import eu.etaxonomy.cdm.model.common.Annotation;
import eu.etaxonomy.cdm.model.common.CdmBase;
import eu.etaxonomy.cdm.model.common.Credit;
-import eu.etaxonomy.cdm.model.common.DefinedTerm;
import eu.etaxonomy.cdm.model.common.EventBase;
import eu.etaxonomy.cdm.model.common.Extension;
import eu.etaxonomy.cdm.model.common.ExtensionType;
import eu.etaxonomy.cdm.model.common.LanguageString;
import eu.etaxonomy.cdm.model.common.Marker;
import eu.etaxonomy.cdm.model.common.MarkerType;
-import eu.etaxonomy.cdm.model.common.OriginalSourceType;
-import eu.etaxonomy.cdm.model.common.Representation;
-import eu.etaxonomy.cdm.model.common.TermType;
-import eu.etaxonomy.cdm.model.common.TermVocabulary;
+import eu.etaxonomy.cdm.model.common.TimePeriod;
import eu.etaxonomy.cdm.model.common.User;
import eu.etaxonomy.cdm.model.description.CategoricalData;
import eu.etaxonomy.cdm.model.description.CommonTaxonName;
import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
+import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
import eu.etaxonomy.cdm.model.description.Distribution;
import eu.etaxonomy.cdm.model.description.Feature;
-import eu.etaxonomy.cdm.model.description.FeatureNode;
-import eu.etaxonomy.cdm.model.description.FeatureTree;
import eu.etaxonomy.cdm.model.description.IIdentificationKey;
import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
import eu.etaxonomy.cdm.model.description.MeasurementUnit;
import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
import eu.etaxonomy.cdm.model.description.TextData;
import eu.etaxonomy.cdm.model.description.TextFormat;
-import eu.etaxonomy.cdm.model.description.WorkingSet;
import eu.etaxonomy.cdm.model.location.Country;
import eu.etaxonomy.cdm.model.location.NamedArea;
import eu.etaxonomy.cdm.model.location.Point;
import eu.etaxonomy.cdm.model.location.ReferenceSystem;
import eu.etaxonomy.cdm.model.media.AudioFile;
+import eu.etaxonomy.cdm.model.media.ExternalLink;
+import eu.etaxonomy.cdm.model.media.ExternalLinkType;
import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
import eu.etaxonomy.cdm.model.media.ImageFile;
import eu.etaxonomy.cdm.model.media.Media;
import eu.etaxonomy.cdm.model.molecular.SingleRead;
import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment.Shift;
-import eu.etaxonomy.cdm.model.name.BacterialName;
-import eu.etaxonomy.cdm.model.name.BotanicalName;
-import eu.etaxonomy.cdm.model.name.CultivarPlantName;
import eu.etaxonomy.cdm.model.name.HybridRelationship;
import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
import eu.etaxonomy.cdm.model.name.NameRelationship;
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.Registration;
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
-import eu.etaxonomy.cdm.model.name.ViralName;
-import eu.etaxonomy.cdm.model.name.ZoologicalName;
+import eu.etaxonomy.cdm.model.name.TaxonName;
+import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
import eu.etaxonomy.cdm.model.occurrence.Collection;
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
+import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
import eu.etaxonomy.cdm.model.taxon.Classification;
import eu.etaxonomy.cdm.model.taxon.Synonym;
-import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
-import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
+import eu.etaxonomy.cdm.model.taxon.SynonymType;
import eu.etaxonomy.cdm.model.taxon.Taxon;
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
+import eu.etaxonomy.cdm.model.taxon.TaxonNodeAgentRelation;
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
+import eu.etaxonomy.cdm.model.term.DefinedTerm;
+import eu.etaxonomy.cdm.model.term.Representation;
+import eu.etaxonomy.cdm.model.term.TermTree;
+import eu.etaxonomy.cdm.model.term.TermTreeNode;
+import eu.etaxonomy.cdm.model.term.TermType;
+import eu.etaxonomy.cdm.model.term.TermVocabulary;
import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
/**
* depend on general parameter than concrete data values.
