import java.util.UUID;
import javax.persistence.Entity;
-import javax.persistence.Enumerated;
import javax.persistence.Transient;
import javax.validation.constraints.NotNull;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
+import org.hibernate.annotations.Type;
import org.hibernate.envers.Audited;
import org.hibernate.search.annotations.Indexed;
private static final UUID uuidCultivar = UUID.fromString("5e98415b-dc6e-440b-95d6-ea33dbb39ad0");
private static final UUID uuidUnknownRank = UUID.fromString("5c4d6755-2cf6-44ca-9220-cccf8881700b");
- private static Map<String, UUID> abbrevMap = null;
+ private static Map<String, UUID> idInVocMap = null;
private static Map<String, UUID> labelMap = null;
protected static Map<UUID, Rank> termMap = null;
*/
@XmlAttribute(name ="RankClass")
@NotNull
- @Enumerated //TODO use UserType
+ @Type(type = "eu.etaxonomy.cdm.hibernate.EnumUserType",
+ parameters = {@org.hibernate.annotations.Parameter(name="enumClass", value="eu.etaxonomy.cdm.model.name.RankClass")}
+ )
private RankClass rankClass;
- // ********************* CONSTRUCTORS ************************************+/
-
- //for hibernate use only
- protected Rank() {}
+//********************************** Constructor *********************************/
+
+ //for hibernate use only
+ @Deprecated
+ protected Rank() {
+ super(TermType.Rank);
+ }
/**
* Class constructor: creates an additional rank instance with a description
/**
- * Returns the rank identified through a name (abbreviated or not).
+ * Returns the rank identified through a label or the identifier within the vocabulary
* Preliminary implementation for BotanicalNameParser.
*
* @param strRank the string identifying the rank
* @return the rank
*/
- public static Rank getRankByNameOrAbbreviation(String strRank) throws UnknownCdmTypeException{
- return getRankByNameOrAbbreviation(strRank, false);
+ public static Rank getRankByNameOrIdInVoc(String strRank) throws UnknownCdmTypeException{
+ return getRankByNameOrIdInVoc(strRank, false);
}
/**
- * Returns the rank identified through a name (abbreviated or not) for a given nomenclatural code.
+ * Returns the rank identified through a label or the identifier within the vocabulary
+ * for a given nomenclatural code.
* Preliminary implementation for BotanicalNameParser.
*
* @param strRank the string identifying the rank
* @param nc the nomenclatural code
* @return the rank
*/
- public static Rank getRankByNameOrAbbreviation(String strRank, NomenclaturalCode nc)
- throws UnknownCdmTypeException{
- return getRankByNameOrAbbreviation(strRank, nc, false);
+ public static Rank getRankByNameOrIdInVoc(String strRank, NomenclaturalCode nc) throws UnknownCdmTypeException{
+ return getRankByNameOrIdInVoc(strRank, nc, false);
}
// TODO
// Preliminary implementation for BotanicalNameParser.
// not yet complete
/**
- * Returns the rank identified through a name (abbreviated or not).
+ * Returns the rank identified through a label or the identifier within the vocabulary.
* Preliminary implementation for BotanicalNameParser.
*
* @param strRank the string identifying the rank
* unknown or not yet implemented
* @return the rank
*/
- public static Rank getRankByNameOrAbbreviation(String strRank, boolean useUnknown)
- throws UnknownCdmTypeException{
+ public static Rank getRankByNameOrIdInVoc(String strRank, boolean useUnknown) throws UnknownCdmTypeException{
try {
- return getRankByAbbreviation(strRank);
+ return getRankByIdInVoc(strRank);
} catch (UnknownCdmTypeException e) {
return getRankByName(strRank, useUnknown);
}
// Preliminary implementation for BotanicalNameParser.
// not yet complete
/**
- * Returns the rank identified through a name (abbreviated or not).
+ * Returns the rank identified through a label or the identifier within the vocabulary.
* Preliminary implementation for BotanicalNameParser.
