TaxonXTransformer xref

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1   /**
2   * Copyright (C) 2007 EDIT
3   * European Distributed Institute of Taxonomy 
4   * http://www.e-taxonomy.eu
5   * 
6   * The contents of this file are subject to the Mozilla Public License Version 1.1
7   * See LICENSE.TXT at the top of this package for the full license terms.
8   */
9   
10  package eu.etaxonomy.cdm.io.taxonx;
11  
12  import org.apache.log4j.Logger;
13  
14  import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
15  import eu.etaxonomy.cdm.model.description.Feature;
16  import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
17  import eu.etaxonomy.cdm.model.name.Rank;
18  import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
19  import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
20  import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
21  import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
22  
23  /**
24   * @author a.mueller
25   * @created 29.07.2008
26   * @version 1.0
27   */
28  public final class TaxonXTransformer {
29  	@SuppressWarnings("unused")
30  	private static final Logger logger = Logger.getLogger(TaxonXTransformer.class);
31   
32  	//Facts
33  	public static int FACT_DESCRIPTION = 1;
34  	public static int FACT_GROWTH_FORM = 2;
35  	public static int FACT_HARDINESS = 3;
36  	public static int FACT_ECOLOGY = 4;
37  	public static int FACT_PHENOLOGY = 5;
38  	public static int FACT_KARYOLOGY = 6;
39  	public static int FACT_ILLUSTRATION = 7;
40  	public static int FACT_IDENTIFICATION = 8;
41  	public static int FACT_OBSERVATION = 9;
42  	public static int FACT_DISTIRBUTION_EM = 10;
43  	public static int FACT_DISTIRBUTION_WORLD = 11;
44  	
45  	//TypeDesignation
46  	public static SpecimenTypeDesignationStatus typeStatusId2TypeStatus (int typeStatusId)  throws UnknownCdmTypeException{
47  		switch (typeStatusId){
48  			case 1: return SpecimenTypeDesignationStatus.HOLOTYPE();
49  			case 2: return SpecimenTypeDesignationStatus.LECTOTYPE();
50  			case 3: return SpecimenTypeDesignationStatus.NEOTYPE();
51  			case 4: return SpecimenTypeDesignationStatus.EPITYPE();
52  			case 5: return SpecimenTypeDesignationStatus.ISOLECTOTYPE();
53  			case 6: return SpecimenTypeDesignationStatus.ISONEOTYPE();
54  			case 7: return SpecimenTypeDesignationStatus.ISOTYPE();
55  			case 8: return SpecimenTypeDesignationStatus.PARANEOTYPE();
56  			case 9: return SpecimenTypeDesignationStatus.PARATYPE();
57  			case 10: return SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE();
58  			case 11: return SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE();
59  			case 12: return SpecimenTypeDesignationStatus.SYNTYPE();
60  			case 21: return SpecimenTypeDesignationStatus.ICONOTYPE();
61  			case 22: return SpecimenTypeDesignationStatus.PHOTOTYPE();
62  			default: {
63  				throw new UnknownCdmTypeException("Unknown TypeDesignationStatus (id=" + Integer.valueOf(typeStatusId).toString() + ")");
64  			}
65  		}
66  	}
67  	
68  	
69  	
70  	
71  	/** Creates an cdm-Rank by the tcs rank
72  	 */
73  	public static Rank rankString2Rank (String strRank) throws UnknownCdmTypeException{
74  		String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonRank#";
75  		String tcsGenus = tcsRoot + "Genus";
76  		String tcsSpecies = tcsRoot + "Species";
77  //		String tcsGenus = tcsRoot + "Genus";
78  		
79  		if (strRank == null){return null;
80  		}else if (tcsGenus.equals(strRank)){return Rank.GENUS();
81  		}else if (tcsSpecies.equals(strRank)){return Rank.SPECIES();
82  		}	
83  		else {
84  			throw new UnknownCdmTypeException("Unknown Rank " + strRank);
85  		}
86  	}
87  	
88  	/** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
89  	 */
90  	public static Feature descriptionType2feature (String descriptionType) throws UnknownCdmTypeException{
91  		if (descriptionType == null){ return null;
92  //		}else if ("abstract".equals(descriptionType)){return Feature.XX();
93  //		}else if ("acknowledgments".equals(descriptionType)){return Feature.ICZN();
94  		}else if ("biology_ecology".equals(descriptionType)){return Feature.BIOLOGY_ECOLOGY();
95  		}else if ("description".equals(descriptionType)){return Feature.DESCRIPTION();
96  		}else if ("cultivation".equals(descriptionType)){return Feature.CULTIVATION();
97  		}else if ("conservation".equals(descriptionType)){return Feature.CONSERVATION();
98  		}else if ("diagnosis".equals(descriptionType)){return Feature.DIAGNOSIS();
