source: trunk/doc/3rd-party-components.txt @ 4507

Last change on this file since 4507 was 4495, checked in by Nicklas Nordborg, 14 years ago

References #1087: Update to Hibernate 3.3.0

The new JARs are in place. TestAll? is working.

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1==================================================================
2$Id: 3rd-party-components.txt 4495 2008-09-09 06:47:12Z nicklas $
3
4  Copyright (C) 2005 Johan Enell, Nicklas Nordborg
5  Copyright (C) 2006 Jari Hakkinen, Nicklas Nordborg, Gregory Vincic
6  Copyright (C) 2007 Johan Enell, Jari Hakkinen, 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 this program; if not, write to the Free Software
23Foundation, Inc., 59 Temple Place - Suite 330,
24Boston, MA  02111-1307, USA.
25==================================================================
26
27=================================
283rd-party components used by BASE
29=================================
30
31Here is list of 3rd-party components used by BASE. All the jar files
32needed are included in the <base>/lib directory or in
33<base>/www/plugins sub-directories for plug-ins based on others
34work. The URLs given here can be used if you need more information or
35need to update some component.
36
37
38Hibernate 3
39-----------
40An object/relational persistence and query service for Java. Shields
41us from most SQL and gives us database independece.
42
43More info : http://www.hibernate.org/
44Version   : 3.3.0.SP1
45License   : LGPL (hibernate.license.txt)
46Jar files : hibernate3.jar, antlr-2.7.6.jar, c3p0-0.9.1.jar,
47            commons-collections-3.1.jar, dom4j-1.6.1.jar, ehcache-1.2.3.jar,
48            javassist-3.4.GA.jar, jta-1.1.jar, slf4j-api.1.5.2.jar,
49            slf4j-log4j12-1.5.2.jar
50
51Note: Most of the jar files above are other 3rd-party components used by Hibernate.
52BASE doesn't use these components directly.
53
54Log4j
55-----
56A logging system that makes it easy to turn on or off debugging just by
57editing a configuration file. This component is also used by Hibernate
58and we are using the same version that ships with Hibernate.
59
60More info : http://logging.apache.org/log4j/docs/
61Version   : 1.2.14
62License   : Apache License 2.0 (apache.license-2.0.txt)
63Jar files : log4j-1.2.14.jar
64
65JDOM
66----
67A library for parsing and generating XML files.
68
69More info : http://www.jdom.org/
70Version   : 1.0
71License   : Apache-style open source license (jdom.license.txt)
72Jar files : jdom.jar, jaxen-1.1-beta-7.jar, saxpath.jar
73
74
75Java Advanced Imaging (JAI)
76---------------------------
77An image toolkit from SUN. The package consists of a few jar files and
78libraries for native code for different operating systems. At the moment
79we are only using the jar files but we must also distribute the native
80code libraries in order to follow the license.
81
82More info : http://java.sun.com/products/java-media/jai/index.jsp
83Version   : 1.1.2
84License   : Sun Microsystems Binary Code License (jai.license.txt)
85Jar files : jai_core.jar, jai_codec.jar, mlibwrapper_jai.jar
86Other     : lbmlib_jai.so, checkmmx.exe, mlib_jai.dll, mlib_jai_mmx.dll
87
88
89Java Servlet API
90----------------
91Required for creating servlets and tag libraries. From SUN. This
92library is only required for compiling and are not included in the
93distribution. The web server/servlet container should already have
94these API installed (that's what makes it a servlet container).
95
96More info : http://java.sun.com/products/servlet/index.jsp
97Version   : 2.5
98License   : N/A
99Jar files : jsp-api.jar, servlet-api.jar
100
101
102Xerces
103------
104A toolkit for handling XML documents. From the Apache Software
105Foundation. These libraries are also needed by JDOM.
106
107More info : http://xml.apache.org/xerces2-j/index.html
108Version   : 2.9.0
109License   : Apache Software License (xerces.license.txt)
110Jar files : xerces-2.9.0.jar, xml-apis.jar
111
112
113MySQL Connector/J
114-----------------
115A JDBC driver for the MySQL database from MySQL. This library is only
116needed if you are using MySQL as your database.
117
118More info : http://www.mysql.com/products/connector/j/
119Version   : 5.1.6
120License   : GPLv2 (gpl-2.license.txt)
121Jar files : mysql-connector-java-5.1.6-bin.jar
122
123
124PostgreSQL JDBC driver
125----------------------
126A JDBC driver for the PostgreSQL database. This library is only
127needed if you are using PostgreSQL as your database.
128
129More info : http://jdbc.postgresql.org/
130Version   : 8.3.603
131License   : BSD License (postgres.license.txt)
132Jar files : postgresql-8.3-603.jdbc4.jar
133
134
135X-Doclet
136--------
137Used at compile-time only to generate the XML files needed by
138Hibernate for the database mapping. These libraries are not included in
139the distribution.
