Author: jm
Date: 2011-10-24 09:47:11 -0700 (Mon, 24 Oct 2011)
New Revision: 27280
Added:
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/pom.xml
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/java/
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/java/CyActivator.java
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/java/org/
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/java/org/cytoscape/
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/java/org/cytoscape/cmdline/
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/java/org/cytoscape/cmdline/internal/
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/java/org/cytoscape/cmdline/internal/CommandLineArgsImpl.java
csplugins/trunk/toronto/jm/cykaraf/launcher/
csplugins/trunk/toronto/jm/cykaraf/launcher/pom.xml
csplugins/trunk/toronto/jm/cykaraf/launcher/src/
csplugins/trunk/toronto/jm/cykaraf/launcher/src/main/
csplugins/trunk/toronto/jm/cykaraf/launcher/src/main/java/
csplugins/trunk/toronto/jm/cykaraf/launcher/src/main/java/org/
csplugins/trunk/toronto/jm/cykaraf/launcher/src/main/java/org/cytoscape/
csplugins/trunk/toronto/jm/cykaraf/launcher/src/main/java/org/cytoscape/launcher/
csplugins/trunk/toronto/jm/cykaraf/launcher/src/main/java/org/cytoscape/launcher/internal/
csplugins/trunk/toronto/jm/cykaraf/launcher/src/main/java/org/cytoscape/launcher/internal/Launcher.java
Modified:
csplugins/trunk/toronto/jm/cykaraf/distribution/pom.xml
csplugins/trunk/toronto/jm/cykaraf/distribution/src/main/descriptors/config-dev.xml
csplugins/trunk/toronto/jm/cykaraf/distribution/src/main/resources/etc/custom.properties
csplugins/trunk/toronto/jm/cykaraf/distribution/src/main/xsl/template.xslt
csplugins/trunk/toronto/jm/cykaraf/features/src/main/resources/features.xml
Log:
Added custom launcher which provides CommandLineArgs service
Added JAXB implementation to list of system packages (required by PSI-MI)
Re-enabled commented out bundles
Added: csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/pom.xml
===================================================================
--- csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/pom.xml
(rev 0)
+++ csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/pom.xml 2011-10-24
16:47:11 UTC (rev 27280)
@@ -0,0 +1,68 @@
+<?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";>
+
+ <parent>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>3.0.0-alpha9-SNAPSHOT</version>
+ </parent>
+
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>cmdline-impl</artifactId>
+ <version>3.0.0-alpha7-SNAPSHOT</version>
+
+ <name>Command Line Provider Implementation</name>
+
+ <properties>
+
<bundle.symbolicName>org.cytoscape.cmdline-impl</bundle.symbolicName>
+ <bundle.namespace>org.cytoscape.cmdline</bundle.namespace>
+ </properties>
+
+ <packaging>bundle</packaging>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.osgi</groupId>
+ <artifactId>org.osgi.core</artifactId>
+ <version>${osgi.api.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>service-api</artifactId>
+ <version>3.0.0-alpha8-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape.distribution</groupId>
+ <artifactId>launcher</artifactId>
+ <version>3.0.0-alpha7-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>cmdline</artifactId>
+ <version>3.0.0-alpha7-SNAPSHOT</version>
+ </dependency>
+ </dependencies>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+
<version>${maven-bundle-plugin.version}</version>
+ <extensions>true</extensions>
+ <configuration>
+ <instructions>
+
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
+
<Bundle-Version>${project.version}</Bundle-Version>
+
<Export-Package>!${bundle.namespace}.internal.*,${bundle.namespace}.*;version="${project.version}"</Export-Package>
+
<Private-Package>${bundle.namespace}.internal.*</Private-Package>
+ <_include>-osgi.bnd</_include>
+ </instructions>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
Added:
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/java/CyActivator.java