*
* @author a.mueller
- * @created 3013-12-02
+ * @since 3013-12-02
*
*
*/
public void fillWithData(Session session){
- List<CdmBase> cdmBases = new ArrayList<CdmBase>();
+ List<CdmBase> cdmBases = new ArrayList<>();
createAgents(cdmBases);
private void createSupplemental(List<CdmBase> cdmBases) {
- Reference<?> ref = ReferenceFactory.newBook();
+ Reference ref = ReferenceFactory.newBook();
Annotation annotation = Annotation.NewDefaultLanguageInstance("annotation");
ref.addAnnotation(annotation);
//Others
try {
LSIDAuthority lsidAuthority = new LSIDAuthority("My authority");
- lsidAuthority.addNamespace("lsidNamespace", TaxonNameBase.class);
+ lsidAuthority.addNamespace("lsidNamespace", TaxonName.class);
cdmBases.add(lsidAuthority);
} catch (MalformedLSIDException e) {
e.printStackTrace();
private void createAgents(List<CdmBase> cdmBases) {
//Person
Person person = Person.NewTitledInstance("Person Title");
- person.setFirstname("first name");
- person.setLastname("last name");
+ person.setGivenName("first name");
+ person.setFamilyName("last name");
person.setLifespan(TimePeriodParser.parseString("1905-1995"));
person.setPrefix("prefix");
person.setSuffix("suffix");
Taxon referencedTaxon = getTaxon();
cdmBases.add(referencedTaxon);
- languageString.addIntextReference(IntextReference.NewTaxonInstance(referencedTaxon, languageString, 2, 5));
+ languageString.addIntextReference(IntextReference.NewInstance(referencedTaxon, languageString, 2, 5));
textData.putModifyingText(eng, "nice diagnosis");
handleAnnotatableEntity(textData);
handleAnnotatableEntity(languageString);
textData.addModifier(DefinedTerm.SEX_HERMAPHRODITE());
textData.putModifyingText(Language.ENGLISH(), "no modification");
textData.setTimeperiod(TimePeriodParser.parseString("1970-1980"));
- Reference<?> ref = ReferenceFactory.newArticle();
+ Reference ref = ReferenceFactory.newArticle();
DescriptionElementSource source = textData.addSource(OriginalSourceType.Import, "22", "taxon description table", ref, "detail");
- source.setNameUsedInSource(BotanicalName.NewInstance(Rank.GENUS()));
+ source.setNameUsedInSource(TaxonNameFactory.NewBotanicalInstance(Rank.GENUS()));
+ ExternalLink link = ExternalLink.NewInstance(ExternalLinkType.WebSite,
+ URI.create("http://wwww.abd.de"), "Somehow useful link", 445);
+ source.addLink(link);
handleAnnotatableEntity(source);
taxonDescription.addDescriptionSource(ref);
handleAnnotatableEntity(specDesc);
//Name description
- TaxonNameBase<?,?> name = BotanicalName.NewInstance(Rank.GENUS());
+ TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
TaxonNameDescription nameDesc = TaxonNameDescription.NewInstance(name);
cdmBases.add(name);
handleAnnotatableEntity(nameDesc);
//Feature Tree
- FeatureTree featureTree = FeatureTree.NewInstance();
+ TermTree<Feature> featureTree = TermTree.NewInstance();
// featureTree
- FeatureNode descriptionFeatureNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
- FeatureNode leaveLengthNode = FeatureNode.NewInstance(leaveLength);
- featureTree.getRootChildren().add(descriptionFeatureNode);
- descriptionFeatureNode.addChild(leaveLengthNode);
+ TermTreeNode<Feature> descriptionFeatureNode = featureTree.getRoot().addChild(Feature.DESCRIPTION());
+ TermTreeNode<Feature> leaveLengthNode = descriptionFeatureNode.addChild(leaveLength);
handleIdentifiableEntity(featureTree);
State inapplicableState = State.NewInstance("inapplicableState", "inapplicableState", null);
cdmBases.add(leaveLengthNode);
- WorkingSet workingSet = WorkingSet.NewInstance();
- workingSet.addDescription(taxonDescription);
- workingSet.setLabel("My Workingset");
- workingSet.getDescriptiveSystem();
- handleAnnotatableEntity(workingSet);
+ //DescriptiveDataSet
+ DescriptiveDataSet descriptiveDataSet = DescriptiveDataSet.NewInstance();
+ descriptiveDataSet.addDescription(taxonDescription);
+ descriptiveDataSet.setLabel("My Descriptive Dataset");
+ descriptiveDataSet.getDescriptiveSystem();
+ handleAnnotatableEntity(descriptiveDataSet);
+ descriptiveDataSet.addGeoFilterArea(Country.GERMANY());
+ Classification classification = Classification.NewInstance("DescriptiveDataSet subtree classification");
+ Taxon subTreeTaxon = getTaxon();
