EDIT

/**

* Copyright (C) 2008 EDIT

* European Distributed Institute of Taxonomy 

* http://www.e-taxonomy.eu

*/

package eu.etaxonomy.cdm.app.util;

import java.util.ArrayList;

import java.util.GregorianCalendar;

import java.util.List;

import jxl.write.DateTime;

import org.apache.log4j.Logger;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.api.application.CdmApplicationController;

import eu.etaxonomy.cdm.common.AccountStore;

import eu.etaxonomy.cdm.database.CdmDataSource;

import eu.etaxonomy.cdm.database.DataSourceNotFoundException;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.jaxb.DataSet;

import eu.etaxonomy.cdm.model.agent.AgentBase;

import eu.etaxonomy.cdm.model.agent.Institution;

import eu.etaxonomy.cdm.model.agent.InstitutionalMembership;

import eu.etaxonomy.cdm.model.agent.Person;

import eu.etaxonomy.cdm.model.common.AnnotatableEntity;

import eu.etaxonomy.cdm.model.common.DefinedTermBase;

import eu.etaxonomy.cdm.model.common.IdentifiableSource;

import eu.etaxonomy.cdm.model.common.Language;

import eu.etaxonomy.cdm.model.common.TimePeriod;

import eu.etaxonomy.cdm.model.common.VersionableEntity;

import eu.etaxonomy.cdm.model.common.init.TermNotFoundException;

import eu.etaxonomy.cdm.model.description.DescriptionElementBase;

import eu.etaxonomy.cdm.model.description.Feature;

import eu.etaxonomy.cdm.model.description.IndividualsAssociation;

import eu.etaxonomy.cdm.model.description.QuantitativeData;

import eu.etaxonomy.cdm.model.description.StatisticalMeasure;

import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;

import eu.etaxonomy.cdm.model.description.TaxonDescription;

import eu.etaxonomy.cdm.model.description.TaxonInteraction;

import eu.etaxonomy.cdm.model.description.TaxonNameDescription;

import eu.etaxonomy.cdm.model.location.NamedArea;

import eu.etaxonomy.cdm.model.location.NamedAreaType;

import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;

import eu.etaxonomy.cdm.model.name.BotanicalName;

import eu.etaxonomy.cdm.model.name.NomenclaturalCode;

import eu.etaxonomy.cdm.model.name.Rank;

import eu.etaxonomy.cdm.model.name.TaxonNameBase;

import eu.etaxonomy.cdm.model.occurrence.Specimen;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

import eu.etaxonomy.cdm.model.reference.IBook;

import eu.etaxonomy.cdm.model.reference.IDatabase;

import eu.etaxonomy.cdm.model.reference.ReferenceBase;

import eu.etaxonomy.cdm.model.reference.ReferenceFactory;

import eu.etaxonomy.cdm.model.taxon.Synonym;

import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonBase;

import eu.etaxonomy.cdm.model.taxon.TaxonNode;

import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;

/**

 * @author a.babadshanjan

 * @created 28.10.2008

 */

public class TestDatabase {

	private static final String server = "192.168.2.10";

	private static final String username = "edit";

	private static final Logger logger = Logger.getLogger(TestDatabase.class);

	public static ICdmDataSource CDM_DB(String dbname) {

		logger.info("Setting DB " + dbname);

		String password = AccountStore.readOrStorePassword(dbname, server, username, null);

		ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, dbname, username, password, NomenclaturalCode.ICBN);

		return datasource;

	}

    public static CdmApplicationController 

    initDb(ICdmDataSource db, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading) {

		logger.info("Initializing database '" + db.getName() + "'");

		CdmApplicationController appCtrInit = null;

		try {

			appCtrInit = CdmApplicationController.NewInstance(db, dbSchemaValidation, omitTermLoading);

		} catch (DataSourceNotFoundException e) {

			logger.error("Could not connect to database");

		}catch (TermNotFoundException e) {

			logger.error("Terms not found in database. " +

			"This error should not happen if preloaded terms are not expected for this application.");

		}

		return appCtrInit;

    }

	public static void loadTestData(String dbname, CdmApplicationController appCtr) {

		logger.info("Loading test data into " + dbname);

		TransactionStatus txStatus = appCtr.startTransaction();

		DataSet dataSet = buildDataSet();

		appCtr.getTermService().save(dataSet.getTerms());

		appCtr.getTaxonService().save(dataSet.getTaxonBases());

		appCtr.commitTransaction(txStatus);

		appCtr.close();

    }

	/**

	 * This method constructs a small sample taxonomic tree to test JAXB marshaling.

	 * The sample tree contains four taxa. The root taxon has two children taxa, and

	 * there is one "free" taxon without a parent and children.