===================================================================
---
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/java/CyActivator.java
(rev 0)
+++
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/java/CyActivator.java
2011-10-24 16:47:11 UTC (rev 27280)
@@ -0,0 +1,17 @@
+import java.util.Properties;
+
+import org.cytoscape.cmdline.CommandLineArgs;
+import org.cytoscape.cmdline.internal.CommandLineArgsImpl;
+import org.cytoscape.service.util.AbstractCyActivator;
+import org.osgi.framework.BundleContext;
+
+
+public class CyActivator extends AbstractCyActivator {
+
+ @Override
+ public void start(BundleContext context) throws Exception {
+ Properties properties = new Properties();
+ registerService(context, new CommandLineArgsImpl(),
CommandLineArgs.class, properties);
+ }
+
+}
Added:
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/java/org/cytoscape/cmdline/internal/CommandLineArgsImpl.java
===================================================================
---
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/java/org/cytoscape/cmdline/internal/CommandLineArgsImpl.java
(rev 0)
+++
csplugins/trunk/toronto/jm/cykaraf/cmdline-impl/src/main/java/org/cytoscape/cmdline/internal/CommandLineArgsImpl.java
2011-10-24 16:47:11 UTC (rev 27280)
@@ -0,0 +1,11 @@
+package org.cytoscape.cmdline.internal;
+
+import org.cytoscape.cmdline.CommandLineArgs;
+import org.cytoscape.launcher.internal.Launcher;
+
+public class CommandLineArgsImpl implements CommandLineArgs {
+ @Override
+ public String[] getArgs() {
+ return Launcher.getStartupArguments();
+ }
+}
Modified: csplugins/trunk/toronto/jm/cykaraf/distribution/pom.xml
===================================================================
--- csplugins/trunk/toronto/jm/cykaraf/distribution/pom.xml 2011-10-24
01:23:23 UTC (rev 27279)
+++ csplugins/trunk/toronto/jm/cykaraf/distribution/pom.xml 2011-10-24
16:47:11 UTC (rev 27280)
@@ -153,6 +153,13 @@
<type>jar</type>
<outputDirectory>target/dependencies/branding</outputDirectory>
</artifactItem>
+ <artifactItem>
+
<groupId>org.cytoscape.distribution</groupId>
+
<artifactId>karaf-launcher</artifactId>
+
<version>3.0.0-alpha7-SNAPSHOT</version>
+
<type>jar</type>
+
<outputDirectory>target/dependencies/launcher</outputDirectory>
+ </artifactItem>
</artifactItems>
</configuration>
</execution>
@@ -257,6 +264,45 @@
</execution>
</executions>
</plugin>
+ <plugin>
+
<groupId>com.google.code.maven-replacer-plugin</groupId>
+ <artifactId>maven-replacer-plugin</artifactId>
+ <version>1.3.9</version>
+ <executions>
+ <execution>
+ <id>patch-karaf-main-unix</id>
+ <phase>compile</phase>
+ <goals>
+ <goal>replace</goal>
+ </goals>
+ <configuration>
+
<file>target/dependencies/unix/apache-karaf-${karaf.version}/bin/karaf</file>
+
<outputFile>target/dependencies/launcher/bin/karaf</outputFile>
+ </configuration>
+ </execution>
+ <execution>
+
<id>patch-karaf-main-windows</id>
+ <phase>compile</phase>
+ <goals>
+ <goal>replace</goal>
+ </goals>
+ <configuration>
+
<file>target/dependencies/windows/apache-karaf-${karaf.version}/bin/karaf.bat</file>
+
<outputFile>target/dependencies/launcher/bin/karaf.bat</outputFile>
+ </configuration>
+ </execution>
+ </executions>
+ <configuration>
+ <regex>false</regex>
+ <unescape>false</unescape>
+ <replacements>
+ <replacement>
+
<token>MAIN=org.apache.karaf.main.Main</token>
+
<value>MAIN=org.cytoscape.launcher.internal.Launcher</value>
+ </replacement>
+ </replacements>
+ </configuration>
+ </plugin>
</plugins>
</build>
</project>
Modified:
csplugins/trunk/toronto/jm/cykaraf/distribution/src/main/descriptors/config-dev.xml
===================================================================
---
csplugins/trunk/toronto/jm/cykaraf/distribution/src/main/descriptors/config-dev.xml
2011-10-24 01:23:23 UTC (rev 27279)
+++
csplugins/trunk/toronto/jm/cykaraf/distribution/src/main/descriptors/config-dev.xml
2011-10-24 16:47:11 UTC (rev 27280)
@@ -3,13 +3,9 @@
<line-ending>keep</line-ending>
<karaf>
<feature-repository>target/features-repo-dev</feature-repository>
- <distribution
