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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:54:17 UTC
[09/49] incubator-taverna-workbench-product git commit: Moved up from
redundant subfolder
Moved up from redundant subfolder
git-svn-id: https://taverna.googlecode.com/svn/taverna/products/taverna-workbench-product/trunk@15220 bf327186-88b3-11dd-a302-d386e5130c1c
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/commit/4e8c4cf7
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/tree/4e8c4cf7
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/diff/4e8c4cf7
Branch: refs/heads/master
Commit: 4e8c4cf76bd1271d7e79aa039f2c738f70d9a041
Parents: 9c70593
Author: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Fri Oct 5 14:22:23 2012 +0000
Committer: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Fri Oct 5 14:22:23 2012 +0000
----------------------------------------------------------------------
pom.xml | 364 +++++++++++++++++++
src/main/assembly/release-assembly.xml | 44 +++
src/main/etc/conf/log4j.properties | 14 +
src/main/etc/conf/logging.properties | 11 +
src/main/etc/conf/taverna.app.properties | 2 +
src/main/etc/taverna.bat | 17 +
src/main/etc/taverna.sh | 25 ++
taverna-workbench-product/pom.xml | 364 -------------------
.../src/main/assembly/release-assembly.xml | 44 ---
.../src/main/etc/conf/log4j.properties | 14 -
.../src/main/etc/conf/logging.properties | 11 -
.../src/main/etc/conf/taverna.app.properties | 2 -
.../src/main/etc/taverna.bat | 17 -
.../src/main/etc/taverna.sh | 25 --
14 files changed, 477 insertions(+), 477 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..e976ff7
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,364 @@
+<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/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <artifactId>taverna-parent</artifactId>
+ <groupId>net.sf.taverna</groupId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>uk.org.taverna.workbench</groupId>
+ <artifactId>taverna-workbench-product</artifactId>
+ <version>3.0.0-SNAPSHOT</version>
+ <name>Taverna Workbench Product</name>
+ <packaging>pom</packaging>
+ <dependencies>
+ <!-- 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>${spring.dm.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.springframework.osgi</groupId>
+ <artifactId>spring-osgi-extender</artifactId>
+ <version>${spring.dm.version}</version>
+ </dependency>
+ <!-- Spring -->
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>org.springframework.context</artifactId>
+ <version>${spring.version}</version>
+ </dependency>
+
+ <!-- Java Extension Implementations -->
+ <!-- <dependency> <groupId>com.sun.xml</groupId> <artifactId>com.springsource.com.sun.xml.bind</artifactId>
+ <version>2.2.0</version> </dependency> -->
+ <dependency>
+ <groupId>javax.xml.bind</groupId>
+ <artifactId>com.springsource.javax.xml.bind</artifactId>
+ <version>2.2.0</version>
+ </dependency>
+ <dependency>
+ <groupId>javax.activation</groupId>
+ <artifactId>com.springsource.javax.activation</artifactId>
+ <version>1.1.1</version>
+ </dependency>
+ <dependency> <!-- required by bsh -->
+ <groupId>javax.servlet</groupId>
+ <artifactId>com.springsource.javax.servlet</artifactId>
+ <version>2.5.0</version>
+ </dependency>
+ <dependency>
+ <groupId>javax.jms</groupId>
+ <artifactId>com.springsource.javax.jms</artifactId>
+ <version>1.1.0</version>
+ </dependency>
+ <dependency>
+ <groupId>javax.xml.soap</groupId>
+ <artifactId>com.springsource.javax.xml.soap</artifactId>
+ <version>1.3.0</version>
+ </dependency>
+ <dependency>
+ <groupId>javax.xml.stream</groupId>
+ <artifactId>com.springsource.javax.xml.stream</artifactId>
+ <version>1.0.1</version>
+ </dependency>
+ <dependency>
+ <groupId>javax.mail</groupId>
+ <artifactId>com.springsource.javax.mail</artifactId>
+ <version>${mail.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>com.springsource.org.apache.commons.codec</artifactId>
+ <version>${commons.codec.version}</version>
+ </dependency>
+
+ <!-- OSGi Enterprise Services -->
+ <dependency>
+ <groupId>uk.org.taverna.osgi.services</groupId>
+ <artifactId>xml-parser-service</artifactId>
+ <version>${osgi.services.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.osgi.services</groupId>
+ <artifactId>xml-transformer-service</artifactId>
+ <version>${osgi.services.version}</version>
+ </dependency>
+
+ <!-- Taverna Activities -->
+ <!-- <dependency> <groupId>net.sf.taverna.t2.activities</groupId> <artifactId>all-activities</artifactId>
+ <version>${t2.activities.version}</version> <exclusions> <exclusion> <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>biomoby-activity</artifactId> </exclusion> </exclusions> </dependency> -->
