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/**
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* '$RCSfile$'
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* Purpose: A Class that implements utility methods for a metadata catalog
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* Copyright: 2009 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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* Authors: Michael Daigle
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*
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* '$Author: daigle $'
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* '$Date: 2009-08-04 14:32:58 -0700 (Tue, 04 Aug 2009) $'
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* '$Revision: 5015 $'
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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.util;
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import java.io.PrintWriter;
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import java.sql.SQLException;
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import java.util.Calendar;
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import java.util.Date;
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import java.util.GregorianCalendar;
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import java.util.Hashtable;
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import java.util.SimpleTimeZone;
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import java.util.Stack;
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import java.util.TimeZone;
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import java.util.Vector;
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import javax.servlet.http.HttpServletRequest;
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import javax.servlet.http.HttpServletResponse;
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import org.apache.log4j.Logger;
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import edu.ucsb.nceas.dbadapter.AbstractDatabase;
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import edu.ucsb.nceas.metacat.DBSAXHandler;
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import edu.ucsb.nceas.metacat.McdbException;
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import edu.ucsb.nceas.metacat.NodeRecord;
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import edu.ucsb.nceas.metacat.PermissionController;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.metacat.service.SessionService;
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import edu.ucsb.nceas.metacat.shared.MetacatUtilException;
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import edu.ucsb.nceas.metacat.util.SessionData;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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import edu.ucsb.nceas.utilities.ParseLSIDException;
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import edu.ucsb.nceas.utilities.LSIDUtil;
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/**
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* A suite of utility classes for the metadata catalog server
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*/
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public class DocumentUtil
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{
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private static int documentIdCounter = 0;
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public static AbstractDatabase dbAdapter;
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private static Logger logMetacat = Logger.getLogger(DocumentUtil.class);
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private static char separator = '.';
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private static String prefix = "autogen";
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static {
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try {
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separator = PropertyService.getProperty("document.accNumSeparator").charAt(0);
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} catch (PropertyNotFoundException pnfe) {
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logMetacat.error("DocumentUtil() - Could not retrieve accession number separator. "
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+ "Separator set to '.' : " + pnfe.getMessage());
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}
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try {
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prefix = PropertyService.getProperty("document.accNumPrefix");
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} catch (PropertyNotFoundException pnfe) {
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logMetacat.error("DocumentUtil() - Could not retrieve accession number prefix. "
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+ "Prefix set to " + prefix + ": " + pnfe.getMessage());
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}
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}
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/**
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* Get docid from online/url string
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*/
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public static String getDocIdWithRevFromOnlineURL(String url)
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{
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String docid = null;
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String DOCID = "docid";
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boolean find = false;
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char limited = '&';
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int count = 0; //keep track how many & was found
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Vector list = new Vector();// keep index number for &
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if (url == null) {
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logMetacat.debug("DocumentUtil.getDocIdWithRevFromOnlineURL - url is null and null will be returned");
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return docid;
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}
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// the first element in list is 0
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list.add(new Integer(0));
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for (int i = 0; i < url.length(); i++) {
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if (url.charAt(i) == limited) {
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// count plus 1
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count++;
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list.add(new Integer(i));
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// get substring beween two &
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String str = url.substring(
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((Integer) list.elementAt(count - 1)).intValue(), i);
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logMetacat.debug("DocumentUtil.getDocIdWithRevFromOnlineURL - substring between two & is: " + str);
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//if the subString contains docid, we got it
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if (str.indexOf(DOCID) != -1) {
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//get index of '="
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int start = getIndexForGivenChar(str, '=') + 1;
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int end = str.length();
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docid = str.substring(start, end);
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find = true;
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}//if
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}//if
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}//for
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//if not find, we need check the subtring between the index of last &
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// and
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// the end of string
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if (!find) {
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logMetacat.debug("DocumentUtil.getDocIdWithRevFromOnlineURL - Checking the last substring");
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String str = url.substring(((Integer) list.elementAt(count))
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.intValue() + 1, url.length());
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logMetacat.debug("DocumentUtil.getDocIdWithRevFromOnlineURL - Last substring is: " + str);
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if (str.indexOf(DOCID) != -1) {
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//get index of '="
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int start = getIndexForGivenChar(str, '=') + 1;
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int end = str.length();
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docid = str.substring(start, end);
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find = true;
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}//if
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}//if
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logMetacat.debug("DocumentUtil.getDocIdWithRevFromOnlineURL - The docid from online url is:" + docid);
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return docid.trim();
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}
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/**
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* Eocgorid identifier will look like: ecogrid://knb/tao.1.1
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* The AccessionNumber tao.1.1 will be returned. If the given doesn't
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* contains ecogrid, null will be returned.