base="target/dependencies/windows/apache-karaf-${karaf.version}">
- <scripts>
- <script>bin/karaf.bat</script>
- </scripts>
- </distribution>
<distribution
base="target/dependencies/unix/apache-karaf-${karaf.version}">
<scripts>
+ <script>bin/karaf.bat</script>
<script>bin/karaf</script>
</scripts>
</distribution>
Modified:
csplugins/trunk/toronto/jm/cykaraf/distribution/src/main/resources/etc/custom.properties
===================================================================
---
csplugins/trunk/toronto/jm/cykaraf/distribution/src/main/resources/etc/custom.properties
2011-10-24 01:23:23 UTC (rev 27279)
+++
csplugins/trunk/toronto/jm/cykaraf/distribution/src/main/resources/etc/custom.properties
2011-10-24 16:47:11 UTC (rev 27280)
@@ -1,2 +1,2 @@
karaf.systemBundlesStartLevel=100
-org.osgi.framework.system.packages.extra = org.apache.karaf.branding;
\ No newline at end of file
+org.osgi.framework.system.packages.extra =
org.apache.karaf.branding,org.cytoscape.launcher.internal,com.sun.xml.internal.bind;
\ No newline at end of file
Modified:
csplugins/trunk/toronto/jm/cykaraf/distribution/src/main/xsl/template.xslt
===================================================================
--- csplugins/trunk/toronto/jm/cykaraf/distribution/src/main/xsl/template.xslt
2011-10-24 01:23:23 UTC (rev 27279)
+++ csplugins/trunk/toronto/jm/cykaraf/distribution/src/main/xsl/template.xslt
2011-10-24 16:47:11 UTC (rev 27280)
@@ -37,18 +37,16 @@
</fileSet>
<!-- Copy over bin/* separately to get the correct file mode -->
- <xsl:for-each select="/config/karaf/distribution">
- <fileSet>
- <directory><xsl:value-of select="@base"/></directory>
- <outputDirectory>/framework</outputDirectory>
- <includes>
- <xsl:for-each select="scripts/script">
- <include><xsl:value-of select="."/></include>
- </xsl:for-each>
- </includes>
- <fileMode>0755</fileMode>
- </fileSet>
- </xsl:for-each>
+ <fileSet>
+ <directory>target/dependencies/launcher</directory>
+ <outputDirectory>/framework</outputDirectory>
+ <includes>
+ <xsl:for-each select="scripts/script">
+ <include><xsl:value-of select="."/></include>
+ </xsl:for-each>
+ </includes>
+ <fileMode>0755</fileMode>
+ </fileSet>
<fileSet>
<directory>src/main/bin</directory>
@@ -71,6 +69,14 @@
</fileSet>
<fileSet>
+ <directory>target/dependencies/launcher</directory>
+ <includes>
+ <include>*.jar</include>
+ </includes>
+ <outputDirectory>/framework/lib</outputDirectory>
+ </fileSet>
+
+ <fileSet>
<directory>target/dependencies/splash-launcher/images</directory>
<includes>
<include>CytoscapeSplashScreen.png</include>
Modified:
csplugins/trunk/toronto/jm/cykaraf/features/src/main/resources/features.xml
===================================================================
--- csplugins/trunk/toronto/jm/cykaraf/features/src/main/resources/features.xml
2011-10-24 01:23:23 UTC (rev 27279)
+++ csplugins/trunk/toronto/jm/cykaraf/features/src/main/resources/features.xml
2011-10-24 16:47:11 UTC (rev 27280)
@@ -8,6 +8,7 @@
<bundle
start-level="1">mvn:org.cytoscape/splash-updater-impl/${cytoscape.support.version}</bundle>
+ <bundle
start-level="10">mvn:org.cytoscape/cmdline/${cytoscape.support.version}</bundle>
<bundle
start-level="10">mvn:org.cytoscape/equations-api/${cytoscape.api.version}</bundle>
<bundle
start-level="10">mvn:org.cytoscape/di-util-api/${cytoscape.api.version}</bundle>
<bundle
start-level="10">mvn:org.cytoscape/model-api/${cytoscape.api.version}</bundle>
@@ -29,10 +30,11 @@
<bundle
start-level="10">mvn:org.cytoscape/webservice-api/${cytoscape.api.version}</bundle>
<bundle
start-level="10">mvn:org.cytoscape/application-api/${cytoscape.api.version}</bundle>
+ <bundle
start-level="15">mvn:org.cytoscape/cmdline-impl/${cytoscape.support.version}</bundle>
<bundle
start-level="15">mvn:org.cytoscape/property-impl/${cytoscape.impl.version}</bundle>
- <bundle
start-level="15">mvn:org.cytoscape/graph-render/3.0.0-alpha8-SNAPSHOT</bundle>
- <bundle
start-level="15">mvn:org.cytoscape/util-intr/3.0.0-alpha8-SNAPSHOT</bundle>
- <bundle
start-level="15">mvn:org.cytoscape/spacial/3.0.0-alpha8-SNAPSHOT</bundle>
