source: tags/3.2.2/doc/3rd-party-components.txt

Last change on this file was 5875, checked in by Nicklas Nordborg, 10 years ago

References #1650: Update 3rd-party JAR files

Updated to Hibernate 3.6.8

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1==================================================================
2$Id: 3rd-party-components.txt 5875 2011-11-14 08:00:23Z nicklas $
3
4  Copyright (C) 2005 Johan Enell, Nicklas Nordborg
5  Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Gregory Vincic
6  Copyright (C) 2007 Johan Enell, Jari Häkkinen, Nicklas Nordborg
7
8  This file is part of BASE - BioArray Software Environment.
9  Available at http://base.thep.lu.se/
10
11BASE is free software; you can redistribute it and/or
12modify it under the terms of the GNU General Public License
13as published by the Free Software Foundation; either version 3
14of the License, or (at your option) any later version.
15
16BASE is distributed in the hope that it will be useful,
17but WITHOUT ANY WARRANTY; without even the implied warranty of
18MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
19GNU General Public License for more details.
20
21You should have received a copy of the GNU General Public License
22along with BASE. If not, see <http://www.gnu.org/licenses/>.
23==================================================================
24
25=================================
263rd-party components used by BASE
27=================================
28
29Here is list of 3rd-party components used by BASE. All the jar files
30needed are included in the <base>/lib directory or in
31<base>/www/plugins sub-directories for plug-ins based on others
32work. The URLs given here can be used if you need more information or
33need to update some component.
34
35
36Hibernate 3
37-----------
38An object/relational persistence and query service for Java. Shields
39us from most SQL and gives us database independece.
40
41More info : http://www.hibernate.org/
42Version   : 3.6.8
43License   : LGPL (hibernate.license.txt)
44Jar files : hibernate3.jar, hibernate-jpa-2.0-api-1.0.1.Final.jar,
45            antlr-2.7.6.jar, c3p0-0.9.1.jar, commons-collections-3.1.jar,
46            dom4j-1.6.1.jar, javassist-3.12.0.GA.jar,
47            jta-1.1.jar, slf4j-api.1.6.4.jar, slf4j-log4j12-1.6.4.jar
48
49Note: Most of the jar files above are other 3rd-party components used by Hibernate.
50BASE doesn't use these components directly.
51
52Ehcahce
53-------
54Used by Hibernate for caching entities and query results. Is no
55longer part of the main Hibernate distribution.
56
57More info : http://ehcache.org/
58Version   : 2.4.6
59License   : Apache License 2.0 (apache.license-2.0.txt)
60Jar files : ehcache-core-2.4.6.jar
61
62
63Log4j
64-----
65A logging system that makes it easy to turn on or off debugging just by
66editing a configuration file. This component is also used by Hibernate
67and we are using the same version that ships with Hibernate.
68
69More info : http://logging.apache.org/log4j/1.2/index.html
70Version   : 1.2.16
71License   : Apache License 2.0 (apache.license-2.0.txt)
72Jar files : log4j-1.2.16.jar
73
74JDOM
75----
76A library for parsing and generating XML files.
77
78More info : http://www.jdom.org/
79Version   : 1.1.2
80License   : Apache-style open source license (jdom.license.txt)
81Jar files : jdom-1.1.2.jar, jaxen-1.1.1.jar
82
83
84Xerces
85------
86A toolkit for handling XML documents. From the Apache Software
87Foundation. These libraries are also needed by JDOM.
88
89More info : http://xml.apache.org/xerces2-j/index.html
90Version   : 2.11.0
91License   : Apache Software License (xerces.license.txt)
92Jar files : xerces-2.11.0.jar, xml-apis.jar
93
94
95Java Advanced Imaging (JAI)
96---------------------------
97An image toolkit from SUN. The package consists of a few jar files and
98libraries for native code for different operating systems. At the moment
99we are only using the jar files but we must also distribute the native
100code libraries in order to follow the license.
101
102More info : http://java.sun.com/javase/technologies/desktop/media/jai/
103Version   : 1.1.3
104License   : Sun Microsystems Binary Code License (jai.license.txt)
105Jar files : jai_core.jar, jai_codec.jar
106
107
108Java Servlet API
109----------------
110Required for creating servlets and tag libraries. From SUN. This
111library is only required for compiling and are not included in the
112distribution. The web server/servlet container should already have
113these API installed (that's what makes it a servlet container).
