Metacat

/**

 *  '$RCSfile$'

 *    Purpose: A Class that implements utility methods for a metadata catalog

 *  Copyright: 2000 Regents of the University of California and the

 *             National Center for Ecological Analysis and Synthesis

 *    Authors: Matt Jones, Jivka Bojilova

 *    Release: @release@

 *

 *   '$Author: sgarg $'

 *     '$Date: 2005-10-10 11:22:50 -0700 (Mon, 10 Oct 2005) $'

 * '$Revision: 2665 $'

 *

 * 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;

import java.io.File;

import java.net.MalformedURLException;

import java.net.URL;

import java.util.Hashtable;

import java.util.Stack;

import java.util.Vector;

import java.util.regex.PatternSyntaxException;

import org.apache.log4j.Logger;

import edu.ucsb.nceas.dbadapter.AbstractDatabase;

import edu.ucsb.nceas.utilities.Options;

/**

 * A suite of utility classes for the metadata catalog server

 */

public class MetaCatUtil

{

    public static AbstractDatabase dbAdapter;

    public static Vector pathsForIndexing;

    private static Options options = null;

    private static boolean debug = true;

    private static String[] administrators;

    private static String[] moderators;

    private static String[] allowedSubmitters;

    private static String[] deniedSubmitters;

    private static Logger logMetacat = Logger.getLogger(MetaCatUtil.class);

    static {

    	// Determine our db adapter class and create an instance of that class

        try {

            dbAdapter = (AbstractDatabase) createObject(getOption("dbAdapter"));

        } catch (Exception e) {

            System.err.println("Error in MetaCatUtil static block:"

                    + e.getMessage());

        }

        // read administrator and moderator lists from metacat.properties

        getUserAccessControlLists();

    }

    /**

     * Instantiate a class using the name of the class at runtime

     *

     * @param className the fully qualified name of the class to instantiate

     */

    public static Object createObject(String className) throws Exception

    {

        Object object = null;

        try {

            Class classDefinition = Class.forName(className);

            object = classDefinition.newInstance();

        } catch (InstantiationException e) {

            throw e;

        } catch (IllegalAccessException e) {

            throw e;

        } catch (ClassNotFoundException e) {

            throw e;

        }

        return object;

    }

    /**

     * Utility method to get an option value from the properties file

     *

     * @param optionName the name of the option requested

     * @return the String value for the option, or null if not set

     */

    public static String getOption(String optionName)

    {

        if (options == null) {

            options = Options.getInstance();

        }

        String value = options.getOption(optionName);

        return value;

    }

    /**

     * Utility method to set an option value from the properties file

     *

     * @param optionName the name of the option requested

     */

    public static void setOption(String optionName, String newValue)

    {

        if (options == null) {

            options = Options.getInstance();

        }

        options.setOption(optionName, newValue);

    }

    /** Utility method to convert a file handle into a URL */

    public static URL fileToURL(File file)

    {

        String path = file.getAbsolutePath();

        String fSep = System.getProperty("file.separator");

        if (fSep != null && fSep.length() == 1)

                path = path.replace(fSep.charAt(0), '/');

        if (path.length() > 0 && path.charAt(0) != '/') path = '/' + path;

        try {

            return new URL("file", null, path);

        } catch (java.net.MalformedURLException e) {

            /*

             * According to the spec this could only happen if the file

             */

            throw new Error("unexpected MalformedURLException");

        }

    }

    /**

     * Utility method to parse the query part of a URL into parameters. This

     * method assumes the format of the query par tof the url is an ampersand

     * separated list of name/value pairs, with equal signs separating the name

     * from the value (e.g., name=tom&zip=99801 ). Returns a has of the name

     * value pairs, hashed on name.

