source: trunk/doc/3rd-party-components.txt @ 7328

Last change on this file since 7328 was 7328, checked in by Nicklas Nordborg, 5 years ago

References #2073: Update JDBC driver for PostgreSQL

Noted the change in driver version.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 11.7 KB
Line 
1==================================================================
2$Id: 3rd-party-components.txt 7328 2017-04-06 09:48:24Z 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   : 5.0.7
43License   : LGPL (hibernate.license.txt)
44Jar files : hibernate-core-5.0.7.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-2.0.0.Final.jar,
47            javassist-3.18.1-GA.jar, jboss-logging-3.3.0.Final.jar,
48            c3p0-0.9.5-pre8.jar, hibernate-c3p0-5.0.7.Final.jar, mchange-commons-java-0.2.7.jar,
49            hibernate-ehcache-5.0.7.Final.jar, slf4j-api.1.6.4.jar, slf4j-log4j12-1.6.4.jar,
50            geronimo-jta_1.1_spec-1.1.1.jar
51
52Note: Most of the jar files above are other 3rd-party components used by Hibernate.
53BASE doesn't use these components directly.
54
55Ehcahce
56-------
57Used by Hibernate for caching entities and query results. Is no
58longer part of the main Hibernate distribution.
59
60More info : http://ehcache.org/
61Version   : 2.6.3
62License   : Apache License 2.0 (apache.license-2.0.txt)
63Jar files : ehcache-core-2.6.3.jar
64
65
66Log4j
67-----
68A logging system that makes it easy to turn on or off debugging just by
69editing a configuration file.
70
71More info : http://logging.apache.org/log4j/1.2/index.html
72Version   : 1.2.17
73License   : Apache License 2.0 (apache.license-2.0.txt)
74Jar files : log4j-1.2.17.jar
75
76JDOM
77----
78A library for parsing and generating XML files.
79
80More info : http://www.jdom.org/
81Version   : 2.0.6
82License   : Apache-style open source license (jdom.license.txt)
83Jar files : jdom-2.0.6.jar, jaxen-1.1.6.jar
84
85
86Xerces
87------
88A toolkit for handling XML documents. From the Apache Software
89Foundation. These libraries are also needed by JDOM.
90
91More info : http://xml.apache.org/xerces2-j/index.html
92Version   : 2.11.0
93License   : Apache Software License (xerces.license.txt)
94Jar files : xerces-2.11.0.jar, xml-apis.jar
95
96
97Java Advanced Imaging (JAI)
98---------------------------
99An image toolkit from SUN. The package consists of a few jar files and
100libraries for native code for different operating systems. At the moment
101we are only using the jar files but we must also distribute the native
102code libraries in order to follow the license.
103
104More info : http://www.oracle.com/technetwork/java/current-142188.html
105Version   : 1.1.3
106License   : Sun Microsystems Binary Code License (jai.license.txt)
107Jar files : jai_core.jar, jai_codec.jar
108
109
110Java Servlet API
111----------------
112Required for creating servlets and tag libraries. This
113library is only required for compiling and are not included in the
114distribution. The web server/servlet container should already have
115these API installed. We use files from the Tomcat 8 distribution.
116
117More info : http://tomcat.apache.org/whichversion.html
118Version   : 3.1
119License   : N/A
120Jar files : jsp-api.jar, servlet-api.jar
121
122
123MySQL Connector/J
124-----------------
125A JDBC driver for the MySQL database from MySQL. This library is only
126needed if you are using MySQL as your database.
127
128More info : http://www.mysql.com/products/connector/
129Version   : 5.1.35
130License   : GPLv2 (gpl-2.license.txt)
131Jar files : mysql-connector-java-5.1.35-bin.jar
132
133
134PostgreSQL JDBC driver
135----------------------
136A JDBC driver for the PostgreSQL database. This library is only
137needed if you are using PostgreSQL as your database.
