source: trunk/doc/3rd-party-components.txt @ 7509

Last change on this file since 7509 was 7509, checked in by Nicklas Nordborg, 4 years ago

References #2129: Preparations for Java 11 support

Updated Javassist to version 3.23.1 and PostgreSQL JDBC driver to version 42.2.5.

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1==================================================================
2$Id: 3rd-party-components.txt 7509 2018-11-01 07:32:04Z 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
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   : 5.2.10
43License   : LGPL (hibernate.license.txt)
44Jar files : hibernate-core-5.2.10.Final.jar, hibernate-commons-annotations-5.0.1.Final.jar,
45            hibernate-jpa-2.1-api-1.0.0.Final.jar,
46            antlr-2.7.7.jar, dom4j-1.6.1.jar, jandex-2.0.3.Final.jar,
47            javassist-3.23.1-GA.jar, classmate-1.3.0.jar
48            jboss-logging-3.3.0.Final.jar, jboss-transaction-api_1.2_spec-1.0.1.Final.jar,
49            c3p0-0.9.5.2.jar, hibernate-c3p0-5.2.10.Final.jar, mchange-commons-java-0.2.11.jar,
50            ehcache-2.10.3.jar, hibernate-ehcache-5.2.10.Final.jar,
51            slf4j-api.1.7.25.jar, slf4j-log4j12-1.7.25.jar
52
53Note: Most of the jar files above are other 3rd-party components used by Hibernate.
54BASE doesn't use these components directly.
55
56Log4j
57-----
58A logging system that makes it easy to turn on or off debugging just by
59editing a configuration file.
60
61More info : http://logging.apache.org/log4j/1.2/index.html
62Version   : 1.2.17
63License   : Apache License 2.0 (apache.license-2.0.txt)
64Jar files : log4j-1.2.17.jar
65
66
67JDOM
68----
69A library for parsing and generating XML files.
70
71More info : http://www.jdom.org/
72Version   : 2.0.6
73License   : Apache-style open source license (jdom.license.txt)
74Jar files : jdom-2.0.6.jar, jaxen-1.1.6.jar
75
76
77Xerces
78------
79A toolkit for handling XML documents. From the Apache Software
80Foundation. These libraries are also needed by JDOM.
81
82More info : http://xml.apache.org/xerces2-j/index.html
83Version   : 2.11.0
84License   : Apache Software License (xerces.license.txt)
85Jar files : xerces-2.11.0.jar, xml-apis.jar
86
87
88Java Advanced Imaging (JAI)
89---------------------------
90An image toolkit from SUN. The package consists of a few jar files and
91libraries for native code for different operating systems. At the moment
92we are only using the jar files but we must also distribute the native
93code libraries in order to follow the license.
94
95More info : http://www.oracle.com/technetwork/java/current-142188.html
96Version   : 1.1.3
97License   : Sun Microsystems Binary Code License (jai.license.txt)
98Jar files : jai_core.jar, jai_codec.jar
99
100
101Java Servlet API
102----------------
103Required for creating servlets and tag libraries. This
104library is only required for compiling and are not included in the
105distribution. The web server/servlet container should already have
106these API installed. We use files from the Tomcat 8 distribution.
107
108More info : http://tomcat.apache.org/whichversion.html
109Version   : 3.1
110License   : N/A
111Jar files : jsp-api.jar, servlet-api.jar
112
113
114MySQL Connector/J
115-----------------
116A JDBC driver for the MySQL database from MySQL. This library is only
117needed if you are using MySQL as your database.
118
119More info : http://www.mysql.com/products/connector/
120Version   : 5.1.35
121License   : GPLv2 (gpl-2.license.txt)
122Jar files : mysql-connector-java-5.1.35-bin.jar
123
124
125PostgreSQL JDBC driver
126----------------------
127A JDBC driver for the PostgreSQL database. This library is only
128needed if you are using PostgreSQL as your database.
129
130More info : http://jdbc.postgresql.org/
131Version   : 42.2.5
132License   : BSD License (postgres.license.txt)
133Jar files : postgresql-42.2.5.jar
134
135
136X-Doclet
137--------
138Used at compile-time only to generate the XML files needed by
139Hibernate for the database mapping. These libraries are not included in
140the distribution.
