TcsRdfTransformer 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.tcsrdf;
11  
12  import org.apache.log4j.Logger;
13  import org.springframework.stereotype.Component;
14  
15  import eu.etaxonomy.cdm.model.common.RelationshipBase;
16  import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
17  import eu.etaxonomy.cdm.model.location.NamedArea;
18  import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
19  import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
20  import eu.etaxonomy.cdm.model.name.Rank;
21  import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
22  /*import eu.etaxonomy.cdm.model.reference.Article;
23  import eu.etaxonomy.cdm.model.reference.Book;
24  import eu.etaxonomy.cdm.model.reference.BookSection;
25  import eu.etaxonomy.cdm.model.reference.Journal;
26  import eu.etaxonomy.cdm.model.reference.PersonalCommunication;
27  import eu.etaxonomy.cdm.model.reference.PrintSeries;*/
28  import eu.etaxonomy.cdm.model.reference.ReferenceBase;
29  import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
30  //import eu.etaxonomy.cdm.model.reference.WebPage;
31  import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
32  import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
33  import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
34  import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
35  
36  /**
37   * @author a.mueller
38   * @created 29.05.2008
39   * @version 1.0
40   */
41  public final class TcsRdfTransformer {
42  	@SuppressWarnings("unused")
43  	private static final Logger logger = Logger.getLogger(TcsRdfTransformer.class);
44   
45  
46  	//TypeDesignation
47  	public static SpecimenTypeDesignationStatus typeStatusId2TypeStatus (int typeStatusId)  throws UnknownCdmTypeException{
48  		switch (typeStatusId){
49  			case 1: return SpecimenTypeDesignationStatus.HOLOTYPE();
50  			case 2: return SpecimenTypeDesignationStatus.LECTOTYPE();
51  			case 3: return SpecimenTypeDesignationStatus.NEOTYPE();
52  			case 4: return SpecimenTypeDesignationStatus.EPITYPE();
53  			case 5: return SpecimenTypeDesignationStatus.ISOLECTOTYPE();
54  			case 6: return SpecimenTypeDesignationStatus.ISONEOTYPE();
55  			case 7: return SpecimenTypeDesignationStatus.ISOTYPE();
56  			case 8: return SpecimenTypeDesignationStatus.PARANEOTYPE();
57  			case 9: return SpecimenTypeDesignationStatus.PARATYPE();
58  			case 10: return SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE();
59  			case 11: return SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE();
60  			case 12: return SpecimenTypeDesignationStatus.SYNTYPE();
61  			case 21: return SpecimenTypeDesignationStatus.ICONOTYPE();
62  			case 22: return SpecimenTypeDesignationStatus.PHOTOTYPE();
63  			default: {
64  				throw new UnknownCdmTypeException("Unknown TypeDesignationStatus (id=" + Integer.valueOf(typeStatusId).toString() + ")");
65  			}
66  		}
67  	}
68  	
69  	
70  	
71  	
72  	/** Creates an cdm-Rank by the tcs rank
73  	 */
74  	public static Rank rankString2Rank (String strRank) throws UnknownCdmTypeException{
75  		String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonRank#";
76  		String tcsFamily = tcsRoot + "Family";
77  		String tcsSubFamily = tcsRoot + "Subfamily";
78  		String tcsTribe = tcsRoot + "Tribe";
79  		String tcsSubtribe = tcsRoot + "Subtribe";
80  		String tcsGenus = tcsRoot + "Genus";
81  		String tcsSpecies = tcsRoot + "Species";
82  		String tcsSubSpecies = tcsRoot + "Subspecies";
