Revision 20fed6a1
Added by Alexander Oppermann about 10 years ago
.gitattributes | ||
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1869 | 1869 |
cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TermListController.java -text |
1870 | 1870 |
cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/VocabularyController.java -text |
1871 | 1871 |
cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/VocabularyListController.java -text |
1872 |
cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/csv/CsvDemoController.java -text
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|
1873 |
cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/csv/CsvExportController.java -text
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|
1872 |
cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/checklist/ChecklistDemoController.java -text
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|
1873 |
cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/checklist/CsvExportController.java -text
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|
1874 | 1874 |
cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/dto/NameCatalogueController.java -text |
1875 | 1875 |
cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/dto/PolytomousKeyNodeDtoController.java -text |
1876 | 1876 |
cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/ext/ExternalBhleController.java -text |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/demo/CsvDemoExport.java | ||
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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 |
*/ |
... | ... | |
64 | 64 |
super(); |
65 | 65 |
this.ioName = this.getClass().getSimpleName(); |
66 | 66 |
} |
67 |
|
|
67 |
|
|
68 | 68 |
|
69 | 69 |
/** Retrieves data from a CDM DB and serializes them CDM to CSV. |
70 |
* Starts with root taxa and traverses the classification to retrieve
|
|
71 |
* children taxa, synonyms, relationships, descriptive data, red list
|
|
72 |
* status (features).
|
|
70 |
* Starts with root taxa and traverses the classification to retrieve |
|
71 |
* children taxa, synonyms, relationships, descriptive data, red list |
|
72 |
* status (features). |
|
73 | 73 |
* Taxa that are not part of the classification are not found. |
74 |
*
|
|
74 |
* |
|
75 | 75 |
* @param exImpConfig |
76 | 76 |
* @param dbname |
77 | 77 |
* @param filename |
... | ... | |
82 | 82 |
TransactionStatus txStatus = startTransaction(true); |
83 | 83 |
List<NamedArea> selectedAreas = config.getNamedAreas(); |
84 | 84 |
Set<Classification> classificationSet = assembleClassificationSet(config); |
85 |
|
|
85 |
|
|
86 | 86 |
PrintWriter writer = null; |
87 | 87 |
ByteArrayOutputStream byteArrayOutputStream; |
88 | 88 |
try { |
89 |
byteArrayOutputStream = config.getByteArrayOutputStream(); |
|
90 |
writer = new PrintWriter(byteArrayOutputStream); |
|
91 |
|
|
89 |
if(config.getByteArrayOutputStream() != null){ |
|
90 |
byteArrayOutputStream = config.getByteArrayOutputStream(); |
|
91 |
writer = new PrintWriter(byteArrayOutputStream); |
|
92 |
} |
|
92 | 93 |
//geographical Filter |
93 | 94 |
List<TaxonNode> taxonNodes = handleGeographicalFilter(state, classificationSet); |
94 |
|
|
95 |
|
|
95 | 96 |
//sorting List |
96 | 97 |
sortTaxonNodes(taxonNodes); |
97 |
|
|
98 |
List<CsvDemoRecord> recordList = null; |
|
99 |
if(config.getRecordList() != null){ |
|
100 |
recordList = config.getRecordList(); |
|
101 |
} |
|
102 |
|
|
98 | 103 |
for (TaxonNode node : taxonNodes){ |
99 | 104 |
Taxon taxon = CdmBase.deproxy(node.getTaxon(), Taxon.class); |
100 | 105 |
CsvDemoRecord record = assembleRecord(state); |
101 | 106 |
NonViralName<?> name = CdmBase.deproxy(taxon.getName(), NonViralName.class); |
102 | 107 |
Classification classification = node.getClassification(); |
103 |
config.setClassificationTitleCache(classification.getTitleCache());
|
|
108 |
config.setClassificationTitleCache(classification.getTitleCache()); |
|
104 | 109 |
if (! this.recordExists(taxon)){ |
105 | 110 |
handleTaxonBase(record, taxon, name, taxon, classification, null, false, false, config, node); |
106 |
record.write(writer); |
|
111 |
if(config.getByteArrayOutputStream() != null){ |
|
112 |
record.write(writer); |
|
113 |
} |
|
114 |
if(recordList != null){ |
|
115 |
recordList.add(record); |
|
116 |
} |
|
117 |
|
|
107 | 118 |
this.addExistingRecord(taxon); |
108 | 119 |
} |
109 | 120 |
//misapplied names |
110 | 121 |
handleMisapplication(taxon, writer, classification, record, config, node); |
111 |
writer.flush(); |
|
122 |
if(writer != null){ |
|
123 |
writer.flush(); |
|
124 |
} |
|
112 | 125 |
} |
113 | 126 |
} catch (ClassCastException e) { |
114 | 127 |
e.printStackTrace(); |
115 | 128 |
} |
116 | 129 |
finally{ |
117 |
writer.close(); |
|
118 |
this.clearExistingRecordIds(); |
|
130 |
if(writer != null){ |
|
131 |
writer.close(); |
|
132 |
} |
|
133 |
this.clearExistingRecordIds(); |
|
119 | 134 |
} |
120 | 135 |
commitTransaction(txStatus); |
121 | 136 |
return; |
122 | 137 |
|
123 | 138 |
} |
124 | 139 |
|
125 |
|
|
126 |
|
|
140 |
|
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141 |
|
|
142 |
|
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127 | 143 |
//TODO: Exception handling |
128 | 144 |
/** |
129 |
*
|
|
145 |
* |
|
130 | 146 |
* @param config |
131 | 147 |
* @return |
132 | 148 |
*/ |
... | ... | |
143 | 159 |
|
144 | 160 |
//TODO: Exception handling |
145 | 161 |
/** |
146 |
*
|
|
162 |
* |
|
147 | 163 |
* @param state |
148 | 164 |
* @return |
149 | 165 |
*/ |
... | ... | |
159 | 175 |
} |
160 | 176 |
|
161 | 177 |
/** |
162 |
* Takes positive List of areas and iterates over a given classification
|
|
163 |
* and their {@link Taxon} to return all {@link Taxon} with the desired
|
|
178 |
* Takes positive List of areas and iterates over a given classification |
|
179 |
* and their {@link Taxon} to return all {@link Taxon} with the desired |
|
164 | 180 |
* geographical attribute. |
165 |
*
|
|
181 |
* |
|
166 | 182 |
* <p><p> |
167 | 183 |
* |
168 | 184 |
* If selectedAreas is null all {@link TaxonNode}s of the given {@link Classification} will be returned. |
169 |
*
|
|
170 |
* @param selectedAreas
|
|
185 |
* |
|
186 |
* @param selectedAreas |
|
171 | 187 |
* @param classificationSet |
172 | 188 |
* @return |
173 | 189 |
*/ |
... | ... | |
223 | 239 |
// CsvTaxRecordRedlist record = new CsvTaxRecordRedlist(metaRecord, config); |
224 | 240 |
