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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.tcsrdf;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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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.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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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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* @since 29.05.2008
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*/
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public final class TcsRdfTransformer {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(TcsRdfTransformer.class);
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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 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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/** Creates an cdm-Rank by the tcs rank
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*/
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public static Rank rankString2Rank (String strRank) throws UnknownCdmTypeException{
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String tcsRoot = "http://rs.tdwg.org/ontology/voc/taxonrank#";
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String tcsFamily = "family";
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String tcsSubFamily = "subfamily";
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String tcsTribe = "tribe";
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String tcsSubtribe = "subtribe";
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String tcsGenus = "genus";
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String tcsSection = "section";
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String tcsSpecies = "species";
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String tcsSubSpecies = "subspecies";
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String tcsVariety = "variety";
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String tcsSubVariety = "subvariety";
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String tcsForm = "form";
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String tcsAbbFamily = "fam.";
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String tcsAbbrSubFamily = "subfam.";
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String tcsAbbrTribe = "trib.";
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String tcsAbbrSubtribe = "subtrib.";
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String tcsAbbrGenus = "gen.";
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String tcsAbbrSubGenus = "subgen.";
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String tcsAbbrSection = "sect.";
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String tcsAbbrSubSection = "subsect.";
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String tcsAbbrSeries = "ser.";
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String tcsAbbrSpecies = "spec.";
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String tcsAbbrSubSpecies = "subsp.";
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String tcsAbbrVariety = "var.";
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String tcsAbbrSubVariety ="subvar.";
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String tcsAbbrForm = "f.";
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String tcsAbbrForma = "forma";
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String tcsAbbrSubForm = "subf.";
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String tcsAbbrInfraspecUnranked ="[infrasp.unranked]";
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String tcsAbbrInfragenUnranked ="[infragen.unranked]";
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String tcsAbbrNothoSubSpecies = "nothosubsp.";
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if (strRank == null){return null;
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}else{
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strRank = strRank.toLowerCase();
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}
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if (tcsFamily.equals(strRank) || tcsRoot.concat(tcsFamily).equals(strRank)){return Rank.FAMILY();
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}else if (tcsSubFamily.equals(strRank)|| tcsRoot.concat(tcsSubFamily).equals(strRank)){return Rank.SUBFAMILY();
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}else if (tcsTribe.equals(strRank)|| tcsRoot.concat(tcsTribe).equals(strRank)){return Rank.TRIBE();
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}else if (tcsSubtribe.equals(strRank)|| tcsRoot.concat(tcsSubtribe).equals(strRank)){return Rank.SUBTRIBE();
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}else if (tcsGenus.equals(strRank)|| tcsRoot.concat(tcsGenus).equals(strRank)){return Rank.GENUS();
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}else if (tcsSection.equals(strRank)|| tcsRoot.concat(tcsSection).equals(strRank)){return Rank.SECTION_BOTANY();
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}else if (tcsSpecies.equals(strRank)|| tcsRoot.concat(tcsSpecies).equals(strRank)){return Rank.SPECIES();
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}else if (tcsVariety.equals(strRank)|| tcsRoot.concat(tcsVariety).equals(strRank)){return Rank.VARIETY();
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}else if (tcsSubVariety.equals(strRank)|| tcsRoot.concat(tcsSubVariety).equals(strRank)){return Rank.SUBVARIETY();
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}else if (tcsSubSpecies.equals(strRank) || tcsRoot.concat(tcsSubSpecies).equals(strRank)){return Rank.SUBSPECIES();
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}else if (tcsForm.equals(strRank)|| tcsRoot.concat(tcsForm).equals(strRank)){return Rank.FORM();
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}else if (tcsAbbFamily.equals(strRank)){return Rank.FAMILY();
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}else if (tcsAbbrSubFamily.equals(strRank)){return Rank.SUBFAMILY();
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}else if (tcsAbbrTribe.equals(strRank)){return Rank.TRIBE();
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}else if (tcsAbbrSubtribe.equals(strRank)){return Rank.SUBTRIBE();
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}else if (tcsAbbrGenus.equals(strRank)){return Rank.GENUS();
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}else if (tcsAbbrSubGenus.equals(strRank)){return Rank.SUBGENUS();
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}else if (tcsAbbrSection.equals(strRank)){return Rank.SECTION_BOTANY();
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}else if (tcsAbbrSubSection.equals(strRank)){return Rank.SUBSECTION_BOTANY();
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}else if (tcsAbbrSeries.equals(strRank)){return Rank.SERIES();
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}else if (tcsAbbrSpecies.equals(strRank)){return Rank.SPECIES();
