/* Copyright (c) 2009 Peter Troshin
 *  
 *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     
 * 
 *  This library is free software; you can redistribute it and/or modify it under the terms of the
 *  Apache License version 2 as published by the Apache Software Foundation
 * 
 *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
 *  License for more details.
 * 
 *  A copy of the license is in apache_license.txt. It is also available here:
 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
 * 
 * Any republication or derived work distributed in source code form
 * must include this copyright and license notice.
 */

package compbio.engine.client;

import java.io.File;
import java.util.Arrays;
import java.util.List;

import org.apache.log4j.Logger;

import compbio.engine.client.CommandBuilder.Parameter;
import compbio.engine.conf.PropertyHelperManager;
import compbio.util.PropertyHelper;
import compbio.util.Util;

public abstract class SkeletalExecutable<T> implements Executable<T> {

    protected static final PropertyHelper ph = PropertyHelperManager
	    .getPropertyHelper();

    private static Logger log = Logger.getLogger(SkeletalExecutable.class);

    protected String inputFile = "input.txt";
    protected String outputFile = "output.txt";
    protected String errorFile = "error.txt";

    private boolean isInputSet = false;
    private boolean isOutputSet = false;
    private boolean isErrorSet = false;

    /**
     * This has to allow duplicate parameters as different options may have the
     * same value e.g. Muscle -weight1 clustalw -weight2 clustalw
     */
    protected CommandBuilder<T> cbuilder;

    public SkeletalExecutable() {
	cbuilder = new CommandBuilder<T>(" ");
    }

    public SkeletalExecutable(String parameterKeyValueDelimiter) {
	assert parameterKeyValueDelimiter != null;
	cbuilder = new CommandBuilder<T>(parameterKeyValueDelimiter);
    }

    public SkeletalExecutable<T> setInput(String inFile) {
	if (compbio.util.Util.isEmpty(inFile)) {
	    throw new IllegalArgumentException("Input file must not be NULL");
	}
	this.inputFile = inFile;
	this.isInputSet = true;
	return this;
    }

    public SkeletalExecutable<T> setOutput(String outFile) {
	if (compbio.util.Util.isEmpty(outFile)
		|| PathValidator.isAbsolutePath(outFile)) {
	    throw new IllegalArgumentException(
		    "Output file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "
			    + outFile);
	}
	this.outputFile = outFile;
	this.isOutputSet = true;
	return this;
    }

    public SkeletalExecutable<T> setError(String errFile) {
	if (compbio.util.Util.isEmpty(errFile)
		|| PathValidator.isAbsolutePath(errFile)) {
	    throw new IllegalArgumentException(
		    "Error file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "
			    + errFile);
	}
	this.errorFile = errFile;
	this.isErrorSet = true;
	return this;
    }

    @Override
    public CommandBuilder<T> getParameters(ExecProvider provider) {
	/*
	 * Prevent modification of the parameters unintentionally. This is
	 * important to preserve executable parameters intact as engine could
	 * add things into the array as it see fit. For instance
	 * ExecutableWrapper (part of local engines) add command line as the
	 * first element of an array.
	 */
	paramValueUpdater();
	return cbuilder;
    }

    @Override
    public Executable<T> addParameters(List<String> parameters) {
	cbuilder.addParams(parameters);
	return this;
    }

    public Executable<T> setParameter(String parameter) {
	cbuilder.setParam(parameter);
	return this;
    }

    /**
     * This is a generic method of changing values of the parameters with
     * properties
     * 
     * This method iterates via commands for an executable finding matches from
     * the Executable.properties file and replacing values in CommandBuilder
     * with a combination of value from CommandBuilder to merge path from
     * properties
     */
    void paramValueUpdater() {
	for (Parameter command : cbuilder.getCommandList()) {
	    if (command.value == null) {
		continue;
	    }
	    String propertyPath = compbio.engine.client.Util.getExecProperty(
		    command.name + ".path", getType());
	    if (Util.isEmpty(propertyPath)) {
		continue;
	    }
	    if (new File(command.value).isAbsolute()) {
		// Matrix can be found so no actions necessary
		// This method has been called already and the matrix name
		// is modified to contain full path // no further actions is
		// necessary
		continue;
	    }
	    String absMatrixPath = compbio.engine.client.Util
		    .convertToAbsolute(propertyPath);
	    command.value = absMatrixPath + File.separator + command.value;
	    cbuilder.setParam(command);
	}
    }

    /**
     * This method cannot really tell whether the files has actually been
     * created or not. It must be overridden as required.
     * 
     * @see compbio.engine.client.Executable#getCreatedFiles()
     */
    @Override
    public List<String> getCreatedFiles() {
	return Arrays.asList(getOutput(), getError());
    }

    @Override
    public String getInput() {
	return inputFile;
    }

    protected boolean isInputSet() {
	return isInputSet;
    }

    protected boolean isOutputSet() {
	return isOutputSet;
    }

    protected boolean isErrorSet() {
	return isErrorSet;
    }

    @Override
    public String getOutput() {
	return outputFile;
    }

    @Override
    public String getError() {
	return errorFile;
    }

    @Override
    public String toString() {
	String value = "Input: " + this.getInput() + "\n";
	value += "Output: " + this.getOutput() + "\n";
	value += "Error: " + this.getError() + "\n";
	value += "Class: " + this.getClass() + "\n";
	value += "Params: " + cbuilder + "\n";
	return value;
    }

    @Override
    public Executable<?> loadRunConfiguration(RunConfiguration rconfig) {
	if (!compbio.util.Util.isEmpty(rconfig.getOutput())) {
	    setOutput(rconfig.getOutput());
	}
	if (!compbio.util.Util.isEmpty(rconfig.getError())) {
	    setError(rconfig.getError());
	}
	if (!compbio.util.Util.isEmpty(rconfig.getInput())) {
	    setInput(rconfig.getInput());
	}
	this.cbuilder = (CommandBuilder<T>) rconfig.getParameters();
	return this;
    }

    @Override
    public boolean equals(Object obj) {
	if (obj == null) {
	    return false;
	}
	if (!(obj instanceof SkeletalExecutable<?>)) {
	    return false;
	}
	SkeletalExecutable<?> exec = (SkeletalExecutable<?>) obj;
	if (!Util.isEmpty(this.inputFile) && !Util.isEmpty(exec.inputFile)) {
	    if (!this.inputFile.equals(exec.inputFile)) {
		return false;
	    }
	}
	if (!Util.isEmpty(this.outputFile) && !Util.isEmpty(exec.outputFile)) {
	    if (!this.outputFile.equals(exec.outputFile)) {
		return false;
	    }
	}
	if (!Util.isEmpty(this.errorFile) && !Util.isEmpty(exec.errorFile)) {
	    if (!this.errorFile.equals(exec.errorFile)) {
		return false;
	    }
	}
	if (!this.cbuilder.equals(exec.cbuilder)) {
	    return false;
	}
	return true;
    }

    @Override
    public int hashCode() {
	int code = inputFile.hashCode();
	code += outputFile.hashCode();
	code += errorFile.hashCode();
	code *= this.cbuilder.hashCode();
	return code;
    }

    public String getClusterSettings() {
	String settings = ph.getProperty(getType().getSimpleName()
		.toLowerCase()
		+ ".cluster.settings");
	return settings == null ? "" : settings;
    }

    public abstract Class<? extends Executable<?>> getType();

}