package org.ngbw.examples;


import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.Future;

import org.ngbw.sdk.UserAuthenticationException;
import org.ngbw.sdk.Workbench;
import org.ngbw.sdk.WorkbenchSession;
import org.ngbw.sdk.common.util.Resource;
import org.ngbw.sdk.core.shared.TaskRunStage;
import org.ngbw.sdk.core.types.DataFormat;
import org.ngbw.sdk.core.types.DataType;
import org.ngbw.sdk.core.types.EntityType;
import org.ngbw.sdk.database.Folder;
import org.ngbw.sdk.database.Task;
import org.ngbw.sdk.database.TaskInputSourceDocument;
import org.ngbw.sdk.database.TaskLogMessage;
import org.ngbw.sdk.database.TaskOutputSourceDocument;
import org.ngbw.sdk.database.User;


public class RaxmlTaskSample 
{
	// Register Tool
	@SuppressWarnings("unchecked")
	public static void main(String[] args)
	{
		try {
			/*================================================================
			 * Login
			 *================================================================*/
			String username = "terri";
			String password = "berryterri";

			Workbench workbench = Workbench.getInstance();
			WorkbenchSession session = null;
			try 
			{
				session = workbench.getSession(username, password);
			} catch (UserAuthenticationException e) 
			{
				System.err.println(e.toString());
			}

			User user = session.getUser();

			/*================================================================
			 * Folder setup
			 *	If we don't have any folders create one, otherwise use the first
			 *================================================================*/
			String folderLabel = "Auto Folder";
			Folder folder = findFolderByLabel(user.findFolders(), folderLabel);

			if (folder == null) {
				folder = new Folder(user);

				folder.setLabel(folderLabel);

				folder.save();
			}

			/*================================================================
			 * Task setup
			 *================================================================*/

			Task task = new Task(folder);

			task.setToolId("RAXMLHPC");
			task.setLabel("raxml-" + System.currentTimeMillis());


			Map<String, String> paramMap = task.toolParameters();
			paramMap.put("datatype_", "dna");
			paramMap.put("mlsearch_", "0");
			paramMap.put("invariable_", "");
			paramMap.put("matrix_", "DAYHOFF");
			paramMap.put("empirical_", "");
			paramMap.put("bootstop_", "auto");
			paramMap.put("bootstrap_seed_", "12345");
			paramMap.put("parsimony_seed_", "12345");

			String infile = "src/main/java/org/ngbw/examples/tooltest/RAXMLHPC/RAXMLHPC_in.txt";
			byte[] data = Resource.getResource(infile).getBytes();
			TaskInputSourceDocument inputDoc = new TaskInputSourceDocument("unused_name", EntityType.NUCLEIC_ACID, DataType.SEQUENCE_ALIGNMENT, DataFormat.PHYLIP, data, false);
			List<TaskInputSourceDocument> inputList = new ArrayList<TaskInputSourceDocument>();

			inputList.add(inputDoc);

			task.input().put("infile_", inputList);

			task.setStage(TaskRunStage.READY);

			task.save();

			Future<Task> ah = workbench.saveAndSubmitTask(task, folder, null);

			try 
			{
				//boolean isDone = false;
				System.out.println("Waiting for TaskAgent to finish");
				/*
			while (isDone == false) 
				isDone = ah.isDone();
				 */
				task = ah.get();
				System.out.println("TaskAgent is done");
			} catch (InterruptedException e) 
			{
				// TODO Auto-generated catch block
				e.printStackTrace();
			} catch (ExecutionException e) 
			{
				// TODO Auto-generated catch block
				e.printStackTrace();
			}

			for (TaskLogMessage msg : task.logMessages())
				System.out.println(msg);

			Map<String, List<TaskOutputSourceDocument>> outputMap = task.output();

			for (String param : outputMap.keySet()) 
			{
				List<TaskOutputSourceDocument> paramOutput = outputMap.get(param);

				for (TaskOutputSourceDocument file : paramOutput)
				{
					System.out.println(file.getName() + ": " + file.getType());
					System.out.println();
					System.out.println(new String(file.getData()));
				}
			}

			task.delete();
		}
		catch (Exception err) {
			err.printStackTrace(System.err);

			System.exit(-1);
		}
	}// end main

	private static Folder findFolderByLabel(List<Folder> folders, String label)
	{
		for (Iterator<Folder> elements = folders.iterator() ; elements.hasNext() ; ) {
			Folder folder = elements.next();

			if (folder.getLabel().equals(label))
				return folder;
		}

		return null;
	}
}