenceSourceFilter(occurrenceSourceFilter);
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config.setWebMarkerFilter(webMarkerFilter);
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config.setUseSingleClassification(useSingleClassification);
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//TDWG codes
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config.setSplitTdwgCodes(isSplitTdwgCodes);
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config.setUseEmAreaVocabulary(useEmAreaVocabulary);
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config.setCheck(check);
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config.setEditor(editor);
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config.setRecordsPerTransaction(partitionSize);
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config.setSwitchSpeciesGroup(switchSpeciesGroup);
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// invoke import
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CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<>();
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bmImport.invoke(config);
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renameRanks(config, bmImport);
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createFeatureTree(config, bmImport);
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changeCommonNameLabel(config, bmImport);
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createUsersAndRoles(config, bmImport);
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createPreferences(config, bmImport);
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System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
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}
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/**
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* @param config
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* @param bmImport
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*/
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private void createPreferences(BerlinModelImportConfigurator config,
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CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
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if (config.isDoUser() && (config.getCheck().isImport() )){
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ICdmRepository app = bmImport.getCdmAppController();
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//area voc
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CdmPreference areaVocPref = CdmPreference.NewTaxEditorInstance(PreferencePredicate.AvailableDistributionAreaVocabularies, BerlinModelTransformer.uuidVocCaucasusAreas.toString());
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areaVocPref.setAllowOverride(false);
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app.getPreferenceService().set(areaVocPref);
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//occ status list
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String status ="42946bd6-9c22-45ad-a910-7427e8f60bfd;9eb99fe6-59e2-4445-8e6a-478365bd0fa9;c3ee7048-15b7-4be1-b687-9ce9c1a669d6;643cf9d1-a5f1-4622-9837-82ef961e880b;0c54761e-4887-4788-9dfa-7190c88746e3;83eb0aa0-1a45-495a-a3ca-bf6958b74366;aeec2947-2700-4623-8e32-9e3a430569d1;ddeac4f2-d8fa-43b8-ad7e-ca13abdd32c7;310373bf-7df4-4d02-8cb3-bcc7448805fc;5c397f7b-59ef-4c11-a33c-45691ceda91b;925662c1-bb10-459a-8c53-da5a738ac770;61cee840-801e-41d8-bead-015ad866c2f1;e191e89a-a751-4b0c-b883-7f1de70915c9";
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CdmPreference statusListPref = CdmPreference.NewTaxEditorInstance(PreferencePredicate.AvailableDistributionAreaVocabularies, status);
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statusListPref.setAllowOverride(false);
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app.getPreferenceService().set(statusListPref);
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//distr. editor activated
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CdmPreference distrEditorActive = CdmPreference.NewTaxEditorInstance(PreferencePredicate.DistributionEditorActivated, "true");
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statusListPref.setAllowOverride(true);
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app.getPreferenceService().set(distrEditorActive);
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//idInVoc for areas
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CdmPreference distrEditorShowIdInVocForAreas = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowIdInVocabulary, "true");
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distrEditorShowIdInVocForAreas.setAllowOverride(true);
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app.getPreferenceService().set(distrEditorShowIdInVocForAreas);
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//areas sort order
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CdmPreference distrEditorSorted = CdmPreference.NewTaxEditorInstance(PreferencePredicate.AreasSortedByIdInVocabulary, "true");
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distrEditorSorted.setAllowOverride(true);
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app.getPreferenceService().set(distrEditorSorted);
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//distr. status uses symbol
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//?? correct?
