Refactoring of all SequenceAnnotation web services

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

diff --git a/webservices/compbio/ws/server/DisemblWS.java b/webservices/compbio/ws/server/DisemblWS.java
index 061f9a6..059695f 100644 (file)
--- a/webservices/compbio/ws/server/DisemblWS.java
+++ b/webservices/compbio/ws/server/DisemblWS.java
@@ -1,132 +1,30 @@
 package compbio.ws.server;\r
 \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.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.disorder.Disembl;\r
 \r
 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "DisemblWS")\r
-public class DisemblWS implements SequenceAnnotation<Disembl> {\r
-\r
-       // Ask for resource injection\r
-       @Resource\r
-       WebServiceContext wsContext;\r
-\r
-       private static Logger statLog = Logger.getLogger("DisemblWS-stats");\r
+public class DisemblWS extends SAService<Disembl>\r
+               implements\r
+                       SequenceAnnotation<Disembl> {\r
 \r
        private static Logger log = Logger.getLogger(DisemblWS.class);\r
 \r
-       private static final RunnerConfig<Disembl> disemblOptions = Util\r
-                       .getSupportedOptions(Disembl.class);\r
-\r
-       private static final PresetManager<Disembl> disemblPresets = Util\r
-                       .getPresets(Disembl.class);\r
-\r
-       ConfiguredExecutable<Disembl> init(List<FastaSequence> sequences)\r
-                       throws JobSubmissionException {\r
-               Disembl disembl = new Disembl();\r
-               disembl.setInput("fasta.in").setOutput("disembl.out");\r
-               return Configurator.configureExecutable(disembl, 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<Disembl> disembl = (ConfiguredExecutable<Disembl>) asyncEngine\r
-                               .getResults(jobId);\r
-               HashMap<String, HashSet<Score>> mas = disembl.getResults();\r
-               log.trace(jobId + " getDisorder : " + mas);\r
-               return mas;\r
-       }\r
-\r
-       @Override\r
-       public Limit<Disembl> getLimit(String presetName) {\r
-               return new Disembl().getLimit(presetName);\r
-       }\r
-\r
-       @Override\r
-       public LimitsManager<Disembl> getLimits() {\r
-               return new Disembl().getLimits();\r
-       }\r
-\r
-       @Override\r
-       public ChunkHolder pullExecStatistics(String jobId, long position) {\r
-               // Execution stat is not supported\r
-               return new ChunkHolder("", -1);\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<Disembl> getPresets() {\r
-               return disemblPresets;\r
-       }\r
-\r
-       @Override\r
-       public RunnerConfig<Disembl> getRunnerOptions() {\r
-               return disemblOptions;\r
-       }\r
-\r
-       String analize(List<FastaSequence> sequences,\r
-                       ConfiguredExecutable<Disembl> confExec, Logger log, String method,\r
-                       Limit<Disembl> 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<Disembl> confDisembl = init(sequences);\r
-\r
-               return analize(sequences, confDisembl, null, "analize", getLimit(""));\r
+       public DisemblWS() {\r
+               super(new Disembl(), log);\r
        }\r
 \r
        /*\r