+/* 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.io.File;\r
-import java.util.HashMap;\r
-import java.util.HashSet;\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.Score;\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.conservation.AACon;\r
import compbio.runner.disorder.Jronn;\r
\r
-@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "JronnWS")\r
-public class JronnWS implements SequenceAnnotation<Jronn> {\r
-\r
- // Ask for resource injection\r
- @Resource\r
- WebServiceContext wsContext;\r
-\r
- private static Logger statLog = Logger.getLogger("JronnWS-stats");\r
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "JronnWS")\r
+public class JronnWS extends SequenceAnnotationService<Jronn>\r
+ implements\r
+ SequenceAnnotation<Jronn> {\r
\r
private static Logger log = Logger.getLogger(JronnWS.class);\r
\r
- private static final RunnerConfig<Jronn> jronnOptions = Util\r
- .getSupportedOptions(Jronn.class);\r
-\r
- private static final PresetManager<Jronn> jronnPresets = Util\r
- .getPresets(Jronn.class);\r
-\r
- ConfiguredExecutable<Jronn> init(List<FastaSequence> sequences)\r
- throws JobSubmissionException {\r
- Jronn jronn = new Jronn();\r
- jronn.setInput("fasta.in").setOutput("jronn.out");\r
- return Configurator.configureExecutable(jronn, sequences);\r
- }\r
-\r
- @Override\r
- public HashMap<String, HashSet<Score>> getAnnotation(String jobId)\r
- throws ResultNotAvailableException {\r
- WSUtil.validateJobId(jobId);\r
- AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
- ConfiguredExecutable<Jronn> jronn = (ConfiguredExecutable<Jronn>) asyncEngine\r
- .getResults(jobId);\r
- HashMap<String, HashSet<Score>> mas = jronn.getResults();\r
- log.trace(jobId + " getConservation : " + mas);\r
- return mas;\r
- }\r
-\r
- @Override\r
- public Limit<Jronn> getLimit(String presetName) {\r
- return new Jronn().getLimit(presetName);\r
- }\r
-\r
- @Override\r
- public LimitsManager<Jronn> getLimits() {\r
- return new Jronn().getLimits();\r
+ public JronnWS() {\r
+ super(new Jronn(), log);\r
}\r
\r
@Override\r
public ChunkHolder pullExecStatistics(String jobId, long position) {\r
WSUtil.validateJobId(jobId);\r
String file = Configurator.getWorkDirectory(jobId) + File.separator\r
- + Jronn.getStatFile();\r
+ + AACon.getStatFile();\r
return WSUtil.pullFile(file, position);\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<Jronn> getPresets() {\r
- return jronnPresets;\r
- }\r
-\r
- @Override\r
- public RunnerConfig<Jronn> getRunnerOptions() {\r
- return jronnOptions;\r
- }\r
-\r
- String analize(List<FastaSequence> sequences,\r
- ConfiguredExecutable<Jronn> confExec, Logger log, String method,\r
- Limit<Jronn> 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<Jronn> confJronn = init(sequences);\r
-\r
- return analize(sequences, confJronn, null, "analize", getLimit(""));\r
- }\r
-\r
- @Override\r
- public String customAnalize(List<FastaSequence> sequences,\r
- List<Option<Jronn>> options) throws UnsupportedRuntimeException,\r
- LimitExceededException, JobSubmissionException,\r
- WrongParameterException {\r
- WSUtil.validateFastaInput(sequences);\r
- ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
-\r
- List<String> params = WSUtil.getCommands(options,\r
- AACon.KEY_VALUE_SEPARATOR);\r
- confJronn.addParameters(params);\r
- return analize(sequences, confJronn, null, "customAnalize",\r
- getLimit(""));\r
- }\r
-\r
- @Override\r
- public String presetAnalize(List<FastaSequence> sequences,\r
- Preset<Jronn> preset) throws UnsupportedRuntimeException,\r
- LimitExceededException, JobSubmissionException,\r
- WrongParameterException {\r
- WSUtil.validateFastaInput(sequences);\r
- if (preset == null) {\r
- throw new WrongParameterException("Preset must be provided!");\r
- }\r
- ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
- confJronn.addParameters(preset.getOptions());\r
- Limit<Jronn> limit = getLimit(preset.getName());\r
- return WSUtil.align(sequences, confJronn, null, "presetAnalize", limit);\r
- }\r
-\r
}\r
git://source.jalview.org / jabaws.git / blobdiff