Revision 0a1bd040
Added by Andreas Müller over 4 years ago
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/PesiFindIdenticalNamesActivator.java | ||
---|---|---|
28 | 28 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
29 | 29 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
30 | 30 |
import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController; |
31 |
import eu.etaxonomy.cdm.io.pesi.merging.PesiMergeObject; |
|
32 | 31 |
import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer; |
33 | 32 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
34 | 33 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
... | ... | |
47 | 46 |
private static final Logger logger = Logger.getLogger(PesiFindIdenticalNamesActivator.class); |
48 | 47 |
|
49 | 48 |
//static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.localH2(); |
50 |
// static final ICdmDataSource pesiSource = CdmDestinations.cdm_test_local_faunaEu_mysql(); |
|
51 | 49 |
static final ICdmDataSource pesiSource = CdmDestinations.cdm_pesi2019_final(); |
52 | 50 |
|
53 | 51 |
static final String path = System.getProperty("user.home")+File.separator+".cdmLibrary"+File.separator+"pesi"+File.separator+"pesimerge"; |
54 | 52 |
|
55 |
private static UUID faunaEuSourceUuid = PesiTransformer.uuidSourceRefFaunaEuropaea;
|
|
53 |
private static UUID emSourceUuid = PesiTransformer.uuidSourceRefEuroMed;
|
|
56 | 54 |
private static UUID ermsSourceUuid = PesiTransformer.uuidSourceRefErms; |
55 |
private static UUID faunaEuSourceUuid = PesiTransformer.uuidSourceRefFaunaEuropaea; |
|
57 | 56 |
private static UUID ifSourceUuid = PesiTransformer.uuidSourceRefIndexFungorum; |
58 |
private static UUID emSourceUuid = PesiTransformer.uuidSourceRefEuroMed; |
|
59 | 57 |
private static List<UUID> sourceRefUuids = new ArrayList<>(); |
60 |
private static Map<UUID,String> sources = new HashMap<>(); |
|
58 |
private static Map<UUID,String> sourcesLabels = new HashMap<>();
|
|
61 | 59 |
|
62 | 60 |
static { |
63 | 61 |
sourceRefUuids.addAll(Arrays.asList(new UUID[]{emSourceUuid, ermsSourceUuid, faunaEuSourceUuid, ifSourceUuid})); |
64 |
sources.put(emSourceUuid, "E+M"); |
|
65 |
sources.put(ermsSourceUuid, "ERMS"); |
|
66 |
sources.put(faunaEuSourceUuid, "FauEu"); |
|
67 |
sources.put(ifSourceUuid, "IF"); |
|
62 |
sourcesLabels.put(emSourceUuid, "E+M");
|
|
63 |
sourcesLabels.put(ermsSourceUuid, "ERMS");
|
|
64 |
sourcesLabels.put(faunaEuSourceUuid, "FauEu");
|
|
65 |
sourcesLabels.put(ifSourceUuid, "IF");
|
|
68 | 66 |
} |
69 | 67 |
|
70 | 68 |
private void invoke(ICdmDataSource source){ |
... | ... | |
96 | 94 |
return; |
97 | 95 |
} |
98 | 96 |
System.out.println("Start creating merging objects"); |
99 |
List<Map<UUID, PesiMergeObject>> mergingObjects = createMergeObjects(namesOfIdenticalTaxa, app);
|
|
97 |
List<Map<UUID, List<PesiMergeObject>>> mergingObjects = createMergeObjects(namesOfIdenticalTaxa, app);
|
|
100 | 98 |
app.commitTransaction(tx); |
101 | 99 |
|
102 | 100 |
boolean resultOK = true; |
103 | 101 |
System.out.println("Start creating csv files"); |
104 |
resultOK &= writeSameNamesDifferentAuthorToCsv(mergingObjects, sources, path + "_authors.csv");
|
|
105 |
resultOK &= writeSameNamesDifferentStatusToCsv(mergingObjects, sources, path + "_status.csv");
|
|
106 |
resultOK &= writeSameNamesToCsvFile(mergingObjects, sources, path + "_names.csv");
|
|
107 |
resultOK &= writeSameNamesDifferentPhylumToCsv(mergingObjects, sources, path + "_phylum.csv");
|
|
108 |
resultOK &= writeSameNamesDifferentParentToCsv(mergingObjects, sources, path + "_parent.csv");
|
