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/**
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* Copyright (C) 2009 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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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.test.function;
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import java.io.IOException;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.hibernate.Query;
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import org.hibernate.Session;
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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.api.application.CdmApplicationUtils;
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import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
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import eu.etaxonomy.cdm.api.service.ITaxonService;
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import eu.etaxonomy.cdm.api.service.UpdateResult;
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import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
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import eu.etaxonomy.cdm.api.service.description.AggregationMode;
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import eu.etaxonomy.cdm.api.service.description.DistributionAggregationConfiguration;
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import eu.etaxonomy.cdm.api.service.description.StructuredDescriptionAggregationConfiguration;
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import eu.etaxonomy.cdm.api.service.dto.GroupedTaxonDTO;
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import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;
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import eu.etaxonomy.cdm.config.AccountStore;
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import eu.etaxonomy.cdm.database.CdmDataSource;
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import eu.etaxonomy.cdm.database.CdmPersistentDataSource;
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import eu.etaxonomy.cdm.database.DataSourceNotFoundException;
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import eu.etaxonomy.cdm.database.DatabaseTypeEnum;
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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.filter.TaxonNodeFilter;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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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.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.model.term.TermTree;
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import eu.etaxonomy.cdm.model.term.init.TermNotFoundException;
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public class Datasource {
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private static final Logger logger = Logger.getLogger(Datasource.class);
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private void testNewConfigControler(){
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DbSchemaValidation schema = DbSchemaValidation.VALIDATE;
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String server;
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String database;
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String username;
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ICdmDataSource dataSource;
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// List<CdmPersistentDataSource> lsDataSources = CdmPersistentDataSource.getAllDataSources();
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// System.out.println(lsDataSources);
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// dataSource = lsDataSources.get(1);
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// DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
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// server = "localhost";
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// database = "cdm_test";
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//// database = "cdm_production_edaphobase";
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// username = "edit";
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// dataSource = CdmDataSource.NewMySqlInstance(server, database, username, AccountStore.readOrStorePassword(server, database, username, null));
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// server = "160.45.63.171";
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// database = "xxx";
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// username = "edit";
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// dataSource = CdmDataSource.NewMySqlInstance(server, database, username, AccountStore.readOrStorePassword(server, database, username, null));
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server = "test.e-taxonomy.eu";
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database = "cdm_rem_conf_am";
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username = "edit";
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dataSource = CdmDataSource.NewMySqlInstance(server, database, username, AccountStore.readOrStorePassword(server, database, username, null));
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// String server = "localhost";
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// String database = "testCDM";
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// String username = "postgres";
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// dataSource = CdmDataSource.NewInstance(DatabaseTypeEnum.PostgreSQL, server, database, DatabaseTypeEnum.PostgreSQL.getDefaultPort(), username, AccountStore.readOrStorePassword(server, database, username, null));
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// //SQLServer
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// server = "BGBM-PESISQL";
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// database = "cdm36";
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// int port = 1433;
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// username = "cdmupdater";
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// dataSource = CdmDataSource.NewSqlServer2012Instance(server, database, port, username, AccountStore.readOrStorePassword(server, database, username, null));
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//
