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Revision 01146fd8

ID01146fd8f4be51a8c9fbe654b8bf9f139571a78b
Parent 519ba447
Child 5a407e53

Added by Andreas Müller about 1 month ago

cleanup

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/app/cyprus/CyprusImagesActivator.java
254 254
//            IImageMetadata metadata = Sanselan.getMetadata(file);
255 255
            ImageMetadata metadata = Imaging.getMetadata(file);
256 256
            List<? extends ImageMetadataItem> items = metadata.getItems();
257
            for (Object object : items){
258
                ImageMetadataItem metadataItem = (ImageMetadataItem) object;
257
            for (ImageMetadataItem metadataItem : items){
259 258
//                System.out.println(item.getKeyword() +  ":    " + item.getText());
260 259
                if (metadataItem instanceof GenericImageMetadataItem){
261 260
                    GenericImageMetadataItem item = (GenericImageMetadataItem) metadataItem;
app-import/src/main/java/eu/etaxonomy/cdm/app/proibiosphere/TaxonXImportLauncher.java
227 227

  
228 228
        //System.out.println(documents);
229 229
        for (String docId : docs.keySet()){
230
            List<String> treatments = new ArrayList<String>(new HashSet<String>(docs.get(docId)));
230
            List<String> treatments = new ArrayList<>(new HashSet<>(docs.get(docId)));
231 231

  
232
            Map<Integer, List<String>> startPages = new HashMap<Integer, List<String>>();
232
            Map<Integer, List<String>> startPages = new HashMap<>();
233 233
            for (String treatment:treatments) {
234 234
                List<String>tmplist = startPages.get(Integer.valueOf(treatment.split("---")[0]));
235 235
                if (tmplist == null) {
236
                    tmplist = new ArrayList<String>();
236
                    tmplist = new ArrayList<>();
237 237
                }
238 238
                tmplist.add(treatment.split("---")[3]);
239 239
                startPages.put(Integer.valueOf(treatment.split("---")[0]),tmplist);
240 240
            }
241
            List<Integer> pages = new ArrayList<Integer>();
241
            List<Integer> pages = new ArrayList<>();
242 242
            pages.addAll(startPages.keySet());
243 243

  
244 244
            Collections.sort(pages);
......
247 247
            log.info("Document "+docId+" should have "+treatments.size()+" treatments");
248 248
                List<URI> uritmp = documentMap.get(docId);
249 249
                if (uritmp == null) {
250
                    uritmp = new ArrayList<URI>();
250
                    uritmp = new ArrayList<>();
251 251
                }
252 252
                for (int page:pages) {
253 253
                    for (String treatment: startPages.get(page)) {
......
265 265
                documentMap.put(docId, uritmp);
266 266
            }
267 267

  
268

  
269

  
270

  
271

  
272

  
273 268
        return documentMap;
274 269

  
275 270
    }
......
303 298
			String[] filterList, String urlstr)
304 299
					throws MalformedURLException, IOException {
305 300

  
306
		Map<String, List<String>> documents = new HashMap<String, List<String>>();
301
		Map<String, List<String>> documents = new HashMap<>();
307 302
		List<String> docList;
308 303
		String inputLine;
309 304
		for(String filter : filterList){
......
318 313
		    URL plaziURL = new URL(urlstr);
319 314
		    BufferedReader in = new BufferedReader(new InputStreamReader(plaziURL.openStream()));
320 315

  
321

  
322 316
		    //TODO lastUpdate field
323 317
		    //            if(!plaziNotServer){
324 318
		    while ((inputLine = in.readLine()) != null) {
......
345 339
		return documents;
346 340
	}
347 341

  
348
    /**
349
     * @param document
350
     * @return
351
     */
352 342
    private static boolean doImportDocument(String document, int nbtreatments) {
353 343

  
354 344
        if (nbtreatments>400) {
......
390 380
        */
391 381
    }
392 382

  
393
    /**
394
     * @return
395
     */
396 383
    private static boolean askIfReuseSecundum() {
397 384
        //        logger.info("getFullReference for "+ name);
398 385
        JTextArea textArea = new JTextArea("Reuse the secundum present in the current classification? " +
......
412 399
        }
413 400
    }
414 401

  
415
    /**
416
     * @return
417
     */
418 402
    private static Reference askForSecundum() {
419 403
        //        logger.info("getFullReference for "+ name);
420 404
        JTextArea textArea = new JTextArea("Enter the secundum name");
......
437 421
        ref.setTitle(s);
438 422
        return ref;
439 423
    }
440

  
441

  
442 424
}
app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraDistributionParser.java
47 47
/**
48 48
 * @author a.mueller
49 49
 * @since 17.10.2008
50
 * @version 1.0
51 50
 */
52 51
public class DipteraDistributionParser {
53 52
	private static final Logger logger = Logger.getLogger(DipteraDistributionParser.class);
......
90 89
		app.commitTransaction(txStatus);
91 90
	}
92 91

  
93
	static Set<String> unrekognizedStrings = new HashSet<String>();
92
	static Set<String> unrekognizedStrings = new HashSet<>();
94 93
	static int countNot = 0;
95 94
	static int countYes = 0;
96 95

  
......
218 217
	}
219 218

  
220 219

  
221
	static List<String> stopWords = new ArrayList<String>();
222
	static List<String> unknownAreas = new ArrayList<String>();
223
	static List<String> higherAreas = new ArrayList<String>();
220
	static List<String> stopWords = new ArrayList<>();
221
	static List<String> unknownAreas = new ArrayList<>();
222
	static List<String> higherAreas = new ArrayList<>();
224 223

  
225 224
	private String adaptWordsToTdwg(String word){
226 225
		word = word.replace(",", "").replace(";", "");
......
409 408
		higherAreas.add("NT");
410 409
	}
411 410

  
412

  
413
	/**
414
	 * @param args
415
	 */
416 411
	public static void main(String[] args) {
417 412
		CdmApplicationController app = null;
418 413
		DbSchemaValidation val = DbSchemaValidation.UPDATE;
app-import/src/main/java/eu/etaxonomy/cdm/io/PalmaeImageImport.java
218 218
						String mimeType = imageinfo.getMimeType();
219 219
						String suffix = "jpg";
220 220

  
221

  
222 221
						// URL for this image
223 222
						URL url = null;
224 223
						try {
......
227 226
							logger.warn("URL is malformed: "+ url);
228 227
						}
229 228

  
230

  
231 229
						ImageFile imageFile = ImageFile.NewInstance(url.toURI(),null, imageinfo.getHeight(), imageinfo.getWidth());
232 230

  
233

  
234 231
						MediaRepresentation representation = MediaRepresentation.NewInstance(mimeType, suffix);
235 232
						representation.addRepresentationPart(imageFile);
236 233

  
app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraPictureImport.java
6 6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7 7
* See LICENSE.TXT at the top of this package for the full license terms.
8 8
*/
9