99  		}else if ("Description".equals(descriptionType)){return Feature.DESCRIPTION();
100 		}else if ("discussion".equals(descriptionType)){return Feature.DISCUSSION();
101 		}else if ("distribution".equals(descriptionType)){return Feature.DISTRIBUTION();
102 		}else if ("etymology".equals(descriptionType)){return Feature.ETYMOLOGY();
103 		}else if ("key".equals(descriptionType)){return Feature.KEY();
104 		}else if ("introduction".equals(descriptionType)){return Feature.INTRODUCTION();
105 		}else if ("materials_examined".equals(descriptionType)){return Feature.MATERIALS_EXAMINED();
106 		}else if ("materials_methods".equals(descriptionType)){return Feature.MATERIALS_METHODS();
107 //		}else if ("multiple".equals(descriptionType)){return Feature.multi;
108 //		}else if ("synopsis".equals(descriptionType)){return Feature.synopsis;
109 		}else if ("uses".equals(descriptionType)){return Feature.USES();
110 		}else if ("vernacular".equals(descriptionType)){return Feature.COMMON_NAME();
111 		}else if ("anatomy".equals(descriptionType)){return Feature.ANATOMY();
112 		}else {
113 			throw new UnknownCdmTypeException("Unknown Description Type: " + descriptionType);
114 		}
115 	}
116 	
117 	public static boolean isReverseRelationshipCategory (String tcsRelationshipCategory){
118 		String str = tcsRelationshipCategory.replace("http://rs.tdwg.org/ontology/voc/TaxonConcept#", "");
119 		if ("HasSynonym".equalsIgnoreCase(str) 
120 				|| "IsParentTaxonOf".equalsIgnoreCase(str) 
121 				|| "IsIncludedIn".equalsIgnoreCase(str) 
122 				|| "DoesNotInclude".equalsIgnoreCase(str) 
123 									){
124 			
125 			return true;
126 		}
127 		return false;
128 	}
129 	
130 	/** Creates an cdm-RelationshipTermBase by the tcsRelationshipCategory
131 	 */
132 	public static RelationshipTermBase tcsRelationshipCategory2Relationship (String tcsRelationshipCategory) throws UnknownCdmTypeException{
133 		String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonConcept#";
134 		String doesNotInclude  = tcsRoot + "DoesNotInclude";
135 		String doesNotOverlap  = tcsRoot + "DoesNotOverlap";
136 		String excludes  = tcsRoot + "Excludes";
137 		String hasSynonym  = tcsRoot + "HasSynonym";
138 		String hasVernacular  = tcsRoot + "HasVernacular";
139 		String includes  = tcsRoot + "Includes";
140 		String isAmbiregnalOf  = tcsRoot + "IsAmbiregnalOf";
141 		String isAnamorphOf  = tcsRoot + "IsAnamorphOf";
142 		String isChildTaxonOf  = tcsRoot + "IsChildTaxonOf";
143 		String isCongruentTo  = tcsRoot + "IsCongruentTo";
144 		String isFemaleParentOf  = tcsRoot + "IsFemaleParentOf";
145 		String isFirstParentOf  = tcsRoot + "IsFirstParentOf";
146 		String isHybridChildOf  = tcsRoot + "IsHybridChildOf";
147 		String isHybridParentOf  = tcsRoot + "IsHybridParentOf";
148 		String isIncludedIn  = tcsRoot + "IsIncludedIn";
149 		String isMaleParentOf  = tcsRoot + "IsMaleParentOf";
150 		String isNotCongruentTo  = tcsRoot + "IsNotCongruentTo";
151 		String isNotIncludedIn  = tcsRoot + "IsNotIncludedIn";
152 		String isParentTaxonOf  = tcsRoot + "IsParentTaxonOf";
153 		String isSecondParentOf  = tcsRoot + "IsSecondParentOf";
154 		String isSynonymFor  = tcsRoot + "IsSynonymFor";
155 		String isTeleomorphOf  = tcsRoot + "IsTeleomorphOf";
156 		String isVernacularFor  = tcsRoot + "IsVernacularFor";
157 		String overlaps  = tcsRoot + "Overlaps";
158 
159 		if (tcsRelationshipCategory == null){ return null;
160 		
161 		//Synonym relationships
162 		}else if (isSynonymFor.equals(tcsRelationshipCategory)){return SynonymRelationshipType.SYNONYM_OF(); 
163 		}else if (hasSynonym.equals(tcsRelationshipCategory)){/*isReverse = true; */ return SynonymRelationshipType.SYNONYM_OF(); 
164 		
165 		//Taxon relationships
166 		}else if (isChildTaxonOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(); 
167 		}else if (isParentTaxonOf.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(); 
168 		
169 		//concept relationships
170 		}else if (doesNotOverlap.equals(tcsRelationshipCategory)){return TaxonRelationshipType.DOES_NOT_OVERLAP(); 
171 		}else if (excludes.equals(tcsRelationshipCategory)){return TaxonRelationshipType.EXCLUDES(); 
172 		}else if (includes.equals(tcsRelationshipCategory)){return TaxonRelationshipType.INCLUDES(); 
173 		}else if (isCongruentTo.equals(tcsRelationshipCategory)){return TaxonRelationshipType.CONGRUENT_TO(); 
174 		}else if (isNotCongruentTo.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOT_CONGRUENT_TO(); 
175 		}else if (isNotIncludedIn.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOT_INCLUDED_IN(); 
