-/* Copyright (c) 2009 Peter Troshin\r
+/* Copyright (c) 2011 Peter Troshin\r
* \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \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
import java.io.File;\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.MsaWS;\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
import compbio.metadata.ChunkHolder;\r
import compbio.metadata.JobStatus;\r
import compbio.metadata.JobSubmissionException;\r
import compbio.metadata.WrongParameterException;\r
import compbio.runner.Util;\r
import compbio.runner.msa.ClustalW;\r
-import compbio.util.Timer;\r
-import compbio.ws.client.Services;\r
\r
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ClustalWS")\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ClustalWS")\r
public class ClustalWS implements MsaWS<ClustalW> {\r
\r
- // Ask for resource injection\r
- @Resource\r
- private WebServiceContext wsContext;\r
+ private static Logger log = Logger.getLogger(ClustalWS.class);\r
\r
- private static Logger log = Logger.getLogger(ClustalWS.class);\r
+ private static final RunnerConfig<ClustalW> clustalOptions = Util\r
+ .getSupportedOptions(ClustalW.class);\r
\r
- private static volatile WSLogger logger;\r
+ private static final PresetManager<ClustalW> clustalPresets = Util\r
+ .getPresets(ClustalW.class);\r
\r
- private static final RunnerConfig<ClustalW> clustalOptions = Util\r
- .getSupportedOptions(ClustalW.class);\r
+ private static final LimitsManager<ClustalW> limitMan = compbio.engine.client.Util\r
+ .getLimits(new ClustalW().getType());\r
\r
- private static final PresetManager<ClustalW> clustalPresets = Util\r
- .getPresets(ClustalW.class);\r
+ @Override\r
+ public String align(List<FastaSequence> sequences)\r
+ throws JobSubmissionException {\r
\r
- /*\r
- * Initialise the logger. This cannot be done in the constructor as the\r
- * WebServiceContext is not available at the object construction time\r
- */\r
- private WSLogger getLogger() {\r
- if (logger == null) {\r
- synchronized (ClustalWS.class) {\r
- if (logger == null) {\r
- logger = WSLogger.getStatLogger(Services.ClustalWS,\r
- wsContext);\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
+ return WSUtil.align(sequences, confClust, log, "align", getLimit(""));\r
+ }\r
+\r
+ ConfiguredExecutable<ClustalW> init(List<FastaSequence> dataSet)\r
+ throws JobSubmissionException {\r
+ ClustalW clustal = new ClustalW();\r
+ clustal.setInput(SkeletalExecutable.INPUT)\r
+ .setOutput(SkeletalExecutable.OUTPUT)\r
+ .setError(SkeletalExecutable.ERROR);\r
+ ConfiguredExecutable<ClustalW> confClust = Configurator\r
+ .configureExecutable(clustal, dataSet);\r
+ return confClust;\r
+ }\r
+\r
+ @Override\r
+ public String presetAlign(List<FastaSequence> sequences,\r
+ Preset<ClustalW> preset) throws JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ if (preset == null) {\r
+ throw new WrongParameterException("Preset must be provided!");\r
}\r
- }\r
+ Limit<ClustalW> limit = getLimit(preset.getName());\r
+ ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
+ confClust.addParameters(preset.getOptions());\r
+ return WSUtil.align(sequences, confClust, log, "presetAlign", limit);\r
}\r
- return logger;\r
- }\r
-\r
- @Override\r
- public String align(List<FastaSequence> sequences)\r
- throws JobSubmissionException {\r
- WSUtil.validateFastaInput(sequences);\r
- ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
- return WSUtil.align(sequences, confClust, getLogger(), "align",\r
- getLimit(""));\r
- }\r
-\r
- ConfiguredExecutable<ClustalW> init(List<FastaSequence> dataSet)\r
- throws JobSubmissionException {\r
- ClustalW clustal = new ClustalW();\r
- ConfiguredExecutable<ClustalW> confClust = Configurator\r
- .configureExecutable(clustal, dataSet);\r
- return confClust;\r
- }\r
-\r
- @Override\r
- public String presetAlign(List<FastaSequence> sequences,\r
- Preset<ClustalW> preset) throws JobSubmissionException,\r
- WrongParameterException {\r
- WSUtil.validateFastaInput(sequences);\r
- if (preset == null) {\r
- throw new WrongParameterException("Preset must be provided!");\r
+\r
+ @Override\r
+ public String customAlign(List<FastaSequence> sequences,\r
+ List<Option<ClustalW>> options) throws JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
+ List<String> params = WSUtil.getCommands(options,\r
+ ClustalW.KEY_VALUE_SEPARATOR);\r
+ confClust.addParameters(params);\r
+ log.info("Setting parameters: " + params);\r
+ return WSUtil.align(sequences, confClust, log, "customAlign",\r
+ getLimit(""));\r
+ }\r
+\r
+ @Override\r
+ public RunnerConfig<ClustalW> getRunnerOptions() {\r