+ <!-- <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>beanshell-activity</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency> -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>stringconstant-activity</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency>
+
+ <!-- Taverna Activities UI -->
+ <!-- <dependency> <groupId>net.sf.taverna.t2.ui-activities</groupId> <artifactId>all-activity-uis</artifactId>
+ <version>${t2.activities.version}</version> <exclusions> <exclusion> <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>biomoby-activity-ui</artifactId> </exclusion> </exclusions> </dependency> -->
+ <!-- <dependency>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>beanshell-activity-ui</artifactId>
+ <version>${t2.ui.activities.version}</version>
+ </dependency> -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>stringconstant-activity-ui</artifactId>
+ <version>${t2.ui.activities.version}</version>
+ </dependency>
+
+ <!-- Taverna Workbench -->
+ <dependency>
+ <groupId>uk.org.taverna.workbench</groupId>
+ <artifactId>taverna-workbench</artifactId>
+ <version>0.1.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>workbench-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>activity-palette-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>configuration-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>edits-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>file-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>menu-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+ <!-- <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>report-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency> -->
+
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>perspective-design</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>contextual-views</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+
+ <!-- <dependency>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>menu-items</artifactId>
+ <version>${t2.ui.exts.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>loop-ui</artifactId>
+ <version>${t2.ui.exts.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>parallelize-ui</artifactId>
+ <version>${t2.ui.exts.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>retry-ui</artifactId>
+ <version>${t2.ui.exts.version}</version>
+ </dependency> -->
+
+
+ <!-- Taverna Platform -->
+ <dependency>
+ <groupId>uk.org.taverna.platform</groupId>
+ <artifactId>taverna-capability-impl</artifactId>
+ <version>${platform.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.platform</groupId>
+ <artifactId>taverna-data-impl</artifactId>
+ <version>${platform.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.platform</groupId>
+ <artifactId>taverna-run-impl</artifactId>
+ <version>${platform.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.platform</groupId>
+ <artifactId>taverna-execution-impl</artifactId>
+ <version>${platform.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.platform</groupId>
+ <artifactId>taverna-execution-local</artifactId>
+ <version>${platform.version}</version>
+ </dependency>
+
+ <!-- Taverna Configuration -->
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-configuration-impl</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-app-configuration-impl</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-database-configuration-impl</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+
+ <!-- Scufl2 -->
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-rdfxml</artifactId>
+ <version>0.9.3-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-t2flow</artifactId>
+ <version>0.9.3-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-validation-structural</artifactId>
+ <version>0.9.3-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-validation-correctness</artifactId>
+ <version>0.9.3-SNAPSHOT</version>
+ </dependency>
+
+ <!-- Taverna Security -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.security</groupId>
+ <artifactId>credential-manager-impl</artifactId>
+ <version>${t2.security.version}</version>
+ </dependency>
+
+ <!-- Taverna Workflow Engine -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>workflowmodel-impl</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>workflowmodel-core-extensions</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>reference-impl</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>reference-core-extensions</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+
+ <!-- Taverna Provenance -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>provenance-derby</artifactId>
