source: branches/hibernate-5.2/doc/3rd-party-components.txt @ 7362

Last change on this file since 7362 was 7362, checked in by Nicklas Nordborg, 5 years ago

References #2084: Upgrade to Hibernate 5.2

Replaced old JAR files with new versions. Causes 131 compile errors and 1477 warnings.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 11.5 KB
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1==================================================================
2$Id: 3rd-party-components.txt 7362 2017-05-16 06:47:12Z 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-3.20.0-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   : 42.0.0
132License   : BSD License (postgres.license.txt)
133Jar files : postgresql-42.0.0.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
210JSON.simple
211-----------
212JSON.simple is a simple Java toolkit for JSON. You can use JSON.simple to encode or decode JSON text.
213
214More info : http://code.google.com/p/json-simple/
215Version   : 1.1.1
216License   : Apache License 2.0 (apache.license-2.0.txt)
217Jar files : json-simple-1.1.1.jar
218
219
220Silk icon set
221-------------
222A very nice icon set containing 1000 icons. The entire icon set
223is available in the "misc" directory. We have converted the icons
224to GIF format (since we didn't want to scan through all web pages
225and replace .gif with .png). We have also created some new icons which
226are merely combinations of other icons, ie. taking an arrow on one icon
227an putting it on another.
228
229More info : http://www.famfamfam.com/lab/icons/silk/
230Version   : 1.3
231License   : Creative Commons Attribution 2.5 License
232            (http://creativecommons.org/licenses/by/2.5/)
233
234
235SvnAnt
236------
237An 'ant' task implementation for accessing subversion from the ant buildfile.
238
239More info : http://subclipse.tigris.org/svnant.html
240Version   : 1.4-dev (http://subclipse.tigris.org/svn/subclipse/trunk/svnant@5584)
241License   : Apache Software License 1.1 (apache.license.txt)
242Jar files : Everything in lib/svn/
243
244
245Docbook
246-------
247A set of DTD:s and stylesheets for creating documentation. We use
248the DocBook styler suite (see below) but has upgraded it to Docbook 4.5.
249
250More info: http://www.docbook.org/
251Version  : 4.5
252License  : docbook.license.txt
253Files    : Everything in lib/docbook/docbook and dist/commons-logging-1.1.jar
254
255
256Docbook styler guide
257--------------------
258An extension to docbook created by Dawid Weiss which simplifies
259file inclusion and building from ant.
260
261More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en
262Version  : 2004_06_22-21_12
263License  : docbook.styler.guide.txt
264Files    : Everything in lib/docbook except the 'docbook' subdirectory
265
266Example code syntax highlighter
267-------------------------------
268A javascript library that can be used to dynamically highlight
269the syntax in program examples. We have made minor changes to
270make it support the HTML produced by Docbook (ie. find the language
271from the 'language' attribute instead of the 'class' attribute).
272
273More info: http://alexgorbatchev.com/SyntaxHighlighter/
274Version  : 1.5.1
275License  : LGPL (lgpl.txt)
276Files    : Everything in the /doc/src/docbook/script and
277           /doc/src/docbook/css directories
278
279Affymetrix Fusion SDK
280---------------------
281Package for reading various Affymetrix file formats. We use a modified
282version that for some file formats can read from an InputStream instead
283of from a File object. This avoids a lot of copying and decompressing.
284
285More info: http://www.affymetrix.com/support/developer/fusion/index.affx
286         : (original version)
287         : http://dev.thep.lu.se/basehacks/wiki/AffxFusion
288         : (modified version)
289Version  : 1.09
290License  : LGPL (lgpl.txt)
291Files    : AffxFusion.jar
292
293TAR file support
294----------------
295Package for reading and writing TAR files.
296
297More info: http://www.trustice.com/java/tar/
298Version  : 2.5
299License  : tar.license.txt
300Files    : tar.jar
301
302BZIP file support
303-----------------
304Package for reading and writing BZIP files.
305
306More info: http://www.kohsuke.org/bzip2/
307Version  : unknown
308License  : Apache software license (apache.license.txt)
309Files    : bzip2.jar
310
311Parallel GZIP compression
312-------------------------
313Package for multi-threaded compression to GZIP format.
314Modified to fix issue with files > 2GB. Source is included
315with the BASE core code.
316
317More info: https://github.com/shevek/parallelgzip
318         : http://base.thep.lu.se/ticket/2006
319         : http://base.thep.lu.se/ticket/2016
320Version  : 1.0.1
321License  : Apache software license (parallelgzip-LICENSE.txt)
322Files    : None. Distributed as source only. All code is in org/anarres/parallelgzip package.
323
324SecondString
325------------
326A package with some fuzzy string matching algorithms developed
327by researchers at Carnegie Mellon University.
328
329More info : http://secondstring.sourceforge.net/
330Version   : CVS trunk checkout (2008-08-25)
331License   : University of Illinois/NCSA Open Source (secondstring-LICENSE.txt)
332Files     : secondstring.jar
333
334
335jsDraw2D
336--------
337A vector graphics package for JavaScript.
338
339More info : http://jsdraw2d.jsfiction.com/
340Version   : 1.1.0
341License   : LGPL v3
342Files     : www/include/scripts/js-draw.js
343
344JavaSysMon
345----------
346A library for accessing CPU and memory information on some selected
347operating systems (including Linux, Windows and Mac OSX). It uses
348native libraries targeted for each platform
349
350More info : http://github.com/jezhumble/javasysmon
351Version   : 0.3.5
352License   : javasysmon-LICENSE.txt
353Files     : javasysmon-0.3.5.jar
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