package uk.ac.ebi.intenz.webapp.controller;
   
   import java.io.IOException;
   import java.sql.SQLException;
   import java.util.Map;
   import java.util.PropertyResourceBundle;
   import java.util.StringTokenizer;
   
   import javax.servlet.ServletContext;
  import javax.servlet.ServletException;
  
  import org.apache.log4j.Logger;
  
  import uk.ac.ebi.intenz.domain.constants.Status;
  import uk.ac.ebi.intenz.domain.enzyme.EnzymeClass;
  import uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber;
  import uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry;
  import uk.ac.ebi.intenz.domain.enzyme.EnzymeSubSubclass;
  import uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass;
  import uk.ac.ebi.intenz.domain.exceptions.DomainException;
  import uk.ac.ebi.intenz.domain.exceptions.EcException;
  import uk.ac.ebi.intenz.mapper.EnzymeClassMapper;
  import uk.ac.ebi.intenz.mapper.EnzymeEntryMapper;
  import uk.ac.ebi.intenz.mapper.EnzymeSubSubclassMapper;
  import uk.ac.ebi.intenz.mapper.EnzymeSubclassMapper;
  import uk.ac.ebi.intenz.webapp.utilities.IntEnzMessenger;
  import uk.ac.ebi.rhea.mapper.MapperException;
  
  /**
   * This command processes all inquiries about EC numbers.
   * 
   * @author Michael Darsow
   * @version 0.9 - 21-July-2003
   */
  public class SearchECCommand extends DatabaseCommand {
  
  	public static final Logger LOGGER = Logger.getLogger(SearchECCommand.class);
  
  	private final EnzymeClassMapper classMapper = new EnzymeClassMapper();
  	private final EnzymeSubclassMapper subclassMapper = new EnzymeSubclassMapper();
  	private final EnzymeSubSubclassMapper subSubclassMapper = new EnzymeSubSubclassMapper();
  
  	/**
  	 * @throws ServletException
  	 * @throws IOException
  	 * @throws MapperException
  	 */
  	public void process() throws ServletException, IOException {
  		String paramEc = request.getParameter("ec");
  		String paramStatus = request.getParameter("status");
  		EnzymeCommissionNumber ec = null;
  		String forwardPageName = null;
  
  		if (paramEc == null) {
  			request.setAttribute("message",
  					"The <b>ec</b> parameter has to be set to be able to search for an EC.");
  			forward("/error.jsp");
  			return;
  		}
  
  		// First check if the given EC is valid.
  		try {
  			ec = EnzymeCommissionNumber.valueOf(paramEc);
  			if (ec == null) {
  				request.setAttribute("message", "The EC <b>" + paramEc
  						+ "</b> you used with this inquiry is not valid.");
  				forward("/error.jsp");
  				return;
  			}
  		} catch (EcException e) {
  			request.setAttribute("message", "The EC <b>" + paramEc
  					+ "</b> you used with this inquiry is not valid.");
  			forward("/error.jsp");
  			return;
  		}
  
  		switch (ec.getType()) {
  		case CLASS:
  			forwardPageName = setClassData(ec);
  			break;
  		case SUBCLASS:
  			forwardPageName = setSubclassData(ec);
  			break;
  		case SUBSUBCLASS:
  			forwardPageName = setSubSubclassData(ec);
  			break;
  		case ENZYME:
  		case PRELIMINARY:
  			forwardPageName = setEnzymeData(ec, getStatus(paramStatus, ec));
  			break;
  		}
  		forward(forwardPageName);
  	}
  
  	/**
  	 * Adjusts the requested status.
  	 * 
  	 * @param paramStatus
  	 *            the requested status, if any.
 	 * @param ec
 	 *            the requested EC number.
 	 * @return
 	 */
 	private Status getStatus(String paramStatus, EnzymeCommissionNumber ec) {
 		switch (ec.getType()) {
 		case PRELIMINARY:
 			return Status.PRELIMINARY;
 		default:
 			return paramStatus == null ? Status.APPROVED : Status
 					.fromCode(paramStatus);
 		}
 	}
 
 	private String setClassData(EnzymeCommissionNumber ec) {
 		assert ec != null;
 
 		EnzymeClass enzymeClass = findEnzymeClass(ec);
 		if (enzymeClass != null) {
 			request.setAttribute("result", enzymeClass);
 			return "/class.jsp";
 		} else {
 			if (request.getAttribute("message") != null) {
 				return "/error.jsp";
 			} else {
 				request.setAttribute("message", "No entry found for EC: <b>"
 						+ ec.toString() + "</b>.");
 				return "/notFound.jsp"; // No result found.
 			}
 		}
 	}
 
 	private String setSubclassData(EnzymeCommissionNumber ec) {
 		assert ec != null;
 