114
115More info : http://java.sun.com/products/servlet/index.jsp
116Version   : 2.5
117License   : N/A
118Jar files : jsp-api.jar, servlet-api.jar
119
120
121MySQL Connector/J
122-----------------
123A JDBC driver for the MySQL database from MySQL. This library is only
124needed if you are using MySQL as your database.
125
126More info : http://www.mysql.com/products/connector/
127Version   : 5.1.18
128License   : GPLv2 (gpl-2.license.txt)
129Jar files : mysql-connector-java-5.1.18-bin.jar
130
131
132PostgreSQL JDBC driver
133----------------------
134A JDBC driver for the PostgreSQL database. This library is only
135needed if you are using PostgreSQL as your database.
136
137More info : http://jdbc.postgresql.org/
138Version   : 9.1.901
139License   : BSD License (postgres.license.txt)
140Jar files : postgresql-9.1-901.jdbc4.jar
141
142
143X-Doclet
144--------
145Used at compile-time only to generate the XML files needed by
146Hibernate for the database mapping. These libraries are not included in
147the distribution.
148
149More info : http://xdoclet.sourceforge.net/xdoclet/index.html
150Version   : 1.2
151License   : XDoclet License (xdoclet.license.txt)
152Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar,
153            xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar,
154            commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
155
156
157Java Math Expression Parser
158---------------------------
159Parses and evaluates mathematical expressions in string. Supports
160most operators and funcations as well as variables.
161
162More info : http://www.singularsys.com/jep/
163Version   : 2.4.0
164License   : GPLv2 (gpl-2.license.txt)
165Jar files : jep-2.4.0.jar
166
167
168JFreeChart
169----------
170Plotting package for bar charts, line charts, pie charts and xy plots.
171
172More info : http://www.jfree.org/jfreechart/
173Version   : 1.0.13
174License   : LGPL (lgpl.txt)
175Jar files : jfreechart-1.0.13.jar jcommon-1.0.16.jar
176
177
178Apache HttpComponents
179---------------------
180Package for doing work with HTTP (eg. downloading files).
181
182More info : http://hc.apache.org/
183Version   : 4.1.2/4.1.3
184License   : Apache License 2.0 (apache.license-2.0.txt)
185Jar files : httpclient-4.1.2.jar, httpcore-4.1.3.jar, commons-codec-1.4.jar,
186            commons-logging-1.1.1.jar
187
188Apache Commons Email
189---------------------
190Package for sending email. Depends on JavaMail 1.4.
191
192More info : http://commons.apache.org/email/
193Version   : 1.2
194License   : Apache License 2.0 (apache.license-2.0.txt)
195Jar files : commons-email-1.2.jar
196
197
198JavaMail
199---------
200Low-level package for sending email. Used by Apache commons email.
201
202More info : http://www.oracle.com/technetwork/java/index-jsp-139225.html
203Version   : 1.4.3
204License   : Sun (mail-LICENSE.txt)
205Jar files : mail-1.4.3.jar
206
207
208jBCrypt
209-------
210Package for safe encryption of passwords using the 'bcrypt' algorithm.
211
212More info : http://www.mindrot.org/projects/jBCrypt/
213Version   : 0.3
214License   : ISC/BSD licence (jbcrypt-license.txt)
215Jar files : None. Distributed as source only. All code is in net/sf/basedb/util/bcrypt/BCrypt.java
216
217JSON.simple
218-----------
219JSON.simple is a simple Java toolkit for JSON. You can use JSON.simple to encode or decode JSON text.
220
221More info : http://code.google.com/p/json-simple/
222Version   : 1.1
223License   : Apache License 2.0 (apache.license-2.0.txt)
224Jar files : json-simple-1.1.jar
225
226
227JSON-js
228-------
229JSON parser/encoder for Javascript. Only needed for those browsers that
230doesn't have native support for JSON.
231
232More info : https://github.com/douglascrockford/JSON-js
233Version   : 2011-01-18
234License   : Public Domain
235Files     : www/include/scipts/json2.js
236
237
238Silk icon set
239-------------
240A very nice icon set containing 1000 icons. The entire icon set
241is available in the "misc" directory. We have converted the icons
242to GIF format (since we didn't want to scan through all web pages
243and replace .gif with .png). We have also created some new icons which
244are merely combinations of other icons, ie. taking an arrow on one icon
245an putting it on another.
