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/**
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* '$RCSfile$'
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* Purpose: A Class that implements utility methods for a metadata catalog
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* Copyright: 2000 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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* Authors: Matt Jones, Jivka Bojilova
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* Release: @release@
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*
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* '$Author: tao $'
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* '$Date: 2004-05-11 18:00:52 -0700 (Tue, 11 May 2004) $'
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* '$Revision: 2165 $'
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 2 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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package edu.ucsb.nceas.metacat;
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import java.io.File;
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import java.net.MalformedURLException;
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import java.net.URL;
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import java.util.Hashtable;
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import java.util.Stack;
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import java.util.Vector;
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import edu.ucsb.nceas.dbadapter.AbstractDatabase;
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import edu.ucsb.nceas.utilities.Options;
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/**
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* A suite of utility classes for the metadata catalog server
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*/
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public class MetaCatUtil
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{
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public static AbstractDatabase dbAdapter;
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private static Options options = null;
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private static boolean debug = true;
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/**
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* Determine our db adapter class and create an instance of that class
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*/
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static {
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try {
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dbAdapter = (AbstractDatabase) createObject(getOption("dbAdapter"));
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} catch (Exception e) {
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System.err.println("Error in MetaCatUtil static block:"
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+ e.getMessage());
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}
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}
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/**
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* Instantiate a class using the name of the class at runtime
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*
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* @param className the fully qualified name of the class to instantiate
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*/
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public static Object createObject(String className) throws Exception
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{
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Object object = null;
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try {
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Class classDefinition = Class.forName(className);
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object = classDefinition.newInstance();
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} catch (InstantiationException e) {
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throw e;
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} catch (IllegalAccessException e) {
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throw e;
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} catch (ClassNotFoundException e) {
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throw e;
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}
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return object;
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}
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/**
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* Utility method to get an option value from the properties file
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*
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* @param optionName the name of the option requested
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* @return the String value for the option, or null if not set
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*/
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public static String getOption(String optionName)
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{
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if (options == null) {
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options = Options.getInstance();
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}
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String value = options.getOption(optionName);
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return value;
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}
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/** Utility method to convert a file handle into a URL */
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public static URL fileToURL(File file)
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{
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String path = file.getAbsolutePath();
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String fSep = System.getProperty("file.separator");
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if (fSep != null && fSep.length() == 1)
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path = path.replace(fSep.charAt(0), '/');
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if (path.length() > 0 && path.charAt(0) != '/') path = '/' + path;
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try {
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return new URL("file", null, path);
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} catch (java.net.MalformedURLException e) {
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/*
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* According to the spec this could only happen if the file
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*/
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throw new Error("unexpected MalformedURLException");
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}
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}
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/**
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* Utility method to parse the query part of a URL into parameters. This
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* method assumes the format of the query par tof the url is an ampersand
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* separated list of name/value pairs, with equal signs separating the name
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* from the value (e.g., name=tom&zip=99801 ). Returns a has of the name
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* value pairs, hashed on name.
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*/
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public static Hashtable parseQuery(String query)
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throws MalformedURLException
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{
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String[][] params = new String[200][2];
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Hashtable parameters = new Hashtable();
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String temp = "";
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boolean ampflag = true;
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boolean poundflag = false;
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int arrcount = 0;
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if (query != null) {
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for (int i = 0; i < query.length(); i++) {
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// go throught the remainder of the query one character at a
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// time.
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if (query.charAt(i) == '=') {
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// if the current char is a # then the preceding should be
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// a name
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if (!poundflag && ampflag) {
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params[arrcount][0] = temp.trim();
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temp = "";
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} else {
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//if there are two #s or &s in a row throw an
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// exception.
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throw new MalformedURLException(
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"metacatURL: Two parameter names "
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+ "not allowed in sequence");
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}
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poundflag = true;
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ampflag = false;
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} else if (query.charAt(i) == '&' || i == query.length() - 1) {
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//the text preceding the & should be the param value.
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if (i == query.length() - 1) {
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//if at the end of the string grab the last value and
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// append it.
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if (query.charAt(i) != '=') {
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//ignore an extra & on the end of the string
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temp += query.charAt(i);
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}
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}
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if (!ampflag && poundflag) {
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params[arrcount][1] = temp.trim();
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parameters
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.put(params[arrcount][0], params[arrcount][1]);
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temp = "";
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arrcount++; //increment the array to the next row.
