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");
}
}
unzip apache-airavata-server-0.7-bin.zip cd apache-airavata-server-0.7/bin ./airavata-server.sh
unzip apache-airavata-xbaya-gui-0.7-bin.zip cd apache-airavata-xbaya-gui-0.7/bin ./xbaya-gui.sh
unzip apache-airavata-server-0.7-bin.zip cd apache-airavata-server-0.7/bin ./airavata-server.sh2. Unzip Airavata XBaya distribution and start XBaya.
unzip apache-airavata-xbaya-gui-0.7-bin.zip cd apache-airavata-xbaya-gui-0.7/bin ./xbaya-gui.shThen you'll get the XBaya UI.
yum install tomcat62) Install 64-bit version of Oracle Java SE6 JRE.
sh jre-6u37-linux-x64-rpm.bin rm -f /usr/bin/java ln -s /etc/alternatives/java /usr/bin/java alternatives --install /usr/bin/java java /usr/java/jre1.6.0_37/bin/java 500 alternatives --set java /usr/java/jre1.6.0_37/bin/java3) Create mws home directories and sub-directories
mkdir -p /opt/mws/etc /opt/mws/hooks /opt/mws/plugins /opt/mws/log chown -R tomcat:tomcat /opt/mws # Depending on your OS, the Tomcat username might be tomcat6. chmod -R 555 /opt/mws chmod u+w /opt/mws/plugins /opt/mws/log4) Extract mws tarball to a tempory directory.
mkdir /tmp/mws-install cd /tmp/mws-install tar xvzf $HOME/Downloads/mws-5) Set up the MWS configuration file..tar.gz cd /tmp/mws-install/mws-
mws-config-cloud.groovy and mws-config-hpc.groovy mws-config-cloud.groovy provides sample configuration for the Moab Cloud Suite mws-config-hpc.groovy provides sample configuration for the Moab HPC Suites
CATALINA_OPTS="-DMWS_HOME=/opt/mws -Xms256m -Xmx3g -XX:MaxPermSize=384m"7) Start Tomcat and deploy mws.war.
chkconfig tomcat6 on service tomcat6 stop cp /tmp/mws-install/mws-8) Visit http://localhost:8080/mws/ in a web browser to verify that MWS is running. You will see some sample queries and a few other actions./mws.war /var/lib/tomcat6/webapps service tomcat6 start