Revision deeccd97
Added by Andreas Kohlbecker over 8 years ago
| src/main/java/org/cybertaxonomy/utis/checklist/EEA_BDC_Client.java | ||
|---|---|---|
| 303 | 303 |
.toList(); |
| 304 | 304 |
for(Vertex tv : titleVs) {
|
| 305 | 305 |
Source source = new Source(); |
| 306 |
logger.error(tv.toString());
|
|
| 306 |
logger.debug(tv.toString());
|
|
| 307 | 307 |
source.setName(tv.getProperty(GraphSail.VALUE).toString()); |
| 308 | 308 |
taxonBase.getSources().add(source); |
| 309 | 309 |
} |
| ... | ... | |
| 337 | 337 |
.inE(RdfSchema.EUNIS_SPECIES.property("eunisPrimaryName")).outV().dedup()
|
| 338 | 338 |
.toList(); |
| 339 | 339 |
for(Vertex synonymV : synonymVs) {
|
| 340 |
String typeUri = queryClient.relatedVertexValue(synonymV, RdfSchema.RDF, "type");
|
|
| 341 |
String status = null;
|
|
| 342 |
try {
|
|
| 343 |
status = URI.create(typeUri).getFragment();
|
|
| 344 |
} catch (Exception e) {
|
|
| 340 |
// http://www.w3.org/1999/02/22-rdf-syntax-ns#type is used inconsistently, accepted taxa can have type SpeciesSynonym
|
|
| 341 |
// and are their own synonym in this case !
|
|
| 342 |
// using http://eunis.eea.europa.eu/rdf/species-schema.rdf#taxonomicRank is the recommended way to detect synonyms and to avoid
|
|
| 343 |
// adding the accepted taxon as its own synonym
|
|
| 344 |
String taxonomicRank = queryClient.relatedVertexValue(synonymV, RdfSchema.EUNIS_SPECIES, "taxonomicRank");
|
|
| 345 | 345 |
|
| 346 |
} |
|
| 347 | 346 |
|
| 348 |
if (status != null && status.equals("SpeciesSynonym")) {
|
|
| 347 |
if (taxonomicRank != null && taxonomicRank.equals("Synonym")) {
|
|
| 349 | 348 |
|
| 350 | 349 |
Synonym synonym = new Synonym(); |
| 351 | 350 |
|
| 352 | 351 |
TaxonName taxonName = createTaxonName(synonymV); |
| 353 |
synonym.setTaxonomicStatus(status); |
|
| 352 |
synonym.setTaxonomicStatus(taxonomicRank); |
|
| 353 |
synonym.setUrl(synonymV.getProperty(GraphSail.VALUE).toString()); |
|
| 354 | 354 |
synonym.setTaxonName(taxonName); |
| 355 | 355 |
synonym.setAccordingTo(queryClient.relatedVertexValue(synonymV, RdfSchema.DWC, "nameAccordingToID")); |
| 356 | 356 |
|
| src/main/java/org/cybertaxonomy/utis/query/TinkerPopClient.java | ||
|---|---|---|
| 59 | 59 |
*/ |
| 60 | 60 |
public class TinkerPopClient implements IQueryClient {
|
| 61 | 61 |
|
| 62 |
protected Logger logger = LoggerFactory.getLogger(TinkerPopClient.class); |
|
| 62 |
protected static final Logger logger = LoggerFactory.getLogger(TinkerPopClient.class);
|
|
| 63 | 63 |
|
| 64 | 64 |
private Neo4jStore graphStore = null; |
| 65 | 65 |
|
| src/test/java/org/cybertaxonomy/utis/checklist/EEA_BDC_ClientTest.java | ||
|---|---|---|
| 6 | 6 |
import org.cybertaxonomy.utis.tnr.msg.Classification; |
| 7 | 7 |
import org.cybertaxonomy.utis.tnr.msg.NameType; |
| 8 | 8 |
import org.cybertaxonomy.utis.tnr.msg.Response; |
| 9 |
import org.cybertaxonomy.utis.tnr.msg.Synonym; |
|
| 9 | 10 |
import org.cybertaxonomy.utis.tnr.msg.TnrMsg; |
