| 1 |
51
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jones
|
/**
|
| 2 |
203
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jones
|
* '$RCSfile$'
|
| 3 |
|
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* Purpose: A Class that implements utility methods for a metadata catalog
|
| 4 |
|
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* Copyright: 2000 Regents of the University of California and the
|
| 5 |
|
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* National Center for Ecological Analysis and Synthesis
|
| 6 |
309
|
bojilova
|
* Authors: Matt Jones, Jivka Bojilova
|
| 7 |
1538
|
berkley
|
*
|
| 8 |
203
|
jones
|
* '$Author$'
|
| 9 |
|
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* '$Date$'
|
| 10 |
|
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* '$Revision$'
|
| 11 |
669
|
jones
|
*
|
| 12 |
|
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* This program is free software; you can redistribute it and/or modify
|
| 13 |
|
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* it under the terms of the GNU General Public License as published by
|
| 14 |
|
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* the Free Software Foundation; either version 2 of the License, or
|
| 15 |
|
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* (at your option) any later version.
|
| 16 |
|
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*
|
| 17 |
|
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* This program is distributed in the hope that it will be useful,
|
| 18 |
|
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
| 19 |
|
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
| 20 |
|
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* GNU General Public License for more details.
|
| 21 |
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*
|
| 22 |
|
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* You should have received a copy of the GNU General Public License
|
| 23 |
|
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* along with this program; if not, write to the Free Software
|
| 24 |
|
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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| 25 |
51
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jones
|
*/
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| 26 |
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| 27 |
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package edu.ucsb.nceas.metacat;
|
| 28 |
|
|
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| 29 |
185
|
jones
|
import java.io.File;
|
| 30 |
3420
|
walbridge
|
import java.io.FileInputStream;
|
| 31 |
3269
|
tao
|
import java.io.FileOutputStream;
|
| 32 |
|
|
import java.io.FileWriter;
|
| 33 |
3420
|
walbridge
|
import java.io.IOException;
|
| 34 |
3269
|
tao
|
import java.io.PrintWriter;
|
| 35 |
|
|
import java.io.StringReader;
|
| 36 |
2068
|
jones
|
import java.net.MalformedURLException;
|
| 37 |
185
|
jones
|
import java.net.URL;
|
| 38 |
3269
|
tao
|
import java.text.SimpleDateFormat;
|
| 39 |
2893
|
sgarg
|
import java.util.HashMap;
|
| 40 |
309
|
bojilova
|
import java.util.Hashtable;
|
| 41 |
3673
|
barteau
|
import java.util.Properties;
|
| 42 |
1545
|
tao
|
import java.util.Stack;
|
| 43 |
887
|
berkley
|
import java.util.Vector;
|
| 44 |
2558
|
sgarg
|
import java.util.regex.PatternSyntaxException;
|
| 45 |
50
|
jones
|
|
| 46 |
2591
|
sgarg
|
import org.apache.log4j.Logger;
|
| 47 |
|
|
|
| 48 |
3420
|
walbridge
|
import com.oreilly.servlet.multipart.FilePart;
|
| 49 |
|
|
|
| 50 |
777
|
bojilova
|
import edu.ucsb.nceas.dbadapter.AbstractDatabase;
|
| 51 |
1951
|
jones
|
import edu.ucsb.nceas.utilities.Options;
|
| 52 |
747
|
bojilova
|
|
| 53 |
50
|
jones
|
/**
|
| 54 |
|
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* A suite of utility classes for the metadata catalog server
|
| 55 |
|
|
*/
|
| 56 |
2068
|
jones
|
public class MetaCatUtil
|
| 57 |
|
|
{
|
| 58 |
50
|
jones
|
|
| 59 |
2068
|
jones
|
public static AbstractDatabase dbAdapter;
|
| 60 |
109
|
bojilova
|
|
| 61 |
2521
|
sgarg
|
public static Vector pathsForIndexing;
|
| 62 |
2893
|
sgarg
|
|
| 63 |
3673
|
barteau
|
private static HashMap skinconfigs = new HashMap();
|
| 64 |
2521
|
sgarg
|
|
| 65 |
3034
|
perry
|
private static edu.ucsb.nceas.utilities.Options options = null;
|
| 66 |
747
|
bojilova
|
|
| 67 |
2068
|
jones
|
private static boolean debug = true;
|
| 68 |
2558
|
sgarg
|
|
| 69 |
|
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private static String[] administrators;
|
| 70 |
|
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|
| 71 |
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private static String[] moderators;
|
| 72 |
2068
|
jones
|
|
| 73 |
2576
|
sgarg
|
private static String[] allowedSubmitters;
|
| 74 |
|
|
|
| 75 |
|
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private static String[] deniedSubmitters;
|
| 76 |
2665
|
sgarg
|
|
| 77 |
|
|
private static Logger logMetacat = Logger.getLogger(MetaCatUtil.class);
|
| 78 |
2576
|
sgarg
|
|
| 79 |
2068
|
jones
|
static {
|
| 80 |
2591
|
sgarg
|
// Determine our db adapter class and create an instance of that class
|
| 81 |
2068
|
jones
|
try {
|
| 82 |
|
|
dbAdapter = (AbstractDatabase) createObject(getOption("dbAdapter"));
|
| 83 |
|
|
} catch (Exception e) {
|
| 84 |
|
|
System.err.println("Error in MetaCatUtil static block:"
|
| 85 |
|
|
+ e.getMessage());
|
| 86 |
3034
|
perry
|
e.printStackTrace();
|
| 87 |
2068
|
jones
|
}
|
| 88 |
2558
|
sgarg
|
|
| 89 |
|
|
// read administrator and moderator lists from metacat.properties
|
| 90 |
2576
|
sgarg
|
getUserAccessControlLists();
|
| 91 |
747
|
bojilova
|
}
|
| 92 |
2665
|
sgarg
|
|
| 93 |
2068
|
jones
|
/**
|
| 94 |
|
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* Instantiate a class using the name of the class at runtime
|
| 95 |
2165
|
tao
|
*
|
| 96 |
2068
|
jones
|
* @param className the fully qualified name of the class to instantiate
|
| 97 |
|
|
*/
|
| 98 |
|
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public static Object createObject(String className) throws Exception
|
| 99 |
|
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{
|
| 100 |
747
|
bojilova
|
|
| 101 |
2068
|
jones
|
Object object = null;
|
| 102 |
|
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try {
|
| 103 |
|
|
Class classDefinition = Class.forName(className);
|
| 104 |
|
|
object = classDefinition.newInstance();
|
| 105 |
|
|
} catch (InstantiationException e) {
|
| 106 |
|
|
throw e;
|
| 107 |
|
|
} catch (IllegalAccessException e) {
|
| 108 |
|
|
throw e;
|
| 109 |
|
|
} catch (ClassNotFoundException e) {
|
| 110 |
|
|
throw e;
|
| 111 |
|
|
}
|
| 112 |
|
|
return object;
|
| 113 |
|
|
}
|
| 114 |
1217
|
tao
|
|
| 115 |
2068
|
jones
|
/**
|
| 116 |
|
|
* Utility method to get an option value from the properties file
|
| 117 |
2165
|
tao
|
*
|
| 118 |
2068
|
jones
|
* @param optionName the name of the option requested
|
| 119 |
|
|
* @return the String value for the option, or null if not set
|
| 120 |
|
|
*/
|
| 121 |
|
|
public static String getOption(String optionName)
|
| 122 |
|
|
{
|
| 123 |
|
|
if (options == null) {
|
| 124 |
3034
|
perry
|
options = edu.ucsb.nceas.utilities.Options.getInstance();
|
| 125 |
2068
|
jones
|
}
|
| 126 |
3034
|
perry
|
if (options == null) {
|
| 127 |
3078
|
jones
|
Logger logMetacat = Logger.getLogger(MetaCatUtil.class);
|
| 128 |
|
|
logMetacat.info("options is null");
|
| 129 |
3034
|
perry
|
}
|
| 130 |
2068
|
jones
|
String value = options.getOption(optionName);
|
| 131 |
|
|
return value;
|
| 132 |
|
|
}
|
| 133 |
2554
|
tao
|
|
| 134 |
|
|
/**
|
| 135 |
|
|
* Utility method to set an option value from the properties file
|
| 136 |
|
|
*
|
| 137 |
|
|
* @param optionName the name of the option requested
|
| 138 |
|
|
*/
|
| 139 |
|
|
public static void setOption(String optionName, String newValue)
|
| 140 |
|
|
{
|
| 141 |
|
|
if (options == null) {
|
| 142 |
3034
|
perry
|
options = edu.ucsb.nceas.utilities.Options.getInstance();
|
| 143 |
2554
|
tao
|
}
|
| 144 |
|
|
options.setOption(optionName, newValue);
|
| 145 |
|
|
|
| 146 |
|
|
}
|
| 147 |
1538
|
berkley
|
|
| 148 |
2068
|
jones
|
/** Utility method to convert a file handle into a URL */
|
| 149 |
|
|
public static URL fileToURL(File file)
|
| 150 |
|
|
{
|
| 151 |
|
|
String path = file.getAbsolutePath();
|
| 152 |
|
|
String fSep = System.getProperty("file.separator");
|
| 153 |
|
|
if (fSep != null && fSep.length() == 1)
|
| 154 |
|
|
path = path.replace(fSep.charAt(0), '/');
|
| 155 |
|
|
if (path.length() > 0 && path.charAt(0) != '/') path = '/' + path;
|
| 156 |
|
|
try {
|
| 157 |
|
|
return new URL("file", null, path);
|
| 158 |
|
|
} catch (java.net.MalformedURLException e) {
|
| 159 |
|
|
/*
|
| 160 |
|
|
* According to the spec this could only happen if the file
|
| 161 |
|
|
*/
|
| 162 |
|
|
throw new Error("unexpected MalformedURLException");
|
| 163 |
|
|
}
|
| 164 |
747
|
bojilova
|
}
|
| 165 |
|
|
|
| 166 |
2068
|
jones
|
/**
|
| 167 |
|
|
* Utility method to parse the query part of a URL into parameters. This
|
| 168 |
|
|
* method assumes the format of the query par tof the url is an ampersand
|
| 169 |
|
|
* separated list of name/value pairs, with equal signs separating the name
|
| 170 |
|
|
* from the value (e.g., name=tom&zip=99801 ). Returns a has of the name
|
| 171 |
|
|
* value pairs, hashed on name.