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// //H2
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// String path = "C:\\Users\\a.mueller\\.cdmLibrary\\writableResources\\h2\\LocalH2";
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//// String path = "C:\\Users\\pesiimport\\.cdmLibrary\\writableResources\\h2\\LocalH2";
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//// String path = "C:\\Users\\a.mueller\\eclipse\\svn\\cdmlib-trunk\\cdmlib-remote-webapp\\src\\test\\resources\\h2";
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// username = "sa";
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// dataSource = CdmDataSource.NewH2EmbeddedInstance("cdm", username, "", path);
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// dataSource = CdmDataSource.NewH2EmbeddedInstance(database, username, "sa");
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// server = "160.45.63.201";
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// database = "cdm_integration_cichorieae";
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// username = "edit";
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// dataSource = CdmDataSource.NewMySqlInstance(server, database, username, AccountStore.readOrStorePassword(server, database, username, null));
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//CdmPersistentDataSource.save(dataSource.getName(), dataSource);
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CdmApplicationController appCtr;
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appCtr = CdmApplicationController.NewInstance(dataSource, schema);
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// appCtr.getOccurrenceService().findRootUnitDTOs(UUID.fromString("2debf5ee-cb57-40bc-af89-173d1d17cefe"));
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// aggregateDDS(appCtr);
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aggregateDistribution(appCtr);
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appCtr.close();
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System.exit(0);
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}
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private void aggregateDistribution(CdmApplicationController app){
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System.out.println("agg distr");
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DefaultProgressMonitor monitor = DefaultProgressMonitor.NewInstance();
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UUID descriptaceaeUuid = UUID.fromString("5a37c47c-347c-49f8-88ba-2720b194dfb9");
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TaxonNodeFilter filter = TaxonNodeFilter.NewSubtreeInstance(descriptaceaeUuid);
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filter.setIncludeUnpublished(true);
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List<AggregationMode> aggregationModes = AggregationMode.byToParent();
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TermTree<PresenceAbsenceTerm> statusOrder = null;
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List<UUID> superAreas = new ArrayList<>();
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DistributionAggregationConfiguration config = DistributionAggregationConfiguration.NewInstance(aggregationModes, superAreas, filter, statusOrder, monitor);
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config.setAdaptBatchSize(false);
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UpdateResult result = config.getTaskInstance().invoke(config, app);
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System.out.println(result);
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}
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private void aggregateDDS(CdmApplicationController app){
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System.out.println("find dds");
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DescriptiveDataSet dds = app.getDescriptiveDataSetService().find(21);
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UUID facciniaSubtreeUuid = UUID.fromString("cf0bc346-a203-4ad7-ad25-477098361db6");
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UUID arenarioAdamssubtreeUuid = UUID.fromString("0215e668-0a65-42cd-85e0-d97ce78e758b");
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TaxonNodeFilter filter = TaxonNodeFilter.NewSubtreeInstance(arenarioAdamssubtreeUuid);
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filter.setIncludeUnpublished(true);
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DefaultProgressMonitor monitor = DefaultProgressMonitor.NewInstance();
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StructuredDescriptionAggregationConfiguration config = StructuredDescriptionAggregationConfiguration.NewInstance(filter, monitor);
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config.setDatasetUuid(dds.getUuid());
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config.setAggregationMode(AggregationMode.byWithinTaxonAndToParent());
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config.setAdaptBatchSize(false);
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UpdateResult result = config.getTaskInstance().invoke(config, app);
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System.out.println(result);
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// app.getLongRunningTasksService().invoke(config);
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}
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private void listClassification(CdmApplicationController appCtr, List<String> propertyPaths) {
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try {
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List<Classification> list = appCtr.getClassificationService().list(null, null, null, null, propertyPaths);
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} catch (Exception e) {
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e.printStackTrace();
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logger.warn(e.getMessage());
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}
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}
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private void testGroupedTaxa(CdmApplicationController appCtr) {
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UUID classificationUuid = UUID.fromString("91231ebf-1c7a-47b9-a56c-b45b33137244");