176 		}else if (overlaps.equals(tcsRelationshipCategory)){return TaxonRelationshipType.OVERLAPS(); 
177 		//reverse concept relationships
178 		}else if (isIncludedIn.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.INCLUDES();
179 		}else if (doesNotInclude.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.NOT_INCLUDED_IN(); 
180 		
181 	//TODO	
182 //		}else if (hasVernacular.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
183 //		}else if (isAmbiregnalOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
184 //		}else if (isAnamorphOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
185 //		}else if (isFemaleParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
186 //		}else if (isFirstParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
187 //		}else if (isHybridChildOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
188 //		}else if (isHybridParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
189 //		}else if (isMaleParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
190 //		}else if (isSecondParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
191 //		}else if (isTeleomorphOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
192 //		}else if (isVernacularFor.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
193 		
194 		}else {
195 			throw new UnknownCdmTypeException("Unknown RelationshipCategory " + tcsRelationshipCategory);
196 		}
197 	}
198 	
199 	
200 	/** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
201 	 */
202 	public static NomenclaturalStatusType nomStatusString2NomStatus (String nomStatus) throws UnknownCdmTypeException{
203 	
204 		if (nomStatus == null){ return null;
205 		}else if ("Valid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.VALID();
206 		
207 		}else if ("Alternative".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
208 		}else if ("nom. altern.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
209 		
210 		}else if ("Ambiguous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.AMBIGUOUS();
211 		
212 		}else if ("Doubtful".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.DOUBTFUL();
213 		
214 		}else if ("Confusum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONFUSUM();
215 		
216 		}else if ("Illegitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
217 		}else if ("nom. illeg.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
218 		
219 		}else if ("Superfluous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
220 		}else if ("nom. superfl.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
221 		
222 		}else if ("Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
223 		}else if ("nom. rej.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
224 		
225 		}else if ("Utique Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED();
226 		
227 		}else if ("Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED_PROP();
228 		
229 		}else if ("Orthography Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP();
230 		
231 		}else if ("Legitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.LEGITIMATE();
232 		
233 		}else if ("Novum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
234 		}else if ("nom. nov.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
235 		
236 		}else if ("Utique Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED_PROP();
237 		
238 		}else if ("Orthography Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED();
239 		
240 		}else if ("Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED_PROP();
241 		
242 		}else if ("Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
243 		}else if ("nom. cons.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
244 		
245 		}else if ("Sanctioned".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SANCTIONED();
246 		
247 		}else if ("Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
248 		}else if ("nom. inval.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
249 		
250 		}else if ("Nudum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
251 		}else if ("nom. nud.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
252 		
253 		}else if ("Combination Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.COMBINATION_INVALID();
254 		
255 		}else if ("Provisional".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
256 		}else if ("nom. provis.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
257 		}
258 		else {
259 			throw new UnknownCdmTypeException("Unknown Nomenclatural status type " + nomStatus);
260 		}
261 	}
262 	
263 }