|
| 172 |
|
|
*/
|
| 173 |
|
|
public static Hashtable parseQuery(String query)
|
| 174 |
|
|
throws MalformedURLException
|
| 175 |
|
|
{
|
| 176 |
|
|
String[][] params = new String[200][2];
|
| 177 |
|
|
Hashtable parameters = new Hashtable();
|
| 178 |
747
|
bojilova
|
|
| 179 |
2068
|
jones
|
String temp = "";
|
| 180 |
|
|
boolean ampflag = true;
|
| 181 |
|
|
boolean poundflag = false;
|
| 182 |
|
|
int arrcount = 0;
|
| 183 |
185
|
jones
|
|
| 184 |
2068
|
jones
|
if (query != null) {
|
| 185 |
|
|
for (int i = 0; i < query.length(); i++) {
|
| 186 |
566
|
jones
|
|
| 187 |
2068
|
jones
|
// go throught the remainder of the query one character at a
|
| 188 |
|
|
// time.
|
| 189 |
|
|
if (query.charAt(i) == '=') {
|
| 190 |
|
|
// if the current char is a # then the preceding should be
|
| 191 |
|
|
// a name
|
| 192 |
|
|
if (!poundflag && ampflag) {
|
| 193 |
|
|
params[arrcount][0] = temp.trim();
|
| 194 |
|
|
temp = "";
|
| 195 |
|
|
} else {
|
| 196 |
|
|
//if there are two #s or &s in a row throw an
|
| 197 |
|
|
// exception.
|
| 198 |
|
|
throw new MalformedURLException(
|
| 199 |
|
|
"metacatURL: Two parameter names "
|
| 200 |
|
|
+ "not allowed in sequence");
|
| 201 |
|
|
}
|
| 202 |
|
|
poundflag = true;
|
| 203 |
|
|
ampflag = false;
|
| 204 |
|
|
} else if (query.charAt(i) == '&' || i == query.length() - 1) {
|
| 205 |
|
|
//the text preceding the & should be the param value.
|
| 206 |
|
|
if (i == query.length() - 1) {
|
| 207 |
|
|
//if at the end of the string grab the last value and
|
| 208 |
|
|
// append it.
|
| 209 |
|
|
if (query.charAt(i) != '=') {
|
| 210 |
|
|
//ignore an extra & on the end of the string
|
| 211 |
|
|
temp += query.charAt(i);
|
| 212 |
|
|
}
|
| 213 |
|
|
}
|
| 214 |
566
|
jones
|
|
| 215 |
2068
|
jones
|
if (!ampflag && poundflag) {
|
| 216 |
|
|
params[arrcount][1] = temp.trim();
|
| 217 |
|
|
parameters
|
| 218 |
|
|
.put(params[arrcount][0], params[arrcount][1]);
|
| 219 |
|
|
temp = "";
|
| 220 |
|
|
arrcount++; //increment the array to the next row.
|
| 221 |
|
|
} else {
|
| 222 |
|
|
//if there are two =s or &s in a row through an
|
| 223 |
|
|
// exception
|
| 224 |
|
|
throw new MalformedURLException(
|
| 225 |
|
|
"metacatURL: Two parameter values "
|
| 226 |
|
|
+ "not allowed in sequence");
|
| 227 |
|
|
}
|
| 228 |
|
|
poundflag = false;
|
| 229 |
|
|
ampflag = true;
|
| 230 |
|
|
} else {
|
| 231 |
|
|
//get the next character in the string
|
| 232 |
|
|
temp += query.charAt(i);
|
| 233 |
|
|
}
|
| 234 |
731
|
bojilova
|
}
|
| 235 |
566
|
jones
|
}
|
| 236 |
2068
|
jones
|
return parameters;
|
| 237 |
566
|
jones
|
}
|
| 238 |
2665
|
sgarg
|
|
| 239 |
2068
|
jones
|
public static Vector getOptionList(String optiontext)
|
| 240 |
|
|
{
|
| 241 |
|
|
Vector optionsVector = new Vector();
|
| 242 |
|
|
if (optiontext.indexOf(",") == -1) {
|
| 243 |
|
|
optionsVector.addElement(optiontext);
|
| 244 |
|
|
return optionsVector;
|
| 245 |
|
|
}
|
| 246 |
1538
|
berkley
|
|
| 247 |
2068
|
jones
|
while (optiontext.indexOf(",") != -1) {
|
| 248 |
|
|
String s = optiontext.substring(0, optiontext.indexOf(","));
|
| 249 |
|
|
optionsVector.addElement(s.trim());
|
| 250 |
|
|
optiontext = optiontext.substring(optiontext.indexOf(",") + 1,
|
| 251 |
|
|
optiontext.length());
|
| 252 |
|
|
if (optiontext.indexOf(",") == -1) { //catch the last list entry
|
| 253 |
|
|
optionsVector.addElement(optiontext.trim());
|
| 254 |
|
|
}
|
| 255 |
|
|
}
|
| 256 |
|
|
return optionsVector;
|
| 257 |
887
|
berkley
|
}
|
| 258 |
1538
|
berkley
|
|
| 259 |
3755
|
tao
|
/** Normalizes a string read from DB. So it will be compatible to HTML */
|
| 260 |
2068
|
jones
|
public static String normalize(String s)
|
| 261 |
887
|
berkley
|
{
|
| 262 |
2068
|
jones
|
StringBuffer str = new StringBuffer();
|
| 263 |
|
|
|
| 264 |
2339
|
sgarg
|
int len = (s != null) ? s.length() : 0;
|
| 265 |
|
|
for (int i = 0; i < len; i++) {
|
| 266 |
|
|
char ch = s.charAt(i);
|
| 267 |
|
|
switch (ch) {
|
| 268 |
|
|
case '<': {
|
| 269 |
|
|
str.append("<");
|
| 270 |
|
|
break;
|
| 271 |
|
|
}
|
| 272 |
|
|
case '>': {
|
| 273 |
|
|
str.append(">");
|
| 274 |
|
|
break;
|
| 275 |
|
|
}
|
| 276 |
|
|
case '&': {
|
| 277 |
2449
|
sgarg
|
/*
|
| 278 |
|
|
* patch provided by Johnoel Ancheta from U of Hawaii
|
| 279 |
|
|
*/
|
| 280 |
|
|
// check if & is for a character reference &#xnnnn;
|
| 281 |
|
|
if (i + 1 < len - 1 && s.charAt(i + 1) == '#') {
|
| 282 |
|
|
str.append("&#");
|
| 283 |
|
|
i += 2;
|
| 284 |
|
|
|
| 285 |
|
|
ch = s.charAt(i);
|
| 286 |
|
|
while (i < len && ch != ';') {
|
| 287 |
|
|
str.append(ch);
|
| 288 |
|
|
i++;
|
| 289 |
|
|
ch = s.charAt(i);
|
| 290 |
|
|
}
|
| 291 |
|
|
str.append(';');
|
| 292 |
2557
|
sgarg
|
} else
|
| 293 |
|
|
// check if & is in front of amp;
|
| 294 |
|
|
// (we dont yet check for other HTML 4.0 Character entities)
|
| 295 |
3755
|
tao
|
if (i + 4 < len && s.charAt(i + 1) == 'a'
|
| 296 |
2557
|
sgarg
|
&& s.charAt(i + 2) == 'm'
|
| 297 |
|
|
&& s.charAt(i + 3) == 'p'
|
| 298 |
|
|
&& s.charAt(i + 4) == ';'){
|
| 299 |
2449
|
sgarg
|
str.append("&");
|
| 300 |
2997
|
sgarg
|
i += 4;
|
| 301 |
3755
|
tao
|
}
|
| 302 |
|
|
else if (i + 3 < len && s.charAt(i + 1) == 'l'
|
| 303 |
|
|
&& s.charAt(i + 2) == 't'
|
| 304 |