	 */

	private static DataSet buildDataSet() {

		List<AgentBase> agents = new ArrayList<AgentBase>();

	    List<VersionableEntity> agentData = new ArrayList<VersionableEntity>();

	    //List<Agent> agentData = new ArrayList<Agent>();

	    //List<TermBase> terms = new ArrayList<TermBase>();

	    List<DefinedTermBase> terms = new ArrayList<DefinedTermBase>();

	    List<ReferenceBase> references = new ArrayList<ReferenceBase>();

	    List<TaxonNameBase> taxonomicNames = new ArrayList<TaxonNameBase>();

	    List<TaxonBase> taxonBases = new ArrayList<TaxonBase>();

	    List<Feature> features = new ArrayList<Feature>();

	    Feature feature1 = Feature.BIOLOGY_ECOLOGY();

	    TaxonNameDescription taxNameDescription = TaxonNameDescription.NewInstance();

	    taxNameDescription.addFeature(feature1);

	    QuantitativeData element = QuantitativeData.NewInstance();

	    StatisticalMeasurementValue statisticalValue = StatisticalMeasurementValue.NewInstance();

	    statisticalValue.setType(StatisticalMeasure.MAX());

	    statisticalValue.setValue((float) 2.1);

	    element.addStatisticalValue(statisticalValue);

	    taxNameDescription.addElement(element);

	    SpecimenOrObservationBase specimen = Specimen.NewInstance();

	    specimen.setIndividualCount(12);

	    Feature featureIndAss = Feature.INDIVIDUALS_ASSOCIATION();

	    TaxonNameDescription newTaxNameDesc = TaxonNameDescription.NewInstance();

	    newTaxNameDesc.addFeature(featureIndAss);

	    IndividualsAssociation indAss = IndividualsAssociation.NewInstance();

	    indAss.setAssociatedSpecimenOrObservation(specimen);

	    newTaxNameDesc.addElement(indAss);

//	    List<Synonym> synonyms = new ArrayList<Synonym>();

	    List<AnnotatableEntity> homotypicalGroups;

		ReferenceBase citRef, sec;

		BotanicalName name1, name2, name21, nameRoot1, nameFree, synName11, synName12, synName2, synNameFree;

		BotanicalName nameRoot2, nameR2_1, nameR2_2;

		Taxon child1, child2, child21, root1T, root2T, freeT;

		Taxon childR2_1, childR2_2;

		TaxonNode child1Node, child2Node, child21Node, root1TNode, root2TNode, freeTNode;

		TaxonNode childR2_1Node, childR2_2Node;

		TaxonomicTree taxTree, taxTree2;

		Synonym syn11, syn12, syn2, synFree;

		Rank rankSpecies, rankSubspecies, rankGenus;

		// agents 

		// - persons, institutions 

		Person linne = new Person("Carl", "Linne", "L.");

		linne.setTitleCache("Linne & Karl", true);

		GregorianCalendar birth = new GregorianCalendar(1707, 4, 23);

		GregorianCalendar death = new GregorianCalendar(1778, 0, 10);

		TimePeriod period = TimePeriod.NewInstance(birth, death);

		linne.setLifespan(period);

//		Keyword keyword = Keyword.NewInstance("plantarum", "lat", "");

//		linne.addKeyword(keyword);

		Institution institute = Institution.NewInstance();

		agents.add(linne);

		agents.add(institute);

		// agent data

		// - contacts, addresses, memberships

		//Contact contact1 = new Contact();

		//contact1.setEmail("someone@somewhere.org");

		InstitutionalMembership membership 

		= new InstitutionalMembership(institute, linne, period, "Biodiversity", "Head");

		//agentData.add(contact1);

		agentData.add(membership);

		// terms

		// - ranks, keywords

		rankSpecies = Rank.SPECIES();

		rankSubspecies = Rank.SUBSPECIES();

		rankGenus = Rank.GENUS();

//		terms.add(keyword);

        // taxonomic names

		nameRoot1 = BotanicalName.NewInstance(rankGenus,"Calendula",null,null,null,linne,null,"p.100", null);

		nameRoot1.addDescription(taxNameDescription);

		nameRoot1.addDescription(newTaxNameDesc);

		name1 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"arvensis",null,linne,null,"p.1", null);

		synName11 = BotanicalName.NewInstance(rankSpecies,"Caltha",null,"arvensis",null,linne,null,"p.11", null);

		synName12 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"sancta",null,linne,null,"p.12", null);

		name2 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzae",null,linne,null,"p.2", null);

		synName2 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"echinata",null,linne,null,"p.2", null);

		name21 = BotanicalName.NewInstance(rankSubspecies,"Calendula",null,"lanzea","something",linne,null,"p.1", null);

		//name211 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null);

