Revert "temporarily empty repository"

This reverts commit 7e9155d1e302395db281b7b7e99889beec8e3446.

diff --git a/.gitignore b/.gitignore
new file mode 100644 (file)
index 0000000..456c7e0
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,4 @@
+.project\r
+.settings\r
+.classpath\r
+target\r

diff --git a/.travis.yml b/.travis.yml
new file mode 100644 (file)
index 0000000..dff5f3a
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1 @@
+language: java

diff --git a/CITATION.txt b/CITATION.txt
new file mode 100644 (file)
index 0000000..ee89568
--- /dev/null
+++ b/CITATION.txt
@@ -0,0 +1,18 @@
+Wolstencroft, K., Haines, R., Fellows, D., Williams, A., Withers, D.,\r
+  Owen, S., Soiland-Reyes, S., Dunlop, I., Nenadic, A., Fisher, P., Bhagat, J.,\r
+  Belhajjame, K., Bacall, F., Hardisty, A., Nieva de la Hidalga, A.,\r
+  Balcazar Vargas, M.P., Sufi, S., and Goble, C.  2013.\r
+The Taverna workflow suite: designing and executing workflows of Web Services\r
+on the desktop, web or in the cloud.  Nucl. Acids Res. gkt328v1\r
+http://doi.org/doi:10.1093/nar/gkt328\r
+\r
+@article{Wolstencroft02052013,\r
+  author = {Wolstencroft, Katherine and Haines, Robert and Fellows, Donal and Williams, Alan and Withers, David and Owen, Stuart and Soiland-Reyes, Stian and Dunlop, Ian and Nenadic, Aleksandra and Fisher, Paul and Bhagat, Jiten and Belhajjame, Khalid and Bacall, Finn and Hardisty, Alex and Nieva de la Hidalga, Abraham and Balcazar Vargas, Maria P. and Sufi, Shoaib and Goble, Carole}, \r
+  title = {The {Taverna} workflow suite: designing and executing workflows of {Web Services} on the desktop, web or in the cloud},\r
+  year = {2013}, \r
+  doi = {10.1093/nar/gkt328}, \r
+  abstract ={The Taverna workflow tool suite (http://www.taverna.org.uk) is designed to combine distributed Web Services and/or local tools into complex analysis pipelines. These pipelines can be executed on local desktop machines or through larger infrastructure (such as supercomputers, Grids or cloud environments), using the Taverna Server. In bioinformatics, Taverna workflows are typically used in the areas of high-throughput omics analyses (for example, proteomics or transcriptomics), or for evidence gathering methods involving text mining or data mining. Through Taverna, scientists have access to several thousand different tools and resources that are freely available from a large range of life science institutions. Once constructed, the workflows are reusable, executable bioinformatics protocols that can be shared, reused and repurposed. A repository of public workflows is available at http://www.myexperiment.org. This article provides an update to the Taverna tool suite, highlighting new features and developments in the workbench and the Taverna Server.}, \r
+  URL = {http://nar.oxfordjournals.org/content/early/2013/05/02/nar.gkt328.abstract}, \r
+  eprint = {http://nar.oxfordjournals.org/content/early/2013/05/02/nar.gkt328.full.pdf+html}, \r
+  journal = {Nucleic Acids Research} \r
+}\r

diff --git a/LICENSE b/LICENSE
new file mode 100644 (file)
index 0000000..68c771a
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,176 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
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+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
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+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
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+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
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diff --git a/README.md b/README.md
new file mode 100644 (file)
index 0000000..c754b25
--- /dev/null
+++ b/README.md
@@ -0,0 +1,26 @@
+# Taverna Workbench 3.x
+
+## Installing
+
+Pre-requisites: 
+* [Maven 3](http://maven.apache.org/download.cgi) 
+* [Java JDK 7](http://www.oracle.com/technetwork/java/javase/downloads/index.html)
+
+Installing:
+
+    git checkout devel
+    mvn install
+    cd target/taverna-workbench-3.0.1-SNAPSHOT-dev/taverna-workbench-3.0.1-SNAPSHOT
+    ./taverna.sh # or taverna.bat
+
+# License
+
+(c) 2005-2014 University of Manchester
+
+Licensed under [Lesser GPL 2.1](https://www.gnu.org/licenses/lgpl-2.1.html). 
+
+
+# Contact
+
+Post to the [https://lists.sourceforge.net/lists/listinfo/taverna-hackers](taverna-hackers) list 
+for any questions, or contact the [http://www.taverna.org.uk/about/contact-us/](myGrid support).