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} else {
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//if there are two =s or &s in a row through an
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// exception
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throw new MalformedURLException(
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"metacatURL: Two parameter values "
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+ "not allowed in sequence");
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}
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poundflag = false;
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ampflag = true;
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} else {
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//get the next character in the string
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temp += query.charAt(i);
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}
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}
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}
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return parameters;
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}
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/**
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* Utility method to print debugging messages. User can set debug level for
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* this message. The number is fewer, the message is more important
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*
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* @param msg, the content of the message
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* @param debugLevel, an integer indicating the message debug leve
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*/
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public static void debugMessage(String msg, int debugLevel)
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{
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if (debug) {
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int limit = 1;
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try {
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limit = Integer.parseInt(getOption("debuglevel"));
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} catch (Exception e) {
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System.out.println(e.getMessage());
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}
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//don't allow the user set debugLevel less than or equals 0
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if (debugLevel <= 0) {
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debugLevel = 1;
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}
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if (debugLevel < limit) {
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System.err.println("@debugprefix@ " + msg);
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}
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}
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}
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public static Vector getOptionList(String optiontext)
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{
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Vector optionsVector = new Vector();
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if (optiontext.indexOf(",") == -1) {
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optionsVector.addElement(optiontext);
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return optionsVector;
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}
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while (optiontext.indexOf(",") != -1) {
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String s = optiontext.substring(0, optiontext.indexOf(","));
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optionsVector.addElement(s.trim());
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optiontext = optiontext.substring(optiontext.indexOf(",") + 1,
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optiontext.length());
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if (optiontext.indexOf(",") == -1) { //catch the last list entry
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optionsVector.addElement(optiontext.trim());
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}
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}
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return optionsVector;
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}
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/** Normalizes the given string. Taken from configXML.java */
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public static String normalize(String s)
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{
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StringBuffer str = new StringBuffer();
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int len = (s != null) ? s.length() : 0;
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for (int i = 0; i < len; i++) {
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char ch = s.charAt(i);
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switch (ch) {
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case '<':
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{
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str.append("<");
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break;
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}
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case '>':
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{
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str.append(">");
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break;
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}
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case '&':
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{
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str.append("&");
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break;
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}
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case '"':
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{
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str.append(""");
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break;
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}
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case '\r':
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case '\n':
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{
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// else, default append char
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}
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default:
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{
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str.append(ch);
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}
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}
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}
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return (str.toString());
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}
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/**
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* Get docid from online/url string
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*/
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public static String getDocIdWithRevFromOnlineURL(String url)
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{
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String docid = null;
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String DOCID = "docid";
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boolean find = false;
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char limited = '&';
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int count = 0; //keep track how many & was found
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Vector list = new Vector();// keep index number for &
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if (url == null) {
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MetaCatUtil.debugMessage("url is null and null will be returned",
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30);
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return docid;
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}
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// the first element in list is 0
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list.add(new Integer(0));
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for (int i = 0; i < url.length(); i++) {
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if (url.charAt(i) == limited) {
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// count plus 1
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count++;
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list.add(new Integer(i));
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// get substring beween two &
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String str = url.substring(
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((Integer) list.elementAt(count - 1)).intValue(), i);
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MetaCatUtil.debugMessage("substring between two & is: " + str,
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30);
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//if the subString contains docid, we got it
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if (str.indexOf(DOCID) != -1) {
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//get index of '="
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int start = getIndexForGivenChar(str, '=') + 1;
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int end = str.length();
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docid = str.substring(start, end);
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find = true;
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}//if
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}//if
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}//for
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//if not find, we need check the subtring between the index of last &
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// and
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// the end of string
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if (!find) {
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MetaCatUtil.debugMessage("Checking the last substring", 35);
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String str = url.substring(((Integer) list.elementAt(count))
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.intValue() + 1, url.length());
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MetaCatUtil.debugMessage("Last substring is: " + str, 30);
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if (str.indexOf(DOCID) != -1) {
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//get index of '="
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int start = getIndexForGivenChar(str, '=') + 1;
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int end = str.length();
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docid = str.substring(start, end);
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find = true;
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}//if
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}//if
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MetaCatUtil.debugMessage("The docid from online url is:" + docid, 30);
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return docid.trim();
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}
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342
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|
343
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/**
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* Eocgorid identifier will look like: ecogrid://knb/tao.1.1
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* The AccessionNumber tao.1.1 will be returned. If the given doesn't
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* contains ecogrid, null will be returned.