 		EnzymeSubclass enzymeSubclass = findEnzymeSubclass(ec);
 		if (enzymeSubclass != null) {
 			request.setAttribute("result", enzymeSubclass);
 			return "/subclass.jsp";
 		} else {
 			if (request.getAttribute("message") != null) {
 				return "/error.jsp";
 			} else {
 				request.setAttribute("message", "No entry found for EC: <b>"
 						+ ec.toString() + "</b>.");
 				return "/notFound.jsp"; // No result found.
 			}
 		}
 	}
 
 	private String setSubSubclassData(EnzymeCommissionNumber ec) {
 		assert ec != null;
 
 		EnzymeSubSubclass enzymeSubSubclass = findEnzymeSubSubclass(ec);
 		if (enzymeSubSubclass != null) {
 			request.setAttribute("result", enzymeSubSubclass);
 			return "/subsubclass.jsp";
 		} else {
 			if (request.getAttribute("message") != null) {
 				return "/error.jsp";
 			} else {
 				request.setAttribute("message", "No entry found for EC: <b>"
 						+ ec.toString() + "</b>.");
 				return "/notFound.jsp"; // No result found.
 			}
 		}
 	}
 
 	private String setEnzymeData(EnzymeCommissionNumber ec, Status status) {
 		assert ec != null && status != null;
 		EnzymeEntry enzymeEntry = findEnzymeEntry(ec, status);
 		if (enzymeEntry != null) {
 			request.setAttribute("result", enzymeEntry);
 			return "/entry.jsp";
 		} else {
 			if (request.getAttribute("message") != null) {
 				return "/error.jsp";
 			} else {
 				request.setAttribute("message", "No entry found for EC: <b>"
 						+ ec.toString() + "</b>.");
 				return "/notFound.jsp"; // No result found.
 			}
 		}
 	}
 
 	/**
 	 * Calls the according <code>find()</code> method and handles empty results
 	 * and SQL exceptions.
 	 * 
 	 * @param ec
 	 *            Number of enzyme class to search for.
 	 * @return An <code>EnzymeClass</code> instance or <code>null</code>.
 	 */
 	protected EnzymeClass findEnzymeClass(EnzymeCommissionNumber ec) {
 		if (ec == null)
 			throw new NullPointerException();
 
 		EnzymeClass enzymeClass = null;
 		ServletContext application = request.getSession().getServletContext();
 		@SuppressWarnings("unchecked")
 		Map<EnzymeCommissionNumber, EnzymeClass> classes = (Map<EnzymeCommissionNumber, EnzymeClass>) application
 				.getAttribute("classes");
 
 		// Check if object already stored in the cache.
 		if (classes.containsKey(ec)) {
 			enzymeClass = (EnzymeClass) classes.get(ec);
 		} else { // If the object is not stored in the cache load it from the
 					// database.
 			try {
 				enzymeClass = classMapper.find(Integer.toString(ec.getEc1()),
 						con);
 				if (enzymeClass != null) {
 					classes.put(ec, enzymeClass);
 					application.setAttribute("classes", classes);
 				}
 			} catch (SQLException e) {
 				LOGGER.error("Finding enzyme class", e);
 				IntEnzMessenger.sendError(this.getClass().toString(), e
 						.getMessage(), (String) request.getSession()
 						.getAttribute("user"));
 				request.setAttribute("message", e.getMessage());
 				return null;
 			} catch (DomainException e) {
 				LOGGER.error("Finding enzyme class", e);
 				PropertyResourceBundle intenzMessages = (PropertyResourceBundle) request
 						.getSession().getServletContext()
 						.getAttribute("intenz.messages");
 				IntEnzMessenger.sendError(this.getClass().toString(),
 						intenzMessages.getString(e.getMessageKey()),
 						(String) request.getSession().getAttribute("user"));
 				request.setAttribute("message", e.getMessage());
 				return null;
 			}
 		}
 
 		return enzymeClass;
 	}
 
 	/**
 	 * Calls the according <code>find()</code> method and handles empty results
 	 * and SQL exceptions.
 	 * 
 	 * @param ec
 	 *            Number of enzyme class to search for.
 	 * @return An <code>EnzymeClass</code> instance or <code>null</code>.
 	 * @throws NullPointerException
 	 *             if any of the parameters is <code>null</code>.
 	 */
 	protected EnzymeSubclass findEnzymeSubclass(EnzymeCommissionNumber ec) {
 		if (ec == null)
 			throw new NullPointerException();
 
 		EnzymeSubclass enzymeSubclass = null;
 		ServletContext application = request.getSession().getServletContext();
 		@SuppressWarnings("unchecked")
 		Map<EnzymeCommissionNumber, EnzymeSubclass> subclasses = (Map<EnzymeCommissionNumber, EnzymeSubclass>) application
 				.getAttribute("subclasses");
 