diff --git a/pom.xml b/pom.xml
new file mode 100644 (file)
index 0000000..accb5c5
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,772 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+       <modelVersion>4.0.0</modelVersion>
+       <parent>
+               <groupId>net.sf.taverna</groupId>
+               <artifactId>taverna-parent</artifactId>
+               <version>3.0.1-SNAPSHOT</version>
+       </parent>
+       <groupId>uk.org.taverna.workbench</groupId>
+       <artifactId>taverna-workbench-product</artifactId>
+       <name>Taverna Workbench [Developer]</name>
+       <packaging>taverna-application</packaging>
+       <profiles>
+               <profile>
+                       <id>dev</id>
+                       <activation>
+                               <activeByDefault>true</activeByDefault>
+                       </activation>
+                       <properties>
+                               <assembly.descriptor>src/main/assembly/developer-assembly.xml</assembly.descriptor>
+                               <profile.updateSite>http://updates.taverna.org.uk/workbench/3.0/dev/</profile.updateSite>
+                               <profile.pluginSite>http://updates.taverna.org.uk/workbench/3.0/dev/plugins/</profile.pluginSite>
+                       </properties>
+                       <distributionManagement>
+                               <repository>
+                                       <id>dev</id>
+                                       <url>file:///local/www/taverna/updates/3/workbench/3.0/dev</url>
+                               </repository>
+                               <snapshotRepository>
+                                       <id>dev</id>
+                                       <url>file:///local/www/taverna/updates/3/workbench/3.0/dev</url>
+                               </snapshotRepository>
+                       </distributionManagement>
+               </profile>
+               <profile>
+                       <id>beta</id>
+                       <properties>
+                               <assembly.descriptor>src/main/assembly/nightly-assembly.xml</assembly.descriptor>
+                               <profile.updateSite>http://updates.taverna.org.uk/workbench/3.0/beta/</profile.updateSite>
+                               <profile.pluginSite>http://updates.taverna.org.uk/workbench/3.0/beta/plugins/</profile.pluginSite>
+                       </properties>
+                       <distributionManagement>
+                               <repository>
+                                       <id>beta</id>
+                                       <url>file:///local/www/taverna/updates/3/workbench/3.0/beta</url>
+                               </repository>
+                               <snapshotRepository>
+                                       <id>beta</id>
+                                       <url>file:///local/www/taverna/updates/3/workbench/3.0/beta</url>
+                               </snapshotRepository>
+                       </distributionManagement>
+               </profile>
+               <profile>
+                       <id>stable</id>
+                       <properties>
+                               <assembly.descriptor>src/main/assembly/release-assembly.xml</assembly.descriptor>
+                               <profile.updateSite>http://updates.taverna.org.uk/workbench/3.0/stable/</profile.updateSite>
+                               <profile.pluginSite>http://updates.taverna.org.uk/workbench/3.0/stable/plugins/</profile.pluginSite>
+                       </properties>
+                       <distributionManagement>
+                               <repository>
+                                       <id>stable</id>
+                                       <url>file:///local/www/taverna/updates/3/workbench/3.0/stable</url>
+                               </repository>
+                               <snapshotRepository>
+                                       <id>stable</id>
+                                       <url>file:///local/www/taverna/updates/3/workbench/3.0/stable</url>
+                               </snapshotRepository>
+                       </distributionManagement>
+               </profile>
+               <profile>
+                       <id>nightly</id>
+                       <properties>
+                               <assembly.descriptor>src/main/assembly/nightly-assembly.xml</assembly.descriptor>
+                               <profile.updateSite>http://updates.taverna.org.uk/workbench/3.0/dev/</profile.updateSite>
+                               <profile.pluginSite>http://updates.taverna.org.uk/workbench/3.0/dev/plugins/</profile.pluginSite>
+                       </properties>
+                       <distributionManagement>
+                               <repository>
+                                       <id>dev</id>
+                                       <url>file:///local/www/taverna/updates/3/workbench/3.0/dev</url>
+                               </repository>
+                               <snapshotRepository>
+                                       <id>dev</id>
+                                       <url>file:///local/www/taverna/updates/3/workbench/3.0/dev</url>
+                               </snapshotRepository>
+                       </distributionManagement>
+               </profile>
+       </profiles>
+       <build>
+               <finalName>taverna-workbench-${project.version}</finalName>
+               <plugins>
+                       <plugin>
+                               <groupId>org.apache.maven.plugins</groupId>
+                               <artifactId>maven-assembly-plugin</artifactId>
+                               <version>2.4</version>
+                               <executions>
+                                       <execution>
+                                               <phase>package</phase>
+                                               <goals>
+                                                       <goal>single</goal>
+                                               </goals>
+                                       </execution>
+                               </executions>
+                               <configuration>
+                                       <descriptors>
+                                               <descriptor>${assembly.descriptor}</descriptor>
+                                       </descriptors>
+                                       <archiverConfig>
+                                               <directoryMode>493</directoryMode> <!-- 493(dec) = 755(oct) -->
+                                               <defaultDirectoryMode>493</defaultDirectoryMode>
+                                       </archiverConfig>
+                               </configuration>
+                       </plugin>
+                       <plugin>
+                               <groupId>org.codehaus.mojo</groupId>
+                               <artifactId>buildnumber-maven-plugin</artifactId>
+                               <version>1.0-beta-3</version>
+                               <executions>
+                                       <execution>
+                                               <id>buildnumber-validate</id>
+                                               <phase>validate</phase>
+                                               <goals>
+                                                       <goal>create</goal>
+                                               </goals>
+                                       </execution>
+                               </executions>
+                               <configuration>
+                                       <format>{0,date,yyyyMMdd}T{0,date,HHmm}</format>
+                                       <items>
+                                               <item>timestamp</item>
+                                       </items>
+                               </configuration>
+                       </plugin>
+                       <plugin>
+                               <groupId>net.sf.taverna.t2.maven.plugins</groupId>
+                               <artifactId>taverna-maven-plugin</artifactId>
+                               <version>0.3.1-SNAPSHOT</version>
+                               <extensions>true</extensions>
+                               <configuration>
+                                       <buildNumber>${buildNumber}</buildNumber>
