package com.cipres.mrBayesPlugin.utilities;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.net.NoRouteToHostException;
import java.net.UnknownHostException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.zip.GZIPInputStream;

import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
import org.ngbw.directclient.CiCipresException;
import org.ngbw.directclient.CiClient;
import org.ngbw.directclient.CiJob;
import org.ngbw.directclient.CiResultFile;
import org.ngbw.restdatatypes.ErrorData;
import org.ngbw.restdatatypes.LimitStatus;
import org.ngbw.restdatatypes.ParamError;

import com.biomatters.geneious.publicapi.components.Dialogs;
import com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceException;
import com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService;
import com.biomatters.geneious.publicapi.plugin.DocumentImportException;
import com.biomatters.geneious.publicapi.plugin.PluginUtilities;
import com.cipres.mrBayesPlugin.models.UserModel;
import com.cipres.mrBayesPlugin.models.UserModel.Job;

import jebl.util.ProgressListener;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Utility class that handles any CIPRES actions such as submit, and list jobs
 * @author rjzheng
 *
 */
public class CipresUtilities {
	
	private static final Logger slf4jLogger = LoggerFactory.getLogger(CipresUtilities.class);
	private static final String HOMEDIR = System.getProperty("user.home");
	private static final String FILESEP = File.separator;
	private static final String NEWLINE = System.getProperty("line.separator");
	//private static final String CONFIGFILE = "pycipres.conf";
	public static final String CONFIGFILE = "geneious_cipres.conf";
	public static final String SERVICEURL = "https://cipresrest.sdsc.edu/cipresrest/v1";
	//public static final String APPNAME = "MRBAYES_XSEDE";
	public static final String APPNAME = "Geneious_Cipres";
	//public static final String APPID = "MRBAYES_XSEDE-1CA75045991B494BB3ED2D1F597AB503";
	public static final String APPID = "Geneious_Cipres-24704BCC103749D8BD17369694AB1F72";
	public static final String DASH = "-";
	public static final String COLON = ":";
	public static final String UNDERSCORE = "_";
	public static final String REPORTEMAIL = "mmiller@sdsc.edu";
	
	public static ClientCheckResult clientCheck(CiClient myClient){
		try {
			myClient.listJobs();
			return ClientCheckResult.TRUE;
		} catch (CiCipresException e) {
			if (e.getHttpStatus() == 401)
				return ClientCheckResult.UNAUTHORIZED;
			else
				return ClientCheckResult.FALSE;
		}
		catch (Exception ne) 
		{
			if ((ne instanceof UnknownHostException) || (ne instanceof NoRouteToHostException) ||
					(ne.toString().contains("UnknownHostException")) || (ne.toString().contains("NoRouteToHostException")))
					Dialogs.showMessageDialog("The CIPRES server cannot be reached.\nPlease check your internet connetion.");
				else
					throw ne;			
		}
		return ClientCheckResult.FALSE;
	}
	
	/**
	 * 
	 * @return config file path
	 */
	public static String getConfigFilePath(){
		return HOMEDIR + FILESEP + CONFIGFILE;
	}
	
	public static boolean checkEmptyString(String testStr){
		boolean check = false;
		if(testStr == null || testStr.trim().equals("")){
			check = true;
		}
		return check;
	}
	
	public static boolean isNewUser()
	{
        File configFile = new File(CipresUtilities.getConfigFilePath());
        return !configFile.exists();       	
	}
	
	/**
	 * Fetch and save user's jobs
	 * @param myClient
	 * @param user
	 * @throws CiCipresException
	 */
	public static void listJobs(CiClient myClient, UserModel user) throws CiCipresException
	{
		//Create a handler instance
		DataHandlingUtilities handler = DataHandlingUtilities.getInstance();
		handler.clearJobs();
		
		//Fetch jobs from CIPRES
		Collection<CiJob> jobs = myClient.listJobs(); 
		
		//Save jobs
		for (CiJob job : jobs)
		{
			Job newJob = user.new Job();
			newJob.setJobName(job.getClientJobName());
			newJob.setJobStage(job.getJobStage());
			newJob.setDate(job.getDateSubmitted());
			
			handler.addJob(newJob);
			
		}
		
		//Set user's jobs
		user.setJobs(handler.getJobs());
	}
	
	public static Collection<CiJob> getJobs(CiClient myClient) throws CiCipresException{
		//Create a handler instance
		DataHandlingUtilities handler = DataHandlingUtilities.getInstance();
		handler.clearJobs();
		
		//Fetch jobs from CIPRES
		Collection<CiJob> jobs = myClient.listJobs();
		
		return jobs;
	}
	
	public static JSONArray updateList(CiClient myClient, UserModel user) throws ParseException{
		
