package org.ngbw.pise.commandrenderer;


import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.Future;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.ngbw.sdk.api.tool.CommandRenderer;
import org.ngbw.sdk.common.util.StringUtils;
import org.ngbw.sdk.common.util.SuperString;
import org.ngbw.sdk.tool.InputStreamCollector;
import org.ngbw.sdk.tool.RenderedCommand;


/**
 * This Class implements CommandRenderer this implementation takes care of
 * PiseXML and Perl contents
 * <br />
 * @author Rami
 * <br />
 * @author R. Hannes Niedner
 * 
 */

public class PiseCommandRenderer implements CommandRenderer {
	private static Log log = LogFactory.getLog(PiseCommandRenderer.class
			.getName());
	//JAXB marshaller with mapped beans in the pise subpackage keyed to the cfg file url
	private final Map<URL , PiseMarshaller> cfgMap = new HashMap<URL , PiseMarshaller>();
	//pise PiseMarshaller for the submitted cfgFileURL
	private PiseMarshaller piseMarshaller;
	//parameter map (parameter name -> parameter value)
	private Map<String, byte[]> parameters;
	// private variable for the toUnixCmd() method
	private String[] unixCmdGroup = null;
	private String[] unixCmdGroupNegative = null;
	private Map<String, String[]> inputDataMapTab = null;
	
	private RenderedCommand renderedCommand= null;

	
	public PiseCommandRenderer() {
		super();
		init();
	}
	
	private void init() {
		parameters = null;
		piseMarshaller = null;
		unixCmdGroup = new String[100];
		unixCmdGroupNegative = new String[100];
		inputDataMapTab = new HashMap<String, String[]>();
		renderedCommand = new RenderedCommand();
	}

	public RenderedCommand render(URL url, Map<String, byte[]> parameters) {
		try {
			if(log.isDebugEnabled())
				log.debug("render command from " + parameters.size() + " parameters using config:" + url);
			init();
			this.parameters = parameters;
			piseMarshaller = initPiseMarshaller(url);
			List<String> commandList = toUnixCmd();
			if(log.isDebugEnabled())
				log.debug("toUnixCmd returns a list with " + commandList.size() + " elements");
			String[] commandArray = new String[commandList.size()];
			renderedCommand.setCommand(commandList.toArray(commandArray));
			if (log.isDebugEnabled()) {
				log.debug("Returned command: " + StringUtils.join(renderedCommand.getCommand(), " "));
				Map<String, String> input = renderedCommand.getInputFileMap();
				Map<String, String> output = renderedCommand.getOutputFileMap();
				for(String parameter : input.keySet())
					log.debug("Input: " + parameter + ": " + input.get(parameter));
				for(String parameter : output.keySet())
					log.debug("Output: " + parameter + ": " + output.get(parameter));
			}
			return renderedCommand;
		}
		catch (Exception err) {
			throw new RuntimeException(err);
		}
	}

	//private methods

	//initialize the JAXB Marshaller
	private PiseMarshaller initPiseMarshaller(URL url) {
		if (url == null)
			throw new NullPointerException("Tool config file URL is null!");
		if (cfgMap.containsKey(url) == false)
		try {
			PiseMarshaller pm = new PiseMarshaller(url.openStream());
			cfgMap.put(url, pm);
		} catch (IOException e) {
			throw new RuntimeException("Cannot initialize PiseMarshaller.", e);
		}
		return cfgMap.get(url);
	}
	
	//all parameter names in the submitted maps have an underscore appended
	//thus we declare our own private getters and setters for the value
	private Set<String> getParameterSet() {
		Set<String> keySet = new HashSet<String>();
		for (String key : parameters.keySet()) {
			//the regex secefies the only a trailing _
			//and the replaceFirst will only take this one
			String paramName = key.replaceFirst("_$", "");
			keySet.add(paramName);
		}
		return keySet;
	}
	