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CdmPreference distrEditorStatusUseSymbols = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowSymbolForStatus, "false");
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distrEditorStatusUseSymbols.setAllowOverride(true);
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app.getPreferenceService().set(distrEditorStatusUseSymbols);
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//media view
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CdmPreference showMediaView = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowMediaView, "false");
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showMediaView.setAllowOverride(false);
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app.getPreferenceService().set(showMediaView);
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//multi classification
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CdmPreference multiClassification = CdmPreference.NewTaxEditorInstance(PreferencePredicate.DisableMultiClassification, "false");
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multiClassification.setAllowOverride(false);
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app.getPreferenceService().set(multiClassification);
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//taxon node wizard
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CdmPreference showTaxonNodeWizard = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowTaxonNodeWizard, "false");
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showTaxonNodeWizard.setAllowOverride(false);
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app.getPreferenceService().set(showTaxonNodeWizard);
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352
|
|
353
|
//import+export
|
354
|
CdmPreference showImportExportMenu = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowImportExportMenu, "false");
|
355
|
showImportExportMenu.setAllowOverride(true);
|
356
|
app.getPreferenceService().set(showImportExportMenu);
|
357
|
|
358
|
//show specimen
|
359
|
CdmPreference showSpecimen = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowSpecimen, "false");
|
360
|
showSpecimen.setAllowOverride(false);
|
361
|
app.getPreferenceService().set(showSpecimen);
|
362
|
}
|
363
|
}
|
364
|
|
365
|
//Rename Ranks (still needed?)
|
366
|
private void renameRanks(BerlinModelImportConfigurator config,
|
367
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
|
368
|
|
369
|
if (config.isDoTaxonNames() && (config.getCheck().isImport() ) ){
|
370
|
ICdmRepository app = bmImport.getCdmAppController();
|
371
|
TransactionStatus tx = app.startTransaction();
|
372
|
try {
|
373
|
Rank sectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());
|
374
|
Representation repr = sectBot.getRepresentation(Language.ENGLISH());
|
375
|
repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());
|
376
|
repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());
|
377
|
sectBot.setTitleCache(null, false); //to definitely update the titleCache also
|
378
|
app.getTermService().saveOrUpdate(sectBot);
|
379
|
|
380
|
Rank subSectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());
|
381
|
repr = subSectBot.getRepresentation(Language.ENGLISH());
|
382
|
repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());
|
383
|
repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());
|
384
|
subSectBot.setTitleCache(null, false); //to definitely update the titleCache also
|
385
|
