JAL-3337 Tidied up j8libs in THIRDPARTYLIBS. Replaced jersey-*-1.19.jar with jersey...

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index 296ae17..348827e 100644 (file)
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -15,53 +15,78 @@ Licensing information for each library is given below:
 
 j8lib:
 
-JGoogleAnalytics_0.3.jar       APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
-Jmol-14.6.4_2016.10.26.jar     GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
-VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr
 activation.jar 
 apache-mime4j-0.6.jar
 axis.jar
-castor-1.1-cycle-xml.jar
+biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
+biojava-ontology-4.1.0.jar     LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
 commons-codec-1.3.jar
-commons-discovery.jar
+commons-compress-1.18.jar
 commons-logging-1.1.1.jar
-commons-logging.jar
-commons-net-3.3.jar
-groovy-all-2.4.6-indy.jar      APL 2.0 License - downloaded and extracted from https://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.6.zip
+getdown-core.jar       Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
+groovy-all-2.4.12-indy.jar     APL 2.0 License - downloaded and extracted from https://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.6.zip
+htsjdk-2.12.0.jar      built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
 httpclient-4.0.3.jar
 httpcore-4.0.1.jar
 httpmime-4.0.3.jar
+intervalstore-v1.0.jar
+jabaws-min-client-2.2.0.jar
+java-json.jar
 jaxrpc.jar
+jersey-client-1.19.4.jar       CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
+jersey-core-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
+jersey-json-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
+jetty-http-9.2.10.v20150310.jar
+jetty-io-9.2.10.v20150310.jar
+jetty-server-9.2.10.v20150310.jar
+jetty-util-9.2.10.v20150310.jar
+jfreesvg-2.1.jar       GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/
+JGoogleAnalytics_0.3.jar       APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
 jhall.jar
-jswingreader-0.3.jar : Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
+Jmol-14.6.4_2016.10.26.jar     GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
+json_simple-1.1.jar    Apache 2.0 license - downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
+jsoup-1.8.1.jar
+jsr311-api-1.1.1.jar
+jswingreader-0.3.jar   Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
+libquaqua64-8.0.jnilib.jar     quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
+libquaqua-8.0.jnilib.jar       quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
 log4j-1.2.8.jar
 mail.jar
-miglayout-4.0-swing.jar        BSD http://www.migcalendar.com/miglayout/versions/4.0/license.txt
-min-jaba-client.jar
+miglayout-4.0-swing.jar        BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt
+quaqua-filechooser-only-8.0.jar        quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
 regex.jar
 saaj.jar
+servlet-api-3.1.jar
+slf4j-api-1.7.7.jar
+slf4j-log4j12-1.7.7.jar
 vamsas-client.jar
+VAqua5-patch.jar       This is a patched version of VAqua v5 (latest stable) by Alan Snyder et al. GPLv3 with Classpath exception, also includes contributions from Quaqua: http://violetlib.org/vaqua/overview.html - see doc/patching-vaqua.txt for patch details, and http://issues.jalview.org/browse/JAL-2988 for details of the bug that the patch addresses.
+VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr
 wsdl4j.jar
 xercesImpl.jar
 xml-apis.jar
-json_simple-1.1.jar : Apache 2.0 license : downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
-jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfree.org/jfreesvg/
-
-quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
-
-vaqua5-patch: This is a patched version of VAqua v5 (latest stable) by Alan Snyder et al. GPLv3 with Classpath exception, also includes contributions from Quaqua: http://violetlib.org/vaqua/overview.html - see doc/patching-vaqua.txt for patch details, and http://issues.jalview.org/browse/JAL-2988 for details of the bug that the patch addresses.
-
-lib/htsjdk-2.12.jar: built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
-
-lib/biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
-
-lib/biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
 