  
10 9
package eu.etaxonomy.cdm.io.algaterra;
11 10

  
12 11
import java.sql.ResultSet;
......
34 33
import eu.etaxonomy.cdm.model.taxon.Taxon;
35 34
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
36 35

  
37

  
38 36
/**
39 37
 * Import for AlgaTerra images from table
40 38
 * @author a.mueller
......
42 40
 */
43 41
@Component
44 42
public class AlgaTerraPictureImport  extends AlgaTerraImageImportBase {
45
	private static final Logger logger = Logger.getLogger(AlgaTerraPictureImport.class);
46 43

  
44
    private static final long serialVersionUID = 3910940848080132170L;
45
    private static final Logger logger = Logger.getLogger(AlgaTerraPictureImport.class);
47 46

  
48 47
	private static int modCount = 5000;
49 48
	private static final String pluralString = "pictures";
......
53 52
		super(dbTableName, pluralString);
54 53
	}
55 54

  
56

  
57
	/* (non-Javadoc)
58
	 * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()
59
	 */
60 55
	@Override
61 56
	protected String getIdQuery(BerlinModelImportState state) {
62 57
		String result = " SELECT p.PictureId "
......
66 61
		return result;
67 62
	}
68 63

  
69
	/* (non-Javadoc)
70
	 * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
71
	 */
72 64
	@Override
73 65
	protected String getRecordQuery(BerlinModelImportConfigurator config) {
74 66
			String strQuery =
......
77 69
	            " FROM Picture p INNER JOIN Fact f ON p.PictureId = f.ExtensionFk LEFT OUTER JOIN PTaxon pt ON f.PTNameFk = pt.PTNameFk AND f.PTRefFk = pt.PTRefFk "
78 70
	            + 	" WHERE f.FactCategoryFk = 205 AND ( p.PictureID IN (" + ID_LIST_TOKEN + ")     )"
79 71
	            + " ORDER BY p.PictureId, f.factId, pt.RIdentifier ";
80
            ;
81 72
		return strQuery;
82 73
	}
83 74

  
84
	/* (non-Javadoc)
85
	 * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
86
	 */
87 75
	@Override
88 76
    public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
89 77
		boolean success = true;
90 78

  
91 79
		AlgaTerraImportState state = (AlgaTerraImportState)bmState;
92 80

  
93
//		Set<SpecimenOrObservationBase> specimenToSave = new HashSet<SpecimenOrObservationBase>();
94
		Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
81
		Set<TaxonBase> taxaToSave = new HashSet<>();
95 82

  
96
//		Map<String, DerivedUnitBase> ecoFactMap = (Map<String, DerivedUnitBase>) partitioner.getObjectMap(AlgaTerraSpecimenImportBase.ECO_FACT_DERIVED_UNIT_NAMESPACE);
97 83
		Map<String, TaxonBase> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
98 84
		Map<String, DerivedUnit> specimenMap = partitioner.getObjectMap(AlgaTerraFactEcologyImport.FACT_ECOLOGY_NAMESPACE);
99 85

  
100 86
		ResultSet rs = partitioner.getResultSet();
101 87

  
102 88
		try {
103

  
104 89
			int i = 0;
105

  
106 90
			//for each reference
107 91
            while (rs.next()){
108 92

  
......
111 95
				int pictureId = rs.getInt("PictureID");
112 96
				int taxonId = rs.getInt("RIdentifier");
113 97
				int factId = rs.getInt("FactId");
114

  
115

  
116 98
				//TODO etc. Created, Notes, Copyright, TermsOfUse etc.
117

  
118 99
				try {
119 100

  
120 101
					TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(taxonId));
......
132 113

  
133 114
						taxaToSave.add(taxon);
134 115
					}
135

  
136

  
137 116
				} catch (Exception e) {
138 117
					logger.warn("Exception in " + getTableName() + ": PictureId " + pictureId + ". " + e.getMessage());
139 118
					e.printStackTrace();
140 119
				}
141

  
142 120
            }
143 121

  
144
//            logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
145

  
146 122
			logger.warn(pluralString + " to save: " + taxaToSave.size());
147
//			getOccurrenceService().save(taxaToSave);
148 123
			getTaxonService().save(taxaToSave);
149 124

  
150 125
			return success;
......
154 129
		}
155 130
	}
156 131

  
157

  
158

  
159 132
	private void handlePictureSpecificFields(ResultSet rs, Media media, AlgaTerraImportState state, Map<String, DerivedUnit> specimenMap) throws SQLException {
160 133
		Integer specimenFactId = nullSafeInt(rs, "FactFk");
161 134
		if (specimenFactId != null){
......
173 146
				}
174 147
			}
175 148
		}
176

  
177 149
	}
178 150

  
179

  
180 151
	@Override
181 152
	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
182 153

  
183 154
	    String nameSpace;
184 155
		Set<String> idSet;
185
		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
156
		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
186 157

  
187 158
		try{
188
			Set<String> taxonIdSet = new HashSet<String>();
189
			Set<String> specimenIdSet = new HashSet<String>();
159
			Set<String> taxonIdSet = new HashSet<>();
160
			Set<String> specimenIdSet = new HashSet<>();
190 161

  
191 162
			while (rs.next()){
192 163
				handleForeignKey(rs, taxonIdSet, "RIdentifier");
......
214 185
		return result;
215 186
	}
216 187

  
217

  
218 188
	@Override
219 189
	protected boolean doCheck(BerlinModelImportState state){
220 190
		IOValidator<BerlinModelImportState> validator = new AlgaTerraTypeImportValidator();
......
226 196
		AlgaTerraImportConfigurator config = ((AlgaTerraImportState) bmState).getAlgaTerraConfigurator();
227 197
		return !  ( config.isDoTypes() && config.isDoImages()) ;
228 198
	}
229

  
230 199
}
app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelAuthorTeamImport.java
34 34
import eu.etaxonomy.cdm.model.common.CdmBase;
35 35
import eu.etaxonomy.cdm.strategy.cache.agent.INomenclaturalAuthorCacheStrategy;
36 36

  
37

  
38 37
/**
39 38
 * @author a.mueller
40 39
 * @since 20.03.2008
......
225 224
		return success;
226 225
	}
227 226

  
228

  
229
	/**
230
     * @param state
231
     * @param team
232
     * @param authorTeamCache
233
     * @param fullAuthorTeamCache
234
     * @param preliminaryFlag
235
     * @return
236
     */
237 227
    private TeamOrPersonBase<?> handleTeam(BerlinModelImportState state, Team team, String authorTeamCache,
238 228
            String fullAuthorTeamCache, boolean preliminaryFlag, int authorTeamId) {
239 229

