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package edu.ucsb.nceas.metacat.dataone;
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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: Peter Slaughter
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*
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* '$Author: tao $'
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* '$Date: 2015-07-15 11:07:27 -0700 (Wed, 15 Jul 2015) $'
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* '$Revision: 9249 $'
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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.math.BigInteger;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.concurrent.ExecutorService;
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import java.util.concurrent.Executors;
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import org.apache.log4j.Logger;
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import org.dataone.client.v2.CNode;
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import org.dataone.client.v2.itk.D1Client;
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import org.dataone.service.exceptions.InvalidRequest;
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import org.dataone.service.exceptions.InvalidToken;
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import org.dataone.service.exceptions.NotAuthorized;
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import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.exceptions.NotImplemented;
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import org.dataone.service.exceptions.ServiceFailure;
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import org.dataone.service.exceptions.VersionMismatch;
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import org.dataone.service.types.v1.AccessPolicy;
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import org.dataone.service.types.v1.AccessRule;
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import org.dataone.service.types.v1.Identifier;
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import org.dataone.service.types.v1.NodeReference;
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import org.dataone.service.types.v1.ObjectFormatIdentifier;
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import org.dataone.service.types.v1.ObjectInfo;
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import org.dataone.service.types.v1.ObjectList;
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import org.dataone.service.types.v1.Permission;
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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 org.dataone.service.types.v2.SystemMetadata;
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import edu.ucsb.nceas.metacat.AccessionNumberException;
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import edu.ucsb.nceas.metacat.IdentifierManager;
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import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlException;
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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.GeneralPropertyException;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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import edu.ucsb.nceas.utilities.SortedProperties;
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public class SyncAccessPolicy {
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private static Logger logMetacat = Logger.getLogger(SyncAccessPolicy.class);
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/**
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* Synchronize access policy (from system metadata) of d1 member node with
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* the corresponding controlling node.
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*
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* @param objList
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* list of d1 objects to be synced
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* @return syncedIds a list of pids that were synced with the CN
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* @throws ServiceFailure
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* @throws InvalidToken
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* @throws NotAuthorized
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* @throws NotFound
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* @throws NotImplemented
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* @throws McdbDocNotFoundException
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* @throws InvalidRequest
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* @throws VersionMismatch
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* @throws SQLException
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* @throws AccessionNumberException
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* @throws NumberFormatException
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*/
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private List<Identifier> sync(ObjectList objList) throws ServiceFailure,
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InvalidToken, NotAuthorized, NotFound, NotImplemented,
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McdbDocNotFoundException, InvalidRequest, VersionMismatch,
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NumberFormatException, AccessionNumberException, SQLException,
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Exception {
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AccessPolicy cnAccessPolicy = null;
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AccessPolicy mnAccessPolicy = null;
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Identifier pid = new Identifier();
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ObjectInfo objInfo = null;
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Session session = null;
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List<Identifier> syncedIds = new ArrayList<Identifier>();
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SystemMetadata cnSysMeta = null;
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SystemMetadata mnSysMeta = null;
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CNode cn = null;
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try {
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cn = D1Client.getCN();
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logMetacat.debug("Will sync access policies to CN id: "
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+ cn.getNodeId() + " with info: " + cn.toString());
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} catch (ServiceFailure sf) {
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logMetacat
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.error("Unable to get Coordinating node name for this MN");
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throw new AccessControlException(
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"Unable to get Coordinating node name for this MN");
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}
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for (int i = objList.getStart(); i < objList.getCount(); i++) {
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objInfo = objList.getObjectInfo(i);
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pid = objInfo.getIdentifier();
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logMetacat.debug("Getting SM for pid: " + pid.getValue() + " i: "
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+ i);
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try {
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// Get sm, access policy for requested localId
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mnSysMeta = IdentifierManager.getInstance().getSystemMetadata(
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pid.getValue());
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} catch (McdbDocNotFoundException e) {
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logMetacat.error("Error syncing access policy of pid: "
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+ pid.getValue() + " pid not found: " + e.getMessage());
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continue;
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} catch (Exception e) {
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logMetacat.error("Error syncing access policy of pid: "
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+ pid.getValue() + ". Message: " + e.getMessage());
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continue;
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}
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logMetacat
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.debug("Getting access policy for pid: " + pid.getValue());
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mnAccessPolicy = mnSysMeta.getAccessPolicy();
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// Get sm, access policy for requested pid from the CN
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try {
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cnSysMeta = cn.getSystemMetadata(null, pid);
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} catch (Exception e) {
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logMetacat.error("Error getting system metadata for pid: "
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+ pid.getValue() + " from cn: " + e.getMessage());
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continue;
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}
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logMetacat.debug("Getting access policy from CN for pid: "
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+ pid.getValue());
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cnAccessPolicy = cnSysMeta.getAccessPolicy();
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logMetacat.debug("Diffing access policies (MN,CN) for pid: "
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+ pid.getValue());
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// Compare access policies of MN and CN, and update if different.
