ErmsSourceUsesImport 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.erms;
11  
12  import static eu.etaxonomy.cdm.io.erms.ErmsTransformer.SOURCE_USE_ADDITIONAL_SOURCE;
13  import static eu.etaxonomy.cdm.io.erms.ErmsTransformer.SOURCE_USE_BASIS_OF_RECORD;
14  import static eu.etaxonomy.cdm.io.erms.ErmsTransformer.SOURCE_USE_EMENDATION;
15  import static eu.etaxonomy.cdm.io.erms.ErmsTransformer.SOURCE_USE_NEW_COMBINATION_REFERENCE;
16  import static eu.etaxonomy.cdm.io.erms.ErmsTransformer.SOURCE_USE_ORIGINAL_DESCRIPTION;
17  import static eu.etaxonomy.cdm.io.erms.ErmsTransformer.SOURCE_USE_REDESCRIPTION;
18  import static eu.etaxonomy.cdm.io.erms.ErmsTransformer.SOURCE_USE_SOURCE_OF_SYNONYMY;
19  import static eu.etaxonomy.cdm.io.erms.ErmsTransformer.SOURCE_USE_STATUS_SOURCE;
20  
21  import java.sql.ResultSet;
22  import java.sql.SQLException;
23  import java.util.HashMap;
24  import java.util.HashSet;
25  import java.util.Map;
26  import java.util.Set;
27  
28  import org.apache.log4j.Logger;
29  import org.springframework.stereotype.Component;
30  
31  import eu.etaxonomy.cdm.common.CdmUtils;
32  import eu.etaxonomy.cdm.io.common.IImportConfigurator;
33  import eu.etaxonomy.cdm.io.common.IOValidator;
34  import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
35  import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
36  import eu.etaxonomy.cdm.io.erms.validation.ErmsSourceUsesImportValidator;
37  import eu.etaxonomy.cdm.model.common.CdmBase;
38  import eu.etaxonomy.cdm.model.common.DescriptionElementSource;
39  import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
40  import eu.etaxonomy.cdm.model.description.CommonTaxonName;
41  import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
42  import eu.etaxonomy.cdm.model.description.Feature;
43  import eu.etaxonomy.cdm.model.description.TaxonDescription;
44  import eu.etaxonomy.cdm.model.description.TextData;
45  import eu.etaxonomy.cdm.model.name.TaxonNameBase;
46  import eu.etaxonomy.cdm.model.reference.ReferenceBase;
47  import eu.etaxonomy.cdm.model.taxon.Synonym;
48  import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
49  import eu.etaxonomy.cdm.model.taxon.Taxon;
50  import eu.etaxonomy.cdm.model.taxon.TaxonBase;
51  
52  /**
53   * @author a.mueller
54   * @created 20.02.2010
55   * @version 1.0
56   */
57  @Component
58  public class ErmsSourceUsesImport  extends ErmsImportBase<CommonTaxonName> {
59  	private static final Logger logger = Logger.getLogger(ErmsSourceUsesImport.class);
60  	
61  	private DbImportMapping mapping; //not needed
62  	
63  	
64  	private int modCount = 10000;
65  	private static final String pluralString = "source uses";
66  	private static final String dbTableName = "tu_sources";
67  	private static final Class cdmTargetClass = null;
68  
69  	public ErmsSourceUsesImport(){
70  		super(pluralString, dbTableName, cdmTargetClass);
71  	}
72  
73  
74  	/* (non-Javadoc)
75  	 * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getIdQuery()
76  	 */
77  	@Override
78  	protected String getIdQuery() {
79  		String strQuery = " SELECT sourceuse_id, source_id, tu_id " + " " +
80  						" FROM tu_sources " + 
81  						" ORDER BY sourceuse_id, source_id, tu_id  ";
82  		return strQuery;	
83  	}
84  
85  
86  
87  	/* (non-Javadoc)
88  	 * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getRecordQuery(eu.etaxonomy.cdm.io.erms.ErmsImportConfigurator)
89  	 */
90  	@Override
91  	protected String getRecordQuery(ErmsImportConfigurator config) {
92  		String strRecordQuery = 
93  			" SELECT * " + 
94  			" FROM tu_sources INNER JOIN sourceuses ON tu_sources.sourceuse_id = sourceuses.sourceuse_id" +
95  			" WHERE ( tu_sources.sourceuse_id IN (" + ID_LIST_TOKEN + ") AND " +
96  			" 		tu_sources.source_id IN (" + ID_LIST_TOKEN + ") AND " + 
97  			"		tu_sources.tu_id IN (" + ID_LIST_TOKEN + ")  )";
98  		return strRecordQuery;
99  	}
100 
101 	
102 	public boolean doPartition(ResultSetPartitioner partitioner, ErmsImportState state) {
