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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.io.berlinModel;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.common.ResultWrapper;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
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import eu.etaxonomy.cdm.model.description.PresenceTerm;
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import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.reference.Article;
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import eu.etaxonomy.cdm.model.reference.Book;
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import eu.etaxonomy.cdm.model.reference.CdDvd;
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import eu.etaxonomy.cdm.model.reference.Database;
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import eu.etaxonomy.cdm.model.reference.Generic;
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import eu.etaxonomy.cdm.model.reference.Journal;
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import eu.etaxonomy.cdm.model.reference.Patent;
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import eu.etaxonomy.cdm.model.reference.PersonalCommunication;
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import eu.etaxonomy.cdm.model.reference.PrintSeries;
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import eu.etaxonomy.cdm.model.reference.Proceedings;
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import eu.etaxonomy.cdm.model.reference.Report;
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import eu.etaxonomy.cdm.model.reference.SectionBase;
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import eu.etaxonomy.cdm.model.reference.StrictReferenceBase;
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import eu.etaxonomy.cdm.model.reference.Thesis;
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import eu.etaxonomy.cdm.model.reference.WebPage;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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/**
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* @author a.mueller
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* @created 20.03.2008
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* @version 1.0
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*/
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public final class BerlinModelTransformer {
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private static final Logger logger = Logger.getLogger(BerlinModelTransformer.class);
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//REFERENCES
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public static int REF_ARTICLE = 1;
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public static int REF_PART_OF_OTHER_TITLE = 2;
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public static int REF_BOOK = 3;
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public static int REF_DATABASE = 4;
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public static int REF_INFORMAL = 5;
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public static int REF_NOT_APPLICABLE = 6;
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public static int REF_WEBSITE = 7;
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public static int REF_CD = 8;
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public static int REF_JOURNAL = 9;
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public static int REF_UNKNOWN = 10;
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public static int REF_PRINT_SERIES = 55;
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public static int REF_CONFERENCE_PROCEEDINGS = 56;
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public static int REF_JOURNAL_VOLUME = 57;
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//NameStatus
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public static int NAME_ST_NOM_INVAL = 1;
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public static int NAME_ST_NOM_ILLEG = 2;
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public static int NAME_ST_NOM_NUD = 3;
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public static int NAME_ST_NOM_REJ = 4;
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public static int NAME_ST_NOM_REJ_PROP = 5;
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public static int NAME_ST_NOM_UTIQUE_REJ = 6;
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public static int NAME_ST_NOM_UTIQUE_REJ_PROP = 7;
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public static int NAME_ST_NOM_CONS = 8;
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public static int NAME_ST_NOM_CONS_PROP = 9;
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public static int NAME_ST_ORTH_CONS = 10;
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public static int NAME_ST_ORTH_CONS_PROP = 11;
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public static int NAME_ST_NOM_SUPERFL = 12;
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public static int NAME_ST_NOM_AMBIG = 13;
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public static int NAME_ST_NOM_PROVIS = 14;
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public static int NAME_ST_NOM_DUB = 15;
