/*
  File: CyAttributesReader.java

  Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)

  This library is free software; you can redistribute it and/or modify it
  under the terms of the GNU Lesser General Public License as published
  by the Free Software Foundation; either version 2.1 of the License, or
  any later version.

  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.  The software and
  documentation provided hereunder is on an "as is" basis, and the
  Institute for Systems Biology and the Whitehead Institute
  have no obligations to provide maintenance, support,
  updates, enhancements or modifications.  In no event shall the
  Institute for Systems Biology and the Whitehead Institute
  be liable to any party for direct, indirect, special,
  incidental or consequential damages, including lost profits, arising
  out of the use of this software and its documentation, even if the
  Institute for Systems Biology and the Whitehead Institute
  have been advised of the possibility of such damage.  See
  the GNU Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public License
  along with this library; if not, write to the Free Software Foundation,
  Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
package cytoscape.data.readers;


import java.io.BufferedReader;
import java.io.IOException;
import java.io.Reader;
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.StringTokenizer;

import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
import cytoscape.data.attr.MultiHashMapDefinition;
import cytoscape.data.writers.CyAttributesWriter;
import cytoscape.logger.CyLogger;

import org.cytoscape.equations.EqnCompiler;
import org.cytoscape.equations.Equation;

import java.net.URLDecoder;
import java.text.MessageFormat;


public class CyAttributesReader {
	public static final String DECODE_PROPERTY = "cytoscape.decode.attributes";
	private static final String badDecodeMessage =
		"Trouble when decoding attribute value, first occurence line no. {0}" +
		"\nIgnore if attributes file was created before 2.6.3 or wasn't creatad by Cytoscape." +
		"\nUse -Dcytoscape.decode.attributes=false when starting Cytoscape to turn off decoding.";

	private boolean badDecode;
	private int lineNum;
	private boolean doDecoding;
	final Map<String, Map<String, Class>> idsToAttribNameToTypeMapMap;
	private final CyLogger logger;


	CyAttributesReader() {
		logger = CyLogger.getLogger(CyAttributesReader.class);
		lineNum = 0;
		doDecoding = Boolean.valueOf(System.getProperty(DECODE_PROPERTY, "true"));
		idsToAttribNameToTypeMapMap = new HashMap<String, Map<String, Class>>();
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param cyAttrs DOCUMENT ME!
	 * @param fileIn DOCUMENT ME!
	 *
	 * @throws IOException DOCUMENT ME!
	 */
	public static void loadAttributes(final CyAttributes cyAttrs, final Reader fileIn) throws IOException {
		CyAttributesReader ar = new CyAttributesReader();
		ar.loadAttributesInternal(cyAttrs, fileIn);
	}

	private Class mapCytoscapeAttribTypeToEqnType(final byte attribType) {
		switch (attribType) {
		case CyAttributes.TYPE_BOOLEAN:
			return Boolean.class;
		case CyAttributes.TYPE_INTEGER:
			return Long.class;
		case CyAttributes.TYPE_FLOATING:
			return Double.class;
		case CyAttributes.TYPE_STRING:
			return String.class;
		case CyAttributes.TYPE_SIMPLE_LIST:
			return List.class;
		default:
			return null;
		}
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param cyAttrs DOCUMENT ME!
	 * @param fileIn DOCUMENT ME!
	 *
	 * @throws IOException DOCUMENT ME!
	 */
	public void loadAttributesInternal(CyAttributes cyAttrs, Reader fileIn)
		throws IOException
	{
		badDecode = false;
		boolean guessedAttrType = false; // We later set this to true if we have to guess the attribute type.

		try {
			final BufferedReader reader;

			if (fileIn instanceof BufferedReader) {
				reader = (BufferedReader) fileIn;
			} else {
				reader = new BufferedReader(fileIn);
			}

			String attributeName;
			byte type = -1;

			{
				final String firstLine = reader.readLine();
				lineNum++;

				if (firstLine == null) {
					return;
				}

				final String searchStr = "class=";
				final int inx = firstLine.indexOf(searchStr);

				if (inx < 0) {
					attributeName = firstLine.trim();
				} else {
					attributeName = firstLine.substring(0, inx - 1).trim();

