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Revision 15d48661

Added by Andreas Müller over 4 years ago

cleanup

View differences:

cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/validate/PesiErmsValidator.java
304 304

  
305 305
    private boolean testSingleTaxon(ResultSet srcRS, ResultSet destRS) throws SQLException {
306 306
        String id = String.valueOf(srcRS.getInt("id"));
307
        //not complete yet
307
        //complete
308 308
        boolean success = equals("Taxon ID", "tu_id: " + srcRS.getInt("id"), destRS.getString("IdInSource"), id);
309 309
        success &= equals("Taxon source", "ERMS export for PESI", destRS.getString("sourceName"), id);
310 310

  
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsTaxonImport.java
177 177
		return;
178 178
	}
179 179

  
180
	Integer lastTaxonId = null;
180
    Integer lastTaxonId = null;
181 181
    @Override
182 182
    protected boolean ignoreRecord(ResultSet rs) throws SQLException {
183 183
        Integer id = rs.getInt("id");
......
262 262
    private void handleNameStatus(TaxonName name, ResultSet rs, ErmsImportState state) throws SQLException {
263 263
        NomenclaturalStatusType nomStatus = null;
264 264
        int tuStatus = rs.getInt("tu_status");
265
        //the order is bottom up from SQL script as there values are overriden from top to bottom
265
        //the order is bottom up from SQL script as their values are overridden from top to bottom
266 266
        if (tuStatus == 8){
267 267
            //species inquirenda
268 268
            nomStatus = getNomenclaturalStatusType(state, ErmsTransformer.uuidNomStatusSpeciesInquirenda, "species inquirenda", "species inquirenda", null, Language.LATIN(), null);
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsTransformer.java
715 715
                synType = null;
716 716
                taxonRelType = TaxonRelationshipType.PRO_PARTE_SYNONYM_FOR();
717 717
            }else if (unacceptreason.matches("(?i)(misidentifications?|misapplied .*name|.*misapplication.*|incorrect identification)")){
718
                //see ErmsTaxonImport.getAcceptedTaxaKeys()
718
                //see ErmsTaxonImport.getAcceptedTaxaKeys(); this differs from SQL script
719 719
                synType = null;
720 720
                taxonRelType = TaxonRelationshipType.MISAPPLIED_NAME_FOR();
721 721
            }else if (unacceptreason.matches("(?i)(.*jun.*syn.*|\\(synonym\\)|reverted genus transfer)")){
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaImportConfigurator.java
11 11
import org.apache.log4j.Logger;
12 12

  
13 13
import eu.etaxonomy.cdm.database.ICdmDataSource;
14
import eu.etaxonomy.cdm.io.common.IImportConfigurator;
15 14
import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;
16 15
import eu.etaxonomy.cdm.io.common.Source;
17 16
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
......
24 23
 * @author a.babadshanjan
25 24
 * @since 08.05.2009
26 25
 */
27
public class FaunaEuropaeaImportConfigurator extends ImportConfiguratorBase<FaunaEuropaeaImportState, Source> implements IImportConfigurator {
26
public class FaunaEuropaeaImportConfigurator
27
            extends ImportConfiguratorBase<FaunaEuropaeaImportState, Source>{
28 28

  
29 29
    private static final long serialVersionUID = 3218446329444903409L;
30 30
    private static final Logger logger = Logger.getLogger(FaunaEuropaeaImportConfigurator.class);
31 31

  
32
	//TODO
33 32
	private static IInputTransformer defaultTransformer = null;
34 33

  
35 34
	private boolean doBasionyms = true;
......
54 53
		return doTypes;
55 54
	}
56 55

  
57

  
58

  
59

  
60 56
	/* Max number of taxa to be saved with one service call */
61 57
	private int limitSave = 5000;
62 58
	private Reference auctReference;
......
75 71
				FaunaEuropaeaAdditionalTaxonDataImport.class,
76 72
				FaunaEuropaeaVernacularNamesImport.class
77 73
		};
78
	};
74
	}
79 75

  
80 76
	public static FaunaEuropaeaImportConfigurator NewInstance(Source source, ICdmDataSource destination){
81 77
		return new FaunaEuropaeaImportConfigurator(source, destination);
82
}
78
	}
83 79

  
84 80
	private FaunaEuropaeaImportConfigurator(Source source, ICdmDataSource destination) {
85 81
		super(defaultTransformer);
......
100 96
//	}
101 97

  
102 98

  
103
	/* (non-Javadoc)
104
	 * @see eu.etaxonomy.cdm.io.common.ImportConfiguratorBase#getSourceReference()
105
	 */
106 99
	@Override
107 100
	public Reference getSourceReference() {
108 101
		//TODO
......
119 112
		return sourceReference;
120 113
	}
121 114