103 		boolean success = true ;
104 		ErmsImportConfigurator config = state.getConfig();
105 		Set objectsToSave = new HashSet<IdentifiableEntity>();
106 		
107 // 		DbImportMapping<?, ?> mapping = getMapping();
108 //		mapping.initialize(state, cdmTargetClass);
109 		
110 		ResultSet rs = partitioner.getResultSet();
111 		try{
112 			while (rs.next()){
113 				//success &= mapping.invoke(rs,referencesToSave);
114 				
115 				//read and normalize values
116 				int sourceUseId = rs.getInt("sourceuse_id");
117 				int sourceId = rs.getInt("source_id");
118 				String strSourceId = String.valueOf(sourceId);
119 				int taxonId = rs.getInt("tu_id");
120 				String strTaxonId = String.valueOf(taxonId);
121 				String strPageNr = rs.getString("pagenr");
122 				if (CdmUtils.isEmpty(strPageNr)){
123 					strPageNr = null;
124 				}
125 				ReferenceBase ref = (ReferenceBase)state.getRelatedObject(ErmsReferenceImport.REFERENCE_NAMESPACE, strSourceId);
126 				
127 				try {
128 				IdentifiableEntity objectToSave = null;
129 				//invoke methods for each sourceUse type
130 				if (sourceUseId == SOURCE_USE_ORIGINAL_DESCRIPTION){
131 					objectToSave = makeOriginalDescription(partitioner, state, ref, strTaxonId, strPageNr);
132 				}else if (sourceUseId == SOURCE_USE_BASIS_OF_RECORD){
133 					objectToSave = makeBasisOfRecord(partitioner, state, ref, strTaxonId, strPageNr);
134 				}else if (sourceUseId == SOURCE_USE_ADDITIONAL_SOURCE){
135 					objectToSave = makeAdditionalSource(partitioner, state, ref, strTaxonId, strPageNr);
136 				}else if (sourceUseId == SOURCE_USE_SOURCE_OF_SYNONYMY){
137 					objectToSave = makeSourceOfSynonymy(partitioner, state, ref, strTaxonId, strPageNr);
138 				}else if (sourceUseId == SOURCE_USE_REDESCRIPTION){
139 					objectToSave = makeRedescription(partitioner, state, ref, strTaxonId, strPageNr);
140 				}else if (sourceUseId == SOURCE_USE_NEW_COMBINATION_REFERENCE){
141 					objectToSave = makeCombinationReference(partitioner, state, ref, strTaxonId, strPageNr);
142 				}else if (sourceUseId == SOURCE_USE_STATUS_SOURCE){
143 					objectToSave = makeStatusSource(partitioner, state, ref, strTaxonId, strPageNr);
144 				}else if (sourceUseId == SOURCE_USE_EMENDATION){
145 					objectToSave = makeEmendation(partitioner, state, ref, strTaxonId, strPageNr);
146 				}
147 				if(objectToSave != null){
148 					objectsToSave.add(objectToSave);
149 				}
150 				} catch (Exception e) {
151 					e.printStackTrace();
152 					success = false;
153 			}
154 			}
155 		} catch (SQLException e) {
156 			logger.error("SQLException:" +  e);
157 			return false;
158 		}
159 	
160 		partitioner.startDoSave();
161 		getCommonService().save(objectsToSave);
162 		return success;
163 	}
164 
165 
166 	/**
167 	 * @param strTaxonId 
168 	 * @param ref 
169 	 * @param state 
170 	 * @param partitioner 
171 	 * @param strPageNr 
172 	 * 
173 	 */
174 	private TaxonNameBase makeOriginalDescription(ResultSetPartitioner partitioner, ErmsImportState state, ReferenceBase ref, String strTaxonId, String strPageNr) {
175 		TaxonNameBase taxonName = (TaxonNameBase)state.getRelatedObject(ErmsTaxonImport.NAME_NAMESPACE, strTaxonId);
176 		taxonName.setNomenclaturalReference(ref);
177 		taxonName.setNomenclaturalMicroReference(strPageNr);
178 		return taxonName;
179 	}
180 	
181 	/**
182 	 * @param partitioner
183 	 * @param state
184 	 * @param ref
185 	 * @param strTaxonId
186 	 * @param strPageNr
187 	 */
188 	private boolean isFirstBasisOfRecord = true; 
189 	private IdentifiableEntity makeBasisOfRecord(ResultSetPartitioner partitioner, ErmsImportState state, ReferenceBase ref, String strTaxonId, String strPageNr) {
190 		if (isFirstBasisOfRecord){
191 			logger.warn("Basis of record not yet implemented");
192 			isFirstBasisOfRecord = false;
193 		}
194 		return null;
195 	}
196 	
197 	/**
198 	 * @param partitioner
199 	 * @param state
200 	 * @param ref
201 	 * @param strTaxonId
