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package eu.dnetlib.enabling.database.utils;
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import java.io.StringReader;
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import java.sql.*;
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import java.sql.Date;
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import java.text.ParseException;
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import java.text.SimpleDateFormat;
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import java.util.*;
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import java.util.concurrent.ArrayBlockingQueue;
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import java.util.concurrent.BlockingQueue;
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import java.util.concurrent.Executors;
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import java.util.concurrent.TimeUnit;
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import java.util.concurrent.atomic.AtomicReference;
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import java.util.regex.Pattern;
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import javax.sql.DataSource;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Queues;
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import com.google.common.collect.Sets;
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import eu.dnetlib.enabling.database.DataSourceFactory;
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import eu.dnetlib.enabling.database.TransactionTemplateFactory;
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import eu.dnetlib.enabling.database.objects.DnetDatabase;
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import eu.dnetlib.enabling.database.rmi.DatabaseException;
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import eu.dnetlib.miscutils.datetime.DateUtils;
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import eu.dnetlib.miscutils.functional.string.Sanitizer;
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import org.apache.commons.lang.BooleanUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.velocity.app.VelocityEngine;
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import org.dom4j.Document;
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import org.dom4j.DocumentHelper;
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import org.dom4j.Element;
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import org.dom4j.Node;
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import org.dom4j.io.SAXReader;
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import org.joda.time.DateTime;
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import org.joda.time.format.ISODateTimeFormat;
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import org.springframework.beans.factory.annotation.Required;
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import org.springframework.dao.DataAccessException;
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import org.springframework.jdbc.core.JdbcTemplate;
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import org.springframework.jdbc.support.rowset.SqlRowSet;
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import org.springframework.transaction.support.TransactionTemplate;
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import org.springframework.ui.velocity.VelocityEngineUtils;
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public class DatabaseUtils {
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public static final String DNET_RESOURCE_ID_FIELD = "_dnet_resource_identifier_";
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public static final int BLOCKING_QUEUE_TIMEOUT = 300;
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private static final String SQL_DATE_FORMAT = "yyyy-MM-dd";
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private static final Log log = LogFactory.getLog(DatabaseUtils.class); // NOPMD by marko on 11/24/08 5:02 PM
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private static final int BLOCKING_QUEUE_SIZE = 200;
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private static final Set<String> TRUE_VALUES = Sets.newHashSet("true", "t", "yes", "y", "vero", "v");
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private static final Set<String> FALSE_VALUES = Sets.newHashSet("false", "f", "no", "n", "falso");
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private DataSourceFactory dataSourceFactory;
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private JdbcTemplateFactory jdbcTemplateFactory;
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private TransactionTemplateFactory transactionTemplateFactory;
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private String defaultDB;
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private VelocityEngine velocityEngine;
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private String dbPrefix;
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private int numbersOfRecordsForTransaction;
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private int fetchSize = 100;
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public List<String> listCommonDBTables(final String database) throws DatabaseException {
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String query =
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"SELECT table_name FROM information_schema.tables " + "WHERE table_schema = 'public' " + "AND table_type != 'VIEW' "
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+ "AND table_name NOT LIKE '%_log'";
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return getTypedListFromSql(database, query, String.class);
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}
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public List<String> listCommonDBViews(final String database) throws DatabaseException {
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String query =
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"SELECT table_name FROM information_schema.tables " + "WHERE table_schema = 'public' " + "AND table_type = 'VIEW' "
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+ "AND table_name NOT LIKE '%_log'";
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return getTypedListFromSql(database, query, String.class);
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}