+                                       <updateSite>${profile.updateSite}</updateSite>
+                                       <pluginSite>${profile.pluginSite}</pluginSite>
+                                       <frameworkConfigurations>
+                                               <frameworkConfiguration>
+                                                       <name>org.osgi.framework.bootdelegation</name>
+                                                       <value>sun.*,com.sun.*,java.*,javax.*,org.xml.*,org.w3c.*,apple.*,com.apple.*,org.omg.*,org.ietf.jgss.*,org.jcp.xml.dsig.internal.*</value>
+                                               </frameworkConfiguration>
+                                               <frameworkConfiguration>
+                                                       <name>org.osgi.framework.system.packages.extra</name>
+                                                       <value>com.sun.org.apache.xml.internal.utils,org.apache.log4j;version=1.2.16</value>
+                                               </frameworkConfiguration>
+                                               <frameworkConfiguration>
+                                                       <name>org.osgi.framework.storage.clean</name>
+                                                       <value>onFirstInit</value>
+                                               </frameworkConfiguration>
+                                       </frameworkConfigurations>
+                               </configuration>
+                       </plugin>
+                       <plugin>
+                               <groupId>org.apache.maven.plugins</groupId>
+                               <artifactId>maven-jar-plugin</artifactId>
+                               <version>2.4</version>
+                               <configuration>
+                                       <skipIfEmpty>true</skipIfEmpty>
+                               </configuration>
+                       </plugin>
+               </plugins>
+               <pluginManagement>
+                       <plugins>
+                               <!--This plugin's configuration is used to store Eclipse m2e settings
+                                       only. It has no influence on the Maven build itself. -->
+                               <plugin>
+                                       <groupId>org.eclipse.m2e</groupId>
+                                       <artifactId>lifecycle-mapping</artifactId>
+                                       <version>1.0.0</version>
+                                       <configuration>
+                                               <lifecycleMappingMetadata>
+                                                       <pluginExecutions>
+                                                               <pluginExecution>
+                                                                       <pluginExecutionFilter>
+                                                                               <groupId>
+                                                                                       net.sf.taverna.t2.maven.plugins
+                                                                               </groupId>
+                                                                               <artifactId>
+                                                                                       taverna-maven-plugin
+                                                                               </artifactId>
+                                                                               <versionRange>
+                                                                                       [0.3.1-SNAPSHOT,)
+                                                                               </versionRange>
+                                                                               <goals>
+                                                                                       <goal>
+                                                                                               profile-generate
+                                                                                       </goal>
+                                                                               </goals>
+                                                                       </pluginExecutionFilter>
+                                                                       <action>
+                                                                               <execute>
+                                                                                       <runOnIncremental>false</runOnIncremental>
+                                                                               </execute>
+                                                                       </action>
+                                                               </pluginExecution>
+                                                       </pluginExecutions>
+                                               </lifecycleMappingMetadata>
+                                       </configuration>
+                               </plugin>
+                       </plugins>
+               </pluginManagement>
+       </build>
+       <dependencies>
+
+               <!-- Explicit org.osgi.* with <scope>provided as these are also provided
+                       by the felix osgi package. Avoids: Caused by: java.lang.SecurityException:
+                       class "org.osgi.framework.hooks.bundle.CollisionHook"'s signer information
+                       does not match signer information of other classes in the same package -->
+
+               <dependency>
+                       <groupId>org.osgi</groupId>
+                       <artifactId>org.osgi.core</artifactId>
+                       <version>4.3.1</version>
+                       <scope>provided</scope>
+               </dependency>
+               <dependency>
+                       <groupId>org.osgi</groupId>
+                       <artifactId>org.osgi.compendium</artifactId>
+                       <version>4.3.1</version>
+                       <scope>provided</scope>
+               </dependency>
+
+               <dependency>
+                       <groupId>log4j</groupId>
+                       <artifactId>log4j</artifactId>
+                       <version>1.2.17</version>
+                       <scope>provided</scope>
+               </dependency>
+
+               <!-- Spring DM -->
+               <dependency>
+                       <groupId>net.sourceforge.cglib</groupId>
+                       <artifactId>com.springsource.net.sf.cglib</artifactId>
+                       <version>2.1.3</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.springframework.osgi</groupId>
+                       <artifactId>spring-osgi-annotation</artifactId>
+                       <version>2.0.0.M1</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.springframework.osgi</groupId>
+                       <artifactId>spring-osgi-extender</artifactId>
+                       <version>2.0.0.M1</version>
+               </dependency>
+
+               <!-- Spring -->
+               <dependency>
+                       <groupId>org.springframework</groupId>
+                       <artifactId>org.springframework.context</artifactId>
+                       <version>3.0.5.RELEASE</version>
+               </dependency>
+
+               <!-- Java Extension Implementations -->
+               <dependency>
+                       <groupId>javax.xml.bind</groupId>
+                       <artifactId>com.springsource.javax.xml.bind</artifactId>
+                       <version>2.2.0</version>
+               </dependency>
+               <dependency>
+                       <groupId>javax.activation</groupId>
+                       <artifactId>com.springsource.javax.activation</artifactId>
+                       <version>1.1.1</version>
+               </dependency>
+               <dependency> <!-- required by bsh -->
+                       <groupId>javax.servlet</groupId>
+                       <artifactId>com.springsource.javax.servlet</artifactId>
+                       <version>2.5.0</version>
+               </dependency>
+               <dependency>
+                       <groupId>javax.jms</groupId>
+                       <artifactId>com.springsource.javax.jms</artifactId>
+                       <version>1.1.0</version>
+               </dependency>
+               <dependency>