|
109 |
resultOK &= writeSameNamesDifferentRankToCsv(mergingObjects, sources, path + "_rank.csv");
|
|
102 |
resultOK &= writeSameNamesToCsvFile(mergingObjects, path + "_namesAll.csv");
|
|
103 |
resultOK &= writeSameNamesDifferentAuthorToCsv(mergingObjects, path + "_authors.csv");
|
|
104 |
resultOK &= writeSameNamesDifferentStatusToCsv(mergingObjects, path + "_status.csv");
|
|
105 |
resultOK &= writeSameNamesDifferentPhylumToCsv(mergingObjects, path + "_phylum.csv"); |
|
106 |
resultOK &= writeSameNamesDifferentParentToCsv(mergingObjects, path + "_parent.csv"); |
|
107 |
resultOK &= writeSameNamesDifferentRankToCsv(mergingObjects, path + "_rank.csv"); |
|
110 | 108 |
|
111 | 109 |
System.out.println("End find identical names for PESI: " + resultOK + ". Results written to " + path); |
112 | 110 |
} |
113 | 111 |
|
114 | 112 |
private boolean writeSameNamesToCsvFile( |
115 |
List<Map<UUID, PesiMergeObject>> mergingObjects, Map<UUID,String> sources, String sFileName) {
|
|
113 |
List<Map<UUID,List<PesiMergeObject>>> mergingObjects, String sFileName) {
|
|
116 | 114 |
|
117 | 115 |
String header = "same names (all)"; |
118 | 116 |
String methodName = null; |
119 |
return writeDifference(header, methodName, mergingObjects, sources, sFileName);
|
|
117 |
return writeDifference(header, methodName, mergingObjects, sFileName); |
|
120 | 118 |
} |
121 | 119 |
|
122 | 120 |
private boolean writeSameNamesDifferentPhylumToCsv( |
123 |
List<Map<UUID, PesiMergeObject>> mergingObjects, Map<UUID,String> sources, String sFileName){
|
|
121 |
List<Map<UUID,List<PesiMergeObject>>> mergingObjects, String sFileName){
|
|
124 | 122 |
|
125 | 123 |
String header = "same names but different phylum"; |
126 | 124 |
String methodName = "getPhylum"; |
127 |
return writeDifference(header, methodName, mergingObjects, sources, sFileName);
|
|
125 |
return writeDifference(header, methodName, mergingObjects, sFileName); |
|
128 | 126 |
} |
129 | 127 |
|
130 | 128 |
private boolean writeSameNamesDifferentParentToCsv( |
131 |
List<Map<UUID, PesiMergeObject>> mergingObjects, Map<UUID,String> sources, String sFileName){
|
|
129 |
List<Map<UUID,List<PesiMergeObject>>> mergingObjects, String sFileName){
|
|
132 | 130 |
|
133 | 131 |
String header = "same names but different parent"; |
134 | 132 |
String methodName = "getParentString"; |
135 |
return writeDifference(header, methodName, mergingObjects, sources, sFileName);
|
|
133 |
return writeDifference(header, methodName, mergingObjects, sFileName); |
|
136 | 134 |
} |
137 | 135 |
|
138 | 136 |
private boolean writeSameNamesDifferentRankToCsv( |
139 |
List<Map<UUID, PesiMergeObject>> mergingObjects, Map<UUID,String> sources, String sFileName){
|
|
137 |
List<Map<UUID,List<PesiMergeObject>>> mergingObjects, String sFileName){
|
|
140 | 138 |
|
141 | 139 |
String header = "same names but different rank"; |
142 | 140 |
String methodName = "getRank"; |
143 |
return writeDifference(header, methodName, mergingObjects, sources, sFileName);
|
|
141 |
return writeDifference(header, methodName, mergingObjects, sFileName); |
|
144 | 142 |
} |
145 | 143 |
|
146 | 144 |
private boolean writeSameNamesDifferentStatusToCsv( |
147 |
List<Map<UUID, PesiMergeObject>> mergingObjects, Map<UUID,String> sources, String sFileName){
|
|
145 |
List<Map<UUID,List<PesiMergeObject>>> mergingObjects, String sFileName){
|
|
148 | 146 |
|
149 | 147 |
String header = "same names but different status"; |
150 | 148 |
String methodName = "isStatus"; |
151 |
return writeDifference(header, methodName, mergingObjects, sources, sFileName);
|
|
149 |