TaxonRelationshipType relType = TaxonRelationshipType.MISAPPLIED_NAME_FOR(); |
225 | 241 |
NonViralName<?> name = CdmBase.deproxy(misappliedName.getName(), NonViralName.class); |
226 |
|
|
242 |
|
|
227 | 243 |
if (! this.recordExists(misappliedName)){ |
228 | 244 |
handleTaxonBase(record, misappliedName, name, taxon, classification, relType, false, false, config, node); |
229 | 245 |
record.write(writer); |
230 | 246 |
this.addExistingRecord(misappliedName); |
231 | 247 |
} |
232 |
}
|
|
248 |
} |
|
233 | 249 |
} |
234 | 250 |
|
235 | 251 |
/** |
236 | 252 |
* handles the information record for the actual {@link Taxon} including {@link Classification classification}, Taxon Name, Taxon ID, |
237 |
* Taxon Status, Synonyms, {@link Feature features} data
|
|
253 |
* Taxon Status, Synonyms, {@link Feature features} data |
|
238 | 254 |
* @param record the concrete information record |
239 | 255 |
* @param taxonBase {@link Taxon} |
240 | 256 |
* @param name |
241 | 257 |
* @param acceptedTaxon |
242 | 258 |
* @param parent |
243 | 259 |
* @param basionym |
244 |
* @param isPartial
|
|
245 |
* @param isProParte
|
|
246 |
* @param config
|
|
247 |
* @param node
|
|
260 |
* @param isPartial |
|
261 |
* @param isProParte |
|
262 |
* @param config |
|
263 |
* @param node |
|
248 | 264 |
* @param type |
249 | 265 |
*/ |
250 | 266 |
private void handleTaxonBase(CsvDemoRecord record,TaxonBase<?> taxonBase, |
251 |
NonViralName<?> name, Taxon acceptedTaxon, Classification classification,
|
|
252 |
RelationshipTermBase<?> relType, boolean isProParte, boolean isPartial,
|
|
267 |
NonViralName<?> name, Taxon acceptedTaxon, Classification classification, |
|
268 |
RelationshipTermBase<?> relType, boolean isProParte, boolean isPartial, |
|
253 | 269 |
CsvDemoExportConfigurator config, TaxonNode node) { |
254 | 270 |
|
255 | 271 |
Taxon taxon = (Taxon) taxonBase; |
256 | 272 |
List<Feature> features = config.getFeatures(); |
257 |
record.setHeadLinePrinted(config.isHasHeaderLines()); |
|
258 |
if(config.isRedlistFeatures()){ |
|
259 |
if(features != null){ |
|
260 |
record.setPrintFeatures(features); |
|
261 |
} |
|
273 |
if(config.getByteArrayOutputStream() != null){ |
|
274 |
record.setHeadLinePrinted(config.isHasHeaderLines()); |
|
275 |
if(config.isRedlistFeatures()){ |
|
276 |
if(features != null){ |
|
277 |
record.setPrintFeatures(features); |
|
278 |
} |
|
279 |
} |
|
280 |
config.setHasHeaderLines(false); |
|
262 | 281 |
} |
263 |
config.setHasHeaderLines(false); |
|
264 |
|
|
265 | 282 |
if(config.isClassification()){ |
266 | 283 |
record.setDatasetName(classification.getTitleCache()); |
267 | 284 |
} |
268 | 285 |
if(config.isTaxonName()){ |
269 |
record.setScientificName(name.getNameCache());
|
|
286 |
record.setScientificName(name.getNameCache()); |
|
270 | 287 |
} |
271 | 288 |
if(config.isTaxonNameID()){ |
272 | 289 |
record.setScientificNameId(name.getUuid().toString()); |
... | ... | |
326 | 343 |
} |
327 | 344 |
if(config.isRedlistFeatures()){ |
328 | 345 |
if(features!= null) { |
329 |
|
|
346 |
|
|
330 | 347 |
List<List<String>> featureCells = new ArrayList<List<String>>(features.size()); |
331 | 348 |
for(int i = 0; i < features.size(); i++) { |
332 | 349 |
featureCells.add(new ArrayList<String>()); |
333 | 350 |
} |
334 | 351 |
handleRelatedRedlistStatus(record, taxon, false, featureCells, features); |
335 | 352 |
handleRelatedRedlistStatus(record, taxon, true, featureCells, features); |
336 |
|
|
353 |
|
|
337 | 354 |
} |
338 | 355 |
} |
339 |
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|
356 |
|
|
340 | 357 |
if(config.isExternalID()){ |
341 | 358 |
Set<IdentifiableSource> sources = taxonBase.getSources(); |
342 | 359 |
for(IdentifiableSource source:sources){ |
... | ... | |
344 | 361 |
/* |
345 | 362 |
* TODO: handle this more generic. |
346 | 363 |
* see ticket #4040 |
347 |
*
|
|
364 |
* |
|
348 | 365 |
*/ |
349 | 366 |
if(citation.getId() == 22){ |
350 | 367 |
String idInSource = source.getIdInSource(); |
... | ... | |
352 | 369 |
idInSource = ""; |
353 | 370 |
} |
354 | 371 |
record.setExternalID(idInSource); |
355 |
|
|
372 |
|
|
356 | 373 |
} |
357 | 374 |
} |
358 | 375 |
} |
... | ... | |
362 | 379 |
* @param record |
363 | 380 |
* @param name |
364 | 381 |
* @param type |
365 |
* @param isPartial
|
|
366 |
* @param isProParte
|
|
382 |
* @param isPartial |
|
383 |
* @param isProParte |
|
367 | 384 |
*/ |
368 | 385 |
private void handleTaxonomicStatus( |
369 | 386 |
CsvDemoRecord record, |
370 |
NonViralName<?> name,
|
|
387 |
NonViralName<?> name, |
|
371 | 388 |
RelationshipTermBase<?> type, |
372 | 389 |
boolean isProParte, |
373 | 390 |
boolean isPartial) { |
... | ... | |
389 | 406 |
logger.warn(message); |
390 | 407 |
status = "partialSynonym"; |
391 | 408 |
} |
392 |
|
|
409 |
|
|
393 | 410 |
record.setTaxonomicStatus(status); |
394 | 411 |
} |
395 | 412 |
} |
396 | 413 |
|
397 | 414 |
/** |
398 |
*
|
|
415 |
* |
|
399 | 416 |
* This method concatenates several synonyms in a list. |
400 |
*
|
|
417 |
* |
|
401 | 418 |
* @param record |
402 | 419 |
* @param taxon |
403 | 420 |
*/ |
404 | 421 |
private void handleSynonyms(CsvDemoRecord record, Taxon taxon) { |
405 |
|
|
422 |
|
|
406 | 423 |
Set<SynonymRelationship> synRels = taxon.getSynonymRelations(); |
407 |
ArrayList<String> synonyms = new ArrayList<String>();
|
|
424 |
ArrayList<String> synonyms = new ArrayList<String>(); |
|
408 | 425 |
for (SynonymRelationship synRel :synRels ){ |
409 | 426 |
Synonym synonym = synRel.getSynonym(); |
410 | 427 |
SynonymRelationshipType type = synRel.getType(); |
... | ... | |
418 | 435 |
} |
419 | 436 |
|
420 | 437 |
/** |
421 |
*
|
|
438 |
* |
|
422 | 439 |
* @param record |
423 | 440 |
* @param taxon |
424 | 441 |
*/ |
425 | 442 |
private void handleDiscriptionData(CsvDemoRecord record, Taxon taxon) { |
426 |
|
|
443 |
|
|
427 | 444 |
Set<TaxonDescription> descriptions = taxon.getDescriptions(); |
428 | 445 |
ArrayList<String> distributions = new ArrayList<String>(); |
429 | 446 |
for (TaxonDescription description : descriptions){ |
... | ... | |
439 | 456 |
record.setCountryCode(distributions); |
440 | 457 |
} |
441 | 458 |
/** |
442 |
*
|
|
459 |
* |
|
443 | 460 |
* @param record |
444 | 461 |
* @param taxon |
445 | 462 |
* @param featureCells |
446 |
* @param features
|
|
463 |
* @param features |
|
447 | 464 |
*/ |
448 | 465 |
private void handleRedlistStatus(CsvDemoRecord record, Taxon taxon, List<List<String>> featureCells, List<Feature> features){ |
