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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.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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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.SynonymType;
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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);
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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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TaxonNameBase<?,?> name1, name2, name21, nameRoot1, nameFree, synName11, synName12, synName2, synNameFree;
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TaxonNameBase<?,?> 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 = TaxonNameFactory.NewBotanicalInstance(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 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Calendula",null,"arvensis",null,linne,null,"p.1", null);
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synName11 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Caltha",null,"arvensis",null,linne,null,"p.11", null);
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synName12 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Calendula",null,"sancta",null,linne,null,"p.12", null);
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name2 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Calendula",null,"lanzae",null,linne,null,"p.2", null);
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synName2 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Calendula",null,"echinata",null,linne,null,"p.2", null);
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name21 = TaxonNameFactory.NewBotanicalInstance(rankSubspecies,"Calendula",null,"lanzea","something",linne,null,"p.1", null);
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//name211 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null);
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//name212 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null);
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nameRoot2 =
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TaxonNameFactory.NewBotanicalInstance(rankGenus,"Sonchus",null,null,null,linne,null,"p.200", null);
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nameR2_1 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Sonchus",null,"child1",null,linne,null,"p.1", null);
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nameR2_2 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Sonchus",null,"child2",null,linne,null,"p.2", null);
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nameFree = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Cichorium",null,"intybus",null,linne,null,"p.200", null);
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synNameFree = TaxonNameFactory.NewBotanicalInstance(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, SynonymType.HOMOTYPIC_SYNONYM_OF());
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child1.addSynonym(syn12, SynonymType.HETEROTYPIC_SYNONYM_OF());
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child2.addSynonym(syn2, SynonymType.HETEROTYPIC_SYNONYM_OF());
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freeT.addSynonym(synFree, SynonymType.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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|
332
|
|
|
333
|
DataSet dataSet = new DataSet();
|
|
334
|
|
|
335
|
logger.warn("WARNING: TestDatabase has been commented in parts. Mainly, must be adapted to classification.");
|
|
336
|
|
|
337
|
dataSet.setTerms(terms);
|
|
338
|
dataSet.setAgents(agents);
|
|
339
|
// dataSet.setAgentData(agentData); //TODO
|
|
340
|
dataSet.setReferences(references);
|
|
341
|
dataSet.setTaxonomicNames(taxonomicNames);
|
|
342
|
dataSet.setTaxonBases((List)taxonBases);
|
|
343
|
|
|
344
|
|
|
345
|
return dataSet;
|
|
346
|
|
|
347
|
}
|
|
348
|
}
|