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* @param identifier String
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* @return String
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*/
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public static String getAccessionNumberFromEcogridIdentifier(String identifier)
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{
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String accessionNumber = null;
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if (identifier != null && identifier.startsWith(DBSAXHandler.ECOGRID))
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{
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// find the last "/" in identifier
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int indexOfLastSlash = identifier.lastIndexOf("/");
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int start = indexOfLastSlash+1;
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int end = identifier.length();
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accessionNumber = identifier.substring(start, end);
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}
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MetaCatUtil.debugMessage("The accession number from url is " +
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accessionNumber, 10);
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return accessionNumber;
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}
|
365
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|
366
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private static int getIndexForGivenChar(String str, char character)
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367
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{
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368
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int index = -1;
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369
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// make sure str is not null
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370
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if (str == null) {
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MetaCatUtil.debugMessage(
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"The given str is null and -1 will be returned", 30);
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return index;
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}
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// got though the string
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376
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for (int i = 0; i < str.length(); i++) {
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377
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// find the first one then break the loop
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378
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if (str.charAt(i) == character) {
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379
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index = i;
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break;
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381
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}//if
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382
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}//for
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MetaCatUtil.debugMessage("the index for char " + character + " is: "
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384
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+ index, 30);
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return index;
|
386
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}
|
387
|
|
388
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/**
|
389
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* Utility method to get docid from a given string
|
390
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*
|
391
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* @param string, the given string should be these two format: 1) str1.str2
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392
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* in this case docid= str1.str2 2) str1.str2.str3, in this case
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393
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* docid =str1.str2
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394
|
* @param the sperator char
|
395
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*/
|
396
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public static String getDocIdFromString(String str)
|
397
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{
|
398
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String docId = null;
|
399
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if (str == null) {
|
400
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MetaCatUtil.debugMessage(
|
401
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"The given str is null and null will be returned"
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402
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+ " in getDocIdfromString", 30);
|
403
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return docId;
|
404
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} //make sure docid is not null
|
405
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int dotNumber = 0;//count how many dots in given string
|
406
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int indexOfLastDot = 0;
|
407
|
|
408
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//assume that seperator is one charactor string
|
409
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char seperator = getOption("accNumSeparator").charAt(0);
|
410
|
|
411
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for (int i = 0; i < str.length(); i++) {
|
412
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if (str.charAt(i) == seperator) {
|
413
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dotNumber++;//count how many dots