 		// Check if object already stored in the cache.
 		if (subclasses.containsKey(ec)) {
 			enzymeSubclass = (EnzymeSubclass) subclasses.get(ec);
 		} else { // If the object is not stored in the cache load it from the
 			try {
 				enzymeSubclass = subclassMapper.find(
 						Integer.toString(ec.getEc1()),
 						Integer.toString(ec.getEc2()), con);
 				if (enzymeSubclass != null) {
 					subclasses.put(ec, enzymeSubclass);
 					application.setAttribute("subclasses", subclasses);
 				}
 			} catch (SQLException e) {
 				LOGGER.error("Finding enzyme subclass", e);
 				IntEnzMessenger.sendError(this.getClass().toString(), e
 						.getMessage(), (String) request.getSession()
 						.getAttribute("user"));
 				request.setAttribute("message", e.getMessage());
 				return null;
 			} catch (DomainException e) {
 				LOGGER.error("Finding enzyme subclass", e);
 				PropertyResourceBundle intenzMessages = (PropertyResourceBundle) request
 						.getSession().getServletContext()
 						.getAttribute("intenz.messages");
 				IntEnzMessenger.sendError(this.getClass().toString(),
 						intenzMessages.getString(e.getMessageKey()),
 						(String) request.getSession().getAttribute("user"));
 				request.setAttribute("message", e.getMessage());
 				return null;
 			}
 		}
 		return enzymeSubclass;
 	}
 
 	/**
 	 * Calls the according <code>find()</code> method and handles empty results
 	 * and SQL exceptions.
 	 * 
 	 * @param ec
 	 *            Number of enzyme class to search for.
 	 * @return An <code>EnzymeClass</code> instance or <code>null</code>.
 	 * @throws NullPointerException
 	 *             if any of the parameters is <code>null</code>.
 	 */
 	protected EnzymeSubSubclass findEnzymeSubSubclass(EnzymeCommissionNumber ec) {
  		if (ec == null)
 			throw new NullPointerException();
 
 		EnzymeSubSubclass enzymeSubSubclass = null;
 		ServletContext application = request.getSession().getServletContext();
 		@SuppressWarnings("unchecked")
 		Map<EnzymeCommissionNumber, EnzymeSubSubclass> subsubclasses = (Map<EnzymeCommissionNumber, EnzymeSubSubclass>) application
 				.getAttribute("subsubclasses");
 
 		// Check if object already stored in the cache.
 		if (subsubclasses.containsKey(ec)) {
 			enzymeSubSubclass = (EnzymeSubSubclass) subsubclasses.get(ec);
 		} else { // If the object is not stored in the cache load it from the
 					// database.
 			try {
 				enzymeSubSubclass = subSubclassMapper.find(ec.getEc1(),
 						ec.getEc2(), ec.getEc3(), con);
 				if (enzymeSubSubclass != null) {
 					subsubclasses.put(ec, enzymeSubSubclass);
 					application.setAttribute("subsubclasses", subsubclasses);
 				}
 			} catch (DomainException e) {
 				LOGGER.error("Finding enzyme subSubclass", e);
 				PropertyResourceBundle intenzMessages = (PropertyResourceBundle) request
 						.getSession().getServletContext()
 						.getAttribute("intenz.messages");
 				IntEnzMessenger.sendError(this.getClass().toString(),
 						intenzMessages.getString(e.getMessageKey()),
 						(String) request.getSession().getAttribute("user"));
 				request.setAttribute("message", e.getMessage());
 				return null;
 			} catch (Exception e) {
 				LOGGER.error("Finding enzyme subSubclass", e);
 				IntEnzMessenger.sendError(this.getClass().toString(),
 						e.getMessage(),
 						(String) request.getSession().getAttribute("user"));
 				request.setAttribute("message", e.getMessage());
 				return null;
 			}
 		}
 		return enzymeSubSubclass;
 	}
 