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public static int NAME_ST_NOM_NOV = 16;
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public static int NAME_ST_NOM_CONFUS = 17;
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public static int NAME_ST_NOM_ALTERN = 18;
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public static int NAME_ST_COMB_INVAL = 19;
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//NameRelationShip
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public static int NAME_REL_IS_BASIONYM_FOR = 1;
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public static int NAME_REL_IS_LATER_HOMONYM_OF = 2;
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public static int NAME_REL_IS_REPLACED_SYNONYM_FOR = 3;
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public static int NAME_REL_IS_VALIDATION_OF = 4;
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public static int NAME_REL_IS_LATER_VALIDATION_OF = 5;
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public static int NAME_REL_IS_TYPE_OF = 6;
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public static int NAME_REL_IS_CONSERVED_TYPE_OF =7;
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public static int NAME_REL_IS_REJECTED_TYPE_OF = 8;
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public static int NAME_REL_IS_FIRST_PARENT_OF = 9;
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public static int NAME_REL_IS_SECOND_PARENT_OF = 10;
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public static int NAME_REL_IS_FEMALE_PARENT_OF = 11;
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public static int NAME_REL_IS_MALE_PARENT_OF = 12;
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public static int NAME_REL_IS_CONSERVED_AGAINST =13;
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public static int NAME_REL_IS_REJECTED_IN_FAVOUR_OF = 14;
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public static int NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF = 15;
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public static int NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF = 16;
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public static int NAME_REL_HAS_SAME_TYPE_AS = 18;
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public static int NAME_REL_IS_LECTOTYPE_OF = 61;
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public static int NAME_REL_TYPE_NOT_DESIGNATED = 62;
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//NameFacts
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public static String NAME_FACT_PROTOLOGUE = "Protologue";
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public static String NAME_FACT_ALSO_PUBLISHED_IN = "Also published in";
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//TaxonRelationShip
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public static int TAX_REL_IS_INCLUDED_IN = 1;
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public static int TAX_REL_IS_SYNONYM_OF = 2;
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public static int TAX_REL_IS_MISAPPLIED_NAME_OF = 3;
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public static int TAX_REL_IS_PROPARTE_SYN_OF = 4;
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public static int TAX_REL_IS_PARTIAL_SYN_OF = 5;
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public static int TAX_REL_IS_HETEROTYPIC_SYNONYM_OF = 6;
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public static int TAX_REL_IS_HOMOTYPIC_SYNONYM_OF = 7;
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public static int TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF = 101;
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public static int TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF = 102;
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public static int TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF = 103;
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public static int TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF = 104;
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//TaxonStatus
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public static int T_STATUS_ACCEPTED = 1;
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public static int T_STATUS_SYNONYM = 2;
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public static int T_STATUS_PARTIAL_SYN = 3;
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public static int T_STATUS_PRO_PARTE_SYN = 4;
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public static int T_STATUS_UNRESOLVED = 5;
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public static int T_STATUS_ORPHANED = 6;
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//Facts
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public static int FACT_DESCRIPTION = 1;
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public static int FACT_GROWTH_FORM = 2;
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public static int FACT_HARDINESS = 3;
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public static int FACT_ECOLOGY = 4;
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public static int FACT_PHENOLOGY = 5;
