org.apache.airavata.gfac.gsissh.handler.GSISSHInputHandler Maven / Gradle / Ivy
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* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
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*
* http://www.apache.org/licenses/LICENSE-2.0
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* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
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package org.apache.airavata.gfac.gsissh.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.context.MessageContext;
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.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.InputDataObjectType;
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.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.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Properties;
import java.util.Set;
/**
* Recoverability for this handler assumes the same input values will come in the second
* run, and assume nobody is changing registry during the original submission and re-submission
*/
public class GSISSHInputHandler extends AbstractHandler {
private static final Logger log = LoggerFactory.getLogger(GSISSHInputHandler.class);
public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
super.invoke(jobExecutionContext);
int index = 0;
int oldIndex = 0;
List oldFiles = new ArrayList();
MessageContext inputNew = new MessageContext();
DataTransferDetails detail = new DataTransferDetails();
TransferStatus status = new TransferStatus();
StringBuffer data = new StringBuffer("|");
Cluster cluster = null;
try {
String hostAddress = jobExecutionContext.getHostName();
if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
}
cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster();
if (cluster == null) {
throw new GFacException("Security context is not set properly");
} else {
log.info("Successfully retrieved the Security Context");
}
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");
}
}
if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
try {
GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
} catch (ApplicationSettingsException e) {
log.error(e.getMessage());
try {
GFacUtils.saveErrorDetails(jobExecutionContext, e.getCause().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());
}
}
log.info("Invoking SCPInputHandler");
MessageContext input = jobExecutionContext.getInMessageContext();
Set parameters = input.getParameters().keySet();
for (String paramName : parameters) {
InputDataObjectType inputParamType = (InputDataObjectType) input.getParameters().get(paramName);
String paramValue = inputParamType.getValue();
//TODO: Review this with type
if (inputParamType.getType() == DataType.URI) {
if (index < oldIndex) {
log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
inputParamType.setValue(oldFiles.get(index));
data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
} else {
String stageInputFile = stageInputFiles(cluster, jobExecutionContext, paramValue);
inputParamType.setValue(stageInputFile);
StringBuffer temp = new StringBuffer(data.append(stageInputFile).append(",").toString());
status.setTransferState(TransferState.UPLOAD);
detail.setTransferStatus(status);
detail.setTransferDescription("Input Data Staged: " + stageInputFile);
registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
}
} // FIXME: what is the thrift model DataType equivalent for URIArray type?
// else if ("URIArray".equals(inputParamType.getType().getType().toString())) {
// List split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
// List newFiles = new ArrayList();
// for (String paramValueEach : split) {
// if (index < oldIndex) {
// log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
// newFiles.add(oldFiles.get(index));
// data.append(oldFiles.get(index++)).append(",");
// } else {
// String stageInputFiles = stageInputFiles(cluster, jobExecutionContext, paramValueEach);
// status.setTransferState(TransferState.UPLOAD);
// detail.setTransferStatus(status);
// detail.setTransferDescription("Input Data Staged: " + stageInputFiles);
// registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
// StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
// GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
// newFiles.add(stageInputFiles);
// }
//
// }
// ((URIArrayType) inputParamType.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
// }
inputNew.getParameters().put(paramName, inputParamType);
}
} catch (Exception e) {
log.error(e.getMessage());
status.setTransferState(TransferState.FAILED);
detail.setTransferDescription(e.getLocalizedMessage());
detail.setTransferStatus(status);
try {
GFacUtils.saveErrorDetails(jobExecutionContext, e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
} catch (Exception e1) {
throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
}
throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
}
jobExecutionContext.setInMessageContext(inputNew);
}
private static String stageInputFiles(Cluster cluster, JobExecutionContext jobExecutionContext, String paramValue) throws IOException, GFacException {
int i = paramValue.lastIndexOf(File.separator);
String substring = paramValue.substring(i + 1);
try {
String targetFile = jobExecutionContext.getInputDir() + File.separator + substring;
if (paramValue.startsWith("file")) {
paramValue = paramValue.substring(paramValue.indexOf(":") + 1, paramValue.length());
}
boolean success = false;
int j = 1;
while(!success){
try {
cluster.scpTo(targetFile, paramValue);
success = true;
} catch (Exception e) {
log.info(e.getLocalizedMessage());
Thread.sleep(2000);
if(j==3) {
throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
}
}
j++;
}
return targetFile;
} catch (Exception e) {
throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
}
}
public void initProperties(Properties properties) throws GFacHandlerException {
}
public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
this.invoke(jobExecutionContext);
}
}