app.getTermService().saveOrUpdate(subSectBot);
|
386
|
app.commitTransaction(tx);
|
387
|
} catch (Exception e) {
|
388
|
e.printStackTrace();
|
389
|
logger.error("Exception in renameRanks: " + e.getMessage());
|
390
|
}
|
391
|
}
|
392
|
}
|
393
|
|
394
|
//create feature tree
|
395
|
private void createFeatureTree(BerlinModelImportConfigurator config,
|
396
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport){
|
397
|
if (config.isDoFacts() && (config.getCheck().isImport() ) ){
|
398
|
try {
|
399
|
ICdmRepository app = bmImport.getCdmAppController();
|
400
|
TransactionStatus tx = app.startTransaction();
|
401
|
|
402
|
//make feature tree
|
403
|
FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
|
404
|
tree.setTitleCache("Euro+Med Feature Tree", true);
|
405
|
FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
|
406
|
tree.getRoot().addChild(imageNode);
|
407
|
FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
|
408
|
tree.getRoot().addChild(distributionNode, 1);
|
409
|
FeatureNode commonNameNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
|
410
|
tree.getRoot().addChild(commonNameNode, 2);
|
411
|
app.getFeatureTreeService().saveOrUpdate(tree);
|
412
|
|
413
|
app.commitTransaction(tx);
|
414
|
} catch (Exception e) {
|
415
|
e.printStackTrace();
|
416
|
logger.error("Exception in createFeatureTree: " + e.getMessage());
|
417
|
}
|
418
|
}
|
419
|
}
|
420
|
|
421
|
//Change common name label
|
422
|
private void changeCommonNameLabel(BerlinModelImportConfigurator config,
|
423
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
|
424
|
if (config.isDoFacts() && (config.getCheck().isImport() ) ){
|
425
|
try {
|
426
|
ICdmRepository app = bmImport.getCdmAppController();
|
427
|
TransactionStatus tx = app.startTransaction();
|
428
|
|
429
|
DefinedTermBase<?> commonNameFeature = app.getTermService().find(Feature.COMMON_NAME().getUuid());
|
430
|
commonNameFeature.setLabel("Common Names", Language.ENGLISH());
|
431
|
commonNameFeature.setTitleCache(null, false); //to definitely update the titleCache also
|
432
|
app.getTermService().saveOrUpdate(commonNameFeature);
|
433
|
|
434
|
app.commitTransaction(tx);
|
435
|
} catch (Exception e) {
|
436
|
e.printStackTrace();
|
437
|
logger.error("Exception in changeCommonNameLabel: " + e.getMessage());
|
438
|
}
|
439
|
}
|
440
|
}
|
441
|
|
442
|
//1. run transmission engine #3979
|
443
|
private void runTransmissionEngine(BerlinModelImportConfigurator config,
|
444
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
|
445
|
|
446
|
if (doRunTransmissionEngine && (config.getCheck().isImport() ) ){
|
447
|
try {
|
448
|
ICdmRepository app = bmImport.getCdmAppController();
|
449
|
|
450
|
final List<String> term_init_strategy = Arrays.asList(new String []{
|
451
|
"representations"
|
452
|
});
|
453
|
|
454
|
UUID uuidSuperAreaLevel = BerlinModelTransformer.uuidEuroMedAreaLevelFirst;
|
455
|
NamedAreaLevel euroMedLevel1 = (NamedAreaLevel)app.getTermService().find(uuidSuperAreaLevel);
|
456
|
|
457
|
Pager<NamedArea> areaPager = app.getTermService().list(
|
458
|
euroMedLevel1,
|
459
|
(NamedAreaType) null,
|
460
|
null,
|
461
|
null,
|
462
|
(List<OrderHint>) null,
|
463
|
term_init_strategy);
|
464
|
TransmissionEngineDistribution transmissionEngineDistribution = (TransmissionEngineDistribution)app.getBean("transmissionEngineDistribution");
|
465
|
transmissionEngineDistribution.accumulate(
|
466
|
AggregationMode.byAreasAndRanks,
|
467
|
areaPager.getRecords(),
|
468
|
