Revision 91b69818
Added by Andreas Kohlbecker over 7 years ago
app-import/src/main/java/eu/etaxonomy/cdm/app/util/TestDatabase.java | ||
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/** |
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* Copyright (C) 2008 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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*/ |
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package eu.etaxonomy.cdm.app.util; |
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import java.util.ArrayList; |
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import java.util.GregorianCalendar; |
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import java.util.List; |
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import org.apache.log4j.Logger; |
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import org.springframework.transaction.TransactionStatus; |
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import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
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import eu.etaxonomy.cdm.common.AccountStore; |
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import eu.etaxonomy.cdm.database.CdmDataSource; |
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import eu.etaxonomy.cdm.database.DbSchemaValidation; |
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import eu.etaxonomy.cdm.database.ICdmDataSource; |
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import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController; |
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import eu.etaxonomy.cdm.io.jaxb.DataSet; |
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import eu.etaxonomy.cdm.model.agent.AgentBase; |
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import eu.etaxonomy.cdm.model.agent.Institution; |
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import eu.etaxonomy.cdm.model.agent.InstitutionalMembership; |
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import eu.etaxonomy.cdm.model.agent.Person; |
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import eu.etaxonomy.cdm.model.common.AnnotatableEntity; |
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import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
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import eu.etaxonomy.cdm.model.common.TimePeriod; |
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import eu.etaxonomy.cdm.model.common.VersionableEntity; |
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import eu.etaxonomy.cdm.model.description.Feature; |
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation; |
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import eu.etaxonomy.cdm.model.description.QuantitativeData; |
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure; |
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import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue; |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
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import eu.etaxonomy.cdm.model.description.TaxonInteraction; |
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription; |
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import eu.etaxonomy.cdm.model.location.Country; |
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import eu.etaxonomy.cdm.model.location.NamedAreaType; |
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import eu.etaxonomy.cdm.model.name.BotanicalName; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
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import eu.etaxonomy.cdm.model.taxon.Classification; |
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import eu.etaxonomy.cdm.model.taxon.Synonym; |
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
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import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
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/** |
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* @author a.babadshanjan |
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* @created 28.10.2008 |
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*/ |
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public class TestDatabase { |
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private static final String server = "192.168.2.10"; |
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private static final String username = "edit"; |
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private static final Logger logger = Logger.getLogger(TestDatabase.class); |
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public static ICdmDataSource CDM_DB(String dbname) { |
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logger.info("Setting DB " + dbname); |
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String password = AccountStore.readOrStorePassword(dbname, server, username, null); |
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ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, dbname, username, password, NomenclaturalCode.ICNAFP); |
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return datasource; |
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} |
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public static CdmApplicationController initDb(ICdmDataSource db, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading) { |
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logger.info("Initializing database '" + db.getName() + "'"); |
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CdmApplicationController appCtrInit = CdmIoApplicationController.NewInstance(db, dbSchemaValidation, omitTermLoading); |
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return appCtrInit; |
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} |
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public static void loadTestData(String dbname, CdmApplicationController appCtr) { |
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logger.info("Loading test data into " + dbname); |
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TransactionStatus txStatus = appCtr.startTransaction(); |
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DataSet dataSet = buildDataSet(); |
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appCtr.getTermService().save(dataSet.getTerms()); |
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appCtr.getTaxonService().save((List)dataSet.getTaxonBases()); |
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appCtr.commitTransaction(txStatus); |
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appCtr.close(); |
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} |
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/** |
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* This method constructs a small sample classification to test JAXB marshaling. |
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* The sample tree contains four taxa. The root taxon has two children taxa, and |
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* there is one "free" taxon without a parent and children. |
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*/ |
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private static DataSet buildDataSet() { |
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List<AgentBase> agents = new ArrayList<AgentBase>(); |