83  		String tcsVariety = tcsRoot + "Variety";
84  		String tcsSubVariety = tcsRoot + "Sub-Variety";
85  		String tcsForm = tcsRoot + "Form";
86  		
87  		
88  		
89  		if (strRank == null){return null;
90  		}else if (tcsFamily.equals(strRank)){return Rank.FAMILY();
91  		}else if (tcsSubFamily.equals(strRank)){return Rank.SUBFAMILY();
92  		}else if (tcsTribe.equals(strRank)){return Rank.TRIBE();
93  		}else if (tcsSubtribe.equals(strRank)){return Rank.SUBTRIBE();
94  		}else if (tcsGenus.equals(strRank)){return Rank.GENUS();
95  		}else if (tcsSpecies.equals(strRank)){return Rank.SPECIES();
96  		}else if (tcsVariety.equals(strRank)){return Rank.VARIETY();
97  		}else if (tcsSubVariety.equals(strRank)){return Rank.SUBVARIETY();
98  		}else if (tcsSubSpecies.equals(strRank)){return Rank.SUBSPECIES();
99  		}else if (tcsForm.equals(strRank)){return Rank.FORM();
100 		}	
101 		else {
102 			throw new UnknownCdmTypeException("Unknown Rank " + strRank);
103 		}
104 	}
105 	
106 	/** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
107 	 */
108 	public static NomenclaturalCode nomCodeString2NomCode (String nomCode) throws UnknownCdmTypeException{
109 		
110 		String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonName#";
111 		String tcsICBN = tcsRoot + "ICBN";
112 		String tcsICZN = tcsRoot + "ICZN";
113 		String tcsICNCP = tcsRoot + "ICNCP";
114 		String tcsBacteriological = tcsRoot + "BACTERIOLOGICAL";
115 		String tcsViral = tcsRoot + "VIRAL";
116 		
117 		if (nomCode == null){ return null;
118 		}else if (tcsICBN.equals(nomCode)){return NomenclaturalCode.ICBN;
119 		}else if (tcsICZN.equals(nomCode)){return NomenclaturalCode.ICZN;
120 		}else if (tcsICNCP.equals(nomCode)){return NomenclaturalCode.ICNCP;
121 		}else if (tcsBacteriological.equals(nomCode)){return NomenclaturalCode.ICNB;
122 		}else if (tcsViral.equals(nomCode)){return NomenclaturalCode.ICVCN;
123 		}	
124 		else {
125 			throw new UnknownCdmTypeException("Unknown Nomenclatural Code " + nomCode);
126 		}
127 	}
128 	
129 	public static boolean isReverseRelationshipCategory (String tcsRelationshipCategory){
130 		String str = tcsRelationshipCategory.replace("http://rs.tdwg.org/ontology/voc/TaxonConcept#", "");
131 		if ("HasSynonym".equalsIgnoreCase(str) 
132 				|| "IsParentTaxonOf".equalsIgnoreCase(str) 
133 				|| "IsIncludedIn".equalsIgnoreCase(str) 
134 				|| "DoesNotInclude".equalsIgnoreCase(str) 
135 									){
136 			
137 			return true;
138 		}
139 		return false;
140 	}
141 	
142 	/** Creates an cdm-Rank by the tcs rank
143 	 */
144 	public static ReferenceBase pubTypeStr2PubType (String strPubType) throws UnknownCdmTypeException{
145 		String tcsRoot = "http://rs.tdwg.org/ontology/voc/PublicationCitation#";
146 		String tcsBook = tcsRoot + "Book";
147 		String tcsJournal = tcsRoot + "Journal";
148 		String tcsWebPage = tcsRoot + "WebPage";
149 		String tcsCommunication = tcsRoot + "Communication";
150 		String tcsBookSeries = tcsRoot + "BookSeries";
151 		String tcsArticle = tcsRoot + "JournalArticle";
152 		String tcsBookSection = tcsRoot + "BookSection";
153 		
154 		
155 //		Artwork	An Artwork type publication.
156 //		AudiovisualMaterial	A Audiovisual Material type publication.
157 //		BookSeries	A Book Series type publication.
158 //		Commentary	A Commentary type publication.
159 //		Communication	A Communication type publication.
160 //		ComputerProgram	A Computer Program type publication.
161 //		ConferenceProceedings	A Conference Proceedings type publication.
