Refactoring of all SequenceAnnotation web services

[jabaws.git] / webservices / compbio / ws / server / ClustalWS.java

diff --git a/webservices/compbio/ws/server/ClustalWS.java b/webservices/compbio/ws/server/ClustalWS.java
index 93d0c7f..22fad0c 100644 (file)
--- a/webservices/compbio/ws/server/ClustalWS.java
+++ b/webservices/compbio/ws/server/ClustalWS.java
@@ -21,9 +21,7 @@ package compbio.ws.server;
 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
@@ -46,20 +44,12 @@ import compbio.metadata.RunnerConfig;
 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
 public class ClustalWS implements MsaWS<ClustalW> {\r
 \r
-       // Ask for resource injection\r
-       @Resource\r
-       private WebServiceContext wsContext;\r
-\r
        private static Logger log = Logger.getLogger(ClustalWS.class);\r
 \r
-       private static volatile WSLogger logger;\r
-\r
        private static final RunnerConfig<ClustalW> clustalOptions = Util\r
                        .getSupportedOptions(ClustalW.class);\r
 \r
@@ -69,30 +59,13 @@ public class ClustalWS implements MsaWS<ClustalW> {
        private static final LimitsManager<ClustalW> limitMan = compbio.engine.client.Util\r
                        .getLimits(new ClustalW().getType());\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
-                               }\r
-                       }\r
-               }\r
-               return logger;\r
-       }\r
-\r
        @Override\r
        public String align(List<FastaSequence> sequences)\r
                        throws JobSubmissionException {\r
 \r
                WSUtil.validateFastaInput(sequences);\r
                ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
-               return WSUtil.align(sequences, confClust, getLogger(), "align",\r
-                               getLimit(""));\r
+               return WSUtil.align(sequences, confClust, log, "align", getLimit(""));\r
        }\r
 \r
        ConfiguredExecutable<ClustalW> init(List<FastaSequence> dataSet)\r
@@ -114,8 +87,7 @@ public class ClustalWS implements MsaWS<ClustalW> {
                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
+               return WSUtil.align(sequences, confClust, log, "presetAlign", limit);\r
        }\r
 \r
        @Override\r
@@ -128,39 +100,35 @@ public class ClustalWS implements MsaWS<ClustalW> {
                                ClustalW.KEY_VALUE_SEPARATOR);\r
                confClust.addParameters(params);\r
                log.info("Setting parameters: " + params);\r
-               return WSUtil.align(sequences, confClust, getLogger(), "customAlign",\r
+               return WSUtil.align(sequences, confClust, log, "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
+\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
+\r
                return al;\r
        }\r
 \r
        @Override\r
        public Limit<ClustalW> getLimit(String presetName) {\r
-               Timer timer = Timer.getMilliSecondsTimer();\r
                if (limitMan == null) {\r
                        // No limit is configured\r
                        return null;\r
                }\r
                Limit<ClustalW> limit = limitMan.getLimitByName(presetName);\r
-               getLogger().logAll(timer, "getLimit");\r
                return limit;\r
        }\r
 \r
@@ -171,37 +139,30 @@ public class ClustalWS implements MsaWS<ClustalW> {
 \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
+\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