|
|
&& s.charAt(i + 3) == ';' ){
|
| 305 |
|
|
// check if & is in front of it;
|
| 306 |
|
|
str.append("<");
|
| 307 |
|
|
i += 3;
|
| 308 |
|
|
}
|
| 309 |
|
|
else if (i + 3 < len && s.charAt(i + 1) == 'g'
|
| 310 |
|
|
&& s.charAt(i + 2) == 't'
|
| 311 |
|
|
&& s.charAt(i + 3) == ';' ){
|
| 312 |
|
|
// check if & is in front of gt;
|
| 313 |
|
|
// (we dont yet check for other HTML 4.0 Character entities)
|
| 314 |
|
|
str.append(">");
|
| 315 |
|
|
i += 3;
|
| 316 |
|
|
}
|
| 317 |
|
|
else if (i + 5 < len && s.charAt(i + 1) == 'q'
|
| 318 |
|
|
&& s.charAt(i + 2) == 'u'
|
| 319 |
|
|
&& s.charAt(i + 3) == 'o'
|
| 320 |
|
|
&& s.charAt(i + 4) == 't'
|
| 321 |
|
|
&& s.charAt(i + 5) == ';')
|
| 322 |
|
|
{
|
| 323 |
|
|
// check if & is in front of quot;
|
| 324 |
|
|
// (we dont yet check for other HTML 4.0 Character entities)
|
| 325 |
|
|
str.append(""");
|
| 326 |
|
|
i += 5;
|
| 327 |
|
|
}
|
| 328 |
|
|
else if (i + 5 < len && s.charAt(i + 1) == 'a'
|
| 329 |
|
|
&& s.charAt(i + 2) == 'p'
|
| 330 |
|
|
&& s.charAt(i + 3) == 'o'
|
| 331 |
|
|
&& s.charAt(i + 4) == 's'
|
| 332 |
|
|
&& s.charAt(i + 5) == ';')
|
| 333 |
|
|
{
|
| 334 |
|
|
// check if & is in front of apostrophe;
|
| 335 |
|
|
// (we dont yet check for other HTML 4.0 Character entities)
|
| 336 |
|
|
str.append("'");
|
| 337 |
|
|
i += 5;
|
| 338 |
|
|
}
|
| 339 |
|
|
else{
|
| 340 |
2557
|
sgarg
|
str.append("&");
|
| 341 |
3755
|
tao
|
}
|
| 342 |
2449
|
sgarg
|
/////////
|
| 343 |
2339
|
sgarg
|
break;
|
| 344 |
|
|
}
|
| 345 |
3150
|
tao
|
case '"':
|
| 346 |
|
|
str.append(""");
|
| 347 |
|
|
break;
|
| 348 |
3755
|
tao
|
case '\'':
|
| 349 |
|
|
str.append("'");
|
| 350 |
|
|
break;
|
| 351 |
2449
|
sgarg
|
default: {
|
| 352 |
|
|
if ( (ch<128) && (ch>31) ) {
|
| 353 |
2339
|
sgarg
|
str.append(ch);
|
| 354 |
|
|
}
|
| 355 |
|
|
else if (ch<32) {
|
| 356 |
2449
|
sgarg
|
if (ch == 10) { // new line
|
| 357 |
2339
|
sgarg
|
str.append(ch);
|
| 358 |
|
|
}
|
| 359 |
2449
|
sgarg
|
if (ch == 13) { // carriage return
|
| 360 |
2339
|
sgarg
|
str.append(ch);
|
| 361 |
|
|
}
|
| 362 |
2449
|
sgarg
|
if (ch == 9) { // tab
|
| 363 |
2339
|
sgarg
|
str.append(ch);
|
| 364 |
|
|
}
|
| 365 |
|
|
// otherwise skip
|
| 366 |
|
|
}
|
| 367 |
|
|
else {
|
| 368 |
|
|
str.append("&#");
|
| 369 |
|
|
str.append(Integer.toString(ch));
|
| 370 |
|
|
str.append(';');
|
| 371 |
|
|
}
|
| 372 |
|
|
}
|
| 373 |
|
|
}
|
| 374 |
|
|
}
|
| 375 |
2437
|
sgarg
|
return str.toString();
|
| 376 |
887
|
berkley
|
}
|
| 377 |
1538
|
berkley
|
|
| 378 |
2068
|
jones
|
/**
|
| 379 |
|
|
* Get docid from online/url string
|
| 380 |
|
|
*/
|
| 381 |
|
|
public static String getDocIdWithRevFromOnlineURL(String url)
|
| 382 |
894
|
berkley
|
{
|
| 383 |
2068
|
jones
|
String docid = null;
|
| 384 |
|
|
String DOCID = "docid";
|
| 385 |
|
|
boolean find = false;
|
| 386 |
|
|
char limited = '&';
|
| 387 |
|
|
int count = 0; //keep track how many & was found
|
| 388 |
|
|
Vector list = new Vector();// keep index number for &
|
| 389 |
|
|
if (url == null) {
|
| 390 |
2665
|
sgarg
|
logMetacat.info("url is null and null will be returned");
|
| 391 |
2068
|
jones
|
return docid;
|
| 392 |
|
|
}
|
| 393 |
|
|
// the first element in list is 0
|
| 394 |
|
|
list.add(new Integer(0));
|
| 395 |
|
|
for (int i = 0; i < url.length(); i++) {
|
| 396 |
|
|
if (url.charAt(i) == limited) {
|
| 397 |
|
|
// count plus 1
|
| 398 |
|
|
count++;
|
| 399 |
|
|
list.add(new Integer(i));
|
| 400 |
|
|
// get substring beween two &
|
| 401 |
|
|
String str = url.substring(
|
| 402 |
|
|
((Integer) list.elementAt(count - 1)).intValue(), i);
|
| 403 |
2665
|
sgarg
|
logMetacat.info("substring between two & is: " + str);
|
| 404 |
2068
|
jones
|
//if the subString contains docid, we got it
|
| 405 |
|
|
if (str.indexOf(DOCID) != -1) {
|
| 406 |
|
|
//get index of '="
|
| 407 |
|
|
int start = getIndexForGivenChar(str, '=') + 1;
|
| 408 |
|
|
int end = str.length();
|
| 409 |
|
|
docid = str.substring(start, end);
|
| 410 |
|
|
find = true;
|
| 411 |
|
|
}//if
|
| 412 |
|
|
}//if
|
| 413 |
|
|
}//for
|
| 414 |
|
|
//if not find, we need check the subtring between the index of last &
|
| 415 |
|
|
// and
|
| 416 |
|
|
// the end of string
|
| 417 |
|
|
if (!find) {
|
| 418 |
2665
|
sgarg
|
logMetacat.info("Checking the last substring");
|
| 419 |
2068
|
jones
|
String str = url.substring(((Integer) list.elementAt(count))
|
| 420 |
|
|
.intValue() + 1, url.length());
|
| 421 |
2665
|
sgarg
|
logMetacat.info("Last substring is: " + str);
|
| 422 |
2068
|
jones
|
if (str.indexOf(DOCID) != -1) {
|
| 423 |
|
|
//get index of '="
|
| 424 |
|
|
int start = getIndexForGivenChar(str, '=') + 1;
|
| 425 |
|
|
int end = str.length();
|
| 426 |
|
|
docid = str.substring(start, end);
|
| 427 |
|
|
find = true;
|
| 428 |
|
|
}//if
|
| 429 |
|
|
}//if
|
| 430 |
2665
|
sgarg
|
logMetacat.info("The docid from online url is:" + docid);
|
| 431 |
2068
|
jones
|
return docid.trim();
|
| 432 |
894
|
berkley
|
}
|
| 433 |
2068
|
jones
|
|
| 434 |
2165
|
tao
|
|
| 435 |
|
|
/**
|
| 436 |
|
|
* Eocgorid identifier will look like: ecogrid://knb/tao.1.1
|
| 437 |
|
|
* The AccessionNumber tao.1.1 will be returned. If the given doesn't
|
| 438 |
|
|
* contains ecogrid, null will be returned.