     */

    public static Hashtable parseQuery(String query)

            throws MalformedURLException

    {

        String[][] params = new String[200][2];

        Hashtable parameters = new Hashtable();

        String temp = "";

        boolean ampflag = true;

        boolean poundflag = false;

        int arrcount = 0;

        if (query != null) {

            for (int i = 0; i < query.length(); i++) {

                // go throught the remainder of the query one character at a

                // time.

                if (query.charAt(i) == '=') {

                    // if the current char is a # then the preceding should be

                    // a name

                    if (!poundflag && ampflag) {

                        params[arrcount][0] = temp.trim();

                        temp = "";

                    } else {

                        //if there are two #s or &s in a row throw an

                        // exception.

                        throw new MalformedURLException(

                                "metacatURL: Two parameter names "

                                        + "not allowed in sequence");

                    }

                    poundflag = true;

                    ampflag = false;

                } else if (query.charAt(i) == '&' || i == query.length() - 1) {

                    //the text preceding the & should be the param value.

                    if (i == query.length() - 1) {

                        //if at the end of the string grab the last value and

                        // append it.

                        if (query.charAt(i) != '=') {

                            //ignore an extra & on the end of the string

                            temp += query.charAt(i);

                        }

                    }

                    if (!ampflag && poundflag) {

                        params[arrcount][1] = temp.trim();

                        parameters

                                .put(params[arrcount][0], params[arrcount][1]);

                        temp = "";

                        arrcount++; //increment the array to the next row.

                    } else {

                        //if there are two =s or &s in a row through an

                        // exception

                        throw new MalformedURLException(

                                "metacatURL: Two parameter values "

                                        + "not allowed in sequence");

                    }

                    poundflag = false;

                    ampflag = true;

                } else {

                    //get the next character in the string

                    temp += query.charAt(i);

                }

            }

        }

        return parameters;

    }

    /**

     * Utility method to print debugging messages. User can set debug level for

     * this message. The number is fewer, the message is more important

     *

     * @param msg, the content of the message

     * @param debugLevel, an integer indicating the message debug leve

     */

    /** 

     * Commenting out the function for now...

     * public static void debugMessage(String msg, int debugLevel)

     * {

     *   if (debug) {

     *       int limit = 1;

     *       try {

     *           limit = Integer.parseInt(getOption("debuglevel"));

     *

     *       } catch (Exception e) {

     *           System.out.println(e.getMessage());

     *       }

     *       //don't allow the user set debugLevel less than or equals 0

     *       if (debugLevel <= 0) {

     *           debugLevel = 1;

     *       }

     *

     *       if (debugLevel < limit) {

     *           System.err.println("@debugprefix@ " + msg);

     *       }

     *   }

     *}

     */

    /**

     * Utility method to print debugging messages. User can set debug level for

     * this message. The number is fewer, the message is more important

     *

     * @param msg, the content of the message

     * @param debugLevel, an integer indicating the message debug leve

     */

    public static void printMessage(String msg)

    {

    	System.err.println("@debugprefix@ " + msg);

    }

    public static Vector getOptionList(String optiontext)

    {

        Vector optionsVector = new Vector();

        if (optiontext.indexOf(",") == -1) {

            optionsVector.addElement(optiontext);

            return optionsVector;

        }

        while (optiontext.indexOf(",") != -1) {

            String s = optiontext.substring(0, optiontext.indexOf(","));

            optionsVector.addElement(s.trim());

            optiontext = optiontext.substring(optiontext.indexOf(",") + 1,

                    optiontext.length());

            if (optiontext.indexOf(",") == -1) { //catch the last list entry

                optionsVector.addElement(optiontext.trim());

            }

        }

        return optionsVector;

    }

    /** Normalizes the given string. Taken from configXML.java */

    public static String normalize(String s)

    {

        StringBuffer str = new StringBuffer();

             int len = (s != null) ? s.length() : 0;

             for (int i = 0; i < len; i++) {

                 char ch = s.charAt(i);

                 switch (ch) {

                     case '<': {

                         str.append("<");

                         break;

                     }

                     case '>': {

                         str.append(">");

                         break;

                     }

                     case '&': {

                         /*

                          * patch provided by Johnoel Ancheta from U of Hawaii

                          */

                         // check if & is for a character reference &#xnnnn;