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public Map<String, TableDates> getTableDatesForDB(final String db) throws DatabaseException {
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Map<String, TableDates> res = new HashMap<String, TableDates>();
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for (String table : listCommonDBTables(db)) {
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try {
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TableDates dates = new TableDates();
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String query =
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"select lastinsert, lastupdate, lastdelete from " + "(select max(date) as lastinsert from " + table
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+ "_log where operation='insert') as t1, " + "(select max(date) as lastupdate from " + table
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+ "_log where operation='update') as t2, " + "(select max(date) as lastdelete from " + table
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+ "_log where operation='delete') as t3";
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SqlRowSet srs = executeSql(db, query, SqlRowSet.class);
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if (srs.next()) {
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dates.setLastInsert(srs.getDate("lastinsert"));
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dates.setLastUpdate(srs.getDate("lastupdate"));
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dates.setLastDelete(srs.getDate("lastdelete"));
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}
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res.put(table, dates);
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} catch (Exception e) {
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log.warn("Error obtaing dates for table " + table, e);
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}
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}
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return res;
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}
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public List<DnetDatabase> listAllDatabases() throws DatabaseException {
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final String query =
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"SELECT d.datname AS db, COALESCE(dsc.description,'')='isManaged' AS managed FROM pg_database d LEFT OUTER JOIN pg_shdescription dsc ON (d.oid = dsc.objoid) WHERE d.datname LIKE '"
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+ dbPrefix + "%' ORDER BY d.datname DESC";
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final JdbcTemplate jdbcTemplate = getJdbcTemplate(defaultDB);
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final List<DnetDatabase> list = Lists.newArrayList();
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for (Map<String, Object> map : jdbcTemplate.queryForList(query)) {
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list.add(new DnetDatabase(map.get("db").toString(), Boolean.parseBoolean(map.get("managed").toString())));
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}
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return list;
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}
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public <T> List<T> getTypedListFromSql(final String dbName, final String query, final Class<T> clazz) throws DatabaseException {
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try {
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List<T> list = new ArrayList<T>();
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for (Object obj : getJdbcTemplate(dbName).queryForList(query, clazz)) {
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list.add(clazz.cast(obj));
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}
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return list;
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} catch (DataAccessException e) {
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throw new DatabaseException(e);
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}
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}
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public List<String> getSimpleListFromSql(final String dbName, final String query) throws DatabaseException {
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JdbcTemplate jdbcTemplate = getJdbcTemplate(dbName);
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try {
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List<String> list = new ArrayList<>();
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for (Object obj : jdbcTemplate.queryForList(query)) {
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list.add(obj.toString());
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}
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return list;
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} catch (DataAccessException e) {
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throw new DatabaseException(e);
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}
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}
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public void executeSql(final String db, final String query) throws DatabaseException {
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executeSql(db, query, Void.class);
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}
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@SuppressWarnings("unchecked")
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public <T> T executeSql(final String dbName, final String query, final Class<T> clazz) throws DatabaseException {
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150
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if (clazz == BlockingQueue.class) {
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log.debug("Creating Queue");
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final ArrayBlockingQueue<Map<String, Object>> queue = Queues.newArrayBlockingQueue(BLOCKING_QUEUE_SIZE);
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Executors.newSingleThreadExecutor().submit(() -> {
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final DataSource ds = dataSourceFactory.createDataSource(dbName);
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try (final Connection con = getConnection(ds);