+ <bundle
start-level="15">mvn:org.cytoscape/graph-render/${cytoscape.impl.version}</bundle>
+ <bundle
start-level="15">mvn:org.cytoscape/util-intr/${cytoscape.impl.version}</bundle>
+ <bundle
start-level="15">mvn:org.cytoscape/spacial/${cytoscape.impl.version}</bundle>
<bundle
start-level="2">mvn:cytoscape-temp/l2fprod-common-sheet/7.3</bundle>
@@ -112,14 +114,10 @@
<bundle
start-level="70">mvn:org.cytoscape/editor-impl/${cytoscape.impl.version}</bundle>
<bundle
start-level="70">mvn:org.cytoscape/layout-prefuse-impl/${cytoscape.impl.version}</bundle>
<bundle
start-level="70">mvn:org.cytoscape/linkout-impl/${cytoscape.impl.version}</bundle>
- <!--
<bundle
start-level="70">mvn:org.cytoscape/psi-mi-impl/${cytoscape.impl.version}</bundle>
- -->
<bundle
start-level="70">mvn:org.cytoscape/network-analyzer-impl/${cytoscape.impl.version}</bundle>
<bundle
start-level="70">mvn:org.cytoscape/table-import-impl/${cytoscape.impl.version}</bundle>
- <!--
<bundle
start-level="70">mvn:org.cytoscape/webservice-biomart-client-impl/${cytoscape.impl.version}</bundle>
- -->
<bundle
start-level="70">mvn:org.cytoscape/webservice-ncbi-client-impl/${cytoscape.impl.version}</bundle>
<bundle
start-level="70">mvn:org.cytoscape/filter-impl/${cytoscape.impl.version}</bundle>
<bundle
start-level="70">mvn:org.cytoscape/sbml-impl/${cytoscape.impl.version}</bundle>
Added: csplugins/trunk/toronto/jm/cykaraf/launcher/pom.xml
===================================================================
--- csplugins/trunk/toronto/jm/cykaraf/launcher/pom.xml
(rev 0)
+++ csplugins/trunk/toronto/jm/cykaraf/launcher/pom.xml 2011-10-24 16:47:11 UTC
(rev 27280)
@@ -0,0 +1,53 @@
+<?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";>
+
+ <parent>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>3.0.0-alpha9-SNAPSHOT</version>
+ </parent>
+
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.cytoscape.distribution</groupId>
+ <artifactId>karaf-launcher</artifactId>
+ <version>3.0.0-alpha7-SNAPSHOT</version>
+
+ <name>Cytoscape Launcher</name>
+
+ <properties>
+
<bundle.symbolicName>org.cytoscape.launcher</bundle.symbolicName>
+ <bundle.namespace>org.cytoscape.launcher</bundle.namespace>
+ <karaf.version>2.2.3</karaf.version>
+ </properties>
+
+ <packaging>bundle</packaging>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.karaf</groupId>
+ <artifactId>org.apache.karaf.main</artifactId>
+ <version>${karaf.version}</version>
+ </dependency>
+ </dependencies>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+
<version>${maven-bundle-plugin.version}</version>
+ <extensions>true</extensions>
+ <configuration>
+ <instructions>
+
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
+
<Bundle-Version>${project.version}</Bundle-Version>
+
<Export-Package>!${bundle.namespace}.internal.*,${bundle.namespace}.*;version="${project.version}"</Export-Package>
+
<Private-Package>${bundle.namespace}.internal.*</Private-Package>
+ <_include>-osgi.bnd</_include>
+ </instructions>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
Added:
csplugins/trunk/toronto/jm/cykaraf/launcher/src/main/java/org/cytoscape/launcher/internal/Launcher.java
===================================================================
---
csplugins/trunk/toronto/jm/cykaraf/launcher/src/main/java/org/cytoscape/launcher/internal/Launcher.java
(rev 0)
+++
csplugins/trunk/toronto/jm/cykaraf/launcher/src/main/java/org/cytoscape/launcher/internal/Launcher.java
2011-10-24 16:47:11 UTC (rev 27280)
@@ -0,0 +1,18 @@
+package org.cytoscape.launcher.internal;
+
+import org.apache.karaf.main.Main;
+
+public class Launcher {
+ private static String[] startupArguments;
+
+ public static void main(String[] args) throws Exception {
+ startupArguments = args;
+ Main.main(args);
+ }
+
+ public static String[] getStartupArguments() {
+ String[] result = new String[startupArguments.length];
+ System.arraycopy(startupArguments, 0, result, 0,
startupArguments.length);
+ return result;
+ }
+}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
