source: trunk/doc/3rd-party-components.txt @ 7821

Last change on this file since 7821 was 7821, checked in by Nicklas Nordborg, 17 months ago

References #2214: Upgrade Hibernate and other 3-rd party components

Updated PostgreSQL JDBC driver to 42.2.13.

  • Property svn:eol-style set to native
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File size: 12.3 KB
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1==================================================================
2$Id: 3rd-party-components.txt 7821 2020-06-08 08:56:09Z 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   : 5.4.17
43License   : LGPL (hibernate.license.txt)
44Jar files : hibernate-core-5.4.17.Final.jar, hibernate-commons-annotations-5.1.0.Final.jar,
45            javax.persistence-api-2.2.jar,
46            antlr-2.7.7.jar, dom4j-2.1.3.jar, jandex-2.1.3.Final.jar,
47            javassist-3.24.0-GA.jar, byte-buddy-1.10.10.jar, classmate-1.5.1.jar
48            jboss-logging-3.3.2.Final.jar, jboss-transaction-api_1.2_spec-1.1.1.Final.jar,
49            c3p0-0.9.5.3.jar, hibernate-c3p0-5.4.17.Final.jar, mchange-commons-java-0.2.15.jar,
50            ehcache-2.10.6.jar, hibernate-ehcache-5.4.17.Final.jar,
51            slf4j-api.1.7.25.jar, slf4j-log4j12-1.7.25.jar,
52            FastInfoset-1.2.15.jar, istack-commons-runtime-3.0.7.jar, stax-ex-1.8.jar,
53            txw2-2.3.1.jar
54
55Note: Most of the jar files above are other 3rd-party components used by Hibernate.
56BASE doesn't use these components directly.
57
58Log4j
59-----
60A logging system that makes it easy to turn on or off debugging just by
61editing a configuration file.
62
63More info : http://logging.apache.org/log4j/1.2/index.html
64Version   : 1.2.17
65License   : Apache License 2.0 (apache.license-2.0.txt)
66Jar files : log4j-1.2.17.jar
67
68
69JDOM
70----
71A library for parsing and generating XML files.
72
73More info : http://www.jdom.org/
74Version   : 2.0.6
75License   : Apache-style open source license (jdom.license.txt)
76Jar files : jdom-2.0.6.jar, jaxen-1.1.6.jar
77
78
79Xerces
80------
81A toolkit for handling XML documents. From the Apache Software
82Foundation. These libraries are also needed by JDOM.
83
84More info : http://xml.apache.org/xerces2-j/index.html
85Version   : 2.11.0
86License   : Apache Software License (xerces.license.txt)
87Jar files : xerces-2.11.0.jar, xml-apis.jar
88
89
90Java Servlet API
91----------------
92Required for creating servlets and tag libraries. This
93library is only required for compiling and are not included in the
94distribution. The web server/servlet container should already have
95these API installed. We use files from the Tomcat 9 distribution.
96
97More info : http://tomcat.apache.org/whichversion.html
98Version   : 4.0
99License   : N/A
100Jar files : jsp-api.jar, servlet-api.jar
101
102
103MySQL Connector/J
104-----------------
105A JDBC driver for the MySQL database from MySQL. This library is only
106needed if you are using MySQL as your database.
107
108More info : http://www.mysql.com/products/connector/
109Version   : 8.0.13
110License   : GPLv2 (mysql-connector-LICENSE.txt)
111Jar files : mysql-connector-java-8.0.13.jar
112
113
114PostgreSQL JDBC driver
115----------------------
116A JDBC driver for the PostgreSQL database. This library is only
117needed if you are using PostgreSQL as your database.
118
119More info : http://jdbc.postgresql.org/
120Version   : 42.2.13
121License   : BSD License (postgres.license.txt)
122Jar files : postgresql-42.2.13.jar
123
124
125X-Doclet
126--------
127Used at compile-time only to generate the XML files needed by
128Hibernate for the database mapping. These libraries are not included in
129the distribution.
130
131More info : http://xdoclet.sourceforge.net/xdoclet/index.html
132Version   : 1.2
133License   : XDoclet License (xdoclet.license.txt)
134Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar,
135            xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar,
136            commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
137
138
139Java Math Expression Parser
140---------------------------
141Parses and evaluates mathematical expressions in string. Supports
142most operators and funcations as well as variables.