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final PreparedStatement stm = getStm(query, con);
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final ResultSet rs = stm.executeQuery()) {
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rs.setFetchSize(getFetchSize());
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boolean timeout = false;
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log.info(String.format("[Thread Id %s] starting to populate queue", Thread.currentThread().getId()));
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while (rs.next()) {
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ResultSetMetaData md = rs.getMetaData();
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Map<String, Object> row = new HashMap<>();
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for (int i = 1; i <= md.getColumnCount(); i++) {
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row.put(md.getColumnName(i), rs.getObject(i));
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}
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if (!enqueue(queue, row)) {
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timeout = true;
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break;
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}
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}
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if (timeout) {
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log.warn(String.format("[Thread Id %s] queue full, consumer did not consume for %s seconds, I give up",
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Thread.currentThread().getId(), BLOCKING_QUEUE_TIMEOUT));
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return;
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}
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// An empty Map indicates the end of the resultset
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enqueue(queue, new HashMap<>());
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} catch (SQLException e) {
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throw new RuntimeException(e);
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}
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});
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log.debug("Returned Queue");
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return (T) queue;
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}
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final JdbcTemplate jdbcTemplate = jdbcTemplateFactory.createJdbcTemplate(dbName);
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if (clazz == Integer.class) return (T) jdbcTemplate.queryForObject(query, Integer.class);
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else if (clazz == List.class) return (T) jdbcTemplate.queryForList(query);
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else if (clazz == Map.class) return (T) jdbcTemplate.queryForMap(query);
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else if (clazz == SqlRowSet.class) return (T) jdbcTemplate.queryForRowSet(query);
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else {
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jdbcTemplate.update(query);
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return null;
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}
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}
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202
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203
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private boolean enqueue(final ArrayBlockingQueue<Map<String, Object>> q, final Map<String, Object> row) {
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try {
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205
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return q.offer(row, BLOCKING_QUEUE_TIMEOUT, TimeUnit.SECONDS);
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206
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} catch (InterruptedException e) {
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log.error("Error putting element in queue");
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throw new RuntimeException(e);
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}
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210
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}
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211
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212
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private PreparedStatement getStm(final String query, final Connection con) throws SQLException {
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213
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final PreparedStatement stm = con.prepareStatement(query, ResultSet.TYPE_FORWARD_ONLY);
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stm.setFetchSize(getFetchSize());
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215
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return stm;
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}
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217
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218
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private Connection getConnection(final DataSource dataSource) throws SQLException {
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final Connection conn = dataSource.getConnection();
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conn.setAutoCommit(false);
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return conn;
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}
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223
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224
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public boolean contains(final String db, final String table, final String column, final String value) throws DatabaseException {
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225
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String query = "";
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226
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try {
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227
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verifyParameters(db, table, column);
