+/* Copyright (c) 2011 Peter Troshin\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
+ * \r
+ * This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ * Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ * License for more details.\r
+ * \r
+ * A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
package compbio.ws.server;\r
\r
import java.util.List;\r
\r
-import javax.annotation.Resource;\r
import javax.jws.WebService;\r
-import javax.xml.ws.WebServiceContext;\r
\r
import org.apache.log4j.Logger;\r
\r
+import compbio.data.msa.JABAService;\r
import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.ScoreManager;\r
-import compbio.engine.AsyncExecutor;\r
-import compbio.engine.Configurator;\r
-import compbio.engine.client.ConfiguredExecutable;\r
-import compbio.metadata.ChunkHolder;\r
-import compbio.metadata.JobStatus;\r
import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.Limit;\r
import compbio.metadata.LimitExceededException;\r
-import compbio.metadata.LimitsManager;\r
import compbio.metadata.Option;\r
import compbio.metadata.Preset;\r
-import compbio.metadata.PresetManager;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.metadata.RunnerConfig;\r
import compbio.metadata.UnsupportedRuntimeException;\r
import compbio.metadata.WrongParameterException;\r
-import compbio.runner.Util;\r
import compbio.runner.disorder.GlobPlot;\r
\r
-@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "GlobPlotWS")\r
-public class GlobPlotWS implements SequenceAnnotation<GlobPlot> {\r
-\r
- // Ask for resource injection\r
- @Resource\r
- WebServiceContext wsContext;\r
-\r
- private static Logger statLog = Logger.getLogger("GlobPlotWS-stats");\r
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "GlobPlotWS")\r
+public class GlobPlotWS extends SequenceAnnotationService<GlobPlot>\r
+ implements\r
+ SequenceAnnotation<GlobPlot> {\r
\r
private static Logger log = Logger.getLogger(GlobPlotWS.class);\r
\r
- private static final RunnerConfig<GlobPlot> globPlotOptions = Util\r
- .getSupportedOptions(GlobPlot.class);\r
-\r
- private static final PresetManager<GlobPlot> globPlotPresets = Util\r
- .getPresets(GlobPlot.class);\r
-\r
- ConfiguredExecutable<GlobPlot> init(List<FastaSequence> sequences)\r
- throws JobSubmissionException {\r
- GlobPlot globPlot = new GlobPlot();\r
- globPlot.setInput("fasta.in").setOutput("globPlot.out");\r
- return Configurator.configureExecutable(globPlot, sequences);\r
- }\r
-\r
- @Override\r
- public ScoreManager getAnnotation(String jobId)\r
- throws ResultNotAvailableException {\r
- WSUtil.validateJobId(jobId);\r
- AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
- ConfiguredExecutable<GlobPlot> globPlot = (ConfiguredExecutable<GlobPlot>) asyncEngine\r
- .getResults(jobId);\r
- ScoreManager mas = globPlot.getResults();\r
- log.trace(jobId + " getConservation : " + mas);\r
- return mas;\r
- }\r
-\r
- @Override\r
- public Limit<GlobPlot> getLimit(String presetName) {\r
- return new GlobPlot().getLimit(presetName);\r
- }\r
-\r
- @Override\r
- public LimitsManager<GlobPlot> getLimits() {\r
- return new GlobPlot().getLimits();\r
- }\r
-\r
- @Override\r
- public ChunkHolder pullExecStatistics(String jobId, long position) {\r
- // Execution stat is not supported\r
- return new ChunkHolder("", -1);\r
- }\r
-\r
- @Override\r
- public boolean cancelJob(String jobId) {\r
- WSUtil.validateJobId(jobId);\r
- return WSUtil.cancelJob(jobId);\r
- }\r
-\r
- @Override\r
- public JobStatus getJobStatus(String jobId) {\r
- WSUtil.validateJobId(jobId);\r
- return WSUtil.getJobStatus(jobId);\r
- }\r
-\r
- @Override\r
- public PresetManager<GlobPlot> getPresets() {\r
- return globPlotPresets;\r
- }\r
-\r
- @Override\r
- public RunnerConfig<GlobPlot> getRunnerOptions() {\r
- return globPlotOptions;\r
- }\r
-\r
- String analize(List<FastaSequence> sequences,\r
- ConfiguredExecutable<GlobPlot> confExec, Logger log, String method,\r
- Limit<GlobPlot> limit) throws JobSubmissionException {\r
- if (limit != null && limit.isExceeded(sequences)) {\r
- throw LimitExceededException.newLimitExceeded(limit, sequences);\r
- }\r
-\r
- compbio.runner.Util.writeInput(sequences, confExec);\r
- AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
- String jobId = engine.submitJob(confExec);\r
- return jobId;\r
- }\r
-\r
- @Override\r
- public String analize(List<FastaSequence> sequences)\r
- throws UnsupportedRuntimeException, LimitExceededException,\r
- JobSubmissionException {\r
- WSUtil.validateFastaInput(sequences);\r
- ConfiguredExecutable<GlobPlot> confGlobPlot = init(sequences);\r
-\r
- return analize(sequences, confGlobPlot, null, "analize", getLimit(""));\r
+ public GlobPlotWS() {\r
+ super(new GlobPlot(), log);\r
}\r
\r
/*\r