Rank.UNRANKED_INFRASPECIFIC(), //or do we even want to start from lower (UNKNOWN?)
|
469
|
Rank.GENUS(),
|
470
|
null,
|
471
|
DefaultProgressMonitor.NewInstance());
|
472
|
} catch (Exception e) {
|
473
|
e.printStackTrace();
|
474
|
logger.error("Exception in markAreasAsHidden: " + e.getMessage());
|
475
|
}
|
476
|
}
|
477
|
}
|
478
|
|
479
|
// //5.Mark areas to be hidden #3979 .5
|
480
|
// private void markAreasAsHidden(BerlinModelImportConfigurator config,
|
481
|
// CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
|
482
|
//
|
483
|
// if (config.isDoOccurrence() && (config.getCheck().isImport())){
|
484
|
// try {
|
485
|
// ICdmRepository app = bmImport.getCdmAppController();
|
486
|
// TransactionStatus tx = app.startTransaction();
|
487
|
//
|
488
|
// MarkerType hiddenAreaMarkerType = MarkerType.NewInstance("Used to hide distributions for the named areas in publications", "Hidden Area", null);
|
489
|
// hiddenAreaMarkerType.setUuid(BerlinModelTransformer.uuidHiddenArea);
|
490
|
// @SuppressWarnings("unchecked")
|
491
|
// TermVocabulary<MarkerType> vocUserDefinedMarkerTypes = app.getVocabularyService().find(CdmImportBase.uuidUserDefinedMarkerTypeVocabulary);
|
492
|
// if (vocUserDefinedMarkerTypes == null){
|
493
|
// String message = "Marker type vocabulary could not be found. Hidden areas not added.";
|
494
|
// logger.error(message);
|
495
|
// System.out.println(message);
|
496
|
// }else{
|
497
|
// vocUserDefinedMarkerTypes.addTerm(hiddenAreaMarkerType);
|
498
|
// app.getVocabularyService().saveOrUpdate(vocUserDefinedMarkerTypes);
|
499
|
//
|
500
|
// //Add hidden area marker to Rs(C) and Rs(N)
|
501
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs);
|
502
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_B);
|
503
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_C);
|
504
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_E);
|
505
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_N);
|
506
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_K);
|
507
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_W);
|
508
|
// }
|
509
|
// app.commitTransaction(tx);
|
510
|
// } catch (Exception e) {
|
511
|
// e.printStackTrace();
|
512
|
// logger.error("Exception in markAreasAsHidden: " + e.getMessage());
|
513
|
// }
|
514
|
// }
|
515
|
// }
|
516
|
//
|
517
|
// private void hideArea(ICdmRepository app, MarkerType hiddenAreaMarkerType, UUID areaUuid) {
|
518
|
// NamedArea area = (NamedArea)app.getTermService().find(areaUuid);
|
519
|
// area.addMarker(Marker.NewInstance(hiddenAreaMarkerType, true));
|
520
|
// app.getTermService().saveOrUpdate(area);
|
521
|
// }
|
522
|
|
523
|
//2. import shapefile attributes #3979 .2
|
524
|
private void importShapefile(BerlinModelImportConfigurator config,
|
525
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
|
526
|
|
527
|
if (config.isDoOccurrence() && (config.getCheck().isImport())){
|
528
|
|
529
|
try {
|
530
|
UUID areaVocabularyUuid = BerlinModelTransformer.uuidVocEuroMedAreas;
|
531
|
List<String> idSearchFields = Arrays.asList(new String[]{"EMAREA","PARENT"});
|
532
|
String wmsLayerName = "euromed_2013";
|
533
|
Set<UUID> areaUuidSet = null;
|
534
|
|
535
|
ICdmRepository app = bmImport.getCdmAppController();
|
536
|
IEditGeoService geoService = (IEditGeoService)app.getBean("editGeoService");
|
537
|
|
538
|
Map<NamedArea, String> resultMap;
|
539
|
try {
|
540
|
InputStream in = CaucasusEuroMedActivator.class.getResourceAsStream("/euromed/euromed_2013.csv");
|
541
|
