Author: mes Date: 2011-09-20 15:47:02 -0700 (Tue, 20 Sep 2011) New Revision: 26897
Added: core3/impl/trunk/io-impl/impl/ core3/impl/trunk/io-impl/impl/osgi.bnd core3/impl/trunk/io-impl/impl/pom.xml core3/impl/trunk/io-impl/impl/src/ core3/impl/trunk/io-impl/performance/ core3/impl/trunk/io-impl/performance/pom.xml core3/impl/trunk/io-impl/performance/src/ core3/impl/trunk/io-impl/performance/src/main/ core3/impl/trunk/io-impl/performance/src/main/java/ core3/impl/trunk/io-impl/performance/src/main/java/org/ core3/impl/trunk/io-impl/performance/src/main/java/org/cytoscape/ core3/impl/trunk/io-impl/performance/src/main/java/org/cytoscape/io/ core3/impl/trunk/io-impl/performance/src/main/java/org/cytoscape/io/read/ core3/impl/trunk/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/ core3/impl/trunk/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java Removed: core3/impl/trunk/io-impl/osgi.bnd core3/impl/trunk/io-impl/pom.xml core3/impl/trunk/io-impl/src/ Log: adding performance subdir Copied: core3/impl/trunk/io-impl/impl/osgi.bnd (from rev 26895, core3/impl/trunk/io-impl/osgi.bnd) =================================================================== --- core3/impl/trunk/io-impl/impl/osgi.bnd (rev 0) +++ core3/impl/trunk/io-impl/impl/osgi.bnd 2011-09-20 22:47:02 UTC (rev 26897) @@ -0,0 +1,6 @@ +#----------------------------------------------------------------- +# Use this file to add customized Bnd instructions for the bundle +#----------------------------------------------------------------- + +Import-Package: * +Private-Package: org.cytoscape.io.internal, org.cytoscape.io.internal.* Copied: core3/impl/trunk/io-impl/impl/pom.xml (from rev 26895, core3/impl/trunk/io-impl/pom.xml) =================================================================== --- core3/impl/trunk/io-impl/impl/pom.xml (rev 0) +++ core3/impl/trunk/io-impl/impl/pom.xml 2011-09-20 22:47:02 UTC (rev 26897) @@ -0,0 +1,71 @@ +<?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>io-impl-parent</artifactId> + <version>3.0.0-alpha8-SNAPSHOT</version> + </parent> + + <properties> + <bundle.symbolicName>org.cytoscape.io-impl</bundle.symbolicName> + <bundle.namespace>org.cytoscape.io</bundle.namespace> + </properties> + + <modelVersion>4.0.0</modelVersion> + <artifactId>io-impl</artifactId> + + <name>${bundle.symbolicName} [${bundle.namespace}]</name> + + <packaging>bundle</packaging> + + <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>${project.version}</Bundle-Version> + <_include>-osgi.bnd</_include> + </instructions> + </configuration> + </plugin> + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-surefire-plugin</artifactId> + <version>${maven-surefire-plugin.version}</version> + <configuration> + <argLine>-Xmx2G</argLine> + <redirectTestOutputToFile>true</redirectTestOutputToFile> + </configuration> + </plugin> + <plugin> + <groupId>org.jvnet.jaxb2.maven2</groupId> + <artifactId>maven-jaxb2-plugin</artifactId> + <version>0.7.4</version> + <executions> + <execution> + <id>vizmap</id> + <goals> + <goal>generate</goal> + </goals> + <configuration> + <schemaDirectory>src/main/resources/xsd</schemaDirectory> + <schemaIncludes> + <include>vizmap.xsd</include> + </schemaIncludes> + <generatePackage>org.cytoscape.io.internal.util.vizmap.model</generatePackage> + <verbose>true</verbose> + <removeOldOutput>false</removeOldOutput> + <forceRegenerate>false</forceRegenerate> + </configuration> + </execution> + </executions> + </plugin> + </plugins> + </build> +</project> Deleted: core3/impl/trunk/io-impl/osgi.bnd =================================================================== --- core3/impl/trunk/io-impl/osgi.bnd 2011-09-20 22:21:01 UTC (rev 26896) +++ core3/impl/trunk/io-impl/osgi.bnd 2011-09-20 22:47:02 UTC (rev 26897) @@ -1,6 +0,0 @@ -#----------------------------------------------------------------- -# Use this file to add customized Bnd instructions for the bundle -#----------------------------------------------------------------- - -Import-Package: * -Private-Package: org.cytoscape.io.internal, org.cytoscape.io.internal.