import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;
import eu.etaxonomy.cdm.model.name.NonViralName;
import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;
import fr.lis.ikeyplus.IO.SDDSaxParser;
import fr.lis.ikeyplus.model.DataSet;
import fr.lis.ikeyplus.model.ICharacter;
pkNode = createPkNode(null, statement);
//TODO handle rank
- NonViralName<?> nonViralName = NonViralName.NewInstance(Rank.UNKNOWN_RANK());
+ NonViralName<?> nonViralName = TaxonNameBase.NewNonViralInstance(Rank.UNKNOWN_RANK());
nonViralName.setTitleCache(taxon.getName(), true);
eu.etaxonomy.cdm.model.taxon.Taxon cdmTaxon = eu.etaxonomy.cdm.model.taxon.Taxon.NewInstance(
nonViralName, null); //FIXME !!!!!!
\r
NonViralName<?> tnb = null;\r
if (!id.equals("")) {\r
- tnb = NonViralName.NewInstance(defaultRank);\r
+ tnb = TaxonNameBase.NewNonViralInstance(defaultRank);\r
IdentifiableSource source = null;\r
if (isNotBlank(uri)) {\r
//TODO type\r
private Taxon handleCDNoScope(Namespace sddNamespace,\r
SDDImportState cdmState, Element elCodedDescription ) {\r
Taxon taxon = null;\r
- NonViralName<?> nonViralName = NonViralName.NewInstance(defaultRank);\r
+ NonViralName<?> nonViralName = TaxonNameBase.NewNonViralInstance(defaultRank);\r
String id = new String("" + taxonNamesCount);\r
IdentifiableSource source = IdentifiableSource.NewDataImportInstance(id, "TaxonName");\r
importRepresentation(elCodedDescription, sddNamespace, nonViralName, id, cdmState);\r
if (nc != null){
name = nc.getNewTaxonNameInstance(rank);
}else{
- name = NonViralName.NewInstance(rank);
+ name = TaxonNameBase.NewNonViralInstance(rank);
}
if (StringUtils.isNotBlank(commonDetermination.genus)){
name.setGenusOrUninomial(commonDetermination.genus);
* @return
*/
private NonViralName<?> makeTaxonName(SpecimenCdmExcelImportState state, DeterminationLight determinationLight) {
- NonViralName<?> name = NonViralName.NewInstance(null);
+ NonViralName<?> name = TaxonNameBase.NewNonViralInstance(null);
NomenclaturalCode nc = state.getConfig().getNomenclaturalCode();
if (nc != null){
name = (NonViralName<?>)nc.getNewTaxonNameInstance(null);
import eu.etaxonomy.cdm.model.media.Media;
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
import eu.etaxonomy.cdm.model.name.NonViralName;
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;
import eu.etaxonomy.cdm.model.occurrence.Collection;
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
taxonName = parseScientificName(scientificName);
}
else{
- taxonName = NonViralName.NewInstance(null);
+ taxonName = TaxonNameBase.NewNonViralInstance(null);
taxonName.setTitleCache(scientificName, true);
}
getNameService().save(taxonName);
}
if(nomenclatureCode == null){
- taxonName = NonViralName.NewInstance(null);
+ taxonName = TaxonNameBase.NewNonViralInstance(null);
taxonName.setTitleCache(scientificName, true);
return taxonName;
}
// }
//TODO: parsing of ViralNames?
if(problem){
- taxonName = NonViralName.NewInstance(null);
+ taxonName = TaxonNameBase.NewNonViralInstance(null);
taxonName.setTitleCache(scientificName, true);
}
return taxonName;
if (nomCode != null){
nameBase = nomCode.getNewTaxonNameInstance(rank);
}else{
- nameBase = NonViralName.NewInstance(rank);
+ nameBase = TaxonNameBase.NewNonViralInstance(rank);
}
childName = "Simple";
obligatory = true;
import eu.etaxonomy.cdm.model.common.RelationshipTermBase;\r
import eu.etaxonomy.cdm.model.description.CommonTaxonName;\r
import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
-import eu.etaxonomy.cdm.model.name.NonViralName;\r
import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.model.reference.Reference;\r
import eu.etaxonomy.cdm.model.taxon.Classification;\r
\r
\r
} else{\r
- basionymName = NonViralName.NewInstance(name.getRank());\r
+ basionymName = TaxonNameBase.NewNonViralInstance(name.getRank());\r
childName = "RelatedName";\r
obligatory = true;\r
Element elName = XmlHelp.getSingleChildElement(success, elBasionym, childName, tcsNamespace, obligatory);\r
}else{\r
String title = elToTaxonConcept.getTextNormalize();\r
//TODO synonym?\r
- TaxonNameBase<?,?> taxonName = NonViralName.NewInstance(null);\r
+ TaxonNameBase<?,?> taxonName = TaxonNameBase.NewNonViralInstance(null);\r
taxonName.setTitleCache(title, true);\r
logger.warn("Free text related taxon seems to be bug in TCS");\r
if (isSynonym){\r
extends TaxonNameBase<T, INonViralNameCacheStrategy>
implements INonViralName{
- private static final long serialVersionUID = 4441110073881088033L;
-
+ private static final long serialVersionUID = -9083811681449792683L;
// ************************** CONSTRUCTORS *************/
* @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy
* @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
*/
- public static NonViralName NewInstance(Rank rank){
+ public static NonViralName NewNonViralInstance(Rank rank){
return new NonViralName(rank, null);
}
* @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy
* @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
*/
- public static NonViralName NewInstance(Rank rank, HomotypicalGroup homotypicalGroup){
+ public static NonViralName NewNonViralInstance(Rank rank, HomotypicalGroup homotypicalGroup){
return new NonViralName(rank, homotypicalGroup);
}
import eu.etaxonomy.cdm.model.common.CdmBase;
import eu.etaxonomy.cdm.model.name.NonViralName;
import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;
/**
* @author cmathew
public void testPropertyChange() {
CdmBase.setNewEntityListener(this);
- NonViralName<?> b = NonViralName.NewInstance(Rank.SPECIES());
+ NonViralName<?> b = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());
Annotation newAnnotation = Annotation.NewDefaultLanguageInstance("test");
b.addAnnotation(newAnnotation);
Assert.assertEquals(newAnnotation, lastPropValue);
/**
* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
+* European Distributed Institute of Taxonomy
* http://www.e-taxonomy.eu
-*
+*
* The contents of this file are subject to the Mozilla Public License Version 1.1
* See LICENSE.TXT at the top of this package for the full license terms.