+                       <groupId>javax.xml.soap</groupId>
+                       <artifactId>com.springsource.javax.xml.soap</artifactId>
+                       <version>1.3.0</version>
+               </dependency>
+               <dependency>
+                       <groupId>javax.xml.stream</groupId>
+                       <artifactId>com.springsource.javax.xml.stream</artifactId>
+                       <version>1.0.1</version>
+               </dependency>
+               <dependency>
+                       <groupId>javax.mail</groupId>
+                       <artifactId>com.springsource.javax.mail</artifactId>
+                       <version>1.4.1</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.apache.commons</groupId>
+                       <artifactId>com.springsource.org.apache.commons.codec</artifactId>
+                       <version>1.4.0</version>
+               </dependency>
+
+               <!-- OSGi Compendium Services -->
+               <dependency>
+                       <groupId>uk.org.taverna.osgi.services</groupId>
+                       <artifactId>xml-parser-service</artifactId>
+                       <version>0.1.1</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.osgi.services</groupId>
+                       <artifactId>xml-transformer-service</artifactId>
+                       <version>0.1.1</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.apache.felix</groupId>
+                       <artifactId>org.apache.felix.eventadmin</artifactId>
+                       <version>1.3.2</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.apache.felix</groupId>
+                       <artifactId>org.apache.felix.configadmin</artifactId>
+                       <version>1.6.0</version>
+               </dependency>
+
+               <!-- Taverna Activities -->
+               <dependency>
+                       <groupId>net.sf.taverna.t2.activities</groupId>
+                       <artifactId>apiconsumer-activity</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.activities</groupId>
+                       <artifactId>beanshell-activity</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.activities</groupId>
+                       <artifactId>biomart-activity</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.activities</groupId>
+                       <artifactId>dataflow-activity</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <!-- <dependency> <groupId>net.sf.taverna.t2.activities</groupId> <artifactId>external-tool-activity</artifactId>
+                       <version>2.0.1-SNAPSHOT</version> </dependency> -->
+               <dependency>
+                       <groupId>net.sf.taverna.t2.activities</groupId>
+                       <artifactId>localworker-activity</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.activities</groupId>
+                       <artifactId>rest-activity</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.activities</groupId>
+                       <artifactId>rshell-activity</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.activities</groupId>
+                       <artifactId>soaplab-activity</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.activities</groupId>
+                       <artifactId>spreadsheet-import-activity</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.activities</groupId>
+                       <artifactId>stringconstant-activity</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.activities</groupId>
+                       <artifactId>wsdl-activity</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.activities</groupId>
+                       <artifactId>xpath-activity</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+
+               <!-- Taverna Activities UI -->
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-activities</groupId>
+                       <artifactId>apiconsumer-activity-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-activities</groupId>
+                       <artifactId>beanshell-activity-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-activities</groupId>
+                       <artifactId>biomart-activity-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-activities</groupId>
+                       <artifactId>dataflow-activity-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-activities</groupId>
+                       <artifactId>localworker-activity-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-activities</groupId>
+                       <artifactId>rest-activity-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-activities</groupId>
+                       <artifactId>rshell-activity-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-activities</groupId>
+                       <artifactId>spreadsheet-import-activity-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-activities</groupId>
+                       <artifactId>soaplab-activity-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-activities</groupId>
+                       <artifactId>stringconstant-activity-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-activities</groupId>
+                       <artifactId>wsdl-activity-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-activities</groupId>
+                       <artifactId>unrecognized-activity-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-activities</groupId>
+                       <artifactId>xpath-activity-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+
+               <!-- Taverna Workbench -->
+               <dependency>
+                       <groupId>uk.org.taverna.workbench</groupId>
+                       <artifactId>taverna-workbench</artifactId>
+                       <version>0.1.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-impl</groupId>
+                       <artifactId>workbench-impl</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-impl</groupId>
+                       <artifactId>activity-palette-impl</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-impl</groupId>
+                       <artifactId>configuration-impl</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-impl</groupId>
+                       <artifactId>edits-impl</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-impl</groupId>
+                       <artifactId>file-impl</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-impl</groupId>
+                       <artifactId>menu-impl</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-impl</groupId>
+                       <artifactId>renderers-impl</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-impl</groupId>
+                       <artifactId>selection-impl</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-impl</groupId>
+                       <artifactId>httpproxy-config</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-impl</groupId>
+                       <artifactId>plugin-manager</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-impl</groupId>
+                       <artifactId>update-manager</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <!-- <dependency> <groupId>net.sf.taverna.t2.ui-impl</groupId> <artifactId>report-impl</artifactId>
+                       <version>2.0-SNAPSHOT</version> </dependency> -->
+
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-components</groupId>
+                       <artifactId>perspective-design</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-components</groupId>
+                       <artifactId>perspective-results</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-components</groupId>
+                       <artifactId>contextual-views</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-components</groupId>
+                       <artifactId>credential-manager-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-components</groupId>
+                       <artifactId>data-management-config-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-components</groupId>
+                       <artifactId>run-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+
+               <dependency>
+                       <!-- <dependency> <groupId>net.sf.taverna.t2.ui-exts</groupId> <artifactId>loop-ui</artifactId>
+                               <version>2.0-SNAPSHOT</version> </dependency> -->
+                       <groupId>net.sf.taverna.t2.ui-exts</groupId>
+                       <artifactId>menu-items</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-exts</groupId>
