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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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*
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* '$Author: leinfelder $'
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* '$Date: 2014-04-24 13:28:01 -0700 (Thu, 24 Apr 2014) $'
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* '$Revision: 8748 $'
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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.util;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.PrintWriter;
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import java.net.MalformedURLException;
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import java.util.Hashtable;
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import java.util.Vector;
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import org.apache.commons.fileupload.FileItem;
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import org.apache.commons.io.IOUtils;
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import org.apache.log4j.Logger;
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import com.oreilly.servlet.multipart.FilePart;
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import edu.ucsb.nceas.dbadapter.AbstractDatabase;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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import edu.ucsb.nceas.utilities.FileUtil;
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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 final String XMLFORMAT = "xml";
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public static AbstractDatabase dbAdapter;
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private static boolean debugErrorDisplayed = false;
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private static Logger logMetacat = Logger.getLogger(MetacatUtil.class);
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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 part of 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<String,String> 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<String,String> parameters = new Hashtable<String,String>();
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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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public static Vector<String> getOptionList(String optiontext)
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{
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Vector<String> optionsVector = new Vector<String>();
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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 a string read from DB. So it will be compatible to HTML */
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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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str.append("<");
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break;
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}
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case '>': {
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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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* patch provided by Johnoel Ancheta from U of Hawaii
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*/
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// check if & is for a character reference &#xnnnn;
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if (i + 1 < len - 1 && s.charAt(i + 1) == '#') {
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str.append("&#");
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i += 2;
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ch = s.charAt(i);
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while (i < len && ch != ';') {
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str.append(ch);
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i++;
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ch = s.charAt(i);
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}
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str.append(';');
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} else
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// check if & is in front of amp;
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// (we dont yet check for other HTML 4.0 Character entities)
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if (i + 4 < len && s.charAt(i + 1) == 'a'
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&& s.charAt(i + 2) == 'm'
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&& s.charAt(i + 3) == 'p'
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&& s.charAt(i + 4) == ';'){
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str.append("&");
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i += 4;
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}
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else if (i + 3 < len && s.charAt(i + 1) == 'l'
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&& s.charAt(i + 2) == 't'
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&& s.charAt(i + 3) == ';' ){
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// check if & is in front of it;
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str.append("<");
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i += 3;
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}
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else if (i + 3 < len && s.charAt(i + 1) == 'g'
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&& s.charAt(i + 2) == 't'
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&& s.charAt(i + 3) == ';' ){
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// check if & is in front of gt;
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// (we dont yet check for other HTML 4.0 Character entities)
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str.append(">");
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i += 3;
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}
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else if (i + 5 < len && s.charAt(i + 1) == 'q'
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&& s.charAt(i + 2) == 'u'
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&& s.charAt(i + 3) == 'o'
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&& s.charAt(i + 4) == 't'
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&& s.charAt(i + 5) == ';')
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{
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// check if & is in front of quot;
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// (we dont yet check for other HTML 4.0 Character entities)
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str.append(""");
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i += 5;
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224
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}
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225
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else if (i + 5 < len && s.charAt(i + 1) == 'a'
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&& s.charAt(i + 2) == 'p'
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227
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&& s.charAt(i + 3) == 'o'
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228
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&& s.charAt(i + 4) == 's'
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229
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&& s.charAt(i + 5) == ';')
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230
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{
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231
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// check if & is in front of apostrophe;
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232