*
* @param strRank the string identifying the rank
* unknown or not yet implemented
* @return the rank
*/
- public static Rank getRankByNameOrAbbreviation(String strRank, NomenclaturalCode nc, boolean useUnknown)
+ public static Rank getRankByNameOrIdInVoc(String strRank, NomenclaturalCode nc, boolean useUnknown)
throws UnknownCdmTypeException{
try {
- return getRankByAbbreviation(strRank, nc);
+ return getRankByIdInVoc(strRank, nc);
} catch (UnknownCdmTypeException e) {
return getRankByName(strRank, nc, useUnknown);
}
}
/**
- * Returns the rank identified through an abbreviated name.
+ * Returns the rank identified through the vocabulary identifier.
* Preliminary implementation for BotanicalNameParser.<BR>
* Note: For abbrev = "[unranked]" the result is undefined.
* It maybe the infrageneric unranked or the infraspecific unranked.
* @param abbrev the string for the name abbreviation
* @return the rank
*/
- public static Rank getRankByAbbreviation(String abbrev)
- throws UnknownCdmTypeException{
- return getRankByAbbreviation(abbrev, false);
+ public static Rank getRankByIdInVoc(String abbrev) throws UnknownCdmTypeException{
+ return getRankByIdInVoc(abbrev, false);
}
/**
* Returns the rank identified through an abbreviated name for a given nomenclatural code.
- * See also {@link #getRankByAbbreviation(String, boolean)}
+ * See also {@link #getRankByIdInVoc(String, boolean)}
*
* @param abbrev the string for the name abbreviation
* @param nc the nomenclatural code
* @return the rank
*/
- public static Rank getRankByAbbreviation(String abbrev, NomenclaturalCode nc) throws UnknownCdmTypeException{
- return getRankByAbbreviation(abbrev, nc, false);
+ public static Rank getRankByIdInVoc(String abbrev, NomenclaturalCode nc) throws UnknownCdmTypeException{
+ return getRankByIdInVoc(abbrev, nc, false);
}
// TODO
* If no according abbreviation is available it throws either an UnknownCdmTypeException
* or an #Rank.UNKNOWN() object depending on the useUnknown flag.
*
- * @param abbrev the string for the name abbreviation
+ * @param idInVoc the string for the name abbreviation
* @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
* unknown or not yet existent
* @return the rank
*/
- public static Rank getRankByAbbreviation(String abbrev, boolean useUnknown) throws UnknownCdmTypeException{
+ public static Rank getRankByIdInVoc(String idInVoc, boolean useUnknown) throws UnknownCdmTypeException{
Rank result = null;
- if (abbrev == null){
- throw new NullPointerException("Abbrev is NULL in getRankByAbbreviation");
+ if (idInVoc == null){
+ throw new NullPointerException("idInVoc is NULL in getRankByIdInVoc");
}
- if (abbrev.trim().equals("")){
- //handle empty abbrev as unknown
- abbrev = "oija�m��";
+ if (StringUtils.isBlank(idInVoc)){
+ //handle empty idInVoc as unknown
+ idInVoc = "oijas34\u0155";
}
- if (abbrevMap == null){
+ if (idInVocMap == null){
return null;
}
- UUID uuid = abbrevMap.get(abbrev);
+ idInVoc = normalizeSectionAndSubsection(idInVoc);
+ UUID uuid = idInVocMap.get(idInVoc);
if (uuid != null ){
result = getTermByUuid(uuid);
}
if (result != null){
return result;
}else {
- if (abbrev == null){
- abbrev = "(null)";
+ if (idInVoc == null){
+ idInVoc = "(null)";
}
if (useUnknown){
- logger.info("Unknown rank name: " + abbrev + ". Rank 'UNKNOWN_RANK' created instead");
+ logger.info("Unknown rank name: " + idInVoc + ". Rank 'UNKNOWN_RANK' created instead");
return Rank.UNKNOWN_RANK();
}else{
- throw new UnknownCdmTypeException("Unknown rank abbreviation: " + abbrev);
+ throw new UnknownCdmTypeException("Unknown rank abbreviation: " + idInVoc);
}
}
}
- // TODO
+ private static String normalizeSectionAndSubsection(String idInVoc) {
+ if (idInVoc.equals("sect.")){
+ return "sect.(bot.)";
+ }else if (idInVoc.equals("subsect.")){
+ return "subsect.(bot.)";
+ }
+ return idInVoc;
+ }
+
+ // TODO
// Preliminary implementation to cover Botany and Zoology.
