Web services refactoring & bug fixing

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

diff --git a/webservices/compbio/ws/server/MafftWS.java b/webservices/compbio/ws/server/MafftWS.java
index d2de592..12805af 100644 (file)
--- a/webservices/compbio/ws/server/MafftWS.java
+++ b/webservices/compbio/ws/server/MafftWS.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
@@ -33,6 +31,7 @@ import compbio.data.sequence.FastaSequence;
 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
@@ -50,12 +49,6 @@ import compbio.runner.msa.Mafft;
 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", 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
@@ -64,7 +57,7 @@ public class MafftWS implements MsaWS<Mafft> {
        private static final PresetManager<Mafft> mafftPresets = Util\r
                        .getPresets(Mafft.class);\r
 \r
-       private static final LimitsManager<Mafft> limitMan = compbio.runner.Util\r
+       private static final LimitsManager<Mafft> limitMan = compbio.engine.client.Util\r
                        .getLimits(new Mafft().getType());\r
 \r
        @Override\r
@@ -78,6 +71,9 @@ public class MafftWS implements MsaWS<Mafft> {
        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