|
| 439 |
|
|
* @param identifier String
|
| 440 |
|
|
* @return String
|
| 441 |
|
|
*/
|
| 442 |
|
|
public static String getAccessionNumberFromEcogridIdentifier(String identifier)
|
| 443 |
|
|
{
|
| 444 |
|
|
String accessionNumber = null;
|
| 445 |
|
|
if (identifier != null && identifier.startsWith(DBSAXHandler.ECOGRID))
|
| 446 |
|
|
{
|
| 447 |
|
|
// find the last "/" in identifier
|
| 448 |
|
|
int indexOfLastSlash = identifier.lastIndexOf("/");
|
| 449 |
|
|
int start = indexOfLastSlash+1;
|
| 450 |
|
|
int end = identifier.length();
|
| 451 |
|
|
accessionNumber = identifier.substring(start, end);
|
| 452 |
|
|
}
|
| 453 |
2665
|
sgarg
|
logMetacat.warn("The accession number from url is " +
|
| 454 |
|
|
accessionNumber);
|
| 455 |
2165
|
tao
|
return accessionNumber;
|
| 456 |
|
|
}
|
| 457 |
|
|
|
| 458 |
2068
|
jones
|
private static int getIndexForGivenChar(String str, char character)
|
| 459 |
1557
|
tao
|
{
|
| 460 |
2068
|
jones
|
int index = -1;
|
| 461 |
|
|
// make sure str is not null
|
| 462 |
|
|
if (str == null) {
|
| 463 |
2665
|
sgarg
|
logMetacat.info(
|
| 464 |
|
|
"The given str is null and -1 will be returned");
|
| 465 |
2068
|
jones
|
return index;
|
| 466 |
|
|
}
|
| 467 |
|
|
// got though the string
|
| 468 |
|
|
for (int i = 0; i < str.length(); i++) {
|
| 469 |
|
|
// find the first one then break the loop
|
| 470 |
|
|
if (str.charAt(i) == character) {
|
| 471 |
|
|
index = i;
|
| 472 |
|
|
break;
|
| 473 |
|
|
}//if
|
| 474 |
|
|
}//for
|
| 475 |
2665
|
sgarg
|
logMetacat.info("the index for char " + character + " is: "
|
| 476 |
|
|
+ index);
|
| 477 |
2068
|
jones
|
return index;
|
| 478 |
1557
|
tao
|
}
|
| 479 |
2068
|
jones
|
|
| 480 |
|
|
/**
|
| 481 |
|
|
* Utility method to get docid from a given string
|
| 482 |
2165
|
tao
|
*
|
| 483 |
2068
|
jones
|
* @param string, the given string should be these two format: 1) str1.str2
|
| 484 |
|
|
* in this case docid= str1.str2 2) str1.str2.str3, in this case
|
| 485 |
|
|
* docid =str1.str2
|
| 486 |
|
|
* @param the sperator char
|
| 487 |
|
|
*/
|
| 488 |
|
|
public static String getDocIdFromString(String str)
|
| 489 |
1557
|
tao
|
{
|
| 490 |
2068
|
jones
|
String docId = null;
|
| 491 |
|
|
if (str == null) {
|
| 492 |
2665
|
sgarg
|
logMetacat.info(
|
| 493 |
2068
|
jones
|
"The given str is null and null will be returned"
|
| 494 |
2665
|
sgarg
|
+ " in getDocIdfromString");
|
| 495 |
2068
|
jones
|
return docId;
|
| 496 |
|
|
} //make sure docid is not null
|
| 497 |
|
|
int dotNumber = 0;//count how many dots in given string
|
| 498 |
|
|
int indexOfLastDot = 0;
|
| 499 |
1538
|
berkley
|
|
| 500 |
2068
|
jones
|
//assume that seperator is one charactor string
|
| 501 |
|
|
char seperator = getOption("accNumSeparator").charAt(0);
|
| 502 |
1538
|
berkley
|
|
| 503 |
2068
|
jones
|
for (int i = 0; i < str.length(); i++) {
|
| 504 |
|
|
if (str.charAt(i) == seperator) {
|
| 505 |
|
|
dotNumber++;//count how many dots
|
| 506 |
|
|
indexOfLastDot = i;//keep the last dot postion
|
| 507 |
|
|
}
|
| 508 |
|
|
}//for
|
| 509 |
1538
|
berkley
|
|
| 510 |
2068
|
jones
|
//The string formatt is wrong, because it has more than two or less
|
| 511 |
|
|
// than
|
| 512 |
|
|
//one seperator
|
| 513 |
|
|
if (dotNumber > 2 || dotNumber < 1) {
|
| 514 |
|
|
docId = null;
|
| 515 |
|
|
} else if (dotNumber == 2) //the case for str1.str2.str3
|
| 516 |
|
|
{
|
| 517 |
|
|
docId = str.substring(0, indexOfLastDot);
|
| 518 |
|
|
} else if (dotNumber == 1) //the case for str1.str2
|
| 519 |
|
|
{
|
| 520 |
|
|
docId = str;
|
| 521 |
|
|
}
|
| 522 |
|
|
|
| 523 |
|
|
return docId;
|
| 524 |
|
|
}//getDocIdFromString
|
| 525 |
|
|
|
| 526 |
|
|
/**
|
| 527 |
|
|
* Utility method to get version number from a given string
|
| 528 |
2165
|
tao
|
*
|
| 529 |
2068
|
jones
|
* @param string, the given string should be these two format: 1)
|
| 530 |
|
|
* str1.str2(no version) version =-1; 2) str1.str2.str3, in this
|
| 531 |
|
|
* case version = str3; 3) other, vresion =-2
|
| 532 |
|
|
*/
|
| 533 |
|
|
public static int getVersionFromString(String str)
|
| 534 |
|
|
throws NumberFormatException
|
| 535 |
942
|
tao
|
{
|
| 536 |
2068
|
jones
|
int version = -1;
|
| 537 |
|
|
String versionString = null;
|
| 538 |
|
|
int dotNumber = 0;//count how many dots in given string
|
| 539 |
|
|
int indexOfLastDot = 0;
|
| 540 |
1538
|
berkley
|
|
| 541 |
2068
|
jones
|
//assume that seperator is one charactor string
|
| 542 |
|
|
char seperator = getOption("accNumSeparator").charAt(0);
|
| 543 |
942
|
tao
|
|
| 544 |
2068
|
jones
|
for (int i = 0; i < str.length(); i++) {
|
| 545 |
|
|
if (str.charAt(i) == seperator) {
|
| 546 |
|
|
dotNumber++;//count how many dots
|
| 547 |
|
|
indexOfLastDot = i;//keep the last dot postion
|
| 548 |
|
|
}
|
| 549 |
|
|
}//for
|
| 550 |
2045
|
tao
|
|
| 551 |
2068
|
jones
|
//The string formatt is wrong, because it has more than two or less
|
| 552 |
|
|
// than
|
| 553 |
|
|
//one seperator
|
| 554 |
|
|
if (dotNumber > 2 || dotNumber < 1) {
|
| 555 |
|
|
version = -2;
|
| 556 |
|
|
} else if (dotNumber == 2 && (indexOfLastDot != (str.length() - 1)))
|
| 557 |
|
|
//the case for str1.str2.str3
|
| 558 |
|
|
{
|
| 559 |
|
|
versionString = str.substring((indexOfLastDot + 1), str.length());
|
| 560 |
|
|
version = Integer.parseInt(versionString);
|
| 561 |
|
|
} else if (dotNumber == 1) //the case for str1.str2
|
| 562 |
|
|
{
|
| 563 |
|
|
version = -1;
|
| 564 |
|
|
}
|
| 565 |
1538
|
berkley
|
|
| 566 |
2068
|
jones
|
return version;
|
| 567 |
|
|
}//getVersionFromString
|
| 568 |
1538
|
berkley
|
|
| 569 |
2068
|
jones
|
/**
|
| 570 |
|
|
* Utility method to get version string from a given string
|
| 571 |
2165
|
tao
|
*
|
| 572 |
2068
|
jones
|
* @param string, the given string should be these two format: 1)
|
| 573 |
|
|
* str1.str2(no version) version=null; 2) str1.str2.str3, in
|
| 574 |
|
|
* this case version = str3; 3) other, vresion =null;
|
| 575 |
|
|
*/
|
| 576 |
|
|
public static String getRevisionStringFromString(String str)
|
| 577 |
|
|
throws NumberFormatException
|
| 578 |
942
|
tao
|
{
|
| 579 |
2068
|
jones
|
// String to store the version
|
| 580 |
|
|
String versionString = null;
|
| 581 |
|
|
int dotNumber = 0;//count how many dots in given string
|
| 582 |
|
|
int indexOfLastDot = 0;
|
| 583 |
1538
|
berkley
|
|
| 584 |
2068
|
jones
|
//assume that seperator is one charactor string
|
| 585 |
|
|
char seperator = getOption("accNumSeparator").charAt(0);
|
| 586 |
1538
|
berkley
|
|
| 587 |
2068
|
jones
|
for (int i = 0; i < str.length(); i++) {
|
| 588 |
|
|
if (str.charAt(i) == seperator) {
|
| 589 |
|
|
dotNumber++;//count how many dots
|
| 590 |
|
|
indexOfLastDot = i;//keep the last dot postion
|
| 591 |
|
|
}
|
| 592 |
|
|
}//for
|
| 593 |
1538
|
berkley
|
|
| 594 |
2068
|
jones
|
//The string formatt is wrong, because it has more than two or less
|
| 595 |
|
|
// than
|
| 596 |
|
|
//one seperator
|
| 597 |
|
|
if (dotNumber > 2 || dotNumber < 1) {
|
| 598 |
|
|
versionString = null;
|
| 599 |
|
|
} else if (dotNumber == 2 && (indexOfLastDot != (str.length() - 1))) {
|
| 600 |
|
|
//the case for str1.str2.str3
|
| 601 |
|
|
// indexOfLastDot != (str.length() -1) means get rid of str1.str2.
