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*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* 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
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
* KIND, either express or implied. See the License for the
* specific language governing permissions and limitations
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package org.apache.airavata.gfac.ssh.handler;
import org.apache.airavata.common.exception.ApplicationSettingsException;
import org.apache.airavata.commons.gfac.type.ActualParameter;
import org.apache.airavata.commons.gfac.type.MappingFactory;
import org.apache.airavata.gfac.GFacException;
import org.apache.airavata.gfac.core.context.JobExecutionContext;
import org.apache.airavata.gfac.core.handler.AbstractHandler;
import org.apache.airavata.gfac.core.handler.GFacHandlerException;
import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
import org.apache.airavata.gfac.ssh.util.GFACSSHUtils;
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.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.DataObjectType;
import org.apache.airavata.model.workspace.experiment.DataType;
import org.apache.airavata.registry.cpi.ChildDataType;
import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.Set;
/**
* This handler will copy outputs from airavata installed local directory
* to a remote location, prior to this handler SCPOutputHandler should be invoked
* Should add following configuration to gfac-config.xml and configure the keys properly
* <Handler class="AdvancedSCPOutputHandler">
<property name="privateKeyPath" value="/Users/lahirugunathilake/.ssh/id_dsa"/>
<property name="publicKeyPath" value="/Users/lahirugunathilake/.ssh/id_dsa.pub"/>
<property name="userName" value="airavata"/>
<property name="hostName" value="gw98.iu.xsede.org"/>
<property name="outputPath" value="/home/airavata/outputData"/>
<property name="passPhrase" value="/home/airavata/outputData"/>
<property name="password" value="/home/airavata/outputData"/>
*/
public class AdvancedSCPOutputHandler extends AbstractHandler {
private static final Logger log = LoggerFactory.getLogger(AdvancedSCPOutputHandler.class);
private String password = null;
private String publicKeyPath;
private String passPhrase;
private String privateKeyPath;
private String userName;
private String hostName;
private String outputPath;
public void initProperties(Properties properties) throws GFacHandlerException {
password = (String)properties.get("password");
passPhrase = (String)properties.get("passPhrase");
privateKeyPath = (String)properties.get("privateKeyPath");
publicKeyPath = (String)properties.get("publicKeyPath");
userName = (String)properties.get("userName");
hostName = (String)properties.get("hostName");
outputPath = (String)properties.get("outputPath");
}
@Override
public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
try {
if (jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) == null) {
try {
GFACSSHUtils.addSecurityContext(jobExecutionContext);
} catch (ApplicationSettingsException e) {
log.error(e.getMessage());
throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
}
}
ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
.getApplicationDeploymentDescription().getType();
String standardError = app.getStandardError();
String standardOutput = app.getStandardOutput();
String outputDataDirectory = app.getOutputDataDirectory();
super.invoke(jobExecutionContext);
AuthenticationInfo authenticationInfo = null;
if (password != null) {
authenticationInfo = new DefaultPasswordAuthenticationInfo(this.password);
} else {
authenticationInfo = new DefaultPublicKeyFileAuthentication(this.publicKeyPath, this.privateKeyPath,
this.passPhrase);
}
// Server info
ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/torque-4.2.3.1/bin/"));
outputPath = outputPath + File.separator + jobExecutionContext.getExperimentID() + "-" + jobExecutionContext.getTaskData().getTaskID()
+ File.separator;
pbsCluster.makeDirectory(outputPath);
pbsCluster.scpTo(outputPath, standardError);
pbsCluster.scpTo(outputPath, standardOutput);
List<DataObjectType> outputArray = new ArrayList<DataObjectType>();
Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
Set<String> keys = output.keySet();
for (String paramName : keys) {
ActualParameter actualParameter = (ActualParameter) output.get(paramName);
if ("URI".equals(actualParameter.getType().getType().toString())) {
String downloadFile = MappingFactory.toString(actualParameter);
pbsCluster.scpTo(outputPath, downloadFile);
String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar)+1, downloadFile.length());
DataObjectType dataObjectType = new DataObjectType();
dataObjectType.setValue(outputPath + File.separatorChar + fileName);
dataObjectType.setKey(paramName);
dataObjectType.setType(DataType.URI);
outputArray.add(dataObjectType);
}
}
registry.add(ChildDataType.EXPERIMENT_OUTPUT, outputArray, jobExecutionContext.getExperimentID());
} catch (SSHApiException e) {
log.error("Error transfering files to remote host : " + hostName + " with the user: " + userName);
log.error(e.getMessage());
throw new GFacHandlerException(e);
} catch (Exception e) {
throw new GFacHandlerException(e);
}
}
}