*/
package eu.etaxonomy.cdm.aspectj;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import eu.etaxonomy.cdm.model.name.BotanicalName;
import eu.etaxonomy.cdm.model.name.NonViralName;
import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;
public class PropertyChangeTest implements PropertyChangeListener {
static Logger logger = Logger.getLogger(PropertyChangeTest.class);
private Object lastPropValue;
- public void propertyChange(PropertyChangeEvent e){
- logger.debug("Property [" + e.getPropertyName()
- + "] changed from " + e.getOldValue()
+ @Override
+ public void propertyChange(PropertyChangeEvent e){
+ logger.debug("Property [" + e.getPropertyName()
+ + "] changed from " + e.getOldValue()
+ " to " + e.getNewValue());
lastPropValue = e.getNewValue() == null ? null : e.getNewValue();
}
@Test
public void testPropertyChange() {
- NonViralName b = NonViralName.NewInstance(Rank.SPECIES());
+ NonViralName<?> b = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());
b.addPropertyChangeListener(this);
b.setGenusOrUninomial("Abies");
assertEquals(b.getGenusOrUninomial(), lastPropValue);
b.setAnamorphic(true);
assertEquals(b.isAnamorphic(), lastPropValue);
}
-
+
@Before
public void updateDebugLevel(){
logger.setLevel(Level.INFO);
/**\r
* Copyright (C) 2009 EDIT\r
-* European Distributed Institute of Taxonomy \r
+* European Distributed Institute of Taxonomy\r
* http://www.e-taxonomy.eu\r
-* \r
+*\r
* The contents of this file are subject to the Mozilla Public License Version 1.1\r
* See LICENSE.TXT at the top of this package for the full license terms.\r
*/\r
import eu.etaxonomy.cdm.model.name.HybridRelationshipType;\r
import eu.etaxonomy.cdm.model.name.NonViralName;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.model.reference.Reference;\r
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;\r
import eu.etaxonomy.cdm.model.taxon.Taxon;\r
* @version 1.0\r
*/\r
public class IdentifiableEntityTest {\r
- \r
+\r
private NonViralName<?> abies;\r
private NonViralName<?> abiesMill;\r
private NonViralName<?> abiesAlba;\r
private NonViralName<?> abiesAlbaMill;\r
private NonViralName<?> abiesAlbaxPinusBeta;\r
private NonViralName<?> pinusBeta;\r
- \r
+\r
private Taxon abiesTaxon;\r
private Taxon abiesMillTaxon;\r
- \r
+\r
private NonViralName<?> abiesAutonym;\r
private Taxon abiesAutonymTaxon;\r
- \r
+\r
private NonViralName<?> abiesBalsamea;\r
private Taxon abiesBalsameaTaxon;\r
private Taxon abiesAlbaxPinusBetaTaxon;\r
/**\r
* @throws java.lang.Exception\r
*/\r
- \r
+\r
@BeforeClass\r
public static void setUpBeforeClass() {\r
DefaultTermInitializer vocabularyStore = new DefaultTermInitializer();\r
vocabularyStore.initialize();\r
- \r
+\r
}\r
/**\r
* @throws java.lang.Exception\r
@Before\r
public void setUp() throws Exception {\r
\r
- abies = NonViralName.NewInstance(Rank.GENUS(), null);\r
+ abies = TaxonNameBase.NewNonViralInstance(Rank.GENUS(), null);\r
abies.setNameCache("Abies");\r
abies.setTitleCache("Abies", true);\r
Reference sec = ReferenceFactory.newArticle();\r
sec.setTitle("Abies alba Ref");\r
- \r
+\r
abiesTaxon = Taxon.NewInstance(abies, sec);\r
- \r
- abiesMill = NonViralName.NewInstance(Rank.GENUS(), null);\r
+\r
+ abiesMill = TaxonNameBase.NewNonViralInstance(Rank.GENUS(), null);\r
abiesMill.setNameCache("Abies");\r
abiesMill.setTitleCache("Abies Mill.", true);\r
abiesMillTaxon = Taxon.NewInstance(abiesMill, sec);\r
- \r
- abiesAlba = NonViralName.NewInstance(Rank.SPECIES(), null);\r
+\r
+ abiesAlba = TaxonNameBase.NewNonViralInstance(Rank.SPECIES(), null);\r
abiesAlba.setNameCache("Abies alba");\r
abiesAlba.setTitleCache("Abies alba", true);\r
- \r
- abiesAlbaMichx = NonViralName.NewInstance(Rank.SPECIES(), null);\r
+\r
+ abiesAlbaMichx = TaxonNameBase.NewNonViralInstance(Rank.SPECIES(), null);\r
abiesAlbaMichx.setNameCache("Abies alba");\r
abiesAlbaMichx.setTitleCache("Abies alba Michx.", true);\r
- \r
- abiesAlbaMill = NonViralName.NewInstance(Rank.SPECIES(), null);\r
+\r
+ abiesAlbaMill = TaxonNameBase.NewNonViralInstance(Rank.SPECIES(), null);\r
abiesAlbaMill.setNameCache("Abies alba");\r
abiesAlbaMill.setTitleCache("Abies alba Mill.", true);\r
- \r
- abiesAutonym = NonViralName.NewInstance(Rank.SECTION_BOTANY());\r
+\r
+ abiesAutonym = TaxonNameBase.NewNonViralInstance(Rank.SECTION_BOTANY());\r
abiesAutonym.setGenusOrUninomial("Abies");\r
abiesAutonym.setInfraGenericEpithet("Abies");\r
- \r
+\r
abiesAutonym.setTitleCache("Abies Mill. sect. Abies", true);\r
abiesAutonym.getNameCache();\r
