org.apache.airavata.gfac.gsissh.handler.GSISSHOutputHandler Maven / Gradle / Ivy
The newest version!
/*
*
* 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.
*
*/
package org.apache.airavata.gfac.gsissh.handler;
//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.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.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.DataTransferDetails;
import org.apache.airavata.model.workspace.experiment.ErrorCategory;
import org.apache.airavata.model.workspace.experiment.TaskDetails;
import org.apache.airavata.model.workspace.experiment.TransferState;
import org.apache.airavata.model.workspace.experiment.TransferStatus;
import org.apache.airavata.registry.cpi.ChildDataType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.Set;
public class GSISSHOutputHandler extends AbstractHandler {
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("|");
String hostAddress = jobExecutionContext.getHostName();
try {
if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
}
} catch (Exception e) {
try {
GFacUtils.saveErrorDetails(jobExecutionContext, e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
} catch (GFacException e1) {
log.error(e1.getLocalizedMessage());
}
log.error(e.getMessage());
throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
}
DataTransferDetails detail = new DataTransferDetails();
TransferStatus status = new TransferStatus();
Cluster cluster = null;
try {
cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster();
if (cluster == null) {
GFacUtils.saveErrorDetails(jobExecutionContext, "Security context is not set properly", CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
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.getHandlerData(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 timeStampedExperimentID = GFacUtils.createUniqueNameWithDate(jobExecutionContext.getExperimentID());
TaskDetails taskData = jobExecutionContext.getTaskData();
String outputDataDir = null;
File localStdOutFile;
File localStdErrFile;
//FIXME: AdvancedOutput is remote location and third party transfer should work to make this work
// 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();
String stdOutStr = "";
if (index < oldIndex) {
localStdOutFile = new File(oldFiles.get(index));
data.append(oldFiles.get(index++)).append(",");
} else {
int i = 0;
localStdOutFile = new File(outputDataDir + File.separator + jobExecutionContext.getApplicationName() + ".stdout");
while(stdOutStr.isEmpty()){
try {
cluster.scpFrom(jobExecutionContext.getStandardOutput(), localStdOutFile.getAbsolutePath());
stdOutStr = GFacUtils.readFileToString(localStdOutFile.getAbsolutePath());
} catch (Exception e) {
log.error(e.getLocalizedMessage());
Thread.sleep(2000);
}
i++;
if(i==3)break;
}
StringBuffer temp = new StringBuffer(data.append(localStdOutFile.getAbsolutePath()).append(",").toString());
GFacUtils.saveHandlerData(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 + jobExecutionContext.getApplicationName() + ".stderr");
cluster.scpFrom(jobExecutionContext.getStandardError(), localStdErrFile.getAbsolutePath());
StringBuffer temp = new StringBuffer(data.append(localStdErrFile.getAbsolutePath()).append(",").toString());
GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
}
String stdErrStr = GFacUtils.readFileToString(localStdErrFile.getAbsolutePath());
status.setTransferState(TransferState.STDOUT_DOWNLOAD);
detail.setTransferStatus(status);
detail.setTransferDescription("STDOUT:" + localStdOutFile.getAbsolutePath());
registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
status.setTransferState(TransferState.STDERROR_DOWNLOAD);
detail.setTransferStatus(status);
detail.setTransferDescription("STDERR:" + localStdErrFile.getAbsolutePath());
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) {
OutputDataObjectType outputDataObjectType = (OutputDataObjectType) output.get(paramName);
if (DataType.URI == outputDataObjectType.getType()) {
List outputList = null;
int retry=3;
while(retry>0){
outputList = cluster.listDirectory(jobExecutionContext.getOutputDir());
if (outputList.size() == 1 && outputList.get(0).isEmpty()) {