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UUID taxonUuid1 = UUID.fromString("3bae1c86-1235-4e2e-be63-c7f8c4410527");
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UUID taxonUuid2 = UUID.fromString("235d3872-defe-4b92-bf2f-75a7c91510de");
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List<UUID> taxonUuids = Arrays.asList(new UUID[]{taxonUuid1, taxonUuid2});
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Rank maxRank = DefinedTermBase.getTermByClassAndUUID(Rank.class, UUID.fromString("af5f2481-3192-403f-ae65-7c957a0f02b6"));
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Rank minRank = DefinedTermBase.getTermByClassAndUUID(Rank.class, UUID.fromString("78786e16-2a70-48af-a608-494023b91904"));
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List<GroupedTaxonDTO> groupedTaxa = appCtr.getClassificationService().groupTaxaByHigherTaxon(taxonUuids, classificationUuid, minRank, maxRank);
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System.out.println(groupedTaxa);
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}
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private void addPerson(CdmApplicationController appCtr) {
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TransactionStatus tx = appCtr.startTransaction();
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appCtr.getAgentService().save(Person.NewInstance());
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appCtr.commitTransaction(tx);
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}
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private void deleteHighLevelNode(CdmApplicationController appCtr) {
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TransactionStatus tx = appCtr.startTransaction();
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ITaxonNodeService service = appCtr.getTaxonNodeService();
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TaxonNode node = service.find(60554);
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// service.delete(node);
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ITaxonService taxonService = appCtr.getTaxonService();
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Taxon taxon = node.getTaxon();
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//try {
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taxonService.deleteTaxon(taxon.getUuid(), new TaxonDeletionConfigurator(), node.getClassification().getUuid());
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/*} catch (DataChangeNoRollbackException e) {
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e.printStackTrace();
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}*/
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try {
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appCtr.commitTransaction(tx);
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} catch (Exception e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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TaxonNode node2 = service.find(60554);
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}
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// private void insertSomeData(CdmApplicationController appCtr) {
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// Classification cl = Classification.NewInstance("myClass");
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// TaxonNode node1 = cl.addChildTaxon(Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(null), null), null, null);
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// appCtr.getClassificationService().save(cl);
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//
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// Taxon t2 = Taxon.NewInstance(null, null);
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// t2.setTitleCache("Taxon2", true);
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// TaxonNode node2 = node1.addChildTaxon(t2, null, null);
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//
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// Taxon t3 = Taxon.NewInstance(null, null);
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// t3.setTitleCache("Taxon3", true);
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// TaxonNode node3 = node1.addChildTaxon(t3, 0, null, null);
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//
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// appCtr.getTaxonNodeService().saveOrUpdate(node1);
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//
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// cl.addChildNode(node3, 0, null, null);
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// appCtr.getTaxonNodeService().saveOrUpdate(node3);
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// appCtr.getClassificationService().saveOrUpdate(cl);
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//
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// TermTree<Feature> ft1 = TermTree.NewInstance();
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// FeatureNode fn1 = TermNode.NewInstance((Feature)null);
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// ft1.getRoot().addChild(fn1);
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// appCtr.getFeatureNodeService().save(fn1);
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//
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// TermNode fn2 = TermNode.NewInstance((Feature)null);
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// fn1.addChild(fn2);
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//
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// TermNode fn3 = TermNode.NewInstance((Feature)null);
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// fn1.addChild(fn2, 0);
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//
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// appCtr.getFeatureNodeService().saveOrUpdate(fn1);
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//
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// ft1.getRoot().addChild(fn3, 0);
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// appCtr.getFeatureNodeService().saveOrUpdate(fn3);
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// appCtr.getFeatureTreeService().saveOrUpdate(ft1);
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// }
