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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.handler;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.airavata.common.utils.StringUtil;
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.ToolsException;
import org.apache.airavata.gfac.context.JobExecutionContext;
import org.apache.airavata.gfac.context.MessageContext;
import org.apache.airavata.gfac.context.security.GSISecurityContext;
import org.apache.airavata.gfac.external.GridFtp;
import org.apache.airavata.gfac.provider.GFacProviderException;
import org.apache.airavata.gfac.utils.GFacUtils;
import org.apache.airavata.gfac.utils.OutputUtils;
import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
import org.apache.airavata.schemas.gfac.GlobusHostType;
import org.apache.airavata.schemas.gfac.HostDescriptionType;
import org.apache.airavata.schemas.gfac.StringArrayType;
import org.apache.airavata.schemas.gfac.StringParameterType;
import org.apache.airavata.schemas.gfac.URIArrayType;
import org.apache.airavata.schemas.gfac.URIParameterType;
import org.apache.airavata.schemas.gfac.UnicoreHostType;
import org.apache.airavata.schemas.wec.ApplicationOutputDataHandlingDocument.ApplicationOutputDataHandling;
import org.apache.airavata.schemas.wec.ContextHeaderDocument;
import org.ietf.jgss.GSSCredential;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class GridFTPOutputHandler implements GFacHandler {
private static final Logger log = LoggerFactory.getLogger(GridFTPOutputHandler.class);
public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
log.info("Invoking GridFTPOutputHandler ...");
ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
HostDescriptionType hostType = jobExecutionContext.getApplicationContext().getHostDescription().getType();
String[] gridFTPEndpointArray = null;
String hostName = null;
if(jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof GlobusHostType){
gridFTPEndpointArray = ((GlobusHostType) hostType).getGridFTPEndPointArray();
hostName = ((GlobusHostType) hostType).getHostName();
}
else if (jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof UnicoreHostType){
gridFTPEndpointArray = ((UnicoreHostType) hostType).getGridFTPEndPointArray();
hostName = ((UnicoreHostType) hostType).getHostName();
}
else {
//TODO
}
GridFtp ftp = new GridFtp();
File localStdErrFile = null;
Map<String, ActualParameter> stringMap = new HashMap<String, ActualParameter>();
try {
GSSCredential gssCred = ((GSISecurityContext)jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getGssCredentials();
String[] hostgridFTP = gridFTPEndpointArray;
if (hostgridFTP == null || hostgridFTP.length == 0) {
hostgridFTP = new String[]{hostName};
}
for (String endpoint : gridFTPEndpointArray) {
try {
/*
* Read Stdout and Stderror
*/
URI stdoutURI = GFacUtils.createGsiftpURI(endpoint, app.getStandardOutput());
URI stderrURI = GFacUtils.createGsiftpURI(endpoint, app.getStandardError());
log.info("STDOUT:" + stdoutURI.toString());
log.info("STDERR:" + stderrURI.toString());
File logDir = new File("./service_logs");
if (!logDir.exists()) {
logDir.mkdir();
}
String timeStampedServiceName = GFacUtils.createUniqueNameForService(jobExecutionContext
.getServiceName());
File localStdOutFile = File.createTempFile(timeStampedServiceName, "stdout");
localStdErrFile = File.createTempFile(timeStampedServiceName, "stderr");
String stdout = null;
String stderr = null;
// TODO: what if job is failed
// and this handler is not able to find std* files?
try {
stdout = ftp.readRemoteFile(stdoutURI, gssCred, localStdOutFile);
stderr = ftp.readRemoteFile(stderrURI, gssCred, localStdErrFile);
//TODO: do we also need to set them as output parameters for another job
ApplicationDescription application = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription();
ApplicationDeploymentDescriptionType appDesc = application.getType();
appDesc.setStandardOutput(stdout);
appDesc.setStandardError(stderr);
jobExecutionContext.getApplicationContext().setApplicationDeploymentDescription(application);
}
catch(ToolsException e) {
log.error("Cannot download stdout/err files. One reason could be the job is not successfully finished: "+e.getMessage());
}
Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
Set<String> keys = output.keySet();
for (String paramName : keys) {
ActualParameter actualParameter = (ActualParameter) output.get(paramName);
if ("URIArray".equals(actualParameter.getType().getType().toString())) {
URI outputURI = GFacUtils.createGsiftpURI(endpoint, app.getOutputDataDirectory());
List<String> outputList = ftp.listDir(outputURI, gssCred);
String[] valueList = outputList.toArray(new String[outputList.size()]);
((URIArrayType) actualParameter.getType()).setValueArray(valueList);
// why to instantiate new instance?
// stringMap = new HashMap<String, ActualParameter>();
stringMap.put(paramName, actualParameter);
}else if ("StringArray".equals(actualParameter.getType().getType().toString())) {
String[] valueList = OutputUtils.parseStdoutArray(stdout, paramName);
((StringArrayType) actualParameter.getType()).setValueArray(valueList);
// stringMap = new HashMap<String, ActualParameter>();
stringMap.put(paramName, actualParameter);
} else if ("URI".equals(actualParameter.getType().getType().toString())) {
URI outputURI = GFacUtils.createGsiftpURI(endpoint, app.getOutputDataDirectory());
List<String> outputList = ftp.listDir(outputURI, gssCred);
if (outputList.size() == 0 || outputList.get(0).isEmpty()) {
stringMap = OutputUtils.fillOutputFromStdout(output, stdout, stderr);
} else {
String valueList = outputList.get(0);
((URIParameterType) actualParameter.getType()).setValue(valueList);
stringMap = new HashMap<String, ActualParameter>();
stringMap.put(paramName, actualParameter);
}
}
else {
// This is to handle exception during the output parsing.