		//Create a handler instance
		DataHandlingUtilities handler = DataHandlingUtilities.getInstance();
				
		try {
			CipresUtilities.listJobs(myClient, user);
		} catch (CiCipresException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}
       
//        handler.saveData("jobs.json", handler.getUserJSON());
//        JSONObject retObj = handler.loadData("jobs.json");
		JSONParser parser = new JSONParser();
		Object obj = parser.parse(handler.getUserJSON());
        
        JSONArray retJSONArray = handler.getJobs((JSONObject)obj);
    	
        return retJSONArray;
        
	}
/***	
	public static void deleteJobs(List<String> selected_jobs,
			Collection<CiJob> allJobs) throws CiCipresException
	{
		for(int i = 0; i < selected_jobs.size(); i++){
			for(int x = 0; x < allJobs.size(); x++){
				CiJob job = (CiJob) allJobs.toArray()[x];
				System.out.println("local: " + selected_jobs.get(i));
				System.out.println("cloud" + job.getClientJobName());
				if(selected_jobs.get(i).equals(job.getClientJobName())){
					job.delete();
					selected_jobs.remove(i);
					System.out.println(job.getClientJobName() + " deleted");
					//Dialogs.showContinueCancelDialog("Incorrect user information", "Error!", null, Dialogs.DialogIcon.ERROR);
				}
			}
		}
	}
***/	
	
	/**
	 * @author Madhusudan Gujral (rewritten)
	 * @param selectedJobs
	 * @param allJobs
	 * @throws CiCipresException
	 */
	public static void deleteJobs(List<String> selectedJobs,
			Collection<CiJob> allJobs) throws CiCipresException
	{
		for(String selectedJob: selectedJobs){
			for(CiJob job: allJobs){	
				String jobNameWithDateAndTime = job.getClientJobName() + DASH + job.getDateSubmitted().toString();
				if(selectedJob.equals(jobNameWithDateAndTime)){
					job.delete();
					System.out.println(jobNameWithDateAndTime + " deleted");
				}
			}
		}
	}
	
	/**
	 * @author Madhusudan Gujral
	 */
	public static void downloadJobs(List<SelectedJobInfo> selectedJobs,
			Collection<CiJob> allJobs, String dwnldFldr) throws CiCipresException{
		//slf4jLogger.info("Welcome to the CipresUtilities");
		System.out.println("Welcome to the CipresUtilities");
		
		StringBuilder folderPresentMessage = new StringBuilder();
		StringBuilder importErrorMessage = new StringBuilder();
		StringBuilder exceptionMessage = new StringBuilder();
		boolean check = false;
		boolean imported = false;
				
		for(SelectedJobInfo selectedJobInfo: selectedJobs){
			String selectedJob = selectedJobInfo.getSelectedJobNameWithDate();
			System.out.println("Selected Job: " + selectedJob);
			
			
			 String folderForFiles =  dwnldFldr +
					 FILESEP + selectedJob.replaceAll(" ", "-" ).replaceAll(COLON, UNDERSCORE);
			
			for(CiJob job: allJobs){	
				String jobNameWithDateAndTime = job.getClientJobName() + DASH + job.getDateSubmitted().toString();
				if(selectedJob.equals(jobNameWithDateAndTime)){
					Collection<CiResultFile> resultsFileCollection = job.listResults(true);
					
					for(CiResultFile resultFile: resultsFileCollection){
						String fName = resultFile.getName();
						System.out.println("File name: " + fName);						
						//Dialogs.showMessageDialog(fName);
					
					}
					
					try{
						System.out.println("New folder path: " + folderForFiles);
						File fileFldr = new File(folderForFiles); // Added time stamp to download folder
						int count = 1;
						String baseFolderForFiles = folderForFiles;
						while (fileFldr.exists())
						{
							folderForFiles = baseFolderForFiles + "(" + count + ")";
							fileFldr = new File(folderForFiles);
							++count;
						}
						
						
						if (!fileFldr.exists()) {
				            if (fileFldr.mkdir()){
				            	System.out.println("Download folder: " + folderForFiles);
				            }
				            job.downloadResults(new File(folderForFiles), true);
				            
				            if (selectedJobInfo.getImported())
				            {
				            	String error = addToYourLocalDatabase(resultsFileCollection, folderForFiles, selectedJobInfo.getLocalFolder());
				            	if  (!error.isEmpty())
				            	{
				            		importErrorMessage.append(addToYourLocalDatabase(resultsFileCollection, folderForFiles, selectedJobInfo.getLocalFolder()));
				            		importErrorMessage.append("\n");
				            	}
				            	else
				            		imported = true;
				            }
						}else{
							if(!check){
															
								folderPresentMessage.append("Following jobs could not be downloaded because their folder "
										+ "names are already present in the selected folder." + NEWLINE);
								folderPresentMessage.append(jobNameWithDateAndTime.replaceAll(" ", "-" ) + NEWLINE);
								check = true;
								