                         if (i + 1 < len - 1 && s.charAt(i + 1) == '#') {

                             str.append("&#");

                             i += 2;

                             ch = s.charAt(i);

                             while (i < len && ch != ';') {

                                 str.append(ch);

                                 i++;

                                 ch = s.charAt(i);

                             }

                             str.append(';');

                         } else 

                         // check if & is in front of amp; 

                         // (we dont yet check for other HTML 4.0 Character entities) 

                         if (i + 4 < len -1 && s.charAt(i + 1) == 'a' 

                        	 && s.charAt(i + 2) == 'm' 

                        		 && s.charAt(i + 3) == 'p' 

                        			 && s.charAt(i + 4) == ';'){

                             str.append("&");

                             i += 5;                        	 

                         } else

                             str.append("&");

                         /////////

                         break;

                     }

                    default: {

                         if ( (ch<128) && (ch>31) ) {

                             str.append(ch);

                         }

                         else if (ch<32) {

                             if (ch == 10) { // new line

                                 str.append(ch);

                             }

                             if (ch == 13) { // carriage return

                                 str.append(ch);

                             }

                             if (ch == 9) {  // tab

                                 str.append(ch);

                             }

                             // otherwise skip

                         }

                         else {

                             str.append("&#");

                             str.append(Integer.toString(ch));

                             str.append(';');

                         }

                     }

                 }

             }

             return str.toString();

    }

    /**

     * 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.info("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.info("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.info("Checking the last substring");

            String str = url.substring(((Integer) list.elementAt(count))

                    .intValue() + 1, url.length());

            logMetacat.info("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.info("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.warn("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.info(

                    "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("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.info(

                    "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;

        //assume that seperator is one charactor string

        char seperator = getOption("accNumSeparator").charAt(0);

        for (int i = 0; i < str.length(); i++) {

            if (str.charAt(i) == seperator) {

                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;

        //assume that seperator is one charactor string

        char seperator = getOption("accNumSeparator").charAt(0);

        for (int i = 0; i < str.length(); i++) {

            if (str.charAt(i) == seperator) {

                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;

        //assume that seperator is one charactor string

        char seperator = getOption("accNumSeparator").charAt(0);

        for (int i = 0; i < str.length(); i++) {

            if (str.charAt(i) == seperator) {

                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; }

        String seperator = getOption("accNumSeparator");

        int indexOfLastSeperator = accessionNumber.lastIndexOf(seperator);

        docid = accessionNumber.substring(0, indexOfLastSeperator);

        logMetacat.info("after parsing accessionnumber, 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; }

        String seperator = getOption("accNumSeparator");

        int indexOfLastSeperator = accessionNumber.lastIndexOf(seperator);

        String version = accessionNumber.substring(indexOfLastSeperator,

                                                   accessionNumber.length());

        accessionNumber = accessionNumber.substring(0, indexOfLastSeperator);

        indexOfLastSeperator = accessionNumber.lastIndexOf(seperator);

        docid = accessionNumber.substring(0, indexOfLastSeperator) + version;

        logMetacat.info("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.info("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; }

        String seperator = getOption("accNumSeparator");

        int indexOfLastSeperator = accessionNumber.lastIndexOf(seperator);

        rev = accessionNumber.substring(indexOfLastSeperator + 1,

                accessionNumber.length());

        revNumber = Integer.parseInt(rev);

        logMetacat.info("after parsing accessionnumber, rev is "

                + revNumber);

        return revNumber;

    }

    /**

     * Method to get the name of local replication server

     */

    public static String getLocalReplicationServerName()

    {

        String replicationServerName = null;

        String serverHost = null;

        serverHost = getOption("server");

        // append "context/servelet/replication" to the host name

        replicationServerName = serverHost.trim() + getOption("replicationpath").trim();

        return replicationServerName;

    }

    /**

     * 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; }

        String seperator = MetaCatUtil.getOption("accNumSeparator");

        char charSeperator = seperator.charAt(0);