449 | 466 |
Set<TaxonDescription> descriptions = taxon.getDescriptions(); |
... | ... | |
473 | 490 |
text = text.replaceAll(System.getProperty("line.separator"), ""); |
474 | 491 |
text = text.replaceAll(" ", " "); |
475 | 492 |
cell.add(text); |
476 |
|
|
493 |
|
|
477 | 494 |
} |
478 | 495 |
} |
479 | 496 |
} |
... | ... | |
483 | 500 |
} |
484 | 501 |
|
485 | 502 |
/** |
486 |
*
|
|
503 |
* |
|
487 | 504 |
* @param record |
488 | 505 |
* @param taxon |
489 | 506 |
* @param relationFrom |
490 | 507 |
* @param featureCells |
491 |
* @param features
|
|
508 |
* @param features |
|
492 | 509 |
*/ |
493 | 510 |
private void handleRelatedRedlistStatus(CsvDemoRecord record, Taxon taxon, boolean relationFrom, List<List<String>> featureCells, List<Feature> features) { |
494 | 511 |
|
495 |
if (relationFrom)handleRedlistStatus(record, taxon, featureCells, features); |
|
496 |
|
|
497 |
|
|
512 |
if (relationFrom) { |
|
513 |
handleRedlistStatus(record, taxon, featureCells, features); |
|
514 |
} |
|
515 |
|
|
516 |
|
|
498 | 517 |
Set<TaxonRelationship> taxRels; |
499 | 518 |
if(relationFrom){ |
500 | 519 |
taxRels = taxon.getRelationsFromThisTaxon(); |
... | ... | |
513 | 532 |
} |
514 | 533 |
} |
515 | 534 |
} |
516 |
|
|
535 |
|
|
517 | 536 |
|
518 | 537 |
|
519 | 538 |
/** |
520 |
*
|
|
539 |
* |
|
521 | 540 |
* @param taxonNodes |
522 | 541 |
*/ |
523 | 542 |
private void sortTaxonNodes(List<TaxonNode> taxonNodes) { |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/demo/CsvDemoExportConfigurator.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 |
*/ |
... | ... | |
48 | 48 |
private String defaultBibliographicCitation = null; |
49 | 49 |
private List<UUID> featureExclusions = new ArrayList<UUID>(); |
50 | 50 |
//filter on the classifications to be exported |
51 |
private Set<UUID> classificationUuids = new HashSet<UUID>();
|
|
51 |
private Set<UUID> classificationUuids = new HashSet<UUID>(); |
|
52 | 52 |
private boolean withHigherClassification = false; |
53 | 53 |
private String setSeparator = ";"; |
54 | 54 |
|
55 | 55 |
private boolean doGeographicalFilter = true; |
56 | 56 |
private boolean doDemoExport = false; |
57 | 57 |
private boolean doTaxonConceptExport = false; |
58 |
|
|
58 |
|
|
59 | 59 |
//attributes for export |
60 | 60 |
private boolean classification; |
61 | 61 |
private boolean taxonName; |
... | ... | |
71 | 71 |
private boolean parentID; |
72 | 72 |
private boolean externalID; |
73 | 73 |
private boolean lastChange; |
74 |
|
|
74 |
|
|
75 |
private List<CsvDemoRecord> recordList; |
|
76 |
|
|
75 | 77 |
|
76 | 78 |
|
77 |
|
|
78 |
private List<Feature> features;
|
|
79 |
|
|
80 |
private List<Feature> features;
|
|
79 | 81 |
private String classificationTitleCache; |
80 | 82 |
private List<NamedArea> areas; |
81 | 83 |
|
82 | 84 |
//TODO |
83 | 85 |
private static IExportTransformer defaultTransformer = null; |
84 | 86 |
|
85 |
public static CsvDemoExportConfigurator NewInstance(ICdmDataSource source, File destinationFolder) {
|
|
87 |
public static CsvDemoExportConfigurator NewInstance(ICdmDataSource source, File destinationFolder) { |
|
86 | 88 |
return new CsvDemoExportConfigurator(source, destinationFolder); |
87 | 89 |
} |
88 | 90 |
|
... | ... | |
94 | 96 |
}; |
95 | 97 |
} |
96 | 98 |
|
97 |
|
|
99 |
|
|
98 | 100 |
/** |
99 |
* This is function is only to have a shortcut for
|
|
101 |
* This is function is only to have a shortcut for |
|
100 | 102 |
* a preselection for available fields. One can still |
101 | 103 |
* select fields manually. |
102 | 104 |
* <p><p> |
103 | 105 |
* Only one of the parameter should be true, otherwise you |
104 |
* all fields are set to true and will be exported.
|
|
106 |
* all fields are set to true and will be exported. |
|
105 | 107 |
* <p><p> |
106 |
* In future this function might be removed.
|
|
107 |
*
|
|
108 |
*
|
|
108 |
* In future this function might be removed. |
|
109 |
* |
|
110 |
* |
|
109 | 111 |
* @param doDemoExport |
110 | 112 |
* @param doTaxonConceptExport |
111 | 113 |
*/ |
... | ... | |
130 | 132 |
setLastChange(true); |
131 | 133 |
} |
132 | 134 |
} |
133 |
|
|
134 |
|
|
135 |
|
|
135 |
|
|
136 |
|
|
137 |
|
|
136 | 138 |
/** |
137 | 139 |
* @param url |
138 | 140 |
* @param destination |
... | ... | |
172 | 174 |
/* (non-Javadoc) |
173 | 175 |
* @see eu.etaxonomy.cdm.io.common.IExportConfigurator#getNewState() |
174 | 176 |
*/ |
175 |
public CsvDemoExportState getNewState() { |
|
177 |
@Override |
|
178 |
public CsvDemoExportState getNewState() { |
|
176 | 179 |
return new CsvDemoExportState(this); |
177 | 180 |
} |
178 | 181 |
|
... | ... | |
271 | 274 |
} |
272 | 275 |
|
273 | 276 |
/** |
274 |
* The default value for the taxon.source column. This may be a column linking to a url that provides
|
|
275 |
* data about the given taxon. The id is replaced by a placeholder,
|
|
277 |
* The default value for the taxon.source column. This may be a column linking to a url that provides |
|
278 |
* data about the given taxon. The id is replaced by a placeholder, |
|
276 | 279 |
* e.g. http://wp6-cichorieae.e-taxonomy.eu/portal/?q=cdm_dataportal/taxon/{id}. |
277 | 280 |
* NOTE: This may be replaced in future versions by concrete CDM server implementations. |
278 |
*
|
|
281 |
* |
|
279 | 282 |
* @return the taxonSourceDefault |
280 | 283 |
*/ |
281 | 284 |
|
... | ... | |
327 | 330 |
|
328 | 331 |
public void setFeatures(List<Feature> features) { |
329 | 332 |
this.features = features; |
330 |
|
|
333 |
|
|
331 | 334 |
} |
332 |
|
|
335 |
|
|
333 | 336 |
public List<Feature> getFeatures() { |
334 | 337 |
return features; |
335 |
|
|
338 |
|
|
336 | 339 |
} |
337 | 340 |
|
338 | 341 |
public void setClassificationTitleCache(String classificationTitleCache) { |
339 | 342 |
this.classificationTitleCache = classificationTitleCache; |
340 | 343 |
} |
341 |
|
|
344 |
|
|
342 | 345 |
public String getClassificationTitleCache() { |
343 | 346 |
return classificationTitleCache; |
344 | 347 |
} |
... | ... | |
349 | 352 |
public void setNamedAreas(List<NamedArea> areas) { |
350 | 353 |
// TODO Auto-generated method stub |
351 | 354 |
this.areas = areas; |
352 |
|
|
355 |
|
|
353 | 356 |
} |
354 | 357 |
public List<NamedArea> getNamedAreas(){ |
355 | 358 |
return areas; |
356 | 359 |
} |
357 |
|
|
360 |
|
|
358 | 361 |
public boolean isDoGeographicalFilter() { |
359 | 362 |
return doGeographicalFilter; |