abiesAutonymTaxon = Taxon.NewInstance(abiesAutonym, sec);\r
- \r
- abiesBalsamea = NonViralName.NewInstance(Rank.SECTION_BOTANY());\r
+\r
+ abiesBalsamea = TaxonNameBase.NewNonViralInstance(Rank.SECTION_BOTANY());\r
abiesBalsamea.setGenusOrUninomial("Abies");\r
abiesBalsamea.setInfraGenericEpithet("Balsamea");\r
abiesBalsamea.getNameCache();\r
abiesBalsamea.setTitleCache("Abies sect. Balsamea L.", true);\r
abiesBalsameaTaxon = Taxon.NewInstance(abiesBalsamea, sec);\r
- \r
- abiesAlbaxPinusBeta = NonViralName.NewInstance(Rank.SPECIES());\r
- pinusBeta = NonViralName.NewInstance(Rank.SPECIES());\r
+\r
+ abiesAlbaxPinusBeta = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());\r
+ pinusBeta = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());\r
pinusBeta.setGenusOrUninomial("Pinus");\r
pinusBeta.setSpecificEpithet("beta");\r
abiesAlbaxPinusBeta.setHybridFormula(true);\r
abiesAlbaxPinusBeta.addHybridParent(abiesAlba, HybridRelationshipType.FIRST_PARENT(), null);\r
abiesAlbaxPinusBeta.addHybridParent(pinusBeta, HybridRelationshipType.SECOND_PARENT(), null);\r
- \r
+\r
}\r
\r
/**\r
@After\r
public void tearDown() throws Exception {\r
}\r
- \r
+\r
/**\r
* Test method for {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#compareTo(eu.etaxonomy.cdm.model.common.IdentifiableEntity)}.\r
*/\r
@Test\r
public void testCompareTo() {\r
int result = 0;\r
- \r
+\r
// "Abies" < "Abies Mill."\r
result = abies.compareTo(abiesMill);\r
assertTrue(result < 0);\r
- \r
+\r
abiesTaxon = abies.getTaxa().iterator().next();\r
- \r
+\r
assertTrue(abiesTaxon.compareTo(abiesTaxon) == 0);\r
- \r
+\r
assertTrue(abiesMillTaxon.compareTo(abiesTaxon) > 0);\r
- \r
+\r
assertTrue(abiesTaxon.compareTo(abiesMillTaxon) < 0);\r
- \r
+\r
// "Abies Mill." > "Abies"\r
result = abiesMill.compareTo(abies);\r
assertTrue(result > 0);\r
- \r
+\r
// "Abies" < "Abies alba"\r
result = abies.compareTo(abiesAlba);\r
assertTrue(result < 0);\r
- \r
+\r
// "Abies alba" > "Abies"\r
result = abiesAlba.compareTo(abies);\r
assertTrue(result > 0);\r
// "Abies Mill." < "Abies alba Michx."\r
result = abiesMill.compareTo(abiesAlbaMichx);\r
assertTrue(result < 0);\r
- \r
+\r
// "Abies alba Michx." > "Abies Mill."\r
result = abiesAlbaMichx.compareTo(abiesMill);\r
assertTrue(result > 0);\r
- \r
+\r
//Autonym should sorted without the authorstring\r
- \r
+\r
result = abiesAutonym.compareTo(abiesBalsamea);\r
assertTrue(result < 0);\r
- // Test consistency of compareTo() with equals(): \r
+ // Test consistency of compareTo() with equals():\r
// Is consistent if and only if for every e1 and e2 of class C\r
- // e1.compareTo(e2) == 0 has the same boolean value as e1.equals(e2) \r
- \r
+ // e1.compareTo(e2) == 0 has the same boolean value as e1.equals(e2)\r
+\r
boolean compareResult = false;\r
boolean equalsResult = false;\r
- \r
+\r
compareResult = (abies.compareTo(abies) == 0);\r
equalsResult = abies.equals(abies);\r
assertEquals(compareResult, equalsResult);\r
- \r
+\r
compareResult = (abies.compareTo(abiesAlba) == 0);\r
equalsResult = abies.equals(abiesAlba);\r
assertEquals(compareResult, equalsResult);\r
- \r
+\r
compareResult = (abiesMill.compareTo(abies) == 0);\r
equalsResult = abiesMill.equals(abies);\r
assertEquals(compareResult, equalsResult);\r
- \r
+\r
//Abies alba x Pinus beta < Abies alba xinus\r
BotanicalName abiesAlbaXinus = BotanicalName.NewInstance(Rank.SUBSPECIES());\r
abiesAlbaXinus.setGenusOrUninomial("Abies");\r
result = abiesAlbaxPinusBeta.compareTo(abiesAlbaXinus);\r
assertTrue(result < 0);\r
}\r
- \r
+\r
/**\r
* Test method for {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#addCredit(eu.etaxonomy.cdm.model.common.IdentifiableEntity)}.\r
*/\r
assertEquals("Number of credits should be 3",3,abies.getCredits().size());\r
assertEquals("Credit0 should be last in list", text3, abies.getCredits(2).getText());\r
}\r
- \r
+\r
/**\r
* Test method for {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#addCredit(eu.etaxonomy.cdm.model.common.IdentifiableEntity)}.\r
*/\r
assertNotNull("A list should always be returned",abies.getCredits());\r
assertTrue("No credits should exist",abies.getCredits().isEmpty());\r
}\r
- \r
+\r
@Test\r
public void testClone(){\r
IdentifiableEntity clone = (IdentifiableEntity)abies.clone();\r
*/
@Test
public final void testNonViralNameRank() {
- NonViralName<?> nonViralName = NonViralName.NewInstance(Rank.GENUS());
+ NonViralName<?> nonViralName = TaxonNameBase.NewNonViralInstance(Rank.GENUS());
assertNotNull(nonViralName);
