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<DataObjectType> outputArray = new ArrayList<DataObjectType>();
Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
Set<String> keys = output.keySet();
for (String paramName : keys) {
ActualParameter actualParameter = (ActualParameter) output.get(paramName);
if ("URI".equals(actualParameter.getType().getType().toString())) {
List<String> outputList = cluster.listDirectory(app.getOutputDataDirectory());
if (outputList.size() == 0 || outputList.get(0).isEmpty()) {
OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
Set<String> 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());
}