360 | 363 |
} |
... | ... | |
370 | 373 |
public void setDoDemoExport(boolean doDemoHeadlines) { |
371 | 374 |
this.doDemoExport = doDemoHeadlines; |
372 | 375 |
} |
373 |
|
|
376 |
|
|
374 | 377 |
|
375 | 378 |
public boolean isDoTaxonConceptExport() { |
376 | 379 |
return doTaxonConceptExport; |
... | ... | |
379 | 382 |
public void setDoTaxonConceptExport(boolean doTaxonConceptExport) { |
380 | 383 |
this.doTaxonConceptExport = doTaxonConceptExport; |
381 | 384 |
} |
382 |
|
|
385 |
|
|
383 | 386 |
public boolean isAuthor() { |
384 | 387 |
return author; |
385 | 388 |
} |
... | ... | |
490 | 493 |
public void setExternalID(boolean externalID) { |
491 | 494 |
this.externalID = externalID; |
492 | 495 |
} |
496 |
public List<CsvDemoRecord> getRecordList() { |
|
497 |
return recordList; |
|
498 |
} |
|
499 |
public void setRecordList(List<CsvDemoRecord> recordList) { |
|
500 |
this.recordList = recordList; |
|
501 |
} |
|
493 | 502 |
} |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/demo/CsvDemoRecord.java | ||
---|---|---|
1 | 1 |
// $Id$ |
2 | 2 |
/** |
3 | 3 |
* Copyright (C) 2009 EDIT |
4 |
* European Distributed Institute of Taxonomy
|
|
4 |
* European Distributed Institute of Taxonomy |
|
5 | 5 |
* http://www.e-taxonomy.eu |
6 |
*
|
|
6 |
* |
|
7 | 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
8 | 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
9 | 9 |
*/ |
... | ... | |
15 | 15 |
import java.util.List; |
16 | 16 |
|
17 | 17 |
import org.apache.log4j.Logger; |
18 |
import org.codehaus.jackson.annotate.JsonIgnore; |
|
18 | 19 |
|
19 | 20 |
import eu.etaxonomy.cdm.io.dwca.TermUri; |
20 | 21 |
import eu.etaxonomy.cdm.model.description.Feature; |
... | ... | |
27 | 28 |
*/ |
28 | 29 |
public class CsvDemoRecord extends CsvDemoRecordBase{ |
29 | 30 |
|
30 |
@SuppressWarnings("unused") |
|
31 |
private static final Logger logger = Logger.getLogger(CsvDemoRecord.class); |
|
32 |
|
|
33 |
private String scientificNameId; |
|
34 |
private String scientificName; |
|
35 |
private String taxonomicStatus; |
|
36 |
private CsvDemoId datasetId; |
|
37 |
private String taxonConceptID; |
|
38 |
private String datasetName; |
|
39 |
private ArrayList<String> synonyms; |
|
40 |
private String threadStatus; |
|
41 |
private ArrayList<String> countryCodes; |
|
42 |
private ArrayList<String> headlines; |
|
43 |
private boolean isHeadLinePrinted; |
|
44 |
private List<Feature> features; |
|
45 |
private List<List<String>> featuresCells; |
|
46 |
private CsvDemoExportConfigurator config; |
|
47 |
|
|
48 |
private String authorshipCache; |
|
49 |
|
|
50 |
private String rank; |
|
51 |
|
|
52 |
private String parentUuid; |
|
53 |
|
|
54 |
private String lastUpdated; |
|
55 |
|
|
56 |
private String externalID; |
|
57 |
|
|
58 |
/** |
|
59 |
* |
|
60 |
* @param metaDataRecord |
|
61 |
* @param config |
|
62 |
*/ |
|
63 |
public CsvDemoRecord(CsvDemoMetaDataRecord metaDataRecord, CsvDemoExportConfigurator config){ |
|
64 |
super(metaDataRecord, config); |
|
65 |
this.config = config; |
|
66 |
datasetId = new CsvDemoId(config); |
|
67 |
} |
|
68 |
|
|
69 |
/* (non-Javadoc) |
|
70 |
* @see eu.etaxonomy.cdm.io.dwca.out.DwcaRecordBase#registerKnownFields() |
|
71 |
*/ |
|
72 |
protected void registerKnownFields(){ |
|
73 |
try { |
|
74 |
addKnownField(TermUri.DWC_SCIENTIFIC_NAME); |
|
75 |
addKnownField(TermUri.DWC_TAXONOMIC_STATUS); |
|
76 |
addKnownField(TermUri.DWC_DATASET_NAME); |
|
77 |
addKnownField("countryCode", "http://rs.tdwg.org/dwc/terms/countryCode"); |
|
78 |
} catch (URISyntaxException e) { |
|
79 |
throw new RuntimeException(e); |
|
80 |
} |
|
81 |
} |
|
82 |
|
|
83 |
public void write(PrintWriter writer) { |
|
84 |
if(isHeadLinePrinted()){ |
|
85 |
printHeadline(writer, setHeadlines(), TermUri.DWC_DATASET_NAME); |
|
86 |
isHeadLinePrinted=false; |
|
87 |
} |
|
88 |
if(config.isClassification()){ |
|
89 |
print(datasetName, writer, IS_FIRST, TermUri.DWC_DATASET_NAME); |
|
90 |
} |
|
91 |
if(config.isDoTaxonConceptExport()){ |
|
92 |
if(config.isTaxonName()){ |
|
93 |
print(scientificName, writer, IS_FIRST, TermUri.DWC_SCIENTIFIC_NAME); |
|
94 |
} |
|
95 |
}else{ |
|
96 |
if(config.isTaxonName()){ |
|
97 |
print(scientificName, writer, IS_NOT_FIRST, TermUri.DWC_SCIENTIFIC_NAME); |
|
98 |
} |
|
99 |
} |
|
100 |
if(config.isTaxonNameID()){ |
|
101 |
print(scientificNameId, writer, IS_NOT_FIRST, TermUri.DWC_DATASET_ID); |
|
102 |
} |
|
103 |
if(config.isAuthor()){ |
|
104 |
print(authorshipCache, writer, IS_NOT_FIRST, TermUri.DC_CREATOR); |
|
105 |
} |
|
106 |
if(config.isRank()){ |
|
107 |
print(rank, writer, IS_NOT_FIRST, TermUri.DWC_TAXON_RANK); |
|
108 |
} |
|
109 |
if(config.isTaxonConceptID()){ |
|
110 |
print(taxonConceptID, writer, IS_NOT_FIRST, TermUri.DWC_TAXON_CONCEPT_ID); |
|
111 |
} |
|
112 |
if(config.isTaxonStatus()){ |
|
113 |
print(taxonomicStatus, writer, IS_NOT_FIRST, TermUri.DWC_TAXONOMIC_STATUS); |
|
114 |
} |
|
115 |
if(config.isAcceptedName()){ |
|
116 |
//TODO print accepted Name |
|
117 |
} |
|
118 |
if(config.isParentID()){ |
|
119 |
print(parentUuid, writer, IS_NOT_FIRST, TermUri.DWC_PARENT_NAME_USAGE_ID); |
|
120 |
} |
|
121 |
if(config.isSynonyms()){ |
|
122 |
print(synonyms, TermUri.DWC_SCIENTIFIC_NAME, writer); |
|
123 |
} |
|
124 |
if(config.isDistributions()){ |
|
125 |
print(countryCodes, TermUri.DWC_COUNTRY_CODE, writer); |
|
126 |
} |
|
127 |
if(config.isRedlistFeatures()){ |
|
128 |
if(features != null ||featuresCells != null || !featuresCells.isEmpty()){ |
|
129 |
for(List<String> featureList : featuresCells) { |
|
130 |
print((ArrayList<String>)featureList, TermUri.DWC_LIFESTAGE, writer); |
|
131 |
} |
|
132 |
} |
|
133 |
} |
|
134 |
if(config.isExternalID()){ |
|
135 |
print(externalID, writer, IS_NOT_FIRST,TermUri.DWC_ORIGINAL_NAME_USAGE_ID); |
|
136 |
} |
|
137 |
if(config.isLastChange()){ |
|
138 |
print(lastUpdated, writer, IS_NOT_FIRST,TermUri.DC_MODIFIED); |
|
139 |
} |
|
140 |
writer.println(); |
|
141 |
} |
|
142 |
|
|
143 |
|
|
144 |
//--------------Getter-Setter-Methods------------------// |
|
145 |
|
|
146 |
public String getDatasetName() { |
|
147 |
return datasetName; |
|
148 |
} |
|
149 |
public void setDatasetName(String datasetName) { |
|
150 |
this.datasetName = datasetName; |
|
151 |
} |
|
152 |
public String getScientificName() { |
|
153 |
return scientificName; |
|
154 |
} |
|
155 |
public void setScientificName(String scientificName) { |
|
156 |