}
assertEquals(0, botanicalName1.getHybridParentRelations().size());
assertEquals(0, botanicalName1.getHybridChildRelations().size());
BotanicalName femaleParent = BotanicalName.NewInstance(null);
- NonViralName<?> maleParent = NonViralName.NewInstance(null);
+ NonViralName<?> maleParent = TaxonNameBase.NewNonViralInstance(null);
ZoologicalName child = TaxonNameBase.NewZoologicalInstance(null);
botanicalName1.addHybridParent(femaleParent, HybridRelationshipType.FEMALE_PARENT(), null);
nonViralName1.setInfraSpecificEpithet("infrabus");
nonViralName1.setBinomHybrid(true);
- NonViralName<?> parent = NonViralName.NewInstance(Rank.SPECIES());
- NonViralName<?> parent2 = NonViralName.NewInstance(Rank.SPECIES());
- NonViralName<?> child = NonViralName.NewInstance(Rank.SPECIES());
- NonViralName<?> child2 = NonViralName.NewInstance(Rank.SPECIES());
+ NonViralName<?> parent = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());
+ NonViralName<?> parent2 = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());
+ NonViralName<?> child = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());
+ NonViralName<?> child2 = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());
nonViralName1.addHybridParent(parent, HybridRelationshipType.FIRST_PARENT(), "parent rule");
nonViralName1.addHybridParent(parent2, HybridRelationshipType.SECOND_PARENT(), "parent rule2");
nonViralName1.addHybridChild(child, HybridRelationshipType.FEMALE_PARENT(), "child rule");
\r
@Test\r
public void testClone(){\r
- NonViralName taxonNameBase1 = NonViralName.NewInstance(Rank.SPECIES());\r
- NonViralName<?> genusName = NonViralName.NewInstance(Rank.GENUS());\r
+ NonViralName taxonNameBase1 = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());\r
+ NonViralName<?> genusName = TaxonNameBase.NewNonViralInstance(Rank.GENUS());\r
Taxon taxonBase = Taxon.NewInstance(taxonNameBase1, null);\r
\r
//basionym & homonym\r
- NonViralName<?> basionym = NonViralName.NewInstance(Rank.SPECIES());\r
- NonViralName<?> earlierHomonym = NonViralName.NewInstance(Rank.SPECIES());\r
+ NonViralName<?> basionym = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());\r
+ NonViralName<?> earlierHomonym = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());\r
taxonNameBase1.addBasionym(basionym);\r
taxonNameBase1.addRelationshipToName(earlierHomonym, NameRelationshipType.LATER_HOMONYM(), "later homonym rule");\r
//status\r
Assert.assertEquals(author.getNomenclaturalTitle(), speciesName.getAuthorshipCache());
Assert.assertEquals("Should be 'Abies alba L.'", "Abies alba L.", speciesName.getTitleCache());
- NonViralName hybridName = NonViralName.NewInstance(Rank.SPECIES());
- NonViralName secondParent = NonViralName.NewInstance(Rank.SPECIES());
+ NonViralName<?> hybridName = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());
+ NonViralName<?> secondParent = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());
secondParent.setTitleCache("Second parent Mill.", true);
hybridName.addHybridParent(speciesName, HybridRelationshipType.FIRST_PARENT(), null);
@Test
public void testGetInfraGenericNames(){
String author = "Anyauthor";
- NonViralName nonViralName = NonViralName.NewInstance(Rank.SUBGENUS());
+ NonViralName<?> nonViralName = TaxonNameBase.NewNonViralInstance(Rank.SUBGENUS());
nonViralName.setGenusOrUninomial("Genus");
nonViralName.setInfraGenericEpithet("subgenus");
nonViralName.setAuthorshipCache(author);
import eu.etaxonomy.cdm.model.description.StatisticalMeasure;\r
import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;\r
import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
-import eu.etaxonomy.cdm.model.name.NonViralName;\r
+import eu.etaxonomy.cdm.model.name.INonViralName;\r
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.model.taxon.Taxon;\r
\r
/**\r
* @author m.venin\r
* @created 16.12.2010\r
- * @version 1.0\r
*/\r
\r
public class IdentificationKeyGeneratorTest {\r
- private static final Logger logger = Logger.getLogger(IdentificationKeyGeneratorTest.class);\r
- \r
+ @SuppressWarnings("unused")\r
+ private static final Logger logger = Logger.getLogger(IdentificationKeyGeneratorTest.class);\r
+\r
private Feature feature1;\r
private Feature feature2;\r
private Feature feature3;\r
private Feature feature4;\r
- \r
+\r
private Taxon taxon1;\r
private Taxon taxon2;\r
private Taxon taxon3;\r
private Taxon taxon6;\r
private Taxon taxon7;\r
private Taxon taxon8;\r
- \r
+\r
private TaxonDescription taxond1;\r
private TaxonDescription taxond2;\r
