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* to you under the Apache License, Version 2.0 (the
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package org.apache.airavata.gfac.ssh.handler;
import org.apache.airavata.common.exception.ApplicationSettingsException;
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.core.utils.GFacUtils;
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.authentication.AuthenticationInfo;
import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
import org.apache.airavata.model.appcatalog.appinterface.DataType;
import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
import org.apache.airavata.model.workspace.experiment.ErrorCategory;
import org.apache.airavata.registry.cpi.ChildDataType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.*;
/**
* 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
*
*/
public class AdvancedSCPOutputHandler extends AbstractHandler {
private static final Logger log = LoggerFactory.getLogger(AdvancedSCPOutputHandler.class);
public static final int DEFAULT_SSH_PORT = 22;
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 {
Cluster pbsCluster = null;
AuthenticationInfo authenticationInfo = null;
if (password != null) {
authenticationInfo = new DefaultPasswordAuthenticationInfo(this.password);
} else {
authenticationInfo = new DefaultPublicKeyFileAuthentication(this.publicKeyPath, this.privateKeyPath,
this.passPhrase);
}
try {
String hostName = jobExecutionContext.getHostName();
if (jobExecutionContext.getSecurityContext(hostName) == null) {
try {
GFACSSHUtils.addSecurityContext(jobExecutionContext);
} catch (ApplicationSettingsException e) {
log.error(e.getMessage());
try {
StringWriter errors = new StringWriter();
e.printStackTrace(new PrintWriter(errors));
GFacUtils.saveErrorDetails(jobExecutionContext, errors.toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
} catch (GFacException e1) {
log.error(e1.getLocalizedMessage());
}
throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
}
}
String standardError = jobExecutionContext.getStandardError();
String standardOutput = jobExecutionContext.getStandardOutput();
super.invoke(jobExecutionContext);
// Server info
if(jobExecutionContext.getTaskData().getAdvancedOutputDataHandling() != null && jobExecutionContext.getTaskData().getAdvancedOutputDataHandling().getOutputDataDir() != null){
try{
URL outputPathURL = new URL(jobExecutionContext.getTaskData().getAdvancedOutputDataHandling().getOutputDataDir());
this.userName = outputPathURL.getUserInfo();
this.hostName = outputPathURL.getHost();
outputPath = outputPathURL.getPath();
} catch (MalformedURLException e) {
log.error(e.getLocalizedMessage(),e);
}
}
String key = GFACSSHUtils.prepareSecurityContext(jobExecutionContext, authenticationInfo, this.userName, this.hostName, DEFAULT_SSH_PORT);
pbsCluster = ((SSHSecurityContext)jobExecutionContext.getSecurityContext(key)).getPbsCluster();
if(jobExecutionContext.getTaskData().getAdvancedOutputDataHandling() != null && !jobExecutionContext.getTaskData().getAdvancedOutputDataHandling().isPersistOutputData()){
outputPath = outputPath + File.separator + jobExecutionContext.getExperimentID() + "-" + jobExecutionContext.getTaskData().getTaskID()
+ File.separator;
pbsCluster.makeDirectory(outputPath);
}
boolean stdoutPresent = false , stderrorPresent = false;
List outputArray = new ArrayList();
Map output = jobExecutionContext.getOutMessageContext().getParameters();
Set keys = output.keySet();
for (String paramName : keys) {
OutputDataObjectType outputDataObjectType = (OutputDataObjectType) output.get(paramName);
if (outputDataObjectType.getType() == DataType.URI) {
// for failed jobs outputs are not generated. So we should not download outputs
if (GFacUtils.isFailedJob(jobExecutionContext)){
continue;
}
String downloadFile = outputDataObjectType.getValue();
if(downloadFile == null || !(new File(downloadFile).isFile())){
GFacUtils.saveErrorDetails(jobExecutionContext, "Empty Output returned from the application", CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
throw new GFacHandlerException("Empty Output returned from the application.." );
}
pbsCluster.scpTo(outputPath, downloadFile);
String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar)+1, downloadFile.length());
OutputDataObjectType dataObjectType = new OutputDataObjectType();
dataObjectType.setValue(outputPath + File.separatorChar + fileName);
dataObjectType.setName(paramName);
dataObjectType.setType(DataType.URI);
dataObjectType.setIsRequired(outputDataObjectType.isIsRequired());
dataObjectType.setRequiredToAddedToCommandLine(outputDataObjectType.isRequiredToAddedToCommandLine());
dataObjectType.setApplicationArgument(outputDataObjectType.getApplicationArgument());
dataObjectType.setSearchQuery(outputDataObjectType.getSearchQuery());
outputArray.add(dataObjectType);
}else if (outputDataObjectType.getType() == DataType.STDOUT) {
stdoutPresent = true;
pbsCluster.scpTo(outputPath, standardOutput);
String fileName = standardOutput.substring(standardOutput.lastIndexOf(File.separatorChar)+1, standardOutput.length());
OutputDataObjectType dataObjectType = new OutputDataObjectType();
dataObjectType.setValue(outputPath + File.separatorChar + fileName);
dataObjectType.setName(paramName);
dataObjectType.setType(DataType.STDOUT);
dataObjectType.setIsRequired(outputDataObjectType.isIsRequired());
dataObjectType.setRequiredToAddedToCommandLine(outputDataObjectType.isRequiredToAddedToCommandLine());
dataObjectType.setApplicationArgument(outputDataObjectType.getApplicationArgument());
dataObjectType.setSearchQuery(outputDataObjectType.getSearchQuery());
outputArray.add(dataObjectType);
}else if (outputDataObjectType.getType() == DataType.STDERR) {
stderrorPresent = true;
pbsCluster.scpTo(outputPath, standardError);
String fileName = standardError.substring(standardError.lastIndexOf(File.separatorChar)+1, standardError.length());
OutputDataObjectType dataObjectType = new OutputDataObjectType();
dataObjectType.setValue(outputPath + File.separatorChar + fileName);
dataObjectType.setName(paramName);
dataObjectType.setType(DataType.STDERR);
dataObjectType.setIsRequired(outputDataObjectType.isIsRequired());
dataObjectType.setRequiredToAddedToCommandLine(outputDataObjectType.isRequiredToAddedToCommandLine());
dataObjectType.setApplicationArgument(outputDataObjectType.getApplicationArgument());
dataObjectType.setSearchQuery(outputDataObjectType.getSearchQuery());
outputArray.add(dataObjectType);
}
}
if (!stdoutPresent) {
log.warn("Didn't copy Standard output to client as it is not defined");
}
if (!stderrorPresent) {
log.warn("Didn't copy Standard error to client as it is not defined");
}
registry.add(ChildDataType.EXPERIMENT_OUTPUT, outputArray, jobExecutionContext.getExperimentID());
} catch (SSHApiException e) {
try {
StringWriter errors = new StringWriter();
e.printStackTrace(new PrintWriter(errors));
GFacUtils.saveErrorDetails(jobExecutionContext, errors.toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
} catch (GFacException e1) {
log.error(e1.getLocalizedMessage());
}
log.error("Error transfering files to remote host : " + hostName + " with the user: " + userName);
log.error(e.getMessage());
throw new GFacHandlerException(e);
} catch (Exception e) {
try {
GFacUtils.saveErrorDetails(jobExecutionContext, e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
} catch (GFacException e1) {
log.error(e1.getLocalizedMessage());
}
throw new GFacHandlerException(e);
}
}
@Override
public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
// TODO: Auto generated method body.
}
}
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