T3-903 Updated build to keep it in line with workbench build.
git-svn-id: https://taverna.googlecode.com/svn/taverna/products/net.sf.taverna.t2.taverna-commandline/trunk@16202 bf327186-88b3-11dd-a302-d386e5130c1c
diff --git a/pom.xml b/pom.xml
index 7279369..89b3fdc 100644
--- a/pom.xml
+++ b/pom.xml
@@ -3,15 +3,182 @@
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>
- <artifactId>taverna-parent</artifactId>
<groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
<version>3.0.1-SNAPSHOT</version>
</parent>
- <groupId>net.sf.taverna.t2</groupId>
- <artifactId>taverna-commandline</artifactId>
- <name>Taverna command line utility</name>
- <packaging>pom</packaging>
+ <groupId>uk.org.taverna.workbench</groupId>
+ <artifactId>taverna-command-line-product</artifactId>
+ <name>Taverna Command Line</name>
+ <packaging>taverna-application</packaging>
+ <profiles>
+ <profile>
+ <id>developer</id>
+ <activation>
+ <activeByDefault>true</activeByDefault>
+ </activation>
+ <properties>
+ <assembly.descriptor>src/main/assembly/developer-assembly.xml</assembly.descriptor>
+ <profile.updateSite>http://dev.mygrid.org.uk/taverna/updates/taverna-command-line/</profile.updateSite>
+ <profile.pluginSite>http://dev.mygrid.org.uk/taverna/plugins/taverna-command-line/</profile.pluginSite>
+ </properties>
+ </profile>
+ <profile>
+ <id>nightly</id>
+ <properties>
+ <assembly.descriptor>src/main/assembly/nightly-assembly.xml</assembly.descriptor>
+ <profile.updateSite>http://dev.mygrid.org.uk/taverna/updates/taverna-command-line/</profile.updateSite>
+ <profile.pluginSite>http://dev.mygrid.org.uk/taverna/plugins/taverna-command-line/</profile.pluginSite>
+ </properties>
+ </profile>
+ <profile>
+ <id>release</id>
+ <properties>
+ <assembly.descriptor>src/main/assembly/release-assembly.xml</assembly.descriptor>
+ <profile.updateSite>http://www.mygrid.org.uk/taverna/updates/taverna-command-line/</profile.updateSite>
+ <profile.pluginSite>http://www.mygrid.org.uk/taverna/plugins/taverna-command-line/</profile.pluginSite>
+ </properties>
+ </profile>
+ </profiles>
+ <build>
+ <finalName>taverna-command-line-${project.version}</finalName>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <version>2.4</version>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <descriptors>
+ <descriptor>${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,net.sf.taverna.t2.commandline.options;version=2.0.1</value>
+ </frameworkConfiguration>
+ <frameworkConfiguration>
+ <name>org.osgi.framework.storage.clean</name>
+ <value>onFirstInit</value>
+ </frameworkConfiguration>
+ </frameworkConfigurations>
+ </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>
@@ -36,11 +203,6 @@
</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>
@@ -86,12 +248,12 @@
<dependency>
<groupId>uk.org.taverna.osgi.services</groupId>
<artifactId>xml-parser-service</artifactId>
- <version>${osgi.services.version}</version>
+ <version>0.1.1</version>
</dependency>
<dependency>
<groupId>uk.org.taverna.osgi.services</groupId>
<artifactId>xml-transformer-service</artifactId>
- <version>${osgi.services.version}</version>
+ <version>0.1.1</version>
</dependency>
<dependency>
<groupId>org.apache.felix</groupId>
@@ -107,14 +269,65 @@
<!-- Taverna Activities -->
<dependency>
<groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>all-activities</artifactId>
- <version>${t2.activities.version}</version>
- <exclusions>
- <exclusion>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>biomoby-activity</artifactId>
- </exclusion>
- </exclusions>
+ <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 Commandline -->
@@ -151,29 +364,42 @@
<version>${platform.version}</version>
</dependency>
- <!-- Taverna Configuration -->
+ <!-- Taverna Commons -->
<dependency>
<groupId>uk.org.taverna.configuration</groupId>
<artifactId>taverna-configuration-impl</artifactId>
- <version>${taverna.configuration.version}</version>
+ <version>0.1.1-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>uk.org.taverna.configuration</groupId>
<artifactId>taverna-app-configuration-impl</artifactId>
- <version>${taverna.configuration.version}</version>
+ <version>0.1.1-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>uk.org.taverna.configuration</groupId>
<artifactId>taverna-database-configuration-impl</artifactId>
- <version>${taverna.configuration.version}</version>
+ <version>0.1.1-SNAPSHOT</version>
</dependency>
-
- <!-- Taverna Commons -->
+ <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>
@@ -200,8 +426,37 @@
<!-- Data bundle -->
<dependency>
<groupId>uk.org.taverna.databundle</groupId>
- <artifactId>databundle</artifactId>
- <version>0.1.0-SNAPSHOT</version>
+ <artifactId>databundle</artifactId>