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List<VersionableEntity> agentData = new ArrayList<VersionableEntity>(); |
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//List<Agent> agentData = new ArrayList<Agent>(); |
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//List<TermBase> terms = new ArrayList<TermBase>(); |
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List<DefinedTermBase> terms = new ArrayList<DefinedTermBase>(); |
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List<Reference> references = new ArrayList<Reference>(); |
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List<TaxonNameBase> taxonomicNames = new ArrayList<TaxonNameBase>(); |
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List<TaxonBase> taxonBases = new ArrayList<TaxonBase>(); |
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List<Feature> features = new ArrayList<Feature>(); |
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Feature feature1 = Feature.BIOLOGY_ECOLOGY(); |
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TaxonNameDescription taxNameDescription = TaxonNameDescription.NewInstance(); |
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// taxNameDescription.addFeature(feature1); //no longer supported since v3.3 |
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QuantitativeData element = QuantitativeData.NewInstance(); |
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StatisticalMeasurementValue statisticalValue = StatisticalMeasurementValue.NewInstance(); |
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statisticalValue.setType(StatisticalMeasure.MAX()); |
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statisticalValue.setValue((float) 2.1); |
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element.addStatisticalValue(statisticalValue); |
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taxNameDescription.addElement(element); |
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SpecimenOrObservationBase<?> specimen = DerivedUnit.NewPreservedSpecimenInstance(); |
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specimen.setIndividualCount(12); |
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Feature featureIndAss = Feature.INDIVIDUALS_ASSOCIATION(); |
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TaxonNameDescription newTaxNameDesc = TaxonNameDescription.NewInstance(); |
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// newTaxNameDesc.addFeature(featureIndAss); //no longer supported since v3.3 |
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IndividualsAssociation indAss = IndividualsAssociation.NewInstance(); |
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indAss.setAssociatedSpecimenOrObservation(specimen); |
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newTaxNameDesc.addElement(indAss); |
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// List<Synonym> synonyms = new ArrayList<Synonym>(); |
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List<AnnotatableEntity> homotypicalGroups; |
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Reference citRef, sec; |
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BotanicalName name1, name2, name21, nameRoot1, nameFree, synName11, synName12, synName2, synNameFree; |
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BotanicalName nameRoot2, nameR2_1, nameR2_2; |
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Taxon child1, child2, child21, root1T, root2T, freeT; |
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Taxon childR2_1, childR2_2; |
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TaxonNode child1Node, child2Node, child21Node, root1TNode, root2TNode, freeTNode; |
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TaxonNode childR2_1Node, childR2_2Node; |
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Classification taxTree, taxTree2; |
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Synonym syn11, syn12, syn2, synFree; |
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Rank rankSpecies, rankSubspecies, rankGenus; |
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// agents |
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// - persons, institutions |
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Person linne = new Person("Carl", "Linne", "L."); |
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linne.setTitleCache("Linne & Karl", true); |
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GregorianCalendar birth = new GregorianCalendar(1707, 4, 23); |
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GregorianCalendar death = new GregorianCalendar(1778, 0, 10); |
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TimePeriod period = TimePeriod.NewInstance(birth, death); |
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linne.setLifespan(period); |
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// Keyword keyword = Keyword.NewInstance("plantarum", "lat", ""); |
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// linne.addKeyword(keyword); |
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Institution institute = Institution.NewInstance(); |
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agents.add(linne); |
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agents.add(institute); |
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// agent data |
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// - contacts, addresses, memberships |
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//Contact contact1 = new Contact(); |
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//contact1.setEmail("someone@somewhere.org"); |
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InstitutionalMembership membership |
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= new InstitutionalMembership(institute, linne, period, "Biodiversity", "Head"); |
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//agentData.add(contact1); |
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agentData.add(membership); |
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// terms |
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// - ranks, keywords |
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rankSpecies = Rank.SPECIES(); |
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rankSubspecies = Rank.SUBSPECIES(); |
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rankGenus = Rank.GENUS(); |
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// terms.add(keyword); |
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// taxonomic names |
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nameRoot1 = BotanicalName.NewInstance(rankGenus,"Calendula",null,null,null,linne,null,"p.100", null); |
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nameRoot1.addDescription(taxNameDescription); |
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nameRoot1.addDescription(newTaxNameDesc); |
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name1 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"arvensis",null,linne,null,"p.1", null); |
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synName11 = BotanicalName.NewInstance(rankSpecies,"Caltha",null,"arvensis",null,linne,null,"p.11", null); |
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synName12 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"sancta",null,linne,null,"p.12", null); |