+ return clustalOptions;\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
+\r
+ WSUtil.validateJobId(jobId);\r
+ AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+ ConfiguredExecutable<ClustalW> clustal = (ConfiguredExecutable<ClustalW>) asyncEngine\r
+ .getResults(jobId);\r
+ Alignment al = clustal.getResults();\r
+\r
+ return al;\r
+ }\r
+\r
+ @Override\r
+ public Limit<ClustalW> getLimit(String presetName) {\r
+ if (limitMan == null) {\r
+ // No limit is configured\r
+ return null;\r
+ }\r
+ Limit<ClustalW> limit = limitMan.getLimitByName(presetName);\r
+ return limit;\r
+ }\r
+\r
+ @Override\r
+ public LimitsManager<ClustalW> getLimits() {\r
+ return limitMan;\r
+ }\r
+\r
+ @Override\r
+ public boolean cancelJob(String jobId) {\r
+ WSUtil.validateJobId(jobId);\r
+ boolean result = WSUtil.cancelJob(jobId);\r
+ return result;\r
+ }\r
+\r
+ @Override\r
+ public JobStatus getJobStatus(String jobId) {\r
+ WSUtil.validateJobId(jobId);\r
+ JobStatus status = WSUtil.getJobStatus(jobId);\r
+ return status;\r
+ }\r
+\r
+ @Override\r
+ public PresetManager<ClustalW> getPresets() {\r
+ return clustalPresets;\r
+ }\r
+\r
+ @Override\r
+ public ChunkHolder pullExecStatistics(String jobId, long position) {\r
+\r
+ WSUtil.validateJobId(jobId);\r
+ String file = Configurator.getWorkDirectory(jobId) + File.separator\r
+ + ClustalW.getStatFile();\r
+ ChunkHolder cholder = WSUtil.pullFile(file, position);\r
+ return cholder;\r
}\r
- Limit<ClustalW> limit = getLimit(preset.getName());\r
- ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
- confClust.addParameters(preset.getOptions());\r
- return WSUtil.align(sequences, confClust, getLogger(), "presetAlign",\r
- limit);\r
- }\r
-\r
- @Override\r
- public String customAlign(List<FastaSequence> sequences,\r
- List<Option<ClustalW>> options) throws JobSubmissionException,\r
- WrongParameterException {\r
- WSUtil.validateFastaInput(sequences);\r
- ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
- List<String> params = WSUtil.getCommands(options,\r
- ClustalW.KEY_VALUE_SEPARATOR);\r
- confClust.addParameters(params);\r
- log.info("Setting parameters: " + params);\r
- return WSUtil.align(sequences, confClust, getLogger(), "customAlign",\r
- getLimit(""));\r
- }\r
-\r
- @Override\r
- public RunnerConfig<ClustalW> getRunnerOptions() {\r
- Timer timer = Timer.getMilliSecondsTimer();\r
- getLogger().logAll(timer, "getRunnerOptions");\r
- return clustalOptions;\r
- }\r
-\r
- @SuppressWarnings("unchecked")\r
- @Override\r
- public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
- Timer timer = Timer.getMilliSecondsTimer();\r
- WSUtil.validateJobId(jobId);\r
- AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
- ConfiguredExecutable<ClustalW> clustal = (ConfiguredExecutable<ClustalW>) asyncEngine\r
- .getResults(jobId);\r
- Alignment al = clustal.getResults();\r
- getLogger().log(timer, "getResults", jobId);\r
- return al;\r
- }\r
-\r
- @Override\r
- public Limit<ClustalW> getLimit(String presetName) {\r
- Timer timer = Timer.getMilliSecondsTimer();\r
- Limit<ClustalW> limit = new ClustalW().getLimit(presetName);\r
- getLogger().logAll(timer, "getLimit");\r
- return limit;\r
- }\r
-\r
- @Override\r
- public LimitsManager<ClustalW> getLimits() {\r
- Timer timer = Timer.getMilliSecondsTimer();\r
- LimitsManager<ClustalW> limits = new ClustalW().getLimits();\r
- getLogger().logAll(timer, "getLimits");\r
- return limits;\r
- }\r
-\r
- @Override\r
- public boolean cancelJob(String jobId) {\r
- Timer timer = Timer.getMilliSecondsTimer();\r
- WSUtil.validateJobId(jobId);\r
- boolean result = WSUtil.cancelJob(jobId);\r
- getLogger().logFine(timer, "Cancel");\r
- return result;\r
- }\r
-\r
- @Override\r
- public JobStatus getJobStatus(String jobId) {\r
- Timer timer = Timer.getMilliSecondsTimer();\r
- WSUtil.validateJobId(jobId);\r
- JobStatus status = WSUtil.getJobStatus(jobId);\r
- getLogger().logFine(timer, "getJobStatus");\r
- return status;\r
- }\r
-\r
- @Override\r
- public PresetManager<ClustalW> getPresets() {\r
- Timer timer = Timer.getMilliSecondsTimer();\r
- getLogger().logAll(timer, "pullExecStatistics");\r
- return clustalPresets;\r
- }\r
-\r
- @Override\r
- public ChunkHolder pullExecStatistics(String jobId, long position) {\r
- Timer timer = Timer.getMilliSecondsTimer();\r
- WSUtil.validateJobId(jobId);\r
- String file = Configurator.getWorkDirectory(jobId) + File.separator\r
- + ClustalW.getStatFile();\r
- ChunkHolder cholder = WSUtil.pullFile(file, position);\r
- getLogger().logFine(timer, "pullExecStatistics");\r
- return cholder;\r
- }\r
\r
}\r
git://source.jalview.org / jabaws.git / blobdiff