Metacat

/**

 *  '$RCSfile$'

 *    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.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

{

    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

    /**

     * 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 getDocIdWithoutRevFromInlineDataID(String inlineDataID)

    {

        String docidWithoutRev = null;

        if (inlineDataID == null) { return docidWithoutRev; }

        char charSeperator = separator;

        int targetNumberOfSeperator = 2;// 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.isSessionRegistered(sessionId)) {

    		message = "Session is not logged in";

    	} else {

    		SessionData sessionData = SessionService.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);

        docid.append(calendar.get(Calendar.YEAR));

        docid.append(calendar.get(Calendar.DAY_OF_YEAR));

        docid.append(calendar.get(Calendar.HOUR_OF_DAY));

        docid.append(calendar.get(Calendar.MINUTE));

        docid.append(calendar.get(Calendar.SECOND));

        docid.append(calendar.get(Calendar.MILLISECOND));

        if (revision > 0) {

            docid.append(".").append(revision);

        }

        return docid.toString();

    }

}