X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FTcoffeeWS.java;h=086d870bf9594a18c931aa194f96bb36ed0cfd85;hb=d92ac5284d2c918deda443f89e60cab6f0f8667e;hp=afe2caec0158616cf053914a83213275511f2933;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/webservices/compbio/ws/server/TcoffeeWS.java b/webservices/compbio/ws/server/TcoffeeWS.java
index afe2cae..086d870 100644
--- a/webservices/compbio/ws/server/TcoffeeWS.java
+++ b/webservices/compbio/ws/server/TcoffeeWS.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
@@ -21,12 +21,11 @@ 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;
@@ -34,6 +33,7 @@ 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;
@@ -48,126 +48,130 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;
 import compbio.runner.msa.Tcoffee;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "TcoffeeWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "TcoffeeWS")
 public class TcoffeeWS implements MsaWS<Tcoffee> {
 
-    // Ask for resource injection
-    @Resource
-    WebServiceContext wsContext;
-
-    private static Logger statLog = Logger.getLogger("TcoffeeWS-stats");
-
-    private static Logger log = Logger.getLogger(TcoffeeWS.class);
-
-    private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util
-	    .getSupportedOptions(Tcoffee.class);
-
-    private static final PresetManager<Tcoffee> tcoffeePresets = Util
-	    .getPresets(Tcoffee.class);
-
-    @Override
-    public String align(List<FastaSequence> sequences)
-	    throws JobSubmissionException {
-	WSUtil.validateFastaInput(sequences);
-	ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
-	return WSUtil
-		.align(sequences, confTcoffee, null, "align", getLimit(""));
-    }
-
-    ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)
-	    throws JobSubmissionException {
-	Tcoffee tcoffee = new Tcoffee();
-	tcoffee.setInput("fasta.in").setOutput("fasta.out");
-	ConfiguredExecutable<Tcoffee> confCoffee = Configurator
-		.configureExecutable(tcoffee, sequences);
-	if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {
-	    int clusterCpuNum = Tcoffee.getClusterCpuNum();
-	    if (clusterCpuNum != 0) {
-		tcoffee.setNCore(clusterCpuNum);
-	    }
+	private static Logger log = Logger.getLogger(TcoffeeWS.class);
+
+	private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util
+			.getSupportedOptions(Tcoffee.class);
+
+	private static final PresetManager<Tcoffee> tcoffeePresets = Util
+			.getPresets(Tcoffee.class);
+
+	private static final LimitsManager<Tcoffee> limitMan = compbio.engine.client.Util
+			.getLimits(new Tcoffee().getType());
+
+	@Override
+	public String align(List<FastaSequence> sequences)
+			throws JobSubmissionException {
+		WSUtil.validateFastaInput(sequences);
+		ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
+		return WSUtil.align(sequences, confTcoffee, log, "align", getLimit(""));
 	}
-	return confCoffee;
-    }
-
-    @Override
-    public String customAlign(List<FastaSequence> sequences,
-	    List<Option<Tcoffee>> options) throws JobSubmissionException,
-	    WrongParameterException {
-
-	WSUtil.validateFastaInput(sequences);
-	ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
-	List<String> params = WSUtil.getCommands(options,
-		Tcoffee.KEY_VALUE_SEPARATOR);
-	log.info("Setting parameters:" + params);
-	confTcoffee.addParameters(params);
-	return WSUtil.align(sequences, confTcoffee, null, "customAlign",
-		getLimit(""));
-    }
-
-    @Override
-    public String presetAlign(List<FastaSequence> sequences,
-	    Preset<Tcoffee> preset) throws JobSubmissionException,
-	    WrongParameterException {
-	WSUtil.validateFastaInput(sequences);
-	if (preset == null) {
-	    throw new WrongParameterException("Preset must be provided!");
+
+	ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)
+			throws JobSubmissionException {
+		Tcoffee tcoffee = new Tcoffee();
+		tcoffee.setInput(SkeletalExecutable.INPUT)
+				.setOutput(SkeletalExecutable.OUTPUT)
+				.setError(SkeletalExecutable.ERROR);
+
+		ConfiguredExecutable<Tcoffee> confCoffee = Configurator
+				.configureExecutable(tcoffee, sequences);
+		if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {
+			int clusterCpuNum = SkeletalExecutable
+					.getClusterCpuNum(Tcoffee.class);