143
144More info : http://www.singularsys.com/jep/
145Version   : 2.4.0
146License   : GPLv2 (gpl-2.license.txt)
147Jar files : jep-2.4.0.jar
148
149
150JFreeChart
151----------
152Plotting package for bar charts, line charts, pie charts and xy plots.
153
154More info : http://www.jfree.org/jfreechart/
155Version   : 1.0.19
156License   : LGPL (lgpl.txt)
157Jar files : jfreechart-1.0.19.jar jcommon-1.0.23.jar
158
159
160Apache HttpComponents
161---------------------
162Package for doing work with HTTP (eg. downloading files).
163
164More info : http://hc.apache.org/
165Version   : 4.5.6 and 4.4.10
166License   : Apache License 2.0 (apache.license-2.0.txt)
167Jar files : httpclient-4.5.6.jar, httpcore-4.4.10.jar, commons-codec-1.10.jar,
168            commons-logging-1.2.jar
169
170Apache Commons Email
171---------------------
172Package for sending email. Depends on JavaMail.
173
174More info : http://commons.apache.org/email/
175Version   : 1.5
176License   : Apache License 2.0 (apache.license-2.0.txt)
177Jar files : commons-email-1.5.jar
178
179
180JavaMail
181---------
182Low-level package for sending email. Used by Apache commons email.
183
184More info : https://javaee.github.io/javamail/
185Version   : 1.6.2
186License   : Common Development and Distribution License (CDDL) v1.1 and GNU General Public License (GPL) v2 with Classpath Exception (javax-mail-LICENSE.txt)
187Jar files : javax-mail-1.6.2.jar, jakarta.activation-1.2.1.jar
188
189Apache Commons Collections 4
190----------------------------
191Package for working with collections.
192
193More info : https://commons.apache.org/proper/commons-collections/
194Version   : 4.2
195License   : Apache License 2.0 (apache.license-2.0.txt)
196Jar files : commons-collections4-4.2.jar
197
198jBCrypt
199-------
200Package for safe encryption of passwords using the 'bcrypt' algorithm.
201
202More info : http://www.mindrot.org/projects/jBCrypt/
203Version   : 0.4
204License   : ISC/BSD licence (jbcrypt-license.txt)
205Jar files : None. Distributed as source only. All code is in net/sf/basedb/util/bcrypt/BCrypt.java
206
207
208BouncyCastle
209------------
210Cryptographic provider package
211
212More info : https://www.bouncycastle.org/java.html
213Version   : 160
214License   : bcp-license.txt
215Jar files : bcpkix-jdk15on-160.jar, bcprov-jdk15on-160.jar, bctls-jdk15on-160.jar, eddsa-0.3.0-jar
216
217
218JSON.simple
219-----------
220JSON.simple is a simple Java toolkit for JSON. You can use JSON.simple to encode or decode JSON text.
221We use a modified version that uses Java generics instead of raw object types.
222
223More info: http://code.google.com/p/json-simple/
224         : (original version)
225         : ​http://dev.thep.lu.se/basehacks/wiki/JSON.simple
226         : (modified version)
227Version   : 1.1.1-1
228License   : Apache License 2.0 (apache.license-2.0.txt)
229Jar files : json-simple-1.1.1-1.jar
230
231
232Silk icon set
233-------------
234A very nice icon set containing 1000 icons. The entire icon set
235is available in the "misc" directory. We have converted the icons
236to GIF format (since we didn't want to scan through all web pages
237and replace .gif with .png). We have also created some new icons which
238are merely combinations of other icons, ie. taking an arrow on one icon
239an putting it on another.
240
241More info : http://www.famfamfam.com/lab/icons/silk/
242Version   : 1.3
243License   : Creative Commons Attribution 2.5 License
244            (http://creativecommons.org/licenses/by/2.5/)
245
246
247SvnAnt
248------
249An 'ant' task implementation for accessing subversion from the ant buildfile.
250
251More info : http://subclipse.tigris.org/svnant.html
252Version   : 1.4-dev (http://subclipse.tigris.org/svn/subclipse/trunk/svnant@5584)
253License   : Apache Software License 1.1 (apache.license.txt)
254Jar files : Everything in lib/svn/
255
256
257Docbook
258-------
259A set of DTD:s and stylesheets for creating documentation. We use
260the DocBook styler suite (see below) but has upgraded it to Docbook 4.5.