  
......
308 298
        return result;
309 299
    }
310 300

  
311

  
312
    /**
313
     * @param team
314
     * @param authorTeamCache
315
     * @param authorTeamId
316
     */
317 301
    protected void checkTeamNomenclaturalTitle(Team team, String authorTeamCache, int authorTeamId) {
318 302
        if (team.getCacheStrategy().getNomenclaturalTitle(team).equals(authorTeamCache)){
319 303
            team.setProtectedNomenclaturalTitleCache(false);
......
326 310
        }
327 311
    }
328 312

  
329

  
330
    /**
331
     * @param team
332
     * @param fullAuthorTeamCache
333
     * @param authorTeamId
334
     * @param formatter
335
     */
336 313
    protected void checkTeamTitleCache(Team team, String fullAuthorTeamCache, int authorTeamId) {
337 314
        INomenclaturalAuthorCacheStrategy<Team> formatter = team.getCacheStrategy();
338 315
        if (team.generateTitle().equals(fullAuthorTeamCache)){
......
428 405

  
429 406
    private static final String TEAM_SPLITTER = "(,|&)";
430 407

  
431
    /**
432
     * @param fullAuthorTeamCache
433
     * @param TEAM_SPLITTER
434
     * @return
435
     */
436 408
    protected static String[] splitTeam(String teamCache) {
437 409
        if (teamCache == null){
438 410
            return new String[0];
......
440 412
        return teamCache.split(TEAM_SPLITTER);
441 413
    }
442 414

  
443

  
444
    /**
445
     * @param authorTeamCache
446
     * @return
447
     */
448 415
    protected static boolean hasTeamSeparator(String teamCache) {
449 416
        if (isBlank(teamCache)){
450 417
            return false;
......
455 422
        }
456 423
    }
457 424

  
458

  
459 425
    @Override
460 426
	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state)  {
461 427

  
......
471 437
		return result;
472 438
	}
473 439

  
474
	/**
475
	 * @param rs
476
	 * @return
477
	 * @throws SQLException
478
	 * @throws SQLException
479
	 */
480 440
	private Set<String> makeAuthorIdList(ResultSet rs) {
481
		Set<String> result = new HashSet<String>();
441
		Set<String> result = new HashSet<>();
482 442

  
483 443
		String authorTeamIdList = "";
484 444
		try {
app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelOccurrenceImport.java
6 6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7 7
* See LICENSE.TXT at the top of this package for the full license terms.
8 8
*/
9

  
10 9
package eu.etaxonomy.cdm.io.berlinModel.in;
11 10

  
12 11
import java.sql.ResultSet;
......
45 44
import eu.etaxonomy.cdm.model.term.OrderedTermVocabulary;
46 45
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
47 46

  
48

  
49 47
/**
50 48
 * @author a.mueller
51 49
 * @since 20.03.2008
......
343 341

  
344 342
		try{
345 343
		    Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
346
			Set<String> taxonIdSet = new HashSet<String>();
344
			Set<String> taxonIdSet = new HashSet<>();
347 345
			while (rs.next()){
348 346
				handleForeignKey(rs, taxonIdSet, "taxonId");
349 347
			}
app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonRelationImport.java
74 74
    private static final Logger logger = Logger.getLogger(BerlinModelTaxonRelationImport.class);
75 75

  
76 76
	public static final String TREE_NAMESPACE = "PTRefFk";
77
	private static final Integer AUCT_REF_ID = 5959;
78 77

  
79 78
	private static int modCount = 30000;
80 79
	private static final String pluralString = "taxon relations";
......
154 153
		return;
155 154
	}
156 155

  
157
	/**
158
	 * @return
159
	 * @throws SQLException
160
	 */
161 156
	private Set<String> getTreeReferenceIdSet(BerlinModelImportState state) throws SQLException {
162 157
		Source source = state.getConfig().getSource();
163
		Set<String> result = new HashSet<String>();
158
		Set<String> result = new HashSet<>();
164 159
		ResultSet rs = source.getResultSet(getClassificationQuery(state)) ;
165 160
		while (rs.next()){
166 161
			Object id = rs.getObject("PTRefFk");
app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTypesImport.java
177 177
		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
178 178

  
179 179
		try{
180
			Set<String> nameIdSet = new HashSet<String>();
181
			Set<String> referenceIdSet = new HashSet<String>();
180
			Set<String> nameIdSet = new HashSet<>();
181
			Set<String> referenceIdSet = new HashSet<>();
182 182
			while (rs.next()){
183 183
				handleForeignKey(rs, nameIdSet, "NameFk");
184 184
				handleForeignKey(rs, referenceIdSet, "RefFk");
app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/validation/BerlinModelReferenceImportValidator.java
6 6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7 7
* See LICENSE.TXT at the top of this package for the full license terms.
8 8
*/
9

  
10 9
package eu.etaxonomy.cdm.io.berlinModel.in.validation;
11 10

  
12 11
import java.sql.ResultSet;
......
46 45
		if (result == false ){System.out.println("========================================================");}
47 46

  
48 47
		return result;
49

  
50 48
	}
51 49

  
52

  
53 50
	//******************************** CHECK *************************************************
54 51

  
55 52
		private static boolean checkArticlesWithoutJournal(BerlinModelImportConfigurator config){
......
110 107
	                        " (SELECT refId FROM %s ))" , config.getReferenceIdTable()) ;
111 108
				}
112 109

  
113

  
114 110
				ResultSet rs = source.getResultSet(strQuery);
115 111
				boolean firstRow = true;
116 112
				while (rs.next()){
......
144 140
			}
145 141
		}
146 142

  
147

  
148 143
		private static boolean checkPartOfUnresolved(BerlinModelImportConfigurator config){
149 144
			try {
150 145
				boolean result = true;
......
489 484
				Source source = config.getSource();
490 485
				ResultSet rs = source.getResultSet(strQuery);
491 486
				int colCount = rs.getMetaData().getColumnCount();
492
				Set<String> existingAttributes = new HashSet<String>();
487
				Set<String> existingAttributes = new HashSet<>();
493 488
				for (int c = 0; c < colCount ; c++){
494 489
					existingAttributes.add(rs.getMetaData().getColumnLabel(c+1).toLowerCase());
495 490
				}
......
557 552
			return result;
558 553
		}
559 554

  
560

  
561
		/* (non-Javadoc)
562
		 * @see eu.etaxonomy.cdm.io.common.IOValidator#validate(eu.etaxonomy.cdm.io.common.IoStateBase)
563
		 */
564 555
		@Override
565 556
        @Deprecated  //use validate(state, import) instead
566 557
		public boolean validate(BerlinModelImportState state) {
567 558
			logger.warn("BerlinModelReferenceImport uses wrong validation method");
568 559
			return false;
569 560
		}
570