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public static int FACT_KARYOLOGY = 6;
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public static int FACT_ILLUSTRATION = 7;
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public static int FACT_IDENTIFICATION = 8;
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public static int FACT_OBSERVATION = 9;
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public static int FACT_DISTRIBUTION_EM = 10;
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public static int FACT_DISTRIBUTION_WORLD = 11;
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//TypeDesignation
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public static SpecimenTypeDesignationStatus typeStatusId2TypeStatus (int typeStatusId) throws UnknownCdmTypeException{
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switch (typeStatusId){
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case 0: return null;
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case 1: return SpecimenTypeDesignationStatus.HOLOTYPE();
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case 2: return SpecimenTypeDesignationStatus.LECTOTYPE();
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case 3: return SpecimenTypeDesignationStatus.NEOTYPE();
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case 4: return SpecimenTypeDesignationStatus.EPITYPE();
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case 5: return SpecimenTypeDesignationStatus.ISOLECTOTYPE();
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case 6: return SpecimenTypeDesignationStatus.ISONEOTYPE();
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case 7: return SpecimenTypeDesignationStatus.ISOTYPE();
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case 8: return SpecimenTypeDesignationStatus.PARANEOTYPE();
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case 9: return SpecimenTypeDesignationStatus.PARATYPE();
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case 10: return SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE();
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case 11: return SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE();
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case 12: return SpecimenTypeDesignationStatus.SYNTYPE();
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case 21: return SpecimenTypeDesignationStatus.ICONOTYPE();
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case 22: return SpecimenTypeDesignationStatus.PHOTOTYPE();
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default: {
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throw new UnknownCdmTypeException("Unknown TypeDesignationStatus (id=" + Integer.valueOf(typeStatusId).toString() + ")");
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}
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}
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}
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//TypeDesignation
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public static TaxonRelationshipType taxonRelId2TaxonRelType (int relTaxonTypeId, ResultWrapper<Boolean> isInverse) throws UnknownCdmTypeException{
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isInverse.setValue(false);
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switch (relTaxonTypeId){
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case 0: return null;
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case 11: return TaxonRelationshipType.CONGRUENT_TO();
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case 12: isInverse.setValue(true); return TaxonRelationshipType.INCLUDES();
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case 13: isInverse.setValue(true); return TaxonRelationshipType.CONGRUENT_OR_INCLUDES();
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case 14: return TaxonRelationshipType.INCLUDES();
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case 15: return TaxonRelationshipType.CONGRUENT_OR_INCLUDES();
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case 16: return TaxonRelationshipType.INCLUDED_OR_INCLUDES();
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case 17: return TaxonRelationshipType.CONGRUENT_OR_INCLUDED_OR_INCLUDES();
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case 18: return TaxonRelationshipType.OVERLAPS();
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case 19: return TaxonRelationshipType.CONGRUENT_OR_OVERLAPS();
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case 20: isInverse.setValue(true); return TaxonRelationshipType.INCLUDES_OR_OVERLAPS();
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case 21: isInverse.setValue(true); return TaxonRelationshipType.CONGRUENT_OR_INCLUDES_OR_OVERLAPS();
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case 22: return TaxonRelationshipType.INCLUDES_OR_OVERLAPS();
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case 23: return TaxonRelationshipType.CONGRUENT_OR_INCLUDES_OR_OVERLAPS();
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case 24: return TaxonRelationshipType.INCLUDED_OR_INCLUDES_OR_OVERLAPS();
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case 26: return TaxonRelationshipType.OVERLAPS();
