/**
* '$RCSfile$'
* Purpose: A Class that implements utility methods for a metadata catalog
* Copyright: 2009 Regents of the University of California and the
* National Center for Ecological Analysis and Synthesis
* Authors: Michael Daigle
*
* '$Author: daigle $'
* '$Date: 2009-08-04 14:32:58 -0700 (Tue, 04 Aug 2009) $'
* '$Revision: 5015 $'
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package edu.ucsb.nceas.metacat.util;
import java.io.PrintWriter;
import java.sql.SQLException;
import java.util.Calendar;
import java.util.Date;
import java.util.GregorianCalendar;
import java.util.Hashtable;
import java.util.SimpleTimeZone;
import java.util.Stack;
import java.util.TimeZone;
import java.util.Vector;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.log4j.Logger;
import edu.ucsb.nceas.dbadapter.AbstractDatabase;
import edu.ucsb.nceas.metacat.DBSAXHandler;
import edu.ucsb.nceas.metacat.DBUtil;
import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
import edu.ucsb.nceas.metacat.McdbException;
import edu.ucsb.nceas.metacat.NodeRecord;
import edu.ucsb.nceas.metacat.PermissionController;
import edu.ucsb.nceas.metacat.properties.PropertyService;
import edu.ucsb.nceas.metacat.service.SessionService;
import edu.ucsb.nceas.metacat.shared.MetacatUtilException;
import edu.ucsb.nceas.metacat.util.SessionData;
import edu.ucsb.nceas.utilities.PropertyNotFoundException;
import edu.ucsb.nceas.utilities.ParseLSIDException;
import edu.ucsb.nceas.utilities.LSIDUtil;
/**
* A suite of utility classes for the metadata catalog server
*/
public class DocumentUtil
{
private static int documentIdCounter = 0;
public static AbstractDatabase dbAdapter;
private static Logger logMetacat = Logger.getLogger(DocumentUtil.class);
private static char separator = '.';
private static String prefix = "autogen";
static {
try {
separator = PropertyService.getProperty("document.accNumSeparator").charAt(0);
} catch (PropertyNotFoundException pnfe) {
logMetacat.error("DocumentUtil() - Could not retrieve accession number separator. "
+ "Separator set to '.' : " + pnfe.getMessage());
}
try {
prefix = PropertyService.getProperty("document.accNumPrefix");
} catch (PropertyNotFoundException pnfe) {
logMetacat.error("DocumentUtil() - Could not retrieve accession number prefix. "
+ "Prefix set to " + prefix + ": " + pnfe.getMessage());
}
}
/**
* Get docid from online/url string
*/
public static String getDocIdWithRevFromOnlineURL(String url)
{
String docid = null;
String DOCID = "docid";
boolean find = false;
char limited = '&';
int count = 0; //keep track how many & was found
Vector list = new Vector();// keep index number for &
if (url == null) {
logMetacat.debug("DocumentUtil.getDocIdWithRevFromOnlineURL - url is null and null will be returned");
return docid;
}
// the first element in list is 0
list.add(new Integer(0));
for (int i = 0; i < url.length(); i++) {
if (url.charAt(i) == limited) {
// count plus 1
count++;
list.add(new Integer(i));
// get substring beween two &
String str = url.substring(
((Integer) list.elementAt(count - 1)).intValue(), i);
logMetacat.debug("DocumentUtil.getDocIdWithRevFromOnlineURL - substring between two & is: " + str);
//if the subString contains docid, we got it
if (str.indexOf(DOCID) != -1) {
//get index of '="
int start = getIndexForGivenChar(str, '=') + 1;
int end = str.length();
docid = str.substring(start, end);
find = true;
}//if
}//if
}//for
//if not find, we need check the subtring between the index of last &
// and
// the end of string
if (!find) {
logMetacat.debug("DocumentUtil.getDocIdWithRevFromOnlineURL - Checking the last substring");
String str = url.substring(((Integer) list.elementAt(count))
.intValue() + 1, url.length());
logMetacat.debug("DocumentUtil.getDocIdWithRevFromOnlineURL - Last substring is: " + str);
if (str.indexOf(DOCID) != -1) {
//get index of '="
int start = getIndexForGivenChar(str, '=') + 1;
int end = str.length();
docid = str.substring(start, end);
find = true;
}//if
}//if
logMetacat.debug("DocumentUtil.getDocIdWithRevFromOnlineURL - The docid from online url is:" + docid);
return docid.trim();
}
/**
* Eocgorid identifier will look like: ecogrid://knb/tao.1.1
* The AccessionNumber tao.1.1 will be returned. If the given doesn't
* contains ecogrid, null will be returned.
