X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FDisemblWS.java;h=bf75828321d4b728e76e36d75625a13b4556923d;hb=68fe46f278b4ec408d6c68677bd56199aac749b3;hp=2eac30d61f6c34bd22956cd7cadc98ffb1f5ad41;hpb=9d860c3793c6812f643caa01fc80a0036fa3fe2b;p=jabaws.git

diff --git a/webservices/compbio/ws/server/DisemblWS.java b/webservices/compbio/ws/server/DisemblWS.java
index 2eac30d..bf75828 100644
--- a/webservices/compbio/ws/server/DisemblWS.java
+++ b/webservices/compbio/ws/server/DisemblWS.java
@@ -1,130 +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.Disembl;
 
-@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "DisemblWS")
-public class DisemblWS implements SequenceAnnotation<Disembl> {
-
-	// Ask for resource injection
-	@Resource
-	WebServiceContext wsContext;
-
-	private static Logger statLog = Logger.getLogger("DisemblWS-stats");
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "DisemblWS")
+public class DisemblWS extends SequenceAnnotationService<Disembl>
+		implements
+			SequenceAnnotation<Disembl> {
 
 	private static Logger log = Logger.getLogger(DisemblWS.class);
 
-	private static final RunnerConfig<Disembl> disemblOptions = Util
-			.getSupportedOptions(Disembl.class);
-
-	private static final PresetManager<Disembl> disemblPresets = Util
-			.getPresets(Disembl.class);
-
-	ConfiguredExecutable<Disembl> init(List<FastaSequence> sequences)
-			throws JobSubmissionException {
-		Disembl disembl = new Disembl();
-		disembl.setInput("fasta.in").setOutput("disembl.out");
-		return Configurator.configureExecutable(disembl, sequences);
-	}
-
-	@Override
-	public ScoreManager getAnnotation(String jobId)
-			throws ResultNotAvailableException {
-		WSUtil.validateJobId(jobId);
-		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
-		ConfiguredExecutable<Disembl> disembl = (ConfiguredExecutable<Disembl>) asyncEngine
-				.getResults(jobId);
-		ScoreManager mas = disembl.getResults();
-		log.trace(jobId + " getDisorder : " + mas);
-		return mas;
-	}
-
-	@Override
-	public Limit<Disembl> getLimit(String presetName) {
-		return new Disembl().getLimit(presetName);
-	}
-
-	@Override
-	public LimitsManager<Disembl> getLimits() {
-		return new Disembl().getLimits();
-	}
-
-	@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<Disembl> getPresets() {
-		return disemblPresets;
-	}
-
-	@Override
-	public RunnerConfig<Disembl> getRunnerOptions() {
-		return disemblOptions;
-	}
-
-	String analize(List<FastaSequence> sequences,
-			ConfiguredExecutable<Disembl> confExec, Logger log, String method,
-			Limit<Disembl> 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<Disembl> confDisembl = init(sequences);
-
-		return analize(sequences, confDisembl, null, "analize", getLimit(""));
+	public DisemblWS() {
+		super(new Disembl(), log);
 	}
 
 	/*