140
141More info : http://xdoclet.sourceforge.net/xdoclet/index.html
142Version   : 1.2
143License   : XDoclet License (xdoclet.license.txt)
144Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar,
145            xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar,
146            commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
147
148
149Java Math Expression Parser
150---------------------------
151Parses and evaluates mathematical expressions in string. Supports
152most operators and funcations as well as variables.
153
154More info : http://www.singularsys.com/jep/
155Version   : 2.4.0
156License   : GPLv2 (gpl-2.license.txt)
157Jar files : jep-2.4.0.jar
158
159
160JFreeChart
161----------
162Plotting package for bar charts, line charts, pie charts and xy plots.
163
164More info : http://www.jfree.org/
165Version   : 1.0.3
166License   : LGPL (lgpl.txt)
167Jar files : jfreechart-1.0.3.jar jcommon-1.0.6.jar
168
169
170Silk icon set
171-------------
172A very nice icon set containing 1000 icons. The entire icon set
173is available in the "misc" directory. We have converted the icons
174to GIF format (since we didn't want to scan through all web pages
175and replace .gif with .png). We have also created some new icons which
176are merely combinations of other icons, ie. taking an arrow on one icon
177an putting it on another.
178
179More info : http://www.famfamfam.com/lab/icons/silk/
180Version   : 1.3
181License   : Creative Commons Attribution 2.5 License
182            (http://creativecommons.org/licenses/by/2.5/)
183
184
185SvnAnt
186------
187An 'ant' task implementation for accessing subversion from the ant buildfile.
188
189More info : http://subclipse.tigris.org/svnant.html
190Version   : 1.2.0.RC1
191License   : Apache Software License 1.1 (apache.license.txt)
192Jar files : svnant.jar, svnkit.jar, svnClientAdapter.jar, svnjavahl.jar
193            ganymed.jar
194
195
196Docbook
197-------
198A set of DTD:s and stylesheets for creating documentation. We use
199the DocBook styler suite (see below) but has upgraded it to Docbook 4.5.
200
201More info: http://www.docbook.org/
202Version  : 4.5
203License  : docbook.license.txt
204Files    : Everything in lib/docbook/docbook
205
206
207Docbook styler guide
208--------------------
209An extension to docbook created by Dawid Weiss which simplifies
210file inclusion and building from ant.
211
212More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en
213Version  : 2004_06_22-21_12
214License  : docbook.styler.guide.txt
215Files    : Everything in lib/docbook except the 'docbook' subdirectory
216
217Example code syntax highlighter
218-------------------------------
219A javascript library that can be used to dynamically highlight
220the syntax in program examples. We have made minor changes to
221make it support the HTML produced by Docbook (ie. find the language
222from the 'language' attribute instead of the 'class' attribute).
223
224More info: http://www.dreamprojections.com/syntaxhighlighter
225Version  : 1.5.1
226License  : LGPL (lgpl.txt)
227Files    : Everything in the /doc/src/docbook/script and
228           /doc/src/docbook/css directories
229
230Affymetrix Fusion SDK
231---------------------
232Package for reading various Affymetrix file formats. We use a modified
233version that for some file formats can read from an InputStream instead
234of from a File object. This avoids a lot of copying and decompressing.
235
236More info: http://www.affymetrix.com/support/developer/fusion/index.affx
237         : (original version)
238         : http://dev.thep.lu.se/basehacks/wiki/AffxFusion
239         : (modified version)
240Version  : 1.09
241License  : LGPL (lgpl.txt)
242Files    : AffxFusion.jar
243
244TAR file support
245----------------
246Package for reading and writing TAR files.
247
248More info: http://www.trustice.com/java/tar/
249Version  : 2.5
250License  : tar.license.txt
251Files    : tar.jar
252
253BZIP file support
254-----------------
255Package for reading and writing BZIP files.
256
257More info: http://www.kohsuke.org/bzip2/
258Version  : unknown
259License  : Apache software license (apache.license.txt)
260Files    : bzip2.jar
261
262Axis2
263-----
264A core engine for webservices from Apache.
265
266More info : http://ws.apache.org/axis2/
267Version   : 1.3
268License   : Apache License 2.0 (apache.license-2.0.txt)
269Files     : Everything in the /lib/webservices directory
270
271SecondString
272------------
273A package with some fuzzy string matching algorithms developed
274by researchers at Carnegie Mellon University.
275
276More info : http://secondstring.sourceforge.net/
277Version   : CVS trunk checkout (2008-08-25)
278License   : University of Illinois/NCSA Open Source (secondstring-LICENSE.txt)
279Files     : secondstring.jar
280
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