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// (we dont yet check for other HTML 4.0 Character entities)
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str.append("'");
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234
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i += 5;
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235
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}
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236
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else{
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237
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str.append("&");
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238
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}
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239
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/////////
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240
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break;
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241
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}
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242
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case '"':
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243
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str.append(""");
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244
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break;
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245
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case '\'':
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246
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str.append("'");
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247
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break;
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248
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default: {
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249
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if ( (ch<128) && (ch>31) ) {
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250
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str.append(ch);
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251
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}
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252
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else if (ch<32) {
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253
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if (ch == 10) { // new line
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254
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str.append(ch);
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255
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}
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256
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if (ch == 13) { // carriage return
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257
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str.append(ch);
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258
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}
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259
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if (ch == 9) { // tab
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260
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str.append(ch);
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261
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}
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262
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// otherwise skip
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263
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}
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264
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else {
|
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265
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//Don't transfer special character to numeric entity
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266
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/*str.append("&#");
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267
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str.append(Integer.toString(ch));
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268
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str.append(';');*/
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269
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str.append(ch);
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270
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}
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271
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}
|
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272
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}
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273
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}
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274
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return str.toString();
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275
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}
|
|
276
|
|
|
277
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/**
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278
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* Method to get the name of local replication server
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279
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*/
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280
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public static String getLocalReplicationServerName()
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281
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{
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282
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String replicationServerName = null;
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283
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// String serverHost = null;
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284
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// serverHost = getProperty("server");
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285
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// append "context/servlet/replication" to the host name
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286
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try {
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287
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replicationServerName =
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288
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SystemUtil.getSecureServer()
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289
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+ "/"
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290
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+ PropertyService.getProperty("application.context")
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291
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+ "/servlet/replication";
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292
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} catch (PropertyNotFoundException pnfe) {
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|
293
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logMetacat.error("Could not get local replication server name "
|
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294
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+ "because property could not be found: " + pnfe.getMessage());
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295
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}
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296
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return replicationServerName;
|