this.scientificName = scientificName; |
|
157 |
} |
|
158 |
public String getTaxonomicStatus() { |
|
159 |
return taxonomicStatus; |
|
160 |
} |
|
161 |
public void setTaxonomicStatus(String taxonomicStatus) { |
|
162 |
this.taxonomicStatus = taxonomicStatus; |
|
163 |
} |
|
164 |
public String getDatasetId() { |
|
165 |
return datasetId.getId(); |
|
166 |
} |
|
167 |
public void setDatasetId(Classification classification) { |
|
168 |
this.datasetId.setId(classification); |
|
169 |
} |
|
170 |
public void setSynonyms(ArrayList<String> synonyms){ |
|
171 |
this.synonyms = synonyms; |
|
172 |
} |
|
173 |
public ArrayList<String> getSynonyms(){ |
|
174 |
return synonyms; |
|
175 |
} |
|
176 |
public String getThreadStatus() { |
|
177 |
return threadStatus; |
|
178 |
} |
|
179 |
public void setThreadStatus(String threadStatus) { |
|
180 |
this.threadStatus = threadStatus; |
|
181 |
} |
|
182 |
|
|
183 |
public void setCountryCode(ArrayList<String> countryCodes) { |
|
184 |
this.countryCodes = countryCodes; |
|
185 |
} |
|
186 |
|
|
187 |
//FIXME: hard coded header lines |
|
188 |
private ArrayList<String> setHeadlines(){ |
|
189 |
// if(config.isDoDemoExport()){ |
|
190 |
headlines = new ArrayList<String>(); |
|
191 |
|
|
192 |
if(config.isClassification()){ |
|
193 |
headlines.add("Classification"); |
|
194 |
} |
|
195 |
if(config.isTaxonName()){ |
|
196 |
headlines.add("Wissenschaftlicher Name"); |
|
197 |
} |
|
198 |
if(config.isTaxonNameID()){ |
|
199 |
headlines.add("Taxon ID"); |
|
200 |
} |
|
201 |
if(config.isAuthor()){ |
|
202 |
headlines.add("Autor"); |
|
203 |
} |
|
204 |
if(config.isRank()){ |
|
205 |
headlines.add("Rang"); |
|
206 |
} |
|
207 |
if(config.isTaxonStatus()){ |
|
208 |
headlines.add("Taxon Status"); |
|
209 |
} |
|
210 |
if(config.isAcceptedName()){ |
|
211 |
headlines.add("Akzeptierter Name"); |
|
212 |
} |
|
213 |
if(config.isTaxonConceptID()){ |
|
214 |
headlines.add("Taxon Konzept ID"); |
|
215 |
} |
|
216 |
if(config.isParentID()){ |
|
217 |
headlines.add("Parent ID"); |
|
218 |
} |
|
219 |
if(config.isSynonyms()){ |
|
220 |
headlines.add("Synonym"); |
|
221 |
} |
|
222 |
if(config.isDistributions()){ |
|
223 |
headlines.add("Distribution"); |
|
224 |
} |
|
225 |
if(features != null){ |
|
226 |
if(!features.isEmpty()){ |
|
227 |
for(Feature f : features) { |
|
228 |
headlines.add(f.getLabel()); |
|
229 |
} |
|
230 |
} |
|
231 |
} |
|
232 |
if(config.isExternalID()){ |
|
233 |
headlines.add("External ID"); |
|
234 |
} |
|
235 |
if(config.isLastChange()){ |
|
236 |
headlines.add("Letztes Update"); |
|
237 |
} |
|
238 |
// }else if(config.isDoTaxonConceptExport()){ |
|
239 |
// headlines = new ArrayList<String>(); |
|
240 |
// Collections.addAll(headlines, "Taxon Name UUID","Taxon Name","Author","Rank","Taxon Status","Accepted Name", "Taxon Concept ID", "Parent ID", "Last Change"); |
|
241 |
// } |
|
242 |
return headlines; |
|
243 |
} |
|
244 |
|
|
245 |
public boolean isHeadLinePrinted() { |
|
246 |
return isHeadLinePrinted; |
|
247 |
} |
|
248 |
|
|
249 |
public void setHeadLinePrinted(boolean isHeadLinePrinted) { |
|
250 |
this.isHeadLinePrinted = isHeadLinePrinted; |
|
251 |
} |
|
252 |
|
|
253 |
public void setScientificNameId(String scientificNameId) { |
|
254 |
this.scientificNameId = scientificNameId; |
|
255 |
} |
|
256 |
|
|
257 |
public void setPrintFeatures(List<Feature> features) { |
|
258 |
this.features = features; |
|
259 |
|
|
260 |
} |
|
261 |
|
|
262 |
public void setFeatures(List<List<String>> featureCells) { |
|
263 |
this.featuresCells = featureCells; |
|
264 |
|
|
265 |
} |
|
266 |
|
|
267 |
public void setAuthorName(String authorshipCache) { |
|
268 |
this.authorshipCache = authorshipCache; |
|
269 |
|
|
270 |
} |
|
271 |
|
|
272 |
public void setRank(String rank) { |
|
273 |
this.rank = rank; |
|
274 |
} |
|
275 |
|
|
276 |
public void setParentUUID(String parentUuid) { |
|
277 |
this.parentUuid = parentUuid; |
|
278 |
|
|
279 |
} |
|
280 |
|
|
281 |
public void setLastChange(String lastUpdated) { |
|
282 |
this.lastUpdated = lastUpdated; |
|
283 |
} |
|
284 |
|
|
285 |
public void setTaxonConceptID(String taxonConceptID) { |
|
286 |
this.taxonConceptID = taxonConceptID; |
|
287 |
} |
|
288 |
|
|
289 |
public void setExternalID(String externalID) { |
|
290 |
this.externalID = externalID; |
|
291 |
} |
|
31 |
@SuppressWarnings("unused") |
|
32 |
private static final Logger logger = Logger.getLogger(CsvDemoRecord.class); |
|
33 |
|
|
34 |
private String scientificNameId; |
|
35 |
private String scientificName; |
|
36 |
private String taxonomicStatus; |
|
37 |
private final CsvDemoId datasetId; |
|
38 |
private String taxonConceptID; |
|
39 |
private String datasetName; |
|
40 |
private ArrayList<String> synonyms; |
|
41 |
private String threadStatus; |
|
42 |
private ArrayList<String> countryCodes; |
|
43 |
private ArrayList<String> headlines; |
|
44 |
private Boolean isHeadLinePrinted; |
|
45 |
private List<Feature> features; |
|
46 |
private List<List<String>> featuresCells; |
|
47 |
private final CsvDemoExportConfigurator config; |
|
48 |
private String authorshipCache; |
|
49 |
private String rank; |
|
50 |
private String parentUuid; |
|
51 |
private String lastUpdated; |
|
52 |
private String externalID; |
|
53 |
|
|
54 |
/** |
|
55 |
* |
|
56 |
* @param metaDataRecord |
|
57 |
* @param config |
|
58 |
*/ |
|
59 |
public CsvDemoRecord(CsvDemoMetaDataRecord metaDataRecord, CsvDemoExportConfigurator config){ |
|
60 |
super(metaDataRecord, config); |
|
61 |
this.config = config; |
|
62 |
datasetId = new CsvDemoId(config); |
|
63 |
} |
|
64 |
|
|
65 |
/* (non-Javadoc) |
|
66 |
* @see eu.etaxonomy.cdm.io.dwca.out.DwcaRecordBase#registerKnownFields() |
|
67 |
*/ |
|
68 |
@Override |
|
69 |
protected void registerKnownFields(){ |
|
70 |
try { |
|
71 |
addKnownField(TermUri.DWC_SCIENTIFIC_NAME); |
|
72 |
addKnownField(TermUri.DWC_TAXONOMIC_STATUS); |
|
73 |
addKnownField(TermUri.DWC_DATASET_NAME); |
|
74 |
addKnownField("countryCode", "http://rs.tdwg.org/dwc/terms/countryCode"); |
|
75 |
} catch (URISyntaxException e) { |
|
76 |
throw new RuntimeException(e); |
|
77 |
} |
|
78 |
} |
|
79 |
|
|
80 |
@Override |
|
81 |
public void write(PrintWriter writer) { |
|
82 |
if(isHeadLinePrinted() != null && isHeadLinePrinted() == true){ |
|
83 |
printHeadline(writer, setHeadlines(), TermUri.DWC_DATASET_NAME); |
|
84 |
isHeadLinePrinted=false; |
|
85 |
} |
|
86 |
if(config.isClassification()){ |
|
87 |