  
122

  
123
	/* (non-Javadoc)
124
	 * @see eu.etaxonomy.cdm.io.common.ImportConfiguratorBase#getSourceReference()
125
	 */
126 115
	public Reference getAuctReference() {
127 116
		//TODO
128 117
		if (auctReference == null){
......
134 123
		return auctReference;
135 124
	}
136 125

  
137
	/* (non-Javadoc)
138
	 * @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getSourceNameString()
139
	 */
140 126
	@Override
141 127
    public String getSourceNameString() {
142 128
		if (this.getSource() == null) {
......
146 132
		}
147 133
	}
148 134

  
149
	/* (non-Javadoc)
150
	 * @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getNewState()
151
	 */
152
	@Override
135
	@SuppressWarnings("unchecked")
136
    @Override
153 137
    public FaunaEuropaeaImportState getNewState() {
154 138
		return new FaunaEuropaeaImportState(this);
155 139
	}
156 140

  
157
	/**
158
	 * @return the doBasionyms
159
	 */
160 141
	public boolean isDoBasionyms() {
161 142
		return doBasionyms;
162 143
	}
163

  
164
	/**
165
	 * @param doBasionyms the doBasionyms to set
166
	 */
167 144
	public void setDoBasionyms(boolean doBasionyms) {
168 145
		this.doBasionyms = doBasionyms;
169 146
	}
170 147

  
171
	/**
172
	 * @return the doTaxonomicallyIncluded
173
	 */
174 148
	public boolean isDoTaxonomicallyIncluded() {
175 149
		return doTaxonomicallyIncluded;
176 150
	}
177

  
178
	/**
179
	 * @param doTaxonomicallyIncluded the doTaxonomicallyIncluded to set
180
	 */
181 151
	public void setDoTaxonomicallyIncluded(boolean doTaxonomicallyIncluded) {
182 152
		this.doTaxonomicallyIncluded = doTaxonomicallyIncluded;
183 153
	}
184 154

  
185
	/**
186
	 * @return the doMisappliedNames
187
	 */
188 155
	public boolean isDoMisappliedNames() {
189 156
		return doMisappliedNames;
190 157
	}
191

  
192
	/**
193
	 * @param doMisappliedNames the doMisappliedNames to set
194
	 */
195 158
	public void setDoMisappliedNames(boolean doMisappliedNames) {
196 159
		this.doMisappliedNames = doMisappliedNames;
197 160
	}
198 161

  
199
	/**
200
	 * @return the doHeterotypicSynonyms
201
	 */
202 162
	public boolean isDoHeterotypicSynonyms() {
203 163
		return doHeterotypicSynonyms;
204 164
	}
205

  
206
	/**
207
	 * @param doHeterotypicSynonyms the doHeterotypicSynonyms to set
208
	 */
209 165
	public void setDoHeterotypicSynonyms(boolean doHeterotypicSynonyms) {
210 166
		this.doHeterotypicSynonyms = doHeterotypicSynonyms;
211 167
	}
212 168

  
213
	/**
214
	 * @param auctReference the auctReference to set
215
	 */
216 169
	public void setAuctReference(Reference auctReference) {
217 170
		this.auctReference = auctReference;
218 171
	}
219 172

  
220
	/**
221
	 * @return the limitSave
222
	 */
223 173
	public int getLimitSave() {
224 174
		return limitSave;
225 175
	}
226

  
227
	/**
228
	 * @param limitSave the limitSave to set
229
	 */
230 176
	public void setLimitSave(int limitSave) {
231 177
		this.limitSave = limitSave;
232 178
	}
233 179

  
234
	/**
235
	 * @param doHeterotypicSynonymsForBasionyms the doHeterotypicSynonymsForBasionyms to set
236
	 */
237 180
	public void setDoHeterotypicSynonymsForBasionyms(
238 181
			boolean doHeterotypicSynonymsForBasionyms) {
239 182
		this.doHeterotypicSynonymsForBasionyms = doHeterotypicSynonymsForBasionyms;
240 183
	}
241

  
242
	/**
243
	 * @return the doHeterotypicSynonymsForBasionyms
244
	 */
245 184
	public boolean isDoHeterotypicSynonymsForBasionyms() {
246 185
		return doHeterotypicSynonymsForBasionyms;
247 186
	}
248 187

