added Goksel's model generator jar to conversion module

conversion/pom.xml

@@ -12,6 +12,30 @@
 	<packaging>jar</packaging>
 	<build>
 		<plugins>
+					<!-- Install dependencies to local repository -->
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-install-plugin</artifactId>
+				<executions>
+					<execution>
+					<!-- Update SBOL JAR name here. NOTE: Make sure to update the DEPENDENCY tag down below for SBOL as well. -->
+						<id>install-libSBOLj</id>
+						<phase>clean</phase>
+						<configuration>
+							<file>${basedir}/../lib/vpr.data-2.0.0-withDependencies.jar</file>
+							<repositoryLayout>default</repositoryLayout>
+							<groupId>uk.ac.ncl.ico2s</groupId>
+			<artifactId>vpr-data</artifactId>
+			<version>2.0.0-SNAPSHOT</version>
+							<packaging>jar</packaging>
+							<generatePom>true</generatePom>
+						</configuration>
+						<goals>
+							<goal>install-file</goal>
+						</goals>
+					</execution>
+					</executions>
+			</plugin>
 			<!-- Build an executable JAR -->
 			<plugin>
 				<artifactId>maven-assembly-plugin</artifactId>
@@ -66,7 +90,11 @@
 			<groupId>edu.utah.ece.async</groupId>
 			<artifactId>iBioSim-dataModels</artifactId>
 			<version>0.0.1-SNAPSHOT</version>
-			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>uk.ac.ncl.ico2s</groupId>
+			<artifactId>vpr-data</artifactId>
+			<version>2.0.0-SNAPSHOT</version>
 		</dependency>
 	</dependencies>
 </project>

conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/ModelGenerator.java

@@ -0,0 +1,46 @@
+package edu.utah.ece.async.ibiosim.conversion;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URI;
+
+import org.sbolstandard.core2.SBOLConversionException;
+import org.sbolstandard.core2.SBOLDocument;
+import org.sbolstandard.core2.SBOLReader;
+import org.sbolstandard.core2.SBOLValidationException;
+
+import uk.ac.ncl.ico2s.VPRException;
+import uk.ac.ncl.ico2s.VPRTripleStoreException;
+import uk.ac.ncl.ico2s.sbolstack.SBOLInteractionAdder_GeneCentric;
+
+public class ModelGenerator {
+
+	public SBOLDocument generateModel(String inputFileDir, String inputFileName)
+	{
+		SBOLDocument doc = null;
+		
+			try {
+				doc = SBOLReader.read(new File(inputFileDir + inputFileName));
+				String endpoint="http://synbiohub.org/sparql";  
+				SBOLInteractionAdder_GeneCentric interactionAdder = new SBOLInteractionAdder_GeneCentric(URI.create(endpoint));
+				interactionAdder.addInteractions(doc);
+			} catch (SBOLValidationException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			} catch (IOException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			} catch (SBOLConversionException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			} catch (VPRException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			} catch (VPRTripleStoreException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+			 
+		return doc;
+	}
+}