 
 Libraries for Test Suite
 
-utils/classgraph-4.1.6.jar: BSD License - allows recovery of classpath for programmatic construction of a Java command line to launch Jalview
-                      version 4.1.6 downloaded from https://mvnrepository.com/artifact/io.github.classgraph/classgraph/4.1.6
+utils/axis-ant.jar
+utils/ant-contrib-1.0b3.jar
+utils/hamcrest-core-1.3.jar
+utils/roxes-ant-tasks-1.2-2004-01-30.jar
+utils/proguard_5.3.3.jar
+utils/jhindexer.jar
+utils/junit-4.12.jar
+utils/jhall.jar
+utils/classgraph-4.1.6.jar     BSD License - allows recovery of classpath for programmatic construction of a Java command line to launch Jalview version 4.1.6 downloaded from https://mvnrepository.com/artifact/io.github.classgraph/classgraph/4.1.6
+utils/testnglibs/guava-base-r03.jar
+utils/testnglibs/guava-collections-r03.jar
+utils/testnglibs/bsh-2.0b4.jar
+utils/testnglibs/snakeyaml.jar
+utils/testnglibs/testng-sources.jar
+utils/testnglibs/testng.jar
+utils/testnglibs/junit-4.12.jar
+utils/testnglibs/jcommander.jar
+utils/wsdl4j.jar
 
 
 Additional dependencies
@@ -86,10 +111,8 @@ javax.xml.rpc-api-1.1.2.jar CDDL + GPLv2 with classpath exception - https://oss.
 javax.xml.soap-api.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.xml.soap/blob/master/LICENSE
 jaxb-api-2.3.1.jar     CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1
 jaxb-runtime-2.3.2.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
-jaxws-api.jar  CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md
-jersey-client-1.19.4.jar       CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
-jersey-core-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
-jersey-json-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
+jaxws-api-2.3.1.jar    CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md
+Jmol-14.6.4_2016.10.26-no_netscape.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
 jsr311-api-1.1.1.jar   CDDL License - http://www.opensource.org/licenses/cddl1.php
 mimepull-1.9.11.jar    Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 policy-2.7.6.jar       Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php

diff --git a/build.gradle b/build.gradle
index 76284e9..2332643 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -1205,6 +1205,7 @@ task sourceDist (type: Tar) {
   exclude ("**/*locales")
   exclude ("*locales/**")
   exclude ("utils/InstallAnywhere")
+  exclude (libDir)
   exclude (getdown_files_dir)
   exclude (getdown_website_dir)
 

diff --git a/doc/building.md b/doc/building.md
index 9648b9c..cc3d7f2 100644 (file)
--- a/doc/building.md
+++ b/doc/building.md
@@ -327,6 +327,14 @@ gradle test
 These normally take around 5 - 10 minutes to complete and outputs its full results into 
 the `tests/` folder.  A summary of results should appear in your console.
 
+You can run different defined groups of tests with
+
+```bash
+gradle test -PtestngGroups=Network
+```
+
+Available groups are Functional (default), Network, External.
+
 
 ### Installer packaging with *install4j*
 
@@ -490,4 +498,4 @@ in the `jalview` root folder.
 
 
 ---
-[Jalview Development Team](mailto:help@jalview.org)
\ No newline at end of file
+[Jalview Development Team](mailto:help@jalview.org)

diff --git a/j8lib/jersey-client-1.19.jar b/j8lib/jersey-client-1.19.4.jar
similarity index 82%
rename from j8lib/jersey-client-1.19.jar
rename to j8lib/jersey-client-1.19.4.jar
index c9e0f56..0588ee2 100644 (file)
Binary files a/j8lib/jersey-client-1.19.jar and b/j8lib/jersey-client-1.19.4.jar differ

diff --git a/j8lib/jersey-core-1.19.jar b/j8lib/jersey-core-1.19.4.jar
similarity index 85%
rename from j8lib/jersey-core-1.19.jar
rename to j8lib/jersey-core-1.19.4.jar
index 92feb63..e800c60 100644 (file)
Binary files a/j8lib/jersey-core-1.19.jar and b/j8lib/jersey-core-1.19.4.jar differ

diff --git a/j8lib/jersey-json-1.19.jar b/j8lib/jersey-json-1.19.4.jar
similarity index 85%
rename from j8lib/jersey-json-1.19.jar
rename to j8lib/jersey-json-1.19.4.jar
index b609411..c79271b 100644 (file)
Binary files a/j8lib/jersey-json-1.19.jar and b/j8lib/jersey-json-1.19.4.jar differ