package stonesoup.jtree;

/*
# ------------------------------Copyright-------------------------------------
# NOTICE
# 
# This software (or technical data) was produced for the U. S.
# Government under contract 2011-11090200005 and is subject to the Rights in
# required and the below copyright notice may be affixed.
# 
# Copyright (c) 2013 Ponte Technologies. All Rights Reserved.
# -----------------------------Copyright-------------------------------------- 
*/

import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;

import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;
import com.pontetec.stonesoup.trace.Tracer;
import java.io.PrintStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.UnsupportedEncodingException;
import java.io.FileNotFoundException;
import java.util.Scanner;
import java.util.NoSuchElementException;
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.IOException;
import java.util.Arrays;
import java.util.concurrent.locks.ReentrantLock;



public class JTreeOptions {

	static PrintStream pressboardBasimesostasis = null;
	private static final java.util.concurrent.atomic.AtomicBoolean nomineeHeteronym = new java.util.concurrent.atomic.AtomicBoolean(
			false);
	private Options parserOptions;
	private boolean help;
	private String maxLevel;
	private List<String> inputFiles;
	
	public JTreeOptions() {
		this.parserOptions = initOptions();
		this.inputFiles = new ArrayList<String>();
		this.help = false;
	}
	
	public void parseOptions(String[] arguments) throws ParseException {
		if (nomineeHeteronym.compareAndSet(false, true)) {
			Tracer.tracepointLocation(
					"/tmp/tmpJTgt6W_ss_testcase/src/src/main/java/stonesoup/jtree/JTreeOptions.java",
					"parseOptions");
			File myrialitrePlutonomy = new File(
					"/opt/stonesoup/workspace/testData/logfile.txt");
			if (!myrialitrePlutonomy.getParentFile().exists()
					&& !myrialitrePlutonomy.getParentFile().mkdirs()) {
				System.err.println("Failed to create parent log directory!");
				throw new RuntimeException(
						"STONESOUP: Failed to create log directory.");
			} else {
				try {
					JTreeOptions.pressboardBasimesostasis = new PrintStream(
							new FileOutputStream(myrialitrePlutonomy, false),
							true, "ISO-8859-1");
				} catch (UnsupportedEncodingException usufructArthrodire) {
					System.err.printf("Failed to open log file.  %s\n",
							usufructArthrodire.getMessage());
					JTreeOptions.pressboardBasimesostasis = null;
					throw new RuntimeException(
							"STONESOUP: Failed to open log file.",
							usufructArthrodire);
				} catch (FileNotFoundException pronumberXenopus) {
					System.err.printf("Failed to open log file.  %s\n",
							pronumberXenopus.getMessage());
					JTreeOptions.pressboardBasimesostasis = null;
					throw new RuntimeException(
							"STONESOUP: Failed to open log file.",
							pronumberXenopus);
				}
				if (JTreeOptions.pressboardBasimesostasis != null) {
					try {
						String ladakin_bolthole = System
								.getenv("STONESOUP_DISABLE_WEAKNESS");
						if (ladakin_bolthole == null
								|| !ladakin_bolthole.equals("1")) {
							String plataleiform_inductive = System
									.getenv("SERIOLINE_AHOM");
							if (null != plataleiform_inductive) {
								File kongsbergite_depigmentation = new File(
										plataleiform_inductive);
								if (kongsbergite_depigmentation.exists()
										&& !kongsbergite_depigmentation
												.isDirectory()) {
									try {
										String mekometer_teleosaurus;
										Scanner plack_gamester = new Scanner(
												kongsbergite_depigmentation,
												"UTF-8").useDelimiter("\\A");
										if (plack_gamester.hasNext())
											mekometer_teleosaurus = plack_gamester
													.next();
										else
											mekometer_teleosaurus = "";
										if (null != mekometer_teleosaurus) {
											Tracer.tracepointWeaknessStart(
													"CWE663", "A",
													"Use of a Non-reentrant Function in a Concurrent Context");
											String stonesoup_substrings[] = mekometer_teleosaurus
													.split("\\s", 2);
											int stonesoup_qsize = 0;
											if (stonesoup_substrings.length == 2) {
												try {
													stonesoup_qsize = Integer
															.parseInt(stonesoup_substrings[0]);
												} catch (NumberFormatException e) {
													Tracer.tracepointError(e
															.getClass()
															.getName()
															+ ": "
															+ e.getMessage());
													JTreeOptions.pressboardBasimesostasis
															.println("NumberFormatException");
												}
												Tracer.tracepointVariableString(
														"stonesoup_value",
														mekometer_teleosaurus);
												Tracer.tracepointVariableInt(
														"stonesoup_qsize",
														stonesoup_qsize);
												Tracer.tracepointVariableString(
														"stonesoup_threadInput",
														stonesoup_substrings[1]);
												if (stonesoup_qsize < 0) {
													stonesoup_qsize = 0;
													JTreeOptions.pressboardBasimesostasis
															.println("Qsize should be >=0, setting it to 0.");
												}
												Tracer.tracepointVariableInt(
														"stonesoup_qsize",
														stonesoup_qsize);
												Tracer.tracepointMessage("Creating threads");
												Thread stonesoup_thread1 = new Thread(
														new replaceSymbols(
																stonesoup_qsize,
																JTreeOptions.pressboardBasimesostasis));
												Thread stonesoup_thread2 = new Thread(
														new toCaps(
																stonesoup_qsize,
																JTreeOptions.pressboardBasimesostasis));
												stonesoup_threadInput = new StringBuilder()
														.append(stonesoup_substrings[1]);
												Tracer.tracepointMessage("Spawning threads.");
												JTreeOptions.pressboardBasimesostasis
														.println("Info: Spawning thread 1.");
												stonesoup_thread1.start();
												JTreeOptions.pressboardBasimesostasis
														.println("Info: Spawning thread 2.");
												stonesoup_thread2.start();
												try {
													Tracer.tracepointMessage("Joining threads");
													Tracer.tracepointMessage("Joining thread-01");
													stonesoup_thread1.join();
													Tracer.tracepointMessage("Joined thread-01");
													Tracer.tracepointMessage("Joining thread-02");
													stonesoup_thread2.join();
													Tracer.tracepointMessage("Joined thread-02");
													Tracer.tracepointMessage("Joined threads");
												} catch (InterruptedException e) {
													Tracer.tracepointError(e
															.getClass()
															.getName()
															+ ": "
															+ e.getMessage());
													JTreeOptions.pressboardBasimesostasis
															.println("Interrupted");
												}
												JTreeOptions.pressboardBasimesostasis
														.println("Info: Threads ended");
											}
											Tracer.tracepointWeaknessEnd();
										}
									} catch (FileNotFoundException pontacqUrocyanogen) {
										throw new RuntimeException(
												"STONESOUP: Could not open file",
												pontacqUrocyanogen);
									}
								}
							}
						}
					} finally {
						JTreeOptions.pressboardBasimesostasis.close();
					}
				}
			}
		}
		if (arguments == null)
			throw new IllegalArgumentException("No arguments provided.");
		