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if (!isEqual(mnAccessPolicy, cnAccessPolicy)) {
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try {
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BigInteger serialVersion = cnSysMeta.getSerialVersion();
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logMetacat
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.debug("Requesting CN to set access policy for pid: "
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+ pid.getValue()
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+ ", serial version: "
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+ serialVersion.toString());
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cn.setAccessPolicy(session, pid, mnAccessPolicy,
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serialVersion.longValue());
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logMetacat.debug("Successfully set access policy for pid: " + pid.getValue());
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// Add this pid to the list of pids that were successfully
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// synced
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syncedIds.add(pid);
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} catch (NotAuthorized na) {
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logMetacat
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.error("Error syncing CN with access policy of pid: "
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+ pid.getValue()
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+ " user not authorized: "
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+ na.getMessage());
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// throw na;
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continue;
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} catch (ServiceFailure sf) {
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logMetacat
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.error("Error syncing CN with access policy of pid: "
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+ pid.getValue()
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+ " Service failure: "
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+ "'" + sf.getDescription() + "'");
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sf.printStackTrace();
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logMetacat.debug("Cause: " + "'" + sf.getCause() + "'");
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// throw sf;
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continue;
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} catch (Exception e) {
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logMetacat
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.error("Error syncing CN with access policy of pid: "
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+ pid.getValue() + e.getMessage());
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// throw e;
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continue;
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}
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} else {
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logMetacat.warn("Skipping pid: " + pid.getValue());
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}
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logMetacat.debug("Done checking access policy for pid: "
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+ pid.getValue());
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}
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return syncedIds;
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}
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/**
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* Convenience function that accepts a list of guids to sync
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*
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* @param guidsToSync
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* list of guids to have access policy synced for
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* @return syncedPids - list of pids that were actually synced with the CN
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* @throws NumberFormatException
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* @throws ServiceFailure
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* @throws InvalidToken
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* @throws NotAuthorized
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* @throws NotFound
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* @throws NotImplemented
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* @throws McdbDocNotFoundException
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* @throws InvalidRequest
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* @throws VersionMismatch
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* @throws AccessionNumberException
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* @throws SQLException
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*/
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public List<Identifier> sync(List<String> guidsToSync)
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throws NumberFormatException, ServiceFailure, InvalidToken,
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NotAuthorized, NotFound, NotImplemented, McdbDocNotFoundException,
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InvalidRequest, VersionMismatch, AccessionNumberException,
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SQLException, Exception {
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List<Identifier> syncedPids = null;
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ObjectList objList = new ObjectList();
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SystemMetadata sm = new SystemMetadata();
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int start = 0;
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int count = 0; // guidsToSync.size();
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objList.setStart(start);
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// Convert the guids to d1 objects, as this is what
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// IdentifierManager.getInstance().querySystemMetadata returns in
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// syncAll, and
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// what sync(ObjectList...) expects
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for (String guid : guidsToSync) {
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try {
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sm = IdentifierManager.getInstance().getSystemMetadata(guid);
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count++;
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} catch (Exception e) {
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logMetacat.error("Error syncing access policy of pid: " + guid
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+ ". Message: " + e.getMessage());
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continue;
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}
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ObjectInfo oi = new ObjectInfo();
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Identifier id = new Identifier();
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id.setValue(guid);
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oi.setIdentifier(id);
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oi.setDateSysMetadataModified(sm.getDateSysMetadataModified());
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oi.setChecksum(sm.getChecksum());
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oi.setFormatId(sm.getFormatId());
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oi.setSize(sm.getSize());
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objList.addObjectInfo(oi);
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}
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int total = count;
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objList.setCount(count);
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objList.setTotal(total);
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syncedPids = sync(objList);
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return syncedPids;
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}
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/**
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* For all guids for which current MN is authoritative, check that access
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* policy is synced with CN.
