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package edu.ucsb.nceas.metacat.admin.upgrade;
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/**
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* '$RCSfile$'
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* Copyright: 2012 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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* Authors: Matthew Jones
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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.io.IOException;
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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.sql.Statement;
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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 edu.ucsb.nceas.metacat.admin.AdminException;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.metacat.shared.ServiceException;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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import edu.ucsb.nceas.utilities.SortedProperties;
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/**
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* Optionally upgrade all of the existing identifiers in the tables to be official
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* DOIs that are assigned by a DOI registration authority. This class first checks
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* if GUIDs should be converted to DOIs, and if so, updates all relevant
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* tables and resources in Metacat, and then registers each of the newly minted
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* identifiers with the EZID service. You must have an EZID account for this to
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* work properly.
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*
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* Whether or not identifiers should be converted is determined by several metacat.properties.
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* First, only upgrade if 'guid.assignGUIDs' is true. Next, for each server registered in
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* the xml_replication table, only convert the documents belonging to that server if
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* there is a corresponding property that gives the 'shoulder' or 'prefix'' to be used to
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* convert existing IDs to GUIDs. For example, if servers 1 & 2 are registered in
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* xml_replication, then only convert the IDs for server 1 to GUIDs if the
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* property 'guid.ezid.doishoulder.1' defines a valid doi shoulder.
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*
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* NOTE: Metacat v2.0.5 has changed the name of the systemmetadata* tables to accommodate Oracle
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* length restrictions. The table names have been updated in this utility to enable
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* users to run this utility on v2.0.5+. You can only run this version of the utility on
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* Metacat deployments that have been upgraded to 2.0.5+
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*
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* @author jones
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*/
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public class GenerateGlobalIdentifiers implements UpgradeUtilityInterface {
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private static Log log = LogFactory.getLog(GenerateGlobalIdentifiers.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 String eziduser = null;
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// private String ezidPassword = null;
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/**
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* The main upgrade() procedure, which first upgrades identifiers in the database,
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* then registers these with EZID.
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*/
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public boolean upgrade() throws AdminException {
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boolean success = false;
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log.debug("Upgrading identifiers to DOIs");
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// Check if assignDOIs is true, and if EZID is configured
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boolean shouldUpgrade = false;
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try {
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shouldUpgrade = new Boolean(PropertyService.getProperty("guid.assignGUIDs")).booleanValue();
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if (shouldUpgrade) {
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log.debug("Upgrading identifiers to DOIs");
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success = updateIdentifierReferences();
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}
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} catch (PropertyNotFoundException e) {
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// When the guid properties are not found, do nothing
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shouldUpgrade = false;
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success = true;
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}
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return success;
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}
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/**
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* Loop through the servers registered in this instance of Metacat, and for
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* each server determine if we should convert to GUIDs for the documents associated
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* with that server. If so, convert the identifier table to use a GUID for all
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* documents for that server found in xml_documents and xml_replication.
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* @return true if all conversions succeed
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* @throws AdminException
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*/
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private boolean updateIdentifierReferences() throws AdminException {
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log.debug("Updating identifier references...");
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try {
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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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// eziduser = PropertyService.getProperty("guid.ezid.username");
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// ezidPassword = PropertyService.getProperty("guid.ezid.password");
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} catch (PropertyNotFoundException e) {
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String msg = "PropertyNotFound while trying to convert identifiers: " + e.getMessage();
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log.error(msg, e);
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throw new AdminException(msg);
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}
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// Create a connection, and start a transaction for which FK constraint checking is deferred
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Connection con = openDatabaseConnection();
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deferConstraints(con);
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// Copy the identifier.guid column for later use
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createDuplicateGUIDColumn(con);
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// Look up the maximum server number from the database
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int maxServerId = lookupMaxServers(con);
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// Loop across each replica server, checking if it is to have DOIs assigned
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// This is determined by the presence of a shoulder in the configuration file for
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// that server number
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for (int server = 1; server <= maxServerId; server++) {
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// Get the server's shoulder, or skip if not found
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try {
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String shoulder = PropertyService.getProperty("guid.ezid.doishoulder." + server);
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log.debug("Processing shoulder for server " + server + ": " + shoulder);
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// Update identifiers table (but only for local documents, not replicated documents)
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convertIdentifierTable(con, server, shoulder);
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} catch (PropertyNotFoundException e) {
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// The shoulder was not found for this server, so we just skip it
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log.debug("No shoulder found: " + e.getMessage());
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}
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}
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// Convert other tables once, after the identifier table conversion has established the new
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// global identifiers to be used
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// This incudes: xml_access table, including accessfileid field, systemmetadata,
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// smreplicationpolicy,and smreplicationstatus tables
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convertIdentifierField(con, "xml_access", "guid");
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convertIdentifierField(con, "xml_access", "accessfileid");
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convertIdentifierField(con, "systemmetadata", "guid");
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convertIdentifierField(con, "smreplicationpolicy", "guid");
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convertIdentifierField(con, "smreplicationstatus", "guid");
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// Now clean up the temporary column we created, but note this makes it much
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// harder to revert our changes
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dropDuplicateGUIDColumn(con);
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commitAndCloseConnection(con);
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/*
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// The following SQL commands will revert the changes made by this script as long as the identifier.old_guid column is intact
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start transaction;
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update smreplicationstatus set guid = id.old_guid FROM identifier id WHERE smreplicationstatus.guid = id.guid;
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update smreplicationpolicy set guid = id.old_guid FROM identifier id WHERE smreplicationpolicy.guid = id.guid;
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update systemmetadata set guid = id.old_guid FROM identifier id WHERE systemmetadata.guid = id.guid;
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update xml_access set accessfileid = id.old_guid FROM identifier id WHERE xml_access.accessfileid = id.guid;
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update xml_access set guid = id.old_guid FROM identifier id WHERE xml_access.guid = id.guid;
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update identifier set guid = old_guid;
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alter table identifier drop column old_guid;
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commit;
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*/
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return true;
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}
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/**
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* Open a JDBC connection that will be used for all of the subsequent methods that
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* access or modify the database. All changes are done in one transaction, so need
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* to be done using a single connection.
