X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FJpredWS.java;h=382ef37444f68cd5f8b503785251ae7226923898;hb=68fe46f278b4ec408d6c68677bd56199aac749b3;hp=42529fcbe08ffb7a35d903d2443320b4e1d18026;hpb=a48ecc5f78c22682774e01d66aa9636d2d483431;p=jabaws.git

diff --git a/webservices/compbio/ws/server/JpredWS.java b/webservices/compbio/ws/server/JpredWS.java
index 42529fc..382ef37 100644
--- a/webservices/compbio/ws/server/JpredWS.java
+++ b/webservices/compbio/ws/server/JpredWS.java
@@ -16,153 +16,154 @@
  * must include this copyright and license notice.
  */
 
-package compbio.ws.server;
-
-import java.io.File;
-import java.util.List;
-
-import javax.jws.WebService;
-
-import org.apache.log4j.Logger;
-
-import compbio.data.msa.JABAService;
-import compbio.data.msa.MsaWS;
-import compbio.data.sequence.Alignment;
-import compbio.data.sequence.FastaSequence;
-import compbio.engine.AsyncExecutor;
-import compbio.engine.Configurator;
-import compbio.engine.client.ConfiguredExecutable;
-import compbio.engine.client.Executable;
-import compbio.engine.client.SkeletalExecutable;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Limit;
-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.WrongParameterException;
-import compbio.runner.Util;
-import compbio.runner.predictors.Jpred;
-
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "JpredWS")
-public class JpredWS implements MsaWS<Jpred> {
-
-	private static Logger log = Logger.getLogger(JpredWS.class);
-
-	private static final RunnerConfig<Jpred> jpredOptions = Util.getSupportedOptions(Jpred.class);
-	private static final PresetManager<Jpred> jpredPresets = Util.getPresets(Jpred.class);
-	private static final LimitsManager<Jpred> limitMan = compbio.engine.client.Util.getLimits(new Jpred().getType());
-
-	@Override
-	public String align(List<FastaSequence> sequences)
-			throws JobSubmissionException {
-
-		WSUtil.validateFastaInput(sequences);
-		ConfiguredExecutable<Jpred> confClust = init(sequences);
-		return WSUtil.align(sequences, confClust, log, "align", getLimit(""));
-	}
-
-	ConfiguredExecutable<Jpred> init(List<FastaSequence> dataSet)
-			throws JobSubmissionException {
-		Jpred jpred = new Jpred();
-		jpred.setInput(SkeletalExecutable.INPUT);
-		jpred.setOutput(SkeletalExecutable.OUTPUT);
-		jpred.setError(SkeletalExecutable.ERROR);
-		ConfiguredExecutable<Jpred> confJpred = Configurator.configureExecutable(jpred, dataSet);
-		// Set the number of threads for the cluster execution from conf file
-		if (confJpred.getExecProvider() == Executable.ExecProvider.Cluster) {
-			int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(jpred.getType());
-			if (clusterCpuNum != 0) {
-				jpred.setNCore(clusterCpuNum);
-			}
-		}
-		return confJpred;
-	}
-
-	@Override
-	public String presetAlign(List<FastaSequence> sequences,
-			Preset<Jpred> preset) throws JobSubmissionException,
-			WrongParameterException {
-		WSUtil.validateFastaInput(sequences);
-		if (preset == null) {
-			throw new WrongParameterException("Preset must be provided!");
-		}
-		Limit<Jpred> limit = getLimit(preset.getName());
-		ConfiguredExecutable<Jpred> confClust = init(sequences);
-		confClust.addParameters(preset.getOptions());
-		return WSUtil.align(sequences, confClust, log, "presetAlign", limit);
-	}
-
-	@Override
-	public String customAlign(List<FastaSequence> sequences,
-			List<Option<Jpred>> options) throws JobSubmissionException,
-			WrongParameterException {
-		WSUtil.validateFastaInput(sequences);