return writeDifference(header, methodName, mergingObjects, sFileName); |
|
152 | 150 |
} |
153 | 151 |
|
154 | 152 |
private boolean writeSameNamesDifferentAuthorToCsv( |
155 |
List<Map<UUID, PesiMergeObject>> mergingObjects, Map<UUID,String> sources, String sFileName){
|
|
153 |
List<Map<UUID,List<PesiMergeObject>>> mergingObjects, String sFileName){
|
|
156 | 154 |
|
157 | 155 |
String header = "same names but different author"; |
158 | 156 |
String methodName = "getAuthor"; |
159 |
return writeDifference(header, methodName, mergingObjects, sources, sFileName);
|
|
157 |
return writeDifference(header, methodName, mergingObjects, sFileName); |
|
160 | 158 |
} |
161 | 159 |
|
162 |
private boolean writeDifference(String header, String methodName, |
|
163 |
List<Map<UUID, PesiMergeObject>> mergingObjects, Map<UUID,String> sources, String sFileName) { |
|
160 |
private boolean writeDifference(String header, |
|
161 |
String methodName, |
|
162 |
List<Map<UUID,List<PesiMergeObject>>> mergingObjects, |
|
163 |
String sFileName) { |
|
164 | 164 |
|
165 | 165 |
try{ |
166 | 166 |
Method method = methodName == null? null : PesiMergeObject.class.getMethod(methodName); |
167 | 167 |
|
168 |
// FileWriter writer = new FileWriter(sFileName); |
|
169 | 168 |
Writer writer = new OutputStreamWriter(new FileOutputStream(new File(sFileName)), StandardCharsets.UTF_8); |
170 | 169 |
|
171 | 170 |
//create Header |
172 | 171 |
createHeader(writer, header); |
173 | 172 |
|
174 | 173 |
//write data |
175 |
for (Map<UUID, PesiMergeObject> merging : mergingObjects){ |
|
176 |
if (isDifferent(merging, method)){ |
|
177 |
writeCsvLine(writer, merging, sources) ; |
|
174 |
for (Map<UUID,List<PesiMergeObject>> merging : mergingObjects){ |
|
175 |
boolean isNextNameCache = true; |
|
176 |
List<UUID> mySources = new ArrayList<>(merging.keySet()); |
|
177 |
for (int i = 0; i<mySources.size()-1; i++){ |
|
178 |
for (int j = i+1; j<mySources.size(); j++){ |
|
179 |
boolean differenceExists = false; |
|
180 |
List<PesiMergeObject> mergeList1 = merging.get(mySources.get(i)); |
|
181 |
List<PesiMergeObject> mergeList2 = merging.get(mySources.get(j)); |
|
182 |
for (PesiMergeObject merge1 : mergeList1){ |
|
183 |
for (PesiMergeObject merge2 : mergeList2){ |
|
184 |
differenceExists |= isDifferent(merge1, merge2, method); |
|
185 |
} |
|
186 |
} |
|
187 |
if (differenceExists){ |
|
188 |
for (PesiMergeObject merge1 : mergeList1){ |
|
189 |
for (PesiMergeObject merge2 : mergeList2){ |
|
190 |
writeCsvLine(writer, merge1, merge2, method, isNextNameCache); |
|
191 |
isNextNameCache = false; |
|
192 |
} |
|
193 |
} |
|
194 |
} |
|
195 |
} |
|
178 | 196 |
} |
179 | 197 |
} |
180 | 198 |
writer.flush(); |
181 | 199 |
writer.close(); |
182 | 200 |
return true; |
183 |
}catch(IOException | IllegalAccessException | IllegalArgumentException | InvocationTargetException | NoSuchMethodException | SecurityException e){
|
|
201 |
}catch(NoSuchMethodException | SecurityException | IOException e){
|
|
184 | 202 |
logger.error(e.getMessage()); |
185 | 203 |
return false; |
186 | 204 |
} |
187 | 205 |
} |
188 | 206 |
|
207 |
private boolean isDifferent(PesiMergeObject merge1, PesiMergeObject merge2, Method method){ |
|
208 |
|
|
209 |
try { |
|
210 |
if (method == null){ |
|
211 |
return true; |
|
212 |
} |
|
213 |
Object value1 = method.invoke(merge1); |
|
214 |
Object value2 = method.invoke(merge2); |
|
215 |
return !CdmUtils.nullSafeEqual(value1, value2); |
|
216 |
} catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) { |
|
217 |
e.printStackTrace(); |
|
218 |
