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/**
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* '$RCSfile$'
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* Copyright: 2010 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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*
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* '$Author: jones $'
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* '$Date: 2010-02-03 17:58:12 -0900 (Wed, 03 Feb 2010) $'
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* '$Revision: 5211 $'
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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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package edu.ucsb.nceas.metacat;
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import java.util.*;
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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 org.apache.log4j.Logger;
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import edu.ucsb.nceas.metacat.database.DBConnection;
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import edu.ucsb.nceas.metacat.database.DBConnectionPool;
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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/**
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* Manage the relationship between Metacat local identifiers (LocalIDs) that are
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* codified as the (docid, rev) pair with globally uniqe string identifiers
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* (GUIDs) that are opaque strings. This class provides methods to manage these
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* identifiers, and to search for and look up LocalIDs based on their GUID and
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* vice versa. IdentifierManager is a singleton.
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*
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* @author Matthew Jones
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*/
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public class IdentifierManager {
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public static final String TYPE_SYSTEM_METADATA = "systemmetadata";
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public static final String TYPE_IDENTIFIER = "identifier";
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public static final String DATAONE_SM_DOCTYPE = "http://dataone.org/service/types/SystemMetadata/0.1";
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/**
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* The single instance of the manager that is always returned.
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*/
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private static IdentifierManager self = null;
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private Logger logMetacat = Logger.getLogger(EventLog.class);
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/**
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* A private constructor that initializes the class when getInstance() is
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* called.
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*/
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private IdentifierManager()
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{
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}
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/**
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* Return the single instance of the manager after initializing it if it
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* wasn't previously initialized.
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*
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* @return the single IdentifierManager instance
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*/
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public static IdentifierManager getInstance()
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{
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if (self == null) {
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self = new IdentifierManager();
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}
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return self;
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}
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/**
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* return information on the document with localId. These are the fields
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* from the xml_documents table. They can be used to contstruct metadata
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* about the object that is stored.
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* @param localId
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* @return
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* @throws McdbDocNotFoundException
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*/
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public Hashtable<String, Object> getDocumentInfo(String localId)
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throws McdbDocNotFoundException
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{
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try
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{
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AccessionNumber acc = new AccessionNumber(localId, "NONE");
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localId = acc.getDocid();
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}
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catch(Exception e)
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{
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//do nothing. just try the localId as it is
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}
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Hashtable<String, Object> h = new Hashtable<String, Object>();
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String sql = "select docname, doctype, user_owner, user_updated, " +
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"server_location, rev, date_created, date_updated from " +
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"xml_documents where docid like '" + localId + "'";
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DBConnection dbConn = null;
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int serialNumber = -1;
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try
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{
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// Get a database connection from the pool
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dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getDocumentInfo");
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serialNumber = dbConn.getCheckOutSerialNumber();
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// Execute the insert statement
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PreparedStatement stmt = dbConn.prepareStatement(sql);
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ResultSet rs = stmt.executeQuery();
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if (rs.next())
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{
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String docname = rs.getString(1);
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String doctype = rs.getString(2);
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String user_owner = rs.getString(3);
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String user_updated = rs.getString(4);
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String server_location = rs.getString(5);
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int rev = rs.getInt(6);
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String date_created = rs.getString(7);
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String date_updated = rs.getString(8);
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h.put("docname", docname);
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h.put("doctype", doctype);
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h.put("user_owner", user_owner);
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h.put("user_updated", user_updated);
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h.put("server_location", server_location);
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h.put("rev", new Integer(rev).toString());
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h.put("date_created", date_created);
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h.put("date_updated", date_updated);
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stmt.close();
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}
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else
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{
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stmt.close();
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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throw new McdbDocNotFoundException("2Could not find document " + localId);
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}
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String sql2 = "select principal_name, permission, perm_type, perm_order from xml_access " +
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"where docid like '" + localId + "'";
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System.out.println("executing sql: " + sql2);
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PreparedStatement stmt2 = dbConn.prepareStatement(sql2);
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rs = stmt2.executeQuery();
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Vector accessVector = new Vector();
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while(rs.next())
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{
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Hashtable accessHash = new Hashtable();
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String principal_name = rs.getString(1);
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String permission = rs.getString(2);
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String permissionType = rs.getString(3);
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String permissionOrder = rs.getString(4);
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accessHash.put("principal_name", principal_name);
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accessHash.put("permission", permission);
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accessHash.put("permission_type", permissionType);
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accessHash.put("permission_order", permissionOrder);
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System.out.println("accessHash: " + accessHash.toString());
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accessVector.add(accessHash);
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}
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h.put("access", accessVector);
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}
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catch (SQLException e)
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{
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e.printStackTrace();