|
414
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indexOfLastDot = i;//keep the last dot postion
|
415
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}
|
416
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}//for
|
417
|
|
418
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//The string formatt is wrong, because it has more than two or less
|
419
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// than
|
420
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//one seperator
|
421
|
if (dotNumber > 2 || dotNumber < 1) {
|
422
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docId = null;
|
423
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} else if (dotNumber == 2) //the case for str1.str2.str3
|
424
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{
|
425
|
docId = str.substring(0, indexOfLastDot);
|
426
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} else if (dotNumber == 1) //the case for str1.str2
|
427
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{
|
428
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docId = str;
|
429
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}
|
430
|
|
431
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return docId;
|
432
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}//getDocIdFromString
|
433
|
|
434
|
/**
|
435
|
* Utility method to get version number from a given string
|
436
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*
|
437
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* @param string, the given string should be these two format: 1)
|
438
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* str1.str2(no version) version =-1; 2) str1.str2.str3, in this
|
439
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* case version = str3; 3) other, vresion =-2
|
440
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*/
|
441
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public static int getVersionFromString(String str)
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442
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throws NumberFormatException
|
443
|
{
|
444
|
int version = -1;
|
445
|
String versionString = null;
|
446
|
int dotNumber = 0;//count how many dots in given string
|
447
|
int indexOfLastDot = 0;
|
448
|
|
449
|
//assume that seperator is one charactor string
|
450
|
char seperator = getOption("accNumSeparator").charAt(0);
|
451
|
|
452
|
for (int i = 0; i < str.length(); i++) {
|
453
|
if (str.charAt(i) == seperator) {
|
454
|
dotNumber++;//count how many dots
|
455
|
indexOfLastDot = i;//keep the last dot postion
|
456
|
}
|
457
|
}//for
|
458
|
|
459
|
//The string formatt is wrong, because it has more than two or less
|
460
|
// than
|
461
|
//one seperator
|
462
|
if (dotNumber > 2 || dotNumber < 1) {
|
463
|
version = -2;
|
464
|
} else if (dotNumber == 2 && (indexOfLastDot != (str.length() - 1)))
|
465
|
//the case for str1.str2.str3
|
466
|
{
|
467
|
versionString = str.substring((indexOfLastDot + 1), str.length());
|
468
|
version = Integer.parseInt(versionString);
|
469
|
} else if (dotNumber == 1) //the case for str1.str2
|
470
|
{
|
471
|
version = -1;
|
472
|
}
|
473
|
|
474
|
return version;
|
475
|
}//getVersionFromString
|
476
|
|
477
|
/**
|
478
|
* Utility method to get version string from a given string
|
479
|
*
|
480
|
* @param string, the given string should be these two format: 1)
|
481
|
* str1.str2(no version) version=null; 2) str1.str2.str3, in
|
482
|
* this case version = str3; 3) other, vresion =null;
|
483
|
*/
|
484
|
public static String getRevisionStringFromString(String str)
|
485
|
throws NumberFormatException
|
486
|
{
|
487
|
// String to store the version
|
488
|
String versionString = null;
|
489
|
int dotNumber = 0;//count how many dots in given string
|
490
|
int indexOfLastDot = 0;
|
491
|
|
492
|
//assume that seperator is one charactor string
|
493
|
char seperator = getOption("accNumSeparator").charAt(0);
|
494
|
|
495
|
for (int i = 0; i < str.length(); i++) {
|
496
|
if (str.charAt(i) == seperator) {
|
497
|
dotNumber++;//count how many dots
|
498
|
indexOfLastDot = i;//keep the last dot postion
|
499
|
}
|
500
|
}//for
|
501
|
|
502
|
//The string formatt is wrong, because it has more than two or less
|
503
|
// than
|
504
|
//one seperator
|
505
|
if (dotNumber > 2 || dotNumber < 1) {
|
506
|
versionString = null;
|
507
|
} else if (dotNumber == 2 && (indexOfLastDot != (str.length() - 1))) {
|
508
|
//the case for str1.str2.str3
|
509
|
// indexOfLastDot != (str.length() -1) means get rid of str1.str2.
|
510
|
versionString = str.substring((indexOfLastDot + 1), str.length());
|
511
|
} else if (dotNumber == 1) //the case for str1.str2 or str1.str2.
|
512
|
{
|
513
|
versionString = null;
|
514
|
}
|
515
|
|
516
|
return versionString;
|
517
|
}//getVersionFromString
|
518
|
|
519
|
/**
|
520
|
* This method will get docid from an AccessionNumber. There is no
|
521
|
* assumption the accessnumber will be str1.str2.str3. It can be more. So
|
522
|
* we think the docid will be get rid of last part
|
523
|
*/
|
524
|
public static String getDocIdFromAccessionNumber(String accessionNumber)
|
525
|
{
|
526
|
String docid = null;
|
527
|
if (accessionNumber == null) { return docid; }
|
528
|
String seperator = getOption("accNumSeparator");
|
529
|
int indexOfLastSeperator = accessionNumber.lastIndexOf(seperator);
|
530
|
docid = accessionNumber.substring(0, indexOfLastSeperator);
|
531
|
MetaCatUtil.debugMessage("after parsing accessionnumber, docid is "
|
532
|
+ docid, 30);
|
533
|
return docid;
|
534
|
}
|
535
|
|
536
|
/**
|
537
|
* This method will call both getDocIdFromString and
|
538
|
* getDocIdFromAccessionNumber. So first, if the string looks str1.str2,
|
539
|
* the docid will be str1.str2. If the string is str1.str2.str3, the docid
|
540
|
* will be str1.str2. If the string is str1.str2.str3.str4 or more, the
|
541
|
* docid will be str1.str2.str3. If the string look like str1, null will be
|
542
|
* returned
|
543
|
*
|
544
|
*/
|
545
|
public static String getSmartDocId(String str)
|
546
|
{
|
547
|
String docid = null;
|
548
|
//call geDocIdFromString first.