202 	 * @param strPageNr
203 	 */
204 	private IdentifiableEntity makeAdditionalSource(ResultSetPartitioner partitioner, ErmsImportState state, ReferenceBase ref, String strTaxonId, String strPageNr) {
205 		Feature citationFeature = Feature.CITATION();
206 		DescriptionElementBase element = TextData.NewInstance(citationFeature);
207 		DescriptionElementSource source = element.addSource(null, null, ref, strPageNr);
208 		if (source == null){
209 			logger.warn("Source is null");
210 			return null;
211 		}
212 		TaxonBase taxonBase = (TaxonBase)state.getRelatedObject(ErmsTaxonImport.TAXON_NAMESPACE, strTaxonId);
213 		Taxon taxon;
214 		
215 		//if taxon base is a synonym, add the description to the accepted taxon
216 		if (taxonBase.isInstanceOf(Synonym.class)){
217 			Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);
218 			Set<Taxon> taxa = synonym.getAcceptedTaxa();
219 			if (taxa.size() < 1){
220 				String warning = "Synonym "+ strTaxonId + " has no accepted taxon";
221 				logger.warn(warning);
222 				return null;
223 				//throw new IllegalStateException(warning);
224 			}else if (taxa.size() > 1){
225 				String warning = "Synonym "+ strTaxonId + " has more than 1 accepted taxon";
226 				logger.warn(warning);
227 				return null;
228 				//throw new IllegalStateException(warning);
229 			}
230 			taxon = taxa.iterator().next();
231 			//add synonym name as name used in source
232 			source.setNameUsedInSource(synonym.getName());
233 		}else{
234 			taxon = (Taxon)taxonBase;
235 		}
236 		
237 		//get or create description and add the element
238 		TaxonDescription description;
239 		if (taxon.getDescriptions().size() > 0){
240 			description = taxon.getDescriptions().iterator().next();
241 		}else{
242 			description = TaxonDescription.NewInstance(taxon);
243 		}
244 		description.addElement(element);
245 		return taxon;
246 	}
247 	
248 	/**
249 	 * @param partitioner
250 	 * @param state
251 	 * @param ref
252 	 * @param strTaxonId
253 	 * @param strPageNr
254 	 */
255 	private IdentifiableEntity makeSourceOfSynonymy(ResultSetPartitioner partitioner, ErmsImportState state, ReferenceBase ref, String strTaxonId, String strPageNr) {
256 		TaxonBase taxonBase = (TaxonBase)state.getRelatedObject(ErmsTaxonImport.TAXON_NAMESPACE, strTaxonId);
257 		if (taxonBase == null){
258 			String warning = "taxonBase (id = " + strTaxonId + ") could not be found ";
259 			logger.warn(warning);
260 			return null;
261 		}else if (! taxonBase.isInstanceOf(Synonym.class)){
262 			String warning = "TaxonBase is not of class Synonym but " + taxonBase.getClass().getSimpleName();
263 			logger.warn(warning);
264 			return null;
265 		}
266 		Synonym synonym =CdmBase.deproxy(taxonBase, Synonym.class);
267 		Set<SynonymRelationship> synRels = synonym.getSynonymRelations();
268 		if (synRels.size() != 1){
269 			logger.warn("Synonym has not 1 but " + synRels.size() + " relations!");
270 		}else{
271 			SynonymRelationship synRel = synRels.iterator().next();
272 			synRel.setCitation(ref);
273 			synRel.setCitationMicroReference(strPageNr);
274 		}
275 		return taxonBase;
276 	}
277 	
278 	/**
279 	 * @param partitioner
280 	 * @param state
281 	 * @param ref
282 	 * @param strTaxonId
283 	 * @param strPageNr
284 	 */
285 	private boolean isFirstRediscription = true; 
286 	private IdentifiableEntity makeRedescription(ResultSetPartitioner partitioner, ErmsImportState state, ReferenceBase ref, String strTaxonId, String strPageNr) {
287 		if (isFirstRediscription){
288 			logger.warn("Rediscription not yet implemented");
289 			isFirstRediscription = false;
290 		}
291 		return null;
292 	}
293 
294 	/**
295 	 * @param partitioner
296 	 * @param state
297 	 * @param ref
298 	 * @param strTaxonId
299 	 * @param strPageNr
300 	 */
301 	private IdentifiableEntity makeCombinationReference(ResultSetPartitioner partitioner, ErmsImportState state, ReferenceBase ref, String strTaxonId, String strPageNr) {
302 		// Kopie von Orig. Comb.