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logMetacat.error("Error while getting document info for localid " + localId + " : "
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+ e.getMessage());
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}
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finally
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{
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// Return database connection to the pool
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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}
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return h;
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}
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/**
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* return the newest rev for a given localId
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* @param localId
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* @return
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*/
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public int getLatestRevForLocalId(String localId)
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throws McdbDocNotFoundException
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{
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try
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{
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AccessionNumber acc = new AccessionNumber(localId, "NONE");
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localId = acc.getDocid();
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}
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catch(Exception e)
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{
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//do nothing. just try the localId as it is
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}
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int rev = 0;
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String sql = "select rev from xml_documents where docid like '" + localId + "'";
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DBConnection dbConn = null;
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int serialNumber = -1;
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try
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{
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// Get a database connection from the pool
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dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLatestRevForLocalId");
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serialNumber = dbConn.getCheckOutSerialNumber();
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// Execute the insert statement
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PreparedStatement stmt = dbConn.prepareStatement(sql);
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ResultSet rs = stmt.executeQuery();
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if (rs.next())
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{
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rev = rs.getInt(1);
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stmt.close();
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}
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else
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{
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stmt.close();
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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throw new McdbDocNotFoundException("While trying to get the latest rev, could not find document " + localId);
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}
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}
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catch (SQLException e)
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{
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logMetacat.error("Error while looking up the guid: "
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+ e.getMessage());
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}
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finally
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{
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// Return database connection to the pool
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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}
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return rev;
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}
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/**
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* return all local ids in the object store that do not have associated
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* system metadata and are not themselves system metadata
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*/
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public List<String> getLocalIdsWithNoSystemMetadata()
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{
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Vector<String> ids = new Vector<String>();
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//String sql = "select docid from identifier where guid in (select guid from systemmetadata)";
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//String sql = "select docid from xml_documents where docid not " +
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// "in (select docid from identifier where guid in (select guid from systemmetadata)) " +
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// "and doctype not like '" + DATAONE_SM_DOCTYPE + "'";
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String sql = "select docid, rev from xml_documents where docid not in " +
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"(select docid from systemmetadata) and (docid not in " +
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"(select docid from identifier where guid in (select guid from systemmetadata)))";
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DBConnection dbConn = null;
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int serialNumber = -1;
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try
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{
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// Get a database connection from the pool
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dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLocalIdsWithNoSystemMetadata");
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serialNumber = dbConn.getCheckOutSerialNumber();
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// Execute the insert statement
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PreparedStatement stmt = dbConn.prepareStatement(sql);
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ResultSet rs = stmt.executeQuery();
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while (rs.next())
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{
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String localid = rs.getString(1);
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String rev = rs.getString(2);
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localid += "." + rev;
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System.out.println("id to add SM for: " + localid);
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ids.add(localid);
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}
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stmt.close();
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}
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catch (SQLException e)
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{
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logMetacat.error("Error while looking up the guid: "
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+ e.getMessage());
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}
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finally
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{
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// Return database connection to the pool
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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}
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return ids;
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}
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/**
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* return a listing of all local ids in the object store
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* @return a list of all local ids in metacat
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*/
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public List<String> getAllLocalIds()
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throws Exception
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{
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Vector<String> ids = new Vector<String>();
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String sql = "select docid from xml_documents";
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DBConnection dbConn = null;
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int serialNumber = -1;
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try
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{
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// Get a database connection from the pool
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dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getAllLocalIds");
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serialNumber = dbConn.getCheckOutSerialNumber();
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// Execute the insert statement
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PreparedStatement stmt = dbConn.prepareStatement(sql);
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ResultSet rs = stmt.executeQuery();
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while (rs.next())
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{
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String localid = rs.getString(1);
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ids.add(localid);
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}
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stmt.close();
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}
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catch (SQLException e)
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{
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logMetacat.error("Error while looking up the guid: "
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+ e.getMessage());
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}
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finally
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{
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// Return database connection to the pool
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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}
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return ids;
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}
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/**
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* Lookup a GUID from the database, and return the associated LocalID. If
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* the identifier is not found, throw an exception.