	private String getParameterKey(String parameter) {
		return parameter + "_";
	}
	
	private String getParameterValue(String parameter) {
		String key = getParameterKey(parameter);
		if (parameters.containsKey(key) || parameters.get(key) != null)
			return new String(parameters.get(key));
		else
			return null; 
		// that is expected since parameters with
		// null values are notin the parameter map
	}
	private void setParameterValue(String parameter, String value) {
		String key = parameter + "_";
		parameters.put(key, value.getBytes());
	}
	private void setInputFileName(String parameter, String fileName) {
		String key = parameter + "_";
		renderedCommand.getInputFileMap().put(key, fileName);
	}
	private void setOutputFileName(String parameter, String fileName) {
		renderedCommand.getOutputFileMap().put(parameter, fileName);
	}
	
	private String evaluatePerlStatement(String perlStatement) throws IOException, InterruptedException, ExecutionException {
		if(log.isDebugEnabled())
			log.debug("PerlStatement: " + perlStatement);

		// after some test, we had to create a table containing the different element of 
		// the statement, otherwise it seems not working with one String
		String[] command = new String[3];

		command[0] = "perl";
		command[1] = "-e";
		command[2] = perlStatement;

		Process worker = Runtime.getRuntime().exec(command);
		final Future<String> stdOut = InputStreamCollector.readInputStream(worker.getInputStream());
		final Future<String> stdErr = InputStreamCollector.readInputStream(worker.getErrorStream());
		final int exitCode = worker.waitFor();

		if (exitCode != 0)
			throw new RuntimeException("Exit value was not 0 but " + exitCode + " STDERR: \n" + stdErr.get());

		return stdOut.get().trim();
	}

	private List<String> toUnixCmd() throws IOException, InterruptedException, ExecutionException {

		//String Cmd = null;

		List<String> commandList = new ArrayList<String>();

		//1- A command is constructed from multiple type of parameters:

		// These are the parameters passed as Map argument for this class, which
		// means parameter selected through GUI
		if(log.isDebugEnabled()) 
			log.debug("toUnixCmd: processing " + getParameterSet().size() 
					+ " GUI parameters");
		for (String paramName : getParameterSet()) 
			processParameter(paramName, false);

		// These are the parameters hidden from the GUI, but necessary for
		// generating the command line correctly
		if(log.isDebugEnabled()) 
			log.debug("toUnixCmd: processing " + piseMarshaller.getHiddenSet().size() 
					+ " HIDDEN parameters");
		for (String paramName : piseMarshaller.getHiddenSet())
			processParameter(paramName, true);

		// These are the parameters that generate an outfile, they are hidden
		// from the GUI since the GUI dosen't
		// give the user the possibility to specify the names of the output
		// files, we use a standard filenames for each output file
		// we have added this information (filenames) into the Pise XML file
		// we return these parameter through getOutputFileMap()
		if(log.isDebugEnabled()) 
			log.debug("toUnixCmd: processing " + piseMarshaller.getOutfileSet().size() 
					+ " OUTFILESET parameters");
		for (String paramName : piseMarshaller.getOutfileSet())
			processParameter(paramName, false);

		// These are the parameters passed as Set argument for this class, which
		// mean that the user has selected a User Data Item
		// for each of these parameters. we will return these parameters through
		// getInputFileMap()
		// if the file is a parameter file, the value of the parameter file is
		// returned through getInputDataMap()
		// processInfile_SequenceParameters();

		// similar to outfile, one difference is not all output files are
		// defined as outfile but also as Results
		log.debug("toUnixCmd: processing " + piseMarshaller.getResultSet().size() 
				+ " RESULTSET parameters");
		for (String paramName : piseMarshaller.getResultSet()) 
			processParameter(paramName, true);

		// 2- Arranging inputDataMapTab<String, String[]> into
		// inputDataMap<String,String>
		// inputDataMapTab<String, String[]> is needed since we have to order
		// the values with respect
		// to the Group definition in Pise XML files
		// we also add the paramfile inside the inputfileMap
		for(String key : inputDataMapTab.keySet()) {
			String[] values = inputDataMapTab.get(key);
			StringBuilder valueSb = new StringBuilder();
			for(String value : values) 
				if (value != null)
					valueSb.append(value);
			
			String value = valueSb.toString();
			
			setParameterValue(key, value.replace("\\n", "\n"));
			setInputFileName(key, key);
		}