+                       <artifactId>parallelize-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+               <!-- <dependency> <groupId>net.sf.taverna.t2.ui-exts</groupId> <artifactId>renderers-exts</artifactId>
+                       <version>2.0-SNAPSHOT</version> </dependency> -->
+               <dependency>
+                       <groupId>net.sf.taverna.t2.ui-exts</groupId>
+                       <artifactId>retry-ui</artifactId>
+                       <version>2.0-SNAPSHOT</version>
+               </dependency>
+
+
+               <!-- Taverna Platform -->
+               <dependency>
+                       <groupId>uk.org.taverna.platform</groupId>
+                       <artifactId>taverna-capability-impl</artifactId>
+                       <version>0.1.3-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.platform</groupId>
+                       <artifactId>taverna-run-impl</artifactId>
+                       <version>0.1.3-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.platform</groupId>
+                       <artifactId>taverna-execution-impl</artifactId>
+                       <version>0.1.3-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.platform</groupId>
+                       <artifactId>taverna-execution-local</artifactId>
+                       <version>0.1.3-SNAPSHOT</version>
+               </dependency>
+
+               <!-- Taverna Commons -->
+               <dependency>
+                       <groupId>uk.org.taverna.configuration</groupId>
+                       <artifactId>taverna-configuration-impl</artifactId>
+                       <version>0.1.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.configuration</groupId>
+                       <artifactId>taverna-app-configuration-impl</artifactId>
+                       <version>0.1.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.configuration</groupId>
+                       <artifactId>taverna-database-configuration-impl</artifactId>
+                       <version>0.1.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.commons</groupId>
+                       <artifactId>taverna-download-impl</artifactId>
+                       <version>0.1.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.commons</groupId>
+                       <artifactId>taverna-plugin-impl</artifactId>
+                       <version>0.1.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.commons</groupId>
+                       <artifactId>taverna-services-impl</artifactId>
+                       <version>0.1.0-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.commons</groupId>
+                       <artifactId>taverna-update-impl</artifactId>
+                       <version>0.1.0-SNAPSHOT</version>
+               </dependency>
+
+               <!-- Scufl2 -->
+               <dependency>
+                       <groupId>uk.org.taverna.scufl2</groupId>
+                       <artifactId>scufl2-api</artifactId>
+                       <version>0.13.1</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.scufl2</groupId>
+                       <artifactId>scufl2-rdfxml</artifactId>
+                       <version>0.13.1</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.scufl2</groupId>
+                       <artifactId>scufl2-t2flow</artifactId>
+                       <version>0.13.2-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.scufl2</groupId>
+                       <artifactId>scufl2-validation-structural</artifactId>
+                       <version>0.13.1</version>
+               </dependency>
+               <dependency>
+                       <groupId>uk.org.taverna.scufl2</groupId>
+                       <artifactId>scufl2-validation-correctness</artifactId>
+                       <version>0.13.1</version>
+               </dependency>
+
+               <!-- Data bundle -->
+               <dependency>
+                       <groupId>uk.org.taverna.databundle</groupId>
+                       <artifactId>databundle</artifactId>
+                       <version>0.2.1</version>
+               </dependency>
+               <!-- HTTP client needed by Data Bundle -->
+               <dependency>
+                       <groupId>org.apache.httpcomponents</groupId>
+                       <artifactId>httpclient-osgi</artifactId>
+                       <version>4.2.5</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.apache.httpcomponents</groupId>
+                       <artifactId>httpcore-osgi</artifactId>
+                       <version>4.2.5</version>
+               </dependency>
+               <!-- Jena bundle needed by jsonld-java-jena -->
+               <!-- See https://github.com/stain/jena/tree/jena-bundle/jena-bundle -->
+               <dependency>
+                       <groupId>org.apache.jena</groupId>
+                       <artifactId>jena-bundle</artifactId>
+                       <version>2.11.0-SNAPSHOT</version>
+               </dependency>
+               <!-- slf4j implementation -->
+               <dependency>
+                       <groupId>org.slf4j</groupId>
+                       <artifactId>slf4j-api</artifactId>
+                       <version>1.7.5</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.slf4j</groupId>
+                       <artifactId>slf4j-log4j12</artifactId>
+                       <version>1.7.5</version>
+               </dependency>
+
+               <!-- Taverna Security -->
+               <dependency>
+                       <groupId>net.sf.taverna.t2.security</groupId>
+                       <artifactId>credential-manager-impl</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+
+               <!-- Taverna Workflow Engine -->
+               <dependency>
+                       <groupId>net.sf.taverna.t2.core</groupId>
+                       <artifactId>workflowmodel-impl</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.core</groupId>
+                       <artifactId>workflowmodel-core-extensions</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.core</groupId>
+                       <artifactId>reference-impl</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.core</groupId>
+                       <artifactId>reference-core-extensions</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+
+               <!-- Taverna Provenance -->
+               <dependency>
+                       <groupId>net.sf.taverna.t2.core</groupId>
+                       <artifactId>provenance-derby</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+               <dependency>
+                       <groupId>net.sf.taverna.t2.core</groupId>
+                       <artifactId>provenance-mysql</artifactId>
+                       <version>2.0.1-SNAPSHOT</version>
+               </dependency>
+
+       </dependencies>
+
+       <repositories>
+               <repository>
+                       <releases />
+                       <snapshots>
+                               <enabled>false</enabled>
+                       </snapshots>
+                       <id>mygrid-repository</id>
+                       <name>myGrid Repository</name>
+                       <url>http://www.mygrid.org.uk/maven/repository</url>
+               </repository>
+               <repository>
+                       <releases>
+                               <enabled>false</enabled>
+                       </releases>
+                       <snapshots />
+                       <id>mygrid-snapshot-repository</id>
+                       <name>myGrid Snapshot Repository</name>
+                       <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+               </repository>
+               <repository>
+                       <id>spring-maven-milestone</id>
+                       <name>Springframework Maven Repository</name>
+                       <url>http://maven.springframework.org/milestone</url>
+               </repository>
+               <repository>
+                       <id>com.springsource.repository.bundles.milestone</id>
+                       <name>SpringSource Enterprise Bundle Repository - SpringSource Bundle Milestones</name>
+                       <url>http://repository.springsource.com/maven/bundles/milestone</url>
+               </repository>
+               <repository>
+                       <id>OPS4J</id>
+                       <url>http://repository.ops4j.org/maven2</url>
+               </repository>
+       </repositories>
+</project>