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name2 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzae",null,linne,null,"p.2", null); |
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synName2 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"echinata",null,linne,null,"p.2", null); |
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name21 = BotanicalName.NewInstance(rankSubspecies,"Calendula",null,"lanzea","something",linne,null,"p.1", null); |
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//name211 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null); |
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//name212 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null); |
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nameRoot2 = |
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BotanicalName.NewInstance(rankGenus,"Sonchus",null,null,null,linne,null,"p.200", null); |
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nameR2_1 = BotanicalName.NewInstance(rankSpecies,"Sonchus",null,"child1",null,linne,null,"p.1", null); |
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nameR2_2 = BotanicalName.NewInstance(rankSpecies,"Sonchus",null,"child2",null,linne,null,"p.2", null); |
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nameFree = BotanicalName.NewInstance(rankSpecies,"Cichorium",null,"intybus",null,linne,null,"p.200", null); |
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synNameFree = BotanicalName.NewInstance(rankSpecies,"Cichorium",null,"balearicum",null,linne,null,"p.2", null); |
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taxonomicNames.add(nameRoot1); |
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taxonomicNames.add(name1); |
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taxonomicNames.add(synName11); |
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taxonomicNames.add(synName12); |
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taxonomicNames.add(name2); |
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taxonomicNames.add(name21); |
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taxonomicNames.add(synName2); |
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taxonomicNames.add(nameFree); |
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taxonomicNames.add(synNameFree); |
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taxonomicNames.add(nameRoot2); |
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// references |
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sec = ReferenceFactory.newBook(); |
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sec.setAuthorship(linne); |
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sec.setTitleCache("Plant Specification & Taxonomy", true); |
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references.add(sec); |
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citRef = ReferenceFactory.newDatabase(); |
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citRef.setAuthorship(linne); |
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citRef.setTitleCache("BioCASE", true); |
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references.add(citRef); |
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// taxa |
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root1T = Taxon.NewInstance(nameRoot1, sec); |
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root2T = Taxon.NewInstance(nameRoot2, sec); |
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freeT = Taxon.NewInstance(nameFree, sec); |
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child1 = Taxon.NewInstance(name1, sec); |
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child2 = Taxon.NewInstance(name2, sec); |
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child21 = Taxon.NewInstance(name21, sec); |
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childR2_1 = Taxon.NewInstance(nameR2_1, sec); |
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childR2_2 = Taxon.NewInstance(nameR2_2, sec); |
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//TaxonInteractions |
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TaxonInteraction descBase = TaxonInteraction.NewInstance(); |
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descBase.setTaxon2(root1T); |
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Feature hostplant = Feature.HOSTPLANT(); |
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descBase.setFeature(hostplant); |
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TaxonDescription taxDesc = TaxonDescription.NewInstance(); |
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taxDesc.addElement(descBase); |
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root2T.addDescription(taxDesc); |
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//locations |
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taxDesc = TaxonDescription.NewInstance(); |
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Feature locationFeature = Feature.DISTRIBUTION(); |
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//locationFeature. |
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Country area = Country.NewInstance("", "locationTest", null); |
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area.setType(NamedAreaType.NATURAL_AREA()); |
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//Country woC= Country.NewInstance(); |
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area.addCountry(Country.AFGHANISTAN()); |
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taxDesc.addGeoScope(area); |
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// taxDesc.addFeature(locationFeature); //no longer supported since v3.3 |
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root1T.addDescription(taxDesc); |
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// synonyms |
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synFree = Synonym.NewInstance(synNameFree, sec); |
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syn11 = Synonym.NewInstance(synName11, sec); |
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syn12 = Synonym.NewInstance(synName12, sec); |
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syn2 = Synonym.NewInstance(synName2, sec); |
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child1.addSynonym(syn11, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF()); |
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child1.addSynonym(syn12, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF()); |
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child2.addSynonym(syn2, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF()); |
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freeT.addSynonym(synFree, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF()); |
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taxonBases.add(synFree); |
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taxonBases.add(syn11); |
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taxonBases.add(syn12); |
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taxonBases.add(syn2); |
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// taxonomic children |
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//TODO: Adapt to classification |
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taxTree = Classification.NewInstance("TestTree"); |
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root1TNode = taxTree.addChildTaxon(root1T, sec, null); |