|
| 602 |
|
|
versionString = str.substring((indexOfLastDot + 1), str.length());
|
| 603 |
|
|
} else if (dotNumber == 1) //the case for str1.str2 or str1.str2.
|
| 604 |
|
|
{
|
| 605 |
|
|
versionString = null;
|
| 606 |
|
|
}
|
| 607 |
1538
|
berkley
|
|
| 608 |
2068
|
jones
|
return versionString;
|
| 609 |
|
|
}//getVersionFromString
|
| 610 |
1538
|
berkley
|
|
| 611 |
2068
|
jones
|
/**
|
| 612 |
|
|
* This method will get docid from an AccessionNumber. There is no
|
| 613 |
|
|
* assumption the accessnumber will be str1.str2.str3. It can be more. So
|
| 614 |
|
|
* we think the docid will be get rid of last part
|
| 615 |
|
|
*/
|
| 616 |
|
|
public static String getDocIdFromAccessionNumber(String accessionNumber)
|
| 617 |
1292
|
tao
|
{
|
| 618 |
2068
|
jones
|
String docid = null;
|
| 619 |
|
|
if (accessionNumber == null) { return docid; }
|
| 620 |
|
|
String seperator = getOption("accNumSeparator");
|
| 621 |
|
|
int indexOfLastSeperator = accessionNumber.lastIndexOf(seperator);
|
| 622 |
|
|
docid = accessionNumber.substring(0, indexOfLastSeperator);
|
| 623 |
2665
|
sgarg
|
logMetacat.info("after parsing accessionnumber, docid is "
|
| 624 |
|
|
+ docid);
|
| 625 |
2068
|
jones
|
return docid;
|
| 626 |
|
|
}
|
| 627 |
1538
|
berkley
|
|
| 628 |
2068
|
jones
|
/**
|
| 629 |
2290
|
sgarg
|
* This method will get inline data id without the revision number.
|
| 630 |
|
|
* So if inlineData.1.2 is passed as input, inlineData.2 is returned.
|
| 631 |
|
|
*/
|
| 632 |
|
|
public static String getInlineDataIdWithoutRev(String accessionNumber)
|
| 633 |
|
|
{
|
| 634 |
|
|
String docid = null;
|
| 635 |
|
|
if (accessionNumber == null) { return docid; }
|
| 636 |
|
|
String seperator = getOption("accNumSeparator");
|
| 637 |
|
|
int indexOfLastSeperator = accessionNumber.lastIndexOf(seperator);
|
| 638 |
|
|
String version = accessionNumber.substring(indexOfLastSeperator,
|
| 639 |
|
|
accessionNumber.length());
|
| 640 |
|
|
accessionNumber = accessionNumber.substring(0, indexOfLastSeperator);
|
| 641 |
|
|
indexOfLastSeperator = accessionNumber.lastIndexOf(seperator);
|
| 642 |
|
|
docid = accessionNumber.substring(0, indexOfLastSeperator) + version;
|
| 643 |
2665
|
sgarg
|
logMetacat.info("after parsing accessionnumber, docid is "
|
| 644 |
|
|
+ docid);
|
| 645 |
2290
|
sgarg
|
|
| 646 |
|
|
return docid;
|
| 647 |
|
|
}
|
| 648 |
|
|
|
| 649 |
|
|
/**
|
| 650 |
2068
|
jones
|
* This method will call both getDocIdFromString and
|
| 651 |
|
|
* getDocIdFromAccessionNumber. So first, if the string looks str1.str2,
|
| 652 |
|
|
* the docid will be str1.str2. If the string is str1.str2.str3, the docid
|
| 653 |
|
|
* will be str1.str2. If the string is str1.str2.str3.str4 or more, the
|
| 654 |
|
|
* docid will be str1.str2.str3. If the string look like str1, null will be
|
| 655 |
|
|
* returned
|
| 656 |
2165
|
tao
|
*
|
| 657 |
2068
|
jones
|
*/
|
| 658 |
|
|
public static String getSmartDocId(String str)
|
| 659 |
1292
|
tao
|
{
|
| 660 |
2068
|
jones
|
String docid = null;
|
| 661 |
|
|
//call geDocIdFromString first.
