EDIT

/**

* Copyright (C) 2008 EDIT

* European Distributed Institute of Taxonomy

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

*/

package eu.etaxonomy.cdm.test.integration;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import org.apache.log4j.Logger;

import org.springframework.transaction.TransactionStatus;

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

import eu.etaxonomy.cdm.config.AccountStore;

import eu.etaxonomy.cdm.database.CdmDataSource;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.common.Source;

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.term.Representation;

import eu.etaxonomy.cdm.model.term.TermVocabulary;

/**

 * @author a.babadshanjan

 * @since 15.09.2008

 */

public class TestCdmDbComparator {

	private static final String sourceDbOne = "cdm_test_jaxb";

	private static final String sourceDbTwo = "cdm_test_jaxb2";

	private static final ICdmDataSource sourceOne = TestCdmDbComparator.CDM_DB(sourceDbOne);

	private static final ICdmDataSource sourceTwo = TestCdmDbComparator.CDM_DB(sourceDbTwo);

	private static final String server = "192.168.2.10";

	private static final String username = "edit";

	public static ICdmDataSource CDM_DB(String dbname) {

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

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

	return datasource;

	}

    private final int MAX_ROWS = 60000;

    private final int MAX_TABLES = 150;

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

	private static final String[] table_list = {

//			"Address",

			"AgentBase",

//			"Agent_Agent",

//			"Agent_Annotation",

//			"Agent_DefinedTermBase",

//			"Agent_Extension",

//			"Agent_InstitutionalMembership",

//			"Agent_Marker",

//			"Agent_Media",

//			"Agent_OriginalSource",

//			"Agent_Rights",

			"Annotation",

//			"CDM_VIEW",

//			"CDM_VIEW_CDM_VIEW",

//			"Collection",

//			"Collection_Annotation",

//			"Collection_Extension",

//			"Collection_Marker",

//			"Collection_Media",

//			"Collection_OriginalSource",

//			"Collection_Rights",

//			"Contact",

			"DefinedTermBase",

//			"DefinedTermBase_DefinedTermBase",

//			"DefinedTermBase_Media",

//			"DefinedTermBase_Representation",

//			"DefinedTermBase_TermVocabulary",

//			"DerivationEvent",

//			"DerivationEvent_Annotation",

//			"DerivationEvent_Marker",

			"DescriptionBase",

//			"DescriptionBase_Annotation",

//			"DescriptionBase_DefinedTermBase",

//			"DescriptionBase_DescriptionElementBase",

//			"DescriptionBase_Extension",

//			"DescriptionBase_Marker",

//			"DescriptionBase_OriginalSource",

//			"DescriptionBase_Rights",

			"DescriptionElementBase",

//			"DescriptionElementBase_Annotation",

//			"DescriptionElementBase_DefinedTermBase",

//			"DescriptionElementBase_LanguageString",

//			"DescriptionElementBase_Marker",

//			"DescriptionElementBase_Media",

//			"DescriptionElementBase_StatisticalMeasurementValue",

//			"DeterminationEvent",

//			"DeterminationEvent_Annotation",

//			"DeterminationEvent_Marker",

//			"Extension",

			"FeatureNode",

			"FeatureTree",

//			"FeatureTree_Representation",

//			"GatheringEvent",

//			"GatheringEvent_Annotation",

//			"GatheringEvent_Marker",

			"HomotypicalGroup",

//			"HomotypicalGroup_Annotation",

//			"HomotypicalGroup_Marker",

//			"HybridRelationship",

//			"HybridRelationship_Annotation",

//			"HybridRelationship_Marker",

//			"InstitutionalMembership",

			"LanguageString",

//			"Locus",

			"Marker",

			"Media",

			"MediaRepresentation",

			"MediaRepresentationPart",

//			"Media_Annotation",

//			"Media_Marker",

//			"Media_Rights",

//			"Media_Sequence",

//			"MediaKey_CoveredTaxon",

			"NameRelationship",

//			"NameRelationship_Annotation",

//			"NameRelationship_Marker",

			"NomenclaturalStatus",

//			"NomenclaturalStatus_Annotation",

//			"NomenclaturalStatus_Marker",

			"OriginalSource",