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228
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query = "SELECT " + column + " FROM " + table + " WHERE " + column + " = '" + value + "'";
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229
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List<String> res = getSimpleListFromSql(db, query);
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230
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return res != null && res.size() > 0;
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231
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} catch (Throwable e) {
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232
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throw new DatabaseException("Error performing SQL: " + query, e);
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233
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}
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234
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}
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235
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236
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public List<Map<?, ?>> describeTable(final String database, final String table) throws DatabaseException {
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237
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verifyParameters(database, table);
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238
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239
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try {
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240
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final JdbcTemplate jdbcTemplate = getJdbcTemplate(database);
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241
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List<Map<?, ?>> response = new ArrayList<Map<?, ?>>();
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242
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String query = "SELECT * FROM information_schema.columns WHERE table_name = ?";
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243
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244
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for (Object o : jdbcTemplate.queryForList(query, new Object[] { table })) {
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245
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if (o instanceof Map<?, ?>) {
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246
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response.add((Map<?, ?>) o);
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247
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}
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248
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}
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249
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return response;
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250
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} catch (DataAccessException e) {
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251
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throw new DatabaseException(e);
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252
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}
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253
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}
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254
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255
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public String dumpTableAsXML(final String db, final String t) throws DatabaseException {
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256
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return dumpTableAsDoc(db, t).asXML();
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257
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}
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258
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259
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public Document dumpTableAsDoc(final String db, final String t) throws DatabaseException {
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260
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Document doc = DocumentHelper.createDocument();
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261
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262
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Element root = doc.addElement("DB_TABLE");
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263
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Element head = root.addElement("HEADER");
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264
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265
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head.addElement("DATABASE").addAttribute("value", db);
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266
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head.addElement("TABLE").addAttribute("value", t);
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267
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head.addElement("DATE").addAttribute("value", DateUtils.now_ISO8601());
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268
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269
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Element body = root.addElement("BODY");
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270
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for (Document d : dumpTableAsList(db, t)) {
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271
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body.add(d.getRootElement());
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272
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}
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273
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return doc;
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274
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}
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275
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276
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public List<Document> dumpTableAsList(final String db, final String t) throws DatabaseException {