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private void testDatabaseChange() throws DataSourceNotFoundException{
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CdmApplicationController appCtr;
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appCtr = CdmApplicationController.NewInstance();
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// DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
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// String server = "192.168.2.10";
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// String database = "cdm_test_andreas";
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// String user = "edit";
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// String pwd = "wp5";
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//
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DatabaseTypeEnum dbType = DatabaseTypeEnum.SqlServer2005;
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String server = "LAPTOPHP";
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String database = "cdmTest";
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String username = "edit";
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String password = "";
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ICdmDataSource dataSource = CdmDataSource.NewInstance(DatabaseTypeEnum.SqlServer2005, "LAPTOPHP", "cdmTest", DatabaseTypeEnum.SqlServer2005.getDefaultPort(), "edit", "");
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appCtr.getDatabaseService().saveDataSource("testSqlServer", dataSource);
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try {
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appCtr.getDatabaseService().connectToDatabase(dbType, server, database, username, password);
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} catch (TermNotFoundException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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appCtr.close();
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}
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private void testSqlServer2005(){
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DatabaseTypeEnum databaseTypeEnum = DatabaseTypeEnum.SqlServer2005;
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String server = "LAPTOPHP";
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String database = "cdmTest";
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String username = "edit";
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String password = "";
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ICdmDataSource dataSource = CdmDataSource.NewInstance(databaseTypeEnum, server, database, databaseTypeEnum.getDefaultPort(), username, password);
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CdmPersistentDataSource ds = CdmPersistentDataSource.save("testSqlServer", dataSource);
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CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds);
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Person agent = Person.NewInstance();
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appCtr.getAgentService().save(agent);
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TaxonName tn = TaxonNameFactory.NewBotanicalInstance(null);
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appCtr.getNameService().save(tn);
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appCtr.close();
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}
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private void testLocalHsql(){
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CdmApplicationController appCtr = null;
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try {
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CdmPersistentDataSource ds = CdmPersistentDataSource.NewLocalHsqlInstance();
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appCtr = CdmApplicationController.NewInstance(ds);
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List<?> l = appCtr.getNameService().list(null,5, 1,null,null);
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System.out.println(l);
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//Agent agent = new Agent();
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//appCtr.getAgentService().saveAgent(agent);
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appCtr.close();
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} catch (RuntimeException e) {
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logger.error("Runtime Exception");
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e.printStackTrace();
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if (appCtr != null){
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appCtr.close();
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}
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} catch (DataSourceNotFoundException e) {
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logger.error("Runtime Exception");
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e.printStackTrace();
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}
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}
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private void testLocalH2(){
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340
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DbSchemaValidation validation = DbSchemaValidation.CREATE;
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ICdmDataSource ds =
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CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "", null);
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// ds =
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// CdmPersistentDataSource.NewInstance("localH2");
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CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds, validation);
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boolean exists = appCtr.getUserService().userExists("admin");
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try {
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IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(null);
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String nameCache = "testName";
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name.setNameCache(nameCache);