  
571

  
572

  
573 561
}
app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoTaxonImport.java
6 6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7 7
* See LICENSE.TXT at the top of this package for the full license terms.
8 8
*/
9

  
10 9
package eu.etaxonomy.cdm.io.caryo;
11 10

  
12 11
import java.sql.ResultSet;
......
52 51
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
53 52
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
54 53

  
55

  
56 54
/**
57 55
 * @author a.mueller
58 56
 * @since 20.02.2010
59 57
 */
60 58
@Component
61 59
public class CaryoTaxonImport  extends DbImportBase<CaryoImportState, CaryoImportConfigurator> {
62
	private static final Logger logger = Logger.getLogger(CaryoTaxonImport.class);
60

  
61
    private static final long serialVersionUID = 5369739490456155285L;
62
    private static final Logger logger = Logger.getLogger(CaryoTaxonImport.class);
63 63

  
64 64
	private final int modCount = 10000;
65 65
	private static final String pluralString = "taxa";
66 66
	private static final String dbTableName = "CARYOPHYLLALES";
67 67

  
68

  
69

  
70
	private final Map<String, Taxon> familyMap = new HashMap<String, Taxon>();
71
	private final Map<String, Person> personMap = new HashMap<String, Person>();
72
	private final Map<String, Team> teamMap = new HashMap<String, Team>();
73
	private final Map<String, TeamOrPersonBase> inAuthorMap = new HashMap<String, TeamOrPersonBase>();
74
	private final Map<String, IJournal> journalMap = new HashMap<String, IJournal>();
75
	private final Map<String, IBook> bookMap = new HashMap<String, IBook>();
76

  
68
	private final Map<String, Taxon> familyMap = new HashMap<>();
69
	private final Map<String, Person> personMap = new HashMap<>();
70
	private final Map<String, Team> teamMap = new HashMap<>();
71
	private final Map<String, TeamOrPersonBase> inAuthorMap = new HashMap<>();
72
	private final Map<String, IJournal> journalMap = new HashMap<>();
73
	private final Map<String, IBook> bookMap = new HashMap<>();
77 74

  
78 75
	private Classification classification;
79 76

  
80

  
81

  
82 77
	public CaryoTaxonImport(){
83 78
		super(dbTableName, pluralString);
84 79
	}
85 80

  
86

  
87

  
88

  
89
	/* (non-Javadoc)
90
	 * @see eu.etaxonomy.cdm.io.common.DbImportBase#getIdQuery(eu.etaxonomy.cdm.io.common.DbImportStateBase)
91
	 */
92 81
	@Override
93 82
	protected String getIdQuery(CaryoImportState state) {
94 83
		String strRecordQuery =
......
98 87
		return strRecordQuery;
99 88
	}
100 89

  
101

  
102
	/* (non-Javadoc)
103
	 * @see eu.etaxonomy.cdm.io.common.DbImportBase#getRecordQuery(eu.etaxonomy.cdm.io.common.DbImportConfiguratorBase)
104
	 */
105 90
	@Override
106 91
	protected String getRecordQuery(CaryoImportConfigurator config) {
107 92
		String strRecordQuery =
......
111 96
		return strRecordQuery;
112 97
	}
113 98

  
114

  
115

  
116
	/* (non-Javadoc)
117
	 * @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#doPartition(eu.etaxonomy.cdm.io.common.ResultSetPartitioner, eu.etaxonomy.cdm.io.globis.GlobisImportState)
118
	 */
119 99
	@Override
120 100
	public boolean doPartition(ResultSetPartitioner partitioner, CaryoImportState state) {
121 101
		boolean success = true;
122 102

  
123
		Set<TaxonBase> objectsToSave = new HashSet<TaxonBase>();
124

  
125
//		Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE);
126

  
103
		Set<TaxonBase> objectsToSave = new HashSet<>();
127 104

  
128 105
		classification = getClassification(state);
129 106

  
......
160 137
//        	      ,[Basionym]
161 138
//        	      ,[OriginalCitation]
162 139

  
163

  
164 140
				IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
165 141
				name.setGenusOrUninomial(genus);
166 142
				makeAuthors(name, autoren, id);
......
169 145
				name.setNomenclaturalMicroReference(pages);
170 146
				makeStatus(name, nomStatusStr, id);
171 147

  
172

  
173 148
				Taxon taxon = Taxon.NewInstance(name, state.getTransactionalSourceReference());
174 149
				handleTypes(state, rs, taxon, typeStr, id);
175 150
				handleBasionym(state, rs, taxon, basioStr, id);
......
180 155

  
181 156
				taxon.addSource(OriginalSourceType.Import, String.valueOf(taxonId), "NCUGenID", sec, null);
182 157

  
183

  
184

  
185 158
				objectsToSave.add(taxon);
186 159

  
187 160
            }
......
208 181
			taxon.addSynonym(syn, SynonymType.HOMOTYPIC_SYNONYM_OF());
209 182
			getTaxonService().save(syn);
210 183
		}
211

  
212 184
	}
213 185

  
214

  
215

  
216

  
217 186
	private void handleTypes(CaryoImportState state, ResultSet rs, Taxon taxon, String origType, Integer id) {
218 187
		NameTypeDesignation desig = NameTypeDesignation.NewInstance();
219 188
		String type = origType;
......
264 233
			}
265 234
			name.addTypeDesignation(desig, true);
266 235
		}
267

  
268

  
269 236
	}
270 237

  
271

  
272

  
273

  
274 238
	private String makeTypeNomStatus(IBotanicalName typeName, String type) {
275 239
		if (type.endsWith(", nom. illeg.")){
276 240
			type = type.replaceAll(", nom. illeg.", "");
......
279 243
		return type;
280 244
	}
281 245

  
282

  
283

  
284

  
285 246
	private void makeStatus(IBotanicalName name, String nomStatusStr, Integer id) throws SQLException {
286
//	      ,[NomenclaturalStatus]
287 247

  
288 248
		if (StringUtils.isNotBlank(nomStatusStr)){
289 249
			NomenclaturalStatusType nomStatusType;
......
311 271
			NomenclaturalStatus status = NomenclaturalStatus.NewInstance(nomStatusType);
312 272
			name.addStatus(status);
313 273
		}
314

  
315 274
	}
316 275

  
317

  
318

  
319

  
320 276
	private INomenclaturalReference makeNomRef(CaryoImportState state, ResultSet rs, Integer id) throws SQLException {
321 277
		INomenclaturalReference result;
322 278
		String periodicalTitle = rs.getString("PeriodicalTitle");
......
387 343
		ref.setDatePublished(tp);
388 344
	}
389 345

