TcsXmlTransformer xref

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1   /**
2   * Copyright (C) 2009 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.tcsxml;
11  
12  import org.apache.log4j.Logger;
13  
14  import eu.etaxonomy.cdm.common.ResultWrapper;
15  import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
16  import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
17  import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
18  import eu.etaxonomy.cdm.model.name.Rank;
19  import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
20  /*import eu.etaxonomy.cdm.model.reference.Article;
21  import eu.etaxonomy.cdm.model.reference.Book;
22  import eu.etaxonomy.cdm.model.reference.BookSection;
23  import eu.etaxonomy.cdm.model.reference.Journal;
24  import eu.etaxonomy.cdm.model.reference.PersonalCommunication;
25  import eu.etaxonomy.cdm.model.reference.PrintSeries;*/
26  import eu.etaxonomy.cdm.model.reference.ReferenceBase;
27  import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
28  //import eu.etaxonomy.cdm.model.reference.WebPage;
29  import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
30  import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
31  import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
32  
33  public final class TcsXmlTransformer {
34  	@SuppressWarnings("unused")
35  	private static final Logger logger = Logger.getLogger(TcsXmlTransformer.class);
36   
37  
38  	//TypeDesignation
39  	public static SpecimenTypeDesignationStatus typeStatusId2TypeStatus (int typeStatusId)  throws UnknownCdmTypeException{
40  		switch (typeStatusId){
41  			case 1: return SpecimenTypeDesignationStatus.HOLOTYPE();
42  			case 2: return SpecimenTypeDesignationStatus.LECTOTYPE();
43  			case 3: return SpecimenTypeDesignationStatus.NEOTYPE();
44  			case 4: return SpecimenTypeDesignationStatus.EPITYPE();
45  			case 5: return SpecimenTypeDesignationStatus.ISOLECTOTYPE();
46  			case 6: return SpecimenTypeDesignationStatus.ISONEOTYPE();
47  			case 7: return SpecimenTypeDesignationStatus.ISOTYPE();
48  			case 8: return SpecimenTypeDesignationStatus.PARANEOTYPE();
49  			case 9: return SpecimenTypeDesignationStatus.PARATYPE();
50  			case 10: return SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE();
51  			case 11: return SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE();
52  			case 12: return SpecimenTypeDesignationStatus.SYNTYPE();
53  			case 21: return SpecimenTypeDesignationStatus.ICONOTYPE();
54  			case 22: return SpecimenTypeDesignationStatus.PHOTOTYPE();
55  			default: {
56  				throw new UnknownCdmTypeException("Unknown TypeDesignationStatus (id=" + Integer.valueOf(typeStatusId).toString() + ")");
57  			}
58  		}
59  	}
60  	
61  	
62  	
63  	
64  	/** Creates an cdm-Rank by the tcs rank
65  	 */
66  	public static Rank rankCode2Rank (String strRank) throws UnknownCdmTypeException{
67  		if (strRank == null){return null;
68  		//genus group
69  		}else if (strRank.equals("infragen")){return Rank.INFRAGENUS();
70  		}else if (strRank.equals("subgen")){return Rank.SUBGENUS();
71  		}else if (strRank.equals("gen")){return Rank.GENUS();
72  		//genus subdivision
73  		//TODO 
74  		}else if (strRank.equals("aggr")){return Rank.SPECIESAGGREGATE();
75  		}else if (strRank.equals("taxinfragen")){return Rank.INFRAGENERICTAXON();
76  		}else if (strRank.equals("subser")){return Rank.SUBSERIES();
77  		}else if (strRank.equals("ser")){return Rank.SERIES();
78  		}else if (strRank.equals("subsect")){return Rank.SUBSECTION_BOTANY();
79  		}else if (strRank.equals("sect")){return Rank.SECTION_BOTANY();
80  		//species group
81  		}else if (strRank.equals("subsp_aggr")){return Rank.SUBSPECIFICAGGREGATE();
82  		}else if (strRank.equals("ssp")){return Rank.SUBSPECIES();
83  		}else if (strRank.equals("sp")){return Rank.SPECIES();
84  		//below subspecies
85  		}else if (strRank.equals("cand")){return Rank.CANDIDATE();
86  		}else if (strRank.equals("taxinfrasp")){return Rank.INFRASPECIFICTAXON();
87  		}else if (strRank.equals("fsp")){return Rank.SPECIALFORM();
88  		}else if (strRank.equals("subsubfm")){return Rank.SUBSUBFORM();
89  		}else if (strRank.equals("subfm")){return Rank.SUBFORM();
90  		}else if (strRank.equals("fm")){return Rank.FORM();