  
249

  
250
	/* (non-Javadoc)
251
	 * @see eu.etaxonomy.cdm.io.tcsrdf.IImportConfigurator#isDoOccurrence()
252
	 */
253 188
	public boolean isDoOccurrence() {
254 189
		return doOccurrence;
255 190
	}
256
	/* (non-Javadoc)
257
	 * @see eu.etaxonomy.cdm.io.tcsrdf.IImportConfigurator#setDoOccurrence(boolean)
258
	 */
259 191
	public void setDoOccurrence(boolean doOccurrence) {
260 192
		this.doOccurrence = doOccurrence;
261 193
	}
......
285 217
		this.doReferences = doReferences;
286 218
	}
287 219

  
288
//	public boolean isDoTypes() {
289
//		return doTypes;
290
//	}
291
//	public void setDoTypes(boolean doTypes) {
292
//		this.doTypes = doTypes;
293
//	}
294

  
295 220
	public boolean isDoTaxa() {
296 221
		return doTaxa;
297 222
	}
......
315 240
		this.doAssociatedSpecialists = doAssociatedSpecialists;
316 241
	}
317 242

  
318
    /**
319
     * @return the doInferredSynonyms
320
     */
321 243
    public boolean isDoInferredSynonyms() {
322 244
        return doInferredSynonyms;
323 245
    }
324

  
325 246
    public void setDoInferredSynonyms(boolean doInferredSynonyms){
326 247
        this.doInferredSynonyms = doInferredSynonyms;
327 248
    }
328

  
329 249
}
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java
418 418
				for (TaxonNode node : taxon.getTaxonNodes()){
419 419
					doCount(count++, modCount, pluralString);
420 420
					TaxonNode parentNode = node.getParent();
421
					if (parentNode != null && isPesiTaxon(parentNode.getTaxon())){//exclude root taxa and unpublished parents (relevant for "Valueless" parent for E+M Rubus taxa). Usually a parent should not be unpublished
421
					if (parentNode != null && isPesiTaxon(parentNode.getTaxon())){ //exclude root taxa and unpublished parents (relevant for "Valueless" parent for E+M Rubus taxa). Usually a parent should not be unpublished
422 422
						int childId = state.getDbId( taxon);
423 423
						int parentId = state.getDbId(parentNode.getTaxon());
424 424
						success &= invokeParentTaxonFk(parentId, childId);
......
1387 1387
    }
1388 1388

  
1389 1389
	private static String getDisplayName(TaxonName taxonName, boolean useNameCache) {
1390
		// TODO: extension?
1391 1390
		if (taxonName == null) {
1392 1391
			return null;
1393 1392
		}else{
......
1418 1417
		}
1419 1418
	}
1420 1419

  
1421
	@SuppressWarnings("unused")
1422
	private static String getGUID(TaxonName taxonName) {
1423
		UUID uuid = taxonName.getUuid();
1424
		String result = "NameUUID:" + uuid.toString();
1425
		return result;
1426
	}
1427

  
1428 1420
	/**
1429 1421
	 * Returns the <code>WebShowName</code> attribute for a taxon.
1430 1422
	 * See {@link #getWebShowName(TaxonName)} for further explanations.
......
1461 1453
	 * @see MethodMapper
1462 1454
	 */
1463 1455
	private static String getWebShowName(TaxonName taxonName) {
1464
		//TODO extensions?
1465 1456
		if (taxonName == null) {
1466 1457
			return null;
1467 1458
		}else{
1468
			INonViralNameCacheStrategy cacheStrategy = getCacheStrategy(taxonName);
1459
		    taxonName = CdmBase.deproxy(taxonName);
1460
            INonViralNameCacheStrategy cacheStrategy = getCacheStrategy(taxonName);
1469 1461

  
1470 1462
			HTMLTagRules tagRules = new HTMLTagRules().addRule(TagEnum.name, "i");
1471 1463
			String result = cacheStrategy.getTitleCache(taxonName, tagRules);
......
1521 1513
		return result;
1522 1514
	}
1523 1515

  
1516
    @SuppressWarnings("unused")
1517
    private static String getGUID(TaxonName taxonName) {
1518
        UUID uuid = taxonName.getUuid();
1519
        String result = "NameUUID:" + uuid.toString();
1520
        return result;
1521
    }
1522

  
1523
    static boolean isFirstAbbrevTitle = true;
1524 1524
	/**
1525 1525
	 * Returns the SourceNameCache for the AdditionalSource table
1526
	 * @param taxonName
1527
	 * @return
1528 1526
	 */
1529
	static boolean isFirstAbbrevTitle = true;
1530 1527
	@SuppressWarnings("unused")
1531 1528
	private static String getSourceNameCache(TaxonName taxonName) {
1532 1529
		if (taxonName != null){

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