+ <version>${t2.core.provenance.derby.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>provenance-mysql</artifactId>
+ <version>${t2.core.provenance.mysql.version}</version>
+ </dependency>
+
+ </dependencies>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <version>2.3</version>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <descriptors>
+ <descriptor>src/main/assembly/release-assembly.xml</descriptor>
+ </descriptors>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <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>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/src/main/assembly/release-assembly.xml
----------------------------------------------------------------------
diff --git a/src/main/assembly/release-assembly.xml b/src/main/assembly/release-assembly.xml
new file mode 100644
index 0000000..5687d70
--- /dev/null
+++ b/src/main/assembly/release-assembly.xml
@@ -0,0 +1,44 @@
+<?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>bin</id>
+ <formats>
+ <format>dir</format>
+ <!-- <format>zip</format> -->
+ </formats>
+
+ <dependencySets>
+ <dependencySet>
+ <useTransitiveDependencies>true</useTransitiveDependencies>
+ <outputDirectory>/bundles</outputDirectory>
+ <excludes>
+ <exclude>net.sf.taverna.t2.activities:all-activities</exclude>
+ <exclude>uk.org.taverna.workbench:taverna-workbench</exclude>
+ <exclude>uk.org.taverna.osgi:osgi-launcher</exclude>
+ <exclude>org.eclipse.osgi:org.eclipse.osgi</exclude>
+ </excludes>
+ </dependencySet>
+ <dependencySet>
+ <outputDirectory>/lib</outputDirectory>
+ <includes>
+ <include>uk.org.taverna.workbench:taverna-workbench</include>
+ <include>uk.org.taverna.osgi:osgi-launcher</include>
+ <include>org.apache.log4j:com.springsource.org.apache.log4j</include>
+ <include>uk.org.taverna.configuration:taverna-app-configuration-api</include>
+ <include>uk.org.taverna.configuration:taverna-app-configuration-impl</include>
+ <include>org.osgi:org.osgi.core</include>
+ <include>org.eclipse.osgi:org.eclipse.osgi</include>
+ </includes>
+ </dependencySet>
+ </dependencySets>
+
+ <fileSets>
+ <fileSet>
+ <directory>src/main/etc</directory>
+ <fileMode>0755</fileMode>
+ <outputDirectory></outputDirectory>
+ </fileSet>
+ </fileSets>
+</assembly>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/src/main/etc/conf/log4j.properties
----------------------------------------------------------------------
diff --git a/src/main/etc/conf/log4j.properties b/src/main/etc/conf/log4j.properties
new file mode 100644
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
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/src/main/etc/conf/logging.properties
----------------------------------------------------------------------
diff --git a/src/main/etc/conf/logging.properties b/src/main/etc/conf/logging.properties
new file mode 100644
index 0000000..aa77e69
--- /dev/null
+++ b/src/main/etc/conf/logging.properties
@@ -0,0 +1,11 @@
+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
+java.util.logging.FileHandler.limit = %h/.taverna-3.0.0/logs/taverna-3.0.0.log
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/src/main/etc/conf/taverna.app.properties
----------------------------------------------------------------------
diff --git a/src/main/etc/conf/taverna.app.properties b/src/main/etc/conf/taverna.app.properties
new file mode 100644
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
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/src/main/etc/taverna.bat
----------------------------------------------------------------------
diff --git a/src/main/etc/taverna.bat b/src/main/etc/taverna.bat
new file mode 100644
index 0000000..7da12f3
--- /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 300 MB memory, 140 MB for classes
+set ARGS=-Xmx300m -XX:MaxPermSize=140m
+
+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\taverna-workbench-0.1.0-SNAPSHOT.jar" %*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/src/main/etc/taverna.sh
----------------------------------------------------------------------
diff --git a/src/main/etc/taverna.sh b/src/main/etc/taverna.sh
new file mode 100644
index 0000000..36a24d3
--- /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="$JAVA_HOME/bin/java"
+fi
+
+# 300 MB memory, 140 MB for classes
+exec "$javabin" -Xmx300m -XX:MaxPermSize=140m \
+ "-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/taverna-workbench-0.1.0-SNAPSHOT.jar" \
+ ${1+"$@"}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/taverna-workbench-product/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-workbench-product/pom.xml b/taverna-workbench-product/pom.xml
deleted file mode 100644
index e976ff7..0000000
--- a/taverna-workbench-product/pom.xml
+++ /dev/null
@@ -1,364 +0,0 @@