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child1Node = root1TNode.addChildTaxon(child1, null, null); |
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child2Node = root1TNode.addChildTaxon(child2, null, null); |
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child21Node = child2Node.addChildTaxon(child21, null, null); |
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taxTree2 = Classification.NewInstance("TestTree2"); |
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root2TNode = taxTree2.addChildTaxon(root2T, sec, null); |
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root2TNode.addChildTaxon(child1, sec, "p.1010").setSynonymToBeUsed(syn11); |
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root2TNode.addChildTaxon(child2, null, null); |
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/* |
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root1T.addTaxonomicChild(child1, sec, "p.1010"); |
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root1T.addTaxonomicChild(child2, sec, "p.1020"); |
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child2.addTaxonomicChild(child21, sec, "p.2000"); |
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root2T.addTaxonomicChild(child1, sec, "p.1010"); |
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root2T.addTaxonomicChild(child2, sec, "p.1020"); |
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*/ |
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// |
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taxonBases.add(root1T); |
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taxonBases.add(root2T); |
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taxonBases.add(freeT); |
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taxonBases.add(child1); |
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taxonBases.add(child2); |
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taxonBases.add(child21); |
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taxonBases.add(childR2_1); |
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taxonBases.add(childR2_2); |
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DataSet dataSet = new DataSet(); |
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logger.warn("WARNING: TestDatabase has been commented in parts. Mainly, must be adapted to classification."); |
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dataSet.setTerms(terms); |
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dataSet.setAgents(agents); |
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// dataSet.setAgentData(agentData); //TODO |
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dataSet.setReferences(references); |
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dataSet.setTaxonomicNames(taxonomicNames); |
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dataSet.setTaxonBases((List)taxonBases); |
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return dataSet; |
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} |
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} |
app-import/src/test/java/eu/etaxonomy/cdm/app/util/TestDatabase.java | ||
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/** |
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* Copyright (C) 2008 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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*/ |
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package eu.etaxonomy.cdm.app.util; |
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import java.util.ArrayList; |
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import java.util.GregorianCalendar; |
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import java.util.List; |
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import org.apache.log4j.Logger; |
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import org.springframework.transaction.TransactionStatus; |
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import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
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import eu.etaxonomy.cdm.common.AccountStore; |
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import eu.etaxonomy.cdm.database.CdmDataSource; |
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import eu.etaxonomy.cdm.database.DbSchemaValidation; |
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import eu.etaxonomy.cdm.database.ICdmDataSource; |
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import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController; |
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import eu.etaxonomy.cdm.io.jaxb.DataSet; |
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import eu.etaxonomy.cdm.model.agent.AgentBase; |
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import eu.etaxonomy.cdm.model.agent.Institution; |
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import eu.etaxonomy.cdm.model.agent.InstitutionalMembership; |
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import eu.etaxonomy.cdm.model.agent.Person; |
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import eu.etaxonomy.cdm.model.common.AnnotatableEntity; |
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import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
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import eu.etaxonomy.cdm.model.common.TimePeriod; |
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import eu.etaxonomy.cdm.model.common.VersionableEntity; |
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import eu.etaxonomy.cdm.model.description.Feature; |
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation; |
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import eu.etaxonomy.cdm.model.description.QuantitativeData; |
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure; |
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import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue; |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
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import eu.etaxonomy.cdm.model.description.TaxonInteraction; |
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription; |
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import eu.etaxonomy.cdm.model.location.Country; |
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import eu.etaxonomy.cdm.model.location.NamedAreaType; |
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import eu.etaxonomy.cdm.model.name.BotanicalName; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
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import eu.etaxonomy.cdm.model.taxon.Classification; |
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import eu.etaxonomy.cdm.model.taxon.Synonym; |
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
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import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
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/** |
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* @author a.babadshanjan |
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* @created 28.10.2008 |
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*/ |
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public class TestDatabase { |
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private static final String server = "192.168.2.10"; |