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277
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final JdbcTemplate jdbcTemplate = getJdbcTemplate(db);
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278
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279
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List<Document> list = new ArrayList<Document>();
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280
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for (Object o : jdbcTemplate.queryForList("SELECT * FROM " + t)) {
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281
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if (o instanceof Map<?, ?>) {
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282
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list.add(rowToDocument((Map<?, ?>) o));
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|
283
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}
|
|
284
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}
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285
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return list;
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|
286
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}
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|
287
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|
|
288
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public Document rowToDocument(final Map<?, ?> map) throws DatabaseException {
|
|
289
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Document doc = DocumentHelper.createDocument();
|
|
290
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|
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291
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Element row = doc.addElement("ROW");
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292
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for (Map.Entry<?, ?> entry : map.entrySet()) {
|
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293
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Element col = row.addElement("FIELD");
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294
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col.addAttribute("name", "" + entry.getKey());
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295
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addValue(col, entry.getValue());
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|
296
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}
|
|
297
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return doc;
|
|
298
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}
|
|
299
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|
|
300
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public Document getRowByResourceId(final String database, final String table, final String resourceId) throws DatabaseException {
|
|
301
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verifyParameters(database, table);
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|
302
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|
|
303
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JdbcTemplate jdbcTemplate = getJdbcTemplate(database);
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|
304
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String query = "SELECT * FROM " + table + " WHERE " + DNET_RESOURCE_ID_FIELD + "=?";
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|
305
|
|
|
306
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Map<?, ?> map = jdbcTemplate.queryForMap(query, resourceId);
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307
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Document doc = DocumentHelper.createDocument();
|
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308
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|
|
309
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Element root = doc.addElement("DB_RECORD");
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|
310
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Element head = root.addElement("HEADER");
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311
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head.addElement("RESOURCE_IDENTIFIER").addAttribute("value", resourceId);
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312
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head.addElement("DATABASE").addAttribute("value", database);
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|
313
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head.addElement("TABLE").addAttribute("value", table);
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|
314
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head.addElement("DATE").addAttribute("value", DateUtils.now_ISO8601());
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|
315
|
|
|
316
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Element body = root.addElement("BODY");
|
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317
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|
|
318
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Element row = body.addElement("ROW");
|
|
319
|
|
|
320
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for (Map.Entry<?, ?> entry : map.entrySet()) {
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|
321
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Element col = row.addElement("FIELD");
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322
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col.addAttribute("name", "" + entry.getKey());
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323
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addValue(col, entry.getValue());
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324
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}
|
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325
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|
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326
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return doc;
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|
327
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}
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|
328
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|
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329