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//TODO other relationshipTypes
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//FIXME doubtful
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case 43: return TaxonRelationshipType.CONGRUENT_TO();
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default: {
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throw new UnknownCdmTypeException("Unknown TypeDesignationStatus (id=" + Integer.valueOf(relTaxonTypeId).toString() + ")");
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}
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}
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}
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//TypeDesignation
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public static HybridRelationshipType relNameId2HybridRel (int relNameId) throws UnknownCdmTypeException{
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switch (relNameId){
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case 0: return null;
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case 9: return HybridRelationshipType.FIRST_PARENT();
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case 10: return HybridRelationshipType.SECOND_PARENT();
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case 11: return HybridRelationshipType.FEMALE_PARENT();
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case 12: return HybridRelationshipType.MALE_PARENT();
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default: {
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throw new UnknownCdmTypeException("Unknown HybridRelationshipType (id=" + Integer.valueOf(relNameId).toString() + ")");
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}
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}
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}
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229
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//OccStatus
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public static PresenceAbsenceTermBase<?> occStatus2PresenceAbsence (int occStatusId) throws UnknownCdmTypeException{
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switch (occStatusId){
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case 0: return null;
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case 110: return PresenceTerm.CULTIVATED_REPORTED_IN_ERROR();
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case 120: return PresenceTerm.CULTIVATED();
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case 210: return PresenceTerm.INTRODUCED_REPORTED_IN_ERROR();
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case 220: return PresenceTerm.INTRODUCED_PRESENCE_QUESTIONABLE();
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case 230: return PresenceTerm.INTRODUCED_FORMERLY_INTRODUCED();
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case 240: return PresenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED();
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case 250: return PresenceTerm.INTRODUCED();
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case 260: return PresenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION();
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241
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case 270: return PresenceTerm.INTRODUCED_ADVENTITIOUS();
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case 280: return PresenceTerm.INTRODUCED_NATURALIZED();
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case 310: return PresenceTerm.NATIVE_REPORTED_IN_ERROR();
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case 320: return PresenceTerm.NATIVE_PRESENCE_QUESTIONABLE();
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case 330: return PresenceTerm.NATIVE_FORMERLY_NATIVE();
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246
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case 340: return PresenceTerm.NATIVE_DOUBTFULLY_NATIVE();
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case 350: return PresenceTerm.NATIVE();
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248
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case 999: {
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249
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logger.warn("endemic for EM can not be transformed in legal status");
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250
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//TODO preliminary
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251
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return PresenceTerm.PRESENT();
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252
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}
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253
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default: {
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254
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throw new UnknownCdmTypeException("Unknown occurrence status (id=" + Integer.valueOf(occStatusId).toString() + ")");
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255
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}
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256