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*
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* @return void
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*/
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public void syncAll() throws ServiceFailure, InvalidToken, NotAuthorized,
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NotFound, NotImplemented, McdbDocNotFoundException, InvalidRequest,
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VersionMismatch, NumberFormatException, AccessionNumberException,
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SQLException, PropertyNotFoundException, ServiceException,
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Exception {
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SyncTask st = new SyncTask();
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// Create a single thread to run the sync of all guids in
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ExecutorService executor = Executors.newSingleThreadExecutor();
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logMetacat.debug("syncAll starting thread");
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executor.execute(st);
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// Only one task will run on this thread
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executor.shutdown();
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// return syncedIds;
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}
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/**
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* Perform syncAll in a single thread.
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*
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* @return void
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*/
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private class SyncTask implements Runnable {
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@Override
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public void run() {
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312
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// For the following query parameters - null indicates that the
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// query
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// will not be
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// constrained by the parameter.
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Date startTime = null;
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Date endTime = null;
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ObjectFormatIdentifier objectFormatId = null;
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//Boolean replicaStatus = false; // return only pids for which this mn
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NodeReference thisMN = new NodeReference();
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try {
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String currentNodeId = PropertyService.getInstance().getProperty("dataone.nodeId"); // return only pids for which this mn
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thisMN.setValue(currentNodeId);
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} catch (Exception e) {
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logMetacat.error("SyncAccessPolicy.run - can't get the node id of this member node from the metacat property file since :"+e.getMessage());
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return;
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}
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// is
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ObjectList objsToSync = null;
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Integer count = 0;
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Integer start = 0;
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Integer total = 0;
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List<Identifier> tmpIds = null;
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// If even one sync error encounted, don't set property that will disable
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// "syncAll" button in admin/replication web page.
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boolean syncError = false;
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List<Identifier> syncedIds = new ArrayList<Identifier>();
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339
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try {
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341
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count = Integer.valueOf(PropertyService
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.getProperty("database.webResultsetSize"));
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} catch (NumberFormatException e1) {
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logMetacat
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.error("Error in propery file for format of database.webResultsetSize, will use 1000");
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e1.printStackTrace();
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count = 1000;
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} catch (PropertyNotFoundException e1) {
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349
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logMetacat
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350
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.error("Error reading propery file for database.webResultsetSize, will use 1000");
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e1.printStackTrace();
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352
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count = 1000;
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353
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}
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354
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355
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// Get the total count of guids before we start syncing
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Identifier id = null;
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boolean isSid = false;
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358
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try {
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359
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360
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objsToSync = IdentifierManager.getInstance()
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361
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.querySystemMetadata(startTime, endTime,
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objectFormatId, thisMN, start, count, id, isSid);
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363
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364
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logMetacat.debug("syncTask total # of guids: "
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365
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+ objsToSync.getTotal() + ", count for this page: "
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366
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+ objsToSync.getCount());
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367
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} catch (Exception e) {
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368
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logMetacat.error("Error syncing ids");
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369
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}
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370
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371
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total = objsToSync.getTotal();
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372
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373
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// The first loop might have fewer results than the requested count
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374
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// value from the properties file,
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375
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// so in this case use count returned from IdentiferManger for the
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376
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// loop count/increment (loop will only execute once).