|
| 662 |
|
|
docid = getDocIdFromString(str);
|
| 663 |
|
|
// If docid is null, try to call getDocIdFromAccessionNumber
|
| 664 |
|
|
// it will handle the seperator more than2
|
| 665 |
|
|
if (docid == null) {
|
| 666 |
|
|
docid = getDocIdFromAccessionNumber(str);
|
| 667 |
|
|
}
|
| 668 |
2665
|
sgarg
|
logMetacat.info("The docid get from smart docid getor is "
|
| 669 |
|
|
+ docid);
|
| 670 |
2068
|
jones
|
return docid;
|
| 671 |
1292
|
tao
|
}
|
| 672 |
2068
|
jones
|
|
| 673 |
|
|
/**
|
| 674 |
|
|
* This method will get revision from an AccessionNumber. There is no
|
| 675 |
|
|
* assumption the accessnumber will be str1.str2.str3. It can be more. So
|
| 676 |
|
|
* we think the docid will be get rid of last part
|
| 677 |
|
|
*/
|
| 678 |
|
|
public static int getRevisionFromAccessionNumber(String accessionNumber)
|
| 679 |
|
|
throws NumberFormatException
|
| 680 |
1292
|
tao
|
{
|
| 681 |
2068
|
jones
|
String rev = null;
|
| 682 |
|
|
int revNumber = -1;
|
| 683 |
|
|
if (accessionNumber == null) { return revNumber; }
|
| 684 |
|
|
String seperator = getOption("accNumSeparator");
|
| 685 |
|
|
int indexOfLastSeperator = accessionNumber.lastIndexOf(seperator);
|
| 686 |
|
|
rev = accessionNumber.substring(indexOfLastSeperator + 1,
|
| 687 |
|
|
accessionNumber.length());
|
| 688 |
|
|
revNumber = Integer.parseInt(rev);
|
| 689 |
2665
|
sgarg
|
logMetacat.info("after parsing accessionnumber, rev is "
|
| 690 |
|
|
+ revNumber);
|
| 691 |
2068
|
jones
|
return revNumber;
|
| 692 |
1292
|
tao
|
}
|
| 693 |
2068
|
jones
|
|
| 694 |
|
|
/**
|
| 695 |
|
|
* Method to get the name of local replication server
|
| 696 |
|
|
*/
|
| 697 |
|
|
public static String getLocalReplicationServerName()
|
| 698 |
1292
|
tao
|
{
|
| 699 |
2068
|
jones
|
String replicationServerName = null;
|
| 700 |
|
|
String serverHost = null;
|
| 701 |
|
|
serverHost = getOption("server");
|
| 702 |
|
|
// append "context/servelet/replication" to the host name
|
| 703 |
2574
|
tao
|
replicationServerName = serverHost.trim() + getOption("replicationpath").trim();
|
| 704 |
2068
|
jones
|
return replicationServerName;
|
| 705 |
|
|
|
| 706 |
1292
|
tao
|
}
|
| 707 |
1538
|
berkley
|
|
| 708 |
2068
|
jones
|
/**
|
| 709 |
|
|
* Method to get docidwithrev from eml2 inline data id The eml inline data
|
| 710 |
|
|
* id would look like eml.200.2.3
|
| 711 |
|
|
*/
|
| 712 |
|
|
public static String getDocIdWithoutRevFromInlineDataID(String inlineDataID)
|
| 713 |
2045
|
tao
|
{
|
| 714 |
2068
|
jones
|
String docidWithoutRev = null;
|
| 715 |
|
|
if (inlineDataID == null) { return docidWithoutRev; }
|
| 716 |
|
|
String seperator = MetaCatUtil.getOption("accNumSeparator");
|
| 717 |
|
|
char charSeperator = seperator.charAt(0);
|
| 718 |
|
|
int targetNumberOfSeperator = 2;// we want to know his index
|
| 719 |
|
|
int numberOfSeperator = 0;
|
| 720 |
|
|
for (int i = 0; i < inlineDataID.length(); i++) {
|
| 721 |
|
|
// meet seperator, increase number of seperator
|
| 722 |
|
|
if (inlineDataID.charAt(i) == charSeperator) {
|
| 723 |
|
|
numberOfSeperator++;
|
| 724 |
|
|
}
|
| 725 |
|
|
// if number of seperator reach the target one, record the index(i)
|
| 726 |
|
|
// and get substring and terminate the loop
|
| 727 |
|
|
if (numberOfSeperator == targetNumberOfSeperator) {
|
| 728 |
|
|
docidWithoutRev = inlineDataID.substring(0, i);
|
| 729 |
|
|
break;
|
| 730 |
|
|
}
|
| 731 |
|
|
}
|
| 732 |
1538
|
berkley
|
|
| 733 |
2665
|
sgarg
|
logMetacat.info("Docid without rev from inlinedata id: "
|
| 734 |
|
|
+ docidWithoutRev);
|
| 735 |
2068
|
jones
|
return docidWithoutRev;
|
| 736 |
1538
|
berkley
|
|
| 737 |
2068
|
jones
|
}
|
| 738 |
1538
|
berkley
|
|
| 739 |
2068
|
jones
|
/**
|
| 740 |
|
|
* Revise stack change a stack to opposite order
|
| 741 |
|
|
*/
|
| 742 |
|
|
public static Stack reviseStack(Stack stack)
|
| 743 |
|
|
{
|
| 744 |
|
|
Stack result = new Stack();
|
| 745 |
|
|
// make sure the parameter is correct
|
| 746 |
|
|
if (stack == null || stack.isEmpty()) {
|
| 747 |
|
|
result = stack;
|
| 748 |
|
|
return result;
|
| 749 |
|
|
}
|
| 750 |
1538
|
berkley
|
|
| 751 |
2068
|
jones
|
while (!stack.isEmpty()) {
|
| 752 |
|
|
Object obj = stack.pop();
|
| 753 |
|
|
result.push(obj);
|
| 754 |
|
|
}
|
| 755 |
|
|
return result;
|
| 756 |
1598
|
tao
|
}
|
| 757 |
1538
|
berkley
|
|
| 758 |
2068
|
jones
|
/** A method to replace whitespace in url */
|
| 759 |
|
|
public static String replaceWhiteSpaceForURL(String urlHasWhiteSpace)
|
| 760 |
1598
|
tao
|
{
|
| 761 |
2068
|
jones
|
StringBuffer newUrl = new StringBuffer();
|
| 762 |
|
|
String whiteSpaceReplace = "%20";
|
| 763 |
|
|
if (urlHasWhiteSpace == null || urlHasWhiteSpace.trim().equals("")) { return null; }
|
| 764 |
1598
|
tao
|
|
| 765 |
2068
|
jones
|
for (int i = 0; i < urlHasWhiteSpace.length(); i++) {
|
| 766 |
|
|
char ch = urlHasWhiteSpace.charAt(i);
|
| 767 |
|
|
if (!Character.isWhitespace(ch)) {
|
| 768 |
|
|
newUrl.append(ch);
|
| 769 |
|
|
} else {
|
| 770 |
|
|
//it is white sapce, replace it by %20
|
| 771 |
|
|
newUrl = newUrl.append(whiteSpaceReplace);
|
| 772 |
|
|
}
|
| 773 |
1598
|
tao
|
|
| 774 |
2068
|
jones
|
}//for
|
| 775 |
2665
|
sgarg
|
logMetacat.info("The new string without space is:"
|
| 776 |
|
|
+ newUrl.toString());
|
| 777 |
2068
|
jones
|
return newUrl.toString();
|
| 778 |
1598
|
tao
|
|
| 779 |
2068
|
jones
|
}// replaceWhiteSpaceForUR
|
| 780 |
|
|
|
| 781 |
2558
|
sgarg
|
/**
|
| 782 |
|
|
* A method to read administrators and moderators list from the metacat.properties
|
| 783 |
|
|
**/
|
| 784 |
2576
|
sgarg
|
public static void getUserAccessControlLists(){
|
| 785 |
|
|
administrators = getListFromOption("administrators");
|
| 786 |
|
|
moderators = getListFromOption("moderators");
|
| 787 |
|
|
allowedSubmitters = getListFromOption("allowedSubmitters");
|
| 788 |
|
|
deniedSubmitters = getListFromOption("deniedSubmitters");
|
| 789 |
|
|
}
|
| 790 |
|
|
|
| 791 |
|
|
/**
|
| 792 |
|
|
* A method to read value of a given option from the metacat.properties
|
| 793 |
|
|
* into specified String array
|
| 794 |
|
|
**/
|
| 795 |
|
|
private static String[] getListFromOption(String optionName){
|
| 796 |
|
|
String[] list = null;
|
| 797 |
|
|
String listString = MetaCatUtil.getOption(optionName);
|
| 798 |
|
|
|
| 799 |
2558
|
sgarg
|
try {
|
| 800 |
2576
|
sgarg
|
if ( listString != null && !listString.trim().equals("")) {
|
| 801 |
|
|
list = listString.split(":");
|
| 802 |
|
|
} else {
|
| 803 |
|
|
list = null;
|
| 804 |
2566
|
tao
|
}
|
| 805 |
|
|
|
| 806 |
2558
|
sgarg
|
} catch (PatternSyntaxException pse) {
|
| 807 |
2576
|
sgarg
|
list = null;
|
| 808 |
2665
|
sgarg
|
logMetacat.error("Error in MetacatServlet.init: "
|
| 809 |
|
|
+ pse.getMessage());
|
| 810 |
2558
|
sgarg
|
}
|
| 811 |
2576
|
sgarg
|
return list;
|
| 812 |
2558
|
sgarg
|
}
|
| 813 |
2576
|
sgarg
|
|
| 814 |
2558
|
sgarg
|
/**
|
| 815 |
2576
|
sgarg
|
* A method to check if the specified user is part of the moderators list
|
| 816 |
2558
|
sgarg
|
**/
|
| 817 |
2576
|
sgarg
|
private static boolean onList(String list[], String username, String[] groups){
|
| 818 |
|
|
|
| 819 |
|
|
if(list == null){
|
| 820 |
|
|
return false;
|
| 821 |
|
|
}
|
| 822 |
|
|
|
| 823 |
|
|
// Check that the user is authenticated as an administrator account
|
| 824 |
|
|
for (int i = 0; i < list.length; i++) {
|
| 825 |
2558
|
sgarg
|
// check the given admin dn is a group dn...