-		ConfiguredExecutable<Jpred> confClust = init(sequences);
-		List<String> params = WSUtil.getCommands(options, Jpred.KEY_VALUE_SEPARATOR);
-		confClust.addParameters(params);
-		log.info("Setting parameters: " + params);
-		return WSUtil.align(sequences, confClust, log, "customAlign", getLimit(""));
-	}
-
-	@Override
-	public RunnerConfig<Jpred> getRunnerOptions() {
-		return jpredOptions;
-	}
-
-	@SuppressWarnings("unchecked")
-	@Override
-	public Alignment getResult(String jobId) throws ResultNotAvailableException {
-		WSUtil.validateJobId(jobId);
-		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
-		ConfiguredExecutable<Jpred> jpred = (ConfiguredExecutable<Jpred>) asyncEngine.getResults(jobId);
-		return jpred.getResults();
-	}
-
-	@Override
-	public Limit<Jpred> getLimit(String presetName) {
-		if (limitMan == null) {
-			// No limit is configured
-			return null;
-		}
-		Limit<Jpred> limit = limitMan.getLimitByName(presetName);
-		return limit;
-	}
-
-	@Override
-	public LimitsManager<Jpred> getLimits() {
-		return limitMan;
-	}
-
-	@Override
-	public boolean cancelJob(String jobId) {
-		WSUtil.validateJobId(jobId);
-		boolean result = WSUtil.cancelJob(jobId);
-		return result;
-	}
-
-	@Override
-	public JobStatus getJobStatus(String jobId) {
-		WSUtil.validateJobId(jobId);
-		JobStatus status = WSUtil.getJobStatus(jobId);
-		return status;
-	}
-
-	@Override
-	public PresetManager<Jpred> getPresets() {
-		return jpredPresets;
-	}
-
-	@Override
-	public ChunkHolder pullExecStatistics(String jobId, long position) {
-		WSUtil.validateJobId(jobId);
-		String file = Configurator.getWorkDirectory(jobId) + File.separator + Jpred.getStatFile();
-		ChunkHolder cholder = WSUtil.pullFile(file, position);
-		return cholder;
-	}
-
-}
+//package compbio.ws.server;
+//
+//import java.io.File;
+//import java.util.List;
+//
+//import javax.jws.WebService;
+//
+//import org.apache.log4j.Logger;
+//
+//import compbio.data.msa.JABAService;
+//import compbio.data.msa.MsaWS;
+//import compbio.data.sequence.Alignment;
+//import compbio.data.sequence.JpredAlignment;
+//import compbio.data.sequence.FastaSequence;
+//import compbio.engine.AsyncExecutor;
+//import compbio.engine.Configurator;
+//import compbio.engine.client.ConfiguredExecutable;
+//import compbio.engine.client.Executable;
+//import compbio.engine.client.SkeletalExecutable;
+//import compbio.engine.client.EngineUtil;
+//import compbio.metadata.ChunkHolder;
+//import compbio.metadata.JobStatus;
+//import compbio.metadata.JobSubmissionException;
+//import compbio.metadata.Limit;
+//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.WrongParameterException;
+//import compbio.runner.RunnerUtil;
+//import compbio.runner.predictors.Jpred;
+//
+//@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "JpredWS")
+//public class JpredWS implements MsaWS<Jpred> {
+//
+//	private static Logger log = Logger.getLogger(JpredWS.class);
+//
+//	private static final RunnerConfig<Jpred> jpredOptions = RunnerUtil.getSupportedOptions(Jpred.class);
+//	private static final PresetManager<Jpred> jpredPresets = RunnerUtil.getPresets(Jpred.class);
+//	private static final LimitsManager<Jpred> limitMan = EngineUtil.getLimits(new Jpred().getType());
+//
+//	@Override
+//	public String align(List<FastaSequence> sequences)
+//			throws JobSubmissionException {
+//		WSUtil.validateFastaInput(sequences);
+//		ConfiguredExecutable<Jpred> confClust = init(sequences);
