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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
* under the License.
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package org.apache.airavata.gfac.ssh.handler;
import org.apache.airavata.common.exception.ApplicationSettingsException;
import org.apache.airavata.common.utils.StringUtil;
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.context.MessageContext;
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.schemas.gfac.ApplicationDeploymentDescriptionType;
import org.apache.airavata.schemas.gfac.URIArrayType;
import org.apache.airavata.schemas.gfac.URIParameterType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.util.*;
/**
* This handler will copy input data from gateway machine to airavata
* installed machine, later running handlers can copy the input files to computing resource
* <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="inputPath" value="/home/airavata/outputData"/>
*/
public class AdvancedSCPInputHandler extends AbstractHandler {
private static final Logger log = LoggerFactory.getLogger(AdvancedSCPInputHandler.class);
private String password = null;
private String publicKeyPath;
private String passPhrase;
private String privateKeyPath;
private String userName;
private String hostName;
private String inputPath;
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");
inputPath = (String)properties.get("inputPath");
}
public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
MessageContext inputNew = new MessageContext();
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();
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 = null;
// here doesn't matter what the job manager is because we are only doing some file handling
// not really dealing with monitoring or job submission, so we pa
pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/torque-4.2.3.1/bin/"));
String parentPath = inputPath + File.separator + jobExecutionContext.getExperimentID() + File.separator + jobExecutionContext.getTaskData().getTaskID();
(new File(parentPath)).mkdirs();
MessageContext input = jobExecutionContext.getInMessageContext();
Set<String> parameters = input.getParameters().keySet();
for (String paramName : parameters) {
ActualParameter actualParameter = (ActualParameter) input.getParameters().get(paramName);
String paramValue = MappingFactory.toString(actualParameter);
//TODO: Review this with type
if ("URI".equals(actualParameter.getType().getType().toString())) {
((URIParameterType) actualParameter.getType()).setValue(stageInputFiles(pbsCluster, paramValue, parentPath));
} else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
List<String> newFiles = new ArrayList<String>();
for (String paramValueEach : split) {
String stageInputFiles = stageInputFiles(pbsCluster, paramValueEach, parentPath);
newFiles.add(stageInputFiles);
}
((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
}
inputNew.getParameters().put(paramName, actualParameter);
}
} catch (Exception e) {
log.error(e.getMessage());
throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
}
jobExecutionContext.setInMessageContext(inputNew);
}
private String stageInputFiles(Cluster cluster, String paramValue, String parentPath) throws GFacException {
try {
cluster.scpFrom(paramValue, parentPath);
return "file://" + parentPath + File.separator + (new File(paramValue)).getName();
} catch (SSHApiException e) {
log.error("Error tranfering remote file to local file, remote path: " + paramValue);
throw new GFacException(e);
}
}
}