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}else if (tcsAbbrSubSpecies.equals(strRank) || tcsAbbrNothoSubSpecies.equals(strRank)){return Rank.SUBSPECIES();
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}else if (tcsAbbrVariety.equals(strRank)){return Rank.VARIETY();
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}else if (tcsAbbrSubVariety.equals(strRank)){return Rank.SUBVARIETY();
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}else if (tcsAbbrForm.equals(strRank) ||tcsAbbrForma.equals(strRank)){return Rank.FORM();
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}else if (tcsAbbrSubForm.equals(strRank)){return Rank.SUBFORM();
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}else if (tcsAbbrInfraspecUnranked.equals(strRank)){return Rank.UNRANKED_INFRASPECIFIC();
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}else if (tcsAbbrInfragenUnranked.equals(strRank)){return Rank.UNRANKED_INFRAGENERIC();
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}else{
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throw new UnknownCdmTypeException("Unknown Rank " + strRank);
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}
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}
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/** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
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*/
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public static NomenclaturalCode nomCodeString2NomCode (String nomCode) throws UnknownCdmTypeException{
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String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonName#";
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String tcsBotanical = tcsRoot + "botanical";
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String tcsICBN = tcsRoot + "ICBN";
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String tcsICZN = tcsRoot + "ICZN";
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String tcsICNCP = tcsRoot + "ICNCP";
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String tcsBacteriological = tcsRoot + "BACTERIOLOGICAL";
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String tcsViral = tcsRoot + "VIRAL";
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if (nomCode == null){ return null;
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}else if (tcsICBN.equals(nomCode)){return NomenclaturalCode.ICNAFP;
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}else if (tcsBotanical.equals(nomCode)){return NomenclaturalCode.ICNAFP;
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}else if (tcsICZN.equals(nomCode)){return NomenclaturalCode.ICZN;
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}else if (tcsICNCP.equals(nomCode)){return NomenclaturalCode.ICNCP;
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}else if (tcsBacteriological.equals(nomCode)){return NomenclaturalCode.ICNP;
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}else if (tcsViral.equals(nomCode)){return NomenclaturalCode.ICVCN;
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}
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else {
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throw new UnknownCdmTypeException("Unknown Nomenclatural Code " + nomCode);
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}
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}
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public static boolean isReverseRelationshipCategory (String tcsRelationshipCategory){
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String str = tcsRelationshipCategory.replace("http://rs.tdwg.org/ontology/voc/TaxonConcept#", "");
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if ("HasSynonym".equalsIgnoreCase(str)
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|| "IsParentTaxonOf".equalsIgnoreCase(str)
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|| "IsIncludedIn".equalsIgnoreCase(str)
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|| "DoesNotInclude".equalsIgnoreCase(str)
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){
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return true;
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}
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return false;
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}
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/** Creates an cdm-Rank by the tcs rank
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*/
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public static Reference pubTypeStr2PubType (String strPubType) throws UnknownCdmTypeException{
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String tcsRoot = "http://rs.tdwg.org/ontology/voc/PublicationCitation#";
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String tcsBook = tcsRoot + "Book";
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String tcsJournal = tcsRoot + "Journal";
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String tcsWebPage = tcsRoot + "WebPage";
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String tcsCommunication = tcsRoot + "Communication";
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String tcsBookSeries = tcsRoot + "BookSeries";
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String tcsArticle = tcsRoot + "JournalArticle";
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String tcsBookSection = tcsRoot + "BookSection";
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// Artwork An Artwork type publication.
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// AudiovisualMaterial A Audiovisual Material type publication.
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// BookSeries A Book Series type publication.
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// Commentary A Commentary type publication.
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// Communication A Communication type publication.
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// ComputerProgram A Computer Program type publication.
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// ConferenceProceedings A Conference Proceedings type publication.
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// Determination A Determination type publication.
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// EditedBook A Edited Book type publication.
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// Generic A generic publication.
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// Journal A Journal type publication.
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// MagazineArticle A Magazine Article type publication.
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// Map A Map type publication.
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// NewspaperArticle A Newspaper Article type publication.
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// Patent A Patent type publication.
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// Report A Report type publication.
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// SubReference A Sub-Reference type publication.
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// Thesis A Thesis type publication.
