source: trunk/doc/3rd-party-components.txt @ 5870

Last change on this file since 5870 was 5870, checked in by Nicklas Nordborg, 10 years ago

References #1650: Update 3rd-party JAR files

Updated Apache HttpComponents? to 4.12/4.1.3

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1==================================================================
2$Id: 3rd-party-components.txt 5870 2011-11-11 09:55:23Z 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
43License   : LGPL (hibernate.license.txt)
44Jar files : hibernate3.jar, hibernate-jpa-2.0-api-1.0.0.Final.jar,
45            antlr-2.7.6.jar, c3p0-0.9.1.jar, commons-collections-3.1.jar,
46            dom4j-1.6.1.jar, ehcache-1.5.0.jar, javassist-3.12.0.GA.jar,
47            jta-1.1.jar, slf4j-api.1.5.8.jar, slf4j-log4j12-1.5.8.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
52Log4j
53-----
54A logging system that makes it easy to turn on or off debugging just by
55editing a configuration file. This component is also used by Hibernate
56and we are using the same version that ships with Hibernate.
57
58More info : http://logging.apache.org/log4j/1.2/index.html
59Version   : 1.2.16
60License   : Apache License 2.0 (apache.license-2.0.txt)
61Jar files : log4j-1.2.16.jar
62
63JDOM
64----
65A library for parsing and generating XML files.
66
67More info : http://www.jdom.org/
68Version   : 1.1.2
69License   : Apache-style open source license (jdom.license.txt)
70Jar files : jdom-1.1.2.jar, jaxen-1.1.1.jar
71
72
73Xerces
74------
75A toolkit for handling XML documents. From the Apache Software
76Foundation. These libraries are also needed by JDOM.
77
78More info : http://xml.apache.org/xerces2-j/index.html
79Version   : 2.11.0
80License   : Apache Software License (xerces.license.txt)
81Jar files : xerces-2.11.0.jar, xml-apis.jar
82
83
84Java Advanced Imaging (JAI)
85---------------------------
86An image toolkit from SUN. The package consists of a few jar files and
87libraries for native code for different operating systems. At the moment
88we are only using the jar files but we must also distribute the native
89code libraries in order to follow the license.
90
91More info : http://java.sun.com/javase/technologies/desktop/media/jai/
92Version   : 1.1.3
93License   : Sun Microsystems Binary Code License (jai.license.txt)
94Jar files : jai_core.jar, jai_codec.jar
95
96
97Java Servlet API
98----------------
99Required for creating servlets and tag libraries. From SUN. This
100library is only required for compiling and are not included in the
101distribution. The web server/servlet container should already have
102these API installed (that's what makes it a servlet container).
103
104More info : http://java.sun.com/products/servlet/index.jsp
105Version   : 2.5
106License   : N/A
107Jar files : jsp-api.jar, servlet-api.jar
108
109
110MySQL Connector/J
111-----------------
112A JDBC driver for the MySQL database from MySQL. This library is only
113needed if you are using MySQL as your database.
114
115More info : http://www.mysql.com/products/connector/
116Version   : 5.1.18
117License   : GPLv2 (gpl-2.license.txt)
118Jar files : mysql-connector-java-5.1.18-bin.jar
119
120
121PostgreSQL JDBC driver
122----------------------
123A JDBC driver for the PostgreSQL database. This library is only
124needed if you are using PostgreSQL as your database.
125
126More info : http://jdbc.postgresql.org/
127Version   : 9.1.901
128License   : BSD License (postgres.license.txt)
129Jar files : postgresql-9.1-901.jdbc4.jar
130
131
132X-Doclet
133--------
134Used at compile-time only to generate the XML files needed by
135Hibernate for the database mapping. These libraries are not included in
136the distribution.
137
138More info : http://xdoclet.sourceforge.net/xdoclet/index.html
139Version   : 1.2
140License   : XDoclet License (xdoclet.license.txt)
141Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar,
142            xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar,
143            commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
144
145
146Java Math Expression Parser
147---------------------------
148Parses and evaluates mathematical expressions in string. Supports
149most operators and funcations as well as variables.
150
151More info : http://www.singularsys.com/jep/
152Version   : 2.4.0
153License   : GPLv2 (gpl-2.license.txt)
154Jar files : jep-2.4.0.jar
155
156
157JFreeChart
158----------
159Plotting package for bar charts, line charts, pie charts and xy plots.
160
161More info : http://www.jfree.org/jfreechart/
162Version   : 1.0.13
163License   : LGPL (lgpl.txt)
164Jar files : jfreechart-1.0.13.jar jcommon-1.0.16.jar
165
166
167Apache HttpComponents
168---------------------
169Package for doing work with HTTP (eg. downloading files).
170
171More info : http://hc.apache.org/
172Version   : 4.1.2/4.1.3
173License   : Apache License 2.0 (apache.license-2.0.txt)
174Jar files : httpclient-4.1.2.jar, httpcore-4.1.3.jar, commons-codec-1.4.jar,
175            commons-logging-1.1.1.jar
176
177Apache Commons Email
178---------------------
179Package for sending email. Depends on JavaMail 1.4.
180
181More info : http://commons.apache.org/email/
182Version   : 1.2
183License   : Apache License 2.0 (apache.license-2.0.txt)
184Jar files : commons-email-1.2.jar
185
186
187JavaMail
188---------
189Low-level package for sending email. Used by Apache commons email.
190
191More info : http://www.oracle.com/technetwork/java/index-jsp-139225.html
192Version   : 1.4.3
193License   : Sun (mail-LICENSE.txt)