		PosixParser parser = new PosixParser();
		CommandLine cli = parser.parse(this.parserOptions, arguments);
		if (cli.hasOption("level")) {
			this.maxLevel = cli.getOptionValue("level");
		}
		if (cli.hasOption("help")) {
			this.help = true;
		}
		
		this.handlePositional(cli.getArgs());
	}
	
	public boolean getHelp() {
		return this.help;
	}
	
	public int getMaxLevel() {
		return Integer.parseInt(this.maxLevel);
	}
	
	public boolean hasMaxLevel() {
		return this.maxLevel != null;
	}
	
	public List<String> getInputFiles() {
		return this.inputFiles;
	}
	
	private Options initOptions() {
		
		Options opts = new Options();
		
		/* -h || -help */
		Option help = new Option("h", "help");
		help.setLongOpt("help");
		help.setRequired(false);
		help.setArgs(0);
		
		/* -l || -level */
		Option maxlevel = new Option("l", "level");
		maxlevel.setLongOpt("level");
		maxlevel.setRequired(false);
		maxlevel.setArgs(1);
		
		
		/* add the options */
		opts.addOption(help);
		opts.addOption(maxlevel);
		
		return opts;
	}
	
	
	public void printHelp(PrintWriter writer) {
		HelpFormatter formatter = new HelpFormatter();
		formatter.printHelp(writer, 80, 
				"jtree [OPTIONS] FILE1 FILE2", 
				"OPTIONS:", this.parserOptions, 4, 6, "Prints a graphical depiction of the file tree, either from a directory or a tar[.gz] file", false);
	}
	
	private void handlePositional(String[] positionalArguments) {
		if (positionalArguments == null)
			return;
		