  
390

  
391

  
392

  
393 346
	private Integer[] getDay(String pre, Integer id) {
394 347
		Integer[] result = new Integer[2];
395 348
		if (! StringUtils.isBlank(pre)){
......
442 395
		return result;
443 396
	}
444 397

  
445

  
446 398
	private TeamOrPersonBase<?> getInAuthor(String inAutorStr) {
447 399
		if (StringUtils.isBlank(inAutorStr)){
448 400
			return null;
......
454 406
		return inAuthor;
455 407
	}
456 408

  
457

  
458

  
459 409
	private void makeAuthors(IBotanicalName name, String autoren, Integer id) {
460 410
		String[] parsedAuthorTeams = getParsedAuthors(autoren);
461 411
		name.setBasionymAuthorship(getTeam(parsedAuthorTeams[0], id));
462 412
		name.setExBasionymAuthorship(getTeam(parsedAuthorTeams[1], id));
463 413
		name.setCombinationAuthorship(getTeam(parsedAuthorTeams[2], id));
464 414
		name.setExCombinationAuthorship(getTeam(parsedAuthorTeams[3], id));
465

  
466 415
	}
467 416

  
468 417
	private TeamOrPersonBase<?> getNomRefAuthor(String authorStr, Integer id) {
......
471 420
		return team;
472 421
	}
473 422

  
474

  
475 423
	private TeamOrPersonBase<?> getTeam(String author, Integer id) {
476 424
		if (StringUtils.isBlank(author)){
477 425
			return null;
......
488 436
		return result;
489 437
	}
490 438

  
491

  
492 439
	private void doInAuthors(CaryoImportState state) throws SQLException {
493 440
		Source source = state.getConfig().getSource();
494 441
		String sql = "SELECT DISTINCT inAutor FROM " + getTableName() + " WHERE inAutor IS NOT NULL AND inAutor <> '' ";
......
502 449
				getAgentService().save(team);
503 450
			}
504 451
		}
505

  
506 452
	}
507 453

  
508

  
509 454
	private void doAuthors(CaryoImportState state) throws SQLException {
510 455
		Source source = state.getConfig().getSource();
511 456
		String sql = "SELECT DISTINCT Autoren FROM " + getTableName() + " WHERE Autoren IS NOT NULL AND Autoren <> '' ";
......
520 465
		}
521 466
	}
522 467

  
523

  
524

  
525

  
526 468
	private void doTypeAuthors(CaryoImportState state) {
527 469
		doTeam("Dinter & Derenb.");
528 470
		doTeam("Marloth");
......
604 546
		doTeam("Maerkl.");
605 547
		doTeam("Vierh.");
606 548
		doTeam("Exell");
607

  
608 549
	}
609 550

  
610

  
611

  
612

  
613
	/**
614
	 * @param teamStr
615
	 * @return
616
	 */
617 551
	protected void doTeam(String teamStr) {
618 552
		if (StringUtils.isBlank(teamStr)){
619 553
			return;
......
655 589
		return result;
656 590
	}
657 591

  
658

  
659

  
660

  
661 592
	private String[] getParsedAuthors(String autorenStr) {
662 593
		String[] result = new String[4];
663 594
		String basioFull = null;
......
680 611
		return result;
681 612
	}
682 613

  
683

  
684

  
685

  
686 614
	private String[] splitExAuthors(String author) {
687 615
		String[] result = new String[2];
688 616
		if (author != null){
......
697 625
		return result;
698 626
	}
699 627

  
700

  
701

  
702

  
703 628
	private void doBooks(CaryoImportState state) throws SQLException {
704 629
		Source source = state.getConfig().getSource();
705 630
		String sql = "SELECT DISTINCT BookTitle FROM " + getTableName() + " WHERE BookTitle IS NOT NULL AND BookTitle <> '' ";
......
718 643
		}
719 644
	}
720 645

  
721

  
722

  
723

  
724 646
	private void doJournals(CaryoImportState state) throws SQLException {
725 647
		Source source = state.getConfig().getSource();
726 648
		String sqlPeriodical = "SELECT DISTINCT PeriodicalTitle FROM " + getTableName() + " WHERE PeriodicalTitle IS NOT NULL AND PeriodicalTitle <> '' ";
......
739 661
		}
740 662
	}
741 663

  
742

  
743

  
744

  
745 664
	private void doFamilies(CaryoImportState state) throws SQLException {
746 665
		Source source = state.getConfig().getSource();
747 666
		String sqlFamily = "SELECT DISTINCT Family FROM " + getTableName() + " WHERE Family IS NOT NULL";
......
760 679
				getTaxonService().save(taxon);
761 680
			}
762 681
		}
763

  
764 682
	}
765 683

  
766 684
	private Classification getClassification(CaryoImportState state) {
......
776 694
		return this.classification;
777 695
	}
778 696

  
779

  
780

  
781

  
782

  
783 697
	@Override
784 698
	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, CaryoImportState state) {
785 699
//		String nameSpace;
786 700
//		Class cdmClass;
787 701
//		Set<String> idSet;
788
		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
702
		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
789 703
//		try{
790
//			Set<String> taxonIdSet = new HashSet<String>();
704
//			Set<String> taxonIdSet = new HashSet<>();
791 705
//
792 706
//			while (rs.next()){
793 707
////				handleForeignKey(rs, taxonIdSet, "taxonId");
......
807 721
		return result;
808 722
	}
809 723

  
810
	/* (non-Javadoc)
811
	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
812
	 */
813 724
	@Override
814 725
	protected boolean doCheck(CaryoImportState state){
815 726
		return true;
816 727
	}
817 728

  
818

  
819
	/* (non-Javadoc)
820
	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
821
	 */
822 729
	@Override
823 730
    protected boolean isIgnore(CaryoImportState state){
824 731
		return ! state.getConfig().isDoTaxa();
825 732
	}
826

  
827

  
828

  
829

  
830

  
831

  
832

  
833 733
}
app-import/src/main/java/eu/etaxonomy/cdm/io/cyprus/CyprusExcelImport.java
6 6
 * The contents of this file are subject to the Mozilla Public License Version 1.1
7 7
 * See LICENSE.TXT at the top of this package for the full license terms.
8 8
 */
9

  
10 9
package eu.etaxonomy.cdm.io.cyprus;
11 10

  
12 11
import java.util.Arrays;
......
49 48
 * @author a.babadshanjan
50 49
 * @since 08.01.2009
51 50
 */
52

  
53 51
@Component
54 52
public class CyprusExcelImport
55 53
        extends ExcelImportBase<CyprusImportState, CyprusImportConfigurator, ExcelRowBase> {
......
58 56

  
59 57
    private static final Logger logger = Logger.getLogger(CyprusExcelImport.class);
60 58