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377
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if (objsToSync.getCount() < count)
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378
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count = objsToSync.getCount();
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379
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|
380
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for (int i = 0; (i + count - 1) < total; i += count) {
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381
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try {
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382
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logMetacat.debug("syncTask # requested: " + count
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383
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+ ", start: " + start + ", total: " + total
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384
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+ ", count: " + objsToSync.getCount());
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385
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tmpIds = sync(objsToSync);
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syncedIds.addAll(tmpIds);
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387
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|
388
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// Set start for the next db retrieval, loop interation
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389
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start += objsToSync.getCount();
|
390
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if (start >= total)
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391
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break;
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392
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objsToSync = IdentifierManager
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393
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.getInstance()
|
394
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.querySystemMetadata(startTime, endTime,
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objectFormatId, thisMN, start, count, id, isSid);
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396
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} catch (Exception e) {
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397
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logMetacat.error("Error syncing ids");
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398
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syncError = true;
|
399
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break;
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400
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}
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401
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}
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402
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logMetacat
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403
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.debug("syncTask thread completed. Number of guids synced: "
|
404
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+ syncedIds.size());
|
405
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if (!syncError) {
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406
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try {
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407
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PropertyService.setProperty(
|
408
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"dataone.syncaccesspolicies.synced",
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409
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Boolean.TRUE.toString());
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410
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} catch (GeneralPropertyException e) {
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411
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logMetacat
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.error("Unable to update property dataone.syncaccesspolicies.synced=true");
|
413
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}
|
414
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}
|
415
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}
|
416
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}
|
417
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|
418
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/**
|
419
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* Compare two d1 system metadata access policies for equivalence.
|
420
|
*
|
421
|
* @param ap1
|
422
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* - first access policy in the comparison
|
423
|
* @param ap2
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424
|
* - second access policy in the comparison
|
425
|
* @return boolean - true if access policies are equivalent
|
426
|
*/
|
427
|
public boolean isEqual(AccessPolicy ap1, AccessPolicy ap2) {
|
428
|
|
429
|
// can't check when either is null
|
430
|
if (ap1 == null || ap2 == null) {
|
431
|
return false;
|
432
|
}
|
433
|
|
434
|
// Access Policy -> Access Rule -> (Subject, Permission)
|
435
|
// i.e. Subject="slaughter", Permission="read,write,changePermission"
|
436
|
// Get the list of access rules for each access policy
|
437
|
List<AccessRule> allowList1 = ap1
|
438
|
.getAllowList();
|
439
|
List<AccessRule> allowList2 = ap2
|
440
|
.getAllowList();
|
441
|
|
442
|
HashMap<Subject, Set<Permission>> userPerms1 = new HashMap<Subject, Set<Permission>>();
|
443
|
HashMap<Subject, Set<Permission>> userPerms2 = new HashMap<Subject, Set<Permission>>();
|
444
|
|
445
|
// Load the permissions from the access rules into a hash of sets, i.e.,
|
446
|
// so that we end up with this:
|
447
|
// hash key: set of permissions, i.e.