+ <version>0.1.0-SNAPSHOT</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 -->
@@ -247,28 +502,6 @@
</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 />
diff --git a/src/main/assembly/dependencies-component.xml b/src/main/assembly/dependencies-component.xml
new file mode 100644
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>${project.build.directory}/taverna-tmp</directory>
+ <fileMode>0755</fileMode>
+ <outputDirectory></outputDirectory>
+ </fileSet>
+ </fileSets>
+
+</component>
\ No newline at end of file
diff --git a/src/main/assembly/developer-assembly.xml b/src/main/assembly/developer-assembly.xml
new file mode 100644
index 0000000..ae2a7c3
--- /dev/null
+++ b/src/main/assembly/developer-assembly.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<assembly
+ xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+ <id>dev</id>
+ <formats>
+ <format>dir</format>
+ </formats>
+ <componentDescriptors>
+ <componentDescriptor>dependencies-component.xml</componentDescriptor>
+ </componentDescriptors>
+</assembly>
diff --git a/src/main/assembly/nightly-assembly.xml b/src/main/assembly/nightly-assembly.xml
new file mode 100644
index 0000000..f82e793
--- /dev/null
+++ b/src/main/assembly/nightly-assembly.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<assembly
+ xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+ <id>nightly</id>
+ <baseDirectory>taverna-command-line-${project.version}-${buildNumber}-nightly</baseDirectory>
+ <formats>
+ <!-- <format>dir</format> -->
+ <format>zip</format>
+ </formats>
+ <componentDescriptors>
+ <componentDescriptor>dependencies-component.xml</componentDescriptor>
+ </componentDescriptors>
+</assembly>
diff --git a/src/main/assembly/release-assembly.xml b/src/main/assembly/release-assembly.xml
index 2b73719..61da752 100644
--- a/src/main/assembly/release-assembly.xml
+++ b/src/main/assembly/release-assembly.xml
@@ -3,47 +3,13 @@
xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
- <id>bin</id>
+ <id>release</id>
+ <baseDirectory>taverna-command-line-${project.version}</baseDirectory>
<formats>
- <format>dir</format>
+ <!-- <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.commandline:taverna-command-line</exclude>
- <exclude>uk.org.taverna.osgi:osgi-launcher</exclude>
- <exclude>uk.org.taverna.commandline:arguments</exclude>
- <exclude>org.eclipse:org.eclipse.osgi</exclude>
- </excludes>
- </dependencySet>
- <dependencySet>
- <outputDirectory>/lib</outputDirectory>
- <includes>
- <include>uk.org.taverna.commandline:taverna-command-line</include>
- <include>uk.org.taverna.osgi:osgi-launcher</include>
- <include>net.sf.taverna.t2.taverna-commandline:taverna-commandline-common</include>
- <include>org.apache.commons:com.springsource.org.apache.commons.cli</include>
- <include>org.apache.commons:com.springsource.org.apache.commons.io</include>
- <include>org.apache.log4j:com.springsource.org.apache.log4j</include>
- <include>uk.org.taverna.commandline:arguments</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:org.eclipse.osgi</include>
- </includes>
- </dependencySet>
- </dependencySets>
-
- <fileSets>
- <fileSet>
- <directory>src/main/etc</directory>
- <fileMode>0755</fileMode>
- <outputDirectory></outputDirectory>
- </fileSet>
- </fileSets>
+ <componentDescriptors>
+ <componentDescriptor>dependencies-component.xml</componentDescriptor>
+ </componentDescriptors>
</assembly>
diff --git a/src/main/etc/conf/logging.properties b/src/main/etc/conf/logging.properties
index aa77e69..b03a43f 100644
--- a/src/main/etc/conf/logging.properties
+++ b/src/main/etc/conf/logging.properties
@@ -8,4 +8,3 @@
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
diff --git a/src/main/etc/executeworkflow.bat b/src/main/etc/executeworkflow.bat
index a7c6be4..722816c 100644
--- a/src/main/etc/executeworkflow.bat
+++ b/src/main/etc/executeworkflow.bat
@@ -6,12 +6,12 @@
set TAVERNA_HOME=%~dp0
-REM 300 MB memory, 140 MB for classes
-set ARGS=-Xmx300m -XX:MaxPermSize=140m
+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\taverna-command-line-0.1.2-SNAPSHOT.jar" %*
+java %ARGS% -jar "%TAVERNA_HOME%lib\uk.org.taverna.commandline\taverna-command-line-0.1.2-SNAPSHOT.jar" %*
diff --git a/src/main/etc/executeworkflow.sh b/src/main/etc/executeworkflow.sh
index 91866c2..663d37f 100644
--- a/src/main/etc/executeworkflow.sh
+++ b/src/main/etc/executeworkflow.sh
@@ -16,10 +16,10 @@
javabin="$JAVA_HOME/bin/java"
fi
-# 300 MB memory, 140 MB for classes
-exec "$javabin" -Xmx300m -XX:MaxPermSize=140m \
+# 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 "$taverna_home/lib/taverna-command-line-0.1.2-SNAPSHOT.jar" \
+ -jar "$taverna_home/lib/uk.org.taverna.commandline/taverna-command-line-0.1.2-SNAPSHOT.jar" \
${1+"$@"}