-<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/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <artifactId>taverna-parent</artifactId>
- <groupId>net.sf.taverna</groupId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>uk.org.taverna.workbench</groupId>
- <artifactId>taverna-workbench-product</artifactId>
- <version>3.0.0-SNAPSHOT</version>
- <name>Taverna Workbench Product</name>
- <packaging>pom</packaging>
- <dependencies>
- <!-- 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>${spring.dm.version}</version>
- </dependency>
- <dependency>
- <groupId>org.springframework.osgi</groupId>
- <artifactId>spring-osgi-extender</artifactId>
- <version>${spring.dm.version}</version>
- </dependency>
- <!-- Spring -->
- <dependency>
- <groupId>org.springframework</groupId>
- <artifactId>org.springframework.context</artifactId>
- <version>${spring.version}</version>
- </dependency>
-
- <!-- Java Extension Implementations -->
- <!-- <dependency> <groupId>com.sun.xml</groupId> <artifactId>com.springsource.com.sun.xml.bind</artifactId>
- <version>2.2.0</version> </dependency> -->
- <dependency>
- <groupId>javax.xml.bind</groupId>
- <artifactId>com.springsource.javax.xml.bind</artifactId>
- <version>2.2.0</version>
- </dependency>
- <dependency>
- <groupId>javax.activation</groupId>
- <artifactId>com.springsource.javax.activation</artifactId>
- <version>1.1.1</version>
- </dependency>
- <dependency> <!-- required by bsh -->
- <groupId>javax.servlet</groupId>
- <artifactId>com.springsource.javax.servlet</artifactId>
- <version>2.5.0</version>
- </dependency>
- <dependency>
- <groupId>javax.jms</groupId>
- <artifactId>com.springsource.javax.jms</artifactId>
- <version>1.1.0</version>
- </dependency>
- <dependency>
- <groupId>javax.xml.soap</groupId>
- <artifactId>com.springsource.javax.xml.soap</artifactId>
- <version>1.3.0</version>
- </dependency>
- <dependency>
- <groupId>javax.xml.stream</groupId>
- <artifactId>com.springsource.javax.xml.stream</artifactId>
- <version>1.0.1</version>
- </dependency>
- <dependency>
- <groupId>javax.mail</groupId>
- <artifactId>com.springsource.javax.mail</artifactId>
- <version>${mail.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.commons</groupId>
- <artifactId>com.springsource.org.apache.commons.codec</artifactId>
- <version>${commons.codec.version}</version>
- </dependency>
-
- <!-- OSGi Enterprise Services -->
- <dependency>
- <groupId>uk.org.taverna.osgi.services</groupId>
- <artifactId>xml-parser-service</artifactId>
- <version>${osgi.services.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.osgi.services</groupId>
- <artifactId>xml-transformer-service</artifactId>
- <version>${osgi.services.version}</version>
- </dependency>
-
- <!-- Taverna Activities -->
- <!-- <dependency> <groupId>net.sf.taverna.t2.activities</groupId> <artifactId>all-activities</artifactId>
- <version>${t2.activities.version}</version> <exclusions> <exclusion> <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>biomoby-activity</artifactId> </exclusion> </exclusions> </dependency> -->
- <!-- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>beanshell-activity</artifactId>
- <version>${t2.activities.version}</version>
- </dependency> -->
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>stringconstant-activity</artifactId>
- <version>${t2.activities.version}</version>
- </dependency>
-
- <!-- Taverna Activities UI -->
- <!-- <dependency> <groupId>net.sf.taverna.t2.ui-activities</groupId> <artifactId>all-activity-uis</artifactId>
- <version>${t2.activities.version}</version> <exclusions> <exclusion> <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>biomoby-activity-ui</artifactId> </exclusion> </exclusions> </dependency> -->
- <!-- <dependency>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
- <artifactId>beanshell-activity-ui</artifactId>
- <version>${t2.ui.activities.version}</version>
- </dependency> -->
- <dependency>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
- <artifactId>stringconstant-activity-ui</artifactId>
- <version>${t2.ui.activities.version}</version>
- </dependency>
-
- <!-- Taverna Workbench -->
- <dependency>
- <groupId>uk.org.taverna.workbench</groupId>
- <artifactId>taverna-workbench</artifactId>
- <version>0.1.0-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>workbench-impl</artifactId>
- <version>${t2.ui.impl.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>activity-palette-impl</artifactId>
- <version>${t2.ui.impl.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>configuration-impl</artifactId>
- <version>${t2.ui.impl.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>edits-impl</artifactId>
