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: tao $'

 *     '$Date: 2004-03-15 14:08:39 -0800 (Mon, 15 Mar 2004) $'

 * '$Revision: 2045 $'

 *

 * 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.URL;

import java.net.MalformedURLException;

import java.sql.Connection;

import java.sql.DriverManager;

import java.sql.SQLException;

import java.util.PropertyResourceBundle;

import java.util.Hashtable;

import java.util.Enumeration;

import java.util.Stack;

import java.util.Vector;

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;

  private static Options options = null;

  private static boolean debug = true;

  //private Hashtable connectionPool = new Hashtable();

  /**

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

   */

  static {

    try {

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

    } catch (Exception e) {

      System.err.println("Error in MetaCatUtil static block:" + e.getMessage());

    }

  }

  /**

   * 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 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

          protocol were not recognized. */

       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

   */

  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);

      }

    }

  }

  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 '&':

      {

        str.append("&");

        break;

      }

      case '"':

      {

        str.append(""");

        break;

      }

      case '\r':

      case '\n':

      {

        // else, default append char

      }

      default:

      {

        str.append(ch);

      }

      }

    }

    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)

    {

      MetaCatUtil.debugMessage("url is null and null will be returned", 30);

      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);

        MetaCatUtil.debugMessage("substring between two & is: " + str, 30);

        //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)

    {

      MetaCatUtil.debugMessage("Checking the last substring", 35);

      String str = url.substring(((Integer)list.elementAt(count)).intValue() +1, 

                                 url.length());

      MetaCatUtil.debugMessage("Last substring is: " + str, 30);

      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

    MetaCatUtil.debugMessage("The docid from online url is:"+ docid, 30);

    return docid.trim();

  }

  private static int getIndexForGivenChar(String str, char character)

  {

    int index = -1;

    // make sure str is not null

    if(str == null)

    {

      MetaCatUtil.debugMessage("The given str is null and -1 will be returned",

                                30);

      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

    MetaCatUtil.debugMessage("the index for char "+ character +

                             " is: "+index, 30);

    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)

    {

      MetaCatUtil.debugMessage("The given str is null and null will be returned"

                                +" in getDocIdfromString", 30);

      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);

     MetaCatUtil.debugMessage("after parsing accessionnumber, docid is " + 

                              docid, 30);

     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);        

      }

      MetaCatUtil.debugMessage("The docid get from smart docid getor is " +

                                docid, 30);

      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);

     MetaCatUtil.debugMessage("after parsing accessionnumber, rev is " + 

                               revNumber, 30);

     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+getOption("replicationpath");

     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;

       }

     }

     MetaCatUtil.debugMessage("Docid without rev from inlinedata id: " +

                               docidWithoutRev, 35);

     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

   MetaCatUtil.debugMessage("The new string without space is:"+ 

                             newUrl.toString(), 35);

   return newUrl.toString();

  }// replaceWhiteSpaceForUR

}