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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.model.description;
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import java.text.ParseException;
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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.UUID;
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import javax.persistence.Entity;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;
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import javax.xml.bind.annotation.XmlAttribute;
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import javax.xml.bind.annotation.XmlRootElement;
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import javax.xml.bind.annotation.XmlType;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.hibernate.envers.Audited;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.OrderedTermBase;
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import eu.etaxonomy.cdm.model.common.TermType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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/**
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* This class represents terms describing the {@link AbsenceTerm absence}
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* (like "extinct") or the {@link PresenceTerm presence} (like "cultivated") of a
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* {@link Taxon taxon} in a {@link NamedArea named area}. These terms are only
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* used for {@link Distribution distributions}.
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*
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* @author m.doering
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* @created 08-Nov-2007 13:06:44
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* @author a.mueller
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "PresenceAbsenceTerm")
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@XmlRootElement(name = "PresenceAbsenceTerm")
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@Entity
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//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
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//@Indexed(index = "eu.etaxonomy.cdm.model.common.DefinedTermBase")
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@Audited
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public class PresenceAbsenceTerm extends OrderedTermBase<PresenceAbsenceTerm> {
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private static final long serialVersionUID = 1036807546935584396L;
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private static final Logger logger = Logger.getLogger(PresenceAbsenceTerm.class);
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//presence base
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private static final UUID uuidP=UUID.fromString("cef81d25-501c-48d8-bbea-542ec50de2c2");
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private static final UUID uuidPD=UUID.fromString("75a60279-a4c2-4f53-bc57-466028a4b3db");
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//presence
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private static final UUID uuidN=UUID.fromString("ddeac4f2-d8fa-43b8-ad7e-ca13abdd32c7");
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private static final UUID uuidNQ=UUID.fromString("925662c1-bb10-459a-8c53-da5a738ac770");
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private static final UUID uuidND=UUID.fromString("310373bf-7df4-4d02-8cb3-bcc7448805fc");
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private static final UUID uuidC=UUID.fromString("9eb99fe6-59e2-4445-8e6a-478365bd0fa9");
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private static final UUID uuidCQ=UUID.fromString("4f31bfc8-3058-4d83-aea5-3a1fe9773f9f");
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private static final UUID uuidI=UUID.fromString("643cf9d1-a5f1-4622-9837-82ef961e880b");
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private static final UUID uuidIQ=UUID.fromString("83eb0aa0-1a45-495a-a3ca-bf6958b74366");
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private static final UUID uuidID=UUID.fromString("0c54761e-4887-4788-9dfa-7190c88746e3");
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private static final UUID uuidIP=UUID.fromString("da159544-b0dd-4599-a9c9-640826af8c17");
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private static final UUID uuidIA=UUID.fromString("42946bd6-9c22-45ad-a910-7427e8f60bfd");
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private static final UUID uuidIN=UUID.fromString("e191e89a-a751-4b0c-b883-7f1de70915c9");
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private static final UUID uuidIC=UUID.fromString("fac8c347-8262-44a1-b0a4-db4de451c021");
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private static final UUID uuidE=UUID.fromString("c3ee7048-15b7-4be1-b687-9ce9c1a669d6");
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private static final UUID uuidNA=UUID.fromString("4e04990a-66fe-4fdf-856c-f40772fbcf0a");
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private static final UUID uuidIV=UUID.fromString("dc536e3d-a753-4bbe-a386-dd8aff35c234");
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//absence
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private static final UUID uuidAbsence=UUID.fromString("59709861-f7d9-41f9-bb21-92559cedd598");
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private static final UUID uuidReportedInError = UUID.fromString("38604788-cf05-4607-b155-86db456f7680");
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private static final UUID uuidNF=UUID.fromString("61cee840-801e-41d8-bead-015ad866c2f1");
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private static final UUID uuidIF=UUID.fromString("aeec2947-2700-4623-8e32-9e3a430569d1");
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private static final UUID uuidCF=UUID.fromString("9d4d3431-177a-4abe-8e4b-1558573169d6");
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private static final UUID uuidNE=UUID.fromString("5c397f7b-59ef-4c11-a33c-45691ceda91b");
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private static final UUID uuidIE=UUID.fromString("b74dc30b-ee93-496d-8c00-4d00abae1ec7");
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protected static Map<UUID, PresenceAbsenceTerm> termMap = null;
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private String defaultColor = "000000";
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@XmlAttribute(name = "absenceTerm")
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private boolean absenceTerm = false;
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//********* METHODS **************************************/
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/**
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* Creates a new empty presence term.