/**
* Returns the rank identified through an abbreviated name for a given nomenclatural code.
* Preliminary implementation for ICBN and ICZN.
- * See also {@link #getRankByAbbreviation(String, boolean)}
+ * See also {@link #getRankByIdInVoc(String, boolean)}
*
* @param abbrev the string for the name abbreviation
* unknown or not yet implemented
* @return the rank
*/
- public static Rank getRankByAbbreviation(String abbrev, NomenclaturalCode nc, boolean useUnknown)
+ public static Rank getRankByIdInVoc(String abbrev, NomenclaturalCode nc, boolean useUnknown)
throws UnknownCdmTypeException{
if (nc != null && nc.equals(NomenclaturalCode.ICZN)) {
}
}
}
- return getRankByAbbreviation(abbrev, useUnknown);
+ return getRankByIdInVoc(abbrev, useUnknown);
}
// TODO
}else if (rankName.equalsIgnoreCase("tax.infragen.")){ return Rank.INFRAGENERICTAXON();
}else if (rankName.equalsIgnoreCase("tax.infrasp.")){ return Rank.INFRASPECIFICTAXON();
// old ranks
- }else if (rankName.equalsIgnoreCase("proles")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
- }else if (rankName.equalsIgnoreCase("race")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
- }else if (rankName.equalsIgnoreCase("taxon")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
- }else if (rankName.equalsIgnoreCase("sublusus")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
+ }else if (rankName.equalsIgnoreCase("proles")){ return Rank.PROLES();
+ }else if (rankName.equalsIgnoreCase("race")){ return Rank.RACE();
+ }else if (rankName.equalsIgnoreCase("sublusus")){ return Rank.SUBLUSUS();
+ }else if (rankName.equalsIgnoreCase("taxon")){ return Rank.INFRASPECIFICTAXON(); //to create the name put 'taxon' and the infraspeciesepi to the field unnamed namephrase
+
}else{
if (rankName == null){
rankName = "(null)"; //see NPE above
@Override
- public Rank readCsvLine(Class<Rank> termClass, List<String> csvLine, Map<UUID, DefinedTermBase> terms) {
- Rank rank = super.readCsvLine(termClass, csvLine, terms);
- RankClass rankClass = RankClass.byKey(csvLine.get(5));
+ public Rank readCsvLine(Class<Rank> termClass, List<String> csvLine, Map<UUID, DefinedTermBase> terms, boolean abbrevAsId) {
+ Rank rank = super.readCsvLine(termClass, csvLine, terms, abbrevAsId);
+ RankClass rankClass = RankClass.getByKey(csvLine.get(5));
assert rankClass != null: "XXXXXXXXXXXXXXXXXXXXX Rank class must not be null: " + csvLine ;
rank.setRankClass(rankClass);
return rank;
Representation representation = rank.getRepresentation(lang);
String abbrevLabel = representation.getAbbreviatedLabel();
String label = representation.getLabel();
- if (abbrevLabel == null){
- logger.warn("Abbreviated label for rank is NULL.Can't add rank: " + CdmUtils.Nz(rank.getLabel()));
- return;
- }
+
//initialize maps
- if (abbrevMap == null){
- abbrevMap = new HashMap<String, UUID>();
+ if (idInVocMap == null){
+ idInVocMap = new HashMap<String, UUID>();
}
if (labelMap == null){
labelMap = new HashMap<String, UUID>();
}
- //add to map
- abbrevMap.put(abbrevLabel, rank.getUuid());
labelMap.put(label.toLowerCase(), rank.getUuid());
+ //add to map
+ if (StringUtils.isBlank(abbrevLabel)){
+ logger.info("Abbreviated label for rank is NULL or empty.Can't add rank to abbrevLabel map: " + CdmUtils.Nz(rank.getLabel()));
+ }else{
+ idInVocMap.put(abbrevLabel, rank.getUuid());
+ }
}
BGBM BDI Projects / cdmlib.git / blobdiff