Reader reader = new InputStreamReader(in, "UTF-8");
|
542
|
|
543
|
resultMap = geoService.mapShapeFileToNamedAreas(
|
544
|
reader, idSearchFields , wmsLayerName , areaVocabularyUuid, areaUuidSet);
|
545
|
Map<String, String> flatResultMap = new HashMap<>(resultMap.size());
|
546
|
for(NamedArea area : resultMap.keySet()){
|
547
|
flatResultMap.put(area.getTitleCache() + " [" + area.getUuid() + "]", resultMap.get(area));
|
548
|
}
|
549
|
} catch (IOException e) {
|
550
|
String message = "IOException when reading from mapping file or creating result map.";
|
551
|
logger.error(message);
|
552
|
System.out.println(message);
|
553
|
}
|
554
|
} catch (Exception e) {
|
555
|
e.printStackTrace();
|
556
|
logger.error("Exception in importShapefile: " + e.getMessage());
|
557
|
}
|
558
|
}
|
559
|
}
|
560
|
|
561
|
//4. Create users and assign roles #3979
|
562
|
private void createUsersAndRoles(BerlinModelImportConfigurator config,
|
563
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
|
564
|
|
565
|
try {
|
566
|
if (config.isDoRelTaxa() && (config.getCheck().isImport())){
|
567
|
ICdmRepository app = bmImport.getCdmAppController();
|
568
|
TransactionStatus tx = app.startTransaction();
|
569
|
|
570
|
//eraabstraube
|
571
|
String eraabstraube = "e.raabstraube";
|
572
|
List<User> users = app.getUserService().listByUsername(eraabstraube, MatchMode.EXACT, null, null, null, null, null);
|
573
|
User userEraabStraube;
|
574
|
if (users.isEmpty()){
|
575
|
userEraabStraube = User.NewInstance(eraabstraube, eraabstraube);
|
576
|
}else{
|
577
|
userEraabStraube = users.get(0);
|
578
|
}
|
579
|
if (userEraabStraube.getPerson() == null){
|
580
|
Person eckhard = Person.NewInstance();
|
581
|
eckhard.setFamilyName("von Raab-Straube");
|
582
|
eckhard.setGivenName("Eckhard");
|
583
|
eckhard.setPrefix("Dr.");
|
584
|
userEraabStraube.setPerson(eckhard);
|
585
|
}
|
586
|
app.getUserService().saveOrUpdate(userEraabStraube);
|
587
|
|
588
|
//groups
|
589
|
Group groupEditor = app.getGroupService().load(Group.GROUP_EDITOR_UUID);
|
590
|
groupEditor.addMember(userEraabStraube);
|
591
|
app.getGroupService().saveOrUpdate(groupEditor);
|
592
|
|
593
|
Group groupProjectManager = app.getGroupService().load(Group.GROUP_PROJECT_MANAGER_UUID);
|
594
|
groupProjectManager.addMember(userEraabStraube);
|
595
|
app.getGroupService().saveOrUpdate(groupProjectManager);
|
596
|
|
597
|
String[] publishRoles = new String[]{Role.ROLE_PUBLISH.toString()};
|
598
|
Group groupPublisher = checkGroup(app.getGroupService(), Group.GROUP_PUBLISHER_UUID, "Publisher", publishRoles);
|
599
|
groupPublisher.addMember(userEraabStraube);
|
600
|
app.getGroupService().saveOrUpdate(groupPublisher);
|
601
|
|
602
|
UUID uuidEuroMedPlantBaseGroup = UUID.fromString("91be42ea-ad04-4458-9836-389277e773db");
|
603
|
String[] emPlantBaseRoles = new String[]{"TAXONNODE.[CREATE,READ,UPDATE,DELETE]"};
|
604
|
Group euroMedPlantbase = checkGroup(app.getGroupService(), uuidEuroMedPlantBaseGroup, "Euro+Med Plantbase", emPlantBaseRoles);
|
605
|
euroMedPlantbase.addMember(userEraabStraube);
|
606
|
app.getGroupService().saveOrUpdate(euroMedPlantbase);
|
607
|
|
608
|
//cichorieae-editor
|
609
|
String cichorieaeEditor = "cichorieae-editor";
|
610
|
app.getUserService().listByUsername(cichorieaeEditor, MatchMode.EXACT, null, null, null, null, null);
|
611
|
User userCichEditor;
|
612
|
if (users.isEmpty()){
|
613
|
userCichEditor = User.NewInstance(cichorieaeEditor, cichorieaeEditor);
|
614
|
}else{
|
615
|