* Added: core3/impl/trunk/io-impl/performance/pom.xml =================================================================== --- core3/impl/trunk/io-impl/performance/pom.xml (rev 0) +++ core3/impl/trunk/io-impl/performance/pom.xml 2011-09-20 22:47:02 UTC (rev 26897) @@ -0,0 +1,83 @@ +<?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> + <artifactId>io-impl-parent</artifactId> + <groupId>org.cytoscape</groupId> + <version>3.0.0-alpha8-SNAPSHOT</version> + </parent> + + <properties> + <bundle.symbolicName>org.cytoscape.io-impl-performance</bundle.symbolicName> + <bundle.namespace>org.cytoscape.io</bundle.namespace> + </properties> + + <modelVersion>4.0.0</modelVersion> + <groupId>org.cytoscape</groupId> + <artifactId>io-impl-performance</artifactId> + + <name>${bundle.symbolicName}</name> + + <packaging>jar</packaging> + + <build> + <plugins> + <plugin> + <artifactId>maven-assembly-plugin</artifactId> + <version>${maven-assembly-plugin.version}</version> + <configuration> + <descriptorRefs> + <descriptorRef>jar-with-dependencies</descriptorRef> + </descriptorRefs> + <archive> + <manifest> + <mainClass>org.cytoscape.io.read.sif.PerfTest</mainClass> + </manifest> + </archive> + </configuration> + <executions> + <execution> + <id>make-assembly</id> <!-- this is used for inheritance merges --> + <phase>package</phase> <!-- append to the packaging phase. --> + <goals> + <goal>attached</goal> <!-- goals == mojos --> + </goals> + </execution> + </executions> + </plugin> + </plugins> + </build> + + <!-- + This is where any additional implementation dependencies necessary for + running the integration tests should reside, NOT in the top level pom.xml. + --> + <dependencies> + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>io-impl</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>model-impl</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>event-impl</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>model-impl</artifactId> + <version>${project.version}</version> + <type>test-jar</type> + </dependency> + <dependency> + <groupId>org.ops4j.pax.logging</groupId> + <artifactId>pax-logging-api</artifactId> + <version>1.5.2</version> + </dependency> + </dependencies> +</project> Added: core3/impl/trunk/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java =================================================================== --- core3/impl/trunk/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java (rev 0) +++ core3/impl/trunk/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java 2011-09-20 22:47:02 UTC (rev 26897) @@ -0,0 +1,19 @@ +package org.cytoscape.io.read.sif; + + + + + +public class PerfTest { + + + public static void main(String[] args) { + new PerfTest().runTestLoop(); + } + + public PerfTest() { + } + + public void runTestLoop() { + } +} Deleted: core3/impl/trunk/io-impl/pom.xml =================================================================== --- core3/impl/trunk/io-impl/pom.xml 2011-09-20 22:21:01 UTC (rev 26896) +++ core3/impl/trunk/io-impl/pom.xml 2011-09-20 22:47:02 UTC (rev 26897) @@ -1,236 +0,0 @@ -<?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>impl-parent</artifactId> - <version>3.0.0-alpha8-SNAPSHOT</version> - </parent> - - <properties> - <bundle.symbolicName>org.cytoscape.io-impl</bundle.symbolicName> - <bundle.namespace>org.cytoscape.io</bundle.namespace> - </properties> - - <modelVersion>4.0.0</modelVersion> - <artifactId>io-impl</artifactId> - - <name>${bundle.symbolicName} [${bundle.namespace}]</name> - - <packaging>bundle</packaging> - - - <repositories> - <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots --> - <repository> - <id>cytoscape_snapshots</id> - <snapshots> - <enabled>true</enabled> - </snapshots> - <releases> - <enabled>false</enabled> - </releases> - <name>Cytoscape Snapshots</name> - <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url> - </repository> - <!-- bootstrap for cytoscape dependencies, namely the parent POM releases --> - <repository> - <id>cytoscape_releases</id> - <snapshots> - <enabled>false</enabled> - </snapshots> - <releases> - <enabled>true</enabled> - </releases> - <name>Cytoscape Releases</name> - <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url> - </repository> - </repositories> - - <build> - <resources> - <resource> - <directory>src/main/resources</directory> - </resource> - <resource> - <directory>.