X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FMafftWS.java;h=f293ae79d154209d638e330d86b4379e7e8d32d8;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=cdb159c5a7f9f6609dac6479274c83ac96684dde;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/webservices/compbio/ws/server/MafftWS.java b/webservices/compbio/ws/server/MafftWS.java
index cdb159c..f293ae7 100644
--- a/webservices/compbio/ws/server/MafftWS.java
+++ b/webservices/compbio/ws/server/MafftWS.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;
@@ -47,119 +47,122 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;
 import compbio.runner.msa.Mafft;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MafftWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "MafftWS")
 public class MafftWS implements MsaWS<Mafft> {
 
-    // Ask for resource injection
-    @Resource
-    WebServiceContext wsContext;
-
-    private static Logger statLog = Logger.getLogger("MafftWS-stats");
-
-    private static Logger log = Logger.getLogger(MafftWS.class);
-
-    private static final RunnerConfig<Mafft> mafftOptions = Util
-	    .getSupportedOptions(Mafft.class);
-
-    private static final PresetManager<Mafft> mafftPresets = Util
-	    .getPresets(Mafft.class);
-
-    @Override
-    public String align(List<FastaSequence> sequences)
-	    throws JobSubmissionException {
-	WSUtil.validateFastaInput(sequences);
-	ConfiguredExecutable<Mafft> confMafft = init(sequences);
-	return WSUtil.align(sequences, confMafft, null, "align", getLimit(""));
-    }
-
-    ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)
-	    throws JobSubmissionException {
-	Mafft mafft = new Mafft();
-	mafft.setInput("fasta.in").setOutput("fasta.out");
-	return Configurator.configureExecutable(mafft, dataSet);
-    }
-
-    @Override
-    public String customAlign(List<FastaSequence> sequences,
-	    List<Option<Mafft>> options) throws JobSubmissionException,
-	    WrongParameterException {
-	WSUtil.validateFastaInput(sequences);
-	ConfiguredExecutable<Mafft> confMafft = init(sequences);
-	List<String> params = WSUtil.getCommands(options,
-		Mafft.KEY_VALUE_SEPARATOR);
-	log.info("Setting parameters: " + params);
-	confMafft.addParameters(params);
-	return WSUtil.align(sequences, confMafft, null, "customAlign",
-		getLimit(""));
-    }
-
-    @Override
-    public String presetAlign(List<FastaSequence> sequences,
-	    Preset<Mafft> preset) throws JobSubmissionException,
-	    WrongParameterException {
-	WSUtil.validateFastaInput(sequences);
-	if (preset == null) {
-	    throw new WrongParameterException("Preset must be provided!");
+	private static Logger log = Logger.getLogger(MafftWS.class);
+
+	private static final RunnerConfig<Mafft> mafftOptions = Util
+			.getSupportedOptions(Mafft.class);
+
+	private static final PresetManager<Mafft> mafftPresets = Util
+			.getPresets(Mafft.class);
+
+	private static final LimitsManager<Mafft> limitMan = compbio.engine.client.Util
+			.getLimits(new Mafft().getType());
+
+	@Override
+	public String align(List<FastaSequence> sequences)
+			throws JobSubmissionException {
+		WSUtil.validateFastaInput(sequences);
+		ConfiguredExecutable<Mafft> confMafft = init(sequences);
+		return WSUtil.align(sequences, confMafft, log, "align", getLimit(""));
+	}
+
+	ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)
+			throws JobSubmissionException {
+		Mafft mafft = new Mafft();
+		mafft.setInput(SkeletalExecutable.INPUT)
+				.setOutput(SkeletalExecutable.OUTPUT)
+				.setError(SkeletalExecutable.ERROR);
+		return Configurator.configureExecutable(mafft, dataSet);
+	}
+
+	@Override