141
142More info : http://xdoclet.sourceforge.net/xdoclet/index.html
143Version   : 1.2
144License   : XDoclet License (xdoclet.license.txt)
145Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar,
146            xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar,
147            commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
148
149
150Java Math Expression Parser
151---------------------------
152Parses and evaluates mathematical expressions in string. Supports
153most operators and funcations as well as variables.
154
155More info : http://www.singularsys.com/jep/
156Version   : 2.4.0
157License   : GPLv2 (gpl-2.license.txt)
158Jar files : jep-2.4.0.jar
159
160
161JFreeChart
162----------
163Plotting package for bar charts, line charts, pie charts and xy plots.
164
165More info : http://www.jfree.org/jfreechart/
166Version   : 1.0.19
167License   : LGPL (lgpl.txt)
168Jar files : jfreechart-1.0.19.jar jcommon-1.0.23.jar
169
170
171Apache HttpComponents
172---------------------
173Package for doing work with HTTP (eg. downloading files).
174
175More info : http://hc.apache.org/
176Version   : 4.4.1
177License   : Apache License 2.0 (apache.license-2.0.txt)
178Jar files : httpclient-4.4.1.jar, httpcore-4.4.1.jar, commons-codec-1.9.jar,
179            commons-logging-1.2.jar
180
181Apache Commons Email
182---------------------
183Package for sending email. Depends on JavaMail 1.5.
184
185More info : http://commons.apache.org/email/
186Version   : 1.3.3
187License   : Apache License 2.0 (apache.license-2.0.txt)
188Jar files : commons-email-1.3.3.jar
189
190
191JavaMail
192---------
193Low-level package for sending email. Used by Apache commons email.
194
195More info : https://java.net/projects/javamail/pages/Home
196Version   : 1.5.3
197License   : Common Development and Distribution License (CDDL) v1.1 and GNU General Public License (GPL) v2 with Classpath Exception (javax-mail-LICENSE.txt)
198Jar files : javax-mail-1.5.3.jar
199
200
201jBCrypt
202-------
203Package for safe encryption of passwords using the 'bcrypt' algorithm.
204
205More info : http://www.mindrot.org/projects/jBCrypt/
206Version   : 0.4
207License   : ISC/BSD licence (jbcrypt-license.txt)
208Jar files : None. Distributed as source only. All code is in net/sf/basedb/util/bcrypt/BCrypt.java
209
210
211BouncyCastle
212------------
213Cryptographic provider package
214
215More info : https://www.bouncycastle.org/java.html
216Version   : 159
217License   : bcp-license.txt
218Jar files : bcpkix-jdk15on-159.jar, bcprov-jdk15on-159.jar, bctls-jdk15on-159.jar, eddsa-0.2.0-jar
219
220
221JSON.simple
222-----------
223JSON.simple is a simple Java toolkit for JSON. You can use JSON.simple to encode or decode JSON text.
224
225More info : http://code.google.com/p/json-simple/
226Version   : 1.1.1
227License   : Apache License 2.0 (apache.license-2.0.txt)
228Jar files : json-simple-1.1.1.jar
229
230
231Silk icon set
232-------------
233A very nice icon set containing 1000 icons. The entire icon set
234is available in the "misc" directory. We have converted the icons
235to GIF format (since we didn't want to scan through all web pages
236and replace .gif with .png). We have also created some new icons which
237are merely combinations of other icons, ie. taking an arrow on one icon
238an putting it on another.
239
240More info : http://www.famfamfam.com/lab/icons/silk/
241Version   : 1.3
242License   : Creative Commons Attribution 2.5 License
243            (http://creativecommons.org/licenses/by/2.5/)
244
245
246SvnAnt
247------
248An 'ant' task implementation for accessing subversion from the ant buildfile.