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}
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257
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}
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258
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259
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260
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//FactCategory
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261
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public static Feature factCategory2Feature (int factCategoryId) throws UnknownCdmTypeException{
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262
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switch (factCategoryId){
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263
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case 0: return null;
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264
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case 1: return Feature.DESCRIPTION();
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265
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case 4: return Feature.ECOLOGY();
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266
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case 5: return Feature.PHENOLOGY();
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267
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case 12: return Feature.COMMON_NAME();
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268
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case 13: return Feature.OCCURRENCE();
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269
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case 99: return Feature.CITATION();
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270
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default: {
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271
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throw new UnknownCdmTypeException("Unknown FactCategory (id=" + Integer.valueOf(factCategoryId).toString() + ")");
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272
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}
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273
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}
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274
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}
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275
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276
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277
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278
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public static Rank rankId2Rank (ResultSet rs, boolean useUnknown) throws UnknownCdmTypeException{
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279
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Rank result;
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280
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try {
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281
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int rankId = rs.getInt("rankFk");
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282
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283
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String abbrev = rs.getString("rankAbbrev");
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284
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String rankName = rs.getString("rank");
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285
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if (logger.isDebugEnabled()){logger.debug(rankId);}
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286
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if (logger.isDebugEnabled()){logger.debug(abbrev);}
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287
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if (logger.isDebugEnabled()){logger.debug(rankName);}
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288
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289
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try {
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290
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result = Rank.getRankByNameOrAbbreviation(abbrev);
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291
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} catch (UnknownCdmTypeException e) {
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292
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try {
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293
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result = Rank.getRankByNameOrAbbreviation(rankName);
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294
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} catch (UnknownCdmTypeException e1) {
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295
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switch (rankId){
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296
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case 0: return null;
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297
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case 1: return Rank.KINGDOM();
