+/* 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.Arrays;\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.Annotation;\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
\r
-@WebService(endpointInterface = "compbio.data.msa.Annotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "AAConWS")\r
-public class AAConWS implements Annotation<AACon> {\r
-\r
- // Ask for resource injection\r
- @Resource\r
- WebServiceContext wsContext;\r
-\r
- private static Logger statLog = Logger.getLogger("AAConWS-stats");\r
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "AAConWS")\r
+public class AAConWS extends SequenceAnnotationService<AACon>\r
+ implements\r
+ SequenceAnnotation<AACon> {\r
\r
private static Logger log = Logger.getLogger(AAConWS.class);\r
\r
- private static final RunnerConfig<AACon> aaconOptions = Util\r
- .getSupportedOptions(AACon.class);\r
-\r
- private static final PresetManager<AACon> aaconPresets = Util\r
- .getPresets(AACon.class);\r
-\r
- ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)\r
- throws JobSubmissionException {\r
- AACon aacon = new AACon();\r
- aacon.setInput("fasta.in").setOutput("aacon.out");\r
- return Configurator.configureExecutable(aacon, sequences);\r
+ public AAConWS() {\r
+ super(new AACon(), log);\r
}\r
\r
- @Override\r
- public HashSet<Score> getConservation(String jobId)\r
- throws ResultNotAvailableException {\r
- WSUtil.validateJobId(jobId);\r
- AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
- ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine\r
- .getResults(jobId);\r
- HashSet<Score> mas = aacon.getResults();\r
- log.trace(jobId + " getConservation : " + mas);\r
- return mas;\r
- }\r
/*\r
* @SuppressWarnings("unchecked") public JalviewAnnotation\r
* getJalviewAnnotation(String jobId) throws ResultNotAvailableException {\r
*/\r
\r
@Override\r
- public Limit<AACon> getLimit(String presetName) {\r
- return new AACon().getLimit(presetName);\r
- }\r
-\r
- @Override\r
- public LimitsManager<AACon> getLimits() {\r
- return new AACon().getLimits();\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
- + 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<AACon> getPresets() {\r
- return aaconPresets;\r
- }\r
-\r
- @Override\r
- public RunnerConfig<AACon> getRunnerOptions() {\r
- return aaconOptions;\r
- }\r
-\r
- String analize(List<FastaSequence> sequences,\r
- ConfiguredExecutable<AACon> confExec, Logger log, String method,\r
- Limit<AACon> 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
+ WSUtil.validateAAConInput(sequences);\r
ConfiguredExecutable<AACon> confAAcon = init(sequences);\r
\r
// set default conservation method to fastest - SHENKIN\r
// TODO: This violates encapsulation, should be moved to the runners\r
// level.\r
confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));\r
- return analize(sequences, confAAcon, null, "analize", getLimit(""));\r
- }\r
-\r
- @Override\r
- public String customAnalize(List<FastaSequence> sequences,\r
- List<Option<AACon>> options) throws UnsupportedRuntimeException,\r
- LimitExceededException, JobSubmissionException,\r
- WrongParameterException {\r
- WSUtil.validateFastaInput(sequences);\r
- ConfiguredExecutable<AACon> confAACon = init(sequences);\r
- // Could not do that! Space separated values\r
- // will all be treated as keys! thus duplicates removed\r
- // String params = cbuilder.getCommand();\r
- List<String> params = WSUtil.getCommands(options,\r
- AACon.KEY_VALUE_SEPARATOR);\r
- confAACon.addParameters(params);\r
- return analize(sequences, confAACon, null, "customAnalize",\r
+ return WSUtil.analize(sequences, confAAcon, log, "AAConWS analize",\r
getLimit(""));\r
}\r
\r
@Override\r
- public String presetAnalize(List<FastaSequence> sequences,\r
- Preset<AACon> 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<AACon> confAAcon = init(sequences);\r
- confAAcon.addParameters(preset.getOptions());\r
- Limit<AACon> limit = getLimit(preset.getName());\r
- return WSUtil.align(sequences, confAAcon, null, "presetAnalize", limit);\r
+ public ChunkHolder pullExecStatistics(String jobId, long position) {\r
+ WSUtil.validateJobId(jobId);\r
+ String file = Configurator.getWorkDirectory(jobId) + File.separator\r
+ + AACon.getStatFile();\r
+ return WSUtil.pullFile(file, position);\r
}\r
\r
}\r
git://source.jalview.org / jabaws.git / blobdiff