| 10 | 11 |
import org.cybertaxonomy.utis.utils.TnrMsgException; |
| 11 | 12 |
import org.cybertaxonomy.utis.utils.TnrMsgUtils; |
| 12 | 13 |
import org.junit.BeforeClass; |
| 13 | 14 |
import org.junit.Test; |
| 15 |
import org.slf4j.Logger; |
|
| 16 |
import org.slf4j.LoggerFactory; |
|
| 14 | 17 |
|
| 15 | 18 |
public class EEA_BDC_ClientTest {
|
| 16 | 19 |
|
| 20 |
protected static final Logger logger = LoggerFactory.getLogger(EEA_BDC_ClientTest.class); |
|
| 21 |
|
|
| 17 | 22 |
static EEA_BDC_Client client; |
| 18 | 23 |
|
| 19 | 24 |
@BeforeClass |
| ... | ... | |
| 48 | 53 |
Response response = tnrMsg.getQuery().get(0).getResponse().get(0); |
| 49 | 54 |
assertEquals("Canis aureus", response.getMatchingNameString());
|
| 50 | 55 |
assertEquals("Canis aureus", response.getTaxon().getTaxonName().getCanonicalName());
|
| 56 |
logger.info("Accepted: " + response.getTaxon().getTaxonName().getFullName() + " (" + response.getTaxon().getUrl() + ")");
|
|
| 51 | 57 |
assertTrue(response.getSynonym().size() > 0); |
| 58 |
for(Synonym syn : response.getSynonym()) {
|
|
| 59 |
logger.info("Synonym: " + syn.getTaxonName().getFullName() + " (" + syn.getUrl() + ")");
|
|
| 60 |
} |
|
| 52 | 61 |
Classification c = response.getTaxon().getClassification(); |
| 53 | 62 |
assertEquals("Canidae", c.getFamily());
|
| 54 | 63 |
assertEquals("Carnivora", c.getOrder());
|
| ... | ... | |
| 56 | 65 |
assertEquals("Animalia", c.getKingdom());
|
| 57 | 66 |
} |
| 58 | 67 |
|
| 68 |
@Test |
|
| 69 |
public void scientificNameExact_withSynonym_Test() throws DRFChecklistException, TnrMsgException {
|
|
| 70 |
|
|
| 71 |
TnrMsg tnrMsg = TnrMsgUtils.createRequest(SearchMode.scientificNameExact, "Prinobius myardi", true); |
|
| 72 |
client.queryChecklist(tnrMsg); |
|
| 73 |
String outputXML = TnrMsgUtils.convertTnrMsgToXML(tnrMsg); |
|
| 74 |
System.out.println(outputXML); |
|
| 75 |
assertEquals(1, tnrMsg.getQuery().get(0).getResponse().size()); |
|
| 76 |
Response response = tnrMsg.getQuery().get(0).getResponse().get(0); |
|
| 77 |
assertEquals("Prinobius myardi", response.getMatchingNameString());
|
|
| 78 |
assertEquals("Prinobius myardi", response.getTaxon().getTaxonName().getCanonicalName());
|
|
| 79 |
assertTrue(response.getSynonym().size() > 0); |
|
| 80 |
boolean prionus_germari_found = false; |
|
| 81 |
for(Synonym syn : response.getSynonym()) {
|
|
| 82 |
logger.info(syn.getTaxonName().getFullName()); |
|
| 83 |
if(syn.getTaxonName().getCanonicalName().equals("Prionus germari")) {
|
|
| 84 |
prionus_germari_found = true; |
|
| 85 |
} |
|
| 86 |
} |
|
| 87 |
assertTrue(prionus_germari_found); |
|
| 88 |
Classification c = response.getTaxon().getClassification(); |
|
| 89 |
} |
|
| 90 |
|
|
| 59 | 91 |
@Test |
| 60 | 92 |
public void genus_Test() throws DRFChecklistException, TnrMsgException {
|
| 61 | 93 |
|
Also available in: Unified diff
better detection of synonyms to avoid adding the accepted taxon as its own synonym