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* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
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*
* http://www.apache.org/licenses/LICENSE-2.0
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* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
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package org.apache.airavata.gfac.ssh.util;
import org.apache.airavata.common.exception.ApplicationSettingsException;
import org.apache.airavata.common.utils.ServerSettings;
import org.apache.airavata.common.utils.StringUtil;
import org.apache.airavata.commons.gfac.type.ActualParameter;
import org.apache.airavata.commons.gfac.type.HostDescription;
import org.apache.airavata.commons.gfac.type.MappingFactory;
import org.apache.airavata.gfac.Constants;
import org.apache.airavata.gfac.GFacException;
import org.apache.airavata.gfac.core.context.JobExecutionContext;
import org.apache.airavata.gfac.core.context.MessageContext;
import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
import org.apache.airavata.gsi.ssh.api.Cluster;
import org.apache.airavata.gsi.ssh.api.SSHApiException;
import org.apache.airavata.gsi.ssh.api.ServerInfo;
import org.apache.airavata.gsi.ssh.api.authentication.AuthenticationInfo;
import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
import org.apache.airavata.gsi.ssh.impl.PBSCluster;
import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
import org.apache.airavata.gsi.ssh.util.CommonUtils;
import org.apache.airavata.model.workspace.experiment.ComputationalResourceScheduling;
import org.apache.airavata.model.workspace.experiment.TaskDetails;
import org.apache.airavata.schemas.gfac.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.*;
public class GFACSSHUtils {
private final static Logger logger = LoggerFactory.getLogger(GFACSSHUtils.class);
public static void addSecurityContext(JobExecutionContext jobExecutionContext) throws GFacException, ApplicationSettingsException {
HostDescription registeredHost = jobExecutionContext.getApplicationContext().getHostDescription();
if (registeredHost.getType() instanceof GlobusHostType || registeredHost.getType() instanceof UnicoreHostType
|| registeredHost.getType() instanceof GsisshHostType) {
logger.error("This is a wrong method to invoke to non ssh host types,please check your gfac-config.xml");
} else if (registeredHost.getType() instanceof SSHHostType) {
Properties configurationProperties = ServerSettings.getProperties();
String sshUserName = configurationProperties.getProperty(Constants.SSH_USER_NAME);
String sshPrivateKey = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY);
String sshPrivateKeyPass = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY_PASS);
String sshPassword = configurationProperties.getProperty(Constants.SSH_PASSWORD);
String sshPublicKey = configurationProperties.getProperty(Constants.SSH_PUBLIC_KEY);
SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
AuthenticationInfo authenticationInfo = null;
// we give higher preference to the password over keypair ssh authentication
if (sshPassword != null) {
authenticationInfo = new DefaultPasswordAuthenticationInfo(sshPassword);
} else {
authenticationInfo = new DefaultPublicKeyFileAuthentication(sshPublicKey, sshPrivateKey, sshPrivateKeyPass);
}
ServerInfo serverInfo = new ServerInfo(sshUserName, registeredHost.getType().getHostAddress());
Cluster pbsCluster = null;
try {
String installedParentPath = "/";
if (((SSHHostType) registeredHost.getType()).getHpcResource()) {
installedParentPath = ((HpcApplicationDeploymentType)
jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType()).getInstalledParentPath();
}
pbsCluster = new PBSCluster(serverInfo, authenticationInfo,
CommonUtils.getPBSJobManager(installedParentPath));
} catch (SSHApiException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
sshSecurityContext.setPbsCluster(pbsCluster);
sshSecurityContext.setUsername(sshUserName);
jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT, sshSecurityContext);