diff --git a/src/main/assembly/dependencies-component.xml b/src/main/assembly/dependencies-component.xml
new file mode 100644 (file)
index 0000000..0e8640e
--- /dev/null
+++ b/src/main/assembly/dependencies-component.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<component
+       xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/component/1.1.2"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/component/1.1.2 http://maven.apache.org/xsd/component-1.1.2.xsd">
+
+       <fileSets>
+               <fileSet>
+                       <directory>src/main/etc</directory>
+                       <fileMode>0755</fileMode>
+                       <outputDirectory></outputDirectory>
+                       <filtered>true</filtered>
+               </fileSet>
+               <fileSet>
+                       <directory>${project.build.directory}/taverna-tmp</directory>
+                       <fileMode>0755</fileMode>
+                       <outputDirectory></outputDirectory>
+               </fileSet>
+       </fileSets>
+
+</component>
\ No newline at end of file

diff --git a/src/main/assembly/developer-assembly.xml b/src/main/assembly/developer-assembly.xml
new file mode 100644 (file)
index 0000000..ae2a7c3
--- /dev/null
+++ b/src/main/assembly/developer-assembly.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<assembly
+       xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+       <id>dev</id>
+       <formats>
+               <format>dir</format>
+       </formats>
+       <componentDescriptors>
+               <componentDescriptor>dependencies-component.xml</componentDescriptor>
+       </componentDescriptors>
+</assembly>