+ TaxonNode subtree = classification.addChildTaxon(subTreeTaxon, null, null);
+ descriptiveDataSet.addTaxonSubtree(subtree);
+
+ cdmBases.add(classification);
+ cdmBases.add(subtree);
//polytomous keys
media.addRepresentation(mediaRepresentation);
media.putTitle(Language.ENGLISH(), "Media title");
- media.setMediaCreated(DateTime.now());
+ media.setMediaCreated(TimePeriod.NewInstance(DateTime.now()));
media.putDescription(Language.ENGLISH(), "Media description");
handleIdentifiableEntity(media);
sequence.setGeneticAccessionNumber("GenNO12345");
sequence.setBoldProcessId("boldId");
sequence.setHaplotype("haplotype");
- Reference<?> sequenceCitation = getReference();
+ Reference sequenceCitation = getReference();
sequence.addCitation(sequenceCitation);
handleAnnotatableEntity(sequence);
private void createTaxon(List<CdmBase> cdmBases) {
- Reference<?> sec = getReference();
- TaxonNameBase<?,?> name = BotanicalName.NewInstance(Rank.GENUS());
+ Reference sec = getReference();
+ TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
Taxon taxon = Taxon.NewInstance(name, sec);
handleIdentifiableEntity(taxon);
- TaxonNameBase<?,?> synName = BotanicalName.NewInstance(Rank.GENUS());
- Synonym syn = Synonym.NewInstance(synName, sec);
- SynonymRelationship synRel = taxon.addSynonym(syn, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(),
- getReference(), "123");
+ TaxonName synName = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
+ Synonym syn = Synonym.NewInstance(synName, sec, "123");
+ taxon.addSynonym(syn, SynonymType.HETEROTYPIC_SYNONYM_OF());
taxon.setDoubtful(true);
- handleAnnotatableEntity(synRel);
handleIdentifiableEntity(syn);
TaxonRelationship taxRel = taxon.addTaxonRelation(concept, TaxonRelationshipType.CONGRUENT_TO(),
sec, "444");
taxon.setTaxonStatusUnknown(true);
- taxon.setUnplaced(true);
- taxon.setExcluded(true);
handleAnnotatableEntity(taxRel);
classification.addGeoScope(Country.GERMANY());
classification.putDescription(Language.ENGLISH(), "An interesting classification");
-
TaxonNode node = classification.addChildTaxon(taxon, sec,"22");
handleIdentifiableEntity(classification);
handleAnnotatableEntity(node);
+ node.putExcludedNote(Language.DEFAULT(), "Excluded note");
+ DefinedTerm agentRelationType = DefinedTerm.NewTaxonNodeAgentRelationTypeInstance(null, "agentRelation", "ar");
+ Person agent = Person.NewTitledInstance("Related agent");
+ TaxonNodeAgentRelation agentRelation = node.addAgentRelation(agentRelationType, agent);
+ handleAnnotatableEntity(agentRelation);
Taxon childTaxon = Taxon.NewInstance(synName, sec);
node.addChildTaxon(childTaxon, sec, "44");
+ node.setUnplaced(true);
+ node.setExcluded(true);
cdmBases.add(taxon);
cdmBases.add(concept);
cdmBases.add(childTaxon);
cdmBases.add(classification);
+ cdmBases.add(agentRelationType);
}
private void createReference(List<CdmBase> cdmBases) {
- Reference<?> reference = ReferenceFactory.newArticle();
+ Reference reference = ReferenceFactory.newArticle();
Person author = Person.NewTitledInstance("Author team");
reference.setAuthorship(author);
reference.setTitle("ref title");
reference.setAbbrevTitle("abbrev title");
- reference.setDatePublished(TimePeriodParser.parseString("1999"));
+ reference.setDatePublished(TimePeriodParser.parseStringVerbatim("1999"));
reference.setEdition("edition");
reference.setEditor("editor");
Institution institution = Institution.NewInstance();
reference.setVolume("vol. 3");
reference.setUri(URI.create("http://rer.abc.de"));
- Reference<?> journal = ReferenceFactory.newJournal();
+ Reference journal = ReferenceFactory.newJournal();
reference.setInJournal(journal);
handleIdentifiableEntity(reference);
mediaSpecimen.setAccessionNumber("accessionNumber");
// mediaSpecimen.setCollectorsNumber("collectorsNumber");
mediaSpecimen.setBarcode("barcode");
- BotanicalName storedUnder = BotanicalName.NewInstance(Rank.SPECIES());
+ TaxonName storedUnder = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
storedUnder.setTitleCache("Stored under", true);
mediaSpecimen.setStoredUnder(storedUnder);
mediaSpecimen.setExsiccatum("exsiccatum");
handleAnnotatableEntity(event);
handleEventBase(event);
-
//SpecOrObservationBase
fieldUnit.setSex(DefinedTerm.SEX_FEMALE());
