X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FJronnWS.java;h=cdc66ac24ef57e9cecaacb79e56e56560f10ac80;hb=68fe46f278b4ec408d6c68677bd56199aac749b3;hp=97d4cebe88846faac4a385564a521548b935c56b;hpb=021b24f125d8b1e8390e99b4a835469dabdd7be1;p=jabaws.git

diff --git a/webservices/compbio/ws/server/JronnWS.java b/webservices/compbio/ws/server/JronnWS.java
index 97d4ceb..cdc66ac 100644
--- a/webservices/compbio/ws/server/JronnWS.java
+++ b/webservices/compbio/ws/server/JronnWS.java
@@ -1,169 +1,52 @@
+/* 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.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.SequenceAnnotation;
-import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.ScoreManager;
-import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
-import compbio.engine.client.ConfiguredExecutable;
 import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Limit;
-import compbio.metadata.LimitExceededException;
-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.UnsupportedRuntimeException;
-import compbio.metadata.WrongParameterException;
-import compbio.runner.Util;
 import compbio.runner.conservation.AACon;
 import compbio.runner.disorder.Jronn;
 
-@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "JronnWS")
-public class JronnWS implements SequenceAnnotation<Jronn> {
-
-	// Ask for resource injection
-	@Resource
-	WebServiceContext wsContext;
-
-	private static Logger statLog = Logger.getLogger("JronnWS-stats");
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "JronnWS")
+public class JronnWS extends SequenceAnnotationService<Jronn>
+		implements
+			SequenceAnnotation<Jronn> {
 
 	private static Logger log = Logger.getLogger(JronnWS.class);
 
-	private static final RunnerConfig<Jronn> jronnOptions = Util
-			.getSupportedOptions(Jronn.class);
-
-	private static final PresetManager<Jronn> jronnPresets = Util
-			.getPresets(Jronn.class);
-
-	private static final LimitsManager<Jronn> limitMan = compbio.engine.client.Util
-			.getLimits(new Jronn().getType());
-
-	ConfiguredExecutable<Jronn> init(List<FastaSequence> sequences)
-			throws JobSubmissionException {
-		Jronn jronn = new Jronn();
-		return Configurator.configureExecutable(jronn, sequences);
-	}
-
-	@Override
-	public ScoreManager getAnnotation(String jobId)
-			throws ResultNotAvailableException {
-		WSUtil.validateJobId(jobId);
-		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
-		ConfiguredExecutable<Jronn> jronn = (ConfiguredExecutable<Jronn>) asyncEngine
-				.getResults(jobId);
-		ScoreManager mas = jronn.getResults();
-		log.trace(jobId + " getConservation : " + mas);
-		return mas;
-	}
-
-	@Override
-	public Limit<Jronn> getLimit(String presetName) {
-		if (limitMan == null) {
-			return null;
-		}
-		return limitMan.getLimitByName(presetName);
-	}
-
-	@Override
-	public LimitsManager<Jronn> getLimits() {
-		return limitMan;
+	public JronnWS() {
+		super(new Jronn(), log);
 	}
 
 	@Override
 	public ChunkHolder pullExecStatistics(String jobId, long position) {
 		WSUtil.validateJobId(jobId);
 		String file = Configurator.getWorkDirectory(jobId) + File.separator
-				+ Jronn.getStatFile();
+				+ AACon.getStatFile();
 		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<Jronn> getPresets() {
-		return jronnPresets;
-	}
-
-	@Override
-	public RunnerConfig<Jronn> getRunnerOptions() {
-		return jronnOptions;
-	}
-
-	String analize(List<FastaSequence> sequences,
-			ConfiguredExecutable<Jronn> confExec, Logger log, String method,
-			Limit<Jronn> limit) throws JobSubmissionException {
-		if (limit != null && limit.isExceeded(sequences)) {
-			throw LimitExceededException.newLimitExceeded(limit, sequences);
-		}
-
-		compbio.runner.Util.writeInput(sequences, confExec);
-		AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
-		String jobId = engine.submitJob(confExec);
-		return jobId;
-	}
-
-	@Override
-	public String analize(List<FastaSequence> sequences)
-			throws UnsupportedRuntimeException, LimitExceededException,
-			JobSubmissionException {
-		WSUtil.validateFastaInput(sequences);
-		ConfiguredExecutable<Jronn> confJronn = init(sequences);
-
-		return analize(sequences, confJronn, null, "analize", getLimit(""));
-	}
-
-	@Override
-	public String customAnalize(List<FastaSequence> sequences,
-			List<Option<Jronn>> options) throws UnsupportedRuntimeException,
-			LimitExceededException, JobSubmissionException,
-			WrongParameterException {
-		WSUtil.validateFastaInput(sequences);
-		ConfiguredExecutable<Jronn> confJronn = init(sequences);
-
-		List<String> params = WSUtil.getCommands(options,
-				AACon.KEY_VALUE_SEPARATOR);
-		confJronn.addParameters(params);
-		return analize(sequences, confJronn, null, "customAnalize",
-				getLimit(""));
-	}
-
-	@Override
-	public String presetAnalize(List<FastaSequence> sequences,
-			Preset<Jronn> preset) throws UnsupportedRuntimeException,
-			LimitExceededException, JobSubmissionException,
-			WrongParameterException {
-		WSUtil.validateFastaInput(sequences);
-		if (preset == null) {
-			throw new WrongParameterException("Preset must be provided!");
-		}
-		ConfiguredExecutable<Jronn> confJronn = init(sequences);
-		confJronn.addParameters(preset.getOptions());
-		Limit<Jronn> limit = getLimit(preset.getName());
-		return WSUtil.align(sequences, confJronn, null, "presetAnalize", limit);
-	}
-
 }