91  		}else if (strRank.equals("subsubvar")){return Rank.SUBSUBVARIETY();
92  		}else if (strRank.equals("subvar")){return Rank.SUBVARIETY();
93  		}else if (strRank.equals("var")){return Rank.VARIETY();
94  		//TODO -> see documentation, Bacteria status
95  //		}else if (strRank.equals("pv")){return Rank;
96  //		}else if (strRank.equals("bv")){return Rank.;
97  		}else if (strRank.equals("infrasp")){return Rank.INFRASPECIES();
98  		//above superfamily
99  		}else if (strRank.equals("infraord")){return Rank.INFRAORDER();
100 		}else if (strRank.equals("ord")){return Rank.ORDER();
101 		}else if (strRank.equals("superord")){return Rank.SUPERORDER();
102 		}else if (strRank.equals("infracl")){return Rank.INFRACLASS();
103 		}else if (strRank.equals("subcl")){return Rank.SUBCLASS();
104 		}else if (strRank.equals("cl")){return Rank.CLASS();
105 		}else if (strRank.equals("supercl")){return Rank.SUPERCLASS();
106 		}else if (strRank.equals("infraphyl_div")){return Rank.INFRAPHYLUM();
107 		}else if (strRank.equals("subphyl_div")){return Rank.SUBPHYLUM();
108 		}else if (strRank.equals("phyl_div")){return Rank.PHYLUM();
109 		}else if (strRank.equals("superphyl_div")){return Rank.SUPERPHYLUM();
110 		}else if (strRank.equals("infrareg")){return Rank.INFRAKINGDOM();
111 		}else if (strRank.equals("subreg")){return Rank.SUBKINGDOM();
112 		}else if (strRank.equals("reg")){return Rank.KINGDOM();
113 		}else if (strRank.equals("superreg")){return Rank.SUPERKINGDOM();
114 		}else if (strRank.equals("dom")){return Rank.DOMAIN();
115 		}else if (strRank.equals("taxsupragen")){return Rank.SUPRAGENERICTAXON();
116 		//family group
117 		}else if (strRank.equals("infrafam")){return Rank.FAMILY();
118 		}else if (strRank.equals("subfam")){return Rank.FAMILY();
119 		}else if (strRank.equals("fam")){return Rank.FAMILY();
120 		}else if (strRank.equals("superfam")){return Rank.FAMILY();
121 		//family subdivision
122 		}else if (strRank.equals("intratrib")){return Rank.FAMILY();
123 		}else if (strRank.equals("subtrib")){return Rank.FAMILY();
124 		}else if (strRank.equals("trib")){return Rank.FAMILY();
125 		}else if (strRank.equals("supertrib")){return Rank.FAMILY();
126 		}	
127 		else {
128 			throw new UnknownCdmTypeException("Unknown Rank " + strRank);
129 		}
130 	}
131 	
132 	/** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
133 	 */
134 	public static NomenclaturalCode nomCodeString2NomCode (String nomCode) throws UnknownCdmTypeException{
135 		if (nomCode != null){
136 			nomCode = nomCode.trim();
137 		}
138 		if (nomCode == null){ return null;
139 		}else if (nomCode.equals("Botanical")){return NomenclaturalCode.ICBN;
140 		}else if (nomCode.equals("Zoological")){return NomenclaturalCode.ICZN;
141 		}else if (nomCode.equals("Viral")){return NomenclaturalCode.ICVCN;
142 		}else if (nomCode.equals("Bacteriological")){return NomenclaturalCode.ICNB;
143 		}else if (nomCode.equals("CultivatedPlant")){return NomenclaturalCode.ICNCP;
144 		//TODO code Indeterminate
145 //		}else if (nomCode.equals("Indeterminate")){return NomenclaturalCode.XXX();
146 		}	
147 		else {
148 			throw new UnknownCdmTypeException("Unknown Nomenclatural Code " + nomCode);
149 		}
150 	}
151 	
152 	public static boolean isReverseRelationshipCategory (String tcsRelationshipCategory){
153 		String str = tcsRelationshipCategory.replace("http://rs.tdwg.org/ontology/voc/TaxonConcept#", "");
154 		if ("HasSynonym".equalsIgnoreCase(str) 
155 				|| "IsParentTaxonOf".equalsIgnoreCase(str) 
156 				|| "IsIncludedIn".equalsIgnoreCase(str) 
157 				|| "DoesNotInclude".equalsIgnoreCase(str) 
158 									){
159 			
160 			return true;
161 		}
162 		return false;
163 	}
164 	
165 	/** Creates an cdm-Rank by the tcs rank
166 	 */
167 	public static ReferenceBase pubTypeStr2PubType (String strPubType) throws UnknownCdmTypeException{
168 		String tcsRoot = "http://rs.tdwg.org/ontology/voc/PublicationCitation#";
169 		String tcsBook = tcsRoot + "Book";
170 		String tcsJournal = tcsRoot + "Journal";
171 		String tcsWebPage = tcsRoot + "WebPage";
172 		String tcsCommunication = tcsRoot + "Communication";
173 		String tcsBookSeries = tcsRoot + "BookSeries";
174 		String tcsArticle = tcsRoot + "JournalArticle";
175 		String tcsBookSection = tcsRoot + "BookSection";
176 		
177 		
178 //		Artwork	An Artwork type publication.