* @param identifier String
* @return String
*/
public static String getAccessionNumberFromEcogridIdentifier(String identifier)
{
String accessionNumber = null;
if (identifier != null && identifier.startsWith(DBSAXHandler.ECOGRID))
{
// find the last "/" in identifier
int indexOfLastSlash = identifier.lastIndexOf("/");
int start = indexOfLastSlash+1;
int end = identifier.length();
accessionNumber = identifier.substring(start, end);
}
logMetacat.info("DocumentUtil.getAccessionNumberFromEcogridIdentifier - The accession number from url is " +
accessionNumber);
return accessionNumber;
}
private static int getIndexForGivenChar(String str, char character)
{
int index = -1;
// make sure str is not null
if (str == null) {
logMetacat.debug("DocumentUtil.getIndexForGivenChar - " +
"The given str is null and -1 will be returned");
return index;
}
// got though the string
for (int i = 0; i < str.length(); i++) {
// find the first one then break the loop
if (str.charAt(i) == character) {
index = i;
break;
}//if
}//for
logMetacat.info("DocumentUtil.getIndexForGivenChar - the index for char " +
character + " is: " + index);
return index;
}
/**
* Utility method to get docid from a given string
*
* @param string, the given string should be these two format: 1) str1.str2
* in this case docid= str1.str2 2) str1.str2.str3, in this case
* docid =str1.str2
* @param the sperator char
*/
public static String getDocIdFromString(String str)
{
String docId = null;
if (str == null) {
logMetacat.debug(
"DocumentUtil.getDocIdFromString - The given str is null and null will be returned"
+ " in getDocIdfromString");
return docId;
} //make sure docid is not null
int dotNumber = 0;//count how many dots in given string
int indexOfLastDot = 0;
for (int i = 0; i < str.length(); i++) {
if (str.charAt(i) == separator) {
dotNumber++;//count how many dots
indexOfLastDot = i;//keep the last dot postion
}
}//for
//The string formatt is wrong, because it has more than two or less
// than
//one seperator
if (dotNumber > 2 || dotNumber < 1) {
docId = null;
} else if (dotNumber == 2) //the case for str1.str2.str3
{
docId = str.substring(0, indexOfLastDot);
} else if (dotNumber == 1) //the case for str1.str2
{
docId = str;
}
return docId;
}//getDocIdFromString
/**
* Utility method to get version number from a given string
*
* @param string, the given string should be these two format: 1)
* str1.str2(no version) version =-1; 2) str1.str2.str3, in this
* case version = str3; 3) other, vresion =-2
*/
public static int getVersionFromString(String str)
throws NumberFormatException
{
int version = -1;
String versionString = null;
int dotNumber = 0;//count how many dots in given string
int indexOfLastDot = 0;
for (int i = 0; i < str.length(); i++) {
if (str.charAt(i) == separator) {
dotNumber++;//count how many dots
indexOfLastDot = i;//keep the last dot postion
}
}//for
//The string formatt is wrong, because it has more than two or less
// than
//one seperator
if (dotNumber > 2 || dotNumber < 1) {
version = -2;
} else if (dotNumber == 2 && (indexOfLastDot != (str.length() - 1)))
//the case for str1.str2.str3
{
versionString = str.substring((indexOfLastDot + 1), str.length());
version = Integer.parseInt(versionString);
} else if (dotNumber == 1) //the case for str1.str2
{
version = -1;
}
return version;
}//getVersionFromString
/**
* Utility method to get version string from a given string
*
* @param string, the given string should be these two format: 1)
* str1.str2(no version) version=null; 2) str1.str2.str3, in
* this case version = str3; 3) other, vresion =null;
*/
public static String getRevisionStringFromString(String str)
throws NumberFormatException
{
// String to store the version
String versionString = null;
int dotNumber = 0;//count how many dots in given string
int indexOfLastDot = 0;
for (int i = 0; i < str.length(); i++) {
if (str.charAt(i) == separator) {
dotNumber++;//count how many dots
indexOfLastDot = i;//keep the last dot postion
}
}//for
//The string formatt is wrong, because it has more than two or less
// than
//one seperator
if (dotNumber > 2 || dotNumber < 1) {
versionString = null;
} else if (dotNumber == 2 && (indexOfLastDot != (str.length() - 1))) {
//the case for str1.str2.str3
// indexOfLastDot != (str.length() -1) means get rid of str1.str2.
versionString = str.substring((indexOfLastDot + 1), str.length());
} else if (dotNumber == 1) //the case for str1.str2 or str1.str2.