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298
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case 3: return Rank.SUBKINGDOM();
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299
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case 5: return Rank.PHYLUM();
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300
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case 7: return Rank.SUBPHYLUM();
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301
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case 8: return Rank.DIVISION();
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302
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case 9: return Rank.SUBDIVISION();
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303
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case 10: return Rank.CLASS();
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304
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case 13: return Rank.SUBCLASS();
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305
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case 16: return Rank.SUPERORDER();
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306
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case 18: return Rank.ORDER();
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307
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case 19: return Rank.SUBORDER();
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308
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case 20: return Rank.FAMILY();
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309
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case 25: return Rank.SUBFAMILY();
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310
|
case 30: return Rank.TRIBE();
|
|
311
|
case 35: return Rank.SUBTRIBE();
|
|
312
|
case 40: return Rank.GENUS();
|
|
313
|
case 42: return Rank.SUBGENUS();
|
|
314
|
case 45: return Rank.SECTION();
|
|
315
|
case 47: return Rank.SUBSECTION();
|
|
316
|
case 50: return Rank.SERIES();
|
|
317
|
case 52: return Rank.SUBSERIES();
|
|
318
|
case 58: return Rank.SPECIESAGGREGATE();
|
|
319
|
//FIXME
|
|
320
|
//case 59: return Rank.SPECIESAGGREGATE();
|
|
321
|
case 60: return Rank.SPECIES();
|
|
322
|
case 65: return Rank.SUBSPECIES();
|
|
323
|
case 68: return Rank.CONVAR();
|
|
324
|
case 70: return Rank.VARIETY();
|
|
325
|
case 73: return Rank.SUBVARIETY();
|
|
326
|
case 80: return Rank.FORM();
|
|
327
|
case 82: return Rank.SUBFORM();
|
|
328
|
case 84: return Rank.SPECIALFORM();
|
|
329
|
case 98: return Rank.INFRAGENERICTAXON();
|
|
330
|
case 99: return Rank.INFRASPECIFICTAXON();
|
|
331
|
|
|
332
|
case 750: return Rank.SUPERCLASS();
|
|
333
|
case 780: return Rank.INFRACLASS();
|
|
334
|
case 820: return Rank.INFRAORDER();
|
|
335
|
|
|
336
|
case 830: return Rank.SUPERFAMILY();
|
|
337
|
|
|
338
|
default: {
|
|
339
|
if (useUnknown){
|
|
340
|
logger.error("Rank unknown. Created UNKNOWN_RANK");
|
|
341
|
return Rank.UNKNOWN_RANK();
|
|
342
|
}
|
|
343
|
throw new UnknownCdmTypeException("Unknown Rank id" + Integer.valueOf(rankId).toString());
|
|
344
|
}
|
|
345
|
}
|
|
346
|
}
|
|
347
|
}
|
|
348
|
return result;
|
|
349
|
} catch (SQLException e) {
|
|
350
|
e.printStackTrace();
|
|
351
|
logger.warn("Exception occurred. Created UNKNOWN_RANK instead");
|
|
352
|
return Rank.UNKNOWN_RANK();
|
|
353
|
}
|
|
354
|
}
|
|
355
|
|
|
356
|
|
|
357
|
public static Integer rank2RankId (Rank rank){
|
|
358
|
if (rank.equals(null)){return null;}
|
|
359
|
else if (rank.equals(Rank.KINGDOM())){ return 1;}
|
|
360
|
else if (rank.equals(Rank.SUBKINGDOM())){ return 3;}
|
|
361
|
else if (rank.equals(Rank.PHYLUM())){ return 5;}
|
|
362
|
else if (rank.equals(Rank.SUBPHYLUM())){ return 7;}
|
|
363
|
else if (rank.equals(Rank.DIVISION())){ return 8;}
|
|
364
|
else if (rank.equals(Rank.SUBDIVISION())){ return 9;}
|
|
365
|
|
|
366
|
else if (rank.equals(Rank.CLASS())){ return 10;}
|
|
367
|
else if (rank.equals(Rank.SUBCLASS())){ return 13;}
|
|
368
|
else if (rank.equals(Rank.SUPERORDER())){ return 16;}
|
|
369
|
else if (rank.equals(Rank.ORDER())){ return 18;}
|
|
370
|
else if (rank.equals(Rank.SUBORDER())){ return 19;}
|
|
371
|
else if (rank.equals(Rank.FAMILY())){ return 20;}
|
|
372
|
else if (rank.equals(Rank.SUBFAMILY())){ return 25;}
|
|
373
|
else if (rank.equals(Rank.TRIBE())){ return 30;}
|
|
374
|
else if (rank.equals(Rank.SUBTRIBE())){ return 35;}
|
|
375
|
else if (rank.equals(Rank.GENUS())){ return 40;}
|
|
376
|
else if (rank.equals(Rank.SUBGENUS())){ return 42;}
|
|
377
|
else if (rank.equals(Rank.SECTION())){ return 45;}
|
|
378
|
else if (rank.equals(Rank.SUBSECTION())){ return 47;}
|
|
379
|
else if (rank.equals(Rank.SERIES())){ return 50;}
|
|
380
|
else if (rank.equals(Rank.SUBSERIES())){ return 52;}
|
|
381
|
else if (rank.equals(Rank.SPECIESAGGREGATE())){ return 58;}
|
|
382
|
//TODO
|
|
383
|
// else if (rank.equals(Rank.XXX())){ return 59;}
|
|
384
|
else if (rank.equals(Rank.SPECIES())){ return 60;}
|
|
385
|
else if (rank.equals(Rank.SUBSPECIES())){ return 65;}
|
|
386
|
else if (rank.equals(Rank.CONVAR())){ return 68;}
|
|
387
|
else if (rank.equals(Rank.VARIETY())){ return 70;}
|
|
388
|
else if (rank.equals(Rank.SUBVARIETY())){ return 73;}