//			"OriginalSource_Annotation",

//			"OriginalSource_Marker",

//			"Person_Keyword",

			"Reference",

//			"ReferenceBase_Annotation",

//			"ReferenceBase_Extension",

//			"ReferenceBase_Marker",

//			"ReferenceBase_Media",

//			"ReferenceBase_OriginalSource",

//			"ReferenceBase_Rights",

//			"RelationshipTermBase_inverseRepresentation",

			"Representation",

//			"Rights",

//			"Sequence",

//			"Sequence_Annotation",

//			"Sequence_Extension",

//			"Sequence_Marker",

//			"Sequence_Media",

//			"Sequence_OriginalSource",

//			"Sequence_ReferenceBase",

//			"Sequence_Rights",

			"SpecimenOrObservationBase",

//			"SpecimenOrObservationBase_Annotation",

//			"SpecimenOrObservationBase_DerivationEvent",

//			"SpecimenOrObservationBase_Extension",

//			"SpecimenOrObservationBase_Marker",

//			"SpecimenOrObservationBase_Media",

//			"SpecimenOrObservationBase_OriginalSource",

//			"SpecimenOrObservationBase_Rights",

//			"StateData",

//			"StateData_DefinedTermBase",

//			"StatisticalMeasurementValue",

//			"StatisticalMeasurementValue_DefinedTermBase",

			"TaxonBase",

//			"TaxonBase_Annotation",

//			"TaxonBase_Extension",

//			"TaxonBase_Marker",

//			"TaxonBase_OriginalSource",

//			"TaxonBase_Rights",

			"TaxonName",

//			"TaxonName_Annotation",

//			"TaxonName_Extension",

//			"TaxonName_HybridRelationship",

//			"TaxonName_Marker",

//			"TaxonName_NomenclaturalStatus",

//			"TaxonName_OriginalSource",

//			"TaxonName_Rights",

//			"TaxonName_TypeDesignationBase",

			"TaxonRelationship",

//			"TaxonRelationship_Annotation",

//			"TaxonRelationship_Marker",

			"TermVocabulary",

//			"TermVocabulary_Representation",

			"TypeDesignationBase",

//			"TypeDesignationBase_Annotation",

//			"TypeDesignationBase_Marker",

	};

//	@Autowired

//	@Qualifier("cdmDao")

//	private ICdmEntityDao cdmDao;

//	@Autowired

//	protected void setDao(ICdmEntityDao dao) {

//		logger.debug("setting DAO");

//		this.cdmDao = dao;

//	}

//	@Autowired

//	private SessionFactory factory;

//

//	protected Session getSession(){

//	Session session = factory.getCurrentSession();

//	return session;

//}

//    public ResultSet getResultSet (String query){

//    	ResultSet rs;

//    	try {

//            this.getConnection(); //establish connection

//        	if (query == null){

//        		return null;

//        	}

//            mStmt = mConn.createStatement();

//            rs = mStmt.executeQuery(query);

//            return rs;

//        }catch(SQLException e){

//            logger.error("Problems when creating Resultset for query \n  " + query + " \n" + "Exception: " + e);

//            return null;

//        }

//    }

	private Map<String, List<String>> doLoadDataFromDb(String dbname, Source source) {

		Map<String, List<String>> dbTables = new HashMap<String, List<String>>();

		logger.info("Loading data from DB " + dbname);

		CdmApplicationController appCtr = null;

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

		DbSchemaValidation dbSchemaValidation = DbSchemaValidation.VALIDATE;

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

		appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation, true);

    	TransactionStatus txStatus = appCtr.startTransaction(true);

    	// get data from DB

    	try {

    		dbTables = retrieveAllTables(appCtr);

    	} catch (Exception e) {

    		logger.error("error setting data");

    		e.printStackTrace();

    	}

    	appCtr.commitTransaction(txStatus);

    	appCtr.close();

    	return dbTables;

    }

	private Map<String, List<CdmBase>> doLoadDataFromDb_(String dbname) {

		Map<String, List<CdmBase>> dbTables = new HashMap<String, List<CdmBase>>();

		logger.info("Loading data from DB " + dbname);

		CdmApplicationController appCtr = null;

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

		DbSchemaValidation dbSchemaValidation = DbSchemaValidation.VALIDATE;