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* @param identifier String
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* @return String
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*/
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public static String getAccessionNumberFromEcogridIdentifier(String identifier)
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{
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String accessionNumber = null;
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if (identifier != null && identifier.startsWith(DBSAXHandler.ECOGRID))
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{
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// find the last "/" in identifier
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int indexOfLastSlash = identifier.lastIndexOf("/");
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int start = indexOfLastSlash+1;
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int end = identifier.length();
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accessionNumber = identifier.substring(start, end);
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}
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logMetacat.info("DocumentUtil.getAccessionNumberFromEcogridIdentifier - The accession number from url is " +
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accessionNumber);
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return accessionNumber;
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}
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private static int getIndexForGivenChar(String str, char character)
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{
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int index = -1;
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// make sure str is not null
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if (str == null) {
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logMetacat.debug("DocumentUtil.getIndexForGivenChar - " +
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"The given str is null and -1 will be returned");
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return index;
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}
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// got though the string
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for (int i = 0; i < str.length(); i++) {
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// find the first one then break the loop
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if (str.charAt(i) == character) {
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index = i;
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break;
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}//if
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}//for
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logMetacat.info("DocumentUtil.getIndexForGivenChar - the index for char " +
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character + " is: " + index);
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return index;
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}
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/**
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* Utility method to get docid from a given string
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*
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* @param string, the given string should be these two format: 1) str1.str2
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* in this case docid= str1.str2 2) str1.str2.str3, in this case
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* docid =str1.str2
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* @param the sperator char
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*/
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public static String getDocIdFromString(String str)
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{
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String docId = null;
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if (str == null) {
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logMetacat.debug(
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"DocumentUtil.getDocIdFromString - The given str is null and null will be returned"
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+ " in getDocIdfromString");
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return docId;
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} //make sure docid is not null
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int dotNumber = 0;//count how many dots in given string
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int indexOfLastDot = 0;
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for (int i = 0; i < str.length(); i++) {
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if (str.charAt(i) == separator) {
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dotNumber++;//count how many dots
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indexOfLastDot = i;//keep the last dot postion
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}
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}//for
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//The string formatt is wrong, because it has more than two or less
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// than
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//one seperator
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if (dotNumber > 2 || dotNumber < 1) {
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docId = null;
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} else if (dotNumber == 2) //the case for str1.str2.str3
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{
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docId = str.substring(0, indexOfLastDot);
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} else if (dotNumber == 1) //the case for str1.str2
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{
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docId = str;
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}
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return docId;
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}//getDocIdFromString
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/**
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* Utility method to get version number from a given string
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*
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* @param string, the given string should be these two format: 1)
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* str1.str2(no version) version =-1; 2) str1.str2.str3, in this
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* case version = str3; 3) other, vresion =-2
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*/
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public static int getVersionFromString(String str)
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throws NumberFormatException
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{
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int version = -1;
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String versionString = null;
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int dotNumber = 0;//count how many dots in given string
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int indexOfLastDot = 0;
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for (int i = 0; i < str.length(); i++) {
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if (str.charAt(i) == separator) {
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dotNumber++;//count how many dots
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indexOfLastDot = i;//keep the last dot postion
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}
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}//for
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//The string formatt is wrong, because it has more than two or less
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// than
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//one seperator
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if (dotNumber > 2 || dotNumber < 1) {
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version = -2;
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} else if (dotNumber == 2 && (indexOfLastDot != (str.length() - 1)))
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//the case for str1.str2.str3
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{
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versionString = str.substring((indexOfLastDot + 1), str.length());
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version = Integer.parseInt(versionString);
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} else if (dotNumber == 1) //the case for str1.str2
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{
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version = -1;
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}
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return version;
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}//getVersionFromString
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/**
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* Utility method to get version string from a given string
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*
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* @param string, the given string should be these two format: 1)
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* str1.str2(no version) version=null; 2) str1.str2.str3, in
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* this case version = str3; 3) other, vresion =null;
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*/
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public static String getRevisionStringFromString(String str)
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throws NumberFormatException
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{
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// String to store the version
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String versionString = null;
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int dotNumber = 0;//count how many dots in given string
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int indexOfLastDot = 0;
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for (int i = 0; i < str.length(); i++) {
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if (str.charAt(i) == separator) {
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dotNumber++;//count how many dots
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indexOfLastDot = i;//keep the last dot postion
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}
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}//for
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//The string formatt is wrong, because it has more than two or less
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// than
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//one seperator
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if (dotNumber > 2 || dotNumber < 1) {
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versionString = null;
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} else if (dotNumber == 2 && (indexOfLastDot != (str.length() - 1))) {
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//the case for str1.str2.str3
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// indexOfLastDot != (str.length() -1) means get rid of str1.str2.