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private static final String username = "edit"; |
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private static final Logger logger = Logger.getLogger(TestDatabase.class); |
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public static ICdmDataSource CDM_DB(String dbname) { |
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logger.info("Setting DB " + dbname); |
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String password = AccountStore.readOrStorePassword(dbname, server, username, null); |
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ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, dbname, username, password, NomenclaturalCode.ICNAFP); |
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return datasource; |
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} |
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public static CdmApplicationController initDb(ICdmDataSource db, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading) { |
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logger.info("Initializing database '" + db.getName() + "'"); |
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CdmApplicationController appCtrInit = CdmIoApplicationController.NewInstance(db, dbSchemaValidation, omitTermLoading); |
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return appCtrInit; |
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} |
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public static void loadTestData(String dbname, CdmApplicationController appCtr) { |
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logger.info("Loading test data into " + dbname); |
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TransactionStatus txStatus = appCtr.startTransaction(); |
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DataSet dataSet = buildDataSet(); |
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appCtr.getTermService().save(dataSet.getTerms()); |
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appCtr.getTaxonService().save((List)dataSet.getTaxonBases()); |
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appCtr.commitTransaction(txStatus); |
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appCtr.close(); |
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} |
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/** |
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* This method constructs a small sample classification to test JAXB marshaling. |
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* The sample tree contains four taxa. The root taxon has two children taxa, and |
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* there is one "free" taxon without a parent and children. |
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*/ |
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private static DataSet buildDataSet() { |
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List<AgentBase> agents = new ArrayList<AgentBase>(); |
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List<VersionableEntity> agentData = new ArrayList<VersionableEntity>(); |
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//List<Agent> agentData = new ArrayList<Agent>(); |
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//List<TermBase> terms = new ArrayList<TermBase>(); |
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List<DefinedTermBase> terms = new ArrayList<DefinedTermBase>(); |
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List<Reference> references = new ArrayList<Reference>(); |
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List<TaxonNameBase> taxonomicNames = new ArrayList<TaxonNameBase>(); |
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List<TaxonBase> taxonBases = new ArrayList<TaxonBase>(); |
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List<Feature> features = new ArrayList<Feature>(); |
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Feature feature1 = Feature.BIOLOGY_ECOLOGY(); |
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TaxonNameDescription taxNameDescription = TaxonNameDescription.NewInstance(); |
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// taxNameDescription.addFeature(feature1); //no longer supported since v3.3 |
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QuantitativeData element = QuantitativeData.NewInstance(); |
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StatisticalMeasurementValue statisticalValue = StatisticalMeasurementValue.NewInstance(); |
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statisticalValue.setType(StatisticalMeasure.MAX()); |
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statisticalValue.setValue((float) 2.1); |
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element.addStatisticalValue(statisticalValue); |
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taxNameDescription.addElement(element); |
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SpecimenOrObservationBase<?> specimen = DerivedUnit.NewPreservedSpecimenInstance(); |
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specimen.setIndividualCount(12); |
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Feature featureIndAss = Feature.INDIVIDUALS_ASSOCIATION(); |
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TaxonNameDescription newTaxNameDesc = TaxonNameDescription.NewInstance(); |
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// newTaxNameDesc.addFeature(featureIndAss); //no longer supported since v3.3 |
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IndividualsAssociation indAss = IndividualsAssociation.NewInstance(); |
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indAss.setAssociatedSpecimenOrObservation(specimen); |
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newTaxNameDesc.addElement(indAss); |
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// List<Synonym> synonyms = new ArrayList<Synonym>(); |
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List<AnnotatableEntity> homotypicalGroups; |
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Reference citRef, sec; |
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BotanicalName name1, name2, name21, nameRoot1, nameFree, synName11, synName12, synName2, synNameFree; |
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BotanicalName nameRoot2, nameR2_1, nameR2_2; |
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Taxon child1, child2, child21, root1T, root2T, freeT; |
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Taxon childR2_1, childR2_2; |
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TaxonNode child1Node, child2Node, child21Node, root1TNode, root2TNode, freeTNode; |
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TaxonNode childR2_1Node, childR2_2Node; |
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Classification taxTree, taxTree2; |
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Synonym syn11, syn12, syn2, synFree; |
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Rank rankSpecies, rankSubspecies, rankGenus; |
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// agents |
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// - persons, institutions |
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Person linne = new Person("Carl", "Linne", "L."); |
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linne.setTitleCache("Linne & Karl", true); |