162 //		Determination	A Determination type publication.
163 //		EditedBook	A Edited Book type publication.
164 //		Generic	A generic publication.
165 //		Journal	A Journal type publication.
166 //		MagazineArticle	A Magazine Article type publication.
167 //		Map	A Map type publication.
168 //		NewspaperArticle	A Newspaper Article type publication.
169 //		Patent	A Patent type publication.
170 //		Report	A Report type publication.
171 //		SubReference	A Sub-Reference type publication.
172 //		Thesis	A Thesis type publication.
173 
174 		ReferenceFactory refFactory = ReferenceFactory.newInstance();
175 		if (strPubType == null){return null;
176 		}else if (tcsBookSection.equals(strPubType)){return refFactory.newBookSection();
177 		}else if (tcsBook.equals(strPubType)){return refFactory.newBook();
178 		}else if (tcsArticle.equals(strPubType)){return refFactory.newArticle();
179 		}else if (tcsJournal.equals(strPubType)){return refFactory.newJournal();
180 		}else if (tcsWebPage.equals(strPubType)){return refFactory.newWebPage();
181 		}else if (tcsCommunication.equals(strPubType)){return refFactory.newPersonalCommunication();
182 		}else if (tcsBookSeries.equals(strPubType)){return refFactory.newPrintSeries();
183 		}	
184 		else {
185 			throw new UnknownCdmTypeException("Unknown publication type " + strPubType);
186 		}
187 	}
188 	
189 	/** Creates an cdm-RelationshipTermBase by the tcsRelationshipCategory
190 	 */
191 	public static RelationshipTermBase tcsRelationshipCategory2Relationship (String tcsRelationshipCategory) throws UnknownCdmTypeException{
192 		String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonConcept#";
193 		String doesNotInclude  = tcsRoot + "DoesNotInclude";
194 		String doesNotOverlap  = tcsRoot + "DoesNotOverlap";
195 		String excludes  = tcsRoot + "Excludes";
196 		String hasSynonym  = tcsRoot + "HasSynonym";
197 		String hasVernacular  = tcsRoot + "HasVernacular";
198 		String includes  = tcsRoot + "Includes";
199 		String isAmbiregnalOf  = tcsRoot + "IsAmbiregnalOf";
200 		String isAnamorphOf  = tcsRoot + "IsAnamorphOf";
201 		String isChildTaxonOf  = tcsRoot + "IsChildTaxonOf";
202 		String isCongruentTo  = tcsRoot + "IsCongruentTo";
203 		String isFemaleParentOf  = tcsRoot + "IsFemaleParentOf";
204 		String isFirstParentOf  = tcsRoot + "IsFirstParentOf";
205 		String isHybridChildOf  = tcsRoot + "IsHybridChildOf";
206 		String isHybridParentOf  = tcsRoot + "IsHybridParentOf";
207 		String isIncludedIn  = tcsRoot + "IsIncludedIn";
208 		String isMaleParentOf  = tcsRoot + "IsMaleParentOf";
209 		String isNotCongruentTo  = tcsRoot + "IsNotCongruentTo";
210 		String isNotIncludedIn  = tcsRoot + "IsNotIncludedIn";
211 		String isParentTaxonOf  = tcsRoot + "IsParentTaxonOf";
212 		String isSecondParentOf  = tcsRoot + "IsSecondParentOf";
213 		String isSynonymFor  = tcsRoot + "IsSynonymFor";
214 		String isTeleomorphOf  = tcsRoot + "IsTeleomorphOf";
215 		String isVernacularFor  = tcsRoot + "IsVernacularFor";
216 		String overlaps  = tcsRoot + "Overlaps";
217 
218 		if (tcsRelationshipCategory == null){ return null;
219 		
220 		//Synonym relationships
221 		}else if (isSynonymFor.equals(tcsRelationshipCategory)){return SynonymRelationshipType.SYNONYM_OF(); 
222 		}else if (hasSynonym.equals(tcsRelationshipCategory)){/*isReverse = true; */ return SynonymRelationshipType.SYNONYM_OF(); 
223 		
224 		//Taxon relationships
225 		}else if (isChildTaxonOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(); 
226 		}else if (isParentTaxonOf.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(); 
227 		
228 		//concept relationships
229 		}else if (doesNotOverlap.equals(tcsRelationshipCategory)){return TaxonRelationshipType.DOES_NOT_OVERLAP(); 
230 		}else if (excludes.equals(tcsRelationshipCategory)){return TaxonRelationshipType.EXCLUDES(); 
231 		}else if (includes.equals(tcsRelationshipCategory)){return TaxonRelationshipType.INCLUDES(); 
232 		}else if (isCongruentTo.equals(tcsRelationshipCategory)){return TaxonRelationshipType.CONGRUENT_TO(); 
233 		}else if (isNotCongruentTo.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOT_CONGRUENT_TO(); 
234 		}else if (isNotIncludedIn.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOT_INCLUDED_IN(); 
235 		}else if (overlaps.equals(tcsRelationshipCategory)){return TaxonRelationshipType.OVERLAPS(); 
236 		//reverse concept relationships