return true; |
|
219 |
} |
|
220 |
} |
|
221 |
|
|
222 |
//old method when all sources were in 1 line |
|
189 | 223 |
private boolean isDifferent(Map<UUID, PesiMergeObject> merging, Method method) |
190 | 224 |
throws IllegalAccessException, IllegalArgumentException, InvocationTargetException { |
191 | 225 |
|
... | ... | |
208 | 242 |
return false; |
209 | 243 |
} |
210 | 244 |
|
211 |
private void createHeader(Writer writer, String firstLine) throws IOException{ |
|
212 |
writer.append(firstLine); |
|
213 |
writer.append('\n'); |
|
214 |
|
|
215 |
for (int i=1; i<=2; i++){ |
|
216 |
writer.append("source"+i); |
|
217 |
writer.append(';'); |
|
218 |
writer.append("name uuid"+i); |
|
219 |
writer.append(';'); |
|
220 |
writer.append("name id"+i); |
|
221 |
writer.append(';'); |
|
222 |
writer.append("name"+i); |
|
223 |
writer.append(';'); |
|
224 |
writer.append("author"+i); |
|
225 |
writer.append(';'); |
|
226 |
writer.append("rank"+i); |
|
227 |
writer.append(';'); |
|
228 |
writer.append("status"+i); |
|
229 |
writer.append(';'); |
|
230 |
writer.append("phylum"+i); |
|
231 |
writer.append(';'); |
|
232 |
writer.append("parent"+i); |
|
233 |
writer.append(';'); |
|
234 |
writer.append("parent rank"+i); |
|
235 |
writer.append(';'); |
|
236 |
} |
|
237 |
writer.append('\n'); |
|
245 |
private void createHeader(Writer writer, String firstLine){ |
|
246 |
try { |
|
247 |
writer.append(firstLine); |
|
248 |
writer.append('\n'); |
|
249 |
writeHeaderPair(writer, "taxon uuid"); |
|
250 |
writeHeaderPair(writer, "taxon id"); |
|
251 |
writer.append("next name cache").append(";"); |
|
252 |
writer.append("diff").append(";"); |
|
253 |
writeHeaderPair(writer, "source"); |
|
254 |
writeHeaderPair(writer, "name uuid"); |
|
255 |
writeHeaderPair(writer, "idInSource"); |
|
256 |
writeHeaderPair(writer, "nameCache"); |
|
257 |
writeHeaderPair(writer, "author"); |
|
258 |
writeHeaderPair(writer, "rank"); |
|
259 |
writeHeaderPair(writer, "kingdom"); |
|
260 |
writeHeaderPair(writer, "phylum"); |
|
261 |
writeHeaderPair(writer, "family"); |
|
262 |
writeHeaderPair(writer, "parentString"); |
|
263 |
writeHeaderPair(writer, "parentRankString"); |
|
264 |
writeHeaderPair(writer, "status"); |
|
265 |
writer.append('\n'); |
|
266 |
} catch (IOException e) { |
|
267 |
e.printStackTrace(); |
|
268 |
} |
|
238 | 269 |
} |
239 | 270 |
|
240 |
private void writeCsvLine(Writer writer, Map<UUID,PesiMergeObject> mergeObjects, Map<UUID,String> sources) throws IOException{ |
|
271 |
private void writeHeaderPair(Writer writer, String header) throws IOException { |
|
272 |
writer.append(header+"1").append(';'); |
|
273 |
writer.append(header+"2").append(';'); |
|
274 |
} |
|
275 |
|
|
276 |
private void writeCsvLine(Writer writer, |
|
277 |
PesiMergeObject merge1, PesiMergeObject merge2, |
|
278 |
Method method, boolean isNextNameCache){ |
|
279 |
|
|
280 |
writePair(writer, merge1, merge2, "UuidTaxon"); |
|
281 |
writePair(writer, merge1, merge2, "IdTaxon"); |
|
282 |
writeSingleValue(writer, isNextNameCache?"1":"0"); |
|
283 |
boolean different = isDifferent(merge1, merge2, method); |
|
284 |
writeSingleValue(writer, different?"1":"0"); |
|
285 |
writeSingleValue(writer, sourcesLabels.get(UUID.fromString(merge1.getUuidSource()))); |
|
286 |
writeSingleValue(writer, sourcesLabels.get(UUID.fromString(merge2.getUuidSource()))); |
|
287 |
writePair(writer, merge1, merge2, "UuidName"); |
|
288 |
writePair(writer, merge1, merge2, "IdInSource"); |
|
289 |
writePair(writer, merge1, merge2, "NameCache"); |
|
290 |
writePair(writer, merge1, merge2, "Author"); |
|