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private void addValue(final Element elem, final Object value) throws DatabaseException {
|
|
330
|
if (value instanceof Array) {
|
|
331
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try {
|
|
332
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for (Object o : (Object[]) ((Array) value).getArray()) {
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333
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addValue(elem.addElement("ITEM"), o);
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|
334
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}
|
|
335
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} catch (Exception e) {
|
|
336
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throw new DatabaseException("Error procsessing a Array", e);
|
|
337
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}
|
|
338
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} else if (value != null) {
|
|
339
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elem.addText(Sanitizer.sanitize(value.toString()));
|
|
340
|
} else {
|
|
341
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elem.addAttribute("isNull", "true");
|
|
342
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}
|
|
343
|
}
|
|
344
|
|
|
345
|
private void verifyParameters(final String... params) throws DatabaseException {
|
|
346
|
Pattern pattern = Pattern.compile("\\w{1,128}");
|
|
347
|
|
|
348
|
for (String p : params) {
|
|
349
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log.debug("TESTING SQL PARAM:" + p);
|
|
350
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if (p == null) throw new DatabaseException("Parameter is null");
|
|
351
|
else if (!pattern.matcher(p).matches()) throw new DatabaseException("Parameter [" + p + "] contains an invalid character");
|
|
352
|
else {
|
|
353
|
log.debug("TEST OK");
|
|
354
|
}
|
|
355
|
}
|
|
356
|
}
|
|
357
|
|
|
358
|
public void importFromIterable(final String db, final Iterable<String> iterable) throws DatabaseException {
|
|
359
|
verifyParameters(db);
|
|
360
|
|
|
361
|
final DataSource dataSource = dataSourceFactory.createDataSource(db);
|
|
362
|
final JdbcTemplate jdbcTemplate = getJdbcTemplate(db);
|
|
363
|
final TransactionTemplate transactionTemplate = transactionTemplateFactory.createTransactionTemplate(dataSource);
|
|
364
|
|
|
365
|
int counterTotal = 0;
|
|
366
|
|
|
367
|
long start = DateUtils.now();
|
|
368
|
|
|
369
|
List<GenericRow> rows = new ArrayList<GenericRow>();
|
|
370
|
for (String prof : iterable) {
|
|
371
|
rows.addAll(obtainListOfRows(prof));
|
|
372
|
if (rows.size() > numbersOfRecordsForTransaction) {
|
|
373
|
counterTotal += rows.size();
|
|
374
|
importTransaction(jdbcTemplate, transactionTemplate, rows);
|
|
375
|
rows.clear();
|
|
376
|
}
|
|
377
|
}
|
|
378
|
counterTotal += rows.size();
|
|
379
|
importTransaction(jdbcTemplate, transactionTemplate, rows);
|
|
380
|
|
|
381
|
long end = DateUtils.now();
|
|
382
|
|
|
383
|
log.info("**********************************************************");
|
|
384
|
log.info("Processed " + counterTotal + " rows in " + ((end - start) / 1000) + " seconds");
|
|
385
|
log.info("**********************************************************");
|
|
386
|
}
|
|
387
|
|
|
388
|
private void importTransaction(final JdbcTemplate jdbcTemplate, final TransactionTemplate transactionTemplate, List<GenericRow> rows)
|
|
389
|
throws DatabaseException {
|
|
390
|
if (rows != null && rows.size() > 0) {
|
|
391
|
importTransactionInternal(jdbcTemplate, transactionTemplate, rows);
|
|
392
|
}
|
|
393
|
}
|
|
394
|
|
|
395
|
private List<GenericRow> importTransactionInternal(final JdbcTemplate jdbcTemplate,
|
|
396
|
final TransactionTemplate transactionTemplate,
|
|
397
|
final List<GenericRow> rows) throws DatabaseException {
|
|
398
|
|
|
399
|
final AtomicReference<DatabaseException> error = new AtomicReference<DatabaseException>();
|
|
400
|
|
|
401
|
try {
|
|
402
|
return transactionTemplate.execute(status -> {
|
|
403
|
final List<GenericRow> ok = Lists.newArrayList();
|
|
404
|
try {
|
|
405
|
for (GenericRow row : rows) {
|
|
406
|
if (row.isToDelete()) {
|
|
407
|
deleteRow(jdbcTemplate, row.getTable(), row.getFields());
|
|
408
|
} else {
|
|
409
|
addOrUpdateRow(jdbcTemplate, row.getTable(), row.getFields());
|
|
410
|
}
|
|
411
|
ok.add(row);
|
|
412
|
}
|
|
413
|
} catch (DatabaseException e) {
|
|
414
|
log.warn("Transaction failed", e);
|
|
415
|
status.setRollbackOnly();
|
|
416
|
error.set(e);
|
|
417
|
}
|
|
418
|
return ok;
|
|
419
|
});
|
|
420
|
} finally {
|
|
421
|
if (error.get() != null) {
|
|
422
|
throw error.get();
|
|
423
|
}
|
|
424
|
}
|
|
425
|
}
|
|
426
|
|
|
427
|
protected void addOrUpdateRow(final JdbcTemplate jdbcTemplate, final String table, final Map<String, Object> rowFields) throws DatabaseException {
|
|
428
|
try {
|
|
429
|
|
|
430
|
if (log.isDebugEnabled()) {
|
|
431
|
log.debug("Adding or updating element to table " + table);
|
|
432
|
}
|
|
433
|
verifyParameters(table);
|
|
434
|
verifyParameters(rowFields.keySet().toArray(new String[rowFields.size()]));
|
|
435
|
|
|
436
|
String fields = "";
|
|
437
|
String values = "";
|
|
438
|
List<Object> list = new ArrayList<Object>();
|
|
439
|
|
|
440
|
for (Map.Entry<String, Object> e : rowFields.entrySet()) {
|
|
441
|
if (!fields.isEmpty()) {
|
|
442
|
fields += ",";
|
|
443
|
}
|
|
444
|
fields += e.getKey();
|
|
445
|
if (!values.isEmpty()) {
|
|
446
|
values += ",";
|
|
447
|
}
|
|
448
|
values += "?";
|
|
449
|
list.add(e.getValue());
|
|
450
|
}
|
|
451
|
|
|
452
|
int count = 0;
|
|
453
|
if (rowFields.containsKey(DNET_RESOURCE_ID_FIELD)) {
|
|
454
|
List<Object> list2 = new ArrayList<Object>();
|
|
455
|
list2.addAll(list);
|
|
456
|
list2.add(rowFields.get(DNET_RESOURCE_ID_FIELD));
|
|
457
|
count =
|
|
458
|
jdbcTemplate.update("UPDATE " + table + " SET (" + fields + ") = (" + values + ") WHERE " + DNET_RESOURCE_ID_FIELD + "=?",
|
|
459
|
list2.toArray());
|
|
460
|
}
|
|
461
|
if (count == 0) {
|
|
462
|
jdbcTemplate.update("INSERT INTO " + table + " (" + fields + ") VALUES (" + values + ")", list.toArray());
|
|
463
|
}
|
|
464
|
} catch (final Exception e) {
|
|
465
|
throw new DatabaseException("Error adding or updating record", e);
|
|
466
|
}
|
|
467
|
}
|
|
468
|
|
|
469
|
protected void deleteRow(final JdbcTemplate jdbcTemplate, final String table, final Map<String, Object> rowFields) throws DatabaseException {
|
|
470
|
if (log.isDebugEnabled()) {