		// 3- Creating the command line by ordering them with respect to their
		// group
		if (unixCmdGroup[0] != null) {
			commandList.add(unixCmdGroup[0]);
			if (log.isDebugEnabled())
				log.debug("for unixCmdGroup[0] commandList.add: " + unixCmdGroup[0]);
		}
		
		for (int j = 1; j < unixCmdGroup.length; j++) {
			// Arranging positve groups
			if (unixCmdGroup[j] != null) {
				commandList.add(unixCmdGroup[j]);
				if (log.isDebugEnabled())
					log.debug("for unixCmdGroup[" + j + "] commandList.add: " + unixCmdGroup[j]);
			}
		}

		// Arranging the negative groups
		//for (int k = unixCmdGroupNegative.length - 1; k > 0; k--) {

		for (int k=1 ; k <unixCmdGroupNegative.length - 1; k++) {
			if (unixCmdGroupNegative[k] != null) {
				commandList.add(0, unixCmdGroupNegative[k]);
				if (log.isDebugEnabled())
					log.debug("for unixCmdGroupNegative[" + k + "] commandList.add: " + unixCmdGroupNegative[k]);
			}
		}
		return commandList;
	}

	private void processParameter(String paramName, boolean hidden) throws IOException, InterruptedException, ExecutionException {
		if(log.isDebugEnabled()) 
			log.debug("START: processParameter: " + paramName + " (hidden: " + hidden + ")");
		//accesses the value by appending an underscore to the paramName
		String parameterValue = hidden ? null : getParameterValue(paramName);

		String format = piseMarshaller.getFormat(paramName);
		String group = piseMarshaller.getGroup(paramName);
		String precond = piseMarshaller.getPrecond(paramName);
		String type = piseMarshaller.getType(paramName);
		String vdef = piseMarshaller.getVdef(paramName);
		String separator = piseMarshaller.getSeparator(paramName);
		String filenames = piseMarshaller.getFileNames(paramName);
		String paramfile = piseMarshaller.getParamFile(paramName);

		log.debug(paramName +"=" + parameterValue + ", type=" + type);

		//TODO: are they needed???
		@SuppressWarnings("unused")
		String isCommand = piseMarshaller.getIsCommand(paramName);
		@SuppressWarnings("unused")
		String ishidden = piseMarshaller.getIsHidden(paramName);

		// this method signature is different than preceding ones since
		// flist is a list of format, we should return exactly the format
		// that corresponds with the entered value which is capture in the
		// parameters
		String flist = piseMarshaller.getflistValue(paramName, parameterValue);
		String perlFormat = null;
		String perlPrecond = null;

		if (type.equals("Results") && group == null)
			group = "-99"; // this group is not going to be used at all
		// group is never null except for some parameters that are Results;
		// however each time we have a format we need to know where the
		// parameter will be positioned in
		// the command line or parameter file
		if (log.isDebugEnabled())
			log.debug("Group: " + group);
		int groupValue=1;
		if (group !=null)
		 groupValue = Integer.parseInt(group);

		// here we assume that flist and format are mutually exclusive
		// however the case where we have a format and a flist, the flist will
		// override format
		// I don't see the sense of having both in the same parameter
		if (flist != null)
			format = flist;

		// Some parameters have multiple choices list, so we should arrange them
		// with respect of their separator
		// it's safer to repalce in parameters than replacing into the original
		// paramMap
		if (type != null && type.equals("List"))
			if (separator == null) {
				setParameterValue(paramName, SuperString.valueOf(parameterValue,
						'@').concatenate());
			} else {
				setParameterValue(paramName, SuperString.valueOf(parameterValue,
						separator.toCharArray()[1]).concatenate());
			}

		if (precond != null) {
			precond = restitutionPrecond(precond, paramName, vdef);
			//perlPrecond = new EvaluatePerlStatement(precond);
			perlPrecond = evaluatePerlStatement(precond);
			if (log.isDebugEnabled())
				log.debug("Precond evaluation: " + perlPrecond);
		}

		if (format != null) {
			format = restitutionFormat(format, paramName, vdef);
			//perlFormat = new EvaluatePerlStatement(format);
			perlFormat = evaluatePerlStatement(format);
			if (log.isDebugEnabled())
				log.debug("Format evaluation: " + perlFormat);
		}

