| 1 | ================================================================== |
|---|
| 2 | $Id: 3rd-party-components.txt 7874 2020-10-22 06:21:45Z 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 | |
|---|
| 11 | BASE is free software; you can redistribute it and/or |
|---|
| 12 | modify it under the terms of the GNU General Public License |
|---|
| 13 | as published by the Free Software Foundation; either version 3 |
|---|
| 14 | of the License, or (at your option) any later version. |
|---|
| 15 | |
|---|
| 16 | BASE is distributed in the hope that it will be useful, |
|---|
| 17 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
|---|
| 18 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
|---|
| 19 | GNU General Public License for more details. |
|---|
| 20 | |
|---|
| 21 | You should have received a copy of the GNU General Public License |
|---|
| 22 | along with BASE. If not, see <http://www.gnu.org/licenses/>. |
|---|
| 23 | ================================================================== |
|---|
| 24 | |
|---|
| 25 | ================================= |
|---|
| 26 | 3rd-party components used by BASE |
|---|
| 27 | ================================= |
|---|
| 28 | |
|---|
| 29 | Here is list of 3rd-party components used by BASE. All the jar files |
|---|
| 30 | needed are included in the <base>/lib directory or in |
|---|
| 31 | <base>/www/plugins sub-directories for plug-ins based on others |
|---|
| 32 | work. The URLs given here can be used if you need more information or |
|---|
| 33 | need to update some component. |
|---|
| 34 | |
|---|
| 35 | |
|---|
| 36 | Hibernate |
|---|
| 37 | --------- |
|---|
| 38 | An object/relational persistence and query service for Java. Shields |
|---|
| 39 | us from most SQL and gives us database independece. |
|---|
| 40 | |
|---|
| 41 | More info : http://www.hibernate.org/ |
|---|
| 42 | Version : 5.4.17 |
|---|
| 43 | License : LGPL (hibernate.license.txt) |
|---|
| 44 | Jar 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 | |
|---|
| 55 | Note: Most of the jar files above are other 3rd-party components used by Hibernate. |
|---|
| 56 | BASE doesn't use these components directly. |
|---|
| 57 | |
|---|
| 58 | Log4j |
|---|
| 59 | ----- |
|---|
| 60 | A logging system that makes it easy to turn on or off debugging just by |
|---|
| 61 | editing a configuration file. |
|---|
| 62 | |
|---|
| 63 | More info : http://logging.apache.org/log4j/1.2/index.html |
|---|
| 64 | Version : 1.2.17 |
|---|
| 65 | License : Apache License 2.0 (apache.license-2.0.txt) |
|---|
| 66 | Jar files : log4j-1.2.17.jar |
|---|
| 67 | |
|---|
| 68 | |
|---|
| 69 | JDOM |
|---|
| 70 | ---- |
|---|
| 71 | A library for parsing and generating XML files. |
|---|
| 72 | |
|---|
| 73 | More info : http://www.jdom.org/ |
|---|
| 74 | Version : 2.0.6 |
|---|
| 75 | License : Apache-style open source license (jdom.license.txt) |
|---|
| 76 | Jar files : jdom-2.0.6.jar, jaxen-1.1.6.jar |
|---|
| 77 | |
|---|
| 78 | |
|---|
| 79 | Xerces |
|---|
| 80 | ------ |
|---|
| 81 | A toolkit for handling XML documents. From the Apache Software |
|---|
| 82 | Foundation. These libraries are also needed by JDOM. |
|---|
| 83 | |
|---|
| 84 | More info : http://xml.apache.org/xerces2-j/index.html |
|---|
| 85 | Version : 2.11.0 |
|---|