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*
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* @see #NewInstance(String, String, String)
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*/
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public static PresenceAbsenceTerm NewInstance(){
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return new PresenceAbsenceTerm();
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}
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/**
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* Creates a new presence term with a description (in the {@link Language#DEFAULT() default language}),
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* a label and a label abbreviation.
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*
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* @param term the string (in the default language) describing the
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* new presence term to be created
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* @param label the string identifying the new presence term to be created
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* @param labelAbbrev the string identifying (in abbreviated form) the
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* new presence term to be created
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* @see #NewInstance()
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*/
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public static PresenceAbsenceTerm NewPresenceInstance(String term, String label, String labelAbbrev){
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return new PresenceAbsenceTerm(term, label, labelAbbrev, false);
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}
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/**
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* Creates a new absence term with a description (in the {@link Language#DEFAULT() default language}),
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* a label and a label abbreviation.
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*
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* @param term the string (in the default language) describing the
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* new presence term to be created
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* @param label the string identifying the new presence term to be created
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* @param labelAbbrev the string identifying (in abbreviated form) the
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* new presence term to be created
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* @see #NewInstance()
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*/
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public static PresenceAbsenceTerm NewAbsenceInstance(String term, String label, String labelAbbrev){
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return new PresenceAbsenceTerm(term, label, labelAbbrev, true);
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}
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//********************************** Constructor *******************************************************************/
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//for hibernate use only
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@Deprecated
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protected PresenceAbsenceTerm() {
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super(TermType.PresenceAbsenceTerm);
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}
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/**
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* Class constructor: creates a new presence or absence term with a description
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* (in the {@link Language#DEFAULT() default language}), a label and a label abbreviation.
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*
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* @param term the string (in the default language) describing the
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* new presence or absence term to be created
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* @param label the string identifying the new presence or absence term to be created
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* @param labelAbbrev the string identifying (in abbreviated form) the
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* new presence or absence term to be created
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* @param isAbsenceTerm boolean value indicating if this term represents an absence or not
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* @see #PresenceAbsenceTermBase()
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*/
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protected PresenceAbsenceTerm(String term, String label, String labelAbbrev, boolean isAbsenceTerm) {
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super(TermType.PresenceAbsenceTerm, term, label, labelAbbrev);
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this.setAbsenceTerm(isAbsenceTerm);
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}
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//******************************* STATIC METHODS *****************************************
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protected static PresenceAbsenceTerm getTermByUuid(UUID uuid){
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if (termMap == null || termMap.isEmpty()){
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return getTermByClassAndUUID(PresenceAbsenceTerm.class, uuid);
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} else {
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return termMap.get(uuid);
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}
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}
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//TODO read from label(abbrevs) like in TDWGArea
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public static PresenceAbsenceTerm getPresenceAbsenceTermByAbbreviation(String abbrev) {
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if (abbrev == null) { throw new NullPointerException("abbrev is 'null' in getPresenceTermByAbbreviation");
