package com.cipres.mrBayesPlugin;

import java.io.File;
import java.io.FileInputStream;
import java.util.Collection;
import java.util.List;
import java.util.Properties;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;

import javax.swing.JPanel;

import org.json.simple.JSONArray;
import org.json.simple.parser.ParseException;
import org.ngbw.directclient.CiApplication;
import org.ngbw.directclient.CiCipresException;
import org.ngbw.directclient.CiClient;
import org.ngbw.directclient.CiJob;

import com.biomatters.geneious.publicapi.components.Dialogs;
import com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions;
import com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument;
import com.biomatters.geneious.publicapi.plugin.DocumentOperation;
import com.biomatters.geneious.publicapi.plugin.DocumentOperationException;
import com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature;
import com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions;
import com.biomatters.geneious.publicapi.plugin.Options;
import com.cipres.mrBayesPlugin.models.UserModel;
import com.cipres.mrBayesPlugin.ui.JobManagePanel;
import com.cipres.mrBayesPlugin.ui.LoginOptions;
import com.cipres.mrBayesPlugin.utilities.CipresUtilities;
import com.cipres.mrBayesPlugin.utilities.ClientCheckResult;
import com.cipres.mrBayesPlugin.utilities.DataHandlingUtilities;

import jebl.util.CompositeProgressListener;
import jebl.util.ProgressListener;


/**
 * 
 * @author rjzheng
 * @author mgujral
 * 
 */
public class CipresMrBayesToolbar extends DocumentOperation{
	
	private static final String APPNAME = CipresUtilities.APPNAME;
	public static CiClient myClient;
	private JPanel displayGuiModel;
	private static Boolean newUser = true;
	
	public static Boolean getNewUser(){
		return newUser;
	}
	
	public String getUniqueId(){
		return "MrBayes_CIPRES";
	}
	
	@Override
	public GeneiousActionOptions getActionOptions() {
		return new GeneiousActionOptions("CIPRES...").setMainMenuLocation(GeneiousActionOptions.MainMenu.Tools);
		
	}

	@Override
	public String getHelp() {
		return "Getting Help";
	}

	@Override
	public DocumentSelectionSignature[] getSelectionSignatures() {
		return new DocumentSelectionSignature[0];
	}
	
	
	//Geneious will display the Options returned from this method as a panel before calling performOperation().
	public Options getOptions(final AnnotatedPluginDocument[] docs) throws DocumentOperationException{
        Options options = null;
       
        if (CipresUtilities.isNewUser())
        {
			options = new LoginOptions();
	        options.canRestoreDefaults();
        }
        
        return options;
    }

    //This is the method that does all the work.  Geneious passes a list of the documents that were selected when the user
    //started the operation, a progressListener, and the options panel that we returned in the getOptionsPanel() method above.
    public List performOperation(AnnotatedPluginDocument[] docs, ProgressListener progress, Options options) throws DocumentOperationException{
    	String userName = null;
    	String password = null;
    	
    	if (options instanceof LoginOptions)
    	{
    		LoginOptions loginOpt = (LoginOptions)options;
    		userName = loginOpt.getUsername();
    		password = loginOpt.getPassword();
    	}
    	newUser = !CipresMrBayesInitializer.Instance.initialize(userName, password);
    	if (newUser == false)
    	{
    		myClient = CipresMrBayesInitializer.Instance.getMyClient();
    		JSONArray retJSONArray = null;
    		try {
    			retJSONArray = CipresUtilities.updateList(myClient, CipresMrBayesInitializer.Instance.getUserModel());
    		} catch (ParseException e) {
    			e.printStackTrace();
    		}

    		displayGuiModel = new JobManagePanel().createPanel(retJSONArray);
    		
    		DialogOptions dialogOptions = new DialogOptions(new Dialogs.DialogAction[] {Dialogs.CANCEL}, "CIPRES jobs");
    	
    		Dialogs.showDialog(dialogOptions, displayGuiModel);
    	}
    	
        return null;
   }
    
    public static void main(String[] args){
    	CiApplication app = CiApplication.getInstance();
    	String url = app.getRestUrl();
        String appName = app.getAppname();
        String appKey = app.getAppKey();
        
        System.out.println("URL: " + url);
        System.out.println("AppName: " + appName);
        System.out.println("AppKey: " + appKey);
    }
}