| 86 | License : Apache Software License (xerces.license.txt) |
|---|
| 87 | Jar files : xerces-2.11.0.jar, xml-apis.jar |
|---|
| 88 | |
|---|
| 89 | |
|---|
| 90 | Java Servlet API |
|---|
| 91 | ---------------- |
|---|
| 92 | Required for creating servlets and tag libraries. This |
|---|
| 93 | library is only required for compiling and are not included in the |
|---|
| 94 | distribution. The web server/servlet container should already have |
|---|
| 95 | these API installed. We use files from the Tomcat 9 distribution. |
|---|
| 96 | |
|---|
| 97 | More info : http://tomcat.apache.org/whichversion.html |
|---|
| 98 | Version : 4.0 |
|---|
| 99 | License : N/A |
|---|
| 100 | Jar files : jsp-api.jar, servlet-api.jar |
|---|
| 101 | |
|---|
| 102 | |
|---|
| 103 | MySQL Connector/J |
|---|
| 104 | ----------------- |
|---|
| 105 | A JDBC driver for the MySQL database from MySQL. This library is only |
|---|
| 106 | needed if you are using MySQL as your database. |
|---|
| 107 | |
|---|
| 108 | More info : https://dev.mysql.com/downloads/connector/j/ |
|---|
| 109 | Version : 8.0.22 |
|---|
| 110 | License : GPLv2 (mysql-connector-LICENSE.txt) |
|---|
| 111 | Jar files : mysql-connector-java-8.0.22.jar |
|---|
| 112 | |
|---|
| 113 | |
|---|
| 114 | PostgreSQL JDBC driver |
|---|
| 115 | ---------------------- |
|---|
| 116 | A JDBC driver for the PostgreSQL database. This library is only |
|---|
| 117 | needed if you are using PostgreSQL as your database. |
|---|
| 118 | |
|---|
| 119 | More info : http://jdbc.postgresql.org/ |
|---|
| 120 | Version : 42.2.13 |
|---|
| 121 | License : BSD License (postgres.license.txt) |
|---|
| 122 | Jar files : postgresql-42.2.13.jar |
|---|
| 123 | |
|---|
| 124 | |
|---|
| 125 | X-Doclet |
|---|
| 126 | -------- |
|---|
| 127 | Used at compile-time only to generate the XML files needed by |
|---|
| 128 | Hibernate for the database mapping. These libraries are not included in |
|---|
| 129 | the distribution. |
|---|
| 130 | |
|---|
| 131 | More info : http://xdoclet.sourceforge.net/xdoclet/index.html |
|---|
| 132 | Version : 1.2 |
|---|
| 133 | License : XDoclet License (xdoclet.license.txt) |
|---|
| 134 | Jar 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 | |
|---|
| 139 | Java Math Expression Parser |
|---|
| 140 | --------------------------- |
|---|
| 141 | Parses and evaluates mathematical expressions in string. Supports |
|---|
| 142 | most operators and funcations as well as variables. |
|---|
| 143 | |
|---|
| 144 | More info : http://www.singularsys.com/jep/ |
|---|
| 145 | Version : 2.4.0 |
|---|
| 146 | License : GPLv2 (gpl-2.license.txt) |
|---|
| 147 | Jar files : jep-2.4.0.jar |
|---|
| 148 | |
|---|
| 149 | |
|---|
| 150 | JFreeChart |
|---|
| 151 | ---------- |
|---|
| 152 | Plotting package for bar charts, line charts, pie charts and xy plots. |
|---|
| 153 | |
|---|
| 154 | More info : http://www.jfree.org/jfreechart/ |
|---|
| 155 | Version : 1.0.19 |
|---|
| 156 | License : LGPL (lgpl.txt) |
|---|
| 157 | Jar files : jfreechart-1.0.19.jar jcommon-1.0.23.jar |
|---|
| 158 | |
|---|
| 159 | |
|---|
| 160 | Apache HttpComponents |
|---|
| 161 | --------------------- |
|---|
| 162 | Package for doing work with HTTP (eg. downloading files). |
|---|
| 163 | |
|---|
| 164 | More info : http://hc.apache.org/ |
|---|
| 165 | Version : 4.5.6 and 4.4.10 |