179 //		AudiovisualMaterial	A Audiovisual Material type publication.
180 //		BookSeries	A Book Series type publication.
181 //		Commentary	A Commentary type publication.
182 //		Communication	A Communication type publication.
183 //		ComputerProgram	A Computer Program type publication.
184 //		ConferenceProceedings	A Conference Proceedings type publication.
185 //		Determination	A Determination type publication.
186 //		EditedBook	A Edited Book type publication.
187 //		Generic	A generic publication.
188 //		Journal	A Journal type publication.
189 //		MagazineArticle	A Magazine Article type publication.
190 //		Map	A Map type publication.
191 //		NewspaperArticle	A Newspaper Article type publication.
192 //		Patent	A Patent type publication.
193 //		Report	A Report type publication.
194 //		SubReference	A Sub-Reference type publication.
195 //		Thesis	A Thesis type publication.
196 
197 		ReferenceFactory refFactory = ReferenceFactory.newInstance();
198 		if (strPubType == null){return null;
199 		}else if (tcsBookSection.equals(strPubType)){return refFactory.newBookSection();
200 		}else if (tcsBook.equals(strPubType)){return refFactory.newBook();
201 		}else if (tcsArticle.equals(strPubType)){return refFactory.newArticle();
202 		}else if (tcsJournal.equals(strPubType)){return refFactory.newJournal();
203 		}else if (tcsWebPage.equals(strPubType)){return refFactory.newWebPage();
204 		}else if (tcsCommunication.equals(strPubType)){return refFactory.newPersonalCommunication();
205 		}else if (tcsBookSeries.equals(strPubType)){return refFactory.newPrintSeries();
206 		}	
207 		else {
208 			throw new UnknownCdmTypeException("Unknown publication type " + strPubType);
209 		}
210 	}
211 	
212 	/** Creates an cdm-RelationshipTermBase by the tcsRelationshipCategory
213 	 */
214 	public static RelationshipTermBase tcsRelationshipType2Relationship (String tcsRelationshipType, ResultWrapper<Boolean> inverse) throws UnknownCdmTypeException{
215 		if (tcsRelationshipType == null){ return null;
216 		
217 		//Synonym relationships
218 //		}else if (tcsRelationshipType.equals("is synonym for")){return SynonymRelationshipType.SYNONYM_OF(); 
219 		}else if (tcsRelationshipType.equals("has synonym")){inverse.setValue(true); return SynonymRelationshipType.SYNONYM_OF(); 
220 		
221 		//Taxon relationships
222 		}else if (tcsRelationshipType.equals("is child taxon of")){return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(); 
223 		}else if (tcsRelationshipType.equals("is parent taxon of")){inverse.setValue(true);  return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(); 
224 		
225 		//concept relationships
226 		}else if (tcsRelationshipType.equals("does not overlap")){return TaxonRelationshipType.DOES_NOT_OVERLAP(); 
227 		}else if (tcsRelationshipType.equals("excludes")){return TaxonRelationshipType.EXCLUDES(); 
228 		}else if (tcsRelationshipType.equals("includes")){return TaxonRelationshipType.INCLUDES(); 
229 		}else if (tcsRelationshipType.equals("is congruent to")){return TaxonRelationshipType.CONGRUENT_TO(); 
230 		}else if (tcsRelationshipType.equals("is not congruent to")){return TaxonRelationshipType.NOT_CONGRUENT_TO(); 
231 		}else if (tcsRelationshipType.equals("is not included in")){return TaxonRelationshipType.NOT_INCLUDED_IN(); 
232 		}else if (tcsRelationshipType.equals("overlaps")){return TaxonRelationshipType.OVERLAPS(); 
233 		//reverse concept relationships
234 		}else if (tcsRelationshipType.equals("is included in")){inverse.setValue(true); return TaxonRelationshipType.INCLUDES();
235 		}else if (tcsRelationshipType.equals("does not include")){inverse.setValue(true); return TaxonRelationshipType.NOT_INCLUDED_IN(); 
236 		
237 	//TODO
238 		
239 //		}else if (tcsRelationshipType.equals("has vernacular")){return TaxonRelationshipType.X; 
240 //		}else if (tcsRelationshipType.equals("is vernacular for")){return TaxonRelationshipType.X; 
241 //		}else if (tcsRelationshipType.equals("is ambiregnal of")){return TaxonRelationshipType.X; 
