Revision 9c97664e
Added by Andreas Kohlbecker over 8 years ago
| src/main/java/org/bgbm/biovel/drf/checklist/EEA_BDC_Client.java | ||
|---|---|---|
| 165 | 165 |
|
| 166 | 166 |
// TaxonName |
| 167 | 167 |
taxonName.setFullName(queryClient.objectAsString(taxonR, RdfSchema.RDFS, "label")); |
| 168 |
NameParser ecatParser = new NameParser(); |
|
| 169 |
String nameCanonical = ecatParser.parseToCanonical(taxonName.getFullName()); |
|
| 170 |
taxonName.setCanonicalName(nameCanonical); |
|
| 168 |
// TODO rename CanonicalName to scientificName? compare with dwc:scientificName |
|
| 169 |
taxonName.setCanonicalName(queryClient.objectAsString(taxonR, RdfSchema.EUNIS_SPECIES, "binominalName")); |
|
| 171 | 170 |
taxonName.setRank(queryClient.objectAsString(taxonR, RdfSchema.EUNIS_SPECIES, "taxonomicRank")); |
| 172 | 171 |
|
| 173 | 172 |
// Taxon |
| ... | ... | |
| 394 | 393 |
|
| 395 | 394 |
logger.debug("processing " + (isAccepted ? "accepted taxon" : "synonym or other") + " " + taxonR.getURI());
|
| 396 | 395 |
|
| 397 |
// TODO: is this possible with this service? |
|
| 398 |
// tnrResponse.setMatchingNameString(record.getScientificname()); |
|
| 399 | 396 |
|
| 400 | 397 |
// case when accepted name |
| 401 | 398 |
if(isAccepted) {
|
| 402 | 399 |
Taxon taxon = generateTaxon(model, taxonR); |
| 403 | 400 |
tnrResponse.setTaxon(taxon); |
| 404 | 401 |
tnrResponse.setMatchingNameType(NameType.TAXON); |
| 402 |
tnrResponse.setMatchingNameString(taxon.getTaxonName().getCanonicalName()); |
|
| 405 | 403 |
|
| 406 | 404 |
} else {
|
| 407 | 405 |
// case when synonym |
| ... | ... | |
| 414 | 412 |
logger.error("No accepted taxon found for " + synonymR.getURI());
|
| 415 | 413 |
} |
| 416 | 414 |
tnrResponse.setMatchingNameType(NameType.SYNONYM); |
| 417 |
// TODO find accepted it is linked via eunisPrimaryName and (synonymFor)
|
|
| 415 |
tnrResponse.setMatchingNameString(queryClient.objectAsString(synonymR, RdfSchema.EUNIS_SPECIES, "binomialName"));
|
|
| 418 | 416 |
} |
| 419 | 417 |
|
| 420 | 418 |
if(request.isAddSynonymy()) {
|
| src/main/java/org/bgbm/biovel/drf/query/SparqlClient.java | ||
|---|---|---|
| 294 | 294 |
try {
|
| 295 | 295 |
boolean hasNoPropertiesInGraph = !_subject.listProperties().hasNext(); |
| 296 | 296 |
if(_subject.isURIResource() && hasNoPropertiesInGraph ) {
|
| 297 |
// FIXME the same uri resource is loaded multiple times |
|
| 298 |
// create an in memory model as cache for the models loaded |
|
| 299 |
// in the getFromUri() method |
|
| 300 |
// so that all resources loaded are put into that model |
|
| 301 |
// clean up the cache when it reaches a specific size |
|
| 297 | 302 |
logger.debug("loading UriResource " + _subject.getURI());
|
| 298 | 303 |
_subject = getFromUri(_subject.getURI()); |
| 299 | 304 |
} |
| src/main/java/org/bgbm/biovel/drf/utils/TnrMsgUtils.java | ||
|---|---|---|
| 31 | 31 |
import org.bgbm.biovel.drf.tnr.msg.Query; |
| 32 | 32 |
import org.bgbm.biovel.drf.tnr.msg.Query.ClientStatus; |
| 33 | 33 |
import org.bgbm.biovel.drf.tnr.msg.Query.Request; |
| 34 |
import org.bgbm.biovel.drf.tnr.msg.TaxonName; |
|
| 35 |
import org.bgbm.biovel.drf.tnr.msg.TnrMsg; |
|
| 36 | 34 |
import org.bgbm.biovel.drf.tnr.msg.Response; |
| 35 |
import org.bgbm.biovel.drf.tnr.msg.TnrMsg; |
|
| 37 | 36 |
import org.w3c.dom.Document; |
| 38 | 37 |
import org.w3c.dom.Node; |