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* @return the Connection created
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* @throws AdminException
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*/
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private Connection openDatabaseConnection() throws AdminException {
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Connection con = null;
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try {
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Driver d = (Driver) Class.forName(driver).newInstance();
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DriverManager.registerDriver(d);
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con = DriverManager.getConnection(url, user, password);
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} catch (InstantiationException e) {
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String msg = "InstantiationException updating creating DB connection: " + e.getMessage();
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log.error(msg, e);
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throw new AdminException(msg);
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} catch (IllegalAccessException e) {
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String msg = "IllegalAccessException updating creating DB connection: " + e.getMessage();
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log.error(msg, e);
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throw new AdminException(msg);
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} catch (ClassNotFoundException e) {
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String msg = "ClassNotFoundException updating creating DB connection: " + e.getMessage();
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log.error(msg, e);
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throw new AdminException(msg);
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} catch (SQLException e) {
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String msg = "SQLException updating creating DB connection: " + e.getMessage();
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log.error(msg, e);
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throw new AdminException(msg);
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}
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return con;
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}
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/**
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* Start a transaction on the given connection, and defer all constraints so
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* that changes to foreign keys will not be checked until after all of the
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* identifiers have been updated in all tables. Without this, we would get
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* FK constraint violations as we changed the tables.
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* @param con the connection to the database
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* @throws AdminException
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*/
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private void deferConstraints(Connection con) throws AdminException {
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try {
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con.setAutoCommit(false);
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Statement sqlStatement = con.createStatement();
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boolean hasResults = sqlStatement.execute("SET CONSTRAINTS ALL DEFERRED;");
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log.debug("Constraints Deferred.");
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} catch (SQLException e) {
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String msg = "SQLException while disabling constraints: " + e.getMessage();
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log.error(msg, e);
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throw new AdminException(msg);
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}
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}
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/**
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* Temporarily save the current identifier.guid in a backup column (old_guid), to be used
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* for updating additional tables.
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* @param con the connection to the database with an open transaction
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* @throws AdminException
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*/
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private void createDuplicateGUIDColumn(Connection con) throws AdminException {
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try {
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Statement sqlStatement = con.createStatement();
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boolean hasResults = sqlStatement.execute("ALTER TABLE identifier ADD COLUMN old_guid TEXT;");
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log.debug("old_guid column added.");
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sqlStatement = con.createStatement();
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hasResults = sqlStatement.execute("UPDATE identifier SET old_guid = guid;");
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log.debug("Copied original identifiers to old_guid column.");
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} catch (SQLException e) {
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String msg = "SQLException while duplicating GUID column: " + e.getMessage();
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log.error(msg, e);
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throw new AdminException(msg);
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}
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}
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/**
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* Drop the temporary GUID backup column (old_guid) once upgrading identifiers
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* is complete.
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* @param con the connection to the database with an open transaction
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* @throws AdminException
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*/
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private void dropDuplicateGUIDColumn(Connection con) throws AdminException {
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try {
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Statement sqlStatement = con.createStatement();
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boolean hasResults = sqlStatement.execute("ALTER TABLE identifier DROP COLUMN old_guid;");
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log.debug("old_guid column dropped.");
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} catch (SQLException e) {
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String msg = "SQLException dropping GUID column: " + e.getMessage();
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log.error(msg, e);
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throw new AdminException(msg);
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}
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}
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/**
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* Query the database to determine which servers are registered and can be
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* inspected for potential identifier upgrades.