					String foo = firstLine.substring(inx);
					final StringTokenizer tokens = new StringTokenizer(foo);
					foo = tokens.nextToken();

					String className = foo.substring(searchStr.length()).trim();

					if (className.endsWith(")")) {
						className = className.substring(0, className.length() - 1);
					}

					if (className.equalsIgnoreCase("java.lang.String")
					    || className.equalsIgnoreCase("String")) {
						type = MultiHashMapDefinition.TYPE_STRING;
					} else if (className.equalsIgnoreCase("java.lang.Boolean")
					           || className.equalsIgnoreCase("Boolean")) {
						type = MultiHashMapDefinition.TYPE_BOOLEAN;
					} else if (className.equalsIgnoreCase("java.lang.Integer")
					           || className.equalsIgnoreCase("Integer")) {
						type = MultiHashMapDefinition.TYPE_INTEGER;
					} else if (className.equalsIgnoreCase("java.lang.Double")
					           || className.equalsIgnoreCase("Double")
					           || className.equalsIgnoreCase("java.lang.Float")
					           || className.equalsIgnoreCase("Float")) {
						type = MultiHashMapDefinition.TYPE_FLOATING_POINT;
					}
				}
			}

			if (attributeName.indexOf("(") >= 0) {
				attributeName = attributeName.substring(0, attributeName.indexOf("(")).trim();
			}

			boolean firstLine = true;
			boolean list = false;

			while (true) {
				final String line = reader.readLine();
				lineNum++;

				if (line == null)
					break;

				// Empty line?
				if ("".equals(line.trim())) {
					continue;
				}

				int inx = line.indexOf('=');
				String key = line.substring(0, inx).trim();
				String val = line.substring(inx + 1).trim();
				final boolean equation = val.startsWith("=");

				key = decodeString(key);

				if (firstLine && val.startsWith("("))
					list = true;

				if (list) {
					// Chop away leading '(' and trailing ')'.
					val = val.substring(1).trim();
					val = val.substring(0, val.length() - 1).trim();

					String[] elms = val.split("::");
					final ArrayList elmsBuff = new ArrayList();

					for (String vs : elms) {
						vs = decodeString(vs);
						vs = decodeSlashEscapes(vs);
						elmsBuff.add(vs);
					}

					if (firstLine) {
						if (type < 0) {
							guessedAttrType = true;
							while (true) {
								try {
									new Integer((String) elmsBuff.get(0));
									type = MultiHashMapDefinition.TYPE_INTEGER;
									break;
								} catch (Exception e) {
								}

								try {
									new Double((String) elmsBuff.get(0));
									type = MultiHashMapDefinition.TYPE_FLOATING_POINT;
									break;
								} catch (Exception e) {
								}
								type = MultiHashMapDefinition.TYPE_STRING;
								break;
							}
						}

						firstLine = false;
					}

					for (int i = 0; i < elmsBuff.size(); i++) {
						if (type == MultiHashMapDefinition.TYPE_INTEGER) {
							elmsBuff.set(i, new Integer((String) elmsBuff.get(i)));
						} else if (type == MultiHashMapDefinition.TYPE_BOOLEAN) {
							elmsBuff.set(i, new Boolean((String) elmsBuff.get(i)));
						} else if (type == MultiHashMapDefinition.TYPE_FLOATING_POINT) {
							elmsBuff.set(i, new Double((String) elmsBuff.get(i)));
						} else {
							// A string; do nothing.
						}
					}

					cyAttrs.setListAttribute(key, attributeName, elmsBuff);
				} else { // Not a list.
					val = decodeString(val);
					val = decodeSlashEscapes(val);

					if (firstLine) {
						if (type < 0) {
							guessedAttrType = true;
							while (true) {
								try {
									new Integer(val);
									type = MultiHashMapDefinition.TYPE_INTEGER;
									break;
								} catch (Exception e) {
								}