237 		}else if (isIncludedIn.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.INCLUDES();
238 		}else if (doesNotInclude.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.NOT_INCLUDED_IN(); 
239 		
240 	//TODO	
241 //		}else if (hasVernacular.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
242 //		}else if (isAmbiregnalOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
243 //		}else if (isAnamorphOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
244 //		}else if (isFemaleParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
245 //		}else if (isFirstParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
246 //		}else if (isHybridChildOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
247 //		}else if (isHybridParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
248 //		}else if (isMaleParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
249 //		}else if (isSecondParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
250 //		}else if (isTeleomorphOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
251 //		}else if (isVernacularFor.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X; 
252 		
253 		}else {
254 			throw new UnknownCdmTypeException("Unknown RelationshipCategory " + tcsRelationshipCategory);
255 		}
256 	}
257 	
258 	
259 	/** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
260 	 */
261 	public static NomenclaturalStatusType nomStatusString2NomStatus (String nomStatus) throws UnknownCdmTypeException{
262 	
263 		if (nomStatus == null){ return null;
264 		}else if ("Valid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.VALID();
265 		
266 		}else if ("Alternative".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
267 		}else if ("nom. altern.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
268 		
269 		}else if ("Ambiguous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.AMBIGUOUS();
270 		
271 		}else if ("Doubtful".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.DOUBTFUL();
272 		
273 		}else if ("Confusum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONFUSUM();
274 		
275 		}else if ("Illegitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
276 		}else if ("nom. illeg.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
277 		
278 		}else if ("Superfluous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
279 		}else if ("nom. superfl.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
280 		
281 		}else if ("Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
282 		}else if ("nom. rej.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
283 		
284 		}else if ("Utique Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED();
285 		
286 		}else if ("Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED_PROP();
287 		
288 		}else if ("Orthography Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP();
289 		
290 		}else if ("Legitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.LEGITIMATE();
291 		
292 		}else if ("Novum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
293 		}else if ("nom. nov.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
294 		
295 		}else if ("Utique Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED_PROP();
296 		
297 		}else if ("Orthography Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED();
298 		
299 		}else if ("Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED_PROP();
300 		
301 		}else if ("Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
302 		}else if ("nom. cons.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
303 		
304 		}else if ("Sanctioned".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SANCTIONED();
305 		
306 		}else if ("Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
307 		}else if ("nom. inval.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
308 		
309 		}else if ("Nudum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
310 		}else if ("nom. nud.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
311 		
312 		}else if ("Combination Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.COMBINATION_INVALID();
313 		
314 		}else if ("Provisional".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
315 		}else if ("nom. provis.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
316 		}
317 		else {
318 			throw new UnknownCdmTypeException("Unknown Nomenclatural status type " + nomStatus);
319 		}
320 	}
321 	
322 	
323 }