This is a followup to my earlier posts [1] [2]. Here we will execute the application mentioned in [2] programmetically using Airavata.
References
[1] - http://heshans.blogspot.com/2013/04/run-ec2-jobs-with-airavata-part-i.html
[2] - http://heshans.blogspot.com/2013/04/run-ec2-jobs-with-airavata-part-ii.html
import org.apache.airavata.commons.gfac.type.*;
import org.apache.airavata.gfac.GFacAPI;
import org.apache.airavata.gfac.GFacConfiguration;
import org.apache.airavata.gfac.GFacException;
import org.apache.airavata.gfac.context.security.AmazonSecurityContext;
import org.apache.airavata.gfac.context.ApplicationContext;
import org.apache.airavata.gfac.context.JobExecutionContext;
import org.apache.airavata.gfac.context.MessageContext;
import org.apache.airavata.schemas.gfac.*;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import java.io.File;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
/**
* Your Amazon instance should be in a running state before running this test.
*/
public class EC2ProviderTest {
private JobExecutionContext jobExecutionContext;
private static final String hostName = "ec2-host";
private static final String hostAddress = "ec2-address";
private static final String sequence1 = "RR042383.21413#CTGGCACGGAGTTAGCCGATCCTTATTCATAAAGTACATGCAAACGGGTATCCATA" +
"CTCGACTTTATTCCTTTATAAAAGAAGTTTACAACCCATAGGGCAGTCATCCTTCACGCTACTTGGCTGGTTCAGGCCTGCGCCCATTGACCAATATTCCTCA" +
"CTGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGC" +
"CTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAG" +
"GCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCGTGCCGCCGGTCGCCATCAGTCTTAGCAAGCTAAGACCATGCTGCCCCTGACTTGCATGT" +
"GTTAAGCCTGTAGCTTAGCGTTC";
private static final String sequence2 = "RR042383.31934#CTGGCACGGAGTTAGCCGATCCTTATTCATAAAGTACATGCAAACGGGTATCCATA" +
"CCCGACTTTATTCCTTTATAAAAGAAGTTTACAACCCATAGGGCAGTCATCCTTCACGCTACTTGGCTGGTTCAGGCTCTCGCCCATTGACCAATATTCCTCA" +
"CTGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGC" +
"CTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAAATCTTCCTTTCAGAA" +
"GGCTATCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCGTGCG";
/* Following variables are needed to be set in-order to run the test. Since these are account specific information,
I'm not adding the values here. It's the responsibility of the person who's running the test to update
these variables accordingly.
*/
/* Username used to log into your ec2 instance eg.ec2-user */
private String userName = "";
/* Secret key used to connect to the image */
private String secretKey = "";
/* Access key used to connect to the image */
private String accessKey = "";
/* Instance id of the running instance of your image */
private String instanceId = "";
@Before
public void setUp() throws Exception {
URL resource = GramProviderTest.class.getClassLoader().getResource("gfac-config.xml");
assert resource != null;
System.out.println(resource.getFile());
GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()), null, null);
/* EC2 Host */
HostDescription host = new HostDescription(Ec2HostType.type);
host.getType().setHostName(hostName);
host.getType().setHostAddress(hostAddress);
/* App */
ApplicationDescription ec2Desc = new ApplicationDescription(Ec2ApplicationDeploymentType.type);
Ec2ApplicationDeploymentType ec2App = (Ec2ApplicationDeploymentType)ec2Desc.getType();
String serviceName = "Gnome_distance_calculation_workflow";
ec2Desc.getType().addNewApplicationName().setStringValue(serviceName);
ec2App.setJobType(JobTypeType.EC_2);
ec2App.setExecutable("/home/ec2-user/run.sh");
ec2App.setExecutableType("sh");
/* Service */
ServiceDescription serv = new ServiceDescription();
serv.getType().setName("GenomeEC2");
List inputList = new ArrayList();
InputParameterType input1 = InputParameterType.Factory.newInstance();
input1.setParameterName("genome_input1");
input1.setParameterType(StringParameterType.Factory.newInstance());
inputList.add(input1);
InputParameterType input2 = InputParameterType.Factory.newInstance();
input2.setParameterName("genome_input2");
input2.setParameterType(StringParameterType.Factory.newInstance());
inputList.add(input2);
InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList.size()]);
List outputList = new ArrayList();
OutputParameterType output = OutputParameterType.Factory.newInstance();
output.setParameterName("genome_output");
output.setParameterType(StringParameterType.Factory.newInstance());
outputList.add(output);
OutputParameterType[] outputParamList = outputList
.toArray(new OutputParameterType[outputList.size()]);
serv.getType().setInputParametersArray(inputParamList);
serv.getType().setOutputParametersArray(outputParamList);
jobExecutionContext = new JobExecutionContext(gFacConfiguration,serv.getType().getName());
ApplicationContext applicationContext = new ApplicationContext();
jobExecutionContext.setApplicationContext(applicationContext);
applicationContext.setServiceDescription(serv);
applicationContext.setApplicationDeploymentDescription(ec2Desc);
applicationContext.setHostDescription(host);
AmazonSecurityContext amazonSecurityContext =
new AmazonSecurityContext(userName, accessKey, secretKey, instanceId);
jobExecutionContext.addSecurityContext(AmazonSecurityContext.AMAZON_SECURITY_CONTEXT, amazonSecurityContext);
MessageContext inMessage = new MessageContext();
ActualParameter genomeInput1 = new ActualParameter();
((StringParameterType)genomeInput1.getType()).setValue(sequence1);
inMessage.addParameter("genome_input1", genomeInput1);
ActualParameter genomeInput2 = new ActualParameter();
((StringParameterType)genomeInput2.getType()).setValue(sequence2);
inMessage.addParameter("genome_input2", genomeInput2);
MessageContext outMessage = new MessageContext();
ActualParameter echo_out = new ActualParameter();
outMessage.addParameter("distance", echo_out);
jobExecutionContext.setInMessageContext(inMessage);
jobExecutionContext.setOutMessageContext(outMessage);
}
@Test
public void testGramProvider() throws GFacException {
GFacAPI gFacAPI = new GFacAPI();
gFacAPI.submitJob(jobExecutionContext);
MessageContext outMessageContext = jobExecutionContext.getOutMessageContext();
Assert.assertEquals(MappingFactory.
toString((ActualParameter) outMessageContext.getParameter("genome_output")), "476");
}
}
References
[2] - http://heshans.blogspot.com/2013/04/run-ec2-jobs-with-airavata-part-ii.html