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if (strPubType == null){return null;
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}else if (tcsBookSection.equals(strPubType)){return ReferenceFactory.newBookSection();
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}else if (tcsBook.equals(strPubType)){return ReferenceFactory.newBook();
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}else if (tcsArticle.equals(strPubType)){return ReferenceFactory.newArticle();
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}else if (tcsJournal.equals(strPubType)){return ReferenceFactory.newJournal();
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}else if (tcsWebPage.equals(strPubType)){return ReferenceFactory.newWebPage();
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}else if (tcsCommunication.equals(strPubType)){return ReferenceFactory.newPersonalCommunication();
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}else if (tcsBookSeries.equals(strPubType)){return ReferenceFactory.newPrintSeries();
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}
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else {
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throw new UnknownCdmTypeException("Unknown publication type " + strPubType);
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}
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}
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/** Creates an cdm-RelationshipTermBase by the tcsRelationshipCategory
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*/
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public static RelationshipTermBase<?> tcsRelationshipCategory2Relationship (String tcsRelationshipCategory) throws UnknownCdmTypeException{
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String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonConcept#";
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String doesNotInclude = tcsRoot + "DoesNotInclude";
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String doesNotOverlap = tcsRoot + "DoesNotOverlap";
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String excludes = tcsRoot + "Excludes";
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String hasSynonym = tcsRoot + "HasSynonym";
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String hasVernacular = tcsRoot + "HasVernacular";
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String includes = tcsRoot + "Includes";
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String isAmbiregnalOf = tcsRoot + "IsAmbiregnalOf";
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String isAnamorphOf = tcsRoot + "IsAnamorphOf";
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String isChildTaxonOf = tcsRoot + "IsChildTaxonOf";
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String isCongruentTo = tcsRoot + "IsCongruentTo";
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String isFemaleParentOf = tcsRoot + "IsFemaleParentOf";
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String isFirstParentOf = tcsRoot + "IsFirstParentOf";
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String isHybridChildOf = tcsRoot + "IsHybridChildOf";
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String isHybridParentOf = tcsRoot + "IsHybridParentOf";
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String isIncludedIn = tcsRoot + "IsIncludedIn";
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String isMaleParentOf = tcsRoot + "IsMaleParentOf";
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String isNotCongruentTo = tcsRoot + "IsNotCongruentTo";
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String isNotIncludedIn = tcsRoot + "IsNotIncludedIn";
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String isParentTaxonOf = tcsRoot + "IsParentTaxonOf";
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String isSecondParentOf = tcsRoot + "IsSecondParentOf";
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String isSynonymFor = tcsRoot + "IsSynonymFor";
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String isTeleomorphOf = tcsRoot + "IsTeleomorphOf";
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String isVernacularFor = tcsRoot + "IsVernacularFor";
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String overlaps = tcsRoot + "Overlaps";
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if (tcsRelationshipCategory == null){ return null;
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//Synonym relationships
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}else if (isSynonymFor.equals(tcsRelationshipCategory)){return SynonymType.SYNONYM_OF();
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}else if (hasSynonym.equals(tcsRelationshipCategory)){/*isReverse = true; */ return SynonymType.SYNONYM_OF();
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//Taxon relationships
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}else if (isChildTaxonOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();
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}else if (isParentTaxonOf.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();
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//concept relationships
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}else if (doesNotOverlap.equals(tcsRelationshipCategory)){return TaxonRelationshipType.DOES_NOT_OVERLAP();
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}else if (excludes.equals(tcsRelationshipCategory)){return TaxonRelationshipType.EXCLUDES();
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}else if (includes.equals(tcsRelationshipCategory)){return TaxonRelationshipType.INCLUDES();
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}else if (isCongruentTo.equals(tcsRelationshipCategory)){return TaxonRelationshipType.CONGRUENT_TO();
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}else if (isNotCongruentTo.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOT_CONGRUENT_TO();
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}else if (isNotIncludedIn.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOT_INCLUDED_IN();
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}else if (overlaps.equals(tcsRelationshipCategory)){return TaxonRelationshipType.OVERLAPS();
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//reverse concept relationships
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}else if (isIncludedIn.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.INCLUDES();
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}else if (doesNotInclude.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.NOT_INCLUDED_IN();
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//TODO
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// }else if (hasVernacular.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isAmbiregnalOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isAnamorphOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isFemaleParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isFirstParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isHybridChildOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isHybridParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isMaleParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isSecondParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isTeleomorphOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isVernacularFor.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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}else {
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throw new UnknownCdmTypeException("Unknown RelationshipCategory " + tcsRelationshipCategory);
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}
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}
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/** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
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*/
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public static NomenclaturalStatusType nomStatusString2NomStatus (String nomStatus) throws UnknownCdmTypeException{
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if (nomStatus == null){ return null;
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}else if ("Valid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.VALID();
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}else if ("Alternative".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
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}else if ("nom. altern.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
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}else if ("Ambiguous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.AMBIGUOUS();
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}else if ("Doubtful".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.DOUBTFUL();
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}else if ("Confusum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONFUSUM();
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}else if ("Illegitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
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}else if ("nom. illeg.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
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}else if ("Superfluous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
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}else if ("nom. superfl.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
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}else if ("Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
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}else if ("nom. rej.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
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}else if ("Utique Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED();
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}else if ("Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED_PROP();
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}else if ("Orthography Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP();
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}else if ("Legitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.LEGITIMATE();
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}else if ("Novum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
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323
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}else if ("nom. nov.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
|
324
|
|
325
|
}else if ("Utique Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED_PROP();
|
326
|
|
327
|
}else if ("Orthography Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED();
|
328
|
|
329
|
}else if ("Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED_PROP();
|
330
|
|
331
|
}else if ("Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
|
332
|
}else if ("nom. cons.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
|
333
|
|
334
|
}else if ("Sanctioned".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SANCTIONED();
|
335
|
|
336
|
}else if ("Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
|
337
|
}else if ("nom. inval.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
|
338
|
|
339
|
}else if ("Nudum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
|
340
|
}else if ("nom. nud.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
|
341
|
|
342
|
}else if ("Combination Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.COMBINATION_INVALID();
|
343
|
|
344
|
}else if ("Provisional".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
|
345
|
}else if ("nom. provis.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
|
346
|
}
|
347
|
else {
|
348
|
throw new UnknownCdmTypeException("Unknown Nomenclatural status type " + nomStatus);
|
349
|
}
|
350
|
}
|
351
|
|
352
|
|
353
|
}
|