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versionString = str.substring((indexOfLastDot + 1), str.length());
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} else if (dotNumber == 1) //the case for str1.str2 or str1.str2.
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{
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versionString = null;
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}
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return versionString;
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}//getVersionFromString
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/**
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* This method will get docid from an AccessionNumber. There is no
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* assumption the accessnumber will be str1.str2.str3. It can be more. So
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* we think the docid will be get rid of last part
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*/
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public static String getDocIdFromAccessionNumber(String accessionNumber)
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{
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String docid = null;
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if (accessionNumber == null) { return docid; }
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int indexOfLastSeperator = accessionNumber.lastIndexOf(separator);
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docid = accessionNumber.substring(0, indexOfLastSeperator);
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logMetacat.debug("DocumentUtil.getDocIdFromAccessionNumber - after parsing accession number, docid is "
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+ docid);
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return docid;
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}
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/**
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* This method will get inline data id without the revision number.
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* So if inlineData.1.2 is passed as input, inlineData.2 is returned.
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*/
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public static String getInlineDataIdWithoutRev(String accessionNumber)
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{
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String docid = null;
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if (accessionNumber == null) { return docid; }
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int indexOfLastSeperator = accessionNumber.lastIndexOf(separator);
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String version = accessionNumber.substring(indexOfLastSeperator,
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accessionNumber.length());
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accessionNumber = accessionNumber.substring(0, indexOfLastSeperator);
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indexOfLastSeperator = accessionNumber.lastIndexOf(separator);
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docid = accessionNumber.substring(0, indexOfLastSeperator) + version;
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logMetacat.debug("DocumentUtil.getInlineDataIdWithoutRev - after parsing accessionnumber, docid is "
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+ docid);
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return docid;
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}
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/**
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* This method will call both getDocIdFromString and
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* getDocIdFromAccessionNumber. So first, if the string looks str1.str2,
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* the docid will be str1.str2. If the string is str1.str2.str3, the docid
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* will be str1.str2. If the string is str1.str2.str3.str4 or more, the
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* docid will be str1.str2.str3. If the string look like str1, null will be
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* returned
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*
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*/
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public static String getSmartDocId(String str)
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{
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String docid = null;
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//call geDocIdFromString first.