291 |
writePair(writer, merge1, merge2, "Rank"); |
|
292 |
writePairNode(writer, merge1, merge2, "Kingdom"); |
|
293 |
writePairNode(writer, merge1, merge2, "Phylum"); |
|
294 |
writePairNode(writer, merge1, merge2, "Family"); |
|
295 |
writePair(writer, merge1, merge2, "ParentString"); |
|
296 |
writePair(writer, merge1, merge2, "ParentRankString"); |
|
297 |
writeSingleValue(writer, merge1.isStatus()?"accepted":"synonym"); |
|
298 |
writeSingleValue(writer, merge2.isStatus()?"accepted":"synonym"); |
|
299 |
try { |
|
300 |
writer.append('\n'); |
|
301 |
} catch (IOException e) { |
|
302 |
e.printStackTrace(); |
|
303 |
} |
|
304 |
} |
|
305 |
|
|
306 |
private void writeSingleValue(Writer writer, String value) { |
|
307 |
try { |
|
308 |
writer.append(value).append(";"); |
|
309 |
} catch (Exception e) { |
|
310 |
e.printStackTrace(); |
|
311 |
} |
|
312 |
} |
|
313 |
|
|
314 |
private void writePairNode(Writer writer, PesiMergeObject merge1, PesiMergeObject merge2, String methodName) { |
|
315 |
try { |
|
316 |
Method method = PesiMergeObject.class.getDeclaredMethod("get"+methodName); |
|
317 |
TaxonNodeDto value = (TaxonNodeDto) method.invoke(merge1); |
|
318 |
writer.append(value==null?"":value.getTitleCache()).append(";"); |
|
319 |
value = (TaxonNodeDto) method.invoke(merge2); |
|
320 |
writer.append(value==null?"":value.getTitleCache()).append(";"); |
|
321 |
} catch (Exception e) { |
|
322 |
e.printStackTrace(); |
|
323 |
} |
|
324 |
} |
|
325 |
|
|
326 |
private void writePair(Writer writer, PesiMergeObject merge1, PesiMergeObject merge2, String methodName) { |
|
327 |
try { |
|
328 |
Method method = PesiMergeObject.class.getDeclaredMethod("get"+methodName); |
|
329 |
String value1 = (String) method.invoke(merge1); |
|
330 |
writer.append(normalize(value1)).append(";"); |
|
331 |
String value2 = (String) method.invoke(merge2); |
|
332 |
writer.append(normalize(value2)).append(";"); |
|
333 |
} catch (Exception e) { |
|
334 |
e.printStackTrace(); |
|
335 |
} |
|
336 |
} |
|
337 |
|
|
338 |
private String normalize(String val) { |
|
339 |
return CdmUtils.Nz(val).replace(";", "@"); |
|
340 |
} |
|
341 |
|
|
342 |
private void writeCsvLine(Writer writer, Map<UUID,PesiMergeObject> mergeObjects, Map<UUID,String> sources) throws IOException{ |
|
241 | 343 |
|
242 | 344 |
for (UUID uuid : sourceRefUuids){ |
243 | 345 |
PesiMergeObject merging = mergeObjects.get(uuid); |
... | ... | |
262 | 364 |
writer.append('\n'); |
263 | 365 |
} |
264 | 366 |
|
265 |
private List<Map<UUID,PesiMergeObject>> createMergeObjects(Map<String, Map<UUID, Set<TaxonName>>> names, |
|
367 |
private List<Map<UUID,List<PesiMergeObject>>> createMergeObjects( |
|
368 |
Map<String, Map<UUID, Set<TaxonName>>> identicalNames, |
|
266 | 369 |
CdmApplicationController appCtr){ |
267 | 370 |
|
268 |
List<Map<UUID,PesiMergeObject>> merge = new ArrayList<>();
|
|
371 |
List<Map<UUID,List<PesiMergeObject>>> merge = new ArrayList<>();
|
|
269 | 372 |
|
270 |
List<String> nameCaches = new ArrayList<>(names.keySet());
|
|
373 |
List<String> nameCaches = new ArrayList<>(identicalNames.keySet());
|
|
271 | 374 |
nameCaches.sort(StringComparator.Instance); |
272 | 375 |
for (String nameCache: nameCaches){ |
273 |
createSingleMergeObject(appCtr, merge, names.get(nameCache));
|
|
376 |
createSingleMergeObject(appCtr, merge, identicalNames.get(nameCache));
|
|
274 | 377 |
} |
275 |
|
|
276 | 378 |
return merge; |
277 | 379 |
} |
278 | 380 |
|
279 |
|
|
280 |
private void createSingleMergeObject(CdmApplicationController appCtr, List<Map<UUID,PesiMergeObject>> merge,
|
|
