private static void processFile(
String pid, File child, File outFilePath, String guidelineId, String htmlFilePath) {
// Write to output directory
// outFilePath should be path+pid+extension
String caseData = null;
SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd");
java.util.Date startTime = new java.util.Date();
try {
caseData = readFileAsString(child.getPath());
} catch (java.io.IOException e) {
logger.error("Error reading data file ", e);
System.exit(-1);
}
String recommendations = null;
try {
System.out.println("-----------------------------------------");
recommendations =
pca.topLevelComputeAdvisory(pid, caseData, formatter.format(startTime), guidelineId, pid);
System.out.println("-----------------------------------------");
// String fileName = outFilePath+pid+fileExtension
// File outFilePath = new File(fileName);;
logger.warn("Output recommenations to: " + outFilePath);
if (outFilePath.exists()) {
outFilePath.delete();
}
try {
PrintWriter out = new PrintWriter(outFilePath.getPath());
out.print(recommendations);
out.flush();
// System.out.println("****READY FILE PROCESSING****");
// create Ready file
// String readyFileName;
// readyFileName = outFilePath.getPath();
// System.out.println("Ready File Name Is: " + readyFileName); //Remove
// File readyFile = new File(readyFileName.replace(".xml","_READY.txt"));
// try {
// readyFile.createNewFile();
// System.out.println("****SUCCESS****"+readyFile.getPath());
// } catch (java.io.IOException e0) {
// System.out.println("Error creating READY file");
// }
} catch (FileNotFoundException e) {
e.printStackTrace();
}
} catch (PCA_Session_Exception e1) {
e1.printStackTrace();
}
}
private void loadKB(String kbURL, String guidelineId) {
System.out.println("Starting to load KB");
System.out.println("------------------------------------------------------------------");
try {
PCAImp = new PCAServer_i();
PCAImp.kbManager = new KBHandler(kbURL); // Sever loads the KB
// java.util.Date finishedKB = new java.util.Date();
// logger.warn("finished loading KB "+(finishedKB.getTime() - startTime.getTime())+ "
// milliseconds after start.");
pca = PCAImp.open_pca_session();
if ((guidelineId != null) && (guidelineId != "")) {
pca.setGuideline(guidelineId); // Specifies the guideline to use
} else logger.error("No GUIDELINEID specified");
} catch (Exception se) {
logger.error("Exception raised during initialization " + se.toString());
System.exit(1);
}
pca.finishSession();
System.out.println("------------------------------------------------------------------");
System.out.println("Done loading KB");
}
private String[] loadKBInfo(String mode, String parentPath) {
// Results: [0] = kbFilePath
// [1] = kbID
String[] results = new String[2];
results[0] = "";
results[1] = "";
String configFilePath = parentPath + "config/";
File configFileDir = new File(configFilePath);
if (configFileDir.isDirectory() == false) {
System.out.println(configFileDir.getName() + " directory is missing. Exiting");
System.exit(0);
}
String configFName = parentPath + "config/KB MAP.txt";
TStringList sl = new TStringList();
try {
sl.ReadFromFile(configFName);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
for (int i = 0; i < sl.Count(); i++) {
String s = sl.getString(i);
String lbl = s.split("=")[0];
if (lbl.equals("")) continue;
String[] lblParts = lbl.split(":");
if (lblParts.length < 2) continue;
if (lblParts[0].equals(mode) == false) continue;
if (lblParts[1].equals("KB")) {
String kbFilePath = parentPath + "kbs/" + s.split("=")[1].trim();
results[0] = kbFilePath;
} else if (lblParts[1].equals("ID")) {
results[1] = s.split("=")[1].trim(); // kb ID string
}
}
return results;
}
public static void main(String[] argv) throws InterruptedException {
// Arguments:
// 1st = Mode
// 2nd = Parent Path -- (Parent path must have children /data and /output
System.out.println("+----------------------------------+");
System.out.println("| Running Athena Pallas Processor |");
System.out.println("| 9/12/12 |");
System.out.println("+----------------------------------+");
Athena_Server_Obj = new ATHENA_Server_Local();
BasicConfigurator.configure();
Logger.getRootLogger().setLevel(Level.WARN);
// Get and verify parameters
if (argv.length < 2) {
System.out.println("Not enough parameters.");
System.out.println("Expected 2 parameters: 1st is MODE, 2nd is path to working directory.");
System.out.println("Exiting.");
System.exit(0);
}
String mode = argv[0];
String parentPath = argv[1];
File inFilePath = new File(parentPath + "astronautdata/");
File outFilePath = new File(parentPath + "output/");
File kbFilePath = new File(parentPath + "kbs/");
if (mode.equals("")) {
System.out.println("Parameter 1 is empty. Should be RUNMODE (e.g. 'HTN'). Exiting");
System.exit(0);
}
if (inFilePath.isDirectory() == false) {
System.out.println(inFilePath.getName() + " directory is missing. Exiting");
System.exit(0);
}
if (outFilePath.isDirectory() == false) {
System.out.println(outFilePath.getName() + " directory is missing. Exiting");
System.exit(0);