private TaxonDescription taxond3;\r
private TaxonDescription taxond6;\r
private TaxonDescription taxond7;\r
private TaxonDescription taxond8;\r
- \r
+\r
private Set<TaxonDescription> taxa;\r
private List<Feature> features;\r
- \r
+\r
private PolytomousKeyGenerator generator;\r
- \r
+\r
@Before\r
public void setUp() throws Exception {\r
feature1 = Feature.NewInstance("","Shape of the head","");\r
feature2 = Feature.NewInstance("","Presence of wings","");\r
feature3 = Feature.NewInstance("","Length of wings","");\r
feature4 = Feature.NewInstance("","Colour","");\r
- \r
- NonViralName tn1 = NonViralName.NewInstance(null);\r
- NonViralName tn2 = NonViralName.NewInstance(null);\r
- NonViralName tn3 = NonViralName.NewInstance(null);\r
- NonViralName tn4 = NonViralName.NewInstance(null);\r
- NonViralName tn5 = NonViralName.NewInstance(null);\r
- NonViralName tn6 = NonViralName.NewInstance(null);\r
- NonViralName tn7 = NonViralName.NewInstance(null);\r
- NonViralName tn8 = NonViralName.NewInstance(null);\r
- \r
+\r
+ INonViralName tn1 = TaxonNameBase.NewNonViralInstance(null);\r
+ INonViralName tn2 = TaxonNameBase.NewNonViralInstance(null);\r
+ INonViralName tn3 = TaxonNameBase.NewNonViralInstance(null);\r
+ INonViralName tn4 = TaxonNameBase.NewNonViralInstance(null);\r
+ INonViralName tn5 = TaxonNameBase.NewNonViralInstance(null);\r
+ INonViralName tn6 = TaxonNameBase.NewNonViralInstance(null);\r
+ INonViralName tn7 = TaxonNameBase.NewNonViralInstance(null);\r
+ INonViralName tn8 = TaxonNameBase.NewNonViralInstance(null);\r
+\r
taxon1 = Taxon.NewInstance(tn1, null);\r
taxon2 = Taxon.NewInstance(tn2, null);\r
taxon3 = Taxon.NewInstance(tn3, null);\r
taxon6 = Taxon.NewInstance(tn6, null);\r
taxon7 = Taxon.NewInstance(tn7, null);\r
taxon8 = Taxon.NewInstance(tn8, null);\r
- \r
+\r
taxond1 = TaxonDescription.NewInstance(taxon1);\r
taxond2 = TaxonDescription.NewInstance(taxon2);\r
taxond3 = TaxonDescription.NewInstance(taxon3);\r
taxond6 = TaxonDescription.NewInstance(taxon6);\r
taxond7 = TaxonDescription.NewInstance(taxon7);\r
taxond8 = TaxonDescription.NewInstance(taxon8);\r
- \r
+\r
CategoricalData catd11 = CategoricalData.NewInstance();\r
catd11.setFeature(feature1);\r
StateData sd11 = StateData.NewInstance();\r
State s12 = State.NewInstance("","Circular","");\r
sd11.setState(s11);\r
catd11.addStateData(sd11);\r
- \r
+\r
CategoricalData catd12 = CategoricalData.NewInstance();\r
catd12.setFeature(feature1);\r
StateData sd12 = StateData.NewInstance();\r
sd12.setState(s11);\r
catd12.addStateData(sd12);\r
- \r
+\r
CategoricalData catd13 = CategoricalData.NewInstance();\r
catd13.setFeature(feature1);\r
StateData sd13 = StateData.NewInstance();\r
sd13.setState(s11);\r
catd13.addStateData(sd13);\r
- \r
+\r
CategoricalData catd14 = CategoricalData.NewInstance();\r
catd14.setFeature(feature1);\r
StateData sd14 = StateData.NewInstance();\r
sd14.setState(s11);\r
catd14.addStateData(sd14);\r
- \r
+\r
CategoricalData catd15 = CategoricalData.NewInstance();\r
catd15.setFeature(feature1);\r
StateData sd15 = StateData.NewInstance();\r
sd15.setState(s12);\r
catd15.addStateData(sd15);\r
- \r
+\r
CategoricalData catd16 = CategoricalData.NewInstance();\r
catd16.setFeature(feature1);\r
StateData sd16 = StateData.NewInstance();\r
sd16.setState(s12);\r
catd16.addStateData(sd16);\r
- \r
+\r
CategoricalData catd17 = CategoricalData.NewInstance();\r
catd17.setFeature(feature1);\r
StateData sd17 = StateData.NewInstance();\r
sd17.setState(s12);\r
catd17.addStateData(sd17);\r
- \r
+\r
CategoricalData catd18 = CategoricalData.NewInstance();\r
catd18.setFeature(feature1);\r
StateData sd18 = StateData.NewInstance();\r
sd18.setState(s12);\r
catd18.addStateData(sd18);\r
- \r
+\r
/*************************/\r
- \r
+\r
CategoricalData catd21 = CategoricalData.NewInstance();\r
catd21.setFeature(feature2);\r
StateData sd21 = StateData.NewInstance();\r
State s22 = State.NewInstance("","No","");\r
sd21.setState(s21);\r
catd21.addStateData(sd21);\r
- \r
+\r
CategoricalData catd22 = CategoricalData.NewInstance();\r
catd22.setFeature(feature2);\r
StateData sd22 = StateData.NewInstance();\r
sd22.setState(s21);\r
catd22.addStateData(sd22);\r
- \r
+\r
CategoricalData catd23 = CategoricalData.NewInstance();\r
catd23.setFeature(feature2);\r
StateData sd23 = StateData.NewInstance();\r
sd23.setState(s21);\r
catd23.addStateData(sd23);\r
- \r
+\r
CategoricalData catd24 = CategoricalData.NewInstance();\r
catd24.setFeature(feature2);\r
StateData sd24 = StateData.NewInstance();\r