		//name212 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null);

		nameRoot2 = 

			BotanicalName.NewInstance(rankGenus,"Sonchus",null,null,null,linne,null,"p.200", null);

		nameR2_1 = BotanicalName.NewInstance(rankSpecies,"Sonchus",null,"child1",null,linne,null,"p.1", null);

		nameR2_2 = BotanicalName.NewInstance(rankSpecies,"Sonchus",null,"child2",null,linne,null,"p.2", null);

		nameFree = BotanicalName.NewInstance(rankSpecies,"Cichorium",null,"intybus",null,linne,null,"p.200", null);

		synNameFree = BotanicalName.NewInstance(rankSpecies,"Cichorium",null,"balearicum",null,linne,null,"p.2", null);

		taxonomicNames.add(nameRoot1);

		taxonomicNames.add(name1);

		taxonomicNames.add(synName11);

		taxonomicNames.add(synName12);

		taxonomicNames.add(name2);

		taxonomicNames.add(name21);

		taxonomicNames.add(synName2);

		taxonomicNames.add(nameFree);

		taxonomicNames.add(synNameFree);

		taxonomicNames.add(nameRoot2);

        // references

		ReferenceFactory refFactory = ReferenceFactory.newInstance();

		sec = refFactory.newBook();

		sec.setAuthorTeam(linne);

		sec.setTitleCache("Plant Specification & Taxonomy", true);

		references.add(sec);

		citRef = refFactory.newDatabase();

		citRef.setAuthorTeam(linne);

		citRef.setTitleCache("BioCASE", true);

		references.add(citRef);

		// taxa

		root1T = Taxon.NewInstance(nameRoot1, sec);

		root2T = Taxon.NewInstance(nameRoot2, sec);

		freeT = Taxon.NewInstance(nameFree, sec);

		child1 = Taxon.NewInstance(name1, sec);

		child2 = Taxon.NewInstance(name2, sec);

		child21 = Taxon.NewInstance(name21, sec);

		childR2_1 = Taxon.NewInstance(nameR2_1, sec);

		childR2_2 = Taxon.NewInstance(nameR2_2, sec);

		//TaxonInteractions

		TaxonInteraction descBase = TaxonInteraction.NewInstance();

		descBase.setTaxon2(root1T);

		Feature hostplant = Feature.HOSTPLANT();

		descBase.setFeature(hostplant);

		TaxonDescription taxDesc = TaxonDescription.NewInstance();

		taxDesc.addElement(descBase);

		root2T.addDescription(taxDesc);

		//locations

		taxDesc = TaxonDescription.NewInstance();

		Feature locationFeature = Feature.DISTRIBUTION();

		//locationFeature.

		WaterbodyOrCountry area = WaterbodyOrCountry.NewInstance("", "locationTest", null);

		area.setType(NamedAreaType.NATURAL_AREA());

		//WaterbodyOrCountry woC= WaterbodyOrCountry.NewInstance();

		area.addWaterbodyOrCountry(WaterbodyOrCountry.AFGHANISTAN());

		taxDesc.addGeoScope(area);

		taxDesc.addFeature(locationFeature);

		root1T.addDescription(taxDesc);

		// synonyms

		synFree = Synonym.NewInstance(synNameFree, sec);

		syn11 = Synonym.NewInstance(synName11, sec);

		syn12 = Synonym.NewInstance(synName12, sec);

		syn2 = Synonym.NewInstance(synName2, sec);

		child1.addSynonym(syn11, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF());

		child1.addSynonym(syn12, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());

		child2.addSynonym(syn2, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());

		freeT.addSynonym(synFree, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());

		taxonBases.add(synFree);

		taxonBases.add(syn11);

		taxonBases.add(syn12);

		taxonBases.add(syn2);

		// taxonomic children

		//TODO: Adapt to taxonomic tree

		taxTree = TaxonomicTree.NewInstance("TestTree");

		root1TNode = taxTree.addRoot(root1T, null, sec);

		child1Node = root1TNode.addChild(child1);

		child2Node = root1TNode.addChild(child2);

		child21Node = child2Node.addChild(child21);

		taxTree2 = TaxonomicTree.NewInstance("TestTree2");

		root2TNode = taxTree2.addRoot(root2T, null, sec);

		root2TNode.addChild(child1, sec, "p.1010", syn11);

		root2TNode.addChild(child2);

		/*

		root1T.addTaxonomicChild(child1, sec, "p.1010");

		root1T.addTaxonomicChild(child2, sec, "p.1020");

		child2.addTaxonomicChild(child21, sec, "p.2000");

		root2T.addTaxonomicChild(child1, sec, "p.1010");

		root2T.addTaxonomicChild(child2, sec, "p.1020");

		*/

		//

		taxonBases.add(root1T);

		taxonBases.add(root2T);

		taxonBases.add(freeT);

		taxonBases.add(child1);

		taxonBases.add(child2);

		taxonBases.add(child21);

		taxonBases.add(childR2_1);

		taxonBases.add(childR2_2);

		DataSet dataSet = new DataSet();

		logger.warn("WARNING: TestDatabase has been commented in parts. Mainly, must be adapted to taxonomic tree.");

		dataSet.setTerms(terms);

		dataSet.setAgents(agents);

//		dataSet.setAgentData(agentData); //TODO

		dataSet.setReferences(references);

		dataSet.setTaxonomicNames(taxonomicNames);

		dataSet.setTaxonBases(taxonBases);

		return dataSet;

	}

}