261
262More info: http://www.docbook.org/
263Version  : 4.5
264License  : docbook.license.txt
265Files    : Everything in lib/docbook/docbook and dist/commons-logging-1.1.jar
266
267
268Docbook styler guide
269--------------------
270An extension to docbook created by Dawid Weiss which simplifies
271file inclusion and building from ant.
272
273More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en
274Version  : 2004_06_22-21_12
275License  : docbook.styler.guide.txt
276Files    : Everything in lib/docbook except the 'docbook' subdirectory
277
278Example code syntax highlighter
279-------------------------------
280A javascript library that can be used to dynamically highlight
281the syntax in program examples. We have made minor changes to
282make it support the HTML produced by Docbook (ie. find the language
283from the 'language' attribute instead of the 'class' attribute).
284
285More info: http://alexgorbatchev.com/SyntaxHighlighter/
286Version  : 1.5.1
287License  : LGPL (lgpl.txt)
288Files    : Everything in the /doc/src/docbook/script and
289           /doc/src/docbook/css directories
290
291Affymetrix Fusion SDK
292---------------------
293Package for reading various Affymetrix file formats. We use a modified
294version that for some file formats can read from an InputStream instead
295of from a File object. This avoids a lot of copying and decompressing.
296
297More info: http://www.affymetrix.com/support/developer/fusion/index.affx
298         : (original version)
299         : http://dev.thep.lu.se/basehacks/wiki/AffxFusion
300         : (modified version)
301Version  : 1.09
302License  : LGPL (lgpl.txt)
303Files    : AffxFusion.jar
304
305TAR file support
306----------------
307Package for reading and writing TAR files.
308
309More info: http://www.trustice.com/java/tar/
310Version  : 2.5
311License  : tar.license.txt
312Files    : tar.jar
313
314BZIP file support
315-----------------
316Package for reading and writing BZIP files.
317
318More info: http://www.kohsuke.org/bzip2/
319Version  : unknown
320License  : Apache software license (apache.license.txt)
321Files    : bzip2.jar
322
323Parallel GZIP compression
324-------------------------
325Package for multi-threaded compression to GZIP format.
326
327More info: https://github.com/shevek/parallelgzip
328Version  : 1.0.5
329License  : Apache software license (parallelgzip-LICENSE.txt)
330Files    : parallelgzip-1.0.5.jar
331
332SecondString
333------------
334A package with some fuzzy string matching algorithms developed
335by researchers at Carnegie Mellon University.
336
337More info : http://secondstring.sourceforge.net/
338Version   : CVS trunk checkout (2008-08-25)
339License   : University of Illinois/NCSA Open Source (secondstring-LICENSE.txt)
340Files     : secondstring.jar
341
342
343jsDraw2D
344--------
345A vector graphics package for JavaScript.
346
347More info : http://jsdraw2d.jsfiction.com/
348Version   : 1.1.0
349License   : LGPL v3
350Files     : www/include/scripts/js-draw.js
351
352JavaSysMon
353----------
354A library for accessing CPU and memory information on some selected
355operating systems (including Linux, Windows and Mac OSX). It uses
356native libraries targeted for each platform
357
358More info : http://github.com/jezhumble/javasysmon
359Version   : 0.3.5
360License   : javasysmon-LICENSE.txt
361Files     : javasysmon-0.3.5.jar
362
363Yauaa: Yet Another UserAgent Analyzer
364-------------------------------------
365A library for extracting information from the User-Agent header sent
366by browsers.
367
368More info : https://github.com/nielsbasjes/yauaa
369Version   : 5.17
370License   : Apache License, Version 2.0 (yauaa-LICENSE.txt)
371Files     : yauaa-5.17.jar, prefixmap-1.1.jar, commons-lang3-3.10.jar, kryo-4.0.2.jar
372
373Apache POI
374----------
375A library for reading and writing Excel (and other Microsoft Office)
376files.
377
378More info : https://poi.apache.org/
379Version   : 4.0.1
380License   : Apache License, Version 2.0 (poi-license.txt)
381Files     : poi-4.0.1.jar, poi-ooxml-4.0.1.jar, poi-ooxml-schemas-4.0.1.jar
382            commons-compress-1.18.jar, commons-math3-3.6.1.jar, xmlbeans-3.0.1.jar
383
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