|---|
| 166 | License : Apache License 2.0 (apache.license-2.0.txt) |
|---|
| 167 | Jar files : httpclient-4.5.6.jar, httpcore-4.4.10.jar, commons-codec-1.10.jar, |
|---|
| 168 | commons-logging-1.2.jar |
|---|
| 169 | |
|---|
| 170 | Apache Commons Email |
|---|
| 171 | --------------------- |
|---|
| 172 | Package for sending email. Depends on JavaMail. |
|---|
| 173 | |
|---|
| 174 | More info : http://commons.apache.org/email/ |
|---|
| 175 | Version : 1.5 |
|---|
| 176 | License : Apache License 2.0 (apache.license-2.0.txt) |
|---|
| 177 | Jar files : commons-email-1.5.jar |
|---|
| 178 | |
|---|
| 179 | |
|---|
| 180 | JavaMail |
|---|
| 181 | --------- |
|---|
| 182 | Low-level package for sending email. Used by Apache commons email. |
|---|
| 183 | |
|---|
| 184 | More info : https://javaee.github.io/javamail/ |
|---|
| 185 | Version : 1.6.2 |
|---|
| 186 | License : Common Development and Distribution License (CDDL) v1.1 and GNU General Public License (GPL) v2 with Classpath Exception (javax-mail-LICENSE.txt) |
|---|
| 187 | Jar files : javax-mail-1.6.2.jar, jakarta.activation-1.2.1.jar |
|---|
| 188 | |
|---|
| 189 | Apache Commons Collections 4 |
|---|
| 190 | ---------------------------- |
|---|
| 191 | Package for working with collections. |
|---|
| 192 | |
|---|
| 193 | More info : https://commons.apache.org/proper/commons-collections/ |
|---|
| 194 | Version : 4.2 |
|---|
| 195 | License : Apache License 2.0 (apache.license-2.0.txt) |
|---|
| 196 | Jar files : commons-collections4-4.2.jar |
|---|
| 197 | |
|---|
| 198 | jBCrypt |
|---|
| 199 | ------- |
|---|
| 200 | Package for safe encryption of passwords using the 'bcrypt' algorithm. |
|---|
| 201 | |
|---|
| 202 | More info : http://www.mindrot.org/projects/jBCrypt/ |
|---|
| 203 | Version : 0.4 |
|---|
| 204 | License : ISC/BSD licence (jbcrypt-license.txt) |
|---|
| 205 | Jar files : None. Distributed as source only. All code is in net/sf/basedb/util/bcrypt/BCrypt.java |
|---|
| 206 | |
|---|
| 207 | |
|---|
| 208 | BouncyCastle |
|---|
| 209 | ------------ |
|---|
| 210 | Cryptographic provider package |
|---|
| 211 | |
|---|
| 212 | More info : https://www.bouncycastle.org/java.html |
|---|
| 213 | Version : 165 |
|---|
| 214 | License : bcp-license.txt |
|---|
| 215 | Jar files : bcpkix-jdk15on-165.jar, bcprov-jdk15on-165.jar, bctls-jdk15on-165.jar, eddsa-0.3.0-jar |
|---|
| 216 | |
|---|
| 217 | |
|---|
| 218 | JSON.simple |
|---|
| 219 | ----------- |
|---|
| 220 | JSON.simple is a simple Java toolkit for JSON. You can use JSON.simple to encode or decode JSON text. |
|---|
| 221 | We use a modified version that uses Java generics instead of raw object types. |
|---|
| 222 | |
|---|
| 223 | More info: http://code.google.com/p/json-simple/ |
|---|
| 224 | : (original version) |
|---|
| 225 | : http://dev.thep.lu.se/basehacks/wiki/JSON.simple |
|---|
| 226 | : (modified version) |
|---|
| 227 | Version : 1.1.1-1 |
|---|
| 228 | License : Apache License 2.0 (apache.license-2.0.txt) |
|---|
| 229 | Jar files : json-simple-1.1.1-1.jar |
|---|
| 230 | |
|---|
| 231 | |
|---|
| 232 | Silk icon set |
|---|
| 233 | ------------- |
|---|
| 234 | A very nice icon set containing 1000 icons. The entire icon set |
|---|
| 235 | is available in the "misc" directory. We have converted the icons |
|---|