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*
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* @param guid the global identifier to look up
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* @return String containing the corresponding LocalId
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* @throws McdbDocNotFoundException if the identifier is not found
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*/
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public String getLocalId(String guid) throws McdbDocNotFoundException
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{
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return this.getLocalId(guid, TYPE_IDENTIFIER);
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}
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/**
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* Determine if an identifier exists already, returning true if so.
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*
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* @param guid the global identifier to look up
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* @return boolean true if the identifier exists
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*/
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public boolean identifierExists(String guid)
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{
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boolean idExists = false;
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try {
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String id = getLocalId(guid);
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if (id != null) {
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idExists = true;
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}
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} catch (McdbDocNotFoundException e) {
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idExists = false;
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}
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return idExists;
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}
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/**
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* Create a mapping between two identifiers, one representing an
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* unconstrained, globally unique string (guid), and one a localId
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* in the Metacat docid format (scope.id.revision).
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* This mapping allows one to find the global id (guid) from the localId.
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*
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* @param guid the global string identifier to be mapped
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* @param localId the local identifier to be mapped
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*/
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public void createMapping(String guid, String localId)
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{
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createGenericMapping(guid, localId, TYPE_IDENTIFIER);
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}
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/**
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*
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* @param guid
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* @param rev
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* @return
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*/
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public String generateLocalId(String guid, int rev)
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{
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return generateLocalId(guid, rev, false);
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}
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|
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/**
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* Given a global identifier (guid), create a suitable local identifier that
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* follows Metacat's docid semantics and format (scope.id.rev), and create
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386
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* a mapping between these two identifiers. This effectively reserves both
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* the global and the local identifier, as they will now be present in the
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* identifier mapping table. If the incoming guid has the syntax of a
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* Metacat docid (scope.id.rev), then simply use it.
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*
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* @param guid the global string identifier
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* @param rev the revision number to be used in the localId
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* @return String containing the localId to be used for Metacat operations
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394
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*/
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public String generateLocalId(String guid, int rev, boolean isSystemMetadata)
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396
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{
|
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String localId = "";
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boolean conformsToDocidFormat = false;
|
399
|
|
400
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// Check if the guid passed in is already in docid (scope.id.rev) format
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try {
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AccessionNumber acc = new AccessionNumber(guid, "NONE");
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if (new Integer(acc.getRev()).intValue() > 0) {
|