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name.setTitleCache(nameCache, true);
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Reference ref = ReferenceFactory.newGeneric();
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ref.setTitleCache("mySec", true);
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Taxon taxon = Taxon.NewInstance(name, ref);
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TaxonDescription description = TaxonDescription.NewInstance();
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taxon.addDescription(description);
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NamedArea area1 = appCtr.getTermService().getAreaByTdwgAbbreviation("GER");
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Distribution distribution = Distribution.NewInstance(area1, PresenceAbsenceTerm.PRESENT());
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description.addElement(distribution);
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List<Distribution> distrList = new ArrayList<Distribution>();
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distrList.add(distribution);
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List<NamedArea> areaList = new ArrayList<NamedArea>();
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areaList.add(area1);
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// distribution.getInDescription().get
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appCtr.getTaxonService().save(taxon);
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System.out.println(taxon.getDescriptions().size());
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TransactionStatus txStatus = appCtr.startTransaction();
|
374
|
|
375
|
Session session = appCtr.getSessionFactory().getCurrentSession();
|
376
|
|
377
|
//String hqlQuery = "from DescriptionBase d join d.elements as e "
|
378
|
// String hqlQuery = "from Taxon t join t.descriptions as d "+
|
379
|
// " inner join d.elements e on e member of d "
|
380
|
// +
|
381
|
// "";//" where e.area = :namedArea " ;
|
382
|
String hqlQuery = "Select t from Distribution e join e.inDescription d join d.taxon t join t.name n "+
|
383
|
" WHERE e.area in (:namedArea) AND n.nameCache = :nameCache ";
|
384
|
Query query = session.createQuery(hqlQuery);
|
385
|
|
386
|
//query.setEntity("namedArea", area1);
|
387
|
query.setParameter("nameCache", nameCache);
|
388
|
query.setParameterList("namedArea", areaList);
|
389
|
List resultList = query.list();
|
390
|
//List list = appCtr.getCommonService().getHqlResult(hqlQuery);
|
391
|
|
392
|
for (Object o:resultList){
|
393
|
System.out.println(o);
|
394
|
}
|
395
|
appCtr.commitTransaction(txStatus);
|
396
|
|
397
|
//System.out.println(l);
|
398
|
//Agent agent = new Agent();
|
399
|
//appCtr.getAgentService().saveAgent(agent);
|
400
|
appCtr.close();
|
401
|
} catch (RuntimeException e) {
|
402
|
logger.error("Runtime Exception");
|
403
|
e.printStackTrace();
|
404
|
appCtr.close();
|
405
|
|
406
|
}
|
407
|
}
|
408
|
|
409
|
private boolean testWritableResourceDirectory() throws IOException{
|
410
|
CdmApplicationUtils.getWritableResourceDir();
|
411
|
return true;
|
412
|
}
|
413
|
|
414
|
private boolean testH2(){
|
415
|
// testLocalH2();
|
416
|
// if (true)return true;
|
417
|
|
418
|
DbSchemaValidation validation = DbSchemaValidation.CREATE;
|
419
|
ICdmDataSource ds =
|
420
|
CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "", null);
|
421
|
//CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "");
|
422
|
// ds =
|
423
|
// CdmPersistentDataSource.NewInstance("localH2");
|
424
|
CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds, validation);
|
425
|
try {
|
426
|
TaxonName botName1 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
427
|
TaxonName botName2 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
428
|
IBotanicalName hybridName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
429
|
botName1.addRelationshipToName(botName2, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), null, null);
|
430
|
UUID uuid1 = botName1.getUuid();
|
431
|
UUID uuid2 = botName2.getUuid();
|
432
|
try {
|
433
|
Logger loggerTrace = Logger.getLogger("org.hibernate.type");
|
434
|
//loggerTrace.setLevel(Level.TRACE);
|
435
|
System.out.println(logger.getName());
|
436
|
|
437
|
appCtr.getNameService().save(botName1);
|
438
|
ResultSet rs = ds.executeQuery("Select count(*) as n FROM NameRelationship");
|
439
|
rs.next();
|
440
|
int c = rs.getInt("n");
|
441
|
System.out.println("Begin :" + c);
|
442
|
|
443
|
botName1.removeRelationToTaxonName(botName2);
|
444
|
botName1.setSpecificEpithet("DELETED");
|
445
|
botName2.addHybridParent(hybridName, HybridRelationshipType.FIRST_PARENT(), null);
|
446
|
|
447
|
TransactionStatus tx = appCtr.startTransaction();
|
448
|
appCtr.getNameService().saveOrUpdate(botName2);
|
449
|
rs = ds.executeQuery("Select count(*) as n FROM NameRelationship");
|
450
|
rs.next();
|
451
|
c = rs.getInt("n");
|
452
|
System.out.println("End: " + c);
|
453
|
|
454
|
appCtr.commitTransaction(tx);
|
455
|
|
456
|
appCtr.getNameService().saveOrUpdate(botName1);
|
457
|
|
458
|
rs = ds.executeQuery("Select count(*) as n FROM NameRelationship");
|
459
|
rs.next();
|
460
|
c = rs.getInt("n");
|
461
|
System.out.println("End: " + c);
|
462
|
|
463
|
} catch (SQLException e) {
|
464
|
// TODO Auto-generated catch block
|
465
|
e.printStackTrace();
|
466
|
}
|
467
|
|
468
|
|
469
|
//Agent agent = new Agent();
|
470
|
//appCtr.getAgentService().saveAgent(agent);
|
471
|
appCtr.close();
|
472
|
return true;
|
473
|
} catch (RuntimeException e) {
|
474
|
logger.error("Runtime Exception");
|
475
|
e.printStackTrace();
|
476
|
appCtr.close();
|
477
|
|
478
|
}
|
479
|
return false;
|
480
|
}
|
481
|
|
482
|
private void test(){
|
483
|
System.out.println("Start Datasource");
|
484
|
testNewConfigControler();
|
485
|
//testDatabaseChange();
|
486
|
|
487
|
//testSqlServer();
|
488
|
|
489
|
//CdmUtils.findLibrary(au.com.bytecode.opencsv.CSVReader.class);
|
490
|
//testPostgreServer();
|
491
|
//testLocalHsql();
|
492
|
//testLocalH2();
|
493
|
//testWritableResourceDirectory();
|
494
|
// testH2();
|
495
|
System.out.println("\nEnd Datasource");
|
496
|
}
|
497
|
|
498
|
/**
|
499
|
* @param args
|
500
|
*/
|
501
|
public static void main(String[] args) {
|
502
|
Datasource cc = new Datasource();
|
503
|
cc.test();
|
504
|
}
|
505
|
|
506
|
}
|