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

		appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation, true);

    	TransactionStatus txStatus = appCtr.startTransaction(true);

    	// get data from DB

    	try {

    		dbTables = retrieveAllTables_(appCtr);

    	} catch (Exception e) {

    		logger.error("error setting data");

    		e.printStackTrace();

    	}

    	appCtr.commitTransaction(txStatus);

    	appCtr.close();

    	return dbTables;

    }

	private Map<String, List<String>> doLoadDataFromDb__(String dbname, Source source) {

		Map<String, List<String>> dbTables = new HashMap<String, List<String>>();

		logger.info("Loading data from DB " + dbname);

    	try {

    		dbTables = retrieveAllTables__(source);

    	} catch (Exception e) {

    		logger.error("error setting data");

    		e.printStackTrace();

    	}

    	return dbTables;

    }

    private Map<String, List<CdmBase>> retrieveAllTables_(CdmApplicationController appCtr) {

		Map<String, List<CdmBase>> tables_ = new HashMap<String, List<CdmBase>>(table_list.length);

		//List<Agent> agents = appCtr.getAgentService().getAllAgents(MAX_ROWS, 0);

		try {

			//get data from database

			for (int i = 0; i < table_list.length; i++) {

	    		logger.debug("Retrieving table '" + table_list[i] + "'");

	    		System.out.println("Retrieving table '" + table_list[i] + "'");

				List<CdmBase> rows = new ArrayList<>(MAX_ROWS);

//				rows = appCtr.getCommonService().count (table_list[i], MAX_ROWS, 0);

    			tables_.put(table_list[i], rows);

			}

		} catch (Exception e) {

    		logger.error("error retrieving data");

    		e.printStackTrace();

		}

//		return tables;

		return tables_;

    }

    private Map<String, List<String>> retrieveAllTables___(Source source) {

		Map<String, List<String>> tables = new HashMap<>(table_list.length);

		try {

			//get data from database

			for (int i = 0; i < table_list.length; i++) {

				List<String> rows = new ArrayList<>(MAX_ROWS);

//					Session session = factory.getCurrentSession();

//					if ( sessionObject != null ) {

//						session.update(sessionObject);

//					}

//					Query query = session.createQuery("select term from DefinedTermBase term join fetch term.representations representation where representation.label = :label");

//					query.setParameter("label", queryString);

//					Query query = session.createQuery("select from " + table_list[i]);

//				    rows = query.list();

				//FIXME: NullPointerException (cdmDao is null)

				    //rows = cdmDao.list(MAX_ROWS, 0);

					tables.put(table_list[i], rows);

				}

		} catch (Exception e) {

    		logger.error("error retrieving data");

    		e.printStackTrace();

		}

		return tables;

    }

    private Map<String, List<String>> retrieveAllTables__(Source source) {

//		IImportConfigurator config = new BerlinModelImportConfigurator;

//		BerlinModelImportConfigurator bmiConfig = (BerlinModelImportConfigurator)config;

//		Source source = bmiConfig.getSource();

//		ResultSet rs = berlinModelSource.getResultSet();

		Map<String, List<String>> tables = new HashMap<>(table_list.length);

		try {

			//get data from database

			for (int i = 0; i < table_list.length; i++) {

				String strQuery =

					" SELECT * FROM " + table_list[i];

				logger.debug("SQL Statement: " +  strQuery);

				//ResultSet rs = berlinModelSource.getResultSet();

				//ResultSet rs = source.getResultSet(strQuery) ;

				ResultSet rs = source.getResultSet(strQuery) ;

				List<String> rows = new ArrayList<>(MAX_ROWS);

				while (rs.next()) {

					rows.add(rs.toString());

				}

				tables.put(table_list[i], rows);

			}

		} catch (SQLException e) {

			logger.error("SQLException:" +  e);

		}

		return tables;

    }

    private Map<String, List<String>> retrieveAllTables(CdmApplicationController appCtr) {

		Map<String, List<String>> tables = new HashMap<>(table_list.length);

		List<String> agentTableContent = new ArrayList<>(MAX_ROWS);

		List<? extends AgentBase> agents = appCtr.getAgentService().list(null,MAX_ROWS, 0,null,null);

		for (AgentBase agent: agents ) {

			//TODO: Want the entire row as string not just toString() of the object.

