X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FClustalWS.java;h=3ba7d62bfe1265220a8a6b641081a637bd1e8784;hb=a966c1a63f4365f34a0567514dee6d1bc4d3af91;hp=93d0c7f534181a172ac74b8fb59105dc0d144b2a;hpb=021b24f125d8b1e8390e99b4a835469dabdd7be1;p=jabaws.git

diff --git a/webservices/compbio/ws/server/ClustalWS.java b/webservices/compbio/ws/server/ClustalWS.java
index 93d0c7f..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;
@@ -46,20 +46,12 @@ 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 volatile WSLogger logger;
-
 	private static final RunnerConfig<ClustalW> clustalOptions = Util
 			.getSupportedOptions(ClustalW.class);
 
@@ -69,35 +61,21 @@ public class ClustalWS implements MsaWS<ClustalW> {
 	private static final LimitsManager<ClustalW> limitMan = compbio.engine.client.Util
 			.getLimits(new ClustalW().getType());
 
-	/*
-	 * 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);
-				}
-			}
-		}
-		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(""));
+		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;
@@ -114,8 +92,7 @@ public class ClustalWS implements MsaWS<ClustalW> {
 		Limit<ClustalW> limit = getLimit(preset.getName());
 		ConfiguredExecutable<ClustalW> confClust = init(sequences);
 		confClust.addParameters(preset.getOptions());
-		return WSUtil.align(sequences, confClust, getLogger(), "presetAlign",
-				limit);
+		return WSUtil.align(sequences, confClust, log, "presetAlign", limit);
 	}
 
 	@Override
@@ -128,39 +105,35 @@ public class ClustalWS implements MsaWS<ClustalW> {
 				ClustalW.KEY_VALUE_SEPARATOR);
 		confClust.addParameters(params);
 		log.info("Setting parameters: " + params);
-		return WSUtil.align(sequences, confClust, getLogger(), "customAlign",
+		return WSUtil.align(sequences, confClust, log, "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();
 		if (limitMan == null) {
 			// No limit is configured
 			return null;
 		}
 		Limit<ClustalW> limit = limitMan.getLimitByName(presetName);
-		getLogger().logAll(timer, "getLimit");
 		return limit;
 	}
 
@@ -171,37 +144,30 @@ public class ClustalWS implements MsaWS<ClustalW> {
 
 	@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;
 	}