        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.info("Docid without rev from inlinedata id: "

                + docidWithoutRev);

        return docidWithoutRev;

    }

    /**

     * Revise stack change a stack to opposite order

     */

    public static Stack reviseStack(Stack 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;

    }

    /** A method to replace whitespace in url */

    public static String replaceWhiteSpaceForURL(String urlHasWhiteSpace)

    {

        StringBuffer newUrl = new StringBuffer();

        String whiteSpaceReplace = "%20";

        if (urlHasWhiteSpace == null || urlHasWhiteSpace.trim().equals("")) { return null; }

        for (int i = 0; i < urlHasWhiteSpace.length(); i++) {

            char ch = urlHasWhiteSpace.charAt(i);

            if (!Character.isWhitespace(ch)) {

                newUrl.append(ch);

            } else {

                //it is white sapce, replace it by %20

                newUrl = newUrl.append(whiteSpaceReplace);

            }

        }//for

        logMetacat.info("The new string without space is:"

                + newUrl.toString());

        return newUrl.toString();

    }// replaceWhiteSpaceForUR

    /** 

     * A method to read administrators and moderators list from the metacat.properties 

     **/

    public static void getUserAccessControlLists(){

    	administrators = getListFromOption("administrators");

    	moderators = getListFromOption("moderators");

    	allowedSubmitters = getListFromOption("allowedSubmitters");

    	deniedSubmitters = getListFromOption("deniedSubmitters");

    }

    /** 

     * A method to read value of a given option from the metacat.properties 

     * into specified String array

     **/

    private static String[] getListFromOption(String optionName){

    	String[] list = null;

    	String listString = MetaCatUtil.getOption(optionName);

        try {

            if ( listString != null && !listString.trim().equals("")) {

            	list = listString.split(":");

            } else {

            	list = null;

            }

        } catch (PatternSyntaxException pse) {

        	list = null;

            logMetacat.error("Error in MetacatServlet.init: "

                + pse.getMessage());

        }

        return list;

    }

    /** 

     * A method to check if the specified user is part of the moderators list 

     **/

    private static boolean onList(String list[], String username, String[] groups){

    	if(list == null){

    		return false;

    	}

    	// Check that the user is authenticated as an administrator account

        for (int i = 0; i < list.length; i++) {

            // check the given admin dn is a group dn...

        	if(groups != null && list[i].startsWith("cn=")){

            	// is a group dn

        		for (int j = 0; j < groups.length; j++) {

        			if (groups[j].equals(list[i])) {

                		return true;

                	}	

        		}   		

            } else { 

            	// is a user dn

            	if (username != null && username.equals(list[i])) {

    	    		return true;

            	}	

            }

        }

        return false;

    }

    /** 

     * A method to check if the specified user is part of the administrators list 

     **/

    public static boolean isAdministrator(String username, String[] groups){

    	return (onList(administrators, username, groups));

    }

    /** 

     * A method to check if the specified user is part of the moderators list 

     **/

    public static boolean isModerator(String username, String[] groups){

    	return (onList(moderators, username, groups));

    }

    /** 

     * A method to check if the specified user is part of the moderators list 

     **/

    public static boolean isAllowedSubmitter(String username, String[] groups){

    	if(allowedSubmitters != null){

    		return (onList(allowedSubmitters, username, groups));

    	} else {

    		// no allowedSubmitters list specified - 

    		// hence everyone should be allowed

    		return true;

    	}

   }

    /** 

     * A method to check if the specified user is part of the moderators list 

     **/

    public static boolean isDeniedSubmitter(String username, String[] groups){

		return (onList(deniedSubmitters, username, groups));

    }

    /** 

     * A method to check if the specified user can insert the document 

     **/

    public static boolean canInsertOrUpdate(String username, String[] groups){

    	return (isAllowedSubmitter(username, groups) 

    			&& !isDeniedSubmitter(username, groups));

    }

}