138
139More info : http://jdbc.postgresql.org/
140Version   : 42.0.0
141License   : BSD License (postgres.license.txt)
142Jar files : postgresql-42.0.0.jar
143
144
145X-Doclet
146--------
147Used at compile-time only to generate the XML files needed by
148Hibernate for the database mapping. These libraries are not included in
149the distribution.
150
151More info : http://xdoclet.sourceforge.net/xdoclet/index.html
152Version   : 1.2
153License   : XDoclet License (xdoclet.license.txt)
154Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar,
155            xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar,
156            commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
157
158
159Java Math Expression Parser
160---------------------------
161Parses and evaluates mathematical expressions in string. Supports
162most operators and funcations as well as variables.
163
164More info : http://www.singularsys.com/jep/
165Version   : 2.4.0
166License   : GPLv2 (gpl-2.license.txt)
167Jar files : jep-2.4.0.jar
168
169
170JFreeChart
171----------
172Plotting package for bar charts, line charts, pie charts and xy plots.
173
174More info : http://www.jfree.org/jfreechart/
175Version   : 1.0.19
176License   : LGPL (lgpl.txt)
177Jar files : jfreechart-1.0.19.jar jcommon-1.0.23.jar
178
179
180Apache HttpComponents
181---------------------
182Package for doing work with HTTP (eg. downloading files).
183
184More info : http://hc.apache.org/
185Version   : 4.4.1
186License   : Apache License 2.0 (apache.license-2.0.txt)
187Jar files : httpclient-4.4.1.jar, httpcore-4.4.1.jar, commons-codec-1.9.jar,
188            commons-logging-1.2.jar
189
190Apache Commons Email
191---------------------
192Package for sending email. Depends on JavaMail 1.5.
193
194More info : http://commons.apache.org/email/
195Version   : 1.3.3
196License   : Apache License 2.0 (apache.license-2.0.txt)
197Jar files : commons-email-1.3.3.jar
198
199
200JavaMail
201---------
202Low-level package for sending email. Used by Apache commons email.
203
204More info : https://java.net/projects/javamail/pages/Home
205Version   : 1.5.3
206License   : Common Development and Distribution License (CDDL) v1.1 and GNU General Public License (GPL) v2 with Classpath Exception (javax-mail-LICENSE.txt)
207Jar files : javax-mail-1.5.3.jar
208
209
210jBCrypt
211-------
212Package for safe encryption of passwords using the 'bcrypt' algorithm.
213
214More info : http://www.mindrot.org/projects/jBCrypt/
215Version   : 0.4
216License   : ISC/BSD licence (jbcrypt-license.txt)
217Jar files : None. Distributed as source only. All code is in net/sf/basedb/util/bcrypt/BCrypt.java
218
219JSON.simple
220-----------
221JSON.simple is a simple Java toolkit for JSON. You can use JSON.simple to encode or decode JSON text.
222
223More info : http://code.google.com/p/json-simple/
224Version   : 1.1.1
225License   : Apache License 2.0 (apache.license-2.0.txt)
226Jar files : json-simple-1.1.1.jar
227
228
229Silk icon set
230-------------
231A very nice icon set containing 1000 icons. The entire icon set
232is available in the "misc" directory. We have converted the icons
233to GIF format (since we didn't want to scan through all web pages
234and replace .gif with .png). We have also created some new icons which
235are merely combinations of other icons, ie. taking an arrow on one icon
236an putting it on another.
237
238More info : http://www.famfamfam.com/lab/icons/silk/
239Version   : 1.3
240License   : Creative Commons Attribution 2.5 License
241            (http://creativecommons.org/licenses/by/2.5/)
242
243
244SvnAnt
245------
246An 'ant' task implementation for accessing subversion from the ant buildfile.