		/*
		 * if (isCommand !=null && ishidden ==null) {
		 * Cmd=perlFormat;}
		 */

		// Start testing if precondition is true or false
		// if the precondition exits and false, we should do nothing
		// if the precondition exits and true, we should test if format exists
		// this format can be the part of the command line or part of the param
		// file
		// however if we are writting in the command line or in a param file
		// we should see if this parameter is (input file) or generate a file
		// (outfile, param)
		// then we have to add the file to the corresponding Map
		// if it is a parameter file we should also capture the value to be
		// written in this file
		if (log.isDebugEnabled())
			log.debug("precond: " + precond);
		if (precond == null) {
			// add an element to the CMD
			if (perlFormat != null) {
				// check if should be written to a file or to cmd
				if (paramfile != null) {
					String[] value;
					if (inputDataMapTab.containsKey(paramfile) == false || inputDataMapTab.get(paramfile) == null)
						inputDataMapTab.put(paramfile, new String[100]);
						
					value = inputDataMapTab.get(paramfile);

					if (value[groupValue] != null)
						value[groupValue] += perlFormat;
					else
						value[groupValue] = perlFormat;
					
					if (log.isDebugEnabled())
						log.debug("parameter: " + paramName + " put in inputDataMap: '" + paramfile + "' -> '" + value[groupValue] + "'");

				} else {
					if (groupValue >= 0) {
						if (unixCmdGroup[groupValue] != null)
							unixCmdGroup[groupValue] += " " + perlFormat;
						else
							unixCmdGroup[groupValue] = perlFormat;
						
						if (log.isDebugEnabled()) {
							log.debug("unixCmdGroup[" + groupValue + "] = " + unixCmdGroup[groupValue]);
						}
					} else {
						if (unixCmdGroupNegative[Math.abs(groupValue)] != null)
							unixCmdGroupNegative[Math.abs(groupValue)] += " " + perlFormat;
						else
							unixCmdGroupNegative[Math.abs(groupValue)] = perlFormat;
						
						if (log.isDebugEnabled()) {
							log.debug("unixCmdGroupNegative[" + Math.abs(groupValue) + "] = " + unixCmdGroupNegative[Math.abs(groupValue)]);
						}
					}
				}
			}

			if (filenames != null) {
				// filenames not null for infile and sequence means we have assigned
				// standard names for these input files
				if (type.equals("InFile") || type.equals("Sequence")){
					setInputFileName(paramName, filenames);

					if (log.isDebugEnabled())
						log.debug("setInputFileName: '" + paramName + "' -> '" + filenames + "'");
				}
				// Most output filenames are given in Results
				// but can also be defined in Switch, List,
				// OutFile, etc.
				else {
					setOutputFileName(paramName, filenames);

					if (log.isDebugEnabled())
						log.debug("setOutputFileName: '" + paramName + "' -> '" + filenames + "'");
				}
			}
		} else {
			if (log.isDebugEnabled())
				log.debug("perlPrecond: " + (perlPrecond == null ? "null" : perlPrecond));
			if (log.isDebugEnabled())
				log.debug("perlFormat: " + (perlFormat == null ? "null" : perlFormat));
			// evaluate precond before adding an element to the CMD
			if (perlPrecond != null) {
				if (log.isDebugEnabled())
					log.debug("Boolean.valueOf(perlPrecond.trim()) == " + Boolean.valueOf(perlPrecond));
				if (Boolean.valueOf(perlPrecond)) {
					if (perlFormat != null) {
						// check if should be written to a file or to cmd
						if (log.isDebugEnabled())
							log.debug("paramfile: " + (paramfile == null ? "null" : paramfile));
						if (paramfile != null) {
							String[] value;
							if (inputDataMapTab.containsKey(paramfile) == false || inputDataMapTab.get(paramfile) == null)
								inputDataMapTab.put(paramfile, new String[100]);
							
							value = inputDataMapTab.get(paramfile);

							if (value[groupValue] != null)
								value[groupValue] += perlFormat;
							else
								value[groupValue] = perlFormat;