}
}
public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext,
ApplicationDeploymentDescriptionType app, Cluster cluster) {
JobDescriptor jobDescriptor = new JobDescriptor();
// this is common for any application descriptor
jobDescriptor.setInputDirectory(app.getInputDataDirectory());
jobDescriptor.setOutputDirectory(app.getOutputDataDirectory());
jobDescriptor.setExecutablePath(app.getExecutableLocation());
jobDescriptor.setStandardOutFile(app.getStandardOutput());
jobDescriptor.setStandardErrorFile(app.getStandardError());
Random random = new Random();
int i = random.nextInt();
jobDescriptor.setJobName(app.getApplicationName().getStringValue() + String.valueOf(i));
jobDescriptor.setWorkingDirectory(app.getStaticWorkingDirectory());
List<String> inputValues = new ArrayList<String>();
MessageContext input = jobExecutionContext.getInMessageContext();
Map<String, Object> inputs = input.getParameters();
Set<String> keys = inputs.keySet();
for (String paramName : keys) {
ActualParameter actualParameter = (ActualParameter) inputs.get(paramName);
if ("URIArray".equals(actualParameter.getType().getType().toString()) || "StringArray".equals(actualParameter.getType().getType().toString())
|| "FileArray".equals(actualParameter.getType().getType().toString())) {
String[] values = null;
if (actualParameter.getType() instanceof URIArrayType) {
values = ((URIArrayType) actualParameter.getType()).getValueArray();
} else if (actualParameter.getType() instanceof StringArrayType) {
values = ((StringArrayType) actualParameter.getType()).getValueArray();
} else if (actualParameter.getType() instanceof FileArrayType) {
values = ((FileArrayType) actualParameter.getType()).getValueArray();
}
String value = StringUtil.createDelimiteredString(values, " ");
inputValues.add(value);
} else {
String paramValue = MappingFactory.toString(actualParameter);
inputValues.add(paramValue);
}
}
jobDescriptor.setInputValues(inputValues);
// this part will fill out the hpcApplicationDescriptor
if (app instanceof HpcApplicationDeploymentType) {
HpcApplicationDeploymentType applicationDeploymentType
= (HpcApplicationDeploymentType) app;
jobDescriptor.setShellName("/bin/bash");
jobDescriptor.setAllEnvExport(true);
jobDescriptor.setMailOptions("n");
jobDescriptor.setNodes(applicationDeploymentType.getNodeCount());
jobDescriptor.setProcessesPerNode(applicationDeploymentType.getProcessorsPerNode());
jobDescriptor.setMaxWallTime(String.valueOf(applicationDeploymentType.getMaxWallTime()));
jobDescriptor.setJobSubmitter(applicationDeploymentType.getJobSubmitterCommand());
if (applicationDeploymentType.getProjectAccount() != null) {
if (applicationDeploymentType.getProjectAccount().getProjectAccountNumber() != null) {
jobDescriptor.setAcountString(applicationDeploymentType.getProjectAccount().getProjectAccountNumber());
}
}
if (applicationDeploymentType.getQueue() != null) {
if (applicationDeploymentType.getQueue().getQueueName() != null) {
jobDescriptor.setQueueName(applicationDeploymentType.getQueue().getQueueName());
}
}
jobDescriptor.setOwner(((PBSCluster) cluster).getServerInfo().getUserName());
TaskDetails taskData = jobExecutionContext.getTaskData();
if (taskData != null && taskData.isSetTaskScheduling()) {
ComputationalResourceScheduling computionnalResource = taskData.getTaskScheduling();
if (computionnalResource.getNodeCount() > 0) {
jobDescriptor.setNodes(computionnalResource.getNodeCount());
}
if (computionnalResource.getComputationalProjectAccount() != null) {
jobDescriptor.setAcountString(computionnalResource.getComputationalProjectAccount());
}
if (computionnalResource.getQueueName() != null) {
jobDescriptor.setQueueName(computionnalResource.getQueueName());
}
if (computionnalResource.getTotalCPUCount() > 0) {
jobDescriptor.setProcessesPerNode(computionnalResource.getTotalCPUCount());
}
if (computionnalResource.getWallTimeLimit() > 0) {
jobDescriptor.setMaxWallTime(String.valueOf(computionnalResource.getWallTimeLimit()));
}
}
}
return jobDescriptor;
}
}