			agentTableContent.add(agent.toString());

		}

		tables.put("agents", agentTableContent);

		//List<Annotation> annotations = appCtr.getTermService().getAllAnnotations(MAX_ROWS, 0);

		List<String> definedTermBaseTableContent = new ArrayList<>(MAX_ROWS);

		List<DefinedTermBase> definedTermBases = appCtr.getTermService().list(null,MAX_ROWS, 0,null,null);

		for (DefinedTermBase definedTermBase: definedTermBases ) {

			definedTermBaseTableContent.add(definedTermBase.toString());

		}

		tables.put("definedTermBases", definedTermBaseTableContent);

		//List<DescriptionBase> descriptionBases = appCtr.getDescriptionService().getAllDescriptionBases(MAX_ROWS, 0);

		//List<DescriptionElementBase> descriptionElementBases = appCtr.getDescriptionService().getAllDescriptionElementBases(MAX_ROWS, 0);

		//List<HomotypicalGroup> homotypicalGroups = appCtr.getNameService().getAllHomotypicalGroups(MAX_ROWS, 0);

		List<LanguageString> languageStrings = appCtr.getTermService().getAllLanguageStrings(MAX_ROWS, 0);

		//List<Marker> markers = appCtr.getTermService().getAllMarkers(MAX_ROWS, 0);

		//List<NameRelationship> nameRelationships = appCtr.getNameService().getAllNameRelationships(MAX_ROWS, 0);

		List<NomenclaturalStatus> nomenclaturalStatus = appCtr.getNameService().getAllNomenclaturalStatus(MAX_ROWS, 0);

		//List<OriginalSource> originalSources = appCtr.getNameService().getAllOriginalSources(MAX_ROWS, 0);

		List<Reference> references = appCtr.getReferenceService().list(null,MAX_ROWS, 0,null,null);

		List<Representation> representations = appCtr.getTermService().getAllRepresentations(MAX_ROWS, 0);

		List<SpecimenOrObservationBase> specimenOrObservationBases = appCtr.getOccurrenceService().list(null,MAX_ROWS, 0,null,null);

//		List<TaxonBase> taxonBases = appCtr.getTaxonService().getAllTaxa(MAX_ROWS, 0);

//		List<TaxonName> taxonNames = appCtr.getNameService().getAllNames(MAX_ROWS, 0);

		//List<TaxonRelationship> taxonRelationships = appCtr.getTaxonService().getAllTaxonRelationships(MAX_ROWS, 0);

		List<TermVocabulary> termVocabularies = appCtr.getVocabularyService().list(null,MAX_ROWS, 0,null,null);

		List<TypeDesignationBase<?>> typeDesignationBases = appCtr.getNameService().getAllTypeDesignations(MAX_ROWS, 0);

		return tables;

	}

     private void compareTables(String tableName, List<CdmBase> tablesDbOne, List<CdmBase> tablesDbTwo) {

		int tableOneSize = tablesDbOne.size();

		int tableTwoSize = tablesDbTwo.size();

		int tableMinSize = 0;

		int tableMaxSize = 0;

		if (tableOneSize != tableTwoSize) {

			logger.warn("Table '" + tableName + "', Rows differ: " + tablesDbOne.size() + ", " + tablesDbTwo.size());

            tableMinSize = Math.min(tableOneSize, tableTwoSize);

            tableMaxSize = Math.max(tableOneSize, tableTwoSize);

		} else {

			logger.info("Table '" + tableName + "': " + tablesDbOne.size());

		}

		int different = 0;

		try {

		for (int i = 0; i < tableMinSize; i++) {

			CdmBase obj1 = tablesDbOne.get(i);

			CdmBase obj2 = tablesDbTwo.get(i);

			// This compares only whether both tables contain the same objects.