						} else {
							if (groupValue >= 0) {
								if (unixCmdGroup[groupValue] != null)
									unixCmdGroup[groupValue] += " "
											+ perlFormat;
								else
									unixCmdGroup[groupValue] = perlFormat
											.toString();
								
								if (log.isDebugEnabled()) {
									log.debug("unixCmdGroup[" + groupValue + "] = " + unixCmdGroup[groupValue]);
								}
							} else {
								if (unixCmdGroupNegative[Math.abs(groupValue)] != null)
									unixCmdGroupNegative[Math.abs(groupValue)] += " "
											+ perlFormat;
								else
									unixCmdGroupNegative[Math.abs(groupValue)] = perlFormat
											.toString();
								
								if (log.isDebugEnabled()) {
									log.debug("unixCmdGroupNegative[" + Math.abs(groupValue) + "] = " + unixCmdGroupNegative[Math.abs(groupValue)]);
								}
							}
						}
					}

					// some filesnames are given in the any type such as Switch,
					// list, etc.
					if (filenames != null) {
						if (type.equals("InFile") == false
								&& type.equals("Sequence") == false) {
							setOutputFileName(paramName, filenames);

							if (log.isDebugEnabled())
								log.debug("type = " + type + ": setOutputFileName: '" + paramName + "' -> '" + filenames + "'");
						}

					// this statement is redanduant with the preceding one if
					// all the filenames of output are given in Results
						if (type.equals("Results")) {
							setOutputFileName(paramName, filenames);

							if (log.isDebugEnabled())
								log.debug("type = " + type + ": setOutputFileName: '" + paramName + "' -> '" + filenames + "'");
						}
					// filenames not null for infile and sequence means we have
					// assigned standard names for these input files
						if (type.equals("InFile") || type.equals("Sequence")) {
							setInputFileName(paramName, filenames);

							if (log.isDebugEnabled())
								log.debug("type = " + type + ": setInputFileName: '" + paramName + "' -> '" + filenames + "'");
						}
					}
				}
			}

		}
		if(log.isDebugEnabled()) 
			log.debug("END : processParameter: " + paramName + " (hidden: " + hidden + ")\n");
	}

	/*
		TL: I'm adding this method to work around the problem where we want to know whether
		the user uploaded a file, or pasted in some text, by checking to see if $param_name
		is in the map.  The problem with doing something like "($param_name)?...:..." is
		that the restitution replaces $param_name with the contents of the file or pasted in
		text, and if that contains a double quote or other character that has meaning to perl,
		the resulting perl expression may be garbage.  Instead we can say "(defined $param_name) ?
		...:..." and this method will replace the conditional with 1 or 0.

		- replaces "defined $value" with 1 (since in swami, $value is always defined)
		- replaces "defined $vdef" with 1 if there is a vdef attribute in the pise xml element, 0 otherwise
		- replaces "defined $param_name" with 1 if param_name is in the map of params we received from the gui, 
		0 otherwise.
	*/
	private String replaceDefined(String str, String parameterValue, String vdef)
	{
		StringBuffer buf = new StringBuffer();

		// Find the text "defined", followed by whitespace, followed by "$", followed by one or more
		// "word" characters (i.e letter, number or underscore).  Capture the "word" into group 1.
		Pattern p = Pattern.compile("defined\\s\\$(\\w+)");

		Matcher matcher = p.matcher(str);
		while(matcher.find())
		{
			// replacement text depends on the word that follows the $, that is, group(1).
			// but we'll be replacing the full string that was matched, in other words "defined $something"
			// will be replace with "0" or "1" depending on what $something is.
			String var = matcher.group(1);
			if (var.equals("value"))
			{
				matcher.appendReplacement(buf, (parameterValue == null) ? "0" : "1");
			} else if (var.equals("vdef"))
			{
				matcher.appendReplacement(buf, (vdef == null) ? "0" : "1");
			} else
			{
				boolean defined = getParameterSet().contains(var);
				matcher.appendReplacement(buf, defined ? "1": "0");
			}
		}
		matcher.appendTail(buf);
		return buf.toString();
	}


	/*
		Returns a perl statement which will be passed to "perl -e".  The stdout from
		running perl -e on the statement will  produce the text "true" or "false".  We pass
		the stdout to java's Boolean.valueOf() to get a boolean evaluation of the precond.