|
|
389
|
else if (rank.equals(Rank.FORM())){ return 80;}
|
|
390
|
else if (rank.equals(Rank.SUBFORM())){ return 82;}
|
|
391
|
else if (rank.equals(Rank.SPECIALFORM())){ return 84;}
|
|
392
|
else if (rank.equals(Rank.INFRAGENERICTAXON())){ return 98;}
|
|
393
|
else if (rank.equals(Rank.INFRASPECIFICTAXON())){ return 99;}
|
|
394
|
|
|
395
|
else if (rank.equals(Rank.SUPERCLASS())){ return 750;}
|
|
396
|
else if (rank.equals(Rank.INFRACLASS())){ return 780;}
|
|
397
|
else if (rank.equals(Rank.INFRAORDER())){ return 820;}
|
|
398
|
else if (rank.equals(Rank.SUPERFAMILY())){ return 830;}
|
|
399
|
|
|
400
|
else {
|
|
401
|
//TODO Exception
|
|
402
|
logger.warn("Rank not yet supported in Berlin Model: "+ rank.getLabel());
|
|
403
|
return null;
|
|
404
|
}
|
|
405
|
}
|
|
406
|
|
|
407
|
public static Integer textData2FactCategoryFk (Feature feature){
|
|
408
|
if (feature.equals(Feature.DESCRIPTION())){
|
|
409
|
return 1;
|
|
410
|
}else if (feature.equals(Feature.ECOLOGY())){
|
|
411
|
return 4;
|
|
412
|
}else if (feature.equals(Feature.PHENOLOGY())){
|
|
413
|
return 5;
|
|
414
|
}else if (feature.equals(Feature.COMMON_NAME())){
|
|
415
|
return 12;
|
|
416
|
}else if (feature.equals(Feature.OCCURRENCE())){
|
|
417
|
return 13;
|
|
418
|
}else if (feature.equals(Feature.CITATION())){
|
|
419
|
return 99;
|
|
420
|
}else{
|
|
421
|
logger.warn("Unknown Feature. Used DESCRIPTION instead");
|
|
422
|
return 4;
|
|
423
|
}
|
|
424
|
}
|
|
425
|
|
|
426
|
|
|
427
|
public static Integer taxonBase2statusFk (TaxonBase<?> taxonBase){
|
|
428
|
if (taxonBase.isInstanceOf(Taxon.class)){
|
|
429
|
return T_STATUS_ACCEPTED;
|
|
430
|
}else if (taxonBase.isInstanceOf(Synonym.class)){
|
|
431
|
return T_STATUS_SYNONYM;
|
|
432
|
}else{
|
|
433
|
logger.warn("Unknown ");
|
|
434
|
return T_STATUS_UNRESOLVED;
|
|
435
|
}
|
|
436
|
//TODO
|
|
437
|
// public static int T_STATUS_PARTIAL_SYN = 3;
|
|
438
|
// public static int T_STATUS_PRO_PARTE_SYN = 4;
|
|
439
|
// public static int T_STATUS_UNRESOLVED = 5;
|
|
440
|
// public static int T_STATUS_ORPHANED = 6;
|
|
441
|
}
|
|
442
|
|
|
443
|
public static Integer ref2refCategoryId (StrictReferenceBase<?> ref){
|
|
444
|
if (ref == null){
|
|
445
|
return null;
|
|
446
|
}
|
|
447
|
else if (ref instanceof Article){ return REF_ARTICLE;}
|
|
448
|
else if (ref instanceof SectionBase){ return REF_PART_OF_OTHER_TITLE;}
|
|
449
|
else if (ref instanceof Book){ return REF_BOOK;}
|
|
450
|
else if (ref instanceof Database){ return REF_DATABASE;}
|
|
451
|
// else if (ref instanceof SectionBas){ return REF_INFORMAL;}
|
|
452
|
// else if (ref instanceof SectionBas){ return REF_NOT_APPLICABLE;}
|
|
453
|
else if (ref instanceof WebPage){ return REF_WEBSITE;}
|
|
454
|
else if (ref instanceof CdDvd){ return REF_CD;}
|
|
455
|
else if (ref instanceof Journal){ return REF_JOURNAL;}
|
|
456
|
else if (ref instanceof Generic){ return REF_UNKNOWN;}
|
|
457
|
else if (ref instanceof PrintSeries){
|
|
458
|
logger.warn("Print Series is not a standard Berlin Model category");
|
|
459
|
return REF_PRINT_SERIES;
|
|
460
|
}
|
|
461
|
else if (ref instanceof Proceedings){
|
|
462
|
logger.warn("Proceedings is not a standard Berlin Model category");
|
|
463
|
return REF_CONFERENCE_PROCEEDINGS;
|
|
464
|
}
|
|
465
|
// else if (ref instanceof ){ return REF_JOURNAL_VOLUME;}
|
|
466
|
else if (ref instanceof Patent){ return REF_NOT_APPLICABLE;}
|
|
467
|
else if (ref instanceof PersonalCommunication){ return REF_INFORMAL;}
|
|
468
|
else if (ref instanceof Report){ return REF_NOT_APPLICABLE;}
|
|
469
|
else if (ref instanceof Thesis){ return REF_NOT_APPLICABLE;}
|
|
470
|
else if (ref instanceof Report){ return REF_NOT_APPLICABLE;}
|
|
471
|
|
|
472
|
else {
|
|
473
|
//TODO Exception
|
|
474
|
logger.warn("Reference type not yet supported in Berlin Model: "+ ref.getClass().getSimpleName());
|
|
475
|
return null;
|
|
476
|
}
|
|
477
|
}
|
|
478
|
|
|
479
|
|
|
480
|
public static Integer taxRelation2relPtQualifierFk (RelationshipBase<?,?,?> rel){
|
|
481
|
if (rel == null){
|
|
482
|
return null;
|
|
483
|
}
|
|
484
|
// else if (rel instanceof SynonymRelationship){
|
|
485
|
// return ;
|
|
486
|
// }else if (rel instanceof TaxonRelationship){
|
|
487
|
RelationshipTermBase<?> type = rel.getType();
|
|
488
|
if (type.equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())) {return TAX_REL_IS_INCLUDED_IN;
|
|
489
|
}else if (type.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())) {return TAX_REL_IS_MISAPPLIED_NAME_OF;
|
|
490
|
}else if (type.equals(SynonymRelationshipType.SYNONYM_OF())) {return TAX_REL_IS_SYNONYM_OF;
|
|
491
|
}else if (type.equals(SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF())) {return TAX_REL_IS_HOMOTYPIC_SYNONYM_OF;
|
|
492
|
}else if (type.equals(SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF())) {return TAX_REL_IS_HETEROTYPIC_SYNONYM_OF;
|
|
493
|
}else if (type.equals(TaxonRelationshipType.CONGRUENT_TO())) {return 11;
|
|
494
|
// public static int TAX_REL_IS_PROPARTE_SYN_OF = 4;
|
|
495
|
// public static int TAX_REL_IS_PARTIAL_SYN_OF = 5;
|
|
496
|
// public static int TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF = 101;
|
|
497
|
// public static int TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF = 102;