- <version>${t2.ui.impl.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>file-impl</artifactId>
- <version>${t2.ui.impl.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>menu-impl</artifactId>
- <version>${t2.ui.impl.version}</version>
- </dependency>
- <!-- <dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>report-impl</artifactId>
- <version>${t2.ui.impl.version}</version>
- </dependency> -->
-
- <dependency>
- <groupId>net.sf.taverna.t2.ui-components</groupId>
- <artifactId>perspective-design</artifactId>
- <version>${t2.ui.components.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-components</groupId>
- <artifactId>contextual-views</artifactId>
- <version>${t2.ui.components.version}</version>
- </dependency>
-
- <!-- <dependency>
- <groupId>net.sf.taverna.t2.ui-exts</groupId>
- <artifactId>menu-items</artifactId>
- <version>${t2.ui.exts.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-exts</groupId>
- <artifactId>loop-ui</artifactId>
- <version>${t2.ui.exts.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-exts</groupId>
- <artifactId>parallelize-ui</artifactId>
- <version>${t2.ui.exts.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-exts</groupId>
- <artifactId>retry-ui</artifactId>
- <version>${t2.ui.exts.version}</version>
- </dependency> -->
-
-
- <!-- Taverna Platform -->
- <dependency>
- <groupId>uk.org.taverna.platform</groupId>
- <artifactId>taverna-capability-impl</artifactId>
- <version>${platform.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.platform</groupId>
- <artifactId>taverna-data-impl</artifactId>
- <version>${platform.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.platform</groupId>
- <artifactId>taverna-run-impl</artifactId>
- <version>${platform.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.platform</groupId>
- <artifactId>taverna-execution-impl</artifactId>
- <version>${platform.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.platform</groupId>
- <artifactId>taverna-execution-local</artifactId>
- <version>${platform.version}</version>
- </dependency>
-
- <!-- Taverna Configuration -->
- <dependency>
- <groupId>uk.org.taverna.configuration</groupId>
- <artifactId>taverna-configuration-impl</artifactId>
- <version>${taverna.configuration.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.configuration</groupId>
- <artifactId>taverna-app-configuration-impl</artifactId>
- <version>${taverna.configuration.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.configuration</groupId>
- <artifactId>taverna-database-configuration-impl</artifactId>
- <version>${taverna.configuration.version}</version>
- </dependency>
-
- <!-- Scufl2 -->
- <dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-rdfxml</artifactId>
- <version>0.9.3-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-t2flow</artifactId>
- <version>0.9.3-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-validation-structural</artifactId>
- <version>0.9.3-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-validation-correctness</artifactId>
- <version>0.9.3-SNAPSHOT</version>
- </dependency>
-
- <!-- Taverna Security -->
- <dependency>
- <groupId>net.sf.taverna.t2.security</groupId>
- <artifactId>credential-manager-impl</artifactId>
- <version>${t2.security.version}</version>
- </dependency>
-
- <!-- Taverna Workflow Engine -->
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-impl</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-core-extensions</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-impl</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-core-extensions</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
-
- <!-- Taverna Provenance -->
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>provenance-derby</artifactId>
- <version>${t2.core.provenance.derby.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>provenance-mysql</artifactId>
- <version>${t2.core.provenance.mysql.version}</version>
- </dependency>
-
- </dependencies>
-
- <build>
- <plugins>
- <plugin>
- <artifactId>maven-assembly-plugin</artifactId>
- <version>2.3</version>
- <executions>
- <execution>
- <phase>package</phase>
- <goals>
- <goal>single</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <descriptors>
- <descriptor>src/main/assembly/release-assembly.xml</descriptor>
- </descriptors>
- </configuration>
- </plugin>
- </plugins>
- </build>
-
- <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>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/taverna-workbench-product/src/main/assembly/release-assembly.xml
----------------------------------------------------------------------
diff --git a/taverna-workbench-product/src/main/assembly/release-assembly.xml b/taverna-workbench-product/src/main/assembly/release-assembly.xml