	*/
	private String restitutionPrecond(String precond, String paramName, String vdef) {
		// find every substring in precond starting with $
		// if the substring is $value replace it with the value of the parameter
		// identified in paramMap with key
		// if the substring is $x replace it with the value of the parameter
		// identified in paramMap with x

		log.debug("Original Precondition:      " + precond);

		String paramValue = getParameterValue(paramName);
		precond = replaceDefined(precond, paramValue, vdef);

		log.debug("Precondition after replaceDefined:      " + precond);

		Pattern p = Pattern.compile("\\$\\w*");
		Matcher m = p.matcher("Precond: " + precond);

		while (m.find()) {
			if (m.group().contains("$value"))
				precond = precond.replace("$value", "\"" + paramValue + "\"");
			else if (m.group().contains("$vdef"))
				precond = precond.replace("$vdef", "\"" + vdef + "\"");
			else
			// we should ignore restitution if the pattern match $
			// preceding bug restituted $ by "null"
			if (m.group().equalsIgnoreCase("$") == false) {
				
				String myKey = m.group().substring(1);
				
				/*
				In the special case where the code references $param_name and param_name isn't
				in our map, we return "print ''", which when run, outputs nothing, which evaluates
				to false.
				*/
				if (getParameterSet().contains(myKey) == false)
					return "print \"\"";

				precond = precond.replace(m.group(), "\""
						+ getParameterValue(myKey)
						+ "\"");
			}
		}

		//In perl ("false")? print"true" : print "false"
		// returns true
		// so we are replacing all true by 1 and all false by 0 
		precond = precond.replaceAll("false", "0");
		precond = precond.replaceAll("true", "1");

		// precond returns a True or False depends on the condition being
		// verified
		precond = "(" + precond + ")? print \"true\" : print \"false\";";

		if (log.isDebugEnabled())
			log.debug("Restituted Precondition: " + precond);
		return precond;
	}

	private String restitutionFormat(String format, String paramName, String vdef) {

		log.debug("Original Format:      " + format);
		
		String paramValue = getParameterValue(paramName);
		format = replaceDefined(format, paramValue, vdef);

		log.debug("Format after replaceDefined:      " + format);

		Pattern p = Pattern.compile("\\$\\w*");
		Matcher m = p.matcher(format);

		while (m.find())
			if (m.group().contains("$value")) {
				//if (paramMap.containsKey(key) == false)
				//	throw new RuntimeException("Missing value for parameter: " + key);
				format = format.replace("$value", paramValue);
			} else if (m.group().contains("$vdef")) {
			{
				//format = format.replace("$vdef", "\"" + vdef + "\"");
				format = format.replace("$vdef", vdef);
			}
			} else {
				String myKey = m.group().substring(1);
				String myValue = null;

				if (getParameterSet().contains(myKey) == false)
				{
					//TL: modified for raxmlhpc.xml "model" parameter.  Need to get default
					//value of parameters that haven't been set in the gui but are referenced in this
					//parameter's code element.
					myValue = piseMarshaller.getVdef(myKey);
					if (myValue == null) // no vDef element in the pise xml
					{
						//throw new RuntimeException("Missing value for parameter: " + myKey);
						// or we could set myValue to "", or the old behavior was 
						// return "print \"\"";
						myValue = "";
					}
				} else
				{
					myValue = getParameterValue(myKey);
				}
				format = format.replace(m.group(), myValue);
			}

		// A format can be a simple "..." or a condition (...)? "...":"..."
		if (format.contains("?")) {
			format = format.substring(0, format.indexOf("?") + 1) + " print "
					+ format.substring(format.indexOf("?") + 1);
			format = format.substring(0, format.indexOf(":") + 1) + " print "
					+ format.substring(format.indexOf(":") + 1);
		} else
			format = "print " + format;
		// format returns the value to be written into the command line

		format = format.replaceAll("false", "0");
		format = format.replaceAll("true", "1");

		if (log.isDebugEnabled())
			log.debug("Restituted Format: " + format);

		return format;
	}
}