-/* 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.runner.Util;\r
import compbio.runner.msa.Mafft;\r
\r
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MafftWS")\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "MafftWS")\r
public class MafftWS implements MsaWS<Mafft> {\r
\r
- // Ask for resource injection\r
- @Resource\r
- WebServiceContext wsContext;\r
-\r
- private static Logger statLog = Logger.getLogger("MafftWS-stats");\r
-\r
- private static Logger log = Logger.getLogger(MafftWS.class);\r
-\r
- private static final RunnerConfig<Mafft> mafftOptions = Util\r
- .getSupportedOptions(Mafft.class);\r
-\r
- private static final PresetManager<Mafft> mafftPresets = Util\r
- .getPresets(Mafft.class);\r
-\r
- @Override\r
- public String align(List<FastaSequence> sequences)\r
- throws JobSubmissionException {\r
- WSUtil.validateFastaInput(sequences);\r
- ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
- return WSUtil.align(sequences, confMafft, null, "align", getLimit(""));\r
- }\r
-\r
- ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)\r
- throws JobSubmissionException {\r
- Mafft mafft = new Mafft();\r
- mafft.setInput("fasta.in").setOutput("fasta.out");\r
- return Configurator.configureExecutable(mafft, dataSet);\r
- }\r
-\r
- @Override\r
- public String customAlign(List<FastaSequence> sequences,\r
- List<Option<Mafft>> options) throws JobSubmissionException,\r
- WrongParameterException {\r
- WSUtil.validateFastaInput(sequences);\r
- ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
- List<String> params = WSUtil.getCommands(options,\r
- Mafft.KEY_VALUE_SEPARATOR);\r
- log.info("Setting parameters: " + params);\r
- confMafft.addParameters(params);\r
- return WSUtil.align(sequences, confMafft, null, "customAlign",\r
- getLimit(""));\r
- }\r
-\r
- @Override\r
- public String presetAlign(List<FastaSequence> sequences,\r
- Preset<Mafft> preset) throws JobSubmissionException,\r
- WrongParameterException {\r
- WSUtil.validateFastaInput(sequences);\r
- if (preset == null) {\r
- throw new WrongParameterException("Preset must be provided!");\r
+ private static Logger log = Logger.getLogger(MafftWS.class);\r
+\r
+ private static final RunnerConfig<Mafft> mafftOptions = Util\r
+ .getSupportedOptions(Mafft.class);\r
+\r
+ private static final PresetManager<Mafft> mafftPresets = Util\r
+ .getPresets(Mafft.class);\r
+\r
+ private static final LimitsManager<Mafft> limitMan = compbio.engine.client.Util\r
+ .getLimits(new Mafft().getType());\r
+\r
+ @Override\r
+ public String align(List<FastaSequence> sequences)\r
+ throws JobSubmissionException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
+ return WSUtil.align(sequences, confMafft, log, "align", getLimit(""));\r
+ }\r
+\r
+ ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)\r
+ throws JobSubmissionException {\r
+ Mafft mafft = new Mafft();\r
+ mafft.setInput(SkeletalExecutable.INPUT)\r
+ .setOutput(SkeletalExecutable.OUTPUT)\r
+ .setError(SkeletalExecutable.ERROR);\r
+ return Configurator.configureExecutable(mafft, dataSet);\r
+ }\r
+\r
+ @Override\r
+ public String customAlign(List<FastaSequence> sequences,\r
+ List<Option<Mafft>> options) throws JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
+ List<String> params = WSUtil.getCommands(options,\r
+ Mafft.KEY_VALUE_SEPARATOR);\r
+ log.info("Setting parameters: " + params);\r
+ confMafft.addParameters(params);\r
+ return WSUtil.align(sequences, confMafft, log, "customAlign",\r
+ getLimit(""));\r
+ }\r
+\r
+ @Override\r
+ public String presetAlign(List<FastaSequence> sequences,\r
+ Preset<Mafft> preset) throws JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ if (preset == null) {\r
+ throw new WrongParameterException("Preset must be provided!");\r
+ }\r
+ ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
+ confMafft.addParameters(preset.getOptions());\r
+ // This will return default limit if a specific the limit for a\r
+ // particular preset is not found\r
+ Limit<Mafft> limit = getLimit(preset.getName());\r
+\r
+ return WSUtil.align(sequences, confMafft, log, "presetAlign", limit);\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
+ WSUtil.validateJobId(jobId);\r
+ AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+ ConfiguredExecutable<Mafft> mafft = (ConfiguredExecutable<Mafft>) asyncEngine\r
+ .getResults(jobId);\r
+ Alignment al = mafft.getResults();\r
+ // log(jobId, "getResults");\r
+ return al;\r
+ }\r
+\r
+ @Override\r
+ public Limit<Mafft> getLimit(String presetName) {\r
+ if (limitMan == null) {\r
+ // Limit is not defined\r
+ return null;\r
+ }\r
+ return limitMan.getLimitByName(presetName);\r
+ }\r
+\r
+ @Override\r
+ public LimitsManager<Mafft> getLimits() {\r
+ return limitMan;\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
+ + new Mafft().getError();\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<Mafft> getPresets() {\r
+ return mafftPresets;\r
+ }\r
+\r
+ @Override\r
+ public RunnerConfig<Mafft> getRunnerOptions() {\r
+ return mafftOptions;\r
}\r
- ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
- confMafft.addParameters(preset.getOptions());\r
- // This will return default limit if a specific the limit for a\r
- // particular preset is not found\r
- Limit<Mafft> limit = getLimit(preset.getName());\r
-\r
- return WSUtil.align(sequences, confMafft, null, "presetAlign", limit);\r
- }\r
-\r
- @SuppressWarnings("unchecked")\r
- @Override\r
- public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
- WSUtil.validateJobId(jobId);\r
- AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
- ConfiguredExecutable<Mafft> mafft = (ConfiguredExecutable<Mafft>) asyncEngine\r
- .getResults(jobId);\r
- Alignment al = mafft.getResults();\r
- //log(jobId, "getResults");\r
- return al;\r
- }\r
-\r
- @Override\r
- public Limit<Mafft> getLimit(String presetName) {\r
- return new Mafft().getLimit(presetName);\r
- }\r
-\r
- @Override\r
- public LimitsManager<Mafft> getLimits() {\r
- return new Mafft().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
- + new Mafft().getError();\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<Mafft> getPresets() {\r
- return mafftPresets;\r
- }\r
-\r
- @Override\r
- public RunnerConfig<Mafft> getRunnerOptions() {\r
- return mafftOptions;\r
- }\r
\r
}\r
git://source.jalview.org / jabaws.git / blobdiff