==================================================================
$Id: 3rd-party-components.txt 8144 2023-04-21 11:43:05Z nicklas $
Copyright (C) 2005 Johan Enell, Nicklas Nordborg
Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Gregory Vincic
Copyright (C) 2007 Johan Enell, Jari Häkkinen, Nicklas Nordborg
This file is part of BASE - BioArray Software Environment.
Available at http://base.thep.lu.se/
BASE is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 3
of the License, or (at your option) any later version.
BASE is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with BASE. If not, see .
==================================================================
=================================
3rd-party components used by BASE
=================================
Here is list of 3rd-party components used by BASE. All the jar files
needed are included in the /lib directory or in
/www/plugins sub-directories for plug-ins based on others
work. The URLs given here can be used if you need more information or
need to update some component.
Hibernate
---------
An object/relational persistence and query service for Java. Shields
us from most SQL and gives us database independece.
More info : http://www.hibernate.org/
Version : 5.5.6
License : LGPL (hibernate.license.txt)
Jar files : hibernate-core-5.6.15.Final.jar, hibernate-commons-annotations-5.1.2.Final.jar,
javax.persistence-api-2.2.jar,
antlr-2.7.7.jar, jandex-2.4.2.Final.jar,
byte-buddy-1.12.23.jar, classmate-1.5.1.jar
jboss-logging-3.4.3.Final.jar, jboss-transaction-api_1.2_spec-1.1.1.Final.jar,
c3p0-0.9.5.5.jar, hibernate-c3p0-5.6.15.Final.jar, mchange-commons-java-0.2.19.jar,
ehcache-2.10.6.jar, hibernate-ehcache-5.6.15.Final.jar,
slf4j-api.1.7.25.jar, slf4j-log4j12-1.7.25.jar,
FastInfoset-1.2.15.jar, istack-commons-runtime-3.0.7.jar, stax-ex-1.8.jar,
txw2-2.3.1.jar
Note: Most of the jar files above are other 3rd-party components used by Hibernate.
BASE doesn't use these components directly.
Log4j
-----
A logging system that makes it easy to turn on or off debugging just by
editing a configuration file.
More info : http://logging.apache.org/log4j/1.2/index.html
Version : 1.2.17
License : Apache License 2.0 (apache.license-2.0.txt)
Jar files : log4j-1.2.17.jar
JDOM
----
A library for parsing and generating XML files.
More info : http://www.jdom.org/
Version : 2.0.6
License : Apache-style open source license (jdom.license.txt)
Jar files : jdom-2.0.6.jar, jaxen-1.1.6.jar
Xerces
------
A toolkit for handling XML documents. From the Apache Software
Foundation. These libraries are also needed by JDOM.
More info : http://xml.apache.org/xerces2-j/index.html
Version : 2.11.0
License : Apache Software License (xerces.license.txt)
Jar files : xerces-2.11.0.jar, xml-apis.jar
Java Servlet API
----------------
Required for creating servlets and tag libraries. This
library is only required for compiling and are not included in the
distribution. The web server/servlet container should already have
these API installed. We use files from the Tomcat 9 distribution.
More info : http://tomcat.apache.org/whichversion.html
Version : 4.0
License : N/A
Jar files : jsp-api.jar, servlet-api.jar
MySQL Connector/J
-----------------
A JDBC driver for the MySQL database from MySQL. This library is only
needed if you are using MySQL as your database.
More info : https://dev.mysql.com/downloads/connector/j/
Version : 8.0.22
License : GPLv2 (mysql-connector-LICENSE.txt)
Jar files : mysql-connector-java-8.0.22.jar
PostgreSQL JDBC driver
----------------------
A JDBC driver for the PostgreSQL database. This library is only
needed if you are using PostgreSQL as your database.
More info : http://jdbc.postgresql.org/
Version : 42.5.1
License : BSD License (postgres.license.txt)
Jar files : postgresql-42.5.1.jar
X-Doclet
--------
Used at compile-time only to generate the XML files needed by
Hibernate for the database mapping. These libraries are not included in
the distribution.