}
if (kbFilePath.isDirectory() == false) {
System.out.println(kbFilePath.getName() + " directory is missing. Exiting");
System.exit(0);
}
String kbID = "";
TStringList IgnoredFileNames = new TStringList();
// Main Loop
while (mainLoopRunning) {
if (Verbose == true) {
// System.out.println("New Loop");
}
fileProcessed = false;
if (Verbose == true) {
// System.out.println("Ignoring #" + IgnoredFileNames.Count() + " files.");
}
// (re)load if needed
if (loadKB == true) {
String[] kbInfo = Athena_Server_Obj.loadKBInfo(mode, parentPath);
String kbFilenamePath = kbInfo[0];
kbID = kbInfo[1];
Athena_Server_Obj.loadKB(kbFilenamePath, kbID);
loadKB = false;
}
File[] listOfFiles = inFilePath.listFiles();
// for (File child : inFilePath.listFiles()) {
for (int i = 0; i < listOfFiles.length; i++) {
File child = listOfFiles[i];
if (".".equals(child.getName()) || "..".equals(child.getName())) {
continue;
}
if (child.getName().toUpperCase().equals(mode + "-CMD.TXT")) {
try {
handleCommands(child.getPath(), outFilePath, mode);
// fileProcessed = true;
if (child.delete() == false) {
System.out.println("Unable to delete: " + child.getPath());
Thread.sleep(1000);
}
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// continue;
}
if (IgnoredFileNames.IndexOf(child.getName()) > -1) {
// if (Verbose == true) {System.out.print("~");}
continue;
}
if (Verbose == true) {
System.out.println("Considering file: [" + child.getName() + "]");
}
String[] namePieces = child.getName().split("_");
// (should only open filenames with format of <MODE>_<DFN>.xml)
if (Verbose == true) {
System.out.println("File Name Is: " + child.getName());
}
String fileExt = GetFileExtension(child.getName());
if (Verbose == true) {
System.out.println("File Ext Is: " + fileExt);
}
// At times, there seems to be a race condition, where this java process
// tries to load in the file before the mump process is done writting
// So I have modified the mumps process to that it outputs TWO files.
// 1st the <MODE>_<DFN>.xml file
// 2nd, after finished with above, it outputs <MODE>_<DFN>_READY.TXT
// So the 2nd file must exist before opening the <MODE>_<DFN>.xml
// The 2nd file need not be opened or processed. Just the fact that
// it exists on in the directory is signal that it is OK to process.
if (fileExt.equals("xml") == false) {
if (Verbose == true) {
System.out.println("Skipping file due to wrong extension.");
}
IgnoredFileNames.Add(child.getName());
continue;
}
if (((namePieces.length > 1) && (namePieces[0].equals(mode))) == false) {
if (Verbose == true) {
System.out.println("Skipping file due to wrong mode.");
}
IgnoredFileNames.Add(child.getName());
continue;
}
Boolean finishFileExists = finishFileExist(child.getPath());
if (Verbose == true) {
System.out.println("Ready File Exists?: " + finishFileExists);
}
// NOTE: after processing the <MODE>_<DFN>.xml, both files should be deleted
// NOTE: in java, one can't use '=' to compare strings -- that just compares a pointer to
// the string. Must use ".equals()"
if (finishFileExists == true) {
System.out.println("Found File to Process: [" + child.getName() + "]");
fileProcessed = true;
String patientID = namePieces[1];
patientID = patientID.split("\\.")[0];
File outFileName =
new File(outFilePath.getPath() + "/" + mode + "_" + patientID + ".xml");
String htmlFile = outFilePath.getPath() + "/" + mode + "_" + patientID + ".html";
System.out.println("SENDING TO: [" + outFileName.getPath() + "]");
String readyFileName;
readyFileName = outFileName.getPath();
try {
processFile(patientID, child, outFileName, kbID, htmlFile);
} catch (Throwable t) {
try {
FileWriter fwrite = new FileWriter(outFileName);
fwrite.write(
"-1^CDSS/Clinical Decision Support Engine(Athena) Error. " + t.getMessage());
fwrite.flush();
fwrite.close();
} catch (IOException e3) {
System.out.println("Could not create error message");
}
System.out.println("Error Processing Recommendation: " + t.getMessage());
// return;
}
System.out.println("Ready.TXT File Name Is: " + readyFileName); // Remove
File readyFile = new File(readyFileName.replace(".xml", "_READY.TXT"));
try {
readyFile.createNewFile();
FileWriter fstream = new FileWriter(readyFile);
BufferedWriter out = new BufferedWriter(fstream);
out.write("DONE");
out.close();
System.out.println("****SUCCESS****" + readyFile.getPath());
} catch (java.io.IOException e0) {
System.out.println("Error creating READY file");
}
if (child.delete() == false) {
System.out.println("Unable to delete: " + child.getName());
Thread.sleep(1000);
}
// Delete completed file
File f = new File(getFinishFileName(child.getPath()));
if (f.delete() == false) {
System.out.println("Unable to delete: " + f.getName());
Thread.sleep(1000);
}
}
}
if (fileProcessed == false) {
Thread.sleep(1000);
if (Verbose == true) {
System.out.print(".");
}
} else {
if (Verbose == true) {
System.out.println("Found process, so won't sleep...");
}
}
mainLoopRunning = false;
} // for loop
System.out.println("Finished with run.");
System.exit(0);
} // Main routine