/**
 * 
 */
package oboannotator.application;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Scanner;

import oboannotator.ontology.OBO_toLexiconConverter;
import oboannotator.util.AppConfig;
import oboannotator.util.UserCommand;
import oboannotator.util.Util;


/**
 * @author ahmedabdeenhamed
 *
 */
public class OBO_AnnotatorTool {

	private static String DICTIONARY_PATH ="/Users/ahmedabdeenhamed/Projects/concept-mapper-project/oboannotator/resources/dict";
	private static final String DICTIONARY_EXTENSION=".xml";
	private static boolean INCLUDE=false;
	private static boolean UPDATE=false;
	private static boolean ADD=false;
	
	/** 
	 * @param args
	 */
	public static void main(String[] args) {
		
		Hashtable<String, String> fileOrderNamePair = new Hashtable<String, String>();
		ArrayList<String> userSelectedEnginesToInclude = new ArrayList<String>();
		String aggAEName = null;
		String aggAEDir = null;
		String primAEName = null;
		String primAEDir = null;
		String ontologyURI= null;	
		String dictionaryName=null;
		
		System.out.println("               					-|----------------------------------|-");
		System.out.println("               					-|Welcome to MBL OBO-Annotator Tool!|-");
		System.out.println("               					-|----------------------------------|-");		
		
		System.out.println("\n\n");
		System.out.println("			|------------------------------------------------------------------------------|");
		System.out.println("			| This application allows users to do the following:                           |");
		System.out.println("			| 1) Add new dictionaries from exiting Ontologies                              |");
		System.out.println("			| - For Adding new dictionaries, users should enter the command 'A'            |");
		System.out.println("			|                                                                              |");
		System.out.println("			| 2) Update existing dictionaries from the list below:                         |");
		System.out.println("			| - For Updating compiled dictionaries, users should enter the command Udict#  |");
		System.out.println("			|                                                                              |");
		System.out.println("			| 3) Include existing dictionares from the list below:                         |");
		System.out.println("			| - For Including a dictionary, users must enter the dictionary#  on the list  |");
		System.out.println("			|------------------------------------------------------------------------------|");
		
		System.out.println("\n");	
		System.out.println("Please enter the dictionaries directory: ");
		String dictDir = new Scanner(System.in).nextLine().toString();
		if(dictDir.equals("") || dictDir==null){
			System.out.println("Invalid directory, application is terminating now...");
			System.exit(0);
		}
		fileOrderNamePair = Util.getFilesByDirectoryName(dictDir);
		
		
		System.out.println("Following is a list of the available dictionaries:");
		// display existing dictionaries and their order on the hashtable
		for(int i = 0; i < fileOrderNamePair.size(); i++){
			System.out.println(new Integer(i+1).toString() + ": " + fileOrderNamePair.get(new Integer(i+1).toString()));
		}
		System.out.println("\n");
		System.out.print("Please enter your commands seperated by commas \",\": \n");		
		String userInput = new Scanner(System.in).nextLine().toString();
		ArrayList<UserCommand> uComms = Util.interpretUserInput(userInput);
		if(uComms==null){
			System.out.println("Invalid Entry, application is terminating now....");
			System.exit(0);
		}

		
		for(UserCommand uComm: uComms){
			if(uComm.getCommand().equals("INCLUDE_DICTIONARY")){
				// turn the INCLUDE flag to true...
				OBO_AnnotatorTool.INCLUDE=true;
				
				Integer anInt = new Integer(uComm.getIntCommand());
				if(fileOrderNamePair.get(anInt.toString())==null){
					System.out.println("Invalid descriptor, command is ignored...");
					continue;
				}				
				
				if(primAEDir==null){
					System.out.print("Please enter primitive AE directory: \n");		
					primAEDir = new Scanner(System.in).nextLine().toString();
					if(primAEDir.equals("") || primAEDir==null){
						System.out.println("Invalid directory, command is ignored...");
						continue;
					}
				}
				System.out.println("\nINCLUDE-DICTIONARY: " + fileOrderNamePair.get(anInt.toString()) + " command is in action...");
				System.out.println("----------------------------------------------");
				//userSelectedList.add(fileOrderNamePair.get(uComm.getIntCommand()));			
				