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conformsToDocidFormat = true;
|
405
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}
|
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} catch (NumberFormatException e) {
|
407
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// No action needed, simply detecting invalid AccessionNumbers
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408
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} catch (AccessionNumberException e) {
|
409
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// No action needed, simply detecting invalid AccessionNumbers
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} catch (SQLException e) {
|
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|
// No action needed, simply detecting invalid AccessionNumbers
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412
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}
|
413
|
|
414
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if (conformsToDocidFormat) {
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// if it conforms, use it for both guid and localId
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localId = guid;
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} else {
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// if not, then generate a new unique localId
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localId = DocumentUtil.generateDocumentId(rev);
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}
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421
|
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422
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// Register this new pair in the identifier mapping table
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423
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System.out.println("creating mapping in generateLocalId");
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if(!isSystemMetadata)
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{ //don't do this if we're generating for system metadata
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createMapping(guid, localId);
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}
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428
|
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return localId;
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430
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}
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431
|
|
432
|
/**
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433
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* given a local identifer, look up the guid. Throw McdbDocNotFoundException
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434
|
* if the docid, rev is not found in the identifiers or systemmetadata tables
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435
|
*
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436
|
* @param docid the docid to look up
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437
|
* @param rev the revision of the docid to look up
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438
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* @return String containing the mapped guid
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439
|
* @throws McdbDocNotFoundException if the docid, rev is not found
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440
|
*/
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441
|
public String getGUID(String docid, int rev)
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442
|
throws McdbDocNotFoundException
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443
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{
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444
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System.out.println("getting guid for " + docid);
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445
|
String query = "select guid from identifier where docid = ? and rev = ?";
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446
|
String guid = null;
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447
|
boolean found = false;
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448
|
|
449
|
DBConnection dbConn = null;
|
450
|
int serialNumber = -1;
|
451
|
try {
|
452
|
// Get a database connection from the pool
|
453
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getGUID");
|
454
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
455
|
|
456
|
// Execute the insert statement
|
457
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
458
|
stmt.setString(1, docid);
|
459
|
stmt.setInt(2, rev);
|
460
|
ResultSet rs = stmt.executeQuery();
|
461
|
if (rs.next())
|
462
|
{
|
463
|
guid = rs.getString(1);
|
464
|
}
|
465
|
else
|
466
|
{
|
467
|
query = "select guid from systemmetadata where docid = ? and rev = ?";
|
468
|
stmt = dbConn.prepareStatement(query);
|
469
|
stmt.setString(1, docid);
|
470
|
stmt.setInt(2, rev);
|
471
|
rs = stmt.executeQuery();
|
472
|
if(rs.next())
|
473
|
{
|
474
|
guid = rs.getString(1);
|
475
|
}
|
476
|
else
|
477
|
{
|
478
|
throw new McdbDocNotFoundException("No guid registered for docid " + docid + "." + rev);
|
479
|
}
|
480
|
}
|
481
|
|
482
|
} catch (SQLException e) {
|
483
|
logMetacat.error("Error while looking up the guid: "
|
484
|
+ e.getMessage());
|
485
|
} finally {
|
486
|
// Return database connection to the pool
|
487
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
488
|
}
|
489
|
|
490
|
return guid;
|
491
|
}
|
492
|
|
493
|
/**
|
494
|
* insert a system metadata id for a local id
|
495
|
*
|
496
|
* @param guid the id to insert
|
497
|
* @param localId the systemMetadata object to get the local id for
|
498
|
*/
|
499
|
public void createSystemMetadataMapping(String guid, String localId)
|
500
|
{
|
501
|
createGenericMapping(guid, localId, TYPE_SYSTEM_METADATA);
|
502
|
}
|
503
|
|
504
|
/**
|
505
|
* update a mapping
|
506
|
* @param guid
|
507
|
* @param localId
|
508
|
*/
|
509
|
public void updateSystemMetadataMapping(String guid, String localId)
|
510
|
{
|
511
|
int serialNumber = -1;
|
512
|
DBConnection dbConn = null;
|
513
|
try {
|
514
|