+	public String customAlign(List<FastaSequence> sequences,
+			List<Option<Mafft>> options) throws JobSubmissionException,
+			WrongParameterException {
+		WSUtil.validateFastaInput(sequences);
+		ConfiguredExecutable<Mafft> confMafft = init(sequences);
+		List<String> params = WSUtil.getCommands(options,
+				Mafft.KEY_VALUE_SEPARATOR);
+		log.info("Setting parameters: " + params);
+		confMafft.addParameters(params);
+		return WSUtil.align(sequences, confMafft, log, "customAlign",
+				getLimit(""));
+	}
+
+	@Override
+	public String presetAlign(List<FastaSequence> sequences,
+			Preset<Mafft> preset) throws JobSubmissionException,
+			WrongParameterException {
+		WSUtil.validateFastaInput(sequences);
+		if (preset == null) {
+			throw new WrongParameterException("Preset must be provided!");
+		}
+		ConfiguredExecutable<Mafft> confMafft = init(sequences);
+		confMafft.addParameters(preset.getOptions());
+		// This will return default limit if a specific the limit for a
+		// particular preset is not found
+		Limit<Mafft> limit = getLimit(preset.getName());
+
+		return WSUtil.align(sequences, confMafft, log, "presetAlign", limit);
+	}
+
+	@SuppressWarnings("unchecked")
+	@Override
+	public Alignment getResult(String jobId) throws ResultNotAvailableException {
+		WSUtil.validateJobId(jobId);
+		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
+		ConfiguredExecutable<Mafft> mafft = (ConfiguredExecutable<Mafft>) asyncEngine
+				.getResults(jobId);
+		Alignment al = mafft.getResults();
+		// log(jobId, "getResults");
+		return al;
+	}
+
+	@Override
+	public Limit<Mafft> getLimit(String presetName) {
+		if (limitMan == null) {
+			// Limit is not defined
+			return null;
+		}
+		return limitMan.getLimitByName(presetName);
+	}
+
+	@Override
+	public LimitsManager<Mafft> getLimits() {
+		return limitMan;
+	}
+
+	@Override
+	public ChunkHolder pullExecStatistics(String jobId, long position) {
+		WSUtil.validateJobId(jobId);
+		String file = Configurator.getWorkDirectory(jobId) + File.separator
+				+ new Mafft().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<Mafft> getPresets() {
+		return mafftPresets;
+	}
+
+	@Override
+	public RunnerConfig<Mafft> getRunnerOptions() {
+		return mafftOptions;
 	}
-	ConfiguredExecutable<Mafft> confMafft = init(sequences);
-	confMafft.addParameters(preset.getOptions());
-	// This will return default limit if a specific the limit for a
-	// particular preset is not found
-	Limit<Mafft> limit = getLimit(preset.getName());
-
-	return WSUtil.align(sequences, confMafft, null, "presetAlign", limit);
-    }
-
-    @SuppressWarnings("unchecked")
-    @Override
-    public Alignment getResult(String jobId) throws ResultNotAvailableException {
-	WSUtil.validateJobId(jobId);
-	AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
-	ConfiguredExecutable<Mafft> mafft = (ConfiguredExecutable<Mafft>) asyncEngine
-		.getResults(jobId);
-	Alignment al = mafft.getResults();
-	//log(jobId, "getResults");
-	return al;
-    }
-
-    @Override
-    public Limit<Mafft> getLimit(String presetName) {
-	return new Mafft().getLimit(presetName);
-    }
-
-    @Override
-    public LimitsManager<Mafft> getLimits() {
-	return new Mafft().getLimits();
-    }
-
-    @Override
-    public ChunkHolder pullExecStatistics(String jobId, long position) {
-	WSUtil.validateJobId(jobId);
-	String file = Configurator.getWorkDirectory(jobId) + File.separator
-		+ new Mafft().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<Mafft> getPresets() {
-	return mafftPresets;
-    }
-
-    @Override
-    public RunnerConfig<Mafft> getRunnerOptions() {
-	return mafftOptions;
-    }
 
 }