{
versionString = null;
}
return versionString;
}//getVersionFromString
/**
* If the given docid only have one seperter, we need
* append rev for it. The rev come from xml_documents
*/
public static String appendRev(String docid)
throws PropertyNotFoundException, SQLException, McdbDocNotFoundException {
String newAccNum = null;
String separator = PropertyService.getProperty("document.accNumSeparator");
int firstIndex = docid.indexOf(separator);
int lastIndex = docid.lastIndexOf(separator);
if (firstIndex == lastIndex) {
//only one seperater
int rev = DBUtil.getLatestRevisionInDocumentTable(docid);
if (rev == -1) {
throw new McdbDocNotFoundException("the requested docid '"
+ docid+ "' does not exist");
} else {
newAccNum = docid+ separator+ rev;
}
} else {
// in other suituation we don't change the docid
newAccNum = docid;
}
//logMetacat.debug("The docid will be read is "+newAccNum);
return newAccNum;
}
/**
* This method will get docid from an AccessionNumber. There is no
* assumption the accessnumber will be str1.str2.str3. It can be more. So
* we think the docid will be get rid of last part
*/
public static String getDocIdFromAccessionNumber(String accessionNumber)
{
String docid = null;
if (accessionNumber == null) { return docid; }
int indexOfLastSeperator = accessionNumber.lastIndexOf(separator);
docid = accessionNumber.substring(0, indexOfLastSeperator);
logMetacat.debug("DocumentUtil.getDocIdFromAccessionNumber - after parsing accession number, docid is "
+ docid);
return docid;
}
/**
* This method will get inline data id without the revision number.
* So if inlineData.1.2 is passed as input, inlineData.2 is returned.
*/
public static String getInlineDataIdWithoutRev(String accessionNumber)
{
String docid = null;
if (accessionNumber == null) { return docid; }
int indexOfLastSeperator = accessionNumber.lastIndexOf(separator);
String version = accessionNumber.substring(indexOfLastSeperator,
accessionNumber.length());
accessionNumber = accessionNumber.substring(0, indexOfLastSeperator);
indexOfLastSeperator = accessionNumber.lastIndexOf(separator);
docid = accessionNumber.substring(0, indexOfLastSeperator) + version;
logMetacat.debug("DocumentUtil.getInlineDataIdWithoutRev - after parsing accessionnumber, docid is "
+ docid);
return docid;
}
/**
* This method will call both getDocIdFromString and
* getDocIdFromAccessionNumber. So first, if the string looks str1.str2,
* the docid will be str1.str2. If the string is str1.str2.str3, the docid
* will be str1.str2. If the string is str1.str2.str3.str4 or more, the
* docid will be str1.str2.str3. If the string look like str1, null will be
* returned
*
*/
public static String getSmartDocId(String str)
{
String docid = null;
//call geDocIdFromString first.
docid = getDocIdFromString(str);
// If docid is null, try to call getDocIdFromAccessionNumber
// it will handle the seperator more than2
if (docid == null) {
docid = getDocIdFromAccessionNumber(str);
}
logMetacat.debug("DocumentUtil.getSmartDocId - The docid get from smart docid getor is "
+ docid);
return docid;
}
/**
* This method will get revision from an AccessionNumber. There is no
* assumption the accessnumber will be str1.str2.str3. It can be more. So
* we think the docid will be get rid of last part
*/
public static int getRevisionFromAccessionNumber(String accessionNumber)
throws NumberFormatException
{
String rev = null;
int revNumber = -1;
if (accessionNumber == null) { return revNumber; }
int indexOfLastSeperator = accessionNumber.lastIndexOf(separator);
rev = accessionNumber.substring(indexOfLastSeperator + 1,
accessionNumber.length());
revNumber = Integer.parseInt(rev);
logMetacat.debug("DocumentUtil.getRevisionFromAccessionNumber - after parsing accessionnumber, rev is "
+ revNumber);
return revNumber;
}
/**
* Method to get docidwithrev from eml2 inline data id The eml inline data
* id would look like eml.200.2.3
*/
public static String getDocIdFromInlineDataID(String inlineDataID)
{
String docidWithoutRev = null;
if (inlineDataID == null) { return docidWithoutRev; }
char charSeperator = separator;
int targetNumberOfSeperator = 3;// we want to know his index
int numberOfSeperator = 0;
for (int i = 0; i < inlineDataID.length(); i++) {
// meet seperator, increase number of seperator
if (inlineDataID.charAt(i) == charSeperator) {
numberOfSeperator++;
}
// if number of seperator reach the target one, record the index(i)
// and get substring and terminate the loop
if (numberOfSeperator == targetNumberOfSeperator) {
docidWithoutRev = inlineDataID.substring(0, i);
break;
}
}
logMetacat.debug("DocumentUtil.getDocIdWithoutRevFromInlineDataID - Docid without rev from inlinedata id: "
+ docidWithoutRev);
return docidWithoutRev;
}
/**
* Revise stack change a stack to opposite order
*/
