X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FClustalWS.java;h=3ba7d62bfe1265220a8a6b641081a637bd1e8784;hb=a966c1a63f4365f34a0567514dee6d1bc4d3af91;hp=4b38157a3af73f27aec3f62089813d368a788886;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/webservices/compbio/ws/server/ClustalWS.java b/webservices/compbio/ws/server/ClustalWS.java
index 4b38157..3ba7d62 100644
--- a/webservices/compbio/ws/server/ClustalWS.java
+++ b/webservices/compbio/ws/server/ClustalWS.java
@@ -1,6 +1,6 @@
-/* Copyright (c) 2009 Peter Troshin
+/* Copyright (c) 2011 Peter Troshin
  *  
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0   
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
  * 
  *  This library is free software; you can redistribute it and/or modify it under the terms of the
  *  Apache License version 2 as published by the Apache Software Foundation
@@ -21,18 +21,18 @@ 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.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.SkeletalExecutable;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
 import compbio.metadata.JobSubmissionException;
@@ -46,158 +46,129 @@ import compbio.metadata.RunnerConfig;
 import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;
 import compbio.runner.msa.ClustalW;
-import compbio.util.Timer;
-import compbio.ws.client.Services;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ClustalWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ClustalWS")
 public class ClustalWS implements MsaWS<ClustalW> {
 
-    // Ask for resource injection
-    @Resource
-    private WebServiceContext wsContext;
+	private static Logger log = Logger.getLogger(ClustalWS.class);
 
-    private static Logger log = Logger.getLogger(ClustalWS.class);
+	private static final RunnerConfig<ClustalW> clustalOptions = Util
+			.getSupportedOptions(ClustalW.class);
 
-    private static volatile WSLogger logger;
+	private static final PresetManager<ClustalW> clustalPresets = Util
+			.getPresets(ClustalW.class);
 
-    private static final RunnerConfig<ClustalW> clustalOptions = Util
-	    .getSupportedOptions(ClustalW.class);
+	private static final LimitsManager<ClustalW> limitMan = compbio.engine.client.Util
+			.getLimits(new ClustalW().getType());
 
-    private static final PresetManager<ClustalW> clustalPresets = Util
-	    .getPresets(ClustalW.class);
+	@Override
+	public String align(List<FastaSequence> sequences)
+			throws JobSubmissionException {
 