								try {
									new Double(val);
									type = MultiHashMapDefinition.TYPE_FLOATING_POINT;
									break;
								} catch (Exception e) {
								}

								type = MultiHashMapDefinition.TYPE_STRING;
								break;
							}
						}

						firstLine = false;
					}

					if (equation) {
						final Class eqnReturnType;
						switch (type) {
						case CyAttributes.TYPE_INTEGER:
							eqnReturnType = Long.class;
							break;
						case CyAttributes.TYPE_FLOATING:
							eqnReturnType = Double.class;
							break;
						case CyAttributes.TYPE_BOOLEAN:
							eqnReturnType = Boolean.class;
							break;
						case CyAttributes.TYPE_STRING:
							eqnReturnType = String.class;
							break;
						case CyAttributes.TYPE_SIMPLE_LIST:
							eqnReturnType = List.class;
							break;
						default:
							final String message = "don't know which equation return type to register on line " + lineNum + "!";
							System.err.println(message);
							logger.warn(message);
							continue;
						}
						final EqnAttrTracker eqnAttrTracker = Cytoscape.getEqnAttrTracker();
						eqnAttrTracker.recordEquation(cyAttrs, key, attributeName, val, eqnReturnType);
					}
					else if (type == MultiHashMapDefinition.TYPE_INTEGER)
						cyAttrs.setAttribute(key, attributeName, new Integer(val));
					else if (type == MultiHashMapDefinition.TYPE_BOOLEAN)
						cyAttrs.setAttribute(key, attributeName, new Boolean(val));
					else if (type == MultiHashMapDefinition.TYPE_FLOATING_POINT)
						cyAttrs.setAttribute(key, attributeName, new Double(val));
					else
						cyAttrs.setAttribute(key, attributeName, val);
				}
			}
		} catch (Exception e) {
			String message;
			if (guessedAttrType) {
				message = "failed parsing attributes file at line: " + lineNum
					+ " with exception: " + e.getMessage()
					+ " This is most likely due to a missing attribute type on the first line.\n"
					+ "Attribute type should be one of the following: "
					+ "(class=String), (class=Boolean), (class=Integer), or (class=Double). "
					+ "(\"Double\" stands for a floating point a.k.a. \"decimal\" number.)"
					+ " This should be added to end of the first line.";
			}
			else
				message = "failed parsing attributes file at line: " + lineNum
					+ " with exception: " + e.getMessage();
			logger.warn(message, e);
			throw new IOException(message);
		}
	}

	private String decodeString(String in) throws IOException {
		if (doDecoding) {
			try {
				in = URLDecoder.decode(in, CyAttributesWriter.ENCODING_SCHEME);
			}
			catch (IllegalArgumentException iae) {
				if (!badDecode) {
					logger.info(MessageFormat.format(badDecodeMessage, lineNum), iae);
					badDecode = true;
				}
			}
		}

		return in;
	}

	private static String decodeSlashEscapes(String in) {
		final StringBuilder elmBuff = new StringBuilder();
		int inx2;

		for (inx2 = 0; inx2 < in.length(); inx2++) {
			char ch = in.charAt(inx2);

			if (ch == '\\') {
				if ((inx2 + 1) < in.length()) {
					inx2++;

					char ch2 = in.charAt(inx2);

					if (ch2 == 'n') {
						elmBuff.append('\n');
					} else if (ch2 == 't') {
						elmBuff.append('\t');
					} else if (ch2 == 'b') {
						elmBuff.append('\b');
					} else if (ch2 == 'r') {
						elmBuff.append('\r');
					} else if (ch2 == 'f') {
						elmBuff.append('\f');
					} else {
						elmBuff.append(ch2);
					}
				} else {
					/* val ends in '\' - just ignore it. */ }
			} else {
				elmBuff.append(ch);
			}
		}

		return elmBuff.toString();
	}

	public boolean isDoDecoding() {
		return doDecoding;
	}

	public void setDoDecoding(boolean doDec) {
		doDecoding = doDec;
	}
}