sd24.setState(s21);\r
catd24.addStateData(sd24);\r
- \r
+\r
CategoricalData catd25 = CategoricalData.NewInstance();\r
catd25.setFeature(feature2);\r
StateData sd25 = StateData.NewInstance();\r
sd25.setState(s21);\r
catd25.addStateData(sd25);\r
- \r
+\r
CategoricalData catd26 = CategoricalData.NewInstance();\r
catd26.setFeature(feature2);\r
StateData sd26 = StateData.NewInstance();\r
sd26.setState(s21);\r
catd26.addStateData(sd26);\r
- \r
+\r
CategoricalData catd27 = CategoricalData.NewInstance();\r
catd27.setFeature(feature2);\r
StateData sd27 = StateData.NewInstance();\r
sd27.setState(s21);\r
catd27.addStateData(sd27);\r
- \r
+\r
CategoricalData catd28 = CategoricalData.NewInstance();\r
catd28.setFeature(feature2);\r
StateData sd28 = StateData.NewInstance();\r
sd28.setState(s22);\r
catd28.addStateData(sd28);\r
- \r
+\r
/*************************/\r
- \r
+\r
QuantitativeData qtd31 = QuantitativeData.NewInstance();\r
StatisticalMeasurementValue smv311 = StatisticalMeasurementValue.NewInstance();\r
smv311.setValue(0);\r
smv312.setType(sm312);\r
qtd31.addStatisticalValue(smv311);\r
qtd31.addStatisticalValue(smv312);\r
- \r
+\r
QuantitativeData qtd32 = QuantitativeData.NewInstance();\r
StatisticalMeasurementValue smv321 = StatisticalMeasurementValue.NewInstance();\r
smv321.setValue(0);\r
smv322.setType(sm322);\r
qtd32.addStatisticalValue(smv321);\r
qtd32.addStatisticalValue(smv322);\r
- \r
+\r
QuantitativeData qtd33 = QuantitativeData.NewInstance();\r
StatisticalMeasurementValue smv331 = StatisticalMeasurementValue.NewInstance();\r
smv331.setValue(6);\r
smv332.setType(sm332);\r
qtd33.addStatisticalValue(smv331);\r
qtd33.addStatisticalValue(smv332);\r
- \r
+\r
QuantitativeData qtd34 = QuantitativeData.NewInstance();\r
StatisticalMeasurementValue smv341 = StatisticalMeasurementValue.NewInstance();\r
smv341.setValue(6);\r
smv342.setType(sm342);\r
qtd34.addStatisticalValue(smv341);\r
qtd34.addStatisticalValue(smv342);\r
- \r
+\r
QuantitativeData qtd35 = QuantitativeData.NewInstance();\r
StatisticalMeasurementValue smv351 = StatisticalMeasurementValue.NewInstance();\r
smv351.setValue(0);\r
smv352.setType(sm352);\r
qtd35.addStatisticalValue(smv351);\r
qtd35.addStatisticalValue(smv352);\r
- \r
+\r
QuantitativeData qtd36 = QuantitativeData.NewInstance();\r
StatisticalMeasurementValue smv361 = StatisticalMeasurementValue.NewInstance();\r
smv361.setValue(0);\r
smv362.setType(sm362);\r
qtd36.addStatisticalValue(smv361);\r
qtd36.addStatisticalValue(smv362);\r
- \r
+\r
QuantitativeData qtd37 = QuantitativeData.NewInstance();\r
StatisticalMeasurementValue smv371 = StatisticalMeasurementValue.NewInstance();\r
smv371.setValue(6);\r
smv372.setType(sm372);\r
qtd37.addStatisticalValue(smv371);\r
qtd37.addStatisticalValue(smv372);\r
- \r
+\r
// QuantitativeData qtd38 = QuantitativeData.NewInstance();\r
// StatisticalMeasurementValue smv381 = StatisticalMeasurementValue.NewInstance();\r
// smv381.setValue(6);\r
// smv382.setType(sm382);\r
// qtd38.addStatisticalValue(smv381);\r
// qtd38.addStatisticalValue(smv382);\r
- \r
+\r
/*************************/\r
- \r
+\r
CategoricalData catd41 = CategoricalData.NewInstance();\r
catd41.setFeature(feature4);\r
StateData sd41 = StateData.NewInstance();\r
State s42 = State.NewInstance("","Yellow","");\r
sd41.setState(s41);\r
catd41.addStateData(sd41);\r
- \r
+\r
CategoricalData catd42 = CategoricalData.NewInstance();\r
catd42.setFeature(feature4);\r
StateData sd42 = StateData.NewInstance();\r
sd42.setState(s42);\r
catd42.addStateData(sd42);\r
- \r
+\r
CategoricalData catd43 = CategoricalData.NewInstance();\r
catd43.setFeature(feature4);\r
StateData sd43 = StateData.NewInstance();\r
sd43.setState(s41);\r
catd43.addStateData(sd43);\r
- \r
+\r
CategoricalData catd44 = CategoricalData.NewInstance();\r
catd44.setFeature(feature4);\r
StateData sd44 = StateData.NewInstance();\r
sd44.setState(s42);\r
catd44.addStateData(sd44);\r
- \r
+\r
CategoricalData catd45 = CategoricalData.NewInstance();\r
catd45.setFeature(feature4);\r
StateData sd45 = StateData.NewInstance();\r
sd45.setState(s41);\r
catd45.addStateData(sd45);\r
- \r
+\r
CategoricalData catd46 = CategoricalData.NewInstance();\r
catd46.setFeature(feature4);\r
StateData sd46 = StateData.NewInstance();\r
sd46.setState(s41);\r
catd46.addStateData(sd46);\r
- \r
+\r
CategoricalData catd47 = CategoricalData.NewInstance();\r
catd47.setFeature(feature4);\r
StateData sd47 = StateData.NewInstance();\r
sd47.setState(s41);\r
catd47.addStateData(sd47);\r