242 //		}else if (tcsRelationshipType.equals("is hybrid child of")){return TaxonRelationshipType.X; 
243 //		}else if (tcsRelationshipType.equals("is hybrid parent of")){return TaxonRelationshipType.X; 
244 //		}else if (tcsRelationshipType.equals("is male parent of")){return TaxonRelationshipType.X; 
245 //		}else if (tcsRelationshipType.equals("is first parent of")){return TaxonRelationshipType.X; 
246 //		}else if (tcsRelationshipType.equals("is female parent of")){return TaxonRelationshipType.X; 
247 //		}else if (tcsRelationshipType.equals("is second parent of")){return TaxonRelationshipType.X; 
248 //		}else if (tcsRelationshipType.equals("is teleomorph of")){return TaxonRelationshipType.X; 
249 //		}else if (tcsRelationshipType.equals("is anamorph of")){return TaxonRelationshipType.X; 
250 		
251 		}else {
252 			throw new UnknownCdmTypeException("Unknown RelationshipCategory " + tcsRelationshipType);
253 		}
254 	}
255 	
256 	
257 	/** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
258 	 */
259 	public static NomenclaturalStatusType nomStatusString2NomStatus (String nomStatus) throws UnknownCdmTypeException{
260 	
261 		if (nomStatus == null){ return null;
262 		}else if ("Valid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.VALID();
263 		
264 		}else if ("Alternative".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
265 		}else if ("nom. altern.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
266 		
267 		}else if ("Ambiguous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.AMBIGUOUS();
268 		
269 		}else if ("Doubtful".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.DOUBTFUL();
270 		
271 		}else if ("Confusum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONFUSUM();
272 		
273 		}else if ("Illegitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
274 		}else if ("nom. illeg.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
275 		
276 		}else if ("Superfluous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
277 		}else if ("nom. superfl.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
278 		
279 		}else if ("Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
280 		}else if ("nom. rej.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
281 		
282 		}else if ("Utique Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED();
283 		
284 		}else if ("Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED_PROP();
285 		
286 		}else if ("Orthography Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP();
287 		
288 		}else if ("Legitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.LEGITIMATE();
289 		
290 		}else if ("Novum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
291 		}else if ("nom. nov.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
292 		
293 		}else if ("Utique Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED_PROP();
294 		
295 		}else if ("Orthography Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED();
296 		
297 		}else if ("Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED_PROP();
298 		
299 		}else if ("Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
300 		}else if ("nom. cons.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
301 		
302 		}else if ("Sanctioned".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SANCTIONED();
303 		
304 		}else if ("Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
305 		}else if ("nom. inval.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
306 		
307 		}else if ("Nudum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
308 		}else if ("nom. nud.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
309 		
310 		}else if ("Combination Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.COMBINATION_INVALID();
311 		
312 		}else if ("Provisional".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
313 		}else if ("nom. provis.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
314 		}
315 		else {
316 			throw new UnknownCdmTypeException("Unknown Nomenclatural status type " + nomStatus);
317 		}
318 	}
319 	
320 	
321 }