							}else{
								folderPresentMessage.append(jobNameWithDateAndTime.replaceAll(" ", "-" ) + NEWLINE);
							}
						}
						//job.downloadResults(new File(folderForFiles), true);
					}catch(Exception e){
						System.out.println("Problem in downloading file: ");
						e.printStackTrace();
						if (exceptionMessage.length() == 0 )
							exceptionMessage.append("Below exception(s) occurred while downloading data. Please try your download again in a few minutes. Thank you!\n");
						exceptionMessage.append(e.toString());
						exceptionMessage.append("\n");
					}
				}
			}			
		}
		
		if(!checkEmptyString(folderPresentMessage.toString())){
			Dialogs.showMessageDialog(folderPresentMessage.toString().trim());
		}
		else if (!importErrorMessage.toString().isEmpty())
			Dialogs.showMessageDialog(importErrorMessage.toString());
		else if (!exceptionMessage.toString().isEmpty())
			Dialogs.showMessageDialog(exceptionMessage.toString());				
		else
			Dialogs.showMessageDialog("The results of selected job(s) have been downloaded" + (imported? " and imported to Sources Panel." : "."));
	
	}
	
	public static void submitJob(String tool,
			Map<String,Collection<String>> vParams, Map<String,String> inputParams, 
			Map<String,String> metadata) throws CiCipresException{
		CiJob jobStatus = null;
		try
		{
			System.err.println("SubmitJob enter");
			DataHandlingUtilities handler = DataHandlingUtilities.getInstance();
			CiClient myClient = handler.getClient();
			
			if(CipresUtilities.clientCheck(myClient) == ClientCheckResult.TRUE){
				try
				{
					jobStatus = myClient.submitJob(tool, vParams, inputParams, metadata);
				}
				catch (CiCipresException ce)
				{
					StringBuffer sb = new StringBuffer();
		            ErrorData ed = ce.getErrorData();
		            sb.append("Cipres error code=");
		            sb.append(ed.code);
		            sb.append(", message=");
		            sb.append(ed.displayMessage);
		            sb.append("\n\n");
		            if (ed.code == ErrorData.FORM_VALIDATION)
		            {
		                for (ParamError pe : ed.paramError)
		                {
		                    sb.append(pe.param);
		                    sb.append(": ");
		                    sb.append(pe.error);
		                    sb.append("\n");
		                }
		            } else if (ed.code == ErrorData.USAGE_LIMIT)
		            {
		                LimitStatus ls = ed.limitStatus;
		                sb.append("Usage Limit Error, type=");
		                sb.append(ls.type);
		                sb.append(", ceiling=");
		                sb.append(ls.ceiling);
		                sb.append("\n");
		            }
		            Dialogs.showMessageDialog(sb.toString(), "Error Message(s) from REST Server");
		            throw ce;
				}
			}else{
				System.err.println("No Client Found");
			}
		}
		catch (Exception ne) 
		{
			if ((ne instanceof UnknownHostException) || (ne instanceof NoRouteToHostException) ||
					(ne.toString().contains("UnknownHostException")) || (ne.toString().contains("NoRouteToHostException")))
					Dialogs.showMessageDialog("The CIPRES server cannot be reached.\nPlease check your internet connetion.");
				else
					throw ne;			
		}
		
		if (jobStatus != null)
			jobStatus.show(true);
	} 
	
	public static String addToYourLocalDatabase(Collection<CiResultFile> resultsFileCollection, String sourceFolder, String targetFolder)
	{		
		WritableDatabaseService database= (WritableDatabaseService) PluginUtilities.getGeneiousService("LocalDocuments");
		try {
			if (targetFolder != null && !targetFolder.isEmpty())
			{
				String[] subfolders = targetFolder.split("/");
		
				for (String subfolder : subfolders)
				{
					if (!subfolder.trim().isEmpty())
						database = database.createChildFolder(subfolder);
				}
			}
			//boolean allowStdErrOut = false;
			List<String> unzipFiles = new ArrayList<String>();
			for (CiResultFile file : resultsFileCollection)
			{
				//if (file.getName().equals("stderr.txt") && file.getLength() > 0)
				//	allowStdErrOut = true;
				//if (file.getName().endsWith(".ckp.gz"))
				//	continue;
				if (file.getName().endsWith(".gz"))
				{
					String sourceFile = sourceFolder + File.separator + file.getName();
					String targetFile = sourceFolder + File.separator + file.getName().substring(0, file.getName().length()-3);
					unzipGZFile(sourceFile, targetFile);
					unzipFiles.add(targetFile);
				}
			}
			