- \r
+\r
CategoricalData catd48 = CategoricalData.NewInstance();\r
catd48.setFeature(feature4);\r
StateData sd48 = StateData.NewInstance();\r
sd48.setState(s41);\r
catd48.addStateData(sd48);\r
- \r
+\r
/*************************/\r
- \r
+\r
taxond1.addElement(catd11);\r
taxond1.addElement(catd21);\r
taxond1.addElement(qtd31);\r
taxond1.addElement(catd41);\r
- \r
+\r
taxond2.addElement(catd12);\r
taxond2.addElement(catd22);\r
taxond2.addElement(qtd32);\r
taxond2.addElement(catd42);\r
- \r
+\r
taxond3.addElement(catd13);\r
taxond3.addElement(catd23);\r
taxond3.addElement(qtd33);\r
taxond3.addElement(catd43);\r
- \r
+\r
taxond4.addElement(catd14);\r
taxond4.addElement(catd24);\r
taxond4.addElement(qtd34);\r
taxond4.addElement(catd44);\r
- \r
+\r
taxond5.addElement(catd15);\r
taxond5.addElement(catd25);\r
taxond5.addElement(qtd35);\r
taxond5.addElement(catd45);\r
- \r
+\r
taxond6.addElement(catd16);\r
taxond6.addElement(catd26);\r
taxond6.addElement(qtd36);\r
taxond6.addElement(catd46);\r
- \r
+\r
taxond7.addElement(catd17);\r
taxond7.addElement(catd27);\r
taxond7.addElement(qtd37);\r
taxond7.addElement(catd47);\r
- \r
+\r
taxond8.addElement(catd18);\r
taxond8.addElement(catd28);\r
// taxond8.addElement(qtd38); // This taxon has no wings\r
taxond8.addElement(catd48);\r
- \r
+\r
/*************************/\r
- \r
+\r
features = new ArrayList<Feature>();\r
features.add(feature1);\r
features.add(feature2);\r
features.add(feature3);\r
features.add(feature4);\r
- \r
+\r
taxa = new HashSet<TaxonDescription>();\r
taxa.add(taxond1);\r
taxa.add(taxond2);\r
taxa.add(taxond6);\r
taxa.add(taxond7);\r
taxa.add(taxond8);\r
- \r
+\r
}\r
- \r
+\r
//*************************** TESTS *********************** /\r
- \r
+\r
\r
@Test\r
public void testInvoke() {\r
// generator.invoke();\r
// assertNotNull("Key should exist (merge mode ON).",generator.invoke());;\r
}\r
- \r
+\r
@Test\r
public void testInvokeWithDependencies() {\r
// generator = new IdentificationKeyGenerator();\r
// generator.invoke();\r
// assertNotNull("Key should exist (dependencies are present).",generator.invoke());;\r
}\r
- \r
+\r
}\r
import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.name.NonViralName;
import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;
import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
import eu.etaxonomy.cdm.model.taxon.Taxon;
// to a taxon name with no name cache to begin with
Reference sec = ReferenceFactory.newDatabase();
referenceService.save(sec);
- Taxon taxon = Taxon.NewInstance(NonViralName.NewInstance(Rank.SERIES()), sec);
+ Taxon taxon = Taxon.NewInstance(TaxonNameBase.NewNonViralInstance(Rank.SERIES()), sec);
taxon.setTitleCache("Tax" + "CdmCacher", true);
taxonService.save(taxon);
NonViralName<?> nvn = (NonViralName<?>)taxon.getName();
import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.description.CategoricalData;
import eu.etaxonomy.cdm.model.description.Feature;
-import eu.etaxonomy.cdm.model.description.FeatureTree;
import eu.etaxonomy.cdm.model.description.FeatureNode;
+import eu.etaxonomy.cdm.model.description.FeatureTree;
import eu.etaxonomy.cdm.model.description.MeasurementUnit;
import eu.etaxonomy.cdm.model.description.QuantitativeData;
import eu.etaxonomy.cdm.model.description.State;
import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
import eu.etaxonomy.cdm.model.description.TaxonDescription;
import eu.etaxonomy.cdm.model.description.TextData;
-import eu.etaxonomy.cdm.model.name.NonViralName;
+import eu.etaxonomy.cdm.model.name.INonViralName;
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;
import eu.etaxonomy.cdm.model.taxon.Taxon;
import eu.etaxonomy.cdm.test.integration.CdmIntegrationTest;
@Ignore //FIXME Remove @Ignore once maximes code is completely comitted
public class NaturalLanguageGeneratorTest extends CdmIntegrationTest {
-
+
@SuppressWarnings("unused")
private static final Logger logger = Logger.getLogger(NaturalLanguageGeneratorTest.class);
-
+
@SpringBeanByType
private INaturalLanguageGenerator generator;
-
+
private FeatureTree featureTree;
private TaxonDescription description;
Set<Feature> featureSet = new HashSet<Feature>();
@Before
public void setUp() throws Exception {
// set up your test objects here
-
- NonViralName tnb = NonViralName.NewInstance(null);
+
+ INonViralName tnb = TaxonNameBase.NewNonViralInstance(null);
Taxon taxon = Taxon.NewInstance(tnb, null);
description = TaxonDescription.NewInstance(taxon);
-
+
featureTree= FeatureTree.NewInstance();
