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org.apache.airavata.gfac.gsissh.handler.GSISSHOutputHandler Maven / Gradle / Ivy
/*
*
* 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.gsissh.handler;
import java.io.File;
import java.io.IOException;
import java.util.*;
import net.schmizz.sshj.connection.ConnectionException;
import net.schmizz.sshj.transport.TransportException;
import org.apache.airavata.common.exception.ApplicationSettingsException;
import org.apache.airavata.common.utils.Constants;
import org.apache.airavata.commons.gfac.type.ActualParameter;
import org.apache.airavata.commons.gfac.type.ApplicationDescription;
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.AbstractRecoverableHandler;
import org.apache.airavata.gfac.core.handler.GFacHandlerException;
import org.apache.airavata.gfac.core.provider.GFacProviderException;
import org.apache.airavata.gfac.core.utils.GFacUtils;
import org.apache.airavata.gfac.core.utils.OutputUtils;
import org.apache.airavata.gfac.gsissh.security.GSISecurityContext;
import org.apache.airavata.gfac.gsissh.util.GFACGSISSHUtils;
import org.apache.airavata.gsi.ssh.api.Cluster;
import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
import org.apache.airavata.model.workspace.experiment.*;
import org.apache.airavata.registry.cpi.ChildDataType;
import org.apache.airavata.registry.cpi.RegistryModelType;
import org.apache.airavata.registry.cpi.RegistryException;
import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
import org.apache.airavata.schemas.gfac.GsisshHostType;
import org.apache.xmlbeans.XmlException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class GSISSHOutputHandler extends AbstractRecoverableHandler {
private static final Logger log = LoggerFactory.getLogger(GSISSHOutputHandler.class);
public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
super.invoke(jobExecutionContext);
int index = 0;
int oldIndex = 0;
List oldFiles = new ArrayList();
StringBuffer data = new StringBuffer("|");
if (jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof GsisshHostType) { // this is because we don't have the right jobexecution context
// so attempting to get it from the registry
if (Constants.PUSH.equals(((GsisshHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType()).getMonitorMode())) {
log.warn("During the out handler chain jobExecution context came null, so trying to handler");
ApplicationDescription applicationDeploymentDescription = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription();
TaskDetails taskData = null;
try {
taskData = (TaskDetails) jobExecutionContext.getRegistry().get(RegistryModelType.TASK_DETAIL, jobExecutionContext.getTaskData().getTaskID());
} catch (RegistryException e) {
log.error("Error retrieving job details from Registry");
throw new GFacHandlerException("Error retrieving job details from Registry", e);
}
JobDetails jobDetails = taskData.getJobDetailsList().get(0);
String jobDescription = jobDetails.getJobDescription();
if (jobDescription != null) {
JobDescriptor jobDescriptor = null;
try {
jobDescriptor = JobDescriptor.fromXML(jobDescription);
} catch (XmlException e1) {
e1.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
applicationDeploymentDescription.getType().setScratchWorkingDirectory(
jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory());
applicationDeploymentDescription.getType().setInputDataDirectory(jobDescriptor.getInputDirectory());
applicationDeploymentDescription.getType().setOutputDataDirectory(jobDescriptor.getOutputDirectory());
applicationDeploymentDescription.getType().setStandardError(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile());
applicationDeploymentDescription.getType().setStandardOutput(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile());
}
}
}
try {
if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
}
} catch (ApplicationSettingsException e) {
log.error(e.getMessage());
throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
} catch (GFacException e) {
log.error(e.getMessage());
throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
}
DataTransferDetails detail = new DataTransferDetails();
TransferStatus status = new TransferStatus();
ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
.getApplicationDeploymentDescription().getType();
try {
Cluster cluster = null;
if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
} else {
cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
}
if (cluster == null) {
throw new GFacProviderException("Security context is not set properly");
} else {
log.info("Successfully retrieved the Security Context");
}
// Get the Stdouts and StdErrs
String pluginData = GFacUtils.getPluginData(jobExecutionContext, this.getClass().getName());
if (pluginData != null) {
try {
oldIndex = Integer.parseInt(pluginData.split("\\|")[0].trim());
oldFiles = Arrays.asList(pluginData.split("\\|")[1].split(","));
if (oldIndex == oldFiles.size()) {
log.info("Old data looks good !!!!");
} else {
oldIndex = 0;
oldFiles.clear();
}
} catch (NumberFormatException e) {
log.error("Previously stored data " + pluginData + " is wrong so we continue the operations");
}
}
String timeStampedServiceName = GFacUtils.createUniqueNameForService(jobExecutionContext.getServiceName());
TaskDetails taskData = jobExecutionContext.getTaskData();
String outputDataDir = null;
File localStdOutFile;
File localStdErrFile;
if (taskData.getAdvancedOutputDataHandling() != null) {
outputDataDir = taskData.getAdvancedOutputDataHandling().getOutputDataDir();
}
if (outputDataDir == null) {
outputDataDir = File.separator + "tmp";
}
outputDataDir = outputDataDir + File.separator + jobExecutionContext.getExperimentID() + "-" + jobExecutionContext.getTaskData().getTaskID();