|
| 826 |
2585
|
tao
|
if(groups != null && list[i].startsWith("cn=")){
|
| 827 |
2576
|
sgarg
|
// is a group dn
|
| 828 |
2558
|
sgarg
|
for (int j = 0; j < groups.length; j++) {
|
| 829 |
2576
|
sgarg
|
if (groups[j].equals(list[i])) {
|
| 830 |
2558
|
sgarg
|
return true;
|
| 831 |
|
|
}
|
| 832 |
|
|
}
|
| 833 |
|
|
} else {
|
| 834 |
|
|
// is a user dn
|
| 835 |
2585
|
tao
|
if (username != null && username.equals(list[i])) {
|
| 836 |
2576
|
sgarg
|
return true;
|
| 837 |
2558
|
sgarg
|
}
|
| 838 |
|
|
}
|
| 839 |
|
|
}
|
| 840 |
|
|
return false;
|
| 841 |
|
|
}
|
| 842 |
2576
|
sgarg
|
|
| 843 |
|
|
/**
|
| 844 |
|
|
* A method to check if the specified user is part of the administrators list
|
| 845 |
|
|
**/
|
| 846 |
|
|
public static boolean isAdministrator(String username, String[] groups){
|
| 847 |
|
|
return (onList(administrators, username, groups));
|
| 848 |
|
|
}
|
| 849 |
2558
|
sgarg
|
|
| 850 |
|
|
/**
|
| 851 |
|
|
* A method to check if the specified user is part of the moderators list
|
| 852 |
|
|
**/
|
| 853 |
|
|
public static boolean isModerator(String username, String[] groups){
|
| 854 |
2576
|
sgarg
|
return (onList(moderators, username, groups));
|
| 855 |
2558
|
sgarg
|
}
|
| 856 |
2576
|
sgarg
|
|
| 857 |
|
|
/**
|
| 858 |
|
|
* A method to check if the specified user is part of the moderators list
|
| 859 |
|
|
**/
|
| 860 |
|
|
public static boolean isAllowedSubmitter(String username, String[] groups){
|
| 861 |
|
|
if(allowedSubmitters != null){
|
| 862 |
|
|
return (onList(allowedSubmitters, username, groups));
|
| 863 |
|
|
} else {
|
| 864 |
|
|
// no allowedSubmitters list specified -
|
| 865 |
|
|
// hence everyone should be allowed
|
| 866 |
|
|
return true;
|
| 867 |
|
|
}
|
| 868 |
|
|
}
|
| 869 |
|
|
|
| 870 |
|
|
/**
|
| 871 |
|
|
* A method to check if the specified user is part of the moderators list
|
| 872 |
|
|
**/
|
| 873 |
|
|
public static boolean isDeniedSubmitter(String username, String[] groups){
|
| 874 |
|
|
return (onList(deniedSubmitters, username, groups));
|
| 875 |
|
|
}
|
| 876 |
|
|
|
| 877 |
|
|
/**
|
| 878 |
|
|
* A method to check if the specified user can insert the document
|
| 879 |
|
|
**/
|
| 880 |
|
|
public static boolean canInsertOrUpdate(String username, String[] groups){
|
| 881 |
|
|
return (isAllowedSubmitter(username, groups)
|
| 882 |
|
|
&& !isDeniedSubmitter(username, groups));
|
| 883 |
|
|
}
|
| 884 |
3269
|
tao
|
|
| 885 |
|
|
/**
|
| 886 |
|
|
* Writes debug information into a file. In metacat.properties, if property writeDebugToFile is
|
| 887 |
|
|
* set to true, the debug information will be written to debug file, which value is the property
|
| 888 |
|
|
* debugOutputFile in metacat.properties.
|
| 889 |
|
|
*
|
| 890 |
|
|
*/
|
| 891 |
|
|
public static void writeDebugToFile(String debugInfo)
|
| 892 |
|
|
{
|
| 893 |
|
|
String debug = MetaCatUtil.getOption("writeDebugToFile");
|
| 894 |
|
|
if (debug != null && debug.equalsIgnoreCase("true"))
|
| 895 |
|
|
{
|
| 896 |
|
|
try
|
| 897 |
|
|
{
|
| 898 |
|
|
File outputFile = new File(MetaCatUtil.getOption("debugOutputFile"));
|
| 899 |
|
|
FileOutputStream fos = new FileOutputStream(outputFile, true);
|
| 900 |
|
|
PrintWriter pw = new PrintWriter(fos);
|
| 901 |
|
|
pw.println(debugInfo);
|
| 902 |
|
|
pw.flush();
|
| 903 |
|
|
pw.close();
|
| 904 |
|
|
fos.close();
|
| 905 |
|
|
|
| 906 |
|
|
}
|
| 907 |
|
|
catch(Exception io)
|
| 908 |
|
|
{
|
| 909 |
|
|
logMetacat.warn("Eorr in MetacatUtil.writeDebugToFile "+io.getMessage()) ;
|
| 910 |
|
|
}
|
| 911 |
|
|
}
|
| 912 |
|
|
|
| 913 |
|
|
}
|
| 914 |
3275
|
tao
|
|
| 915 |
|
|
/**
|
| 916 |
|
|
* Writes debug information into a file in delimitered format
|
| 917 |
|
|
* @param debugInfo the debug information
|
| 918 |
|
|
* @param newLine append the debug info to a line or not
|
| 919 |
|
|
*/
|
| 920 |
|
|
public static void writeDebugToDelimiteredFile(String debugInfo, boolean newLine)
|
| 921 |
|
|
{
|
| 922 |
|
|
String debug = MetaCatUtil.getOption("writeDebugToFile");
|
| 923 |
|
|
if (debug != null && debug.equalsIgnoreCase("true"))
|
| 924 |
|
|
{
|
| 925 |
|
|
try
|
| 926 |
|
|
{
|
| 927 |
|
|
File outputFile = new File(MetaCatUtil.getOption("delimiteredOutputFile"));
|
| 928 |
|
|
FileOutputStream fos = new FileOutputStream(outputFile, true);
|
| 929 |
|
|
PrintWriter pw = new PrintWriter(fos);
|
| 930 |
|
|
if (newLine)
|
| 931 |
|
|
{
|
| 932 |
|
|
pw.println(debugInfo);
|
| 933 |
|
|
}
|
| 934 |
|
|
else
|
| 935 |
|
|
{
|
| 936 |
|
|
pw.print(debugInfo);
|
| 937 |
|
|
}
|
| 938 |
|
|
pw.flush();
|
| 939 |
|
|
pw.close();
|
| 940 |
|
|
fos.close();
|
| 941 |
|
|
|
| 942 |
|
|
}
|
| 943 |
|
|
catch(Exception io)
|
| 944 |
|
|
{
|
| 945 |
|
|
logMetacat.warn("Eorr in writeDebugToDelimiteredFile "+io.getMessage()) ;
|
| 946 |
|
|
}
|
| 947 |
|
|
}
|
| 948 |
|
|
|
| 949 |
|
|
}
|
| 950 |
3420
|
walbridge
|
|
| 951 |
|
|
/**
|
| 952 |
|
|
* Write the uploaded file to disk for temporary storage before moving it
|
| 953 |
|
|
* to its final Metacat location.