FeatureNode root = FeatureNode.NewInstance();
featureTree.setRoot(root);
FeatureNode qNode = FeatureNode.NewInstance(qFeature);
root.addChild(qNode);
}
-
+
@Test
public void testGenerateNaturalLanguageDescription() {
assertNotNull("FeatureTree should exist", featureTree);
assertTrue("Empty text",!stringBuilder.equals(""));
System.out.println(stringBuilder.toString());
}
-
+
public void buildBranches(FeatureNode parent, String[][][] children, int level, int depth, int nodeNumber) {
int i = nodeNumber;
int j;
buildBranches(child, children,level+1,depth, j);
}
}
-
+
}
/* (non-Javadoc)
@Override
public void createTestDataSet() throws FileNotFoundException {
// TODO Auto-generated method stub
-
+
}
-
+
}
//service = new TaxonServiceImpl();
//nameService = new NameServiceImpl();
- t1n = NonViralName.NewInstance(null);
+ t1n = TaxonNameBase.NewNonViralInstance(null);
t1 = Taxon.NewInstance(t1n, reference);
- t2n = NonViralName.NewInstance(null);
+ t2n = TaxonNameBase.NewNonViralInstance(null);
t2 = Taxon.NewInstance(t2n, reference);
- s1n = NonViralName.NewInstance(null);
+ s1n = TaxonNameBase.NewNonViralInstance(null);
s1 = Synonym.NewInstance(s1n, reference);
- s2n = NonViralName.NewInstance(null);
+ s2n = TaxonNameBase.NewNonViralInstance(null);
s2 = Synonym.NewInstance(s2n, reference);
// referencing
@Test
public final void testChangeSynonymWithMultipleSynonymsInHomotypicalGroupToAcceptedTaxon() {
t1.addSynonym(s1, heteroTypicSynonymType);
- TaxonNameBase<?,?> otherHeteroSynonymName = NonViralName.NewInstance(null);
+ TaxonNameBase<?,?> otherHeteroSynonymName = TaxonNameBase.NewNonViralInstance(null);
t1.addHeterotypicSynonymName(otherHeteroSynonymName);
- TaxonNameBase<?,?> homotypicSynonymName = NonViralName.NewInstance(null);
+ TaxonNameBase<?,?> homotypicSynonymName = TaxonNameBase.NewNonViralInstance(null);
Synonym homotypicSynonym = Synonym.NewInstance(homotypicSynonymName, t1.getSec());
t1.addHomotypicSynonym(homotypicSynonym);
t1.addSynonym(s1, heteroTypicSynonymType);
//s2 - heterotypic
- TaxonNameBase otherHeteroSynonymName = NonViralName.NewInstance(null);
+ TaxonNameBase otherHeteroSynonymName = TaxonNameBase.NewNonViralInstance(null);
Synonym s2 = Synonym.NewInstance(otherHeteroSynonymName, t1.getSec());
t1.addSynonym(s2, heteroTypicSynonymType);
- TaxonNameBase<?,?> otherHeteroSynonymNameB = NonViralName.NewInstance(null);
+ TaxonNameBase<?,?> otherHeteroSynonymNameB = TaxonNameBase.NewNonViralInstance(null);
otherHeteroSynonymName.addBasionym(otherHeteroSynonymNameB);
Synonym s2b = Synonym.NewInstance(otherHeteroSynonymNameB, t1.getSec());
t1.addSynonym(s2b, heteroTypicSynonymType);
//homotypic
- TaxonNameBase<?,?> homotypicSynonymName = NonViralName.NewInstance(null);
+ TaxonNameBase<?,?> homotypicSynonymName = TaxonNameBase.NewNonViralInstance(null);
Synonym homotypicSynonym = Synonym.NewInstance(homotypicSynonymName, t1.getSec());
t1.addHomotypicSynonym(homotypicSynonym);
t1.getName().addBasionym(homotypicSynonymName);
Reference reference = ReferenceFactory.newGeneric();
String referenceDetail = "test";
- NonViralName<?> t1n = NonViralName.NewInstance(null);
+ NonViralName<?> t1n = TaxonNameBase.NewNonViralInstance(null);
Taxon t1 = Taxon.NewInstance(t1n, reference);
- NonViralName<?> t2n = NonViralName.NewInstance(null);
+ NonViralName<?> t2n = TaxonNameBase.NewNonViralInstance(null);
Taxon t2 = Taxon.NewInstance(t2n, reference);
- NonViralName<?> s1n = NonViralName.NewInstance(null);
+ NonViralName<?> s1n = TaxonNameBase.NewNonViralInstance(null);
Synonym s1 = Synonym.NewInstance(s1n, reference);
t1.addSynonym(s1, heteroTypicSynonymType);
service.saveOrUpdate(t1);
public void testAppController() {
logger.info("Create name objects...");
- NonViralName<?> nvn = NonViralName.NewInstance(Rank.SPECIES());
+ NonViralName<?> nvn = TaxonNameBase.NewNonViralInstance(Rank.SPECIES());
BotanicalName bn = BotanicalName.NewInstance(Rank.SUBSPECIES());
ZoologicalName zn = TaxonNameBase.NewZoologicalInstance(Rank.FAMILY());
appCtr = CdmApplicationController.NewInstance(dbSchemaValidation);
- TaxonNameBase<?,?> name = NonViralName.NewInstance(null);
+ TaxonNameBase<?,?> name = TaxonNameBase.NewNonViralInstance(null);
name.setTitleCache("Abies alba", true);
- TaxonNameBase<?,?> name2 = NonViralName.NewInstance(null);
+ TaxonNameBase<?,?> name2 = TaxonNameBase.NewNonViralInstance(null);
name2.setTitleCache("Abies beta", true);
//appCtr.getNameService().saveTaxonName(name);
BGBM BDI Projects / cdmlib.git / commitdiff