Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix
diff --git a/genomix/genomix-hadoop/pom.xml b/genomix/genomix-hadoop/pom.xml
index 8ca2fa3..f305c49 100755
--- a/genomix/genomix-hadoop/pom.xml
+++ b/genomix/genomix-hadoop/pom.xml
@@ -160,6 +160,8 @@
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>genomix-hyracks</artifactId>
<version>0.2.6-SNAPSHOT</version>
+ <type>test-jar</type>
+ <scope>test</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
diff --git a/genomix/genomix-pregelix/pom.xml b/genomix/genomix-pregelix/pom.xml
index f609d3b..95227c5 100644
--- a/genomix/genomix-pregelix/pom.xml
+++ b/genomix/genomix-pregelix/pom.xml
@@ -1,60 +1,61 @@
<?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>
- <groupId>edu.uci.ics.pregelix</groupId>
- <artifactId>genomix-pregelix</artifactId>
- <packaging>jar</packaging>
- <version>0.2.6-SNAPSHOT</version>
- <name>genomix-pregelix</name>
+<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>
+ <groupId>edu.uci.ics.pregelix</groupId>
+ <artifactId>genomix-pregelix</artifactId>
+ <packaging>jar</packaging>
+ <version>0.2.6-SNAPSHOT</version>
+ <name>genomix-pregelix</name>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
- <profiles>
- <profile>
- <id>macosx</id>
- <activation>
- <os>
- <name>mac os x</name>
- </os>
- <jdk>1.7</jdk>
- </activation>
- <properties>
- <jvm.extraargs>-Djava.nio.channels.spi.SelectorProvider=sun.nio.ch.KQueueSelectorProvider</jvm.extraargs>
- </properties>
- </profile>
- </profiles>
+ <profiles>
+ <profile>
+ <id>macosx</id>
+ <activation>
+ <os>
+ <name>mac os x</name>
+ </os>
+ <jdk>1.7</jdk>
+ </activation>
+ <properties>
+ <jvm.extraargs>-Djava.nio.channels.spi.SelectorProvider=sun.nio.ch.KQueueSelectorProvider</jvm.extraargs>
+ </properties>
+ </profile>
+ </profiles>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-compiler-plugin</artifactId>
- <version>2.0.2</version>
- <configuration>
- <source>1.7</source>
- <target>1.7</target>
- <fork>true</fork>
- </configuration>
- </plugin>
- <plugin>
- <artifactId>maven-assembly-plugin</artifactId>
- <configuration>
- <descriptorRefs>
- <descriptorRef>jar-with-dependencies</descriptorRef>
- </descriptorRefs>
- </configuration>
- <executions>
- <execution>
- <id>make-my-jar-with-dependencies</id>
- <phase>package</phase>
- <goals>
- <goal>single</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <version>2.0.2</version>
+ <configuration>
+ <source>1.7</source>
+ <target>1.7</target>
+ <fork>true</fork>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <descriptorRefs>
+ <descriptorRef>jar-with-dependencies</descriptorRef>
+ </descriptorRefs>
+ </configuration>
+ <executions>
+ <execution>
+ <id>make-my-jar-with-dependencies</id>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>appassembler-maven-plugin</artifactId>
@@ -78,207 +79,207 @@
</execution>
</executions>
</plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-surefire-plugin</artifactId>
- <version>2.7.2</version>
- <configuration>
- <forkMode>pertest</forkMode>
- <argLine>-enableassertions -Xmx2047m -Dfile.encoding=UTF-8
- -Djava.util.logging.config.file=src/test/resources/logging.properties</argLine>
- <includes>
- <include>**/*TestSuite.java</include>
- <include>**/*Test.java</include>
- </includes>
- </configuration>
- </plugin>
- <plugin>
- <artifactId>maven-clean-plugin</artifactId>
- <configuration>
- <filesets>
- <fileset>
- <directory>.</directory>
- <includes>
- <include>teststore*</include>
- <include>edu*</include>
- <include>actual*</include>
- <include>build*</include>
- <include>expect*</include>
- <include>ClusterController*</include>
- <include>edu.uci.*</include>
- </includes>
- </fileset>
- </filesets>
- </configuration>
- </plugin>
- </plugins>
- </build>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>2.7.2</version>
+ <configuration>
+ <forkMode>pertest</forkMode>
+ <argLine>-enableassertions -Xmx2047m -Dfile.encoding=UTF-8
+ -Djava.util.logging.config.file=src/test/resources/logging.properties</argLine>
+ <includes>
+ <include>**/*TestSuite.java</include>
+ <include>**/*Test.java</include>
+ </includes>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-clean-plugin</artifactId>
+ <configuration>
+ <filesets>
+ <fileset>
+ <directory>.</directory>
+ <includes>
+ <include>teststore*</include>
+ <include>edu*</include>
+ <include>actual*</include>
+ <include>build*</include>
+ <include>expect*</include>
+ <include>ClusterController*</include>
+ <include>edu.uci.*</include>
+ </includes>
+ </fileset>
+ </filesets>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
- <dependencies>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>4.8.1</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>pregelix-core</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>genomix-data</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-api</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-data-std</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-control-cc</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-control-nc</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>com.kenai.nbpwr</groupId>
- <artifactId>org-apache-commons-io</artifactId>