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} else if (abbrev.equalsIgnoreCase("c")) { return PresenceAbsenceTerm.CULTIVATED();
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} else if (abbrev.equalsIgnoreCase("e")) { return PresenceAbsenceTerm.ENDEMIC_FOR_THE_RELEVANT_AREA();
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} else if (abbrev.equalsIgnoreCase("i")) { return PresenceAbsenceTerm.INTRODUCED();
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} else if (abbrev.equalsIgnoreCase("ia")) { return PresenceAbsenceTerm.INTRODUCED_ADVENTITIOUS();
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} else if (abbrev.equalsIgnoreCase("ic")) { return PresenceAbsenceTerm.INTRODUCED_CULTIVATED();
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} else if (abbrev.equalsIgnoreCase("id")) { return PresenceAbsenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED();
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} else if (abbrev.equalsIgnoreCase("in")) { return PresenceAbsenceTerm.INTRODUCED_NATURALIZED();
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} else if (abbrev.equalsIgnoreCase("ip")) { return PresenceAbsenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION();
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} else if (abbrev.equalsIgnoreCase("iq")) { return PresenceAbsenceTerm.INTRODUCED_PRESENCE_QUESTIONABLE();
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} else if (abbrev.equalsIgnoreCase("n")) { return PresenceAbsenceTerm.NATIVE();
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} else if (abbrev.equalsIgnoreCase("nd")) { return PresenceAbsenceTerm.NATIVE_DOUBTFULLY_NATIVE();
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} else if (abbrev.equalsIgnoreCase("nq")) { return PresenceAbsenceTerm.NATIVE_PRESENCE_QUESTIONABLE();
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} else if (abbrev.equalsIgnoreCase("p")) { return PresenceAbsenceTerm.PRESENT();
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} else if (abbrev.equalsIgnoreCase("na")) { return PresenceAbsenceTerm.NATURALISED();
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} else if (abbrev.equalsIgnoreCase("iv")) { return PresenceAbsenceTerm.INVASIVE();
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//absence
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} else if (abbrev.equalsIgnoreCase("cf")) { return PresenceAbsenceTerm.CULTIVATED_REPORTED_IN_ERROR();
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} else if (abbrev.equalsIgnoreCase("if")) { return PresenceAbsenceTerm.INTRODUCED_REPORTED_IN_ERROR();
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} else if (abbrev.equalsIgnoreCase("nf")) { return PresenceAbsenceTerm.NATIVE_REPORTED_IN_ERROR();
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} else if (abbrev.equalsIgnoreCase("ne")) { return PresenceAbsenceTerm.NATIVE_FORMERLY_NATIVE();
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} else if (abbrev.equalsIgnoreCase("ie")) { return PresenceAbsenceTerm.INTRODUCED_FORMERLY_INTRODUCED();
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} else {
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logger.warn("Unknown presence or absence status term abbreviation: " + abbrev);
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return null;
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}
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}
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public static final PresenceAbsenceTerm PRESENT(){
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return getTermByUuid(uuidP);
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}
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public static final PresenceAbsenceTerm PRESENT_DOUBTFULLY(){
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return getTermByUuid(uuidPD);
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}
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public static final PresenceAbsenceTerm CULTIVATED(){
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return getTermByUuid(uuidC);
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}
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public static final PresenceAbsenceTerm CULTIVATED_PRESENCE_QUESTIONABLE(){
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return getTermByUuid(uuidCQ);
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}
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public static final PresenceAbsenceTerm ENDEMIC_FOR_THE_RELEVANT_AREA(){
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return getTermByUuid(uuidE);
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}
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public static final PresenceAbsenceTerm INTRODUCED(){
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return getTermByUuid(uuidI);
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}
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public static final PresenceAbsenceTerm INTRODUCED_ADVENTITIOUS(){
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return getTermByUuid(uuidIA);
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}
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public static final PresenceAbsenceTerm INTRODUCED_CULTIVATED(){
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return getTermByUuid(uuidIC);
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}
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public static final PresenceAbsenceTerm INTRODUCED_DOUBTFULLY_INTRODUCED(){
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return getTermByUuid(uuidID);
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}
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public static final PresenceAbsenceTerm INTRODUCED_NATURALIZED(){
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return getTermByUuid(uuidIN);
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}
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public static final PresenceAbsenceTerm INTRODUCED_PRESENCE_QUESTIONABLE(){
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return getTermByUuid(uuidIQ);
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}
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public static final PresenceAbsenceTerm INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION(){
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return getTermByUuid(uuidIP);