			for (CiResultFile file : resultsFileCollection)
			{
				if (file.getName().endsWith("TXT") || file.getName().endsWith("conf") || file.getName().endsWith("STDERR") || file.getName().endsWith("STDOUT") ||
					file.getName().contains((CharSequence)".ckp.") || file.getName().endsWith(".gz"))
				{
					//if (file.getName().endsWith("JOBINFO.TXT") || file.getName().endsWith("conf") || file.getName().endsWith("STDERR") || file.getName().endsWith("STDOUT"))
					
					continue;
				}
				
				
				if (file.getName().endsWith("txt"))
				{
					//if (!allowStdErrOut || (!file.getName().equals("stderr.txt")  && !file.getName().equals("stdout.txt")))
					//if (!file.getName().equals("stderr.txt")  && !file.getName().equals("stdout.txt"))
					//	continue;
					if (file.getName().startsWith("_scheduler") ||
						file.getName().equals("done.txt") ||
						file.getName().equals("start.txt") ||
						file.getName().equals("term.txt"))
						continue;
						
					if (file.getLength() == 0)
						continue;
				
				}
				
				String fileName = file.getName();
				if (file.getName().endsWith(".p") || file.getName().endsWith(".tstat") || file.getName().endsWith(".vstat"))
				{
					Path source = Paths.get(sourceFolder + File.separator + file.getName());
					
					if (fileName.contains(".txt"))
					{
						CharSequence cs1 = new StringBuffer(".txt");
						CharSequence cs2 = new StringBuffer("");
						fileName = fileName.replace(cs1, cs2);
					}		
					fileName = fileName + ".txt";

					try
					{
						Files.move(source, source.resolveSibling(fileName));
					}
					catch (Exception e)
					{
						fileName = file.getName();
					}
				}
					
					
				File importfile = new File(sourceFolder + File.separator + fileName);
				//File importfile = new File(sourceFolder + File.separator + file.getName());     //new File("C:\\Users\\mzhuang\\MyGeneious_job_download\\Three-Kingdoms-Thu-Apr-25-12_19_16-PDT-2019\\infile.nex.run1.p");
				try {
					System.out.println("Importing " + importfile.getAbsolutePath());
					PluginUtilities.importDocumentsToDatabase(importfile, database, ProgressListener.EMPTY);
				} catch (DocumentImportException | IOException e) {
				
					e.printStackTrace();
				}
			}
			for (String file : unzipFiles)
			{
				if (file.endsWith("TXT") || file.endsWith("conf") || file.endsWith("STDERR") || file.endsWith("STDOUT") ||
					file.contains((CharSequence)".ckp.") || file.endsWith(".gz"))
				{
					//if (file.getName().endsWith("JOBINFO.TXT") || file.getName().endsWith("conf") || file.getName().endsWith("STDERR") || file.getName().endsWith("STDOUT"))
					
					continue;
				}
				if (file.endsWith("txt"))
				{
					if (!file.equals("stderr.txt")  && !file.equals("stdout.txt"))
						continue;
					//if (file.getLength() == 0)
					//	continue;
				}
				File importfile = new File(file);
				
		
				try {
					PluginUtilities.importDocumentsToDatabase(importfile, database, ProgressListener.EMPTY);
				} catch (DocumentImportException | IOException e) {
				
					e.printStackTrace();
				}
			}
		} catch (DatabaseServiceException e) {
			
			return e.getMessage();
		}
		return "";
	}
	
	private static void unzipGZFile(String sourceFile, String targetFile)
	{
		FileInputStream fis = null;
		GZIPInputStream gzis = null;
		FileOutputStream fos = null;
	    try {
	        // Create a file input stream to read the source file.
	        fis = new FileInputStream(sourceFile);
	
	        // Create a gzip input stream to decompress the source
	        // file defined by the file input stream.
	        gzis = new GZIPInputStream(fis);
	
	        // Create file output stream where the decompress result
	        // will be stored.
	        fos = new FileOutputStream(targetFile);
	
	        // Create a buffer and temporary variable used during the
	        // file decompress process.
	        byte[] buffer = new byte[1024];
	        int length;
	
	        // Read from the compressed source file and write the
	        // decompress file.
	        while ((length = gzis.read(buffer)) > 0) {
	            fos.write(buffer, 0, length);
	        }
	    } catch (IOException e) {
	        e.printStackTrace();
	    }
	    finally
	    {
	    	try
	    	{
	    		if (gzis != null)
	    			gzis.close();
	    		if (fis != null)
	    			fis.close();
	    		if (fos != null)
	    			fos.close();
	    	}
	    	catch (IOException e)
	    	{}
	    }
	}

}