  
61
	public static Set<String> validMarkers = new HashSet<String>(Arrays.asList(new String[]{"", "valid", "accepted", "a", "v", "t"}));
62
	public static Set<String> synonymMarkers = new HashSet<String>(Arrays.asList(new String[]{"", "invalid", "synonym", "s", "i"}));
59
	public static Set<String> validMarkers = new HashSet<>(Arrays.asList(new String[]{"", "valid", "accepted", "a", "v", "t"}));
60
	public static Set<String> synonymMarkers = new HashSet<>(Arrays.asList(new String[]{"", "invalid", "synonym", "s", "i"}));
63 61

  
64 62

  
65 63
	@Override
......
67 65
		return ! state.getConfig().isDoTaxa();
68 66
	}
69 67

  
70

  
71
	/* (non-Javadoc)
72
	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
73
	 */
74 68
	@Override
75 69
	protected boolean doCheck(CyprusImportState state) {
76 70
		logger.warn("DoCheck not yet implemented for CyprusExcelImport");
......
91 85
	protected static final String RED_DATA_BOOK_CATEGORY_COLUMN = "red data book category";
92 86
	protected static final String SYSTEMATICS_COLUMN = "systematics";
93 87

  
94

  
95

  
96 88
	// TODO: This enum is for future use (perhaps).
97 89
	protected enum Columns {
98 90
//		Id("Id"),
......
122 114
		}
123 115
	}
124 116

  
125

  
126 117
	@Override
127 118
    protected void analyzeRecord(Map<String, String> record, CyprusImportState state) {
128 119

  
......
154 145
    			continue;
155 146
    		}
156 147

  
157

  
158 148
    		if (key.equalsIgnoreCase(SPECIES_COLUMN)) {
159 149
//    			int ivalue = floatString2IntValue(value);
160 150
    			cyprusRow.setSpecies(value);
......
231 221
				getTermService().save(endemism);
232 222

  
233 223
				//status
234

  
235 224
				UUID indigenousUuid = transformer.getPresenceTermUuid("IN");
236 225
				indigenous = this.getPresenceTerm(state, indigenousUuid, "indigenous", "Indigenous", "IN", false);
237 226
				getTermService().save(indigenous);
......
243 232
				cultivatedDoubtful = this.getPresenceTerm(state, cultivatedDoubtfulUuid, "cultivated?", "Cultivated?", "CU?", false);
244 233
				getTermService().save(cultivatedDoubtful);
245 234

  
246

  
247 235
				UUID casualUuid = transformer.getPresenceTermUuid("CA");
248 236
				casual = this.getPresenceTerm(state, casualUuid, "casual", "Casual", "CA", false);
249 237
				getTermService().save(casual);
......
251 239
				casualDoubtful = this.getPresenceTerm(state, casualDoubtfulUuid, "casual?", "Casual?", "CA?", false);
252 240
				getTermService().save(casualDoubtful);
253 241

  
254

  
255 242
				UUID nonInvasiveUuid = transformer.getPresenceTermUuid("NN");
256 243
				nonInvasive = this.getPresenceTerm(state, nonInvasiveUuid, "naturalized  non-invasive", "Naturalized  non-invasive", "NN", false);
257 244
				getTermService().save(nonInvasive);
......
349 336
		return;
350 337
    }
351 338

  
352

  
353 339
	private void makeHigherTaxa(CyprusImportState state, CyprusRow taxonLight, Taxon speciesTaxon, Reference citation, String microCitation) {
354 340
		String divisionStr = taxonLight.getDivision();
355 341
		String genusStr = taxonLight.getGenus();
......
434 420
		}
435 421
	}
436 422

  
437

  
438 423
	private void makeStatus(String statusString, Taxon mainTaxon) {
439 424
		//status
440 425
		if (StringUtils.isNotBlank(statusString)){
......
483 468
		}
484 469
	}
485 470

  
486

  
487 471
	private void makeRedBookCategory(String redBookCategory, Taxon mainTaxon) {
488 472
		//red data book category
489 473
		if (StringUtils.isNotBlank(redBookCategory)){
......
494 478
		}
495 479
	}
496 480

  
497

  
498

  
499

  
500 481
	/**
501 482
	 *  Stores parent-child, synonym and common name relationships
502 483
	 */
......
506 487
		return;
507 488
	}
508 489

  
509

  
510

  
511
	/**
512
	 * @param state
513
	 * @param rank
514
	 * @param taxonNameStr
515
	 * @param authorStr
516
	 * @param nameStatus
517
	 * @param nc
518
	 * @return
519
	 */
520 490
	private TaxonBase<?> createTaxon(CyprusImportState state, Rank rank, String taxonNameStr,
521 491
			Class<?> statusClass, NomenclaturalCode nc) {
522 492
		TaxonBase<?> taxonBase;
......
530 500
			taxonNameBase = parser.parseFullName(taxonNameStr, nc, rank);
531 501

  
532 502
			//taxonNameBase.setNameCache(taxonNameStr);
533

  
534 503
		}
535 504

  
536 505
		//Create the taxon
......
565 534
		}
566 535
		return success;
567 536
	}
568

  
569

  
570

  
571 537
}
app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisTransformer.java
1 1
/**
2 2
* Copyright (C) 2007 EDIT
3
* European Distributed Institute of Taxonomy 
3
* European Distributed Institute of Taxonomy
4 4
* http://www.e-taxonomy.eu
5
* 
5
*
6 6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7 7
* See LICENSE.TXT at the top of this package for the full license terms.
8 8
*/
9

  
10 9
package eu.etaxonomy.cdm.io.globis;
11 10

  
12 11
import java.util.HashSet;
......
21 20
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
22 21
import eu.etaxonomy.cdm.model.common.ExtensionType;
23 22
import eu.etaxonomy.cdm.model.description.Feature;
24
import eu.etaxonomy.cdm.model.location.NamedArea;
25 23
import eu.etaxonomy.cdm.model.location.Country;
24
import eu.etaxonomy.cdm.model.location.NamedArea;
26 25

  
27 26
/**
28 27
 * @author a.mueller
29 28
 * @since 01.03.2010
30
 * @version 1.0
31 29
 */
32 30
public final class GlobisTransformer extends InputTransformerBase {
33
	private static final Logger logger = Logger.getLogger(GlobisTransformer.class);
34
	
31

  
32
    private static final long serialVersionUID = 8353340999086630728L;
33
    private static final Logger logger = Logger.getLogger(GlobisTransformer.class);
35 34

  
36 35
	//marker types
37 36
	public static final UUID uuidCheckedMarkerType = UUID.fromString("f2a7926f-def1-49a6-b642-9b81e6b1e35c");
38 37
	public static final UUID uuidOldRecordMarkerType = UUID.fromString("8616edc5-00d4-40ca-aca4-d48ec32231e9");
39 38
	public static final UUID uuidNotAvailableMarkerType = UUID.fromString("6931e584-6fc2-44ab-9084-e6452f8cd5d1");
40
	