-    /*
-     * Initialise the logger. This cannot be done in the constructor as the
-     * WebServiceContext is not available at the object construction time
-     */
-    private WSLogger getLogger() {
-	if (logger == null) {
-	    synchronized (ClustalWS.class) {
-		if (logger == null) {
-		    logger = WSLogger.getStatLogger(Services.ClustalWS,
-			    wsContext);
+		WSUtil.validateFastaInput(sequences);
+		ConfiguredExecutable<ClustalW> confClust = init(sequences);
+		return WSUtil.align(sequences, confClust, log, "align", getLimit(""));
+	}
+
+	ConfiguredExecutable<ClustalW> init(List<FastaSequence> dataSet)
+			throws JobSubmissionException {
+		ClustalW clustal = new ClustalW();
+		clustal.setInput(SkeletalExecutable.INPUT)
+				.setOutput(SkeletalExecutable.OUTPUT)
+				.setError(SkeletalExecutable.ERROR);
+		ConfiguredExecutable<ClustalW> confClust = Configurator
+				.configureExecutable(clustal, dataSet);
+		return confClust;
+	}
+
+	@Override
+	public String presetAlign(List<FastaSequence> sequences,
+			Preset<ClustalW> preset) throws JobSubmissionException,
+			WrongParameterException {
+		WSUtil.validateFastaInput(sequences);
+		if (preset == null) {
+			throw new WrongParameterException("Preset must be provided!");
 		}
-	    }
+		Limit<ClustalW> limit = getLimit(preset.getName());
+		ConfiguredExecutable<ClustalW> confClust = init(sequences);
+		confClust.addParameters(preset.getOptions());
+		return WSUtil.align(sequences, confClust, log, "presetAlign", limit);
 	}
-	return logger;
-    }
-
-    @Override
-    public String align(List<FastaSequence> sequences)
-	    throws JobSubmissionException {
-	WSUtil.validateFastaInput(sequences);
-	ConfiguredExecutable<ClustalW> confClust = init(sequences);
-	return WSUtil.align(sequences, confClust, getLogger(), "align",
-		getLimit(""));
-    }
-
-    ConfiguredExecutable<ClustalW> init(List<FastaSequence> dataSet)
-	    throws JobSubmissionException {
-	ClustalW clustal = new ClustalW();
-	ConfiguredExecutable<ClustalW> confClust = Configurator
-		.configureExecutable(clustal, dataSet);
-	return confClust;
-    }
-
-    @Override
-    public String presetAlign(List<FastaSequence> sequences,
-	    Preset<ClustalW> preset) throws JobSubmissionException,
-	    WrongParameterException {
-	WSUtil.validateFastaInput(sequences);
-	if (preset == null) {
-	    throw new WrongParameterException("Preset must be provided!");
+
+	@Override
+	public String customAlign(List<FastaSequence> sequences,
+			List<Option<ClustalW>> options) throws JobSubmissionException,
+			WrongParameterException {
+		WSUtil.validateFastaInput(sequences);
+		ConfiguredExecutable<ClustalW> confClust = init(sequences);
+		List<String> params = WSUtil.getCommands(options,
+				ClustalW.KEY_VALUE_SEPARATOR);
+		confClust.addParameters(params);
+		log.info("Setting parameters: " + params);
+		return WSUtil.align(sequences, confClust, log, "customAlign",
+				getLimit(""));
+	}
+
+	@Override
+	public RunnerConfig<ClustalW> getRunnerOptions() {
+		return clustalOptions;
+	}
+
+	@SuppressWarnings("unchecked")
+	@Override
+	public Alignment getResult(String jobId) throws ResultNotAvailableException {
+
+		WSUtil.validateJobId(jobId);
+		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
+		ConfiguredExecutable<ClustalW> clustal = (ConfiguredExecutable<ClustalW>) asyncEngine
+				.getResults(jobId);
+		Alignment al = clustal.getResults();
+
+		return al;
+	}
+
+	@Override
+	public Limit<ClustalW> getLimit(String presetName) {
+		if (limitMan == null) {
+			// No limit is configured
+			return null;
+		}
+		Limit<ClustalW> limit = limitMan.getLimitByName(presetName);
+		return limit;
+	}
+
+	@Override
+	public LimitsManager<ClustalW> 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<ClustalW> getPresets() {
+		return clustalPresets;
+	}
+
+	@Override
+	public ChunkHolder pullExecStatistics(String jobId, long position) {
+
+		WSUtil.validateJobId(jobId);
+		String file = Configurator.getWorkDirectory(jobId) + File.separator
+				+ ClustalW.getStatFile();
+		ChunkHolder cholder = WSUtil.pullFile(file, position);
+		return cholder;
 	}
-	Limit<ClustalW> limit = getLimit(preset.getName());
-	ConfiguredExecutable<ClustalW> confClust = init(sequences);
-	confClust.addParameters(preset.getOptions());
-	return WSUtil.align(sequences, confClust, getLogger(), "presetAlign",
-		limit);
-    }
-
-    @Override
-    public String customAlign(List<FastaSequence> sequences,
-	    List<Option<ClustalW>> options) throws JobSubmissionException,
-	    WrongParameterException {
-	WSUtil.validateFastaInput(sequences);
-	ConfiguredExecutable<ClustalW> confClust = init(sequences);
-	List<String> params = WSUtil.getCommands(options,
-		ClustalW.KEY_VALUE_SEPARATOR);
-	confClust.addParameters(params);
-	log.info("Setting parameters: " + params);
-	return WSUtil.align(sequences, confClust, getLogger(), "customAlign",
-		getLimit(""));
-    }
-
-    @Override
-    public RunnerConfig<ClustalW> getRunnerOptions() {
-	Timer timer = Timer.getMilliSecondsTimer();
-	getLogger().logAll(timer, "getRunnerOptions");
-	return clustalOptions;
-    }
-
-    @SuppressWarnings("unchecked")
-    @Override
-    public Alignment getResult(String jobId) throws ResultNotAvailableException {
-	Timer timer = Timer.getMilliSecondsTimer();
-	WSUtil.validateJobId(jobId);
-	AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
-	ConfiguredExecutable<ClustalW> clustal = (ConfiguredExecutable<ClustalW>) asyncEngine
-		.getResults(jobId);
-	Alignment al = clustal.getResults();
-	getLogger().log(timer, "getResults", jobId);
-	return al;
-    }
-
-    @Override
-    public Limit<ClustalW> getLimit(String presetName) {
-	Timer timer = Timer.getMilliSecondsTimer();
-	Limit<ClustalW> limit = new ClustalW().getLimit(presetName);
-	getLogger().logAll(timer, "getLimit");
-	return limit;
-    }
-
-    @Override
-    public LimitsManager<ClustalW> getLimits() {
-	Timer timer = Timer.getMilliSecondsTimer();
-	LimitsManager<ClustalW> limits = new ClustalW().getLimits();
-	getLogger().logAll(timer, "getLimits");
-	return limits;
-    }
-
-    @Override
-    public boolean cancelJob(String jobId) {
-	Timer timer = Timer.getMilliSecondsTimer();
-	WSUtil.validateJobId(jobId);
-	boolean result = WSUtil.cancelJob(jobId);
-	getLogger().logFine(timer, "Cancel");
-	return result;
-    }
-
-    @Override
-    public JobStatus getJobStatus(String jobId) {
-	Timer timer = Timer.getMilliSecondsTimer();
-	WSUtil.validateJobId(jobId);
-	JobStatus status = WSUtil.getJobStatus(jobId);
-	getLogger().logFine(timer, "getJobStatus");
-	return status;
-    }
-
-    @Override
-    public PresetManager<ClustalW> getPresets() {
-	Timer timer = Timer.getMilliSecondsTimer();
-	getLogger().logAll(timer, "pullExecStatistics");
-	return clustalPresets;
-    }
-
-    @Override
-    public ChunkHolder pullExecStatistics(String jobId, long position) {
-	Timer timer = Timer.getMilliSecondsTimer();
-	WSUtil.validateJobId(jobId);
-	String file = Configurator.getWorkDirectory(jobId) + File.separator
-		+ ClustalW.getStatFile();
-	ChunkHolder cholder = WSUtil.pullFile(file, position);
-	getLogger().logFine(timer, "pullExecStatistics");
-	return cholder;
-    }
 
 }