diff --git a/src/main/assembly/nightly-assembly.xml b/src/main/assembly/nightly-assembly.xml
new file mode 100644 (file)
index 0000000..d5b631d
--- /dev/null
+++ b/src/main/assembly/nightly-assembly.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<assembly
+       xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+       <id>nightly</id>
+       <baseDirectory>taverna-workbench-${project.version}-${buildNumber}-nightly</baseDirectory>
+       <formats>
+               <!-- <format>dir</format> -->
+               <format>zip</format>
+       </formats>
+       <componentDescriptors>
+               <componentDescriptor>dependencies-component.xml</componentDescriptor>
+       </componentDescriptors>
+</assembly>

diff --git a/src/main/assembly/release-assembly.xml b/src/main/assembly/release-assembly.xml
new file mode 100644 (file)
index 0000000..a83f9b8
--- /dev/null
+++ b/src/main/assembly/release-assembly.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<assembly
+       xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+       <id>release</id>
+       <baseDirectory>taverna-workbench-${project.version}</baseDirectory>
+       <formats>
+               <!-- <format>dir</format> -->
+               <format>zip</format>
+       </formats>
+       <componentDescriptors>
+               <componentDescriptor>dependencies-component.xml</componentDescriptor>
+       </componentDescriptors>
+</assembly>