</directory> - <includes> - <include>plugin.xml</include> - <include>plugin.properties</include> - <include>icons/**</include> - </includes> - </resource> - </resources> - <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>${project.version}</Bundle-Version> - <_include>-osgi.bnd</_include> - </instructions> - </configuration> - </plugin> - <plugin> - <groupId>org.apache.maven.plugins</groupId> - <artifactId>maven-surefire-plugin</artifactId> - <version>${maven-surefire-plugin.version}</version> - <configuration> - <argLine>-Xmx2G</argLine> - <redirectTestOutputToFile>true</redirectTestOutputToFile> - </configuration> - </plugin> - <plugin> - <groupId>org.jvnet.jaxb2.maven2</groupId> - <artifactId>maven-jaxb2-plugin</artifactId> - <version>0.7.4</version> - <executions> - <execution> - <id>vizmap</id> - <goals> - <goal>generate</goal> - </goals> - <configuration> - <schemaDirectory>src/main/resources/xsd</schemaDirectory> - <schemaIncludes> - <include>vizmap.xsd</include> - </schemaIncludes> - <generatePackage>org.cytoscape.io.internal.util.vizmap.model</generatePackage> - <verbose>true</verbose> - <removeOldOutput>false</removeOldOutput> - <forceRegenerate>false</forceRegenerate> - </configuration> - </execution> - </executions> - </plugin> - </plugins> - </build> - - <dependencies> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>di-util-api</artifactId> - </dependency> - <dependency> - <groupId>org.springframework</groupId> - <artifactId>spring-core</artifactId> - <version>${spring.version}</version> - <scope>provided</scope> - </dependency> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>equations-api</artifactId> - </dependency> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>io-api</artifactId> - </dependency> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>presentation-api</artifactId> - </dependency> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>layout-api</artifactId> - </dependency> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>model-api</artifactId> - </dependency> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>core-task-api</artifactId> - </dependency> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>property-api</artifactId> - </dependency> - <!-- 3rd party libraries --> - - <dependency> - <groupId>com.lowagie.text</groupId> - <artifactId>com.springsource.com.lowagie.text</artifactId> - <version>2.0.8</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>opencsv</artifactId> - <version>2.1</version> - </dependency> - - <!-- freehep --> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-graphicsio</artifactId> - <version>2.1.1</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-graphicsio-svg</artifactId> - <version>2.1.1</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-graphics2d</artifactId> - <version>2.1.1</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-graphicsio-ps</artifactId> - <version>2.1.1</version> - </dependency> - - <!-- For Testing --> - <dependency> - <groupId>junit</groupId> - <artifactId>junit</artifactId> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.mockito</groupId> - <artifactId>mockito-all</artifactId> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>model-impl</artifactId> - <version>${project.version}</version> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>model-impl</artifactId> - <version>${project.version}</version> - <type>test-jar</type> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>viewmodel-impl</artifactId> - <version>${project.version}</version> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>viewmodel-impl</artifactId> - <version>${project.version}</version> - <type>test-jar</type> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>service-api</artifactId> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.cytoscape</groupId> - <artifactId>event-api</artifactId> - <type>test-jar</type> - <scope>test</scope> - </dependency> - 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