JAL-4199 Update slivka client

[jalview.git] / src / jalview / ws / slivkaws / SlivkaWSInstance.java

diff --git a/src/jalview/ws/slivkaws/SlivkaWSInstance.java b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
index 613c702..d3701ac 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaWSInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
@@ -30,7 +30,7 @@ import javajs.http.ClientProtocolException;
 
 import java.util.Collection;
 import uk.ac.dundee.compbio.slivkaclient.Job;
-import uk.ac.dundee.compbio.slivkaclient.JobRequest;
+import uk.ac.dundee.compbio.slivkaclient.RequestValues;
 import uk.ac.dundee.compbio.slivkaclient.Parameter;
 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
@@ -75,7 +75,7 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
           WsParamSetI preset, List<ArgumentI> args) throws Throwable
   {
     var parameters = service.getParameters();
-    var request = new JobRequest();
+    var request = new RequestValues();
     for (Parameter param : parameters)
     {
       if (param instanceof Parameter.FileParameter)
@@ -126,8 +126,8 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
         }
       }
     }
-    var job = service.submitJob(request);
-    return new JobId(service.getName(), service.getName(), job.getId());
+    var jobId = client.submitJob(service, request);
+    return new JobId(service.getName(), service.getName(), jobId);
   }
 
   @Override
@@ -135,8 +135,7 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
   {
     try
     {
-      var slivkaJob = client.getJob(job.getJobId());
-      job.setState(stateMap.get(slivkaJob.getStatus()));
+      job.setState(stateMap.get(client.fetchJobStatus(job.getJobId())));
     } catch (IOException e)
     {
       throw new IOError(e);
@@ -146,8 +145,7 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
   @Override
   public final boolean updateJobProgress(WsJob job) throws IOException
   {      
-    var slivkaJob = client.getJob(job.getJobId());
-    Collection<RemoteFile> files = slivkaJob.getResults();
+    Collection<RemoteFile> files = client.fetchFilesList(job.getJobId());
     RemoteFile logFile=null;
     for (RemoteFile f : files)
     {
@@ -161,7 +159,7 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
     if (logFile!=null)
     {
       ByteArrayOutputStream output = new ByteArrayOutputStream();
-      logFile.writeTo(output);
+      client.writeFileTo(logFile, output);
       if (output.size() > job.getNextChunk())
       {
         newContent = true;
@@ -185,7 +183,7 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
       if (errLogFile!=null)
       {
         ByteArrayOutputStream output = new ByteArrayOutputStream();
-        errLogFile.writeTo(output);
+        client.writeFileTo(errLogFile, output);
         if (output.size() > 0)
         {
           newContent = true;