deleted file mode 100644
index 5687d70..0000000
--- a/taverna-workbench-product/src/main/assembly/release-assembly.xml
+++ /dev/null
@@ -1,44 +0,0 @@
-<?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>bin</id>
- <formats>
- <format>dir</format>
- <!-- <format>zip</format> -->
- </formats>
-
- <dependencySets>
- <dependencySet>
- <useTransitiveDependencies>true</useTransitiveDependencies>
- <outputDirectory>/bundles</outputDirectory>
- <excludes>
- <exclude>net.sf.taverna.t2.activities:all-activities</exclude>
- <exclude>uk.org.taverna.workbench:taverna-workbench</exclude>
- <exclude>uk.org.taverna.osgi:osgi-launcher</exclude>
- <exclude>org.eclipse.osgi:org.eclipse.osgi</exclude>
- </excludes>
- </dependencySet>
- <dependencySet>
- <outputDirectory>/lib</outputDirectory>
- <includes>
- <include>uk.org.taverna.workbench:taverna-workbench</include>
- <include>uk.org.taverna.osgi:osgi-launcher</include>
- <include>org.apache.log4j:com.springsource.org.apache.log4j</include>
- <include>uk.org.taverna.configuration:taverna-app-configuration-api</include>
- <include>uk.org.taverna.configuration:taverna-app-configuration-impl</include>
- <include>org.osgi:org.osgi.core</include>
- <include>org.eclipse.osgi:org.eclipse.osgi</include>
- </includes>
- </dependencySet>
- </dependencySets>
-
- <fileSets>
- <fileSet>
- <directory>src/main/etc</directory>
- <fileMode>0755</fileMode>
- <outputDirectory></outputDirectory>
- </fileSet>
- </fileSets>
-</assembly>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/taverna-workbench-product/src/main/etc/conf/log4j.properties
----------------------------------------------------------------------
diff --git a/taverna-workbench-product/src/main/etc/conf/log4j.properties b/taverna-workbench-product/src/main/etc/conf/log4j.properties
deleted file mode 100644
index 5014f2b..0000000
--- a/taverna-workbench-product/src/main/etc/conf/log4j.properties
+++ /dev/null
@@ -1,14 +0,0 @@
-# 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
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/taverna-workbench-product/src/main/etc/conf/logging.properties
----------------------------------------------------------------------
diff --git a/taverna-workbench-product/src/main/etc/conf/logging.properties b/taverna-workbench-product/src/main/etc/conf/logging.properties
deleted file mode 100644
index aa77e69..0000000
--- a/taverna-workbench-product/src/main/etc/conf/logging.properties
+++ /dev/null
@@ -1,11 +0,0 @@
-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
-java.util.logging.FileHandler.limit = %h/.taverna-3.0.0/logs/taverna-3.0.0.log
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/taverna-workbench-product/src/main/etc/conf/taverna.app.properties
----------------------------------------------------------------------
diff --git a/taverna-workbench-product/src/main/etc/conf/taverna.app.properties b/taverna-workbench-product/src/main/etc/conf/taverna.app.properties
deleted file mode 100644
index 9634438..0000000
--- a/taverna-workbench-product/src/main/etc/conf/taverna.app.properties
+++ /dev/null
@@ -1,2 +0,0 @@
-taverna.app.name=taverna-workbench-3.0.0
-taverna.app.title=Taverna Workbench 3.0.0
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/taverna-workbench-product/src/main/etc/taverna.bat
----------------------------------------------------------------------
diff --git a/taverna-workbench-product/src/main/etc/taverna.bat b/taverna-workbench-product/src/main/etc/taverna.bat
deleted file mode 100644
index 7da12f3..0000000
--- a/taverna-workbench-product/src/main/etc/taverna.bat
+++ /dev/null
@@ -1,17 +0,0 @@
-@ECHO OFF
-
-REM Taverna startup script
-
-REM distribution directory
-set TAVERNA_HOME=%~dp0
-
-
-REM 300 MB memory, 140 MB for classes
-set ARGS=-Xmx300m -XX:MaxPermSize=140m
-
-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\taverna-workbench-0.1.0-SNAPSHOT.jar" %*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-product/blob/4e8c4cf7/taverna-workbench-product/src/main/etc/taverna.sh
----------------------------------------------------------------------
diff --git a/taverna-workbench-product/src/main/etc/taverna.sh b/taverna-workbench-product/src/main/etc/taverna.sh
deleted file mode 100644
index 36a24d3..0000000
--- a/taverna-workbench-product/src/main/etc/taverna.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/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="$JAVA_HOME/bin/java"
-fi
-
-# 300 MB memory, 140 MB for classes
-exec "$javabin" -Xmx300m -XX:MaxPermSize=140m \
- "-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/taverna-workbench-0.1.0-SNAPSHOT.jar" \
- ${1+"$@"}