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297
|
|
|
298
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}
|
|
299
|
|
|
300
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/** A method to replace whitespace in url */
|
|
301
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public static String replaceWhiteSpaceForURL(String urlHasWhiteSpace)
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302
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{
|
|
303
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StringBuffer newUrl = new StringBuffer();
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304
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String whiteSpaceReplace = "%20";
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305
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if (urlHasWhiteSpace == null || urlHasWhiteSpace.trim().equals("")) { return null; }
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306
|
|
|
307
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for (int i = 0; i < urlHasWhiteSpace.length(); i++) {
|
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308
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char ch = urlHasWhiteSpace.charAt(i);
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309
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if (!Character.isWhitespace(ch)) {
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310
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newUrl.append(ch);
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311
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} else {
|
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312
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//it is white sapce, replace it by %20
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313
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newUrl = newUrl.append(whiteSpaceReplace);
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|
314
|
}
|
|
315
|
|
|
316
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}//for
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317
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logMetacat.info("The new string without space is:"
|
|
318
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+ newUrl.toString());
|
|
319
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return newUrl.toString();
|
|
320
|
|
|
321
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}// replaceWhiteSpaceForUR
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|
322
|
|
|
323
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/**
|
|
324
|
* Writes debug information into a file. In metacat.properties, if property
|
|
325
|
* application.writeDebugToFile is set to true, the debug information will be written to
|
|
326
|
* debug file, which value is the property application.debugOutputFile in
|
|
327
|
* metacat.properties.
|
|
328
|
*
|
|
329
|
*/
|
|
330
|
public static void writeDebugToFile(String debugInfo) {
|
|
331
|
String debug = "false";
|
|
332
|
try {
|
|
333
|
debug = PropertyService.getProperty("application.writeDebugToFile");
|
|
334
|
if (debug != null && debug.equalsIgnoreCase("true")) {
|
|
335
|
File outputFile =
|
|
336
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new File(PropertyService.getProperty("application.debugOutputFile"));
|
|
337
|
FileOutputStream fos = new FileOutputStream(outputFile, true);
|
|
338
|
PrintWriter pw = new PrintWriter(fos);
|
|
339
|
pw.println(debugInfo);
|
|
340
|
pw.flush();
|
|
341
|
pw.close();
|
|
342
|
fos.close();
|
|
343
|
}
|
|
344
|
} catch (PropertyNotFoundException pnfe) {
|
|
345
|
// only log debug to file warning once
|
|
346
|
if (!debugErrorDisplayed) {
|
|
347
|
logMetacat.warn("Could not get debug property. Write debug to "
|
|
348
|
+ "file is set to false: " + pnfe.getMessage());
|
|
349
|
debugErrorDisplayed = true;
|
|
350
|
}
|
|
351
|
} catch (Exception io) {
|
|
352
|
logMetacat.warn("Error in MetacatUtil.writeDebugToFile "
|
|
353
|
+ io.getMessage());
|
|
354
|
}
|
|
355
|
}
|
|
356
|
|
|
357
|
/**
|
|
358
|
* Writes debug information into a file in delimitered format
|
|
359
|
*
|
|
360
|
* @param debugInfo
|
|
361
|
* the debug information
|
|
362
|
* @param newLine
|
|
363
|
* append the debug info to a line or not
|
|
364
|
*/
|
|
365
|
public static void writeDebugToDelimiteredFile(String debugInfo, boolean newLine) {
|
|
366
|
String debug = "false";
|
|
367
|
try {
|
|
368
|
debug = PropertyService.getProperty("application.writeDebugToFile");
|
|
369
|
if (debug != null && debug.equalsIgnoreCase("true")) {
|
|
370
|
File outputFile = new File(PropertyService
|
|
371
|
.getProperty("application.delimiteredOutputFile"));
|
|
372
|
FileOutputStream fos = new FileOutputStream(outputFile, true);
|
|
373
|
PrintWriter pw = new PrintWriter(fos);
|
|
374
|
if (newLine) {
|
|
375
|
pw.println(debugInfo);
|
|
376
|
} else {
|
|
377
|
pw.print(debugInfo);
|
|
378
|
}
|
|
379
|
pw.flush();
|
|
380
|
pw.close();
|
|
381
|
fos.close();
|
|
382
|
}
|
|
383
|
} catch (PropertyNotFoundException pnfe) {
|
|
384
|
// only log debug to file warning once
|
|
385
|
if (!debugErrorDisplayed) {
|
|
386
|
logMetacat.warn("Could not get delimited debug property. Write debug to "
|
|
387
|
+ "file is set to false: " + pnfe.getMessage());
|
|
388
|
debugErrorDisplayed = true;
|
|
389
|
}
|
|
390
|
} catch (Exception io) {
|
|
391
|
logMetacat.warn("Eorr in writeDebugToDelimiteredFile "
|
|
392
|
+ io.getMessage());
|
|
393
|
}
|
|
394
|
}
|
|
395
|
|
|
396
|
/**
|
|
397
|
* Write the uploaded file to disk for temporary storage before moving it to
|
|
398
|
* its final Metacat location.
|
|
399
|
*
|
|
400
|
* @param filePart
|
|
401
|
* the FilePart object containing the file form element
|
|
402
|
* @param fileName
|
|
403
|
* the name of the file to be written to disk
|
|
404
|
* @return tempFilePath a String containing location of temporary file
|
|
405
|
*/
|
|
406
|
public static File writeTempUploadFile (FileItem fi, String fileName) throws Exception {
|
|
407
|
File tempFile = null;
|
|
408
|
String tempDirPath = null;
|
|
409
|
try {
|
|
410
|
tempDirPath = PropertyService.getProperty("application.tempDir") + FileUtil.getFS() + "uploads";
|
|
411
|
} catch (PropertyNotFoundException pnfe) {
|
|
412
|
logMetacat.warn("Temp property not found. An attempt will be made "
|
|
413
|
+ "to use system temp directory: " + pnfe.getMessage());
|
|
414
|
}
|
|
415
|
long fileSize;
|
|
416
|
File tempDir;
|
|
417
|
|
|
418
|
if ((fileName == null) || fileName.equals("")) {
|
|
419
|
return tempFile;
|
|
420
|
}
|
|
421
|
|
|
422
|
// the tempfilepath token isn't set, use Java default
|
|
423
|
if (tempDirPath == null) {
|
|
424
|
String javaTempDir = System.getProperty("java.io.tempdir");
|
|
425
|
if (javaTempDir == null) {
|
|
426
|
// no paths set, use unix default
|
|
427
|
tempDirPath = "/tmp";
|
|
428
|
} else {
|
|
429
|
tempDirPath = javaTempDir;
|
|
430
|
}
|
|
431
|
}
|
|
432
|
|
|
433
|
tempDir = new File(tempDirPath);
|
|
434
|
|
|
435
|
// Create the temporary directory if it doesn't exist
|
|
436
|
try {
|
|
437
|
if (!tempDir.exists()) {
|
|
438
|
tempDir.mkdirs();
|
|
439
|
}
|
|
440
|
} catch (SecurityException e) {
|
|
441
|
throw new IOException("Can't create directory: " + tempDir.getPath() + ". Error: "
|
|
442
|
+ e.getMessage());
|
|
443
|
}
|
|
444
|
|
|
445
|
//tempFile = new File(tempDirPath, fileName);
|
|
446
|
tempFile = File.createTempFile("upload", ".tmp", tempDir);
|
|
447
|
fi.write(tempFile);
|
|
448
|
fileSize = fi.getSize();
|
|
449
|
|
|
450
|
if (fileSize == 0) {
|
|
451
|
logMetacat.warn("Uploaded file '" + fileName + "'is empty!");
|
|
452
|
}
|
|
453
|
|
|
454
|
logMetacat.debug("Temporary file is: " + tempFile.getAbsolutePath());
|
|
455
|
|
|
456
|
return tempFile;
|
|
457
|
}
|
|
458
|
|
|
459
|
/**
|
|
460
|
*
|
|
461
|
* Copy a file between two locations specified as strings. Fails if either
|
|
462
|
* path cannot be created. Based on the public domain FileCopy class in
|
|
463
|
* _Java in a Nutshell_.