print(datasetName, writer, IS_FIRST, TermUri.DWC_DATASET_NAME); |
|
88 |
} |
|
89 |
if(config.isDoTaxonConceptExport()){ |
|
90 |
if(config.isTaxonName()){ |
|
91 |
print(scientificName, writer, IS_FIRST, TermUri.DWC_SCIENTIFIC_NAME); |
|
92 |
} |
|
93 |
}else{ |
|
94 |
if(config.isTaxonName()){ |
|
95 |
print(scientificName, writer, IS_NOT_FIRST, TermUri.DWC_SCIENTIFIC_NAME); |
|
96 |
} |
|
97 |
} |
|
98 |
if(config.isTaxonNameID()){ |
|
99 |
print(scientificNameId, writer, IS_NOT_FIRST, TermUri.DWC_DATASET_ID); |
|
100 |
} |
|
101 |
if(config.isAuthor()){ |
|
102 |
print(authorshipCache, writer, IS_NOT_FIRST, TermUri.DC_CREATOR); |
|
103 |
} |
|
104 |
if(config.isRank()){ |
|
105 |
print(rank, writer, IS_NOT_FIRST, TermUri.DWC_TAXON_RANK); |
|
106 |
} |
|
107 |
if(config.isTaxonConceptID()){ |
|
108 |
print(taxonConceptID, writer, IS_NOT_FIRST, TermUri.DWC_TAXON_CONCEPT_ID); |
|
109 |
} |
|
110 |
if(config.isTaxonStatus()){ |
|
111 |
print(taxonomicStatus, writer, IS_NOT_FIRST, TermUri.DWC_TAXONOMIC_STATUS); |
|
112 |
} |
|
113 |
if(config.isAcceptedName()){ |
|
114 |
//TODO print accepted Name |
|
115 |
} |
|
116 |
if(config.isParentID()){ |
|
117 |
print(parentUuid, writer, IS_NOT_FIRST, TermUri.DWC_PARENT_NAME_USAGE_ID); |
|
118 |
} |
|
119 |
if(config.isSynonyms()){ |
|
120 |
print(synonyms, TermUri.DWC_SCIENTIFIC_NAME, writer); |
|
121 |
} |
|
122 |
if(config.isDistributions()){ |
|
123 |
print(countryCodes, TermUri.DWC_COUNTRY_CODE, writer); |
|
124 |
} |
|
125 |
if(config.isRedlistFeatures()){ |
|
126 |
if(features != null ||featuresCells != null || !featuresCells.isEmpty()){ |
|
127 |
for(List<String> featureList : featuresCells) { |
|
128 |
print((ArrayList<String>)featureList, TermUri.DWC_LIFESTAGE, writer); |
|
129 |
} |
|
130 |
} |
|
131 |
} |
|
132 |
if(config.isExternalID()){ |
|
133 |
print(externalID, writer, IS_NOT_FIRST,TermUri.DWC_ORIGINAL_NAME_USAGE_ID); |
|
134 |
} |
|
135 |
if(config.isLastChange()){ |
|
136 |
print(lastUpdated, writer, IS_NOT_FIRST,TermUri.DC_MODIFIED); |
|
137 |
} |
|
138 |
writer.println(); |
|
139 |
} |
|
140 |
|
|
141 |
|
|
142 |
//--------------Getter-Setter-Methods------------------// |
|
143 |
|
|
144 |
/* public String getDatasetName() { |
|
145 |
return datasetName; |
|
146 |
}*/ |
|
147 |
public void setDatasetName(String datasetName) { |
|
148 |
this.datasetName = datasetName; |
|
149 |
} |
|
150 |
public String getScientificName() { |
|
151 |
return scientificName; |
|
152 |
} |
|
153 |
public void setScientificName(String scientificName) { |
|
154 |
this.scientificName = scientificName; |
|
155 |
} |
|
156 |
/* public String getTaxonomicStatus() { |
|
157 |
return taxonomicStatus; |
|
158 |
}*/ |
|
159 |
public void setTaxonomicStatus(String taxonomicStatus) { |
|
160 |
this.taxonomicStatus = taxonomicStatus; |
|
161 |
} |
|
162 |
/* public String getDatasetId() { |
|
163 |
return datasetId.getId(); |
|
164 |
}*/ |
|
165 |
public void setDatasetId(Classification classification) { |
|
166 |
this.datasetId.setId(classification); |
|
167 |
} |
|
168 |
public void setSynonyms(ArrayList<String> synonyms){ |
|
169 |
this.synonyms = synonyms; |
|
170 |
} |
|
171 |
/* public ArrayList<String> getSynonyms(){ |
|
172 |
return synonyms; |
|
173 |
}*/ |
|
174 |
/* public String getThreadStatus() { |
|
175 |
return threadStatus; |
|
176 |
}*/ |
|
177 |
public void setThreadStatus(String threadStatus) { |
|
178 |
this.threadStatus = threadStatus; |
|
179 |
} |
|
180 |
|
|
181 |
public void setCountryCode(ArrayList<String> countryCodes) { |
|
182 |
this.countryCodes = countryCodes; |
|
183 |
} |
|
184 |
|
|
185 |
//FIXME: hard coded header lines |
|
186 |
private ArrayList<String> setHeadlines(){ |
|
187 |
// if(config.isDoDemoExport()){ |
|
188 |
headlines = new ArrayList<String>(); |
|
189 |
|
|
190 |
if(config.isClassification()){ |
|
191 |
headlines.add("Classification"); |
|
192 |
} |
|
193 |
if(config.isTaxonName()){ |
|
194 |
headlines.add("Wissenschaftlicher Name"); |
|
195 |
} |
|
196 |
if(config.isTaxonNameID()){ |
|
197 |
headlines.add("Taxon ID"); |
|
198 |
} |
|
199 |
if(config.isAuthor()){ |
|
200 |
headlines.add("Autor"); |
|
201 |
} |
|
202 |
if(config.isRank()){ |
|
203 |
headlines.add("Rang"); |
|
204 |
} |
|
205 |
if(config.isTaxonStatus()){ |
|
206 |
headlines.add("Taxon Status"); |
|
207 |
} |
|
208 |
if(config.isAcceptedName()){ |
|
209 |
headlines.add("Akzeptierter Name"); |
|
210 |
} |
|
211 |
if(config.isTaxonConceptID()){ |
|
212 |
headlines.add("Taxon Konzept ID"); |
|
213 |
} |
|
214 |
if(config.isParentID()){ |
|
215 |
headlines.add("Parent ID"); |
|
216 |
} |
|
217 |
if(config.isSynonyms()){ |
|
218 |
headlines.add("Synonym"); |
|
219 |
} |
|
220 |
if(config.isDistributions()){ |
|
221 |
headlines.add("Distribution"); |
|
222 |
} |
|
223 |
if(features != null){ |
|
224 |
if(!features.isEmpty()){ |
|
225 |
for(Feature f : features) { |
|
226 |
headlines.add(f.getLabel()); |
|
227 |
} |
|
228 |
} |
|
229 |
} |
|
230 |
if(config.isExternalID()){ |
|
231 |
headlines.add("External ID"); |
|
232 |
} |
|
233 |
if(config.isLastChange()){ |
|
234 |
headlines.add("Letztes Update"); |
|
235 |
} |
|
236 |
// }else if(config.isDoTaxonConceptExport()){ |
|
237 |
// headlines = new ArrayList<String>(); |
|
238 |
// Collections.addAll(headlines, "Taxon Name UUID","Taxon Name","Author","Rank","Taxon Status","Accepted Name", "Taxon Concept ID", "Parent ID", "Last Change"); |
|
239 |
// } |
|
240 |
return headlines; |
|
241 |
} |
|
242 |
@JsonIgnore |
|
243 |
public Boolean isHeadLinePrinted() { |
|
244 |
return isHeadLinePrinted; |
|
245 |
} |
|
246 |
|
|
247 |
public void setHeadLinePrinted(Boolean isHeadLinePrinted) { |
|
248 |
this.isHeadLinePrinted = isHeadLinePrinted; |
|
249 |
} |
|
250 |
|
|
251 |
public void setScientificNameId(String scientificNameId) { |
|
252 |
this.scientificNameId = scientificNameId; |
|
253 |
} |
|
254 |
|
|
255 |
public void setPrintFeatures(List<Feature> features) { |
|
256 |
this.features = features; |
|
257 |
|
|
258 |
} |
|
259 |
|
|
260 |
public void setFeatures(List<List<String>> featureCells) { |
|
261 |
this.featuresCells = featureCells; |
|
262 |
|
|
263 |
} |
|
264 |
|
|
265 |
public void setAuthorName(String authorshipCache) { |
|
266 |
this.authorshipCache = authorshipCache; |
|
267 |
} |
|
268 |
|
|
269 |
public void setRank(String rank) { |
|
270 |
this.rank = rank; |
|
271 |
} |
|
272 |
|
|
273 |
public void setParentUUID(String parentUuid) { |