			// It doesn't check whether all field values are the same.

			logger.debug("Row # " + i + ":");

			if (obj1.equals(obj2) != true) {

				different++;

				logger.debug("Table 1 = " + obj1);

				logger.debug("Table 2 = " + obj2);

			} else {

				logger.debug("Entry = " + obj1);

			}

		}

		if (different > 0) {

			logger.info("# Rows identical: " + (tableMaxSize - different));

			logger.warn("# Rows different: " + different);

		}

		} catch (org.hibernate.LazyInitializationException e){

			logger.error("LazyInitializationException");

		}

	}

    	private void doCompareDatabases(Map<String, List<CdmBase>> tablesDbOne, Map<String, List<CdmBase>> tablesDbTwo) {

		logger.debug("# Tables in DB 1: " + tablesDbOne.size());

		logger.debug("# Tables in DB 2: " + tablesDbTwo.size());

		for (String tableName: tablesDbOne.keySet()) {

			logger.info("Comparing table '" + tableName + "'");

			List<CdmBase> dbOneTableRows = new ArrayList<>();

			List<CdmBase> dbTwoTableRows = new ArrayList<>();

			dbOneTableRows = tablesDbOne.get(tableName);

			dbTwoTableRows = tablesDbTwo.get(tableName);

//			Collections.sort(dbOneTableRows);

//			Collections.sort(dbTwoTableRows);

			int different = 0;

			int tableSize = dbOneTableRows.size();

			for (int i = 0; i < tableSize; i++) {

//				String str1 = dbOneTableRows.get(i);

//				String str2 = dbTwoTableRows.get(i);

				CdmBase str1 = dbOneTableRows.get(i);

				CdmBase str2 = dbTwoTableRows.get(i);

				if (str1.equals(str2) != true) {

					different++;

					logger.debug("Rows differ:");

					logger.debug("Table 1 Row = " + str1);

					logger.debug("Table 2 Row = " + str2);

				}

				i++;

			}

			if (different > 0) {

				logger.info("Compared table '" + tableName + "':");

				logger.info("# Rows total: " + tableSize);

				logger.info("# Rows identical: " + (tableSize - different));

				logger.warn("# Rows different: " + different);

			}

		}

		logger.info("End database comparison");

	}

//	private void test_(){

//

//		Map<String, List<CdmBase>> tablesDbOne = doLoadDataFromDb_(sourceDbOne);

//		Map<String, List<CdmBase>> tablesDbTwo = doLoadDataFromDb_(sourceDbTwo);

//	    doCompareDatabases(tablesDbOne, tablesDbTwo);

//

//	}

	private void test(){

		CdmApplicationController appCtrOne = null;

		CdmApplicationController appCtrTwo = null;

		logger.info("Comparing '" + sourceDbOne + "' and '" + sourceDbTwo + "'");

		try {

			appCtrOne = CdmApplicationController.NewInstance(sourceOne, DbSchemaValidation.VALIDATE, true);

			appCtrTwo = CdmApplicationController.NewInstance(sourceTwo, DbSchemaValidation.VALIDATE, true);

		} catch (Exception e) {

			logger.error("Error creating application controller");

			e.printStackTrace();

			System.exit(1);

			return;

		}

		try {

			//get data from database

	    	TransactionStatus txStatOne = appCtrOne.startTransaction(true);

	    	TransactionStatus txStatTwo = appCtrTwo.startTransaction(true);

			for (int i = 0; i < table_list.length; i++) {

				List<CdmBase> rowsDbOne = new ArrayList<>(MAX_ROWS);

				List<CdmBase> rowsDbTwo = new ArrayList<>(MAX_ROWS);

//				rowsDbOne = appCtrOne.getCommonService().count(table_list[i], MAX_ROWS, 0);

//				rowsDbTwo = appCtrTwo.getCommonService().count(table_list[i], MAX_ROWS, 0);

				compareTables(table_list[i], rowsDbOne, rowsDbTwo);

			}

	    	appCtrTwo.commitTransaction(txStatTwo);

	    	appCtrOne.commitTransaction(txStatOne);

	    	//java.lang.IllegalStateException: Cannot deactivate transaction synchronization - not active

	    	appCtrOne.close();

	    	appCtrTwo.close();

			logger.info("End database comparison");

		} catch (Exception e) {

    		logger.error("Error retrieving or comparing data");

    		e.printStackTrace();

		}

	}

	/**

	 * @param args

	 */

	public static void  main(String[] args) {

		TestCdmDbComparator diff = new TestCdmDbComparator();

    	diff.test();

	}

}