|
| 954 |
|
|
*
|
| 955 |
|
|
* @param filePart the FilePart object containing the file form element
|
| 956 |
|
|
* @param fileName the name of the file to be written to disk
|
| 957 |
|
|
* @return tempFilePath a String containing location of temporary file
|
| 958 |
|
|
*/
|
| 959 |
|
|
public static String writeTempFile (FilePart filePart, String fileName) {
|
| 960 |
|
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
| 961 |
|
|
String tempFilePath = null;
|
| 962 |
|
|
String tempDirPath = getOption("temp-dir");
|
| 963 |
|
|
long fileSize;
|
| 964 |
|
|
File tempFile;
|
| 965 |
|
|
File tempDir;
|
| 966 |
|
|
|
| 967 |
|
|
if ((fileName == null) || fileName.equals("")) {
|
| 968 |
|
|
return tempFilePath;
|
| 969 |
|
|
}
|
| 970 |
|
|
|
| 971 |
|
|
// the tempfilepath token isn't set, use Java default
|
| 972 |
|
|
if (tempDirPath == null) {
|
| 973 |
|
|
String javaTempDir = System.getProperty("java.io.tempdir");
|
| 974 |
|
|
if (javaTempDir == null) {
|
| 975 |
|
|
// no paths set, use unix default
|
| 976 |
|
|
tempDirPath = "/tmp";
|
| 977 |
|
|
} else {
|
| 978 |
|
|
tempDirPath = javaTempDir;
|
| 979 |
|
|
}
|
| 980 |
|
|
}
|
| 981 |
|
|
|
| 982 |
|
|
tempDir = new File(tempDirPath);
|
| 983 |
|
|
|
| 984 |
|
|
// Create the temporary directory if it doesn't exist
|
| 985 |
|
|
try {
|
| 986 |
|
|
if (!tempDir.exists()) {
|
| 987 |
|
|
tempDir.mkdirs();
|
| 988 |
|
|
}
|
| 989 |
|
|
} catch (SecurityException e) {
|
| 990 |
|
|
logMetacat.error("Can't create directory: " + tempDir.getPath() +
|
| 991 |
|
|
". Error: " + e.getMessage());
|
| 992 |
|
|
}
|
| 993 |
|
|
try {
|
| 994 |
|
|
tempFile = new File(tempDirPath, fileName);
|
| 995 |
|
|
fileSize = filePart.writeTo(tempFile);
|
| 996 |
|
|
tempFilePath = tempDirPath + File.separator + fileName;
|
| 997 |
|
|
|
| 998 |
|
|
if (fileSize == 0) {
|
| 999 |
|
|
logMetacat.error("Uploaded file '" + fileName + "'is empty!");
|
| 1000 |
|
|
}
|
| 1001 |
|
|
} catch (IOException e) {
|
| 1002 |
|
|
logMetacat.error("IO exception which writing temporary file: " +
|
| 1003 |
|
|
tempFilePath + " " + e.getMessage());
|
| 1004 |
|
|
}
|
| 1005 |
|
|
|
| 1006 |
|
|
logMetacat.info("Temporary file is: " + tempFilePath);
|
| 1007 |
|
|
|
| 1008 |
|
|
return tempFilePath;
|
| 1009 |
|
|
}
|
| 1010 |
|
|
|
| 1011 |
|
|
/**
|
| 1012 |
|
|
*
|
| 1013 |
|
|
* Copy a file between two locations specified as strings. Fails
|
| 1014 |
|
|
* if either path cannot be created. Based on the public domain
|
| 1015 |
|
|
* FileCopy class in _Java in a Nutshell_.
|
| 1016 |
|
|
*
|
| 1017 |
|
|
* @param sourceName the source file to read from disk
|
| 1018 |
|
|
* @param destName the destination file on disk
|
| 1019 |
|
|
*/
|
| 1020 |
|
|
public static void copyFile(String sourceName, String destName) throws IOException {
|
| 1021 |
|
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
| 1022 |
|
|
|
| 1023 |
|
|
File sourceFile = new File(sourceName);
|
| 1024 |
|
|
File destFile = new File(destName);
|
| 1025 |
|
|
FileInputStream source = null;
|
| 1026 |
|
|
FileOutputStream dest = null;
|
| 1027 |
|
|
byte[] buffer;
|
| 1028 |
|
|
int bytesRead;
|
| 1029 |
|
|
|
| 1030 |
|
|
try {
|
| 1031 |
|
|
if (!sourceFile.exists() || !sourceFile.isFile()) {
|
| 1032 |
|
|
logMetacat.error("File copy: no such source" +
|
| 1033 |
|
|
" file: " + sourceName);
|
| 1034 |
|
|
}
|
| 1035 |
|
|
if (!sourceFile.canRead()) {
|
| 1036 |
|
|
logMetacat.error("File copy: source file " +
|
| 1037 |
|
|
"is unreadable: " + sourceName);
|
| 1038 |
|
|
}
|
| 1039 |
|
|
|
| 1040 |
|
|
if (destFile.exists()) {
|
| 1041 |
|
|
if (destFile.isFile()) {
|
| 1042 |
|
|
if (!destFile.canWrite()) {
|
| 1043 |
|
|
logMetacat.error("File copy: destination " +
|
| 1044 |
|
|
"file is unwriteable: " + destFile);
|
| 1045 |
|
|
}
|
| 1046 |
|
|
} else {
|
| 1047 |
|
|
logMetacat.error("File copy: destination file " +
|
| 1048 |
|
|
"is not a file: " + destFile);
|
| 1049 |
|
|
}
|
| 1050 |
|
|
} else {
|
| 1051 |
|
|
File parentDir = parent(destFile);
|
| 1052 |
|
|
|
| 1053 |
|
|
if (!parentDir.exists())
|
| 1054 |
|
|
{
|
| 1055 |
|
|
logMetacat.error("File copy: destination diretory " +
|
| 1056 |
|
|
" doesn't exist: " + destName);
|
| 1057 |
|
|
}
|
| 1058 |
|
|
if (!parentDir.canWrite()) {
|
| 1059 |
|
|
logMetacat.error("File copy: destination directory " +
|
| 1060 |
|
|
" is unwritable: " + destName);
|
| 1061 |
|
|
}
|
| 1062 |
|
|
}
|
| 1063 |
|
|
|
| 1064 |
|
|
// Verbose error checking done, copy the file object
|
| 1065 |
|
|
source = new FileInputStream(sourceFile);
|
| 1066 |
|
|
dest = new FileOutputStream(destFile);
|
| 1067 |
|
|
buffer = new byte[1024];
|
| 1068 |
|
|
|
| 1069 |
|
|
while (true) {
|
| 1070 |
|
|
bytesRead = source.read(buffer);
|
| 1071 |
|
|
if (bytesRead == -1) {
|
| 1072 |
|
|
break;
|
| 1073 |
|
|
}
|
| 1074 |
|
|
dest.write(buffer, 0, bytesRead);
|
| 1075 |
|
|
}
|
| 1076 |
|
|
}
|
| 1077 |
|
|
finally {
|
| 1078 |
|
|
if (source != null) {
|
| 1079 |
|
|
try { source.close(); } catch (IOException e) { ; }
|
| 1080 |
|
|
}
|
| 1081 |
|
|
if (dest != null) {
|
| 1082 |
|
|
try { dest.close(); } catch (IOException e) { ; }
|
| 1083 |
|
|
}
|
| 1084 |
|
|
}
|
| 1085 |
|
|
}
|
| 1086 |
|
|
|
| 1087 |
|
|
private static File parent(File f) {
|
| 1088 |
|
|
String dirname = f.getParent();
|
| 1089 |
|
|
if (dirname == null) {
|
| 1090 |
|
|
if (f.isAbsolute()) return new File(File.separator);
|
| 1091 |
|
|
else return new File(System.getProperty("user.dir"));
|
| 1092 |
|
|
}
|
| 1093 |
|
|
return new File(dirname);
|
| 1094 |
|
|
}
|
| 1095 |
|
|
|
| 1096 |
3673
|
barteau
|
/**
|
| 1097 |
|
|
* Adds the Properties and skin to the list of skin configurations.
|
| 1098 |
|
|
* @param skinName String qformat
|
| 1099 |
|
|
* @param skinProperties Properties instance
|
| 1100 |
|
|
*/
|
| 1101 |
|
|
public static void addSkinConfig(String skinName, Properties skinProperties) {
|
| 1102 |
|
|
skinconfigs.put(skinName, skinProperties);
|
| 1103 |
|
|
}
|
| 1104 |
|
|
|
| 1105 |
|
|
/**
|
| 1106 |
|
|
* Return the Properties for a given skin name.
|
| 1107 |
|
|
* @param skinName String qformat
|
| 1108 |
|
|
* @return Properties, or null if none exist for the skin.
|
| 1109 |
|
|
*/
|
| 1110 |
|
|
public static Properties getSkinConfig(String skinName) {
|
| 1111 |
|
|
Properties result;
|
| 1112 |
|
|
|
| 1113 |
|
|
result = (Properties) skinconfigs.get(skinName);
|
| 1114 |
|
|
return(result);
|
| 1115 |
|
|
}
|
| 1116 |
|
|
|
| 1117 |
|
|
/**
|
| 1118 |
|
|
* Returns true if Properties exist for a given skin name, false otherwise.
|
| 1119 |
|
|
* @param skinName String qformat
|
| 1120 |
|
|
* @return boolean
|
| 1121 |
|
|
*/
|
| 1122 |
|
|
public static boolean hasSkinConfig(String skinName) {
|
| 1123 |
|
|
boolean result;
|
| 1124 |
|
|
|
| 1125 |
|
|
result = skinconfigs.containsKey(skinName);
|
| 1126 |
|
|
return(result);
|
| 1127 |
|
|
}
|
| 1128 |
50
|
jones
|
}
|