package org.ngbw.examples;

import java.io.File;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import org.ngbw.sdk.Workbench;
import org.ngbw.sdk.WorkbenchSession;
import org.ngbw.sdk.common.util.FileUtils;
import org.ngbw.sdk.common.util.Resource;
import org.ngbw.sdk.database.User;
import org.ngbw.sdk.jobs.Job;
import org.ngbw.sdk.jobs.JobFile;
import org.ngbw.sdk.jobs.JobMetadata;
import org.ngbw.sdk.jobs.JobOutput;
import org.ngbw.sdk.jobs.JobStatus;
import org.ngbw.sdk.tool.DisabledResourceException;


/*
	Submits a job for the specified user.
		InputData is the path to a directory that contains the data for the test.  It can be either a path
		on the file system or a (relative) resource path.  The directory must contain the 2 files described below
		and may also contain the input files referenced in testInput.properties (either with filesystem or
		resource paths).
			testParam.properties: 
				Name=value pairs, corresponding to visible params for the tool.
				The special property toolId comes first in the file and isn't a parameter for a 
				tool but tells us which tool to run.
			testInput.properties: 
				Name=value pairs, where name is an input file param name and value
				is path to the file or resource with the data.
*/
public class TestJob 
{
	private static char[] buffer = new char[1024];
	private static final String USERNAME = "test1";
	private static final String PASSWORD = "test1";
	private static final String testSpec1 = "examples/new_tooltest/CLUSTALW";
	private static final String testSpec2 = "examples/new_tooltest/READSEQ";
	private static final String testSpec3 = "examples/new_tooltest/RAXMLHPC2BB";
	private static final String testSpec4 = "examples/new_tooltest/BEAST_TG";
	private static final String paramFile = "/testParam.properties";
	private static final String inputFile = "/testInput.properties";

	//Workbench object instances
	private static Workbench workbench = Workbench.getInstance();

	public static String runJob(User user, String path) throws DisabledResourceException, Exception
	{
		Map<String,String> testParam = Resource.getResource(path + paramFile).getPropertiesAsMap();
		Map<String,String> testInput = Resource.getResource(path + inputFile).getPropertiesAsMap();

		String toolId = testParam.get("toolId").trim();
		testParam.remove("toolId");

		/*
			Copy data from each testInput item to a tmp file because 
			the submission mechanism may modify the contents of the file (to convert the encoding).
			Also because the path given in testInput may refer to a resource, not a file.
		*/

		HashMap<String, File> inputFiles = new HashMap<String, File>();
		for (Map.Entry<String, String> entry : testInput.entrySet())
		{
			String name = entry.getKey();
			String value = entry.getValue();
			byte[] data;
			data = Resource.getResource(value).getBytes();
			File tmpFile = File.createTempFile("TestJob", null);
			FileUtils.writeFile(tmpFile, data);
			inputFiles.put(name, tmpFile);
		}

		/*
			I modified Job.submit to make 4th param Map<String, List<String>> so that we could
			handle pisexml "List" parameters, but haven't really updated this code to handle it.
			As a temporary workaround I'm just taking our testParam and changing the type of
			map below.  The caveat is that this won't correctly handle List type parameters in pise files.
		*/
		Map<String, List<String>> toolParameters = new HashMap<String, List<String>>(testParam.size());
		for (String key : testParam.keySet())
		{
			ArrayList<String> al = new ArrayList<String>(1);
			al.add(testParam.get(key));
			toolParameters.put(key, al);
		}
		JobMetadata md = new JobMetadata();
		String jh = Job.submit(user, null, md, toolId, toolParameters, inputFiles, false);
		return jh;
	}

	
	public static void main(String[] args) throws Exception
	{
		WorkbenchSession session = null;

		session = workbench.getSession(USERNAME, PASSWORD);
		User user = session.getUser();
		String jobHandle;
		JobStatus jobStatus;

		jobHandle = runJob(user, testSpec1);
		jobStatus = new JobStatus(jobHandle, user, null);
		System.out.println("Submitted job " + jobStatus.getJobHandle());
		displayStatus(jobStatus); 

		jobHandle = runJob(user, testSpec2);
		jobStatus = new JobStatus(jobHandle, user, null);
		System.out.println("Submitted job " + jobStatus.getJobHandle());
		displayStatus(jobStatus);

		jobHandle = runJob(user, testSpec3);
		jobStatus = new JobStatus(jobHandle, user, null);
		System.out.println("Submitted job " + jobStatus.getJobHandle());
		displayStatus(jobStatus);

		jobHandle = runJob(user, testSpec4);
		jobStatus = new JobStatus(jobHandle, user, null);
		System.out.println("Submitted job " + jobStatus.getJobHandle());
		displayStatus(jobStatus);
	}


	static void displayStatus(JobStatus status)
	{
		System.out.println("\nJOB STATUS " + status.getJobHandle());
		System.out.println("Terminal Stage: " + status.isTerminalStage());
		System.out.println("Job Stage: " + status.getJobStage());
		System.out.println("Date Submitted: " + status.getDateSubmitted().toString());
	}

	static void displayOutput(JobFile file, User user) throws Exception
	{
		System.out.println("\nResult File " + file.getFilename());
		System.out.println("Parameter: " + file.getParameterName());
		System.out.println("OutputDocumentId: " + file.getOutputDocumentId());
		System.out.println("Length: " + file.getLength());

		InputStream is = null;
		InputStreamReader reader = null;
		try
		{
			//is = Job.getOutputContent(file.getJobHandle(), file.getOutputDocumentId(), user);
			JobOutput output = Job.getOutput(file.getJobHandle(),  user, null);
			JobFile jf = output.getDocumentInfo(file.getOutputDocumentId());
			is = output.getDocument(jf);


			reader = new InputStreamReader(is);
			int len = reader.read(buffer, 0, buffer.length);
			if (len > -1)
			{
				System.out.println(buffer + " ...\n");
			} else
			{
				System.out.println("EOF trying to read contents.");
			}
		}
		catch(Exception e)
		{
			System.out.println("Error reading contents: " + e.getMessage());
		}
		finally
		{
			if (reader != null) { reader.close(); }
			if (is != null) { is.close(); }
		}

	}
}