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/* Copyright (c) 2011 Peter Troshin
*
* 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
*
* This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
* even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
* License for more details.
*
* A copy of the license is in apache_license.txt. It is also available here:
* @see: http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Any republication or derived work distributed in source code form
* 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.data.sequence.Program;
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.msa.ClustalO;
@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "ClustalOWS")
public class ClustalOWS implements MsaWS<ClustalO> {
private static Logger log = Logger.getLogger(ClustalOWS.class);
private static final RunnerConfig<ClustalO> clustalOptions = RunnerUtil.getSupportedOptions(ClustalO.class);
private static final PresetManager<ClustalO> clustalPresets = RunnerUtil.getPresets(ClustalO.class);
private static final LimitsManager<ClustalO> limitMan = EngineUtil.getLimits(new ClustalO().getType());
@Override
public String align(List<FastaSequence> sequences)
throws JobSubmissionException {
WSUtil.validateFastaInput(sequences);
ConfiguredExecutable<ClustalO> confClust = init(sequences);
return WSUtil.align(sequences, confClust, log, "align", getLimit(""));
}
ConfiguredExecutable<ClustalO> init(List<FastaSequence> dataSet)
throws JobSubmissionException {
ClustalO clustal = new ClustalO();
clustal.setInput(SkeletalExecutable.INPUT);
clustal.setOutput(SkeletalExecutable.OUTPUT);
clustal.setError(SkeletalExecutable.ERROR);
ConfiguredExecutable<ClustalO> confClust = Configurator.configureExecutable(clustal, dataSet);
// Set the number of threads for the cluster execution from conf file
if (confClust.getExecProvider() == Executable.ExecProvider.Cluster) {
int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(clustal.getType());
if (clusterCpuNum != 0) {
clustal.setNCore(clusterCpuNum);
}
}
return confClust;
}
@Override
public String presetAlign(List<FastaSequence> sequences,
Preset<ClustalO> preset) throws JobSubmissionException,
WrongParameterException {
WSUtil.validateFastaInput(sequences);
if (preset == null) {
throw new WrongParameterException("Preset must be provided!");
}
Limit<ClustalO> limit = getLimit(preset.getName());
ConfiguredExecutable<ClustalO> confClust = init(sequences);
confClust.addParameters(preset.getOptions());
return WSUtil.align(sequences, confClust, log, "presetAlign", limit);
}
@Override
public String customAlign(List<FastaSequence> sequences,
List<Option<ClustalO>> options) throws JobSubmissionException,
WrongParameterException {
WSUtil.validateFastaInput(sequences);
ConfiguredExecutable<ClustalO> confClust = init(sequences);
List<String> params = WSUtil.getCommands(options, ClustalO.KEY_VALUE_SEPARATOR);
confClust.addParameters(params);
log.info("Setting parameters: " + params);
return WSUtil.align(sequences, confClust, log, "customAlign", getLimit(""));
}
@Override
public RunnerConfig<ClustalO> getRunnerOptions() {
return clustalOptions;
}
@SuppressWarnings("unchecked")
@Override
public Alignment getResult(String jobId) throws ResultNotAvailableException {
WSUtil.validateJobId(jobId);
AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
ConfiguredExecutable<ClustalO> clustal = (ConfiguredExecutable<ClustalO>) asyncEngine.getResults(jobId);
Alignment al = clustal.getResults();
return new Alignment (al.getSequences(),Program.ClustalO, '-');
}
@Override
public Limit<ClustalO> getLimit(String presetName) {
if (limitMan == null) {
// No limit is configured
return null;
}
Limit<ClustalO> limit = limitMan.getLimitByName(presetName);
return limit;
}
@Override
public LimitsManager<ClustalO> 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<ClustalO> getPresets() {
return clustalPresets;
}
@Override
public ChunkHolder pullExecStatistics(String jobId, long position) {
WSUtil.validateJobId(jobId);
String file = Configurator.getWorkDirectory(jobId) + File.separator + ClustalO.getStatFile();
ChunkHolder cholder = WSUtil.pullFile(file, position);
return cholder;
}
}
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