39

  
41 40
	//extension types
42 41
	public static final UUID uuidExtTypeNotAvailableReason = UUID.fromString("d7dd5632-8c65-4058-b804-d1291560ac4c");
43
	
44
	public NamedArea getNamedAreaByKey(String area)  {
45
		Set<String> unhandledCountries = new HashSet<String>();
46
		
42

  
43
	@Override
44
    public NamedArea getNamedAreaByKey(String area)  {
45
		Set<String> unhandledCountries = new HashSet<>();
46

  
47 47
		if (StringUtils.isBlank(area)){return null;
48 48
		}else if (area.equals("Argentina")){return Country.ARGENTINAARGENTINEREPUBLIC();
49 49
		}else if (area.equals("Bolivia")){return Country.BOLIVIAREPUBLICOF();
......
60 60
		}else if (area.equals("France")){return Country.FRANCEFRENCHREPUBLIC();
61 61
		}else if (area.equals("Poland")){return Country.POLANDPOLISHPEOPLESREPUBLIC();
62 62
		}else if (area.equals("Brazil")){return Country.BRAZILFEDERATIVEREPUBLICOF();
63
		
63

  
64 64
		}else if (area.equals("Cuba")){return Country.BRAZILFEDERATIVEREPUBLICOF();
65 65
		}else if (area.equals("Guatemala")){return Country.GUATEMALAREPUBLICOF();
66 66
		}else if (area.equals("Colombia")){return Country.COLOMBIAREPUBLICOF();
67 67
		}else if (area.equals("India")){return Country.INDIAREPUBLICOF();
68
		
68

  
69 69
		}else if (area.equals("Mexico")){return Country.MEXICOUNITEDMEXICANSTATES();
70 70
		}else if (area.equals("Peru")){return Country.PERUREPUBLICOF();
71 71
		}else if (area.equals("Ecuador")){return Country.ECUADORREPUBLICOF();
......
87 87
		}else if (area.equals("Botswana")){return Country.BOTSWANAREPUBLICOF();
88 88
		}else if (area.equals("Burundi")){return Country.BURUNDIREPUBLICOF();
89 89
		}else if (area.equals("Cameroon")){return Country.CAMEROONUNITEDREPUBLICOF();
90
		
90

  
91 91
		}else if (area.equals("Congo")){return Country.CONGOPEOPLESREPUBLICOF();
92 92
		}else if (area.equals("Zaire")){return Country.CONGODEMOCRATICREPUBLICOF();
93 93
		}else if (area.equals("Equatorial Guinea")){return Country.EQUATORIALGUINEAREPUBLICOF();
94 94
		}else if (area.equals("Gabon")){return Country.GABONGABONESEREPUBLIC();
95 95
		}else if (area.equals("Liberia")){return Country.LIBERIAREPUBLICOF();
96
		
96

  
97 97
		}else if (area.equals("Togo")){return Country.TOGOTOGOLESEREPUBLIC();
98 98
		}else if (area.equals("Guinea")){return Country.GUINEAREVOLUTIONARYPEOPLESREPCOF();
99 99
		}else if (area.equals("Guinea-Bissau")){return Country.GUINEABISSAUREPUBLICOF();
100
		
100

  
101 101
		}else if (area.equals("Malawi")){return Country.MALAWIREPUBLICOF();
102 102
		}else if (area.equals("Mozambique")){return Country.MOZAMBIQUEPEOPLESREPUBLICOF();
103 103
		}else if (area.equals("Nigeria")){return Country.NIGERIAFEDERALREPUBLICOF();
......
106 106
		}else if (area.equals("Sudan")){return Country.SUDANDEMOCRATICREPUBLICOFTHE();
107 107
		}else if (area.equals("Madagascar")){return Country.MADAGASCARREPUBLICOF();
108 108
		}else if (area.equals("Comoros")){return Country.COMOROSUNIONOFTHE();
109
		
109

  
110 110
		}else if (area.equals("Vietnam")){return Country.VIETNAMSOCIALISTREPUBLICOF();
111 111
		}else if (area.equals("Thailand")){return Country.THAILANDKINGDOMOF();
112 112
		}else if (area.equals("Bhutan")){return Country.BHUTANKINGDOMOF();
......
115 115
		}else if (area.equals("Nepal")){return Country.NEPALKINGDOMOF();
116 116
		}else if (area.equals("Pakistan")){return Country.PAKISTANISLAMICREPUBLICOF();
117 117
		}else if (area.equals("Singapore")){return Country.SINGAPOREREPUBLICOF();
118
		
118

  
119 119
		}else if (area.equals("Honduras")){return Country.HONDURASREPUBLICOF();
120 120
		}else if (area.equals("Nicaragua")){return Country.NICARAGUAREPUBLICOF();
121 121
		}else if (area.equals("Trinidad and Tobago")){return Country.TRINIDADANDTOBAGOREPUBLICOF();
......
125 125
		}else if (area.equals("North Korea")){return Country.KOREADEMOCRATICPEOPLESREPUBLICOF();
126 126
		}else if (area.equals("South Korea")){return Country.KOREAREPUBLICOF();
127 127
		}else if (area.equals("Taiwan")){return Country.TAIWANPROVINCEOFCHINA();
128
		
128

  
129 129
		}else if (area.equals("Somalia")){return Country.SOMALIASOMALIREPUBLIC();
130 130
		}else if (area.equals("Albania")){return Country.ALBANIAPEOPLESSOCIALISTREPUBLICOF();
131 131
		}else if (area.equals("Algeria")){return Country.ALGERIAPEOPLESDEMOCRATICREPUBLICOF();
132
		
132

  
133 133
		}else if (area.equals("Andorra")){return Country.ANDORRAPRINCIPALITYOF();
134 134
		}else if (area.equals("Austria")){return Country.AUSTRIAREPUBLICOF();
135 135
		}else if (area.equals("Azerbaijan")){return Country.AZERBAIJANREPUBLICOF();
......
137 137
		}else if (area.equals("Croatia")){return Country.HRVATSKA();
138 138
		}else if (area.equals("Greece")){return Country.GREECEHELLENICREPUBLIC();
139 139
		}else if (area.equals("Hungary")){return Country.HUNGARYHUNGARIANPEOPLESREPUBLIC();
140
		