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GregorianCalendar birth = new GregorianCalendar(1707, 4, 23); |
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GregorianCalendar death = new GregorianCalendar(1778, 0, 10); |
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TimePeriod period = TimePeriod.NewInstance(birth, death); |
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linne.setLifespan(period); |
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// Keyword keyword = Keyword.NewInstance("plantarum", "lat", ""); |
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// linne.addKeyword(keyword); |
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Institution institute = Institution.NewInstance(); |
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agents.add(linne); |
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agents.add(institute); |
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// agent data |
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// - contacts, addresses, memberships |
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//Contact contact1 = new Contact(); |
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//contact1.setEmail("someone@somewhere.org"); |
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InstitutionalMembership membership |
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= new InstitutionalMembership(institute, linne, period, "Biodiversity", "Head"); |
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//agentData.add(contact1); |
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agentData.add(membership); |
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// terms |
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// - ranks, keywords |
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rankSpecies = Rank.SPECIES(); |
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rankSubspecies = Rank.SUBSPECIES(); |
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rankGenus = Rank.GENUS(); |
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// terms.add(keyword); |
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// taxonomic names |
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nameRoot1 = BotanicalName.NewInstance(rankGenus,"Calendula",null,null,null,linne,null,"p.100", null); |
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nameRoot1.addDescription(taxNameDescription); |
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nameRoot1.addDescription(newTaxNameDesc); |
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name1 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"arvensis",null,linne,null,"p.1", null); |
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synName11 = BotanicalName.NewInstance(rankSpecies,"Caltha",null,"arvensis",null,linne,null,"p.11", null); |
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synName12 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"sancta",null,linne,null,"p.12", null); |
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name2 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzae",null,linne,null,"p.2", null); |
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synName2 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"echinata",null,linne,null,"p.2", null); |
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name21 = BotanicalName.NewInstance(rankSubspecies,"Calendula",null,"lanzea","something",linne,null,"p.1", null); |
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//name211 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null); |
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//name212 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null); |
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nameRoot2 = |
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BotanicalName.NewInstance(rankGenus,"Sonchus",null,null,null,linne,null,"p.200", null); |
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nameR2_1 = BotanicalName.NewInstance(rankSpecies,"Sonchus",null,"child1",null,linne,null,"p.1", null); |
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nameR2_2 = BotanicalName.NewInstance(rankSpecies,"Sonchus",null,"child2",null,linne,null,"p.2", null); |
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nameFree = BotanicalName.NewInstance(rankSpecies,"Cichorium",null,"intybus",null,linne,null,"p.200", null); |
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synNameFree = BotanicalName.NewInstance(rankSpecies,"Cichorium",null,"balearicum",null,linne,null,"p.2", null); |
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taxonomicNames.add(nameRoot1); |
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taxonomicNames.add(name1); |
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taxonomicNames.add(synName11); |
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taxonomicNames.add(synName12); |
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taxonomicNames.add(name2); |
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taxonomicNames.add(name21); |
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taxonomicNames.add(synName2); |
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taxonomicNames.add(nameFree); |
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taxonomicNames.add(synNameFree); |
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taxonomicNames.add(nameRoot2); |
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// references |
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sec = ReferenceFactory.newBook(); |
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sec.setAuthorship(linne); |
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sec.setTitleCache("Plant Specification & Taxonomy", true); |
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references.add(sec); |
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citRef = ReferenceFactory.newDatabase(); |
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citRef.setAuthorship(linne); |
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citRef.setTitleCache("BioCASE", true); |
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references.add(citRef); |
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// taxa |
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root1T = Taxon.NewInstance(nameRoot1, sec); |
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root2T = Taxon.NewInstance(nameRoot2, sec); |
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freeT = Taxon.NewInstance(nameFree, sec); |
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child1 = Taxon.NewInstance(name1, sec); |
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child2 = Taxon.NewInstance(name2, sec); |
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child21 = Taxon.NewInstance(name21, sec); |
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childR2_1 = Taxon.NewInstance(nameR2_1, sec); |
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childR2_2 = Taxon.NewInstance(nameR2_2, sec); |
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//TaxonInteractions |
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TaxonInteraction descBase = TaxonInteraction.NewInstance(); |
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descBase.setTaxon2(root1T); |
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Feature hostplant = Feature.HOSTPLANT(); |