| 39 | 38 |
import org.xml.sax.SAXException; |
| ... | ... | |
| 266 | 265 |
return null; |
| 267 | 266 |
} |
| 268 | 267 |
|
| 268 |
public static TnrMsg createRequest(SearchMode searchMode, String queryString, boolean addSynonymy) {
|
|
| 269 |
TnrMsg msg = new TnrMsg(); |
|
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Query q = new Query(); |
|
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Request r = new Request(); |
|
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r.setQueryString(queryString); |
|
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r.setSearchMode(searchMode.name()); |
|
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r.setAddSynonymy(addSynonymy); |
|
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q.setRequest(r); |
|
| 276 |
msg.getQuery().add(q); |
|
| 277 |
return msg; |
|
| 278 |
} |
|
| 269 | 279 |
|
| 270 | 280 |
|
| 271 | 281 |
|
| src/test/java/org/bgbm/biovel/drf/checklist/EEA_BDC_ClientTest.java | ||
|---|---|---|
| 1 | 1 |
package org.bgbm.biovel.drf.checklist; |
| 2 | 2 |
|
| 3 |
import java.util.Iterator;
|
|
| 4 |
import java.util.List;
|
|
| 3 |
import static org.junit.Assert.assertEquals;
|
|
| 4 |
import static org.junit.Assert.assertTrue;
|
|
| 5 | 5 |
|
| 6 | 6 |
import org.bgbm.biovel.drf.input.DRFCSVInputParser; |
| 7 |
import org.bgbm.biovel.drf.tnr.msg.Response; |
|
| 7 | 8 |
import org.bgbm.biovel.drf.tnr.msg.TnrMsg; |
| 8 |
import org.bgbm.biovel.drf.utils.BiovelUtils; |
|
| 9 | 9 |
import org.bgbm.biovel.drf.utils.TnrMsgException; |
| 10 | 10 |
import org.bgbm.biovel.drf.utils.TnrMsgUtils; |
| 11 | 11 |
import org.junit.BeforeClass; |
| ... | ... | |
| 14 | 14 |
public class EEA_BDC_ClientTest {
|
| 15 | 15 |
|
| 16 | 16 |
private static DRFCSVInputParser parser; |
| 17 |
static EEA_BDC_Client client; |
|
| 17 | 18 |
|
| 18 | 19 |
@BeforeClass |
| 19 | 20 |
public static void setup() {
|
| 20 |
parser = new DRFCSVInputParser(); |
|
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client = new EEA_BDC_Client(); |
|
| 22 |
client.setChecklistInfo(client.buildServiceProviderInfo()); |
|
| 21 | 23 |
} |
| 22 | 24 |
|
| 23 | 25 |
@Test |
| 24 |
public void scientificNameExactTest() throws DRFChecklistException, TnrMsgException {
|
|
| 25 |
parser = new DRFCSVInputParser(); |
|
| 26 |
|
|
| 27 |
List<TnrMsg> tnrMsgs = parser.parse(BiovelUtils.getResourceAsString("/org/bgbm/biovel/drf/tnr/eunis-scientificNameExact.csv","UTF-8"));
|
|
| 26 |
public void scientificNameExact_Synonym_Test() throws DRFChecklistException, TnrMsgException {
|
|
| 28 | 27 |
|
| 29 |
EEA_BDC_Client client = new EEA_BDC_Client(); |
|
| 30 |
client.setChecklistInfo(client.buildServiceProviderInfo()); |
|
| 31 |
|
|
| 32 |
Iterator<TnrMsg> tnrMsgItr = tnrMsgs.iterator(); |
|
| 33 |
while(tnrMsgItr.hasNext()) {
|
|
| 34 |
TnrMsg tnrMsg = tnrMsgItr.next(); |
|
| 35 |
TnrMsgUtils.updateWithSearchMode(tnrMsg, SearchMode.scientificNameExact); |
|
| 36 |
client.queryChecklist(tnrMsg); |
|
| 37 |
String outputXML = TnrMsgUtils.convertTnrMsgToXML(tnrMsg); |
|
| 38 |
System.out.println(outputXML); |
|
| 39 |
} |
|
| 28 |
TnrMsg tnrMsg = TnrMsgUtils.createRequest(SearchMode.scientificNameExact, "Canis dalmatinus", false); |
|
| 29 |
client.queryChecklist(tnrMsg); |
|
| 30 |
String outputXML = TnrMsgUtils.convertTnrMsgToXML(tnrMsg); |
|
| 31 |