userCichEditor = users.get(0);
|
616
|
}
|
617
|
app.getUserService().saveOrUpdate(userCichEditor);
|
618
|
|
619
|
//groups
|
620
|
groupEditor.addMember(userCichEditor);
|
621
|
app.getGroupService().saveOrUpdate(groupEditor);
|
622
|
|
623
|
UUID uuidCichorieaeSubtree = null;
|
624
|
UUID uuidCichorieae = UUID.fromString("63c7dbeb-b9a2-48b8-a75f-e3fe5e161f7c");
|
625
|
Taxon cich = (Taxon)app.getTaxonService().find(uuidCichorieae);
|
626
|
if (cich != null){
|
627
|
if (!cich.getTaxonNodes().isEmpty()){
|
628
|
TaxonNode cichNode = cich.getTaxonNodes().iterator().next();
|
629
|
uuidCichorieaeSubtree = cichNode.getUuid();
|
630
|
}
|
631
|
}
|
632
|
|
633
|
String[] cichorieaeRoles = new String[]{};
|
634
|
if (uuidCichorieaeSubtree != null){
|
635
|
cichorieaeRoles = new String[]{"TAXONNODE.[CREATE,READ,UPDATE,DELETE]{"+uuidCichorieaeSubtree.toString()+"}"};
|
636
|
}else{
|
637
|
String message = "Cichorieae node could not be found for cichorieae-editor role";
|
638
|
logger.warn(message);
|
639
|
System.out.println(message);
|
640
|
}
|
641
|
UUID uuidCichorieaeGroup = UUID.fromString("a630938d-dd4f-48c2-9406-91def487b11e");
|
642
|
String cichorieaeGroupName = "Cichorieae";
|
643
|
Group cichorieaeGroup = checkGroup(app.getGroupService(), uuidCichorieaeGroup, cichorieaeGroupName, cichorieaeRoles);
|
644
|
cichorieaeGroup.addMember(userCichEditor);
|
645
|
app.getGroupService().saveOrUpdate(cichorieaeGroup);
|
646
|
|
647
|
app.commitTransaction(tx);
|
648
|
}
|
649
|
} catch (Exception e) {
|
650
|
e.printStackTrace();
|
651
|
logger.error("Exception in createUsersAndRoles: " + e.getMessage());
|
652
|
}
|
653
|
}
|
654
|
|
655
|
/**
|
656
|
* copied from {@link FirstDataInserter#checkGroup}
|
657
|
*/
|
658
|
private Group checkGroup(IGroupService groupService, UUID groupUuid, String groupName, String[] requiredAuthorities) {
|
659
|
Group group = groupService.load(groupUuid);
|
660
|
if(group == null){
|
661
|
group = Group.NewInstance();
|
662
|
group.setUuid(groupUuid);
|
663
|
logger.info("New Group '" + groupName + "' created");
|
664
|
}
|
665
|
group.setName(groupName); // force name
|
666
|
|
667
|
Set<GrantedAuthority> grantedAuthorities = group.getGrantedAuthorities();
|
668
|
|
669
|
for(String a : requiredAuthorities){
|
670
|
boolean isMissing = true;
|
671
|
for(GrantedAuthority ga : grantedAuthorities){
|
672
|
if(a.equals(ga.getAuthority())){
|
673
|
isMissing = false;
|
674
|
break;
|
675
|
}
|
676
|
}
|
677
|
if(isMissing){
|
678
|
GrantedAuthorityImpl newGa = GrantedAuthorityImpl.NewInstance(a);
|
679
|
group.addGrantedAuthority(newGa);
|
680
|
logger.info("New GrantedAuthority '" + a + "' added to '" + groupName + "'");
|
681
|
}
|
682
|
}
|
683
|
groupService.saveOrUpdate(group);
|
684
|
logger.info("Check of group '" + groupName + "' done");
|
685
|
return group;
|
686
|
}
|
687
|
|
688
|
|
689
|
/**
|
690
|
* @param args
|
691
|
*/
|
692
|
public static void main(String[] args) {
|
693
|
CaucasusEuroMedActivator importActivator = new CaucasusEuroMedActivator();
|
694
|
Source source = berlinModelSource;
|
695
|
ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
|
696
|
|
697
|
importActivator.importEm2CDM(source, cdmRepository, hbm2dll);
|
698
|
if (includePesiExport){
|
699
|
//not available from here since E+M was moved to app-import
|
700
|
// PesiExportActivatorEM exportActivator = new PesiExportActivatorEM();
|
701
|
// exportActivator.doExport(cdmRepository);
|
702
|
}
|
703
|
System.exit(0);
|
704
|
|
705
|
}
|
706
|
|
707
|
}
|