+//		return WSUtil.align(sequences, confClust, log, "align", getLimit(""));
+//	}
+//
+//	ConfiguredExecutable<Jpred> init(List<FastaSequence> dataSet)
+//			throws JobSubmissionException {
+//		Jpred jpred = new Jpred();
+//		jpred.setInput(SkeletalExecutable.INPUT);
+//		jpred.setOutput(SkeletalExecutable.OUTPUT);
+//		jpred.setError(SkeletalExecutable.ERROR);
+//		ConfiguredExecutable<Jpred> confJpred = Configurator.configureExecutable(jpred, dataSet);
+//		// Set the number of threads for the cluster execution from conf file
+//		if (confJpred.getExecProvider() == Executable.ExecProvider.Cluster) {
+//			int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(jpred.getType());
+//			if (clusterCpuNum != 0) {
+//				jpred.setNCore(clusterCpuNum);
+//			}
+//		}
+//		return confJpred;
+//	}
+//
+//	@Override
+//	public String presetAlign(List<FastaSequence> sequences,
+//			Preset<Jpred> preset) throws JobSubmissionException,
+//			WrongParameterException {
+//		WSUtil.validateFastaInput(sequences);
+//		if (preset == null) {
+//			throw new WrongParameterException("Preset must be provided!");
+//		}
+//		Limit<Jpred> limit = getLimit(preset.getName());
+//		ConfiguredExecutable<Jpred> confClust = init(sequences);
+//		confClust.addParameters(preset.getOptions());
+//		return WSUtil.align(sequences, confClust, log, "presetAlign", limit);
+//	}
+//
+//	@Override
+//	public String customAlign(List<FastaSequence> sequences,
+//			List<Option<Jpred>> options) throws JobSubmissionException,
+//			WrongParameterException {
+//		WSUtil.validateFastaInput(sequences);
+//		ConfiguredExecutable<Jpred> confClust = init(sequences);
+//		List<String> params = WSUtil.getCommands(options, Jpred.KEY_VALUE_SEPARATOR);
+//		confClust.addParameters(params);
+//		log.info("Setting parameters: " + params);
+//		return WSUtil.align(sequences, confClust, log, "customAlign", getLimit(""));
+//	}
+//
+//	@Override
+//	public RunnerConfig<Jpred> getRunnerOptions() {
+//		return jpredOptions;
+//	}
+//
+//	@SuppressWarnings("unchecked")
+//	@Override
+//	public Alignment getResult(String jobId) throws ResultNotAvailableException {
+//		WSUtil.validateJobId(jobId);
+//		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
+//		ConfiguredExecutable<Jpred> jpred = (ConfiguredExecutable<Jpred>) asyncEngine.getResults(jobId);
+//		return (Alignment)jpred.getResults();
+//	}
+//
+//	@Override
+//	public Limit<Jpred> getLimit(String presetName) {
+//		if (limitMan == null) {
+//			// No limit is configured
+//			return null;
+//		}
+//		Limit<Jpred> limit = limitMan.getLimitByName(presetName);
+//		return limit;
+//	}
+//
+//	@Override
+//	public LimitsManager<Jpred> getLimits() {
+//		return limitMan;
+//	}
+//
+//	@Override
+//	public boolean cancelJob(String jobId) {
+//		WSUtil.validateJobId(jobId);
+//		boolean result = WSUtil.cancelJob(jobId);
+//		return result;
+//	}
+//
+//	@Override
+//	public JobStatus getJobStatus(String jobId) {
+//		WSUtil.validateJobId(jobId);
+//		JobStatus status = WSUtil.getJobStatus(jobId);
+//		return status;
+//	}
+//
+//	@Override
+//	public PresetManager<Jpred> getPresets() {
+//		return jpredPresets;
+//	}
+//
+//	@Override
+//	public ChunkHolder pullExecStatistics(String jobId, long position) {
+//		WSUtil.validateJobId(jobId);
+//		String file = Configurator.getWorkDirectory(jobId) + File.separator + Jpred.getStatFile();
+//		ChunkHolder cholder = WSUtil.pullFile(file, position);
+//		return cholder;
+//	}
+//
+//}