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descBase.setFeature(hostplant); |
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TaxonDescription taxDesc = TaxonDescription.NewInstance(); |
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taxDesc.addElement(descBase); |
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root2T.addDescription(taxDesc); |
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//locations |
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taxDesc = TaxonDescription.NewInstance(); |
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Feature locationFeature = Feature.DISTRIBUTION(); |
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//locationFeature. |
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Country area = Country.NewInstance("", "locationTest", null); |
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area.setType(NamedAreaType.NATURAL_AREA()); |
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//Country woC= Country.NewInstance(); |
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area.addCountry(Country.AFGHANISTAN()); |
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taxDesc.addGeoScope(area); |
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// taxDesc.addFeature(locationFeature); //no longer supported since v3.3 |
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root1T.addDescription(taxDesc); |
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280 |
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// synonyms |
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282 |
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synFree = Synonym.NewInstance(synNameFree, sec); |
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syn11 = Synonym.NewInstance(synName11, sec); |
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syn12 = Synonym.NewInstance(synName12, sec); |
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syn2 = Synonym.NewInstance(synName2, sec); |
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child1.addSynonym(syn11, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF()); |
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child1.addSynonym(syn12, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF()); |
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child2.addSynonym(syn2, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF()); |
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freeT.addSynonym(synFree, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF()); |
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taxonBases.add(synFree); |
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taxonBases.add(syn11); |
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taxonBases.add(syn12); |
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taxonBases.add(syn2); |
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297 |
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// taxonomic children |
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299 |
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//TODO: Adapt to classification |
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taxTree = Classification.NewInstance("TestTree"); |
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302 |
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root1TNode = taxTree.addChildTaxon(root1T, sec, null); |
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304 |
child1Node = root1TNode.addChildTaxon(child1, null, null); |
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305 |
child2Node = root1TNode.addChildTaxon(child2, null, null); |
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306 |
child21Node = child2Node.addChildTaxon(child21, null, null); |
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307 |
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taxTree2 = Classification.NewInstance("TestTree2"); |
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309 |
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310 |
root2TNode = taxTree2.addChildTaxon(root2T, sec, null); |
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root2TNode.addChildTaxon(child1, sec, "p.1010").setSynonymToBeUsed(syn11); |
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312 |
root2TNode.addChildTaxon(child2, null, null); |
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313 |
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314 |
/* |
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315 |
root1T.addTaxonomicChild(child1, sec, "p.1010"); |
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316 |
root1T.addTaxonomicChild(child2, sec, "p.1020"); |
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317 |
child2.addTaxonomicChild(child21, sec, "p.2000"); |
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318 |
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root2T.addTaxonomicChild(child1, sec, "p.1010"); |
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320 |
root2T.addTaxonomicChild(child2, sec, "p.1020"); |
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*/ |
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322 |
// |
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323 |
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324 |
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325 |
taxonBases.add(root1T); |
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326 |
taxonBases.add(root2T); |
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taxonBases.add(freeT); |
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328 |
taxonBases.add(child1); |
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329 |
taxonBases.add(child2); |
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330 |
taxonBases.add(child21); |
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331 |
taxonBases.add(childR2_1); |
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332 |
taxonBases.add(childR2_2); |
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333 |
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334 |
DataSet dataSet = new DataSet(); |
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335 |
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336 |
logger.warn("WARNING: TestDatabase has been commented in parts. Mainly, must be adapted to classification."); |
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337 |
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338 |
dataSet.setTerms(terms); |
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339 |
dataSet.setAgents(agents); |
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340 |
// dataSet.setAgentData(agentData); //TODO |
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341 |
dataSet.setReferences(references); |
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342 |
dataSet.setTaxonomicNames(taxonomicNames); |
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343 |
dataSet.setTaxonBases((List)taxonBases); |
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344 |
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345 |
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346 |
return dataSet; |
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347 |
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348 |
} |
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349 |
} |
Also available in: Unified diff
moving TestDatabase back to main - a couple of classes had complie errors