public static Stack<NodeRecord> reviseStack(Stack<NodeRecord> stack)
{
Stack result = new Stack();
// make sure the parameter is correct
if (stack == null || stack.isEmpty()) {
result = stack;
return result;
}
while (!stack.isEmpty()) {
Object obj = stack.pop();
result.push(obj);
}
return result;
}
public static void isAuthorized(PrintWriter out, Hashtable<String,String[]> params,
HttpServletRequest request, HttpServletResponse response) throws MetacatUtilException {
String resourceLsid;
String[] resourceLsids = params.get("resourceLsid");
if (resourceLsids == null) {
throw new MetacatUtilException("DocumentUtil.isAuthorized - " +
"resourceLsid parameter cannot be null.");
}
resourceLsid = resourceLsids[0];
String permission;
String[] permissions = params.get("permission");
if (permissions == null) {
throw new MetacatUtilException("DocumentUtil.isAuthorized - " +
"permission parameter cannot be null.");
}
permission = permissions[0];
String sessionId;
String[] sessionIds = params.get("sessionId");
if (sessionIds == null) {
throw new MetacatUtilException("DocumentUtil.isAuthorized - " +
"sessionId parameter cannot be null.");
}
sessionId = sessionIds[0];
String isAuthorized = "false";
String message = "";
String result = "<resourceAuthorization>";
result += "<resourceId>" + resourceLsid + "</resourceId>";
result += "<permission>" + permission + "</permission>";
result += "<sessionId>" + sessionId + "</sessionId>";
if (!SessionService.getInstance().isSessionRegistered(sessionId)) {
message = "Session is not logged in";
} else {
SessionData sessionData = SessionService.getInstance().getRegisteredSession(sessionId);
String docId = null;
try {
docId = LSIDUtil.getDocId(resourceLsid, true);
PermissionController pc = new PermissionController(docId);
if (pc.hasPermission(sessionData.getUserName(), sessionData.getGroupNames(), permission)) {
isAuthorized = "true";
message = " docid: " + docId + " is authorized for session";
}
} catch (ParseLSIDException ple) {
message = "unparseable resource lsid: " + ple.getMessage();
} catch (McdbException me) {
message = "could not create permission controller for docid: " + docId + " : " + me.getMessage();
} catch (SQLException sqle) {
message = "SQL error getting permissions for docid: " + docId + " : " + sqle.getMessage();
}
}
result += "<isAuthorized>" + isAuthorized + "</isAuthorized>";
result += "<message>" + message + "</message>";
result += "</resourceAuthorization>";
out.write(result);
}
/**
* Create a unique docid for use in inserts and updates using the default
* prefix from the document.accNumPrefix property. Does not include the
* 'revision' part of the id if revision is '0', otherwise sets the
* revision number to 'revision'.
*
* @param idPrefix the prefix to be used to construct the scope portion of the docid
* @param revision the integer revision to use for this docid
* @return a String docid based on the current date and time
*/
public static String generateDocumentId(int revision) {
return generateDocumentId(prefix, revision);
}
/**
* Create a unique docid for use in inserts and updates using the prefix
* that is provided. Does not include the 'revision' part of the id if
* revision is '0', otherwise sets the revision number to 'revision'.
*
* @param idPrefix the prefix to be used to construct the scope portion of the docid
* @param revision the integer revision to use for this docid
* @return a String docid based on the current date and time
*/
public static String generateDocumentId(String idPrefix, int revision)
{
StringBuffer docid = new StringBuffer(idPrefix);
docid.append(".");
// Create a calendar to get the date formatted properly
String[] ids = TimeZone.getAvailableIDs(-8 * 60 * 60 * 1000);
SimpleTimeZone pdt = new SimpleTimeZone(-8 * 60 * 60 * 1000, ids[0]);
pdt.setStartRule(Calendar.APRIL, 1, Calendar.SUNDAY, 2 * 60 * 60 * 1000);
pdt.setEndRule(Calendar.OCTOBER, -1, Calendar.SUNDAY, 2 * 60 * 60 * 1000);
Calendar calendar = new GregorianCalendar(pdt);
Date trialTime = new Date();
calendar.setTime(trialTime);
// using yyyymmddhhmmssmmm by convention (zero padding to preserve places)
// will help with looking at logs and especially database tables.
// for each millisecond we can support up to 99 before resetting to 0
// NOTE: if you make it larger, docid is too big for a Long
if (documentIdCounter > 100) {
documentIdCounter = 0;
}
docid.append(String.format("%04d%02d%02d%02d%02d%02d%03d%02d",
calendar.get(Calendar.YEAR),
calendar.get(Calendar.MONTH) + 1, // adjust 0-11 range to 1-12
calendar.get(Calendar.DAY_OF_MONTH),
calendar.get(Calendar.HOUR_OF_DAY),
calendar.get(Calendar.MINUTE),
calendar.get(Calendar.SECOND),
calendar.get(Calendar.MILLISECOND),
documentIdCounter++)
);
if (revision > 0) {
docid.append(".").append(revision);
}
return docid.toString();
}
}