More info : http://xdoclet.sourceforge.net/xdoclet/index.html
Version : 1.2
License : XDoclet License (xdoclet.license.txt)
Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar,
xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar,
commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
Java Math Expression Parser
---------------------------
Parses and evaluates mathematical expressions in string. Supports
most operators and funcations as well as variables.
More info : http://www.singularsys.com/jep/
Version : 2.4.0
License : GPLv2 (gpl-2.license.txt)
Jar files : jep-2.4.0.jar
JFreeChart
----------
Plotting package for bar charts, line charts, pie charts and xy plots.
More info : http://www.jfree.org/jfreechart/
Version : 1.0.19
License : LGPL (lgpl.txt)
Jar files : jfreechart-1.0.19.jar jcommon-1.0.23.jar
Apache HttpComponents
---------------------
Package for doing work with HTTP (eg. downloading files).
More info : http://hc.apache.org/
Version : 4.5.13 and 4.4.14
License : Apache License 2.0 (apache.license-2.0.txt)
Jar files : httpclient-4.5.13.jar, httpcore-4.4.14.jar, commons-codec-1.11.jar,
commons-logging-1.2.jar
Apache Commons Email
---------------------
Package for sending email. Depends on JavaMail.
More info : http://commons.apache.org/email/
Version : 1.5
License : Apache License 2.0 (apache.license-2.0.txt)
Jar files : commons-email-1.5.jar
JavaMail
---------
Low-level package for sending email. Used by Apache commons email.
More info : https://javaee.github.io/javamail/
Version : 1.6.2
License : Common Development and Distribution License (CDDL) v1.1 and GNU General Public License (GPL) v2 with Classpath Exception (javax-mail-LICENSE.txt)
Jar files : javax-mail-1.6.2.jar, jakarta.activation-1.2.1.jar
Apache Commons Collections 4
----------------------------
Package for working with collections.
More info : https://commons.apache.org/proper/commons-collections/
Version : 4.4
License : Apache License 2.0 (apache.license-2.0.txt)
Jar files : commons-collections4-4.4.jar
jBCrypt
-------
Package for safe encryption of passwords using the 'bcrypt' algorithm.
More info : http://www.mindrot.org/projects/jBCrypt/
Version : 0.4
License : ISC/BSD licence (jbcrypt-license.txt)
Jar files : None. Distributed as source only. All code is in net/sf/basedb/util/bcrypt/BCrypt.java
BouncyCastle
------------
Cryptographic provider package
More info : https://www.bouncycastle.org/java.html
Version : 172
License : bcp-license.txt
Jar files : bcpkix-jdk18on-172.jar, bcprov-jdk18on-172.jar, bctls-jdk18on-172.jar, eddsa-0.3.0-jar
JSON.simple
-----------
JSON.simple is a simple Java toolkit for JSON. You can use JSON.simple to encode or decode JSON text.
We use a modified version that uses Java generics instead of raw object types.
More info: http://code.google.com/p/json-simple/
: (original version)
: http://dev.thep.lu.se/basehacks/wiki/JSON.simple
: (modified version)
Version : 1.1.1-1
License : Apache License 2.0 (apache.license-2.0.txt)
Jar files : json-simple-1.1.1-1.jar
Silk icon set
-------------
A very nice icon set containing 1000 icons. The entire icon set
is available in the "misc" directory. We have converted the icons
to GIF format (since we didn't want to scan through all web pages
and replace .gif with .png). We have also created some new icons which
are merely combinations of other icons, ie. taking an arrow on one icon
an putting it on another.
More info : http://www.famfamfam.com/lab/icons/silk/
Version : 1.3
License : Creative Commons Attribution 2.5 License
(http://creativecommons.org/licenses/by/2.5/)
SvnKit
------
Java implementation for accessing subversion from the ant buildfile.
More info : https://svnkit.com/
Version : 1.10.3
License : TMate License (lib/svnkit/LICENSE.txt)
Jar files : Everything in lib/svnkit/
Docbook
-------
A set of DTD:s and stylesheets for creating documentation. We use
the DocBook styler suite (see below) but has upgraded it to Docbook 4.5.