|
274 |
this.parentUuid = parentUuid; |
|
275 |
|
|
276 |
} |
|
277 |
|
|
278 |
public void setLastChange(String lastUpdated) { |
|
279 |
this.lastUpdated = lastUpdated; |
|
280 |
} |
|
281 |
|
|
282 |
public void setTaxonConceptID(String taxonConceptID) { |
|
283 |
this.taxonConceptID = taxonConceptID; |
|
284 |
} |
|
285 |
|
|
286 |
public void setExternalID(String externalID) { |
|
287 |
this.externalID = externalID; |
|
288 |
} |
|
289 |
/** |
|
290 |
* @return the scientificNameId |
|
291 |
*/ |
|
292 |
/* public String getScientificNameId() { |
|
293 |
return scientificNameId; |
|
294 |
}*/ |
|
295 |
|
|
296 |
/** |
|
297 |
* @return the taxonConceptID |
|
298 |
*/ |
|
299 |
public String getTaxonConceptID() { |
|
300 |
return taxonConceptID; |
|
301 |
} |
|
302 |
/* |
|
303 |
public ArrayList<String> getCountryCodes() { |
|
304 |
return countryCodes; |
|
305 |
} |
|
306 |
*/ |
|
307 |
/** |
|
308 |
* @return the authorshipCache |
|
309 |
*/ |
|
310 |
public String getAuthor() { |
|
311 |
return authorshipCache; |
|
312 |
} |
|
313 |
|
|
314 |
/** |
|
315 |
* @return the rank |
|
316 |
*/ |
|
317 |
public String getRank() { |
|
318 |
return rank; |
|
319 |
} |
|
320 |
|
|
321 |
/** |
|
322 |
* @return the parentUuid |
|
323 |
*/ |
|
324 |
public String getParentUuid() { |
|
325 |
return parentUuid; |
|
326 |
} |
|
327 |
|
|
328 |
/** |
|
329 |
* @return the lastUpdated |
|
330 |
*/ |
|
331 |
public String getLastUpdated() { |
|
332 |
return lastUpdated; |
|
333 |
} |
|
334 |
|
|
335 |
/** |
|
336 |
* @return the externalID |
|
337 |
*/ |
|
338 |
public String getExternalID() { |
|
339 |
return externalID; |
|
340 |
} |
|
341 |
|
|
292 | 342 |
} |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/demo/CsvDemoRecordBase.java | ||
---|---|---|
1 | 1 |
// $Id$ |
2 | 2 |
/** |
3 | 3 |
* Copyright (C) 2009 EDIT |
4 |
* European Distributed Institute of Taxonomy
|
|
4 |
* European Distributed Institute of Taxonomy |
|
5 | 5 |
* http://www.e-taxonomy.eu |
6 |
*
|
|
6 |
* |
|
7 | 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
8 | 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
9 | 9 |
*/ |
... | ... | |
59 | 59 |
protected static final boolean IS_FIRST = false; |
60 | 60 |
protected static final boolean IS_NOT_FIRST = true; |
61 | 61 |
// protected static final String SEP = ","; |
62 |
|
|
62 |
|
|
63 | 63 |
protected Map<String, URI> knownFields = new HashMap<String, URI>(); |
64 | 64 |
protected Set<TermUri> knownTermFields = new HashSet<TermUri>(); |
65 |
|
|
65 |
|
|
66 | 66 |
public abstract void write(PrintWriter writer); |
67 | 67 |
protected abstract void registerKnownFields(); |
68 |
|
|
68 |
|
|
69 | 69 |
protected int count; |
70 |
private CsvDemoMetaDataRecord metaDataRecord; |
|
70 |
private final CsvDemoMetaDataRecord metaDataRecord;
|
|
71 | 71 |
protected CsvDemoExportConfigurator config; |
72 | 72 |
|
73 | 73 |
private Integer id; |
74 | 74 |
private UUID uuid; |
75 | 75 |
|
76 |
|
|
76 |
|
|
77 | 77 |
protected CsvDemoRecordBase(CsvDemoMetaDataRecord metaDataRecord, CsvDemoExportConfigurator config){ |
78 | 78 |
this.metaDataRecord = metaDataRecord; |
79 | 79 |
this.count = metaDataRecord.inc(); |
80 | 80 |
this.config = config; |
81 | 81 |
} |
82 |
|
|
83 |
|
|
82 |
|
|
83 |
|
|
84 | 84 |
public void setId(Integer id) { |
85 | 85 |
this.id = id; |
86 | 86 |
} |
... | ... | |
93 | 93 |
this.uuid = uuid; |
94 | 94 |
} |
95 | 95 |
|
96 |
public UUID getUuid() { |
|
96 |
/* public UUID getUuid() {
|
|
97 | 97 |
return uuid; |
98 |
} |
|
98 |
}*/
|
|
99 | 99 |
|
100 | 100 |
protected void printNotes(Set<Annotation> notes, PrintWriter writer, boolean addSeparator, TermUri fieldKey) { |
101 | 101 |
printNotes(notes, writer, addSeparator, fieldKey.getUriString()); |
... | ... | |
105 | 105 |
String value = null; |
106 | 106 |
print(value, writer, addSeparator, fieldKey); |
107 | 107 |
} |
108 |
|
|
108 |
|
|
109 | 109 |
// protected void print(Object object, PrintWriter writer, boolean addSeparator, TermUri fieldKey) { |
110 | 110 |
// print(object == null ? null : object.toString(), writer, addSeparator, fieldKey); |
111 | 111 |
// } |
... | ... | |
122 | 122 |
print(agent == null ? null : getAgent(agent), writer, addSeparator, fieldKey); |
123 | 123 |
} |
124 | 124 |
|
125 |
|
|
125 |
|
|
126 | 126 |
protected void print(Language language, PrintWriter writer, boolean addSeparator, TermUri fieldKey) { |
127 | 127 |
print(language, writer, addSeparator, fieldKey.getUriString()); |
128 | 128 |
} |
... | ... | |
135 | 135 |
protected void print(LSID lsid, PrintWriter writer, boolean addSeparator, String fieldKey) { |
136 | 136 |
print(lsid == null ? null : String.valueOf(lsid.toString()), writer, addSeparator, fieldKey); |
137 | 137 |
} |
138 |
|
|
138 |
|
|
139 | 139 |
protected void print(Set<Rights> rights, PrintWriter writer, boolean addSeparator, TermUri fieldKey) { |
140 | 140 |
print(rights, writer, addSeparator, fieldKey.getUriString()); |
141 | 141 |
} |
... | ... | |
149 | 149 |
protected void print(URI uri, PrintWriter writer, boolean addSeparator, String fieldKey) { |
150 | 150 |
print(uri == null ? null : String.valueOf(uri), writer, addSeparator, fieldKey); |
151 | 151 |
} |
152 |
|
|
152 |
|
|
153 | 153 |
protected void print(Point point, PrintWriter writer, boolean addSeparator, TermUri latitudeKey, TermUri longitudeKey) { |
154 | 154 |
print(point, writer, addSeparator, latitudeKey.getUriString(), longitudeKey.getUriString()); |
155 | 155 |
} |
156 |
|
|
156 |
|
|
157 | 157 |
protected void print(Point point, PrintWriter writer, boolean addSeparator, String latitudeKey, String longitudeKey) { |
158 | 158 |
if (point == null){ |
159 | 159 |
String toPrint = null; |
... | ... | |
168 | 168 |
} |
169 | 169 |
protected void print(Boolean boolValue, PrintWriter writer, boolean addSeparator, TermUri fieldKey) { |
170 | 170 |
print(boolValue, writer, addSeparator, fieldKey.getUriString()); |
171 |
}
|
|
171 |
} |
|
172 | 172 |
protected void print(Boolean boolValue, PrintWriter writer, boolean addSeparator, String fieldKey) { |
173 | 173 |
print(boolValue == null ? null : String.valueOf(boolValue), writer, addSeparator, fieldKey); |
174 | 174 |
} |
... | ... | |
179 | 179 |
protected void print(Integer intValue, PrintWriter writer, boolean addSeparator, String fieldKey) { |
180 | 180 |
print(intValue == null ? null : String.valueOf(intValue), writer, addSeparator, fieldKey); |