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docid = getDocIdFromString(str);
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// If docid is null, try to call getDocIdFromAccessionNumber
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// it will handle the seperator more than2
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if (docid == null) {
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docid = getDocIdFromAccessionNumber(str);
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}
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logMetacat.debug("DocumentUtil.getSmartDocId - The docid get from smart docid getor is "
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+ docid);
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return docid;
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}
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|
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/**
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* This method will get revision from an AccessionNumber. There is no
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* assumption the accessnumber will be str1.str2.str3. It can be more. So
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* we think the docid will be get rid of last part
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*/
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public static int getRevisionFromAccessionNumber(String accessionNumber)
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throws NumberFormatException
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{
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String rev = null;
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int revNumber = -1;
|
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if (accessionNumber == null) { return revNumber; }
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int indexOfLastSeperator = accessionNumber.lastIndexOf(separator);
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rev = accessionNumber.substring(indexOfLastSeperator + 1,
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accessionNumber.length());
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revNumber = Integer.parseInt(rev);
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logMetacat.debug("DocumentUtil.getRevisionFromAccessionNumber - after parsing accessionnumber, rev is "
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+ revNumber);
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return revNumber;
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}
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|
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/**
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* Method to get docidwithrev from eml2 inline data id The eml inline data
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* id would look like eml.200.2.3
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*/
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public static String getDocIdFromInlineDataID(String inlineDataID)
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{
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String docidWithoutRev = null;
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if (inlineDataID == null) { return docidWithoutRev; }
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char charSeperator = separator;
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int targetNumberOfSeperator = 3;// we want to know his index
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int numberOfSeperator = 0;
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for (int i = 0; i < inlineDataID.length(); i++) {
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// meet seperator, increase number of seperator
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if (inlineDataID.charAt(i) == charSeperator) {
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numberOfSeperator++;
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}
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// if number of seperator reach the target one, record the index(i)
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408
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// and get substring and terminate the loop
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if (numberOfSeperator == targetNumberOfSeperator) {
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docidWithoutRev = inlineDataID.substring(0, i);
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break;
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}
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}
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|
415
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logMetacat.debug("DocumentUtil.getDocIdWithoutRevFromInlineDataID - Docid without rev from inlinedata id: "
|
416
|
+ docidWithoutRev);
|
417
|
return docidWithoutRev;
|
418
|
|
419
|
}
|
420
|
|
421
|
/**
|
422
|
* Revise stack change a stack to opposite order
|
423
|
*/
|
424
|
public static Stack<NodeRecord> reviseStack(Stack<NodeRecord> stack)
|
425
|
{
|
426
|
Stack result = new Stack();
|
427
|
// make sure the parameter is correct
|
428
|
if (stack == null || stack.isEmpty()) {
|
429
|
result = stack;
|
430
|
return result;
|
431
|
}
|
432
|
|
433
|
while (!stack.isEmpty()) {
|
434
|
Object obj = stack.pop();
|
435
|
result.push(obj);
|
436
|
}
|
437
|
return result;
|
438
|
}
|
439
|
|
440
|
public static void isAuthorized(PrintWriter out, Hashtable<String,String[]> params,
|
441
|
HttpServletRequest request, HttpServletResponse response) throws MetacatUtilException {
|
442
|
|
443
|
String resourceLsid;
|
444
|
String[] resourceLsids = params.get("resourceLsid");
|
445
|
if (resourceLsids == null) {
|
446
|
throw new MetacatUtilException("DocumentUtil.isAuthorized - " +
|
447
|
"resourceLsid parameter cannot be null.");
|
448
|
}
|
449
|
resourceLsid = resourceLsids[0];
|
450
|
|
451
|
String permission;
|
452
|
String[] permissions = params.get("permission");
|
453
|
if (permissions == null) {
|
454
|
throw new MetacatUtilException("DocumentUtil.isAuthorized - " +
|
455
|
"permission parameter cannot be null.");
|
456
|
}
|
457
|
permission = permissions[0];
|
458
|
|
459
|
String sessionId;
|
460
|
String[] sessionIds = params.get("sessionId");
|
461
|
if (sessionIds == null) {
|
462
|
throw new MetacatUtilException("DocumentUtil.isAuthorized - " +
|
463
|
"sessionId parameter cannot be null.");
|
464
|
}
|
465
|
sessionId = sessionIds[0];
|
466
|
|
467
|
String isAuthorized = "false";
|
468
|
String message = "";
|
469
|
|
470
|
String result = "<resourceAuthorization>";
|
471
|
result += "<resourceId>" + resourceLsid + "</resourceId>";
|
472
|
result += "<permission>" + permission + "</permission>";
|
473
|
result += "<sessionId>" + sessionId + "</sessionId>";
|
474
|
|
475
|
if (!SessionService.getInstance().isSessionRegistered(sessionId)) {
|
476
|
message = "Session is not logged in";
|
477
|
} else {
|
478
|
SessionData sessionData = SessionService.getInstance().getRegisteredSession(sessionId);
|
479
|
|
480
|
String docId = null;
|
481
|
try {
|
482
|
docId = LSIDUtil.getDocId(resourceLsid, true);
|
483
|
PermissionController pc = new PermissionController(docId);
|
484
|
if (pc.hasPermission(sessionData.getUserName(), sessionData.getGroupNames(), permission)) {
|
485
|
isAuthorized = "true";
|
486
|
message = " docid: " + docId + " is authorized for session";
|
487
|
}
|
488
|
} catch (ParseLSIDException ple) {
|
489
|
message = "unparseable resource lsid: " + ple.getMessage();
|
490
|
} catch (McdbException me) {
|
491
|
message = "could not create permission controller for docid: " + docId + " : " + me.getMessage();
|
492
|
} catch (SQLException sqle) {
|
493
|
message = "SQL error getting permissions for docid: " + docId + " : " + sqle.getMessage();
|
494
|
}
|
495
|
}
|
496
|
|
497
|
result += "<isAuthorized>" + isAuthorized + "</isAuthorized>";
|
498
|
result += "<message>" + message + "</message>";
|
499
|
result += "</resourceAuthorization>";
|
500
|
|
501
|
out.write(result);
|
502
|
}
|
503
|
|
504
|
/**
|
505
|
* Create a unique docid for use in inserts and updates using the default
|
506
|
* prefix from the document.accNumPrefix property. Does not include the
|
507
|
* 'revision' part of the id if revision is '0', otherwise sets the
|
508
|
* revision number to 'revision'.