 	/**
 	 * Gets the type of the EC number.
 	 * <p/>
 	 * The following types are possible (in [] the value returned by this
 	 * method):
 	 * <ul>
 	 * <li>Class EC (e.g. EC 1) [1]</li>
 	 * <li>Subclass EC (e.g. EC 1.1) [2]</li>
 	 * <li>Sub-subclass EC (e.g. EC 1.1.1) [3]</li>
 	 * <li>Entry EC (e.g. EC 1.1.1.1) [4]</li>
 	 * </ul>
 	 * 
 	 * @param ec
 	 *            The EC string.
 	 * @return Integer code for the type.
 	 */
 	protected int analyseECType(String ec) {
 		int count = 0;
 		for (StringTokenizer stringTokenizer = new StringTokenizer(ec, "."); stringTokenizer
 				.hasMoreTokens();) {
 			stringTokenizer.nextToken();
 			count++;
 		}
 
 		return count;
 	}
 
 	// ------------------- PRIVATE METHODS ------------------------
 
 	/**
 	 * Calls the according <code>find()</code> method and handles empty results
 	 * and SQL exceptions.
 	 * 
 	 * @param ec
 	 *            EC number of enzyme to search for.
 	 * @param status
 	 *            the enzyme status.
 	 * @return An <code>EnzymeEntry</code> instance or <code>null</code>.
 	 * @throws NullPointerException
 	 *             if any of the parameters is <code>null</code>.
 	 */
 	protected EnzymeEntry findEnzymeEntry(EnzymeCommissionNumber ec,
 			Status status) {
 		if (ec == null || status == null)
 			throw new NullPointerException();
 
 		EnzymeEntry enzymeEntry = null;
 		ServletContext application = request.getSession().getServletContext();
 		@SuppressWarnings("unchecked")
 		Map<EnzymeEntryCacheKey, EnzymeEntry> entries = (Map<EnzymeEntryCacheKey, EnzymeEntry>) application
 				.getAttribute("entries_ec");
 
 		// Check if object already stored in the cache.
 		EnzymeEntryCacheKey key = new EnzymeEntryCacheKey(ec, status);
 		if (entries.containsKey(key)) {
 			enzymeEntry = (EnzymeEntry) entries.get(key);
 		} else {
 			try {
 				Long enzyme_id = enzymeEntryMapper.findIDInMappingTable(
 						ec.toString(), status, con);
 				if (enzyme_id.longValue() == -1)
 					return null;
 				enzymeEntry = enzymeEntryMapper.findById(enzyme_id, con);
 				if (enzymeEntry != null)
 					entries.put(key, enzymeEntry);
 			} catch (SQLException e) {
 				IntEnzMessenger.sendError(this.getClass().toString(), e
 						.getMessage(), (String) request.getSession()
 						.getAttribute("user"));
 				request.setAttribute("message", e.getMessage());
 			} catch (MapperException e) {
 				IntEnzMessenger.sendError(this.getClass().toString(), e
 						.getMessage(), (String) request.getSession()
 						.getAttribute("user"));
 				request.setAttribute("message", e.getMessage());
 			} catch (DomainException e) {
 				LOGGER.error("Finding enzyme entry", e);
 				PropertyResourceBundle intenzMessages = (PropertyResourceBundle) request
 						.getSession().getServletContext()
 						.getAttribute("intenz.messages");
 				IntEnzMessenger.sendError(this.getClass().toString(),
 						intenzMessages.getString(e.getMessageKey()),
 						(String) request.getSession().getAttribute("user"));
 				request.setAttribute("message", e.getMessage());
 			} finally {
 				try {
 					con.close();
 				} catch (SQLException e) {
 					IntEnzMessenger.sendError(this.getClass().toString(), e
 							.getMessage(), (String) request.getSession()
 							.getAttribute("user"));
 					request.setAttribute("message", e.getMessage());
 					return null;
 				}
 			}
 		}
 		return enzymeEntry;
 	}
 
 	protected static class EnzymeEntryCacheKey {
 		private EnzymeCommissionNumber ec;
 		private Status status;
 
 		public EnzymeEntryCacheKey(EnzymeCommissionNumber ec, Status status) {
 			this.ec = ec;
 			this.status = status;
 		}
 
 		public boolean equals(Object o) {
 			if (this == o)
 				return true;
 			if (!(o instanceof SearchECCommand.EnzymeEntryCacheKey))
 				return false;
 
 			final SearchECCommand.EnzymeEntryCacheKey enzymeEntryCacheKey = (SearchECCommand.EnzymeEntryCacheKey) o;
 
 			if (ec != null ? !ec.equals(enzymeEntryCacheKey.ec)
 					: enzymeEntryCacheKey.ec != null)
 				return false;
 			if (status != null ? !status.equals(enzymeEntryCacheKey.status)
 					: enzymeEntryCacheKey.status != null)
 				return false;
 
 			return true;
 		}
 
 		public int hashCode() {
 			int result;
 			result = (ec != null ? ec.hashCode() : 0);
 			result = 29 * result + (status != null ? status.hashCode() : 0);
 			return result;
 		}
 
 		public String toString() {
 			StringBuffer output = new StringBuffer();
 			output.append("EC: ");
 			output.append(ec.toString());
 			output.append("\n");
 			output.append("Status: ");
 			output.append(status.toString());
 			output.append("\n");
 			return output.toString();
 		}
 	}
 }