More info: http://www.docbook.org/
Version : 4.5
License : docbook.license.txt
Files : Everything in lib/docbook/docbook and dist/commons-logging-1.1.jar
Docbook styler guide
--------------------
An extension to docbook created by Dawid Weiss which simplifies
file inclusion and building from ant.
More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en
Version : 2004_06_22-21_12
License : docbook.styler.guide.txt
Files : Everything in lib/docbook except the 'docbook' subdirectory
Example code syntax highlighter
-------------------------------
A javascript library that can be used to dynamically highlight
the syntax in program examples. We have made minor changes to
make it support the HTML produced by Docbook (ie. find the language
from the 'language' attribute instead of the 'class' attribute).
More info: http://alexgorbatchev.com/SyntaxHighlighter/
Version : 1.5.1
License : LGPL (lgpl.txt)
Files : Everything in the /doc/src/docbook/script and
/doc/src/docbook/css directories
Affymetrix Fusion SDK
---------------------
Package for reading various Affymetrix file formats. We use a modified
version that for some file formats can read from an InputStream instead
of from a File object. This avoids a lot of copying and decompressing.
More info: http://www.affymetrix.com/support/developer/fusion/index.affx
: (original version)
: http://dev.thep.lu.se/basehacks/wiki/AffxFusion
: (modified version)
Version : 1.09
License : LGPL (lgpl.txt)
Files : AffxFusion.jar
ZIP file support
----------------
A library for reading and writing ZIP files.
More info: https://github.com/srikanth-lingala/zip4j
Version : 2.11.2
License : zip4j-license.txt
Files : zip4j-2.11.2.jar
TAR file support
----------------
Package for reading and writing TAR files.
More info: http://www.trustice.com/java/tar/
Version : 2.5
License : tar.license.txt
Files : tar.jar
BZIP file support
-----------------
Package for reading and writing BZIP files.
More info: http://www.kohsuke.org/bzip2/
Version : unknown
License : Apache software license (apache.license.txt)
Files : bzip2.jar
Parallel GZIP compression
-------------------------
Package for multi-threaded compression to GZIP format.
More info: https://github.com/shevek/parallelgzip
Version : 1.0.5
License : Apache software license (parallelgzip-LICENSE.txt)
Files : parallelgzip-1.0.5.jar
SecondString
------------
A package with some fuzzy string matching algorithms developed
by researchers at Carnegie Mellon University.
More info : http://secondstring.sourceforge.net/
Version : CVS trunk checkout (2008-08-25)
License : University of Illinois/NCSA Open Source (secondstring-LICENSE.txt)
Files : secondstring.jar
jsDraw2D
--------
A vector graphics package for JavaScript.
More info : http://jsdraw2d.jsfiction.com/
Version : 1.1.0
License : LGPL v3
Files : www/include/scripts/js-draw.js
JavaSysMon
----------
A library for accessing CPU and memory information on some selected
operating systems (including Linux, Windows and Mac OSX). It uses
native libraries targeted for each platform
More info : http://github.com/jezhumble/javasysmon
Version : 0.3.5
License : javasysmon-LICENSE.txt
Files : javasysmon-0.3.5.jar
Yauaa: Yet Another UserAgent Analyzer
-------------------------------------
A library for extracting information from the User-Agent header sent
by browsers.
More info : https://github.com/nielsbasjes/yauaa
Version : 5.23
License : Apache License, Version 2.0 (yauaa-LICENSE.txt)
Files : yauaa-5.23.jar, prefixmap-1.1.jar, commons-lang3-3.10.jar, kryo-4.0.2.jar
Apache POI
----------
A library for reading and writing Excel (and other Microsoft Office)
files.
More info : https://poi.apache.org/
Version : 5.0.0
License : Apache License, Version 2.0 (poi-license.txt)
Files : poi-5.0.0.jar, poi-ooxml-5.0.0.jar, poi-ooxml-lite-5.0.0.jar
commons-compress-1.20.jar, commons-math3-3.6.1.jar, xmlbeans-4.0.0.jar