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leinfelder
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package edu.ucsb.nceas.metacat.admin.upgrade;
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/**
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* '$RCSfile$'
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* Purpose: A Class for upgrading the database to version 1.5
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* Copyright: 2000 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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* Authors: Saurabh Garg
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*
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* '$Author$'
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* '$Date$'
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* '$Revision$'
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 2 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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import java.sql.Connection;
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import java.sql.Driver;
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import java.sql.DriverManager;
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import java.sql.PreparedStatement;
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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.List;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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7622
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leinfelder
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import org.apache.wicket.protocol.http.mock.MockHttpServletRequest;
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7506
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leinfelder
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import org.dataone.service.types.v1.Event;
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import org.dataone.service.types.v1.Identifier;
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import org.dataone.service.types.v1.Session;
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import org.dataone.service.types.v1.Subject;
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import edu.ucsb.nceas.metacat.IdentifierManager;
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import edu.ucsb.nceas.metacat.admin.AdminException;
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import edu.ucsb.nceas.metacat.dataone.MNodeService;
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import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.utilities.SortedProperties;
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/**
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* Used for forcibly removing invalid replicas from a target node.
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* These replicas exist from legacy Metacat replication that may have introduced
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* whitespace differences and entity escaping in the XML representations.
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* Removing these replicas is considered 'safe' because the source node[s] house the
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* original content that should be re-replicated (by DataONE).
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* @see https://redmine.dataone.org/issues/3539
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* @author leinfelder
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*
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*/
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public class RemoveInvalidReplicas implements UpgradeUtilityInterface {
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protected static Log log = LogFactory.getLog(RemoveInvalidReplicas.class);
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private String driver = null;
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private String url = null;
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private String user = null;
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private String password = null;
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private boolean dryRun = false;
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leinfelder
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private int serverLocation = 0;
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public int getServerLocation() {
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return serverLocation;
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}
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public void setServerLocation(int serverLocation) {
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this.serverLocation = serverLocation;
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}
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public boolean upgrade() throws AdminException {
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boolean success = true;
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leinfelder
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// do not allow this. ever.
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if (serverLocation == 1) {
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throw new AdminException("This is a DESTRUCTIVE action. Cannot remove original objects from home server: " + serverLocation);
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}
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Connection sqlca = null;
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PreparedStatement pstmt = null;
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try {
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log.debug("dryRun: " + dryRun);
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// get the properties
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driver = PropertyService.getProperty("database.driver");
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url = PropertyService.getProperty("database.connectionURI");
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user = PropertyService.getProperty("database.user");
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password = PropertyService.getProperty("database.password");
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// Create a JDBC connection to the database
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Driver d = (Driver) Class.forName(driver).newInstance();
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DriverManager.registerDriver(d);
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sqlca = DriverManager.getConnection(url, user, password);
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sqlca.setAutoCommit(true);
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// find the replicas that failed to synch
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List<String> invalidReplicas = new ArrayList<String>();
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pstmt = sqlca.prepareStatement(
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leinfelder
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"SELECT distinct guid " +
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leinfelder
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"FROM xml_documents xml, identifier id, access_log log " +
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leinfelder
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"WHERE id.docid = xml.docid " +
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"AND id.rev = xml.rev " +
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"AND log.docid = id.docid || '.' || id.rev " +
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leinfelder
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"AND xml.server_location = ? " +
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"AND log.event = ? " +
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"UNION " +
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leinfelder
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"SELECT distinct guid " +
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"FROM xml_revisions xml, identifier id, access_log log " +
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"WHERE id.docid = xml.docid " +
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"AND id.rev = xml.rev " +
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"AND log.docid = id.docid || '.' || id.rev " +
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"AND xml.server_location = ? " +
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"AND log.event = ? ");
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pstmt.setInt(1, serverLocation);
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pstmt.setString(2, Event.SYNCHRONIZATION_FAILED.xmlValue());
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pstmt.setInt(3, serverLocation);
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pstmt.setString(4, Event.SYNCHRONIZATION_FAILED.xmlValue());
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log.debug("Finding invalid (failed replicas with SQL: " + pstmt.toString());
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ResultSet rs = pstmt.executeQuery();
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while (rs.next()) {
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invalidReplicas.add(rs.getString(1));
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}
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log.debug("invalidReplicas count: " + invalidReplicas.size());
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// prepare statement for removing from identifier table
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pstmt = sqlca.prepareStatement("DELETE FROM identifier WHERE guid = ? ");
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// for using the MN API as the MN itself
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MockHttpServletRequest request = new MockHttpServletRequest(null, null, null);
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Session session = new Session();
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Subject subject = MNodeService.getInstance(request).getCapabilities().getSubject(0);
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session.setSubject(subject);
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// remove them from the system in two steps
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for (String identifier: invalidReplicas) {
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log.debug("Removing invalid replica: " + identifier);
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// using the MN.delete() method first
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Identifier pid = new Identifier();
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pid.setValue(identifier);
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try {
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if (!dryRun) {
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MNodeService.getInstance(request).delete(session, pid);
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log.debug("Deleted invalid replica object: " + pid.getValue());
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// remove SM from database
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IdentifierManager.getInstance().deleteSystemMetadata(identifier);
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log.debug("Deleted invalid replica SystemMetadata for: " + pid.getValue());
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// remove the identifier from the database
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if (IdentifierManager.getInstance().mappingExists(identifier)) {
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String localId = IdentifierManager.getInstance().getLocalId(identifier);
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IdentifierManager.getInstance().removeMapping(identifier, localId);
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log.debug("Removed localId mapping: " + localId);
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} else {
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// remove from the identifier table manually
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pstmt.setString(1, identifier);
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int count = pstmt.executeUpdate();
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log.debug("Removed identifier entry with SQL: " + pstmt.toString());
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// warn if we saw something unexpected
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if (count <= 0) {
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log.warn("Delete returned unexpected count for pid: " + identifier);
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}
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}
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// purge from Hz map
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HazelcastService.getInstance().getSystemMetadataMap().evict(pid);
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log.debug("Evicted identifier from HZ map: " + pid.getValue());
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}
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} catch (Exception e) {
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log.error("Could not delete invalid replica: " + identifier, e);
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continue;
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}
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}
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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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success = false;
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} finally {
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// clean up
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if (sqlca != null) {
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try {
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sqlca.close();
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} catch (SQLException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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}
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}
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log.debug("Done removing failed/invalid replicas");
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return success;
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}
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leinfelder
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public static void main(String [] args){
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try {
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// set up the properties based on the test/deployed configuration of the workspace
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SortedProperties testProperties =
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new SortedProperties("test/test.properties");
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testProperties.load();
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String metacatContextDir = testProperties.getProperty("metacat.contextDir");
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PropertyService.getInstance(metacatContextDir + "/WEB-INF");
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// now run it
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RemoveInvalidReplicas upgrader = new RemoveInvalidReplicas();
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if (args.length > 0) {
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String serverLocation = args[0];
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upgrader.setServerLocation(Integer.parseInt(serverLocation));
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}
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//upgrader.dryRun = true;
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upgrader.upgrade();
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} catch (Exception ex) {
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System.out.println("Exception:" + ex.getMessage());
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ex.printStackTrace();
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}
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}
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}
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