303 		//TODO ist das wirklich der richtige Name, oder muss ein verknüpfter Name verwendet werden
304 		TaxonNameBase taxonName = (TaxonNameBase)state.getRelatedObject(ErmsTaxonImport.NAME_NAMESPACE, strTaxonId);
305 		taxonName.setNomenclaturalReference(ref);
306 		taxonName.setNomenclaturalMicroReference(strPageNr);
307 		return taxonName;
308 	}
309 
310 
311 	/**
312 	 * @param partitioner
313 	 * @param state
314 	 * @param ref
315 	 * @param strTaxonId
316 	 * @param strPageNr
317 	 */
318 	private boolean isFirstStatusSource = true; 
319 	private IdentifiableEntity makeStatusSource(ResultSetPartitioner partitioner, ErmsImportState state, ReferenceBase ref, String strTaxonId, String strPageNr) {
320 		if (isFirstStatusSource){
321 			logger.warn("StatusSource not yet implemented");
322 			isFirstStatusSource = false;
323 		}
324 		return null;
325 	}
326 
327 	/**
328 	 * @param partitioner
329 	 * @param state
330 	 * @param ref
331 	 * @param strTaxonId
332 	 * @param strPageNr
333 	 */
334 	private boolean isFirstEmendation = true; 
335 	private IdentifiableEntity makeEmendation(ResultSetPartitioner partitioner, ErmsImportState state, ReferenceBase ref, String strTaxonId, String strPageNr) {
336 		if (isFirstEmendation){
337 			logger.warn("Emmendation not yet implemented");
338 			isFirstEmendation = false;
339 		}
340 		return null;
341 	}
342 
343 
344 
345 	/* (non-Javadoc)
346 	 * @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet, eu.etaxonomy.cdm.io.common.ImportStateBase)
347 	 */
348 	public CommonTaxonName createObject(ResultSet rs, ErmsImportState state)
349 			throws SQLException {
350 		return null;  //not needed
351 	}
352 
353 	/* (non-Javadoc)
354 	 * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
355 	 */
356 	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
357 		String nameSpace;
358 		Class cdmClass;
359 		Set<String> idSet;
360 		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
361 		
362 		try{
363 			Set<String> taxonIdSet = new HashSet<String>();
364 			Set<String> nameIdSet = new HashSet<String>();
365 			Set<String> referenceIdSet = new HashSet<String>();
366 			while (rs.next()){
367 				handleForeignKey(rs, taxonIdSet, "tu_id");
368 				handleForeignKey(rs, nameIdSet, "tu_id");
369 				handleForeignKey(rs, referenceIdSet, "source_id");
370 			}
371 			
372 			//name map
373 			nameSpace = ErmsTaxonImport.NAME_NAMESPACE;
374 			cdmClass = TaxonNameBase.class;
375 			idSet = nameIdSet;
376 			Map<String, TaxonNameBase> nameMap = (Map<String, TaxonNameBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
377 			result.put(nameSpace, nameMap);
378 			
379 			//taxon map
380 			nameSpace = ErmsTaxonImport.TAXON_NAMESPACE;
381 			cdmClass = TaxonBase.class;
382 			idSet = taxonIdSet;
383 			Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
384 			result.put(nameSpace, taxonMap);
385 			
386 			//reference map
387 			nameSpace = ErmsReferenceImport.REFERENCE_NAMESPACE;
388 			cdmClass = ReferenceBase.class;
389 			idSet = referenceIdSet;
390 			Map<String, ReferenceBase> referenceMap = (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(ReferenceBase.class, idSet, nameSpace);
391 			result.put(nameSpace, referenceMap);
392 	
393 				
394 		} catch (SQLException e) {
395 			throw new RuntimeException(e);
396 		}
397 		return result;
398 
399 	}
400 	
401 	/* (non-Javadoc)
402 	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
403 	 */
404 	@Override
405 	protected boolean doCheck(ErmsImportState state){
406 		IOValidator<ErmsImportState> validator = new ErmsSourceUsesImportValidator();
407 		return validator.validate(state);
408 	}
409 	
410 	/* (non-Javadoc)
411 	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
412 	 */
413 	protected boolean isIgnore(ErmsImportState state){
414 		boolean result = state.getConfig().getDoReferences() != IImportConfigurator.DO_REFERENCES.ALL;
415 		result &= state.getConfig().isDoTaxa();
416 		return state.getConfig().getDoReferences() != IImportConfigurator.DO_REFERENCES.ALL;
417 	}
418 
419 
420 	/* (non-Javadoc)
421 	 * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping()
422 	 */
423 	@Override
424 	protected DbImportMapping<?, ?> getMapping() {
425 		logger.warn("getMapping not yet implemented for EmrsSourceUsesImport");
426 		return null;  // not needed because Mapping is not implemented in this class yet
427 	}
428 
429 }