249
250More info : http://subclipse.tigris.org/svnant.html
251Version   : 1.4-dev (http://subclipse.tigris.org/svn/subclipse/trunk/svnant@5584)
252License   : Apache Software License 1.1 (apache.license.txt)
253Jar files : Everything in lib/svn/
254
255
256Docbook
257-------
258A set of DTD:s and stylesheets for creating documentation. We use
259the DocBook styler suite (see below) but has upgraded it to Docbook 4.5.
260
261More info: http://www.docbook.org/
262Version  : 4.5
263License  : docbook.license.txt
264Files    : Everything in lib/docbook/docbook and dist/commons-logging-1.1.jar
265
266
267Docbook styler guide
268--------------------
269An extension to docbook created by Dawid Weiss which simplifies
270file inclusion and building from ant.
271
272More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en
273Version  : 2004_06_22-21_12
274License  : docbook.styler.guide.txt
275Files    : Everything in lib/docbook except the 'docbook' subdirectory
276
277Example code syntax highlighter
278-------------------------------
279A javascript library that can be used to dynamically highlight
280the syntax in program examples. We have made minor changes to
281make it support the HTML produced by Docbook (ie. find the language
282from the 'language' attribute instead of the 'class' attribute).
283
284More info: http://alexgorbatchev.com/SyntaxHighlighter/
285Version  : 1.5.1
286License  : LGPL (lgpl.txt)
287Files    : Everything in the /doc/src/docbook/script and
288           /doc/src/docbook/css directories
289
290Affymetrix Fusion SDK
291---------------------
292Package for reading various Affymetrix file formats. We use a modified
293version that for some file formats can read from an InputStream instead
294of from a File object. This avoids a lot of copying and decompressing.
295
296More info: http://www.affymetrix.com/support/developer/fusion/index.affx
297         : (original version)
298         : http://dev.thep.lu.se/basehacks/wiki/AffxFusion
299         : (modified version)
300Version  : 1.09
301License  : LGPL (lgpl.txt)
302Files    : AffxFusion.jar
303
304TAR file support
305----------------
306Package for reading and writing TAR files.
307
308More info: http://www.trustice.com/java/tar/
309Version  : 2.5
310License  : tar.license.txt
311Files    : tar.jar
312
313BZIP file support
314-----------------
315Package for reading and writing BZIP files.
316
317More info: http://www.kohsuke.org/bzip2/
318Version  : unknown
319License  : Apache software license (apache.license.txt)
320Files    : bzip2.jar
321
322Parallel GZIP compression
323-------------------------
324Package for multi-threaded compression to GZIP format.
325
326More info: https://github.com/shevek/parallelgzip
327Version  : 1.0.5
328License  : Apache software license (parallelgzip-LICENSE.txt)
329Files    : parallelgzip-1.0.5.jar
330
331SecondString
332------------
333A package with some fuzzy string matching algorithms developed
334by researchers at Carnegie Mellon University.
335
336More info : http://secondstring.sourceforge.net/
337Version   : CVS trunk checkout (2008-08-25)
338License   : University of Illinois/NCSA Open Source (secondstring-LICENSE.txt)
339Files     : secondstring.jar
340
341
342jsDraw2D
343--------
344A vector graphics package for JavaScript.
345
346More info : http://jsdraw2d.jsfiction.com/
347Version   : 1.1.0
348License   : LGPL v3
349Files     : www/include/scripts/js-draw.js
350
351JavaSysMon
352----------
353A library for accessing CPU and memory information on some selected
354operating systems (including Linux, Windows and Mac OSX). It uses
355native libraries targeted for each platform
356
357More info : http://github.com/jezhumble/javasysmon
358Version   : 0.3.5
359License   : javasysmon-LICENSE.txt
360Files     : javasysmon-0.3.5.jar
361
362Yauaa: Yet Another UserAgent Analyzer
363-------------------------------------
364A library for extracting information from the User-Agent header sent
365by browsers.
366
367More info : https://github.com/nielsbasjes/yauaa
368Version   : 2.2
369License   : Apache License, Version 2.0 (yauaa-LICENSE.txt)
370Files     : yauaa-2.2.jar, snakeyaml-1.18.jar, commons-collections4-4.1.jar
371            commons-lang3-3.6.jar
372
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