				System.out.println("Please enter the primitive engine associated with the dictionary: ");
				primAEName = new Scanner(System.in).nextLine().toString();
				if(primAEName.equals("") || primAEName==null){
					System.out.println("Invalid engine name, command is ignored...");
					continue;
				}				
				userSelectedEnginesToInclude.add(primAEName);
//				if(aggregateEnginesFileName==null){
//					System.out.println("Please enter a name for the new aggregate engine: ");
//					aggregateEnginesFileName = new Scanner(System.in).nextLine().toString();
//				}			
			}else if(uComm.getCommand().equals("ADD_NEW_DICTIONARY")){
				
				// 1- Ask for ontology URI
				// 2- Ask for a unique dictionary name
				// 3- add the new dctionary name
				System.out.println("\nADD-NEW-DICTIONARY command is in action...");
				System.out.println("-------------------------------------------");
				System.out.println("Enter Ontology URI that you would like to add: ");
				ontologyURI = new Scanner(System.in).nextLine();				
				if (ontologyURI.equals("") || ontologyURI==null){
					System.out.println("Invalid ontology URI, command is ignored....");
					continue;
				}

				System.out.println("Enter a dictionary name for your ontology: ");
				dictionaryName = new Scanner(System.in).nextLine();
				if (dictionaryName.equals("") || dictionaryName==null){
					System.out.println("Invalid dictionary name, command is ignored....");
					continue;
				}
				System.out.println("Creating dictionary, this might take several minutes.....");
				OBO_toLexiconConverter.compileDictionaryFromOboUri(ontologyURI, dictionaryName, dictDir, AppConfig.ADD_NEW_DICTION);
				
				// generating the associated descriptor for a primitive engine 
				System.out.println("Enter a primitive engine name to assocaite with the created dictionary: ");
				primAEName = new Scanner(System.in).nextLine();
				if (primAEName==null || primAEName.equals("")){
					System.out.println("Invalid descriptor name, command is ignored....");
					continue;
				} 
				System.out.println("Enter a directory location for the primitive engine: ");
				primAEDir = new Scanner(System.in).nextLine();
				if (primAEDir==null || primAEDir.equals("")){
					System.out.println("Invalid directory name, command is ignored....");
					continue;
				}
				
				System.out.println("Generating the primitive analysis engine for the dictionary...");
				try {
					UserCustomedAEApplication.composePrimitiveAE(dictionaryName, "ADD");
				} catch (IOException e) {
					System.out.println("Error message is: " + e.getMessage());
				}				
			}else if(uComm.getCommand().equals("UPDATE_DICTIONARY")){
				Integer anInt = new Integer(uComm.getCommandOption());
				//System.out.println("\n\n---------------------------------");
				if(fileOrderNamePair.get(anInt.toString())==null){
					System.out.println("Invalid file number, command is ignored....");
					continue;
				}
				System.out.println("\nUPDATE-DICTIONARY "  + fileOrderNamePair.get(anInt.toString()) + " command is in action...");
				System.out.println("-------------------------------------------");
				System.out.println("Enter Ontology URI that you would like to update:");
				ontologyURI = new Scanner(System.in).nextLine();
				if (ontologyURI.equals("") || ontologyURI==null){
					System.out.println("Invalid ontology URI, command is ignored....");
					continue;
				}
				System.out.println("Updating dictionary, this might take several minutes.....");
				dictionaryName = fileOrderNamePair.get(anInt.toString());
				OBO_toLexiconConverter.compileDictionaryFromOboUri(ontologyURI, dictionaryName, dictDir, AppConfig.UPDATE_DICTION);
								
				// lookup the file name from the hashtable using the intCommand
				// then override that file on the file system......				
			}else{
				System.out.println("This should never get executed");
			}			
		}
		if(OBO_AnnotatorTool.INCLUDE){
			System.out.println("Please enter a name for the new aggregate engine: ");
			aggAEName = new Scanner(System.in).nextLine().toString();
			if (aggAEName.equals("") || aggAEName==null){
				System.out.println("Invalid file name, operation is ignored....");
				System.exit(0);
			}
			
			System.out.println("Please enter the path where for the new aggregate engine: ");
			aggAEDir = new Scanner(System.in).nextLine().toString();
			if (aggAEDir.equals("") || aggAEDir==null){
				System.out.println("Invalid directory name, operation is ignored....");
				System.exit(0);
			}			
			// take the files and create a new descriptor
			try {
				UserCustomedAEApplication.composeAggregateAE(userSelectedEnginesToInclude);
			} catch (IOException e) {
				System.out.println("Here is the error: \n" + e.getMessage());
				e.printStackTrace();
			}				
		}
		System.out.println("\n\n");
		System.out.println("Exiting the OBO-Annotator Tool ....");
		System.out.println("Goodbye ...");		
	}
}