|
549
|
docid = getDocIdFromString(str);
|
550
|
// If docid is null, try to call getDocIdFromAccessionNumber
|
551
|
// it will handle the seperator more than2
|
552
|
if (docid == null) {
|
553
|
docid = getDocIdFromAccessionNumber(str);
|
554
|
}
|
555
|
MetaCatUtil.debugMessage("The docid get from smart docid getor is "
|
556
|
+ docid, 30);
|
557
|
return docid;
|
558
|
}
|
559
|
|
560
|
/**
|
561
|
* This method will get revision from an AccessionNumber. There is no
|
562
|
* assumption the accessnumber will be str1.str2.str3. It can be more. So
|
563
|
* we think the docid will be get rid of last part
|
564
|
*/
|
565
|
public static int getRevisionFromAccessionNumber(String accessionNumber)
|
566
|
throws NumberFormatException
|
567
|
{
|
568
|
String rev = null;
|
569
|
int revNumber = -1;
|
570
|
if (accessionNumber == null) { return revNumber; }
|
571
|
String seperator = getOption("accNumSeparator");
|
572
|
int indexOfLastSeperator = accessionNumber.lastIndexOf(seperator);
|
573
|
rev = accessionNumber.substring(indexOfLastSeperator + 1,
|
574
|
accessionNumber.length());
|
575
|
revNumber = Integer.parseInt(rev);
|
576
|
MetaCatUtil.debugMessage("after parsing accessionnumber, rev is "
|
577
|
+ revNumber, 30);
|
578
|
return revNumber;
|
579
|
}
|
580
|
|
581
|
/**
|
582
|
* Method to get the name of local replication server
|
583
|
*/
|
584
|
public static String getLocalReplicationServerName()
|
585
|
{
|
586
|
String replicationServerName = null;
|
587
|
String serverHost = null;
|
588
|
serverHost = getOption("server");
|
589
|
// append "context/servelet/replication" to the host name
|
590
|
replicationServerName = serverHost + getOption("replicationpath");
|
591
|
return replicationServerName;
|
592
|
|
593
|
}
|
594
|
|
595
|
/**
|
596
|
* Method to get docidwithrev from eml2 inline data id The eml inline data
|
597
|
* id would look like eml.200.2.3
|
598
|
*/
|
599
|
public static String getDocIdWithoutRevFromInlineDataID(String inlineDataID)
|
600
|
{
|
601
|
String docidWithoutRev = null;
|
602
|
if (inlineDataID == null) { return docidWithoutRev; }
|
603
|
String seperator = MetaCatUtil.getOption("accNumSeparator");
|
604
|
char charSeperator = seperator.charAt(0);
|
605
|
int targetNumberOfSeperator = 2;// we want to know his index
|
606
|
int numberOfSeperator = 0;
|
607
|
for (int i = 0; i < inlineDataID.length(); i++) {
|
608
|
// meet seperator, increase number of seperator
|
609
|
if (inlineDataID.charAt(i) == charSeperator) {
|
610
|
numberOfSeperator++;
|
611
|
}
|
612
|
// if number of seperator reach the target one, record the index(i)
|
613
|
// and get substring and terminate the loop
|
614
|
if (numberOfSeperator == targetNumberOfSeperator) {
|
615
|
docidWithoutRev = inlineDataID.substring(0, i);
|
616
|
break;
|
617
|
}
|
618
|
}
|
619
|
|
620
|
MetaCatUtil.debugMessage("Docid without rev from inlinedata id: "
|
621
|
+ docidWithoutRev, 35);
|
622
|
return docidWithoutRev;
|
623
|
|
624
|
}
|
625
|
|
626
|
/**
|
627
|
* Revise stack change a stack to opposite order
|
628
|
*/
|
629
|
public static Stack reviseStack(Stack stack)
|
630
|
{
|
631
|
Stack result = new Stack();
|
632
|
// make sure the parameter is correct
|
633
|
if (stack == null || stack.isEmpty()) {
|
634
|
result = stack;
|
635
|
return result;
|
636
|
}
|
637
|
|
638
|
while (!stack.isEmpty()) {
|
639
|
Object obj = stack.pop();
|
640
|
result.push(obj);
|
641
|
}
|
642
|
return result;
|
643
|
}
|
644
|
|
645
|
/** A method to replace whitespace in url */
|
646
|
public static String replaceWhiteSpaceForURL(String urlHasWhiteSpace)
|
647
|
{
|
648
|
StringBuffer newUrl = new StringBuffer();
|
649
|
String whiteSpaceReplace = "%20";
|
650
|
if (urlHasWhiteSpace == null || urlHasWhiteSpace.trim().equals("")) { return null; }
|
651
|
|
652
|
for (int i = 0; i < urlHasWhiteSpace.length(); i++) {
|
653
|
char ch = urlHasWhiteSpace.charAt(i);
|
654
|
if (!Character.isWhitespace(ch)) {
|
655
|
newUrl.append(ch);
|
656
|
} else {
|
657
|
//it is white sapce, replace it by %20
|
658
|
newUrl = newUrl.append(whiteSpaceReplace);
|
659
|
}
|
660
|
|
661
|
}//for
|
662
|
MetaCatUtil.debugMessage("The new string without space is:"
|
663
|
+ newUrl.toString(), 35);
|
664
|
return newUrl.toString();
|
665
|
|
666
|
}// replaceWhiteSpaceForUR
|
667
|
|
668
|
}
|