|
|
471
|
log.debug("Deleting element from table " + table);
|
|
472
|
}
|
|
473
|
verifyParameters(table);
|
|
474
|
verifyParameters(rowFields.keySet().toArray(new String[rowFields.size()]));
|
|
475
|
|
|
476
|
List<Object> list = new ArrayList<Object>();
|
|
477
|
|
|
478
|
String where = "";
|
|
479
|
|
|
480
|
for (Map.Entry<String, Object> e : rowFields.entrySet()) {
|
|
481
|
if (!where.isEmpty()) {
|
|
482
|
where += " AND ";
|
|
483
|
}
|
|
484
|
where += e.getKey() + "=?";
|
|
485
|
list.add(e.getValue());
|
|
486
|
}
|
|
487
|
|
|
488
|
if (where.isEmpty()) throw new DatabaseException("Delete condition is empty");
|
|
489
|
int n = jdbcTemplate.update("DELETE FROM " + table + " WHERE " + where, list.toArray());
|
|
490
|
|
|
491
|
if (log.isDebugEnabled()) {
|
|
492
|
log.debug("Number of Deleted records: " + n);
|
|
493
|
}
|
|
494
|
}
|
|
495
|
|
|
496
|
public void deleteRowByResourceId(final String database, final String table, final String resourceIdentifier) throws DatabaseException {
|
|
497
|
verifyParameters(database, table, resourceIdentifier);
|
|
498
|
final JdbcTemplate jdbcTemplate = getJdbcTemplate(database);
|
|
499
|
jdbcTemplate.update("DELETE FROM " + table + " WHERE " + DNET_RESOURCE_ID_FIELD + "=?", resourceIdentifier);
|
|
500
|
}
|
|
501
|
|
|
502
|
public void clearTable(final String database, final String table) throws DatabaseException {
|
|
503
|
verifyParameters(database, table);
|
|
504
|
|
|
505
|
final JdbcTemplate jdbcTemplate = getJdbcTemplate(database);
|
|
506
|
jdbcTemplate.update("DELETE FROM " + table);
|
|
507
|
}
|
|
508
|
|
|
509
|
public void prepareManagementOfTable(final String database, final String table) throws DatabaseException {
|
|
510
|
verifyParameters(database, table);
|
|
511
|
final JdbcTemplate jdbcTemplate = getJdbcTemplate(database);
|
|
512
|
|
|
513
|
if (!isManagedTable(jdbcTemplate, table)) {
|
|
514
|
jdbcTemplate.update(getSQLFromTemplate("manageTable", database, table, null));
|
|
515
|
log.info("Added management of table " + table);
|
|
516
|
}
|
|
517
|
}
|
|
518
|
|
|
519
|
public void removeManagementOfTable(final String database, final String table) throws DatabaseException {
|
|
520
|
verifyParameters(database, table);
|
|
521
|
final JdbcTemplate jdbcTemplate = getJdbcTemplate(database);
|
|
522
|
|
|
523
|
if (isManagedTable(jdbcTemplate, table)) {
|
|
524
|
jdbcTemplate.update(getSQLFromTemplate("unmanageTable", database, table, null));
|
|
525
|
log.info("Removed management of table " + table);
|
|
526
|
}
|
|
527
|
}
|
|
528
|
|
|
529
|
public boolean isManagedTable(final String database, final String table) throws DatabaseException {
|
|
530
|
verifyParameters(database, table);
|
|
531
|
final JdbcTemplate jdbcTemplate = getJdbcTemplate(database);
|
|
532
|
return isManagedTable(jdbcTemplate, table);
|
|
533
|
}
|
|
534
|
|
|
535
|
private boolean isManagedTable(final JdbcTemplate jdbcTemplate, final String table) {
|
|
536
|
return jdbcTemplate.queryForObject("SELECT count(*) FROM information_schema.columns WHERE table_name = ? AND column_name = ?", Integer.class,
|
|
537
|
table, DNET_RESOURCE_ID_FIELD) == 1;
|
|
538
|
}
|
|
539
|
|
|
540
|
public boolean isLoggedTable(final String database, final String table) throws DatabaseException {
|
|
541
|
verifyParameters(database, table);
|
|
542
|
final JdbcTemplate jdbcTemplate = getJdbcTemplate(database);
|
|
543
|
return isLoggedTable(jdbcTemplate, table);
|
|
544
|
}
|
|
545
|
|
|
546
|
private boolean isLoggedTable(final JdbcTemplate jdbcTemplate, final String table) {
|
|
547
|
return jdbcTemplate.queryForObject("SELECT count(*) FROM information_schema.tables WHERE table_name = ?", Integer.class,
|
|
548
|
table + "_log") == 1;
|
|
549
|
}
|
|
550
|
|
|
551
|
public String getDefaultDnetIdentifier(final String database, final String table) throws DatabaseException {
|
|
552
|
verifyParameters(database, table);
|
|
553
|
final JdbcTemplate jdbcTemplate = getJdbcTemplate(database);
|
|
554
|
if (isManagedTable(jdbcTemplate, table)) return jdbcTemplate.queryForObject(
|
|
555
|
"SELECT column_default FROM information_schema.columns WHERE table_name = ? AND column_name = ?", new Object[] {
|
|
556
|
table, DNET_RESOURCE_ID_FIELD }, String.class);
|
|
557
|
return "";
|
|
558
|
}
|
|
559
|
|
|
560
|
public void reassignDefaultDnetIdentifiers(final String db) throws DatabaseException {
|
|
561
|
for (String t : listCommonDBTables(db)) {
|
|
562
|
reassignDefaultDnetIdentifiers(db, t);
|
|
563
|
}
|
|
564
|
}
|
|
565
|
|
|
566
|
public void reassignDefaultDnetIdentifiers(final String db, final String t) throws DatabaseException {
|
|
567
|
if (!isManagedTable(db, t)) return;
|
|
568
|
|
|
569
|
SqlRowSet rows =
|
|
570
|
executeSql(db, "SELECT pg_attribute.attname as pkey FROM pg_index, pg_class, pg_attribute " + "WHERE pg_class.oid = '" + t + "'::regclass "
|
|
571
|
+ "AND indrelid = pg_class.oid " + "AND pg_attribute.attrelid = pg_class.oid "
|
|
572
|
+ "AND pg_attribute.attnum = any(pg_index.indkey) AND indisprimary " + "ORDER BY pkey", SqlRowSet.class);
|
|
573
|
|
|
574
|
String defaultValue = "";
|
|
575
|
while (rows.next()) {
|
|
576
|
if (!defaultValue.isEmpty()) {
|
|
577
|
defaultValue += "||'@@'||";
|
|
578
|
}
|
|
579
|
defaultValue += rows.getString("pkey");
|
|
580
|
}
|
|
581
|
executeSql(db, "UPDATE " + t + " SET " + DatabaseUtils.DNET_RESOURCE_ID_FIELD + " = " + defaultValue);
|
|
582
|
log.info("Reassigned dnetId for table " + t);
|
|
583
|
}
|
|
584
|
|
|
585
|
public String getSQLFromTemplate(final String sqlTemplate, final String db, final String table, Map<String, Object> map) {
|
|
586
|
if (map == null) {
|
|
587
|
map = new HashMap<String, Object>();
|
|
588
|
}
|
|
589
|
|
|
590
|
map.put("mainDB", defaultDB);
|
|
591
|
map.put("db", db);
|
|
592
|
map.put("table", table);
|
|
593
|
map.put("idField", DNET_RESOURCE_ID_FIELD);
|
|
594
|
|
|
595
|
return VelocityEngineUtils.mergeTemplateIntoString(velocityEngine, "eu/dnetlib/enabling/database/velocity/" + sqlTemplate + ".sql.vm", "UTF-8", map);
|
|
596
|
}
|
|
597
|
|
|
598
|
public List<GenericRow> obtainListOfRows(final String xml) throws DatabaseException {
|
|
599
|
try {
|
|
600
|
Document doc = new SAXReader().read(new StringReader(xml));
|
|
601
|
|
|
602
|
List<GenericRow> list = new ArrayList<GenericRow>();
|
|
603
|
|
|
604
|
for (Object or : doc.selectNodes("//ROW")) {
|
|
605
|
Element row = (Element) or;
|
|
606
|
|
|
607
|