DefinedTerm lifeStage = DefinedTerm.NewStageInstance("Live stage", "stage", null);
DefinedTerm kindOfUnit = DefinedTerm.NewKindOfUnitInstance("Kind of unit", "Kind of unit", null);
cdmBases.add(kindOfUnit);
fieldUnit.setKindOfUnit(kindOfUnit);
- fieldUnit.setIndividualCount(3);
+ fieldUnit.setIndividualCount("3");
fieldUnit.putDefinition(Language.ENGLISH(), "definition");
fieldUnit.setPublish(true);
handleIdentifiableEntity(fieldUnit);
private void createTaxonName(List<CdmBase> cdmBases) {
- BacterialName bacName = BacterialName.NewInstance(Rank.GENUS());
+ TaxonName bacName = TaxonNameFactory.NewBacterialInstance(Rank.GENUS());
bacName.setSubGenusAuthorship("sub Genus author");
bacName.setNameApprobation("nameApprobation");
handleIdentifiableEntity(bacName);
- CultivarPlantName botName = CultivarPlantName.NewInstance(Rank.SUBSPECIES());
+ TaxonName botName = TaxonNameFactory.NewCultivarInstance(Rank.SUBSPECIES());
botName.setAnamorphic(true);
botName.setCultivarName("cultivarName");
botName.setGenusOrUninomial("Genus");
botName.setExBasionymAuthorship(exBasionymAuthorship);
handleIdentifiableEntity(botName);
handleAnnotatableEntity(botName.getHomotypicalGroup());
- BotanicalName botName2 = BotanicalName.NewInstance(Rank.SPECIES());
+ TaxonName botName2 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
HybridRelationship hybridRel = botName2.addHybridChild(botName, HybridRelationshipType.FIRST_PARENT(), "Rule 1.2.3");
hybridRel.setCitation(ReferenceFactory.newBook());
hybridRel.setCitationMicroReference("p. 123");
handleAnnotatableEntity(hybridRel);
- ZoologicalName zooName = ZoologicalName.NewInstance(Rank.GENUS());
+ TaxonName zooName = TaxonNameFactory.NewZoologicalInstance(Rank.GENUS());
zooName.setBreed("breed");
zooName.setPublicationYear(1922);
zooName.setOriginalPublicationYear(1987);
handleIdentifiableEntity(zooName);
//TypeDesignation
- ZoologicalName speciesZooName = ZoologicalName.NewInstance(Rank.SPECIES());
+ TaxonName speciesZooName = TaxonNameFactory.NewZoologicalInstance(Rank.SPECIES());
NameTypeDesignation nameDesig = zooName.addNameTypeDesignation(speciesZooName, getReference(), "111", "original name",
NameTypeDesignationStatus.AUTOMATIC(), true, true, true, true);
handleAnnotatableEntity(nameDesig);
getReference(), "p,22", "original name", false, true);
handleAnnotatableEntity(specimenDesig);
- ViralName viralName = ViralName.NewInstance(Rank.GENUS());
+ TaxonName viralName = TaxonNameFactory.NewViralInstance(Rank.GENUS());
viralName.setAcronym("acronym");
handleIdentifiableEntity(viralName);
-
+ //Registration
+ Registration registration = Registration.NewInstance("registration identifier",
+ "specificIdentifier", speciesZooName, null);
+ registration.addTypeDesignation(specimenDesig);
+ registration.setRegistrationDate(DateTime.now());
+ Registration blockingRegistration = Registration.NewInstance();
+ registration.addBlockedBy(blockingRegistration);
+ registration.setInstitution(Institution.NewInstance());
+ User submitter = User.NewInstance("submitter", "12345");
+ registration.setSubmitter(submitter);
+ handleAnnotatableEntity(registration);;
+
+ cdmBases.add(submitter);
cdmBases.add(bacName);
cdmBases.add(botName);
cdmBases.add(viralName);
cdmBases.add(zooName);
+ cdmBases.add(botName2);
}
private void handleEventBase(EventBase event){
Extension.NewInstance(identifiableEntity, "extension", ExtensionType.INFORMAL_CATEGORY());
//Identifier
- Identifier<?> identifier = Identifier.NewInstance(identifiableEntity, "ident23", DefinedTerm.SEX_FEMALE());
+ Identifier<?> identifier = identifiableEntity.addIdentifier("ident23", DefinedTerm.SEX_FEMALE());
handleAnnotatableEntity(identifier);
}
- private Reference<?> getReference() {
- Reference<?> result = ReferenceFactory.newGeneric();
+ private Reference getReference() {
+ Reference result = ReferenceFactory.newGeneric();
result.setTitle("some generic reference");
return result;
}
private Taxon getTaxon() {
- Reference<?> sec = getReference();
- TaxonNameBase<?,?> name = BotanicalName.NewInstance(Rank.GENUS());
+ Reference sec = getReference();
+ TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
Taxon taxon = Taxon.NewInstance(name, sec);
return taxon;
BGBM BDI Projects / cdmlib.git / blobdiff