|
509
|
*
|
510
|
* @param idPrefix the prefix to be used to construct the scope portion of the docid
|
511
|
* @param revision the integer revision to use for this docid
|
512
|
* @return a String docid based on the current date and time
|
513
|
*/
|
514
|
public static String generateDocumentId(int revision) {
|
515
|
return generateDocumentId(prefix, revision);
|
516
|
}
|
517
|
|
518
|
/**
|
519
|
* Create a unique docid for use in inserts and updates using the prefix
|
520
|
* that is provided. Does not include the 'revision' part of the id if
|
521
|
* revision is '0', otherwise sets the revision number to 'revision'.
|
522
|
*
|
523
|
* @param idPrefix the prefix to be used to construct the scope portion of the docid
|
524
|
* @param revision the integer revision to use for this docid
|
525
|
* @return a String docid based on the current date and time
|
526
|
*/
|
527
|
public static String generateDocumentId(String idPrefix, int revision)
|
528
|
{
|
529
|
StringBuffer docid = new StringBuffer(idPrefix);
|
530
|
docid.append(".");
|
531
|
|
532
|
// Create a calendar to get the date formatted properly
|
533
|
String[] ids = TimeZone.getAvailableIDs(-8 * 60 * 60 * 1000);
|
534
|
SimpleTimeZone pdt = new SimpleTimeZone(-8 * 60 * 60 * 1000, ids[0]);
|
535
|
pdt.setStartRule(Calendar.APRIL, 1, Calendar.SUNDAY, 2 * 60 * 60 * 1000);
|
536
|
pdt.setEndRule(Calendar.OCTOBER, -1, Calendar.SUNDAY, 2 * 60 * 60 * 1000);
|
537
|
Calendar calendar = new GregorianCalendar(pdt);
|
538
|
Date trialTime = new Date();
|
539
|
calendar.setTime(trialTime);
|
540
|
// using yyyymmddhhmmssmmm by convention (zero padding to preserve places)
|
541
|
// will help with looking at logs and especially database tables.
|
542
|
// for each millisecond we can support up to 99 before resetting to 0
|
543
|
// NOTE: if you make it larger, docid is too big for a Long
|
544
|
if (documentIdCounter > 100) {
|
545
|
documentIdCounter = 0;
|
546
|
}
|
547
|
docid.append(String.format("%04d%02d%02d%02d%02d%02d%03d%02d",
|
548
|
calendar.get(Calendar.YEAR),
|
549
|
calendar.get(Calendar.MONTH) + 1, // adjust 0-11 range to 1-12
|
550
|
calendar.get(Calendar.DAY_OF_MONTH),
|
551
|
calendar.get(Calendar.HOUR_OF_DAY),
|
552
|
calendar.get(Calendar.MINUTE),
|
553
|
calendar.get(Calendar.SECOND),
|
554
|
calendar.get(Calendar.MILLISECOND),
|
555
|
documentIdCounter++)
|
556
|
);
|
557
|
if (revision > 0) {
|
558
|
docid.append(".").append(revision);
|
559
|
}
|
560
|
return docid.toString();
|
561
|
}
|
562
|
}
|