|
448
|
// ----------------------------
|
449
|
// user1: read, write
|
450
|
// user2: read
|
451
|
// user3: read, write, change permissions
|
452
|
// With the permissions in this structure, they can be easily compared
|
453
|
Set<Permission> perms = null;
|
454
|
// Process first access policy
|
455
|
// Loop through access rules of this allowList
|
456
|
for (AccessRule accessRule : allowList1) {
|
457
|
for (Subject s : accessRule.getSubjectList()) {
|
458
|
if (userPerms1.containsKey(s)) {
|
459
|
perms = userPerms1.get(s);
|
460
|
} else {
|
461
|
perms = new HashSet<Permission>();
|
462
|
}
|
463
|
for (Permission p : accessRule.getPermissionList()) {
|
464
|
perms.add(p);
|
465
|
}
|
466
|
userPerms1.put(s, perms);
|
467
|
}
|
468
|
}
|
469
|
|
470
|
// Process second access policy
|
471
|
for (AccessRule accessRule : allowList2) {
|
472
|
for (Subject s : accessRule.getSubjectList()) {
|
473
|
if (userPerms2.containsKey(s)) {
|
474
|
perms = userPerms2.get(s);
|
475
|
} else {
|
476
|
perms = new HashSet<Permission>();
|
477
|
}
|
478
|
for (Permission p : accessRule.getPermissionList()) {
|
479
|
perms.add(p);
|
480
|
}
|
481
|
userPerms2.put(s, perms);
|
482
|
}
|
483
|
}
|
484
|
|
485
|
// Check if the number of access rules is the same for mn and cn. If not
|
486
|
// then consider them not equal, without performing diff of each access
|
487
|
// rule.
|
488
|
if (userPerms1.entrySet().size() != userPerms2.entrySet().size())
|
489
|
return false;
|
490
|
|
491
|
// Now perform the comparison of each access rule of access policy 1 to
|
492
|
// ap 2.
|
493
|
// This test assumes that the mn perms are more complete than the cn
|
494
|
// perms.
|
495
|
logMetacat.debug("Performing comparison of access policies");
|
496
|
for (Map.Entry<Subject, Set<Permission>> entry : userPerms1.entrySet()) {
|
497
|
// User name
|
498
|
Subject s1 = entry.getKey();
|
499
|
// Perms that the user holds
|
500
|
Set<Permission> p1 = entry.getValue();
|
501
|
logMetacat
|
502
|
.debug("Checking access policy of user: " + s1.getValue());
|
503
|
|
504
|
// Does this user exist in both access policies?
|
505
|
if (userPerms2.containsKey(s1)) {
|
506
|
if (!p1.equals(userPerms2.get(s1))) {
|
507
|
logMetacat.debug("User access policies not equal");
|
508
|
return false;
|
509
|
}
|
510
|
} else {
|
511
|
logMetacat.debug("User access policy not found on CN");
|
512
|
return false;
|
513
|
}
|
514
|
}
|
515
|
|
516
|
// All comparisons have been passed, so the two access policies are
|
517
|
// equivalent
|
518
|
logMetacat.debug("Access policies are the same");
|
519
|
return true;
|
520
|
}
|
521
|
|
522
|
/**
|
523
|
* Run pid synch script on the given pids Each argument is an individual pid
|
524
|
* because pids cannot contain whitespace.
|
525
|
*
|
526
|
* @param args
|
527
|
* @throws Exception
|
528
|
*/
|
529
|
public static void main(String[] args) throws Exception {
|
530
|
|
531
|
// set up the properties based on the test/deployed configuration of the
|
532
|
// workspace
|
533
|
SortedProperties testProperties = new SortedProperties(
|
534
|
"test/test.properties");
|
535
|
testProperties.load();
|
536
|
String metacatContextDir = testProperties
|
537
|
.getProperty("metacat.contextDir");
|
538
|
PropertyService.getInstance(metacatContextDir + "/WEB-INF");
|
539
|
|
540
|
ArrayList<String> guids = null;
|
541
|
SyncAccessPolicy syncAP = new SyncAccessPolicy();
|
542
|
|
543
|
if (args.length > 0) {
|
544
|
try {
|
545
|
guids = new ArrayList<String>(Arrays.asList(args));
|
546
|
logMetacat.warn("Trying to syncing access policy for "
|
547
|
+ args.length + " pids");
|
548
|
List<Identifier> synchedPids = syncAP.sync(guids);
|
549
|
logMetacat.warn("Sunk access policies for "
|
550
|
+ synchedPids.size() + " pids");
|
551
|
} catch (Exception e) {
|
552
|
logMetacat.error(
|
553
|
"Error syncing pids, message: " + e.getMessage(), e);
|
554
|
System.exit(1);
|
555
|
}
|
556
|
}
|
557
|
}
|
558
|
}
|