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.FileUtils;
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 BlastTaskSample {
	// Register Tool
	@SuppressWarnings("unchecked")
	public static void main(String[] args) {
		try {
			/*================================================================
			 * Login
			 *================================================================*/
			String username = "t";
			String password = "t";
			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
			 *================================================================*/
			String folderLabel = "Test 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("BLASTP");
			task.setLabel("BlastTask-" + System.currentTimeMillis());


			Map<String, String> paramMap = task.toolParameters();
			paramMap.put("protein_db_", "UNIPROT");
			paramMap.put("blast2_", "blastp");
			paramMap.put("filter_", "1");
			paramMap.put("lower_case_", "0");
			paramMap.put("Expect_", "10");
			paramMap.put("gapped_alig_", "1");
			paramMap.put("mismatch_", "-3");
			paramMap.put("match_", "1");
			paramMap.put("matrix_", "BLOSUM62");
			paramMap.put("gc_query_", "1");
			paramMap.put("gc_db_", "1");
			paramMap.put("strand_", "3");
			paramMap.put("Descriptions_", "500");
			paramMap.put("Alignments_", "250");
			paramMap.put("view_alignments_", "0");
			paramMap.put("show_gi_", "0");
			paramMap.put("believe_", "0");
			paramMap.put("htmloutput_", "0");
			paramMap.put("external_links_", "0");
			paramMap.put("one_HSP_per_line_", "0");
			paramMap.put("image_query_", "0");


			byte[] data = FileUtils.readFile("../samplefiles/queryp.fasta");
			TaskInputSourceDocument inputDoc = new TaskInputSourceDocument("infile.fsa", EntityType.PROTEIN, DataType.SEQUENCE, DataFormat.FASTA, data, false);
			List<TaskInputSourceDocument> inputList = new ArrayList<TaskInputSourceDocument>();

			inputList.add(inputDoc);

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

			task.setStage(TaskRunStage.READY);

			task.save();

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

			try {
				System.out.println("Waiting for TaskAgent to finish");
				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;
	}
}