181 | 181 |
} |
182 |
|
|
182 |
|
|
183 | 183 |
protected void printId(Integer intValue, PrintWriter writer, boolean addSeparator, String fieldKey) { |
184 | 184 |
print(intValue == null ? null : String.valueOf(intValue), writer, addSeparator, fieldKey); |
185 | 185 |
} |
... | ... | |
194 | 194 |
protected void print(String value, PrintWriter writer, boolean addSeparator, TermUri fieldKey, String defaultValue) { |
195 | 195 |
print(value, writer, addSeparator, fieldKey.getUriString(), defaultValue); |
196 | 196 |
} |
197 |
|
|
197 |
|
|
198 | 198 |
protected void print(String value, PrintWriter writer, boolean addSeparator, String fieldKey) { |
199 | 199 |
print(value, writer, addSeparator, fieldKey, null); |
200 | 200 |
} |
201 |
|
|
201 |
|
|
202 | 202 |
protected void print(String value, PrintWriter writer, boolean addSeparator, String fieldKey, String defaultValue) { |
203 | 203 |
if (count == 1 && addSeparator == IS_NOT_FIRST){ |
204 | 204 |
registerFieldKey(URI.create(fieldKey), defaultValue); |
... | ... | |
208 | 208 |
if (StringUtils.isNotBlank(value)){ |
209 | 209 |
//Replace quotes by double quotes |
210 | 210 |
value = value.replace("\"", "\"\""); |
211 |
|
|
211 |
|
|
212 | 212 |
value = value.replace(config.getLinesTerminatedBy(), "\\r"); |
213 |
|
|
213 |
|
|
214 | 214 |
//replace all line brakes according to best practices: http://code.google.com/p/gbif-ecat/wiki/BestPractices |
215 | 215 |
value = value.replace("\r\n", "\\r"); |
216 | 216 |
value = value.replace("\r", "\\r"); |
217 | 217 |
value = value.replace("\n", "\\r"); |
218 |
|
|
218 |
|
|
219 | 219 |
strToPrint += config.getFieldsEnclosedBy() + value + config.getFieldsEnclosedBy(); |
220 | 220 |
} |
221 | 221 |
writer.print(strToPrint); |
222 | 222 |
} |
223 | 223 |
} |
224 |
|
|
224 |
|
|
225 | 225 |
/** |
226 | 226 |
* @param writer |
227 | 227 |
* @param list |
... | ... | |
243 | 243 |
* @param list |
244 | 244 |
* @param termUri |
245 | 245 |
* @param writer |
246 |
*
|
|
246 |
* |
|
247 | 247 |
* Method for concatenating strings, especially for the red list use case |
248 | 248 |
*/ |
249 | 249 |
protected void print(ArrayList<String> list, TermUri termUri, PrintWriter writer){ |
... | ... | |
264 | 264 |
print(element, writer, IS_FIRST, termUri); |
265 | 265 |
writer.write(","); |
266 | 266 |
logger.info(element); |
267 |
|
|
267 |
|
|
268 | 268 |
} |
269 | 269 |
} |
270 | 270 |
} |
271 | 271 |
} |
272 |
|
|
273 |
|
|
272 |
|
|
273 |
|
|
274 | 274 |
private void registerFieldKey(URI key, String defaultValue) { |
275 | 275 |
this.metaDataRecord.addFieldEntry(key, defaultValue); |
276 | 276 |
} |
277 | 277 |
|
278 |
|
|
278 |
|
|
279 | 279 |
protected String getRights(Rights rights) { |
280 | 280 |
if (rights == null){ |
281 | 281 |
return ""; |
... | ... | |
337 | 337 |
return result; |
338 | 338 |
} |
339 | 339 |
} |
340 |
|
|
340 |
|
|
341 | 341 |
protected String getSex(DefinedTerm sex) { |
342 | 342 |
String result = CsvDemoExportTransformer.transformToGbifSex(sex); |
343 | 343 |
if (result == null){ |
... | ... | |
350 | 350 |
return result; |
351 | 351 |
} |
352 | 352 |
} |
353 |
|
|
353 |
|
|
354 | 354 |
protected String getLifeStage(DefinedTerm stage) { |
355 | 355 |
String result = CsvDemoExportTransformer.transformToGbifLifeStage(stage); |
356 | 356 |
if (result == null){ |
... | ... | |
376 | 376 |
return result; |
377 | 377 |
} |
378 | 378 |
} |
379 |
|
|
379 |
|
|
380 | 380 |
protected String getEstablishmentMeans(PresenceAbsenceTermBase<?> status) { |
381 | 381 |
String result = CsvDemoExportTransformer.transformToGbifEstablishmentMeans(status); |
382 | 382 |
if (result == null){ |
... | ... | |
390 | 390 |
} |
391 | 391 |
} |
392 | 392 |
|
393 |
|
|
394 |
|
|
393 |
|
|
394 |
|
|
395 | 395 |
protected String getAgent(AgentBase<?> agent) { |
396 | 396 |
if (agent == null){ |
397 | 397 |
return ""; |
... | ... | |
400 | 400 |
return agent.getTitleCache(); |
401 | 401 |
} |
402 | 402 |
} |
403 |
|
|
403 |
|
|
404 | 404 |
|
405 | 405 |
protected String getFeature(Feature feature) { |
406 | 406 |
if (feature == null){ |
... | ... | |
411 | 411 |
} |
412 | 412 |
} |
413 | 413 |
|
414 |
|
|
414 |
|
|
415 | 415 |
protected String getTimePeriod(TimePeriod period) { |
416 | 416 |
if (period == null){ |
417 | 417 |
return ""; |
... | ... | |
420 | 420 |
return period.toString(); |
421 | 421 |
} |
422 | 422 |
} |
423 |
|
|
423 |
|
|
424 | 424 |
protected String getTimePeriodPart(TimePeriod period, boolean useEnd) { |
425 | 425 |
if (period == null){ |
426 | 426 |
return ""; |
... | ... | |
449 | 449 |
return result; |
450 | 450 |
} |
451 | 451 |
} |
452 |
|
|
452 |
|
|
453 | 453 |
|
454 | 454 |
protected String getDesignationType(TypeDesignationStatusBase<?> status) { |
455 | 455 |
if (status == null){ |
... | ... | |
469 | 469 |
return result; |
470 | 470 |
} |
471 | 471 |
} |
472 |
|
|
473 |
|
|
472 |
|
|
473 |
|
|
474 | 474 |
protected void addKnownField(String string, String uri) throws URISyntaxException { |
475 | 475 |
this.knownFields.put(string, new URI(uri)); |
476 | 476 |
} |
477 |
|
|
477 |
|
|
478 | 478 |
protected void addKnownField(TermUri term) throws URISyntaxException { |
479 | 479 |
this.knownTermFields.add(term); |
480 | 480 |
} |
cdmlib-remote-webapp/src/main/webapp/WEB-INF/json-views.xml | ||
---|---|---|
29 | 29 |
<property name="jsonConfig" ref="nameCatalogueJsonConfig" /> |
30 | 30 |
</bean> |
31 | 31 |
|
32 |
<bean name="**/csv/* **/export" class="eu.etaxonomy.cdm.remote.view.JsonView"> |
|
33 |
<property name="jsonConfig" ref="nameCatalogueJsonConfig" /> |
|
34 |
</bean> |
|
35 |
|
|
32 | 36 |
<!-- portal service --> |
33 | 37 |
<bean name="**/portal/* **/portal/**/*" class="eu.etaxonomy.cdm.remote.view.JsonView"> |
34 | 38 |
<property name="jsonConfig" ref="jsonConfigPortal" /> |
cdmlib-remote-webapp/src/main/webapp/WEB-INF/xml-views.xml | ||
---|---|---|
51 | 51 |
<property name="jsonConfig" ref="nameCatalogueJsonConfig" /> |
52 | 52 |
<property name="dataSourceProperties" ref="dataSourceProperties" /> |
53 | 53 |
</bean> |
54 |
|
|
55 |
<bean name="**/csv/* **/export" class="eu.etaxonomy.cdm.remote.view.JsonView"> |
|
56 |
<property name="type" value="XML" /> |
|
57 |
<property name="jsonConfig" ref="nameCatalogueJsonConfig" /> |
|
58 |
<property name="dataSourceProperties" ref="dataSourceProperties" /> |
|
59 |
</bean> |
Also available in: Unified diff
redlist WS export added .json and .xml functionality