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}
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public static final PresenceAbsenceTerm NATIVE(){
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return getTermByUuid(uuidN);
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}
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public static final PresenceAbsenceTerm NATIVE_DOUBTFULLY_NATIVE(){
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return getTermByUuid(uuidND);
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}
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public static final PresenceAbsenceTerm NATIVE_PRESENCE_QUESTIONABLE(){
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return getTermByUuid(uuidNQ);
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}
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public static final PresenceAbsenceTerm INVASIVE(){
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return getTermByUuid(uuidIV);
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}
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public static final PresenceAbsenceTerm NATURALISED(){
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return getTermByUuid(uuidNA);
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}
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public static final PresenceAbsenceTerm ABSENT(){
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return getTermByUuid(uuidAbsence);
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}
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public static final PresenceAbsenceTerm REPORTED_IN_ERROR(){
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return getTermByUuid(uuidReportedInError);
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}
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public static final PresenceAbsenceTerm NATIVE_REPORTED_IN_ERROR(){
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return getTermByUuid(uuidNF);
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}
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public static final PresenceAbsenceTerm CULTIVATED_REPORTED_IN_ERROR(){
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return getTermByUuid(uuidCF);
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}
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public static final PresenceAbsenceTerm INTRODUCED_REPORTED_IN_ERROR(){
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return getTermByUuid(uuidIF);
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}
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public static final PresenceAbsenceTerm NATIVE_FORMERLY_NATIVE(){
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return getTermByUuid(uuidNE);
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}
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public static final PresenceAbsenceTerm INTRODUCED_FORMERLY_INTRODUCED(){
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return getTermByUuid(uuidIE);
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}
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//******************************** METHODS ****************************/
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@Override
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public void resetTerms(){
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termMap = null;
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}
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@Override
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protected void setDefaultTerms(TermVocabulary<PresenceAbsenceTerm> termVocabulary) {
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termMap = new HashMap<UUID, PresenceAbsenceTerm>();
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for (PresenceAbsenceTerm term : termVocabulary.getTerms()){
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termMap.put(term.getUuid(), term);
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}
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}
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@Override
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public PresenceAbsenceTerm readCsvLine(Class<PresenceAbsenceTerm> termClass, List<String> csvLine, Map<UUID,DefinedTermBase> terms, boolean abbrevAsId){
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PresenceAbsenceTerm newInstance = super.readCsvLine(termClass, csvLine, terms, abbrevAsId);
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318
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String abbreviatedLabel = csvLine.get(4);
|
|
319
|
// String uuid = (String)csvLine.get(0);
|
|
320
|
// map.put(abbreviatedLabel, UUID.fromString(uuid));
|
|
321
|
String symbol = csvLine.get(5);
|
|
322
|
newInstance.setSymbol(symbol);
|
|
323
|
String color = csvLine.get(6);
|
|
324
|
try {
|
|
325
|
newInstance.setDefaultColor(color);
|
|
326
|
} catch (ParseException e) {
|
|
327
|
throw new RuntimeException(e);
|
|
328
|
}
|
|
329
|
boolean isAbsence = csvLine.get(7).equals("1") ? true : false;
|
|
330
|
newInstance.setAbsenceTerm(isAbsence);
|
|
331
|
|
|
332
|
newInstance.getRepresentation(Language.DEFAULT()).setAbbreviatedLabel(abbreviatedLabel);
|
|
333
|
newInstance.setSymbol(abbreviatedLabel);
|
|
334
|
return newInstance;
|
|
335
|
}
|
|
336
|
|
|
337
|
/**
|
|
338
|
* @return the defaultColor
|
|
339
|
*/
|
|
340
|
public String getDefaultColor() {
|
|
341
|
return defaultColor;
|
|
342
|
}
|
|
343
|
|
|
344
|
/**
|
|
345
|
* @param defaultColor the defaultColor to set
|
|
346
|
* @throws ParseException
|
|
347
|
*/
|
|
348
|
//TODO make format checking a hibernate validation rule
|
|
349
|
public void setDefaultColor(String defaultColor) throws ParseException {
|
|
350
|
String regEx = "[0-9a-fA-F]{6}";
|
|
351
|
if (StringUtils.isEmpty(defaultColor)){
|
|
352
|
this.defaultColor = null;
|
|
353
|
}else if (StringUtils.isEmpty(defaultColor) || defaultColor.matches(regEx)){
|
|
354
|
this.defaultColor = defaultColor;
|
|
355
|
}else{
|
|
356
|
throw new java.text.ParseException("Default color is not of correct format. Required is 'FFFFFF'", -1);
|
|
357
|
}
|
|
358
|
}
|
|
359
|
|
|
360
|
/**
|
|
361
|
* Compares this OrderedTermBase with the specified OrderedTermBase for
|
|
362
|
* order. Returns a -1, 0, or +1 if the orderId of this object is greater
|
|
363
|
* than, equal to, or less than the specified object.