Thread.sleep(10000);
} else if (outputList.size() > 0) {
break;
}else{
Thread.sleep(10000);
}
retry--;
if(retry==0){
}
Thread.sleep(10000);
}
if (outputList.size() == 0 || outputList.get(0).isEmpty() || outputList.size() > 1) {
OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
Set strings = output.keySet();
outputArray.clear();
for (String key : strings) {
OutputDataObjectType outputDataObjectType1 = (OutputDataObjectType) output.get(key);
if (DataType.URI == outputDataObjectType1.getType()) {
String downloadFile = outputDataObjectType1.getValue();
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.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
}
jobExecutionContext.addOutputFile(localFile);
outputDataObjectType1.setValue(localFile);
OutputDataObjectType dataObjectType = new OutputDataObjectType();
dataObjectType.setValue(localFile);
dataObjectType.setName(key);
dataObjectType.setType(DataType.URI);
outputArray.add(dataObjectType);
}else if (DataType.STDOUT == outputDataObjectType1.getType()) {
String localFile;
if (index < oldIndex) {
localFile = oldFiles.get(index);
data.append(oldFiles.get(index++)).append(",");
} else {
String fileName = localStdOutFile.getName();
localFile = outputDataDir + File.separator + fileName;
StringBuffer temp = new StringBuffer(data.append(localFile).append(",").toString());
GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
}
jobExecutionContext.addOutputFile(localFile);
outputDataObjectType1.setValue(localFile);
OutputDataObjectType dataObjectType = new OutputDataObjectType();
dataObjectType.setValue(localFile);
dataObjectType.setName(key);
dataObjectType.setType(DataType.STDOUT);
outputArray.add(dataObjectType);
}else if (DataType.STDERR == outputDataObjectType1.getType()) {
String localFile;
if (index < oldIndex) {
localFile = oldFiles.get(index);
data.append(oldFiles.get(index++)).append(",");
} else {
String fileName = localStdErrFile.getName();
localFile = outputDataDir + File.separator + fileName;
StringBuffer temp = new StringBuffer(data.append(localFile).append(",").toString());
GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
}
jobExecutionContext.addOutputFile(localFile);
outputDataObjectType1.setValue(localFile);
OutputDataObjectType dataObjectType = new OutputDataObjectType();
dataObjectType.setValue(localFile);
dataObjectType.setName(key);
dataObjectType.setType(DataType.STDERR);
outputArray.add(dataObjectType);
}
}
break;
} else if(outputList.size() == 1) { //FIXME: this is ultrascan specific
String valueList = outputList.get(0);
String outputFile;
if (index < oldIndex) {
outputFile = oldFiles.get(index);
data.append(oldFiles.get(index++)).append(",");
} else {
cluster.scpFrom(jobExecutionContext.getOutputDir() + File.separator + valueList, outputDataDir);
outputFile = outputDataDir + File.separator + valueList;
jobExecutionContext.addOutputFile(outputFile);
StringBuffer temp = new StringBuffer(data.append(outputFile).append(",").toString());
GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
}
jobExecutionContext.addOutputFile(outputFile);
outputDataObjectType.setValue(outputFile);
OutputDataObjectType dataObjectType = new OutputDataObjectType();
dataObjectType.setValue(valueList);
dataObjectType.setName(paramName);
dataObjectType.setType(DataType.URI);
outputArray.add(dataObjectType);
}
} else {
OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
// break;
}
}
if (outputArray == null || outputArray.isEmpty()) {
if(jobExecutionContext.getTaskData().getAdvancedOutputDataHandling() == null){
throw new GFacHandlerException(
"Empty Output returned from the Application, Double check the application"
+ "and ApplicationDescriptor output Parameter Names"
);
}
}
// Why we set following?
jobExecutionContext.setStandardError(localStdErrFile.getAbsolutePath());
jobExecutionContext.setStandardOutput(localStdOutFile.getAbsolutePath());
jobExecutionContext.setOutputDir(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());
fireTaskOutputChangeEvent(jobExecutionContext, outputArray);
} 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.getCause().toString(), 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);
}
}