/**
 * 
 */
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.ontology.OntoUtil;
import oboannotator.util.AppConfig;
import oboannotator.util.UserCommand;
import oboannotator.util.Util;


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

	/**
	 * @param args
	 */
	public static void main(String[] args) {	     
		Hashtable<String, String> fileOrderNamePair = new Hashtable<String, String>();
		ArrayList<String> userSelectedEnginesList = new ArrayList<String>();
		String primAEName = null;
		String ontologyURI= null;	
		String dictionaryName=null;
		
		
		System.out.println("                                 |--------------------------------------------------------|");
		System.out.println("                                 |          Welcome to OBO-Annotator Application          |");
		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("Following is the list of available dictionary\n");
		//String primitiveDescriptorsLocation = AppConfig.PRIMITIVE_AE_LOCATION; 		
		//System.out.print("current directory" + primitiveDescriptorsLocation);
		
		System.out.println(AppConfig.DICTIONARY_AE_DIR);
		fileOrderNamePair = Util.getFilesByDirectoryName(AppConfig.DICTIONARY_AE_DIR);		
		//System.out.println(fileOrderNamePair);
		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(AppConfig.INCLUDE_DICTION)){
				// turn the INCLUDE flag to true...
				AppConfig.INCLUDE=true;
				
				Integer anInt = new Integer(uComm.getIntCommand());
				if(fileOrderNamePair.get(anInt.toString())==null){
					System.out.println("Invalid descriptor, command is ignored...");
					continue;
				}										
				primAEName = fileOrderNamePair.get(anInt.toString());
			
				userSelectedEnginesList.add(primAEName);			
			}else if(uComm.getCommand().equals(AppConfig.ADD_NEW_DICTION)){
				
				// 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.....");
				
				if(OntoUtil.oboOrOwl(ontologyURI).equals(OntoUtil.OBO)){
					OBO_toLexiconConverter.compileDictionaryFromOboUri(ontologyURI, dictionaryName, AppConfig.DICTIONARY_DIR, AppConfig.ADD_NEW_DICTION);
				}

				if(OntoUtil.oboOrOwl(ontologyURI).equals(OntoUtil.OWL)){
					OBO_toLexiconConverter.compileDictionaryFromOwlURI(ontologyURI, dictionaryName, AppConfig.DICTIONARY_DIR, AppConfig.ADD_NEW_DICTION);
				}
				
				System.out.println("Generating the primitive analysis engine for the dictionary...");
				try {
					UserCustomedAEApplication.composePrimitiveAE(dictionaryName, AppConfig.ADD_NEW_DICTION);
				} catch (IOException e) {
					System.out.println("Error message is: " + e.getMessage());
				}				
			}else if(uComm.getCommand().equals(AppConfig.UPDATE_DICTION)){
				Integer anInt = new Integer(uComm.getCommandOption());
				if(fileOrderNamePair.get(anInt.toString())==null){
					System.out.println("Invalid dictionary name, 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());
				
				String validDictionaryName = Util.removeString(dictionaryName, "AE.xml");

				if(OntoUtil.oboOrOwl(ontologyURI).equals(OntoUtil.OBO)){
					OBO_toLexiconConverter.compileDictionaryFromOboUri(ontologyURI, validDictionaryName, AppConfig.DICTIONARY_DIR, AppConfig.ADD_NEW_DICTION);
				}

				if(OntoUtil.oboOrOwl(ontologyURI).equals(OntoUtil.OWL)){
					OBO_toLexiconConverter.compileDictionaryFromOwlURI(ontologyURI, validDictionaryName, AppConfig.DICTIONARY_DIR, AppConfig.ADD_NEW_DICTION);
				}				
				
				System.out.println("Upadting the primitive analysis engine for the dictionary...");
				try {
					UserCustomedAEApplication.composePrimitiveAE(dictionaryName, AppConfig.UPDATE_DICTION);
				} catch (IOException e) {
					System.out.println("Error message is: " + e.getMessage());
				}												
				// 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(AppConfig.INCLUDE){
			// take the files and create a new descriptor
			try {
				UserCustomedAEApplication.composeAggregateAE(userSelectedEnginesList);
				
				// annotate documents...
				OBO_DocumentAnalyzer.annotateDocuments(AppConfig.AGGREGATE_AE_DIR+AppConfig.USER_ASSEMBLED_AGGREGATE_AE, AppConfig.INPUT_FILES_DIR);
			} catch (IOException e) {
				System.out.println("Here is the error: \n" + e.getMessage());
				e.printStackTrace();
			}				
		}
		System.out.println("\n\n");
		System.out.println("Application finished processing ...");
		System.out.println("Exiting the OBO-Annotator Tool ...");
		System.out.println("Goodbye!");				
	}
}