381 |
private void createSingleMergeObject(CdmApplicationController appCtr, |
|
382 |
List<Map<UUID,List<PesiMergeObject>>> merge,
|
|
281 | 383 |
Map<UUID, Set<TaxonName>> identicalNames) { |
282 | 384 |
|
283 |
Map<UUID,PesiMergeObject> mergeMap = new HashMap<>();
|
|
385 |
Map<UUID,List<PesiMergeObject>> mergeMap = new HashMap<>();
|
|
284 | 386 |
|
285 | 387 |
for (UUID sourceUuid : identicalNames.keySet()){ |
286 | 388 |
Set<TaxonName> names = identicalNames.get(sourceUuid); |
287 |
if (names.isEmpty()){ |
|
288 |
continue; |
|
289 |
} |
|
290 |
TaxonName name = names.iterator().next(); |
|
291 |
String nameAndIdStr = name.getTitleCache() + "; id = " + name.getId(); |
|
292 |
if (names.size()>1){ |
|
293 |
logger.warn("Multiple names per source not yet handled. Take arbitrary one: " + nameAndIdStr); |
|
294 |
} |
|
295 |
|
|
296 |
PesiMergeObject mergeObject = new PesiMergeObject(); |
|
297 |
mergeMap.put(sourceUuid, mergeObject); |
|
298 |
|
|
299 |
Set<TaxonBase> taxonBases = name.getTaxonBases(); |
|
300 |
if (taxonBases.isEmpty()){ |
|
301 |
logger.warn("No taxonbase attached to name. This is not yet handled: " + nameAndIdStr); |
|
302 |
continue; |
|
303 |
} |
|
304 |
if (taxonBases.size() > 1) { |
|
305 |
//TODO: find the two correct names |
|
306 |
logger.warn("Name has not exact 1 but " + taxonBases.size() + " taxon base attached. This is not yet handled. Take arbitrary one."); |
|
307 |
} |
|
308 |
|
|
309 |
//uuid |
|
310 |
mergeObject.setUuidName(name.getUuid().toString()); |
|
389 |
List<PesiMergeObject> pmoList = new ArrayList<>(); |
|
390 |
mergeMap.put(sourceUuid, pmoList); |
|
391 |
|
|
392 |
for (TaxonName name : names){ |
|
393 |
String nameAndIdStr = name.getTitleCache() + "; id = " + name.getId(); |
|
394 |
@SuppressWarnings("rawtypes") |
|
395 |
Set<TaxonBase> taxonBases = name.getTaxonBases(); |
|
396 |
if (taxonBases.isEmpty()){ |
|
397 |
logger.warn("No taxonbase attached to name. This is not yet handled: " + nameAndIdStr); |
|
398 |
continue; |
|
399 |
} |
|
400 |
for (TaxonBase<?> taxonBase : taxonBases) { |
|
401 |
if (!taxonBase.isPublish()){ |
|
402 |
continue; |
|
403 |
} |
|
404 |
PesiMergeObject mergeObject = PesiMergeObject.NewInstance(); |
|
405 |
pmoList.add(mergeObject); |
|
311 | 406 |
|
312 |
//nameCache |
|
313 |
mergeObject.setNameCache(name.getNameCache()); |
|
407 |
//uuid |
|
408 |
mergeObject.setUuidSource(sourceUuid.toString()); |
|
409 |
mergeObject.setUuidName(name.getUuid().toString()); |
|
410 |
mergeObject.setUuidTaxon(taxonBase.getUuid().toString()); |
|
411 |
mergeObject.setIdTaxon(String.valueOf(taxonBase.getId())); |
|
314 | 412 |
|
315 |
//authorship
|
|
316 |
mergeObject.setAuthor(name.getAuthorshipCache());
|
|
413 |
//nameCache
|
|
414 |
mergeObject.setNameCache(name.getNameCache());
|
|
317 | 415 |
|
318 |
//rank
|
|
319 |
mergeObject.setRank(name.getRank().getLabel());
|
|
416 |
//authorship
|
|
417 |
mergeObject.setAuthor(name.getAuthorshipCache());
|
|
320 | 418 |
|
321 |
//Phylum |
|
322 |
TaxonNodeDto phylum = getPhylum(appCtr, name); |
|
323 |
mergeObject.setPhylum(phylum); |
|
419 |
//rank |
|
420 |
mergeObject.setRank(name.getRank().getLabel()); |
|
324 | 421 |
|
325 |
//idInSource |
|
326 |
Iterator<IdentifiableSource> sources = name.getSources().iterator(); |
|
327 |
//TODO idInSource - what if multiple sources exist? |
|
328 |
if (sources.hasNext()){ |
|
329 |
IdentifiableSource source = sources.next(); |
|
330 |
String idInSource = source.getIdInSource(); |
|
331 |
mergeObject.setIdInSource(idInSource); |
|
332 |
} |
|
422 |
//Kingdom |
|
423 |