diff --git a/src/main/etc/conf/log4j.properties b/src/main/etc/conf/log4j.properties
new file mode 100644 (file)
index 0000000..5014f2b
--- /dev/null
+++ b/src/main/etc/conf/log4j.properties
@@ -0,0 +1,14 @@
+# By default, WARN (our external libraries)
+log4j.rootLogger=INFO, CONSOLE
+
+# Get rid of some xml sec warnings
+log4j.logger.org.apache.ws.security=ERROR
+log4j.logger.org.apache.commons.httpclient=ERROR
+
+# Default output to console is restrictive
+log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
+log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
+log4j.appender.CONSOLE.layout.ConversionPattern=%-5p %d{ISO8601} (%c:%L) - %m%n
+
+# Output WARN and above to console -
+log4j.appender.CONSOLE.Threshold=ERROR
\ No newline at end of file

diff --git a/src/main/etc/conf/logging.properties b/src/main/etc/conf/logging.properties
new file mode 100644 (file)
index 0000000..b03a43f
--- /dev/null
+++ b/src/main/etc/conf/logging.properties
@@ -0,0 +1,10 @@
+handlers = java.util.logging.ConsoleHandler, java.util.logging.FileHandler
+
+.level = ALL
+
+java.util.logging.ConsoleHandler.level = WARNING
+java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
+
+java.util.logging.FileHandler.level = ALL
+java.util.logging.FileHandler.count = 5
+java.util.logging.FileHandler.limit = 1048576

diff --git a/src/main/etc/conf/taverna.app.properties b/src/main/etc/conf/taverna.app.properties
new file mode 100644 (file)
index 0000000..9634438
--- /dev/null
+++ b/src/main/etc/conf/taverna.app.properties
@@ -0,0 +1,2 @@
+taverna.app.name=taverna-workbench-3.0.0
+taverna.app.title=Taverna Workbench 3.0.0

diff --git a/src/main/etc/taverna.bat b/src/main/etc/taverna.bat
new file mode 100644 (file)
index 0000000..ebc9580
--- /dev/null
+++ b/src/main/etc/taverna.bat
@@ -0,0 +1,17 @@
+@ECHO OFF
+
+REM Taverna startup script
+
+REM distribution directory
+set TAVERNA_HOME=%~dp0
+
+
+REM 1 GB memory, 400 MB for classes
+set ARGS=-Xmx1g -XX:MaxPermSize=400m
+
+REM Taverna system properties
+set ARGS=%ARGS% "-Dlog4j.configuration=file:///%TAVERNA_HOME%conf/log4j.properties"
+set ARGS=%ARGS% "-Djava.util.logging.config.file=%TAVERNA_HOME%conf/logging.properties"
+set ARGS=%ARGS% "-Dtaverna.app.startup=%TAVERNA_HOME%."
+
+java %ARGS% -jar "%TAVERNA_HOME%lib\uk.org.taverna.workbench\taverna-workbench-0.1.0-SNAPSHOT.jar" %*

diff --git a/src/main/etc/taverna.sh b/src/main/etc/taverna.sh
new file mode 100644 (file)
index 0000000..aedd87b
--- /dev/null
+++ b/src/main/etc/taverna.sh
@@ -0,0 +1,25 @@
+#!/bin/sh
+
+set -e
+
+## resolve links - $0 may be a symlink
+prog="$0"
+
+real_path() {
+    readlink -m "$1" 2>/dev/null || python -c 'import os,sys;print os.path.realpath(sys.argv[1])' "$1"
+}
+
+realprog=`real_path "$prog"`
+taverna_home=`dirname "$realprog"`
+javabin=java
+if test -x "$JAVA_HOME/bin/java"; then
+    javabin="$JAVA_HOME/bin/java"
+fi
+
+# 1 GB memory, 400 MB for classes
+exec "$javabin" -Xmx1g -XX:MaxPermSize=400m \
+  "-Dlog4j.configuration=file://$taverna_home/conf/log4j.properties " \
+  "-Djava.util.logging.config.file=$taverna_home/conf/logging.properties " \
+  "-Dtaverna.app.startup=$taverna_home" \
+  -jar "$taverna_home/lib/uk.org.taverna.workbench/taverna-workbench-0.1.0-SNAPSHOT.jar" \
+  ${1+"$@"}