+			if (clusterCpuNum != 0) {
+				tcoffee.setNCore(clusterCpuNum);
+			}
+		}
+		return confCoffee;
+	}
+
+	@Override
+	public String customAlign(List<FastaSequence> sequences,
+			List<Option<Tcoffee>> options) throws JobSubmissionException,
+			WrongParameterException {
+
+		WSUtil.validateFastaInput(sequences);
+		ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
+		List<String> params = WSUtil.getCommands(options,
+				Tcoffee.KEY_VALUE_SEPARATOR);
+		log.info("Setting parameters:" + params);
+		confTcoffee.addParameters(params);
+		return WSUtil.align(sequences, confTcoffee, log, "customAlign",
+				getLimit(""));
+	}
+
+	@Override
+	public String presetAlign(List<FastaSequence> sequences,
+			Preset<Tcoffee> preset) throws JobSubmissionException,
+			WrongParameterException {
+		WSUtil.validateFastaInput(sequences);
+		if (preset == null) {
+			throw new WrongParameterException("Preset must be provided!");
+		}
+		ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
+		confTcoffee.addParameters(preset.getOptions());
+		Limit<Tcoffee> limit = getLimit(preset.getName());
+		return WSUtil.align(sequences, confTcoffee, log, "presetAlign", limit);
+	}
+
+	@SuppressWarnings("unchecked")
+	@Override
+	public Alignment getResult(String jobId) throws ResultNotAvailableException {
+		WSUtil.validateJobId(jobId);
+		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
+		ConfiguredExecutable<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine
+				.getResults(jobId);
+		Alignment al = tcoffee.getResults();
+		// log(jobId, "getResults");
+		return al;
+	}
+
+	@Override
+	public Limit<Tcoffee> getLimit(String presetName) {
+		if (limitMan == null) {
+			// Limit is not defined
+			return null;
+		}
+		return limitMan.getLimitByName(presetName);
+	}
+
+	@Override
+	public LimitsManager<Tcoffee> getLimits() {
+		return limitMan;
+	}
+
+	@Override
+	public ChunkHolder pullExecStatistics(String jobId, long position) {
+		WSUtil.validateJobId(jobId);
+		String file = Configurator.getWorkDirectory(jobId) + File.separator
+				+ new Tcoffee().getError();
+		return WSUtil.pullFile(file, position);
+	}
+
+	@Override
+	public boolean cancelJob(String jobId) {
+		WSUtil.validateJobId(jobId);
+		return WSUtil.cancelJob(jobId);
+	}
+
+	@Override
+	public JobStatus getJobStatus(String jobId) {
+		WSUtil.validateJobId(jobId);
+		return WSUtil.getJobStatus(jobId);
+	}
+
+	@Override
+	public PresetManager<Tcoffee> getPresets() {
+		return tcoffeePresets;
+	}
+
+	@Override
+	public RunnerConfig<Tcoffee> getRunnerOptions() {
+		return tcoffeeOptions;
 	}
-	ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
-	confTcoffee.addParameters(preset.getOptions());
-	Limit<Tcoffee> limit = getLimit(preset.getName());
-	return WSUtil.align(sequences, confTcoffee, null, "presetAlign", limit);
-    }
-
-    @SuppressWarnings("unchecked")
-    @Override
-    public Alignment getResult(String jobId) throws ResultNotAvailableException {
-	WSUtil.validateJobId(jobId);
-	AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
-	ConfiguredExecutable<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine
-		.getResults(jobId);
-	Alignment al = tcoffee.getResults();
-	//log(jobId, "getResults");
-	return al;
-    }
-
-    @Override
-    public Limit<Tcoffee> getLimit(String presetName) {
-	return new Tcoffee().getLimit(presetName);
-    }
-
-    @Override
-    public LimitsManager<Tcoffee> getLimits() {
-	return new Tcoffee().getLimits();
-    }
-
-    @Override
-    public ChunkHolder pullExecStatistics(String jobId, long position) {
-	WSUtil.validateJobId(jobId);
-	String file = Configurator.getWorkDirectory(jobId) + File.separator
-		+ new Tcoffee().getError();
-	return WSUtil.pullFile(file, position);
-    }
-
-    @Override
-    public boolean cancelJob(String jobId) {
-	WSUtil.validateJobId(jobId);
-	return WSUtil.cancelJob(jobId);
-    }
-
-    @Override
-    public JobStatus getJobStatus(String jobId) {
-	WSUtil.validateJobId(jobId);
-	return WSUtil.getJobStatus(jobId);
-    }
-
-    @Override
-    public PresetManager<Tcoffee> getPresets() {
-	return tcoffeePresets;
-    }
-
-    @Override
-    public RunnerConfig<Tcoffee> getRunnerOptions() {
-	return tcoffeeOptions;
-    }
 
 }