System.out.println(outputXML); |
|
| 32 |
assertEquals(1, tnrMsg.getQuery().get(0).getResponse().size()); |
|
| 33 |
Response response = tnrMsg.getQuery().get(0).getResponse().get(0); |
|
| 34 |
assertEquals("Canis dalmatinus", response.getMatchingNameString());
|
|
| 35 |
assertEquals("Canis aureus", response.getTaxon().getTaxonName().getCanonicalName());
|
|
| 40 | 36 |
} |
| 41 | 37 |
|
| 42 | 38 |
@Test |
| 43 |
public void scientificNameLikeTest() throws DRFChecklistException, TnrMsgException {
|
|
| 44 |
parser = new DRFCSVInputParser(); |
|
| 39 |
public void scientificNameExact_Accepted_Test() throws DRFChecklistException, TnrMsgException {
|
|
| 45 | 40 |
|
| 46 |
List<TnrMsg> tnrMsgs = parser.parse(BiovelUtils.getResourceAsString("/org/bgbm/biovel/drf/tnr/eunis-scientificNameLike.csv","UTF-8"));
|
|
| 41 |
TnrMsg tnrMsg = TnrMsgUtils.createRequest(SearchMode.scientificNameExact, "Canis lupus", true); |
|
| 42 |
client.queryChecklist(tnrMsg); |
|
| 43 |
String outputXML = TnrMsgUtils.convertTnrMsgToXML(tnrMsg); |
|
| 44 |
System.out.println(outputXML); |
|
| 45 |
assertEquals(1, tnrMsg.getQuery().get(0).getResponse().size()); |
|
| 46 |
Response response = tnrMsg.getQuery().get(0).getResponse().get(0); |
|
| 47 |
assertEquals("Canis lupus", response.getMatchingNameString());
|
|
| 48 |
assertEquals("Canis lupus", response.getTaxon().getTaxonName().getCanonicalName());
|
|
| 49 |
assertTrue(response.getSynonym().size() > 0); |
|
| 50 |
} |
|
| 47 | 51 |
|
| 48 |
EEA_BDC_Client client = new EEA_BDC_Client(); |
|
| 49 |
client.setChecklistInfo(client.buildServiceProviderInfo()); |
|
| 52 |
@Test |
|
| 53 |
public void scientificNameLikeTest_1() throws DRFChecklistException, TnrMsgException {
|
|
| 54 |
TnrMsg tnrMsg = TnrMsgUtils.createRequest(SearchMode.scientificNameExact, "Cani", false); |
|
| 55 |
client.queryChecklist(tnrMsg); |
|
| 56 |
String outputXML = TnrMsgUtils.convertTnrMsgToXML(tnrMsg); |
|
| 57 |
System.out.println(outputXML); |
|
| 58 |
assertTrue(tnrMsg.getQuery().get(0).getResponse().size() > 1); |
|
| 59 |
} |
|
| 50 | 60 |
|
| 51 |
Iterator<TnrMsg> tnrMsgItr = tnrMsgs.iterator(); |
|
| 52 |
while(tnrMsgItr.hasNext()) {
|
|
| 53 |
TnrMsg tnrMsg = tnrMsgItr.next(); |
|
| 54 |
TnrMsgUtils.updateWithSearchMode(tnrMsg, SearchMode.scientificNameLike); |
|
| 55 |
client.queryChecklist(tnrMsg); |
|
| 56 |
String outputXML = TnrMsgUtils.convertTnrMsgToXML(tnrMsg); |
|
| 57 |
System.out.println(outputXML); |
|
| 58 |
} |
|
| 61 |
@Test |
|
| 62 |
public void scientificNameLikeTest_2() throws DRFChecklistException, TnrMsgException {
|
|
| 63 |
TnrMsg tnrMsg = TnrMsgUtils.createRequest(SearchMode.scientificNameExact, "Abies par", false); |
|
| 64 |
client.queryChecklist(tnrMsg); |
|
| 65 |
String outputXML = TnrMsgUtils.convertTnrMsgToXML(tnrMsg); |
|
| 66 |
System.out.println(outputXML); |
|
| 67 |
assertTrue(tnrMsg.getQuery().get(0).getResponse().size() > 1); |
|
| 59 | 68 |
} |
| 60 | 69 |
} |
| 61 | 70 |
|
| src/test/resources/org/bgbm/biovel/drf/tnr/eunis-scientificNameExact.csv | ||
|---|---|---|
| 1 |
taxonName |
|
| 2 |
Canis lupus |
|
| 3 |
Abies pardei |
|
| 4 |
|
|
| src/test/resources/org/bgbm/biovel/drf/tnr/eunis-scientificNameLike.csv | ||
|---|---|---|
| 1 |
taxonName |
|
| 2 |
Abies par |
|
| 3 |
Cani |
|
Also available in: Unified diff
tests with more detailed expectations