247
248More info : http://subclipse.tigris.org/svnant.html
249Version   : 1.4-dev (http://subclipse.tigris.org/svn/subclipse/trunk/svnant@5584)
250License   : Apache Software License 1.1 (apache.license.txt)
251Jar files : Everything in lib/svn/
252
253
254Docbook
255-------
256A set of DTD:s and stylesheets for creating documentation. We use
257the DocBook styler suite (see below) but has upgraded it to Docbook 4.5.
258
259More info: http://www.docbook.org/
260Version  : 4.5
261License  : docbook.license.txt
262Files    : Everything in lib/docbook/docbook and dist/commons-logging-1.1.jar
263
264
265Docbook styler guide
266--------------------
267An extension to docbook created by Dawid Weiss which simplifies
268file inclusion and building from ant.
269
270More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en
271Version  : 2004_06_22-21_12
272License  : docbook.styler.guide.txt
273Files    : Everything in lib/docbook except the 'docbook' subdirectory
274
275Example code syntax highlighter
276-------------------------------
277A javascript library that can be used to dynamically highlight
278the syntax in program examples. We have made minor changes to
279make it support the HTML produced by Docbook (ie. find the language
280from the 'language' attribute instead of the 'class' attribute).
281
282More info: http://alexgorbatchev.com/SyntaxHighlighter/
283Version  : 1.5.1
284License  : LGPL (lgpl.txt)
285Files    : Everything in the /doc/src/docbook/script and
286           /doc/src/docbook/css directories
287
288Affymetrix Fusion SDK
289---------------------
290Package for reading various Affymetrix file formats. We use a modified
291version that for some file formats can read from an InputStream instead
292of from a File object. This avoids a lot of copying and decompressing.
293
294More info: http://www.affymetrix.com/support/developer/fusion/index.affx
295         : (original version)
296         : http://dev.thep.lu.se/basehacks/wiki/AffxFusion
297         : (modified version)
298Version  : 1.09
299License  : LGPL (lgpl.txt)
300Files    : AffxFusion.jar
301
302TAR file support
303----------------
304Package for reading and writing TAR files.
305
306More info: http://www.trustice.com/java/tar/
307Version  : 2.5
308License  : tar.license.txt
309Files    : tar.jar
310
311BZIP file support
312-----------------
313Package for reading and writing BZIP files.
314
315More info: http://www.kohsuke.org/bzip2/
316Version  : unknown
317License  : Apache software license (apache.license.txt)
318Files    : bzip2.jar
319
320Parallel GZIP compression
321-------------------------
322Package for multi-threaded compression to GZIP format.
323Modified to fix issue with files > 2GB. Source is included
324with the BASE core code.
325
326More info: https://github.com/shevek/parallelgzip
327         : http://base.thep.lu.se/ticket/2006
328         : http://base.thep.lu.se/ticket/2016
329Version  : 1.0.1
330License  : Apache software license (parallelgzip-LICENSE.txt)
331Files    : None. Distributed as source only. All code is in org/anarres/parallelgzip package.
332
333SecondString
334------------
335A package with some fuzzy string matching algorithms developed
336by researchers at Carnegie Mellon University.
337
338More info : http://secondstring.sourceforge.net/
339Version   : CVS trunk checkout (2008-08-25)
340License   : University of Illinois/NCSA Open Source (secondstring-LICENSE.txt)
341Files     : secondstring.jar
342
343
344jsDraw2D
345--------
346A vector graphics package for JavaScript.
347
348More info : http://jsdraw2d.jsfiction.com/
349Version   : 1.1.0
350License   : LGPL v3
351Files     : www/include/scripts/js-draw.js
352
353JavaSysMon
354----------
355A library for accessing CPU and memory information on some selected
356operating systems (including Linux, Windows and Mac OSX). It uses
357native libraries targeted for each platform
358
359More info : http://github.com/jezhumble/javasysmon
360Version   : 0.3.5
361License   : javasysmon-LICENSE.txt
362Files     : javasysmon-0.3.5.jar
Note: See TracBrowser for help on using the repository browser.