TaxonNodeDto kingdom = getHigherTaxon(appCtr, name, Rank.KINGDOM()); |
|
424 |
mergeObject.setKingdom(kingdom); |
|
333 | 425 |
|
334 |
//status and parent |
|
335 |
Set<Taxon> taxa = name.getTaxa(); |
|
336 |
taxa = getReallyAcceptedTaxa(taxa); |
|
337 |
if (!taxa.isEmpty()){ |
|
338 |
mergeObject.setStatus(true); |
|
339 |
Iterator<Taxon> taxaIterator = taxa.iterator(); |
|
340 |
Taxon taxon = null; |
|
341 |
while (taxaIterator.hasNext()){ |
|
342 |
taxon = taxaIterator.next(); |
|
343 |
if (!taxon.isMisapplication()){ |
|
344 |
break; |
|
426 |
//Phylum/Division |
|
427 |
TaxonNodeDto phylum = getHigherTaxon(appCtr, name, Rank.PHYLUM()); |
|
428 |
if(phylum == null){ |
|
429 |
phylum = getHigherTaxon(appCtr, name, Rank.DIVISION()); |
|
345 | 430 |
} |
346 |
} |
|
347 |
@SuppressWarnings("null") |
|
348 |
Set<TaxonNode> nodes = taxon.getTaxonNodes(); |
|
349 |
Iterator<TaxonNode> taxonNodeIterator = nodes.iterator(); |
|
350 |
TaxonNode parentNode = null; |
|
351 |
while (taxonNodeIterator.hasNext()){ |
|
352 |
TaxonNode node = taxonNodeIterator.next(); |
|
353 |
if (!node.isTopmostNode()){ |
|
354 |
parentNode = node.getParent(); |
|
431 |
mergeObject.setPhylum(phylum); |
|
432 |
|
|
433 |
//Family |
|
434 |
TaxonNodeDto family = getHigherTaxon(appCtr, name, Rank.FAMILY()); |
|
435 |
mergeObject.setFamily(family); |
|
436 |
|
|
437 |
//idInSource |
|
438 |
Iterator<IdentifiableSource> sources = name.getSources().iterator(); |
|
439 |
//TODO idInSource - what if multiple sources exist? |
|
440 |
if (sources.hasNext()){ |
|
441 |
IdentifiableSource source = sources.next(); |
|
442 |
String idInSource = source.getIdInSource(); |
|
443 |
mergeObject.setIdInSource(idInSource); |
|
355 | 444 |
} |
356 |
} |
|
357 |
//TODO: ändern mit erweitertem Initializer.. |
|
358 |
if (parentNode != null){ |
|
359 |
TaxonName parentName = CdmBase.deproxy(parentNode.getTaxon().getName()); |
|
360 |
String parentNameCache = parentName.getNameCache(); |
|
361 |
mergeObject.setParentString(parentNameCache); |
|
362 |
mergeObject.setParentRankString(parentName.getRank().getLabel()); |
|
363 |
} |
|
364 |
}else{ |
|
365 |
mergeObject.setStatus(false); |
|
366 |
TaxonNode parentNode = getAcceptedNode(name); |
|
367 |
//TODO: ändern mit erweitertem Initializer.. |
|
368 |
if (parentNode != null){ |
|
369 |
TaxonName parentName = CdmBase.deproxy(parentNode.getTaxon().getName()); |
|
370 |
String parentNameCache = parentName.getNameCache(); |
|
371 |
mergeObject.setParentString(parentNameCache); |
|
372 |
mergeObject.setParentRankString(parentName.getRank().getLabel()); |
|
445 |
|
|
446 |
//status and parent |
|
447 |
makeStatusAndParent(name, mergeObject); |
|
373 | 448 |
} |
374 | 449 |
} |
375 | 450 |
} |
376 | 451 |
|
452 |
merge.add(mergeMap); |
|
453 |
|
|
377 | 454 |
|
378 | 455 |
//set parent informations |
379 | 456 |
|
... | ... | |
399 | 476 |
mergeObject.setParentStringInFaunaEu(parentName.getNameCache()); |
400 | 477 |
}*/ |
401 | 478 |
|
402 |
merge.add(mergeMap); |
|
479 |
|
|
403 | 480 |
} |
404 | 481 |
|
405 |
private TaxonNodeDto getPhylum(CdmApplicationController appCtr, TaxonName name) { |
|
406 |
TaxonNodeDto phylum = null; |
|
407 |
if (name.getRank().equals(Rank.PHYLUM())) { |
|
482 |
private void makeStatusAndParent(TaxonName name, PesiMergeObject mergeObject) { |
|
483 |
Set<Taxon> taxa = name.getTaxa(); |
|
484 |
taxa = getReallyAcceptedTaxa(taxa); |
|
485 |
if (!taxa.isEmpty()){ |
|
486 |
mergeObject.setStatus(true); |
|
487 |
Iterator<Taxon> taxaIterator = taxa.iterator(); |
|
488 |
Taxon taxon = null; |
|
489 |