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* @param con the connection to the database with an open transaction
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* @throws AdminException
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*/
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private int lookupMaxServers(Connection con) throws AdminException {
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int maxServers = 0;
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try {
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Statement sqlStatement = con.createStatement();
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boolean hasResults = sqlStatement.execute("SELECT max(serverid) AS maxserverid FROM xml_replication;");
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if (hasResults) {
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ResultSet rs = sqlStatement.getResultSet();
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if (rs.next()) {
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maxServers = rs.getInt(1);
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log.debug("MaxServerID: " + maxServers);
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} else {
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String msg = "Could not determine max serverid; database query cursor had zero rows.";
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log.error(msg);
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throw new AdminException(msg);
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}
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} else {
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String msg = "Could not determine max serverid; database query failed to return results.";
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log.error(msg);
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throw new AdminException(msg);
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}
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} catch (SQLException e) {
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String msg = "SQLException while looking up serverId: " + e.getMessage();
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log.error(msg, e);
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throw new AdminException(msg);
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}
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return maxServers;
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}
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/**
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* Convert identifiers to DOI GUIDs in the identifier table for any documents found in
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* xml_documents or xml_revisions that reside on a server for which a DOI shoulder prefix
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* has been assigned.
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*
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* @param con the connection to the database with an open transaction
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* @param server the id of the server whose documents are to be converted
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* @param shoulder the DOI shoulder to be used for converting
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* @return true if conversion is successful
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* @throws AdminException
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*/
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private boolean convertIdentifierTable(Connection con, int server, String shoulder) throws AdminException {
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PreparedStatement pstmt = null;
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try {
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String sql_1 =
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"UPDATE identifier " +
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"SET guid = p.doi " +
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"FROM (" +
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"SELECT guid, ? || guid as doi " +
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"FROM identifier id2, ";
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String sql_2 =
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" xd " +
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"WHERE id2.docid = xd.docid AND id2.rev = xd.rev " +
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"AND xd.server_location = ? " +
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") p " +
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"WHERE identifier.guid = p.guid;";
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// Convert identifiers found in xml_documents
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pstmt = con.prepareStatement(sql_1 + "xml_documents" + sql_2);
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pstmt.setString(1, shoulder);
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pstmt.setInt(2, server);
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pstmt.execute();
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// Convert identifiers found in xml_revisions
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pstmt = con.prepareStatement(sql_1 + "xml_revisions" + sql_2);
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pstmt.setString(1, shoulder);
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pstmt.setInt(2, server);
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pstmt.execute();
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log.debug("Finished shoulder for server " + server + ": " + shoulder);
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361
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362
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} catch (SQLException e) {
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String msg = "SQLException updating identifier table: " + e.getMessage();
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log.error(msg, e);
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throw new AdminException(msg);
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}
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367
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return true;
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}
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370
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|
371
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/**
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* Convert the given field in the given table to use the new identifier.guid that
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* has been assigned.
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*
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* @param con the connection to the database with an open transaction
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* @param table the name of the table with identifiers to be converted
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* @param field the name of the field containing identifiers to be converted
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* @return true if conversion was successful
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* @throws AdminException
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*/
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private boolean convertIdentifierField(Connection con, String table, String field) throws AdminException {
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PreparedStatement pstmt = null;
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try {
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384
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|
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String sql_1 =
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"UPDATE " + table + " " +
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"SET " + field + " = id.guid " +
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"FROM identifier id " +
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"WHERE " + table + "."+ field + " = id.old_guid;";
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// Convert identifiers found in the given table and field
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pstmt = con.prepareStatement(sql_1);
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pstmt.execute();
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log.debug("Finished converting table " + table + " (" + field +")" );
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396
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} catch (SQLException e) {
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String msg = "SQLException while converting identifier field: " + e.getMessage();
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log.error(msg, e);
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throw new AdminException(msg);
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}
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402
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403
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return true;
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}
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405
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|
406
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/**
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* Commit the current transaction on the connection, and close the connection.
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408
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* @param con the connection to the database with an open transaction
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409
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* @return true if the connection is successfully closed
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410
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* @throws AdminException
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*/
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private boolean commitAndCloseConnection(Connection con) throws AdminException {
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413
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try {
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414
|
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log.debug("Committing and closing connection.");
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con.commit();
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con.close();
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} catch (SQLException e) {
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419
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String msg = "SQLException while commiting and closing connection: " + e.getMessage();
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log.error(msg, e);
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throw new AdminException(msg);
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422
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}
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423
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|
424
|
return true;
|
425
|
}
|
426
|
|
427
|
/**
|
428
|
* Main method, solely for testing. Not used in ordinary operation.
|
429
|
*/
|
430
|
public static void main(String [] ags){
|
431
|
|
432
|
try {
|
433
|
// set up the properties based on the test/deployed configuration of the workspace
|
434
|
SortedProperties testProperties =
|
435
|
new SortedProperties("test/test.properties");
|
436
|
testProperties.load();
|
437
|
String metacatContextDir = testProperties.getProperty("metacat.contextDir");
|
438
|
PropertyService.getInstance(metacatContextDir + "/WEB-INF");
|
439
|
// now run it
|
440
|
GenerateGlobalIdentifiers upgrader = new GenerateGlobalIdentifiers();
|
441
|
upgrader.upgrade();
|
442
|
} catch (IOException e) {
|
443
|
e.printStackTrace();
|
444
|
} catch (PropertyNotFoundException e) {
|
445
|
e.printStackTrace();
|
446
|
} catch (ServiceException e) {
|
447
|
e.printStackTrace();
|
448
|
} catch (AdminException e) {
|
449
|
e.printStackTrace();
|
450
|
}
|
451
|
}
|
452
|
}
|