(new File(outputDataDir)).mkdirs();
if (index < oldIndex) {
localStdOutFile = new File(oldFiles.get(index));
data.append(oldFiles.get(index++)).append(",");
} else {
localStdOutFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stdout");
cluster.scpFrom(app.getStandardOutput(), localStdOutFile.getAbsolutePath());
Thread.sleep(1000);
StringBuffer temp = new StringBuffer(data.append(localStdOutFile.getAbsolutePath()).append(",").toString());
GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
}
if (index < oldIndex) {
localStdErrFile = new File(oldFiles.get(index));
data.append(oldFiles.get(index++)).append(",");
} else {
localStdErrFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stderr");
cluster.scpFrom(app.getStandardError(), localStdErrFile.getAbsolutePath());
Thread.sleep(1000);
StringBuffer temp = new StringBuffer(data.append(localStdErrFile.getAbsolutePath()).append(",").toString());
GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
}
String stdOutStr = GFacUtils.readFileToString(localStdOutFile.getAbsolutePath());
String stdErrStr = GFacUtils.readFileToString(localStdErrFile.getAbsolutePath());
status.setTransferState(TransferState.COMPLETE);
detail.setTransferStatus(status);
detail.setTransferDescription("STDOUT:" + stdOutStr);
registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
status.setTransferState(TransferState.COMPLETE);
detail.setTransferStatus(status);
detail.setTransferDescription("STDERR:" + stdErrStr);
registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
//todo this is a mess we have to fix this
List outputArray = new ArrayList();
Map output = jobExecutionContext.getOutMessageContext().getParameters();
Set keys = output.keySet();
for (String paramName : keys) {
ActualParameter actualParameter = (ActualParameter) output.get(paramName);
if ("URI".equals(actualParameter.getType().getType().toString())) {
List outputList = cluster.listDirectory(app.getOutputDataDirectory());
if (outputList.size() == 0 || outputList.get(0).isEmpty()) {
OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
Set strings = output.keySet();
outputArray.clear();
for (String key : strings) {
ActualParameter actualParameter1 = (ActualParameter) output.get(key);
if ("URI".equals(actualParameter1.getType().getType().toString())) {
String downloadFile = MappingFactory.toString(actualParameter1);
String localFile;
if (index < oldIndex) {
localFile = oldFiles.get(index);
data.append(oldFiles.get(index++)).append(",");
} else {
cluster.scpFrom(downloadFile, outputDataDir);
String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar) + 1, downloadFile.length());
localFile = outputDataDir + File.separator + fileName;
StringBuffer temp = new StringBuffer(data.append(localFile).append(",").toString());
GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
}
jobExecutionContext.addOutputFile(localFile);
MappingFactory.fromString(actualParameter1, localFile);
DataObjectType dataObjectType = new DataObjectType();
dataObjectType.setValue(localFile);
dataObjectType.setKey(key);
dataObjectType.setType(DataType.URI);
outputArray.add(dataObjectType);
}
}
break;
} else {
String valueList = outputList.get(0);
String outputFile;
if (index < oldIndex) {
outputFile = oldFiles.get(index);
data.append(oldFiles.get(index++)).append(",");
} else {
cluster.scpFrom(app.getOutputDataDirectory() + File.separator + valueList, outputDataDir);
outputFile = outputDataDir + File.separator + valueList;
jobExecutionContext.addOutputFile(outputFile);
StringBuffer temp = new StringBuffer(data.append(outputFile).append(",").toString());
GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
}
jobExecutionContext.addOutputFile(outputFile);
DataObjectType dataObjectType = new DataObjectType();
dataObjectType.setValue(valueList);
dataObjectType.setKey(paramName);
dataObjectType.setType(DataType.URI);
outputArray.add(dataObjectType);
}
} else {
OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
break;
}
}
if (outputArray == null || outputArray.isEmpty()) {
throw new GFacHandlerException(
"Empty Output returned from the Application, Double check the application"
+ "and ApplicationDescriptor output Parameter Names"
);
}
app.setStandardError(localStdErrFile.getAbsolutePath());
app.setStandardOutput(localStdOutFile.getAbsolutePath());
app.setOutputDataDirectory(outputDataDir);
status.setTransferState(TransferState.DOWNLOAD);
detail.setTransferStatus(status);
detail.setTransferDescription(outputDataDir);
registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
registry.add(ChildDataType.EXPERIMENT_OUTPUT, outputArray, jobExecutionContext.getExperimentID());
} catch (XmlException e) {
throw new GFacHandlerException("Cannot read output:" + e.getMessage(), e);
} catch (ConnectionException e) {
throw new GFacHandlerException(e.getMessage(), e);
} catch (TransportException e) {
throw new GFacHandlerException(e.getMessage(), e);
} catch (IOException e) {
throw new GFacHandlerException(e.getMessage(), e);
} catch (Exception e) {
try {
status.setTransferState(TransferState.FAILED);
detail.setTransferStatus(status);
detail.setTransferDescription(e.getLocalizedMessage());
registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
GFacUtils.saveErrorDetails(jobExecutionContext, e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
} catch (Exception e1) {
throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
}
throw new GFacHandlerException("Error in retrieving results", e);
}
}
public void initProperties(Properties properties) throws GFacHandlerException {
}
public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
this.invoke(jobExecutionContext);
}
}
