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.Probcons;\r
\r
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ProbconsWS")\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ProbconsWS")\r
public class ProbconsWS implements MsaWS<Probcons> {\r
\r
- // Ask for resource injection\r
- @Resource\r
- WebServiceContext wsContext;\r
-\r
- private static Logger statLog = Logger.getLogger("ProbconsWS-stats");\r
-\r
private static Logger log = Logger.getLogger(ProbconsWS.class);\r
\r
private static final RunnerConfig<Probcons> probconsOptions = Util\r
.getSupportedOptions(Probcons.class);\r
\r
- private static final LimitsManager<Probcons> limitMan = compbio.runner.Util\r
+ private static final LimitsManager<Probcons> limitMan = compbio.engine.client.Util\r
.getLimits(new Probcons().getType());\r
\r
@Override\r
ConfiguredExecutable<Probcons> init(List<FastaSequence> dataSet)\r
throws JobSubmissionException {\r
Probcons probcons = new Probcons();\r
- probcons.setInput("fasta.in").setOutput("alignment.out");\r
+ probcons.setInput(SkeletalExecutable.INPUT)\r
+ .setOutput(SkeletalExecutable.OUTPUT)\r
+ .setError(SkeletalExecutable.ERROR);\r
return Configurator.configureExecutable(probcons, dataSet);\r
}\r
\r
\r
@Override\r
public Limit<Probcons> getLimit(String presetName) {\r
+ if (limitMan == null) {\r
+ // Limit is not defined\r
+ return null;\r
+ }\r
return limitMan.getLimitByName(presetName);\r
}\r
\r