|
|
464
|
*
|
|
465
|
* @param sourceName
|
|
466
|
* the source file to read from disk
|
|
467
|
* @param destName
|
|
468
|
* the destination file on disk
|
|
469
|
*/
|
|
470
|
public static void copyFile(String sourceName, String destName) throws IOException {
|
|
471
|
|
|
472
|
File sourceFile = new File(sourceName);
|
|
473
|
File destFile = new File(destName);
|
|
474
|
FileInputStream source = null;
|
|
475
|
FileOutputStream dest = null;
|
|
476
|
byte[] buffer;
|
|
477
|
int bytesRead;
|
|
478
|
|
|
479
|
try {
|
|
480
|
if (!sourceFile.exists() || !sourceFile.isFile()) {
|
|
481
|
logMetacat.error("File copy: no such source" +
|
|
482
|
" file: " + sourceName);
|
|
483
|
}
|
|
484
|
if (!sourceFile.canRead()) {
|
|
485
|
logMetacat.error("File copy: source file " +
|
|
486
|
"is unreadable: " + sourceName);
|
|
487
|
}
|
|
488
|
|
|
489
|
if (destFile.exists()) {
|
|
490
|
if (destFile.isFile()) {
|
|
491
|
if (!destFile.canWrite()) {
|
|
492
|
logMetacat.error("File copy: destination " +
|
|
493
|
"file is unwriteable: " + destFile);
|
|
494
|
}
|
|
495
|
} else {
|
|
496
|
logMetacat.error("File copy: destination file " +
|
|
497
|
"is not a file: " + destFile);
|
|
498
|
}
|
|
499
|
} else {
|
|
500
|
File parentDir = parent(destFile);
|
|
501
|
|
|
502
|
if (!parentDir.exists())
|
|
503
|
{
|
|
504
|
logMetacat.error("File copy: destination diretory " +
|
|
505
|
" doesn't exist: " + destName);
|
|
506
|
}
|
|
507
|
if (!parentDir.canWrite()) {
|
|
508
|
logMetacat.error("File copy: destination directory " +
|
|
509
|
" is unwritable: " + destName);
|
|
510
|
}
|
|
511
|
}
|
|
512
|
|
|
513
|
// Verbose error checking done, copy the file object
|
|
514
|
source = new FileInputStream(sourceFile);
|
|
515
|
dest = new FileOutputStream(destFile);
|
|
516
|
buffer = new byte[1024];
|
|
517
|
|
|
518
|
while (true) {
|
|
519
|
bytesRead = source.read(buffer);
|
|
520
|
if (bytesRead == -1) {
|
|
521
|
break;
|
|
522
|
}
|
|
523
|
dest.write(buffer, 0, bytesRead);
|
|
524
|
}
|
|
525
|
}
|
|
526
|
finally {
|
|
527
|
if (source != null) {
|
|
528
|
try { source.close(); } catch (IOException e) { ; }
|
|
529
|
}
|
|
530
|
if (dest != null) {
|
|
531
|
try { dest.close(); } catch (IOException e) { ; }
|
|
532
|
}
|
|
533
|
}
|
|
534
|
}
|
|
535
|
|
|
536
|
private static File parent(File f) {
|
|
537
|
String dirname = f.getParent();
|
|
538
|
if (dirname == null) {
|
|
539
|
if (f.isAbsolute()) return new File(File.separator);
|
|
540
|
else return new File(System.getProperty("user.dir"));
|
|
541
|
}
|
|
542
|
return new File(dirname);
|
|
543
|
}
|
|
544
|
}
|