while (taxaIterator.hasNext()){ |
|
490 |
taxon = taxaIterator.next(); |
|
491 |
if (!taxon.isMisapplication()){ |
|
492 |
break; |
|
493 |
} |
|
494 |
} |
|
495 |
@SuppressWarnings("null") |
|
496 |
Set<TaxonNode> nodes = taxon.getTaxonNodes(); |
|
497 |
Iterator<TaxonNode> taxonNodeIterator = nodes.iterator(); |
|
498 |
TaxonNode parentNode = null; |
|
499 |
while (taxonNodeIterator.hasNext()){ |
|
500 |
TaxonNode node = taxonNodeIterator.next(); |
|
501 |
if (!node.isTopmostNode()){ |
|
502 |
parentNode = node.getParent(); |
|
503 |
} |
|
504 |
} |
|
505 |
if (parentNode != null){ |
|
506 |
TaxonName parentName = CdmBase.deproxy(parentNode.getTaxon().getName()); |
|
507 |
String parentNameCache = parentName.getNameCache(); |
|
508 |
mergeObject.setParentString(parentNameCache); |
|
509 |
mergeObject.setParentRankString(parentName.getRank().getLabel()); |
|
510 |
} |
|
511 |
}else{ |
|
512 |
mergeObject.setStatus(false); |
|
513 |
TaxonNode parentNode = getAcceptedNode(name); |
|
514 |
if (parentNode != null){ |
|
515 |
TaxonName parentName = CdmBase.deproxy(parentNode.getTaxon().getName()); |
|
516 |
String parentNameCache = parentName.getNameCache(); |
|
517 |
mergeObject.setParentString(parentNameCache); |
|
518 |
mergeObject.setParentRankString(parentName.getRank().getLabel()); |
|
519 |
} |
|
520 |
} |
|
521 |
} |
|
522 |
|
|
523 |
private TaxonNodeDto getHigherTaxon(CdmApplicationController appCtr, TaxonName name, Rank rank) { |
|
524 |
if (name.getRank().equals(rank)) { |
|
408 | 525 |
Taxon taxon = getAcceptedTaxon(name); |
409 | 526 |
if (taxon != null) { |
527 |
if (taxon.getTaxonNodes().isEmpty()){ |
|
528 |
return null; //probably MAN |
|
529 |
} |
|
410 | 530 |
if (taxon.getTaxonNodes().size()>1){ |
411 |
logger.warn("More than 1 node not yet handled for getPhylum. Take arbitrary one.");
|
|
531 |
logger.warn("More than 1 node not yet handled for getHigherTaxon. Take arbitrary one.");
|
|
412 | 532 |
} |
413 | 533 |
TaxonNode node = taxon.getTaxonNodes().iterator().next(); |
414 |
phylum = new TaxonNodeDto(node);
|
|
534 |
return new TaxonNodeDto(node);
|
|
415 | 535 |
} |
416 |
|
|
417 | 536 |
} |
418 |
if (phylum == null && !name.getRank().isHigher(Rank.PHYLUM())){ |
|
537 |
if (name.getRank().isHigher(rank)){ |
|
538 |
return null; |
|
539 |
}else{ |
|
419 | 540 |
Taxon taxon = getAcceptedTaxon(name); |
420 |
if (!taxon.getTaxonNodes().isEmpty()){ |
|
541 |
if (taxon.getTaxonNodes().isEmpty()){ |
|
542 |
return null; |
|
543 |
}else{ |
|
421 | 544 |
if (taxon.getTaxonNodes().size()>1){ |
422 |
logger.warn("More than 1 node not yet handled for getPhylum. Take arbitrary one.");
|
|
545 |
logger.warn("More than 1 node not yet handled for getHigherTaxon. Take arbitrary one.");
|
|
423 | 546 |
} |
424 | 547 |
TaxonNode node = taxon.getTaxonNodes().iterator().next(); |
425 |
phylum = appCtr.getTaxonNodeService().taxonNodeDtoParentRank(node.getClassification(), Rank.PHYLUM(), name); |
|
548 |
List<TaxonNodeDto> higherDtos = appCtr.getTaxonNodeService().taxonNodeDtoParentRank(node.getClassification(), rank, taxon); |
|
549 |
if (higherDtos.isEmpty()){ |
|
550 |
return null; |
|
551 |
}else { |
|
552 |
if (higherDtos.size() > 1){ |
|
553 |
logger.warn("More than 1 higher dto. This is not yet implemented: " + taxon.getTitleCache()); |
|
554 |
} |
|
555 |
return higherDtos.get(0); |
|
556 |
} |
|
426 | 557 |
} |
427 | 558 |
} |
428 |
return phylum; |
|
429 | 559 |
} |
430 | 560 |
|
431 | 561 |
private TaxonNode getAcceptedNode(TaxonName ermsName) { |
Also available in: Unified diff
ref #1447 Improve FindIdenticalNames for PESI