stringMap = OutputUtils.fillOutputFromStdout(output, stdout, stderr);
}
}
if (stringMap == null || stringMap.isEmpty()) {
throw new GFacHandlerException("Empty Output returned from the Application, Double check the application" +
"and ApplicationDescriptor output Parameter Names");
}
// If users has given an output Data path to download the output files this will download the file on machine where GFac is installed
ContextHeaderDocument.ContextHeader currentContextHeader = jobExecutionContext.getContextHeader();
if(currentContextHeader != null && currentContextHeader.getWorkflowOutputDataHandling() != null){
ApplicationOutputDataHandling[] handlings = currentContextHeader.getWorkflowOutputDataHandling().getApplicationOutputDataHandlingArray();
if(handlings != null && handlings.length != 0){
String outputDataDirectory = handlings[0].getOutputDataDirectory();
if(outputDataDirectory != null && !"".equals(outputDataDirectory)){
stageOutputFiles(jobExecutionContext,outputDataDirectory);
}
}
}
} catch (ToolsException e) {
log.error(e.getMessage());
throw new GFacHandlerException(e.getMessage(), e, readLastLinesofStdOut(localStdErrFile.getPath(), 20));
} catch (URISyntaxException e) {
log.error(e.getMessage());
throw new GFacHandlerException("URI is malformatted:" + e.getMessage(), e, readLastLinesofStdOut(localStdErrFile.getPath(), 20));
}
}
} catch (Exception e) {
log.error(e.getMessage());
throw new GFacHandlerException(e.getMessage(), e, readLastLinesofStdOut(localStdErrFile.getPath(), 20));
}
}
private static String readLastLinesofStdOut(String path, int count) {
StringBuffer buffer = new StringBuffer();
FileInputStream in = null;
try {
in = new FileInputStream(path);
} catch (FileNotFoundException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
BufferedReader br = new BufferedReader(new InputStreamReader(in));
List<String> strLine = new ArrayList<String>();
String tmp = null;
int numberofLines = 0;
try {
while ((tmp = br.readLine()) != null) {
strLine.add(tmp);
numberofLines++;
}
} catch (IOException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
if (numberofLines > count) {
for (int i = numberofLines - count; i < numberofLines; i++) {
buffer.append(strLine.get(i));
buffer.append("\n");
}
} else {
for (int i = 0; i < numberofLines; i++) {
buffer.append(strLine.get(i));
buffer.append("\n");
}
}
try {
in.close();
} catch (IOException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
return buffer.toString();
}
private static void stageOutputFiles(JobExecutionContext jobExecutionContext, String outputFileStagingPath) throws GFacProviderException,GFacException {
HostDescriptionType hostType = jobExecutionContext.getApplicationContext().getHostDescription().getType();
String[] gridFTPEndpointArray = null;
if(jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof GlobusHostType){
gridFTPEndpointArray = ((GlobusHostType) hostType).getGridFTPEndPointArray();
}
else if (jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof UnicoreHostType){
gridFTPEndpointArray = ((UnicoreHostType) hostType).getGridFTPEndPointArray();
}
else {
//TODO
}
MessageContext outputNew = new MessageContext();
MessageContext output = jobExecutionContext.getOutMessageContext();
Map<String, Object> parameters = output.getParameters();
for (String paramName : parameters.keySet()) {
ActualParameter actualParameter = (ActualParameter) parameters
.get(paramName);
GridFtp ftp = new GridFtp();
GSSCredential gssCred = ((GSISecurityContext)jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getGssCredentials();
try {
if ("URI".equals(actualParameter.getType().getType().toString())) {
for (String endpoint : gridFTPEndpointArray) {
((URIParameterType) actualParameter.getType()).setValue(doStaging(outputFileStagingPath,
MappingFactory.toString(actualParameter), ftp, gssCred, endpoint));
}
} else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
List<String> split = Arrays.asList(StringUtil.getElementsFromString(MappingFactory.toString(actualParameter)));
List<String> newFiles = new ArrayList<String>();
for (String endpoint : gridFTPEndpointArray) {
for (String paramValueEach : split) {
newFiles.add(doStaging(outputFileStagingPath, paramValueEach, ftp, gssCred, endpoint));
}
((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
}
}
} catch (URISyntaxException e) {
log.error(e.getMessage());
throw new GFacProviderException(e.getMessage(), e);
} catch (ToolsException e) {
log.error(e.getMessage());
throw new GFacProviderException(e.getMessage(), e);
}
outputNew.getParameters().put(paramName, actualParameter);
}
jobExecutionContext.setOutMessageContext(outputNew);
}
private static String doStaging(String outputFileStagingPath, String paramValue, GridFtp ftp, GSSCredential gssCred, String endpoint) throws URISyntaxException, ToolsException {
URI srcURI = GFacUtils.createGsiftpURI(endpoint, paramValue);
String fileName = new File(srcURI.getPath()).getName();
File outputpath = new File(outputFileStagingPath);
if(!outputpath.exists()){
outputpath.mkdirs();
}
File outputFile = new File(outputpath.getAbsolutePath() + File.separator + fileName);
ftp.readRemoteFile(srcURI,
gssCred, outputFile);
return outputFileStagingPath + File.separator + fileName;
}
public void initProperties(Map<String, String> properties) throws GFacHandlerException, GFacException {
}
}