String table = row.valueOf("@table");
|
|
608
|
|
|
609
|
if ((table == null) || table.isEmpty()) throw new DatabaseException("Attribute table is missing in XSLT");
|
|
610
|
|
|
611
|
boolean toDelete = "deleted".equals(row.valueOf("@status"));
|
|
612
|
|
|
613
|
Map<String, Object> fields = new HashMap<String, Object>();
|
|
614
|
|
|
615
|
for (Object of : row.selectNodes("./FIELD")) {
|
|
616
|
Node node = (Node) of;
|
|
617
|
String key = node.valueOf("@name");
|
|
618
|
String type = node.valueOf("@type");
|
|
619
|
String format = node.valueOf("@format");
|
|
620
|
String valueS = node.getText().trim();
|
|
621
|
|
|
622
|
if ((key != null) && !key.isEmpty()) {
|
|
623
|
Object value = valueS;
|
|
624
|
if (type != null) {
|
|
625
|
|
|
626
|
try {
|
|
627
|
// probably an empty string in a typed field means null
|
|
628
|
if ("".equals(valueS)) {
|
|
629
|
value = null;
|
|
630
|
} else if (type.equals("int")) {
|
|
631
|
value = Integer.parseInt(valueS);
|
|
632
|
} else if (type.equals("float")) {
|
|
633
|
value = Float.parseFloat(valueS);
|
|
634
|
} else if (type.equals("boolean")) {
|
|
635
|
value = parseBoolean(valueS);
|
|
636
|
} else if (type.equals("date")) {
|
|
637
|
value = parseDate(valueS, format);
|
|
638
|
} else if (type.equals("iso8601Date")) {
|
|
639
|
DateTime date = ISODateTimeFormat.dateTimeParser().parseDateTime(valueS);
|
|
640
|
value = date.toDate();
|
|
641
|
// value = new DateUtils().parse(valueS);
|
|
642
|
}
|
|
643
|
} catch (IllegalArgumentException e) {
|
|
644
|
log.fatal("cannot convert '" + valueS + "' to " + type, e);
|
|
645
|
throw e;
|
|
646
|
}
|
|
647
|
}
|
|
648
|
fields.put(key, value);
|
|
649
|
}
|
|
650
|
}
|
|
651
|
|
|
652
|
list.add(new GenericRow(table, fields, toDelete));
|
|
653
|
}
|
|
654
|
return list;
|
|
655
|
} catch (Exception e) {
|
|
656
|
log.error("Error obtaining list of rows from xml: " + xml);
|
|
657
|
throw new DatabaseException(e);
|
|
658
|
}
|
|
659
|
}
|
|
660
|
|
|
661
|
protected boolean parseBoolean(final String s) {
|
|
662
|
if (TRUE_VALUES.contains(s.toLowerCase().trim())) return true;
|
|
663
|
if (FALSE_VALUES.contains(s.toLowerCase().trim())) return false;
|
|
664
|
|
|
665
|
return BooleanUtils.toBoolean(s);
|
|
666
|
}
|
|
667
|
|
|
668
|
public void setManaged(final String dbName, final boolean managed) throws DatabaseException {
|
|
669
|
verifyParameters(dbName);
|
|
670
|
JdbcTemplate jdbcTemplate = getJdbcTemplate(dbName);
|
|
671
|
if (managed) {
|
|
672
|
jdbcTemplate.update("COMMENT ON DATABASE " + dbName + " IS 'isManaged'");
|
|
673
|
} else {
|
|
674
|
jdbcTemplate.update("COMMENT ON DATABASE " + dbName + " IS NULL");
|
|
675
|
}
|
|
676
|
}
|
|
677
|
|
|
678
|
// public for testing
|
|
679
|
public Date parseDate(final String date, String format) {
|
|
680
|
if ((format == null) || format.isEmpty()) {
|
|
681
|
format = SQL_DATE_FORMAT;
|
|
682
|
}
|
|
683
|
try {
|
|
684
|
java.util.Date parsed = new SimpleDateFormat(format).parse(date);
|
|
685
|
String ret = new SimpleDateFormat(SQL_DATE_FORMAT).format(parsed);
|
|
686
|
return Date.valueOf(ret);
|
|
687
|
} catch (ParseException e) {
|
|
688
|
return null;
|
|
689
|
}
|
|
690
|
}
|
|
691
|
|
|
692
|
private JdbcTemplate getJdbcTemplate(final String dbName) {
|
|
693
|
JdbcTemplate jdbcTemplate = jdbcTemplateFactory.createJdbcTemplate(dbName);
|
|
694
|
jdbcTemplate.setFetchSize(getFetchSize());
|
|
695
|
return jdbcTemplate;
|
|
696
|
}
|
|
697
|
|
|
698
|
@Required
|
|
699
|
public void setVelocityEngine(final VelocityEngine velocityEngine) {
|
|
700
|
this.velocityEngine = velocityEngine;
|
|
701
|
}
|
|
702
|
|
|
703
|
public String getDbPrefix() {
|
|
704
|
return dbPrefix;
|
|
705
|
}
|
|
706
|
|
|
707
|
@Required
|
|
708
|
public void setDbPrefix(final String dbPrefix) {
|
|
709
|
this.dbPrefix = dbPrefix;
|
|
710
|
}
|
|
711
|
|
|
712
|
public DataSourceFactory getDataSourceFactory() {
|
|
713
|
return dataSourceFactory;
|
|
714
|
}
|
|
715
|
|
|
716
|
@Required
|
|
717
|
public void setDataSourceFactory(final DataSourceFactory dataSourceFactory) {
|
|
718
|
this.dataSourceFactory = dataSourceFactory;
|
|
719
|
}
|
|
720
|
|
|
721
|
public JdbcTemplateFactory getJdbcTemplateFactory() {
|
|
722
|
return jdbcTemplateFactory;
|
|
723
|
}
|
|
724
|
|
|
725
|
@Required
|
|
726
|
public void setJdbcTemplateFactory(final JdbcTemplateFactory jdbcTemplateFactory) {
|
|
727
|
this.jdbcTemplateFactory = jdbcTemplateFactory;
|
|
728
|
}
|
|
729
|
|
|
730
|
public TransactionTemplateFactory getTransactionTemplateFactory() {
|
|
731
|
return transactionTemplateFactory;
|
|
732
|
}
|
|
733
|
|
|
734
|
@Required
|
|
735
|
public void setTransactionTemplateFactory(final TransactionTemplateFactory transactionTemplateFactory) {
|
|
736
|
this.transactionTemplateFactory = transactionTemplateFactory;
|
|
737
|
}
|
|
738
|
|
|
739
|
public int getNumbersOfRecordsForTransaction() {
|
|
740
|
return numbersOfRecordsForTransaction;
|
|
741
|
}
|
|
742
|
|
|
743
|
@Required
|
|
744
|
public void setNumbersOfRecordsForTransaction(final int numbersOfRecordsForTransaction) {
|
|
745
|
this.numbersOfRecordsForTransaction = numbersOfRecordsForTransaction;
|
|
746
|
}
|
|
747
|
|
|
748
|
public String getDefaultDB() {
|
|
749
|
return defaultDB;
|
|
750
|
}
|
|
751
|
|
|
752
|
@Required
|
|
753
|
public void setDefaultDB(final String defaultDB) {
|
|
754
|
this.defaultDB = defaultDB;
|
|
755
|
}
|
|
756
|
|
|
757
|
public int getFetchSize() {
|
|
758
|
return fetchSize;
|
|
759
|
}
|
|
760
|
|
|
761
|
public void setFetchSize(final int fetchSize) {
|
|
762
|
this.fetchSize = fetchSize;
|
|
763
|
}
|
|
764
|
|
|
765
|
public class TableDates {
|
|
766
|
|
|
767
|
private java.sql.Date lastInsert;
|
|
768
|
private java.sql.Date lastUpdate;
|
|
769
|
private java.sql.Date lastDelete;
|
|
770
|
|
|
771
|
public java.sql.Date getLastInsert() {
|
|
772
|
return lastInsert;
|
|
773
|
}
|
|
774
|
|
|
775
|
public void setLastInsert(final Date lastInsert) {
|
|
776
|
this.lastInsert = lastInsert;
|
|
777
|
}
|
|
778
|
|
|
779
|
public Date getLastUpdate() {
|
|
780
|
return lastUpdate;
|
|
781
|
}
|
|
782
|
|
|
783
|
public void setLastUpdate(final Date lastUpdate) {
|
|
784
|
this.lastUpdate = lastUpdate;
|
|
785
|
}
|
|
786
|
|
|
787
|
public Date getLastDelete() {
|
|
788
|
return lastDelete;
|
|
789
|
}
|
|
790
|
|
|
791
|
public void setLastDelete(final Date lastDelete) {
|
|
792
|
this.lastDelete = lastDelete;
|
|
793
|
}
|
|
794
|
}
|
|
795
|
|
|
796
|
}
|