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Merge pull request #7 from CIDARLAB/LookupTable
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Lookup table
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@shamseen
shamseen authored Jul 24, 2017
2 parents 7504f9a + c52764b commit c7b0e75
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Showing 7 changed files with 1,220 additions and 769 deletions.
302 changes: 151 additions & 151 deletions pom.xml
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Original file line number Diff line number Diff line change
@@ -1,194 +1,194 @@
<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">
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>
<groupId>org.cidarlab</groupId>
<artifactId>eugene</artifactId>
<version>2.0.0-SNAPSHOT</version>
<packaging>jar</packaging>
<modelVersion>4.0.0</modelVersion>
<groupId>org.cidarlab</groupId>
<artifactId>eugene</artifactId>
<version>2.0.0-SNAPSHOT</version>
<packaging>jar</packaging>

<build>
<resources>
<build>
<resources>

<!-- Rule-files for JBoss Drools ``Sparrow'' -->
<resource>
<directory>src/main/rules</directory>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>
<!-- Rule-files for JBoss Drools ``Sparrow'' -->
<resource>
<directory>src/main/rules</directory>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>


<plugins>
<plugins>

<!-- Packing Eugene v2.0 including all dependencies -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.5</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>org.cidarlab.eugene.Eugene</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<!-- Packing Eugene v2.0 including all dependencies -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.5</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>org.cidarlab.eugene.Eugene</mainClass>
</manifest>
</archive>
</configuration>
</plugin>


<!-- Packaging Eugene v2.0 w/o dependencies -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.5</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>org.cidarlab.eugene.Eugene</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<!-- Packaging Eugene v2.0 w/o dependencies -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.5</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>org.cidarlab.eugene.Eugene</mainClass>
</manifest>
</archive>
</configuration>
</plugin>

<!-- Maven - Java compiler - Java7 -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<!-- Maven - Java compiler - Java7 -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>

</plugins>
</build>
</plugins>
</build>


<!-- REPOSITORIES for downloading dependencies
on libSBOLj and BioJava
-->
<repositories>
on libSBOLj and BioJava
-->
<repositories>
<repository>
<id>Sonatype OSS Snapshot Repository</id>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</repository>

<repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url>
</repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url>
</repository>
</repositories>


<!-- DEPENDENCIES -->
<dependencies>
<dependencies>

<dependency>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java</artifactId>
<version>2.6.0</version>
</dependency>
<dependency>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java</artifactId>
<version>2.6.0</version>
</dependency>

<dependency>
<groupId>uk.com.robust-it</groupId>
<artifactId>cloning</artifactId>
<version>1.7.4</version>
</dependency>
<dependency>
<groupId>uk.com.robust-it</groupId>
<artifactId>cloning</artifactId>
<version>1.7.4</version>
</dependency>

<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.3.2</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.3.2</version>
</dependency>

<!-- JUNit -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
</dependency>
<!-- JUNit -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
</dependency>

<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.3.5</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.3.5</version>
</dependency>

<!-- DROOLS dependencies -->
<dependency>
<groupId>org.drools</groupId>
<artifactId>drools-core</artifactId>
<version>5.6.0.Final</version>
</dependency>
<dependency>
<groupId>org.drools</groupId>
<artifactId>drools-templates</artifactId>
<version>5.6.0.Final</version>
</dependency>
<dependency>
<groupId>org.drools</groupId>
<artifactId>knowledge-api</artifactId>
<version>5.6.0.Final</version>
</dependency>
<!-- DROOLS dependencies -->
<dependency>
<groupId>org.drools</groupId>
<artifactId>drools-core</artifactId>
<version>5.6.0.Final</version>
</dependency>
<dependency>
<groupId>org.drools</groupId>
<artifactId>drools-templates</artifactId>
<version>5.6.0.Final</version>
</dependency>
<dependency>
<groupId>org.drools</groupId>
<artifactId>knowledge-api</artifactId>
<version>5.6.0.Final</version>
</dependency>

<!-- ALL HAIL SBOL -->
<dependency>
<!-- ALL HAIL SBOL -->
<dependency>
<groupId>org.sbolstandard</groupId>
<artifactId>libSBOLj</artifactId>
<version>0.7.0-SNAPSHOT</version>
</dependency>


<!-- miniEugene-core dependency -->
<dependency>
<groupId>org.cidarlab</groupId>
<artifactId>miniEugene-core</artifactId>
<version>1.0</version>
</dependency>
<!-- miniEugene-core dependency -->
<dependency>
<groupId>org.cidarlab</groupId>
<artifactId>miniEugene-core</artifactId>
<version>1.0</version>
</dependency>

<!-- JaCoP Constraint Solver -->
<dependency>
<groupId>org.jacop</groupId>
<artifactId>jacop</artifactId>
<version>4.4.0</version>
</dependency>
<!-- JaCoP Constraint Solver -->
<dependency>
<groupId>org.jacop</groupId>
<artifactId>jacop</artifactId>
<version>4.4.0</version>
</dependency>

<!-- BioJava -->
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava3-core</artifactId>
<version>3.0</version>
</dependency>
<!-- BioJava -->
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava3-core</artifactId>
<version>3.0</version>
</dependency>

<dependency>
<groupId>org.biojava</groupId>
<artifactId>core</artifactId>
<version>1.9.0</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>core</artifactId>
<version>1.9.0</version>
</dependency>

<!-- SLF4J -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.5</version>
</dependency>
<!-- SLF4J -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.5</version>
</dependency>

<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<version>1.6.4</version>
</dependency>

</dependencies>
<!-- MongoDB driver for mLab -->
<dependency>
<groupId>org.mongodb</groupId>
<artifactId>mongo-java-driver</artifactId>
<version>3.4.2</version>
</dependency>
</dependencies>
</project>
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