| 236 | to GIF format (since we didn't want to scan through all web pages |
|---|
| 237 | and replace .gif with .png). We have also created some new icons which |
|---|
| 238 | are merely combinations of other icons, ie. taking an arrow on one icon |
|---|
| 239 | an putting it on another. |
|---|
| 240 | |
|---|
| 241 | More info : http://www.famfamfam.com/lab/icons/silk/ |
|---|
| 242 | Version : 1.3 |
|---|
| 243 | License : Creative Commons Attribution 2.5 License |
|---|
| 244 | (http://creativecommons.org/licenses/by/2.5/) |
|---|
| 245 | |
|---|
| 246 | |
|---|
| 247 | SvnKit |
|---|
| 248 | ------ |
|---|
| 249 | Java implementation for accessing subversion from the ant buildfile. |
|---|
| 250 | |
|---|
| 251 | More info : https://svnkit.com/ |
|---|
| 252 | Version : 1.10.1 |
|---|
| 253 | License : TMate License (lib/svnkit/LICENSE.txt) |
|---|
| 254 | Jar files : Everything in lib/svnkit/ |
|---|
| 255 | |
|---|
| 256 | |
|---|
| 257 | Docbook |
|---|
| 258 | ------- |
|---|
| 259 | A set of DTD:s and stylesheets for creating documentation. We use |
|---|
| 260 | the DocBook styler suite (see below) but has upgraded it to Docbook 4.5. |
|---|
| 261 | |
|---|
| 262 | More info: http://www.docbook.org/ |
|---|
| 263 | Version : 4.5 |
|---|
| 264 | License : docbook.license.txt |
|---|
| 265 | Files : Everything in lib/docbook/docbook and dist/commons-logging-1.1.jar |
|---|
| 266 | |
|---|
| 267 | |
|---|
| 268 | Docbook styler guide |
|---|
| 269 | -------------------- |
|---|
| 270 | An extension to docbook created by Dawid Weiss which simplifies |
|---|
| 271 | file inclusion and building from ant. |
|---|
| 272 | |
|---|
| 273 | More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en |
|---|
| 274 | Version : 2004_06_22-21_12 |
|---|
| 275 | License : docbook.styler.guide.txt |
|---|
| 276 | Files : Everything in lib/docbook except the 'docbook' subdirectory |
|---|
| 277 | |
|---|
| 278 | Example code syntax highlighter |
|---|
| 279 | ------------------------------- |
|---|
| 280 | A javascript library that can be used to dynamically highlight |
|---|
| 281 | the syntax in program examples. We have made minor changes to |
|---|
| 282 | make it support the HTML produced by Docbook (ie. find the language |
|---|
| 283 | from the 'language' attribute instead of the 'class' attribute). |
|---|
| 284 | |
|---|
| 285 | More info: http://alexgorbatchev.com/SyntaxHighlighter/ |
|---|
| 286 | Version : 1.5.1 |
|---|
| 287 | License : LGPL (lgpl.txt) |
|---|
| 288 | Files : Everything in the /doc/src/docbook/script and |
|---|
| 289 | /doc/src/docbook/css directories |
|---|
| 290 | |
|---|
| 291 | Affymetrix Fusion SDK |
|---|
| 292 | --------------------- |
|---|
| 293 | Package for reading various Affymetrix file formats. We use a modified |
|---|
| 294 | version that for some file formats can read from an InputStream instead |
|---|
| 295 | of from a File object. This avoids a lot of copying and decompressing. |
|---|
| 296 | |
|---|
| 297 | More 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) |
|---|
| 301 | Version : 1.09 |
|---|
| 302 | License : LGPL (lgpl.txt) |
|---|
| 303 | Files : AffxFusion.jar |
|---|
| 304 | |
|---|
| 305 | TAR file support |
|---|
| 306 | ---------------- |
|---|
| 307 | Package for reading and writing TAR files. |
|---|