|
|
364
|
* <p>
|
|
365
|
* <b>Note:</b> The compare logic of this method is the <b>inverse logic</b>
|
|
366
|
* of the the one implemented in
|
|
367
|
* {@link java.lang.Comparable#compareTo(java.lang.Object)}
|
|
368
|
*
|
|
369
|
* @param orderedTerm
|
|
370
|
* the OrderedTermBase to be compared
|
|
371
|
* @param skipVocabularyCheck
|
|
372
|
* whether to skip checking if both terms to compare are in the
|
|
373
|
* same vocabulary
|
|
374
|
* @throws NullPointerException
|
|
375
|
* if the specified object is null
|
|
376
|
*/
|
|
377
|
@Override
|
|
378
|
protected int performCompareTo(PresenceAbsenceTerm presenceAbsenceTerm, boolean skipVocabularyCheck) {
|
|
379
|
|
|
380
|
PresenceAbsenceTerm presenceAbsenceTermLocal = CdmBase.deproxy(presenceAbsenceTerm, PresenceAbsenceTerm.class);
|
|
381
|
if(! skipVocabularyCheck){
|
|
382
|
if (this.vocabulary == null || presenceAbsenceTermLocal.vocabulary == null){
|
|
383
|
throw new IllegalStateException("An ordered term (" + this.toString() + " or " +
|
|
384
|
presenceAbsenceTermLocal.toString() + ") of class " + this.getClass() + " or " +
|
|
385
|
presenceAbsenceTermLocal.getClass() + " does not belong to a vocabulary and therefore "
|
|
386
|
+ "can not be compared");
|
|
387
|
}
|
|
388
|
if (presenceAbsenceTermLocal.isAbsenceTerm() != this.isAbsenceTerm() ){
|
|
389
|
if (presenceAbsenceTermLocal.isAbsenceTerm()){
|
|
390
|
return 1;
|
|
391
|
}else{
|
|
392
|
return -1;
|
|
393
|
}
|
|
394
|
|
|
395
|
}
|
|
396
|
}
|
|
397
|
|
|
398
|
int orderThat;
|
|
399
|
int orderThis;
|
|
400
|
try {
|
|
401
|
orderThat = presenceAbsenceTermLocal.orderIndex;//OLD: this.getVocabulary().getTerms().indexOf(orderedTerm);
|
|
402
|
orderThis = orderIndex; //OLD: this.getVocabulary().getTerms().indexOf(this);
|
|
403
|
} catch (RuntimeException e) {
|
|
404
|
throw e;
|
|
405
|
}
|
|
406
|
if (orderThis > orderThat){
|
|
407
|
return -1;
|
|
408
|
}else if (orderThis < orderThat){
|
|
409
|
return 1;
|
|
410
|
}else {
|
|
411
|
return 0;
|
|
412
|
}
|
|
413
|
}
|
|
414
|
|
|
415
|
|
|
416
|
public boolean isAbsenceTerm() {
|
|
417
|
return absenceTerm;
|
|
418
|
}
|
|
419
|
|
|
420
|
public void setAbsenceTerm(boolean isAbsenceTerm) {
|
|
421
|
this.absenceTerm = isAbsenceTerm;
|
|
422
|
}
|
|
423
|
|
|
424
|
|
|
425
|
}
|