246
247More info : http://www.famfamfam.com/lab/icons/silk/
248Version   : 1.3
249License   : Creative Commons Attribution 2.5 License
250            (http://creativecommons.org/licenses/by/2.5/)
251
252
253SvnAnt
254------
255An 'ant' task implementation for accessing subversion from the ant buildfile.
256
257More info : http://subclipse.tigris.org/svnant.html
258Version   : 1.3.0
259License   : Apache Software License 1.1 (apache.license.txt)
260Jar files : svnant.jar, svnkit.jar, svnClientAdapter.jar, svnjavahl.jar
261            ganymed.jar
262
263
264Docbook
265-------
266A set of DTD:s and stylesheets for creating documentation. We use
267the DocBook styler suite (see below) but has upgraded it to Docbook 4.5.
268
269More info: http://www.docbook.org/
270Version  : 4.5
271License  : docbook.license.txt
272Files    : Everything in lib/docbook/docbook and dist/commons-logging-1.1.jar
273
274
275Docbook styler guide
276--------------------
277An extension to docbook created by Dawid Weiss which simplifies
278file inclusion and building from ant.
279
280More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en
281Version  : 2004_06_22-21_12
282License  : docbook.styler.guide.txt
283Files    : Everything in lib/docbook except the 'docbook' subdirectory
284
285Example code syntax highlighter
286-------------------------------
287A javascript library that can be used to dynamically highlight
288the syntax in program examples. We have made minor changes to
289make it support the HTML produced by Docbook (ie. find the language
290from the 'language' attribute instead of the 'class' attribute).
291
292More info: http://alexgorbatchev.com/SyntaxHighlighter/
293Version  : 1.5.1
294License  : LGPL (lgpl.txt)
295Files    : Everything in the /doc/src/docbook/script and
296           /doc/src/docbook/css directories
297
298Affymetrix Fusion SDK
299---------------------
300Package for reading various Affymetrix file formats. We use a modified
301version that for some file formats can read from an InputStream instead
302of from a File object. This avoids a lot of copying and decompressing.
303
304More info: http://www.affymetrix.com/support/developer/fusion/index.affx
305         : (original version)
306         : http://dev.thep.lu.se/basehacks/wiki/AffxFusion
307         : (modified version)
308Version  : 1.09
309License  : LGPL (lgpl.txt)
310Files    : AffxFusion.jar
311
312TAR file support
313----------------
314Package for reading and writing TAR files.
315
316More info: http://www.trustice.com/java/tar/
317Version  : 2.5
318License  : tar.license.txt
319Files    : tar.jar
320
321BZIP file support
322-----------------
323Package for reading and writing BZIP files.
324
325More info: http://www.kohsuke.org/bzip2/
326Version  : unknown
327License  : Apache software license (apache.license.txt)
328Files    : bzip2.jar
329
330Axis2
331-----
332A core engine for webservices from Apache.
333
334More info : http://ws.apache.org/axis2/
335Version   : 1.6.1
336License   : Apache License 2.0 (apache.license-2.0.txt)
337Files     : Everything in the /lib/webservices directory
338
339SecondString
340------------
341A package with some fuzzy string matching algorithms developed
342by researchers at Carnegie Mellon University.
343
344More info : http://secondstring.sourceforge.net/
345Version   : CVS trunk checkout (2008-08-25)
346License   : University of Illinois/NCSA Open Source (secondstring-LICENSE.txt)
347Files     : secondstring.jar
348
349
350jsDraw2D
351--------
352A vector graphics package for JavaScript.
353
354More info : http://jsdraw2d.jsfiction.com/
355Version   : 1.1.0
356License   : LGPL v3
357Files     : www/include/scripts/js-draw.js
358
359JavaSysMon
360----------
361A library for accessing CPU and memory information on some selected
362operating systems (including Linux, Windows and Mac OSX). It uses
363native libraries targeted for each platform
364
365More info : http://github.com/jezhumble/javasysmon
366Version   : 0.3.1
367License   : javasysmon-LICENSE.txt
368Files     : javasysmon-0.3.1.jar
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