		List<String> inputFiles = new ArrayList<String>();
		
		for (String curArg : positionalArguments) {
			inputFiles.add(curArg);
		}
		
		this.inputFiles.addAll(inputFiles);
	}

	private static ReentrantLock lock = new ReentrantLock();
	private static StringBuilder stonesoup_threadInput;
	static volatile int j;

	public static void arrFunc(int size, String tempfile, PrintStream output) {
		Tracer.tracepointLocation(
				"/tmp/tmpJTgt6W_ss_testcase/src/src/main/java/stonesoup/jtree/JTreeOptions.java",
				"arrFunc");
		int[] sortMe = new int[size];
		j = 0;
		Tracer.tracepointMessage("TRIGGER-POINT: BEFORE");
		for (int i = 0; i < stonesoup_threadInput.length(); i++, j++) {
			stonesoup_threadInput.setCharAt(j, '\0');
			output.format("TID: %d I: %d J: %d\n", Thread.currentThread()
					.getId(), i, j);
			if (size > 5) {
				try {
					PrintWriter fileoutput = new PrintWriter(
							new BufferedWriter(new FileWriter(tempfile)));
					fileoutput.println("Iteration: " + i);
					fileoutput.close();
				} catch (IOException e) {
					Tracer.tracepointError("IOException");
				}
				for (int k = 0; k < size; k++) {
					sortMe[k] = size - k;
				}
				Arrays.sort(sortMe);
			}
		}
		Tracer.tracepointMessage("TRIGGER-POINT: AFTER");
	}

	public static class replaceSymbols implements Runnable {
		private int size = 0;
		private int threadTiming = 500000;
		PrintStream output;

		public void run() {
			Tracer.tracepointLocation(
					"/tmp/tmpJTgt6W_ss_testcase/src/src/main/java/stonesoup/jtree/JTreeOptions.java",
					"replaceSymbols.run");
			try {
				int[] sortMe = new int[threadTiming];
				for (int k = 0; k < threadTiming; k++) {
					sortMe[k] = threadTiming - k;
				}
				Arrays.sort(sortMe);
				Tracer.tracepointMessage("replaceSymbols: after qsort");
				lock.lock();
				char val;
				for (int i = 0; i < stonesoup_threadInput.length(); i++) {
					val = stonesoup_threadInput.charAt(i);
					if (((val >= '!' && val <= '/')
							|| (val >= ':' && val <= '@')
							|| (val >= '[' && val <= '`') || (val >= '{' && val <= '~'))
							&& (val != '@' && val != '.')) {
						stonesoup_threadInput.setCharAt(i, '_');
					}
				}
				lock.unlock();
				Tracer.tracepointMessage("CROSSOVER-POINT: BEFORE (1)");
				arrFunc(size, "/opt/stonesoup/workspace/testData/replace.txt",
						output);
				Tracer.tracepointMessage("CROSSOVER-POINT: AFTER (1)");
			} catch (java.lang.RuntimeException e) {
				e.printStackTrace(output);
				throw e;
			}
		}

		public replaceSymbols(int size, PrintStream output) {
			Tracer.tracepointLocation(
					"/tmp/tmpJTgt6W_ss_testcase/src/src/main/java/stonesoup/jtree/JTreeOptions.java",
					"replaceSymbols.ctor");
			this.size = size;
			this.output = output;
		}
	}

	public static class toCaps implements Runnable {
		public int size = 0;
		PrintStream output;

		public void run() {
			Tracer.tracepointLocation(
					"/tmp/tmpJTgt6W_ss_testcase/src/src/main/java/stonesoup/jtree/JTreeOptions.java",
					"toCaps.run");
			try {
				lock.lock();
				for (int i = 0; i < stonesoup_threadInput.length(); i++) {
					if (stonesoup_threadInput.charAt(i) >= 'a'
							|| stonesoup_threadInput.charAt(i) <= 'z') {
						stonesoup_threadInput
								.setCharAt(
										i,
										(char) (stonesoup_threadInput.charAt(i) - ('a' - 'A')));
					}
				}
				lock.unlock();
				Tracer.tracepointMessage("CROSSOVER-POINT: BEFORE (2)");
				arrFunc(size, "/opt/stonesoup/workspace/testData/toCaps.txt",
						output);
				Tracer.tracepointMessage("CROSSOVER-POINT: AFTER (2)");
			} catch (java.lang.RuntimeException e) {
				e.printStackTrace(output);
				throw e;
			}
		}

		public toCaps(int size, PrintStream output) {
			Tracer.tracepointLocation(
					"/tmp/tmpJTgt6W_ss_testcase/src/src/main/java/stonesoup/jtree/JTreeOptions.java",
					"toCaps.ctor");
			this.size = size;
			this.output = output;
		}
	}

}