140

  
141 141
		}else if (area.equals("Iran")){return Country.IRANISLAMICREPUBLICOF();
142 142
		}else if (area.equals("Iraq")){return Country.IRAQREPUBLICOF();
143 143
		}else if (area.equals("Israel")){return Country.ISRAELSTATEOF();
......
145 145
		}else if (area.equals("Kazakhstan")){return Country.KAZAKHSTANREPUBLICOF();
146 146
		}else if (area.equals("Kyrgyzstan")){return Country.KYRGYZREPUBLIC();
147 147
		}else if (area.equals("Lebanon")){return Country.LEBANONLEBANESEREPUBLIC();
148
		
148

  
149 149
		}else if (area.equals("Luxembourg")){return Country.LUXEMBOURGGRANDDUCHYOF();
150 150
		}else if (area.equals("Macedonia")){return Country.MACEDONIATHEFORMERYUGOSLAVREPUBLICOF();
151 151
		}else if (area.equals("Moldova")){return Country.MOLDOVAREPUBLICOF();
......
154 154
		}else if (area.equals("Serbia")){return Country.SERBIAANDMONTENEGRO();
155 155
		}else if (area.equals("Slovakia")){return Country.SLOVAKIA();
156 156
		}else if (area.equals("Spain")){return Country.SPAINSPANISHSTATE();
157
		
157

  
158 158
		}else if (area.equals("Switzerland")){return Country.SWITZERLANDSWISSCONFEDERATION();
159 159
		}else if (area.equals("Syria")){return Country.SYRIANARABREPUBLIC();
160 160
		}else if (area.equals("Turkey")){return Country.TURKEYREPUBLICOF();
161 161
		}else if (area.equals("Cambodia")){return Country.CAMBODIAKINGDOMOF();
162 162
		}else if (area.equals("Bangladesh")){return Country.BANGLADESHPEOPLESREPUBLICOF();
163
		
163

  
164 164
		}else if (area.equals("Sri Lanka")){return Country.SRILANKADEMOCRATICSOCIALISTREPUBLICOF();
165 165
		}else if (area.equals("Bahamas")){return Country.BAHAMASCOMMONWEALTHOFTHE();
166 166
		}else if (area.equals("Western Samoa")){return Country.SAMOAINDEPENDENTSTATEOF();
......
188 188
		}else if (area.matches("B(y)?elarus")){return Country.BELARUS();
189 189
		}else if (area.equals("Turkey")){return Country.TURKEYREPUBLICOF();
190 190
		}else if (area.equals("Turkmenistan")){return Country.TURKMENISTAN();
191
		
191

  
192 192
		}else if (area.matches("United States: Alaska")){ return TdwgAreaProvider.getAreaByTdwgAbbreviation("ASK");
193
		
194
		
195
		}else{	
193

  
194
		}else{
196 195
			if (unhandledCountries.contains(area)){
197 196
				logger.warn("Unhandled country '" + area + "' replaced by null" );
198 197
				return null;
199 198
			}
200 199
			return null;
201

  
202 200
		}
203

  
204 201
	}
205
	
206
	/* (non-Javadoc)
207
	 * @see eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase#getLanguageUuid(java.lang.String)
208
	 */
202

  
209 203
	@Override
210 204
	public UUID getLanguageUuid(String key)
211 205
			throws UndefinedTransformerMethodException {
212 206
		return super.getLanguageUuid(key);
213 207
	}
214
	
215
	
216
	
217
	
218
	
219

  
220
	/* (non-Javadoc)
221
	 * @see eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase#getExtensionTypeByKey(java.lang.String)
222
	 */
208

  
223 209
	@Override
224 210
	public ExtensionType getExtensionTypeByKey(String key) throws UndefinedTransformerMethodException {
225 211
		if (key == null){return null;
......
227 213
		return null;
228 214
	}
229 215

  
230
	/* (non-Javadoc)
231
	 * @see eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase#getExtensionTypeUuid(java.lang.String)
232
	 */
233 216
	@Override
234 217
	public UUID getExtensionTypeUuid(String key)
235 218
			throws UndefinedTransformerMethodException {
......
240 223
		}
241 224
		return null;
242 225
	}
243
	
244
	/* (non-Javadoc)
245
	 * @see eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase#getExtensionTypeUuid(java.lang.String)
246
	 */
226

  
247 227
	@Override
248 228
	public UUID getMarkerTypeUuid(String key)
249 229
			throws UndefinedTransformerMethodException {
......
251 231
		}else if (key.equalsIgnoreCase("old record")){return uuidOldRecordMarkerType;
252 232
		}else if (key.equalsIgnoreCase("checked")){return uuidCheckedMarkerType;
253 233
		}else if (key.equalsIgnoreCase("not available")){return uuidNotAvailableMarkerType;
254
		
234

  
255 235
		}
256 236
		return null;
257 237
	}
258 238

  
259
	
260

  
261
	/* (non-Javadoc)
262
	 * @see eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase#getFeatureByKey(java.lang.String)
263
	 */
264 239
	@Override
265 240
	public Feature getFeatureByKey(String key) throws UndefinedTransformerMethodException {
266 241
		if (StringUtils.isBlank(key)){return null;
......
273 248
			return null;
274 249
		}
275 250
	}
276

  
277
	
278
	
279
	
280 251
}
app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportClassification.java
6 6
 * The contents of this file are subject to the Mozilla Public License Version 1.1
7 7
 * See LICENSE.TXT at the top of this package for the full license terms.
8 8
 */
9

  
10 9
package eu.etaxonomy.cdm.io.redlist.gefaesspflanzen;
11 10

  
12 11
import java.sql.ResultSet;
......
89 88
        super.doInvoke(state);
90 89
    }
91 90

  
92

  
93 91
    private void importFamilies(Classification gesamtListe, Classification checkliste, RedListGefaesspflanzenImportState state) {
94 92
        for(UUID uuid:state.getFamilyMap().values()){
95 93
            Taxon family = HibernateProxyHelper.deproxy(getTaxonService().load(uuid, true, Arrays.asList(new String[]{"*"})), Taxon.class);
......
229 227
        addTaxonToClassification(classificationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, relationS, taxonBase, id, state);
230 228
    }
231 229

  
232

  
233

  
234 230
    private void addTaxonToClassification(Classification classification, String classificationNamespace, String relationString, final TaxonBase<?> gesamtListeTaxon, long id, RedListGefaesspflanzenImportState state){
235 231
        Taxon taxon = HibernateProxyHelper.deproxy(state.getRelatedObject(classificationNamespace, String.valueOf(id), TaxonBase.class), Taxon.class);
236 232
        //add concept relation to gesamtliste/checkliste
......
338 334
            RedListGefaesspflanzenImportState state) {
339 335
        Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
340 336

  
341
        Set<String> idSet = new HashSet<String>();
337
        Set<String> idSet = new HashSet<>();
342 338
        try {
343 339
            while (rs.next()){
344 340
                idSet.add(String.valueOf(rs.getLong(RedListUtil.NAMNR)));

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