194Jar files : mail-1.4.3.jar
195
196
197jBCrypt
198-------
199Package for safe encryption of passwords using the 'bcrypt' algorithm.
200
201More info : http://www.mindrot.org/projects/jBCrypt/
202Version   : 0.3
203License   : ISC/BSD licence (jbcrypt-license.txt)
204Jar files : None. Distributed as source only. All code is in net/sf/basedb/util/bcrypt/BCrypt.java
205
206JSON.simple
207-----------
208JSON.simple is a simple Java toolkit for JSON. You can use JSON.simple to encode or decode JSON text.
209
210More info : http://code.google.com/p/json-simple/
211Version   : 1.1
212License   : Apache License 2.0 (apache.license-2.0.txt)
213Jar files : json-simple-1.1.jar
214
215
216JSON-js
217-------
218JSON parser/encoder for Javascript. Only needed for those browsers that
219doesn't have native support for JSON.
220
221More info : https://github.com/douglascrockford/JSON-js
222Version   : 2011-01-18
223License   : Public Domain
224Files     : www/include/scipts/json2.js
225
226
227Silk icon set
228-------------
229A very nice icon set containing 1000 icons. The entire icon set
230is available in the "misc" directory. We have converted the icons
231to GIF format (since we didn't want to scan through all web pages
232and replace .gif with .png). We have also created some new icons which
233are merely combinations of other icons, ie. taking an arrow on one icon
234an putting it on another.
235
236More info : http://www.famfamfam.com/lab/icons/silk/
237Version   : 1.3
238License   : Creative Commons Attribution 2.5 License
239            (http://creativecommons.org/licenses/by/2.5/)
240
241
242SvnAnt
243------
244An 'ant' task implementation for accessing subversion from the ant buildfile.
245
246More info : http://subclipse.tigris.org/svnant.html
247Version   : 1.3.0
248License   : Apache Software License 1.1 (apache.license.txt)
249Jar files : svnant.jar, svnkit.jar, svnClientAdapter.jar, svnjavahl.jar
250            ganymed.jar
251
252
253Docbook
254-------
255A set of DTD:s and stylesheets for creating documentation. We use
256the DocBook styler suite (see below) but has upgraded it to Docbook 4.5.
257
258More info: http://www.docbook.org/
259Version  : 4.5
260License  : docbook.license.txt
261Files    : Everything in lib/docbook/docbook and dist/commons-logging-1.1.jar
262
263
264Docbook styler guide
265--------------------
266An extension to docbook created by Dawid Weiss which simplifies
267file inclusion and building from ant.
268
269More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en
270Version  : 2004_06_22-21_12
271License  : docbook.styler.guide.txt
272Files    : Everything in lib/docbook except the 'docbook' subdirectory
273
274Example code syntax highlighter
275-------------------------------
276A javascript library that can be used to dynamically highlight
277the syntax in program examples. We have made minor changes to
278make it support the HTML produced by Docbook (ie. find the language
279from the 'language' attribute instead of the 'class' attribute).
280
281More info: http://alexgorbatchev.com/SyntaxHighlighter/
282Version  : 1.5.1
283License  : LGPL (lgpl.txt)
284Files    : Everything in the /doc/src/docbook/script and
285           /doc/src/docbook/css directories
286
287Affymetrix Fusion SDK
288---------------------
289Package for reading various Affymetrix file formats. We use a modified
290version that for some file formats can read from an InputStream instead
291of from a File object. This avoids a lot of copying and decompressing.
292
293More info: http://www.affymetrix.com/support/developer/fusion/index.affx
294         : (original version)
295         : http://dev.thep.lu.se/basehacks/wiki/AffxFusion
296         : (modified version)
297Version  : 1.09
298License  : LGPL (lgpl.txt)
299Files    : AffxFusion.jar
300
301TAR file support
302----------------
303Package for reading and writing TAR files.
304
305More info: http://www.trustice.com/java/tar/
306Version  : 2.5
307License  : tar.license.txt
308Files    : tar.jar
309
310BZIP file support
311-----------------
312Package for reading and writing BZIP files.
313
314More info: http://www.kohsuke.org/bzip2/
315Version  : unknown
316License  : Apache software license (apache.license.txt)
317Files    : bzip2.jar
318
319Axis2
320-----
321A core engine for webservices from Apache.
322
323More info : http://ws.apache.org/axis2/
324Version   : 1.3
325License   : Apache License 2.0 (apache.license-2.0.txt)
326Files     : Everything in the /lib/webservices directory
327
328SecondString
329------------
330A package with some fuzzy string matching algorithms developed
331by researchers at Carnegie Mellon University.
332
333More info : http://secondstring.sourceforge.net/
334Version   : CVS trunk checkout (2008-08-25)
335License   : University of Illinois/NCSA Open Source (secondstring-LICENSE.txt)
336Files     : secondstring.jar
337
338
339jsDraw2D
340--------
341A vector graphics package for JavaScript.
342
343More info : http://jsdraw2d.jsfiction.com/
344Version   : 1.1.0
345License   : LGPL v3
346Files     : www/include/scripts/js-draw.js
347
348JavaSysMon
349----------
350A library for accessing CPU and memory information on some selected
351operating systems (including Linux, Windows and Mac OSX). It uses
352native libraries targeted for each platform
353
354More info : http://github.com/jezhumble/javasysmon
355Version   : 0.3.1
356License   : javasysmon-LICENSE.txt
357Files     : javasysmon-0.3.1.jar
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