// Parse the localId into scope and rev parts
|
515
|
AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
|
516
|
String docid = acc.getDocid();
|
517
|
int rev = 1;
|
518
|
if(acc.getRev() != null)
|
519
|
{
|
520
|
rev = (new Integer(acc.getRev()).intValue());
|
521
|
}
|
522
|
|
523
|
// Get a database connection from the pool
|
524
|
dbConn =
|
525
|
DBConnectionPool.getDBConnection("IdentifierManager.createMapping");
|
526
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
527
|
|
528
|
// Execute the insert statement
|
529
|
String query = "update systemmetadata set (docid, rev) = (?, ?) where guid='" + guid + "'";
|
530
|
//System.out.println("query: " + query + " for params: (guid:" + guid + ", docid=" + docid + ", rev=" + rev + ")");
|
531
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
532
|
stmt.setString(1, docid);
|
533
|
stmt.setInt(2, rev);
|
534
|
int rows = stmt.executeUpdate();
|
535
|
|
536
|
stmt.close();
|
537
|
} catch (SQLException e) {
|
538
|
e.printStackTrace();
|
539
|
logMetacat.error("SQL error while updating a mapping to the system metadata identifier: "
|
540
|
+ e.getMessage());
|
541
|
} catch (NumberFormatException e) {
|
542
|
e.printStackTrace();
|
543
|
logMetacat.error("NumberFormat error while updating a mapping to the system metadata identifier: "
|
544
|
+ e.getMessage());
|
545
|
} catch (AccessionNumberException e) {
|
546
|
e.printStackTrace();
|
547
|
logMetacat.error("AccessionNumber error while updating a mapping to the system metadata identifier: "
|
548
|
+ e.getMessage());
|
549
|
} finally {
|
550
|
// Return database connection to the pool
|
551
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
552
|
}
|
553
|
}
|
554
|
|
555
|
/**
|
556
|
* return the localId of a system metadata document based on its guid
|
557
|
*/
|
558
|
public String getSystemMetadataLocalId(String guid)
|
559
|
throws McdbDocNotFoundException
|
560
|
{
|
561
|
return this.getLocalId(guid, TYPE_SYSTEM_METADATA);
|
562
|
}
|
563
|
|
564
|
/**
|
565
|
* return a localId based on a guid. The type can either be 'identifier'
|
566
|
* to get an id from the identifier table or 'systemmetadata' to get
|
567
|
* the identifier from the systemidentifier table
|
568
|
*/
|
569
|
private String getLocalId(String guid, String type)
|
570
|
throws McdbDocNotFoundException
|
571
|
{
|
572
|
if(!type.equals(TYPE_IDENTIFIER) &&
|
573
|
!type.equals(TYPE_SYSTEM_METADATA))
|
574
|
{
|
575
|
throw new RuntimeException("cannot lookup the identifier for type " + type +
|
576
|
". Please choose 'identifier' or 'systemmetadata'.");
|
577
|
}
|
578
|
|
579
|
String db_guid = "";
|
580
|
String docid = "";
|
581
|
int rev = 0;
|
582
|
|
583
|
String query = "select guid, docid, rev from " + type + " where guid = ?";
|
584
|
//System.out.println("query: " + query + " for params: (" + guid + ")");
|
585
|
|
586
|
DBConnection dbConn = null;
|
587
|
int serialNumber = -1;
|
588
|
try {
|
589
|
// Get a database connection from the pool
|
590
|
dbConn = DBConnectionPool.getDBConnection("Identifier.getLocalId");
|
591
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
592
|
|
593
|
// Execute the insert statement
|
594
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
595
|
stmt.setString(1, guid);
|
596
|
ResultSet rs = stmt.executeQuery();
|
597
|
if (rs.next()) {
|
598
|
db_guid = rs.getString(1);
|
599
|
docid = rs.getString(2);
|
600
|
rev = rs.getInt(3);
|
601
|
assert(db_guid.equals(guid));
|
602
|
} else {
|
603
|
throw new McdbDocNotFoundException("Document not found:" + guid);
|
604
|
}
|
605
|
stmt.close();
|
606
|
} catch (SQLException e) {
|
607
|
logMetacat.error("Error while looking up the local identifier: "
|
608
|
+ e.getMessage());
|
609
|
} finally {
|
610
|
// Return database connection to the pool
|
611
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
612
|
}
|
613
|
return docid + "." + rev;
|
614
|
}
|
615
|
|
616
|
/**
|
617
|
* create a mapping in the systemmetadata or identifier table
|
618
|
* @param guid
|
619
|
* @param localId
|
620
|
* @param type
|
621
|
*/
|
622
|
private void createGenericMapping(String guid, String localId, String type)
|
623
|
{
|
624
|
if(!type.equals(TYPE_IDENTIFIER) &&
|
625
|
!type.equals(TYPE_SYSTEM_METADATA))
|
626
|
{
|
627
|
throw new RuntimeException("Cannot create mapping for type " + type +
|
628
|
". Please choose 'identifier' or 'systemmetadata'.");
|
629
|
}
|
630
|
|
631
|
int serialNumber = -1;
|
632
|
DBConnection dbConn = null;
|
633
|
try {
|
634
|
|
635
|
// Parse the localId into scope and rev parts
|
636
|
AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
|
637
|
String docid = acc.getDocid();
|
638
|
int rev = 1;
|
639
|
if(acc.getRev() != null)
|
640
|
{
|
641
|
rev = (new Integer(acc.getRev()).intValue());
|
642
|
}
|
643
|
|
644
|
// Get a database connection from the pool
|
645
|
dbConn =
|
646
|
DBConnectionPool.getDBConnection("IdentifierManager.createMapping");
|
647
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
648
|
|
649
|
// Execute the insert statement
|
650
|
String query = "insert into " + type + " (guid, docid, rev) values (?, ?, ?)";
|
651
|
//System.out.println("query: " + query + " for params: (" + guid + ", " + docid + ", " + rev + ")");
|
652
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
653
|
stmt.setString(1, guid);
|
654
|
stmt.setString(2, docid);
|
655
|
stmt.setInt(3, rev);
|
656
|
int rows = stmt.executeUpdate();
|
657
|
|
658
|
stmt.close();
|
659
|
} catch (SQLException e) {
|
660
|
e.printStackTrace();
|
661
|
logMetacat.error("SQL error while creating a mapping to the system metadata identifier: "
|
662
|
+ e.getMessage());
|
663
|
} catch (NumberFormatException e) {
|
664
|
e.printStackTrace();
|
665
|
logMetacat.error("NumberFormat error while creating a mapping to the system metadata identifier: "
|
666
|
+ e.getMessage());
|
667
|
} catch (AccessionNumberException e) {
|
668
|
e.printStackTrace();
|
669
|
logMetacat.error("AccessionNumber error while creating a mapping to the system metadata identifier: "
|
670
|
+ e.getMessage());
|
671
|
} finally {
|
672
|
// Return database connection to the pool
|
673
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
674
|
}
|
675
|
}
|
676
|
}
|
677
|
|