|
|
498
|
// public static int TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF = 103;
|
|
499
|
// public static int TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF = 104;
|
|
500
|
|
|
501
|
}else {
|
|
502
|
//TODO Exception
|
|
503
|
logger.warn("Relationship type not yet supported by Berlin Model export: "+ rel.getType());
|
|
504
|
return null;
|
|
505
|
}
|
|
506
|
}
|
|
507
|
|
|
508
|
public static Integer nomStatus2nomStatusFk (NomenclaturalStatus status){
|
|
509
|
if (status == null){
|
|
510
|
return null;
|
|
511
|
}
|
|
512
|
if (status.equals(NomenclaturalStatusType.INVALID())) {return NAME_ST_NOM_INVAL;
|
|
513
|
}else if (status.equals(NomenclaturalStatusType.ILLEGITIMATE())) {return NAME_ST_NOM_ILLEG;
|
|
514
|
}else if (status.equals(NomenclaturalStatusType.NUDUM())) {return NAME_ST_NOM_NUD;
|
|
515
|
}else if (status.equals(NomenclaturalStatusType.REJECTED())) {return NAME_ST_NOM_REJ;
|
|
516
|
}else if (status.equals(NomenclaturalStatusType.REJECTED_PROP())) {return NAME_ST_NOM_REJ_PROP;
|
|
517
|
}else if (status.equals(NomenclaturalStatusType.UTIQUE_REJECTED())) {return NAME_ST_NOM_UTIQUE_REJ;
|
|
518
|
}else if (status.equals(NomenclaturalStatusType.UTIQUE_REJECTED_PROP())) {return NAME_ST_NOM_UTIQUE_REJ_PROP;
|
|
519
|
}else if (status.equals(NomenclaturalStatusType.CONSERVED())) {return NAME_ST_NOM_CONS;
|
|
520
|
|
|
521
|
}else if (status.equals(NomenclaturalStatusType.CONSERVED_PROP())) {return NAME_ST_NOM_CONS_PROP;
|
|
522
|
}else if (status.equals(NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED())) {return NAME_ST_ORTH_CONS;
|
|
523
|
}else if (status.equals(NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP())) {return NAME_ST_ORTH_CONS_PROP;
|
|
524
|
}else if (status.equals(NomenclaturalStatusType.SUPERFLUOUS())) {return NAME_ST_NOM_SUPERFL;
|
|
525
|
}else if (status.equals(NomenclaturalStatusType.AMBIGUOUS())) {return NAME_ST_NOM_AMBIG;
|
|
526
|
}else if (status.equals(NomenclaturalStatusType.PROVISIONAL())) {return NAME_ST_NOM_PROVIS;
|
|
527
|
}else if (status.equals(NomenclaturalStatusType.DOUBTFUL())) {return NAME_ST_NOM_DUB;
|
|
528
|
}else if (status.equals(NomenclaturalStatusType.NOVUM())) {return NAME_ST_NOM_NOV;
|
|
529
|
|
|
530
|
}else if (status.equals(NomenclaturalStatusType.CONFUSUM())) {return NAME_ST_NOM_CONFUS;
|
|
531
|
}else if (status.equals(NomenclaturalStatusType.ALTERNATIVE())) {return NAME_ST_NOM_ALTERN;
|
|
532
|
}else if (status.equals(NomenclaturalStatusType.COMBINATION_INVALID())) {return NAME_ST_COMB_INVAL;
|
|
533
|
//TODO
|
|
534
|
}else {
|
|
535
|
//TODO Exception
|
|
536
|
logger.warn("NomStatus type not yet supported by Berlin Model export: "+ status);
|
|
537
|
return null;
|
|
538
|
}
|
|
539
|
}
|
|
540
|
|
|
541
|
|
|
542
|
|
|
543
|
public static Integer nameRel2RelNameQualifierFk (RelationshipBase<?,?,?> rel){
|
|
544
|
if (rel == null){
|
|
545
|
return null;
|
|
546
|
}
|
|
547
|
RelationshipTermBase<?> type = rel.getType();
|
|
548
|
if (type.equals(NameRelationshipType.BASIONYM())) {return NAME_REL_IS_BASIONYM_FOR;
|
|
549
|
}else if (type.equals(NameRelationshipType.LATER_HOMONYM())) {return NAME_REL_IS_LATER_HOMONYM_OF;
|
|
550
|
}else if (type.equals(NameRelationshipType.REPLACED_SYNONYM())) {return NAME_REL_IS_REPLACED_SYNONYM_FOR;
|
|
551
|
//TODO
|
|
552
|
}else if (type.equals(NameRelationshipType.VALIDATED_BY_NAME())) {return NAME_REL_IS_VALIDATION_OF;
|
|
553
|
}else if (type.equals(NameRelationshipType.LATER_VALIDATED_BY_NAME())) {return NAME_REL_IS_LATER_VALIDATION_OF;
|
|
554
|
}else if (type.equals(NameRelationshipType.CONSERVED_AGAINST())) {return NAME_REL_IS_CONSERVED_AGAINST;
|
|
555
|
|
|
556
|
|
|
557
|
}else if (type.equals(NameRelationshipType.TREATED_AS_LATER_HOMONYM())) {return NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF;
|
|
558
|
}else if (type.equals(NameRelationshipType.ORTHOGRAPHIC_VARIANT())) {return NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF;
|
|
559
|
// }else if (type.equals(NameRelationshipType.())) {return NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF;
|
|
560
|
}else {
|
|
561
|
//TODO Exception
|
|
562
|
logger.warn("Relationship type not yet supported by Berlin Model export: "+ rel.getType());
|
|
563
|
return null;
|
|
564
|
}
|
|
565
|
|
|
566
|
//NameRelationShip
|
|
567
|
|
|
568
|
// }else if (type.equals(NameRelationshipType.())) {return NAME_REL_IS_REJECTED_IN_FAVOUR_OF;
|
|
569
|
|
|
570
|
// public static int NAME_REL_IS_FIRST_PARENT_OF = 9;
|
|
571
|
// public static int NAME_REL_IS_SECOND_PARENT_OF = 10;
|
|
572
|
// public static int NAME_REL_IS_FEMALE_PARENT_OF = 11;
|
|
573
|
// public static int NAME_REL_IS_MALE_PARENT_OF = 12;
|
|
574
|
//
|
|
575
|
// public static int NAME_REL_IS_REJECTED_IN_FAVOUR_OF = 14;
|
|
576
|
// }else if (type.equals(NameRelationshipType.)) {return NAME_REL_IS_REJECTED_TYPE_OF;
|
|
577
|
//
|
|
578
|
// public static int NAME_REL_HAS_SAME_TYPE_AS = 18;
|
|
579
|
// public static int NAME_REL_IS_LECTOTYPE_OF = 61;
|
|
580
|
// public static int NAME_REL_TYPE_NOT_DESIGNATED = 62;
|
|
581
|
|
|
582
|
// }else if (type.equals(NameRelationshipType.LATER_VALIDATED_BY_NAME())) {return NAME_REL_IS_TYPE_OF;
|
|
583
|
|
|
584
|
|
|
585
|
}
|
|
586
|
|
|
587
|
|
|
588
|
|
|
589
|
|
|
590
|
}
|