| 308 | |
|---|
| 309 | More info: http://www.trustice.com/java/tar/ |
|---|
| 310 | Version : 2.5 |
|---|
| 311 | License : tar.license.txt |
|---|
| 312 | Files : tar.jar |
|---|
| 313 | |
|---|
| 314 | BZIP file support |
|---|
| 315 | ----------------- |
|---|
| 316 | Package for reading and writing BZIP files. |
|---|
| 317 | |
|---|
| 318 | More info: http://www.kohsuke.org/bzip2/ |
|---|
| 319 | Version : unknown |
|---|
| 320 | License : Apache software license (apache.license.txt) |
|---|
| 321 | Files : bzip2.jar |
|---|
| 322 | |
|---|
| 323 | Parallel GZIP compression |
|---|
| 324 | ------------------------- |
|---|
| 325 | Package for multi-threaded compression to GZIP format. |
|---|
| 326 | |
|---|
| 327 | More info: https://github.com/shevek/parallelgzip |
|---|
| 328 | Version : 1.0.5 |
|---|
| 329 | License : Apache software license (parallelgzip-LICENSE.txt) |
|---|
| 330 | Files : parallelgzip-1.0.5.jar |
|---|
| 331 | |
|---|
| 332 | SecondString |
|---|
| 333 | ------------ |
|---|
| 334 | A package with some fuzzy string matching algorithms developed |
|---|
| 335 | by researchers at Carnegie Mellon University. |
|---|
| 336 | |
|---|
| 337 | More info : http://secondstring.sourceforge.net/ |
|---|
| 338 | Version : CVS trunk checkout (2008-08-25) |
|---|
| 339 | License : University of Illinois/NCSA Open Source (secondstring-LICENSE.txt) |
|---|
| 340 | Files : secondstring.jar |
|---|
| 341 | |
|---|
| 342 | |
|---|
| 343 | jsDraw2D |
|---|
| 344 | -------- |
|---|
| 345 | A vector graphics package for JavaScript. |
|---|
| 346 | |
|---|
| 347 | More info : http://jsdraw2d.jsfiction.com/ |
|---|
| 348 | Version : 1.1.0 |
|---|
| 349 | License : LGPL v3 |
|---|
| 350 | Files : www/include/scripts/js-draw.js |
|---|
| 351 | |
|---|
| 352 | JavaSysMon |
|---|
| 353 | ---------- |
|---|
| 354 | A library for accessing CPU and memory information on some selected |
|---|
| 355 | operating systems (including Linux, Windows and Mac OSX). It uses |
|---|
| 356 | native libraries targeted for each platform |
|---|
| 357 | |
|---|
| 358 | More info : http://github.com/jezhumble/javasysmon |
|---|
| 359 | Version : 0.3.5 |
|---|
| 360 | License : javasysmon-LICENSE.txt |
|---|
| 361 | Files : javasysmon-0.3.5.jar |
|---|
| 362 | |
|---|
| 363 | Yauaa: Yet Another UserAgent Analyzer |
|---|
| 364 | ------------------------------------- |
|---|
| 365 | A library for extracting information from the User-Agent header sent |
|---|
| 366 | by browsers. |
|---|
| 367 | |
|---|
| 368 | More info : https://github.com/nielsbasjes/yauaa |
|---|
| 369 | Version : 5.17 |
|---|
| 370 | License : Apache License, Version 2.0 (yauaa-LICENSE.txt) |
|---|
| 371 | Files : yauaa-5.17.jar, prefixmap-1.1.jar, commons-lang3-3.10.jar, kryo-4.0.2.jar |
|---|
| 372 | |
|---|
| 373 | Apache POI |
|---|
| 374 | ---------- |
|---|
| 375 | A library for reading and writing Excel (and other Microsoft Office) |
|---|
| 376 | files. |
|---|
| 377 | |
|---|
| 378 | More info : https://poi.apache.org/ |
|---|
| 379 | Version : 4.1.2 |
|---|
| 380 | License : Apache License, Version 2.0 (poi-license.txt) |
|---|
| 381 | Files : poi-4.1.2.jar, poi-ooxml-4.1.2.jar, poi-ooxml-schemas-4.1.2.jar |
|---|
| 382 | commons-compress-1.19.jar, commons-math3-3.6.1.jar, xmlbeans-3.1.0.jar |
|---|
| 383 | |
|---|
