X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FGlobPlotWS.java;h=d54bcd98a020d03d3e021ee7c054ea670e2af0b7;hb=68fe46f278b4ec408d6c68677bd56199aac749b3;hp=b0588825182bb697c0c405a27769a8a59f651669;hpb=24b1f578d0752ca4e3ee410031af5678b3ff1189;p=jabaws.git

diff --git a/webservices/compbio/ws/server/GlobPlotWS.java b/webservices/compbio/ws/server/GlobPlotWS.java
index b058882..d54bcd9 100644
--- a/webservices/compbio/ws/server/GlobPlotWS.java
+++ b/webservices/compbio/ws/server/GlobPlotWS.java
@@ -1,137 +1,48 @@
+/* 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.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.disorder.GlobPlot;
 
-@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "GlobPlotWS")
-public class GlobPlotWS implements SequenceAnnotation<GlobPlot> {
-
-	// Ask for resource injection
-	@Resource
-	WebServiceContext wsContext;
-
-	private static Logger statLog = Logger.getLogger("GlobPlotWS-stats");
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "GlobPlotWS")
+public class GlobPlotWS extends SequenceAnnotationService<GlobPlot>
+		implements
+			SequenceAnnotation<GlobPlot> {
 
 	private static Logger log = Logger.getLogger(GlobPlotWS.class);
 
-	private static final RunnerConfig<GlobPlot> globPlotOptions = Util
-			.getSupportedOptions(GlobPlot.class);
-
-	private static final PresetManager<GlobPlot> globPlotPresets = Util
-			.getPresets(GlobPlot.class);
-
-	private static final LimitsManager<GlobPlot> limitMan = compbio.runner.Util
-			.getLimits(new GlobPlot().getType());
-
-	ConfiguredExecutable<GlobPlot> init(List<FastaSequence> sequences)
-			throws JobSubmissionException {
-		GlobPlot globPlot = new GlobPlot();
-		globPlot.setInput("fasta.in").setOutput("globPlot.out");
-		return Configurator.configureExecutable(globPlot, sequences);
-	}
-
-	@Override
-	public ScoreManager getAnnotation(String jobId)
-			throws ResultNotAvailableException {
-		WSUtil.validateJobId(jobId);
-		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
-		ConfiguredExecutable<GlobPlot> globPlot = (ConfiguredExecutable<GlobPlot>) asyncEngine
-				.getResults(jobId);
-		ScoreManager mas = globPlot.getResults();
-		log.trace(jobId + " getConservation : " + mas);
-		return mas;
-	}
-
-	@Override
-	public Limit<GlobPlot> getLimit(String presetName) {
-		if (limitMan == null) {
-			// Limit is not defined
-			return null;
-		}
-		return limitMan.getLimitByName(presetName);
-	}
-
-	@Override
-	public LimitsManager<GlobPlot> getLimits() {
-		return limitMan;
-	}
-
-	@Override
-	public ChunkHolder pullExecStatistics(String jobId, long position) {
-		// Execution stat is not supported
-		return new ChunkHolder("", -1);
-	}
-
-	@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<GlobPlot> getPresets() {
-		return globPlotPresets;
-	}
-
-	@Override
-	public RunnerConfig<GlobPlot> getRunnerOptions() {
-		return globPlotOptions;
-	}
-
-	String analize(List<FastaSequence> sequences,
-			ConfiguredExecutable<GlobPlot> confExec, Logger log, String method,
-			Limit<GlobPlot> 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<GlobPlot> confGlobPlot = init(sequences);
-
-		return analize(sequences, confGlobPlot, null, "analize", getLimit(""));
+	public GlobPlotWS() {
+		super(new GlobPlot(), log);
 	}
 
 	/*