package compbio.ws.server;

import java.io.File;
import java.util.List;

import javax.annotation.Resource;
import javax.jws.WebService;
import javax.xml.ws.WebServiceContext;

import org.apache.log4j.Logger;

import compbio.conservation.Method;
import compbio.data.msa.Annotation;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.JalviewAnnotation;
import compbio.data.sequence.MultiAnnotatedSequence;
import compbio.engine.AsyncExecutor;
import compbio.engine.Configurator;
import compbio.engine.client.ConfiguredExecutable;
import compbio.metadata.ChunkHolder;
import compbio.metadata.JobStatus;
import compbio.metadata.JobSubmissionException;
import compbio.metadata.Limit;
import compbio.metadata.LimitExceededException;
import compbio.metadata.LimitsManager;
import compbio.metadata.Option;
import compbio.metadata.Preset;
import compbio.metadata.PresetManager;
import compbio.metadata.ResultNotAvailableException;
import compbio.metadata.RunnerConfig;
import compbio.metadata.UnsupportedRuntimeException;
import compbio.metadata.WrongParameterException;
import compbio.runner.Util;
import compbio.runner.conservation.AACon;

@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MuscleWS")
public class AAConWS implements Annotation<AACon> {

	// Ask for resource injection
	@Resource
	WebServiceContext wsContext;

	private static Logger statLog = Logger.getLogger("AAConWS-stats");

	private static Logger log = Logger.getLogger(AAConWS.class);

	private static final RunnerConfig<AACon> aaconOptions = Util
			.getSupportedOptions(AACon.class);

	private static final PresetManager<AACon> aaconPresets = Util
			.getPresets(AACon.class);

	ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)
			throws JobSubmissionException {
		AACon aacon = new AACon();
		aacon.setInput("fasta.in").setOutput("fasta.out");
		return Configurator.configureExecutable(aacon, sequences);
	}

	@SuppressWarnings("unchecked")
	public MultiAnnotatedSequence<Method> getResult(String jobId)
			throws ResultNotAvailableException {
		WSUtil.validateJobId(jobId);
		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
		ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine
				.getResults(jobId);
		MultiAnnotatedSequence<Method> mas = aacon.getResults();
		// log(jobId, "getResults");
		return mas;
	}

	@SuppressWarnings("unchecked")
	public JalviewAnnotation getJalviewAnnotation(String jobId)
			throws ResultNotAvailableException {
		MultiAnnotatedSequence<Method> result = getResult(jobId);

		// log(jobId, "getResults");
		return result.toJalviewAnnotation();
	}

	public Limit<AACon> getLimit(String presetName) {
		return new AACon().getLimit(presetName);
	}

	public LimitsManager<AACon> getLimits() {
		return new AACon().getLimits();
	}

	public ChunkHolder pullExecStatistics(String jobId, long position) {
		WSUtil.validateJobId(jobId);
		String file = Configurator.getWorkDirectory(jobId) + File.separator
				+ AACon.getStatFile();
		return WSUtil.pullFile(file, position);
	}

	public boolean cancelJob(String jobId) {
		WSUtil.validateJobId(jobId);
		return WSUtil.cancelJob(jobId);
	}

	public JobStatus getJobStatus(String jobId) {
		WSUtil.validateJobId(jobId);
		return WSUtil.getJobStatus(jobId);
	}

	public PresetManager<AACon> getPresets() {
		return aaconPresets;
	}

	public RunnerConfig<AACon> getRunnerOptions() {
		return aaconOptions;
	}

	@Override
	public String analize(List<FastaSequence> sequences)
			throws UnsupportedRuntimeException, LimitExceededException,
			JobSubmissionException {
		// TODO Auto-generated method stub
		return null;
	}

	@Override
	public String customAnalize(List<FastaSequence> sequences,
			List<Option<AACon>> options) throws UnsupportedRuntimeException,
			LimitExceededException, JobSubmissionException,
			WrongParameterException {
		// TODO Auto-generated method stub
		return null;
	}

	@Override
	public String presetAnalize(List<FastaSequence> sequences,
			Preset<AACon> preset) throws UnsupportedRuntimeException,
			LimitExceededException, JobSubmissionException,
			WrongParameterException {
		// TODO Auto-generated method stub
		return null;
	}

}