- <version>1.3.1-201002241208</version>
- <type>nbm</type>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks.examples</groupId>
- <artifactId>hyracks-integration-tests</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-ipc</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>org.apache.hadoop</groupId>
- <artifactId>hadoop-core</artifactId>
- <version>0.20.2</version>
- </dependency>
- <dependency>
- <groupId>org.apache.hadoop</groupId>
- <artifactId>hadoop-test</artifactId>
- <version>0.20.2</version>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-hdfs-core</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-hdfs-core</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>test-jar</type>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>genomix-hyracks</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>genomix-hadoop</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- </dependencies>
+ <dependencies>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.8.1</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>pregelix-core</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>genomix-data</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-dataflow-std</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-api</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-dataflow-common</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-data-std</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-control-cc</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-control-nc</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>com.kenai.nbpwr</groupId>
+ <artifactId>org-apache-commons-io</artifactId>
+ <version>1.3.1-201002241208</version>
+ <type>nbm</type>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks.examples</groupId>
+ <artifactId>hyracks-integration-tests</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-ipc</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.hadoop</groupId>
+ <artifactId>hadoop-core</artifactId>
+ <version>0.20.2</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.hadoop</groupId>
+ <artifactId>hadoop-test</artifactId>
+ <version>0.20.2</version>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-hdfs-core</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-hdfs-core</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>test-jar</type>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>genomix-hyracks</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>genomix-hadoop</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ </dependencies>
- <scm>
- <connection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</connection>
- <developerConnection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</developerConnection>
- <url>http://code.google.com/p/hyracks/source/browse/#svn/trunk/fullstack/pregelix</url>
- </scm>
+ <scm>
+ <connection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</connection>
+ <developerConnection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</developerConnection>
+ <url>http://code.google.com/p/hyracks/source/browse/#svn/trunk/fullstack/pregelix</url>
+ </scm>
- <distributionManagement>
- <repository>
- <id>hyracks-releases</id>
- <url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-releases/</url>
- </repository>
- <snapshotRepository>
- <id>hyracks-snapshots</id>
- <url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-snapshots/</url>
- </snapshotRepository>
- </distributionManagement>
+ <distributionManagement>
+ <repository>
+ <id>hyracks-releases</id>
+ <url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-releases/</url>
+ </repository>
+ <snapshotRepository>
+ <id>hyracks-snapshots</id>
+ <url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-snapshots/</url>
+ </snapshotRepository>
+ </distributionManagement>
- <reporting>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-changelog-plugin</artifactId>
- </plugin>
- </plugins>
- </reporting>
+ <reporting>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-changelog-plugin</artifactId>
+ </plugin>
+ </plugins>
+ </reporting>
- <repositories>
- <repository>
- <id>hyracks-public</id>
- <url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
- </repository>
- <repository>
- <id>jboss-public</id>
- <url>https://repository.jboss.org/nexus/content/groups/public/</url>
- </repository>
- </repositories>
+ <repositories>
+ <repository>
+ <id>hyracks-public</id>
+ <url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
+ </repository>
+ <repository>
+ <id>jboss-public</id>
+ <url>https://repository.jboss.org/nexus/content/groups/public/</url>
+ </repository>
+ </repositories>
- <pluginRepositories>
- <pluginRepository>
- <id>hyracks-public</id>
- <url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
- <releases>
- <updatePolicy>always</updatePolicy>
- </releases>
- </pluginRepository>
- </pluginRepositories>
+ <pluginRepositories>
+ <pluginRepository>
+ <id>hyracks-public</id>
+ <url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
+ <releases>
+ <updatePolicy>always</updatePolicy>
+ </releases>
+ </pluginRepository>
+ </pluginRepositories>
</project>